Leaching alleviates phenol-mediated root rot in Panax notoginseng by modifying the soil microbiota

Plant and Soil - Numerous Bacillus spp. in soils show strong plant growth-promotion effects, but the molecular mechanism of most of these bacteria interacting with plants remains unknown....     

Identification of immune-based prostate cancer subtypes using mRNA expression

Immune infiltration in Prostate Cancer (PCa) was reported to be strongly associated with clinical outcomes. However, previous research could not elucidate the diversity of different immune cell types that contribute to the functioning of the immune response system. In the present study, the CIBERSORT method was employed to evaluate the relative proportions of immune cell profiling in PCa samples, adjacent tumor samples and normal samples. Three types of molecular classification were identified in tumor samples using the ‘CancerSubtypes’ package of the R software. Each subtype had specific molecular and clinical characteristics. In addition, functional enrichment was analyzed in each subtype. The submap and Tumor Immune Dysfunction and Exclusion (TIDE) algorithms were also used to predict clinical response to the immune checkpoint blockade. Moreover, the Genomics of Drug Sensitivity in Cancer (GDSC) database was employed to screen for potential chemotherapeutic targets for the treatment of PCa. The results showed that Cluster I was associated with advanced PCa and was more likely to respond to immunotherapy. The findings demonstrated that differences in immune responses may be important drivers of PCa progression and response to treatment. Therefore, this comprehensive assessment of the 22 immune cell types in the PCa Tumor Environment (TEM) provides insights on the mechanisms of tumor response to immunotherapy and may help clinicians explore the development of new drugs.     

Anatomy of enzyme channels

Background

Enzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is known about how often channels are present or about any structural features such channels may have in common.

Results

Here, we analyze the long channels (i.e. >15 Å) leading to the active sites of 4,306 enzyme structures. We find that over 64% of enzymes contain two or more long channels, their typical length being 28 Å. We show that amino acid compositions of the channel significantly differ both to the composition of the active site, surface and interior of the protein.

Conclusions

The majority of enzymes have buried active sites accessible via a network of access channels. This indicates that enzymes tend to have buried active sites, with channels controlling access to, and egress from, them, and that suggests channels may play a key role in helping determine enzyme substrate.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0379-x) contains supplementary material, which is available to authorized users.     

Archaeal aminoacyl-tRNA synthetases interact with the ribosome to recycle tRNAs

Aminoacyl-tRNA synthetases (aaRS) are essential enzymes catalyzing the formation of aminoacyl-tRNAs, the immediate precursors for encoded peptides in ribosomal protein synthesis. Previous studies have suggested a link between tRNA aminoacylation and high-molecular-weight cellular complexes such as the cytoskeleton or ribosomes. However, the structural basis of these interactions and potential mechanistic implications are not well understood. To biochemically characterize these interactions we have used a system of two interacting archaeal aaRSs: an atypical methanogenic-type seryl-tRNA synthetase and an archaeal ArgRS. More specifically, we have shown by thermophoresis and surface plasmon resonance that these two aaRSs bind to the large ribosomal subunit with micromolar affinities. We have identified the L7/L12 stalk and the proteins located near the stalk base as the main sites for aaRS binding. Finally, we have performed a bioinformatics analysis of synonymous codons in the Methanothermobacter thermautotrophicus genome that supports a mechanism in which the deacylated tRNAs may be recharged by aaRSs bound to the ribosome and reused at the next occurrence of a codon encoding the same amino acid. These results suggest a mechanism of tRNA recycling in which aaRSs associate with the L7/L12 stalk region to recapture the tRNAs released from the preceding ribosome in polysomes.     

In Vitro Antibacterial Activity of a Novel Resin-Based Pulp Capping Material Containing the Quaternary Ammonium Salt MAE-DB and Portland Cement

Background

Vital pulp preservation in the treatment of deep caries is challenging due to bacterial infection. The objectives of this study were to synthesize a novel, light-cured composite material containing bioactive calcium-silicate (Portland cement, PC) and the antimicrobial quaternary ammonium salt monomer 2-methacryloxylethyl dodecyl methyl ammonium bromide (MAE-DB) and to evaluate its effects on Streptococcus mutans growth in vitro.

Methods

The experimental material was prepared from a 2∶1 ratio of PC mixed with a resin of 2-hydroxyethylmethacrylate, bisphenol glycerolate dimethacrylate, and triethylene glycol dimethacrylate (4∶3∶1) containing 5 wt% MAE-DB. Cured resin containing 5% MAE-DB without PC served as the positive control material, and resin without MAE-DB or PC served as the negative control material. Mineral trioxide aggregate (MTA) and calcium hydroxide (Dycal) served as commercial controls. S. mutans biofilm formation on material surfaces and growth in the culture medium were tested according to colony-forming units (CFUs) and metabolic activity after 24 h incubation over freshly prepared samples or samples aged in water for 6 months. Biofilm formation was also assessed by Live/Dead staining and scanning electron microscopy.

Results

S. mutans biofilm formation on the experimental material was significantly inhibited, with CFU counts, metabolic activity, viability staining, and morphology similar to those of biofilms on the positive control material. None of the materials affected bacterial growth in solution. Contact-inhibition of biofilm formation was retained by the aged experimental material. Significant biofilm formation was observed on MTA and Dycal.

Conclusion

The synthesized material containing HEMA-BisGMA-TEGDMA resin with MAE-DB as the antimicrobial agent and PC to support mineralized tissue formation inhibited S. mutans biofilm formation even after aging in water for 6 months, but had no inhibitory effect on bacteria in solution. Therefore, this material shows promise as a pulp capping material for vital pulp preservation in the treatment of deep caries.     

Circulating AIM as an Indicator of Liver Damage and Hepatocellular Carcinoma in Humans

Background

Hepatocellular carcinoma (HCC), the fifth most common cancer type and the third highest cause of cancer death worldwide, develops in different types of liver injuries, and is mostly associated with cirrhosis. However, non-alcoholic fatty liver disease often causes HCC with less fibrosis, and the number of patients with this disease is rapidly increasing. The high mortality rate and the pathological complexity of liver diseases and HCC require blood biomarkers that accurately reflect the state of liver damage and presence of HCC.

Methods and Findings

Here we demonstrate that a circulating protein, apoptosis inhibitor of macrophage (AIM) may meet this requirement. A large-scale analysis of healthy individuals across a wide age range revealed a mean blood AIM of 4.99±1.8 µg/ml in men and 6.06±2.1 µg/ml in women. AIM levels were significantly augmented in the younger generation (20s–40s), particularly in women. Interestingly, AIM levels were markedly higher in patients with advanced liver damage, regardless of disease type, and correlated significantly with multiple parameters representing liver function. In mice, AIM levels increased in response to carbon tetrachloride, confirming that the high AIM observed in humans is the result of liver damage. In addition, carbon tetrachloride caused comparable states of liver damage in AIM-deficient and wild-type mice, indicating no influence of AIM levels on liver injury progression. Intriguingly, certain combinations of AIM indexes normalized to liver marker score significantly distinguished HCC patients from non-HCC patients and thus could be applicable for HCC diagnosis.

Conclusion

AIM potently reveals both liver damage and HCC. Thus, our results may provide the basis for novel diagnostic strategies for this widespread and fatal disease.     

Characterization and engineering of the ethylmalonyl-CoA pathway towards the improved heterologous production of polyketides in Streptomyces venezuelae

Streptomyces venezuelae has an inherent advantage as a heterologous host for polyketide production due to its fast rate of growth that cannot be endowed easily through metabolic engineering. However, the utility of S. venezuelae as a host has been limited thus far due to its inadequate intracellular reserves of the (2S)-ethylmalonyl-CoA building block needed to support the biosynthesis of polyketides preventing the efficient production of the desired metabolite, such as tylactone. Here, via precursor supply engineering, we demonstrated that S. venezuelae can be developed into a more efficient general heterologous host for the quick production of polyketides. We first identified and functionally characterized the ethylmalonyl-CoA pathway which plays a major role in supplying the (2S)-ethylmalonyl-CoA extender unit in S. venezuelae. Next, S. venezuelae was successfully engineered to increase the intracellular ethylmalonyl-CoA concentration by the deletion of the meaA gene encoding coenzyme B₁₂-dependent ethylmalonyl-CoA mutase in combination with ethylmalonate supplementation and was engineered to upregulate the expression of the heterologous tylosin PKS by overexpression of the pathway specific regulatory gene pikD. Thus, a dramatic increase (～10-fold) in tylactone production was achieved. In addition, the detailed insights into the role of the ethylmalonyl-CoA pathway, which is present in most streptomycetes, provides a general strategy to increase the ethylmalonyl-CoA supply for polyketide biosynthesis in the most prolific family of polyketide-producing bacteria.