Roles of Free Electrons and H2O2 in the Optical Breakdown-Induced Photochemical Reduction of Aqueous [AuCl4]-

Free electrons and H2O2 formed in an optical breakdown plasma are found to directly control the kinetics of [AuCl4]− reduction to form Au nanoparticles (AuNPs) during femtosecond laser-assisted synthesis of AuNPs. The formation rates of both free electrons and H2O2 strongly depend on the energy and duration of the 800 nm laser pulses over the ranges of 10−2400 μJ and 30−1500 fs. By monitoring the conversion of [AuCl4]− to AuNPs using in situ UV−vis spectroscopy during laser irradiation, the first- and second-order rate constants in the autocatalytic rate law, k1 and k2, were extracted and compared to the computed free electron densities and experimentally measured H2O2 formation rates. For laser pulse energies of 600 μJ and lower at all pulse durations, the first-order rate constant, k1, was found to be directly proportional to the theoretically calculated plasma volume, in which the electron density exceeds the threshold value of 1.8 × 1020 cm−3. The second-order rate constant, k2, was found to correlate with the measured H2O2 formation rate at all pulse energies and durations, resulting in the empirical relationship k2 ≈ H2O20.5. We have demonstrated that the relative composition of free electrons and H2O2 in the optical breakdown plasma may be controlled by changing the pulse energy and duration, which may make it possible to tune the size and dispersity of AuNPs and other metal nanoparticle products synthesized with femtosecond laser-based methods

Nucleation and growth of gold nanoparticles initiated by nanosecond and femtosecond laser irradiation of aqueous [AuCl4]-

Irradiation of aqueous [AuCl4]with 532 nm nanosecond (ns) laser pulses produces monodisperse (PDI = 0.04) 5 nm Au nanoparticles (AuNPs) without any additives or capping agents via a plasmon- enhanced photothermal autocatalytic mechanism. Compared with 800 nm femtosecond (fs) laser pulses, the AuNP growth kinetics under ns laser irradiation follow the same autocatalytic rate law, but with a significantly lower sensitivity to laser pulse energy. The results are explained using a simple model for simulating heat transfer in liquid water and at the interface with AuNPs. While the extent of water superheating with the ns laser is smaller compared to the fs laser, its significantly longer duration can provide sufficient energy to dissociate a small fraction of the [AuCl4]present, resulting in the formation of AuNPs by coalescence of the resulting Au atoms. Irradiation of initially formed AuNPs at 532 nm results in plasmon-enhanced superheating of water, which greatly accelerates the rate of thermal dissociation of [AuCl4]and accounts for the observed autocatalytic kinetics. The plasmon-enhanced heating under ns laser irradiation fragments the AuNPs and results in nearly uniform 5 nm particles, while the lack of particles’ heating under fs laser irradiation results in the growth of the particles as large as 40 nm

The effect of simulated copper stress on genes associated with the metabolism of polyphosphates and polyhydroxyalkanoates in Bacillus thuringiensis Y1

Aims: Bacillus thuringiensis Y1 is a copper-tolerant bacterium that can serve as a model for the elucidation of the mechanism of energy metabolism under simulated copper stress. This study aimed to elucidate the effects of simulated copper stress on the genes associated with the biosynthesis of polyhydroxyalkanoates (PAH) and the metabolism of polyphosphates (PP). Methodology and results: The gene expression study involved the growth of the bacterium in nutrient broth supplemented with two concentrations of copper sulphate (0.4 mM and 0.8 mM), followed by RNA extraction and quantification of four and 11 genes associated with the metabolism of polyphosphate (PP) and polyhydroxyalkanoates (PAHs) respectively, using reverse transcription quantitative polymerase chain reaction (RT-qPCR). Three genes associated with polyphosphate metabolism, which are polyphosphate kinase (ppk), exopolyphosphatase (ppx) and NAD kinase (ppnk), were all shown to be upregulated by both 0.4 mM and 0.8 mM copper, except for the 5’-nucleotidase (surE) gene that was downregulated under the second treatment. Among the 11 genes associated with the metabolism of polyhydroxyalkanoates, only the 3-ketoacyl-CoA-thiolase (phaA) gene was upregulated in both treatments and highly expressed in the second treatment; the majority were downregulated and repressed. Conclusion, significance and impact of study: The study demonstrated that copper induces the metabolism of polyphosphates in B. thuringiensis Y1 that serve as an alternative source of energy under copper stress. This model can be extended to the study of other species of Bacillus under environmental stress

Genomic data of two bacillus and two pseudomonas strains isolated from the acid mine drainage site at Mamut Copper Mine, Ranau, Malaysia

The genomic data of four bacteria strains isolated from the abandoned Mamut Copper Mine, an Acid Mine Drainage (AMD) site is presented in this report. Two of these strains belong to the genus Bacillus , while the other two belong to the genus Pseudomonas. The draft genome size of Pseu- domonas sp. strain MCMY3 was 6,396,595 bp (GC: 63.3%), Bacillus sp. strain MCMY6 was 6,815,573 bp (GC: 35.2%), Bacillus sp. strain MCMY13 was 5,559,059 bp (GC: 35.5%) and Pseudomonas sp. strain MCMY15 was 7,381,777 bp (GC: 64.8%). These four genomes contained 4 93, 4 95, 4 95 and 579 annotated subsystems, respectively. The sequence data are available at GenBank sequence read archive with ac- cessions numbers SRX7859406, SRX7859404, SRX7859405 and SRX7293032 for strains MCMY3, MCMY6, MCMY13 and MCMY15, respectively

Bacterial diversity of the abandoned Mamut Copper Mine in Sabah, Malaysia and its correlation with copper contamination

The former Mamut Copper Mine, acid mine drainage site represents an anthropogenic altered landscape characterized by its acidic topsoil which is contaminated primarily with copper. Even though the mining operation was ceased at 1999, the bacterial diversity in this area has never been investigated. This study was conducted to ascertain the bacterial diversity of this abandoned copper mine and correlate it to the copper concentration in the soil. Methodology and results: Soil samples were collected from 7 sites near the mine pit and the vicinity. Soil samples were assessed for soil copper elemental concentration using inductively coupled plasma optical emission spectrometry and bacteria were isolated via serial dilution followed by culture on nutrient agar plates. Phylogenetic analysis was done based on the full-length sequences of 16S rRNA gene. Twenty-four phylotypes were obtained from the 7 locations which originated from the phyla Firmicutes, Actinobacteria, Bacteroidetes and Proteobacteria. The results of the study indicated that site 2 (6.030223°; 116.658030°), located in between the mine pit and the mine factory with a copper concentration of 88.96 ppm, possessed the most diverse bacterial community with a Shannon diversity index (H) of 1.68, evenness (EH) of 0.94 and richness (S) of 6. Conclusion, significance and impact of study: Current study revealed that there was a positive correlation between the copper concentration and the H index and the richness, but this was not reflected in the evenness. This is the first report of bacterial diversity from the former Mamut Copper Mine site. The data provided a valuable insight for the future monitoring of the bacterial community in this ecologically important niche

Adaptive Strategies of Bacillus thuringiensis Isolated from Acid Mine Drainage Site in Sabah, Malaysia

The adaptive process in bacteria is driven by specific genetic elements which regulate phenotypic characteristics such as tolerance to high metal ion concentrations and the secretion of protective biofilms. Extreme environments such as those associated with heavy metal pollution and extremes of acidity offer opportunities to study the adaptive mechanisms of microorganisms. This study focused on the genome analysis of Bacillus thuringiensis (Bt MCMY1), a gram positive rod shaped bacterium isolated from an acid mine drainage site in Sabah, Malaysia by using a combination of Single Molecule Real Time DNA Sequencing, Scanning Electron Microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR). The genome size of Bt MCMY1 was determined to be 5,458,152 bases which was encoded on a single chromosome. Analysis of the genome revealed genes associated with resistance to Copper, Mercury, Arsenic, Cobalt, Zinc, Cadmium and Aluminum. Evidence from SEM and FTIR indicated that the bacterial colonies form distinct films which bear the signature of polyhydroxyalkanoates (PHA) and this finding was supported by the genome data indicating the presence of a genetic pathway associated with the biosynthesis of PHAs. This is the first report of a Bacillus sp. isolated from an acid mine drainage site in Sabah, Malaysia and the genome sequence will provide insights into the manner in which B. thuringiensis adapts to acid mine drainage

Methotrexate and low-dose prednisolone downregulate osteoclast function by decreasing receptor activator of nuclear factor-kappa beta expression in monocytes from patients with early rheumatoid arthritis

Objective Rheumatoid arthritis (RA) is a systemic, immune-mediated inflammatory disease that ultimately leads to bone erosions and joint destruction. Methotrexate (MTX) slows bone damage but the mechanism by which it acts is still unknown. In this study, we aimed to assess the effect of MTX and low-dose prednisolone (PDN) on circulating osteoclast (OC) precursors and OC differentiation in patients with RA. Methods Patients with RA before and at least 6 months after MTX therapy were analysed and compared with healthy donors. A blood sample was collected in order to assess receptor activator of NF-kappa beta (RANK) ligand surface expression on circulating leucocytes and frequency and phenotype of monocyte subpopulations. Quantification of serum levels of bone turnover markers and cytokines and OC differentiation assays were performed. Results Classical activation markers of monocytes and RANK increased in patients with RA at baseline, compared with control healthy donors, and after MTX and low-dose PDN (MTX+PDN) exposure they decreased to control levels. Although the number of OC was not different between groups, the percentage of resorbed area and the resorbed area per pit reduced after treatment. Serum soluble receptor activator of nuclear factor-kappa (RANKL) levels increased at baseline compared with healthy donors and normalised after therapy. Conclusion Our results suggest that MTX+PDN play an important role in downregulating OC function, which we believe occurs through the decrease in RANK surface expression in monocytes.Peer reviewe

Whole-exome sequencing reveals ZNF408 as a new gene associated with autosomal recessive retinitis pigmentosa with vitreal alterations

Retinitis pigmentosa (RP) is a group of progressive inherited retinal dystrophies that cause visual impairment as a result of photoreceptor cell death. RP is heterogeneous, both clinically and genetically making difficult to establish precise genotype–phenotype correlations. In a Spanish family with autosomal recessive RP (arRP), homozygosity mapping and whole-exome sequencing led to the identification of a homozygous mutation (c.358_359delGT; p.Ala122Leufs*2) in the ZNF408 gene. A screening performed in 217 additional unrelated families revealed another homozygous mutation (c.1621C>T; p.Arg541Cys) in an isolated RP case. ZNF408 encodes a transcription factor that harbors 10 predicted C2H2-type fingers thought to be implicated in DNA binding. To elucidate the ZNF408 role in the retina and the pathogenesis of these mutations we have performed different functional studies. By immunohistochemical analysis in healthy human retina, we identified that ZNF408 is expressed in both cone and rod photoreceptors, in a specific type of amacrine and ganglion cells, and in retinal blood vessels. ZNF408 revealed a cytoplasmic localization and a nuclear distribution in areas corresponding with the euchromatin fraction. Immunolocalization studies showed a partial mislocalization of the p.Arg541Cys mutant protein retaining part of the WT protein in the cytoplasm. Our study demonstrates that ZNF408, previously associated with Familial Exudative Vitreoretinopathy (FEVR), is a new gene causing arRP with vitreous condensations supporting the evidence that this protein plays additional functions into the human retina.This work is supported by CIBERER (06/07/0036), FIS (PI013/00226), Ministry of Economy and Competitiveness-FEDER (BFU2012-36845), RETICS (RD12/0034/0010), Fundación ONCE, Fundaluce and grants BIO2011-27069 from the Spanish Ministry of Economy and Competitiveness, and PROMETEOII/2014/025 from the Conselleria de Educacio of the Valencia Community. PC is supported by Fundación Conchita Rábago (FCR), MC by Miguel Servet ISCIII (CP/03256) and dS by CAPES Foundation, Ministry of Education of Brazil

Use of ecotoxicity test and ecoscores to improve the management of polluted soils: case of a secondary lead smelter plant

International audienceWith the rise of sustainable development, rehabilitation of brownfield sites located in urban areas has become a major concern. Management of contaminated soils in relation with environmental and sanitary risk concerns is therefore a strong aim needing the development of both useful tools for risk assessment and sustainable remediation techniques. For soils polluted by metals and metalloids (MTE), the criteria for landfilling are currently not based on ecotoxicological tests but on total MTE concentrations and leaching tests. In this study, the ecotoxicity of leachates from MTE polluted soils sampled from an industrial site recycling lead-acid batteries were evaluated by using both modified Escherichia coli strains with luminescence modulated by metals and normalized Daphnia magna and Alivibrio fischeri bioassays. The results were clearly related to the type of microorganisms (crustacean, different strains of bacteria) whose sensitivity varied. Ecotoxicity was also different according to sample location on the site, total concentrations and physico-chemical properties of each soil. For comparison, standard leaching tests were also performed. Potentially phytoavailable fraction of MTE in soils and physico-chemical measures were finally performed in order to highlight the mechanisms. The results demonstrated that the use of a panel of microorganisms is suitable for hazard classification of polluted soils. In addition, calculated eco-scores permit to rank the polluted soils according to their potentially of dangerousness. Influence of soil and MTE characteristics on MTE mobility and ecotoxicity was also highlighted