Microstructure and Chemo-Physical Characterizations of Functional Graphene Oxide-Iron Oxide-Silver Ternary Nanocomposite Synthesized by One-Pot Hydrothermal Method.

In this work, a functional graphene oxide-iron oxide-silver (GO-Fe3O4-Ag) ternary nanocomposite was synthesized by using one-pot hydrothermal treatments of mixture solutions of silver nitrate (AgNO3), ferrous chloride tetrahydrate (FeCl2 4H2O), polyvinylpyrrolidone (PVP), graphene oxide (GO), and ammonium hydroxide solution (NH4OH). The systematic effects of synthesis conditions on the microstructure and formation of binary and ternary composite systems were studied. Importantly, high-crystalline GO-Fe3O4-Ag ternary nanomaterials with average sizes of Fe3O4 particles ~16 nm and of Ag particles ~20 nm were obtained at optimized conditions (125 °C, 2.5 mM of AgNO3 and 5 mL of NH4OH). Magnetic analysis indicated that the saturated magnetization value of Fe3O4-Ag binary composite sample (~73.1 emu/g) was improved as compared with pure Fe3O4 nanoparticles (~60.6 emu/g), while this of GO-Fe3O4-Ag ternary composite sample was about 57.3 emu/g. With exhibited advantages of low-cost, high purity and short synthesis time, the hydrothermal-synthesized GO-Fe3O4-Ag ternary nanocomposite can be a promising candidate for advanced environmental catalyst and biomedical applications.

Anti-Inflammatory and Anti-Urolithiasis Effects of Polyphenolic Compounds from Quercus gilva Blume.

Quercus gilva Bume (QGB, family Fagaceae) is a tall evergreen oak species tree that grows in warm temperate regions in Korea, Japan, China and Taiwan. Quercus plants have long been the basis of traditional medicines. Their clinical benefits according to traditional medicine include relief of urolithiasis, tremors and inflammation. In the present study, the anti-urolithiasis activity including anti-inflammatory and anti-oxidative activities, of some phenolic compounds isolated from QGB were described. Seven compounds were isolated and identified as picraquassioside D (1), quercussioside (2), (+)-lyoniresinol-9'α-O-ß-d-xylopyranoside (3), (+)-catechin (4), (-)-epicatechin (5), procyanidin B-3 (6), and procyanidin B-4 (7). Compounds 5-7 showed potent anti-oxidative and anti-inflammatory activities. These compounds were further tested for their inhibition of the gene expression of the inflammatory cytokines. The three compounds 5-7 showed dose-dependent inhibitory activities on gene expression of COX-2 and IL-1ß. In vivo, urolithiasis was induced more effectively in an animal model of acute urolithiasis by the administration of QGB extract. These results indicate the potential of compounds from QGB in the treatment of urolithiasis.

Enhanced magnetic anisotropy and heating efficiency in multi-functional manganese ferrite/graphene oxide nanostructures.

A promising nanocomposite material composed of MnFe2O4 (MFO) nanoparticles of ∼17 nm diameter deposited onto graphene oxide (GO) nanosheets was successfully synthesized using a modified co-precipitation method. X-ray diffraction, transmission electron microscopy, and selected area electron diffraction confirmed the quality of the synthesized samples. Fourier transform infrared measurements and analysis evidenced that the MFO nanoparticles were attached to the GO surface. Magnetic measurements and analysis using the modified Langevin model evidenced the superparamagnetic characteristic of both the bare MFO nanoparticles and the MFO-GO nanocomposite at room temperature, and an appreciable increase of the effective anisotropy for the MFO-GO sample. Magnetic hyperthermia experiments performed by both calorimetric and ac magnetometry methods indicated that relative to the bare MFO nanoparticles, the heating efficiency of the MFO-GO nanocomposite was similar at low ac fields (0-300 Oe) but became progressively larger with increasing ac fields (>300 Oe). This has been related to the higher effective anisotropy of the MFO-GO nanocomposite. In comparison with the bare MFO nanoparticles, a smaller reduction in the heating efficiency was observed in the MFO-GO composites when embedded in agar or when their concentration was increased, indicating that the GO helped minimize the physical rotation and aggregation of the MFO nanoparticles. These findings can be of practical importance in exploiting this type of nanocomposite for advanced hyperthermia. Magnetoimpedance-based biodetection studies also indicated that the MFO-GO nanocomposite could be used as a promising magnetic biomarker in biosensing applications.

Investigation of the potential of Brevibacillus spp. for the biosynthesis of nonribosomally produced bioactive compounds by combination of genome mining with MALDI-TOF mass spectrometry.

The biosynthetic potential of 11 Brevibacillus spp. strains was investigated by combination of genome mining with mass spectrometric analysis using MALDI-TOF mass spectrometry. These endophytic, plant associated Brevibacillus strains were isolated from crop plants, such as coffee and black pepper, in Vietnam. Draft genomes of these strains were available. They were classified (a) by comparison with type strains and a collection of genome-sequenced Brevibacillus spp. deposited in the NCBI data base as well as (b) by construction of a phylogenetic tree from the core sequences of publicly available genomes of Brevibacillus strains. They were identified as Brevibacillus brevis (1 strain); parabrevis (2 strains); porteri (3 strains); and 5 novel Brevibacillus genomospecies. Our work was specifically focused on the detection and characterization of nonribosomal peptides produced by these strains. Structural characterization of these compounds was performed by LIFT-MALDI-TOF/TOF mass spectrometric sequence analysis. The highlights of our work were the demonstration of the tyrocidines, a well-known family of cyclodecapeptides of great structural variability, as the main products of all investigated strains and the identification of a novel class of pentapeptides produced by B. brevis; B. schisleri; and B. porteri which we designate as brevipentins. Our biosynthetic studies demonstrate that knowledge of their biosynthetic capacity can efficiently assist classification of Brevibacillus species.

Antimicrobial secondary metabolites from the aerial parts of Perilla frutescens.

Phytochemical research of Perilla frutescens aerial parts led to isolation of 12 secondary metabolites, including one new 3-benzoxepin glucoside, perillafrutoside A (1), one new megastigmane glycoside, perillafrutoside B (2), and 10 known compounds. Their chemical structures were identified based on 1D/2D NMR, HRESIMS, and ECD spectroscopic analyses. The structure of 2 was elucidated based on revision of the previously reported stereoisomer, (6R,9R)-blumenyl α-L-rhamnopyranosyl-(1→6)-ß-D-glucopyranoside. Evaluation of their antimicrobial effect revealed that compounds 1 and 5-11 inhibit Enterococcus faecalis growth, compounds 6, 7 and 9 suppress Staphylococcus aureus growth, whereas compounds 6 and 11 attenuate Candida albicans growth. This is the first report of the isolation of 3-5, 8-10 and 12 from the genus Perilla and the antimicrobial effect of compounds 3, 8 and 10.

Plant-Associated Representatives of the Bacillus cereus Group Are a Rich Source of Antimicrobial Compounds.

Seventeen bacterial strains able to suppress plant pathogens have been isolated from healthy Vietnamese crop plants and taxonomically assigned as members of the Bacillus cereus group. In order to prove their potential as biocontrol agents, we perform a comprehensive analysis that included the whole-genome sequencing of selected strains and the mining for genes and gene clusters involved in the synthesis of endo- and exotoxins and secondary metabolites, such as antimicrobial peptides (AMPs). Kurstakin, thumolycin, and other AMPs were detected and characterized by different mass spectrometric methods, such as MALDI-TOF-MS and LIFT-MALDI-TOF/TOF fragment analysis. Based on their whole-genome sequences, the plant-associated isolates were assigned to the following species and subspecies: B. cereus subsp. cereus (6), B. cereus subsp. bombysepticus (5), Bacillus tropicus (2), and Bacillus pacificus. These three isolates represent novel genomospecies. Genes encoding entomopathogenic crystal and vegetative proteins were detected in B. cereus subsp. bombysepticus TK1. The in vitro assays revealed that many plant-associated isolates enhanced plant growth and suppressed plant pathogens. Our findings indicate that the plant-associated representatives of the B. cereus group are a rich source of putative antimicrobial compounds with potential in sustainable agriculture. However, the presence of virulence genes might restrict their application as biologicals in agriculture.

Two plant-associated Bacillus velezensis strains selected after genome analysis, metabolite profiling, and with proved biocontrol potential, were enhancing harvest yield of coffee and black pepper in large field trials.

Elimination of chemically synthesized pesticides, such as fungicides and nematicides, in agricultural products is a key to successful practice of the Vietnamese agriculture. We describe here the route for developing successful biostimulants based on members of the Bacillus subtilis species complex. A number of endospore-forming Gram-positive bacterial strains with antagonistic action against plant pathogens were isolated from Vietnamese crop plants. Based on their draft genome sequence, thirty of them were assigned to the Bacillus subtilis species complex. Most of them were assigned to the species Bacillus velezensis. Whole genome sequencing of strains BT2.4 and BP1.2A corroborated their close relatedness to B. velezensis FZB42, the model strain for Gram-positive plant growth-promoting bacteria. Genome mining revealed that at least 15 natural product biosynthesis gene clusters (BGCs) are well conserved in all B. velezensis strains. In total, 36 different BGCs were identified in the genomes of the strains representing B. velezensis, B. subtilis, Bacillus tequilensis, and Bacillus. altitudinis. In vitro and in vivo assays demonstrated the potential of the B. velezensis strains to enhance plant growth and to suppress phytopathogenic fungi and nematodes. Due to their promising potential to stimulate plant growth and to support plant health, the B. velezensis strains TL7 and S1 were selected as starting material for the development of novel biostimulants, and biocontrol agents efficient in protecting the important Vietnamese crop plants black pepper and coffee against phytopathogens. The results of the large-scale field trials performed in the Central Highlands in Vietnam corroborated that TL7 and S1 are efficient in stimulating plant growth and protecting plant health in large-scale applications. It was shown that treatment with both bioformulations resulted in prevention of the pathogenic pressure exerted by nematodes, fungi, and oomycetes, and increased harvest yield in coffee, and pepper.

High electrochemical performance of ink solution based on manganese cobalt sulfide/reduced graphene oxide nano-composites for supercapacitor electrode materials.

Large scale supercapacitor electrodes were prepared by 3D-printing directly on a graphite paper substrate from ink solution containing manganese cobalt sulfide/reduced graphene oxide (MCS/rGO) nanocomposites. The MCS/rGO composite solution was synthesized through the dispersion of MCS NPs and rGO in dimethylformamide (DMF) solvent at room temperature. Their morphology and composition were investigated by scanning electron microscopy (SEM), transmission electron microscopy (TEM), and energy dispersive X-ray diffraction (EDS). The role of rGO on decreasing charge transfer resistance and enhancing ion exchange was discussed. The MCS/rGO electrode exhibits an excellent specific capacitance of 3812.5 F g-1 at 2 A g-1 and it maintains 1780.8 F g-1 at a high current density of 50 A g-1. The cycling stability of the electrodes reveals capacitance retention of over 92% after 22 000 cycles at 50 A g-1.

Draft Genome Sequences of 59 Endospore-Forming Gram-Positive Bacteria Associated with Crop Plants Grown in Vietnam.

We report the draft genome sequences of 59 Gram-positive bacterial strains that were isolated from Vietnamese crop plants. The strains were assigned to nine different Bacillus and Brevibacillus species. Ten strains classified as being a Bacillus sp. (3 strains), Brevibacillus sp. (6 strains), or Lysinibacillus sp. (1 strain) could not be identified to the species level.

Towards the entire proteome of the model bacterium Bacillus subtilis by gel-based and gel-free approaches.

With the emergence of mass spectrometry in protein science and the availability of complete genome sequences, proteomics has gone through a rapid development. The soil bacterium Bacillus subtilis, as one of the first DNA sequenced species, represents a model for Gram-positive bacteria and its proteome was extensively studied throughout the years. Having the final goal to elucidate how life really functions, one basic requirement is to know the entirety of cellular proteins. This review presents how far we have got in unraveling the proteome of B. subtilis. The application of gel-based and gel-free technologies, the analyses of different subcellular proteome fractions, and the pursuance of various physiological strategies resulted in a coverage of more than one-third of B. subtilis theoretical proteome.

Biosensor based on nanocomposite material for pathogenic virus detection.

This paper introduces a DNA biosensor based on a DNA/chitosan/multi-walled carbon nanotube nanocomposite for pathogenic virus detection. An easy, cost-effective approach to the immobilization of probe DNA sequences on the sensor surface was performed. Cyclic voltammograms were used to characterize the probe DNA sequence immobilization. Complementary sequence hybridization was examined by electrochemical impedance spectroscopy. Results revealed that the developed DNA sensor can detect a target DNA concentration as low as 0.01×10(-12) M. The sensitivity of the prepared sensor was 52.57 kΩ/fM. The reusability and storage stability of the DNA sensor were also investigated. Results showed that the electron-transfer resistance decreased to approximately 35% after 8 weeks and to approximately 80% after 12 weeks of storage.

Global gene expression profiling of Bacillus subtilis in response to ammonium and tryptophan starvation as revealed by transcriptome and proteome analysis.

The global gene expression profile of Bacillus subtilis in response to ammonium and tryptophan starvation was analyzed using transcriptomics and proteomics which gained novel insights into these starvation responses. The results demonstrate that both starvation conditions induce specific, overlapping and general starvation responses. The TnrA regulon, the glutamine synthetase (glnA) as well as the sigma(L)-dependent bkd and roc operons were most strongly and specifically induced after ammonium starvation. These are involved in the uptake and utilization of ammonium and alternative nitrogen sources such as amino acids, gamma-aminobutyrate, nitrate/nitrite, uric acid/urea and oligopeptides. In addition, several carbon catabolite-controlled genes (e.g. acsA, citB), the alpha-acetolactate synthase/-decarboxylase alsSD operon and several aminotransferase genes were specifically induced after ammonium starvation. The induction of sigma(F)- and sigma(E)-dependent sporulation proteins at later time points in ammonium-starved cells was accompanied by an increased sporulation frequency. The specific response to tryptophan starvation includes the TRAP-regulated tryptophan biosynthesis genes, some RelA-dependent genes (e.g. adeC, ald) as well as spo0E. Furthermore, we recognized overlapping responses between ammonium and tryptophan starvation (e.g. dat, maeN) as well as the common induction of the CodY and sigma(H) general starvation regulons and the RelA-dependent stringent response. Many genes encoding proteins of so far unknown functions could be assigned to specifically or commonly induced genes.

The proteome and transcriptome analysis of Bacillus subtilis in response to salicylic acid.

Phenolic acids that are present in plant-soil ecosystems can be considered as toxins which induce specific stress responses in microorganisms. In this paper, we have analyzed the global response of the soil bacterium Bacillus subtilis to salicylic acid using proteomics and transcriptomics. The results demonstrate that salicylic acid caused predominantly the induction of the SigmaB-dependent general stress response in B. subtilis which is not related to the acidic conditions. Treatment of B. subtilis with growth-inhibitory concentrations of 4 mM salicylic acid caused protein damage in B. subtilis as reflected by the induction of the CtsR and Spx regulons. Both phenolic acid decarboxylases (pads) of B. subtilis padC and bsdBCD (yclBCD) were induced by 4 mM salicylic acid that were previously shown to be involved in decarboxylation and detoxification of different phenolic acids. Deletion of the putative LysR-type regulator encoded by the divergently transcribed bsdA (yclA) gene upstream of the bsdBCD operon revealed that BsdA is the transcriptional activator of bsdBCD expression in response to salicylic acid. Phenotype analysis of bsdA and padC single and double mutants demonstrated that both pads confer resistance to salicylic acid in B. subtilis.

Differential gene expression in response to phenol and catechol reveals different metabolic activities for the degradation of aromatic compounds in Bacillus subtilis.

Aromatic organic compounds that are present in the environment can have toxic effects or provide carbon sources for bacteria. We report here the global response of Bacillus subtilis 168 to phenol and catechol using proteome and transcriptome analyses. Phenol induced the HrcA, sigmaB and CtsR heat-shock regulons as well as the Spx disulfide stress regulon. Catechol caused the activation of the HrcA and CtsR heat-shock regulons and a thiol-specific oxidative stress response involving the Spx, PerR and FurR regulons but no induction of the sigmaB regulon. The most surprising result was that several catabolite-controlled genes are derepressed by catechol, even if glucose is taken up under these conditions. This derepression of the carbon catabolite control was dependent on the glucose concentration in the medium, as glucose excess increased the derepression of the CcpA-dependent lichenin utilization licBCAH operon and the ribose metabolism rbsRKDACB operon by catechol. Growth and viability experiments with catechol as sole carbon source suggested that B. subtilis is not able to utilize catechol as a carbon-energy source. In addition, the microarray results revealed the very strong induction of the yfiDE operon by catechol of which the yfiE gene shares similarities to glyoxalases/bleomycin resistance proteins/extradiol dioxygenases. Using recombinant His6-YfiE(Bs) we demonstrate that YfiE shows catechol-2,3-dioxygenase activity in the presence of catechol as the metabolite 2-hydroxymuconic semialdehyde was measured. Furthermore, both genes of the yfiDE operon are essential for the growth and viability of B. subtilis in the presence of catechol. Thus, our studies revealed that the catechol-2,3-dioxygenase YfiE is the key enzyme of a meta cleavage pathway in B. subtilis involved in the catabolism of catechol.

Proteome signatures for stress and starvation in Bacillus subtilis as revealed by a 2-D gel image color coding approach.

In this paper we have defined proteome signatures of Bacillus subtilis in response to heat, salt, peroxide, and superoxide stress as well as after starvation for ammonium, tryptophan, glucose, and phosphate using the 2-D gel-based approach. In total, 79 stress-induced and 155 starvation-induced marker proteins were identified including 50% that are not expressed in the vegetative proteome. Fused proteome maps and a color coding approach have been used to define stress-specific regulons that are involved in specific adaptative functions (HrcA for heat, PerR and Fur for oxidative stress, RecA for peroxide, CymR and S-box for superoxide stress). In addition, starvation-specific regulons are defined that are involved in the uptake or utilization of alternative nutrient sources (TnrA, sigmaL/BkdR for ammonium; tryptophan-activated RNA-binding attenuation protein for tryptophan; CcpA, CcpN, sigmaL/AcoR for glucose; PhoPR for phosphate starvation). The general stress or starvation proteome signatures include the CtsR, Spx, sigmaL/RocR, sigmaB, sigmaH, CodY, sigmaF, and sigmaE regulons. Among these, the Spx-dependent oxidase NfrA was induced by all stress conditions indicating stress-induced protein damages. Finally, a subset of sigmaH-dependent proteins (sporulation response regulator, YvyD, YtxH, YisK, YuxI, YpiB) and the CodY-dependent aspartyl phosphatase RapA were defined as general starvation proteins that indicate the transition to stationary phase caused by starvation.

A comprehensive proteome map of growing Bacillus subtilis cells.

The proteome of growing cells of Bacillus subtilis was analyzed in order to provide the basis for its application in microbial physiology. DNA arrays were used to calculate the number of genes transcribed in growing cells. From the 4100 B. subtilis genes, 2515 were actively transcribed in cells grown under standard conditions. From these genes 1544 proteins should be covered by our standard gel system pI 4-7. Using this standard gel system and supplementary zoom gels (pI 5.5-6.7, 5-6, 4.5-5.5, and 4-5) 693 proteins which are expressed in growing cells were detected that cover more than 40% of the vegetative proteome predicted for this region. Particularly broad coverage and thus comprehensive monitoring will be possible for central carbohydrate metabolism (glycolysis, pentose phosphate shunt, and citric acid cycle), amino acid synthesis pathways, purine and pyrimidine metabolism, fatty acid metabolism, and main cellular functions like replication, transcription, translation, and cell wall synthesis. Comparing the theoretical pI and Mr values with those experimentally determined a reasonable correlation was found for the majority of protein spots. By a color code outliers with dramatic deviations in charge or mass were visualized that may indicate post-translational modifications. In addition to the cytosolic neutral and alkaline proteins, 130 membrane proteins were found relying on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) separation in combination with electrospray ionization-tandem mass spectrometry (ESI-MS/MS) techniques. The vegetative proteome containing 876 proteins in total is now ready for physiological applications. Two main proteome fractions (pI 4-7 and zoom gel pI 4.5-5.5) should be sufficient for such high-throughput physiological proteomics.