Project description:FROG and miniFROG reports are given for the genome-scale metabolic network of Bacillus licheniformis WX-02. The model iWX1009 contains 1009 genes, 1141 metabolites and 1762 reactions and is the study of poly-γ-glutamic acid (γ-PGA) synthesis. The model can be found in the Supplementary data of the Guo et al, 2016 paper cited here.
Project description:Environmental pollution is a worldwide problem, and metals are the largest group of contaminants in soil. Microarray toxicogenomic studies with ecologically relevant organisms such as springtails, supplement traditional ecotoxicological research, but are presently rather descriptive. Classifier analysis, a more analytical application of the microarray technique, is able to predict biological classes of unknown samples. We used the uncorrelated shrunken centroid (USC) method to classify gene expression profiles of the springtail Folsomia candida exposed to soil spiked with six different metals (barium, cadmium, cobalt, chromium, lead, and zinc). We identified a gene set (classifier) of 188 genes that can discriminate between six different metals present in soil, which allowed us to predict the correct classes for samples of an independent test set with an accuracy of 83% (error rate = 0.17). This study shows further that in order to apply classifier analysis to actual contaminated field soil samples, more insight and information is needed on the transcriptional responses of soil organisms to different soil types (properties) and mixtures of contaminants.
Project description:Phosphate (P) fertilization impacts many rhizosphere processes, driving plant P use efficiency. However, less is known about the induced molecular and physiological root-rhizosphere traits in responses to polyphosphates (PolyP), particularly root transcriptome and belowground functional traits responsible for P acquisition. The present study aims to investigate physiological and transcriptomic belowground mechanisms explaining the enhanced durum wheat P acquisition under PolyP (PolyB and PolyC) supply. Root molecular traits were differentially expressed in response to PolyP, where PolyB induced upregulation of OGDH, MDH, and ENO, PAP21 and downregulation of PFK, and LDH genes. The modulation of gene expression can presumably explain the PolyP-induced changes in rhizosphere (root, rhizosphere soil, soil solution) acidification (pH decreased from 8 to 6.3) and acid phosphatase activities, which were concomitant with enhanced rhizosphere soil P availability and shoot Pi content (145% and 36% compared to OrthoP, respectively) along with changes in morphological and transcriptomic root (particularly, the upregulation of AUX1 and ABA transporter genes) traits. These findings provide novel insights that P acquisition from polyphosphates involves the coordinated regulation of genes governing root-rhizosphere processes and root development, ultimately enhancing wheat P acquisition.
Project description:Environmental pollution is a worldwide problem, and metals are the largest group of contaminants in soil. Microarray toxicogenomic studies with ecologically relevant organisms such as springtails, supplement traditional ecotoxicological research, but are presently rather descriptive. Classifier analysis, a more analytical application of the microarray technique, is able to predict biological classes of unknown samples. We used the uncorrelated shrunken centroid (USC) method to classify gene expression profiles of the springtail Folsomia candida exposed to soil spiked with six different metals (barium, cadmium, cobalt, chromium, lead, and zinc). We identified a gene set (classifier) of 188 genes that can discriminate between six different metals present in soil, which allowed us to predict the correct classes for samples of an independent test set with an accuracy of 83% (error rate = 0.17). This study shows further that in order to apply classifier analysis to actual contaminated field soil samples, more insight and information is needed on the transcriptional responses of soil organisms to different soil types (properties) and mixtures of contaminants. Gene expression was measured in springtails after exposure of 2 days to soil containing either EC10 or EC50 of 6 different metals. The exposure experiment was performed in two separate series (1 and 2), both containing a separate non-spiked (LUFA 2.2) soil control. Also, two field soil samples were tested. The samples were divided into a separate training set and a validation set for USC classifier analysis.