Dataset Information

Large-Scale Public Transcriptomic Data Mining Reveals a Tight Connection between the Transport of Nitrogen and Other Transport Processes in Arabidopsis.

ABSTRACT: Movement of nitrogen to the plant tissues where it is needed for growth is an important contribution to nitrogen use efficiency. However, we have very limited knowledge about the mechanisms of nitrogen transport. Loading of nitrogen into the xylem and/or phloem by transporter proteins is likely important, but there are several families of genes that encode transporters of nitrogenous molecules (collectively referred to as N transporters here), each comprised of many gene members. In this study, we leveraged publicly available microarray data of Arabidopsis to investigate the gene networks of N transporters to elucidate their possible biological roles. First, we showed that tissue-specificity of nitrogen (N) transporters was well reflected among the public microarray data. Then, we built coexpression networks of N transporters, which showed relationships between N transporters and particular aspects of plant metabolism, such as phenylpropanoid biosynthesis and carbohydrate metabolism. Furthermore, genes associated with several biological pathways were found to be tightly coexpressed with N transporters in different tissues. Our coexpression networks provide information at the systems-level that will serve as a resource for future investigation of nitrogen transport systems in plants, including candidate gene clusters that may work together in related biological roles.

SUBMITTER: He F

PROVIDER: S-EPMC4981021 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Large-Scale Public Transcriptomic Data Mining Reveals a Tight Connection between the Transport of Nitrogen and Other Transport Processes in Arabidopsis.

He Fei F Karve Abhijit A AA Maslov Sergei S Babst Benjamin A BA

Frontiers in plant science 20160811

Movement of nitrogen to the plant tissues where it is needed for growth is an important contribution to nitrogen use efficiency. However, we have very limited knowledge about the mechanisms of nitrogen transport. Loading of nitrogen into the xylem and/or phloem by transporter proteins is likely important, but there are several families of genes that encode transporters of nitrogenous molecules (collectively referred to as N transporters here), each comprised of many gene members. In this study, ...[more]

PMID: 27563305

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Project description:Elements in mining extracts can be potentially toxic if they are incorporated into soils, sediments or biota. Numerous approaches have been used to assess this problem, and these include sequential extractions and selective extractions. These two methods have limitations and advantages, and their combined use usually provides a rough estimate of the availability or (bio)availability of potentially toxic elements and, therefore, of their real potential as toxicants in food chains. These indirect speciation data are interesting in absolute terms, but in the work described here, this aspect was developed further by assessing the evolution of availability-related speciation in relation to the transport processes from the emission source, which are mainly fluvial- and wind-driven. This objective was achieved by characterizing tailings samples as the source of elements in soils and sediments at increasing distances to investigate the evolution of certain elements. The standard procedures employed included a sequential five-step extraction and a selective extraction with ammonium acetate. The results show that the highest percentages of Zn and Pb in tailings, soils and sediment samples are associated with oxyhydroxides, along with a significant presence of resistant mineralogical forms. In the case of Cd, its association with organic matter is the second-most important trapping mechanism in the area. The physicochemical mechanisms of transport did not transform the main mineralogical associations (oxyhydroxides and resistant mineralogical forms) along the transects, but they produced a chaotic evolution pattern for the other minor matrix associations for Zn and a decrease in exchangeable and carbonate-bound forms for Pb in soils. Interestingly, in sediments, these mobile forms showed a decrease in Zn and a chaotic evolution for Pb. The most probable reason for these observations is that Zn2+ can form smithsonite (ZnCO3) or hydrozincite (Zn5(CO3)2(OH)6), which explains the retention of a carbonate-bound form for Zn in the soil transect. In contrast, Pb and Cd can appear as different mineral phases. The order of (bio)availability was Pb > Zn > Cd in tailings but Cd > Pb > Zn in soils. The physicochemical processes involved in transport from tailings to soils produce an increase in Cd (bio)availability. The trend is a decrease in bioavailability on moving away from the source (tailings), with maximum values obtained for Cd near to the source area (200-400 m).

Dataset Information

Large-Scale Public Transcriptomic Data Mining Reveals a Tight Connection between the Transport of Nitrogen and Other Transport Processes in Arabidopsis.

Publications

Large-Scale Public Transcriptomic Data Mining Reveals a Tight Connection between the Transport of Nitrogen and Other Transport Processes in Arabidopsis.

Similar Datasets

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