Alterations of the human gut microbiome in liver cirrhosis.

Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide. Here we characterize the gut microbiome in liver cirrhosis by comparing 98 patients and 83 healthy control individuals. We build a reference gene set for the cohort containing 2.69 million genes, 36.1% of which are novel. Quantitative metagenomics reveals 75,245 genes that differ in abundance between the patients and healthy individuals (false discovery rate < 0.0001) and can be grouped into 66 clusters representing cognate bacterial species; 28 are enriched in patients and 38 in control individuals. Most (54%) of the patient-enriched, taxonomically assigned species are of buccal origin, suggesting an invasion of the gut from the mouth in liver cirrhosis. Biomarkers specific to liver cirrhosis at gene and function levels are revealed by a comparison with those for type 2 diabetes and inflammatory bowel disease. On the basis of only 15 biomarkers, a highly accurate patient discrimination index is created and validated on an independent cohort. Thus microbiota-targeted biomarkers may be a powerful tool for diagnosis of different diseases.

Phosphoproteomic analysis reveals the effects of PilF phosphorylation on type IV pilus and biofilm formation in Thermus thermophilus HB27.

Thermus thermophilus HB27 is an extremely thermophilic eubacteria with a high frequency of natural competence. This organism is therefore often used as a thermophilic model to investigate the molecular basis of type IV pili-mediated functions, such as the uptake of free DNA, adhesion, twitching motility, and biofilm formation, in hot environments. In this study, the phosphoproteome of T. thermophilus HB27 was analyzed via a shotgun approach and high-accuracy mass spectrometry. Ninety-three unique phosphopeptides, including 67 in vivo phosphorylated sites on 53 phosphoproteins, were identified. The distribution of Ser/Thr/Tyr phosphorylation sites was 57%/36%/7%. The phosphoproteins were mostly involved in central metabolic pathways and protein/cell envelope biosynthesis. According to this analysis, the ATPase motor PilF, a type IV pili-related component, was first found to be phosphorylated on Thr-368 and Ser-372. Through the point mutation of PilF, mimic phosphorylated mutants T368D and S372E resulted in nonpiliated and nontwitching phenotypes, whereas nonphosphorylated mutants T368V and S372A displayed piliation and twitching motility. In addition, mimic phosphorylated mutants showed elevated biofilm-forming abilities with a higher initial attachment rate, caused by increasing exopolysaccharide production. In summary, the phosphorylation of PilF might regulate the pili and biofilm formation associated with exopolysaccharide production.

From nanoplates to microtubes and microrods: a surfactant-free rolling mechanism for facile fabrication and morphology evolution of Ag2S films.

By a simple and facile wet-chemistry technique without any surfactant, various shapes of Ag(2)S crystals--including leaflike pentagonal nanoplates, crinkly nanoscrolls, hexagonal prismlike microtubes, and microrods--were fabricated in situ on a large-area silver-foil surface separately. Detailed experiments revealed that the Ag(2)S nanoplates were formed just by immersing the silver foil in a sulfur/ethanol solution at room temperature and atmospheric pressure, and they subsequently rolled into nanoscrolls and further grew into microtubes and microrods under solvothermal conditions. Inspired by the natural curling of a piece of foliage, we proposed a surfactant-free rolling mechanism to interpret the observed morphological evolution from lamellar to tubular structures. Based on these simple, practical, and green chemical synthetic routes, we can easily synthesize lamellar, scrolled, tubular, and clubbed Ag(2)S crystals by simply adjusting the reaction temperature, pressure, and time. It is very interesting to note that the current rolling process is quite different from the previous reported rolling mechanism that highly depends on the surfactants; we revealed that the lamellar Ag(2)S could be rolled into tubular structures without using any surfactant or other chemical additives, just like the natural rolling process of a piece of foliage. Therefore, this morphology-controlled synthetic route of Ag(2)S crystals may provide new insight into the synthesis of metal sulfide semiconducting micro-/nanocrystals with desired morphologies for further industrial applications. The optical properties of the pentagonal Ag(2)S nanoplates/film were also investigated by UV/Vis and photoluminescence (PL) techniques, which showed large blue-shift of the corresponding UV/Vis and PL spectra.