117 research outputs found
Bananan Genome Hub v2
No full textDroc G, Lariviere D, Guignon V, Yahiaoui N, This D, Garsmeur O, Dereeper A, Hamelin C, Argout X, Dufayard J-F, Lengelle J, Baurens F-C, Cenci A, Pitollat B, D'Hont A, Ruiz M, Rouard M, Bocs . The Banana Genome Hub. Database (2013) doi:10.1093/database/bat03
The AF promotes <i>G. intraradices</i> hyphal growth in the DROC.
No full text<p>The hyphal length of each <i>G. intraradices</i> spore was measured each day for 1 week after adding the AF to the DROC. The cultures containing WT and M161 roots without any additive served as the positive and negative control, respectively. The cultures containing M161 and NAF served as a second negative control. Error bars indicate SE (<i>n</i> = <i>3</i>) of three biological replicates.</p
Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library
No full textTo organize data resulting from the phenotypic characterization of a library of 30 000 T-DNA enhancer trap (ET) insertion lines of rice (Oryza sativa L cv. Nipponbare), we developed the Oryza Tag Line (OTL) database (http://urgi.versailles.inra.fr/OryzaTagLine/). OTL structure facilitates forward genetic search for specific phenotypes, putatively resulting from gene disruption, and/or for GUSA or GFP reporter gene expression patterns, reflecting ET-mediated endogenous gene detection. In the latest version, OTL gathers the detailed morpho-physiological alterations observed during field evaluation and specific screens in a first set of 13 928 lines. Detection of GUS or GFP activity in specific organ/tissues in a subset of the library is also provided. Search in OTL can be achieved through trait ontology category, organ and/or developmental stage, keywords, expression of reporter gene in specific organ/tissue as well as line identification number. OTL now contains the description of 9721 mutant phenotypic traits observed in 2636 lines and 1234 GUS or GFP expression patterns. Each insertion line is documented through a generic passport data including production records, seed stocks and FST information. 8004 and 6101 of the 13 928 lines are characterized by at least one T-DNA and one Tos17 FST, respectively that OTL links to the rice genome browser OryGenesDB
Resilient active seismic response control of structural systems
No full textThis paper proposes a dissipative resilient observer and controller (DROC) design for a network controlled system (NCS) that handles faults, implementation errors, or cyberattacks that can be modeled as bounded controller or observer gain perturbations. It presents linear matrix inequality (LMI) conditions for the robust stability of the system in the presence of bounded perturbations in the observer and controller. Furthermore, a new LMI-based time-delay control (TDC) algorithm that mitigates the effects of perturbations due to time-delays in the NCS is introduced. The robust methodology is applied to active control of a scaled model of a structural system equipped with an active mass driver system. The results demonstrate that the proposed methodology is robust and ensures stable system response due to various types of earthquake base excitations. © The Author(s) 2022
The Rice Annotation Project Database (RAP-DB): 2008 update
No full textThe Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/
Steady-state power distribution in VSC-based MTDC systems and dc grids under mixed P/V and I/V droop control
No full text[EN] This paper proposes a steady-state power distribution derivation method for voltage source converter (VSC)based multi-terminal HVDC (MTDC) systems and dc grids under mixed power/voltage (P/V) and current/voltage (I/V) droop control. P/V and I/V droop control are two commonly used control schemes, which can be combined to achieve co-regulation of powers & currents in MTDC systems and dc grids. The proposed method can be used to estimate the power distributions under different scenarios for MTDC systems and dc grids based on VSCs with mixed P/V and I/V droop control. After determining the initial operating point based on an estimation-correction algorithm, redistributed power due to power disturbances, current changes or converter outages is analyzed in detail considering converter overload. An excess power reduction strategy is further proposed to avoid violation of power limits after converter outage. The accuracy of the proposed method is validated through multiple scenarios in a modular multilevel converter (MMC)-based four-terminal dc grid. The comparison between the proposed method and other approaches in the current literature further demonstrates the advantages of proposed power distribution derivation method.The third author (Muhammad Khalid) would like to acknowledge the support from Deanship of Research Oversight and Coordination (DROC) at King Fahd University of Petroleum and Minerals (KFUPM) through project No. DF201011.Sun, P.; Wang, Y.; Khalid, M.; Blasco-Gimenez, R.; Konstantinou, G. (2023). Steady-state power distribution in VSC-based MTDC systems and dc grids under mixed P/V and I/V droop control. Electric Power Systems Research. 214:1-10. https://doi.org/10.1016/j.epsr.2022.108798S11021
Is cirrhotic cardiomyopathy a risk factor for post-reperfusion syndrome during liver transplantation?
No full textWarm ischemia time, postreperfusion syndrome and initial poor function after liver transplantation: are they connected?
No full textASL/LBD phylogeny suggests that genetic mechanisms of root initiation downstream of auxin are distinct in lycophytes and euphyllophytes
No full textPaleobotanical studies suggest that roots evolved at least twice independently during land plant diversification, once in lycophytes and once in euphyllophytes. Auxin promotes postembryonic root initiation in both groups but from different cell types. In several euphyllophytes, such as Arabidopsis, rice, and maize, AS2/LOB-domain (ASL/LBD) proteins act directly downstream of auxin and are conserved elements necessary for root initiation. It is currently unknown whether similar or different genetic mechanisms act downstream of auxin for root initiation in lycophytes and euphyllophytes. We searched for ASL/LBD proteins in genome sequences spanning the tree of life to retrace their evolutionary history. We performed a phylogenetic analysis of ASL/LBD proteins and mapped the functions of all characterized ASL/LBD onto the phylogenetic trees. We identified a clade specifically associated with root development, which includes no lycophyte sequence. This points toward the existence of distinct genetic mechanisms downstream of auxin for root initiation in lycophytes and euphyllophytes
Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants
No full textAbstract Background Gene ortholog identification is now a major objective for mining the increasing amount of sequence data generated by complete or partial genome sequencing projects. Comparative and functional genomics urgently need a method for ortholog detection to reduce gene function inference and to aid in the identification of conserved or divergent genetic pathways between several species. As gene functions change during evolution, reconstructing the evolutionary history of genes should be a more accurate way to differentiate orthologs from paralogs. Phylogenomics takes into account phylogenetic information from high-throughput genome annotation and is the most straightforward way to infer orthologs. However, procedures for automatic detection of orthologs are still scarce and suffer from several limitations. Results We developed a procedure for ortholog prediction between Oryza sativa and Arabidopsis thaliana. Firstly, we established an efficient method to cluster A. thaliana and O. sativa full proteomes into gene families. Then, we developed an optimized phylogenomics pipeline for ortholog inference. We validated the full procedure using test sets of orthologs and paralogs to demonstrate that our method outperforms pairwise methods for ortholog predictions. Conclusion Our procedure achieved a high level of accuracy in predicting ortholog and paralog relationships. Phylogenomic predictions for all validated gene families in both species were easily achieved and we can conclude that our methodology outperforms similarly based methods.</p
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