The Pd (II) Reduction Mechanisms in Bacillus megaterium Y-4 Revealed by Proteomic Analysis.

Many studies have been conducted on the microbial reduction of Pd (II) to palladium nanoparticles (Pd-NPs) due to the environmental friendliness, low cost, and the decreased toxicity of Pd (II) ions. In this study, we investigate the reduction mechanism of Pd (II) by Bacillus megaterium Y-4 through proteomics. The data are available via ProteomeXchange with identifier PXD049711. Our results revealed that B. megaterium Y-4 may use the endogenous electron donor (NAD(P)H) generated by nirB, tdh, and fabG and reductase to reduce Pd (II) to Pd-NPs. The expression levels of fabG, tdh, gudB, and rocG that generate NAD(P)H were further increased, and the number of reduced Pd-NPs was further increased with the exogenous electron donor sodium formate. Endogenous electron mediators such as quinones and flavins in B. megaterium Y-4 can further enhance Pd (II) reduction. The findings provided invaluable information regarding the reduction mechanism of Pd (II) by B. megaterium Y-4 at the proteome level.

The effect of different angle kappa on higher-order aberrations after small incision lenticule extraction.

This study aimed to compare higher-order aberrations (HOAs) after small incision lenticule extraction (SMILE) in patients with different angle kappa. This is a retrospective report in which 341 right eyes of 341 patients who were subjected to SMILE, which used coaxially sighted corneal light reflex (CSCLR) as the treatment zone centered, treated by the same experienced surgeon (LHB) for correction of myopia and myopic astigmatism, preoperative and postoperative spherical equivalent (SE), angle kappa, total higher-order aberrations (total HOA), spherical aberration (SA), vertical coma (VC), horizontal coma (HC), oblique trefoil (OT), and horizontal trefoil (HT), were compared. SMILE showed outstanding performance in terms of safety, efficacy, and predictability. In addition, a comparison of preoperative and postoperative HOAs exhibited the difference of total HOA (P < 0.01), SA (P < 0.01), VC (P < 0.01), and HC (P < 0.01), which was statistically significant; however, for OT and HT with the longer follow-up time, the statistical difference gradually decreased. For stratification of angle kappa into groups based on decantation, angle kappa was divided into three major groups: r < 0.1 mm, 0.1 ≤ r < 0.2 mm, and r ≥ 0.2 mm; the changes of SA (F = 4.127, P = 0.021) and OT (F = 3.687, P = 0.031) exhibited significant difference after 1 year of SMILE. We performed a correlation analysis of all preoperative and postoperative parameters, and the results indicated that the preoperative total HOA was negatively correlated with preoperative cylindrical diopter (DC), and postoperative total HOA, SA, and coma were affected by spherical diopter (DS) and SE. Moreover, we also found a significant difference of SA and VC in the early postoperative with preoperative. SA was positively correlated with Y values and r of 1 year after SMILE. All of the analyzed parameters in the three groups, except for the trefoil, gradually increased over time; however, the trefoil could gradually stabilize over time. We also divided angle kappa into four groups by quadrants; the result showed that the effects of higher-order aberrations were markedly different from the various quadrants. Patients with large angle kappa were able to increase VC and SA postoperatively, and higher HOAs were more significant in patients with high myopia. The differences in quadrants exhibited a diversity of HOAs; this could be attributed to the corneal surface reestablishment and the alteration of angle kappa, but the trend was not apparent. Although all patients displayed increased HOAs after SMILE, the potential application of CSCLR as the treatment zone centered still showed excellent safety, efficacy, and predictability.

Advantage effect of Dalbergia pinnata on wound healing and scar formation of burns.

ETHNOPHARMACOLOGICAL RELEVANCE: Dalbergia pinnata, as a natural and ethnic medicine in China, has been used for burns and wounds with a long history, which has the effect of invigorating blood and astringent sores. However, there were no reports on the advantage activity of burns. AIM OF STUDY: The purpose of this study was to screen out the best active extract part of Dalbergia pinnata and investigate its therapeutic effect on wound healing and scar resolution. MATERIALS AND METHODS: Rat burn model was established and the healing effects of extracts from Dalbergia pinnata on burn wounds were evaluated by the percentage of wound contraction and period of epithelialization. Histological observation, immunohistochemistry, immunofluorescence and ELISA were used for the examination of inflammatory factors, TGF-ß1, neovascularization and collagen fibers through the period of epithelialization. In addition, the effect of the optimal extraction site on fibroblast cells was evaluated by cell proliferation and cell migration assays. The extracts of Dalbergia pinnata were analyzed by UPLC-Q/TOF-MS or GC-MS technique. RESULTS: Compared to the model group, there were better wound healing, suppressed inflammatory factors, more neovascularization as well as newly formed collagen in the ethyl acetate extract (EAE) and petroleum ether extract (PEE) treatment groups. The ratio of Collagen I and Collagen III was lower in the EAE and PEE treatment groups, suggesting a potential for reduced scarring. Furthermore, EAE and PEE could repair wounds by up-regulating TGF-ß1 in the early stage of wound repair and down-regulating TGF-ß1 in the late stage. In vitro studies showed that both EAE and PEE were able to promote NIH/3T3 cells proliferation and migration compared with the control group. CONCLUSIONS: In this study, EAE and PEE were found to significantly accelerate wound repair and might have an inhibitory effect on the generation of scars. It was also hypothesized that the mechanism might be related to the regulation of TGF-ß1 secretion. This study provided an experimental basis for the development of topical drugs for the treatment of burns with Dalbergia pinnata.

Polysaccharides from Ostrea rivularis rebuild the balance of gut microbiota to ameliorate non-alcoholic fatty liver disease in ApoE-/- mice.

The purpose of this study was to investigate the preventive effects of polysaccharide from Ostrea rivularis (ORP) on high-fat diet (HFD)-induced nonalcoholic fatty liver disease (NAFLD) in mice and the underlying mechanism. The results showed that NAFLD model group mice had significant fatty liver lesions. ORP could significantly reduce TC, TG and LDL level, and increase HDL level in serum of HFD mice. Besides, it could also reduce the contents of serum AST and ALT and alleviate pathological changes of fatty liver disease. ORP could also enhance the intestinal barrier function. 16sRNA analysis showed that ORP could reduce the abundance of Firmicutes and Proteobacteria and the ratio of Firmicutes/ Bacteroidetes at the phylum level. These results suggested that ORP could regulate the composition of gut microbiota in NAFLD mice, enhance intestinal barrier function, reduce intestinal permeability, and finally delay the progress and reduce the occurrence of NAFLD. In brief, ORP is an ideal polysaccharide for prevention and treatment of NAFLD, which can be developed as functional food or candidate drugs.

Synchronous bio-degradation and bio-electricity generation in a Microbial Fuel Cell with aged and fresh leachate from the identical subtropical area.

Seasonal leachate from both sealed and operating landfill in the identical district were employed as the sole substrate in the Microbial Fuel Cell (MFC) to evaluate the power output performance and aqueous organic waste disposal. The electrical performance was characterized to study the power generation, while the Chemical Oxygen Demand (COD) removal ratio and Coulombic Efficiency (CE) were calculated to illustrate the substrate disposal effect. In addition, Scanning Electron Microscope (SEM) on the operated anode was conducted to preliminarily explain the microbial community difference, and the phylogenetic tree constructed on the cultivated microorganism was an insight into the dominant bacteria suitable for leachate degradation. It was found that the MFCs inoculated with seasonal leachate from both sealed and operating landfill could generate electricity successfully. Although the fresh leachate-inoculated MFCs had better electrical output performance (22.7-25.6 W/m3 versus 6.61-7.48 W/m3) and COD removal efficiency (55.8%∼61.7% versus 47.7%∼51.4%), the CEs were only 4.3%∼7.6%, which were lower than the aged leachate inoculated group (5.9%∼11.3%). Based on the SEM images and the phylogenetic tree of the operated anode, the composition impacts on the microbial community and power output performance were verified, which was instructive for the leachate disposal in the MFC.

Engineering a vitamin B12 high-throughput screening system by riboswitch sensor in Sinorhizobium meliloti.

BACKGROUND: As a very important coenzyme in the cell metabolism, Vitamin B12 (cobalamin, VB12) has been widely used in food and medicine fields. The complete biosynthesis of VB12 requires approximately 30 genes, but overexpression of these genes did not result in expected increase of VB12 production. High-yield VB12-producing strains are usually obtained by mutagenesis treatments, thus developing an efficient screening approach is urgently needed. RESULT: By the help of engineered strains with varied capacities of VB12 production, a riboswitch library was constructed and screened, and the btuB element from Salmonella typhimurium was identified as the best regulatory device. A flow cytometry high-throughput screening system was developed based on the btuB riboswitch with high efficiency to identify positive mutants. Mutation of Sinorhizobium meliloti (S. meliloti) was optimized using the novel mutation technique of atmospheric and room temperature plasma (ARTP). Finally, the mutant S. meliloti MC5-2 was obtained and considered as a candidate for industrial applications. After 7 d's cultivation on a rotary shaker at 30 °C, the VB12 titer of S. meliloti MC5-2 reached 156 ± 4.2 mg/L, which was 21.9% higher than that of the wild type strain S. meliloti 320 (128 ± 3.2 mg/L). The genome of S. meliloti MC5-2 was sequenced, and gene mutations were identified and analyzed. CONCLUSION: To our knowledge, it is the first time that a riboswitch element was used in S. meliloti. The flow cytometry high-throughput screening system was successfully developed and a high-yield VB12 producing strain was obtained. The identified and analyzed gene mutations gave useful information for developing high-yield strains by metabolic engineering. Overall, this work provides a useful high-throughput screening method for developing high VB12-yield strains.

Bexarotene protects against traumatic brain injury in mice partially through apolipoprotein E.

Bexarotene has been proved to have neuroprotective effects in many animal models of neurological diseases. However, its neuroprotection in traumatic brain injury (TBI) is still unknown. This study aims to explore the neuroprotective effects of bexarotene on TBI and its possible mechanism. Controlled cortical impact (CCI) model was used to simulate TBI in C57BL/6 mice as well as APOE gene knockout (APOE-KO) mice. After CCI, mice were daily dosed with bexarotene or vehicle solution intraperitoneally. The motor function, learning and memory, inflammatory factors, microglia amount, apoptosis condition around injury site and main side-effects were all measured. The results showed that, after CCI, bexarotene treatment markedly improved the motor function and spatial memory in C57BL/6 compare to APOE-KO mice which showed no improvement. The inflammatory cytokines, microglia amount, cell apoptosis rate, and protein of cleaved caspase-3 around the injury site were markedly upregulated after TBI in both C57BL/6 and APOE-KO mice, and all these upregulation were significantly mitigated by bexarotene treatment in C57BL/6 mice, but not in APOE-KO mice. No side-effects were detected after consecutive administration. Taken together, bexarotene inhibits the inflammatory response as well as cell apoptosis and improves the neurological function of mice after TBI partially through apolipoprotein E. This may make it a promising candidate for the therapeutic treatment after TBI.

Using Formal Concept Analysis to Identify Negative Correlations in Gene Expression Data.

Recently, many biological studies reported that two groups of genes tend to show negatively correlated or opposite expression tendency in many biological processes or pathways. The negative correlation between genes may imply an important biological mechanism. In this study, we proposed a FCA-based negative correlation algorithm (NCFCA) that can effectively identify opposite expression tendency between two gene groups in gene expression data. After applying it to expression data of cell cycle-regulated genes in yeast, we found that six minichromosome maintenance family genes showed the opposite changing tendency with eight core histone family genes. Furthermore, we confirmed that the negative correlation expression pattern between these two families may be conserved in the cell cycle. Finally, we discussed the reasons underlying the negative correlation of six minichromosome maintenance (MCM) family genes with eight core histone family genes. Our results revealed that negative correlation is an important and potential mechanism that maintains the balance of biological systems by repressing some genes while inducing others. It can thus provide new understanding of gene expression and regulation, the causes of diseases, etc.

Furfural and hydroxymethylfurfural tolerance in Escherichia coli ΔacrR regulatory mutants.

The presence of the highly toxic furfural and hydroxymethylfurfural (HMF) in the hydrolysate of lignocellulosic biomass prompted the investigation of the Escherichia coli ΔacrR regulatory mutant for higher tolerance to these compounds, to facilitate the production of biofuels and biochemicals, and further biocatalytic conversions. In comparison with the parental strain, the regulatory mutant with the upregulated efflux pump AcrAB-TolC produced moderately better growth and higher tolerance to concentrations of furfural and HMF between 1 and 2 g L(-1) .

High performance relaxor-based ferroelectric single crystals for ultrasonic transducer applications.

Relaxor-based ferroelectric single crystals Pb(Mg1/3Nb2/3)O3-PbTiO3 (PMN-PT) have drawn much attention in the ferroelectric field because of their excellent piezoelectric properties and high electromechanical coupling coefficients (d33~2000 pC/N, kt~60%) near the morphotropic phase boundary (MPB). Ternary Pb(In1/2Nb1/2)O3-Pb(Mg1/3Nb2/3)O3-PbTiO3 (PIN-PMN-PT) single crystals also possess outstanding performance comparable with PMN-PT single crystals, but have higher phase transition temperatures (rhombohedral to tetragonal Trt, and tetragonal to cubic Tc) and larger coercive field Ec. Therefore, these relaxor-based single crystals have been extensively employed for ultrasonic transducer applications. In this paper, an overview of our work and perspectives on using PMN-PT and PIN-PMN-PT single crystals for ultrasonic transducer applications is presented. Various types of single-element ultrasonic transducers, including endoscopic transducers, intravascular transducers, high-frequency and high-temperature transducers fabricated using the PMN-PT and PIN-PMN-PT crystals and their 2-2 and 1-3 composites are reported. Besides, the fabrication and characterization of the array transducers, such as phased array, cylindrical shaped linear array, high-temperature linear array, radial endoscopic array, and annular array, are also addressed.

Enoyl acyl carrier protein reductase (FabI) catalyzed asymmetric reduction of the C=C double bond of α,ß-unsaturated ketones: preparation of (R)-2-alkyl-cyclopentanones.

Enoyl-ACP reductase (FabI) was identified as a non-OYE 'ene'-reductase for asymmetric reduction of the C=C double bond of α, ß-unsaturated ketones. Reduction of several 2-alkylidenecyclopentanones with A-FabI and E-FabI gave (R)-2-alkylcyclopentanones in 95-90% and 70-81% ee, respectively. The product ee was improved to 99-98% in high yield by subsequent one-pot biooxidation.

Surface chemistry modulates osteoblasts sensitivity to low fluid shear stress.

Low fluid shear stress (FSS) is the mechanical environment encountered by osteoblasts in implanted bones or native bones of bed rest patients. High sensitivity of osteoblasts to low FSS is beneficial to osteogenesis. We hypothesize that this sensitivity might be regulated by chemical microenvironment provided by scaffolds. To confirm this hypothesis, self-assembled monolayers (SAMs) were used to provide various surface chemistries including OH, CH3 , and NH2 while parallel-plate fluid flow system produced low FSS (5 dynes/cm(2) ). Alterations in S-phase cell fraction, alkaline phosphatase activity, fibronectin (Fn), and collagen type I (COL I) secretion compared to those without FSS exposure were detected to characterize the sensitivity. Osteoblasts on OH and CH3 SAMs demonstrated obvious sensitivity while on NH2 SAMs negligible sensitivity was observed. Examination of the cell aspect ratio, orientation, and focal adhesions before and after FSS exposure indicates that the full spreading and robust focal adhesions on NH2 SAMs should be responsible for the negligible sensitivity through increasing the cell tolerance to low FSS. Despite the higher sensitivity, the Fn and COL I depositions on both OH and CH3 SAMs after FSS exposure were still less than on NH2 SAMs without FSS exposure. These results suggest that elaborate design of surface chemical compositions is essential for orchestration of surface chemistry with low FSS to realize both high sensitivity and high matrix secretion, facilitating the formation of functional bone tissues in implanted bone.

Accumulated lipids rather than the rigid cell walls impede the extraction of genetic materials for effective colony PCRs in Chlorella vulgaris.

BACKGROUND: Failure of colony PCRs in green microalga Chlorella vulgaris is typically attributed to the difficulty in disrupting its notoriously rigid cell walls for releasing the genetic materials and therefore the development of an effective colony PCR procedure in C. vulgaris presents a challenge. RESULTS: Here we identified that colony PCR results were significantly affected by the accumulated lipids rather than the rigid cell walls of C. vulgaris. The higher lipids accumulated in C. vulgaris negatively affects the effective amplification by DNA polymerase. Based on these findings, we established a simple and extremely effective colony PCR procedure in C. vulgaris. By simply pipetting/votexing the pellets of C. vulgaris in 10 ul of either TE (10 mM Tris/1 mM EDTA) or 0.2% SDS buffer at room temperature, followed by the addition of 10 ul of either hexane or Phenol:Chloroform:Isoamyl Alcohol in the same PCR tube for extraction. The resulting aqueous phase was readily PCR-amplified as genomic DNA templates as demonstrated by successful amplification of the nuclear 18S rRNA and the chloroplast rbcL gene. This colony PCR protocol is effective and robust in C. vulgaris and also demonstrates its effectiveness in other Chlorella species. CONCLUSIONS: The accumulated lipids rather than the rigid cell walls of C. vulgaris significantly impede the extraction of genetic materials and subsequently the effective colony PCRs. The finding has the potential to aid the isolation of high-quality total RNAs and mRNAs for transcriptomic studies in addition to the genomic DNA isolation in Chlorella.

Size of gene specific inverted repeat--dependent gene deletion In Saccharomyces cerevisiae.

We describe here an approach for rapidly producing scar-free and precise gene deletions in S. cerevisiae with high efficiency. Preparation of the disruption gene cassette in this approach was simply performed by overlap extension-PCR of an invert repeat of a partial or complete sequence of the targeted gene with URA3. Integration of the prepared disruption gene cassette to the designated position of a target gene leads to the formation of a mutagenesis cassette within the yeast genome, which consists of a URA3 gene flanked by the targeted gene and its inverted repeat between two short identical direct repeats. The inherent instability of the inverted sequences in close proximity facilitates the self-excision of the entire mutagenesis cassette deposited in the genome and promotes homologous recombination resulting in a seamless deletion via a single transformation. This rapid assembly circumvents the difficulty during preparation of disruption gene cassettes composed of two inverted repeats of the URA3, which requires the engineering of unique restriction sites for subsequent digestion and T4 DNA ligation in vitro. We further identified that the excision of the entire mutagenesis cassette flanked by two DRs in the transformed S. cerevisiae is dependent on the length of the inverted repeat of which a minimum of 800 bp is required for effective gene deletion. The deletion efficiency improves with the increase of the inverted repeat till 1.2 kb. Finally, the use of gene-specific inverted repeats of target genes enables simultaneous gene deletions. The procedure has the potential for application on other yeast strains to achieve precise and efficient removal of gene sequences.

An extremely simple and effective colony PCR procedure for bacteria, yeasts, and microalgae.

An extremely simple and effective colony PCR procedure is established for both gram-negative and gram-positive bacteria, yeasts, and microalgae. Among the four lysis buffers examined, Y-PER is observed to be more effective than Tris/EDTA, 0.2 % SDS, and 10 mM EDTA in the extraction of PCR-quality genomic DNA from those microorganisms. Vortexing or pipetting agitation of the cells in Y-PER for 5-10 s was sufficient to release genomic DNA for all the test bacteria and yeasts, and most microalgae. Additional incubation at 98 °C for 5 min for further cell disruption was essential only for Chlorella vulgaris due to its notoriously rigid cell wall.

Thermal-independent properties of PIN-PMN-PT single-crystal linear-array ultrasonic transducers.

In this paper, low-frequency 32-element linear-array ultrasonic transducers were designed and fabricated using both ternary Pb(In(1/2)Nb(1/2))-Pb(Mg(1/3)Nb(2/3))-PbTiO(3) (PIN-PMN-PT) and binary Pb(Mg(1/3)Nb(2/3))-PbTiO(3) (PMNPT) single crystals. Performance of the array transducers was characterized as a function of temperature ranging from room temperature to 160°C. It was found that the array transducers fabricated using the PIN-PMN-PT single crystal were capable of satisfactory performance at 160°C, having a -6-dB bandwidth of 66% and an insertion loss of 37 dB. The results suggest that the potential of PIN-PMN-PT linear-array ultrasonic transducers for high-temperature ultrasonic transducer applications is promising.

Screened butanol-tolerant Enterococcus faecium capable of butanol production.

Due to the complex mechanisms involved in butanol-induced stress response, butanol tolerance phenotype is difficult to engineer even in microorganisms with well-defined genetic backgrounds. We therefore aimed to isolate butanol-tolerant microorganisms from environmental samples as potential alternative hosts for butanol production. Soil samples collected were subjected to butanol stress. A microbial strain capable of 2.5-3 % (w/v) butanol tolerance was isolated and identified as Enterococcus faecium by 16S rDNA analysis. The isolate grew readily under both aerobic and anaerobic conditions and was capable of producing butanol anaerobically. In comparison with the obligate anaerobe Clostridium acetobutylicum, the growth under both aerobic and anaerobic conditions of the isolated strain, together with no detection of butyrate and lack of two-phase fermentation suggests different metabolic networks from the obligate anaerobe C. acetobutylicum. Under anaerobic condition, butanol reached up to 0.4 gl(-1) in a batch culture without heterologous introduction of butanol biosynthetic pathway. Besides butanol tolerance, the isolated E. faecium IB1 showed high tolerance to 10 % (w/v) ethanol and 3 % (w/v) isobutanol. With distinct features including high butanol tolerance and natural butanol production, the isolated E. faecium IB1 with minimum metabolic engineering can be explored as a potential host for butanol production.

Increase of ethanol tolerance of Saccharomyces cerevisiae by error-prone whole genome amplification.

Saccharomyces cerevisiae was transformed for higher ethanol tolerance by error-prone whole genome amplification. The resulting PCR products were transformed back to the parental strain for homologous recombination to create a library of mutants with the perturbed genomic networks. A few rounds of transformation led to the isolation of mutants that grew in 9% (v/v) ethanol and 100 g glucose l(-1) compared to untransformed yeast which grew only at 6% (v/v) ethanol and 100 g glucose l(-1).

Expression of arabinogalactan proteins involved in Taxol production by immobilized Taxus cuspidata cells.

The expression of arabinogalactan-proteins (AGPs), known as extracellular signal molecules, in immobilized T. cuspidata cells was investigated by immunofluorescence localization and Western blot analysis. It was found that the relative intensity of JIM13-reactive AGPs and Taxol production by T. cuspidata cells was increased 1.43-fold and 2.2-fold by immobilized cultures on day 25, respectively. Particularly, the expression levels of JIM13-reactive AGPs were much higher in the cells located in central and middle zones of the immobilized support matrices than these in the outer zone or in the suspension. Whether in immobilized T. cuspidata cells or in suspended T. cuspidata cells, the expression level of JIM13-reactive AGPs and Taxol production after two to three subcultures had no significant changes, but the immobilized cells always kept high-level expression of JIM13-reactive AGP and Taxol production during subcultures. Moreover, the enhancement of Taxol production was accompanied with a high-level expression of JIM13-reactive AGPs by T. cuspidata cells after treatment with 200 microM methyl jasmonate. Taken together, these results implicate that the AGPs in T. cuspidata cells may be taken as potential signal molecular involved in regulating the Taxol production by immobilized T. cuspidata cells.

Mung bean lipoxygenase in the production of a C6-aldehyde. Natural green-note flavor generation via biotransformation.

Mung bean was investigated as a novel source of lipoxygenase in the natural production of the green-note aroma compound hexanal. Lipoxygenase extracted from mung bean catalyzed the oxidative reaction of linoleic acid, after which the intermediate hydroperoxide compound was split via green bell pepper hydroperoxide lyase to produce hexanal. In comparison to soybean lipoxygenase, mung bean lipoxygenase was found to be a good substitute as it produced 15.4 mM (76% yield) hexanal while soybean gave 60% yield. The mung bean pH profile comprised a wide peak (optimum pH 6.5) representing lipoxygenase-2 and lipoxygenase-3 isozymes, whereas two narrower peaks representing lipoxygenase-1 and lipoxygenase-2/3 isozymes were observed for soybean (optimum pH 10). Extraction at pH 4.5 was preferred, at which specific lipoxygenase activity was also the highest.