Effect of ambient polycyclic aromatic hydrocarbons and nicotine on the structure of Aβ42 protein

● B[a]P, nicotine and phenanthrene molecules altered the secondary structure of Aβ₄₂. ● β-content of the peptide was significantly enhanced in the presence of the PAHs. ● Nicotine made stable cluster with Aβ₄₂ peptide via hydrogen bonds. ● Phenanthrene due to its small size, interfered with the Aβ₄₂ monomer more strongly. Recent studies have correlated the chronic impact of ambient environmental pollutants like polycyclic aromatic hydrocarbons (PAHs) with the progression of neurodegenerative disorders, either by using statistical data from various cities, or via tracking biomarkers during in-vivo experiments. Among different neurodegenerative disorders, PAHs are known to cause increased risk for Alzheimer’s disease, related to the development of amyloid beta (Aβ) peptide oligomers. However, the complex molecular interactions between peptide monomers and organic pollutants remains obscured. In this work, we performed an atomistic molecular dynamics study via GROMACS to investigate the structure of Aβ₄₂ peptide monomer in the presence of benzo[a]pyrene, nicotine, and phenanthrene. Interestingly the results revealed strong hydrophobic, and hydrogen-bond based interactions between Aβ peptides and these environmental pollutants that resulted in the formation of stable intermolecular clusters. The strong interactions affected the secondary structure of the Aβ₄₂ peptide in the presence of the organic pollutants, with almost 50 % decrease in the α-helix and 2 %–10 % increase in the β-sheets of the peptide. Overall, the undergoing changes in the secondary structure of the peptide monomer in the presence of the pollutants under the study indicates an enhanced formation of Aβ peptide oligomers, and consequent progression of Alzheimer’s disease.     

Evaluation of the spontaneous combustion characteristics of coal of different metamorphic degrees based on a temperature-programmed oil bath experimental system

Research on the micro- and macrocharacteristics of different metamorphic degrees of coal helps improve the control and protection techniques used during spontaneous combustion. Nine coals with different properties were thoroughly investigated in this study. Fourier transform infrared spectroscopy and a self-designed temperature-programmed oil bath experimental system were adopted to analyze the molecular structure and macrocharacteristic parameters of the spontaneous combustion of coal. Additionally, the influence of particle size on spontaneous combustion was considered. Various functional groups were employed as microcharacteristic parameters to capture the principal active groups in oxidation. The gas production rate, oxygen consumption rate, gas concentration, heat energy release rate, and characteristic temperatures were evaluated as macrocharacteristic parameters to investigate the changes in coal during oxidation. The results establish that the microcharacteristics of coal molecules determine the degree of spontaneous combustion based on intrinsic properties and that changes in the macrocharacteristics of the spontaneous combustion of coal reflect the microstructural changes. The contents of the hydroxyl groups, carbonyl groups, alkyl ether and aryl ether in the coal molecules gradually decrease with the metamorphic increase. Oxygen-containing functional groups have higher reactivities and easily react with oxygen, causing the macroparameters, such as the oxygen consumption rate, the gas generation rate and the heat energy release rate, to consistently decrease with the increase of the metamorphic degree. Small-particle-size coal molecules have more active aliphatic hydrocarbons, oxygen-containing functional groups and a larger specific surface area, increasing the chances of adsorbing the oxygen of active groups and promoting the reaction between coal and oxygen. The experimental results indicate that coal samples with higher metamorphic degrees or larger sizes exhibit lower tendencies toward spontaneous combustion. Evaluation of the spontaneous combustion of coal based on a temperature-programmed oil bath experimental system is of great practical importance for preventing the spontaneous combustion of coal during storage, processing and utilization and can serve as a convenient reference for production safety in mining applications.     

水环境中致病菌分子生物学检测技术研究进展

总结了水环境中主要致病菌及其导致的疾病；介绍了检测水环境样品中致病菌的聚合酶链式反应（PCR）、实时定量PCR、等温扩增技术、生物传感器和高通量测序等分子生物学技术研究进展；分析了不同检测技术的优缺点和应用特点；提出了水环境中致病菌分子生物学检测技术的未来发展方向，为水环境中致病菌分析检测和风险控制提供研究思路和技术支撑。     

Molecular diversity of arbuscular mycorrhizal fungi at a large-scale antimony mining area in southern China

Arbuscular mycorrhizal fungi (AMF) have great potential for assisting heavy metal hyperaccumulators in the remediation of contaminated soils. However, little information is available about the community composition of AMF under natural conditions in soils contaminated by antimony (Sb). The objective of this study was to investigate the characteristics of AMF molecular diversity, and to explore the effects of Sb content and soil properties on the AMF community structure in an Sb mining area. Four Sb mine spoils and one adjacent reference area were selected from around the Xikuangshan mine in southern China. The association of AMF molecular diversity and community composition with the rhizosphere soils of the dominant plant species was studied by Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). Results from all five studied sites showed that the diversity of AMF decreased with increasing Sb concentration. Principal component analysis (PCA) indicated that the AMF community structure was markedly different among these groups. Further redundancy analysis (RDA) showed that Sb contaminationwas the dominating factor influencing the AMF community structure in the Sb mine area. However, the multivariate analysis showed that, apart from the soil Sb content, extractable nitrogen content and organic matter content also attributed to AMF sequence distribution type. Some AMF sequences were only found in the highly contaminated area and these might be ideal candidates for improving phytoremediation efficiency in Sb mining regions. Gene sequencing analysis revealed that most species were affiliated with Glomus, suggesting that Glomus was the dominant AMF genus in the studied Sb mining area.     

Interspecific and intraspecific identification of Dendrobium based on the psbAtrnH intergenic region sequences and the 5S rRNA gene spacer sequences北大核心CSCD

This research aimed to investigate the interspecific and intraspecific identification of Dendrobium by using the multi-locus method so as to provide a molecular basis for Dendrobium identification through the combination of chloroplast psbA-trnH intergenic region sequences and ribosome 5S rRNA gene spacer sequences. PCR direct sequencing was applied to detect the chloroplast psbA-trnH intergenic region sequences as well as the ribosome 5S rRNA gene spacer sequences of 12 Dendrobium species, while the psbA-trnH intergenic region sequences of Dendrobium denneanum dq-2 variety and dq- 5line were cloned and sequenced for single nucleotide polymorphism (SNP) analyzing. The sequences were analyzed by the software Sequencher4.14, Bioedit7.0, MEGA5.2 and Dansp5.0; the interspecific and intraspecific Kimara-2-Parameter(K2P) distances were also calculated. The phylogenetic tree (using Neighbor joining method) was constructed with Bulbophyllum odoratissimum and Bletilla striata as outgroup. The results showed an average length of chloroplast psbA-trnH gene sequences in Dendrobium as 742.3 bp, with 72 variable sites, including 33 information sites; the average length of the ribosome 5S rRNA gene spacer sequences in Dendrobium was 336.4 bp, with 213 variable sites including 139 information sites. Using psbAtrnH intergenic region sequences in combination with ribosome 5S rRNA gene spacer sequences can not only identify D. denneanum, D. hancockil, D. thysiflorum, D. devonianum, D. moniliforme, D. chrysotoxum, D. officinale, D. heterocarpum and D. nobile, but also differentiate D. officinale from different geographical populations, and distinguish the dq-2 variety and dq 5line with SNP in the multi locus of D. denneanum.     

Diversity of bacterial isolates during full scale rotary drum composting

Bacterial diversity of full scale rotary drum composter from biodegradable organic waste samples were analyzed through two different approaches, i.e., Culture dependent and independent techniques. Culture-dependent enumerations for indigenous population of bacterial isolates mainly total heterotrophic bacteria (Bacillus species, Pseudomonas species and Enterobacter species), Fecal Coliforms, Fecal Streptococci, Escherichia coli, Salmonella species and Shigella species showed reduction during the composting period. On the other hand, Culture-independent method using PCR amplification of specific 16S rRNA sequences identified the presence of Acinetobacter species, Actinobacteria species, Bacillus species, Clostridium species, Hydrogenophaga species, Butyrivibrio species, Pedobacter species, Empedobactor species and Flavobacterium species by sequences clustering in the phylogenetic tree. Furthermore, correlating physico-chemical analysis of samples with bacterial diversity revealed the bacterial communities have undergone changes, possibly linked to the variations in temperature and availability of new metabolic substrates while decomposing organics at different stages of composting.     

Molecular composition of recycled organic wastes,as determined by solid-state 13C NMR and elemental analyses

Using solid state ¹³C NMR data and elemental composition in a molecular mixing model, we estimated the molecular components of the organic matter in 16 recycled organic (RO) wastes representative of the major materials generated in the Sydney basin area. Close correspondence was found between the measured NMR signal intensities and those predicted by the model for all RO wastes except for poultry manure char. Molecular nature of the organic matter differed widely between the RO wastes. As a proportion of organic C, carbohydrate C ranged from 0.07 to 0.63, protein C from <0.01 to 0.66, lignin C from <0.01 to 0.31, aliphatic C from 0.09 to 0.73, carbonyl C from 0.02 to 0.23, and char C from 0 to 0.45. This method is considered preferable to techniques involving imprecise extraction methods for RO wastes. Molecular composition data has great potential as a predictor of RO waste soil carbon and nutrient outcomes.     

Molecular docking: A potential tool to aid ecotoxicity testing in environmental risk assessment of pharmaceuticals

A cocktail of human pharmaceuticals pollute aquatic environments and there is considerable scientific uncertainty about the effects that this may have on aquatic organisms. Human drug target proteins can be highly conserved in non target species suggesting that similar modes of action (MoA) may occur. The aim of this work was to explore whether molecular docking offers a potential tool to predict the effects of pharmaceutical compounds on non target organisms. Three highly prescribed drugs, diclofenac, ibuprofen and levonorgestrel which regularly pollute freshwater environments were used as examples. Their primary drug targets are cyclooxygenase 2 (COX2) and progesterone receptor (PR). Molecular docking experiments were performed using these drugs and their primary drug target homologues for Danio rerio, Salmo salar, Oncorhynchus mykiss, Xenopus tropicalis, Xenopus laevis and Daphnia pulex. The results show that fish and frog COX2 enzymes are likely to bind diclofenac and ibuprofen in the same way as humans but that D. pulex would not. Binding will probably lead to inhibition of COX function and reduced prostaglandin production. Levonorgestrel was found to bind in the same binding pocket of the progesterone receptor in frogs and fish as the human form. This suggests implications for the fecundity of fish and frogs which are exposed to levonorgestrel. Chronic ecotoxicological effects of these drugs reported in the literature support these findings. Molecular docking may provide a valuable tool for ecotoxicity tests by guiding selection of test species and incorporating the MoA of drugs for relevant chronic test end points in environmental risk assessments.     

Ozonation as an advanced oxidant in treatment of bamboo industry wastewater

The present study employed ozonation process to treat the bamboo industry wastewater (BIWW). The impact of ozone dosage and initial organic concentration on color, COD and TOC removal rates were studied along with characterization of the major organics in raw and treated wastewater. The results suggested the ozone dosage of 3.15 g h⁻¹ (concentration 52.5 mg L⁻¹) was suitable for the treatment. After 25 min ozonation of 1 L raw wastewater, the color, COD and TOC removal efficiencies were 95%, 56% and 40%, respectively, with an influent COD concentration of 835 mg L⁻¹. The ratio of kg O₃ kg⁻¹ COD at 3.15 g h⁻¹ was 2.8 (<3), revealing that ozonation was a cost effective process for tertiary treatment of BIWW. Longer oxidization time was required to achieve similar results for raw wastewater with higher COD concentration. The chromatogram from gel permeation chromatography revealed that ozonation resulted in the breakdown of high molecular weight compounds into lower molecular weight components but could not completely mineralize the organic matter. The majority of these compounds were identified in both raw and ozonated samples via GC-MS analysis. In addition to ester derivatives as the main intermediates of ozonation, 1-chloroctadecane, methyl stearate, benzophenone and α-cyperone were identified as the by-products of ozonation.     

Octanol–air partition coefficients of polybrominated biphenyls

The octanol–air partition coefficients (K_OA) for PBB15, PBB26, PBB31, PBB49, PBB103 and PBB153 were determined as a function of temperature using a gas chromatographic retention time technique with 1,1,1-trichloro-2,2-bis (4-chlorophenyl) ethane (p,p′-DDT) as a reference substance. The internal energies of phase change from octanol to air (Δ_OAU) were calculated for the six compounds and were in the range from 74 to 116 kJ mol⁻¹. Simple regression equations of log K_OA versus relative retention times (RRTs) on gas chromatography (GC), and log K_OA versus molecular connectivity indexes (MCI) were obtained, for which the correlation coefficients (r²) were greater than 0.985 at 283.15 K and 298.15 K. Thus the K_OA values of the remaining PBBs can be predicted by using their RRTs and MCI according to these relationships.