Nitrogen addition may promote soil organic carbon storage and CO2 emission but reduce dissolved organic carbon in Zoige peatland.

With the increase of nitrogen (N) deposition, N input can affect soil C cycling since microbes may trigger a series of activities to balance the supply and demand of nutrients. However, as one of the largest C sinks on earth, the role of extra N addition in affecting peatland soil C and its potential mechanism remains unclear and debated. Therefore, this study chose the largest peatland in China (i.e., Zoige, mostly N-limited) to systematically explore the potential changes of soil C, microbes, and ecoenzymes caused by extra N input at the lab scale incubation. Three different types of soils were collected and incubated with different levels of NH4NO3 solution for 45 days. After incubation, N input generally increased soil organic C (SOC) but decreased dissolved organic carbon (DOC) in Zoige peatland soils. Moreover, CO2 and CH4 emissions were significantly increased after high N input (equal to 5 mg NH4NO3 g-1 dry soils). Through a series of analyses, it was observed that microbial communities and ecoenzyme activities mainly influenced the changes of different C components. Collectively, this study implied that the increasing N deposition might help C sequestration in N-limited peatland soils; simultaneously, the risk of increased CO2 and CH4 by N input in global warming should not be ignored.

Analysis of dynamic protein carbonylation in rice embryo during germination through AP-SWATH.

Seed germination is an important aspect of the plant life cycle, during which, reactive oxygen species (ROS) accumulate. The accumulation of ROS results in an increase in protein oxidation of which carbonylation is the most canonical one. However, there is insufficient information concerning protein oxidation, especially carbonylation and its contribution to seed germination. In this study, biotin hydrazide labeled chromatography combined with sequential window acquisition of all theoretical fragment ion spectra (SWATH) method was used to analyze the dynamic pattern of protein carbonylation in rice embryos during germination. A total of 1872 unique proteins were quantified, among which 288 carbonylated peptides corresponding to 144 proteins were determined based on the filtering through mass shifts of modified amino acids. In addition, 66 carbonylated proteins were further analyzed based on their carbonylation intensity in four stages of germination. These identified carbonylated proteins were mainly involved in maintaining the levels of ROS, abscisic acid and seed reserves. Remarkably, a peroxiredoxin was found with 23 unique carbonylated peptides, and the expression of which was consistent with its increased activity. This study describes the dynamic pattern of carbonylated proteins during seed germination, and may help to further understand the biochemical mechanisms on this process.

Quantitative toxicoproteomic analysis of zebrafish embryos exposed to a retinoid X receptor antagonist UVI3003.

Retinoid X receptor (RXR) antagonists, including some environmental endocrine disruptors, have a teratogenic effect on vertebrate embryos. To investigate the toxicological mechanism on the protein expression level, a quantitative proteomic study was conducted to analyze the proteome alterations of zebrafish (Danio rerio) embryos exposed to gradient concentrations of a representative RXR antagonist UVI3003. Using isobaric Tags for Relative and Absolute Quantitation (iTRAQ) labeling coupled nano high-performance liquid chromatography-tandem mass spectrometry (nano HPLC-MS/MS), in total 6592 proteins were identified, among which 195 proteins were found to be differentially expressed by more than a two-fold change in exposed groups compared with the control. Gene ontology analysis showed that these differential proteins were mostly involved in anatomical structure development, biosynthetic process, ion binding and oxidoreductase activity. Moreover, the biological pathways of translation, lipoprotein metabolism, cell survival and gluconeogenesis were intensively inhibited after exposure. Some significantly downregulated proteins such as apolipoprotein A-I and vitellogenin and upregulated proteins such as calcium activated nucleotidase 1b, glutathione S-transferase and glucose 6-dehydrogenases showed a strong dose-dependent response. The results provided new insight into the molecular details of RXR antagonist-induced teratogenicity and added novel information of pathways and potential biomarkers for evaluation of RXR interfering activity.

Quantitative proteomic analysis of Salmonella enterica serovar Typhimurium under PhoP/PhoQ activation conditions.

The PhoP/PhoQ two-component system plays a central regulatory role in the pathogenesis of Salmonella enterica serovar Typhimurium (S. Typhimurium), and it can be activated by low Mg(2+) concentrations and sublethal concentrations of cationic antimicrobial peptides (CAMP). Therefore, these two PhoP/PhoQ activation signals are considered as in vivo environmental cues sensed by S. Typhimurium for adaptation and survival. In this work, we conducted a SILAC (stable isotope labeling by amino acids in cell culture)-based quantitative proteomic study to survey the proteomic changes of S. Typhimurium in response to low Mg(2+) concentrations or CAMP. We discovered that CAMP activated a portion of the PhoP/PhoQ regulatory network, whereas low Mg(2+) concentrations upregulated nearly all known members of this network, a number of previously unknown proteins, and some proteins regulated by IHF and RpoS. Systematic analysis following metabolic pathways revealed that low Mg(2+) concentrations selectively influenced proteins of certain metabolic functions while CAMP did not. Our study indicates that the low Mg(2+)-concentration condition may lead S. Typhimurium into a growth-control lifestyle, which provides new perspectives about Salmonella's adaptation to the host environment.

Effect of matrine on transforming growth factor ß1 and hepatocyte growth factor in rat liver fibrosis model.

OBJECTIVE: To observe the preventive and control effect of matrine on transforming growth factor (TGF-ß1) and hepatocyte growth factor (HGF) of liver fibrosis tissue in rats. METHODS: A total of 48 SD rats were randomly divided into A, B, C, D groups with 12 in each, group A as the normal control group and groups B, C, D as liver fibrosis models using composite modulus method with carbon tetrachloride (CCL4). Group B was the model group, group C adopted γ-interferon lavage therapy in the second day of modeling, and group D adopted matrine lavage treatment, at 4 and 8 weeks after treatment. Six rats were executed for detection of TGF-ß1 and HGF, liver tissue histology and comparison fibrosis degree changes of rat liver tissue between groups. RESULTS: Groups B, C, D showed a more significantly increased TGF-ß1 at each time point compared with group A (P<0.05); Group B showed a more significantly increased TGF-ß1 than groups C and D at weeks 4 and 8 (P<0.05); group D showed a lowest level of TGF-ß1, followed by groups C and B. HGF of group B decreased more significantly than A group at weeks 4 and 8 (P<0.05); HGF of groups C and D was significantly elevated at 4 and 8 weeks than groups A and B (P<0.05), in which the group D showed the highest level of HGF. According to tissue histologic observation, rat liver tissue structure of group A was clear and normal, tissue structure of group B was destroyed with obvious fibrous tissue hyperplasia and fatty change of hepatic cells; groups C and D showed a slighter liver tissue damage, cell necrosis and connective tissue hyperplasia in collect abbacy than group B with a trend of obvious improvement. CONCLUSIONS: Matrine can reduce TGF-ß1 expression and enhance the activity of HGF, so as to realize the inhibition effect on liver fibrosis in rats.

Quantitative proteomics of Sesuvium portulacastrum leaves revealed that ion transportation by V-ATPase and sugar accumulation in chloroplast played crucial roles in halophyte salt tolerance.

Physiological and proteomic responses of Sesuvium portulacastrum leaves under salinity were investigated. Different from glycophytes, this halophyte had optimal growth at 200-300mM NaCl and accumulated more starch grains in chloroplasts under high salinity. Increased contents of soluble sugars, proline, and Na(+) were observed upon salinity. X-ray microanalysis revealed that Na(+) was mainly compartmentalized into cell vacuole. Quantitative proteomics produced 96 salt responsive proteins, and the majority was chloroplast-located proteins. Gene ontology analysis revealed that proteins involved in ion binding, proton transport, photosynthesis and ATP synthesis were overrepresented. The expressions of a Na(+)/H(+) antiporter and several ATP synthase subunits were activated upon high salinity. ATP hydrolysis assay demonstrated that V-ATPase activity at tonoplast was dramatically increased upon NaCl whereas vacuolar H(+)-pyrophosphatase and plasma membrane P-ATPase activities were not increased, which indicated that sodium compartmentalization was mainly performed by enhancing V-ATPase activity rather than P-ATPase and H(+)-pyrophosphatase. Accumulation of soluble sugars as well as sodium compartmentalization maintained the osmotic balance between vacuole and cytoplasm, which finally established ionic homeostasis in saline cells in true halophytes. BIOLOGICAL SIGNIFICANCE: Physiological and proteomic analyses of S. portulacastrum leaves under different salinities were investigated. This true halophyte accumulated more soluble sugars, starch, proline and Na(+) under high salinity. Differential proteomics produced 96 salt responsive proteins and the majority was involved in ion binding, proton transport, photosynthesis, and ATP synthesis. A Na(+)/H(+) antiporter and several ATP synthase subunits were induced upon high salinity. ATP hydrolysis assay demonstrated that V-ATPase activity at tonoplast was dramatically increased whereas vacuolar H(+)-pyrophosphatase and plasma membrane ATPase activities were stable upon NaCl. These findings demonstrated that the increased Na(+) was compartmentalized into vacuole by enhancing V-ATPase activity rather than H(+)-ATPase.

Isolation of thylakoid membrane complexes from rice by a new double-strips BN/SDS-PAGE and bioinformatics prediction of stromal ridge subunits interaction.

Thylakoid membrane complexes of rice (Oryza sativa L.) play crucial roles in growth and crop production. Understanding of protein interactions within the complex would provide new insights into photosynthesis. Here, a new "Double-Strips BN/SDS-PAGE" method was employed to separate thylakoid membrane complexes in order to increase the protein abundance on 2D-gels and to facilitate the identification of hydrophobic transmembrane proteins. A total of 58 protein spots could be observed and subunit constitution of these complexes exhibited on 2D-gels. The generality of this new approach was confirmed using thylakoid membrane from spinach (Spinacia oleracea) and pumpkin (Cucurita spp). Furthermore, the proteins separated from rice thylakoid membrane were identified by the mass spectrometry (MS). The stromal ridge proteins PsaD and PsaE were identified both in the holo- and core- PSI complexes of rice. Using molecular dynamics simulation to explore the recognition mechanism of these subunits, we showed that salt bridge interactions between residues R19 of PsaC and E168 of PasD as well as R75 of PsaC and E91 of PsaD played important roles in the stability of the complex. This stromal ridge subunits interaction was also supported by the subsequent analysis of the binding free energy, the intramolecular distances and the intramolecular energy.