Fast-Folding Pathways of the Thrombin-Binding Aptamer G-Quadruplex Revealed by a Markov State Model.

G-quadruplex structures participate in many important cellular processes. For a better understanding of their functions, knowledge of the mechanism by which they fold into the functional native structures is necessary. In this work, we studied the folding process of the thrombin-binding aptamer G-quadruplex. Enabled by a computational paradigm that couples an advanced sampling method and a Markov state model, four folding intermediates were identified, including an antiparallel G-hairpin, two G-triplex structures, and a double-hairpin conformation. Likewise, a misfolded structure with a nonnative distribution of syn/anti guanines was also observed. Based on these states, a transition path analysis revealed three fast-folding pathways, along which the thrombin-binding aptamer would fold to the native state directly, with no evidence of potential nonnative competing conformations. The results also showed that the TGT-loop plays an important role in the folding process. The findings of this research may provide general insight about the folding of other G-quadruplex structures.

Effects of the opening of the Qinghai-Tibet Railway on municipal solid waste management generation in Lhasa.

Lhasa, the capital of Tibet, is located on the Tibetan Plateau. Accelerated economic development and flourishing tourism resulting from the opening of the Qinghai-Tibet Railway (QTR) have increased solid waste generation and contamination in recent years. Using data from Lhasa Statistical Yearbooks and previous studies, this study estimates the future population of permanent residents and tourists using the least squares method to extrapolate the population from 2015-2025, and evaluates the effects of the QTR on municipal solid waste (MSW) generation in Lhasa and estimates future MSW generation. There were approximately 1.35 million tourists in 2008 when the QTR had been operating for 2 years and MSW generation was approximately 470 tons per day. The amount of MSW generated increased dramatically with time after opening the QTR. This study estimates that MSW generation will reach 962 tons per day in 2025. Due to the existence of the QTR, increasing numbers of people are traveling to Lhasa, and tourism has driven the development of the local economy. During the studies, the proportion of MSW produced by tourists increased from 2.99% to 20.06%, and it is estimated that it will increase to 33.49% in 2025. If the current trend continues, Lhasa will face significant challenges from garbage disposal. This study analyzes the current situation of urban garbage treatment in Lhasa, and it suggests several options for improvement to MSW generation, transportation equipment, disposal, and resource recycling.

Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor.

Reliable determination of binding kinetics and affinity of DNA hybridization and single-base mismatches plays an essential role in systems biology, personalized and precision medicine. The standard tools are optical-based sensors that are difficult to operate in low cost and to miniaturize for high-throughput measurement. Biosensors based on nanowire field-effect transistors have been developed, but reliable and cost-effective fabrication remains a challenge. Here, we demonstrate that a graphene single-crystal domain patterned into multiple channels can measure time- and concentration-dependent DNA hybridization kinetics and affinity reliably and sensitively, with a detection limit of 10 pM for DNA. It can distinguish single-base mutations quantitatively in real time. An analytical model is developed to estimate probe density, efficiency of hybridization and the maximum sensor response. The results suggest a promising future for cost-effective, high-throughput screening of drug candidates, genetic variations and disease biomarkers by using an integrated, miniaturized, all-electrical multiplexed, graphene-based DNA array.

Phthalate esters in soil, plastic film, and vegetable from greenhouse vegetable production bases in Beijing, China: Concentrations, sources, and risk assessment.

The increased use of plastic film in greenhouse vegetable production (GVP) could result in phthalate ester (PAE) contamination in vegetables. However, limited information is currently available on their occurrence and associated potential risks in GVP systems. The present study documents the occurrence and composition of 15 PAEs in soil, plastic film, and vegetable samples from eight large-scale GVP bases in Beijing, China. Results showed that PAEs are ubiquitous contaminants in these GVP bases. Total PAE concentrations ranged from 0.14 to 2.13mg/kg (mean 0.99mg/kg) in soils and from 0.15 to 6.94mg/kg (mean 1.49mg/kg) in vegetables. Di (2-ethylhexyl) phthalate, di-n-butyl phthalate, and diisobutyl phthalate were the most abundant components, which accounted for >90% of the total PAEs. This investigation also indicated that the widespread application of plastic film in GVP systems may be the primary source of these PAEs. The non-cancer and carcinogenic risks of target PAEs were estimated based on the exposures of vegetable intake. The hazard quotients of PAE in all vegetable samples were lower than 1 and the carcinogenic risks were also at acceptable levels for consumers. The data in this study can provide valuable information to understand the status of potential pollutants, specifically PAEs, in GVP systems.

Occurrence and risk assessment of pharmaceuticals and personal care products and endocrine disrupting chemicals in reclaimed water and receiving groundwater in China.

Groundwater recharge using reclaimed water is considered a promising method to alleviate groundwater depletion. However, pollutants in reclaimed water could be recharged into groundwater during this process, thereby posing a risk to groundwater and human health. In this study, 12 cities in northern China were selected for reclaimed water and groundwater sampling. Analysis of the samples revealed the presence of nine pharmaceutical and personal care products (PPCPs) and five endocrine disrupting compounds (EDCs). In reclaimed water, all the PPCPs and EDCs were found, with sulpiride (SP) and estriol (E3) being most frequently detected. In groundwater samples, only ketoprofen (KP), mefenamic acid (MA), nalidixic acid (NA) and SP were detected among PPCPs, while bisphenol-A (BPA) was dominant among the target EDCs. The risk quotients (RQs) of all target PPCPs and EDCs except 17α-ethinyl estradiol (EE2) and E3 were below 1 in groundwater samples, indicating that EE2 and E3 deserve priority preferential treatment before recharging.

Occurrence of antibiotics in soils and manures from greenhouse vegetable production bases of Beijing, China and an associated risk assessment.

The occurrence of 15 antibiotics in soil and manure samples from 11 large-scale greenhouse vegetable production (GVP) bases in Beijing, China was investigated. Results showed that the greenhouse soils were ubiquitously contaminated with antibiotics, and that antibiotic concentrations were significantly higher in greenhouses than in open field soils. The mean concentrations of four antibiotic classes decreased in the following order: tetracyclines (102µg/kg)>quinolones (86µg/kg)>sulfonamides (1.1µg/kg)>macrolides (0.62µg/kg). This investigation also indicated that fertilization with manure and especially animal feces might be the primary source of antibiotics. A risk assessment based on the calculated risk quotients (RQs) demonstrated that oxytetracycline, chlortetracycline, norfloxacin, ciprofloxacin and enrofloxacin could pose a high risk to soil organisms. These results suggested that the ecological effects of antibiotic contamination in GVP bases and their potential adverse risks on human health need to be given special attention.

[Assessment of chlorophyll content using a new vegetation index based on multi-angular hyperspectral image data].

The fast estimation of chlorophyll content is significant for understanding the crops growth, monitoring the disease and insect, and assessing the yield of crops. This study gets the hyperspectral imagery data by using a self-developed multi-angular acquisition system during the different maize growth period, the reflectance of maize canopy was extracted accurately from the hyperspectral images under different view angles in the principal plane. The hot-dark-spot index (HDS) of red waveband was calculated through the analysis of simulated values by ACRM model and measured values, then this index was used to modify the vegetation index (TCARI), thus a new vegetation index (HD-TCARI) based on the multi-angular observation was proposed. Finally, the multi-angular hyperspectral imagery data was used to validate the vegetation indexes. The result showed that HD-TCARI could effectively reduce the LAI effects on the assessment of chlorophyll content. When the chlorophyll content was greater than 30 µg x cm(-2), the correlation (R2) between HD-TCARI and LAI was only 26.88%-28.72%. In addition, the HD-TCARI could resist the saturation of vegetation index during the assessment of high chlorophyll content. When the LAI varled from 1 to 6, the linear relation between HD-TCARI and chlorophyll content could be improved by 9% compared with TCARI. The ground validation of HD-TCARI by multi-angular hyperspectral image showed that the linear relation between HD-TCARI and chlorophyll content (R2 = 66.74%) was better than the TCARI (R2 = 39.92%), which indicated that HD-TCARI has good potentials for estimating the chlorophyll content.