Water for rural development: Background paper on water for rural development prepared for the World Bank

Water management / Irrigation management / Rural development / Water resources development / Small scale systems / Land management / Groundwater / Environment / Health / Water policy / Institutions / Food consumption / Water supply / Water demand / Water allocation / Crop yield / Cereals / Water scarcity / Food production / Food security / Crop production / Population growth

Land and water productivity of wheat in the Western Indo-Gangetic Plains of India and Pakistan: a comparative analysis

Wheat / Crop yield / Productivity / Climate / Irrigation canals / Watercourses / Water distribution / Water allocation / Policy / India / Pakistan / Gangetic Plains / Kaithal Irrigation Circle / Bhakra Canal / Chaj Sub-Basin / Lower Jehlum Canal

Human and murine IFIT1 proteins do not restrict infection of negative-sense RNA viruses of the Orthomyxoviridae, Bunyaviridae, and Filoviridae families

UNLABELLED: Interferon-induced protein with tetratricopeptide repeats 1 (IFIT1) is a host protein with reported cell-intrinsic antiviral activity against several RNA viruses. The proposed basis for the activity against negative-sense RNA viruses is the binding to exposed 5\u27-triphosphates (5\u27-ppp) on the genome of viral RNA. However, recent studies reported relatively low binding affinities of IFIT1 for 5\u27-ppp RNA, suggesting that IFIT1 may not interact efficiently with this moiety under physiological conditions. To evaluate the ability of IFIT1 to have an impact on negative-sense RNA viruses, we infected Ifit1(-/-) and wild-type control mice and primary cells with four negative-sense RNA viruses (influenza A virus [IAV], La Crosse virus [LACV], Oropouche virus [OROV], and Ebola virus) corresponding to three distinct families. Unexpectedly, a lack of Ifit1 gene expression did not result in increased infection by any of these viruses in cell culture. Analogously, morbidity, mortality, and viral burdens in tissues were identical between Ifit1(-/-) and control mice after infection with IAV, LACV, or OROV. Finally, deletion of the human IFIT1 protein in A549 cells did not affect IAV replication or infection, and reciprocally, ectopic expression of IFIT1 in HEK293T cells did not inhibit IAV infection. To explain the lack of antiviral activity against IAV, we measured the binding affinity of IFIT1 for RNA oligonucleotides resembling the 5\u27 ends of IAV gene segments. The affinity for 5\u27-ppp RNA was approximately 10-fold lower than that for non-2\u27-O-methylated (cap 0) RNA oligonucleotides. Based on this analysis, we conclude that IFIT1 is not a dominant restriction factor against negative-sense RNA viruses. IMPORTANCE: Negative-sense RNA viruses, including influenza virus and Ebola virus, have been responsible for some of the most deadly outbreaks in recent history. The host interferon response and induction of antiviral genes contribute to the control of infections by these viruses. IFIT1 is highly induced after virus infection and reportedly has antiviral activity against several RNA and DNA viruses. However, its role in restricting infection by negative-sense RNA viruses remains unclear. In this study, we evaluated the ability of IFIT1 to inhibit negative-sense RNA virus replication and pathogenesis both in vitro and in vivo. Detailed cell culture and animal studies demonstrated that IFIT1 is not a dominant restriction factor against three different families of negative-sense RNA viruses

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

Background Functional annotations of large plant genome projects mostly provide information on gene function and gene families based on the presence of protein domains and gene homology, but not necessarily in association with gene expression or metabolic and regulatory networks. These additional annotations are necessary to understand the physiology, development and adaptation of a plant and its interaction with the environment. Results RiceCyc is a metabolic pathway networks database for rice. It is a snapshot of the substrates, metabolites, enzymes, reactions and pathways of primary and intermediary metabolism in rice. RiceCyc version 3.3 features 316 pathways and 6,643 peptide-coding genes mapped to 2,103 enzyme-catalyzed and 87 protein-mediated transport reactions. The initial functional annotations of rice genes with InterPro, Gene Ontology, MetaCyc, and Enzyme Commission (EC) numbers were enriched with annotations provided by KEGG and Gramene databases. The pathway inferences and the network diagrams were first predicted based on MetaCyc reference networks and plant pathways from the Plant Metabolic Network, using the Pathologic module of Pathway Tools. This was enriched by manually adding metabolic pathways and gene functions specifically reported for rice. The RiceCyc database is hierarchically browsable from pathway diagrams to the associated genes, metabolites and chemical structures. Through the integrated tool OMICs Viewer, users can upload transcriptomic, proteomic and metabolomic data to visualize expression patterns in a virtual cell. RiceCyc, along with additional species-specific pathway databases hosted in the Gramene project, facilitates comparative pathway analysis. Conclusions Here we describe the RiceCyc network development and discuss its contribution to rice genome annotations. As a case study to demonstrate the use of RiceCyc network as a discovery environment we carried out an integrated bioinformatic analysis of rice metabolic genes that are differentially regulated under diurnal photoperiod and biotic stress treatments. The analysis of publicly available rice transcriptome datasets led to the hypothesis that the complete tryptophan biosynthesis and its dependent metabolic pathways including serotonin biosynthesis are induced by taxonomically diverse pathogens while also being under diurnal regulation. The RiceCyc database is available online for free access at http://www.gramene.org/pathway

The Operational MODIS Cloud Optical and Microphysical Property Product: Overview of the Collection 6 Algorithm and Preliminary Results

Operational Moderate Resolution Imaging Spectroradiometer (MODIS) retrievals of cloud optical and microphysical properties (part of the archived products MOD06 and MYD06, for MODIS Terra and Aqua, respectively) are currently being reprocessed along with other MODIS Atmosphere Team products. The latest "Collection 6" processing stream, which is expected to begin production by summer 2012, includes updates to the previous cloud retrieval algorithm along with new capabilities. The 1 km retrievals, based on well-known solar reflectance techniques, include cloud optical thickness, effective particle radius, and water path, as well as thermodynamic phase derived from a combination of solar and infrared tests. Being both global and of high spatial resolution requires an algorithm that is computationally efficient and can perform over all surface types. Collection 6 additions and enhancements include: (i) absolute effective particle radius retrievals derived separately from the 1.6 and 3.7 !-lm bands (instead of differences relative to the standard 2.1 !-lm retrieval), (ii) comprehensive look-up tables for cloud reflectance and emissivity (no asymptotic theory) with a wind-speed interpolated Cox-Munk BRDF for ocean surfaces, (iii) retrievals for both liquid water and ice phases for each pixel, and a subsequent determination of the phase based, in part, on effective radius retrieval outcomes for the two phases, (iv) new ice cloud radiative models using roughened particles with a specified habit, (v) updated spatially-complete global spectral surface albedo maps derived from MODIS Collection 5, (vi) enhanced pixel-level uncertainty calculations incorporating additional radiative error sources including the MODIS L1 B uncertainty index for assessing band and scene-dependent radiometric uncertainties, (v) and use of a new 1 km cloud top pressure/temperature algorithm (also part of MOD06) for atmospheric corrections and low cloud non-unity emissivity temperature adjustments

Structure-function analysis of the curli accessory protein CsgE defines surfaces essential for coordinating amyloid fiber formation

Curli amyloid fibers are produced as part of the extracellular biofilm matrix and are composed primarily of the major structural subunit CsgA. The CsgE chaperone facilitates the secretion of CsgA through CsgG by forming a cap at the base of the nonameric CsgG outer membrane pore. We elucidated a series of finely tuned nonpolar and charge-charge interactions that facilitate the oligomerization of CsgE and its ability to transport unfolded CsgA to CsgG for translocation. CsgE oligomerization in vitro is temperature dependent and is disrupted by mutations in the W48 and F79 residues. Using nuclear magnetic resonance (NMR), we identified two regions of CsgE involved in the CsgE-CsgA interaction: a head comprising a positively charged patch centered around R47 and a stem comprising a negatively charged patch containing E31 and E85. Negatively charged residues in the intrinsically disordered N- and C-terminal “tails” were not implicated in this interaction. Head and stem residues were mutated and interrogated using in vivo measurements of curli production and in vitro amyloid polymerization assays. The R47 head residue of CsgE is required for stabilization of CsgA- and CsgE-mediated curli fiber formation. Mutation of the E31 and E85 stem residues to positively charged side chains decreased CsgE-mediated curli fiber formation but increased CsgE-mediated stabilization of CsgA. No single-amino-acid substitutions in the head, stem, or tail regions affected the ability of CsgE to cap the CsgG pore as determined by a bile salt sensitivity assay. These mechanistic insights into the directed assembly of functional amyloids in extracellular biofilms elucidate possible targets for biofilm-associated bacterial infections.Curli represent a class of functional amyloid fibers produced by Escherichia coli and other Gram-negative bacteria that serve as protein scaffolds in the extracellular biofilm matrix. Despite the lack of sequence conservation among different amyloidogenic proteins, the structural and biophysical properties of functional amyloids such as curli closely resemble those of amyloids associated with several common neurodegenerative diseases. These parallels are underscored by the observation that certain proteins and chemicals can prevent amyloid formation by the major curli subunit CsgA and by alpha-synuclein, the amyloid-forming protein found in Lewy bodies during Parkinson’s disease. CsgA subunits are targeted to the CsgG outer membrane pore by CsgE prior to secretion and assembly into fibers. Here, we use biophysical, biochemical, and genetic approaches to elucidate a mechanistic understanding of CsgE function in curli biogenesis

Plant Reactome: a resource for plant pathways and comparative analysis

Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX

Electrospun amplified fiber optics

A lot of research is focused on all-optical signal processing, aiming to obtain effective alternatives to existing data transmission platforms. Amplification of light in fiber optics, such as in Erbium-doped fiber amplifiers, is especially important for an efficient signal transmission. However, the complex fabrication methods, involving high-temperature processes performed in highly pure environment, slow down the fabrication and make amplified components expensive with respect to an ideal, high-throughput and room temperature production. Here, we report on near infrared polymer fiber amplifiers, working over a band of about 20 nm. The fibers are cheap, spun with a process entirely carried out at room temperature, and show amplified spontaneous emission with good gain coefficients as well as low optical losses (a few cm^-1). The amplification process is favoured by the high fiber quality and low self-absorption. The found performance metrics promise to be suitable for short-distance operation, and the large variety of commercially-available doping dyes might allow for effective multi-wavelength operation by electrospun amplified fiber optics.Comment: 27 pages, 8 figure

Decoupling algorithms from schedules for easy optimization of image processing pipelines

Using existing programming tools, writing high-performance image processing code requires sacrificing readability, portability, and modularity. We argue that this is a consequence of conflating what computations define the algorithm, with decisions about storage and the order of computation. We refer to these latter two concerns as the schedule, including choices of tiling, fusion, recomputation vs. storage, vectorization, and parallelism. We propose a representation for feed-forward imaging pipelines that separates the algorithm from its schedule, enabling high-performance without sacrificing code clarity. This decoupling simplifies the algorithm specification: images and intermediate buffers become functions over an infinite integer domain, with no explicit storage or boundary conditions. Imaging pipelines are compositions of functions. Programmers separately specify scheduling strategies for the various functions composing the algorithm, which allows them to efficiently explore different optimizations without changing the algorithmic code. We demonstrate the power of this representation by expressing a range of recent image processing applications in an embedded domain specific language called Halide, and compiling them for ARM, x86, and GPUs. Our compiler targets SIMD units, multiple cores, and complex memory hierarchies. We demonstrate that it can handle algorithms such as a camera raw pipeline, the bilateral grid, fast local Laplacian filtering, and image segmentation. The algorithms expressed in our language are both shorter and faster than state-of-the-art implementations.National Science Foundation (U.S.) (Grant 0964004)National Science Foundation (U.S.) (Grant 0964218)National Science Foundation (U.S.) (Grant 0832997)United States. Dept. of Energy (Award DE-SC0005288)Cognex CorporationAdobe System

Synthesis and properties of novel star-shaped oligofluorene conjugated systems with BODIPY cores

Star-shaped conjugated systems with varying oligofluorene arm length and substitution patterns of the central BODIPY core have been synthesised, leading to two families of compounds, T-B1-T-B4 and Y-B1-Y-B4, with T- and Y-shaped motifs, respectively. Thermal stability, cyclic voltammetry, absorption and photoluminescence spectroscopy of each member of these two families were studied in order to determine their suitability as emissive materials in photonic applications