Cell Interactomics and Carcinogenetic Mechanisms

CERN Document Server

Baianu, IC; Report to the Institute of Genomics

2004-01-01

Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quant...

Delay-tolerant mobile network protocol for rice field monitoring using wireless sensor networks

Science.gov (United States)

Guitton, Alexandre; Andres, Frédéric; Cardoso, Jarbas Lopes; Kawtrakul, Asanee; Barbin, Silvio E.

2015-10-01

The monitoring of rice fields can improve productivity by helping farmers throughout the rice cultivation cycle, on various issues: when to harvest, when to treat the crops against disease, when to increase the water level, how to share observations and decisions made in a collaborative way, etc. In this paper, we propose an architecture to monitor a rice field by a wireless sensor network. Our architecture is based on static sensor nodes forming a disconnected network, and mobile nodes communicating with the sensor nodes in a delay-tolerant manner. The data collected by the static sensor nodes are transmitted to mobile nodes, which in turn transmit them to a gateway, connected to a database, for further analysis. We focus on the related architecture, as well as on the energy-efficient protocols intended to perform the data collection.

The L1TD1 Protein Interactome Reveals the Importance of Post-transcriptional Regulation in Human Pluripotency

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Maheswara Reddy Emani

2015-03-01

Full Text Available The RNA-binding protein L1TD1 is one of the most specific and abundant proteins in pluripotent stem cells and is essential for the maintenance of pluripotency in human cells. Here, we identify the protein interaction network of L1TD1 in human embryonic stem cells (hESCs and provide insights into the interactome network constructed in human pluripotent cells. Our data reveal that L1TD1 has an important role in RNA splicing, translation, protein traffic, and degradation. L1TD1 interacts with multiple stem-cell-specific proteins, many of which are still uncharacterized in the context of development. Further, we show that L1TD1 is a part of the pluripotency interactome network of OCT4, SOX2, and NANOG, bridging nuclear and cytoplasmic regulation and highlighting the importance of RNA biology in pluripotency.

"Fuzziness" in the celular interactome: a historical perspective.

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Welch, G Rickey

2012-01-01

Some historical background is given for appreciating the impact of the empirical construct known as the cellular protein-protein interactome, which is a seemingly de novo entity that has arisen of late within the context of postgenomic systems biology. The approach here builds on a generalized principle of "fuzziness" in protein behavior, proposed by Tompa and Fuxreiter.(1) Recent controversies in the analysis and interpretation of the interactome studies are rationalized historically under the auspices of this concept. There is an extensive literature on protein-protein interactions, dating to the mid-1900s, which may help clarify the "fuzziness" in the interactome picture and, also, provide a basis for understanding the physiological importance of protein-protein interactions in vivo.

Neural network modeling of drying of rice in BAU-STR dryer

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Alam, Md. Ashraful; Saha, Chayan Kumer; Alam, Md. Monjurul; Ashraf, Md. Ali; Bala, Bilash Kanti; Harvey, Jagger

2018-05-01

The experimental performance and artificial neural network modeling of rice drying in BAU-STR dryer is presented in this paper. The dryer consists of a biomass stove as a heat source, a perforated inner bin and a perforated outer bin with annular space for grains, and a blower (1 hp) to supply heated air. The dryer capacity was 500 kg of freshly harvested rice. Twenty experimental runs were conducted to investigate the experimental performance of the dryer for drying of rice. An independent multilayer neural network approach was used to predict the performance of the BAU-STR dryer for drying of rice. Ten sets of experimental data were used for training using back propagation algorithm and another ten sets of data were used for testing the artificial neural network model. The prediction of the performance of the dryer was found to be excellent after it was adequately trained. The statistical analysis showed that the errors (MSE and RMSE) were within and acceptable range of ±5% with a coefficient of determination (R2) of 99%. The model can be used to predict the potential of the dryer for different locations, and can also be used in a predictive optimal control algorithm.

Embryonic stem cell interactomics: the beginning of a long road to biological function.

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Yousefi, Maram; Hajihoseini, Vahid; Jung, Woojin; Hosseinpour, Batol; Rassouli, Hassan; Lee, Bonghee; Baharvand, Hossein; Lee, KiYoung; Salekdeh, Ghasem Hosseini

2012-12-01

Embryonic stem cells (ESCs) are capable of unlimited self-renewal while maintaining pluripotency. They are of great interest in regenerative medicine due to their ability to differentiate into all cell types of the three embryonic germ layers. Recently, induced pluripotent stem cells (iPSCs) have shown similarities to ESCs and thus promise great therapeutic potential in regenerative medicine. Despite progress in stem cell biology, our understanding of the exact mechanisms by which pluripotency and self-renewal are established and maintained is largely unknown. A better understanding of these processes may lead to discovery of alternative ways for reprogramming, differentiation and more reliable applications of stem cells in therapies. It has become evident that proteins generally function as members of large complexes that are part of a more complex network. Therefore, the identification of protein-protein interactions (PPI) is an efficient strategy for understanding protein function and regulation. Systematic genome-wide and pathway-specific PPI analysis of ESCs has generated a network of ESC proteins, including major transcription factors. These PPI networks of ESCs may contribute to a mechanistic understanding of self-renewal and pluripotency. In this review we describe different experimental approaches for the identification of PPIs along with various databases. We discuss biological findings and technical challenges encountered with interactome studies of pluripotent stem cells, and provide insight into how interactomics is likely to develop.

An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice

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Liu Lili

2013-06-01

Full Text Available Understanding how metabolic reactions translate the genome of an organism into its phenotype is a grand challenge in biology. Genome-wide association studies (GWAS statistically connect genotypes to phenotypes, without any recourse to known molecular interactions, whereas a molecular mechanistic description ties gene function to phenotype through gene regulatory networks (GRNs, protein-protein interactions (PPIs and molecular pathways. Integration of different regulatory information levels of an organism is expected to provide a good way for mapping genotypes to phenotypes. However, the lack of curated metabolic model of rice is blocking the exploration of genome-scale multi-level network reconstruction. Here, we have merged GRNs, PPIs and genome-scale metabolic networks (GSMNs approaches into a single framework for rice via omics’ regulatory information reconstruction and integration. Firstly, we reconstructed a genome-scale metabolic model, containing 4,462 function genes, 2,986 metabolites involved in 3,316 reactions, and compartmentalized into ten subcellular locations. Furthermore, 90,358 pairs of protein-protein interactions, 662,936 pairs of gene regulations and 1,763 microRNA-target interactions were integrated into the metabolic model. Eventually, a database was developped for systematically storing and retrieving the genome-scale multi-level network of rice. This provides a reference for understanding genotype-phenotype relationship of rice, and for analysis of its molecular regulatory network.

A critical and Integrated View of the Yeast Interactome

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Stephen G. Oliver

2006-04-01

Full Text Available Global studies of protein–protein interactions are crucial to both elucidating gene function and producing an integrated view of the workings of living cells. High-throughput studies of the yeast interactome have been performed using both genetic and biochemical screens. Despite their size, the overlap between these experimental datasets is very limited. This could be due to each approach sampling only a small fraction of the total interactome. Alternatively, a large proportion of the data from these screens may represent false-positive interactions. We have used the Genome Information Management System (GIMS to integrate interactome datasets with transcriptome and protein annotation data and have found significant evidence that the proportion of false-positive results is high. Not all high-throughput datasets are similarly contaminated, and the tandem affinity purification (TAP approach appears to yield a high proportion of reliable interactions for which corroborating evidence is available. From our integrative analyses, we have generated a set of verified interactome data for yeast.

Gene, protein and network of male sterility in rice

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Wang eKun

2013-04-01

Full Text Available Rice is one of the most important model crop plants whose heterosis has been well exploited in commercial hybrid seed production via a variety of types of male sterile lines. Hybrid rice cultivation area is steadily expanding around the world, especially in Southern Asia. Characterization of genes and proteins related to male sterility aims to understand how and why the male sterility occurs, and which proteins are the key players for microspores abortion. Recently, a series of genes and proteins related to cytoplasmic male sterility, photoperiod sensitive male sterility, self-incompatibility and other types of microspores deterioration have been characterized through genetics or proteomics. Especially the latter, offers us a powerful and high throughput approach to discern the novel proteins involving in male-sterile pathways which may help us to breed artificial male-sterile system. This represents an alternative tool to meet the critical challenge of further development of hybrid rice. In this paper, we reviewed the recent developments in our understanding of male sterility in rice hybrid production across gene, protein and integrated network levels, and also, present a perspective on the engineering of male sterile lines for hybrid rice production.

In vitro nuclear interactome of the HIV-1 Tat protein.

LENUS (Irish Health Repository)

Gautier, Virginie W

2009-01-01

BACKGROUND: One facet of the complexity underlying the biology of HIV-1 resides not only in its limited number of viral proteins, but in the extensive repertoire of cellular proteins they interact with and their higher-order assembly. HIV-1 encodes the regulatory protein Tat (86-101aa), which is essential for HIV-1 replication and primarily orchestrates HIV-1 provirus transcriptional regulation. Previous studies have demonstrated that Tat function is highly dependent on specific interactions with a range of cellular proteins. However they can only partially account for the intricate molecular mechanisms underlying the dynamics of proviral gene expression. To obtain a comprehensive nuclear interaction map of Tat in T-cells, we have designed a proteomic strategy based on affinity chromatography coupled with mass spectrometry. RESULTS: Our approach resulted in the identification of a total of 183 candidates as Tat nuclear partners, 90% of which have not been previously characterised. Subsequently we applied in silico analysis, to validate and characterise our dataset which revealed that the Tat nuclear interactome exhibits unique signature(s). First, motif composition analysis highlighted that our dataset is enriched for domains mediating protein, RNA and DNA interactions, and helicase and ATPase activities. Secondly, functional classification and network reconstruction clearly depicted Tat as a polyvalent protein adaptor and positioned Tat at the nexus of a densely interconnected interaction network involved in a range of biological processes which included gene expression regulation, RNA biogenesis, chromatin structure, chromosome organisation, DNA replication and nuclear architecture. CONCLUSION: We have completed the in vitro Tat nuclear interactome and have highlighted its modular network properties and particularly those involved in the coordination of gene expression by Tat. Ultimately, the highly specialised set of molecular interactions identified will

The Interactomic Analysis Reveals Pathogenic Protein Networks in Phomopsis longicolla Underlying Seed Decay of Soybean

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Shuxian Li

2018-04-01

Full Text Available Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla is the primary cause of Phomopsis seed decay (PSD in soybean, Glycine max (L. Merrill. This disease results in poor seed quality and is one of the most economically important seed diseases in soybean. The objectives of this study were to infer protein–protein interactions (PPI and to identify conserved global networks and pathogenicity subnetworks in P. longicolla including orthologous pathways for cell signaling and pathogenesis. The interlog method used in the study identified 215,255 unique PPIs among 3,868 proteins. There were 1,414 pathogenicity related genes in P. longicolla identified using the pathogen host interaction (PHI database. Additionally, 149 plant cell wall degrading enzymes (PCWDE were detected. The network captured five different classes of carbohydrate degrading enzymes, including the auxiliary activities, carbohydrate esterases, glycoside hydrolases, glycosyl transferases, and carbohydrate binding molecules. From the PPI analysis, novel interacting partners were determined for each of the PCWDE classes. The most predominant class of PCWDE was a group of 60 glycoside hydrolases proteins. The glycoside hydrolase subnetwork was found to be interacting with 1,442 proteins within the network and was among the largest clusters. The orthologous proteins FUS3, HOG, CYP1, SGE1, and the g5566t.1 gene identified in this study could play an important role in pathogenicity. Therefore, the P. longicolla protein interactome (PiPhom generated in this study can lead to a better understanding of PPIs in soybean pathogens. Furthermore, the PPI may aid in targeting of genes and proteins for further studies of the pathogenicity mechanisms.

Quantum Interactomics and Cancer Molecular Mechanisms: I. Report Outline

CERN Document Server

Baianu, I C

2004-01-01

Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quant...

Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis.

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Rohit Vashisht

Full Text Available A decade since the availability of Mycobacterium tuberculosis (Mtb genome sequence, no promising drug has seen the light of the day. This not only indicates the challenges in discovering new drugs but also suggests a gap in our current understanding of Mtb biology. We attempt to bridge this gap by carrying out extensive re-annotation and constructing a systems level protein interaction map of Mtb with an objective of finding novel drug target candidates. Towards this, we synergized crowd sourcing and social networking methods through an initiative 'Connect to Decode' (C2D to generate the first and largest manually curated interactome of Mtb termed 'interactome pathway' (IPW, encompassing a total of 1434 proteins connected through 2575 functional relationships. Interactions leading to gene regulation, signal transduction, metabolism, structural complex formation have been catalogued. In the process, we have functionally annotated 87% of the Mtb genome in context of gene products. We further combine IPW with STRING based network to report central proteins, which may be assessed as potential drug targets for development of drugs with least possible side effects. The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach.

Crowd Sourcing a New Paradigm for Interactome Driven Drug Target Identification in Mycobacterium tuberculosis

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Rohira, Harsha; Bhat, Ashwini G.; Passi, Anurag; Mukherjee, Keya; Choudhary, Kumari Sonal; Kumar, Vikas; Arora, Anshula; Munusamy, Prabhakaran; Subramanian, Ahalyaa; Venkatachalam, Aparna; S, Gayathri; Raj, Sweety; Chitra, Vijaya; Verma, Kaveri; Zaheer, Salman; J, Balaganesh; Gurusamy, Malarvizhi; Razeeth, Mohammed; Raja, Ilamathi; Thandapani, Madhumohan; Mevada, Vishal; Soni, Raviraj; Rana, Shruti; Ramanna, Girish Muthagadhalli; Raghavan, Swetha; Subramanya, Sunil N.; Kholia, Trupti; Patel, Rajesh; Bhavnani, Varsha; Chiranjeevi, Lakavath; Sengupta, Soumi; Singh, Pankaj Kumar; Atray, Naresh; Gandhi, Swati; Avasthi, Tiruvayipati Suma; Nisthar, Shefin; Anurag, Meenakshi; Sharma, Pratibha; Hasija, Yasha; Dash, Debasis; Sharma, Arun; Scaria, Vinod; Thomas, Zakir; Chandra, Nagasuma; Brahmachari, Samir K.; Bhardwaj, Anshu

2012-01-01

A decade since the availability of Mycobacterium tuberculosis (Mtb) genome sequence, no promising drug has seen the light of the day. This not only indicates the challenges in discovering new drugs but also suggests a gap in our current understanding of Mtb biology. We attempt to bridge this gap by carrying out extensive re-annotation and constructing a systems level protein interaction map of Mtb with an objective of finding novel drug target candidates. Towards this, we synergized crowd sourcing and social networking methods through an initiative ‘Connect to Decode’ (C2D) to generate the first and largest manually curated interactome of Mtb termed ‘interactome pathway’ (IPW), encompassing a total of 1434 proteins connected through 2575 functional relationships. Interactions leading to gene regulation, signal transduction, metabolism, structural complex formation have been catalogued. In the process, we have functionally annotated 87% of the Mtb genome in context of gene products. We further combine IPW with STRING based network to report central proteins, which may be assessed as potential drug targets for development of drugs with least possible side effects. The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach. PMID:22808064

Data management of protein interaction networks

CERN Document Server

Cannataro, Mario

2012-01-01

Interactomics: a complete survey from data generation to knowledge extraction With the increasing use of high-throughput experimental assays, more and more protein interaction databases are becoming available. As a result, computational analysis of protein-to-protein interaction (PPI) data and networks, now known as interactomics, has become an essential tool to determine functionally associated proteins. From wet lab technologies to data management to knowledge extraction, this timely book guides readers through the new science of interactomics, giving them the tools needed to: Generate

A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE).

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Stacey, R Greg; Skinnider, Michael A; Scott, Nichollas E; Foster, Leonard J

2017-10-23

An organism's protein interactome, or complete network of protein-protein interactions, defines the protein complexes that drive cellular processes. Techniques for studying protein complexes have traditionally applied targeted strategies such as yeast two-hybrid or affinity purification-mass spectrometry to assess protein interactions. However, given the vast number of protein complexes, more scalable methods are necessary to accelerate interaction discovery and to construct whole interactomes. We recently developed a complementary technique based on the use of protein correlation profiling (PCP) and stable isotope labeling in amino acids in cell culture (SILAC) to assess chromatographic co-elution as evidence of interacting proteins. Importantly, PCP-SILAC is also capable of measuring protein interactions simultaneously under multiple biological conditions, allowing the detection of treatment-specific changes to an interactome. Given the uniqueness and high dimensionality of co-elution data, new tools are needed to compare protein elution profiles, control false discovery rates, and construct an accurate interactome. Here we describe a freely available bioinformatics pipeline, PrInCE, for the analysis of co-elution data. PrInCE is a modular, open-source library that is computationally inexpensive, able to use label and label-free data, and capable of detecting tens of thousands of protein-protein interactions. Using a machine learning approach, PrInCE offers greatly reduced run time, more predicted interactions at the same stringency, prediction of protein complexes, and greater ease of use over previous bioinformatics tools for co-elution data. PrInCE is implemented in Matlab (version R2017a). Source code and standalone executable programs for Windows and Mac OSX are available at https://github.com/fosterlab/PrInCE , where usage instructions can be found. An example dataset and output are also provided for testing purposes. PrInCE is the first fast and easy

Interactomes, manufacturomes and relational biology: analogies between systems biology and manufacturing systems

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2011-01-01

Background We review and extend the work of Rosen and Casti who discuss category theory with regards to systems biology and manufacturing systems, respectively. Results We describe anticipatory systems, or long-range feed-forward chemical reaction chains, and compare them to open-loop manufacturing processes. We then close the loop by discussing metabolism-repair systems and describe the rationality of the self-referential equation f = f (f). This relationship is derived from some boundary conditions that, in molecular systems biology, can be stated as the cardinality of the following molecular sets must be about equal: metabolome, genome, proteome. We show that this conjecture is not likely correct so the problem of self-referential mappings for describing the boundary between living and nonliving systems remains an open question. We calculate a lower and upper bound for the number of edges in the molecular interaction network (the interactome) for two cellular organisms and for two manufacturomes for CMOS integrated circuit manufacturing. Conclusions We show that the relevant mapping relations may not be Abelian, and that these problems cannot yet be resolved because the interactomes and manufacturomes are incomplete. PMID:21689427

Gene coexpression network analysis as a source of functional annotation for rice genes.

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Kevin L Childs

Full Text Available With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional

RNA-Binding Proteins Revisited – The Emerging Arabidopsis mRNA Interactome

KAUST Repository

Köster, Tino

2017-04-13

RNA–protein interaction is an important checkpoint to tune gene expression at the RNA level. Global identification of proteins binding in vivo to mRNA has been possible through interactome capture – where proteins are fixed to target RNAs by UV crosslinking and purified through affinity capture of polyadenylated RNA. In Arabidopsis over 500 RNA-binding proteins (RBPs) enriched in UV-crosslinked samples have been identified. As in mammals and yeast, the mRNA interactomes came with a few surprises. For example, a plethora of the proteins caught on RNA had not previously been linked to RNA-mediated processes, for example proteins of intermediary metabolism. Thus, the studies provide unprecedented insights into the composition of the mRNA interactome, highlighting the complexity of RNA-mediated processes.

RNA-Binding Proteins Revisited – The Emerging Arabidopsis mRNA Interactome

KAUST Repository

Kö ster, Tino; Marondedze, Claudius; Meyer, Katja; Staiger, Dorothee

2017-01-01

RNA–protein interaction is an important checkpoint to tune gene expression at the RNA level. Global identification of proteins binding in vivo to mRNA has been possible through interactome capture – where proteins are fixed to target RNAs by UV crosslinking and purified through affinity capture of polyadenylated RNA. In Arabidopsis over 500 RNA-binding proteins (RBPs) enriched in UV-crosslinked samples have been identified. As in mammals and yeast, the mRNA interactomes came with a few surprises. For example, a plethora of the proteins caught on RNA had not previously been linked to RNA-mediated processes, for example proteins of intermediary metabolism. Thus, the studies provide unprecedented insights into the composition of the mRNA interactome, highlighting the complexity of RNA-mediated processes.

Mapping the Small Molecule Interactome by Mass Spectrometry.

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Flaxman, Hope A; Woo, Christina M

2018-01-16

Mapping small molecule interactions throughout the proteome provides the critical structural basis for functional analysis of their impact on biochemistry. However, translation of mass spectrometry-based proteomics methods to directly profile the interaction between a small molecule and the whole proteome is challenging because of the substoichiometric nature of many interactions, the diversity of covalent and noncovalent interactions involved, and the subsequent computational complexity associated with their spectral assignment. Recent advances in chemical proteomics have begun fill this gap to provide a structural basis for the breadth of small molecule-protein interactions in the whole proteome. Innovations enabling direct characterization of the small molecule interactome include faster, more sensitive instrumentation coupled to chemical conjugation, enrichment, and labeling methods that facilitate detection and assignment. These methods have started to measure molecular interaction hotspots due to inherent differences in local amino acid reactivity and binding affinity throughout the proteome. Measurement of the small molecule interactome is producing structural insights and methods for probing and engineering protein biochemistry. Direct structural characterization of the small molecule interactome is a rapidly emerging area pushing new frontiers in biochemistry at the interface of small molecules and the proteome.

Characterization of WRKY co-regulatory networks in rice and Arabidopsis

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Kikuchi Shoshi

2009-09-01

Full Text Available Abstract Background The WRKY transcription factor gene family has a very ancient origin and has undergone extensive duplications in the plant kingdom. Several studies have pointed out their involvement in a range of biological processes, revealing that a large number of WRKY genes are transcriptionally regulated under conditions of biotic and/or abiotic stress. To investigate the existence of WRKY co-regulatory networks in plants, a whole gene family WRKYs expression study was carried out in rice (Oryza sativa. This analysis was extended to Arabidopsis thaliana taking advantage of an extensive repository of gene expression data. Results The presented results suggested that 24 members of the rice WRKY gene family (22% of the total were differentially-regulated in response to at least one of the stress conditions tested. We defined the existence of nine OsWRKY gene clusters comprising both phylogenetically related and unrelated genes that were significantly co-expressed, suggesting that specific sets of WRKY genes might act in co-regulatory networks. This hypothesis was tested by Pearson Correlation Coefficient analysis of the Arabidopsis WRKY gene family in a large set of Affymetrix microarray experiments. AtWRKYs were found to belong to two main co-regulatory networks (COR-A, COR-B and two smaller ones (COR-C and COR-D, all including genes belonging to distinct phylogenetic groups. The COR-A network contained several AtWRKY genes known to be involved mostly in response to pathogens, whose physical and/or genetic interaction was experimentally proven. We also showed that specific co-regulatory networks were conserved between the two model species by identifying Arabidopsis orthologs of the co-expressed OsWRKY genes. Conclusion In this work we identified sets of co-expressed WRKY genes in both rice and Arabidopsis that are functionally likely to cooperate in the same signal transduction pathways. We propose that, making use of data from co

Using artificial neural network and satellite data to predict rice yield in Bangladesh

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Akhand, Kawsar; Nizamuddin, Mohammad; Roytman, Leonid; Kogan, Felix; Goldberg, Mitch

2015-09-01

Rice production in Bangladesh is a crucial part of the national economy and providing about 70 percent of an average citizen's total calorie intake. The demand for rice is constantly rising as the new populations are added in every year in Bangladesh. Due to the increase in population, the cultivation land decreases. In addition, Bangladesh is faced with production constraints such as drought, flooding, salinity, lack of irrigation facilities and lack of modern technology. To maintain self sufficiency in rice, Bangladesh will have to continue to expand rice production by increasing yield at a rate that is at least equal to the population growth until the demand of rice has stabilized. Accurate rice yield prediction is one of the most important challenges in managing supply and demand of rice as well as decision making processes. Artificial Neural Network (ANN) is used to construct a model to predict Aus rice yield in Bangladesh. Advanced Very High Resolution Radiometer (AVHRR)-based remote sensing satellite data vegetation health (VH) indices (Vegetation Condition Index (VCI) and Temperature Condition Index (TCI) are used as input variables and official statistics of Aus rice yield is used as target variable for ANN prediction model. The result obtained with ANN method is encouraging and the error of prediction is less than 10%. Therefore, prediction can play an important role in planning and storing of sufficient rice to face in any future uncertainty.

Bcl2-associated Athanogene 3 Interactome Analysis Reveals a New Role in Modulating Proteasome Activity*

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Chen, Ying; Yang, Li-Na; Cheng, Li; Tu, Shun; Guo, Shu-Juan; Le, Huang-Ying; Xiong, Qian; Mo, Ran; Li, Chong-Yang; Jeong, Jun-Seop; Jiang, Lizhi; Blackshaw, Seth; Bi, Li-Jun; Zhu, Heng; Tao, Sheng-Ce; Ge, Feng

2013-01-01

Bcl2-associated athanogene 3 (BAG3), a member of the BAG family of co-chaperones, plays a critical role in regulating apoptosis, development, cell motility, autophagy, and tumor metastasis and in mediating cell adaptive responses to stressful stimuli. BAG3 carries a BAG domain, a WW domain, and a proline-rich repeat (PXXP), all of which mediate binding to different partners. To elucidate BAG3's interaction network at the molecular level, we employed quantitative immunoprecipitation combined with knockdown and human proteome microarrays to comprehensively profile the BAG3 interactome in humans. We identified a total of 382 BAG3-interacting proteins with diverse functions, including transferase activity, nucleic acid binding, transcription factors, proteases, and chaperones, suggesting that BAG3 is a critical regulator of diverse cellular functions. In addition, we characterized interactions between BAG3 and some of its newly identified partners in greater detail. In particular, bioinformatic analysis revealed that the BAG3 interactome is strongly enriched in proteins functioning within the proteasome-ubiquitination process and that compose the proteasome complex itself, suggesting that a critical biological function of BAG3 is associated with the proteasome. Functional studies demonstrated that BAG3 indeed interacts with the proteasome and modulates its activity, sustaining cell survival and underlying resistance to therapy through the down-modulation of apoptosis. Taken as a whole, this study expands our knowledge of the BAG3 interactome, provides a valuable resource for understanding how BAG3 affects different cellular functions, and demonstrates that biologically relevant data can be harvested using this kind of integrated approach. PMID:23824909

Comparison of gene co-networks reveals the molecular mechanisms of the rice (Oryza sativa L.) response to Rhizoctonia solani AG1 IA infection.

Science.gov (United States)

Zhang, Jinfeng; Zhao, Wenjuan; Fu, Rong; Fu, Chenglin; Wang, Lingxia; Liu, Huainian; Li, Shuangcheng; Deng, Qiming; Wang, Shiquan; Zhu, Jun; Liang, Yueyang; Li, Ping; Zheng, Aiping

2018-05-05

Rhizoctonia solani causes rice sheath blight, an important disease affecting the growth of rice (Oryza sativa L.). Attempts to control the disease have met with little success. Based on transcriptional profiling, we previously identified more than 11,947 common differentially expressed genes (TPM > 10) between the rice genotypes TeQing and Lemont. In the current study, we extended these findings by focusing on an analysis of gene co-expression in response to R. solani AG1 IA and identified gene modules within the networks through weighted gene co-expression network analysis (WGCNA). We compared the different genes assigned to each module and the biological interpretations of gene co-expression networks at early and later modules in the two rice genotypes to reveal differential responses to AG1 IA. Our results show that different changes occurred in the two rice genotypes and that the modules in the two groups contain a number of candidate genes possibly involved in pathogenesis, such as the VQ protein. Furthermore, these gene co-expression networks provide comprehensive transcriptional information regarding gene expression in rice in response to AG1 IA. The co-expression networks derived from our data offer ideas for follow-up experimentation that will help advance our understanding of the translational regulation of rice gene expression changes in response to AG1 IA.

A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize.

Directory of Open Access Journals (Sweden)

Matt eGeisler

2015-06-01

Full Text Available Interactomes are genome-wide roadmaps of protein-protein interactions. They have been produced for humans, yeast, the fruit fly, and Arabidopsis thaliana and have become invaluable tools for generating and testing hypotheses. A predicted interactome for Zea mays (PiZeaM is presented here as an aid to the research community for this valuable crop species. PiZeaM was built using a proven method of interologs (interacting orthologs that were identified using both one-to-one and many-to-many orthology between genomes of maize and reference species. Where both maize orthologs occurred for an experimentally determined interaction in the reference species, we predicted a likely interaction in maize. A total of 49,026 unique interactions for 6,004 maize proteins were predicted. These interactions are enriched for processes that are evolutionarily conserved, but include many otherwise poorly annotated proteins in maize. The predicted maize interactions were further analyzed by comparing annotation of interacting proteins, including different layers of ontology. A map of pairwise gene co-expression was also generated and compared to predicted interactions. Two global subnetworks were constructed for highly conserved interactions. These subnetworks showed clear clustering of proteins by function. Another subnetwork was created for disease response using a bait and prey strategy to capture interacting partners for proteins that respond to other organisms. Closer examination of this subnetwork revealed the connectivity between biotic and abiotic hormone stress pathways. We believe PiZeaM will provide a useful tool for the prediction of protein function and analysis of pathways for Z. mays researchers and is presented in this paper as a reference tool for the exploration of protein interactions in maize.

Sequential Elution Interactome Analysis of the Mind Bomb 1 Ubiquitin Ligase Reveals a Novel Role in Dendritic Spine Outgrowth*

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Mertz, Joseph; Tan, Haiyan; Pagala, Vishwajeeth; Bai, Bing; Chen, Ping-Chung; Li, Yuxin; Cho, Ji-Hoon; Shaw, Timothy; Wang, Xusheng; Peng, Junmin

2015-01-01

The mind bomb 1 (Mib1) ubiquitin ligase is essential for controlling metazoan development by Notch signaling and possibly the Wnt pathway. It is also expressed in postmitotic neurons and regulates neuronal morphogenesis and synaptic activity by mechanisms that are largely unknown. We sought to comprehensively characterize the Mib1 interactome and study its potential function in neuron development utilizing a novel sequential elution strategy for affinity purification, in which Mib1 binding proteins were eluted under different stringency and then quantified by the isobaric labeling method. The strategy identified the Mib1 interactome with both deep coverage and the ability to distinguish high-affinity partners from low-affinity partners. A total of 817 proteins were identified during the Mib1 affinity purification, including 56 high-affinity partners and 335 low-affinity partners, whereas the remaining 426 proteins are likely copurified contaminants or extremely weak binding proteins. The analysis detected all previously known Mib1-interacting proteins and revealed a large number of novel components involved in Notch and Wnt pathways, endocytosis and vesicle transport, the ubiquitin-proteasome system, cellular morphogenesis, and synaptic activities. Immunofluorescence studies further showed colocalization of Mib1 with five selected proteins: the Usp9x (FAM) deubiquitinating enzyme, alpha-, beta-, and delta-catenins, and CDKL5. Mutations of CDKL5 are associated with early infantile epileptic encephalopathy-2 (EIEE2), a severe form of mental retardation. We found that the expression of Mib1 down-regulated the protein level of CDKL5 by ubiquitination, and antagonized CDKL5 function during the formation of dendritic spines. Thus, the sequential elution strategy enables biochemical characterization of protein interactomes; and Mib1 analysis provides a comprehensive interactome for investigating its role in signaling networks and neuronal development. PMID:25931508

A "candidate-interactome" aggregate analysis of genome-wide association data in multiple sclerosis

DEFF Research Database (Denmark)

Mechelli, Rosella; Umeton, Renato; Policano, Claudia

2013-01-01

of genes whose products are known to physically interact with environmental factors that may be relevant for disease pathogenesis) analysis of genome-wide association data in multiple sclerosis. We looked for statistical enrichment of associations among interactomes that, at the current state of knowledge......, may be representative of gene-environment interactions of potential, uncertain or unlikely relevance for multiple sclerosis pathogenesis: Epstein-Barr virus, human immunodeficiency virus, hepatitis B virus, hepatitis C virus, cytomegalovirus, HHV8-Kaposi sarcoma, H1N1-influenza, JC virus, human innate...... immunity interactome for type I interferon, autoimmune regulator, vitamin D receptor, aryl hydrocarbon receptor and a panel of proteins targeted by 70 innate immune-modulating viral open reading frames from 30 viral species. Interactomes were either obtained from the literature or were manually curated...

ARMOUR - A Rice miRNA: mRNA Interaction Resource.

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Sanan-Mishra, Neeti; Tripathi, Anita; Goswami, Kavita; Shukla, Rohit N; Vasudevan, Madavan; Goswami, Hitesh

2018-01-01

ARMOUR was developed as A Rice miRNA:mRNA interaction resource. This informative and interactive database includes the experimentally validated expression profiles of miRNAs under different developmental and abiotic stress conditions across seven Indian rice cultivars. This comprehensive database covers 689 known and 1664 predicted novel miRNAs and their expression profiles in more than 38 different tissues or conditions along with their predicted/known target transcripts. The understanding of miRNA:mRNA interactome in regulation of functional cellular machinery is supported by the sequence information of the mature and hairpin structures. ARMOUR provides flexibility to users in querying the database using multiple ways like known gene identifiers, gene ontology identifiers, KEGG identifiers and also allows on the fly fold change analysis and sequence search query with inbuilt BLAST algorithm. ARMOUR database provides a cohesive platform for novel and mature miRNAs and their expression in different experimental conditions and allows searching for their interacting mRNA targets, GO annotation and their involvement in various biological pathways. The ARMOUR database includes a provision for adding more experimental data from users, with an aim to develop it as a platform for sharing and comparing experimental data contributed by research groups working on rice.

Two novel antimicrobial defensins from rice identified by gene coexpression network analyses.

Science.gov (United States)

Tantong, Supaluk; Pringsulaka, Onanong; Weerawanich, Kamonwan; Meeprasert, Arthitaya; Rungrotmongkol, Thanyada; Sarnthima, Rakrudee; Roytrakul, Sittiruk; Sirikantaramas, Supaart

2016-10-01

Defensins form an antimicrobial peptides (AMP) family, and have been widely studied in various plants because of their considerable inhibitory functions. However, their roles in rice (Oryza sativa L.) have not been characterized, even though rice is one of the most important staple crops that is susceptible to damaging infections. Additionally, a previous study identified 598 rice genes encoding cysteine-rich peptides, suggesting there are several uncharacterized AMPs in rice. We performed in silico gene expression and coexpression network analyses of all genes encoding defensin and defensin-like peptides, and determined that OsDEF7 and OsDEF8 are coexpressed with pathogen-responsive genes. Recombinant OsDEF7 and OsDEF8 could form homodimers. They inhibited the growth of the bacteria Xanthomonas oryzae pv. oryzae, X. oryzae pv. oryzicola, and Erwinia carotovora subsp. atroseptica with minimum inhibitory concentration (MIC) ranging from 0.6 to 63μg/mL. However, these OsDEFs are weakly active against the phytopathogenic fungi Helminthosporium oryzae and Fusarium oxysporum f.sp. cubense. This study describes a useful method for identifying potential plant AMPs with biological activities. Copyright © 2016 Elsevier Inc. All rights reserved.

Transcriptional Network Analysis Reveals Drought Resistance Mechanisms of AP2/ERF Transgenic Rice

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Hongryul Ahn

2017-06-01

Full Text Available This study was designed to investigate at the molecular level how a transgenic version of rice “Nipponbare” obtained a drought-resistant phenotype. Using multi-omics sequencing data, we compared wild-type rice (WT and a transgenic version (erf71 that had obtained a drought-resistant phenotype by overexpressing OsERF71, a member of the AP2/ERF transcription factor (TF family. A comprehensive bioinformatics analysis pipeline, including TF networks and a cascade tree, was developed for the analysis of multi-omics data. The results of the analysis showed that the presence of OsERF71 at the source of the network controlled global gene expression levels in a specific manner to make erf71 survive longer than WT. Our analysis of the time-series transcriptome data suggests that erf71 diverted more energy to survival-critical mechanisms related to translation, oxidative response, and DNA replication, while further suppressing energy-consuming mechanisms, such as photosynthesis. To support this hypothesis further, we measured the net photosynthesis level under physiological conditions, which confirmed the further suppression of photosynthesis in erf71. In summary, our work presents a comprehensive snapshot of transcriptional modification in transgenic rice and shows how this induced the plants to acquire a drought-resistant phenotype.

Interactome of the hepatitis C virus: Literature mining with ANDSystem.

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Saik, Olga V; Ivanisenko, Timofey V; Demenkov, Pavel S; Ivanisenko, Vladimir A

2016-06-15

A study of the molecular genetics mechanisms of host-pathogen interactions is of paramount importance in developing drugs against viral diseases. Currently, the literature contains a huge amount of information that describes interactions between HCV and human proteins. In addition, there are many factual databases that contain experimentally verified data on HCV-host interactions. The sources of such data are the original data along with the data manually extracted from the literature. However, the manual analysis of scientific publications is time consuming and, because of this, databases created with such an approach often do not have complete information. One of the most promising methods to provide actualisation and completeness of information is text mining. Here, with the use of a previously developed method by the authors using ANDSystem, an automated extraction of information on the interactions between HCV and human proteins was conducted. As a data source for the text mining approach, PubMed abstracts and full text articles were used. Additionally, external factual databases were analyzed. On the basis of this analysis, a special version of ANDSystem, extended with the HCV interactome, was created. The HCV interactome contains information about the interactions between 969 human and 11 HCV proteins. Among the 969 proteins, 153 'new' proteins were found not previously referred to in any external databases of protein-protein interactions for HCV-host interactions. Thus, the extended ANDSystem possesses a more comprehensive detailing of HCV-host interactions versus other existing databases. It was interesting that HCV proteins more preferably interact with human proteins that were already involved in a large number of protein-protein interactions as well as those associated with many diseases. Among human proteins of the HCV interactome, there were a large number of proteins regulated by microRNAs. It turned out that the results obtained for protein

Analysis of the robustness of network-based disease-gene prioritization methods reveals redundancy in the human interactome and functional diversity of disease-genes.

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Emre Guney

Full Text Available Complex biological systems usually pose a trade-off between robustness and fragility where a small number of perturbations can substantially disrupt the system. Although biological systems are robust against changes in many external and internal conditions, even a single mutation can perturb the system substantially, giving rise to a pathophenotype. Recent advances in identifying and analyzing the sequential variations beneath human disorders help to comprehend a systemic view of the mechanisms underlying various disease phenotypes. Network-based disease-gene prioritization methods rank the relevance of genes in a disease under the hypothesis that genes whose proteins interact with each other tend to exhibit similar phenotypes. In this study, we have tested the robustness of several network-based disease-gene prioritization methods with respect to the perturbations of the system using various disease phenotypes from the Online Mendelian Inheritance in Man database. These perturbations have been introduced either in the protein-protein interaction network or in the set of known disease-gene associations. As the network-based disease-gene prioritization methods are based on the connectivity between known disease-gene associations, we have further used these methods to categorize the pathophenotypes with respect to the recoverability of hidden disease-genes. Our results have suggested that, in general, disease-genes are connected through multiple paths in the human interactome. Moreover, even when these paths are disturbed, network-based prioritization can reveal hidden disease-gene associations in some pathophenotypes such as breast cancer, cardiomyopathy, diabetes, leukemia, parkinson disease and obesity to a greater extend compared to the rest of the pathophenotypes tested in this study. Gene Ontology (GO analysis highlighted the role of functional diversity for such diseases.

Systematic differences in signal emitting and receiving revealed by PageRank analysis of a human protein interactome.

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Donglei Du

Full Text Available Most protein PageRank studies do not use signal flow direction information in protein interactions because this information was not readily available in large protein databases until recently. Therefore, four questions have yet to be answered: A What is the general difference between signal emitting and receiving in a protein interactome? B Which proteins are among the top ranked in directional ranking? C Are high ranked proteins more evolutionarily conserved than low ranked ones? D Do proteins with similar ranking tend to have similar subcellular locations? In this study, we address these questions using the forward, reverse, and non-directional PageRank approaches to rank an information-directional network of human proteins and study their evolutionary conservation. The forward ranking gives credit to information receivers, reverse ranking to information emitters, and non-directional ranking mainly to the number of interactions. The protein lists generated by the forward and non-directional rankings are highly correlated, but those by the reverse and non-directional rankings are not. The results suggest that the signal emitting/receiving system is characterized by key-emittings and relatively even receivings in the human protein interactome. Signaling pathway proteins are frequent in top ranked ones. Eight proteins are both informational top emitters and top receivers. Top ranked proteins, except a few species-related novel-function ones, are evolutionarily well conserved. Protein-subunit ranking position reflects subunit function. These results demonstrate the usefulness of different PageRank approaches in characterizing protein networks and provide insights to protein interaction in the cell.

Systematic differences in signal emitting and receiving revealed by PageRank analysis of a human protein interactome.

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Du, Donglei; Lee, Connie F; Li, Xiu-Qing

2012-01-01

Most protein PageRank studies do not use signal flow direction information in protein interactions because this information was not readily available in large protein databases until recently. Therefore, four questions have yet to be answered: A) What is the general difference between signal emitting and receiving in a protein interactome? B) Which proteins are among the top ranked in directional ranking? C) Are high ranked proteins more evolutionarily conserved than low ranked ones? D) Do proteins with similar ranking tend to have similar subcellular locations? In this study, we address these questions using the forward, reverse, and non-directional PageRank approaches to rank an information-directional network of human proteins and study their evolutionary conservation. The forward ranking gives credit to information receivers, reverse ranking to information emitters, and non-directional ranking mainly to the number of interactions. The protein lists generated by the forward and non-directional rankings are highly correlated, but those by the reverse and non-directional rankings are not. The results suggest that the signal emitting/receiving system is characterized by key-emittings and relatively even receivings in the human protein interactome. Signaling pathway proteins are frequent in top ranked ones. Eight proteins are both informational top emitters and top receivers. Top ranked proteins, except a few species-related novel-function ones, are evolutionarily well conserved. Protein-subunit ranking position reflects subunit function. These results demonstrate the usefulness of different PageRank approaches in characterizing protein networks and provide insights to protein interaction in the cell.

Characterization of the CLASP2 Protein Interaction Network Identifies SOGA1 as a Microtubule-Associated Protein

DEFF Research Database (Denmark)

Sørensen, Rikke Kruse; Krantz, James; Barker, Natalie

2017-01-01

. The GTPase-activating proteins AGAP1 and AGAP3 were also enriched in the CLASP2 interactome, although subsequent AGAP3 and CLIP2 interactome analysis suggests a preference of AGAP3 for CLIP2. Follow-up MARK2 interactome analysis confirmed reciprocal co-IP of CLASP2 and also revealed MARK2 can co-IP SOGA1......, glycogen synthase, and glycogenin. Investigating the SOGA1 interactome confirmed SOGA1 can reciprocal co-IP both CLASP2 and MARK2 as well as glycogen synthase and glycogenin. SOGA1 was confirmed to colocalize with CLASP2 and also with tubulin, which identifies SOGA1 as a new microtubule-associated protein....... These results introduce the metabolic function of these proposed novel protein networks and their relationship with microtubules as new fields of cytoskeleton-associated protein biology....

DETERMINATION OF SPATIAL INTEGRATION AND SUBSTITUTION OF FOREIGN RICE FOR LOCAL RICE IN GHANA

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Philip Kofi ADOM

2014-11-01

Full Text Available This study tested for spatial integration in the rice market and the substitution of imported rice for local rice in Ghana. It is established that the markets for domestic imported rice are well-integrated, but not complete. The imperfect spatial integration of domestic foreign rice markets implies that the market provides opportunities for arbitrage. Price leadership roles are found to be determined by the kind of sub-inter-regional-trade network defined. However, in all, the Accra market emerged as a dominant market leader in the domestic foreign rice market. There is evidence of significant regional substitution of foreign rice for local rice in the long run, but the result is mixed in the short run. The result that local rice is not a perfect substitute for imported rice implies that price disincentive measures such as increasing the import tariffs on foreign rice will only produce a mild effect on increasing the producer price faced by local rice farmers, but aggravate the burden on households’ budget.

Expression of DISC1-interactome members correlates with cognitive phenotypes related to schizophrenia.

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Rampino, Antonio; Walker, Rosie May; Torrance, Helen Scott; Anderson, Susan Maguire; Fazio, Leonardo; Di Giorgio, Annabella; Taurisano, Paolo; Gelao, Barbara; Romano, Raffaella; Masellis, Rita; Ursini, Gianluca; Caforio, Grazia; Blasi, Giuseppe; Millar, J Kirsty; Porteous, David John; Thomson, Pippa Ann; Bertolino, Alessandro; Evans, Kathryn Louise

2014-01-01

Cognitive dysfunction is central to the schizophrenia phenotype. Genetic and functional studies have implicated Disrupted-in-Schizophrenia 1 (DISC1), a leading candidate gene for schizophrenia and related psychiatric conditions, in cognitive function. Altered expression of DISC1 and DISC1-interactors has been identified in schizophrenia. Dysregulated expression of DISC1-interactome genes might, therefore, contribute to schizophrenia susceptibility via disruption of molecular systems required for normal cognitive function. Here, the blood RNA expression levels of DISC1 and DISC1-interacting proteins were measured in 63 control subjects. Cognitive function was assessed using neuropsychiatric tests and functional magnetic resonance imaging was used to assess the activity of prefrontal cortical regions during the N-back working memory task, which is abnormal in schizophrenia. Pairwise correlations between gene expression levels and the relationship between gene expression levels and cognitive function and N-back-elicited brain activity were assessed. Finally, the expression levels of DISC1, AKAP9, FEZ1, NDEL1 and PCM1 were compared between 63 controls and 69 schizophrenic subjects. We found that DISC1-interactome genes showed correlated expression in the blood of healthy individuals. The expression levels of several interactome members were correlated with cognitive performance and N-back-elicited activity in the prefrontal cortex. In addition, DISC1 and NDEL1 showed decreased expression in schizophrenic subjects compared to healthy controls. Our findings highlight the importance of the coordinated expression of DISC1-interactome genes for normal cognitive function and suggest that dysregulated DISC1 and NDEL1 expression might, in part, contribute to susceptibility for schizophrenia via disruption of prefrontal cortex-dependent cognitive functions.

Expression of DISC1-interactome members correlates with cognitive phenotypes related to schizophrenia.

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Antonio Rampino

Full Text Available Cognitive dysfunction is central to the schizophrenia phenotype. Genetic and functional studies have implicated Disrupted-in-Schizophrenia 1 (DISC1, a leading candidate gene for schizophrenia and related psychiatric conditions, in cognitive function. Altered expression of DISC1 and DISC1-interactors has been identified in schizophrenia. Dysregulated expression of DISC1-interactome genes might, therefore, contribute to schizophrenia susceptibility via disruption of molecular systems required for normal cognitive function. Here, the blood RNA expression levels of DISC1 and DISC1-interacting proteins were measured in 63 control subjects. Cognitive function was assessed using neuropsychiatric tests and functional magnetic resonance imaging was used to assess the activity of prefrontal cortical regions during the N-back working memory task, which is abnormal in schizophrenia. Pairwise correlations between gene expression levels and the relationship between gene expression levels and cognitive function and N-back-elicited brain activity were assessed. Finally, the expression levels of DISC1, AKAP9, FEZ1, NDEL1 and PCM1 were compared between 63 controls and 69 schizophrenic subjects. We found that DISC1-interactome genes showed correlated expression in the blood of healthy individuals. The expression levels of several interactome members were correlated with cognitive performance and N-back-elicited activity in the prefrontal cortex. In addition, DISC1 and NDEL1 showed decreased expression in schizophrenic subjects compared to healthy controls. Our findings highlight the importance of the coordinated expression of DISC1-interactome genes for normal cognitive function and suggest that dysregulated DISC1 and NDEL1 expression might, in part, contribute to susceptibility for schizophrenia via disruption of prefrontal cortex-dependent cognitive functions.

Recent advances in the dissection of drought-stress regulatory networks and strategies for development of drought-tolerant transgenic rice plants.

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Todaka, Daisuke; Shinozaki, Kazuo; Yamaguchi-Shinozaki, Kazuko

2015-01-01

Advances have been made in the development of drought-tolerant transgenic plants, including cereals. Rice, one of the most important cereals, is considered to be a critical target for improving drought tolerance, as present-day rice cultivation requires large quantities of water and as drought-tolerant rice plants should be able to grow in small amounts of water. Numerous transgenic rice plants showing enhanced drought tolerance have been developed to date. Such genetically engineered plants have generally been developed using genes encoding proteins that control drought regulatory networks. These proteins include transcription factors, protein kinases, receptor-like kinases, enzymes related to osmoprotectant or plant hormone synthesis, and other regulatory or functional proteins. Of the drought-tolerant transgenic rice plants described in this review, approximately one-third show decreased plant height under non-stressed conditions or in response to abscisic acid treatment. In cereal crops, plant height is a very important agronomic trait directly affecting yield, although the improvement of lodging resistance should also be taken into consideration. Understanding the regulatory mechanisms of plant growth reduction under drought stress conditions holds promise for developing transgenic plants that produce high yields under drought stress conditions. Plant growth rates are reduced more rapidly than photosynthetic activity under drought conditions, implying that plants actively reduce growth in response to drought stress. In this review, we summarize studies on molecular regulatory networks involved in response to drought stress. In a separate section, we highlight progress in the development of transgenic drought-tolerant rice plants, with special attention paid to field trial investigations.

Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress

KAUST Repository

Yun, Kil-Young; Park, Myoung Ryoul; Mohanty, Bijayalaxmi; Herath, Venura; Xu, Fuyu; Mauleon, Ramil; Wijaya, Edward; Bajic, Vladimir B.; Bruskiewich, Richard; de los Reyes, Benildo G

2010-01-01

-plant level analyses established a holistic view of chilling stress response mechanism of japonica rice. Early response regulatory network triggered by oxidative signals is critical for prolonged survival under sub-optimal temperature. Integration of stress

ARMOUR – A Rice miRNA: mRNA Interaction Resource

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Neeti Sanan-Mishra

2018-05-01

Full Text Available ARMOUR was developed as ARice miRNA:mRNA interaction resource. This informative and interactive database includes the experimentally validated expression profiles of miRNAs under different developmental and abiotic stress conditions across seven Indian rice cultivars. This comprehensive database covers 689 known and 1664 predicted novel miRNAs and their expression profiles in more than 38 different tissues or conditions along with their predicted/known target transcripts. The understanding of miRNA:mRNA interactome in regulation of functional cellular machinery is supported by the sequence information of the mature and hairpin structures. ARMOUR provides flexibility to users in querying the database using multiple ways like known gene identifiers, gene ontology identifiers, KEGG identifiers and also allows on the fly fold change analysis and sequence search query with inbuilt BLAST algorithm. ARMOUR database provides a cohesive platform for novel and mature miRNAs and their expression in different experimental conditions and allows searching for their interacting mRNA targets, GO annotation and their involvement in various biological pathways. The ARMOUR database includes a provision for adding more experimental data from users, with an aim to develop it as a platform for sharing and comparing experimental data contributed by research groups working on rice.

Identification of conserved drought stress responsive gene-network across tissues and developmental stages in rice.

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Smita, Shuchi; Katiyar, Amit; Pandey, Dev Mani; Chinnusamy, Viswanathan; Archak, Sunil; Bansal, Kailash Chander

2013-01-01

Identification of genes that are coexpressed across various tissues and environmental stresses is biologically interesting, since they may play coordinated role in similar biological processes. Genes with correlated expression patterns can be best identified by using coexpression network analysis of transcriptome data. In the present study, we analyzed the temporal-spatial coordination of gene expression in root, leaf and panicle of rice under drought stress and constructed network using WGCNA and Cytoscape. Total of 2199 differentially expressed genes (DEGs) were identified in at least three or more tissues, wherein 88 genes have coordinated expression profile among all the six tissues under drought stress. These 88 highly coordinated genes were further subjected to module identification in the coexpression network. Based on chief topological properties we identified 18 hub genes such as ABC transporter, ATP-binding protein, dehydrin, protein phosphatase 2C, LTPL153 - Protease inhibitor, phosphatidylethanolaminebinding protein, lactose permease-related, NADP-dependent malic enzyme, etc. Motif enrichment analysis showed the presence of ABRE cis-elements in the promoters of > 62% of the coordinately expressed genes. Our results suggest that drought stress mediated upregulated gene expression was coordinated through an ABA-dependent signaling pathway across tissues, at least for the subset of genes identified in this study, while down regulation appears to be regulated by tissue specific pathways in rice.

Grouping annotations on the subcellular layered interactome demonstrates enhanced autophagy activity in a recurrent experimental autoimmune uveitis T cell line.

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Xiuzhi Jia

Full Text Available Human uveitis is a type of T cell-mediated autoimmune disease that often shows relapse-remitting courses affecting multiple biological processes. As a cytoplasmic process, autophagy has been seen as an adaptive response to cell death and survival, yet the link between autophagy and T cell-mediated autoimmunity is not certain. In this study, based on the differentially expressed genes (GSE19652 between the recurrent versus monophasic T cell lines, whose adoptive transfer to susceptible animals may result in respective recurrent or monophasic uveitis, we proposed grouping annotations on a subcellular layered interactome framework to analyze the specific bioprocesses that are linked to the recurrence of T cell autoimmunity. That is, the subcellular layered interactome was established by the Cytoscape and Cerebral plugin based on differential expression, global interactome, and subcellular localization information. Then, the layered interactomes were grouping annotated by the ClueGO plugin based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. The analysis showed that significant bioprocesses with autophagy were orchestrated in the cytoplasmic layered interactome and that mTOR may have a regulatory role in it. Furthermore, by setting up recurrent and monophasic uveitis in Lewis rats, we confirmed by transmission electron microscopy that, in comparison to the monophasic disease, recurrent uveitis in vivo showed significantly increased autophagy activity and extended lymphocyte infiltration to the affected retina. In summary, our framework methodology is a useful tool to disclose specific bioprocesses and molecular targets that can be attributed to a certain disease. Our results indicated that targeted inhibition of autophagy pathways may perturb the recurrence of uveitis.

Cramer-Rao Lower Bound Evaluation for Linear Frequency Modulation Based Active Radar Networks Operating in a Rice Fading Environment.

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Shi, Chenguang; Salous, Sana; Wang, Fei; Zhou, Jianjiang

2016-12-06

This paper investigates the joint target parameter (delay and Doppler) estimation performance of linear frequency modulation (LFM)-based radar networks in a Rice fading environment. The active radar networks are composed of multiple radar transmitters and multichannel receivers placed on moving platforms. First, the log-likelihood function of the received signal for a Rician target is derived, where the received signal scattered off the target comprises of dominant scatterer (DS) component and weak isotropic scatterers (WIS) components. Then, the analytically closed-form expressions of the Cramer-Rao lower bounds (CRLBs) on the Cartesian coordinates of target position and velocity are calculated, which can be adopted as a performance metric to access the target parameter estimation accuracy for LFM-based radar network systems in a Rice fading environment. It is found that the cumulative Fisher information matrix (FIM) is a linear combination of both DS component and WIS components, and it also demonstrates that the joint CRLB is a function of signal-to-noise ratio (SNR), target's radar cross section (RCS) and transmitted waveform parameters, as well as the relative geometry between the target and the radar network architectures. Finally, numerical results are provided to indicate that the joint target parameter estimation performance of active radar networks can be significantly improved with the exploitation of DS component.

Cramer-Rao Lower Bound Evaluation for Linear Frequency Modulation Based Active Radar Networks Operating in a Rice Fading Environment

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Chenguang Shi

2016-12-01

Full Text Available This paper investigates the joint target parameter (delay and Doppler estimation performance of linear frequency modulation (LFM-based radar networks in a Rice fading environment. The active radar networks are composed of multiple radar transmitters and multichannel receivers placed on moving platforms. First, the log-likelihood function of the received signal for a Rician target is derived, where the received signal scattered off the target comprises of dominant scatterer (DS component and weak isotropic scatterers (WIS components. Then, the analytically closed-form expressions of the Cramer-Rao lower bounds (CRLBs on the Cartesian coordinates of target position and velocity are calculated, which can be adopted as a performance metric to access the target parameter estimation accuracy for LFM-based radar network systems in a Rice fading environment. It is found that the cumulative Fisher information matrix (FIM is a linear combination of both DS component and WIS components, and it also demonstrates that the joint CRLB is a function of signal-to-noise ratio (SNR, target’s radar cross section (RCS and transmitted waveform parameters, as well as the relative geometry between the target and the radar network architectures. Finally, numerical results are provided to indicate that the joint target parameter estimation performance of active radar networks can be significantly improved with the exploitation of DS component.

Network-based association of hypoxia-responsive genes with cardiovascular diseases

International Nuclear Information System (INIS)

Wang, Rui-Sheng; Oldham, William M; Loscalzo, Joseph

2014-01-01

Molecular oxygen is indispensable for cellular viability and function. Hypoxia is a stress condition in which oxygen demand exceeds supply. Low cellular oxygen content induces a number of molecular changes to activate regulatory pathways responsible for increasing the oxygen supply and optimizing cellular metabolism under limited oxygen conditions. Hypoxia plays critical roles in the pathobiology of many diseases, such as cancer, heart failure, myocardial ischemia, stroke, and chronic lung diseases. Although the complicated associations between hypoxia and cardiovascular (and cerebrovascular) diseases (CVD) have been recognized for some time, there are few studies that investigate their biological link from a systems biology perspective. In this study, we integrate hypoxia genes, CVD genes, and the human protein interactome in order to explore the relationship between hypoxia and cardiovascular diseases at a systems level. We show that hypoxia genes are much closer to CVD genes in the human protein interactome than that expected by chance. We also find that hypoxia genes play significant bridging roles in connecting different cardiovascular diseases. We construct a hypoxia-CVD bipartite network and find several interesting hypoxia-CVD modules with significant gene ontology similarity. Finally, we show that hypoxia genes tend to have more CVD interactors in the human interactome than in random networks of matching topology. Based on these observations, we can predict novel genes that may be associated with CVD. This network-based association study gives us a broad view of the relationships between hypoxia and cardiovascular diseases and provides new insights into the role of hypoxia in cardiovascular biology. (paper)

Tillering and panicle branching genes in rice.

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Liang, Wei-hong; Shang, Fei; Lin, Qun-ting; Lou, Chen; Zhang, Jing

2014-03-01

Rice (Oryza sativa L.) is one of the most important staple food crops in the world, and rice tillering and panicle branching are important traits determining grain yield. Since the gene MONOCULM 1 (MOC 1) was first characterized as a key regulator in controlling rice tillering and branching, great progress has been achieved in identifying important genes associated with grain yield, elucidating the genetic basis of yield-related traits. Some of these important genes were shown to be applicable for molecular breeding of high-yielding rice. This review focuses on recent advances, with emphasis on rice tillering and panicle branching genes, and their regulatory networks. Copyright © 2013 Elsevier B.V. All rights reserved.

Serum Amyloid P Component (SAP) Interactome in Human Plasma Containing Physiological Calcium Levels.

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Poulsen, Ebbe Toftgaard; Pedersen, Kata Wolff; Marzeda, Anna Maria; Enghild, Jan J

2017-02-14

The pentraxin serum amyloid P component (SAP) is secreted by the liver and found in plasma at a concentration of approximately 30 mg/L. SAP is a 25 kDa homopentamer known to bind both protein and nonprotein ligands, all in a calcium-dependent manner. The function of SAP is unclear but likely involves the humoral innate immune system spanning the complement system, inflammation, and coagulation. Also, SAP is known to bind to the generic structure of amyloid deposits and possibly to protect them against proteolysis. In this study, we have characterized the SAP interactome in human plasma containing the physiological Ca 2+ concentration using SAP affinity pull-down and co-immunoprecipitation experiments followed by mass spectrometry analyses. The analyses resulted in the identification of 33 proteins, of which 24 were direct or indirect interaction partners not previously reported. The SAP interactome can be divided into categories that include apolipoproteins, the complement system, coagulation, and proteolytic regulation.

Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis.

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Klopffleisch, Karsten; Phan, Nguyen; Augustin, Kelsey; Bayne, Robert S; Booker, Katherine S; Botella, Jose R; Carpita, Nicholas C; Carr, Tyrell; Chen, Jin-Gui; Cooke, Thomas Ryan; Frick-Cheng, Arwen; Friedman, Erin J; Fulk, Brandon; Hahn, Michael G; Jiang, Kun; Jorda, Lucia; Kruppe, Lydia; Liu, Chenggang; Lorek, Justine; McCann, Maureen C; Molina, Antonio; Moriyama, Etsuko N; Mukhtar, M Shahid; Mudgil, Yashwanti; Pattathil, Sivakumar; Schwarz, John; Seta, Steven; Tan, Matthew; Temp, Ulrike; Trusov, Yuri; Urano, Daisuke; Welter, Bastian; Yang, Jing; Panstruga, Ralph; Uhrig, Joachim F; Jones, Alan M

2011-09-27

The heterotrimeric G-protein complex is minimally composed of Gα, Gβ, and Gγ subunits. In the classic scenario, the G-protein complex is the nexus in signaling from the plasma membrane, where the heterotrimeric G-protein associates with heptahelical G-protein-coupled receptors (GPCRs), to cytoplasmic target proteins called effectors. Although a number of effectors are known in metazoans and fungi, none of these are predicted to exist in their canonical forms in plants. To identify ab initio plant G-protein effectors and scaffold proteins, we screened a set of proteins from the G-protein complex using two-hybrid complementation in yeast. After deep and exhaustive interrogation, we detected 544 interactions between 434 proteins, of which 68 highly interconnected proteins form the core G-protein interactome. Within this core, over half of the interactions comprising two-thirds of the nodes were retested and validated as genuine in planta. Co-expression analysis in combination with phenotyping of loss-of-function mutations in a set of core interactome genes revealed a novel role for G-proteins in regulating cell wall modification.

Rice agroecosystem and the maintenance of biodiversity

International Nuclear Information System (INIS)

Ahyaudin Ali

2002-01-01

Rice fields are a special type of wetland. They are shallow, constantly disturbed and experience extremes in temperature and dissolved oxygen content. They receive nutrients in the form of fertilizers during rice cultivation. Rice fields; support a variety of flora and fauna that have adapted and adjusted themselves to the extreme conditions. Since rice fields also support populations of wild fish, rice?fish integration should be done in order to optimize land use and provide supplementary income to farmers. Rice?fish farming encourages farmers to judiciously apply pesticides and herbicides in their fields thus helping to control excessive and unwarranted use of these chemicals. Rice fields also support many migratory and nonmigratory bird species and provides habitat for small mammals. Thus the rice agroecosystem helps to maintain aquatic biodiversity. The Muda rice agroecosystem consists of a troika of interconnected ecosystems. The troika consisting of reservoirs, the connecting network of canals and the rice fields; should be investigated further. This data is needed for informed decision-making concerning development and management of the system so that productivity and biodiversity can be maintained and sustained. (Author)

Sustainable rice production in Malaysia beyond 2000

International Nuclear Information System (INIS)

Nashriyah Mat; Ho Nai Kin; Ismail Sahid; Ahyaudin Ali; Lum Keng Yeang; Mashhor Mansor

2002-01-01

This book is a compendium of works carried out by various institutions on subjects related to sustainable rice production. The institutions comprise Department of Agriculture, Malaysian Agricultural Research and Development Institute, Malaysian Institute for Nuclear Technology Research, Muda Agricultural Development Authority, Universiti Kebangsaan Malaysia, Universiti Putra Malaysia, Universiti Sains Malaysia, International Islamic University of Malaysia and the Agrochemical Company Mosanto. Integrated Biodiversity Management parallel with the Integrated Weed / Pest / Disease Management, rice-fish farming networking, agrochemical residue monitoring in rice and marine ecosystems, and application of biotechnology in rice productivity are taken as the future direction towards achieving sustainable rice production beyond 2000. Challenges from social and technical agroecosystem constraints, agricultural input management and maintenance of agroecosystem biodiversity are highlighted. It is imperative that the challenges are surmounted to attain the target that would be reflected by tangible rice output of 10 t/ha, and at the same time maintaining the well-being of rice-farmers. (Author)

Molecular characterization and interactome analysis of Trypanosoma cruzi tryparedoxin II.

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Arias, Diego G; Piñeyro, María Dolores; Iglesias, Alberto A; Guerrero, Sergio A; Robello, Carlos

2015-04-29

Trypanosoma cruzi, the causative agent of Chagas disease, possesses two tryparedoxins (TcTXNI and TcTXNII), belonging to the thioredoxin superfamily. TXNs are oxidoreductases which mediate electron transfer between trypanothione and peroxiredoxins. This constitutes a difference with the host cells, in which these activities are mediated by thioredoxins. These differences make TXNs an attractive target for drug development. In a previous work we characterized TcTXNI, including the redox interactome. In this work we extend the study to TcTXNII. We demonstrate that TcTXNII is a transmembrane protein anchored to the surface of the mitochondria and endoplasmic reticulum, with a cytoplasmatic orientation of the redox domain. It would be expressed during the metacyclogenesis process. In order to continue with the characterization of the redox interactome of T. cruzi, we designed an active site mutant TcTXNII lacking the resolving cysteine, and through the expression of this mutant protein and incubation with T. cruzi proteins, heterodisulfide complexes were isolated by affinity chromatography and identified by mass spectrometry. This allowed us to identify sixteen TcTXNII interacting proteins, which are involved in a wide range of cellular processes, indicating the relevance of TcTXNII, and contributing to our understanding of the redox interactome of T. cruzi. T. cruzi, the causative agent of Chagas disease, constitutes a major sanitary problem in Latin America. The number of estimated infected persons is ca. 8 million, 28 million people are at risk of infection and ~20,000 deaths occur per year in endemic regions. No vaccines are available at present, and most drugs currently in use were developed decades ago and show variable efficacy with undesirable side effects. The parasite is able to live and prolipherate inside macrophage phagosomes, where it is exposed to cytotoxic reactive oxygen and nitrogen species, derived from macrophage activation. Therefore, T. cruzi

Integration of multiple biological features yields high confidence human protein interactome.

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Karagoz, Kubra; Sevimoglu, Tuba; Arga, Kazim Yalcin

2016-08-21

The biological function of a protein is usually determined by its physical interaction with other proteins. Protein-protein interactions (PPIs) are identified through various experimental methods and are stored in curated databases. The noisiness of the existing PPI data is evident, and it is essential that a more reliable data is generated. Furthermore, the selection of a set of PPIs at different confidence levels might be necessary for many studies. Although different methodologies were introduced to evaluate the confidence scores for binary interactions, a highly reliable, almost complete PPI network of Homo sapiens is not proposed yet. The quality and coverage of human protein interactome need to be improved to be used in various disciplines, especially in biomedicine. In the present work, we propose an unsupervised statistical approach to assign confidence scores to PPIs of H. sapiens. To achieve this goal PPI data from six different databases were collected and a total of 295,288 non-redundant interactions between 15,950 proteins were acquired. The present scoring system included the context information that was assigned to PPIs derived from eight biological attributes. A high confidence network, which included 147,923 binary interactions between 13,213 proteins, had scores greater than the cutoff value of 0.80, for which sensitivity, specificity, and coverage were 94.5%, 80.9%, and 82.8%, respectively. We compared the present scoring method with others for evaluation. Reducing the noise inherent in experimental PPIs via our scoring scheme increased the accuracy significantly. As it was demonstrated through the assessment of process and cancer subnetworks, this study allows researchers to construct and analyze context-specific networks via valid PPI sets and one can easily achieve subnetworks around proteins of interest at a specified confidence level. Copyright © 2016 Elsevier Ltd. All rights reserved.

Interactomic approach for evaluating nucleophosmin-binding proteins as biomarkers for Ewing's sarcoma.

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Haga, Ayako; Ogawara, Yoko; Kubota, Daisuke; Kitabayashi, Issay; Murakami, Yasufumi; Kondo, Tadashi

2013-06-01

Nucleophosmin (NPM) is a novel prognostic biomarker for Ewing's sarcoma. To evaluate the prognostic utility of NPM, we conducted an interactomic approach to characterize the NPM protein complex in Ewing's sarcoma cells. A gene suppression assay revealed that NPM promoted cell proliferation and the invasive properties of Ewing's sarcoma cells. FLAG-tag-based affinity purification coupled with liquid chromatography-tandem mass spectrometry identified 106 proteins in the NPM protein complex. The functional classification suggested that the NPM complex participates in critical biological events, including ribosome biogenesis, regulation of transcription and translation, and protein folding, that are mediated by these proteins. In addition to JAK1, a candidate prognostic biomarker for Ewing's sarcoma, the NPM complex, includes 11 proteins known as prognostic biomarkers for other malignancies. Meta-analysis of gene expression profiles of 32 patients with Ewing's sarcoma revealed that 6 of 106 were significantly and independently associated with survival period. These observations suggest a functional role as well as prognostic value of these NPM complex proteins in Ewing's sarcoma. Further, our study suggests the potential applications of interactomics in conjunction with meta-analysis for biomarker discovery. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

RNA/DNA Hybrid Interactome Identifies DXH9 as a Molecular Player in Transcriptional Termination and R-Loop-Associated DNA Damage.

Science.gov (United States)

Cristini, Agnese; Groh, Matthias; Kristiansen, Maiken S; Gromak, Natalia

2018-05-08

R-loops comprise an RNA/DNA hybrid and displaced single-stranded DNA. They play important biological roles and are implicated in pathology. Even so, proteins recognizing these structures are largely undefined. Using affinity purification with the S9.6 antibody coupled to mass spectrometry, we defined the RNA/DNA hybrid interactome in HeLa cells. This consists of known R-loop-associated factors SRSF1, FACT, and Top1, and yet uncharacterized interactors, including helicases, RNA processing, DNA repair, and chromatin factors. We validate specific examples of these interactors and characterize their involvement in R-loop biology. A top candidate DHX9 helicase promotes R-loop suppression and transcriptional termination. DHX9 interacts with PARP1, and both proteins prevent R-loop-associated DNA damage. DHX9 and other interactome helicases are overexpressed in cancer, linking R-loop-mediated DNA damage and disease. Our RNA/DNA hybrid interactome provides a powerful resource to study R-loop biology in health and disease. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Investigation of PARP-1, PARP-2, and PARG interactomes by affinity-purification mass spectrometry

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Isabelle Maxim

2010-04-01

Full Text Available Abstract Background Poly(ADP-ribose polymerases (PARPs catalyze the formation of poly(ADP-ribose (pADPr, a post-translational modification involved in several important biological processes, namely surveillance of genome integrity, cell cycle progression, initiation of the DNA damage response, apoptosis, and regulation of transcription. Poly(ADP-ribose glycohydrolase (PARG, on the other hand, catabolizes pADPr and thereby accounts for the transient nature of poly(ADP-ribosylation. Our investigation of the interactomes of PARP-1, PARP-2, and PARG by affinity-purification mass spectrometry (AP-MS aimed, on the one hand, to confirm current knowledge on these interactomes and, on the other hand, to discover new protein partners which could offer insights into PARPs and PARG functions. Results PARP-1, PARP-2, and PARG were immunoprecipitated from human cells, and pulled-down proteins were separated by gel electrophoresis prior to in-gel trypsin digestion. Peptides were identified by tandem mass spectrometry. Our AP-MS experiments resulted in the identifications of 179 interactions, 139 of which are novel interactions. Gene Ontology analysis of the identified protein interactors points to five biological processes in which PARP-1, PARP-2 and PARG may be involved: RNA metabolism for PARP-1, PARP-2 and PARG; DNA repair and apoptosis for PARP-1 and PARP-2; and glycolysis and cell cycle for PARP-1. Conclusions This study reveals several novel protein partners for PARP-1, PARP-2 and PARG. It provides a global view of the interactomes of these proteins as well as a roadmap to establish the systems biology of poly(ADP-ribose metabolism.

Proteomic-coupled-network analysis of T877A-androgen receptor interactomes can predict clinical prostate cancer outcomes between White (non-Hispanic and African-American groups.

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Naif Zaman

Full Text Available The androgen receptor (AR remains an important contributor to the neoplastic evolution of prostate cancer (CaP. CaP progression is linked to several somatic AR mutational changes that endow upon the AR dramatic gain-of-function properties. One of the most common somatic mutations identified is Thr877-to-Ala (T877A, located in the ligand-binding domain, that results in a receptor capable of promiscuous binding and activation by a variety of steroid hormones and ligands including estrogens, progestins, glucocorticoids, and several anti-androgens. In an attempt to further define somatic mutated AR gain-of-function properties, as a consequence of its promiscuous ligand binding, we undertook a proteomic/network analysis approach to characterize the protein interactome of the mutant T877A-AR in LNCaP cells under eight different ligand-specific treatments (dihydrotestosterone, mibolerone, R1881, testosterone, estradiol, progesterone, dexamethasone, and cyproterone acetate. In extending the analysis of our multi-ligand complexes of the mutant T877A-AR we observed significant enrichment of specific complexes between normal and primary prostatic tumors, which were furthermore correlated with known clinical outcomes. Further analysis of certain mutant T877A-AR complexes showed specific population preferences distinguishing primary prostatic disease between white (non-Hispanic vs. African-American males. Moreover, these cancer-related AR-protein complexes demonstrated predictive survival outcomes specific to CaP, and not for breast, lung, lymphoma or medulloblastoma cancers. Our study, by coupling data generated by our proteomics to network analysis of clinical samples, has helped to define real and novel biological pathways in complicated gain-of-function AR complex systems.

Gene, protein, and network of male sterility in rice

OpenAIRE

Wang, Kun; Peng, Xiaojue; Ji, Yanxiao; Yang, Pingfang; Zhu, Yingguo; Li, Shaoqing

2013-01-01

Rice is one of the most important model crop plants whose heterosis has been well-exploited in commercial hybrid seed production via a variety of types of male-sterile lines. Hybrid rice cultivation area is steadily expanding around the world, especially in Southern Asia. Characterization of genes and proteins related to male sterility aims to understand how and why the male sterility occurs, and which proteins are the key players for microspores abortion. Recently, a series of genes and prot...

Improved microarray-based decision support with graph encoded interactome data.

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Anneleen Daemen

Full Text Available In the past, microarray studies have been criticized due to noise and the limited overlap between gene signatures. Prior biological knowledge should therefore be incorporated as side information in models based on gene expression data to improve the accuracy of diagnosis and prognosis in cancer. As prior knowledge, we investigated interaction and pathway information from the human interactome on different aspects of biological systems. By exploiting the properties of kernel methods, relations between genes with similar functions but active in alternative pathways could be incorporated in a support vector machine classifier based on spectral graph theory. Using 10 microarray data sets, we first reduced the number of data sources relevant for multiple cancer types and outcomes. Three sources on metabolic pathway information (KEGG, protein-protein interactions (OPHID and miRNA-gene targeting (microRNA.org outperformed the other sources with regard to the considered class of models. Both fixed and adaptive approaches were subsequently considered to combine the three corresponding classifiers. Averaging the predictions of these classifiers performed best and was significantly better than the model based on microarray data only. These results were confirmed on 6 validation microarray sets, with a significantly improved performance in 4 of them. Integrating interactome data thus improves classification of cancer outcome for the investigated microarray technologies and cancer types. Moreover, this strategy can be incorporated in any kernel method or non-linear version of a non-kernel method.

Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment

Energy Technology Data Exchange (ETDEWEB)

Mohammadi, Shahin [Purdue Univ., West Lafayette, IN (United States); Gleich, David F. [Purdue Univ., West Lafayette, IN (United States); Kolda, Tamara G. [Sandia National Laboratories (SNL-CA), Livermore, CA (United States); Grama, Ananth [Purdue Univ., West Lafayette, IN (United States)

2015-11-01

Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangular AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.

Searching for cellular partners of hantaviral nonstructural protein NSs: Y2H screening of mouse cDNA library and analysis of cellular interactome.

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Rönnberg, Tuomas; Jääskeläinen, Kirsi; Blot, Guillaume; Parviainen, Ville; Vaheri, Antti; Renkonen, Risto; Bouloy, Michele; Plyusnin, Alexander

2012-01-01

Hantaviruses (Bunyaviridae) are negative-strand RNA viruses with a tripartite genome. The small (S) segment encodes the nucleocapsid protein and, in some hantaviruses, also the nonstructural protein (NSs). The aim of this study was to find potential cellular partners for the hantaviral NSs protein. Toward this aim, yeast two-hybrid (Y2H) screening of mouse cDNA library was performed followed by a search for potential NSs protein counterparts via analyzing a cellular interactome. The resulting interaction network was shown to form logical, clustered structures. Furthermore, several potential binding partners for the NSs protein, for instance ACBD3, were identified and, to prove the principle, interaction between NSs and ACBD3 proteins was demonstrated biochemically.

Assessment of reference gene stability in Rice stripe virus and Rice black streaked dwarf virus infection rice by quantitative Real-time PCR.

Science.gov (United States)

Fang, Peng; Lu, Rongfei; Sun, Feng; Lan, Ying; Shen, Wenbiao; Du, Linlin; Zhou, Yijun; Zhou, Tong

2015-10-24

Stably expressed reference gene(s) normalization is important for the understanding of gene expression patterns by quantitative Real-time PCR (RT-qPCR), particularly for Rice stripe virus (RSV) and Rice black streaked dwarf virus (RBSDV) that caused seriously damage on rice plants in China and Southeast Asia. The expression of fourteen common used reference genes of Oryza sativa L. were evaluated by RT-qPCR in RSV and RBSDV infected rice plants. Suitable normalization reference gene(s) were identified by geNorm and NormFinder algorithms. UBQ 10 + GAPDH and UBC + Actin1 were identified as suitable reference genes for RT-qPCR normalization under RSV and RBSDV infection, respectively. When using multiple reference genes, the expression patterns of OsPRIb and OsWRKY, two virus resistance genes, were approximately similar with that reported previously. Comparatively, by using single reference gene (TIP41-Like), a weaker inducible response was observed. We proposed that the combination of two reference genes could obtain more accurate and reliable normalization of RT-qPCR results in RSV- and RBSDV-infected plants. This work therefore sheds light on establishing a standardized RT-qPCR procedure in RSV- and RBSDV-infected rice plants, and might serve as an important point for discovering complex regulatory networks and identifying genes relevant to biological processes or implicated in virus.

POINeT: protein interactome with sub-network analysis and hub prioritization

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Lai Jin-Mei

2009-04-01

Full Text Available Abstract Background Protein-protein interactions (PPIs are critical to every aspect of biological processes. Expansion of all PPIs from a set of given queries often results in a complex PPI network lacking spatiotemporal consideration. Moreover, the reliability of available PPI resources, which consist of low- and high-throughput data, for network construction remains a significant challenge. Even though a number of software tools are available to facilitate PPI network analysis, an integrated tool is crucial to alleviate the burden on querying across multiple web servers and software tools. Results We have constructed an integrated web service, POINeT, to simplify the process of PPI searching, analysis, and visualization. POINeT merges PPI and tissue-specific expression data from multiple resources. The tissue-specific PPIs and the numbers of research papers supporting the PPIs can be filtered with user-adjustable threshold values and are dynamically updated in the viewer. The network constructed in POINeT can be readily analyzed with, for example, the built-in centrality calculation module and an integrated network viewer. Nodes in global networks can also be ranked and filtered using various network analysis formulas, i.e., centralities. To prioritize the sub-network, we developed a ranking filtered method (S3 to uncover potential novel mediators in the midbody network. Several examples are provided to illustrate the functionality of POINeT. The network constructed from four schizophrenia risk markers suggests that EXOC4 might be a novel marker for this disease. Finally, a liver-specific PPI network has been filtered with adult and fetal liver expression profiles. Conclusion The functionalities provided by POINeT are highly improved compared to previous version of POINT. POINeT enables the identification and ranking of potential novel genes involved in a sub-network. Combining with tissue-specific gene expression profiles, PPIs specific to

A Global Interactome Map of the Dengue Virus NS1 Identifies Virus Restriction and Dependency Host Factors

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Mohamed Lamine Hafirassou

2017-12-01

Full Text Available Dengue virus (DENV infections cause the most prevalent mosquito-borne viral disease worldwide, for which no therapies are available. DENV encodes seven non-structural (NS proteins that co-assemble and recruit poorly characterized host factors to form the DENV replication complex essential for viral infection. Here, we provide a global proteomic analysis of the human host factors that interact with the DENV NS1 protein. Combined with a functional RNAi screen, this study reveals a comprehensive network of host cellular processes involved in DENV infection and identifies DENV host restriction and dependency factors. We highlight an important role of RACK1 and the chaperonin TRiC (CCT and oligosaccharyltransferase (OST complexes during DENV replication. We further show that the OST complex mediates NS1 and NS4B glycosylation, and pharmacological inhibition of its N-glycosylation function strongly impairs DENV infection. In conclusion, our study provides a global interactome of the DENV NS1 and identifies host factors targetable for antiviral therapies.

Weighted Protein Interaction Network Analysis of Frontotemporal Dementia.

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Ferrari, Raffaele; Lovering, Ruth C; Hardy, John; Lewis, Patrick A; Manzoni, Claudia

2017-02-03

The genetic analysis of complex disorders has undoubtedly led to the identification of a wealth of associations between genes and specific traits. However, moving from genetics to biochemistry one gene at a time has, to date, rather proved inefficient and under-powered to comprehensively explain the molecular basis of phenotypes. Here we present a novel approach, weighted protein-protein interaction network analysis (W-PPI-NA), to highlight key functional players within relevant biological processes associated with a given trait. This is exemplified in the current study by applying W-PPI-NA to frontotemporal dementia (FTD): We first built the state of the art FTD protein network (FTD-PN) and then analyzed both its topological and functional features. The FTD-PN resulted from the sum of the individual interactomes built around FTD-spectrum genes, leading to a total of 4198 nodes. Twenty nine of 4198 nodes, called inter-interactome hubs (IIHs), represented those interactors able to bridge over 60% of the individual interactomes. Functional annotation analysis not only reiterated and reinforced previous findings from single genes and gene-coexpression analyses but also indicated a number of novel potential disease related mechanisms, including DNA damage response, gene expression regulation, and cell waste disposal and potential biomarkers or therapeutic targets including EP300. These processes and targets likely represent the functional core impacted in FTD, reflecting the underlying genetic architecture contributing to disease. The approach presented in this study can be applied to other complex traits for which risk-causative genes are known as it provides a promising tool for setting the foundations for collating genomics and wet laboratory data in a bidirectional manner. This is and will be critical to accelerate molecular target prioritization and drug discovery.

Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress

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Wijaya Edward

2010-01-01

Full Text Available Abstract Background The transcriptional regulatory network involved in low temperature response leading to acclimation has been established in Arabidopsis. In japonica rice, which can only withstand transient exposure to milder cold stress (10°C, an oxidative-mediated network has been proposed to play a key role in configuring early responses and short-term defenses. The components, hierarchical organization and physiological consequences of this network were further dissected by a systems-level approach. Results Regulatory clusters responding directly to oxidative signals were prominent during the initial 6 to 12 hours at 10°C. Early events mirrored a typical oxidative response based on striking similarities of the transcriptome to disease, elicitor and wounding induced processes. Targets of oxidative-mediated mechanisms are likely regulated by several classes of bZIP factors acting on as1/ocs/TGA-like element enriched clusters, ERF factors acting on GCC-box/JAre-like element enriched clusters and R2R3-MYB factors acting on MYB2-like element enriched clusters. Temporal induction of several H2O2-induced bZIP, ERF and MYB genes coincided with the transient H2O2 spikes within the initial 6 to 12 hours. Oxidative-independent responses involve DREB/CBF, RAP2 and RAV1 factors acting on DRE/CRT/rav1-like enriched clusters and bZIP factors acting on ABRE-like enriched clusters. Oxidative-mediated clusters were activated earlier than ABA-mediated clusters. Conclusion Genome-wide, physiological and whole-plant level analyses established a holistic view of chilling stress response mechanism of japonica rice. Early response regulatory network triggered by oxidative signals is critical for prolonged survival under sub-optimal temperature. Integration of stress and developmental responses leads to modulated growth and vigor maintenance contributing to a delay of plastic injuries.

Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress

KAUST Repository

Yun, Kil-Young

2010-01-25

Background: The transcriptional regulatory network involved in low temperature response leading to acclimation has been established in Arabidopsis. In japonica rice, which can only withstand transient exposure to milder cold stress (10C), an oxidative-mediated network has been proposed to play a key role in configuring early responses and short-term defenses. The components, hierarchical organization and physiological consequences of this network were further dissected by a systems-level approach.Results: Regulatory clusters responding directly to oxidative signals were prominent during the initial 6 to 12 hours at 10C. Early events mirrored a typical oxidative response based on striking similarities of the transcriptome to disease, elicitor and wounding induced processes. Targets of oxidative-mediated mechanisms are likely regulated by several classes of bZIP factors acting on as1/ocs/TGA-like element enriched clusters, ERF factors acting on GCC-box/JAre-like element enriched clusters and R2R3-MYB factors acting on MYB2-like element enriched clusters.Temporal induction of several H2O2-induced bZIP, ERF and MYB genes coincided with the transient H2O2spikes within the initial 6 to 12 hours. Oxidative-independent responses involve DREB/CBF, RAP2 and RAV1 factors acting on DRE/CRT/rav1-like enriched clusters and bZIP factors acting on ABRE-like enriched clusters. Oxidative-mediated clusters were activated earlier than ABA-mediated clusters.Conclusion: Genome-wide, physiological and whole-plant level analyses established a holistic view of chilling stress response mechanism of japonica rice. Early response regulatory network triggered by oxidative signals is critical for prolonged survival under sub-optimal temperature. Integration of stress and developmental responses leads to modulated growth and vigor maintenance contributing to a delay of plastic injuries. 2010 Yun et al; licensee BioMed Central Ltd.

Synaptic Interactome Mining Reveals p140Cap as a New Hub for PSD Proteins Involved in Psychiatric and Neurological Disorders

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Annalisa Alfieri

2017-06-01

Full Text Available Altered synaptic function has been associated with neurological and psychiatric conditions including intellectual disability, schizophrenia and autism spectrum disorder (ASD. Amongst the recently discovered synaptic proteins is p140Cap, an adaptor that localizes at dendritic spines and regulates their maturation and physiology. We recently showed that p140Cap knockout mice have cognitive deficits, impaired long-term potentiation (LTP and long-term depression (LTD, and immature, filopodia-like dendritic spines. Only a few p140Cap interacting proteins have been identified in the brain and the molecular complexes and pathways underlying p140Cap synaptic function are largely unknown. Here, we isolated and characterized the p140Cap synaptic interactome by co-immunoprecipitation from crude mouse synaptosomes, followed by mass spectrometry-based proteomics. We identified 351 p140Cap interactors and found that they cluster to sub complexes mostly located in the postsynaptic density (PSD. p140Cap interactors converge on key synaptic processes, including transmission across chemical synapses, actin cytoskeleton remodeling and cell-cell junction organization. Gene co-expression data further support convergent functions: the p140Cap interactors are tightly co-expressed with each other and with p140Cap. Importantly, the p140Cap interactome and its co-expression network show strong enrichment in genes associated with schizophrenia, autism, bipolar disorder, intellectual disability and epilepsy, supporting synaptic dysfunction as a shared biological feature in brain diseases. Overall, our data provide novel insights into the molecular organization of the synapse and indicate that p140Cap acts as a hub for postsynaptic complexes relevant to psychiatric and neurological disorders.

Rice Combine Harvester: Its Effects to the Livelihood of Rice-Field Tenants in a Second Class Municipality

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Jesrael Medrano

2016-11-01

Full Text Available Over the past few years, the advancement of modern technology has intensely overhauled society. People use and benefit from modern technology, and the tremendous opportunities it provides play a significant role in almost all aspects of human life. However, too much usage of this has its repercussions as well. Technological and mechanical change in agricultural sector and its impact on the work force have already become one of the neglected concerns of farmers in Amulung, a second class municipality of Cagayan. The newly introduced rice combine harvesters are already dominating the rice fields in Amulung during harvesting seasons. Thus, it replaces the conventional system of harvesting using human labor and sickles. This study is conducted to determine the effects of rice combine harvesters to the livelihood of rice field tenants in Amulung, Cagayan. Using purposive sampling through site selection approach and networking, 25 rice field tenants were selected as participants of this study. In–depth conversations and guided interview had served as the main instruments used by the researchers to gather the needed data. The results showed that rice combine harvesters cause unemployment and migration among the participants and degrade their sense of solidarity and camaraderie. As a result, the participants sought alternative activities which they can be paid off. Also, they engage themselves in livestock and poultry production, and even in informal sector economy just to cope with the prevalence of rice combine harvesters.

Transfer of gaseous iodine from atmosphere to rough rice, brown rice and polished rice

International Nuclear Information System (INIS)

Sumiya, Misako; Uchida, Shigeo; Muramatsu, Yasuyuki; Ohmomo, Yoichiro; Yamaguchi, Shuho; Obata, Hitoshi.

1987-01-01

Experiments were carried out in order to obtain information required for establishing transfer coefficients of gaseous iodine (I 2 ) to rough rice, brown rice and polished rice. The gaseous iodine deposited on young rice plants before the heading period was scarcely found in the rough rice harvested at the full ripe stage. The biological half life of iodine in hull, however, was much slower than that in leaves of 14 days. The translocation of iodine from leaves and stalks to rough rice was not clearly recognized. Therefore, it was deduced that iodine found in brown rice mainly should originate from that deposited on the hull. The distribution ratios of iodine between rough rice and brown rice, and between brown rice and polished rice were 100:4 and 100:30 on 100 grains basis, respectively. If average normalized deposition velocity (V d(m) ) or derived deposition velocity (V s ) are given, the transfer coefficients of gaseous iodine to rough rice (TF r ), brown rice (TF b ) and polished rice (TF p ) could be calculated. (author)

The chicken B-cell line DT40 proteome, beadome and interactomes

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Johanna S. Rees

2015-06-01

Full Text Available In developing a new quantitative AP-MS method for exploring interactomes in the chicken B-cell line DT40, we also surveyed the most abundant proteins in this organism and explored the likely contaminants that bind to a variety of affinity resins that would later be confirmed quantitatively [1]. We present the ‘Top 150 abundant DT40 proteins list’, the DT40 beadomes as well as protein interaction lists for the Phosphatidyl inositol 5-phosphate 4-kinase 2β and Fanconi anaemia protein complexes.

Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice

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Shuchi eSmita

2015-12-01

response in rice. Thus, the co-regulatory network analysis facilitated the identification of complex OsMYB regulatory networks, and candidate target regulon genes of selected guide MYB genes. The results contribute to the candidate gene screening, and experimentally testable hypotheses for potential regulatory MYB TFs, and their targets under stress conditions.

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks

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Kirouac Daniel C

2012-05-01

Full Text Available Abstract Background Understanding the information-processing capabilities of signal transduction networks, how those networks are disrupted in disease, and rationally designing therapies to manipulate diseased states require systematic and accurate reconstruction of network topology. Data on networks central to human physiology, such as the inflammatory signalling networks analyzed here, are found in a multiplicity of on-line resources of pathway and interactome databases (Cancer CellMap, GeneGo, KEGG, NCI-Pathway Interactome Database (NCI-PID, PANTHER, Reactome, I2D, and STRING. We sought to determine whether these databases contain overlapping information and whether they can be used to construct high reliability prior knowledge networks for subsequent modeling of experimental data. Results We have assembled an ensemble network from multiple on-line sources representing a significant portion of all machine-readable and reconcilable human knowledge on proteins and protein interactions involved in inflammation. This ensemble network has many features expected of complex signalling networks assembled from high-throughput data: a power law distribution of both node degree and edge annotations, and topological features of a “bow tie” architecture in which diverse pathways converge on a highly conserved set of enzymatic cascades focused around PI3K/AKT, MAPK/ERK, JAK/STAT, NFκB, and apoptotic signaling. Individual pathways exhibit “fuzzy” modularity that is statistically significant but still involving a majority of “cross-talk” interactions. However, we find that the most widely used pathway databases are highly inconsistent with respect to the actual constituents and interactions in this network. Using a set of growth factor signalling networks as examples (epidermal growth factor, transforming growth factor-beta, tumor necrosis factor, and wingless, we find a multiplicity of network topologies in which receptors couple to downstream

MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria.

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Jiabin Wang

Full Text Available Mitochondrion plays a central role in diverse biological processes in most eukaryotes, and its dysfunctions are critically involved in a large number of diseases and the aging process. A systematic identification of mitochondrial proteomes and characterization of functional linkages among mitochondrial proteins are fundamental in understanding the mechanisms underlying biological functions and human diseases associated with mitochondria. Here we present a database MitProNet which provides a comprehensive knowledgebase for mitochondrial proteome, interactome and human diseases. First an inventory of mammalian mitochondrial proteins was compiled by widely collecting proteomic datasets, and the proteins were classified by machine learning to achieve a high-confidence list of mitochondrial proteins. The current version of MitProNet covers 1124 high-confidence proteins, and the remainders were further classified as middle- or low-confidence. An organelle-specific network of functional linkages among mitochondrial proteins was then generated by integrating genomic features encoded by a wide range of datasets including genomic context, gene expression profiles, protein-protein interactions, functional similarity and metabolic pathways. The functional-linkage network should be a valuable resource for the study of biological functions of mitochondrial proteins and human mitochondrial diseases. Furthermore, we utilized the network to predict candidate genes for mitochondrial diseases using prioritization algorithms. All proteins, functional linkages and disease candidate genes in MitProNet were annotated according to the information collected from their original sources including GO, GEO, OMIM, KEGG, MIPS, HPRD and so on. MitProNet features a user-friendly graphic visualization interface to present functional analysis of linkage networks. As an up-to-date database and analysis platform, MitProNet should be particularly helpful in comprehensive studies of

Functional interactome of Aquaporin 1 sub-family reveals new physiological functions in Arabidopsis Thaliana

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Mohamed Ragab Abdel Gawwad

2013-09-01

Full Text Available Aquaporins are channel proteins found in plasma membranes and intercellular membranes of different cellular compartments, facilitate the water flux, solutes and gases across the cellular plasma membranes. The present study highlights the sub-family plasma membrane intrinsic protein (PIP predicting the 3-D structure and analyzing the functional interactome of it homologs. PIP1 homologs integrate with many proteins with different plant physiological roles in Arabidopsis thaliana including; PIP1A and PIP1B: facilitate the transport of water, diffusion of amino acids and/or peptides from the vacuolar compartment to the cytoplasm, play a role in the control of cell turgor and cell expansion and involved in root water uptake respectively. In addition we found that PIP1B plays a defensive role against Pseudomonas syringae infection through the interaction with the plasma membrane Rps2 protein. Another substantial function of PIP1C via the interaction with PIP2E is the response to nematode infection. Generally, PIP1 sub-family interactome controlling many physiological processes in plant cell like; osmoregulation in plants under high osmotic stress such as under a high salt, response to nematode, facilitate the transport of water across cell membrane and regulation of floral initiation in Arabidopsis thaliana.

Weed management through herbicide application in direct-seeded rice and yield modeling by artificial neural network

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Ghosh, D.; Singh, U.P.; Ray, K.; Das, A.

2016-11-01

In direct seeded rice (DSR) cultivation, weed is the major constraint mainly due to absence of puddling in field. The yield loss due to weed interference is huge, may be up to 100%. In this perspective, the present experiment was conducted to study the efficacy of selected herbicides, and to predict the rice yield using artificial neural network (ANN) models. The dry weight and density of weeds were recorded at different growth stages and consequently herbicidal efficacy was evaluated. Experimental results revealed that pre-emergence (PRE) herbicide effectively controlled the germination of grassy weeds. Application bispyribac-sodium as post-emergence (POST) following PRE herbicides (clomazone or pendimethalin) or as tank-mixture with clomazone effectively reduced the density and biomass accumulation of diverse weed flora in DSR. Herbicidal treatments improved the plant height, yield attributes and grain yield (2.7 to 5.5 times) over weedy check. The sensitivity of the best ANN model clearly depicts that the weed control index (WCI) of herbicides was most important than their weed control efficiency (WCE). Besides, the early control of weeds is a better prescription to improve rice yield. Differences in sensitivity values of WCI and WCE across the crop growth stages also suggest that at 15, 30 and 60 days after sowing, herbicides most effectively controlled sedges, broad leaves and grasses, respectively. Based on the grain yield and herbicidal WCE, it can be concluded that the combined application of pendimethalin or clomazone as PRE followed by bispyribac-sodium as POST or tank-mixture of clomazone + bispyribac sodium can effectively control different weed flushes throughout the crop growth period in DSR. (Author)

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks.

Science.gov (United States)

Lepoivre, Cyrille; Bergon, Aurélie; Lopez, Fabrice; Perumal, Narayanan B; Nguyen, Catherine; Imbert, Jean; Puthier, Denis

2012-01-31

Deciphering gene regulatory networks by in silico approaches is a crucial step in the study of the molecular perturbations that occur in diseases. The development of regulatory maps is a tedious process requiring the comprehensive integration of various evidences scattered over biological databases. Thus, the research community would greatly benefit from having a unified database storing known and predicted molecular interactions. Furthermore, given the intrinsic complexity of the data, the development of new tools offering integrated and meaningful visualizations of molecular interactions is necessary to help users drawing new hypotheses without being overwhelmed by the density of the subsequent graph. We extend the previously developed TranscriptomeBrowser database with a set of tables containing 1,594,978 human and mouse molecular interactions. The database includes: (i) predicted regulatory interactions (computed by scanning vertebrate alignments with a set of 1,213 position weight matrices), (ii) potential regulatory interactions inferred from systematic analysis of ChIP-seq experiments, (iii) regulatory interactions curated from the literature, (iv) predicted post-transcriptional regulation by micro-RNA, (v) protein kinase-substrate interactions and (vi) physical protein-protein interactions. In order to easily retrieve and efficiently analyze these interactions, we developed In-teractomeBrowser, a graph-based knowledge browser that comes as a plug-in for Transcriptome-Browser. The first objective of InteractomeBrowser is to provide a user-friendly tool to get new insight into any gene list by providing a context-specific display of putative regulatory and physical interactions. To achieve this, InteractomeBrowser relies on a "cell compartments-based layout" that makes use of a subset of the Gene Ontology to map gene products onto relevant cell compartments. This layout is particularly powerful for visual integration of heterogeneous biological information

Introduction and Utilization of INGER Rice Germplasm in China

Institute of Scientific and Technical Information of China (English)

TANGSheng-xiang; WEIXing-hua; ELJavier

2004-01-01

The International Network for Genetic Evaluation of Rice (INGER) is a global partnership between international and national agricultural research institutions. INGER focuses on worldwide exchange, evaluation and utilization of improved varieties and elite breeding lines of rice. China has actively participated in the activities of INGER since 1980.During the pasted years, 26 500 INGER entries with diversity genetic background have been introduced and evaluated by Chinese scientists. Among of them, 37 commercial varieties directly from elite INGER entries and 27 rice hybrids using INGER lines as their restorer lines/donors have been released to farmers in China. About 1 900 INGER entries were indirectly utilized as cross parents or pest resistant donors in various national and provincial rice breeding programs. Based on the incomplete statistics, there were 14.5 million cumulated hectares planting these varieties and hybrids, from which 5.44 MT of increased rough rice has been received by farmers. INGER accelerates the transfer of adapted varieties and hybrids to farmers, and increases the diversity of rice germplasm in cultivation. Therefore, INGER cooperation has made great benefit both in economy and society in China.

Introduction and Utilization of INGER Rice Germplasm in China

Institute of Scientific and Technical Information of China (English)

TANG Sheng-xiang; WEI Xing-hua; E L Javier

2004-01-01

The International Network for Genetic Evaluation of Rice (INGER) is a global partnership between international and national agricultural research institutions. INGER focuses on worldwide exchange, evaluation and utilization of improved varieties and elite breeding lines of rice. China has actively participated in the activities of INGER since 1980.During the pasted years, 26 500 INGER entries with diversity genetic background have been introduced and evaluated by Chinese scientists. Among of them, 37 commercial varieties directly from elite INGER entries and 27 rice hybrids using INGER lines as their restorer lines/donors have been released to farmers in China. About 1 900 INGER entries were indirectly utilized as cross parents or pest resistant donors in various national and provincial rice breeding programs. Based on the incomplete statistics, there were 14.5million cumulated hectares planting these varieties and hybrids, from which 5.44 MT of increased rough rice has been received by farmers. INGER accelerates the transfer of adapted varieties and hybrids to farmers, and increases the diversity of rice germplasm in cultivation. Therefore, INGER cooperation has made great benefit both in economy and society in China.

Soybean-Enriched Snacks Based on African Rice

Science.gov (United States)

Marengo, Mauro; Akoto, Hannah F.; Zanoletti, Miriam; Carpen, Aristodemo; Buratti, Simona; Benedetti, Simona; Barbiroli, Alberto; Johnson, Paa-Nii T.; Sakyi-Dawson, Esther O.; Saalia, Firibu K.; Bonomi, Francesco; Pagani, Maria Ambrogina; Manful, John; Iametti, Stefania

2016-01-01

Snacks were produced by extruding blends of partially-defatted soybean flour with flours from milled or parboiled African-grown rice. The interplay between composition and processing in producing snacks with a satisfactory sensory profile was addressed by e-sensing, and by molecular and rheological approaches. Soybean proteins play a main role in defining the properties of the protein network in the products. At the same content in soybean flour, use of parboiled rice flour increases the snack’s hardness. Electronic nose and electronic tongue discriminated samples containing a higher amount of soybean flour from those with a lower soybean flour content. PMID:28231133

PROFEAT Update: A Protein Features Web Server with Added Facility to Compute Network Descriptors for Studying Omics-Derived Networks.

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Zhang, P; Tao, L; Zeng, X; Qin, C; Chen, S Y; Zhu, F; Yang, S Y; Li, Z R; Chen, W P; Chen, Y Z

2017-02-03

The studies of biological, disease, and pharmacological networks are facilitated by the systems-level investigations using computational tools. In particular, the network descriptors developed in other disciplines have found increasing applications in the study of the protein, gene regulatory, metabolic, disease, and drug-targeted networks. Facilities are provided by the public web servers for computing network descriptors, but many descriptors are not covered, including those used or useful for biological studies. We upgraded the PROFEAT web server http://bidd2.nus.edu.sg/cgi-bin/profeat2016/main.cgi for computing up to 329 network descriptors and protein-protein interaction descriptors. PROFEAT network descriptors comprehensively describe the topological and connectivity characteristics of unweighted (uniform binding constants and molecular levels), edge-weighted (varying binding constants), node-weighted (varying molecular levels), edge-node-weighted (varying binding constants and molecular levels), and directed (oriented processes) networks. The usefulness of the network descriptors is illustrated by the literature-reported studies of the biological networks derived from the genome, interactome, transcriptome, metabolome, and diseasome profiles. Copyright © 2016 Elsevier Ltd. All rights reserved.

Complex Systems Analysis of Cell Cycling Models in Carcinogenesis:II. Cell Genome and Interactome, Neoplastic Non-random Transformation Models in Topoi with Lukasiewicz-Logic and MV Algebras

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Baianu, I C

2004-01-01

Quantitative Biology, abstract q-bio.OT/0406045 From: I.C. Baianu Dr. [view email] Date (v1): Thu, 24 Jun 2004 02:45:13 GMT (164kb) Date (revised v2): Fri, 2 Jul 2004 00:58:06 GMT (160kb) Complex Systems Analysis of Cell Cycling Models in Carcinogenesis: II. Authors: I.C. Baianu Comments: 23 pages, 1 Figure Report-no: CC04 Subj-class: Other Carcinogenesis is a complex process that involves dynamically inter-connected modular sub-networks that evolve under the influence of micro-environmentally induced perturbations, in non-random, pseudo-Markov chain processes. An appropriate n-stage model of carcinogenesis involves therefore n-valued Logic treatments of nonlinear dynamic transformations of complex functional genomes and cell interactomes. Lukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous, Boolean or "fuzzy", logic models of genetic activities in vivo....

Introducing the hypothome

DEFF Research Database (Denmark)

Madsen, Claus Desler; Zambach, Sine; Suravajhala, Prashanth

2014-01-01

of doing so is the risk of devaluing the definition of interactomes. By adding proteins that have only been predicted, an interactome can no longer be classified as experimentally verified and the integrity of the interactome will be endured. Therefore, we propose the term 'hypothome' (collection......An interactome is defined as a network of protein-protein interactions built from experimentally verified interactions. Basic science as well as application-based research of potential new drugs can be promoted by including proteins that are only predicted into interactomes. The disadvantage...

Rice Bran Metabolome Contains Amino Acids, Vitamins & Cofactors, and Phytochemicals with Medicinal and Nutritional Properties.

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Zarei, Iman; Brown, Dustin G; Nealon, Nora Jean; Ryan, Elizabeth P

2017-12-01

Rice bran is a functional food that has shown protection against major chronic diseases (e.g. obesity, diabetes, cardiovascular disease and cancer) in animals and humans, and these health effects have been associated with the presence of bioactive phytochemicals. Food metabolomics uses multiple chromatography and mass spectrometry platforms to detect and identify a diverse range of small molecules with high sensitivity and precision, and has not been completed for rice bran. This study utilized global, non-targeted metabolomics to identify small molecules in rice bran, and conducted a comprehensive search of peer-reviewed literature to determine bioactive compounds. Three U.S. rice varieties (Calrose, Dixiebelle, and Neptune), that have been used for human dietary intervention trials, were assessed herein for bioactive compounds that have disease control and prevention properties. The profiling of rice bran by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and gas chromatography-mass spectrometry (GC-MS) identified 453 distinct phytochemicals, 209 of which were classified as amino acids, cofactors & vitamins, and secondary metabolites, and were further assessed for bioactivity. A scientific literature search revealed 65 compounds with health properties, 16 of which had not been previously identified in rice bran. This suite of amino acids, cofactors & vitamins, and secondary metabolites comprised 46% of the identified rice bran metabolome, which substantially enhanced our knowledge of health-promoting rice bran compounds provided during dietary supplementation. Rice bran metabolite profiling revealed a suite of biochemical molecules that can be further investigated and exploited for multiple nutritional therapies and medical food applications. These bioactive compounds may also be biomarkers of dietary rice bran intake. The medicinal compounds associated with rice bran can function as a network across metabolic pathways and this

Comparative Transcriptional Profiling of Three Super-Hybrid Rice Combinations

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Yonggang Peng

2014-03-01

Full Text Available Utilization of heterosis has significantly increased rice yields. However, its mechanism remains unclear. In this study, comparative transcriptional profiles of three super-hybrid rice combinations, LY2163, LY2186 and LYP9, at the flowering and filling stages, were created using rice whole-genome oligonucleotide microarray. The LY2163, LY2186 and LYP9 hybrids yielded 1193, 1630 and 1046 differentially expressed genes (DGs, accounting for 3.2%, 4.4% and 2.8% of the total number of genes (36,926, respectively, after using the z-test (p < 0.01. Functional category analysis showed that the DGs in each hybrid combination were mainly classified into the carbohydrate metabolism and energy metabolism categories. Further analysis of the metabolic pathways showed that DGs were significantly enriched in the carbon fixation pathway (p < 0.01 for all three combinations. Over 80% of the DGs were located in rice quantitative trait loci (QTLs of the Gramene database, of which more than 90% were located in the yield related QTLs in all three combinations, which suggested that there was a correlation between DGs and rice heterosis. Pathway Studio analysis showed the presence of DGs in the circadian regulatory network of all three hybrid combinations, which suggested that the circadian clock had a role in rice heterosis. Our results provide information that can help to elucidate the molecular mechanism underlying rice heterosis.

Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation

DEFF Research Database (Denmark)

Kieffer-Kwon, Kyong-Rim; Tang, Zhonghui; Mathe, Ewy

2013-01-01

IA-PET technologies to map the promoter-enhancer interactomes of pluripotent ES cells and differentiated B lymphocytes. We confirm that enhancer usage varies widely across tissues. Unexpectedly, we find that this feature extends to broadly transcribed genes, including Myc and Pim1 cell-cycle regulators, which...... associate with an entirely different set of enhancers in ES and B cells. By means of high-resolution CpG methylomes, genome editing, and digital footprinting, we show that these enhancers recruit lineage-determining factors. Furthermore, we demonstrate that the turning on and off of enhancers during...

Soybean-Enriched Snacks Based on African Rice

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Mauro Marengo

2016-05-01

Full Text Available Snacks were produced by extruding blends of partially-defatted soybean flour with flours from milled or parboiled African-grown rice. The interplay between composition and processing in producing snacks with a satisfactory sensory profile was addressed by e-sensing, and by molecular and rheological approaches. Soybean proteins play a main role in defining the properties of the protein network in the products. At the same content in soybean flour, use of parboiled rice flour increases the snack’s hardness. Electronic nose and electronic tongue discriminated samples containing a higher amount of soybean flour from those with a lower soybean flour content.

Structures and short linear motif of disordered transcription factor regions provide clues to the interactome of the cellular hub radical-induced cell death1

DEFF Research Database (Denmark)

O'Shea, Charlotte; Staby, Lasse; Bendsen, Sidsel Krogh

2017-01-01

Intrinsically disordered protein regions (IDRs) lack a well-defined three-dimensional structure, but often facilitate key protein functions. Some interactions between IDRs and folded protein domains rely on short linear motifs (SLiMs). These motifs are challenging to identify, but once found can...... point to larger networks of interactions, such as with proteins that serve as hubs for essential cellular functions. The stress-associated plant protein Radical-Induced Cell Death1 (RCD1) is one such hub, interacting with many transcription factors via their flexible IDRs. To identify the SLiM bound......046 formed different structures or were fuzzy in the complexes. These findings allow us to present a model of the stress-associated RCD1-transcription factor interactome and to contribute to the emerging understanding of the interactions between folded hubs and their intrinsically disordered partners....

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks

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Lepoivre Cyrille

2012-01-01

Full Text Available Abstract Background Deciphering gene regulatory networks by in silico approaches is a crucial step in the study of the molecular perturbations that occur in diseases. The development of regulatory maps is a tedious process requiring the comprehensive integration of various evidences scattered over biological databases. Thus, the research community would greatly benefit from having a unified database storing known and predicted molecular interactions. Furthermore, given the intrinsic complexity of the data, the development of new tools offering integrated and meaningful visualizations of molecular interactions is necessary to help users drawing new hypotheses without being overwhelmed by the density of the subsequent graph. Results We extend the previously developed TranscriptomeBrowser database with a set of tables containing 1,594,978 human and mouse molecular interactions. The database includes: (i predicted regulatory interactions (computed by scanning vertebrate alignments with a set of 1,213 position weight matrices, (ii potential regulatory interactions inferred from systematic analysis of ChIP-seq experiments, (iii regulatory interactions curated from the literature, (iv predicted post-transcriptional regulation by micro-RNA, (v protein kinase-substrate interactions and (vi physical protein-protein interactions. In order to easily retrieve and efficiently analyze these interactions, we developed In-teractomeBrowser, a graph-based knowledge browser that comes as a plug-in for Transcriptome-Browser. The first objective of InteractomeBrowser is to provide a user-friendly tool to get new insight into any gene list by providing a context-specific display of putative regulatory and physical interactions. To achieve this, InteractomeBrowser relies on a "cell compartments-based layout" that makes use of a subset of the Gene Ontology to map gene products onto relevant cell compartments. This layout is particularly powerful for visual integration

Broken rice kernels and the kinetics of rice hydration and texture during cooking.

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Saleh, Mohammed; Meullenet, Jean-Francois

2013-05-01

During rice milling and processing, broken kernels are inevitably present, although to date it has been unclear as to how the presence of broken kernels affects rice hydration and cooked rice texture. Therefore, this work intended to study the effect of broken kernels in a rice sample on rice hydration and texture during cooking. Two medium-grain and two long-grain rice cultivars were harvested, dried and milled, and the broken kernels were separated from unbroken kernels. Broken rice kernels were subsequently combined with unbroken rice kernels forming treatments of 0, 40, 150, 350 or 1000 g kg(-1) broken kernels ratio. Rice samples were then cooked and the moisture content of the cooked rice, the moisture uptake rate, and rice hardness and stickiness were measured. As the amount of broken rice kernels increased, rice sample texture became increasingly softer (P hardness was negatively correlated to the percentage of broken kernels in rice samples. Differences in the proportions of broken rice in a milled rice sample play a major role in determining the texture properties of cooked rice. Variations in the moisture migration kinetics between broken and unbroken kernels caused faster hydration of the cores of broken rice kernels, with greater starch leach-out during cooking affecting the texture of the cooked rice. The texture of cooked rice can be controlled, to some extent, by varying the proportion of broken kernels in milled rice. © 2012 Society of Chemical Industry.

Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research

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Rita eSharma

2013-08-01

Full Text Available Glycoside hydrolases (GH catalyze the hydrolysis of glycosidic bonds in cell wall polymers and can have major effects on cell wall architecture. Taking advantage of the massive datasets available in public databases, we have constructed a rice phylogenomic database of GHs (http://ricephylogenomics.ucdavis.edu/cellwalls/gh/. This database integrates multiple data types including the structural features, orthologous relationships, mutant availability and gene expression patterns for each GH family in a phylogenomic context. The rice genome encodes 437 GH genes classified into 34 families. Based on pairwise comparison with eight dicot and four monocot genomes, we identified 138 GH genes that are highly diverged between monocots and dicots, 57 of which have diverged further in rice as compared with four monocot genomes scanned in this study. Chromosomal localization and expression analysis suggest a role for both whole-genome and localized gene duplications in expansion and diversification of GH families in rice. We examined the meta-profiles of expression patterns of GH genes in twenty different anatomical tissues of rice. Transcripts of 51 genes exhibit tissue or developmental stage-preferential expression, whereas, seventeen other genes preferentially accumulate in actively growing tissues. When queried in RiceNet, a probabilistic functional gene network that facilitates functional gene predictions, nine out of seventeen genes form a regulatory network with the well-characterized genes involved in biosynthesis of cell wall polymers including cellulose synthase and cellulose synthase-like genes of rice. Two-thirds of the GH genes in rice are up regulated in response to biotic and abiotic stress treatments indicating a role in stress adaptation. Our analyses identify potential GH targets for cell wall modification.

Investigating differences in light stable isotopes between Thai jasmine rice and Sungyod rice

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Kukusamude, C.; Kongsri, S.

2017-10-01

We report the differences in light stable isotopes between two kinds of Thai rice (Thai jasmine and Sungyod rice). Thai jasmine rice and Sungyod rice were cultivated in the northeast and the south of Thailand. Light isotopes including 13C, 15N and 18O of Thai jasmine rice and Sungyod rice samples were carried out using isotope ratio mass spectrometry (IRMS). Thai jasmine rice (Khao Dawk Mali 105) was cultivated from Thung Kula Rong Hai area, whereas Sungyod rice was cultivated from Phathalung province. Hypothesis testing of difference of each isotope between Thai jasmine rice and Sungyod rice was also studied. The study was the feasibility test whether the light stable isotopes can be the variables to identify Thai jasmine rice and Sungyod rice. The result shows that there was difference in the isotope patterns of Thai jasmine rice and Sungyod rice. Our results may provide the useful information in term of stable isotope profiles of Thai rice.

Network perturbation by recurrent regulatory variants in cancer.

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Kiwon Jang

2017-03-01

Full Text Available Cancer driving genes have been identified as recurrently affected by variants that alter protein-coding sequences. However, a majority of cancer variants arise in noncoding regions, and some of them are thought to play a critical role through transcriptional perturbation. Here we identified putative transcriptional driver genes based on combinatorial variant recurrence in cis-regulatory regions. The identified genes showed high connectivity in the cancer type-specific transcription regulatory network, with high outdegree and many downstream genes, highlighting their causative role during tumorigenesis. In the protein interactome, the identified transcriptional drivers were not as highly connected as coding driver genes but appeared to form a network module centered on the coding drivers. The coding and regulatory variants associated via these interactions between the coding and transcriptional drivers showed exclusive and complementary occurrence patterns across tumor samples. Transcriptional cancer drivers may act through an extensive perturbation of the regulatory network and by altering protein network modules through interactions with coding driver genes.

Extraction of rice bran oil from local rice husk

International Nuclear Information System (INIS)

Anwar, J.; Zaman, W.; Salman, M.; Jabeen, N.

2006-01-01

Rice Bran Oil is widely used in pharmaceutical, food and chemical industries due to its unique properties and high medicinal value. In the present work, extraction of rice bran oil from different samples of rice husk collected from local rice shellers by solvent extraction method has been studied. Experiments were conducted using a soxhelt apparatus, to extract rice bran oil using hexane, petroleum ether, ethanol and methanol as the solvents and the yields obtained under different conditions were compared. Batch extraction tests showed that the rate of extraction decreases with time and the solution approaches saturation at an exponential rate. (author)

Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme

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Moschopoulos Charalampos

2011-06-01

Full Text Available Abstract Background Recent technological advances applied to biology such as yeast-two-hybrid, phage display and mass spectrometry have enabled us to create a detailed map of protein interaction networks. These interaction networks represent a rich, yet noisy, source of data that could be used to extract meaningful information, such as protein complexes. Several interaction network weighting schemes have been proposed so far in the literature in order to eliminate the noise inherent in interactome data. In this paper, we propose a novel weighting scheme and apply it to the S. cerevisiae interactome. Complex prediction rates are improved by up to 39%, depending on the clustering algorithm applied. Results We adopt a two step procedure. During the first step, by applying both novel and well established protein-protein interaction (PPI weighting methods, weights are introduced to the original interactome graph based on the confidence level that a given interaction is a true-positive one. The second step applies clustering using established algorithms in the field of graph theory, as well as two variations of Spectral clustering. The clustered interactome networks are also cross-validated against the confirmed protein complexes present in the MIPS database. Conclusions The results of our experimental work demonstrate that interactome graph weighting methods clearly improve the clustering results of several clustering algorithms. Moreover, our proposed weighting scheme outperforms other approaches of PPI graph weighting.

RiceAtlas, a spatial database of global rice calendars and production.

Science.gov (United States)

Laborte, Alice G; Gutierrez, Mary Anne; Balanza, Jane Girly; Saito, Kazuki; Zwart, Sander J; Boschetti, Mirco; Murty, M V R; Villano, Lorena; Aunario, Jorrel Khalil; Reinke, Russell; Koo, Jawoo; Hijmans, Robert J; Nelson, Andrew

2017-05-30

Knowing where, when, and how much rice is planted and harvested is crucial information for understanding the effects of policy, trade, and global and technological change on food security. We developed RiceAtlas, a spatial database on the seasonal distribution of the world's rice production. It consists of data on rice planting and harvesting dates by growing season and estimates of monthly production for all rice-producing countries. Sources used for planting and harvesting dates include global and regional databases, national publications, online reports, and expert knowledge. Monthly production data were estimated based on annual or seasonal production statistics, and planting and harvesting dates. RiceAtlas has 2,725 spatial units. Compared with available global crop calendars, RiceAtlas is nearly ten times more spatially detailed and has nearly seven times more spatial units, with at least two seasons of calendar data, making RiceAtlas the most comprehensive and detailed spatial database on rice calendar and production.

Transgene Flow from Glufosinate-Resistant Rice to Improved and Weedy Rice in China

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Yong-liang LU

2014-09-01

Full Text Available The development of transgenic rice with novel traits in China can increase rice productivity, but transgene flow to improved or weedy rice has become a major concern. We aimed to evaluate the potential maximum frequencies of transgene flow from glufosinate-resistant rice to improved rice cultivars and weedy rice. Treatments were arranged in randomized complete blocks with three replicates. Experiments were conducted between 2009 and 2010 at the Center for Environmental Safety Supervision and Inspection for Genetically Modified Plants, China National Rice Research Institute, Hangzhou, China. Glufosinate-resistant japonica rice 99-1 was the pollen donor. The pollen recipients were two inbred japonica rice (Chunjiang 016 and Xiushui 09, two inbred indica rice (Zhongzu 14 and Zhongzao 22, two indica hybrid rice (Zhongzheyou 1 and Guodao 1, and one weedy indica rice (Taizhou weedy rice. The offspring of recipients were planted in the field and sprayed with a commercial dose of glufosinate. Leaf tissues of survivors were analyzed by polymerase chain reaction to detect the presence of the transgene. The frequency of gene flow ranged from 0 to 0.488%. In 2009, the order of gene flow frequency was as follows: weedy rice > Chunjiang 016 > Xiushui 09 and Zhongzu 14 > Guodao 1, Zhongzheyou 1 and Zhongzao 22. Gene flow frequencies were generally higher in 2009 than in 2010, but did not differ significantly among rice materials. Gene flow frequency was the highest in weedy rice followed by the inbred japonica rice. The risk of gene flow differed significantly between years and year-to-year variance could mask risk differences among pollen recipients. Gene flow was generally lesser in taller pollen recipients than in shorter ones, but plant height only accounted for about 30% of variation in gene flow. When flowering synchrony was maximized, as in this study, low frequencies of gene flow occurred from herbicide-resistant japonica rice to other cultivars and

Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways.

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Brady, Arthur; Maxwell, Kyle; Daniels, Noah; Cowen, Lenore J

2009-01-01

As increasing amounts of high-throughput data for the yeast interactome become available, more system-wide properties are uncovered. One interesting question concerns the fault tolerance of protein interaction networks: whether there exist alternative pathways that can perform some required function if a gene essential to the main mechanism is defective, absent or suppressed. A signature pattern for redundant pathways is the BPM (between-pathway model) motif, introduced by Kelley and Ideker. Past methods proposed to search the yeast interactome for BPM motifs have had several important limitations. First, they have been driven heuristically by local greedy searches, which can lead to the inclusion of extra genes that may not belong in the motif; second, they have been validated solely by functional coherence of the putative pathways using GO enrichment, making it difficult to evaluate putative BPMs in the absence of already known biological annotation. We introduce stable bipartite subgraphs, and show they form a clean and efficient way of generating meaningful BPMs which naturally discard extra genes included by local greedy methods. We show by GO enrichment measures that our BPM set outperforms previous work, covering more known complexes and functional pathways. Perhaps most importantly, since our BPMs are initially generated by examining the genetic-interaction network only, the location of edges in the protein-protein physical interaction network can then be used to statistically validate each candidate BPM, even with sparse GO annotation (or none at all). We uncover some interesting biological examples of previously unknown putative redundant pathways in such areas as vesicle-mediated transport and DNA repair.

Exploitation of complex network topology for link prediction in biological interactomes

KAUST Repository

Alanis Lobato, Gregorio

2014-01-01

In this work, we propose three novel and powerful approaches for the prediction of interactions in biological networks and conclude that it is possible to mine the topology of these complex system representations and produce reliable

Rice production in relation to soil quality under different rice-based cropping systems

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Tran Ba, Linh; Sleutel, Steven; Nguyen Van, Qui; Thi, Guong Vo; Le Van, Khoa; Cornelis, Wim

2016-04-01

Soil quality of shallow paddy soils may be improved by introducing upland crops and thus a more diverse crop cultivation pattern. Yet, the causal relationship between crop performance and enhanced soil traits in rice-upland crop rotations remains elusive. The objectives of this study were to (i) find correlations among soil properties under different rice-upland crop systems and link selected soil properties to rice growth and yield, (ii) present appropriate values of soil parameters for sustainable rice productivity in heavy clay soil, (iii) evaluate the effect of rotating rice with upland crops on rice yield and economic benefit in a long-term experiment. A rice-upland crop rotational field experiment in the Vietnamese Mekong delta was conducted for 10 years using a randomized complete block design with four treatments and four replications. Treatments were: (i) rice-rice-rice (control - conventional system as farmers' practice), (ii) rice-maize-rice, (iii) rice-mung bean-rice, and (iv) rice-mung bean-maize. Soil and plant sampling were performed after harvest of the rice crop at the end of the final winter-spring cropping season (i.e. year 10). Results show differences in rice growth and yield, and economic benefit as an effect of the crop rotation system. These differences were linked with changes in bulk density, soil porosity, soil aggregate stability index, soil penetration resistance, soil macro-porosity, soil organic carbon, acid hydrolysable soil C and soil nutrient elements, especially at soil depth of 20-30 cm. This is evidenced by the strong correlation (P < 0.01) between rice plant parameters, rice yield and soil properties such as bulk density, porosity, penetration resistance, soil organic carbon and Chydrolysable. It turned out that good rice root growth and rice yield corresponded to bulk density values lower than 1.3 Mg m-3, soil porosity higher than 50%, penetration resistance below 1.0 MPa, and soil organic carbon above 25 g kg-1. The optimal

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

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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.

Cellulose fibers extracted from rice and oat husks and their application in hydrogel.

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Oliveira, Jean Paulo de; Bruni, Graziella Pinheiro; Lima, Karina Oliveira; Halal, Shanise Lisie Mello El; Rosa, Gabriela Silveira da; Dias, Alvaro Renato Guerra; Zavareze, Elessandra da Rosa

2017-04-15

The commercial cellulose fibers and cellulose fibers extracted from rice and oat husks were analyzed by chemical composition, morphology, functional groups, crystallinity and thermal properties. The cellulose fibers from rice and oat husks were used to produce hydrogels with poly (vinyl alcohol). The fibers presented different structural, crystallinity, and thermal properties, depending on the cellulose source. The hydrogel from rice cellulose fibers had a network structure with a similar agglomeration sponge, with more homogeneous pores compared to the hydrogel from oat cellulose fibers. The hydrogels prepared from the cellulose extracted from rice and oat husks showed water absorption capacity of 141.6-392.1% and high opacity. The highest water absorption capacity and maximum stress the compression were presented by rice cellulose hydrogel at 25°C. These results show that the use of agro-industrial residues is promising for the biomaterial field, especially in the preparation of hydrogels. Copyright © 2016 Elsevier Ltd. All rights reserved.

Analysis of rice purchase decision on rice consumer in Bandung city

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Kusno, K.; Imannurdin, A.; Syamsiyah, N.; Djuwendah, E.

2018-03-01

This study was conducted at three kinds of purchase location which were traditional market, rice kiosk, and supermarket in Bandung City, with survey data of 108 respondents which were selected by systematic random sampling. The aim of this study is to (1) identify consumer characteristics, (2) identify which atribute is considered by consumer in buying rice, and (3) analyze the relationship between purchase decision and income class. Data were analyzed by descriptive analysis and Chi Square test. The results showed most consumers in the traditional market were middle-educated and lower middle-income, at the rice kiosk, the consumer were generally middle-educated and middle-income, and in the supermarkets, the majority were high-educated and upper middle-income consumers. “Kepulenan” be the first priority of most consumers, but for the lower-middle class, the main priority was price. Thus, in case of scarcity and rice price increase, the government should immediately arrange market operations which targeting to lower-middle class consumers. There was a significant relationship between (1) the quality of rice consumed, (2) the frequency of rice purchase per month, and (3) attitudes toward rice price increase; each with the income class. Although the price of rice increase, consumers of middle and upper-middle were remain loyal to the quality of rice they consumed. This indicates rice market in Bandung city is an ideal market for premium rice so that traders and producers are expected to maintain the quality of rice, such as keep using superior seeds and applying good cultivation based on Good Agricultural Practice (GAP) rules.

Evidence That a Psychopathology Interactome Has Diagnostic Value, Predicting Clinical Needs: An Experience Sampling Study

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van Os, Jim; Lataster, Tineke; Delespaul, Philippe; Wichers, Marieke; Myin-Germeys, Inez

2014-01-01

Background For the purpose of diagnosis, psychopathology can be represented as categories of mental disorder, symptom dimensions or symptom networks. Also, psychopathology can be assessed at different levels of temporal resolution (monthly episodes, daily fluctuating symptoms, momentary fluctuating mental states). We tested the diagnostic value, in terms of prediction of treatment needs, of the combination of symptom networks and momentary assessment level. Method Fifty-seven patients with a psychotic disorder participated in an ESM study, capturing psychotic experiences, emotions and circumstances at 10 semi-random moments in the flow of daily life over a period of 6 days. Symptoms were assessed by interview with the Positive and Negative Syndrome Scale (PANSS); treatment needs were assessed using the Camberwell Assessment of Need (CAN). Results Psychotic symptoms assessed with the PANSS (Clinical Psychotic Symptoms) were strongly associated with psychotic experiences assessed with ESM (Momentary Psychotic Experiences). However, the degree to which Momentary Psychotic Experiences manifested as Clinical Psychotic Symptoms was determined by level of momentary negative affect (higher levels increasing probability of Momentary Psychotic Experiences manifesting as Clinical Psychotic Symptoms), momentary positive affect (higher levels decreasing probability of Clinical Psychotic Symptoms), greater persistence of Momentary Psychotic Experiences (persistence predicting increased probability of Clinical Psychotic Symptoms) and momentary environmental stress associated with events and activities (higher levels increasing probability of Clinical Psychotic Symptoms). Similarly, the degree to which momentary visual or auditory hallucinations manifested as Clinical Psychotic Symptoms was strongly contingent on the level of accompanying momentary paranoid delusional ideation. Momentary Psychotic Experiences were associated with CAN unmet treatment needs, over and above PANSS

Evaluation of clustering algorithms for protein-protein interaction networks

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van Helden Jacques

2006-11-01

Full Text Available Abstract Background Protein interactions are crucial components of all cellular processes. Recently, high-throughput methods have been developed to obtain a global description of the interactome (the whole network of protein interactions for a given organism. In 2002, the yeast interactome was estimated to contain up to 80,000 potential interactions. This estimate is based on the integration of data sets obtained by various methods (mass spectrometry, two-hybrid methods, genetic studies. High-throughput methods are known, however, to yield a non-negligible rate of false positives, and to miss a fraction of existing interactions. The interactome can be represented as a graph where nodes correspond with proteins and edges with pairwise interactions. In recent years clustering methods have been developed and applied in order to extract relevant modules from such graphs. These algorithms require the specification of parameters that may drastically affect the results. In this paper we present a comparative assessment of four algorithms: Markov Clustering (MCL, Restricted Neighborhood Search Clustering (RNSC, Super Paramagnetic Clustering (SPC, and Molecular Complex Detection (MCODE. Results A test graph was built on the basis of 220 complexes annotated in the MIPS database. To evaluate the robustness to false positives and false negatives, we derived 41 altered graphs by randomly removing edges from or adding edges to the test graph in various proportions. Each clustering algorithm was applied to these graphs with various parameter settings, and the clusters were compared with the annotated complexes. We analyzed the sensitivity of the algorithms to the parameters and determined their optimal parameter values. We also evaluated their robustness to alterations of the test graph. We then applied the four algorithms to six graphs obtained from high-throughput experiments and compared the resulting clusters with the annotated complexes. Conclusion This

Interactome Screening Identifies the ER Luminal Chaperone Hsp47 as a Regulator of the Unfolded Protein Response Transducer IRE1α.

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Sepulveda, Denisse; Rojas-Rivera, Diego; Rodríguez, Diego A; Groenendyk, Jody; Köhler, Andres; Lebeaupin, Cynthia; Ito, Shinya; Urra, Hery; Carreras-Sureda, Amado; Hazari, Younis; Vasseur-Cognet, Mireille; Ali, Maruf M U; Chevet, Eric; Campos, Gisela; Godoy, Patricio; Vaisar, Tomas; Bailly-Maitre, Béatrice; Nagata, Kazuhiro; Michalak, Marek; Sierralta, Jimena; Hetz, Claudio

2018-01-18

Maintenance of endoplasmic reticulum (ER) proteostasis is controlled by a dynamic signaling network known as the unfolded protein response (UPR). IRE1α is a major UPR transducer, determining cell fate under ER stress. We used an interactome screening to unveil several regulators of the UPR, highlighting the ER chaperone Hsp47 as the major hit. Cellular and biochemical analysis indicated that Hsp47 instigates IRE1α signaling through a physical interaction. Hsp47 directly binds to the ER luminal domain of IRE1α with high affinity, displacing the negative regulator BiP from the complex to facilitate IRE1α oligomerization. The regulation of IRE1α signaling by Hsp47 is evolutionarily conserved as validated using fly and mouse models of ER stress. Hsp47 deficiency sensitized cells and animals to experimental ER stress, revealing the significance of Hsp47 to global proteostasis maintenance. We conclude that Hsp47 adjusts IRE1α signaling by fine-tuning the threshold to engage an adaptive UPR. Copyright © 2018 Elsevier Inc. All rights reserved.

PhosphoRice: a meta-predictor of rice-specific phosphorylation sites

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Que Shufu

2012-02-01

Full Text Available Abstract Background As a result of the growing body of protein phosphorylation sites data, the number of phosphoprotein databases is constantly increasing, and dozens of tools are available for predicting protein phosphorylation sites to achieve fast automatic results. However, none of the existing tools has been developed to predict protein phosphorylation sites in rice. Results In this paper, the phosphorylation site predictors, NetPhos 2.0, NetPhosK, Kinasephos, Scansite, Disphos and Predphosphos, were integrated to construct meta-predictors of rice-specific phosphorylation sites using several methods, including unweighted voting, unreduced weighted voting, reduced unweighted voting and weighted voting strategies. PhosphoRice, the meta-predictor produced by using weighted voting strategy with parameters selected by restricted grid search and conditional random search, performed the best at predicting phosphorylation sites in rice. Its Matthew's Correlation Coefficient (MCC and Accuracy (ACC reached to 0.474 and 73.8%, respectively. Compared to the best individual element predictor (Disphos_default, PhosphoRice archieved a significant increase in MCC of 0.071 (P Conclusions PhosphoRice is a powerful tool for predicting unidentified phosphorylation sites in rice. Compared to the existing methods, we found that our tool showed greater robustness in ACC and MCC. PhosphoRice is available to the public at http://bioinformatics.fafu.edu.cn/PhosphoRice.

Rice microstructure

Science.gov (United States)

An understanding of plant structure is desirable to obtain a clear idea of the overall impact of a crop. A mature rice plant consists of leafy components (left in the field post-harvest) and paddy rice (collected). The rice plant is supported by a hollow stem (culm) with leaf sheaths attached to nod...

Toxoplasmosis and Polygenic Disease Susceptibility Genes: Extensive Toxoplasma gondii Host/Pathogen Interactome Enrichment in Nine Psychiatric or Neurological Disorders

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C. J. Carter

2013-01-01

Full Text Available Toxoplasma gondii is not only implicated in schizophrenia and related disorders, but also in Alzheimer's or Parkinson's disease, cancer, cardiac myopathies, and autoimmune disorders. During its life cycle, the pathogen interacts with ~3000 host genes or proteins. Susceptibility genes for multiple sclerosis, Alzheimer's disease, schizophrenia, bipolar disorder, depression, childhood obesity, Parkinson's disease, attention deficit hyperactivity disorder (multiple sclerosis, and autism (, but not anorexia or chronic fatigue are highly enriched in the human arm of this interactome and 18 (ADHD to 33% (MS of the susceptibility genes relate to it. The signalling pathways involved in the susceptibility gene/interactome overlaps are relatively specific and relevant to each disease suggesting a means whereby susceptibility genes could orient the attentions of a single pathogen towards disruption of the specific pathways that together contribute (positively or negatively to the endophenotypes of different diseases. Conditional protein knockdown, orchestrated by T. gondii proteins or antibodies binding to those of the host (pathogen derived autoimmunity and metabolite exchange, may contribute to this disruption. Susceptibility genes may thus be related to the causes and influencers of disease, rather than (and as well as to the disease itself.

[Nitrogen cycling in rice-duck mutual ecosystem during double cropping rice growth season].

Science.gov (United States)

Zhang, Fan; Chen, Yuan-Quan; Sui, Peng; Gao, Wang-Sheng

2012-01-01

Raising duck in paddy rice field is an evolution of Chinese traditional agriculture. In May-October 2010, a field experiment was conducted in a double cropping rice region of Hunan Province, South-central China to study the nitrogen (N) cycling in rice-duck mutual ecosystem during early rice and late rice growth periods, taking a conventional paddy rice field as the control. Input-output analysis method was adopted. The N output in the early rice-duck mutual ecosystem was 239.5 kg x hm(-2), in which, 12.77 kg x hm(-2) were from ducks, and the N output in the late rice-duck mutual ecosystem was 338.7 kg x hm(-2), in which, 23.35 kg x hm(-2) were from ducks. At the present N input level, there existed soil N deficit during the growth seasons of both early rice and late rice. The N input from duck sub-system was mainly from the feed N, and the cycling rate of the duck feces N recycled within the system was 2.5% during early rice growth season and 3.5% during late rice growth season. After late rice harvested, the soil N sequestration was 178.6 kg x hm(-2).

Determination of rice panicle numbers during heading by multi-angle imaging

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Lingfeng Duan

2015-06-01

Full Text Available Plant phenomics has the potential to accelerate progress in understanding gene functions and environmental responses. Progress has been made in automating high-throughput plant phenotyping. However, few studies have investigated automated rice panicle counting. This paper describes a novel method for automatically and nonintrusively determining rice panicle numbers during the full heading stage by analyzing color images of rice plants taken from multiple angles. Pot-grown rice plants were transferred via an industrial conveyer to an imaging chamber. Color images from different angles were automatically acquired as a turntable rotated the plant. The images were then analyzed and the panicle number of each plant was determined. The image analysis pipeline consisted of extracting the i2 plane from the original color image, segmenting the image, discriminating the panicles from the rest of the plant using an artificial neural network, and calculating the panicle number in the current image. The panicle number of the plant was taken as the maximum of the panicle numbers extracted from all 12 multi-angle images. A total of 105 rice plants during the full heading stage were examined to test the performance of the method. The mean absolute error of the manual and automatic count was 0.5, with 95.3% of the plants yielding absolute errors within ± 1. The method will be useful for evaluating rice panicles and will serve as an important supplementary method for high-throughput rice phenotyping.

Effects of Extraction Methods on Phytochemicals of Rice Bran Oils Produced from Colored Rice.

Science.gov (United States)

Mingyai, Sukanya; Srikaeo, Khongsak; Kettawan, Aikkarach; Singanusong, Riantong; Nakagawa, Kiyotaka; Kimura, Fumiko; Ito, Junya

2018-02-01

Rice bran oil (RBO) especially from colored rice is rich in phytochemicals and has become popular in food, cosmetic, nutraceutical and pharmaceutical applications owing to its offering health benefits. This study determined the contents of phytochemicals including oryzanols, phytosterols, tocopherols (Toc) and tocotrienols (T3) in RBOs extracted using different methods namely cold-press extraction (CPE), solvent extraction (SE) and supercritical CO 2 extraction (SC-CO 2 ). Two colored rice, Red Jasmine rice (RJM, red rice) and Hom-nin rice (HN, black rice), were studied in comparison with the popular Thai fragrant rice Khao Dawk Mali 105 (KDML 105, white rice). RBOs were found to be the rich source of oryzanols, phytosterols, Toc and T3. Rice varieties had a greater effect on the phytochemicals concentrations than extraction methods. HN rice showed the significantly highest concentration of all phytochemicals, followed by RJM and KDML 105 rice, indicating that colored rice contained high concentration of phytochemicals in the oil than non-colored rice. The RBO samples extracted by the CPE method had a greater concentration of the phytochemicals than those extracted by the SC-CO 2 and SE methods, respectively. In terms of phytochemical contents, HN rice extracted using CPE method was found to be the best.

Hepatitis C virus infection protein network.

Science.gov (United States)

de Chassey, B; Navratil, V; Tafforeau, L; Hiet, M S; Aublin-Gex, A; Agaugué, S; Meiffren, G; Pradezynski, F; Faria, B F; Chantier, T; Le Breton, M; Pellet, J; Davoust, N; Mangeot, P E; Chaboud, A; Penin, F; Jacob, Y; Vidalain, P O; Vidal, M; André, P; Rabourdin-Combe, C; Lotteau, V

2008-01-01

A proteome-wide mapping of interactions between hepatitis C virus (HCV) and human proteins was performed to provide a comprehensive view of the cellular infection. A total of 314 protein-protein interactions between HCV and human proteins was identified by yeast two-hybrid and 170 by literature mining. Integration of this data set into a reconstructed human interactome showed that cellular proteins interacting with HCV are enriched in highly central and interconnected proteins. A global analysis on the basis of functional annotation highlighted the enrichment of cellular pathways targeted by HCV. A network of proteins associated with frequent clinical disorders of chronically infected patients was constructed by connecting the insulin, Jak/STAT and TGFbeta pathways with cellular proteins targeted by HCV. CORE protein appeared as a major perturbator of this network. Focal adhesion was identified as a new function affected by HCV, mainly by NS3 and NS5A proteins.

Interactome analysis of transcriptional coactivator multiprotein bridging factor 1 unveils a yeast AP-1-like transcription factor involved in oxidation tolerance of mycopathogen Beauveria bassiana.

Science.gov (United States)

Chu, Xin-Ling; Dong, Wei-Xia; Ding, Jin-Li; Feng, Ming-Guang; Ying, Sheng-Hua

2018-02-01

Oxidation tolerance is an important determinant to predict the virulence and biocontrol potential of Beauveria bassiana, a well-known entomopathogenic fungus. As a transcriptional coactivator, multiprotein bridging factor 1 mediates the activity of transcription factor in diverse physiological processes, and its homolog in B. bassiana (BbMBF1) contributes to fungal oxidation tolerance. In this study, the BbMBF1-interactomes under oxidative stress and normal growth condition were deciphered by mass spectrometry integrated with the immunoprecipitation. BbMBF1p factor has a broad interaction with proteins that are involved in various cellular processes, and this interaction is dynamically regulated by oxidative stress. Importantly, a B. bassiana homolog of yeast AP-1-like transcription factor (BbAP-1) was specifically associated with the BbMBF1-interactome under oxidation and significantly contributed to fungal oxidation tolerance. In addition, qPCR analysis revealed that several antioxidant genes are jointly controlled by BbAP-1 and BbMBF1. Conclusively, it is proposed that BbMBF1p protein mediates BbAP-1p factor to transcribe the downstream antioxidant genes in B. bassiana under oxidative stress. This study demonstrates for the first time a proteomic view of the MBF1-interactome in fungi, and presents an initial framework to probe the transcriptional mechanism involved in fungal response to oxidation, which will provide a new strategy to improve the biocontrol efficacy of B. bassiana.

Discrimination of Rice with Different Pretreatment Methods by Using a Voltammetric Electronic Tongue

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Li Wang

2015-07-01

Full Text Available In this study, an application of a voltammetric electronic tongue for discrimination and prediction of different varieties of rice was investigated. Different pretreatment methods were selected, which were subsequently used for the discrimination of different varieties of rice and prediction of unknown rice samples. To this aim, a voltammetric array of sensors based on metallic electrodes was used as the sensing part. The different samples were analyzed by cyclic voltammetry with two sample-pretreatment methods. Discriminant Factorial Analysis was used to visualize the different categories of rice samples; however, radial basis function (RBF artificial neural network with leave-one-out cross-validation method was employed for prediction modeling. The collected signal data were first compressed employing fast Fourier transform (FFT and then significant features were extracted from the voltammetric signals. The experimental results indicated that the sample solutions obtained by the non-crushed pretreatment method could efficiently meet the effect of discrimination and recognition. The satisfactory prediction results of voltammetric electronic tongue based on RBF artificial neural network were obtained with less than five-fold dilution of the sample solution. The main objective of this study was to develop primary research on the application of an electronic tongue system for the discrimination and prediction of solid foods and provide an objective assessment tool for the food industry.

[Effects of fish on field resource utilization and rice growth in rice-fish coculture].

Science.gov (United States)

Zhang, Jian; Hu, Liang Liang; Ren, Wei Zheng; Guo, Liang; Wu, Min Fang; Tang, Jian Jun; Chen, Xin

2017-01-01

Rice field can provide habitat for fish and other aquatic animals. Rice-fish coculture can increase rice yield and simultaneously reduce the use of chemicals through reducing rice pest occurrence and nutrient complementary use. However, how fish uses food sources (e.g. phytoplankton, weeds, duckweed, macro-algal and snail) from rice field, and whether the nutrients releasing from those food sources due to fish transforming can improve rice growth are still unknown. Here, we conducted two field experiments to address these questions. One was to investigate the pattern of fish activity in the field using the method of video recording. The other was to examine the utilization of field resources by fish using stable isotope technology. Rice growth and rice yield were also exa-mined. Results showed that fish tended to be more active and significantly expanded the activity range in the rice-fish coculture compared to fish monoculture (fish not living together with rice plants). The contributions of 3 potential aquatic organisms (duckweed, phytoplankton and snail) to fish dietary were 22.7%, 34.8% and 30.0% respectively under rice-fish coculture without feed. Under the treatment with feed, however, the contributions of these 3 aquatic organisms to the fish die-tary were 8.9%, 5.9% and 1.6% respectively. The feed contribution was 71.0%. Rice-fish coculture significantly increased the nitrogen concentration in rice leaves, prolonged tillering stage by 10-12 days and increased rice spike rate and yield. The results suggested that raising fish in paddy field may transform the nutrients contained in field resources to bioavailable for rice plants through fish feeding activity, which can improve rice growth and rice yield.

Unraveling the WRKY transcription factors network in Arabidopsis Thaliana by integrative approach

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Mouna Choura

2015-06-01

Full Text Available The WRKY transcription factors superfamily are involved in diverse biological processes in plants including response to biotic and abiotic stresses and plant immunity. Protein-protein interaction network is a useful approach for understanding these complex processes. The availability of Arabidopsis Thaliana interactome offers a good opportunity to do get a global view of protein network. In this work, we have constructed the WRKY transcription factor network by combining different sources of evidence and we characterized its topological features using computational tools. We found that WRKY network is a hub-based network involving multifunctional proteins denoted as hubs such as WRKY 70, WRKY40, WRKY 53, WRKY 60, WRKY 33 and WRKY 51. Functional annotation showed seven functional modules particularly involved in biotic stress and defense responses. Furthermore, the gene ontology and pathway enrichment analysis revealed that WRKY proteins are mainly involved in plant-pathogen interaction pathways and their functions are directly related to the stress response and immune system process.

Intranuclear interactomic inhibition of NF-κB suppresses LPS-induced severe sepsis

International Nuclear Information System (INIS)

Park, Sung-Dong; Cheon, So Yeong; Park, Tae-Yoon; Shin, Bo-Young; Oh, Hyunju; Ghosh, Sankar; Koo, Bon-Nyeo; Lee, Sang-Kyou

2015-01-01

Suppression of nuclear factor-κB (NF-κB) activation, which is best known as a major regulator of innate and adaptive immune responses, is a potent strategy for the treatment of endotoxic sepsis. To inhibit NF-κB functions, we designed the intra-nuclear transducible form of transcription modulation domain (TMD) of RelA (p65), called nt-p65-TMD, which can be delivered effectively into the nucleus without influencing the cell viability, and work as interactomic inhibitors via disruption of the endogenous p65-mediated transcription complex. nt-p65-TMD effectively inhibited the secretion of pro-inflammatory cytokines, including TNF-α, IL-1β, or IL-6 from BV2 microglia cells stimulated by lipopolysaccharide (LPS). nt-p65-TMD did not inhibit tyrosine phosphorylation of signaling mediators such as ZAP-70, p38, JNK, or ERK involved in T cell activation, but was capable of suppressing the transcriptional activity of NF-κB without the functional effect on that of NFAT upon T-cell receptor (TCR) stimulation. The transduced nt-p65-TMD in T cell did not affect the expression of CD69, however significantly inhibited the secretion of T cell-specific cytokines such as IL-2, IFN-γ, IL-4, IL-17A, or IL-10. Systemic administration of nt-p65-TMD showed a significant therapeutic effect on LPS-induced sepsis model by inhibiting pro-inflammatory cytokines secretion. Therefore, nt-p65-TMD can be a novel therapeutics for the treatment of various inflammatory diseases, including sepsis, where a transcription factor has a key role in pathogenesis, and further allows us to discover new functions of p65 under normal physiological condition without genetic alteration. - Highlights: • The nt-p65-TMD is intra-nuclear interactomic inhibitor of endogenous p65. • The nt-p65-TMD effectively inhibited the secretion of pro-inflammatory cytokines. • The excellent therapeutic potential of nt-p65-TMD was confirmed in sepsis model

Intranuclear interactomic inhibition of NF-κB suppresses LPS-induced severe sepsis

Energy Technology Data Exchange (ETDEWEB)

Park, Sung-Dong [Translational Research Center for Protein Function Control, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Cheon, So Yeong [Department of Anesthesiology and Pain Medicine, Anesthesia and Pain Research Institute, Yonsei University College of Medicine, Seoul 120-752 (Korea, Republic of); Park, Tae-Yoon; Shin, Bo-Young [Translational Research Center for Protein Function Control, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Oh, Hyunju; Ghosh, Sankar [Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032 (United States); Koo, Bon-Nyeo, E-mail: koobn@yuhs.ac [Department of Anesthesiology and Pain Medicine, Anesthesia and Pain Research Institute, Yonsei University College of Medicine, Seoul 120-752 (Korea, Republic of); Lee, Sang-Kyou, E-mail: sjrlee@yonsei.ac.kr [Translational Research Center for Protein Function Control, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)

2015-08-28

Suppression of nuclear factor-κB (NF-κB) activation, which is best known as a major regulator of innate and adaptive immune responses, is a potent strategy for the treatment of endotoxic sepsis. To inhibit NF-κB functions, we designed the intra-nuclear transducible form of transcription modulation domain (TMD) of RelA (p65), called nt-p65-TMD, which can be delivered effectively into the nucleus without influencing the cell viability, and work as interactomic inhibitors via disruption of the endogenous p65-mediated transcription complex. nt-p65-TMD effectively inhibited the secretion of pro-inflammatory cytokines, including TNF-α, IL-1β, or IL-6 from BV2 microglia cells stimulated by lipopolysaccharide (LPS). nt-p65-TMD did not inhibit tyrosine phosphorylation of signaling mediators such as ZAP-70, p38, JNK, or ERK involved in T cell activation, but was capable of suppressing the transcriptional activity of NF-κB without the functional effect on that of NFAT upon T-cell receptor (TCR) stimulation. The transduced nt-p65-TMD in T cell did not affect the expression of CD69, however significantly inhibited the secretion of T cell-specific cytokines such as IL-2, IFN-γ, IL-4, IL-17A, or IL-10. Systemic administration of nt-p65-TMD showed a significant therapeutic effect on LPS-induced sepsis model by inhibiting pro-inflammatory cytokines secretion. Therefore, nt-p65-TMD can be a novel therapeutics for the treatment of various inflammatory diseases, including sepsis, where a transcription factor has a key role in pathogenesis, and further allows us to discover new functions of p65 under normal physiological condition without genetic alteration. - Highlights: • The nt-p65-TMD is intra-nuclear interactomic inhibitor of endogenous p65. • The nt-p65-TMD effectively inhibited the secretion of pro-inflammatory cytokines. • The excellent therapeutic potential of nt-p65-TMD was confirmed in sepsis model.

Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways.

Directory of Open Access Journals (Sweden)

Arthur Brady

Full Text Available As increasing amounts of high-throughput data for the yeast interactome become available, more system-wide properties are uncovered. One interesting question concerns the fault tolerance of protein interaction networks: whether there exist alternative pathways that can perform some required function if a gene essential to the main mechanism is defective, absent or suppressed. A signature pattern for redundant pathways is the BPM (between-pathway model motif, introduced by Kelley and Ideker. Past methods proposed to search the yeast interactome for BPM motifs have had several important limitations. First, they have been driven heuristically by local greedy searches, which can lead to the inclusion of extra genes that may not belong in the motif; second, they have been validated solely by functional coherence of the putative pathways using GO enrichment, making it difficult to evaluate putative BPMs in the absence of already known biological annotation. We introduce stable bipartite subgraphs, and show they form a clean and efficient way of generating meaningful BPMs which naturally discard extra genes included by local greedy methods. We show by GO enrichment measures that our BPM set outperforms previous work, covering more known complexes and functional pathways. Perhaps most importantly, since our BPMs are initially generated by examining the genetic-interaction network only, the location of edges in the protein-protein physical interaction network can then be used to statistically validate each candidate BPM, even with sparse GO annotation (or none at all. We uncover some interesting biological examples of previously unknown putative redundant pathways in such areas as vesicle-mediated transport and DNA repair.

Effects of White Rice, Brown Rice and Germinated Brown Rice on Antioxidant Status of Type 2 Diabetic Rats

OpenAIRE

Imam, Mustapha Umar; Musa, Siti Nor Asma; Azmi, Nur Hanisah; Ismail, Maznah

2012-01-01

Oxidative stress is implicated in the pathogenesis of diabetic complications, and can be increased by diet like white rice (WR). Though brown rice (BR) and germinated brown rice (GBR) have high antioxidant potentials as a result of their bioactive compounds, reports of their effects on oxidative stress-related conditions such as type 2 diabetes are lacking. We hypothesized therefore that if BR and GBR were to improve antioxidant status, they would be better for rice consuming populations inst...

Evaluation of weather-based rice yield models in India

Science.gov (United States)

Sudharsan, D.; Adinarayana, J.; Reddy, D. Raji; Sreenivas, G.; Ninomiya, S.; Hirafuji, M.; Kiura, T.; Tanaka, K.; Desai, U. B.; Merchant, S. N.

2013-01-01

The objective of this study was to compare two different rice simulation models—standalone (Decision Support System for Agrotechnology Transfer [DSSAT]) and web based (SImulation Model for RIce-Weather relations [SIMRIW])—with agrometeorological data and agronomic parameters for estimation of rice crop production in southern semi-arid tropics of India. Studies were carried out on the BPT5204 rice variety to evaluate two crop simulation models. Long-term experiments were conducted in a research farm of Acharya N G Ranga Agricultural University (ANGRAU), Hyderabad, India. Initially, the results were obtained using 4 years (1994-1997) of data with weather parameters from a local weather station to evaluate DSSAT simulated results with observed values. Linear regression models used for the purpose showed a close relationship between DSSAT and observed yield. Subsequently, yield comparisons were also carried out with SIMRIW and DSSAT, and validated with actual observed values. Realizing the correlation coefficient values of SIMRIW simulation values in acceptable limits, further rice experiments in monsoon (Kharif) and post-monsoon (Rabi) agricultural seasons (2009, 2010 and 2011) were carried out with a location-specific distributed sensor network system. These proximal systems help to simulate dry weight, leaf area index and potential yield by the Java based SIMRIW on a daily/weekly/monthly/seasonal basis. These dynamic parameters are useful to the farming community for necessary decision making in a ubiquitous manner. However, SIMRIW requires fine tuning for better results/decision making.

Mining protein interactomes to improve their reliability and support the advancement of network medicine

KAUST Repository

Alanis Lobato, Gregorio

2015-01-01

networks that are currently available are incomplete and a significant percentage of their interactions are false positives. Fortunately, the structural properties observed in good quality social or technological networks are also present in biological

Mutant-inducing effect of γ-ray irradiation for hybrid rice F1 derived from cross of black glutinous rice x wild rice

International Nuclear Information System (INIS)

Mao Dezhi; Tang Yilan

1998-01-01

The hybrid rice F 1 plant derived from the back crossing of glutinous rice x wild rice was irradiated with γ-ray. The result of investigation to the induced mutant showed that through the selection and backcross, a black glutinous rice strain with the short stem, cold tolerance and high yield was developed. The analysis of the ability of heredity variance showed that the selection was effective for the husk colour, black glutinous and black Indica rice, but ineffective for the white Indica rice and seed setting

Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome.

Science.gov (United States)

Krishnan S, Gopala; Waters, Daniel L E; Henry, Robert J

2014-01-01

Rice is a major source of human food with a predominantly Asian production base. Domestication involved selection of traits that are desirable for agriculture and to human consumers. Wild relatives of crop plants are a source of useful variation which is of immense value for crop improvement. Australian wild rices have been isolated from the impacts of domestication in Asia and represents a source of novel diversity for global rice improvement. Oryza rufipogon is a perennial wild progenitor of cultivated rice. Oryza meridionalis is a related annual species in Australia. We have examined the sequence of the genomes of AA genome wild rices from Australia that are close relatives of cultivated rice through whole genome re-sequencing. Assembly of the resequencing data to the O. sativa ssp. japonica cv. Nipponbare shows that Australian wild rices possess 2.5 times more single nucleotide polymorphisms than in the Asian wild rice and cultivated O. sativa ssp. indica. Analysis of the genome of domesticated rice reveals regions of low diversity that show very little variation (polymorphism deserts). Both the perennial and annual wild rice from Australia show a high degree of conservation of sequence with that found in cultivated rice in the same 4.58 Mbp region on chromosome 5, which suggests that some of the 'polymorphism deserts' in this and other parts of the rice genome may have originated prior to domestication due to natural selection. Analysis of genes in the 'polymorphism deserts' indicates that this selection may have been due to biotic or abiotic stress in the environment of early rice relatives. Despite having closely related sequences in these genome regions, the Australian wild populations represent an invaluable source of diversity supporting rice food security.

Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome.

Directory of Open Access Journals (Sweden)

Gopala Krishnan S

Full Text Available BACKGROUND: Rice is a major source of human food with a predominantly Asian production base. Domestication involved selection of traits that are desirable for agriculture and to human consumers. Wild relatives of crop plants are a source of useful variation which is of immense value for crop improvement. Australian wild rices have been isolated from the impacts of domestication in Asia and represents a source of novel diversity for global rice improvement. Oryza rufipogon is a perennial wild progenitor of cultivated rice. Oryza meridionalis is a related annual species in Australia. RESULTS: We have examined the sequence of the genomes of AA genome wild rices from Australia that are close relatives of cultivated rice through whole genome re-sequencing. Assembly of the resequencing data to the O. sativa ssp. japonica cv. Nipponbare shows that Australian wild rices possess 2.5 times more single nucleotide polymorphisms than in the Asian wild rice and cultivated O. sativa ssp. indica. Analysis of the genome of domesticated rice reveals regions of low diversity that show very little variation (polymorphism deserts. Both the perennial and annual wild rice from Australia show a high degree of conservation of sequence with that found in cultivated rice in the same 4.58 Mbp region on chromosome 5, which suggests that some of the 'polymorphism deserts' in this and other parts of the rice genome may have originated prior to domestication due to natural selection. CONCLUSIONS: Analysis of genes in the 'polymorphism deserts' indicates that this selection may have been due to biotic or abiotic stress in the environment of early rice relatives. Despite having closely related sequences in these genome regions, the Australian wild populations represent an invaluable source of diversity supporting rice food security.

Ethanol production from rice on radioactively contaminated field toward sustainable rice farming

International Nuclear Information System (INIS)

Yokoyama, Shinya; Izumi, Bintaro; Oki, Kazuo

2011-01-01

Radioactive species such as 137 Cs were discharged from Fukushima Daiichi Nuclear Power Plant which was severely damaged by the enormous earthquake and tsunami. Cropland has been radioactively contaminated by 137 Cs etc. and it seems impossible to plant rice due to the non-suitability for food. According to the reports, 137 Cs transferred into the rice from soil is less than 1% on the average. Therefore, it is expected that the concentration of 137 Cs in bioethanol will be well below the tentative restriction value even if bioethanol could be produced from the rice. It is proposed that the rice field should be filled with water to avoid the flow of runoff contaminated by radioactive cesium compounds because they are insoluble in aqueous phase and that bioethanol should be produced from the rice in order to maintain the multifunction of rice field and to continue the agriculture. If rice farming is halted and neglected, agricultural function of rice field as well as local community will be permanently destroyed. (author)

Integrated model for predicting rice yield with climate change

Science.gov (United States)

Park, Jin-Ki; Das, Amrita; Park, Jong-Hwa

2018-04-01

Rice is the chief agricultural product and one of the primary food source. For this reason, it is of pivotal importance for worldwide economy and development. Therefore, in a decision-support-system both for the farmers and in the planning and management of the country's economy, forecasting yield is vital. However, crop yield, which is a dependent of the soil-bio-atmospheric system, is difficult to represent in statistical language. This paper describes a novel approach for predicting rice yield using artificial neural network, spatial interpolation, remote sensing and GIS methods. Herein, the variation in the yield is attributed to climatic parameters and crop health, and the normalized difference vegetation index from MODIS is used as an indicator of plant health and growth. Due importance was given to scaling up the input parameters using spatial interpolation and GIS and minimising the sources of error in every step of the modelling. The low percentage error (2.91) and high correlation (0.76) signifies the robust performance of the proposed model. This simple but effective approach is then used to estimate the influence of climate change on South Korean rice production. As proposed in the RCP8.5 scenario, an upswing in temperature may increase the rice yield throughout South Korea.

Prevalence of Rice Yellow Mottle Virus (RYMV) on Rice Plants ...

African Journals Online (AJOL)

Abstract. Incidence of Rice yellow mottle virus (RYMV) on rice plants (ofada) grown in two local government areas (LGAs) of Ogun State had been evaluated during a two year field survey. Six month old rice plants were observed for symptom expression and leaf samples collected for serological indexing. Of the 60 leaf ...

Effect of Interplanting with Zero Tillage and Straw Manure on Rice Growth and Rice Quality

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Shi-ping LIU

2007-09-01

Full Text Available The interplanting with zero-tillage of rice, i.e. direct sowing rice 10–20 days before wheat harvesting, and remaining about 30-cm high stubble after cutting wheat or rice with no tillage, is a new cultivation technology in wheat-rice rotation system. To study the effects of interplanting with zero tillage and straw manure on rice growth and quality, an experiment was conducted in a wheat-rotation rotation system. Four treatments, i.e. ZIS (Zero-tillage, straw manure and rice interplanting, ZI (Zero-tillage, no straw manure and rice interplanting, PTS (Plowing tillage, straw manure and rice transplanting, and PT (Plowing tillage, no straw manure and rice transplanting, were used. ZIS reduced plant height, leaf area per plant and the biomass of rice plants, but the biomass accumulation of rice at the late stage was quicker than that under conventional transplanting cultivation. In the first year (2002, there was no significant difference in rice yield among the four treatments. However, rice yield decreased in interplanting with zero-tillage in the second year (2003. Compared with the transplanting treatments, the number of filled grains per panicle decreased but 1000-grain weight increased in interplanting with zero-tillage, which were the main factors resulting in higher yield. Interplanting with zero-tillage improved the milling and appearance qualities of rice. The rates of milled and head rice increased while chalky rice rate and chalkiness decreased in interplanting with zero-tillage. Zero-tillage and interplanting also affected rice nutritional and cooking qualities. In 2002, ZIS showed raised protein content, decreased amylose content, softer gel consistency, resulting in improved rice quality. In 2003, zero-tillage and interplanting decreased protein content and showed similar amylose content as compared with transplanting treatments. Moreover, protein content in PTS was obviously increased in comparison with the other three treatments

An overview of the sustainability of rice agroecosystem through rice-fish integration

International Nuclear Information System (INIS)

Ahyaudin Ali

2002-01-01

Rice-fish integration in the rice agroecosystem has been introduced and is expanding in Malaysia. This type of farm integration has resulted in land optimization, thus enabling farmers to grow both fish and rice in one farming system. Introducing fish into the ricefield has also increased seasonal income as well as reduced pesticide use. Although basic ecological knowledge on rice-fish integration has allowed rice-fish integration to be introduced, further research is required to allow for fine tuning of the methodologies used. Thus research on the ecology, management, production methods and the characterization of rice-fish farming system of Malaysia is needed. Further characterization and description is needed on the ecology of the rice-fish farming system of Malaysia in terms of production, food webs, nutrient flow and system diversity. To increase the sustainability efficiency and productivity of the system, implementation of management techniques formulated through research is required. (Author)

Occurrence and partitioning of cadmium, arsenic and lead in mine impacted paddy rice: Hunan, China.

Science.gov (United States)

Williams, Paul N; Lei, Ming; Sun, Guoxin; Huang, Qing; Lu, Ying; Deacon, Claire; Meharg, Andrew A; Zhu, Yong-Guan

2009-02-01

Paddy rice has been likened to nictiana sp in its ability to scavenge cadmium (Cd) from soil, whereas arsenic (As) accumulation is commonly an order of magnitude higher than in other cereal crops. In areas such as those found in parts of Hunan province in south central China, base-metal mining activities and rice farming coexist. Therefore there is a considerable likelihood that lead (Pb), in addition to Cd and As, will accumulate in rice grown in parts of this region above levels suitable for human consumption. To test this hypothesis, a widespread provincial survey of rice from mine spoilt paddies (n = 100), in addition to a follow-up market grain survey (n = 122) conducted in mine impacted areas was undertaken to determine the safety of local rice supply networks. Furthermore, a specific Cd, As, and Pb biogeochemical survey of paddy soil and rice was conducted within southern China, targeting sites impacted by mining of varying intensities to calibrate rice metal(loid) transfer models and transfer factors that can be used to predict tissue loading. Results revealed a number of highly significant correlations between shoot, husk, bran, and endosperm rice tissue fractions and that rice from mining areas was enriched in Cd, As, and Pb. Sixty-five, 50, and 34% of all the mine-impacted field rice was predicted to fail national food standards for Cd, As, and Pb, respectively. Although, not as elevated as the grains from the mine-impacted field survey, it was demonstrated that metal(loid) tainted rice was entering food supply chains intended for direct human consumption.

Objective evaluation of whiteness of cooked rice and rice cakes using a portable spectrophotometer.

Science.gov (United States)

Goto, Hajime; Asanome, Noriyuki; Suzuki, Keitaro; Sano, Tomoyoshi; Saito, Hiroshi; Abe, Yohei; Chuba, Masaru; Nishio, Takeshi

2014-03-01

The whiteness of cooked rice and rice cakes was evaluated using a portable spectrophotometer with a whiteness index (WI). Also, by using boiled rice for measurement of Mido values by Mido Meter, it was possible to infer the whiteness of cooked rice without rice cooking. In the analysis of varietal differences of cooked rice, 'Tsuyahime', 'Koshihikari' and 'Koshinokaori' showed high whiteness, while 'Satonoyuki' had inferior whiteness. The whiteness of rice cakes made from 'Koyukimochi' and 'Dewanomochi' was higher than the whiteness of those made from 'Himenomochi' and 'Koganemochi'. While there was a significant correlation (r = 0.84) between WI values and whiteness scores of cooked rice by the sensory test, no correlation was detected between the whiteness scores and Mido values, indicating that the values obtained by a spectrophotometer differ from those obtained by a Mido Meter. Thus, a spectrophotometer may be a novel device for measurement of rice eating quality.

Correlation exploration of metabolic and genomic diversity in rice

Directory of Open Access Journals (Sweden)

Shinozaki Kazuo

2009-12-01

Full Text Available Abstract Background It is essential to elucidate the relationship between metabolic and genomic diversity to understand the genetic regulatory networks associated with the changing metabolo-phenotype among natural variation and/or populations. Recent innovations in metabolomics technologies allow us to grasp the comprehensive features of the metabolome. Metabolite quantitative trait analysis is a key approach for the identification of genetic loci involved in metabolite variation using segregated populations. Although several attempts have been made to find correlative relationships between genetic and metabolic diversity among natural populations in various organisms, it is still unclear whether it is possible to discover such correlations between each metabolite and the polymorphisms found at each chromosomal location. To assess the correlative relationship between the metabolic and genomic diversity found in rice accessions, we compared the distance matrices for these two "omics" patterns in the rice accessions. Results We selected 18 accessions from the world rice collection based on their population structure. To determine the genomic diversity of the rice genome, we genotyped 128 restriction fragment length polymorphism (RFLP markers to calculate the genetic distance among the accessions. To identify the variations in the metabolic fingerprint, a soluble extract from the seed grain of each accession was analyzed with one dimensional 1H-nuclear magnetic resonance (NMR. We found no correlation between global metabolic diversity and the phylogenetic relationships among the rice accessions (rs = 0.14 by analyzing the distance matrices (calculated from the pattern of the metabolic fingerprint in the 4.29- to 0.71-ppm 1H chemical shift and the genetic distance on the basis of the RFLP markers. However, local correlation analysis between the distance matrices (derived from each 0.04-ppm integral region of the 1H chemical shift against genetic

Puffing of okara/rice blends using a rice cake machine.

Science.gov (United States)

Xie, M; Huff, H; Hsieh, F; Mustapha, A

2008-10-01

Okara is the insoluble byproduct of soymilk and tofu manufactures. It is cheap, high in nutrients, and possesses great potential to be applied to functional human foods. In this study, a puffed okara/rice cake product was developed with blends of okara pellets and parboiled rice. Consumer preference and acceptance tests were conducted for the product. Okara pellets were prepared by grinding the strands obtained from extruding a mixture of dried okara and rice flour (3:2, w/w) with a twin-screw extruder. Okara pellets and parboiled rice were blended in 4 ratios, 90:10, 70:30, 40:60, and 0:100 (w/w), and tempered to 14% and 17% moisture. The blends were puffed at 221, 232, and 243 degrees C for 4, 5, or 6 s. The okara/rice cakes were evaluated for specific volume (SPV), texture, color, and percent weight loss after tumbling. Overall, the decrease in okara content and increase in moisture, heating temperature and time led to greater specific volume (SPV) and hardness, lighter color, and lower percent weight loss after tumbling. The consumer tests indicated that the okara/rice cake containing 70% okara pellets was preferred and the 90% one was liked the least. The possible drivers of liking for the puffed okara/rice cakes could be the okara content, hardness, SPV, bright color, and percent weight loss after tumbling.

Diversity of some endophytic fungi associated with rice black bug Paraeucosmetus pallicornis on rice plant

OpenAIRE

Nur, Amin; La Daha; Nurariaty, Agus; Ade, Rosmana; Muh., Fadlan

2015-01-01

A new rice insect pest was sighted in some rice producing areas of South Sulawesi Province, Indonesia. This pest is rice black bugs Paraeucosmetus pallicornis. The research aimed to isolation of fungi associated with rice black bugs Paraeucosmetus pallicornis, so as to know the cause of a bitter taste to the rice. The isolation of the fungi consist of three kinds of treatment, namely rice black bugs without sterilization, with sterilization and rice black bugs cut and sterilized. The resul...

A multi-stakeholder partnership for the dissemination of alternate wetting and drying water-saving technology for rice farmers in the Philippines

Directory of Open Access Journals (Sweden)

Florencia G. Palis

2017-09-01

Full Text Available To address issues of water scarcity and food security for sustainable rice farming and increasing production, a water-saving technology called alternate wetting and drying (AWD was disseminated in the Philippines. This study assessed the impact of facilitating a network of stakeholders on disseminating AWD in irrigated rice systems in the Philippines. It used both qualitative and quantitative data collected from 2002 to 2012 in study sites in the country. Engaging multi-stakeholders in adaptive research, training, and dissemination facilitated the process of more interaction by partners. All partners joined a knowledge and dissemination alliance for scaling out AWD activities. This in turn effected a policy outcome, and the synergetic interactions of each partner within and outside the current network fast-tracked the dissemination process and adoption of AWD by farmers. The AWD practice resulted in an increase in irrigated rice area but not necessarily in rice production and farmers’ income. It also reduced labor and fuel consumption, especially in deep-well irrigation systems.

RiceAtlas, a spatial database of global rice calendars and production

NARCIS (Netherlands)

Laborte, Alice G.; Gutierrez, Mary Anne; Balanza, Jane Girly; Saito, Kazuki; Zwart, Sander; Boschetti, Mirco; Murty, M. V.R.; Villano, Lorena; Aunario, Jorrel Khalil; Reinke, Russell; Koo, Jawoo; Hijmans, Robert J.; Nelson, Andrew

2017-01-01

Knowing where, when, and how much rice is planted and harvested is crucial information for understanding the effects of policy, trade, and global and technological change on food security. We developed RiceAtlas, a spatial database on the seasonal distribution of the world's rice production. It

The Potency of White Rice (Oryza sativa), Black Rice (Oryza sativa L. indica), and Red Rice (Oryza nivara) as Antioxidant and Tyrosinase Inhibitor

Science.gov (United States)

Batubara, I.; Maharni, M.; Sadiah, S.

2017-04-01

Rice is known to have many beneficial biological activities and is often used as “bedak dingin”, a face powder. The content of vitamins, minerals, fiber, and several types of antioxidants, such as ferulic acid, phytic acid, tocopherol, and oryzanols [1-2] are predicted to be potential as a tyrosinase inhibitor. The purpose of this study is to determine the potency of extracts from there types of rice, namely white, red, and black rice as an antioxidant and tyrosinase inhibitor. The rice was extracted with three different solvents, n-hexane, ethyl acetate, and methanol. The results showed that the highest antioxidant activity using 1,1-diphenyl-2-picrylhydrazyl method was found in the methanol extract of black rice (IC50 290 μg/mL). Meanwhile, ethyl acetate extract of white rice has the highest antioxidant activity withphosphomolybdic acid method (41 mmol α-tocopherol equivalents/g sample). Thus, methanol extract of black rice and ethyl acetate extract of white rice are potential as an antioxidant. For tyrosinase inhibitor, n-hexane extract of red rice (IC50 3156 μg/mL) was the most active extract. The active component for radical scavenging is polar compound and for antioxidant by phosphomolybdate method is less polar compounds in black rice methanol extract based on TLC bioautogram. In conclusion, the black rice is the most potent in antioxidant while red rice is for tyrosinase inhibition.

Effect of Rice bran on the Quality of Rice Flour Breads (Gluten-free)

OpenAIRE

仲上, 晴世; 矢部, えん; Haruyo, Nakagami; En, Yabe

2016-01-01

Over recent years progress has been made in the development of substitute foods for allergy patients. One such is rice flour bread. However, typically rice flour bread uses polysaccharide thickener in substitution for the gluten in wheat. Most polysaccharide thickeners are of dietary fiber origin, and the nutritive value is poor. Therefore, in this study, I made rice flour bread adding rice bran in place of polysaccharide thickener. Various nutrients are included in rice bran, including vitam...

Neuroplasticity pathways and protein-interaction networks are modulated by vortioxetine in rodents

DEFF Research Database (Denmark)

Waller, Jessica A.; Nygaard, Sara Holm; Li, Yan

2017-01-01

species and sexes, different brain regions, and in response to distinct routes of administration and regimens. Conclusions: A recurring theme, based on the present study as well as previous findings, is that networks related to synaptic plasticity, synaptic transmission, signal transduction...... and rat in response to distinct treatment regimens and in different brain regions. Furthermore, analysis of complexes of physically-interacting proteins reveal that biomarkers involved in transcriptional regulation, neurodevelopment, neuroplasticity, and endocytosis are modulated by vortioxetine....... A subsequent qPCR study examining the expression of targets in the protein-protein interactome space in response to chronic vortioxetine treatment over a range of doses provides further biological validation that vortioxetine engages neuroplasticity networks. Thus, the same biology is regulated in different...

Rice peasants and rice research in Colombia

NARCIS (Netherlands)

Spijkers, P.A.N.M.

1983-01-01

Rice has been grown as a food crop in Latin America from early colonial times. In Colombia rice became a prominent subsistence crop especially on the north coast where it has been grown since the 17th century, sometimes also as a commercial crop. During the last twenty years there has been a sharp

Leaf development of cultivated rice and weedy red rice under elevated temperature scenarios

OpenAIRE

Streck,Nereu A.; Uhlmann,Lilian O.; Gabriel,Luana F.

2013-01-01

The objective of this study was to simulate leaf development of cultivated rice genotypes and weedy red rice biotypes in climate change scenarios at Santa Maria, RS, Brazil. A leaf appearance (LAR) model adapted for rice was used to simulate the accumulated leaf number, represented by the Haun Stage, from crop emergence to flag leaf appearance (EM-FL). Three cultivated rice genotypes and two weedy red rice biotypes in six emergence dates were used. The LAR model was run for each emergence dat...

Estimation of global network statistics from incomplete data.

Directory of Open Access Journals (Sweden)

Catherine A Bliss

Full Text Available Complex networks underlie an enormous variety of social, biological, physical, and virtual systems. A profound complication for the science of complex networks is that in most cases, observing all nodes and all network interactions is impossible. Previous work addressing the impacts of partial network data is surprisingly limited, focuses primarily on missing nodes, and suggests that network statistics derived from subsampled data are not suitable estimators for the same network statistics describing the overall network topology. We generate scaling methods to predict true network statistics, including the degree distribution, from only partial knowledge of nodes, links, or weights. Our methods are transparent and do not assume a known generating process for the network, thus enabling prediction of network statistics for a wide variety of applications. We validate analytical results on four simulated network classes and empirical data sets of various sizes. We perform subsampling experiments by varying proportions of sampled data and demonstrate that our scaling methods can provide very good estimates of true network statistics while acknowledging limits. Lastly, we apply our techniques to a set of rich and evolving large-scale social networks, Twitter reply networks. Based on 100 million tweets, we use our scaling techniques to propose a statistical characterization of the Twitter Interactome from September 2008 to November 2008. Our treatment allows us to find support for Dunbar's hypothesis in detecting an upper threshold for the number of active social contacts that individuals maintain over the course of one week.

Can rice field channels contribute to biodiversity conservation in Southern Brazilian wetlands?

Science.gov (United States)

Maltchik, Leonardo; Rolon, Ana Silvia; Stenert, Cristina; Machado, Iberê Farina; Rocha, Odete

2011-12-01

Conservation of species in agroecosystems has attracted attention. Irrigation channels can improve habitats and offer conditions for freshwater species conservation. Two questions from biodiversity conservation point of view are: 1) Can the irrigated channels maintain a rich diversity of macrophytes, macroinvertebrates and amphibians over the cultivation cycle? 2) Do richness, abundance and composition of aquatic species change over the rice cultivation cycle? For this, a set of four rice field channels was randomly selected in Southern Brazilian wetlands. In each channel, six sample collection events were carried out over the rice cultivation cycle (June 2005 to June 2006). A total of 160 taxa were identified in irrigated channels, including 59 macrophyte species, 91 taxa of macroinvertebrate and 10 amphibian species. The richness and abundance of macrophytes, macroinvertebrates and amphibians did not change significantly over the rice cultivation cycle. However, the species composition of these groups in the irrigation channels varied between uncultivated and cultivated periods. Our results showed that the species diversity found in the irrigation channels, together with the permanence of water enables these man-made aquatic networks to function as important systems that can contribute to the conservation of biodiversity in regions where the wetlands were converted into rice fields. The conservation of the species in agriculture, such as rice field channels, may be an important alternative for biodiversity conservation in Southern Brazil, where more than 90% of wetland systems have already been lost and the remaining ones are still at high risk due to the expansion of rice production.

Nutritional test of rice in rats

International Nuclear Information System (INIS)

Horii, Masaji; Yoshikawa, Seiji

1980-01-01

Behaviors on N derived from rice were followed up by means of 15 N-labeled rice. In the first test, the single unpolished rice diet and the diet of rice and bean lecithin (4.5%) produced urinary excretion of 10 - 12% of 15 N, and that of rice and mannan from devil's tongue (3%), 16 - 20%. The single unpolished rice diet showed slightly more urinary excretion of 15 N, and the other 2 diets showed a similar proportion of 15 N in 3 days. The results indicated that the diet containing mannan from devil's tongue resulted in a poor N absorption by rice, a large quantity of N being excreted over a long period of time. This suggested differences and time lags in the excretion of rice N into the stool and urine depending on the diet constitution. With the unpolished rice diet, a small quantity of rice protein was not absorbed, but was excreted. In the 2nd test with 15 N-polished rice, the urinary excretion rate was 11.44% for a single rice diet, 11.16% for a mixed diet of rice and bean (1:1 in protein), 10.99% for rice and egg yolk, 9.66% for rice, bean and egg yolk and 8.10% for rice and bean lecithin. This decrease in urinary excretion indicated a corresponding increase in absorption of rice protein. (Chiba, N.)

RHEOLOGICAL PROPERTIES AND THE ENERGETIC VALUE OF WHEAT FLOUR SUBSTITUTED BY DIFFERENT SHARES OF WHITE AND BROWN RICE FLOUR

Directory of Open Access Journals (Sweden)

Nada Nikolić

2011-09-01

Full Text Available In order to produce dough with a lower gluten content, more enriched with rice components and satisfactory rheological properties, the rheological properties, energetic value and cake baking properties of wheat and white or brown rice flour in shares from 3 to 30% (w/w were investigated in this paper. The water absorption in wheat-rice flour mixtures was lower and decreased to 53.5% and 54.0% along with the increase of the white and the brown rice flour share, respectively, than in wheat flour, where it was 58.8%. In the dough made from rice flour, a gluten network had thinner filaments, about 2 and 1 μm in width for white and brown rice flour, respectively, compared to those in the dough from wheat flour only, where it was about 7 μm. The dough from rice flour had almost twice higher gelatinization maximum than the gelatinization maximum of the wheat flour only. The energetic values of the dough from rice flour were smaller than the energetic value of the wheat flour, for only 1.32%. Based on Cluster analysis, the white or brown rice flour share of 20% was pointed out.

Proteomic Analysis of the Mediator Complex Interactome in Saccharomyces cerevisiae.

Science.gov (United States)

Uthe, Henriette; Vanselow, Jens T; Schlosser, Andreas

2017-02-27

Here we present the most comprehensive analysis of the yeast Mediator complex interactome to date. Particularly gentle cell lysis and co-immunopurification conditions allowed us to preserve even transient protein-protein interactions and to comprehensively probe the molecular environment of the Mediator complex in the cell. Metabolic 15 N-labeling thereby enabled stringent discrimination between bona fide interaction partners and nonspecifically captured proteins. Our data indicates a functional role for Mediator beyond transcription initiation. We identified a large number of Mediator-interacting proteins and protein complexes, such as RNA polymerase II, general transcription factors, a large number of transcriptional activators, the SAGA complex, chromatin remodeling complexes, histone chaperones, highly acetylated histones, as well as proteins playing a role in co-transcriptional processes, such as splicing, mRNA decapping and mRNA decay. Moreover, our data provides clear evidence, that the Mediator complex interacts not only with RNA polymerase II, but also with RNA polymerases I and III, and indicates a functional role of the Mediator complex in rRNA processing and ribosome biogenesis.

Glufosinate herbicide-tolerant (LibertyLink) rice vs. conventional rice in diets for growing-finishing swine.

Science.gov (United States)

Cromwell, G L; Henry, B J; Scott, A L; Gerngross, M F; Dusek, D L; Fletcher, D W

2005-05-01

Genetically modified (GM) rice (LibertyLink, event LLRICE62) that is tolerant to glufosinate ammonium (Liberty) herbicide was compared with a near-isogenic (NI) conventional medium-grain brown rice (cultivar, Bengal) and a commercially milled long-grain brown rice in diets for growing-finishing pigs. The GM and NI rice were grown in 2000. The GM rice was from fields treated (GM+) or not treated (GM-) with glufosinate herbicide. The GM- and NI rice were grown using herbicide regimens typical of southern United States rice production practices. The four rice grains were similar in composition. Growing-finishing pigs (n = 96) were fed fortified rice-soybean meal diets containing the four different rice grains from 25 to 106 kg BW. Diets contained 0.99% lysine initially (growing phase), with lysine decreased to 0.80% (early finishing phase) and 0.65% (late finishing phase), when pigs reached 51 and 77 kg, respectively. The percentage of rice in the four diets was constant during each of the three phases (72.8, 80.0, and 85.8% for the growing, early-finishing, and late-finishing phases, respectively). There were six pen replicates (three pens of barrows and three pens of gilts) and four pigs per pen for each dietary treatment. All pigs were slaughtered at the termination of the study to collect carcass data. At the end of the 98-d experiment, BW gain, feed intake (as-fed basis), and feed:gain ratio did not differ (P > 0.05) for pigs fed the GM+ vs. conventional rice diets, but growth performance traits of pigs fed the GM+ rice diets were superior (P glufosinate herbicide-tolerant rice was similar in composition and nutritional value to conventional rice for growing-finishing pigs.

Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice.

Science.gov (United States)

Wang, Hongru; Vieira, Filipe G; Crawford, Jacob E; Chu, Chengcai; Nielsen, Rasmus

2017-06-01

The domestication history of rice remains controversial, with multiple studies reaching different conclusions regarding its origin(s). These studies have generally assumed that populations of living wild rice, O. rufipogon , are descendants of the ancestral population that gave rise to domesticated rice, but relatively little attention has been paid to the origins and history of wild rice itself. Here, we investigate the genetic ancestry of wild rice by analyzing a diverse panel of rice genomes consisting of 203 domesticated and 435 wild rice accessions. We show that most modern wild rice is heavily admixed with domesticated rice through both pollen- and seed-mediated gene flow. In fact, much presumed wild rice may simply represent different stages of feralized domesticated rice. In line with this hypothesis, many presumed wild rice varieties show remnants of the effects of selective sweeps in previously identified domestication genes, as well as evidence of recent selection in flowering genes possibly associated with the feralization process. Furthermore, there is a distinct geographical pattern of gene flow from aus , indica , and japonica varieties into colocated wild rice. We also show that admixture from aus and indica is more recent than gene flow from japonica , possibly consistent with an earlier spread of japonica varieties. We argue that wild rice populations should be considered a hybrid swarm, connected to domesticated rice by continuous and extensive gene flow. © 2017 Wang et al.; Published by Cold Spring Harbor Laboratory Press.

An Economic Risk Analysis of Weed Suppressive Rice Cultivars in Rice Production

Science.gov (United States)

Weeds are a major constraint to rice production. In the United States, most rice cultivars are not inherently weed-suppressive and require substantial herbicide inputs to achieve agronomic and economic viability. Intensive herbicide application in rice also has many potential drawbacks, resulting in...

Soil to rice transfer factors for 210Pb: a study on rice grown in India

International Nuclear Information System (INIS)

Karunakara, N.; Rao, Chetan; Ujwal, P.; Yashodhara, I.; Sudeep Kumara; Somashekarappa, H.M.; Bhaskara Shenoy, K.; Ravi, P.M.

2013-01-01

India is the second largest producer of rice (Oryza sativa L.) in the world and rice is the essential component of the diet for the majority of the population of India. However, detailed studies aimed at evaluation of radionuclide transfer factors (F v ) for rice grown in India are almost non-existent. This paper presents soil to rice transfer factors for 210 Pb for rice grown in natural field conditions on the West Coast of India. A rice field was developed very close to the Kaiga nuclear power plant for the field studies. For a comparative study of radionuclide transfer factors, rice samples were also collected from the rice fields of nearby villages. The soil to un-hulled rice grain 210 Pb varied in the range <1.2 x10 -2 to 8.1 x 10 -1 with a mean of 1.4 x 10 -1 . The mean values of un-hulled grain to white rice processing retention factors (F r ) was 0.03 for 210 Pb. Using the processing retention factors the soil to white rice transfer factor was estimated and found to have the mean value of 4.2 x 10 -3 . The study has shown that the transfer of 210 Pb was retained in the root and its transfer to above ground organs of rice plant is significantly lower. (author)

A comparative study of competitiveness between different genotypes of weedy rice (Oryza sativa) and cultivated rice.

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Dai, Lei; Dai, Weimin; Song, Xiaoling; Lu, Baorong; Qiang, Sheng

2014-01-01

Competition from weedy rice can cause serious yield losses to cultivated rice. However, key traits that facilitate competitiveness are still not well understood. To explore the mechanisms behind the strong growth and competitive ability, replacement series experiments were established with six genotypes of weedy rice from different regions and one cultivated rice cultivar. (1) Weedy rice from southern China had the greatest impact on growth and yield of cultivated rice throughout the entire growing season. Weedy rice from the northeast was very competitive during the early vegetative stage while the competitive effects of eastern weedy rice were more detrimental at later crop-growth stages. (2) As the proportion of weedy rice increased, plant height, tillers, above-ground biomass, and yield of cultivated rice significantly declined; the crop always being at disadvantage regardless of proportion. (3) Weedy biotypes with greater diversity as estimated by their Shannon indexes were more detrimental to the growth and yield of cultivated rice. Geographic origin (latitude) of weedy rice biotype, its mixture proportion under competition with the crop and its genetic diversity are determinant factors of the outcome of competition and the associated decline in the rice crop yield. © 2013 Society of Chemical Industry. © 2013 Society of Chemical Industry.

Diversity of global rice markets and the science required for consumer-targeted rice breeding

Science.gov (United States)

With the ever-increasing global demand for high quality rice in both local production regions and with Western consumers, we have a strong desire to understand better the importance of different quality traits that make up the rice grain and obtain a full picture of rice quality demographics. Rice ...

Laboratory Screening for Resistance in Rice to Rice Stem Borer Chilo Suppressalis Walker

International Nuclear Information System (INIS)

Singgih Sutrisno

2004-01-01

Rice stem borer Chilo suppressalis Walker is one of the major insect pests in rice in Indonesia. The use of insect pest resistant variety of rice is one of the effective techniques against pests. Breeding of resistance to insect pests rice crops often faced difficulties in obtaining a lot of insect amounts due to the unavailability of enough number insects pests in the field so that a laboratory bioassay is needed. In this experiments five rice varieties were used: a Pelita I/1, Atomita I, Cisadane, Cisanggarung, and IR 36. Rice seedling 7 days of age were put in 1 liter plastic vials for rice resistance test against the attack of insect pest C. suppressalis. The parameters observed were larval and pupal viability, pupal weight, and eggs production. The larval and pupal viability which were reared on of Pelita I/1 and Atomita I rice seedlings were 68.5 % - 55.5 % and 57.3 % - 46.7 % respectively. The respective lowest percentages were found in IR 36 which was about 41.3 % - 29.8 % .The experiment results on the parameters of pupal weight and egg production showed similar results to that on the parameters of larval and pupal viability. Rice variety of IR 36 showed more resistance to the other varieties, while Pelita I/1 and Atomita I showed the most susceptible to the attack of insect pest C. suppressalis. (author)

Creation of transgenic rice plants producing small interfering RNA of Rice tungro spherical virus.

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Le, Dung Tien; Chu, Ha Duc; Sasaya, Takahide

2015-01-01

Rice tungro spherical virus (RTSV), also known as Rice waika virus, does not cause visible symptoms in infected rice plants. However, the virus plays a critical role in spreading Rice tungro bacilliform virus (RTBV), which is the major cause of severe symptoms of rice tungro disease. Recent studies showed that RNA interference (RNAi) can be used to develop virus-resistance transgenic rice plants. In this report, we presented simple procedures and protocols needed for the creation of transgenic rice plants capable of producing small interfering RNA specific against RTSV sequences. Notably, our study showed that 60 out of 64 individual hygromycin-resistant lines (putative transgenic lines) obtained through transformation carried transgenes designed for producing hairpin double-stranded RNA. Northern blot analyses revealed the presence of small interfering RNA of 21- to 24-mer in 46 out of 56 confirmed transgenic lines. Taken together, our study indicated that transgenic rice plants carrying an inverted repeat of 500-bp fragments encoding various proteins of RTSV can produce small interfering RNA from the hairpin RNA transcribed from that transgene. In light of recent studies with other viruses, it is possible that some of these transgenic rice lines might be resistant to RTSV.

A Non-destructive and Continuous Measurement of Gelatinization of Rice in Rice Cooking Process

OpenAIRE

Hagura, Yoshio; Suzuki, Kanichi

2002-01-01

A non-destructive and continuous method to measure gelatinization of rice samples in a rice-water system during rice cooking process was examined. An aluminum pot and a lid of a rice cooker were used as two electrode plates, and changes in dielectric properties (capacitance : C, and dielectric dissipation factor : tan δ) of the samples in the rice cooking process were measured by a capacitance meter. Differential scanning calorimetry (DSC) was used to measure gelatinization enthalpy and to de...

Comprehensively Characterizing the Thioredoxin Interactome In Vivo Highlights the Central Role Played by This Ubiquitous Oxidoreductase in Redox Control*

Science.gov (United States)

Arts, Isabelle S.; Vertommen, Didier; Baldin, Francesca; Laloux, Géraldine; Collet, Jean-François

2016-01-01

Thioredoxin (Trx) is a ubiquitous oxidoreductase maintaining protein-bound cysteine residues in the reduced thiol state. Here, we combined a well-established method to trap Trx substrates with the power of bacterial genetics to comprehensively characterize the in vivo Trx redox interactome in the model bacterium Escherichia coli. Using strains engineered to optimize trapping, we report the identification of a total 268 Trx substrates, including 201 that had never been reported to depend on Trx for reduction. The newly identified Trx substrates are involved in a variety of cellular processes, ranging from energy metabolism to amino acid synthesis and transcription. The interaction between Trx and two of its newly identified substrates, a protein required for the import of most carbohydrates, PtsI, and the bacterial actin homolog MreB was studied in detail. We provide direct evidence that PtsI and MreB contain cysteine residues that are susceptible to oxidation and that participate in the formation of an intermolecular disulfide with Trx. By considerably expanding the number of Trx targets, our work highlights the role played by this major oxidoreductase in a variety of cellular processes. Moreover, as the dependence on Trx for reduction is often conserved across species, it also provides insightful information on the interactome of Trx in organisms other than E. coli. PMID:27081212

7 CFR 868.310 - Grades and grade requirements for the classes Long Grain Milled Rice, Medium Grain Milled Rice...

Science.gov (United States)

2010-01-01

... Grain Milled Rice, Medium Grain Milled Rice, Short Grain Milled Rice, and Mixed Milled Rice. (See also Â... Milled Rice Principles Governing Application of Standards § 868.310 Grades and grade requirements for the classes Long Grain Milled Rice, Medium Grain Milled Rice, Short Grain Milled Rice, and Mixed Milled Rice...

Rice varieties in relation to rice bread quality.

Science.gov (United States)

Han, Hye Min; Cho, Jun Hyeon; Kang, Hang Won; Koh, Bong Kyung

2012-05-01

It is difficult to predict rice bread quality only from the amylose content (AC) or dough characteristics of new lines produced by rice breeding programmes. This study investigated the AC relative to bread baking quality of rice varieties developed in Korea, and identified specific characteristics that contribute to rice bread quality. Manmibyeo, Jinsumi, Seolgaeng and Hanareumbyeo were classified as low AC, YR24088 Acp9, Suweon517, Chenmaai and Goamibyeo as intermediate AC and Milyang261 as high AC. Suweon517, Milyang261 and Manmibyeo had a high water absorption index (WAI), while Goamibyeo, YR24088 Acp9, Jinsumi, Seolgaeng, Hanareumbyeo and Chenmaai had a low WAI. The gelatinisation enthalpy of flour varied from 9.2 J g(-1) in Milyang261 to 14.8 J g(-1) in YR24088 Acp9. After 7 days of storage the rate of flour retrogradation and crumb firmness were weakly correlated, with the exception of Jinsumi. Bread volumes of Jinsumi, Chenmaai, YR24088 Acp9 and Goamibyeo were comparable to that of wheat flour, but the rest were unsuited to bread making because of their low volume and hard crumb texture. Based on volume, texture and crumb firmness ratio, Chenmaai and Goamibyeo were the most appropriate varieties for making bread. An intermediate AC and low WAI were the primary indicators of rice bread flour quality. Copyright © 2011 Society of Chemical Industry.

Salinity alters the protein composition of rice endosperm and the physicochemical properties of rice flour.

Science.gov (United States)

Baxter, Graeme; Zhao, Jian; Blanchard, Christopher

2011-09-01

Salinity is one of the major threats to production of rice and other agricultural crops worldwide. Although numerous studies have shown that salinity can severely reduce rice yield, little is known about its impact on the chemical composition, processing and sensory characteristics of rice. The objective of the current study was to investigate the effect of salinity on the pasting and textural properties of rice flour as well as on the protein content and composition of rice endosperm. Rice grown under saline conditions had significantly lower yields but substantially higher protein content. The increase in protein content was mainly attributed to increases in the amount of glutelin, with lesser contributions from albumin. Salinity also altered the relative proportions of the individual peptides within the glutelin fraction. Flours obtained from rice grown under saline conditions showed significantly higher pasting temperatures, but lower peak and breakdown viscosities. Rice gels prepared from the flour showed significantly higher hardness and adhesiveness values, compared to the freshwater controls. Salinity can significantly affect the pasting and textural characteristics of rice flour. Although some of the effects could be attributed to changes in protein content of the rice flour, especially the increased glutelin level, the impact of salinity on the physicochemical properties of rice is rather complex and may involve the interrelated effects of other rice components such as starch and lipids. Copyright © 2011 Society of Chemical Industry.

Assessing the impacts of climate change on rice yields in the main rice areas of China

International Nuclear Information System (INIS)

Yao, Fengmei; Xu, Yinglong; Lin, Erda; Yokozawa, Masayuki; Zhang, Jiahua

2007-01-01

This paper assesses the impact of climate change on irrigated rice yield using B2 climate change scenario from the Regional Climate Model (RCM) and CERES-rice model during 2071--2090. Eight typical rice stations ranging in latitude, longitude, and elevation that are located in the main rice ecological zones of China are selected for impact assessment. First, Crop Estimation through Resource and Environment Synthesis (CERES)-rice model is validated using farm experiment data in selected stations. The simulated results represent satisfactorily the trend of flowering duration and yields. The deviation of simulation within ± 10% of observed flowering duration and ± 15% of observed yield. Second, the errors of the outputs of RCM due to the difference of topography between station point and grid point is corrected. The corrected output of the RCM used for simulating rice flowering duration and yield is more reliable than the not corrected. Without CO2 direct effect on crop, the results from the assessment explore that B2 climate change scenario would have a negative impact on rice yield at most rice stations and have little impacts at Fuzhou and Kunming. To find the change of inter-annual rice yield, a preliminary assessment is made based on comparative cumulative probability at low and high yield and the coefficient variable of yield between the B2 scenario and baseline. Without the CO2 direct effect on rice yield, the result indicates that frequency for low yield would increase and it reverses for high yield, and the variance for rice yield would increase. It is concluded that high frequency at low yield and high variances of rice yield could pose a threat to rice yield at most selected stations in the main rice areas of China. With the CO2 direct effect on rice yield, rice yield increase in all selected stations

Assessing the impacts of climate change on rice yields in the main rice areas of China

Energy Technology Data Exchange (ETDEWEB)

Yao, Fengmei [College of Earth Sciences, The Graduate University of the Chinese Academy of Sciences, 19A, Yuquan Road, Beijing, 100049 (China); Xu, Yinglong; Lin, Erda [Agricultural Environment and Sustainable Development Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 (China); Yokozawa, Masayuki [National Institute for Agro-environmental Sciences, Tsukuba 305-8604 (Japan); Zhang, Jiahua [Chinese Academy of Meteorological Sciences, Beijing, 100081 (China)

2007-02-15

This paper assesses the impact of climate change on irrigated rice yield using B2 climate change scenario from the Regional Climate Model (RCM) and CERES-rice model during 2071--2090. Eight typical rice stations ranging in latitude, longitude, and elevation that are located in the main rice ecological zones of China are selected for impact assessment. First, Crop Estimation through Resource and Environment Synthesis (CERES)-rice model is validated using farm experiment data in selected stations. The simulated results represent satisfactorily the trend of flowering duration and yields. The deviation of simulation within {+-} 10% of observed flowering duration and {+-} 15% of observed yield. Second, the errors of the outputs of RCM due to the difference of topography between station point and grid point is corrected. The corrected output of the RCM used for simulating rice flowering duration and yield is more reliable than the not corrected. Without CO2 direct effect on crop, the results from the assessment explore that B2 climate change scenario would have a negative impact on rice yield at most rice stations and have little impacts at Fuzhou and Kunming. To find the change of inter-annual rice yield, a preliminary assessment is made based on comparative cumulative probability at low and high yield and the coefficient variable of yield between the B2 scenario and baseline. Without the CO2 direct effect on rice yield, the result indicates that frequency for low yield would increase and it reverses for high yield, and the variance for rice yield would increase. It is concluded that high frequency at low yield and high variances of rice yield could pose a threat to rice yield at most selected stations in the main rice areas of China. With the CO2 direct effect on rice yield, rice yield increase in all selected stations.

Specificity and evolvability in eukaryotic protein interaction networks.

Directory of Open Access Journals (Sweden)

Pedro Beltrao

2007-02-01

Full Text Available Progress in uncovering the protein interaction networks of several species has led to questions of what underlying principles might govern their organization. Few studies have tried to determine the impact of protein interaction network evolution on the observed physiological differences between species. Using comparative genomics and structural information, we show here that eukaryotic species have rewired their interactomes at a fast rate of approximately 10(-5 interactions changed per protein pair, per million years of divergence. For Homo sapiens this corresponds to 10(3 interactions changed per million years. Additionally we find that the specificity of binding strongly determines the interaction turnover and that different biological processes show significantly different link dynamics. In particular, human proteins involved in immune response, transport, and establishment of localization show signs of positive selection for change of interactions. Our analysis suggests that a small degree of molecular divergence can give rise to important changes at the network level. We propose that the power law distribution observed in protein interaction networks could be partly explained by the cell's requirement for different degrees of protein binding specificity.

Radiation disinfestation of Basmati rice

International Nuclear Information System (INIS)

Rao, V.S.; Gholap, A.S.; Adhikari, H.R.; Nair, P.M.

1994-01-01

Effect of low dose γ-radiation on prepackaged Basmati rice was studied in order to achieve disinfestation of rice. Basmati rice procured from local market was repacked in 1 kg pouches made from high density polyethylene (HDP) and biaxially oriented polypropylene: low density polyethylene (BOPP/LDP) laminate and irradiated at doses from 0.25-1.0 kGy. Within one month of storage at room temperature, unirradiated (control) Basmati rice developed heavy infestation. No infestation was observed in any of the irradiated samples even at 0.25 kGy and the rice could be stored for 6 months in a clean state. Irradiation (at 0.25 kGy) did not alter the moisture content of the rice. Likewise, no significant change was noted due to irradiation in the functional properties of rice such as swelling index and water absorption and in total volatile components responsible for flavour of Basmati rice. In organoleptic evaluation, no significant difference was found between the acceptability of irradiated (0.25 kGy) and control rice. These results are significant in view of the high export potential of Basmati rice and the transit losses at present due to infestation. (author). 24 refs., 5 tabs., 1 fig

Cytoplasmic-genetic male sterility gene provides direct evidence for some hybrid rice recently evolving into weedy rice

Science.gov (United States)

Zhang, Jingxu; Lu, Zuomei; Dai, Weimin; Song, Xiaoling; Peng, Yufa; Valverde, Bernal E.; Qiang, Sheng

2015-01-01

Weedy rice infests paddy fields worldwide at an alarmingly increasing rate. There is substantial evidence indicating that many weedy rice forms originated from or are closely related to cultivated rice. There is suspicion that the outbreak of weedy rice in China may be related to widely grown hybrid rice due to its heterosis and the diversity of its progeny, but this notion remains unsupported by direct evidence. We screened weedy rice accessions by both genetic and molecular marker tests for the cytoplasmic male sterility (CMS) genes (Wild abortive, WA, and Boro type, BT) most widely used in the production of indica and japonica three-line hybrid rice as a diagnostic trait of direct parenthood. Sixteen weedy rice accessions of the 358 tested (4.5%) contained the CMS-WA gene; none contained the CMS-BT gene. These 16 accessions represent weedy rices recently evolved from maternal hybrid rice derivatives, given the primarily maternal inheritance of this trait. Our results provide key direct evidence that hybrid rice can be involved in the evolution of some weedy rice accessions, but is not a primary factor in the recent outbreak of weedy rice in China. PMID:26012494

Cytoplasmic-genetic male sterility gene provides direct evidence for some hybrid rice recently evolving into weedy rice.

Science.gov (United States)

Zhang, Jingxu; Lu, Zuomei; Dai, Weimin; Song, Xiaoling; Peng, Yufa; Valverde, Bernal E; Qiang, Sheng

2015-05-27

Weedy rice infests paddy fields worldwide at an alarmingly increasing rate. There is substantial evidence indicating that many weedy rice forms originated from or are closely related to cultivated rice. There is suspicion that the outbreak of weedy rice in China may be related to widely grown hybrid rice due to its heterosis and the diversity of its progeny, but this notion remains unsupported by direct evidence. We screened weedy rice accessions by both genetic and molecular marker tests for the cytoplasmic male sterility (CMS) genes (Wild abortive, WA, and Boro type, BT) most widely used in the production of indica and japonica three-line hybrid rice as a diagnostic trait of direct parenthood. Sixteen weedy rice accessions of the 358 tested (4.5%) contained the CMS-WA gene; none contained the CMS-BT gene. These 16 accessions represent weedy rices recently evolved from maternal hybrid rice derivatives, given the primarily maternal inheritance of this trait. Our results provide key direct evidence that hybrid rice can be involved in the evolution of some weedy rice accessions, but is not a primary factor in the recent outbreak of weedy rice in China.

Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice

OpenAIRE

Wang, Hongru; Garrett Vieira, Filipe Jorge; Crawford, Jacob E.; Chu, Chengcai; Nielsen, Rasmus

2017-01-01

The domestication history of rice remains controversial, with multiple studies reaching different conclusions regarding its origin(s). These studies have generally assumed that populations of living wild rice, O. rufipogon, are descendants of the ancestral population that gave rise to domesticated rice, but relatively little attention has been paid to the origins and history of wild rice itself. Here, we investigate the genetic ancestry of wild rice by analyzing a diverse panel of rice genome...

Transcriptional changes of rice in response to rice black-streaked dwarf virus.

Science.gov (United States)

Ahmed, Mohamed M S; Ji, Wen; Wang, Muyue; Bian, Shiquan; Xu, Meng; Wang, Weiyun; Zhang, Jiangxiang; Xu, Zhihao; Yu, Meimei; Liu, Qiaoquan; Zhang, Changquan; Zhang, Honggen; Tang, Shuzhu; Gu, Minghong; Yu, Hengxiu

2017-09-10

Rice black-streaked dwarf virus (RBSDV), a member of the genus Fijivirus in the family Reoviridae, causes significant economic losses in rice production in China and many other Asian countries. Although a great deal of effort has been made to elucidate the interactions among the virus, insect vectors, host and environmental conditions, few RBSDV proteins involved in pathogenesis have been identified, and the biological basis of disease development in rice remains largely unknown. Transcriptomic information associated with the disease development in rice would be helpful to unravel the biological mechanism. To determine how the rice transcriptome changes in response to RBSDV infection, we carried out RNA-Seq to perform a genome-wide gene expression analysis of a susceptible rice cultivar KTWYJ3. The transcriptomes of RBSDV-infected samples were compared to those of RBSDV-free (healthy) at two time points (time points are represented by group I and II). The results derived from the differential expression analysis in RBSDV-infected libraries vs. healthy ones in group I revealed that 102 out of a total of 281 significant differentially expressed genes (DEGs) were up-regulated and 179 DEGs were down-regulated. Of the 2592 identified DEGs in group II, 1588 DEGs were up-regulated and 1004 DEGs were down-regulated. A total of 66 DEGs were commonly identified in both groups. Of these 66 DEGs, expression patterns for 36 DEGs were similar in both groups. Our analysis demonstrated that some genes related to disease defense and stress resistance were up-regulated while genes associated with chloroplast were down-regulated in response to RBSDV infection. In addition, some genes associated with plant-height were differentially expressed. This result indicates those genes might be involved in dwarf symptoms caused by RBSDV. Taken together, our results provide a genome-wide transcriptome analysis for rice plants in response to RBSDV infection which may contribute to the

Integrated rice-duck farming mitigates the global warming potential in rice season.

Science.gov (United States)

Xu, Guochun; Liu, Xin; Wang, Qiangsheng; Yu, Xichen; Hang, Yuhao

2017-01-01

Integrated rice-duck farming (IRDF), as a mode of ecological agriculture, is an important way to realize sustainable development of agriculture. A 2-year split-plot field experiment was performed to evaluate the effects of IRDF on methane (CH 4 ) and nitrous oxide (N 2 O) emissions and its ecological mechanism in rice season. This experiment was conducted with two rice farming systems (FS) of IRDF and conventional farming (CF) under four paddy-upland rotation systems (PUR): rice-fallow (RF), annual straw incorporating in rice-wheat rotation system (RWS), annual straw-based biogas residues incorporating in rice-wheat rotation system (RWB), and rice-green manure (RGM). During the rice growing seasons, IRDF decreased the CH 4 emission by 8.80-16.68%, while increased the N 2 O emission by 4.23-15.20%, when compared to CF. Given that CH 4 emission contributed to 85.83-96.22% of global warming potential (GWP), the strong reduction in CH 4 emission led to a significantly lower GWP of IRDF as compared to CF. The reason for this trend was because IRDF has significant effect on dissolved oxygen (DO) and soil redox potential (Eh), which were two pivotal factors for CH 4 and N 2 O emissions in this study. The IRDF not only mitigates the GWP, but also increases the rice yield by 0.76-2.43% compared to CF. Moreover, compared to RWS system, RF, RWB and RGM systems significantly reduced CH 4 emission by 50.17%, 44.89% and 39.51%, respectively, while increased N 2 O emission by 10.58%, 14.60% and 23.90%, respectively. And RWS system had the highest GWP. These findings suggest that mitigating GWP and improving rice yield could be simultaneously achieved by the IRDF, and employing suitable PUR would benefit for relieving greenhouse effect. Copyright © 2016 Elsevier B.V. All rights reserved.

Engineered Dwarf Male-Sterile Rice: A Promising Genetic Tool for Facilitating Recurrent Selection in Rice.

Science.gov (United States)

Ansari, Afsana; Wang, Chunlian; Wang, Jian; Wang, Fujun; Liu, Piqing; Gao, Ying; Tang, Yongchao; Zhao, Kaijun

2017-01-01

Rice is a crop feeding half of the world's population. With the continuous raise of yield potential via genetic improvement, rice breeding has entered an era where multiple genes conferring complex traits must be efficiently manipulated to increase rice yield further. Recurrent selection is a sound strategy for manipulating multiple genes and it has been successfully performed in allogamous crops. However, the difficulties in emasculation and hand pollination had obstructed efficient use of recurrent selection in autogamous rice. Here, we report development of the dwarf male-sterile rice that can facilitate recurrent selection in rice breeding. We adopted RNAi technology to synergistically regulate rice plant height and male fertility to create the dwarf male-sterile rice. The RNAi construct pTCK-EGGE, targeting the OsGA20ox2 and OsEAT1 genes, was constructed and used to transform rice via Agrobacterium -mediated transformation. The transgenic T0 plants showing largely reduced plant height and complete male-sterile phenotypes were designated as the dwarf male-sterile plants. Progenies of the dwarf male-sterile plants were obtained by pollinating them with pollens from the wild-type. In the T1 and T2 populations, half of the plants were still dwarf male-sterile; the other half displayed normal plant height and male fertility which were designated as tall and male-fertile plants. The tall and male-fertile plants are transgene-free and can be self-pollinated to generate new varieties. Since emasculation and hand pollination for dwarf male-sterile rice plants is no longer needed, the dwarf male-sterile rice can be used to perform recurrent selection in rice. A dwarf male-sterile rice-based recurrent selection model has been proposed.

The quiet revolution in Asia's rice value chains.

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Reardon, Thomas; Chen, Kevin Z; Minten, Bart; Adriano, Lourdes; Dao, The Anh; Wang, Jianying; Gupta, Sunipa Das

2014-12-01

There is a rapid transformation afoot in the rice value chain in Asia. The upstream is changing quickly-farmers are undertaking capital-led intensification and participating in burgeoning markets for land rental, fertilizer and pesticides, irrigation water, and seed, and shifting from subsistence to small commercialized farms; in some areas landholdings are concentrating. Midstream, in wholesale and milling, there is a quiet revolution underway, with thousands of entrepreneurs investing in equipment, increasing scale, diversifying into higher quality, and the segments are undergoing consolidation and vertical coordination and integration. Mills, especially in China, are packaging and branding, and building agent networks in wholesale markets, and large mills are building direct relationships with supermarkets. The downstream retail segment is undergoing a "supermarket revolution," again with the lead in change in China. In most cases the government is not playing a direct role in the market, but enabling this transformation through infrastructural investment. The transformation appears to be improving food security for cities by reducing margins, offering lower consumer rice prices, and increasing quality and diversity of rice. This paper discusses findings derived from unique stacked surveys of all value chain segments in seven zones, more and less developed, around Bangladesh, China, India, and Vietnam. © 2014 New York Academy of Sciences.

[Study on the Identification of Geographical Indication Wuchang Rice Based on the Content of Inorganic Elements].

Science.gov (United States)

Li, Yong-le; Zheng, Yan-jie; Tang, Lu; Su, Zhi-yi; Xiong, Cen

2016-03-01

Wuchang rice is a geographical indication product in China. Due to its high quality and low production, the phenome- non of fake is more and more serious. An effective identification method of Wuchang rice is urgent needed, for the maintenance of its brand image and interest of consumers. Base on the content of inorganic elements which are analyzed by ICP-AES and ICP-MS in rice, the identification model of Wuchang rice is studied combining with principal component analysis (PCA), Fisher discrimination and artificial neural network (ANN) in this paper. The effect on the identification of samples is poor through PCA, while the samples from Wuchang area and other areas can be identified accurately through Fisher discrimination and ANN. The average accurate identification ratio of training and verification set through Fisher discrimination is 93.5%, while the average accurate identification ratio through ANN is 96.4%. The ability to identify of ANN is better than Fisher discrimination. Wuchang rice can be identified accurately through the result of this research which provides a technology for the protection of geographical indications of this product.

75 FR 56911 - Request for Public Comment on the United States Standards for Rough Rice, Brown Rice for...

Science.gov (United States)

2010-09-17

... for Rough Rice, Brown Rice for Processing, and Milled Rice AGENCY: Grain Inspection, Packers and... reviewing the United States Standards and grading procedures for Rough Rice, Brown Rice for Processing, and Milled Rice under the Agriculture Marketing Act of 1946 (AMA). Since the standards were last revised...

Rice as commodity and anti-commodity

NARCIS (Netherlands)

Richards, P.

2016-01-01

On the Upper West Africa coast rice belongs to two species — African rice (Oryza glaberrima Steud.) and Asian rice (Oryza sativa L.). African rice was domesticated in the region, perhaps three millennia ago, from a presumed wild ancestor, O. barthii. Asian rice was introduced via trans-Saharan

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

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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.

Physicochemical and Antioxidant Properties of Rice Bran Oils Produced from Colored Rice Using Different Extraction Methods.

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Mingyai, Sukanya; Kettawan, Aikkarach; Srikaeo, Khongsak; Singanusong, Riantong

2017-06-01

This study investigated the physicochemical and antioxidant properties of rice bran oil (RBO) produced from the bran of three rice varities; Khao Dawk Mali 105 (white rice), Red Jasmine rice (red rice) and Hom-nin rice (black rice) using three extraction methods including cold-press extraction (CPE), solvent extraction (SE) and supercritical CO 2 extraction (SC-CO 2 ). Yields, color, acid value (AV), free fatty acid (FFA), peroxide value (PV), iodine value (IV), total phenolic compound (TPC), γ-oryzanol, α-tocopherol and fatty acid profile were analyzed. It was found that the yields obtained from SE, SC-CO 2 and CPE extractions were 17.35-20.19%, 14.76-18.16% and 3.22-6.22%, respectively. The RBO from the bran of red and black rice samples exhibited high antioxidant activities. They also contained higher amount of γ-oryzanol and α-tocopherol than those of white rice sample. In terms of extraction methods, SC-CO 2 provided better qualities of RBO as evidenced by their physicochemical and antioxidant properties. This study found that RBO produced from the bran of black rice samples using SC-CO 2 extraction method showed the best physicochemical and antioxidant properties.

Dynamic viscoelasticity of protease-treated rice batters for gluten-free rice bread making.

Science.gov (United States)

Honda, Yuji; Inoue, Nanami; Sugimoto, Reina; Matsumoto, Kenji; Koda, Tomonori; Nishioka, Akihiro

2018-03-01

Papain (cysteine protease), subtilisin (Protin SD-AY10, serine protease), and bacillolysin (Protin SD-NY10, metallo protease) increased the specific volume of gluten-free rice breads by 19-63% compared to untreated bread. In contrast, Newlase F (aspartyl protease) did not expand the volume of the rice bread. In a rheological analysis, the viscoelastic properties of the gluten-free rice batters also depended on the protease categories. Principal component analysis (PCA) analysis suggested that the storage and loss moduli (G' and G″, respectively) at 35 °C, and the maximum values of G' and G″, were important factors in the volume expansion. Judging from the PCA of the viscoelastic parameters of the rice batters, papain and Protin SD-AY10 improved the viscoelasticity for gluten-free rice bread making, and Protin SD-NY effectively expanded the gluten-free rice bread. The rheological properties differed between Protin SD-NY and the other protease treatments.

Efficient Prediction of Progesterone Receptor Interactome Using a Support Vector Machine Model

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Ji-Long Liu

2015-03-01

Full Text Available Protein-protein interaction (PPI is essential for almost all cellular processes and identification of PPI is a crucial task for biomedical researchers. So far, most computational studies of PPI are intended for pair-wise prediction. Theoretically, predicting protein partners for a single protein is likely a simpler problem. Given enough data for a particular protein, the results can be more accurate than general PPI predictors. In the present study, we assessed the potential of using the support vector machine (SVM model with selected features centered on a particular protein for PPI prediction. As a proof-of-concept study, we applied this method to identify the interactome of progesterone receptor (PR, a protein which is essential for coordinating female reproduction in mammals by mediating the actions of ovarian progesterone. We achieved an accuracy of 91.9%, sensitivity of 92.8% and specificity of 91.2%. Our method is generally applicable to any other proteins and therefore may be of help in guiding biomedical experiments.

Characterization of Volatile Flavor Compounds in Chinese Rice Wine Fermented from Enzymatic Extruded Rice.

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Xu, Enbo; Long, Jie; Wu, Zhengzong; Li, Hongyan; Wang, Fang; Xu, Xueming; Jin, Zhengyu; Jiao, Aiquan

2015-07-01

Enzymatic extrusion, instead of traditional steam cooking, to treat rice is an efficient and alternative pretreatment for Chinese rice wine fermentation. In order to determine the formation of volatiles in enzymatic extrusion-processed rice wine (EE), and to confirm its characteristic flavor compounds, headspace solid-phase micro-extraction followed by GC-MS was used. A total of 66 volatile compounds were identified in EE. During fermentation, most volatiles generated from enzymatic extruded rice had the similar trends with those from steam-cooked rice, but the differences in the concentration of volatiles indicated a changed balance of flavors release caused by enzymatic extrusion. Besides, the concentrations and sorts of volatiles in EEs fermented from different rice particle sizes, were not dramatically different. By principal component analysis, EE could be distinctly separated from other traditional Chinese rice wines according to its characteristic volatiles, namely, 2-heptanol, 1-octen-3-ol, ethyl 4-hydroxybenzoate, methylpentyl 2-propenoate, γ-hexalactone, and 4-vinylguaiacol. Enzymatic extrusion liquefaction has been a popular thermal treatment for cereals, and gradually being applied in fermentation and liquor-making industry all over the world. The characterization of volatile flavor compounds in Chinese rice wine processed by enzymatic extrusion liquefaction pretreatment, might be made use not only for a better understanding of this new-type rice wine, but for the further utilization of enzymatic extrusion in other wine or alcohol production as well. © 2015 Institute of Food Technologists®

The Reactive Species Interactome: Evolutionary Emergence, Biological Significance, and Opportunities for Redox Metabolomics and Personalized Medicine.

Science.gov (United States)

Cortese-Krott, Miriam M; Koning, Anne; Kuhnle, Gunter G C; Nagy, Peter; Bianco, Christopher L; Pasch, Andreas; Wink, David A; Fukuto, Jon M; Jackson, Alan A; van Goor, Harry; Olson, Kenneth R; Feelisch, Martin

2017-10-01

Oxidative stress is thought to account for aberrant redox homeostasis and contribute to aging and disease. However, more often than not, administration of antioxidants is ineffective, suggesting that our current understanding of the underlying regulatory processes is incomplete. Recent Advances: Similar to reactive oxygen species and reactive nitrogen species, reactive sulfur species are now emerging as important signaling molecules, targeting regulatory cysteine redox switches in proteins, affecting gene regulation, ion transport, intermediary metabolism, and mitochondrial function. To rationalize the complexity of chemical interactions of reactive species with themselves and their targets and help define their role in systemic metabolic control, we here introduce a novel integrative concept defined as the reactive species interactome (RSI). The RSI is a primeval multilevel redox regulatory system whose architecture, together with the physicochemical characteristics of its constituents, allows efficient sensing and rapid adaptation to environmental changes and various other stressors to enhance fitness and resilience at the local and whole-organism level. To better characterize the RSI-related processes that determine fluxes through specific pathways and enable integration, it is necessary to disentangle the chemical biology and activity of reactive species (including precursors and reaction products), their targets, communication systems, and effects on cellular, organ, and whole-organism bioenergetics using system-level/network analyses. Understanding the mechanisms through which the RSI operates will enable a better appreciation of the possibilities to modulate the entire biological system; moreover, unveiling molecular signatures that characterize specific environmental challenges or other forms of stress will provide new prevention/intervention opportunities for personalized medicine. Antioxid. Redox Signal. 00, 000-000.

Recent applications of multivariate data analysis methods in the authentication of rice and the most analyzed parameters: A review.

Science.gov (United States)

Maione, Camila; Barbosa, Rommel Melgaço

2018-01-24

Rice is one of the most important staple foods around the world. Authentication of rice is one of the most addressed concerns in the present literature, which includes recognition of its geographical origin and variety, certification of organic rice and many other issues. Good results have been achieved by multivariate data analysis and data mining techniques when combined with specific parameters for ascertaining authenticity and many other useful characteristics of rice, such as quality, yield and others. This paper brings a review of the recent research projects on discrimination and authentication of rice using multivariate data analysis and data mining techniques. We found that data obtained from image processing, molecular and atomic spectroscopy, elemental fingerprinting, genetic markers, molecular content and others are promising sources of information regarding geographical origin, variety and other aspects of rice, being widely used combined with multivariate data analysis techniques. Principal component analysis and linear discriminant analysis are the preferred methods, but several other data classification techniques such as support vector machines, artificial neural networks and others are also frequently present in some studies and show high performance for discrimination of rice.

Rice Cluster I, an Important Group of Archaea Producing Methane in Rice Fields

Science.gov (United States)

Conrad, R.

2006-12-01

Rice fields are an important source for the greenhouse gas methane. Methane is a major degradation product of organic matter in the anoxic soil, is partially oxidized in the rhizosphere and is emitted into the atmosphere through the aerenchyma system of the plants. Anaerobic degradation of organic matter by fermenting bacteria eventually results in the production of acetate and hydrogen, the two major substrates for microbial methanogenesis. The community of methanogenic archaea consists of several major orders or families including hydrogen-utilizing Rice Cluster-I (RC-I). Environmental conditions affect the methanogenic degradation process and the community structure of the methanogenic archaea in soil and rhizosphere. For example, populations of acetoclastic Methanosaetaceae and Methanosarcinaceae are enhanced by low and high acetate concentrations, respectively. Stable isotope probing of 16S rRNA showed that RC-I methanogens are mainly active on rice roots and at low H2 concentrations. Growth and population size is largely consistent with energetic conditions. RC-I methanogens on roots seem to be responsible for methane production from plant photosynthates that account for a major part of the emitted methane. Populations of RC-I methanogens in rice field soil are also enhanced at elevated temperatures (40-50°C). Moderately thermophilic members of RC-I methanogens or other methanogenic families were found to be ubiquitously present in soils from rice fields and river marshes. The genome of a RC-I methanogen was completely sequenced out of an enrichment culture using a metagenome approach. Genes found are consistent with life in the rhizosphere and in temporarily drained, oxic soil. We found that the methanogenic community structure on the rice roots is mainly determined by the respective community structure of the soil, but is in addition affected by the rice cultivar. Rice microcosms in which soil and rice roots are mainly colonized by RC-I methanogens produce

Label-free LC-MSe in tissue and serum reveals protein networks underlying differences between benign and malignant serous ovarian tumors.

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Wouter Wegdam

Full Text Available PURPOSE: To identify proteins and (molecular/biological pathways associated with differences between benign and malignant epithelial ovarian tumors. EXPERIMENTAL PROCEDURES: Serum of six patients with a serous adenocarcinoma of the ovary was collected before treatment, with a control group consisting of six matched patients with a serous cystadenoma. In addition to the serum, homogeneous regions of cells exhibiting uniform histology were isolated from benign and cancerous tissue by laser microdissection. We subsequently employed label-free liquid chromatography tandem mass spectrometry (LC-MSe to identify proteins in these serum and tissues samples. Analyses of differential expression between samples were performed using Bioconductor packages and in-house scripts in the statistical software package R. Hierarchical clustering and pathway enrichment analyses were performed, as well as network enrichment and interactome analysis using MetaCore. RESULTS: In total, we identified 20 and 71 proteins that were significantly differentially expressed between benign and malignant serum and tissue samples, respectively. The differentially expressed protein sets in serum and tissue largely differed with only 2 proteins in common. MetaCore network analysis, however inferred GCR-alpha and Sp1 as common transcriptional regulators. Interactome analysis highlighted 14-3-3 zeta/delta, 14-3-3 beta/alpha, Alpha-actinin 4, HSP60, and PCBP1 as critical proteins in the tumor proteome signature based on their relative overconnectivity. The data have been deposited to the ProteomeXchange with identifier PXD001084. DISCUSSION: Our analysis identified proteins with both novel and previously known associations to ovarian cancer biology. Despite the small overlap between differentially expressed protein sets in serum and tissue, APOA1 and Serotransferrin were significantly lower expressed in both serum and cancer tissue samples, suggesting a tissue-derived effect in serum

Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation

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Haberer Georg

2009-06-01

Full Text Available Abstract Background The spatiotemporal regulation of gene expression largely depends on the presence and absence of cis-regulatory sites in the promoter. In the economically highly important grass family, our knowledge of transcription factor binding sites and transcriptional networks is still very limited. With the completion of the sorghum genome and the available rice genome sequence, comparative promoter analyses now allow genome-scale detection of conserved cis-elements. Results In this study, we identified thousands of phylogenetic footprints conserved between orthologous rice and sorghum upstream regions that are supported by co-expression information derived from three different rice expression data sets. In a complementary approach, cis-motifs were discovered by their highly conserved co-occurrence in syntenic promoter pairs. Sequence conservation and matches to known plant motifs support our findings. Expression similarities of gene pairs positively correlate with the number of motifs that are shared by gene pairs and corroborate the importance of similar promoter architectures for concerted regulation. This strongly suggests that these motifs function in the regulation of transcript levels in rice and, presumably also in sorghum. Conclusion Our work provides the first large-scale collection of cis-elements for rice and sorghum and can serve as a paradigm for cis-element analysis through comparative genomics in grasses in general.

Effect of waxy rice flour and cassava starch on freeze-thaw stability of rice starch gels.

Science.gov (United States)

Charoenrein, Sanguansri; Preechathammawong, Nutsuda

2012-10-01

Repeatedly frozen and thawed rice starch gel affects quality. This study investigated how incorporating waxy rice flour (WF) and cassava starch (CS) in rice starch gel affects factors used to measure quality. When rice starch gels containing 0-2% WF and CS were subjected to 5 freeze-thaw cycles, both WF and CS reduced the syneresis in first few cycles. However CS was more effective in reducing syneresis than WF. The different composite arrangement of rice starch with WF or CS caused different mechanisms associated with the rice starch gel retardation of retrogradation, reduced the spongy structure and lowered syneresis. Both swollen granules of rice starch and CS caused an increase in the hardness of the unfrozen and freeze-thawed starch gel while highly swollen WF granules caused softer gels. These results suggested that WF and CS were effective in preserving quality in frozen rice starch based products. Copyright © 2012 Elsevier Ltd. All rights reserved.

Electricity generation from rice husk in Indian rice mills: potential and financial viability

International Nuclear Information System (INIS)

Kapur, T.; Kandpal, T.C.; Garg, H.P.

1998-01-01

Rice husk generated as a by-product of rice processing is an important energy resource. The availability of this resource in India has been assessed and the technologies for exploitation of its energy potential in the rice processing industry discussed. Nomographs have been developed for estimation of the husk required to meet the energy of parboiling, drying and milling operations. The unit cost of electricity using rice husk gasifier-based power generation systems has been calculated and its financial feasibility assessed in comparison with utility-supplied and diesel-generated electricity. With the cost and efficiency data assumed here, the unit cost of electricity produced by rice husk gasifier-dual fuel engine-generator system varies between Rs 2/kWh and Rs 7/kWh. (35 Rs approximates to SUS 1.). (author)

Electricity generation from rice husk in Indian rice mills: potential and financial viability

Energy Technology Data Exchange (ETDEWEB)

Kapur, T.; Kandpal, T.C.; Garg, H.P. [Indian Inst. of Technology, Centre for Energy Studies, New Delhi (India)

1998-12-31

Rice husk generated as a by-product of rice processing is an important energy resource. The availability of this resource in India has been assessed and the technologies for exploitation of its energy potential in the rice processing industry discussed. Nomographs have been developed for estimation of the husk required to meet the energy of parboiling, drying and milling operations. The unit cost of electricity using rice husk gasifier-based power generation systems has been calculated and its financial feasibility assessed in comparison with utility-supplied and diesel-generated electricity. With the cost and efficiency data assumed here, the unit cost of electricity produced by rice husk gasifier-dual fuel engine-generator system varies between Rs 2/kWh and Rs 7/kWh. (35 Rs approximates to SUS 1.). (author)

Evidence for Non-Transmission of Rice Yellow Mottle Virus (RYMV through Rice Seed

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Sy, AA.

2004-01-01

Full Text Available An indexing of the organs (radicle and plumule and components (husk, endosperm and embryo of rice seeds using Enzyme Linked Immunosorbent Assay (ELISA was carried out to detect Rice yellow mottle virus (RYMV and establish the exact location of the virus in the rice seed. RYMV was detected only in the husk (seed coat but not in the endosperm, plumule, radicle, nor embryo. None of the seedlings raised from the seeds expressed RYMV symptoms. No virus particle was detected by the ELISA test in the leaves of the screenhouse-reared plants obtained from seeds of infected plants. The results indicate that RYMV is apparently not transmitted through rice seed probably because the virus is seed-borne in the husk (seed coat of mature rice seeds.

Impact of bio-processing on rice

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ANCA NICOLAU

2011-07-01

Full Text Available The usual way of preparing rice is boiling, thermal process that gives it a lower digestibility as compared to instantiation, extrusion or expandation. Having in view this fact, the possibility to biotechnologically improve the boiled rice digestibility was investigated in a laboratory study. In this respect, boiled rice wassolid state fermented using a strain of Saccharomycopsis fibuligera, an amylase producing yeast originating from ragi. Fermented rice was then analyzed from the point of view of its content in easily assimilable sugars, protein, amino-acids, phosphorus and vitamins from B group. Biochemical analyses revealed that the fermented rice has a ten times higher content of reducing sugars than boiled rice, due to starch hydrolysis, while chromatographic studies proved that the fermented rice contains glucose, maltose, maltotriose and maltotetrose that are easily assimilable carbohydrates.Fermented rice has a protein content that is two times higher than that of boiled rice because it contains the yeast biomass, and is enriched in vitamins from B group (B1, B2, and B6 that are synthesized by the yeast. Inorganic phosphorus present in rice doubles its concentration in fermented rice, which means thatphosphorus bioavailability is increased.The sensorial profile of boiled rice is also improved by fermentation.This study proves the possibility to have a processing method which is relatively cheap, practical and of which the resulting product has good nutritive qualities and does not pose safety problems due to pure culture utilization as starter.

Gibberellic Acid: A Key Phytohormone for Spikelet Fertility in Rice Grain Production.

Science.gov (United States)

Kwon, Choon-Tak; Paek, Nam-Chon

2016-05-23

The phytohormone gibberellic acid (GA) has essential signaling functions in multiple processes during plant development. In the "Green Revolution", breeders developed high-yield rice cultivars that exhibited both semi-dwarfism and altered GA responses, thus improving grain production. Most studies of GA have concentrated on germination and cell elongation, but GA also has a pivotal role in floral organ development, particularly in stamen/anther formation. In rice, GA signaling plays an important role in spikelet fertility; however, the molecular genetic and biochemical mechanisms of GA in male fertility remain largely unknown. Here, we review recent progress in understanding the network of GA signaling and its connection with spikelet fertility, which is tightly associated with grain productivity in cereal crops.

Storage stability of flour-blasted brown rice

Science.gov (United States)

Brown rice was blasted with rice flour rather than sand in a sand blaster to make microscopic nicks and cuts so that water can easily penetrate into the brown rice endosperm and cook the rice in a shorter time. The flour-blasted American Basmati brown rice, long grain brown rice, and parboiled long...

Mapping paddy rice planting area in rice-wetland coexistent areas through analysis of Landsat 8 OLI and MODIS images.

Science.gov (United States)

Zhou, Yuting; Xiao, Xiangming; Qin, Yuanwei; Dong, Jinwei; Zhang, Geli; Kou, Weili; Jin, Cui; Wang, Jie; Li, Xiangping

2016-04-01

Accurate and up-to-date information on the spatial distribution of paddy rice fields is necessary for the studies of trace gas emissions, water source management, and food security. The phenology-based paddy rice mapping algorithm, which identifies the unique flooding stage of paddy rice, has been widely used. However, identification and mapping of paddy rice in rice-wetland coexistent areas is still a challenging task. In this study, we found that the flooding/transplanting periods of paddy rice and natural wetlands were different. The natural wetlands flood earlier and have a shorter duration than paddy rice in the Panjin Plain, a temperate region in China. We used this asynchronous flooding stage to extract the paddy rice planting area from the rice-wetland coexistent area. MODIS Land Surface Temperature (LST) data was used to derive the temperature-defined plant growing season. Landsat 8 OLI imagery was used to detect the flooding signal and then paddy rice was extracted using the difference in flooding stages between paddy rice and natural wetlands. The resultant paddy rice map was evaluated with in-situ ground-truth data and Google Earth images. The estimated overall accuracy and Kappa coefficient were 95% and 0.90, respectively. The spatial pattern of OLI-derived paddy rice map agrees well with the paddy rice layer from the National Land Cover Dataset from 2010 (NLCD-2010). The differences between Rice Landsat and Rice NLCD are in the range of ±20% for most 1-km grid cell. The results of this study demonstrate the potential of the phenology-based paddy rice mapping algorithm, via integrating MODIS and Landsat 8 OLI images, to map paddy rice fields in complex landscapes of paddy rice and natural wetland in the temperate region.

Genome-wide expression analysis of rice ABC transporter family across spatio-temporal samples and in response to abiotic stresses.

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Nguyen, Van Ngoc Tuyet; Moon, Sunok; Jung, Ki-Hong

2014-09-01

Although the super family of ATP-binding cassette (ABC) proteins plays key roles in the physiology and development of plants, the functions of members of this interesting family mostly remain to be clarified, especially in crop plants. Thus, systematic analysis of this family in rice (Oryza sativa), a major model crop plant, will be helpful in the design of effective strategies for functional analysis. Phylogenomic analysis that integrates anatomy and stress meta-profiling data based on a large collection of rice Affymetrix array data into the phylogenic context provides useful clues into the functions for each of the ABC transporter family members in rice. Using anatomy data, we identified 17 root-preferred and 16-shoot preferred genes at the vegetative stage, and 3 pollen, 2 embryo, 2 ovary, 2 endosperm, and 1 anther-preferred gene at the reproductive stage. The stress data revealed significant up-regulation or down-regulation of 47 genes under heavy metal treatment, 16 genes under nutrient deficient conditions, and 51 genes under abiotic stress conditions. Of these, we confirmed the differential expression patterns of 14 genes in root samples exposed to drought stress using quantitative real-time PCR. Network analysis using RiceNet suggests a functional gene network involving nine rice ABC transporters that are differentially regulated by drought stress in root, further enhancing the prediction of biological function. Our analysis provides a molecular basis for the study of diverse biological phenomena mediated by the ABC family in rice and will contribute to the enhancement of crop yield and stress tolerance. Copyright © 2014 Elsevier GmbH. All rights reserved.

International tourist preference of Lodok Rice Field natural elements, the cultural rice field from Manggarai - Indonesia

Science.gov (United States)

March Syahadat, Ray; Trie Putra, Priambudi; Nuraini; Nailufar, Balqis; Fatmala Makhmud, Desy

2017-10-01

Lodok Rice Field or usually known as spiderweb rice field is a system of land division. It cultural rice field only found on Manggarai, Province of East Nusa Tenggara, Indonesia. The landscape of Lodok Rice Field was aesthetic and it has big potential for tourism development. The aim of this study was to know the perception of natural elements of Lodok Rice Field landscape that could influence international tourist to visited Lodok Rice Field. If we know the elements that could influenced the international tourist, we could used the landscape image for tourism media promotion. The methods of this study used scenic beauty estimation (SBE) by 85 respondents from 34 countries and Kruskal Wallis H test. The countries grouped by five continents (Asia, America, Europe, Africa, and Oceania). The result showed that the Asian respondents liked the elements of sky, mountain, and the rice field. Then, the other respondent from another continent liked the elements of sunshine, mountain, and the rice field. Although the Asian had different perception about landscape elements of rice field’s good view, it’s not differ significantly by Kruskal Wallis H test.

Defensive Responses of Rice Genotypes for Resistance Against Rice Leaffolder Cnaphalocrocis medinalis

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M. PUNITHAVALLI

2013-09-01

Full Text Available The experiment was carried out to assess the reaction of different categories of rice genotypes viz., resistant, susceptible, hybrid, scented, popular and wild in response to the infestation by rice leaffolder (RLF, Cnaphalocrocis medinalis (Guenee and to explore the possible use of these genotypes in developing RLF-resistant rice varieties. The changes of various biochemical constituents such as leaf soluble protein, phenol, ortho-dihydroxy phenol, tannin and enzymes viz., peroxidase, phenyl alanine ammonia lyase (PAL were assessed spectrophotometrically in all the rice genotypes before and after RLF infestation. The protein profile was analyzed using sodium dodecyl sulphate-poly acrylamide gel electrophoresis (SDS-PAGE method. A significant constituent of biochemical content such as tannin, phenol and ortho-dihydroxy phenol has been increased along with enzyme activities of peroxidase and PAL in the infested resistant (Ptb 33, TKM6 and LFR831311 and wild rice genotypes (Oryza minuta and O. rhizomatis. A decrease in leaf protein content was evident invariably in all the infested rice genotypes. It is also evident that the contents of biochemicals such as phenol, ortho-dihydroxy phenol and tannin were negatively correlated with leaffolder damage. However, leaf protein content was positively correlated with the damage by rice leaffolder. SDS-PAGE analysis for total protein profiling of healthy and C. medinalis-infested genotypes revealed the enhanced expression of a high molecular weight (> 97 kDa protein in all the genotypes. Besides, there was also an increased induction of a 38 kDa protein in C. medinalis infested resistant genotypes, which was absent in uninfested plants. The present investigation proved that the elevated levels of biochemicals and enzymes may play a vital role in rice plants resistance to RLF.

Dynamic Mapping of Rice Growth Parameters Using HJ-1 CCD Time Series Data

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Jing Wang

2016-11-01

Full Text Available The high temporal resolution (4-day charge-coupled device (CCD cameras onboard small environment and disaster monitoring and forecasting satellites (HJ-1A/B with 30 m spatial resolution and large swath (700 km have substantially increased the availability of regional clear sky optical remote sensing data. For the application of dynamic mapping of rice growth parameters, leaf area index (LAI and aboveground biomass (AGB were considered as plant growth indicators. The HJ-1 CCD-derived vegetation indices (VIs showed robust relationships with rice growth parameters. Cumulative VIs showed strong performance for the estimation of total dry AGB. The cross-validation coefficient of determination ( R C V 2 was increased by using two machine learning methods, i.e., a back propagation neural network (BPNN and a support vector machine (SVM compared with traditional regression equations of LAI retrieval. The LAI inversion accuracy was further improved by dividing the rice growth period into before and after heading stages. This study demonstrated that continuous rice growth monitoring over time and space at field level can be implemented effectively with HJ-1 CCD 10-day composite data using a combination of proper VIs and regression models.

Lead in rice: analysis of baseline lead levels in market and field collected rice grains.

Science.gov (United States)

Norton, Gareth J; Williams, Paul N; Adomako, Eureka E; Price, Adam H; Zhu, Yongguan; Zhao, Fang-Jie; McGrath, Steve; Deacon, Claire M; Villada, Antia; Sommella, Alessia; Lu, Ying; Ming, Lei; De Silva, P Mangala C S; Brammer, Hugh; Dasgupta, Tapash; Islam, M Rafiqul; Meharg, Andrew A

2014-07-01

In a large scale survey of rice grains from markets (13 countries) and fields (6 countries), a total of 1578 rice grain samples were analysed for lead. From the market collected samples, only 0.6% of the samples exceeded the Chinese and EU limit of 0.2 μg g(-1) lead in rice (when excluding samples collected from known contaminated/mine impacted regions). When evaluating the rice grain samples against the Food and Drug Administration's (FDA) provisional total tolerable intake (PTTI) values for children and pregnant women, it was found that only people consuming large quantities of rice were at risk of exceeding the PTTI from rice alone. Furthermore, 6 field experiments were conducted to evaluate the proportion of the variation in lead concentration in rice grains due to genetics. A total of 4 of the 6 field experiments had significant differences between genotypes, but when the genotypes common across all six field sites were assessed, only 4% of the variation was explained by genotype, with 9.5% and 11% of the variation explained by the environment and genotype by environment interaction respectively. Further work is needed to identify the sources of lead contamination in rice, with detailed information obtained on the locations and environments where the rice is sampled, so that specific risk assessments can be performed. Copyright © 2014 Elsevier B.V. All rights reserved.

Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case study.

Science.gov (United States)

Wang, Yongfei; Lin, Shoukai; Song, Qi; Li, Kuan; Tao, Huan; Huang, Jian; Chen, Xinhai; Que, Shufu; He, Huaqin

2014-05-07

Heat shock proteins (Hsps) perform a fundamental role in protecting plants against abiotic stresses. Although researchers have made great efforts on the functional analysis of individual family members, Hsps have not been fully characterized in rice (Oryza sativa L.) and little is known about their interactors. In this study, we combined orthology-based approach with expression association data to screen rice Hsps for the expression patterns of which strongly correlated with that of heat responsive probe-sets. Twenty-seven Hsp candidates were identified, including 12 small Hsps, six Hsp70s, three Hsp60s, three Hsp90s, and three clpB/Hsp100s. Then, using a combination of interolog and expression profile-based methods, we inferred 430 interactors of Hsp70s in rice, and validated the interactions by co-localization and function-based methods. Subsequent analysis showed 13 interacting domains and 28 target motifs were over-represented in Hsp70s interactors. Twenty-four GO terms of biological processes and five GO terms of molecular functions were enriched in the positive interactors, whose expression levels were positively associated with Hsp70s. Hsp70s interaction network implied that Hsp70s were involved in macromolecular translocation, carbohydrate metabolism, innate immunity, photosystem II repair and regulation of kinase activities. Twenty-seven Hsps in rice were identified and 430 interactors of Hsp70s were inferred and validated, then the interacting network of Hsp70s was induced and the function of Hsp70s was analyzed. Furthermore, two databases named Rice Heat Shock Proteins (RiceHsps) and Rice Gene Expression Profile (RGEP), and one online tool named Protein-Protein Interaction Predictor (PPIP), were constructed and could be accessed at http://bioinformatics.fafu.edu.cn/.

Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication.

Science.gov (United States)

Wang, Yu; Bai, Xuefei; Yan, Chenghai; Gui, Yiejie; Wei, Xinghua; Zhu, Qian-Hao; Guo, Longbiao; Fan, Longjiang

2012-11-01

The lack of a MIRNA set and genome sequence of wild rice (Oryza rufipogon) has prevented us from determining the role of MIRNA genes in rice domestication. In this study, a genome, three small RNA populations and a degradome of O. rufipogon were sequenced by Illumina platform and the expression levels of microRNAs (miRNAs) were investigated by miRNA chips. A de novo O. rufipogon genome was assembled using c. 55× coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on c. 5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these, O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting a loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression differences between wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated that MIRNA genes, like protein-coding genes, might have been significantly shaped during rice domestication and could be one of the driving forces that contributed to rice domestication. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

Do rice water weevils and rice stem borers compete when sharing a host plant?

Science.gov (United States)

Shi, Sheng-Wei; He, Yan; Ji, Xiang-Hua; Jiang, Ming-Xing; Cheng, Jia-An

2008-07-01

The rice water weevil (RWW) Lissorhoptrus oryzophilus Kuschel (Coleoptera: Curculionidae) is an invasive insect pest of rice Oryza sativa L. in China. Little is known about the interactions of this weevil with indigenous herbivores. In the present study, adult feeding and population density of the weevil, injury level of striped stem borer Chilo suppressalis (Walker) (Lepidoptera: Pyralidae) and pink stem borer Sesamia inferens (Walker) (Lepidoptera: Noctuidae) to rice, as well as growth status of their host plants were surveyed in a rice field located in Southeastern Zhejiang, China, in 2004 with the objective to discover interspecific interactions on the rice. At tillering stage, both adult feeding of the weevil and injury of the stem borers tended to occur on larger tillers (bearing 5 leaves) compared with small tillers (bearing 2~4 leaves), but the insects showed no evident competition with each other. At booting stage, the stem borers caused more withering/dead hearts and the weevil reached a higher density on the plants which had more productive tillers and larger root system; the number of weevils per tiller correlated negatively with the percentage of withering/dead hearts of plants in a hill. These observations indicate that interspecific interactions exist between the rice water weevil and the rice stem borers with negative relations occurring at booting or earlier developmental stages of rice.

Do rice water weevils and rice stem borers compete when sharing a host plant?*

Science.gov (United States)

Shi, Sheng-wei; He, Yan; Ji, Xiang-hua; Jiang, Ming-xing; Cheng, Jia-an

2008-01-01

The rice water weevil (RWW) Lissorhoptrus oryzophilus Kuschel (Coleoptera: Curculionidae) is an invasive insect pest of rice Oryza sativa L. in China. Little is known about the interactions of this weevil with indigenous herbivores. In the present study, adult feeding and population density of the weevil, injury level of striped stem borer Chilo suppressalis (Walker) (Lepidoptera: Pyralidae) and pink stem borer Sesamia inferens (Walker) (Lepidoptera: Noctuidae) to rice, as well as growth status of their host plants were surveyed in a rice field located in Southeastern Zhejiang, China, in 2004 with the objective to discover interspecific interactions on the rice. At tillering stage, both adult feeding of the weevil and injury of the stem borers tended to occur on larger tillers (bearing 5 leaves) compared with small tillers (bearing 2~4 leaves), but the insects showed no evident competition with each other. At booting stage, the stem borers caused more withering/dead hearts and the weevil reached a higher density on the plants which had more productive tillers and larger root system; the number of weevils per tiller correlated negatively with the percentage of withering/dead hearts of plants in a hill. These observations indicate that interspecific interactions exist between the rice water weevil and the rice stem borers with negative relations occurring at booting or earlier developmental stages of rice. PMID:18600788

Field trial of GABA-fortified rice plants and oral administration of milled rice in spontaneously hypertensive rats.

Science.gov (United States)

Kowaka, Emi; Shimajiri, Yasuka; Kawakami, Kouhei; Tongu, Miki; Akama, Kazuhito

2015-06-01

Hypertension is one of the most critical risk factors accompanying cardiovascular diseases. γ-Aminobutyric acid (GABA) is a non-protein amino acid that functions as a major neurotransmitter in mammals and also as a blood-pressure lowering agent. We previously produced GABA-fortified rice lines of a popular Japonica rice cultivar 'Koshihikari' by genetic manipulation of GABA shunt-related genes. In the study reported here, we grew these same novel rice lines in a field trial and administered the milled rice orally to rats. The yield parameters of the transgenic rice plants were almost unchanged compared to those of untransformed cv. 'Koshihikari' plants, while the rice grains of the transgenic plants contained a high GABA content (3.5 g GABA/kg brown rice; 0.75-0.85 GABA g/kg milled rice) in a greenhouse trial. Oral administration of a diet containing 2.5% GABA-fortified rice, with a daily intake for 8 weeks, had an approximately 20 mmHg anti-hypertensive effect in spontaneous hypertensive rats but not in normotensive Wistar-Kyoto rats. These results suggest that GABA-fortified rice may be applicable as a staple food to control or prevent hypertension.

Effect of acetic acid on rice seeds coated with rice husk ash

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Lizandro Ciciliano Tavares

2013-06-01

Full Text Available Flooded rice cultivation promotes anaerobic conditions, favoring the formation of short chain organic acids such as acetic acid, which may be toxic to the crop. The objective of this study was to evaluate the effect of acetic acid on rice seeds coated with rice husk ash. The experiment was arranged in a 2 x 5 x 5 factorial randomized design, with two cultivars (IRGA 424 and BRS Querência, five doses of coating material (0, 2, 3,4 e 5 g kg-1 seed and five concentrations of acetic acid (0, 3, 6, 9 and 12 mM, with 4 replications, totaling 50 treatments. The variables first count of germination, germination, shoot and root length, dry weight of shoots and roots were recorded. The results showed that coating rice seeds with rice husk ash up to 5 g kg-1 seed does not influence the performance of rice seeds of cultivars IRGA 424 and BRS Querência when exposed to concentrations of 12 mM acetic acid. The presence of acetic acid in the substrates used for seed germination reduced the vigor and viability of seeds of cultivars IRGA 424 and BRS Querência, as well as seedling development, affecting mainly the roots of BRS Querência.

Interactomes to Biological Phase Space: a call to begin thinking at a new level in computational biology.

Energy Technology Data Exchange (ETDEWEB)

Davidson, George S.; Brown, William Michael

2007-09-01

Techniques for high throughput determinations of interactomes, together with high resolution protein collocalizations maps within organelles and through membranes will soon create a vast resource. With these data, biological descriptions, akin to the high dimensional phase spaces familiar to physicists, will become possible. These descriptions will capture sufficient information to make possible realistic, system-level models of cells. The descriptions and the computational models they enable will require powerful computing techniques. This report is offered as a call to the computational biology community to begin thinking at this scale and as a challenge to develop the required algorithms and codes to make use of the new data.3

The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of United States weedy rice.

Science.gov (United States)

Burgos, Nilda Roma; Singh, Vijay; Tseng, Te Ming; Black, Howard; Young, Nelson D; Huang, Zhongyun; Hyma, Katie E; Gealy, David R; Caicedo, Ana L

2014-11-01

The use of herbicide-resistant (HR) Clearfield rice (Oryza sativa) to control weedy rice has increased in the past 12 years to constitute about 60% of rice acreage in Arkansas, where most U.S. rice is grown. To assess the impact of HR cultivated rice on the herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a history of Clearfield rice. Panicles from each weedy type were harvested and tested for resistance to imazethapyr. The majority of plants sampled had at least 20% resistant offspring. These resistant weeds were 97 to 199 cm tall and initiated flowering from 78 to 128 d, generally later than recorded for accessions collected prior to the widespread use of Clearfield rice (i.e. historical accessions). Whereas the majority (70%) of historical accessions had straw-colored hulls, only 30% of contemporary HR weedy rice had straw-colored hulls. Analysis of genotyping-by-sequencing data showed that HR weeds were not genetically structured according to hull color, whereas historical weedy rice was separated into straw-hull and black-hull populations. A significant portion of the local rice crop genome was introgressed into HR weedy rice, which was rare in historical weedy accessions. Admixture analyses showed that HR weeds tend to possess crop haplotypes in the portion of chromosome 2 containing the ACETOLACTATE SYNTHASE gene, which confers herbicide resistance to Clearfield rice. Thus, U.S. HR weedy rice is a distinct population relative to historical weedy rice and shows modifications in morphology and phenology that are relevant to weed management. © 2014 American Society of Plant Biologists. All Rights Reserved.

Residues and accumulation of molinate in rice crops and aquatic weeds in the MUDA rice agroecosystem

International Nuclear Information System (INIS)

Nashriyah Mat; Sabri Junoh; Nuriati Nurdin; Ramli Ishak

2002-01-01

Plant and soil residue levels and its accumulation in rice crops and rice aquatic weed plants were studied. Molinate residue levels in rice, weeds and soil were not significantly different between the recycled and the non-recycled area, even though they were higher in the non-recycled area. In the rice plant, the residue level at 10 DAT (days after treatment) was significantly higher than 30 DAT in the recycled area. In rice aquatic weed plants, the residue level was significantly higher at 10 DAT as compared to 30 DAT in the non-recycled area. Molinate residue levels in soil at 10 DAT and 30 DAT were similar. Molinate accumulated (ratio of molinate concentration in plant over soil) more in the rice crop as compared to rice aquatic weeds at 10 DAT, in both the recycled and the non-recycled areas. (Author)

Arsenic accumulation in rice: Consequences of rice genotypes and management practices to reduce human health risk.

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Islam, Shofiqul; Rahman, Mohammad Mahmudur; Islam, M R; Naidu, Ravi

2016-11-01

Rice is an essential staple food and feeds over half of the world's population. Consumption of rice has increased from limited intake in Western countries some 50years ago to major dietary intake now. Rice consumption represents a major route for inorganic arsenic (As) exposure in many countries, especially for people with a large proportion of rice in their daily diet as much as 60%. Rice plants are more efficient in assimilating As into its grains than other cereal crops and the accumulation may also adversely affect the quality of rice and their nutrition. Rice is generally grown as a lowland crop in flooded soils under reducing conditions. Under these conditions the bioavailability of As is greatly enhanced leading to excessive As bioaccumulation compared to that under oxidizing upland conditions. Inorganic As species are carcinogenic to humans and even at low levels in the diet pose a considerable risk to humans. There is a substantial genetic variation among the rice genotypes in grain-As accumulation as well as speciation. Identifying the extent of genetic variation in grain-As concentration and speciation of As compounds are crucial to determining the rice varieties which accumulate low inorganic As. Varietal selection, irrigation water management, use of fertilizer and soil amendments, cooking practices etc. play a vital role in reducing As exposure from rice grains. In the meantime assessing the bioavailability of As from rice is crucial to understanding human health exposure and reducing the risk. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Effects of rice cleaning and cooking process on the residues of flutolanil, fenobucarb, silafluofen and buprofezin in rice].

Science.gov (United States)

Satoh, Motoaki; Sakaguchi, Masayuki; Kobata, Masakazu; Sakaguchi, Yoko; Tanizawa, Haruna; Miura, Yuri; Sasano, Ryoichi; Nakanishi, Yutaka

2003-02-01

We studied the effect of cleaning and cooking on the residues of flutolanil, fenobucarb, silafluofen and buprofezin in rice. The rice had been sprayed in a paddy field in Wakayama city, with 3 kinds of pesticide application protocols: spraying once at the usual concentration of pesticides, repeated spraying (3 times) with the usual concentration of pesticides and spraying once with 3 times the usual concentration of pesticides. The residue levels of pesticide decreased during the rice cleaning process. Silafluofen, which has a higher log Pow value, remained in the hull of the rice. Fenobucarb, which has a lower log Pow value, penetrated inside the rice. The residue concentration of pesticide in polished rice was higher than that in pre-washed rice processed ready for cooking. During the cooking procedure, the reduction of pesticides in polished rice was higher than that in brown rice.

Molecular evolution of the rice blast resistance gene Pi-ta in invasive weedy rice in the USA.

Directory of Open Access Journals (Sweden)

Seonghee Lee

Full Text Available The Pi-ta gene in rice has been effectively used to control rice blast disease caused by Magnaporthe oryzae worldwide. Despite a number of studies that reported the Pi-ta gene in domesticated rice and wild species, little is known about how the Pi-ta gene has evolved in US weedy rice, a major weed of rice. To investigate the genome organization of the Pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the US, we analyzed nucleotide sequence variation at the Pi-ta gene and its surrounding 2 Mb region in 156 weedy, domesticated and wild rice relatives. We found that the region at and around the Pi-ta gene shows very low genetic diversity in US weedy rice. The patterns of molecular diversity in weeds are more similar to cultivated rice (indica and aus, which have never been cultivated in the US, rather than the wild rice species, Oryza rufipogon. In addition, the resistant Pi-ta allele (Pi-ta found in the majority of US weedy rice belongs to the weedy group strawhull awnless (SH, suggesting a single source of origin for Pi-ta. Weeds with Pi-ta were resistant to two M. oryzae races, IC17 and IB49, except for three accessions, suggesting that component(s required for the Pi-ta mediated resistance may be missing in these accessions. Signatures of flanking sequences of the Pi-ta gene and SSR markers on chromosome 12 suggest that the susceptible pi-ta allele (pi-ta, not Pi-ta, has been introgressed from cultivated to weedy rice by out-crossing.

Molecular Evolution of the Rice Blast Resistance Gene Pi-ta in Invasive Weedy Rice in the USA

Science.gov (United States)

Lee, Seonghee; Jia, Yulin; Jia, Melissa; Gealy, David R.; Olsen, Kenneth M.; Caicedo, Ana L.

2011-01-01

The Pi-ta gene in rice has been effectively used to control rice blast disease caused by Magnaporthe oryzae worldwide. Despite a number of studies that reported the Pi-ta gene in domesticated rice and wild species, little is known about how the Pi-ta gene has evolved in US weedy rice, a major weed of rice. To investigate the genome organization of the Pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the US, we analyzed nucleotide sequence variation at the Pi-ta gene and its surrounding 2 Mb region in 156 weedy, domesticated and wild rice relatives. We found that the region at and around the Pi-ta gene shows very low genetic diversity in US weedy rice. The patterns of molecular diversity in weeds are more similar to cultivated rice (indica and aus), which have never been cultivated in the US, rather than the wild rice species, Oryza rufipogon. In addition, the resistant Pi-ta allele (Pi-ta) found in the majority of US weedy rice belongs to the weedy group strawhull awnless (SH), suggesting a single source of origin for Pi-ta. Weeds with Pi-ta were resistant to two M. oryzae races, IC17 and IB49, except for three accessions, suggesting that component(s) required for the Pi-ta mediated resistance may be missing in these accessions. Signatures of flanking sequences of the Pi-ta gene and SSR markers on chromosome 12 suggest that the susceptible pi-ta allele (pi-ta), not Pi-ta, has been introgressed from cultivated to weedy rice by out-crossing. PMID:22043312

Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks.

Science.gov (United States)

Van Landeghem, Sofie; Van Parys, Thomas; Dubois, Marieke; Inzé, Dirk; Van de Peer, Yves

2016-01-05

Differential networks have recently been introduced as a powerful way to study the dynamic rewiring capabilities of an interactome in response to changing environmental conditions or stimuli. Currently, such differential networks are generated and visualised using ad hoc methods, and are often limited to the analysis of only one condition-specific response or one interaction type at a time. In this work, we present a generic, ontology-driven framework to infer, visualise and analyse an arbitrary set of condition-specific responses against one reference network. To this end, we have implemented novel ontology-based algorithms that can process highly heterogeneous networks, accounting for both physical interactions and regulatory associations, symmetric and directed edges, edge weights and negation. We propose this integrative framework as a standardised methodology that allows a unified view on differential networks and promotes comparability between differential network studies. As an illustrative application, we demonstrate its usefulness on a plant abiotic stress study and we experimentally confirmed a predicted regulator. Diffany is freely available as open-source java library and Cytoscape plugin from http://bioinformatics.psb.ugent.be/supplementary_data/solan/diffany/.

A Systems Approach to Refine Disease Taxonomy by Integrating Phenotypic and Molecular Networks

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Xuezhong Zhou

2018-05-01

Full Text Available The International Classification of Diseases (ICD relies on clinical features and lags behind the current understanding of the molecular specificity of disease pathobiology, necessitating approaches that incorporate growing biomedical data for classifying diseases to meet the needs of precision medicine. Our analysis revealed that the heterogeneous molecular diversity of disease chapters and the blurred boundary between disease categories in ICD should be further investigated. Here, we propose a new classification of diseases (NCD by developing an algorithm that predicts the additional categories of a disease by integrating multiple networks consisting of disease phenotypes and their molecular profiles. With statistical validations from phenotype-genotype associations and interactome networks, we demonstrate that NCD improves disease specificity owing to its overlapping categories and polyhierarchical structure. Furthermore, NCD captures the molecular diversity of diseases and defines clearer boundaries in terms of both phenotypic similarity and molecular associations, establishing a rational strategy to reform disease taxonomy. Keywords: Disease taxonomy, Network medicine, Disease phenotypes, Molecular profiles, Precision medicine

Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication.

Science.gov (United States)

Zhang, Fantao; Xu, Tao; Mao, Linyong; Yan, Shuangyong; Chen, Xiwen; Wu, Zhenfeng; Chen, Rui; Luo, Xiangdong; Xie, Jiankun; Gao, Shan

2016-04-26

It is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.). Compared to other studies which concentrate on rice origin, this study is to genetically elucidate the substantially phenotypic and physiological changes from wild rice to cultivated rice at the whole genome level. Instead of comparing two assembled genomes, this study directly compared the Dongxiang wild rice (DXWR) Illumina sequencing reads with the Nipponbare (O. sativa) complete genome without assembly of the DXWR genome. Based on the results from the comparative genomics analysis, structural variations (SVs) between DXWR and Nipponbare were determined to locate deleted genes which could have been acquired by Nipponbare during rice domestication. To overcome the limit of the SV detection, the DXWR transcriptome was also sequenced and compared with the Nipponbare transcriptome to discover the genes which could have been lost in DXWR during domestication. Both 1591 Nipponbare-acquired genes and 206 DXWR-lost transcripts were further analyzed using annotations from multiple sources. The NGS data are available in the NCBI SRA database with ID SRP070627. These results help better understanding the domestication from wild rice to cultivated rice at the whole genome level and provide a genomic data resource for rice genetic research or breeding. One finding confirmed transposable elements contribute greatly to the genome evolution from wild rice to cultivated rice. Another finding suggested the photophosphorylation and oxidative phosphorylation system in cultivated rice could have adapted to environmental changes simultaneously during domestication.

Discerning molecular interactions: A comprehensive review on biomolecular interaction databases and network analysis tools.

Science.gov (United States)

Miryala, Sravan Kumar; Anbarasu, Anand; Ramaiah, Sudha

2018-02-05

Computational analysis of biomolecular interaction networks is now gaining a lot of importance to understand the functions of novel genes/proteins. Gene interaction (GI) network analysis and protein-protein interaction (PPI) network analysis play a major role in predicting the functionality of interacting genes or proteins and gives an insight into the functional relationships and evolutionary conservation of interactions among the genes. An interaction network is a graphical representation of gene/protein interactome, where each gene/protein is a node, and interaction between gene/protein is an edge. In this review, we discuss the popular open source databases that serve as data repositories to search and collect protein/gene interaction data, and also tools available for the generation of interaction network, visualization and network analysis. Also, various network analysis approaches like topological approach and clustering approach to study the network properties and functional enrichment server which illustrates the functions and pathway of the genes and proteins has been discussed. Hence the distinctive attribute mentioned in this review is not only to provide an overview of tools and web servers for gene and protein-protein interaction (PPI) network analysis but also to extract useful and meaningful information from the interaction networks. Copyright © 2017 Elsevier B.V. All rights reserved.

Effect of Red Yeast Rice and Coconut, Rice Bran or Sunflower Oil Combination in Rats on Hypercholesterolemic Diet.

Science.gov (United States)

Govindarajan, Sumitra; Vellingiri, Kishore

2016-04-01

Dietary supplements provide a novel population based health approach for treating hyperlipidemias. Red yeast rice is known to have lipid lowering effects. Combination of red yeast rice with various oils is taken by different population around the world. In this present work, we aimed to compare the effects of red yeast rice with different oil (coconut, rice bran and sunflower oil) supplementations on lipid levels and oxidative stress in rats fed on hypercholesterolemic diet. A Randomized controlled study was conducted on 28 male Sprague Dawley rats. It included 4 arms-Control arm (hypercholesterolemic diet), Test arm A (hypercholesterolemic diet +Red yeast rice + Rice bran oil), arm B (hypercholesterolemic diet +Red yeast rice + Coconut oil) and arm C (hypercholesterolemic diet +Red yeast rice + Sunflower oil). At the end of one month, serum cholesterol, triglycerides, MDA and paraoxonase was measured. The mean values of analytes between the different groups were compared using student 't-' test. The rats fed with red yeast rice and rice bran oil combination showed significantly lower levels of serum cholesterol, triglycerides and MDA when compared to the controls. The serum paraoxonase levels were significantly higher in this group when compared to the controls. The rats fed with red yeast rice and coconut oil combination showed significantly lower serum cholesterol and MDA levels when compared to the controls. The mean triglyceride and paraoxonase levels did not show any statistically significant difference from the controls. The rats on red yeast rice and sunflower oil combination did not show any statistically significant difference in the lipid levels and oxidative stress parameters. The food combination which had best outcome in preventing the development of hyperlipidemia and oxidative stress in rats fed with hypercholesterolemic diet was red yeast rice and rice bran oil. Combining red yeast rice with coconut oil and sunflower oil gave suboptimal benefits.

Rice-eating quality among consumers in different rice grain preference countries

NARCIS (Netherlands)

Suwannaporn, P.; Linnemann, A.R.

2008-01-01

More rice is eaten nowadays in traditionally nonrice-eating countries. This study investigated consumer eating quality preferences among consumers in target rice export countries to identify opportunities and strategic implications. A quantitative study with 1,128 consumers of target nationalities

[The main nutrients digestibility of genetically modified rice and parental rice in the terminal ileum of pigs].

Science.gov (United States)

Li, Min; Hu, Yi-chun; Piao, Jian-hua; Yang, Xiao-guang

2010-10-01

To compare the digestibility of main nutrients in genetically modified rice with double antisense starch-branching enzyme gene and parental rice. Seven Wuzhishan healthy adult barrows were surgically fitted with a T-cannula at the terminal ileum. After surgery, seven pigs were randomly divided into two groups, and fed genetically modified rice and parental rice by a crossover model. Ileal digesta were collected for analysis of main nutrient digestibility. The apparent digestibility levels of protein in genetically modified rice and parental rice were 69.50% ± 4.50%, 69.61% ± 8.40%, respectively (t = 0.01, P = 0.994); true digestibility levels of protein were 87.55% ± 4.95%, 87.64% ± 9.40%, respectively (t = 0.01, P = 0.994); fat digestibility levels were 72.86% ± 0.34%, 77.89% ± 13.09%, respectively (t = 0.95, P = 0.378); carbohydrate digestibility levels were 72.92% ± 7.43%, 92.35% ± 5.88%, respectively (t = 4.27, P = 0.005). The apparent and true digestibility of 17 amino acids had no significant difference in the two rice. Carbohydrate digestibility in genetically modified rice was significantly lower than that in non-genetically modified rice, other main nutrients digestibility in the two rice have substantial equivalence.

Processing Conditions, Rice Properties, Health and Environment

Directory of Open Access Journals (Sweden)

Nobutaka Nakamura

2011-06-01

Full Text Available Rice is the staple food for nearly two-thirds of the world’s population. Food components and environmental load of rice depends on the rice form that is resulted by different processing conditions. Brown rice (BR, germinated brown rice (GBR and partially-milled rice (PMR contains more health beneficial food components compared to the well milled rice (WMR. Although the arsenic concentration in cooked rice depends on the cooking methods, parboiled rice (PBR seems to be relatively prone to arsenic contamination compared to that of untreated rice, if contaminated water is used for parboiling and cooking. A change in consumption patterns from PBR to untreated rice (non-parboiled, and WMR to PMR or BR may conserve about 43–54 million tons of rice and reduce the risk from arsenic contamination in the arsenic prone area. This study also reveals that a change in rice consumption patterns not only supply more food components but also reduces environmental loads. A switch in production and consumption patterns would improve food security where food grains are scarce, and provide more health beneficial food components, may prevent some diseases and ease the burden on the Earth. However, motivation and awareness of the environment and health, and even a nominal incentive may require for a method switching which may help in building a sustainable society.

Development of Ozone Technology Rice Storage Systems (OTRISS) for Quality Improvement of Rice Production

International Nuclear Information System (INIS)

Nur, M; Kusdiyantini, E; Wuryanti, W; Winarni, T A; Widyanto, S A; Muharam, H

2015-01-01

This research has been carried out by using ozone to address the rapidly declining quality of rice in storage. In the first year, research has focused on the rice storage with ozone technology for small capacity (e.g., household) and the medium capacity (e.g., dormitories, hospitals). Ozone was produced by an ozone generator with Dielectric Barrier Discharge Plasma (DBDP). Ozone technology rice storage system (OTRISS) is using ozone charateristic which is a strong oxidizer. Ozone have a short endurance of existence and then decompose, as a result produce oxygen and radicals of oxygen. These characteristics could kill microorganisms and pests, reduce air humidity and enrich oxygen. All components used in SPBTO assembled using raw materials available in the big cities in Indonesia. Provider of high voltage (High Voltage Power Supply, 40-70 kV, 23 KH, AC) is one of components that have been assembled and tested. Ozone generator is assembled with 7 reactors of Dielectric Barrier Discharge Plasma (DBDP). Rice container that have been prepared for OTRISS have adjusted so can be integrated with generator, power supply and blower to blow air. OTRISS with a capacity of 75 kg and 100 kg have been made and tested. The ability of ozone to eliminate bacteria and fungi have been tested and resulted in a decrease of microorganisms at 3 log CFU/g. Testing in food chemistry showed that ozone treatment of rice had not changed the chemical content that still meet the standard of chemical content and nutritional applicable to ISO standard milled rice. The results of this study are very likely to be used as an alternative to rice storage systems in warehouse. Test and scale-up is being carried out in a mini warehouse whose condition is mimicked to rice in National Rice Storage of Indonesia (Bulog) to ensure quality. Next adaptations would be installed in the rice storage system in the Bulog. (paper)

Mechanisms of UVB-resistance in rice: Cultivar differences in the sensitivity to UVB radiation in rice

International Nuclear Information System (INIS)

Hidema, J.

2001-01-01

In a study on the sensitivity to UVB radiation of rice cultivars of 5 Asian rice ecotypes, results showed that the rice cultivars widely varied in UVB sensitivity; among the Japanese rice cultivars, Sasanishiki was more resistant to UVB, while Norin 1 was less resistant; UV-sensitive Norin 1 was deficient in photorepair of cyclobutane pyrimidine dimers (UV-induced DNA damage), and the sensitivity to UVB radiation significantly correlated with deficient CPD photorepair; and that this deficiency in Norin 1 resulted from a functionally altered photolyase. The results suggest that photorepair capacity is a principal factor in determining UVB sensitivity in rice. The effects of supplemental UVB radiation on the growth and yield of Japanese rice cultivars under field conditions were also studied in Japan since 1993. The results indicate that supplemental UVB radiation had inhibitory effects on the growth and yield of rice. Furthermore, grain size was smaller with supplemental UVB radiation

Contribution of rice straw carbon to CH4 emission from rice paddies using 13C-enriched rice straw

Science.gov (United States)

Watanabe, Akira; Yoshida, Mariko; Kimura, Makoto

1998-04-01

It is generally recognized that the application of rice straw (RS) increases CH4 emission from rice paddies. To estimate the contribution of RS carbon to CH4 emission, a pot experiment was conducted using 13C-enriched RS. The percentage contributions of RS carbon to CH4 emission throughout the rice growth period were 10±1, 32±3, and 43±3% for the treatments with RS applied at the rates of 2, 4, and 6 g kg-1 soil, respectively. The increase in the rate of application of RS increased CH4 emission derived from both RS carbon and other carbon sources. The percentage contribution of RS carbon to CH4 emission was larger in the earlier period (maximum 96%) when the decomposition rate of RS was larger. After RS decomposition had slowed, CH4 emission derived from RS carbon decreased. However, the δ13C values of CH4 emitted from the pots with 13C-enriched RS applied at rates of 4 and 6 g kg-1 soil were significantly higher than those from the pots with natural RS until the harvesting stage. An increased atom-13C% of roots of rice plants growing in the pots with 6 g kg-1 of 13C-enriched RS at around the maximum tiller number stage and a decrease during the following 2 months suggested that rice plants assimilated RS carbon once and then released a portion of it. This supply of RS carbon from roots may be one of the sources of CH4 in the late period of rice growth.

Characterization and evaluation of rice blast resistance of Chinese indica hybrid rice parental lines

Directory of Open Access Journals (Sweden)

Yunyu Wu

2017-12-01

Full Text Available The development of resistant varieties and hybrid combinations has been the most effective and economical strategy to control blast disease caused by Magnaporthe oryzae. However, the distribution of major R genes and blast resistance characterization in hybrid rice parents has not been well investigated, resulting in their limited use in hybrid rice blast-resistance breeding. In the present study, 88 elite indica hybrid rice parental lines were evaluated with 30 isolates of M. oryzae collected from the main planting area of indica hybrid rice in China and were characterized for the presence of 11 major resistance genes using molecular markers. The pathogenicity assays showed that four types of hybrid rice parent line showed some resistance to M. oryzae. However, the proportions of highly resistant lines and the mean resistance frequency (RF varied among the four types, with resistance in decreasing order shown by three-line restorer lines, three-line maintainer lines, two-line sterile lines, and two-line restorer lines. All 88 hybrid rice parental lines carried more than one R gene, but none carried the R genes Pi1 and Pi2. Although Pid3 and Pi9 were present only in three-line restorer lines and Pigm only in three-line maintainer lines, the remaining six R genes (Pib, Pid2, Pi5, Pia, Pi54, and Pita were present in the four types of hybrid rice parent with significantly different distribution frequencies. The correlation between R genes and resistance reactions was investigated. The results are expected to provide useful information for rational utilization of major R genes in hybrid rice breeding programs. Keywords: Hybrid rice parental lines, Magnaporthe oryzae, Pi genes, Resistance evaluation, Molecular markers

Evaluation of Heavy Metals Contamination from Environment to Food Matrix by TXRF: The Case of Rice and Rice Husk

Directory of Open Access Journals (Sweden)

Fabjola Bilo

2015-01-01

Full Text Available This paper is devoted to the chemical analysis of contaminated soils of India and the rice grown in the same area. Total reflection X-ray fluorescence spectroscopy is a well-established technique for elemental chemical analysis of environmental samples, and it can be a useful tool to assess food safety. Metals uptake in rice crop grown in soils from different areas was studied. In this work soil, rice husk and rice samples were analyzed after complete solubilization of samples by microwave acid digestion. Heavy metals concentration detected in rice samples decreases in the following order: Mn > Zn > Cu > Ni > Pb > Cr. The metal content in rice husk was higher than in rice. This study suggests, for the first time, a possible role of heavy metals filter played by rice husk. The knowledge of metals sequestration capability of rice husk may promote some new management practices for rice cultivation to preserve it from pollution.

Innovation Chinese rice wine brewing technology by bi-acidification to exclude rice soaking process.

Science.gov (United States)

Wei, Xiao Lu; Liu, Shuang Ping; Yu, Jian Shen; Yu, Yong Jian; Zhu, Sheng Hu; Zhou, Zhi Lei; Hu, Jian; Mao, Jian

2017-04-01

As a traditional fermented alcoholic beverage of China, Chinese rice wine (CRW) had a long history of more than 5000 years. Rice soaking process was the most crucial step during CRW brewing process, because rice soaking quality directly determined the quality of CRW. However, rice soaking water would cause the eutrophication of water bodies and waste of water. The longer time of rice soaking, the higher the content of biogenic amine, and it would have a huge impact on human health. An innovation brewing technology was carried out to exclude the rice soaking process and the Lactobacillus was added to make up for the total acid. Compared to the traditional brewing technology, the new technology saved water resources and reduced environmental pollution. The concentration of biogenic amine was also decreased by 27.16%, which improving the security of the CRW. The esters increased led to more soft-tasted CRW and less aging time; the quality of CRW would be improved with less alcohol. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Effect of germination on the physicochemical and antioxidant characteristics of rice flour from three rice varieties from Nigeria.

Science.gov (United States)

Chinma, Chiemela Enyinnaya; Anuonye, Julian Chukwuemeka; Simon, Omotade Comfort; Ohiare, Raliat Ozavize; Danbaba, Nahemiah

2015-10-15

This study determined the effect of germination (48 h) on the physicochemical and antioxidant characteristics of rice flour from three rice varieties from Nigeria. Local rice varieties (Jamila, Jeep and Kwandala) were evaluated and compared to an improved variety (MR 219). Physicochemical and antioxidant properties of flours were determined using standard methods. Protein, magnesium, phosphorus, potassium and antioxidant properties of rice flours increased after germination while phytic acid and total starch contents decreased. Foaming capacity and stability of rice flours increased after germination. Germination resulted to changes in pasting and thermal characteristics of rice flours. Germinated rice flours had better physicochemical and antioxidant properties with reduced phytic acid and starch contents compared to MR 219, which can be utilized as functional ingredients in the preparation of rice-based products. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dolce Vita in the Rice Paddy - Characterization of weedy rice groups in Northern Italy and investigation of their evolutionary origins

OpenAIRE

Grimm, Annabelle

2014-01-01

The thesis deals with the topic of the invasive rice form called weedy rice or red rice. Studies focused on the geographical area of Italy. Different populations of weedy rice in Italy were genetically characterized. The evolutionary origins of different weedy rice groups were investigated using molecular, morphological and physiological methods. Invasion of wild rice as well as de-domestication of cultivars could be identified as evolutionary sources of weedy rice in Northern Italy.

Gibberellic Acid: A Key Phytohormone for Spikelet Fertility in Rice Grain Production

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Choon-Tak Kwon

2016-05-01

Full Text Available The phytohormone gibberellic acid (GA has essential signaling functions in multiple processes during plant development. In the “Green Revolution”, breeders developed high-yield rice cultivars that exhibited both semi-dwarfism and altered GA responses, thus improving grain production. Most studies of GA have concentrated on germination and cell elongation, but GA also has a pivotal role in floral organ development, particularly in stamen/anther formation. In rice, GA signaling plays an important role in spikelet fertility; however, the molecular genetic and biochemical mechanisms of GA in male fertility remain largely unknown. Here, we review recent progress in understanding the network of GA signaling and its connection with spikelet fertility, which is tightly associated with grain productivity in cereal crops.

21 CFR 137.350 - Enriched rice.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 2 2010-04-01 2010-04-01 false Enriched rice. 137.350 Section 137.350 Food and... Related Products § 137.350 Enriched rice. (a) The foods for which definitions and standards of identity are prescribed by this section are forms of milled rice (except rice coated with talc and glucose and...

Bioethanol production from rice straw residues

Directory of Open Access Journals (Sweden)

Elsayed B. Belal

2013-01-01

Full Text Available A rice straw -cellulose utilizing mold was isolated from rotted rice straw residues. The efficient rice straw degrading microorganism was identified as Trichoderma reesei. The results showed that different carbon sources in liquid culture such as rice straw, carboxymethyl cellulose, filter paper, sugar cane bagasse, cotton stalk and banana stalk induced T. reesei cellulase production whereas glucose or Potato Dextrose repressed the synthesis of cellulase. T. reesei cellulase was produced by the solid state culture on rice straw medium. The optimal pH and temperature for T. reesei cellulase production were 6 and 25 ºC, respectively. Rice straw exhibited different susceptibilities towards cellulase to their conversion to reducing sugars. The present study showed also that, the general trend of rice straw bioconversion with cellulase was more than the general trend by T. reesei. This enzyme effectively led to enzymatic conversion of acid, alkali and ultrasonic pretreated cellulose from rice straw into glucose, followed by fermentation into ethanol. The combined method of acid pretreatment with ultrasound and subsequent enzyme treatment resulted the highest conversion of lignocellulose in rice straw to sugar and consequently, highest ethanol concentration after 7 days fermentation with S. cerevisae yeast. The ethanol yield in this study was about 10 and 11 g.L-1.

Consumer Preferences and Buying Criteria in Rice: A Study to Identify Market Strategy for Thailand Jasmine Rice Export

NARCIS (Netherlands)

Suwannaporn, P.; Linnemann, A.R.

2008-01-01

Rice consumption per capita in many Asian countries decreased, but it is consumed more in non-rice-eating countries. This study aimed to investigate consumer preferences and attitudes toward Jasmine rice among consumers in target rice export countries to identify opportunities and strategic

Benthic macroinvertebrates in Italian rice fields

Directory of Open Access Journals (Sweden)

Daniela Lupi

2013-02-01

Full Text Available Rice fields can be considered man-managed temporary wetlands. Five rice fields handled with different management strategies, their adjacent channels, and a spring were analysed by their benthic macroinvertebrate community to i evaluate the role of rice agroe- cosystem in biodiversity conservation; ii find indicator species which can be used to compare the ecological status of natural wetlands with rice agroecosystems; and iii find the influence of environmental variables on biodiversity. Different methods of data analysis with increasing degree of complexity – from diversity index up to sophisticated multivariate analysis – were used. The investigation provided a picture of benthic macroinvertebrates inhabiting rice agroecosystems where 173 taxa were identified, 89 of which detected in rice paddies. Among them, 4 phyla (Mollusca, Annelida, Nematomorpha, and Arthropoda, 8 classes (Bivalvia, Gastropoda, Oligochaeta, Hirudinea, Gordioida, Insecta, Branchiopoda, and Malacostraca, 24 orders, 68 families, 127 genera and 159 species have been found. Ten threatened and 3 invasive species were detected in the habitats examined. The information obtained by the different methods of data analysis allowed a more comprehensive view on the value of the components of rice agroecosystems. Data analyses highlighted significant differences between habitats (feeding channel and rice field, with higher diversity observed in channels, and emphasised the role of the water chemical-physical parameters. The period of water permanence in rice fields resulted to be only one of the factors influencing the community of benthic macroinvertebrates. The presence of rare/endangered species allowed characterising some stations, but it was less informative about management strategies in rice paddies because most of these species were absent in rice fields.

Study of Rice Marketing System in Iran

OpenAIRE

Feizabadi, Yaser

2011-01-01

Rice comes second after wheat in Iran`s food consumption economy. Rising population and recent growth in GDP has made Iran one of the greatest rice importer countries all over the world. That is why rice marketing has always been a controversial issue in Iran`s agricultural economics. To study rice marketing system in Iran, this paper aims to calculate rice marketing margin, market efficiency and marketing cost coefficient in seaside Mazandaran province( where 70 percent of domestic rice prod...

Micronutrient-fortified rice can increase hookworm infection risk

DEFF Research Database (Denmark)

de Gier, Brechje; Campos Ponce, Maiza; Perignon, Marlene

2016-01-01

or inflammation after iron supplementation. OBJECTIVE: To study effects of micronutrient-fortified rice on hookworm infection in Cambodian schoolchildren. METHODS: A double-blinded, cluster-randomized trial was conducted in 16 Cambodian primary schools partaking in the World Food Program school meal program....... Three types of multi-micronutrient fortified rice were tested against placebo rice within the school meal program: UltraRice_original, UltraRice_improved and NutriRice. Four schools were randomly assigned to each study group (placebo n = 492, UltraRice_original n = 479, UltraRice_improved n = 500, NutriRice.......6%, but differed considerably among schools (range 0%- 48.1%).Micronutrient-fortified rice significantly increased risk of new hookworm infection. This effect was modified by baseline hookworm prevalence at the school; hookworm infection risk was increased by all three types of fortified rice in schools where...

Brewers’ Rice: A By-Product from Rice Processing Provides Natural Hepatorenal Protection in Azoxymethane-Induced Oxidative Stress in Rats

Directory of Open Access Journals (Sweden)

Bee Ling Tan

2015-01-01

Full Text Available Brewers’ rice, which is known locally as temukut, is a mixture of broken rice, rice bran, and rice germ. Our present study was designed to identify the effect of brewers’ rice on the attenuation of liver and kidney damage induced by azoxymethane (AOM. Alanine transaminase (ALT, alkaline phosphatase (ALP, aspartate transaminase (AST, creatinine, and urea were evaluated to understand potential hepatoprotective effects and the ability of brewers’ rice to attenuate kidney pathology induced by AOM treatment. Liver and kidney tissues were evaluated by hematoxylin and eosin (H&E staining. Overall analyses revealed that brewers’ rice improved the levels of serum markers in a manner associated with better histopathological outcomes, which indicated that brewers’ rice could enhance recovery from hepatocyte and kidney damage. Taken together, these results suggest that brewers’ rice could be used in future applications to combat liver and kidney disease.

IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools.

Science.gov (United States)

Carazzolle, Marcelo Falsarella; de Carvalho, Lucas Miguel; Slepicka, Hugo Henrique; Vidal, Ramon Oliveira; Pereira, Gonçalo Amarante Guimarães; Kobarg, Jörg; Meirelles, Gabriela Vaz

2014-01-01

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two

Dissection of protein interactomics highlights microRNA synergy.

Science.gov (United States)

Zhu, Wenliang; Zhao, Yilei; Xu, Yingqi; Sun, Yong; Wang, Zhe; Yuan, Wei; Du, Zhimin

2013-01-01

Despite a large amount of microRNAs (miRNAs) have been validated to play crucial roles in human biology and disease, there is little systematic insight into the nature and scale of the potential synergistic interactions executed by miRNAs themselves. Here we established an integrated parameter synergy score to determine miRNA synergy, by combining the two mechanisms for miRNA-miRNA interactions, miRNA-mediated gene co-regulation and functional association between target gene products, into one single parameter. Receiver operating characteristic (ROC) analysis indicated that synergy score accurately identified the gene ontology-defined miRNA synergy (AUC = 0.9415, psynergy, implying poor expectancy of widespread synergy. However, targeting more key genes made two miRNAs more likely to act synergistically. Compared to other miRNAs, miR-21 was a highly exceptional case due to frequent appearance in the top synergistic miRNA pairs. This result highlighted its essential role in coordinating or strengthening physiological and pathological functions of other miRNAs. The synergistic effect of miR-21 and miR-1 were functionally validated for their significant influences on myocardial apoptosis, cardiac hypertrophy and fibrosis. The novel approach established in this study enables easy and effective identification of condition-restricted potent miRNA synergy simply by concentrating the available protein interactomics and miRNA-target interaction data into a single parameter synergy score. Our results may be important for understanding synergistic gene regulation by miRNAs and may have significant implications for miRNA combination therapy of cardiovascular disease.

The impact of seasonal rice price changes on rice self-consumption in farm household of rural Java

Science.gov (United States)

Ani, S. W.; Antriyandarti, E.

2018-03-01

Seasonal rice price changes are very volatile and not predictable. This price changes have a heterogeneous impact on public consumption. The problem of seasonal rice price changes is not only experienced by consumers, but also in the farmers side as producers. The objective of this study is to provide a detail overview and description of the changing seasonal rice self-consumption of farm households in rural Java in response to seasonal rice price changes and income shocks to anticipate seasonal scarcity. This paper constructs a theoretical model to address such seasonality of food deprivation by using one year of seasonally farm household panel data, empirically tests the extent to which farmers in rural Java can smooth their rice self-consumption from season to season in response to income shocks. The result shows that rice farmers increase their rice self-consumption when prices are high.

Characterization of hampin/MSL1 as a node in the nuclear interactome

International Nuclear Information System (INIS)

Dmitriev, Ruslan I.; Korneenko, Tatyana V.; Bessonov, Alexander A.; Shakhparonov, Mikhail I.; Modyanov, Nikolai N.; Pestov, Nikolay B.

2007-01-01

Hampin, homolog of Drosophila MSL1, is a partner of histone acetyltransferase MYST1/MOF. Functions of these proteins remain poorly understood beyond their participation in chromatin remodeling complex MSL. In order to identify new proteins interacting with hampin, we screened a mouse cDNA library in yeast two-hybrid system with mouse hampin as bait and found five high-confidence interactors: MYST1, TPR proteins TTC4 and KIAA0103, NOP17 (homolog of a yeast nucleolar protein), and transcription factor GC BP. Subsequently, all these proteins were used as baits in library screenings and more new interactions were found: tumor suppressor RASSF1C and spliceosome component PRP3 for KIAA0103, ring finger RNF10 for RASSF1C, and RNA polymerase II regulator NELF-C for MYST1. The majority of the observed interactions was confirmed in vitro by pull-down of bacterially expressed proteins. Reconstruction of a fragment of mammalian interactome suggests that hampin may be linked to diverse regulatory processes in the nucleus

Diversity of global rice markets and the science required for consumer-targeted rice breeding.

Directory of Open Access Journals (Sweden)

Mariafe Calingacion

Full Text Available With the ever-increasing global demand for high quality rice in both local production regions and with Western consumers, we have a strong desire to understand better the importance of the different traits that make up the quality of the rice grain and obtain a full picture of rice quality demographics. Rice is by no means a 'one size fits all' crop. Regional preferences are not only striking, they drive the market and hence are of major economic importance in any rice breeding / improvement strategy. In this analysis, we have engaged local experts across the world to perform a full assessment of all the major rice quality trait characteristics and importantly, to determine how these are combined in the most preferred varieties for each of their regions. Physical as well as biochemical characteristics have been monitored and this has resulted in the identification of no less than 18 quality trait combinations. This complexity immediately reveals the extent of the specificity of consumer preference. Nevertheless, further assessment of these combinations at the variety level reveals that several groups still comprise varieties which consumers can readily identify as being different. This emphasises the shortcomings in the current tools we have available to assess rice quality and raises the issue of how we might correct for this in the future. Only with additional tools and research will we be able to define directed strategies for rice breeding which are able to combine important agronomic features with the demands of local consumers for specific quality attributes and hence, design new, improved crop varieties which will be awarded success in the global market.

Diversity of Global Rice Markets and the Science Required for Consumer-Targeted Rice Breeding

Science.gov (United States)

Calingacion, Mariafe; Laborte, Alice; Nelson, Andrew; Resurreccion, Adoracion; Concepcion, Jeanaflor Crystal; Daygon, Venea Dara; Mumm, Roland; Reinke, Russell; Dipti, Sharifa; Bassinello, Priscila Zaczuk; Manful, John; Sophany, Sakhan; Lara, Karla Cordero; Bao, Jinsong; Xie, Lihong; Loaiza, Katerine; El-hissewy, Ahmad; Gayin, Joseph; Sharma, Neerja; Rajeswari, Sivakami; Manonmani, Swaminathan; Rani, N. Shobha; Kota, Suneetha; Indrasari, Siti Dewi; Habibi, Fatemeh; Hosseini, Maryam; Tavasoli, Fatemeh; Suzuki, Keitaro; Umemoto, Takayuki; Boualaphanh, Chanthkone; Lee, Huei Hong; Hung, Yiu Pang; Ramli, Asfaliza; Aung, Pa Pa; Ahmad, Rauf; Wattoo, Javed Iqbal; Bandonill, Evelyn; Romero, Marissa; Brites, Carla Moita; Hafeel, Roshni; Lur, Huu-Sheng; Cheaupun, Kunya; Jongdee, Supanee; Blanco, Pedro; Bryant, Rolfe; Thi Lang, Nguyen; Hall, Robert D.; Fitzgerald, Melissa

2014-01-01

With the ever-increasing global demand for high quality rice in both local production regions and with Western consumers, we have a strong desire to understand better the importance of the different traits that make up the quality of the rice grain and obtain a full picture of rice quality demographics. Rice is by no means a ‘one size fits all’ crop. Regional preferences are not only striking, they drive the market and hence are of major economic importance in any rice breeding / improvement strategy. In this analysis, we have engaged local experts across the world to perform a full assessment of all the major rice quality trait characteristics and importantly, to determine how these are combined in the most preferred varieties for each of their regions. Physical as well as biochemical characteristics have been monitored and this has resulted in the identification of no less than 18 quality trait combinations. This complexity immediately reveals the extent of the specificity of consumer preference. Nevertheless, further assessment of these combinations at the variety level reveals that several groups still comprise varieties which consumers can readily identify as being different. This emphasises the shortcomings in the current tools we have available to assess rice quality and raises the issue of how we might correct for this in the future. Only with additional tools and research will we be able to define directed strategies for rice breeding which are able to combine important agronomic features with the demands of local consumers for specific quality attributes and hence, design new, improved crop varieties which will be awarded success in the global market. PMID:24454799

Assessment of Rice Associated Bacterial Ability to Enhance Rice Seed Germination and Rice Growth Promotion

Directory of Open Access Journals (Sweden)

R. Gholamalizadeh

2017-08-01

Full Text Available ABSTRACT The application of beneficial bacteria has recently been used for sustainable agriculture. In current research, 71 bacterial isolates were obtained from rice plant and the rhizosphere soil of different paddy fields in Guilan province, Iran. After primitive investigation, 40 bacteria with typical predominant characteristics were selected. By PCR-RFLP of their 16S r-DNA gene, 8 Operational Taxonomic Units (OTUs totally consisted of 33 isolates were obtained. From all of them, 8 isolates were selected for rice seed germination experiment, then, effective isolates were used for pot experiment to evaluate their ability for promoting rice growth. All of them were able to increase rice growth and yield, but in different potential. These tested isolates were identified as Alcaligenes faecalis (DEp8, O1R4, Pantoea ananatis (AEn1, Bacillus vietnamensis (MR5, Bacillus idriensis (MR2 and Stenotrophomonas maltophilia by partial sequencing of their 16S r-DNA gene. Among them, AEn1 and MR5 produced indole-3- acetic acid (IAA in larger amounts than the other isolates and the isolates AEn1 and O1R4 were able to solubilize phosphate in higher amounts. According to the results obtained, it can be concluded that AEn1, O1R4 and MR5 can be considered as bacterial inoculants to use as alternatives for chemical fertilizers.

Effect of transgenic Bacillus thuringiensis rice lines on mortality and feeding behavior of rice stem borers (Lepidoptera: Crambidae).

Science.gov (United States)

Chen, Hao; Zhang, Guoan; Zhang, Qifa; Lin, Yongjun

2008-02-01

Ten transgenic Bacillus thuringiensis Bt rice, Oryza sativa L., lines with different Bt genes (two Cry1Ac lines, three Cry2A lines, and five Cry9C lines) derived from the same variety Minghui 63 were evaluated in both the laboratory and the field. Bioassays were conducted by using the first instars of two main rice lepidopteran insect species: yellow stem borer, Scirpophaga incertulas (Walker) and Asiatic rice borer, Chilo suppressalis (Walker). All transgenic lines exhibited high toxicity to these two rice borers. Field evaluation results also showed that all transgenic lines were highly insect resistant with both natural infestation and manual infestation of the neonate larvae of S. incertulas compared with the nontransformed Minghui63. Bt protein concentrations in leaves of 10 transgenic rice lines were estimated by the sandwich enzyme-linked immunosorbent assay. The cry9C gene had the highest expression level, next was cry2A gene, and the cry1Ac gene expressed at the lowest level. The feeding behavior of 7-d-old Asiatic rice borer to three classes of Bt transgenic rice lines also was detected by using rice culm cuttings. The results showed that 7-d-old larvae of Asiatic rice borer have the capacity to distinguish Bt and non-Bt culm cuttings and preferentially fed on non-Bt cuttings. When only Bt culm cuttings with three classes of different Bt proteins (CrylAc, Cry2A, and Cry9C) were fed, significant distribution difference of 7-d-old Asiatic rice borer in culm cuttings of different Bt proteins also was found. In the current study, we evaluate different Bt genes in the same rice variety in both the laboratory and the field, and also tested feeding behavior of rice insect to these Bt rice. These data are valuable for the further development of two-toxin Bt rice and establishment of appropriate insect resistance management in the future.

Rice Yellow Mottle Virus stress responsive genes from susceptible and tolerant rice genotypes

Directory of Open Access Journals (Sweden)

Siré Christelle

2008-03-01

Full Text Available Abstract Background The effects of viral infection involve concomitant plant gene variations and cellular changes. A simple system is required to assess the complexity of host responses to viral infection. The genome of the Rice yellow mottle virus (RYMV is a single-stranded RNA with a simple organisation. It is the most well-known monocotyledon virus model. Several studies on its biology, structure and phylogeography have provided a suitable background for further genetic studies. 12 rice chromosome sequences are now available and provide strong support for genomic studies, particularly physical mapping and gene identification. Results The present data, obtained through the cDNA-AFLP technique, demonstrate differential responses to RYMV of two different rice cultivars, i.e. susceptible IR64 (Oryza sativa indica, and partially resistant Azucena (O. s. japonica. This RNA profiling provides a new original dataset that will enable us to gain greater insight into the RYMV/rice interaction and the specificity of the host response. Using the SIM4 subroutine, we took the intron/exon structure of the gene into account and mapped 281 RYMV stress responsive (RSR transcripts on 12 rice chromosomes corresponding to 234 RSR genes. We also mapped previously identified deregulated proteins and genes involved in partial resistance and thus constructed the first global physical map of the RYMV/rice interaction. RSR transcripts on rice chromosomes 4 and 10 were found to be not randomly distributed. Seven genes were identified in the susceptible and partially resistant cultivars, and transcripts were colocalized for these seven genes in both cultivars. During virus infection, many concomitant plant gene expression changes may be associated with host changes caused by the infection process, general stress or defence responses. We noted that some genes (e.g. ABC transporters were regulated throughout the kinetics of infection and differentiated susceptible and

Uptake of C-14 tagged acetate by rice in a paddy soil-to-rice plant system

Energy Technology Data Exchange (ETDEWEB)

Ishii, Nobuyoshi; Tagami, Keiko; Uchida, Shigeo [Research Center for Radiation Protection, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage, Chiba 263-8555 (Japan)

2014-07-01

Geological disposal of Transuranic (TRU) waste is planned to avoid radiation exposure to the public. One of the dominant nuclides contributing to the dose from TRU waste is C-14, which is long-lived and has very poor sorption properties on natural geological media. Therefore, there are some concerns regarding possible migration of C-14 to the living environments. For the public health safety, it is necessary to clarify pathways of C-14 to human beings in the environment. Intake of C-14 from food source is one of important pathways. In the present study, we examined transfer of C-14 to various parts of rice plant in a paddy soil-to-rice plant system. Rice seedlings in Wagner pots (n=12) were grown for about two months from 7 May 2012 under natural light. The grown plants were moved to a closed chamber on 5 July 2012. The rice plants were grown without water supply from 5 July 2012, and then one liter of C-14 tagged acetate (1.85 MBq) was supplied to the rice plants in the spiked group (n=8) just once on 9 July 2012. For the rice plants in the control group (n=4), uncontaminated water was supplied. These rice plants were air-dried after a harvest on 23 August 2012 and divided into four parts: white rice, bran, rice husk, and the stem and leaf part. The activities of C-14 in the divided parts and air-dried soil samples were determined with a liquid scintillation counting system. Radiocarbon was detected even in the rice plants of the control group. However, the C-14 activity in the soil of the control group was less than the detection limit (1.0 Bq/g). The C-14 activities for the control group decreased in the order of rice husk, bran, white rice, and the stem and leaf part. The detection of C-14 in the control group may be caused by the release of C-14 tagged carbon dioxide from the spiked group. That is, C-14 tagged acetate was converted to carbon dioxide by microbial activity in the spiked group, and then some of the released carbon dioxide was assimilated into

Rheological and secondary structural characterization of rice flour-zein composites for noodles slit from gluten-free sheeted dough.

Science.gov (United States)

Jeong, Sungmin; Kim, Hee Won; Lee, Suyong

2017-04-15

Rice flour-zein composites in a hydrated viscoelastic state were utilized to compensate for the role of wheat gluten in gluten-free sheeted dough. The use of zein above its glass transition temperature was able to form a viscoelastic protein network of non-wheat dough with rice flour. The mixing stability and development time of the rice dough were positively increased with increasing levels of zein. The protein secondary structural analysis by FTIR spectroscopy demonstrated that the rice doughs with high levels of zein showed significant increases in β-sheet structures whose intensity was almost doubled by the use of 10% zein. The use of zein at more than 5% (w/w) successfully produced gluten-free dough sheets that could be slit into thin and long noodle strands. In addition, the composites were effective in improving the rheological characteristics of gluten-free noodle strands by increasing their maximum force to extension, compared to wheat-based noodles. Copyright © 2016 Elsevier Ltd. All rights reserved.

Computational prediction and experimental verification of HVA1-like abscisic acid responsive promoters in rice (Oryza sativa).

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Ross, Christian; Shen, Qingxi J

2006-09-01

Abscisic acid (ABA) is one of the central plant hormones, responsible for controlling both maturation and germination in seeds, as well as mediating adaptive responses to desiccation, injury, and pathogen infection in vegetative tissues. Thorough analyses of two barley genes, HVA1 and HVA22, indicate that their response to ABA relies on the interaction of two cis-acting elements in their promoters, an ABA response element (ABRE) and a coupling element (CE). Together, they form an ABA response promoter complex (ABRC). Comparison of promoters of barley HVA1 and it rice orthologue indicates that the structures and sequences of their ABRCs are highly similar. Prediction of ABA responsive genes in the rice genome is then tractable to a bioinformatics approach based on the structures of the well-defined barley ABRCs. Here we describe a model developed based on the consensus, inter-element spacing and orientations of experimentally determined ABREs and CEs. Our search of the rice promoter database for promoters that fit the model has generated a partial list of genes in rice that have a high likelihood of being involved in the ABA signaling network. The ABA inducibility of some of the rice genes identified was validated with quantitative reverse transcription PCR (QPCR). By limiting our input data to known enhancer modules and experimentally derived rules, we have generated a high confidence subset of ABA-regulated genes. The results suggest that the pathways by which cereals respond to biotic and abiotic stresses overlap significantly, and that regulation is not confined to the level transcription. The large fraction of putative regulatory genes carrying HVA1-like enhancer modules in their promoters suggests the ABA signal enters at multiple points into a complex regulatory network that remains largely unmapped.

Comparison of the concentrations of metal elements and isotopes of lead found in rice and rice bran.

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Dai, Shouhui; Yang, Hui; Yang, Lan; Wang, Fuhua; Du, Ruiying; Wen, Dian

2014-08-01

Very few studies have investigated the difference in the distribution of metal elements between rice and rice bran samples. In this study, the concentrations of 27 metal elements (Li, Be, Na, Mg, Al, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Ga, As, Se, Rb, Sr, Ag, Cd, Cs, Ba, Tl, Pb, and U) in 56 polished rice and their corresponding bran samples were determined. A significant difference in concentrations of all elements except Ag and Cd was found between rice and bran (P rice ratios of 1.21 to 36.3. High concentrations of metal elements, especially that of the heavy metal Cr, in bran samples present a potential safety issue for bran products, such as food and feed containing bran. Pb isotope ((204)Pb, (206)Pb, (207)Pb, and (208)Pb) ratios also were determined. The (206)Pb/(207)Pb and (208)Pb/(207)Pb ratios in bran were generally higher than those in rice (P rice and bran samples were distinctly different from each other, indicating that Pb isotope composition is an effective for discriminating between bran and rice samples.

Evaluation of Rice Resistance to Southern Rice Black-Streaked Dwarf Virus and Rice Ragged Stunt Virus through Combined Field Tests, Quantitative Real-Time PCR, and Proteome Analysis.

Science.gov (United States)

Wang, Zhenchao; Yu, Lu; Jin, Linhong; Wang, Wenli; Zhao, Qi; Ran, Longlu; Li, Xiangyang; Chen, Zhuo; Guo, Rong; Wei, Yongtian; Yang, Zhongcheng; Liu, Enlong; Hu, Deyu; Song, Baoan

2017-02-22

Diseases caused by southern rice black-streaked dwarf virus (SRBSDV) and rice ragged stunt virus (RRSV) considerably decrease grain yield. Therefore, determining rice cultivars with high resistance to SRBSDV and RRSV is necessary. In this study, rice cultivars with high resistance to SRBSDV and RRSV were evaluated through field trials in Shidian and Mangshi county, Yunnan province, China. SYBR Green I-based quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to quantitatively detect virus gene expression levels in different rice varieties. The following parameters were applied to evaluate rice resistance: acre yield (A.Y.), incidence of infected plants (I.I.P.), virus load (V.L.), disease index (D.I.), and insect quantity (I.Q.) per 100 clusters. Zhongzheyou1 (Z1) and Liangyou2186 (L2186) were considered the most suitable varieties with integrated higher A.Y., lower I.I.P., V.L., D.I. and I.Q. In order to investigate the mechanism of rice resistance, comparative label-free shotgun liquid chromatography tandem-mass spectrometry (LC-MS/MS) proteomic approaches were applied to comprehensively describe the proteomics of rice varieties' SRBSDV tolerance. Systemic acquired resistance (SAR)-related proteins in Z1 and L2186 may result in the superior resistance of these varieties compared with Fengyouxiangzhan (FYXZ).

Integrative Analysis of the microRNAome and Transcriptome Illuminates the Response of Susceptible Rice Plants to Rice Stripe Virus.

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Jian Yang

Full Text Available Rice stripe virus (RSV is one of the most serious rice viruses in East Asia. To investigate how rice responds to RSV infection, we integrated miRNA expression with parallel mRNA transcription profiling by deep sequencing. A total of 570 miRNAs were identified of which 69 miRNAs (56 up-regulated and 13 down-regulated were significantly modified by RSV infection. Digital gene expression (DGE analysis showed that 1274 mRNAs (431 up-regulated and 843 down-regulated genes were differentially expressed as a result of RSV infection. The differential expression of selected miRNAs and mRNAs was confirmed by qRT-PCR. Gene ontology (GO and pathway enrichment analysis showed that a complex set of miRNA and mRNA networks were selectively regulated by RSV infection. In particular, 63 differentially expressed miRNAs were found to be significantly and negatively correlated with 160 target mRNAs. Interestingly, 22 up-regulated miRNAs were negatively correlated with 24 down-regulated mRNAs encoding disease resistance-related proteins, indicating that the host defense responses were selectively suppressed by RSV infection. The suppression of both osa-miR1423-5p- and osa-miR1870-5p-mediated resistance pathways was further confirmed by qRT-PCR. Chloroplast functions were also targeted by RSV, especially the zeaxanthin cycle, which would affect the stability of thylakoid membranes and the biosynthesis of ABA. All these modifications may contribute to viral symptom development and provide new insights into the pathogenicity mechanisms of RSV.

RICE: A Reliable and Efficient Remote Instrumentation Collaboration Environment

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Prasad Calyam

2008-01-01

Full Text Available Remote access of scientific instruments over the Internet (i.e., remote instrumentation demand high-resolution (2D and 3D video image transfers with simultaneous real-time mouse and keyboard controls. Consequently, user quality of experience (QoE is highly sensitive to network bottlenecks. Further, improper user control while reacting to impaired video caused due to network bottlenecks could result in physical damages to the expensive instrument equipment. Hence, it is vital to understand the interplay between (a user keyboard/mouse actions toward the instrument, and (b corresponding network reactions for transfer of instrument video images toward the user. In this paper, we first present an analytical model for characterizing user and network interplay during remote instrumentation sessions in terms of demand and supply interplay principles of traditional economics. Next, we describe the trends of the model parameters using subjective and objective measurements obtained from QoE experiments. Thereafter, we describe our Remote Instrumentation Collaboration Environment (RICE software that leverages our experiences from the user and network interplay studies, and has functionalities that facilitate reliable and efficient remote instrumentation such as (a network health awareness to detect network bottleneck periods, and (b collaboration tools for multiple participants to interact during research and training sessions.

Determination of Tinopal CBS-X in rice papers and rice noodles using HPLC with fluorescence detection and LC-MS/MS.

Science.gov (United States)

Ko, Kyung Yuk; Lee, Chae A; Choi, Jae Chon; Kim, Meehye

2014-01-01

To date there have been no reports of methods to determine Tinopal CBS-X. We developed a rapid and simple method to determine the Tinopal CBS-X content in rice noodles and rice papers using HPLC equipped with fluorescence detection. Heating the rice noodles and rice papers to 80°C after adding 75% methanol solution induced the release of Tinopal CBS-X from processed rice products. Tinopal CBS-X was separated using an isocratic mobile phase comprising 50% acetonitrile/water containing 0.4% tetrabutyl ammonium hydrogen sulphate at pH 8.0. The samples suspected to be positive by HPLC analysis were then confirmed by LC-MS/MS analysis. This study also investigated the Tinopal CBS-X content of three rice noodle products and two rice papers. The limits of quantification for rice papers and rice noodles were 1.58 and 1.51 µg kg(-1), respectively, and their correlation curves showed good linearity with r(2) ≥ 0.9997 and ≥ 0.9998, respectively. Moreover, rice papers had recoveries of 70.3-83.3% with precision ranging from 5.0% to 7.9%, whereas rice noodles had slightly lower recoveries of 63.4-78.7% and precisions of 8.5-11.5%. Only one rice noodle product contained Tinopal CBS-X, at around 2.1 mg kg(-1), whereas it was not detected in four other samples. Consequently, Tinopal CBS-X from rice noodles and rice papers can be successfully detected using the developed pre-treatment and ion-pairing HPLC system coupled with fluorescence detection.

Medicinal and nutritional importance of rice bran

International Nuclear Information System (INIS)

Ahmad, R.; Salim, M.; Rauf, R.; Baloach, M.K.

2005-01-01

Rice-bran is produced from the outer layer of brown rice and is stabilized through steam-heating. The rice-bran and its products are safe for human and animal consumption. The microbiological safety and rigorous quality-control practices merits its use as nutritional and dietary supplement for overall health-maintenance and as a part of a healthy diet and life-style, as it contributes to the reduction of certain diseases and health-related conditions. Stabilized rice-barn contain 15% of high nutritional- value protein, 20% of high-quality fat with Omega-3 and Omega-6 fatty acids, and nutritional dietary fiber. In addition to several phytonutrients, rice-bran contains vitamins and minerals, while over 100 potent antioxidants have been identified to date. Several scientific papers have reported the analysis and bioavailibility of rice-bran nutrients. Various chemical studies demonstrated the biological effects of the nutrients found in rice-bran. So far, more than 250 scientific publications are available on rice-bran, establishing the striking medicinal properties of rice-bran products. The oil-fraction of rice-bran has concentrated all tire fat-soluble phytonutrient in it, making itself an excellent health-promoting edible oil, as well as message oil The fiber-fraction of rice-bran has a profound effect on the gastrointestinal health, and improves bowel function. Rice-bran fiber along with phytonutrients was found to reduce cholesterol and lipid levels and maintain cardiovascular function. It has beneficial effect on tire kidney and urinary tract health and is helpful in weight-management and fiber replacement diets. (author)

Development of instant noodles from high-iron rice and iron-fortified rice flour

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Suparat Reungmaneepaitoon

2008-08-01

Full Text Available Instant high-iron noodles, prepared from wheat flour and high iron brown rice flour, were developed. Three varieties of rice flour, Suphan Buri 90 (SB, Homnin 313 (HW and Homnin 1000 (HP, containing amylose content of 30.40, 19.10 and 15.74% (w/w and iron content of 1.24, 2.04 and 2.22 (mg/100 g respectively, were used to replace wheat flour for instant fried noodle production. To determine the physicochemical properties and acceptability of instant fried noodles,different percentages (30, 40, 50% (w/w of each rice flour sample were used. The instant fried noodles were fortified with ferrous sulphate at levels of 0, 32, 64% iron of RDI per serving. Increasing amount of iron content in the mixtures decreased the L* value, b* value and increased a* value for the color of the instant fried noodle with brown rice flour. The texture characteristic of the noodles with 30, 40, 50% replacement with each variety of brown rice flour were significantly different from those of wheat noodle. Tensile force of the noodles decreased from 11.57±1.30 g to 6.38±1.45 g (SB, 8.36±0.96 g to 5.71±0.57 g (HP and 10.09±1.20 g to 5.46±1.31 g (HW as the rice flour content increased from 30 to 50%. The sensoryacceptability of the noodles made from each variety of 30% brown rice flour fortified with 32% iron of RDI had higher preference scores for elasticity, firmness, color and overall acceptability, than those with 64% iron of RDI. Instant fried noodles with HW and HP brown rice flour were subjected to consumer test using 100 rural primary school children. The frequency percent of the acceptability scores of the noodle with HP and HW were 88 and 84% respectively. Shelf life studyrevealed that the developed products were still acceptable up to 4 months. These products were claimed to be high iron noodle.

From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks.

KAUST Repository

Cannistraci, C.V.

2013-04-08

Growth and remodelling impact the network topology of complex systems, yet a general theory explaining how new links arise between existing nodes has been lacking, and little is known about the topological properties that facilitate link-prediction. Here we investigate the extent to which the connectivity evolution of a network might be predicted by mere topological features. We show how a link/community-based strategy triggers substantial prediction improvements because it accounts for the singular topology of several real networks organised in multiple local communities - a tendency here named local-community-paradigm (LCP). We observe that LCP networks are mainly formed by weak interactions and characterise heterogeneous and dynamic systems that use self-organisation as a major adaptation strategy. These systems seem designed for global delivery of information and processing via multiple local modules. Conversely, non-LCP networks have steady architectures formed by strong interactions, and seem designed for systems in which information/energy storage is crucial.

The land use potential of flood-prone rice fields using floating rice system in Bojonegoro regency in East Java

Science.gov (United States)

Irianto, H.; Mujiyo; Riptanti, E. W.; Qonita, A.

2018-03-01

Bojonegoro regency occupies the largest flood-prone rice fields of about 14,198 hectares, in East Java province. Floods commonly occur due to Bengawan Solo river over-burst, particularly in rainy season. The fields are potential for cultivating rice, but floods lasting for months causing these areas to be unproductive. The objective of this article is to examine the potential land use of flood prone rice fields in Bojonegoro regency using floating rice system as an effort to maintain productivity in rainy season. The method of this study is referential study about the rice production using floating cultivation system in other regions, which are later compared with the physical condition of the fields in Bojonegoro. The results of analysis show that rice cultivation using floating system can maintain rice production in flood prone areas during rainy season. The potential production of rice is 5-6 tons/ha. However, technical problems for cultivating rice cannot be ignored since farmers are not familiar with cultivating flooded fields. This article also explains alternatives of floating rice cultivation technique, which can be implemented effectively and efficiently. Pioneer work of developing floating rice in Bojonegoro that has been done by the Team of Faculty of Agriculture of UNS, Surakarta, is expected to serve as a medium for accelerating the adoption of cultivation technology innovation to farmers.

Assessment of suitability of selected rice varieties for production of expanded rice

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Vijayalaxmi Kamaraddi

2015-12-01

Full Text Available Expanded rice, prepared from pre-gelatinized milled rice by sand roasting method, is a popular snack food of India. Five high-yielding rice varieties of Hill zone of Karnataka state, viz., IET-13901, KHP-2, KHP-5, KHP-10, and Intan were screened for puffing quality based on their physicochemical, functional, nutritional and organoleptic parameters with Rajamudi as local check. The effect of varietal differences on expansion/puffing quality parameters, in vitro digestibility of starch and protein as well as bioaccessibility of iron, zinc, and calcium were determined. Results indicated a strong positive correlation between amylose content and expansion ratio and a negative correlation between protein and amylose content, length expansion ratio and volume expansion ratio. Expansion characteristics showed that the varieties suitable for production of puffed rice were KHP-2, IET-13901 and Intan. Nutritional analysis showed following ranges of nutrient content in expanded rice: protein, 6.22–8.17%; fat, 0.06–0.14%; and as mg/100 g calcium, 20.5–23.5; iron, 2.01–2.72; zinc, 1.22–1.82; thiamine, 0.315–0.470; riboflavin, 0.051–0.069; and niacin, 3.18–4.68. Nearly 80.3–80.8% starch and 67.6–83.2% protein was digestible. Among all varieties, KHP-2 had lowest amount of rapidly digestible starch (61.4%. Mineral bioaccessibility ranged from 42.7 to 52.1%. Sensory analysis indicated that Intan and KHP-2 were superior and suited for production of expanded rice.

Rice (Oryza) hemoglobins

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Hemoglobins (Hbs) corresponding to non-symbiotic (nsHb) and truncated (tHb) Hbs have been identified in rice (Oryza). This review discusses the major findings from the current studies on rice Hbs. At the molecular level, a family of the nshb genes, consisting of hb1, hb2, hb3, hb4 and hb5, and a sin...

Aerobic rice mechanization: techniques for crop establishment

Science.gov (United States)

Khusairy, K. M.; Ayob, H.; Chan, C. S.; Fauzi, M. I. Mohamed; Mohamad Fakhrul, Z. O.; Shahril Shah, G. S. M.; Azlan, O.; Rasad, M. A.; Hashim, A. M.; Arshad, Z.; E, E. Ibrahim; Saifulizan, M. N.

2015-12-01

Rice being the staple food crops, hundreds of land races in it makes the diversity of rice crops. Aerobic rice production was introduced which requires much less water input to safeguard and sustain the rice production and conserve water due to decreasing water resources, climatic changes and competition from urban and industrial users. Mechanization system plays an important role for the success of aerobic rice cultivation. All farming activities for aerobic rice production are run on aerobic soil conditions. Row seeder mechanization system is developed to replace conventional seeding technique on the aerobic rice field. It is targeted for small and the large scale aerobic rice farmers. The aero - seeder machine is used for the small scale aerobic rice field, while the accord - seeder is used for the large scale aerobic rice field. The use of this mechanization machine can eliminate the tedious and inaccurate seeding operations reduce labour costs and increases work rate. The machine is easy to operate and it can increase crop establishment rate. It reduce missing hill, increasing planting and crop with high yield can be produce. This machine is designed for low costs maintenance and it is easy to dismantle and assemble during maintenance and it is safe to be used.

Enzymatic hydrolsis of pretreated rice straw

Energy Technology Data Exchange (ETDEWEB)

Vlasenko, E.Y.; Shoemaker, S.P. [California Inst. of Food and Agricultural Research, Davis, CA (United States); Ding, H. [California Univ., Davis (Canada). Dept. of Food Science and Technology; Labavitch, J.M. [California Univ., Davis, CA (United States). Dept. of Pomology

1997-02-01

California rice straw is being evaluated as a feedstock for production of power and fuel. This paper examines the initial steps in the process: pretreatment of rice straw and enzymatic hydrolysis of the polysaccharides in the pretreated material to soluble sugars. Rice straw was subjected to three distinct pretreatment procedures: acid-catalyzed steam explosion (Swan Biomass Company), acid hydrolysis (U.S. DOE National Renewable Energy Laboratory), and ammonia fiber explosion or AFEX (Texas A and M University). Standard conditions for each pretreatment were used, but none was optimized for rice straw specifically. Six commercial cellulases, products of Genencor International (USA), Novo (Denmark), Iogen (Canada) and Fermtech (Russia) were used for hydrolysis. The Swan- and the acid-pretreatments effectively removed hemicellulose from rice straw, providing high yields of fermentable sugars. The AFEX-pretreatment was distinctly different from other pretreatments in that it did not significantly solubilize hemicellulose. All three pretreatment procedures substantially increased enzymatic digestibility of rice straw. Three commercial Trichoderma-reesei-derived enzyme preparations: Cellulase 100L (Iogen), Spezyme CP (Genencor), and Al (Fermtech), were more active on pretreated rice straw compared than others tested. Conditions for hydrolysis of rice straw using Cellulase 100L were evaluated. The supplementation of this enzyme preparation with cellobiase (Novozyme 188) significantly improved the parameters of hydrolysis for the Swan- and the acid-pretreated materials, but did not affect the hydrolysis of the AFEX-pretreated rice straw. (Author)

Understanding the evolution of rice technology in China - from traditional agriculture to GM rice today.

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Shen, Xiaobai

2010-01-01

This paper provides an historical survey of the evolution of rice technology in China, from the traditional farming system to genetically modified rice today. Using sociotechnological analytical framework, it analyses rice technology as a socio-technical ensemble - a complex interaction of material and social elements, and discusses the specificity of technology development and its socio-technical outcomes. It points to two imperatives in rice variety development: wholesale transporting agricultural technology and social mechanism to developing countries are likely lead to negative consequences; indigenous innovation including deploying GM technology for seed varietal development and capturing/cultivating local knowledge will provide better solutions.

Rice Hulls as a Renewable Complex Material Resource

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Irina Glushankova

2018-05-01

Full Text Available As a result of rice grain processing, a big amount of waste (up to 20% is produced. It is mainly rice hulls. The main components of rice hulls are cellulose, lignin and mineral ash. The mineral ash quantity in rice hulls varies from 15 up to 20%, by weight of the rice hulls. The mineral ash consists of amorphous silica (opal-type. Due to the high content of silica in rice hulls, the material burns with difficulty under natural conditions, and it is biodegradably destroyed only with difficulty, when composted. Utilization of rice hulls then becomes an ecological problem due to huge rice production and its continuous growth. At the same time, the annual quantity of silica content in rice hulls is comparable with the quantity of amorphous silica produced as a mineral resource. The issue of manufacturing cellular glass silica construction materials from rice hulls as a renewable resource is discussed in this paper. The utilization technology is based on an amorphous silicon oxide with the use of energy from the combustion of the organic component of rice hulls.

Elemental composition of Malawian rice.

Science.gov (United States)

Joy, Edward J M; Louise Ander, E; Broadley, Martin R; Young, Scott D; Chilimba, Allan D C; Hamilton, Elliott M; Watts, Michael J

2017-08-01

Widespread potential dietary deficiencies of calcium (Ca), iron (Fe), iodine (I), selenium (Se) and zinc (Zn) have been identified in Malawi. Several deficiencies are likely to be compounded by high phytic acid (PA) consumption. Rice (Oryza sativa) is commonly consumed in some Malawian populations, and its mineral micronutrient content is important for food security. The considerable irrigation requirements and flooded conditions of paddy soils can also introduce or mobilise potentially toxic elements including arsenic (As), cadmium (Cd) and lead (Pb). The aim of this study was to determine the mineral composition of rice sampled from farmers' fields and markets in Malawi. Rice was sampled from 18 extension planning areas across Malawi with 21 white (i.e. polished) and 33 brown samples collected. Elemental composition was determined by inductively coupled plasma-mass spectrometry (ICP-MS). Arsenic speciation was performed using high-performance liquid chromatography (HPLC)-ICP-MS. Concentration of PA was determined using a PA-total phosphorus assay. Median total concentrations (mg kg -1 , dry weight) of elements important for human nutrition in brown and white rice, respectively, were: Ca = 66.5 and 37.8; Cu = 3.65 and 2.49; Fe = 22.1 and 7.2; I = 0.006 and rice samples, respectively, median PA concentrations were 5438 and 1906 mg kg -1 , and median PA:Zn molar ratios were 29 and 13. Concentrations of potentially toxic elements (mg kg -1 , dry weight) in brown and white rice samples, respectively, were: As = 0.030 and 0.006; Cd  ≤ 0.002 and 0.006; Pb = 0.008 and 0.008. Approximately 95 % of As was found to be inorganic As, where this could be quantified. Malawian rice, like the more widely consumed staple grain maize, contains inadequate Ca, I, Se or Zn to meet dietary requirements. Biofortification strategies could significantly increase Se and Zn concentrations and require further investigation. Concentrations of Fe in rice grain varied

Comparative Proteomic Analysis of Susceptible and Resistant Rice Plants during Early Infestation by Small Brown Planthopper

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Yan Dong

2017-10-01

Full Text Available The small brown planthopper (Laodelphax striatellus Fallén, Homoptera, Delphacidae-SBPH is one of the major destructive pests of rice (Oryza sativa L.. Understanding on how rice responds to SBPH infestation will contribute to developing strategies for SBPH control. However, the response of rice plant to SBPH is poorly understood. In this study, two contrasting rice genotypes, Pf9279-4 (SBPH-resistant and 02428 (SBPH-susceptible, were used for comparative analysis of protein profiles in the leaf sheath of rice plants in responses to SBPH infestation. One hundred and thirty-two protein spots that were differentially expressed between the resistant and susceptible rice lines were identified with significant intensity differences (≥2-fold, P < 0.05 at 0, 6, and 12 h after SBPH infestation. Protein expression profile analysis in the leaf sheath of SBPH-resistant and SBPH-susceptible rice lines after SBPH infestation showed that proteins induced by SBPH feeding were involved mainly in stress response, photosynthesis, protein metabolic process, carbohydrate metabolic process, energy metabolism, cell wall-related proteins, amino acid metabolism and transcriptional regulation. Gene expression analysis of 24 differentially expressed proteins (DEPs showed that more than 50% DEPs were positively correlated with their mRNA levels. Analysis of some physiological indexes mainly involved in the removal of oxygen reactive species showed that the levels of superoxide dismutase (SOD and glutathione (GSH were considerably higher in Pf9279-4 than 02428 during SBPH infestation. The catalase (CAT activity and hydroxyl radical inhibition were lower in Pf9279-4 than 02428. Analysis of enzyme activities indicates that Pf9279-4 rice plants defend against SBPH through the activation of the pathway of the salicylic acid (SA-dependent systemic acquired resistance. In conclusion, this study provides some insights into the molecular networks involved on cellular and

The Impact of Herbicide-Resistant Rice Technology on Phenotypic Diversity and Population Structure of United States Weedy Rice1[W][OPEN

Science.gov (United States)

Burgos, Nilda Roma; Singh, Vijay; Tseng, Te Ming; Black, Howard; Young, Nelson D.; Huang, Zhongyun; Hyma, Katie E.; Gealy, David R.; Caicedo, Ana L.

2014-01-01

The use of herbicide-resistant (HR) Clearfield rice (Oryza sativa) to control weedy rice has increased in the past 12 years to constitute about 60% of rice acreage in Arkansas, where most U.S. rice is grown. To assess the impact of HR cultivated rice on the herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a history of Clearfield rice. Panicles from each weedy type were harvested and tested for resistance to imazethapyr. The majority of plants sampled had at least 20% resistant offspring. These resistant weeds were 97 to 199 cm tall and initiated flowering from 78 to 128 d, generally later than recorded for accessions collected prior to the widespread use of Clearfield rice (i.e. historical accessions). Whereas the majority (70%) of historical accessions had straw-colored hulls, only 30% of contemporary HR weedy rice had straw-colored hulls. Analysis of genotyping-by-sequencing data showed that HR weeds were not genetically structured according to hull color, whereas historical weedy rice was separated into straw-hull and black-hull populations. A significant portion of the local rice crop genome was introgressed into HR weedy rice, which was rare in historical weedy accessions. Admixture analyses showed that HR weeds tend to possess crop haplotypes in the portion of chromosome 2 containing the ACETOLACTATE SYNTHASE gene, which confers herbicide resistance to Clearfield rice. Thus, U.S. HR weedy rice is a distinct population relative to historical weedy rice and shows modifications in morphology and phenology that are relevant to weed management. PMID:25122473

Mercury in rice (Oryza sativa L.) and rice-paddy soils under long-term fertilizer and organic amendment.

Science.gov (United States)

Tang, Zhenya; Fan, Fangling; Wang, Xinyue; Shi, Xiaojun; Deng, Shiping; Wang, Dingyong

2018-04-15

High levels of mercury (Hg), especially methylmercury (MeHg), in rice is of concern due to its potential of entering food chain and the high toxicity to human. The level and form of Hg in rice could be influenced by fertilizers and other soil amendments. Studies were conducted to evaluate the effect of 24 years application of chemical fertilizers and organic amendments on total Hg (THg) and MeHg and their translocation in soil, plants, and rice grain. All treatments led to significantly higher concentrations of MeHg in grain than those from the untreated control. Of nine treatments tested, chemical fertilizers combining with returning rice straw (NPK1+S) led to highest MeHg concentration in grain and soil; while the nitrogen and potassium (NK) treatment led to significantly higher THg in grain. Concentrations of soil MeHg were significantly correlated with THg in soil (r = 0.59 *** ) and MeHg in grain (r = 0.48 *** ). Calcium superphosphate negatively affected plant bioavailability of soil Hg. MeHg concentration in rice was heavily influenced by soil Hg levels. Phosphorus fertilizer was a main source contributing to soil THg, while returning rice straw to the field contributed significantly to MeHg in soil and rice grain. As a result, caution should be exercised in soil treatment or when utilizing Hg-contaminated soils to produce rice for human consumption. Strategic management of rice straw and phosphorus fertilizer could be effective strategies of lowering soil Hg, which would ultimately lower MeHg in rice and the risk of Hg entering food chain. Copyright © 2017 Elsevier Inc. All rights reserved.

Realistic Simulation of Rice Plant

Directory of Open Access Journals (Sweden)

Wei-long DING

2011-09-01

Full Text Available The existing research results of virtual modeling of rice plant, however, is far from perfect compared to that of other crops due to its complex structure and growth process. Techniques to visually simulate the architecture of rice plant and its growth process are presented based on the analysis of the morphological characteristics at different stages. Firstly, the simulations of geometrical shape, the bending status and the structural distortion of rice leaves are conducted. Then, by using an improved model for bending deformation, the curved patterns of panicle axis and various types of panicle branches are generated, and the spatial shape of rice panicle is therefore created. Parametric L-system is employed to generate its topological structures, and finite-state automaton is adopted to describe the development of geometrical structures. Finally, the computer visualization of three-dimensional morphologies of rice plant at both organ and individual levels is achieved. The experimental results showed that the proposed methods of modeling the three-dimensional shapes of organs and simulating the growth of rice plant are feasible and effective, and the generated three-dimensional images are realistic.

Transgenic rice plants expressing synthetic cry2AX1 gene exhibits resistance to rice leaffolder (Cnaphalocrosis medinalis).

Science.gov (United States)

Manikandan, R; Balakrishnan, N; Sudhakar, D; Udayasuriyan, V

2016-06-01

Bacillus thuringiensis is a major source of insecticidal genes imparting insect resistance in transgenic plants. Level of expression of transgenes in transgenic plants is important to achieve desirable level of resistance against target insects. In order to achieve desirable level of expression, rice chloroplast transit peptide sequence was fused with synthetic cry2AX1 gene to target its protein in chloroplasts. Sixteen PCR positive lines of rice were generated by Agrobacterium mediated transformation using immature embryos. Southern blot hybridization analysis of T 0 transgenic plants confirmed the integration of cry2AX1 gene in two to five locations of rice genome and ELISA demonstrated its expression. Concentration of Cry2AX1 in transgenic rice events ranged 5.0-120 ng/g of fresh leaf tissue. Insect bioassay of T 0 transgenic rice plants against neonate larvae of rice leaffolder showed larval mortality ranging between 20 and 80 % in comparison to control plant. Stable inheritance and expression of cry2AX1 gene was demonstrated in T 1 progenies through Southern and ELISA. In T 1 progenies, the highest concentration of Cry2AX1 and mortality of rice leaffolder larvae were recorded as 150 ng/g of fresh leaf tissue and 80 %, respectively. The Cry2AX1 expression even at a very low concentration (120-150 ng/g) in transgenic rice plants was found effective against rice leaffolder larvae.

Late-maturing cooking rice Sensyuraku has excellent properties, equivalent to sake rice, for high-quality sake brewing.

Science.gov (United States)

Anzawa, Yoshihiko; Satoh, Kenji; Satoh, Yuko; Ohno, Satomi; Watanabe, Tsutomu; Katsumata, Kazuaki; Kume, Kazunori; Watanabe, Ken-Ichi; Mizunuma, Masaki; Hirata, Dai

2014-01-01

Low protein content and sufficient grain rigidity are desired properties for the rice used in high-quality sake brewing such as Daiginjo-shu (polishing ratio of the rice, less than 50%). Two kinds of rice, sake rice (SR) and cooking rice (CR), have been used for sake brewing. Compared with those of SR, analyses of CR for high-quality sake brewing using highly polished rice have been limited. Here we described the original screening of late-maturing CR Sensyuraku (SEN) as rice with low protein content and characterization of its properties for high-quality sake brewing. The protein content of SEN was lower than those of SR Gohyakumangoku (GOM) and CR Yukinosei (YUK), and its grain rigidity was higher than that of GOM. The excellent properties of SEN with respect to both water-adsorption and enzyme digestibility were confirmed using a Rapid Visco Analyzer (RVA). Further, we confirmed a clear taste of sake produced from SEN by sensory evaluation. Thus, SEN has excellent properties, equivalent to those of SR, for high-quality sake brewing.

Tungsten (W) bioavailability in paddy rice soils and its accumulation in rice (Oryza sativa).

Science.gov (United States)

James, Blessing; Zhang, Weili; Sun, Pei; Wu, Mingyan; Li, Hong Hong; Khaliq, Muhammad Athar; Jayasuriya, Pathmamali; James, Swithin; Wang, Guo

2017-12-01

The aim of this study was to investigate the accumulation characteristics of tungsten (W) by different indica rice cultivars from the soil and to assess the potential risks to human health via dietary intake of W in rice consumption. A total of 153 rice (ear) samples of 15 cultivars and the corresponding surface soil samples were collected from 7 cities in Fujian Province of southeastern China. The available soil W were extracted using H 2 C 2 O 4 ·2H 2 O-(NH 4 ) 2 C 2 O 4 ·H 2 O at pH 3.3). Results showed that the total soil W ranged from 2.03 mg kg -1 to 15.34 mg kg -1  and available soil W ranged from 0.03 mg kg -1 to 1.61 mg kg -1 . The W concentration in brown rice varied from 7 μg kg -1 to 283 μg kg -1 and was significantly correlated with the available soil W. The highest mean TF avail (transfer factor based on available soil W) was 0.91 for Te-you 627 (hybrid, indica rice), whereas the lowest was 0.08 for Yi-you 673 (hybrid, indica rice). The TF avail decreased with the increase in available soil W, clay content, and cation exchange capacity. The consumption of the brown rice produced from the investigated areas in some cultivars by the present study may cause risks to human health.

Increasing rice plant growth by Trichoderma sp.

Science.gov (United States)

Doni, Febri; Isahak, Anizan; Zain, Che Radziah Che Mohd; Sulaiman, Norela; Fathurahman, F.; Zain, Wan Nur Syazana Wan Mohd.; Kadhimi, Ahsan A.; Alhasnawi, Arshad Naji; Anhar, Azwir; Yusoff, Wan Mohtar Wan

2016-11-01

Trichoderma sp. is a plant growth promoting fungi in many crops. Initial observation on the ability to enhance rice germination and vigor have been reported. In this study, the effectiveness of a local isolate Trichoderma asprellum SL2 to enhance rice seedling growth was assessed experimentally under greenhouse condition using a completely randomized design. Results showed that inoculation of rice plants with Trichoderma asprellum SL2 significantly increase rice plants height, root length, wet weight, leaf number and biomass compared to untreated rice plants (control). The result of this study can serve as a reference for further work on the application of beneficial microorganisms to enhance rice production.

Plant root transcriptome profiling reveals a strain-dependent response during Azospirillum-rice cooperation

Directory of Open Access Journals (Sweden)

Benoît eDrogue

2014-11-01

Full Text Available Cooperation involving Plant Growth-Promoting Rhizobacteria results in improvements of plant growth and health. While pathogenic and symbiotic interactions are known to induce transcriptional changes for genes related to plant defence and development, little is known about the impact of phytostimulating rhizobacteria on plant gene expression. This study aims at identifying genes significantly regulated in rice roots upon Azospirillum inoculation, considering possible favored interaction between a strain and its original host cultivar. Genome-wide analyses of Oryza sativa japonica cultivars Cigalon and Nipponbare were performed, by using microarrays, seven days post inoculation with A. lipoferum 4B (isolated from Cigalon or Azospirillum sp. B510 (isolated from Nipponbare and compared to the respective non-inoculated condition. A total of 7,384 genes were significantly regulated, which represent about 16 % of total rice genes. A set of 34 genes is regulated by both Azospirillum strains in both cultivars, including a gene orthologous to PR10 of Brachypodium, and these could represent plant markers of Azospirillum-rice interactions. The results highlight a strain-dependent response of rice, with 83 % of the differentially expressed genes being classified as combination-specific. Whatever the combination, most of the differentially expressed genes are involved in primary metabolism, transport, regulation of transcription and protein fate. When considering genes involved in response to stress and plant defence, it appears that strain B510, a strain displaying endophytic properties, leads to the repression of a wider set of genes than strain 4B. Individual genotypic variations could be the most important driving force of rice roots gene expression upon Azospirillum inoculation. Strain-dependent transcriptional changes observed for genes related to auxin and ethylene signalling highlight the complexity of hormone signalling networks in the Azospirillum-rice

The rice growth image files - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us The Rice Growth Monitoring for The Phenotypic Functional Analysis The rice growth image file...s Data detail Data name The rice growth image files DOI 10.18908/lsdba.nbdc00945-004 Description of data contents The rice growth ima...ge files categorized based on file size. Data file File name: image files (director...y) File URL: ftp://ftp.biosciencedbc.jp/archive/agritogo-rice-phenome/LATEST/image...ite Policy | Contact Us The rice growth image files - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive ...

[Extruded rice flour as a gluten substitute in the poduction of rice bread].

Science.gov (United States)

Clerici, Maria Teresa Pedrosa Silva; El-Dash, Ahmed A

2006-09-01

Research regarding the production of gluten-free bread (GFB) is very important nutritionally, technically and economically speaking, both to celiac patients and to developing countries who import wheat. The main technological problem in the production of GFB is obtaining a gluten substitute that is both inexpensive and capable of retaining gas during bread fermentation and baking. The use of gelatinized starch as an alternative for gluten seems promising. In this project, rice bread was made using pregelatinized extruded rice flour as a gluten substitute. Pre-gelatinized rice flours (PRF) were manufactured in a single screw Brabender extruder, varying extrusion temperature (108-192 degrees C) and the moisture of the raw material (19.2 - 24.8%), and were used in a proportion of 10 g for every 100 g of raw rice flour, in the production of gluten-free bread. Results showed that rice flour extruded at a high temperature (180 degrees) and low moisture content (20%), rendered bread with the best technological characteristics, presenting crust and crumb color similar to those of conventional wheat bread, although with volume and texture not as satisfactory in the same comparison.

Fermented Brown Rice Flour as Functional Food Ingredient.

Science.gov (United States)

Ilowefah, Muna; Chinma, Chiemela; Bakar, Jamilah; Ghazali, Hasanah M; Muhammad, Kharidah; Makeri, Mohammad

2014-02-12

As fermentation could reduce the negative effects of bran on final cereal products, the utilization of whole-cereal flour is recommended, such as brown rice flour as a functional food ingredient. Therefore, this study aimed to investigate the effect of fermented brown rice flour on white rice flour, white rice batter and its steamed bread qualities. Brown rice batter was fermented using commercial baker's yeast (Eagle brand) according to the optimum conditions for moderate acidity (pH 5.5) to obtain fermented brown rice flour (FBRF). The FBRF was added to white rice flour at 0%, 10%, 20%, 30%, 40% and 50% levels to prepare steamed rice bread. Based on the sensory evaluation test, steamed rice bread containing 40% FBRF had the highest overall acceptability score. Thus, pasting properties of the composite rice flour, rheological properties of its batter, volume and texture properties of its steamed bread were determined. The results showed that peak viscosity of the rice flour containing 40% FBRF was significantly increased, whereas its breakdown, final viscosity and setback significantly decreased. Viscous, elastic and complex moduli of the batter having 40% FBRF were also significantly reduced. However, volume, specific volume, chewiness, resilience and cohesiveness of its steamed bread were significantly increased, while hardness and springiness significantly reduced in comparison to the control. These results established the effectiveness of yeast fermentation in reducing the detrimental effects of bran on the sensory properties of steamed white rice bread and encourage the usage of brown rice flour to enhance the quality of rice products.

Lead enrichment in different genotypes of rice grains.

Science.gov (United States)

Chen, Gang; Sun, Guo-rong; Liu, Ai-ping; Zhou, Wei-dong

2008-03-01

Using environmental scanning electron microscopy and X-ray electron probe microanalysis, the lead content was studied in inner and outer surface of rice glume, surface of caryopsis, center of caryopsis, near aleuronic layer and aleuronic layer in 21 genotypes of rice grains. The results showed that the lead content in different part of 21 genotypes of rice grains changed as inner surface of rice glume > aleuronic layer > near aleuronic layer > surface of caryopsis > outer surface of rice glume > center of caryopsis. There were genetic differences in lead enrichment in different genotypes of rice grains, which reflected as the differences of lead content in the same part and different part of rice grains. In different genotypes of rice grains, there were significant non-linear correlations between lead content in the inner surface of rice glume, center of caryopsis, aleuronic layer and that in the other parts of rice grain. The results also indicated that the lead enrichment in the center of caryopsis regulated by glume and aleuronic layer. In addition, in different genotypes of rice grains, there were differences in regulation of lead enrichment among different parts, which changed non-linearly.

21 CFR 573.160 - Ammoniated rice hulls.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Ammoniated rice hulls. 573.160 Section 573.160... Additive Listing § 573.160 Ammoniated rice hulls. The food additive ammoniated rice hulls may be safely... obtained by the treatment of ground rice hulls with monocalcium phosphate and anhydrous ammonia at a...

Effect of Temperature on Chinese Rice Wine Brewing with High Concentration Presteamed Whole Sticky Rice

Science.gov (United States)

Zhang, Hong-Tao; Xiong, Weili; Hu, Jianhua; Xu, Baoguo; Lin, Chi-Chung; Xu, Ling; Jiang, Lihua

2014-01-01

Production of high quality Chinese rice wine largely depends on fermentation temperature. However, there is no report on the ethanol, sugars, and acids kinetics in the fermentation mash of Chinese rice wine treated at various temperatures. The effects of fermentation temperatures on Chinese rice wine quality were investigated. The compositions and concentrations of ethanol, sugars, glycerol, and organic acids in the mash of Chinese rice wine samples were determined by HPLC method. The highest ethanol concentration and the highest glycerol concentration both were attained at the fermentation mash treated at 23°C. The highest peak value of maltose (90 g/L) was obtained at 18°C. Lactic acid and acetic acid both achieved maximum values at 33°C. The experimental results indicated that temperature contributed significantly to the ethanol production, acid flavor contents, and sugar contents in the fermentation broth of the Chinese rice wines. PMID:24672788

New market opportunities for rice grains

Science.gov (United States)

Breeding efforts for rice have been focusing on increasing yield and improving quality (milling yield and grain quality), while maintaining cooked rice sensory properties to meet consumer preferences. These breeding targets will no doubt continue as the main foci for the rice industry. However, the ...

Down-regulation of OsSPX1 causes high sensitivity to cold and oxidative stresses in rice seedlings.

Directory of Open Access Journals (Sweden)

Chunchao Wang

Full Text Available Rice SPX domain gene, OsSPX1, plays an important role in the phosphate (Pi signaling network. Our previous work showed that constitutive overexpression of OsSPX1 in tobacco and Arabidopsis plants improved cold tolerance while also decreasing total leaf Pi. In the present study, we generated rice antisense and sense transgenic lines of OsSPX1 and found that down-regulation of OsSPX1 caused high sensitivity to cold and oxidative stresses in rice seedlings. Compared to wild-type and OsSPX1-sense transgenic lines, more hydrogen peroxide accumulated in seedling leaves of OsSPX1-antisense transgenic lines for controls, cold and methyl viologen (MV treatments. Glutathione as a ROS scavenger could protect the antisense transgenic lines from cold and MV stress. Rice whole genome GeneChip analysis showed that some oxidative-stress marker genes (e.g. glutathione S-transferase and P450s and Pi-signaling pathway related genes (e.g. OsPHO2 were significantly down-regulated by the antisense of OsSPX1. The microarray results were validated by real-time RT-PCR. Our study indicated that OsSPX1 may be involved in cross-talks between oxidative stress, cold stress and phosphate homeostasis in rice seedling leaves.

Development Radar Absorber Material using Rice Husk Carbon for Anechoic Chamber Application

Science.gov (United States)

Zulpadrianto, Z.; Yohandri, Y.; Putra, A.

2018-04-01

The developments of radar technology in Indonesia are very strategic due to the vast territory and had a high-level cloud cover more than 55% of the time. The objective of this research is to develop radar technology facility in Indonesia using local natural resources. The target of this research is to present a low cost and satisfy quality of anechoic chambers. Anechoic chamber is a space designed to avoid reflection of EM waves from outside or from within the room. The reflection coefficient of the EM wave is influenced by the medium imposed by the EM wave. In laboratory experimental research has been done the development of material radar absorber using rice husk. The rice husk is activated using HCl and KOH by stirring using a magnetic stirrer for 1 Hours. The results of rice husk activation were measured using a Vector Network Analyzer by varying the thickness of the ingredients and the concentration of the activation agent. The VNA measurement is obtained reflection coefficient of -12dB and. -6.22dB for 1M HCL and KOH at thickness 10mm, respectively.

[Effects of Rice Cultivar and Typical Soil Improvement Measures on the Uptake of Cd in Rice Grains].

Science.gov (United States)

Wang, Mei-e; Peng, Chi; Chen, Wei-ping

2015-11-01

Cadmium pollution of rice is a big problem in agricultural food safety. The accident "Cd rice" occurred last year in Youxian County, Hunan Province caused serious social panic. In this study, trials on "Cd rice" controlling techniques specific to the Cd pollution in paddy soil in Youxian were investigated. It was suggested that the average Cd contents in rice grains of the rice variety "Zhu Liang You 06" in Datongqiao and Wangling were 0.167 and 0.127 mg x kg(-1), respectively, which were only equal to 20% of the contents of other varieties. The trials for stabilizing agents revealed that treatments of lime and mineral fertilizer decreased Cd contents in rice grains to 20-30% of the control. Plastic film-mulched treatment decreased the rice grain Cd to 50%. And combined treatment of plastic film-mulched and biochar and silicon foliar-fertilizer decreased 80% of rice Cd content. Single treatments of silicon foliar-fertilizer and combined treatment of silicon foliar-fertilizer and topdressing fertilizer decreased more than 90% of Cd content. Results of BCR revealed that the percentage of cationic exchangeable and/or carbonate associated Cd fraction was more than 55% for most of the soil samples. Lime treatment significantly decreased the percentage of cationic exchangeable and/or carbonate and oxides of Fe and Mn associated Cd and increased the crystalline structure of clay minerals associated Cd. The change rate reached about 20%. Our results suggested concentration of soil Cd and pH were the two significant factors impacting the uptake of Cd by rice grains.

Rice Seedling Substrate Produced by Coal Gangue

Directory of Open Access Journals (Sweden)

SHAO Yu-fei

2017-10-01

Full Text Available Peats are the mostly used material in making rice seedling substrate. However, mining peats could cause environmental problems. In order to reduce or replace peats in rice seedling substrate industry, this paper studied suitable way to configure rice seedling. The coal gangue was used to experiment cultivating rice. Four rice seeding experiments were carried out based on physical and chemical properties of materials attributes. The results showed:(1 Coal gangue was feasible for rice seedling; (2 The maximum adding amount of coal gangue was 80%(volume ratio though the coal gangue need to be activated; (3 In the case of no activated treatment only 38%(volume ratio of coal gangue could be added to the substrate.

From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks.

KAUST Repository

Cannistraci, C.V.; Alanis-Lobato, G.; Ravasi, Timothy

2013-01-01

for the singular topology of several real networks organised in multiple local communities - a tendency here named local-community-paradigm (LCP). We observe that LCP networks are mainly formed by weak interactions and characterise heterogeneous and dynamic systems

Water culture of the rice containing Cs-137

International Nuclear Information System (INIS)

Choi, Yong Ho; Keum, Dong Kwon; Lim, Kwang Muk; Jun, In; Park, Doo Won

2008-10-01

Pot experiments were carried out in a greenhouse in order to produce Cs-137-containing rice seeds as a source material for use in manufacturing reference rice samples of a high Cs-137 activity. Two kinds of soil were used and two pots were prepared for each kind of soil. Rice plants were water-cultured in the pots and Cs-137 was applied to the surface water to induce a Cs-137 contamination of rice seeds via a plant uptake of Cs-137. Mature rice plants were harvested and Cs-137-containing rice seeds were obtained after some treatment of the harvested plants. These produced rice seeds are going to be provided for the KRISS so as to be used in manufacturing reference rice samples for Cs-137

Curating the innate immunity interactome.

LENUS (Irish Health Repository)

Lynn, David J

2010-01-01

The innate immune response is the first line of defence against invading pathogens and is regulated by complex signalling and transcriptional networks. Systems biology approaches promise to shed new light on the regulation of innate immunity through the analysis and modelling of these networks. A key initial step in this process is the contextual cataloguing of the components of this system and the molecular interactions that comprise these networks. InnateDB (http:\\/\\/www.innatedb.com) is a molecular interaction and pathway database developed to facilitate systems-level analyses of innate immunity.

Effect of Temperature on Chinese Rice Wine Brewing with High Concentration Presteamed Whole Sticky Rice

Directory of Open Access Journals (Sweden)

Dengfeng Liu

2014-01-01

Full Text Available Production of high quality Chinese rice wine largely depends on fermentation temperature. However, there is no report on the ethanol, sugars, and acids kinetics in the fermentation mash of Chinese rice wine treated at various temperatures. The effects of fermentation temperatures on Chinese rice wine quality were investigated. The compositions and concentrations of ethanol, sugars, glycerol, and organic acids in the mash of Chinese rice wine samples were determined by HPLC method. The highest ethanol concentration and the highest glycerol concentration both were attained at the fermentation mash treated at 23°C. The highest peak value of maltose (90 g/L was obtained at 18°C. Lactic acid and acetic acid both achieved maximum values at 33°C. The experimental results indicated that temperature contributed significantly to the ethanol production, acid flavor contents, and sugar contents in the fermentation broth of the Chinese rice wines.

Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia.

Science.gov (United States)

Song, Beng-Kah; Chuah, Tse-Seng; Tam, Sheh May; Olsen, Kenneth M

2014-10-01

Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe and northern Asia). Here, we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull colour), we addressed the following questions: (i) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the USA? (ii) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? (iii) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal the following: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild-to-weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed-shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations. © 2014 John Wiley & Sons Ltd.

Simultaneous rough rice drying and rice bran stabilization using infrared radiation heating

Science.gov (United States)

The objective of this study was to develop a new rice drying method by using IR heating followed by tempering. Freshly harvested medium grain rice (M206) samples with different initial moisture contents (IMCs) were used in this study. The samples were dried for one- and two-passes by using a catalyt...

Genetic analysis of rice blast disease resistance genes using USDA rice mini-core and a mapping population

Science.gov (United States)

Rice blast disease caused by the fungal pathogen Magnaporthe oryzae (M. oryzae) is one of the most destructive diseases of cultivated rice, resulting in significant yield loss each year all over the world. Developing and utilizing blast resistant rice varieties is the most economical and effective m...

Comparing the costs and benefits of floating rice-based and intensive rice-based farming systems in the Mekong delta

OpenAIRE

Van Kien Nguyen; Oc Van Vo; Duc Ngoc Huynh

2015-01-01

This paper compares financial costs and benefits of floating rice-based and intensive rice farming systems using data from focus group discussions and household survey in four locations in the Mekong Delta. We argue that the net financial benefit per 1000m2 of integrated floating rice-based farming systems is greater than the net financial benefit of intensive rice farming system. The total net benefit of floating rice-leeks shows the highest net benefit (VND 24.8 mil./1000 m2), followed by f...

The puzzle of Italian rice origin and evolution: determining genetic divergence and affinity of rice germplasm from Italy and Asia.

Directory of Open Access Journals (Sweden)

Xingxing Cai

Full Text Available The characterization of genetic divergence and relationships of a set of germplasm is essential for its efficient applications in crop breeding and understanding of the origin/evolution of crop varieties from a given geographical region. As the largest rice producing country in Europe, Italy holds rice germplasm with abundant genetic diversity. Although Italian rice varieties and the traditional ones in particular have played important roles in rice production and breeding, knowledge concerning the origin and evolution of Italian traditional varieties is still limited. To solve the puzzle of Italian rice origin, we characterized genetic divergence and relationships of 348 rice varieties from Italy and Asia based on the polymorphisms of microsatellite fingerprints. We also included common wild rice O. rufipogon as a reference in the characterization. Results indicated relatively rich genetic diversity (H(e = 0.63-0.65 in Italian rice varieties. Further analyses revealed a close genetic relationship of the Italian traditional varieties with those from northern China, which provides strong genetic evidence for tracing the possible origin of early established rice varieties in Italy. These findings have significant implications for the rice breeding programs, in which appropriate germplasm can be selected from a given region and utilized for transferring unique genetic traits based on its genetic diversity and evolutionary relationships.

Succession of methanogenic archaea in rice straw incorporated into a Japanese rice field: estimation by PCR-DGGE and sequence analyses

Directory of Open Access Journals (Sweden)

Atsuo Sugano

2005-01-01

Full Text Available The succession and phylogenetic profiles of methanogenic archaeal communities associated with rice straw decomposition in rice-field soil were studied by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE analysis followed by 16S rDNA sequencing. Nylon bags containing either leaf sheaths or blades were buried in the plowed layer of a Japanese rice field under drained conditions during the off-crop season and under flooded conditions after transplanting. In addition, rice straw samples that had been buried in the rice field under drained conditions during the off-crop season were temporarily removed during spring plowing and then re-buried in the same rice field under flooded conditions at transplanting. Populations of methanogenic archaea were examined by amplification of the 16S rRNA genes in the DNA extracted from the rice straw samples. No PCR product was produced for samples of leaf sheath or blade prior to burial or after burial under drained conditions, indicating that the methanogen population was very small during decomposition of rice straw under oxic conditions. Many common bands were observed in rice straw samples of leaf sheath and blade during decomposition of rice straw under flooded conditions. Cluster analysis based on DGGE patterns divided methanogenic archaeal communities into two groups before and after the mid-season drainage. Sequence analysis of DGGE bands that were commonly present were closely related to Methanomicrobiales and Rice cluster I. Methanomicrobiales, Rice cluster I and Methanosarcinales were major members before the mid-season drainage, whereas the DGGE bands that characterized methanogenic archaeal communities after the mid-season drainage were closely related to Methanomicrobiales. These results indicate that mid-season drainage affected the methanogenic archaeal communities irrespective of their location on rice straw (sheath and blade and the previous history of decomposition

Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis.

Science.gov (United States)

Narsai, Reena; Devenish, James; Castleden, Ian; Narsai, Kabir; Xu, Lin; Shou, Huixia; Whelan, James

2013-12-01

Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or 'expressology', thus using and combining available information from two pre-eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large-scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au). © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

PICTORIAL INTERLUDES Flake-shaped rice bodies

African Journals Online (AJOL)

removing the rice bodies and the bursa.3. In summary: rice bodies can occur without underlying systemic disorder, have different shapes and sizes, and have specific signal characteristics on. MRI that allow discrimination from synovial chondromatosis. 1. Cheung HS, Ryan LM, Kozin F, McCarty DJ. Synovial origins of rice ...

Rice methylmercury exposure and mitigation: a comprehensive review.

Science.gov (United States)

Rothenberg, Sarah E; Windham-Myers, Lisamarie; Creswell, Joel E

2014-08-01

Rice cultivation practices from field preparation to post-harvest transform rice paddies into hot spots for microbial mercury methylation, converting less-toxic inorganic mercury to more-toxic methylmercury, which is likely translocated to rice grain. This review includes 51 studies reporting rice total mercury and/or methylmercury concentrations, based on rice (Orzya sativa) cultivated or purchased in 15 countries. Not surprisingly, both rice total mercury and methylmercury levels were significantly higher in polluted sites compared to non-polluted sites (Wilcoxon rank sum, p<0.001). However, rice percent methylmercury (of total mercury) did not differ statistically between polluted and non-polluted sites (Wilcoxon rank sum, p=0.35), suggesting comparable mercury methylation rates in paddy soil across these sites and/or similar accumulation of mercury species for these rice cultivars. Studies characterizing the effects of rice cultivation under more aerobic conditions were reviewed to determine the mitigation potential of this practice. Rice management practices utilizing alternating wetting and drying (instead of continuous flooding) caused soil methylmercury levels to spike, resulting in a strong methylmercury pulse after fields were dried and reflooded; however, it is uncertain whether this led to increased translocation of methylmercury from paddy soil to rice grain. Due to the potential health risks, it is advisable to investigate this issue further, and to develop separate water management strategies for mercury polluted and non-polluted sites, in order to minimize methylmercury exposure through rice ingestion. Copyright © 2014 Elsevier Inc. All rights reserved.

Translocations of 2,4-D-14C Herbicides In Weed And Rice Plant On Irrigated Rice Field System

International Nuclear Information System (INIS)

Chairul, Sofnie M.; Idawati; Mulyadi

2000-01-01

The investigation of translocation 2,4-D herbicides using 14 C as tracer on irradiated rice plant system. Condition of the soil was two kinds, that is normal soil and soil 30% up normal. The soil of rice field was spray with 1μCi of 2,4-D non labelled, one week after planting. A part of rice plant and weed was determined the radioactivity after 0, 2, 4, 8, and 10 weeks after spraying. The result showed that radioactivity maximum after zero week was in root and leaf of weeds, the second weeks in root of rice, the forth weeks in rice stick, and eighth weeks in leaf of rice. This result occur at normal condition soil of solid 30 % up normal soil. The residues of 2.4-D in rice was 4,24x10 -3 ppb at normal soil and 3.16x10 -3 ppb at solid 30% up normal soil. This result still lower than rate of WHO/FAO, that is 0,05 ppm

Clustering of 18 Local Black Rice Base on Total Anthocyanin

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Kristamtini Kristamtini

2017-10-01

Full Text Available Black rice has a high anthocyanin content in the pericarp layer, which provides a dark purple color. Anthocyanin serve as an antioxidant that control cholesterol level in the blood, prevent anemia, potentially improve the body's resistance to disease, improve damage to liver cells (hepatitis and chirrosis, prevent impaired kidney function, prevent cancer/tumors, slows down antiaging, and prevent atherosclerosis and cardiovascular disease. Exploration results at AIAT Yogyakarta, Indonesia from 2011 to 2014 obtained 18 cultivar of local black rice Indonesia. The names of the rice are related to the color (black, red or purple formed by anthocyanin deposits in the pericarp layer, seed coat or aleuron. The objective of the study was to classify several types of local black rice from explorations based on the total anthocyanin content. The study was conducted by clustering analyzing the total anthocyanin content of 18 local black rice cultivars in Indonesia. Cluster analysis of total anthocyanin content were done using SAS ver. 9.2. Clustering dendogram shows that there were 4 groups of black rice cultivars based on the total anthocyanin content. Group I consists of Melik black rice, Patalan black rice, Yunianto black rice, Muharjo black rice, Ngatijo black rice, short life of Tugiyo black rice, Andel hitam 1, Jlitheng, and Sragen black rice. Group II consists of Pari ireng, Magelang black hairy rice, Banjarnegara-Wonosobo black rice, and Banjarnegara black rice. Group III consists of NTT black rice, Magelang non hairy black rice, Sembada hitam, and longevity Tugiyo black rice. Group IV consist only one type of black rice namely Cempo ireng. The grouping result indicate the existence of duplicate names among the black rice namely Patalan with Yunianto black rice, and short life Tugiyo with Andel hitam 1 black rice.

Recent advances on bioactivities of black rice.

Science.gov (United States)

Dias, Aécio L de S; Pachikian, Barbara; Larondelle, Yvan; Quetin-Leclercq, Joëlle

2017-11-01

Black rice has been consumed for centuries in Asian countries such as China, Korea or Japan. Nowadays, extracts and derivatives are considered as beneficial functional foods because of their high content in several bioactive molecules such as anthocyanins, other phenolics and terpenoids. The purpose of this review is to summarize and discuss recent developments on black rice bioactivities. Some sterols and triterpenoids with potential anticancer properties already tested in vitro and in vivo have been isolated and identified from bran extracts of black rice. Protection against osteoporosis has been suggested for the first time for black rice extracts. Because of its antioxidant and anti-inflammatory properties, black rice also protects liver and kidney from injuries. One clinical study reported the interest of black rice in case of alcohol withdrawal. Several advances have been recently achieved on the understanding of the potential biological effects of black rice and its derivatives. They further confirm that black rice should be considered as a promising source of health-promoting functional foods targeting a large set of noninfectious diseases. However, more clinical studies are needed to support the findings highlighted in this review.

Generation and comprehensive analysis of an influenza virus polymerase cellular interaction network.

Science.gov (United States)

Tafforeau, Lionel; Chantier, Thibault; Pradezynski, Fabrine; Pellet, Johann; Mangeot, Philippe E; Vidalain, Pierre-Olivier; Andre, Patrice; Rabourdin-Combe, Chantal; Lotteau, Vincent

2011-12-01

The influenza virus transcribes and replicates its genome inside the nucleus of infected cells. Both activities are performed by the viral RNA-dependent RNA polymerase that is composed of the three subunits PA, PB1, and PB2, and recent studies have shown that it requires host cell factors to transcribe and replicate the viral genome. To identify these cellular partners, we generated a comprehensive physical interaction map between each polymerase subunit and the host cellular proteome. A total of 109 human interactors were identified by yeast two-hybrid screens, whereas 90 were retrieved by literature mining. We built the FluPol interactome network composed of the influenza virus polymerase (PA, PB1, and PB2) and the nucleoprotein NP and 234 human proteins that are connected through 279 viral-cellular protein interactions. Analysis of this interactome map revealed enriched cellular functions associated with the influenza virus polymerase, including host factors involved in RNA polymerase II-dependent transcription and mRNA processing. We confirmed that eight influenza virus polymerase-interacting proteins are required for virus replication and transcriptional activity of the viral polymerase. These are involved in cellular transcription (C14orf166, COPS5, MNAT1, NMI, and POLR2A), translation (EIF3S6IP), nuclear transport (NUP54), and DNA repair (FANCG). Conversely, we identified PRKRA, which acts as an inhibitor of the viral polymerase transcriptional activity and thus is required for the cellular antiviral response.

A comprehensive protein-protein interactome for yeast PAS kinase 1 reveals direct inhibition of respiration through the phosphorylation of Cbf1.

Science.gov (United States)

DeMille, Desiree; Bikman, Benjamin T; Mathis, Andrew D; Prince, John T; Mackay, Jordan T; Sowa, Steven W; Hall, Tacie D; Grose, Julianne H

2014-07-15

Per-Arnt-Sim (PAS) kinase is a sensory protein kinase required for glucose homeostasis in yeast, mice, and humans, yet little is known about the molecular mechanisms of its function. Using both yeast two-hybrid and copurification approaches, we identified the protein-protein interactome for yeast PAS kinase 1 (Psk1), revealing 93 novel putative protein binding partners. Several of the Psk1 binding partners expand the role of PAS kinase in glucose homeostasis, including new pathways involved in mitochondrial metabolism. In addition, the interactome suggests novel roles for PAS kinase in cell growth (gene/protein expression, replication/cell division, and protein modification and degradation), vacuole function, and stress tolerance. In vitro kinase studies using a subset of 25 of these binding partners identified Mot3, Zds1, Utr1, and Cbf1 as substrates. Further evidence is provided for the in vivo phosphorylation of Cbf1 at T211/T212 and for the subsequent inhibition of respiration. This respiratory role of PAS kinase is consistent with the reported hypermetabolism of PAS kinase-deficient mice, identifying a possible molecular mechanism and solidifying the evolutionary importance of PAS kinase in the regulation of glucose homeostasis. © 2014 DeMille et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Rice is the seed of the monocot plants Oryza sativa (Asian rice) or ...

African Journals Online (AJOL)

BIOTECH

2013-10-16

Oct 16, 2013 ... of culture. The regenerated plantlets were transferred to pots for acclimatization. About 80% of plants were survived in the greenhouse condition. Key words: Somatic embryogenesis, immature zygotic embryos, Indica rice, plant regeneration. INTRODUCTION. Rice (Oryza sativa L.) is one of the most ...

A Mixed-Methods Study on Acceptability, Tolerability, and Substitution of Brown Rice for White Rice to Lower Blood Glucose Levels among Nigerian Adults

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Sally N. Adebamowo

2017-07-01

Full Text Available BackgroundWhole-grain products such as brown rice have been associated with lower risk of metabolic disorders including diabetes. We examined the acceptability and tolerability of substituting brown rice for white rice and the feasibility of introducing brown rice into the diet through a long-term trial to lower the risk of type 2 diabetes.MethodsFifty-one adults residing in Abuja, Nigeria, participated in this study. Using purposeful sampling for focus group discussions (FGDs, participants were enrolled based on their age (19–25 vs. 40–60 years and body mass index (BMI (normal weight vs. overweight/obese. Participants tasted four meals with different constitution of brown and white rice (25:75%, 50:50%, 75:25%, and 100% brown rice. Twelve FGDs were conducted, six before and six after the food tasting. Two-hour postprandial blood glucose was measured after consumption of each rice meal.ResultsThe mean age of the participants was 39 (±14 years, their mean BMI was 25.6 (±5.2 and about half of them were male. Most of the participants (61% reported that rice was their main source of carbohydrate and 67% consumed rice at least five times/week. Before the food tasting, participants considered white polished rice superior to brown rice with regard to quality, taste, and nutritional value. After the food tasting, most of the participants (49% indicated a preference for the 100% brown rice, 19% preferred the 25% brown rice, 18% preferred the 50% brown rice, and 7% preferred the 75% brown rice meals. Factors that may affect the acceptability of brown rice include its appearance, longer cooking time, cost, limited availability, and poor appreciation of its nutritional value. In general, 2-h postprandial glucose levels were lower, after consumption of meals with higher proportion of brown rice.ConclusionThis study provides valuable insight into the acceptability of brown rice as a substitute for white rice in Nigeria. If confirmed in larger studies

Development of Rice Reprocessing to Strengthen Small Scale Rice Mills in Indramayu West Java

Science.gov (United States)

Firdaus, Y. R.; Hasbullah, R.; Djohar, S.

2018-05-01

Small Rice Mill (SRM) has a very important role in rice production of strong institutional relationships to farmers and rice markets. Nevertheless, the rice produced in low quality and changing consumer preferences cause SRM to have difficulty in maintaining the role. Development of a reprocessing business - called Rice to Rice Processing Plant (R2RP) - as a separate business unit will support their role and existence. This study aimed at analyzing the feasibility of R2RP business that integrates SRM and market as an independent business unit and determines mutual partnership pattern. The study was conducted with special reference to West Java Province. The qualitative method used for non-financial aspects analysis includes raw material, market, technical-technological, management and regulation and partnership pattern. The financial aspect used the quantitative method of Net Present Value (NPV), Net Benefit Cost Ratio (Net B/C), Internal Rate of Return (IRR), Payback Period (PP) and Switching Value to check their sensitivity.The results showed R2R business is feasible for non-financially, technical-technological and financial aspects. Technology has evolved to produce various qualities (premium or medium) after the quality of raw materials (low quality or off-grade rice) using profit optimization. Value of the financial parameters was NPV of Rp 137 billion, Net B/C of 5.80, IRR of 84.27 percent and PP of 2.18 years at capacity of 19,800 tons/year with total investment of Rp 30 billion (Rp 13,500/USD). The switching value analysis showed that a decrease in product prices is sensitively influencing the financial feasibility. To strengthen cooperation that enhancing mutually beneficial relationship, R2R assists equipment investment in and buy raw material from SRM at a rational agreed price.

Vulnerability of Thai rice production to simultaneous climate and socioeconomic changes: a double exposure analysis

Science.gov (United States)

Sangpenchan, R.

2011-12-01

This research explores the vulnerability of Thai rice production to simultaneous exposure by climate and socioeconomic change -- so-called "double exposure." Both processes influence Thailand's rice production system, but the vulnerabilities associated with their interactions are unknown. To understand this double exposure, I adopts a mixed-method, qualitative-quantitative analytical approach consisting of three phases of analysis involving a Vulnerability Scoping Diagram, a Principal Component Analysis, and the EPIC crop model using proxy datasets collected from secondary data sources at provincial scales.The first and second phases identify key variables representing each of the three dimensions of vulnerability -- exposure, sensitivity, and adaptive capacity indicating that the greatest vulnerability in the rice production system occurs in households and areas with high exposure to climate change, high sensitivity to climate and socioeconomic stress, and low adaptive capacity. In the third phase, the EPIC crop model simulates rice yields associated with future climate change projected by CSIRO and MIROC climate models. Climate change-only scenarios project the decrease in yields by 10% from the current productivity during 2016-2025 and 30% during 2045-2054. Scenarios applying both climate change and improved technology and management practices show that a 50% increase in rice production is possible, but requires strong collaboration between sectors to advance agricultural research and technology and requires strong adaptive capacity in the rice production system characterized by well-developed social capital, social networks, financial capacity, and infrastructure and household mobility at the local scale. The vulnerability assessment and climate and crop adaptation simulations used here provide useful information to decision makers developing vulnerability reduction plans in the face of concurrent climate and socioeconomic change.

Labelling of rice seedlings and rice plants with 32P

International Nuclear Information System (INIS)

Achmad Nasroh, K.

1989-01-01

Labelling of rice seedlings and rice plants with 32 P. Labelled rice seedlings can be used to tag insect pests that feed on. Radioactivity counting of 32 P in the endosperm and in the shoot of rice seeds that soaked for 72 hours in KH 2 32 PO 4 solution of 1 μCi/ml were 29,300 and 9,500 cpm respectively. When these labelled seedlings were grown in unlabelled medium the radioactivity in the shoot increased. It was due to the 32 P that was translocated to the shoot from the endosperm. The 32 P translocation reached maximum about one week after the seedling were grown in the unlabelled medium. Labelled seedlings could also be produced by growing 5, 10 and 15 days old seedlings hydroponically in Kimura B solution containing 32 P. Ten days after growing, the radioactivity concentration of the seedlings stem reached about 115,000; 85,000 and 170,000 cpm/mg dry weight for the 5, 10 and 15 days old seedlings respectively. For the implementation of this method, 20 ml labelled Kimura B was needed for labelling of one seedling. The seedlings should be prepared in tap water. During the growth the 32 P in the labelled seedlings was distributed throughout the plant, so that new leaves and tillers became also radioactive. (author). 5 refs

Water Footprint Analysis of Paddy Rice and the Nexus of Water-Land-Rice in Taiwan: 2005-2014

Science.gov (United States)

Wu, T. C.

2018-05-01

This paper explores the water footprint (WF) of paddy rice and the nexus of water-land-food (rice) in Taiwan. The research results indicate that the average annual rice WF for the years 2005-2014 was about 7,580 m3/ton, of which 80% was blue, 17% was green, and 3% was grey. This average annual footprint was about 5.7 times larger than the 2000-2004 average annual WF of rice for countries around the globe of 1325 m3/ton, of which 48% was green, 44% was blue, and 8% was grey. The blue WF is the most important source of water for rice production in Taiwan. The water consumption of the second crop is higher than that of the first crop. The water use efficiency in the southern region of Taiwan is the best, while the northern part of Taiwan exhibits relatively high inefficiency. The rates of change in cultivated land and rice production in Taiwan are decreasing in a stable manner. However, the annual rate of change in the rice WF is unstable. The nexus of land, water, and food should be taken into consideration to protect water availability, maintain agricultural production, and avoid land degradation. The results could offer useful information for agriculture policy and water resource management.

Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks

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Sandip Chakraborty

2016-01-01

Full Text Available Proteins within a molecular network are expected to be subject to different selective pressures depending on their relative hierarchical positions. However, it is not obvious what genes within a network should be more likely to evolve under positive selection. On one hand, only mutations at genes with a relatively high degree of control over adaptive phenotypes (such as those encoding highly connected proteins are expected to be “seen” by natural selection. On the other hand, a high degree of pleiotropy at these genes is expected to hinder adaptation. Previous analyses of the human protein-protein interaction network have shown that genes under long-term, recurrent positive selection (as inferred from interspecific comparisons tend to act at the periphery of the network. It is unknown, however, whether these trends apply to other organisms. Here, we show that long-term positive selection has preferentially targeted the periphery of the yeast interactome. Conversely, in flies, genes under positive selection encode significantly more connected and central proteins. These observations are not due to covariation of genes’ adaptability and centrality with confounding factors. Therefore, the distribution of proteins encoded by genes under recurrent positive selection across protein-protein interaction networks varies from one species to another.

Effect of vanadium application on the paddy rice

Energy Technology Data Exchange (ETDEWEB)

Chiu, T F

1953-01-01

The height, the root length and the weight of rice seedlings were increased by the application of ammonium vanadate. The nitrogen contents of seedlings were generally increased in proportion to the amounts of vanadate applied. Carbon contents of seedlings, however, show little difference. The best result was obtained when V/sub 2/O/sub 3/ 150 ppm was applied, but more than 500 ppm was toxic to rice seedlings, and at 1000 ppm all rice seedlings were killed. N, P, and K fertilizers were added to the rice after transplantation from the nursery, but vanadium was omitted. Little difference was found in growth and yield of the rice plants. Vanadium absorbed by younger rice seedlings has little influence on the latter growth and yields of rice plants.

Development and characterization of emulsions containing purple rice bran and brown rice oils

Science.gov (United States)

The aims of this study were to characterize purple rice bran oil (PRBO) as extracted from the bran, and to produce and characterize a nano-emulsion containing purple rice bran oil. An emulsion was prepared using PRBO (10%), sodium caseinate (5%) and water (85%). The mixture was sonicated followed ...

The economic power of the Golden Rice opposition

NARCIS (Netherlands)

Wesseler, J.H.H.; Zilberman, D.

2014-01-01

Vitamin A enriched rice (Golden Rice) is a cost-efficient solution that can substantially reduce health costs. Despite Golden Rice being available since early 2000, this rice has not been introduced in any country. Governments must perceive additional costs that overcompensate the benefits of the

RESTRUKTURISASI MENIR MENJADI BERAS BERKALSIUM TINGGI DENGAN METODE EKSTRUSI Restructured Fine Grain Rice to High Calcium Rice by Extrusion Method

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Chatarina Wariyah

2012-05-01

Full Text Available Indonesian calcium intake is still low. So, calcium fortification  in such as rice is important. Rice fortification by extru- sion method was conducted by mixing rice flour with fortificant solution, molding and drying. The rice that was resulted from this process is called ultra rice. Menir (finely ground grain rice will be used as raw material of ultra rice. The purposed of this research was to produce high calcium extrusion rice or ultra rice with physical, organoleptic properties and cooking  quality  as normal rice. The specific purposes were to evaluate the effect of the type and amount of binder(gluten and tapioca on the characteristics of ultra rice, to determine type and amount of binder that resulted high cal- cium ultra rice with high acceptability. The result showed that high calcium ultra rice with tapioca as binder had colour,texture and organoleptic properties as normal rice. The ultra rice texture tended harder than IR-64, but cooked-ultra ricewas softer. The colour of ultra rice with tapioca as binder was similar with IR-64, but ultra rice with gluten as binderwas more yellowness. The cooking quality of ultra rice was less acceptable than IR-64. The high acceptability of ultra rice  was made with 4 % tapioca as binder, and the characterictics of this ultra rice were : hardness 140.43N, deforma- tion 63.70 %, the colour with lightness (L 71.08,  yellowness (b 11.00, redness (a -0.27 and good cooking quality. ABSTRAK Angka kecukupan asupan kalsium masyarakat Indonesia saat ini masih rendah. Untuk itu perlu dilakukan fortifikasi pada pangan yang umum  dikonsumsi  masyarakat luas seperti beras. Salah satu cara fortifikasi beras adalah dengan metode ekstrusi yaitu mencampur larutan fortifikan dengan tepung beras, kemudian dicetak dan dikeringkan.  Berasyang dihasilkan sering disebut sebagai beras ultra. Untuk meningkatkan kemanfaatan hasil samping penggilingan padi,maka digunakan menir sebagai bahan baku beras ultra

Preparation of an In-House Reference Material Containing Fumonisins in Thai Rice and Matrix Extension of the Analytical Method for Japanese Rice

Science.gov (United States)

Awaludin, Norhafniza; Nagata, Reiko; Kawasaki, Tomomi; Kushiro, Masayo

2009-01-01

Mycotoxin contamination in rice is less reported, compared to that in wheat or maize, however, some Fusarium fungi occasionally infect rice in the paddy field. Fumonisins are mycotoxins mainly produced by Fusarium verticillioides, which often ruins maize. Rice adherent fungus Gibberella fujikuroi is taxonomically near to F. verticillioides, and there are sporadic reports of fumonisin contamination in rice from Asia, Europe and the United States. Therefore, there exists the potential risk of fumonisin contamination in rice as well as the need for the validated analytical method for fumonisins in rice. Although both natural and spiked reference materials are available for some Fusarium mycotoxins in matrices of wheat and maize, there are no reference materials for Fusarium mycotoxins in rice. In this study, we have developed a method for the preparation of a reference material containing fumonisins in Thai rice. A ShakeMaster grinding machine was used for the preparation of a mixed material of blank Thai rice and F. verticillioides-infected Thai rice. The homogeneity of the mixed material was confirmed by one-way analysis of variance, which led this material to serve as an in-house reference material. Using this reference material, several procedures to extract fumonisins from Thai rice were compared. Accordingly, we proved the applicability of an effective extraction procedure for the determination of fumonisins in Japanese rice. PMID:22069540

Effects of white rice, brown rice and germinated brown rice on antioxidant status of type 2 diabetic rats.

Science.gov (United States)

Imam, Mustapha Umar; Musa, Siti Nor Asma; Azmi, Nur Hanisah; Ismail, Maznah

2012-10-10

Oxidative stress is implicated in the pathogenesis of diabetic complications, and can be increased by diet like white rice (WR). Though brown rice (BR) and germinated brown rice (GBR) have high antioxidant potentials as a result of their bioactive compounds, reports of their effects on oxidative stress-related conditions such as type 2 diabetes are lacking. We hypothesized therefore that if BR and GBR were to improve antioxidant status, they would be better for rice consuming populations instead of the commonly consumed WR that is known to promote oxidative stress. This will then provide further reasons why less consumption of WR should be encouraged. We studied the effects of GBR on antioxidant status in type 2 diabetic rats, induced using a high-fat diet and streptozotocin injection, and also evaluated the effects of WR, BR and GBR on catalase and superoxide dismutase genes. As dietary components, BR and GBR improved glycemia and kidney hydroxyl radical scavenging activities, and prevented the deterioration of total antioxidant status in type 2 diabetic rats. Similarly, GBR preserved liver enzymes, as well as serum creatinine. There seem to be evidence that upregulation of superoxide dismutase gene may likely be an underlying mechanism for antioxidant effects of BR and GBR. Our results provide insight into the effects of different rice types on antioxidant status in type 2 diabetes. The results also suggest that WR consumption, contrary to BR and GBR, may worsen antioxidant status that may lead to more damage by free radicals. From the data so far, the antioxidant effects of BR and GBR are worth studying further especially on a long term to determine their effects on development of oxidative stress-related problems, which WR consumption predisposes to.

Effects of White Rice, Brown Rice and Germinated Brown Rice on Antioxidant Status of Type 2 Diabetic Rats

Directory of Open Access Journals (Sweden)

Maznah Ismail

2012-10-01

Full Text Available Oxidative stress is implicated in the pathogenesis of diabetic complications, and can be increased by diet like white rice (WR. Though brown rice (BR and germinated brown rice (GBR have high antioxidant potentials as a result of their bioactive compounds, reports of their effects on oxidative stress-related conditions such as type 2 diabetes are lacking. We hypothesized therefore that if BR and GBR were to improve antioxidant status, they would be better for rice consuming populations instead of the commonly consumed WR that is known to promote oxidative stress. This will then provide further reasons why less consumption of WR should be encouraged. We studied the effects of GBR on antioxidant status in type 2 diabetic rats, induced using a high-fat diet and streptozotocin injection, and also evaluated the effects of WR, BR and GBR on catalase and superoxide dismutase genes. As dietary components, BR and GBR improved glycemia and kidney hydroxyl radical scavenging activities, and prevented the deterioration of total antioxidant status in type 2 diabetic rats. Similarly, GBR preserved liver enzymes, as well as serum creatinine. There seem to be evidence that upregulation of superoxide dismutase gene may likely be an underlying mechanism for antioxidant effects of BR and GBR. Our results provide insight into the effects of different rice types on antioxidant status in type 2 diabetes. The results also suggest that WR consumption, contrary to BR and GBR, may worsen antioxidant status that may lead to more damage by free radicals. From the data so far, the antioxidant effects of BR and GBR are worth studying further especially on a long term to determine their effects on development of oxidative stress-related problems, which WR consumption predisposes to.

A spectral analysis of rice grains

International Nuclear Information System (INIS)

McIlvaine, M.S.; Cua, F.T.; Navarro, E.F.

1976-06-01

With the advent of extensive nuclear testing and the development and use of highly potent pesticides and fertilizers, the hazardous threats of radioactive contamination due to fallout and to the absorption of pesticide residues have been given due consideration. Among the many forms of life exposed to these threats are food crops and among these is rice. Several rice grain samples - Japanese rice samples ''A'' and ''B'' submitted by the National Grains Authority (NGA) for analysis, random samples of rice being sold to the public at local markets, and ''black rice'' which were picked from along the shores of a Mindoro town were subjected to spectral analysis. Results revealed the presence of trace elements normally found in plants, such as; K-42, I-124, Cl-38, Na-24, Br-82, and Mn-56. No mercury was detected in the sample specimen analyzed

Complementarity of Two Rice Mapping Approaches: Characterizing Strata Mapped by Hypertemporal MODIS and Rice Paddy Identification Using Multitemporal SAR

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Sonia Asilo

2014-12-01

Full Text Available Different rice crop information can be derived from different remote sensing sources to provide information for decision making and policies related to agricultural production and food security. The objective of this study is to generate complementary and comprehensive rice crop information from hypertemporal optical and multitemporal high-resolution SAR imagery. We demonstrate the use of MODIS data for rice-based system characterization and X-band SAR data from TerraSAR-X and CosmoSkyMed for the identification and detailed mapping of rice areas and flooding/transplanting dates. MODIS was classified using ISODATA to generate cropping calendar, cropping intensity, cropping pattern and rice ecosystem information. Season and location specific thresholds from field observations were used to generate detailed maps of rice areas and flooding/transplanting dates from the SAR data. Error matrices were used for the accuracy assessment of the MODIS-derived rice characteristics map and the SAR-derived detailed rice area map, while Root Mean Square Error (RMSE and linear correlation were used to assess the TSX-derived flooding/transplanting dates. Results showed that multitemporal high spatial resolution SAR data is effective for mapping rice areas and flooding/transplanting dates with an overall accuracy of 90% and a kappa of 0.72 and that hypertemporal moderate-resolution optical imagery is effective for the basic characterization of rice areas with an overall accuracy that ranged from 62% to 87% and a kappa of 0.52 to 0.72. This study has also provided the first assessment of the temporal variation in the backscatter of rice from CSK and TSX using large incidence angles covering all rice crop stages from pre-season until harvest. This complementarity in optical and SAR data can be further exploited in the near future with the increased availability of space-borne optical and SAR sensors. This new information can help improve the identification of rice

Rice methylmercury exposure and mitigation: a comprehensive review

Science.gov (United States)

Rothenberg, Sarah E.; Windham-Myers, Lisamarie; Creswell, Joel E.

2014-01-01

Rice cultivation practices from field preparation to post-harvest transform rice paddies into hot spots for microbial mercury methylation, converting less-toxic inorganic mercury to more-toxic methylmercury, which is likely translocated to rice grain. This review includes 51 studies reporting rice total mercury and/or methylmercury concentrations, based on rice (Orzya sativa) cultivated or purchased in 15 countries. Not surprisingly, both rice total mercury and methylmercury levels were significantly higher in polluted sites compared to non-polluted sites (Wilcoxon rank sum, price percent methylmercury (of total mercury) did not differ statistically between polluted and non-polluted sites (Wilcoxon rank sum, p=0.35), suggesting comparable mercury methylation rates in paddy soil across these sites and/or similar accumulation of mercury species for these rice cultivars. Studies characterizing the effects of rice cultivation under more aerobic conditions were reviewed to determine the mitigation potential of this practice. Rice management practices utilizing alternating wetting and drying (instead of continuous flooding) caused soil methylmercury levels to spike, resulting in a strong methylmercury pulse after fields were dried and reflooded; however, it is uncertain whether this led to increased translocation of methylmercury from paddy soil to rice grain. Due to the potential health risks, it is advisable to investigate this issue further, and to develop separate water management strategies for mercury polluted and non-polluted sites, in order to minimize methylmercury exposure through rice ingestion.

Effects of fish and prawn culture on physico-chemical parameters of water and rice yield in rice fields

OpenAIRE

Razzak, M.A.; Nahar, A.; Mirhaj, M.; Becker, K.; Dewan, S.

2009-01-01

An experiment was conducted with five treatments i.e. rice combined with fish having regular urea fertilization (T1), rice combined with prawn having regular urea fertilization (T2), rice combined with fish with supplementary feeding (T3), rice combined with prawn with supplementary feeding (T4) and without fish and prawn (T5) was kept as control. The dissolved oxygen values obtained in treatments with fish both in morning and afternoon were lower than the values of prawn containing treatment...

Tightly Controlled Expression of bHLH142 Is Essential for Timely Tapetal Programmed Cell Death and Pollen Development in Rice

Directory of Open Access Journals (Sweden)

Swee-Suak Ko

2017-07-01

Full Text Available Male sterility is important for hybrid seed production. Pollen development is regulated by a complex network. We previously showed that knockout of bHLH142 in rice (Oryza sativa causes pollen sterility by interrupting tapetal programmed cell death (PCD and bHLH142 coordinates with TDR to modulate the expression of EAT1. In this study, we demonstrated that overexpression of bHLH142 (OE142 under the control of the ubiquitin promoter also leads to male sterility in rice by triggering the premature onset of PCD. Protein of bHLH142 was found to accumulate specifically in the OE142 anthers. Overexpression of bHLH142 induced early expression of several key regulatory transcription factors in pollen development. In particular, the upregulation of EAT1 at the early stage of pollen development promoted premature PCD in the OE142 anthers, while its downregulation at the late stage impaired pollen development by suppressing genes involved in pollen wall biosynthesis, ROS scavenging and PCD. Collectively, these events led to male sterility in OE142. Analyses of related mutants further revealed the hierarchy of the pollen development regulatory gene network. Thus, the findings of this study advance our understanding of the central role played by bHLH142 in the regulatory network leading to pollen development in rice and how overexpression of its expression affects pollen development. Exploitation of this novel functionality of bHLH142 may confer a big advantage to hybrid seed production.

Comprehensive gene expression analysis of rice aleurone cells: probing the existence of an alternative gibberellin receptor.

Science.gov (United States)

Yano, Kenji; Aya, Koichiro; Hirano, Ko; Ordonio, Reynante Lacsamana; Ueguchi-Tanaka, Miyako; Matsuoka, Makoto

2015-02-01

Current gibberellin (GA) research indicates that GA must be perceived in plant nuclei by its cognate receptor, GIBBERELLIN INSENSITIVE DWARF1 (GID1). Recognition of GA by GID1 relieves the repression mediated by the DELLA protein, a model known as the GID1-DELLA GA perception system. There have been reports of potential GA-binding proteins in the plasma membrane that perceive GA and induce α-amylase expression in cereal aleurone cells, which is mechanistically different from the GID1-DELLA system. Therefore, we examined the expression of the rice (Oryza sativa) α-amylase genes in rice mutants impaired in the GA receptor (gid1) and the DELLA repressor (slender rice1; slr1) and confirmed their lack of response to GA in gid1 mutants and constitutive expression in slr1 mutants. We also examined the expression of GA-regulated genes by genome-wide microarray and quantitative reverse transcription-polymerase chain reaction analyses and confirmed that all GA-regulated genes are modulated by the GID1-DELLA system. Furthermore, we studied the regulatory network involved in GA signaling by using a set of mutants defective in genes involved in GA perception and gene expression, namely gid1, slr1, gid2 (a GA-related F-box protein mutant), and gamyb (a GA-related trans-acting factor mutant). Almost all GA up-regulated genes were regulated by the four named GA-signaling components. On the other hand, GA down-regulated genes showed different expression patterns with respect to GID2 and GAMYB (e.g. a considerable number of genes are not controlled by GAMYB or GID2 and GAMYB). Based on these observations, we present a comprehensive discussion of the intricate network of GA-regulated genes in rice aleurone cells. © 2015 American Society of Plant Biologists. All Rights Reserved.

Extracting silica from rice husk treated with potassium permanganate

International Nuclear Information System (INIS)

Javed, S.H.; Naveed, S.

2008-01-01

As an agro-waste material the rice husk is abundantly available is rice growing areas. In many areas rice husk after burning involves disposal problems because of higher quantities of silica present in it. Rice husk contains about 20 per cent silica, which is present in hydrated amorphous form. On thermal treatment the silica converts into crystobalite, which is a crystalline form of silica. However amorphous silica can be produced under controlled conditions ensuring high reactivity and large surface area. Leaching the rice husk with organic acids and alkalies removes the metallic impurities from its surface. How a dilute solution of potassium permanganate affects the rice husk is the subject of this research paper. The rice husk was treated with the dilute solution of potassium permanganate at room temperature and then analyzed by SEM, TGA and the ash by analytical treatment after burning under controlled temperature. The SEM results revealed that the protuberances of the rice husk were eaten away by the solution of potassium permanganate. Pyrolysis of rice husks showed that the thermal degradation of the treated rice husk was faster than the untreated rice husk where as analytical results confirmed the presence of more amorphous silica than untreated rice husk. (author)

Upland rice yield as affected by Brachiaria coverage management

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Adriano S. Nascente

2015-01-01

Full Text Available An important point in no-tillage system is the time between cover crop glyphosate desiccation and rice sowing. This study aimed to verify the effect of Brachiaria ruziziensis management time before rice sowing on rice yield and its components. The experiment was conducted under greenhouse conditions and consisted of four types of B. ruziziensis management: with Brachiaria and with herbicide (WBWH, without Brachiaria shoots and with herbicide (NBWH, without Brachiaria shoots and without herbicide (NBNH, and with Brachiaria and without herbicide (WBNH, at four times: 30, 20, 10, and 0 days, preceding the rice sowing. The amount of B. ruziziensis dry matter increased as the management was done closer to the rice sowing date. The WBWH and WBNH managements (this one causes the lowest rice grain yield must be done 30 days before rice sowing; while NBWH management must be done ten or more days before rice sowing. On the other hand, NBNH management (this one favors the best rice grain yield can be done until rice sowing day. Despite some reduction in rice yield caused by the B. ruziziensis management, when it was done at the proper time the rice grain yield was similar to the control (without Brachiaria sowing and without herbicide application.

Harvest season and head rice yield of upland rice cultivars submitted to parboiling

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Diva Mendonça Garcia

2012-11-01

Full Text Available Normal 0 21 false false false PT-BR X-NONE X-NONE This work aimed to evaluate the effects of parboiling on the yield of upland rice cultivars harvested at different times. The cultivars were BRS Primavera and BRS Sertaneja, harvested at 30 and 47 days after flowering (DAF. For parboiling, samples were soaked in water bath at 65 °C in grain: water ratio of 1:1.6 in order to reach 25% and 30% moisture, and then were autoclaved for 10 minutes at 120 °C and 1.1 kg/cm2 of pressure. After drying up to 13% moisture in a greenhouse with forced air at 40 °C, samples were benefited, followed by separation using the trieur equipment and weighing to obtain the head rice yield. The results showed a higher yield for head rice harvested at 30 DAF than at 47 DAF (BRS Primavera 63.2 and 38.7%; BRS Sertaneja 68.5 and 55.7%, respectively. Parboiling increased the head rice yield, regardless of harvest season, but partly reflected the potential of the cultivar origin: BRS Primavera 70.06%, BRS Sertaneja 74.94%. It is concluded that the harvest season is one of the factors that most influence the quality of industrial rice and the effect of parboiling also depends on the potential of the material source.

Stimulate The Growth of Rice Using Endophytic Bacteria from Lowland Rice Plant Tissue

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Nuni Gofar

2015-07-01

Full Text Available Exploration and selection of endophytic bacteria from healthy food crops grown in lowland ecosystem is important to be conducted in order to get growth-stimulating endophytic bacteria at soil with low fertility level so that capable to optimize initial growth of food crops and subsequently can increase productivity level of lowland soil.The research objective was to isolate and to test the IAA-producing endophytic bacteria isolate in stimulating the rice crop growth at lowland area. Endophytic bacteria are isolated from tissues of rice, corn and peanut crops which grown at shallow swamp land in Ogan Ilir and Ogan Komering Ilir Districts, South Sumatra, Indonesia. There was nine isolates of nitrogen-fixer endophytic bacteria that capable to contribute IAA phytohormone into their growth media. The P31 isolate from rice crop tisssue of 2 months old produce the best rice sprouts than other isolates. This isolate can contribute of about 10 mg kg-1 IAA to its growth medium and increase the crowns dry weight and the roots dry weight respectively with magnitudes of 133% and 225% compared to control treatment. Concentration and absorbtion of N for rice crops innoculated with P31 isolates had increased by 169% and 400%, recpectively. The P31 isolates had been identified as Burkholderia pseudomallei (also known as Pseudomonas pseudomallei.

Study on residues of 14C-Fenitrothion in a model rice-fish ecosystem and in a field rice-fish ecosystem

International Nuclear Information System (INIS)

Zhang Zhongliang; Wang Huaxin; Guo Dazhi; Chen Zhiyu; Wu Suchueng

1993-01-01

Residues of 14 C-fenitrothion in a model rice-fish ecosystem and field rice-fish ecosystem were studied. When equal amounts of the pesticide were applied, the extractable residues in brown rice (equivalent to 34.3±1.9 μg/kg fenitrothion) and rice stems and leaves (20.9±1.5 μg/kg) of the model rice-fish ecosystem were 10-15 times higher than that of the field rice-fish ecosystem (4.48±0.13 μg/kg and 1.27±0.34 μg/kg respectively). Residues in upper part of the soil (6.50±0.1--8.10±0.2 μg/kg) and lower part of the soil (1.30±0.1--1.50±0.1 μg/kg) of the model rice-fish ecosystem were 10-40 times higher than that of the field rice-fish ecosystem (0.17±0.01 μg/kg). The extractable residues in paddy water of the model ecosystem (0.30 ± 0.01 μg/kg) were similar to that of the field ecosystem (0.20±0.02 μg/kg). When the fenitrothion was sprayed on the rice plants, residues in brown rice, fish body, soil and paddy water were lower than those when the pesticide was spread on the surface of the soil. (author). 4 refs, 2 tabs

Vinegar rice (Oryza sativa L.) produced by a submerged fermentation process from alcoholic fermented rice

OpenAIRE

Spinosa,Wilma Aparecida; Santos Júnior,Vitório dos; Galvan,Diego; Fiorio,Jhonatan Luiz; Gomez,Raul Jorge Hernan Castro

2015-01-01

Considering the limited availability of technology for the production of rice vinegar and also due to the potential consumer product market, this study aimed to use alcoholic fermented rice (rice wine (Oryza sativa L.)) for vinegar production. An alcoholic solution with 6.28% (w/v) ethanol was oxidized by a submerged fermentation process to produce vinegar. The process of acetic acid fermentation occurred at 30 ± 0.3°C in a FRINGS® Acetator (Germany) for the production of vineg...

Establishment of a rice-duck integrated farming system and its effects on soil fertility and rice disease control

Science.gov (United States)

Teng, Qing; Hu, Xue-Feng; Cheng, Chang; Luo, Zhi-Qing; Luo, Fan

2015-04-01

Rice-duck integrated farming is an ecological farming system newly established in some areas of southern China . It was reported that the ducks walking around the paddy fields is beneficial to control weed hazards and reduce rice pests and diseases. To study and evaluate the effects of the rice-duck integrated farming on soil fertility and rice disease control, a field experiment of rice cultivation was carried out in the suburb of Shanghai in 2014. It includes a treatment of raising ducks in the fields and a control without ducks. The treatment was implemented by building a duck coop nearby the experimental fields and driving 15 ducks into a plot at daytime since the early stage of rice growth. Each plot is 667 m2 in area. The treatment and control were replicated for three times. No any herbicides, pesticides, fungicides and chemical fertilizers were applied during the experiment to prevent any disturbance to duck growing and rice weed hazards and disease incidences from agrochemicals. The results are as follows: (1) The incidences of rice leaf rollers (Cnaphalocrocis medinalis) and stem borers treated with ducks, 0.45%and 1.18% on average, respectively, are lower than those of the control, 0.74% and 1.44% on average, respectively. At the late stage of rice growth, the incidence of rice sheath blight treated with ducks, 13.15% on average, is significantly lower than that of the control, 16.9% on average; and the incidence of rice planthoppers treated with ducks, 11.3 per hill on average, is also significantly lower than that of the control, 47.4 per hill on average. (2) The number of weeds in the plots treated with ducks, 8.3 per m2 on average, is significantly lower than that of the control, 87.5 m2 on average. (3) Raising ducks in the fields could also enhance soil enzyme activity and nutrient status. At the late stage of rice growth, the activities of urease, phosphatase, sucrase and catalase in the soils treated with ducks are 1.39 times, 1.40 times, 1

Production of glutinous rice flour from broken rice via ultrasonic assisted extraction of amylose.

Science.gov (United States)

Setyawati, Yohana Dwi; Ahsan, Sitti Faika; Ong, Lu Ki; Soetaredjo, Felycia Edi; Ismadji, Suryadi; Ju, Yi-Hsu

2016-07-15

In this study, a modified aqueous leaching method by complex formation of amylose with glycerol was employed for reducing the amylose content of starch in broken white rice to less than 2%, so that the resulting starch can be classified to that of glutinous rice flour. By employing ultrasonication in alkaline condition, extraction of amylose could be performed by washing at lower temperature in shorter time compared to the existing aqueous leaching method. The effects of glycerol concentration, alkali concentration, ultrasonication and treatment time on the amylose content of the treated starch were systematically investigated. Under optimum condition, amylose content of broken white rice starch can be reduced from 27.27% to 1.43% with a yield of 80.42%. The changes in the physicochemical properties of the rice flour before and after treatment were studied. Copyright © 2016 Elsevier Ltd. All rights reserved.

Radiocarbon ages of Sorori ancient rice of Korea

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Kim, Kyeong Ja, E-mail: kjkim@kigam.re.kr [Korea Institute of Geoscience and Mineral Resources, Daejeon (Korea, Republic of); Lee, Yung-Jo; Woo, Jong-Yoon [Institute of Korean Prehistory, Cheongju (Korea, Republic of); Jull, A.J. Timothy [NSF Arizona AMS Laboratory, University of Arizona, Tucson, AZ 85721 (United States)

2013-01-15

Samples of Sorori ancient rice were excavated in 1998 from the Sorori Paleolithic site located at Sorori, Oksan-myeon, Cheong-won County in Chungcheongbuk-do, Korea. We have made new radiocarbon measurements for Sorori samples in 2009 at the NSF Arizona AMS Laboratory. Both ancient rice samples and surrounded peat from the Sorori site were dated. The AMS results confirmed that the ages of the rice and peat soil were 12,520 {+-} 150 and 12,552 {+-} 90 BP, respectively. These radiocarbon ages are consistent with the previously published data of quasi rice measured at Seoul National University and confirm that the Sorori rice is the oldest ancient rice currently reported.

Cropping system diversification for food production in Mindanao rubber plantations: a rice cultivar mixture and rice intercropped with mungbean

Science.gov (United States)

Elazegui, Francisco; Duque, Jo-Anne Lynne Joy E.; Mundt, Christopher C.; Vera Cruz, Casiana M.

2017-01-01

Including food production in non-food systems, such as rubber plantations and biofuel or bioenergy crops, may contribute to household food security. We evaluated the potential for planting rice, mungbean, rice cultivar mixtures, and rice intercropped with mungbean in young rubber plantations in experiments in the Arakan Valley of Mindanao in the Philippines. Rice mixtures consisted of two- or three-row strips of cultivar Dinorado, a cultivar with higher value but lower yield, and high-yielding cultivar UPL Ri-5. Rice and mungbean intercropping treatments consisted of different combinations of two- or three-row strips of rice and mungbean. We used generalized linear mixed models to evaluate the yield of each crop alone and in the mixture or intercropping treatments. We also evaluated a land equivalent ratio for yield, along with weed biomass (where Ageratum conyzoides was particularly abundant), the severity of disease caused by Magnaporthe oryzae and Cochliobolus miyabeanus, and rice bug (Leptocorisa acuta) abundance. We analyzed the yield ranking of each cropping system across site-year combinations to determine mean relative performance and yield stability. When weighted by their relative economic value, UPL Ri-5 had the highest mean performance, but with decreasing performance in low-yielding environments. A rice and mungbean intercropping system had the second highest performance, tied with high-value Dinorado but without decreasing relative performance in low-yielding environments. Rice and mungbean intercropped with rubber have been adopted by farmers in the Arakan Valley. PMID:28194318

Significance of rice sheath photosynthesis: Yield determination by ...

African Journals Online (AJOL)

Using high-yielding hybrid rice Liangyopeijiu (LYP9), its male parent 9311 and hybrid rice Shanyou 63 (SY63) as the experimental materials, the photosynthesis of rice sheath was studied by 14C radio-autography. The results showed that rice sheath could trap sunlight and produce photosynthates, and these ...

Econometric Model of Rice Policy Based On Presidential Instruction

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Abadi Sembiring, Surya; Hutauruk, Julia

2018-01-01

The objective of research is to build an econometric model based on Presidential Instruction rice policy. The data was monthly time series from March 2005 to September 2009. Rice policy model specification using simultaneous equation, consisting of 14 structural equations and four identity equation, which was estimated using Two Stages Least Squares (2SLS) method. The results show that: (1) an increase of government purchasing price of dried harvest paddy has a positive impact on to increase in total rice production and community rice stock, (2) an increase community rice stock lead to decrease the rice imports, (3) an increase of the realization of the distribution of subsidized ZA fertilizers and the realization of the distribution of subsidized NPK fertilizers has a positive impact on to increase in total rice production and community rice stock and to reduce rice imports, (4) the price of the dried harvest paddy is highly responsive to the water content of dried harvest paddy both the short run and long run, (5) the quantity of rice imported is highly responsive to the imported rice price, both short run and long run.

Combined influence of Bt rice and rice dwarf virus on biological parameters of a non-target herbivore, Nephotettix cincticeps (Uhler) (Hemiptera: Cicadellidae).

Science.gov (United States)

Wang, Qianjin; Han, Naishun; Dang, Cong; Lu, Zengbin; Wang, Fang; Yao, Hongwei; Peng, Yufa; Stanley, David; Ye, Gongyin

2017-01-01

The advent of genetically modified (GM) Bt rice creates the possibility of interactions among Bt crops, crop pathogens and non-target herbivores. In particular, information on how pathogen-infected Bt-expressing plants will influence non-target herbivores is necessary to predict the sustainability of GM cropping systems. Laboratory bioassays were conducted to evaluate the potential combined impacts of rice dwarf virus (RDV) and two Bt rice lines, T1C-19 (Cry1C) and T2A-1 (Cry2A), on non-target green rice leafhopper (GRLH), Nephotettix cincticeps (Uhler) (Hemiptera: Cicadellidae). In the first experiment, GRLHs feeding preference tests on Bt rice lines compared to a parental control rice line, MH63, were conducted. As rice plants were uninfected with RDV, GRLHs generally preferred the control MH63 line over the two Bt lines during the initial 8 h, with no significant preference during the following 64 h. As rice plants were infected with RDV, there were no clear preferences between the Bt rice lines and the control MH63 line. In the second experiment, we assessed the combined influence of RDV-infection status and Bt rice lines on GRLH biological parameters. Egg duration, adult weights, and male adult longevity were significantly affected on RDV-infected Bt rice. Other parameters, egg hatching rate, nymph survival and fecundity were not significantly influenced. We infer that interaction effect among two testing Bt rice lines and RDV will not lead to enlarged pest populations, thus demonstrating that growing these two Bt rice lines will poses negligible risk to GRLH in sustainable rice agroecosystems. Long-term field experiments to monitor the population dynamics of GRLHs at large scale need to be carried out to confirm the current results.

Combined influence of Bt rice and rice dwarf virus on biological parameters of a non-target herbivore, Nephotettix cincticeps (Uhler (Hemiptera: Cicadellidae.

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Qianjin Wang

Full Text Available The advent of genetically modified (GM Bt rice creates the possibility of interactions among Bt crops, crop pathogens and non-target herbivores. In particular, information on how pathogen-infected Bt-expressing plants will influence non-target herbivores is necessary to predict the sustainability of GM cropping systems. Laboratory bioassays were conducted to evaluate the potential combined impacts of rice dwarf virus (RDV and two Bt rice lines, T1C-19 (Cry1C and T2A-1 (Cry2A, on non-target green rice leafhopper (GRLH, Nephotettix cincticeps (Uhler (Hemiptera: Cicadellidae. In the first experiment, GRLHs feeding preference tests on Bt rice lines compared to a parental control rice line, MH63, were conducted. As rice plants were uninfected with RDV, GRLHs generally preferred the control MH63 line over the two Bt lines during the initial 8 h, with no significant preference during the following 64 h. As rice plants were infected with RDV, there were no clear preferences between the Bt rice lines and the control MH63 line. In the second experiment, we assessed the combined influence of RDV-infection status and Bt rice lines on GRLH biological parameters. Egg duration, adult weights, and male adult longevity were significantly affected on RDV-infected Bt rice. Other parameters, egg hatching rate, nymph survival and fecundity were not significantly influenced. We infer that interaction effect among two testing Bt rice lines and RDV will not lead to enlarged pest populations, thus demonstrating that growing these two Bt rice lines will poses negligible risk to GRLH in sustainable rice agroecosystems. Long-term field experiments to monitor the population dynamics of GRLHs at large scale need to be carried out to confirm the current results.

Signatures of adaptation in the weedy rice genome

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Weedy rice is a common problem of by product of domestication that has evolved multiple times from cultivated and wild rice relatives. Here we use whole genome sequences to examine the origin and adaptation of the two major US weedy red rice strains, with a comparison to Chinese weedy red rice. We f...

7 CFR 868.301 - Definition of milled rice.

Science.gov (United States)

2010-01-01

... 7 Agriculture 7 2010-01-01 2010-01-01 false Definition of milled rice. 868.301 Section 868.301... FOR CERTAIN AGRICULTURAL COMMODITIES United States Standards for Milled Rice Terms Defined § 868.301 Definition of milled rice. Whole or broken kernels of rice (Oryza sativa L.) from which the hulls and at...

7 CFR 868.201 - Definition of rough rice.

Science.gov (United States)

2010-01-01

... 7 Agriculture 7 2010-01-01 2010-01-01 false Definition of rough rice. 868.201 Section 868.201... FOR CERTAIN AGRICULTURAL COMMODITIES United States Standards for Rough Rice Terms Defined § 868.201 Definition of rough rice. Rice (Oryza sativa L.) which consists of 50 percent or more of paddy kernels (see...

Fermented Brown Rice Flour as Functional Food Ingredient

OpenAIRE

Ilowefah, Muna; Chinma, Chiemela; Bakar, Jamilah; Ghazali, Hasanah; Muhammad, Kharidah; Makeri, Mohammad

2014-01-01

As fermentation could reduce the negative effects of bran on final cereal products, the utilization of whole-cereal flour is recommended, such as brown rice flour as a functional food ingredient. Therefore, this study aimed to investigate the effect of fermented brown rice flour on white rice flour, white rice batter and its steamed bread qualities. Brown rice batter was fermented using commercial baker?s yeast (Eagle brand) according to the optimum conditions for moderate acidity (pH 5.5) to...

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice.

Science.gov (United States)

Brozynska, Marta; Copetti, Dario; Furtado, Agnelo; Wing, Rod A; Crayn, Darren; Fox, Glen; Ishikawa, Ryuji; Henry, Robert J

2017-06-01

The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Deciphering the Environmental Impacts on Rice Quality for Different Rice Cultivated Areas.

Science.gov (United States)

Li, Xiukun; Wu, Lian; Geng, Xin; Xia, Xiuhong; Wang, Xuhong; Xu, Zhengjin; Xu, Quan

2018-01-19

Rice (Oryza sativa L.) is cultivated in a wide range of climatic conditions, and is one of mankind's major staple foods. The interaction of environmental factors with genotype effects major agronomic traits such as yield, quality, and resistance in rice. However, studies on the environmental factors affecting agronomic traits are often difficult to conduct because most environmental factors are dynamic and constantly changing. A series of recombinant inbred lines (RILs) derived from an indica/japonica cross were planted into four typical rice cultivated areas arranging from latitude N22° to N42°. The environmental data from the heading to mature (45 days) stages were recorded for each RIL in the four areas. We determined that light, temperature, and humidity significantly affected the milling quality and cooking quality overall the four areas. Within each area, these environmental factors mainly affected the head rice ratio, grain length, alkali consumption, and amylose and protein content. Moreover, the effect of these environmental factors dynamically changed from heading to mature stage. Compared to light and humidity, temperature was more stable and predictable, and night temperature showed a stronger correlation efficiency to cooking quality than day temperature, and the daily temperature range had contrary effects compared to day and night temperature on grain quality. The present study evaluated the critical phase during the grain filling stage by calculating the dynamic changes of correlation efficiency between the quality traits and climate parameters. Our findings suggest that the sowing date could be adjusted to improve rice quality so as to adjust for environmental changes.

Response Of Lowland Rice To Soil Compaction

International Nuclear Information System (INIS)

Idawati; Haryanto

2000-01-01

Soil compaction, as a new tillage practice for paddy soil, is to substitute pudding in order to reduce land preparation cost. To study response of lowland rice to soil compaction, a pot experiment has been conducted which took place in the greenhouse of P3TIR-BATAN. Soil for experiment was taken from pusakanegara. Two factors (degree of soil compaction and rice variety) were combined. Degree of compaction was split into 3 levels (DI = normal; D215% more compact than normal; 30 % more compact than normal), and rice variety into 2 levels (IR64 and Atomita IV). KH 2 32 PO 4 solution was injected into the soil surrounding rice clump to test the root activity at blooming stage of rice plant. Data resulted from this experiment is presented together with additional data from some other experiments of fertilization in the research s erie to study soil compaction. Some information's from experiment results are as following. Both rice varieties tested gave the same response to soil compaction. Root activity, according to data of 32 P absorbed by plant, was not harmed by soil compaction at the degree tested in the experiment. This prediction is supported by the growth by rice observed at generative growth stage, in pot experiment as well as in field experiment, which showed that soil compaction tested did not decrease rice yield but in opposite in tended to increase the yield. In practising soil compaction in land preparation, fertilizers should be applied by deep placement to have higher increasing is rice yield

Rice epigenomics and epigenetics: challenges and opportunities.

Science.gov (United States)

Chen, Xiangsong; Zhou, Dao-Xiu

2013-05-01

During recent years rice genome-wide epigenomic information such as DNA methylation and histone modifications, which are important for genome activity has been accumulated. The function of a number of rice epigenetic regulators has been studied, many of which are found to be involved in a diverse range of developmental and stress-responsive pathways. Analysis of epigenetic variations among different rice varieties indicates that epigenetic modification may lead to inheritable phenotypic variation. Characterizing phenotypic consequences of rice epigenomic variations and the underlining chromatin mechanism and identifying epialleles related to important agronomic traits may provide novel strategies to enhance agronomically favorable traits and grain productivity in rice. Copyright © 2013 Elsevier Ltd. All rights reserved.

Fungal diversity of rice straw for meju fermentation.

Science.gov (United States)

Kim, Dae-Ho; Kim, Seon-Hwa; Kwon, Soon-Wo; Lee, Jong-Kyu; Hong, Seung-Beom

2013-12-01

Rice straw is closely associated with meju fermentation and it is generally known that the rice straw provides meju with many kinds of microorganisms. In order to elucidate the origin of meju fungi, the fungal diversity of rice straw was examined. Rice straw was collected from 12 Jang factories where meju are produced, and were incubated under nine different conditions by altering the media (MEA, DRBC, and DG18), and temperature (15°C, 25°C, and 35°C). In total, 937 strains were isolated and identified as belonging to 39 genera and 103 species. Among these, Aspergillus, Cladosporium, Eurotium, Fusarium, and Penicillium were the dominant genera. Fusarium asiaticum (56.3%), Cladosporium cladosporioides (48.6%), Aspergillus tubingensis (37.5%), A. oryzae (31.9%), Eurotium repens (27.1%), and E. chevalieri (25.0%) were frequently isolated from the rice straw obtained from many factories. Twelve genera and 40 species of fungi that were isolated in the rice straw in this study were also isolated from meju. Specifically, A. oryzae, C. cladosporioides, E. chevalieri, E. repens, F. asiaticum, and Penicillium polonicum (11.8%), which are abundant species in meju, were also isolated frequently from rice straw. C. cladosporioides, F. asiaticum, and P. polonicum, which are abundant in the low temperature fermentation process of meju fermentation, were frequently isolated from rice straw incubated at 15°C and 25°C, whereas A. oryzae, E. repens, and E. chevalieri, which are abundant in the high temperature fermentation process of meju fermentation, were frequently isolated from rice straw incubated at 25°C and 35°C. This suggests that the mycobiota of rice straw has a large influence in the mycobiota of meju. The influence of fungi on the rice straw as feed and silage for livestock, and as plant pathogens for rice, are discussed as well.

Sulfate-reducing bacteria in rice field soil and on rice roots.

Science.gov (United States)

Wind, T; Stubner, S; Conrad, R

1999-05-01

Rice plants that were grown in flooded rice soil microcosms were examined for their ability to exhibit sulfate reducing activity. Washed excised rice roots showed sulfate reduction potential when incubated in anaerobic medium indicating the presence of sulfate-reducing bacteria. Rice plants, that were incubated in a double-chamber (phylloshpere and rhizosphere separated), showed potential sulfate reduction rates in the anoxic rhizosphere compartment. These rates decreased when oxygen was allowed to penetrate through the aerenchyma system of the plants into the anoxic root compartment, indicating that sulfate reducers on the roots were partially inhibited by oxygen or that sulfate was regenerated by oxidation of reduced S-compounds. The potential activity of sulfate reducers on rice roots was consistent with MPN enumerations showing that H2-utilizing sulfate-reducing bacteria were present in high numbers on the rhizoplane (4.1 x 10(7) g-1 root fresh weight) and in the adjacent rhizosperic soil (2.5 x 10(7) g-1 soil dry weight). Acetate-oxidizing sulfate reducers, on the other hand, showed highest numbers in the unplanted bulk soil (1.9 x 10(6) g-1 soil dry weight). Two sulfate reducing bacteria were isolated from the highest dilutions of the MPN series and were characterized physiologically and phylogenetically. Strain F1-7b which was isolated from the rhizoplane with H2 as electron donor was related to subgroup II of the family Desulfovibrionaceae. Strain EZ-2C2, isolated from the rhizoplane on acetate, grouped together with Desulforhabdus sp. and Syntrophobacter wolinii. Other strains of sulfate-reducing bacteria originated from bulk soil of rice soil microcosms and were isolated using different electron donors. From these isolates, strains R-AcA1, R-IbutA1, R-PimA1 and R-AcetonA170 were Gram-positive bacteria which were affiliated with the genus Desulfotomaculum. The other isolates were members of subgroup II of the Desulfovibrionaceae (R-SucA1 and R-LacA1), were

THE EFFECT OF RICE CULTIVARS ON METHANE EMISSION FROM IRRIGATED RICE FIELD

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P. Setyanto

2016-10-01

Full Text Available Rice plants have been reported to affect methane (CH4 emission from rice fields. The objectives of this study were to determine the effect of rice cultivars on CH4 emission from flooded rice and to develop crop management strategies with low emitting rice cultivars while sustaining high yield. The four rice cultivars studied were Memberamo, Cisadane, IR64, and Way Apoburu. The CH4 emissions were determined in the wet season of 2001/2002 (November-February using an automated closed chamber technique in an irrigated field condition. Farmyard manure at the rate of 5 t ha-1 was given to the plots to ensure carbon was not limited. Root weight, root length, biomass, and number of tillers were determined at 17, 36, and 57 days after transplanting (DAT. The results showed that the mean CH4 emission was highest in the plot planted with Cisadane (94.8 kg CH4 ha-1, and the lowest with IR64 (37.7 kg CH4 ha-1. The plots treated with emberamo and Way Apoburu resulted an intermediate CH4 emission at the average of 61.1 and 58.9 kg CH4 ha-1, respectively. There was no significant difference in yield between the cultivars tested. The yield of Memberamo, Cisadane, IR64, and Way Apoburu were 5.882, 5.764, 5.873 and 6.065 t ha-1, respectively. Statistical analysis showed that there were no significant differences in the root weight and root length among cultivars. However, Cisadane gave the highest dry matter weight (222 g hill-1 at 57 DAT compared to the other cultivars (175-190 g hill-1. Plant tillers did not show significant differences between the cultivars. Regression analysis showed that CH4 flux was significantly related with root weight, root length, aboveground biomass, and number of plant tillers. This finding shows that the use of selected cultivars, such as IR64, can potentially lower CH4 emission without scarifying yield.

Assessment of irradiated rice bran as iron source

International Nuclear Information System (INIS)

Wada, Heden Katsue

2002-01-01

Rice is the largest cereal crop in Brazil. To obtain the polish grain, its external peel is extracted after abrasive process. As a result, rice bran is obtained. It has low cost and high nutritional level, which has been include into malnourished children feeding. There is a considerable controversy related to the rice bran effect on the prevention and control of undernutrition and iron deficiency. The aim os this study was to assess the availability of in vitro iron of in natura and treated rice brans, after different levels of irradiation were applied. Both sorts of bran had their composition analyzed emphasizing the iron and phytate contents. The microbiological quality of the rice bran was also assessed. The pathogenic microorganisms were destroyed only in the in natura rice bran. As the irradiation level applied on the stabilized bran increased, its lipidic fraction reduced an the progressive destruction of the phytates occurred. The high iron content follow its availability in the rice bran, despite of the irradiation level applied, on the rice bran products and its dietetic preparations. (author)

Tier I Rice Model - Version 1.0 - Guidance for Estimating Pesticide Concentrations in Rice Paddies

Science.gov (United States)

Describes a Tier I Rice Model (Version 1.0) for estimating surface water exposure from the use of pesticides in rice paddies. The concentration calculated can be used for aquatic ecological risk and drinking water exposure assessments.

Designing Dietary Recommendations Using System Level Interactomics Analysis and Network-Based Inference

Directory of Open Access Journals (Sweden)

Tingting Zheng

2017-09-01

Full Text Available Background: A range of computational methods that rely on the analysis of genome-wide expression datasets have been developed and successfully used for drug repositioning. The success of these methods is based on the hypothesis that introducing a factor (in this case, a drug molecule that could reverse the disease gene expression signature will lead to a therapeutic effect. However, it has also been shown that globally reversing the disease expression signature is not a prerequisite for drug activity. On the other hand, the basic idea of significant anti-correlation in expression profiles could have great value for establishing diet-disease associations and could provide new insights into the role of dietary interventions in disease.Methods: We performed an integrated analysis of publicly available gene expression profiles for foods, diseases and drugs, by calculating pairwise similarity scores for diet and disease gene expression signatures and characterizing their topological features in protein-protein interaction networks.Results: We identified 485 diet-disease pairs where diet could positively influence disease development and 472 pairs where specific diets should be avoided in a disease state. Multiple evidence suggests that orange, whey and coconut fat could be beneficial for psoriasis, lung adenocarcinoma and macular degeneration, respectively. On the other hand, fructose-rich diet should be restricted in patients with chronic intermittent hypoxia and ovarian cancer. Since humans normally do not consume foods in isolation, we also applied different algorithms to predict synergism; as a result, 58 food pairs were predicted. Interestingly, the diets identified as anti-correlated with diseases showed a topological proximity to the disease proteins similar to that of the corresponding drugs.Conclusions: In conclusion, we provide a computational framework for establishing diet-disease associations and additional information on the role of

Global Rice Watch: Spatial-temporal dynamics, driving factors, and impacts of paddy rice agriculture in the world

Science.gov (United States)

Xiao, X.; Dong, J.; Zhang, G.; Xin, F.; Li, X.

2017-12-01

Paddy rice croplands account for more than 12% of the global cropland areas, and provide food to feed more than 50% of the world population. Spatial patterns and temporal dynamics of paddy rice croplands have changed remarkably in the past decades, driven by growing human population and their changing diet structure, land use (e.g., urbanization, industrialization), climate, markets, and technologies. In this presentation, we will provide a comprehensive review of our current knowledge on (1) the spatial patterns and temporal dynamics of paddy rice croplands from agricultural statistics data and remote sensing approaches; (2) major driving factors for the observed changes in paddy rice areas, including social, economic, climate, land use, markets, crop breeding technology, and farming technology; and (3) major impacts on atmospheric methane concentration, land surface temperature, water resources and use, and so on. We will highlight the results from a few case studies in China and monsoon Asia. We will also call for a global synthesis analysis of paddy rice agriculture, and invite researchers to join the effort to write and edit a book that provides comprehensive and updated knowledge on paddy rice agriculture.

[Quality of pastas supplemented with rice bran].

Science.gov (United States)

Sangronis, E; Rebolledo, M A

1997-06-01

The objective of this research was to investigate the potential of using rice bran as an ingredient in pastas spaghetti type. Two of the pastas were made with semolina from durum as raw material, supplemented with 10 and 20% rice bran. The other two were made with granular flour and the same percentage of rice bran. Proximate composition of raw material was analyzed. Pastas were elaborated in a local industry. Composition, proximal, color, texture, and sensorial quality of pastas were determined. Protein content (13.9-15.0%), ash (1.47-3.09%) and dietary fiber (6.71-8.45%) of pastas increased according to the percentage of rice bran added. The hardest pastas were those elaborated with semolina from durum wheat and with a 10% of substitution. Also, they were the most yellow. The sensory panel found differences in quality among the pastas evaluated. Pastas with 10% rice bran had the best quality. The results demonstrated that is possible to elaborate pastas with 20% as maximum of rice bran resulting products with high protein, ash and dietetic fiber content, but some undesirable characteristics were given by the rice bran as white spots, wrinkles and color changes.

Breeding of ozone resistant rice: Relevance, approaches and challenges

International Nuclear Information System (INIS)

Frei, Michael

2015-01-01

Tropospheric ozone concentrations have been rising across Asia, and will continue to rise during the 21st century. Ozone affects rice yields through reductions in spikelet number, spikelet fertility, and grain size. Moreover, ozone leads to changes in rice grain and straw quality. Therefore the breeding of ozone tolerant rice varieties is warranted. The mapping of quantitative trait loci (QTL) using bi-parental populations identified several tolerance QTL mitigating symptom formation, grain yield losses, or the degradation of straw quality. A genome-wide association study (GWAS) demonstrated substantial natural genotypic variation in ozone tolerance in rice, and revealed that the genetic architecture of ozone tolerance in rice is dominated by multiple medium and small effect loci. Transgenic approaches targeting tolerance mechanisms such as antioxidant capacity are also discussed. It is concluded that the breeding of ozone tolerant rice can contribute substantially to the global food security, and is feasible using different breeding approaches. - Highlights: • Tropospheric ozone affects millions of hectares of rice land. • Ozone affects rice yield and quality. • Breeding approaches to adapt rice to high ozone are discussed. • Challenges in the breeding of ozone resistant rice are discussed. - This review summarizes the effects of tropospheric ozone on rice and outlines approaches and challenges in the breeding of adapted varieties

Estimation of rice yield affected by drought and relation between rice yield and TVDI

Science.gov (United States)

Hongo, C.; Tamura, E.; Sigit, G.

2016-12-01

Impact of climate change is not only seen on food production but also on food security and sustainable development of society. Adaptation to climate change is a pressing issue throughout the world to reduce the risks along with the plans and strategies for food security and sustainable development. As a key adaptation to the climate change, agricultural insurance is expected to play an important role in stabilizing agricultural production through compensating the losses caused by the climate change. As the adaptation, the Government of Indonesia has launched agricultural insurance program for damage of rice by drought, flood and pest and disease. The Government started a pilot project in 2013 and this year the pilot project has been extended to 22 provinces. Having the above as background, we conducted research on development of new damage assessment method for rice using remote sensing data which could be used for evaluation of damage ratio caused by drought in West Java, Indonesia. For assessment of the damage ratio, estimation of rice yield is a key. As the result of our study, rice yield affected by drought in dry season could be estimated at level of 1 % significance using SPOT 7 data taken in 2015, and the validation result was 0.8t/ha. Then, the decrease ratio in rice yield about each individual paddy field was calculated using data of the estimated result and the average yield of the past 10 years. In addition, TVDI (Temperature Vegetation Dryness Index) which was calculated from Landsat8 data in heading season indicated the dryness in low yield area. The result suggests that rice yield was affected by irrigation water shortage around heading season as a result of the decreased precipitation by El Nino. Through our study, it becomes clear that the utilization of remote sensing data can be promising for assessment of the damage ratio of rice production precisely, quickly and quantitatively, and also it can be incorporated into the insurance procedures.

Consumer preference mapping for rice product concepts

NARCIS (Netherlands)

Suwannaporn, P.; Linnemann, A.R.; Chaveesuk, R.

2008-01-01

Purpose - Rice consumption per capita in many Asian countries is decreasing constantly, but American and European citizens are eating more rice nowadays. A preference study among consumers was carried out with the aim of determining new rice product characteristics in order to support export of Thai

Rice straw as a feedstock for biofuels: Availability, recalcitrance, and chemical properties: Rice straw as a feedstock for biofuels

Energy Technology Data Exchange (ETDEWEB)

Satlewal, Alok [Univ. of Tennessee, Knoxville, TN (United States). Dept. of Chemical and Biomolecular Engineering; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Joint Inst. for Biological Sciences, Biosciences Division; Indian Oil Corporation Ltd, Faridabad (India), Dept. of Bioenergy, DBT-IOC Centre for Advanced Bioenergy Research, Research and Development Centre; Agrawal, Ruchi [Indian Oil Corporation Ltd, Faridabad (India), Dept. of Bioenergy, DBT-IOC Centre for Advanced Bioenergy Research, Research and Development Centre; Bhagia, Samarthya [Univ. of Tennessee, Knoxville, TN (United States). Dept. of Chemical and Biomolecular Engineering; Das, Parthapratim [Univ. of Tennessee, Knoxville, TN (United States). Dept. of Chemical and Biomolecular Engineering; Ragauskas, Arthur J. [Univ. of Tennessee, Knoxville, TN (United States). Dept. of Chemical and Biomolecular Engineering

2017-10-17

The surplus availability of rice straw, its limited usage and environment pollution caused by inefficient burning has fostered research for its valorization to biofuels. This review elucidates the current status of rice straw potential around the globe along with recent advances in revealing the critical factors responsible for its recalcitrance and chemical properties. The role and accumulation of high silica content in rice straw has been elucidated with its impact on enzymatic hydrolysis in a biorefinery environment. The correlation of different pretreatment approaches in modifying the physiochemical properties of rice straw and improving the enzymatic accessibility has also been discussed. This study highlights new challenges, resolutions and opportunities for rice straw based biorefineries.

A novel method for transmitting southern rice black-streaked dwarf virus to rice without insect vector.

Science.gov (United States)

Yu, Lu; Shi, Jing; Cao, Lianlian; Zhang, Guoping; Wang, Wenli; Hu, Deyu; Song, Baoan

2017-08-15

Southern rice black-streaked dwarf virus (SRBSDV) has spread from the south of China to the north of Vietnam in the past few years, and has severely influenced rice production. However, previous study of traditional SRBSDV transmission method by the natural virus vector, the white-backed planthopper (WBPH, Sogatella furcifera), in the laboratory, researchers are frequently confronted with lack of enough viral samples due to the limited life span of infected vectors and rice plants and low virus acquisition and inoculation efficiency by the vector. Meanwhile, traditional mechanical inoculation of virus only apply to dicotyledon because of the higher content of lignin in the leaves of the monocot. Therefore, establishing an efficient and persistent-transmitting model, with a shorter virus transmission time and a higher virus transmission efficiency, for screening novel anti-SRBSDV drugs is an urgent need. In this study, we firstly reported a novel method for transmitting SRBSDV in rice using the bud-cutting method. The transmission efficiency of SRBSDV in rice was investigated via the polymerase chain reaction (PCR) method and the replication of SRBSDV in rice was also investigated via the proteomics analysis. Rice infected with SRBSDV using the bud-cutting method exhibited similar symptoms to those infected by the WBPH, and the transmission efficiency (>80.00%), which was determined using the PCR method, and the virus transmission time (30 min) were superior to those achieved that transmitted by the WBPH. Proteomics analysis confirmed that SRBSDV P1, P2, P3, P4, P5-1, P5-2, P6, P8, P9-1, P9-2, and P10 proteins were present in infected rice seedlings infected via the bud-cutting method. The results showed that SRBSDV could be successfully transmitted via the bud-cutting method and plants infected SRBSDV exhibited the symptoms were similar to those transmitted by the WBPH. Therefore, the use of the bud-cutting method to generate a cheap, efficient, reliable supply of

Improvement of rice starch by gamma irradiation

International Nuclear Information System (INIS)

Duan Zhiying; Wu Dianxing; Shen Shengquan; Han Juanying; Xia Yingwu

2003-01-01

Three types of rice cultivars, Indica, Japonica and hybrid rice, with similar intermediate apparent amylose content (AAC) as well as early Indica rice cultivars with different amounts of AAC were selected for studying the effects of gamma irradiation on starch viscosity, physico-chemical properties and starch granule structure. Four major parameters of RVA profile, peak viscosity (PKV), hot paste viscosity (HPV), cool paste viscosity (CPV), setback viscosity (SBV) and consistence viscosity (CSV) were considerably decreased with increasing dose levels. Gamma irradiation reduced the amylose contents in the cultivars with low AAC, intermediate AAC, and glutinous rice, but had no effects on the high AAC cultivar. No visible changes in alkali spreading value (ASV) were detected after irradiation, but the peak time (PKT) were reduced with the dose level. Gel consistency (GC) were significantly increased in the tested cultivars, especially in the high AAC Indica rice, suggesting that it is promising to use gamma irradiation to improve eating and cooking quality of rice

Biophysical and Mechanical properties of rice varieties: attributes to ...

African Journals Online (AJOL)

It requires about 25N for the rice grain (IITA306) to fail at 0.7mm at horizontal and 150N to crack the rice grain in vertical position at 21.0mm, it takes 60N for the rice grain (MAS) to fail at 1.4mm and 150N to crack the rice grain at 22.5mm as well as 58N for the rice grain (R18) to fail at 1.2mm and 125N to crack the rice grain ...

Cell fusion as a tool for rice improvement

Energy Technology Data Exchange (ETDEWEB)

Hayashi, Y; Kyozuka, J; Terada, R; Nishibayashi, S; Shimamoto, K [Plantech Research Institute, Kamoshida, Midori-ku, Yokohama (Japan)

1990-01-01

Full text: Cell fusion offers a unique opportunity to hybridize sexually incompatible species and to mix cytoplasmic genomes in higher plants. Recent progress in plant regeneration from rice protoplasts facilitates an evaluation of the cell fusion method for rice improvement. By using electrofusion of protoplasts, we obtained hybrid/cybrid plants of the following combinations: Hybrids of rice x barnyard grass (E. oryzicola); Hybrids of rice x wild Oryza species; Cybrids of rice with transferred cms cytoplasm. For the latter, protoplasts irradiated with 70 krad x-rays were used. (author)

Golden Rice is an effective source of vitamin A.

Science.gov (United States)

Tang, Guangwen; Qin, Jian; Dolnikowski, Gregory G; Russell, Robert M; Grusak, Michael A

2009-06-01

Genetically engineered "Golden Rice" contains up to 35 microg beta-carotene per gram of rice. It is important to determine the vitamin A equivalency of Golden Rice beta-carotene to project the potential effect of this biofortified grain in rice-consuming populations that commonly exhibit low vitamin A status. The objective was to determine the vitamin A value of intrinsically labeled dietary Golden Rice in humans. Golden Rice plants were grown hydroponically with heavy water (deuterium oxide) to generate deuterium-labeled [2H]beta-carotene in the rice grains. Golden Rice servings of 65-98 g (130-200 g cooked rice) containing 0.99-1.53 mg beta-carotene were fed to 5 healthy adult volunteers (3 women and 2 men) with 10 g butter. A reference dose of [13C10]retinyl acetate (0.4-1.0 mg) in oil was given to each volunteer 1 wk before ingestion of the Golden Rice dose. Blood samples were collected over 36 d. Our results showed that the mean (+/-SD) area under the curve for the total serum response to [2H]retinol was 39.9 +/- 20.7 microg x d after the Golden Rice dose. Compared with that of the [13C10]retinyl acetate reference dose (84.7 +/- 34.6 microg x d), Golden Rice beta-carotene provided 0.24-0.94 mg retinol. Thus, the conversion factor of Golden Rice beta-carotene to retinol is 3.8 +/- 1.7 to 1 with a range of 1.9-6.4 to 1 by weight, or 2.0 +/- 0.9 to 1 with a range of 1.0-3.4 to 1 by moles. Beta-carotene derived from Golden Rice is effectively converted to vitamin A in humans. This trial was registered at clinicaltrials.gov as NCT00680355.

Arsenic in rice: A cause for concern

DEFF Research Database (Denmark)

Hojsak, Iva; Braegger, Christian; Bronsky, Jiri

2015-01-01

Inorganic arsenic intake is likely to affect long-term health. High concentrations are found in some rice-based foods and drinks widely used in infants and young children. In order to reduce exposure we recommend avoidance of rice drinks for infants and young children. For all rice products, stri...

Compressive Load Resistance Characteristics of Rice Grain

OpenAIRE

Sumpun Chaitep; Chaiy R. Metha Pathawee; Pipatpong Watanawanyoo

2008-01-01

Investigation was made to observe the compressive load property of rice gain both rough rice and brown grain. Six rice varieties (indica and japonica) were examined with the moisture content at 10-12%. A compressive load with reference to a principal axis normal to the thickness of the grain were conducted at selected inclined angles of 0°, 15°, 30°, 45°, 60° and 70°. The result showed the compressive load resistance of rice grain based on its characteristic of yield s...

A rice husk gasifier for paddy drying

International Nuclear Information System (INIS)

Mirani, A.A.; Kalwar, S.A.; Ahmad, M.

2013-01-01

Due to energy crisis and constant increase in the price of fossil fuels, the world's trend changes to renewable sources of energy like solar, wind and biomass gasification. Substantial biomass potential is available in Pakistan in the form of agriculture or forest residue (rice straw, rice husk, cotton stalks, corn cobs, wood chips, wood saw, etc.). These can be best utilised for the production of producer gas or synthetic gas that can be used for drying of agricultural crops. The drying process is an important activity of post harvest processing for long-term storage. Rice husk is nowadays commonly used for biomass gasification and its heat content value is about 15MJ/kg. It constitutes about 30 percent of rice production. A rice husk gasifier was developed and evaluated on paddy drying at Japan International Cooperation Agency (JICA), Tsukuba International Center (TBIC), Japan. Rice husk gasifier has following major components; husk feeding system, ash chamber, burner, centrifugal fan, drying chamber, gasifier reactor, air duct and an electric motor of 0.37kW. The average drying plenum air temperature was recorded as 45 degree C during the drying process. The paddy 'IR 28' from initial moisture content of 24% was dried up to 14% moisture content for about 3.33h consuming 3kg/h of rice husk. The efficiency was found to be 58%. The rice husk gasifier can also be used for drying the fruits and vegetables, provided that heat exchanger should be attached with it. The overall performance of rice husk gasifier was satisfactory and will be beneficial for small scale farmers, food processors and millers as well. (author)

Characterization of Mediator Complex and its Associated Proteins from Rice.

Science.gov (United States)

Samanta, Subhasis; Thakur, Jitendra Kumar

2017-01-01

The Mediator complex is a multi-protein complex that acts as a molecular bridge conveying transcriptional messages from the cis element-bound transcription factor to the RNA Polymerase II machinery. It is found in all eukaryotes including members of the plant kingdom. Increasing number of reports from plants regarding different Mediator subunits involved in a multitude of processes spanning from plant development to environmental interactions have firmly established it as a central hub of plant regulatory networks. Routine isolation of Mediator complex in a particular species is a necessity because of many reasons. First, composition of the Mediator complex varies from species to species. Second, the composition of the Mediator complex in a particular species is not static under all developmental and environmental conditions. Besides this, at times, Mediator complex is used in in vitro transcription systems. Rice, a staple food crop of the world, is used as a model monocot crop. Realizing the need of a reliable protocol for the isolation of Mediator complex from plants, we describe here the isolation of Mediator complex from rice.

Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice

Directory of Open Access Journals (Sweden)

Lu Tingting

2012-12-01

Full Text Available Abstract Background Cis-natural antisense transcripts (cis-NATs are RNAs transcribed from the antisense strand of a gene locus, and are complementary to the RNA transcribed from the sense strand. Common techniques including microarray approach and analysis of transcriptome databases are the major ways to globally identify cis-NATs in various eukaryotic organisms. Genome-wide in silico analysis has identified a large number of cis-NATs that may generate endogenous short interfering RNAs (nat-siRNAs, which participate in important biogenesis mechanisms for transcriptional and post-transcriptional regulation in rice. However, the transcriptomes are yet to be deeply sequenced to comprehensively investigate cis-NATs. Results We applied high-throughput strand-specific complementary DNA sequencing technology (ssRNA-seq to deeply sequence mRNA for assessing sense and antisense transcripts that were derived under salt, drought and cold stresses, and normal conditions, in the model plant rice (Oryza sativa. Combined with RAP-DB genome annotation (the Rice Annotation Project Database build-5 data set, 76,013 transcripts corresponding to 45,844 unique gene loci were assembled, in which 4873 gene loci were newly identified. Of 3819 putative rice cis-NATs, 2292 were detected as expressed and giving rise to small RNAs from their overlapping regions through integrated analysis of ssRNA-seq data and small RNA data. Among them, 503 cis-NATs seemed to be associated with specific conditions. The deep sequence data from isolated epidermal cells of rice seedlings further showed that 54.0% of cis-NATs were expressed simultaneously in a population of homogenous cells. Nearly 9.7% of rice transcripts were involved in one-to-one or many-to-many cis-NATs formation. Furthermore, only 17.4-34.7% of 223 many-to-many cis-NAT groups were all expressed and generated nat-siRNAs, indicating that only some cis-NAT groups may be involved in complex regulatory networks. Conclusions

Combination of mass spectrometry-based targeted lipidomics and supervised machine learning algorithms in detecting adulterated admixtures of white rice.

Science.gov (United States)

Lim, Dong Kyu; Long, Nguyen Phuoc; Mo, Changyeun; Dong, Ziyuan; Cui, Lingmei; Kim, Giyoung; Kwon, Sung Won

2017-10-01

The mixing of extraneous ingredients with original products is a common adulteration practice in food and herbal medicines. In particular, authenticity of white rice and its corresponding blended products has become a key issue in food industry. Accordingly, our current study aimed to develop and evaluate a novel discrimination method by combining targeted lipidomics with powerful supervised learning methods, and eventually introduce a platform to verify the authenticity of white rice. A total of 30 cultivars were collected, and 330 representative samples of white rice from Korea and China as well as seven mixing ratios were examined. Random forests (RF), support vector machines (SVM) with a radial basis function kernel, C5.0, model averaged neural network, and k-nearest neighbor classifiers were used for the classification. We achieved desired results, and the classifiers effectively differentiated white rice from Korea to blended samples with high prediction accuracy for the contamination ratio as low as five percent. In addition, RF and SVM classifiers were generally superior to and more robust than the other techniques. Our approach demonstrated that the relative differences in lysoGPLs can be successfully utilized to detect the adulterated mixing of white rice originating from different countries. In conclusion, the present study introduces a novel and high-throughput platform that can be applied to authenticate adulterated admixtures from original white rice samples. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comprehensive Gene Expression Analysis of Rice Aleurone Cells: Probing the Existence of an Alternative Gibberellin Receptor1

Science.gov (United States)

Yano, Kenji; Aya, Koichiro; Hirano, Ko; Ordonio, Reynante Lacsamana; Ueguchi-Tanaka, Miyako; Matsuoka, Makoto

2015-01-01

Current gibberellin (GA) research indicates that GA must be perceived in plant nuclei by its cognate receptor, GIBBERELLIN INSENSITIVE DWARF1 (GID1). Recognition of GA by GID1 relieves the repression mediated by the DELLA protein, a model known as the GID1-DELLA GA perception system. There have been reports of potential GA-binding proteins in the plasma membrane that perceive GA and induce α-amylase expression in cereal aleurone cells, which is mechanistically different from the GID1-DELLA system. Therefore, we examined the expression of the rice (Oryza sativa) α-amylase genes in rice mutants impaired in the GA receptor (gid1) and the DELLA repressor (slender rice1; slr1) and confirmed their lack of response to GA in gid1 mutants and constitutive expression in slr1 mutants. We also examined the expression of GA-regulated genes by genome-wide microarray and quantitative reverse transcription-polymerase chain reaction analyses and confirmed that all GA-regulated genes are modulated by the GID1-DELLA system. Furthermore, we studied the regulatory network involved in GA signaling by using a set of mutants defective in genes involved in GA perception and gene expression, namely gid1, slr1, gid2 (a GA-related F-box protein mutant), and gamyb (a GA-related trans-acting factor mutant). Almost all GA up-regulated genes were regulated by the four named GA-signaling components. On the other hand, GA down-regulated genes showed different expression patterns with respect to GID2 and GAMYB (e.g. a considerable number of genes are not controlled by GAMYB or GID2 and GAMYB). Based on these observations, we present a comprehensive discussion of the intricate network of GA-regulated genes in rice aleurone cells. PMID:25511432

Southern rice black-streaked dwarf virus: a white-backed planthopper transmitted fijivirus threadening rice production in Asia

Directory of Open Access Journals (Sweden)

Guohui eZhou

2013-09-01

Full Text Available Southern rice black-streaked dwarf virus (SRBSDV, a nonenveloped icosahedral virus with a genome of 10 double-stranded RNA segments, is a novel species in the genus Fijivirus (family Reoviridae first recognized in 2008. Rice plants infected with this virus exhibit symptoms similar to those caused by Rice black-streaked dwarf virus. Since 2009, the virus has rapidly spread and caused serious rice losses in East and Southeast Asia. Significant progress has been made in recent years in understanding this disease, especially about the functions of the viral genes, rice–virus–insect interactions, and epidemiology and control measures. The virus can be efficiently transmitted by the white-backed planthopper (WBPH, Sogatella furcifera in a persistent circulative propagative manner but cannot be transmitted by the brown planthopper (Nilaparvata lugens and small brown planthopper (Laodelphax striatellus. Rice, maize, Chinese sorghum (Coix lacryma-jobi and other grass weeds can be infected via WBPH. However, only rice plays a major role in the virus infection cycle because of the vector's preference. In Southeast Asia, WBPH is a long-distance migratory rice pest. The disease cycle can be described as follows: SRBSDV and its WBPH vector overwinter in warm tropical or sub-tropical areas; viruliferous WBPH adults carry the virus from south to north via long-distance migration in early spring, transmit the virus to rice seedlings in the newly colonized areas, and lay eggs on the infected seedlings; the next generation of WBPHs propagate on infected seedlings, become viruliferous, disperse, and cause new disease outbreaks. Several molecular and serological methods have been developed to detect SRBSDV in plant tissues and individual insects. Control measures based on protection from WBPH, including seedbed coverage, chemical seed treatments, and chemical spraying of seedlings, have proven effective in China.

Estimation of rice grain yield from dual-polarization Radarsat-2 SAR data by integrating a rice canopy scattering model and a genetic algorithm

Science.gov (United States)

Zhang, Yuan; Yang, Bin; Liu, Xiaohui; Wang, Cuizhen

2017-05-01

Fast and accurate estimation of rice yield plays a role in forecasting rice productivity for ensuring regional or national food security. Microwave synthetic aperture radar (SAR) data has been proved to have a great potential for rice monitoring and parameters retrieval. In this study, a rice canopy scattering model (RCSM) was revised and then was applied to simulate the backscatter of rice canopy. The combination of RCSM and genetic algorithm (GA) was proposed for retrieving two important rice parameters relating to grain yield, ear length and ear number density, from a C-band, dual-polarization (HH and HV) Radarsat-2 SAR data. The stability of retrieved results of GA inversion was also evaluated by changing various parameter configurations. Results show that RCSM can effectively simulate backscattering coefficients of rice canopy at HH and HV mode with an error of <1 dB. Reasonable selection of GA's parameters is essential for stability and efficiency of rice parameter retrieval. Two rice parameters are retrieved by the proposed RCSM-GA technology with better accuracy. The rice ear length are estimated with error of <1.5 cm, and ear number density with error of <23 #/m2. Rice grain yields are effectively estimated and mapped by the retrieved ear length and number density via a simple yield regression equation. This study further illustrates the capability of C-band Radarsat-2 SAR data on retrieval of rice ear parameters and the practicability of radar remote sensing technology for operational yield estimation.

Current Insights into Research on Rice stripe virus

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Won Kyong Cho

2013-09-01

Full Text Available Rice stripe virus (RSV is one of the most destructive viruses of rice, and greatly reduces rice production in China, Japan, and Korea, where mostly japonica cultivars of rice are grown. RSV is transmitted by the small brown plant-hopper (SBPH in a persistent and circulative-propagative manner. Several methods have been developed for detection of RSV, which is composed of four single-stranded RNAs that encode seven proteins. Genome sequence data and comparative phylogenetic analysis have been used to identify the origin and diversity of RSV isolates. Several rice varieties resistant to RSV have been selected and QTL analysis and fine mapping have been intensively performed to map RSV resistance loci or genes. RSV genes have been used to generate several genetically modified transgenic rice plants with RSV resistance. Recently, genome-wide transcriptome analyses and deep sequencing have been used to identify mRNAs and small RNAs involved in RSV infection; several rice host factors that interact with RSV proteins have also been identified. In this article, we review the current statues of RSV research and propose integrated approaches for the study of interactions among RSV, rice, and the SBPH.

Migration of rice planthoppers and their vectored re-emerging and novel rice viruses in East Asia.

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Otuka, Akira

2013-10-28

This review examines recent studies of the migration of three rice planthoppers, Laodelphax striatellus, Sogatella furcifera, and Nilaparvata lugens, in East Asia. Laodelphax striatellus has recently broken out in Jiangsu province, eastern China. The population density in the province started to increase in the early 2000s and peaked in 2004. In 2005, Rice stripe virus (RSV) viruliferous rate of L. striatellus peaked at 31.3%. Since then, rice stripe disease spread severely across the whole province. Due to the migration of the RSV vectors, the rice stripe disease spread to neighboring countries Japan and Korea. An overseas migration of L. striatellus that occurred in 2008 was analyzed, when a slow-moving cold vortex, a type of low pressure system, reached western Japan from Jiangsu, carrying the insects into Japan. Subsequently the rice stripe diseases struck these areas in Japan severely. In Korea, similar situations occurred in 2009, 2011, and 2012. Their migration sources were also estimated to be in Jiangsu by backward trajectory analysis. Rice black-streaked dwarf virus, whose vector is L. striatellus, has recently re-emerged in eastern China, and the evidence for overseas migrations of the virus, just like the RSV's migrations, has been given. A method of predicting the overseas migration of L. striatellus has been developed by Japanese, Chinese, and Korean institutes. An evaluation of the prediction showed that this method properly predicted migration events that occurred in East Asia from 2008 to 2011. Southern rice black-streaked dwarf virus (SRBSDV) was first found in Guangdong province. Its vector is S. furcifera. An outbreak of SRBSDV occurred in southern China in 2009 and spread to Vietnam the same year. This disease and virus were also found in Japan in 2010. The epidemic triggered many migration studies to investigate concrete spring-summer migration routes in China, and the addition of migration sources for early arrivals in Guangdong and Guangxi

International Conference on Sustainable Rice Production - Policy, Technology and Extension Celebration Activity for International Year of Rice and World Food Day 2004

Institute of Scientific and Technical Information of China (English)

无

2004-01-01

Rice is the staple food of more than half of the world's population. The production, processing and management of paddy rice have provided the basic conditions for the living of mankind. The production of rice has not only created employment opportunities for one billion agricultural population in developing nations, but has also contributed to the development of the splendid culture associated with rice production. Hence, effective and productive rice systems play an influential role in development of economy and improvement of quality of life. In view of this, on 16 December,2002, the UN General Assembly declared the year of 2004 the International Year of Rice.

Rice Genome Research: Current Status and Future Perspectives

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Bin Han

2008-11-01

Full Text Available Rice ( L. is the leading genomics system among the crop plants. The sequence of the rice genome, the first cereal plant genome, was published in 2005. This review summarizes progress made in rice genome annotations, comparative genomics, and functional genomics researches. It also maps out the status of rice genomics globally and provides a vision of future research directions and resource building.

Making connections for life: an in vivo map of the yeast interactome.

Science.gov (United States)

Kast, Juergen

2008-10-01

Proteins are the true workhorses of any cell. To carry out specific tasks, they frequently bind other molecules in their surroundings. Due to their structural complexity and flexibility, the most diverse array of interactions is seen with other proteins. The different geometries and affinities available for such interactions typically bestow specific functions on proteins. Having available a map of protein-protein interactions is therefore of enormous importance for any researcher interested in gaining insight into biological systems at the level of cells and organisms. In a recent report, a novel approach has been employed that relies on the spontaneous folding of complementary enzyme fragments fused to two different proteins to test whether these interact in their actual cellular context [Tarassov et al., Science 320, 1465-1470 (2008)]. Genome-wide application of this protein-fragment complementation assay has resulted in the first map of the in vivo interactome of Saccharomyces cerevisiae. The current data show striking similarities but also significant differences to those obtained using other large-scale approaches for the same task. This warrants a general discussion of the current state of affairs of protein-protein interaction studies and foreseeable future trends, highlighting their significance for a variety of applications and their potential to revolutionize our understanding of the architecture and dynamics of biological systems.

System level mechanisms of adaptation, learning, memory formation and evolvability: the role of chaperone and other networks.

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Gyurko, David M; Soti, Csaba; Stetak, Attila; Csermely, Peter

2014-05-01

During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here, we describe first the protein structure networks of molecular chaperones, then characterize chaperone containing sub-networks of interactomes called as chaperone-networks or chaperomes. We review the role of molecular chaperones in short-term adaptation of cellular networks in response to stress, and in long-term adaptation discussing their putative functions in the regulation of evolvability. We provide a general overview of possible network mechanisms of adaptation, learning and memory formation. We propose that changes of network rigidity play a key role in learning and memory formation processes. Flexible network topology provides ' learning-competent' state. Here, networks may have much less modular boundaries than locally rigid, highly modular networks, where the learnt information has already been consolidated in a memory formation process. Since modular boundaries are efficient filters of information, in the 'learning-competent' state information filtering may be much smaller, than after memory formation. This mechanism restricts high information transfer to the 'learning competent' state. After memory formation, modular boundary-induced segregation and information filtering protect the stored information. The flexible networks of young organisms are generally in a 'learning competent' state. On the contrary, locally rigid networks of old organisms have lost their 'learning competent' state, but store and protect their learnt information efficiently. We anticipate that the above mechanism may operate at the level of both protein-protein interaction and neuronal networks.

Mapping the Interactome of a Major Mammalian Endoplasmic Reticulum Heat Shock Protein 90.

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Feng Hong

Full Text Available Up to 10% of cytosolic proteins are dependent on the mammalian heat shock protein 90 (HSP90 for folding. However, the interactors of its endoplasmic reticulum (ER paralogue (gp96, Grp94 and HSP90b1 has not been systematically identified. By combining genetic and biochemical approaches, we have comprehensively mapped the interactome of gp96 in macrophages and B cells. A total of 511 proteins were reduced in gp96 knockdown cells, compared to levels observed in wild type cells. By immunoprecipitation, we found that 201 proteins associated with gp96. Gene Ontology analysis indicated that these proteins are involved in metabolism, transport, translation, protein folding, development, localization, response to stress and cellular component biogenesis. While known gp96 clients such as integrins, Toll-like receptors (TLRs and Wnt co-receptor LRP6, were confirmed, cell surface HSP receptor CD91, TLR4 pathway protein CD180, WDR1, GANAB and CAPZB were identified as potentially novel substrates of gp96. Taken together, our study establishes gp96 as a critical chaperone to integrate innate immunity, Wnt signaling and organ development.

Impact of Day Intervals on Sequential Infestations of the Rice Leaffolder (Guenée (Lepidoptera: Pyralidae and the White-Backed Rice Planthopper (Horváth on Rice Grain Damage

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Li-Ben Jiang

2014-01-01

Full Text Available The present study illustrates that different day intervals (DIs between the sequential infestations of two pest species, the rice leaffolder (RLF Cnaphalocrocis medinalis Guenée (Lepidoptera: Pyralidae and the white-backed rice planthopper (WBPH Sogatella furcifera Horváth (Hemiptera: Delphacidae, have a significant impact on the rice yield loss rate (YLR and on the carbohydrate contents of rice plants. For WBPH release after RLF release (WRARR, the YLR decreased with the increasing DIs, and the YLR at the 24 DI was significantly lower compared to that at the 6 and 12 DIs and had a minimum value for a simultaneous infestation of the two pest species (SITS. In contrast, for RLF release after WBPH release (RRAWR, the YLR at the 24 DI had a maximum value and was significantly higher compared to that at the 6 and 12 DIs and the SITS. These findings indicate that damaged rice plants gradually recover, with an increase in the DI for WRARR. The above results were demonstrated by biochemical tests. Therefore, the sequential infestation of the two pest species and their DIs should be considered for integrated pest management (IPM and control strategies for rice pests.

Rice Water: A Traditional Ingredient with Anti-Aging Efficacy

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Joana Marto

2018-04-01

Full Text Available The skin healing benefits of rice have been known for centuries. Rice (Oryza sativa water is a food processing waste that can potentially be incorporated into cosmetic formulations. However, no scientific evidence supports their role in skincare products. The aim of this project is to design and develop a topical gel formulation containing rice water and to evaluate its biological properties, namely, the anti-aging and antioxidant rice water properties. Rice water was evaluated in terms of physico-chemical composition and in terms of in vitro biological antioxidant activity and elastase inhibitory effect. Rice water was incorporated into a hydrogel and the developed formulation was subjected to pharmacotechnical tests such as pH and viscosity. Biological and sensory effects were evaluated on a panel of 12 volunteers for 28 days. The safety evaluation study was performed on rice water gel, using the Human Repeat Insult Patch test protocol. Rice water presented in vitro biological antioxidant activity and elastase inhibitory effect. The gel formulation containing 96% rice water was biocompatible with the human skin and presented suitable cosmetic properties. Rice water should be thus considered as an anti-aging ingredient to be used as raw material for skincare applications.

Bioactive compounds and antioxidative activity of colored rice bran

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Yu-Ping Huang

2016-07-01

Full Text Available The profiles of bioactive compounds (including phenolics and flavonoids in free and bound fractions, anthocyanins, proanthocyanidins, vitamin E, and γ-oryzanol of outer and inner rice bran from six colored rice samples collected from local markets were investigated. Proanthocyanidins could only be detected in red rice bran but not in black rice bran. The free fraction of the extracts dominated the total phenolics (72–92% and the total flavonoids (72–96% of colored rice bran. Most of the phenolic acids (83–97% in colored rice bran were present in the bound form. Protocatechualdehyde was identified for the first time in the bound fraction of red rice bran by high performance liquid chromatography-photodiode array/electrospray ionization tandem mass spectrometry. The antioxidative activities of the free fraction of the colored rice bran were attributed to the proanthocyanidins in red colored rice and anthocyanins in black rice, while that of the bound fraction was mainly due to the phenolic acids.

Identification of climate-resilient integrated nutrient management practices for rice-rice cropping system--an empirical approach to uphold food security.

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Subash, N; Gangwar, B; Singh, Rajbir; Sikka, A K

2015-01-01

Yield datasets of long-term experiments on integrated nutrient management in rice-rice cropping systems were used to investigate the relationship of variability in rainfall, temperature, and integrated nutrient management (INM) practices in rice-rice cropping system in three different agroecological regions of India. Twelve treatments with different combinations of inorganic (chemical fertilizer) and organic (farmyard manure, green manure, and paddy straw) were compared with farmer's conventional practice. The intraseasonal variations in rice yields are largely driven by rainfall during kharif rice and by temperature during rabi rice. Half of the standard deviation from the average monthly as well as seasonal rainfall during kharif rice and 1 °C increase or decrease from the average maximum and minimum temperature during rabi rice has been taken as the classification of yield groups. The trends in the date of effective onset of monsoon indicate a 36-day delay during the 30-year period at Rajendranagar, which is statistically significant at 95 % confidence level. The mean annual maximum temperature shows an increasing trend in all the study sites. The length of monsoon also showed a shrinking trend in the rate of 40 days during the 30-year study period at Rajendranagar representing a semiarid region. At Bhubaneshwar, the application of 50 % recommended NPK through chemical fertilizers and 50 % N through green manure resulted in an overall average higher increase of 5.1 % in system productivity under both excess and deficit rainfall years and also during the years having seasonal mean maximum temperature ≥35 °C. However, at Jorhat, the application of 50 % recommended NPK through chemical fertilizers and 50 % N through straw resulted in an overall average higher increase of 7.4 % in system productivity, while at Rajendranagar, the application of 75 % NPK through chemical fertilizers and 25 % N through green manusre resulted in an overall average higher increase of

Identification of climate-resilient integrated nutrient management practices for rice-rice cropping system—an empirical approach to uphold food security

Science.gov (United States)

Subash, N.; Gangwar, B.; Singh, Rajbir; Sikka, A. K.

2015-01-01

Yield datasets of long-term experiments on integrated nutrient management in rice-rice cropping systems were used to investigate the relationship of variability in rainfall, temperature, and integrated nutrient management (INM) practices in rice-rice cropping system in three different agroecological regions of India. Twelve treatments with different combinations of inorganic (chemical fertilizer) and organic (farmyard manure, green manure, and paddy straw) were compared with farmer's conventional practice. The intraseasonal variations in rice yields are largely driven by rainfall during kharif rice and by temperature during rabi rice. Half of the standard deviation from the average monthly as well as seasonal rainfall during kharif rice and 1 °C increase or decrease from the average maximum and minimum temperature during rabi rice has been taken as the classification of yield groups. The trends in the date of effective onset of monsoon indicate a 36-day delay during the 30-year period at Rajendranagar, which is statistically significant at 95 % confidence level. The mean annual maximum temperature shows an increasing trend in all the study sites. The length of monsoon also showed a shrinking trend in the rate of 40 days during the 30-year study period at Rajendranagar representing a semiarid region. At Bhubaneshwar, the application of 50 % recommended NPK through chemical fertilizers and 50 % N through green manure resulted in an overall average higher increase of 5.1 % in system productivity under both excess and deficit rainfall years and also during the years having seasonal mean maximum temperature ≥35 °C. However, at Jorhat, the application of 50 % recommended NPK through chemical fertilizers and 50 % N through straw resulted in an overall average higher increase of 7.4 % in system productivity, while at Rajendranagar, the application of 75 % NPK through chemical fertilizers and 25 % N through green manusre resulted in an overall average higher increase of

From rice bag to table: Fate of phenolic chemical compositions and antioxidant activities in waxy and non-waxy black rice during home cooking.

Science.gov (United States)

Tang, Yayuan; Cai, Weixi; Xu, Baojun

2016-01-15

The objectives of this study were to systematically analyze degradation rate of functional substances, such as total phenolic content (TPC), total flavonoid content (TFC), condensed tannin content (CTC), monomeric anthocyanin content (MAC), cyanidin-3-glucoside (Cy3glc), and peonidin-3-glucoside (Pn3glc), as well as antioxidant activities in cooked waxy and non-waxy black rice through different home cooking manners. Results showed that greater phenolics and antioxidant capacities were detected in non-waxy rice rather than waxy one. All processed black rice exhibited significantly (price. Different processing methods significantly degraded the content and activities of antioxidants of both waxy and non-waxy black rice. Under the same cooking time, black rice porridge retained more active substances than that of cooked rice by rice cooker. Therefore, to maintain bioavailability of active components, black rice porridge may gain more health promoting effects. Copyright © 2015 Elsevier Ltd. All rights reserved.

Inorganic arsenic contents in ready-to-eat rice products and various Korean rice determined by a highly sensitive gas chromatography-tandem mass spectrometry.

Science.gov (United States)

Jung, Mun Yhung; Kang, Ju Hee; Jung, Hyun Jeong; Ma, Sang Yong

2018-02-01

Rice and rice products have been reported to contain high contents of toxic inorganic arsenic (iAs). The inorganic arsenic contents in microwavable ready-to-eat rice products (n=30) and different types of Korean rice (n=102) were determined by a gas chromatography-tandem mass spectrometry (GC-MS/MS). The method showed low limit of detection (0.015pg), high intra- and inter-day repeatability (ready-to-eat rice products was 59μgkg -1 (dry weight basis). The mean iAs contents in polished white, brown, black, and waxy rice were 65, 109, 91, and 66μgkg -1 , respectively. The percentages of ready-to-eat rice products, white, brown, black, and waxy rice containing iAs over the maximum level (100μgkg -1 ) set by EU for the infant foods were 17, 4, 70, 36 and 0%, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

Speciation of arsenic in rice and estimation of daily intake of different arsenic species by Brazilians through rice consumption.

Science.gov (United States)

Batista, Bruno L; Souza, Juliana M O; De Souza, Samuel S; Barbosa, Fernando

2011-07-15

Rice is an important source of essential elements. However, rice may also contain toxic elements such as arsenic. Therefore, in the present study, the concentration of total arsenic and five main chemical species of arsenic (As(3+), As(5+), DMA, MMA and AsB) were evaluated in 44 different rice samples (white, parboiled white, brown, parboiled brown, parboiled organic and organic white) from different Brazilian regions using high-performance liquid chromatography hyphenated to inductively coupled plasma mass spectrometry (HPLC-ICP-MS). The mean level of total arsenic was 222.8 ng g(-1) and the daily intake of inorganic arsenic (the most toxic form) from rice consumption was estimated as 10% of the Provisional Tolerable Daily Intake (PTDI) with a daily ingestion of 88 g of rice. Inorganic arsenic (As(3+), As(5+)) and dimethylarsinic acid (DMA) are the predominant forms in all samples. The percentages of species were 38.7; 39.7; 3.7 and 17.8% for DMA, As(3+), MMA and As(5+), respectively. Moreover, rice samples harvested in the state of Rio Grande do Sul presented more fractions of inorganic arsenic than rice in Minas Gerais or Goiás, which could lead to different risks of arsenic exposure. Copyright © 2011 Elsevier B.V. All rights reserved.

Drought resistant rice mutants, characteristics and discussions on possibilities for planting them in some Arab Countries which import rice

International Nuclear Information System (INIS)

Abo-Hegazi, A.M.T.

1994-01-01

A number of drought resistant mutants of rice were produced from ordinary rice varieties being planted in several parts of Egypt through utilization of gamma rays as a mutagen. The mutants have water requirements less than one half of that of their mother varieties. According to official data, authorities in Egypt insure about 18000 M 3 of irrigation water for every hectare (10000 M 2 ) of rice and about 6700 M 3 , 6900 M 3 for every hectare of corn and ground nuts, respectively. Peanuts and corn are summer crops like the drought resistant rice mutants. The mentioned mutants can produce good yield under water requirements very near to that of corn and peanuts. The wide gap in agricultural food stuffs for the Arab Countries (more than 20000 million US $ annually) includes rice imports usually exceeds 700 million US $ per year> Rice imports of Arab Countries such as Saudi Arabia, Yemen, Syria, Libya and the Sudan, reached 180, 47, 21, 16 and 14 million US $ in 1988 as an example. Such countries could make use of the drought resistant rice mutants for plantation on water requirements very near to those of usual summer crops such as corn and peanuts which is significantly less than one half of water requirements of their mother varieties. Some characteristics of such mutants as well as discussions on possibilities for planting them in some of the nominated Arab Countries are presented. However, arrangements for ensuring the minimum water requirements during the growing period irrespective to rain which in many cases did not accord the growing period of the mutants should be taken if such countries wants to make use of the drought resistant rice mutants. The author believe that most if not all requirements of rice of such countries could locally be ensured through planting of the above mentioned rice mutants. In this case, maximizing the efficiency of utilizing the limited water resources of such countries could also be counted as another cause for presenting this

Development of a Monoclonal Antibody-Based icELISA for the Detection of Ustiloxin B in Rice False Smut Balls and Rice Grains

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Xiaoxiang Fu

2015-08-01

Full Text Available Rice false smut is an emerging and economically-important rice disease caused by infection by the fungal pathogen Villosiclava virens. Ustiloxin B is an antimitotic cyclopeptide mycotoxin isolated from the rice false smut balls that formed in the pathogen-infected rice spikelets. A monoclonal antibody (mAb designated as mAb 1B5A10 was generated with ustiloxin B—ovalbumin conjugate. A highly-sensitive and specific indirect competitive enzyme-linked immunosorbent assay (icELISA was then developed. The median inhibitory concentration (IC50 of the icELISA was 18.0 ng/mL for the detection of ustiloxin B; the limit of detection was 0.6 ng/mL, and the calibration range was from 2.5 to 107.4 ng/mL. The LOD/LOQ values of the developed ELISA used for the determination of ustiloxin B in rice false smut balls and rice grains were 12/50 μg/g and 30/125 ng/g, respectively. The mAb 1B5A10 cross-reacted with ustiloxin A at 13.9% relative to ustiloxin B. Average recoveries of ustiloxin B ranged from 91.3% to 105.1% for rice false smut balls at spiking levels of 0.2 to 3.2 mg/g and from 92.6% to 103.5% for rice grains at spiking levels of 100 to 5000 ng/g. Comparison of ustiloxin B content in rice false smut balls and rice grains detected by both icELISA and high performance liquid chromatography (HPLC demonstrated that the developed icELISA can be employed as an effective and accurate method for the detection of ustiloxin B in rice false smut balls, as well as rice food and feed samples.

Natural variation of rice blast resistance gene Pi-d2

Science.gov (United States)

Studying natural variation of rice resistance (R) genes in cultivated and wild rice relatives can predict resistance stability to rice blast fungus. In the present study, the protein coding regions of rice R gene Pi-d2 in 35 rice accessions of subgroups, aus (AUS), indica (IND), temperate japonica (...

Problems and prospects of mechanical rice-transplanting in Pakistan

International Nuclear Information System (INIS)

Majid, A.; Rehman, A.; Akram, M.; Zafar, A.W.; Ahmed, M.

2003-01-01

Among the many factors, low plant-population is the fundamental reason for poor rice-yield, despite advancements in rice-culture technology. The contracted manual transplanting of paddy seedlings is considered to be one of the key factors responsible for poor stand-establishment of rice in the field. The labourers transplant rice-seedlings at considerably wider distance than the recommended one, resulting in poor establishment of crop-stand and, ultimately, lower yield. The mechanized rice-culture is thought to be a viable substitute for manual rice-culture in Pakistan. Over the years, a lot of effort has been made in this regard, but could not popularize mechanical transplantation of paddy, for a number of reasons. The popularization of mechanical rice-culture in the country needs significant reforms in nursery raising, water management, improvement of soil organic-matter and land-preparation, along with emphasis on local manufacturing of the cost-effective simple mechanical rice transplanter. (author)