Non-parametric multivariate analysis of variance in the proteomic response of potato to drought stress

Metal(loid) speciation in a river subjected to industrial anthropopressure: chemometric and environmental studies

High-performance liquid chromatography (HPLC) coupled with inductively coupled plasma mass spectrometry (ICP-MS) was applied to the speciation of arsenic [As(III), As(V), and AsB (arsenobetaine)], MMA (monomethylarsonic acid), DMA (dimethylarsinic acid), antimony [Sb(III) and Sb(V)], and chromium [Cr(III) and Cr(VI)] in water and bottom sediment samples collected from the urban Bytomka River (Poland). The main objective of the study was the research of As, Cr and Sb species in the Bytomka River, as well as the simplified three-stage sequential chemical extraction of bottom sediments according to the Institute for Reference Materials and Measurements (BCR). The contents of V, Mn, Co, Ni, Cu, Zn, Rb, Sr, Ag, Cd, Te, Ba, Tl, Pb, Fe, Ga, and U in the water and bottom sediments were tested using the ICP-MS technique. The risk assessment code (RAC) indicated a medium risk for As and a high risk for Sb to the environment. Sequential chemical extraction of bottom sediments showed that As and Cr were strongly demobilized. Sb was mainly bound with the ion-exchange fraction and posed a serious threat to the environment. Chemometric analysis with the (dis)similarity analysis and principal component analysis (PCA) allowed for visualization of the variability and correlations of the analyzed elements.

Alterations in the diversity and composition of mice gut microbiota by lytic or temperate gut phage treatment

Phages, the most abundant species in the mammalian gut, have numerous advantages as biocontrol agent over antibiotics. In this study, mice were orally treated with the lytic gut phage PA13076 (group B), the temperate phage BP96115 (group C), no phage (group A), or streptomycin (group D) over 31 days. At the end of the experiment, fecal microbiota diversity and composition was determined and compared using high-throughput sequencing of the V3-V4 hyper-variable region of the 16S rRNA gene and virus-like particles (VLPs) were quantified in feces. There was high diversity and richness of microbiota in the lytic and temperate gut phage-treated mice, with the lytic gut phage causing an increased alpha diversity based on the Chao1 index (p < 0.01). However, the streptomycin treatment reduced the microbiota diversity and richness (p = 0.0299). Both phage and streptomycin treatments reduced the abundance of Bacteroidetes at the phylum level (p < 0.01) and increased the abundance of the phylum Firmicutes. Interestingly, two beneficial genera, Lactobacillus and Bifidobacterium, were enhanced by treatment with the lytic and temperate gut phage. The abundance of the genus Escherichia/Shigella was higher in mice after temperate phage administration than in the control group (p < 0.01), but lower than in the streptomycin group. Moreover, streptomycin treatment increased the abundance of the genera Klebsiella and Escherichia/Shigella (p < 0.01). In terms of the gut virome, fecal VLPs did not change significantly after phage treatment. This study showed that lytic and temperate gut phage treatment modulated the composition and diversity of gut microbiota and the lytic gut phage promoted a beneficial gut ecosystem, while the temperate phage may promote conditions enabling diseases to occur.

Maize proteomic responses to separate or overlapping soil drought and two-spotted spider mite stresses

In maize, leaf proteome responses evoked by soil drought applied separately differ from those evoked by mite feeding or both types of stresses occurring simultaneously. This study focuses on the involvement of proteomic changes in defence responses of a conventional maize cultivar (Bosman) to the two-spotted spider mite infestation, soil drought and both stresses coexisting for 6 days. Under watering cessation or mite feeding applied separately, the protein carbonylation was not directly linked to the antioxidant enzymes' activities. Protein carbonylation increased at higher and lower SOD, APX, GR, POX, PPO activities following soil drought and mite feeding, respectively. Combination of these stresses resulted in protein carbonylation decrease despite the increased activity of all antioxidant enzymes (except the CAT). However, maize protein network modification remains unknown upon biotic/abiotic stresses overlapping. Here, using multivariate chemometric methods, 94 leaf protein spots (out of 358 considered; 2-DE) were identified (LC-MS/MS) as differentiating the studied treatments. Only 43 of them had individual discrimination power. The soil drought increased abundance of leaf proteins related mainly to photosynthesis, carbohydrate metabolism, defence (molecular chaperons) and protection. On the contrary, mite feeding decreased the abundance of photosynthesis related proteins and enhanced the abundance of proteins protecting the mite-infested leaf against photoinhibition. The drought and mites occurring simultaneously increased abundance of proteins that may improve the efficiency of carbon fixation, as well as carbohydrate and amino acid metabolism. Furthermore, increased abundance of the Rubisco large subunit-binding protein (subunit β), fructose-bisphosphate aldolase and mitochondrial precursor of Mn-SOD and decreased abundance of the glycolysis-related enzymes in the mite-free leaf (in the vicinity of mite-infested leaf) illustrate the involvement of these proteins in systemic maize response to mite feeding.

Tuber proteome comparison of five potato varieties by principal component analysis

BACKGROUND

Data analysis of omics data should be performed by multivariate analysis such as principal component analysis (PCA). The way data are clustered in PCA is of major importance to develop some classification systems based on multivariate analysis, such as soft independent modeling of class analogy (SIMCA). In a previous study a one-class classifier based on SIMCA was built using microarray data from a set of potatoes. The PCA grouped the transcriptomic data according to varieties. The present work aimed to use PCA to verify the clustering of the proteomic profiles for the same potato varieties.

RESULTS

Proteomic profiles of five potato varieties (Biogold, Fontane, Innovator, Lady Rosetta and Maris Piper) were evaluated by two-dimensional gel electrophoresis (2-DE) performed on two immobilized pH gradient (IPG) strip lengths, 13 and 24 cm, both under pH range 4-7. For each strip length, two gels were prepared from each variety; in total there were ten gels per analysis. For 13 cm strips, 199-320 spots were detected per gel, and for 24 cm strips, 365-684 spots.

CONCLUSION

All four PCAs performed with these datasets presented clear grouping of samples according to the varieties. The data presented here showed that PCA was applicable for proteomic analysis of potato and was able to separate the samples by varieties. © 2016 Society of Chemical Industry.

Chemometric and environmental assessment of arsenic, antimony, and chromium speciation form occurrence in a water reservoir subjected to thermal anthropopressure

In the study, arsenic, antimony, and chromium concentrations and selected physicochemical parameters in water and sediment samples from the thermal anthroporessure subjected Rybnik Reservoir (Poland) were determined. As(III), As(V), Sb(III), and Sb(V) ions were successfully separated on Dionex IonPac AS7 column, and Cr(III) and Cr(VI) on Dionex IonPac AG7 column. The obtained limits of detection were 0.18, 0.22, 0.009, 0.012, 0.11, and 0.17 μg/L, respectively. Water and bottom sediment samples were collected monthly at three-point transect between January and November 2013. The As(III) and Sb(III) speciation forms dominated in the bottom water, and Cr(VI) concentration in the bottom water was twice as high as the value measured for the surface water. The oxidized arsenic, antimony, and chromium forms dominated in the bottom sediments in the heated water discharge zone of the Rybnik Power Plant. The location of sampling point had a significant influence on the observed transformations and contents of the analyzed speciation forms. The chemometric analysis coupled with the dissimilarity analysis and principal component analysis helped to visualize the variability in the concentrations of the element speciation forms within the researched period and analyzing correlations.