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The explosive growth of microbiome data provides ample opportunities to gain a better understanding of the microbes and their interactions in microbial communities. Given these massive data, optimized data mining methods become important and necessary to perform deep and comprehensive analysis. Among the various priorities for microbiome data mining, the examination of species-species co-occurrence patterns becomes one of the key themes in urgent need.
ResultsHence, in this work, we propose the Meta-Network framework to lucubrate the microbial communities. Rooted in loose definitions of network (two species co-exist in a certain samples rather than all samples) as well as association rule mining (mining more complex forms of correlations like indirect correlation and mutual information), this framework outperforms other methods in restoring the microbial communities, based on two cohorts of microbial communities: (a) the loose definition strategy is capable to generate more reasonable relationships among species in the species-species co-occurrence network; (b) important species-species co-occurrence patterns could not be identified by other existing approaches, but could successfully generated by association rule mining.
ConclusionsResults have shown that the species-species co-occurrence network we generated are much more informative than those based on traditional methods. Meta-Network has consistently constructed more meaningful networks with biologically important clusters, hubs, and provides a general approach towards deciphering the species-species co-occurrence networks.
相似文献The study was conducted at the grain-filling stage to elucidate the physiological and molecular mechanisms of the root to enhance yield under alternate wetting and drying (AWD) compared with conventional irrigation. Measurements of root dry weight (RDW), seed setting rate, total kernel weight, and grain yield were determined along with 2D electrophoresis to detect altered protein expression in response to moderate soil drying (MD) and the subsequent recovery phase as moderate wetting (MW) under AWD compared with continuous wetting under CI. We found significant enhancement in RDW as well as 14.30 % increase in inferior spikelets, seed setting and 10.32 g m−2 increase in final yield. Among the total 55 differentially expressed proteins, 26 proteins were differentially expressed under both MD treatment and MW treatment, whereas 14 proteins under MD and 15 proteins under MW showed distinct expression. Differentially expressed proteins were involved in redox homeostasis, signaling, defense, energy, photoassimilate remobilization and included 14-3-3 proteins, cysteine-rich receptor-like protein kinase, monodehydroascorbate reductase, ascorbate peroxidase, glutathione S-transferases, translationally controlled tumor protein, remorin C-terminal domain containing protein, protein disulfide isomerase, DnaK family protein, cysteine synthase, aminotransferase, phosphoglycerate mutase, pyruvate phosphate dikinase, ATP synthase, and abscisic acid stress ripening (ASR1). The differential expression ratio of the signaling, redox, and defense group proteins was almost the same under MD and MW. ABA signaling, amino acid synthesis, and N remobilization were upregulated under MD, and the enzymes involved in carbohydrate, energy, and transportation metabolism were upregulated under MW. In conclusion, at the rice grain-filling stage, AWD is a potential technique to trigger signaling and the enzymatic protein network for systematic senescence initiation, root enlargement for maximum nutrient uptake, and maximize photoassimilate remobilization for yield enhancement.
相似文献Pseudomonas putida KT2442, a natural producer of polyhydroxyalkanoate, spends a lot of energy and carbon sources to form flagella and pili; therefore, deleting the genes involved in the biosynthesis and assembly of flagella and pili might improve PHA productivity. In this study, two novel deletion systems were constructed in order to efficiently remove the 76 genes involved in the biosynthesis and assembly of flagella and pili in P. putida KT2442. Both systems combine suicide-plasmid-based homologous recombination and mutant lox site-specific recombination and involve three plasmids. The first includes pK18mobsacB, pWJW101, and pWJW102; and the second includes pZJD29c, pDTW202, and pWJW103. These newly constructed systems were successfully used to remove different gene clusters in P. putida KT2442 and showed a high deletion efficiency (above 90%) whether for the second-round or the third-round recombination. Both systems could efficiently delete the gene PP4378 encoding flagellin in putida KT2442, resulting in the mutant strain WJPP01. The second system was used to remove the pili-forming gene cluster PP2357-PP2363 in putida KT2442, resulting in the mutant strain WJPP02, and also used to remove the flagella-forming gene cluster PP4329-PP4397 in WJPP02, resulting in the mutant strain WJPP03. Compared with the wild-type KT2442, the 1.2% genome reduction mutant WJPP03 grew faster, lacked flagella and motility, showed sharply decreased biofilm and 3′,5′-cyclic diguanylic acid (c-di-GMP), but accumulated more polyhydroxyalkanoate. The biomass, polyhydroxyalkanoate yield, and content of WJPP03 increased 19.1, 73.4, and 45.6%, respectively, with sodium hexanoate supplementation, and also increased 11.4, 53.6, and 37.9%, respectively, with lauric acid supplementation.
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