Promoter prediction in nannochloropsis based on densely connected convolutional neural networks.

Promoter is a key DNA element located near the transcription start site, which regulates gene transcription by binding RNA polymerase. Thus, the identification of promoters is an important research field in synthetic biology. Nannochloropsis is an important unicellular industrial oleaginous microalgae, and at present, some studies have identified some promoters with specific functions by biological methods in Nannochloropsis, whereas few studies used computational methods. Here, we propose a method called DNPPro (DenseNet-Predict-Promoter) based on densely connected convolutional neural networks to predict the promoter of Nannochloropsis. First, we collected promoter sequences from six Nannochloropsis strains and removed 80% similarity using CD-HIT for each strain to yield a reliable set of positive datasets. Then, in order to construct a robust classifier, within-group scrambling method was used to generate negative dataset which overcomes the limitation of randomly selecting a non-promoter region from the same genome as a negative sample. Finally, we constructed a densely connected convolutional neural network, with the sequence one-hot encoding as the input. Compared with commonly used sequence processing methods, DNPPro can extract long sequence features to a greater extent. The cross-strain experiment on independent dataset verifies the generalization of our method. At the same time, T-SNE visualization analysis shows that our method can effectively distinguish promoters from non-promoters.

Enantioseparation and dissipation of acephate and its highly toxic metabolite methamidophos in pakchoi by supercritical fluid chromatography tandem mass spectrometry.

Acephate is widely used in crops as racemate. However, the enantioselective dissipation of acephate enantiomers has not been investigated in pakchoi. A sensitive and effective approach was established for determining residues of acephate and its highly toxic metabolite methamidophos enantiomers by supercritical fluid chromatography tandem mass spectrometry. Baseline separations for their enantiomers were achieved by using a Chiralcel OD-H column. The optimal chromatographic conditions were obtained as follows: CO2 /ethanol (95/5) as mobile phase; flow rate, 3.0 mL/min; column temperature, 40°C. The mean recoveries (RSDs) of analytes were in the range of 77-83.1% (6.1-9.9%), 75.4-87.5% (9.3-13.2%), and 81.5-84.2% (7.1-13.4%) at three fortification levels (0.005, 0.05, and 0.5 mg/kg for each enantiomer) for interday assay (n = 18). The method was used to evaluate the enantioselective dissipation of acephate and methamidophos in pakchoi. S-acephate dissipated faster than R-acephate, while the concentration of R-methamidophos was higher than that of S-methamidophos during the entire study period. The results indicated that the R-enantiomer of acephate and methamidophos was preferentially enriched in pakchoi. The established analysis approach and the study data provided useful information for the rational use of acephate in agriculture.

Assessment of heavy metals, fungicide quintozene and its hazardous impurity residues in medical Panax notoginseng (Burk) F.H.Chen root.

A quick, easy, cheap, effective, rugged, and safe extraction approach and gas chromatography/tandem mass spectrometry with programmed temperature vaporization sampling technology were used to determine fungicide quintozene and its hazardous impurity hexachlorobenzene (HCB) in Panax notoginseng root, which is commonly used as a rare traditional Chinese medicine worldwide. The mean recoveries were in the ranges of 94-125 and 84-119% for quintozene and HCB with relative standard deviations of 6.2-16.1% at three concentrations: 0.01, 0.1 and 1 mg kg-1 . Heavy metals arsenic, cadmium, copper and lead were simultaneously detected by an inductively coupled plasma-mass spectrometry approach after digestion with nitric acid. The above methods were used to analyze 50 samples of P. notoginseng roots collected at markets and planting bases from the special local producing areas, namely, Honghe, Kunming and Wenshan in Yunnan province, China. Quintozene and HCB in root samples were determined at <0.0015-1.50 and <0.0015-0.125 mg kg-1 . In the 50 samples, 60, 16, 56, 2 and 6% exceeded the maximum permissible levels in medicinal plants (WM/T2-2004) for quintozene, arsenic, cadmium, lead and copper. The results showed that the method is robust and suitable for measuring quintozene, its hazardous impurity and heavy metals in P. notoginseng roots.

Adaptively Evolving Bacterial Communities for Complete and Selective Reduction of Cr(VI), Cu(II), and Cd(II) in Biocathode Bioelectrochemical Systems.

Bioelectrochemical systems (BESs) have been shown to be useful in removing individual metals from solutions, but effective treatment of electroplating and mining wastewaters requires simultaneous removal of several metals in a single system. To develop multiple-reactor BESs for metals removal, biocathodes were first individually acclimated to three different metals using microbial fuel cells with Cr(VI) or Cu(II) as these metals have relatively high redox potentials, and microbial electrolysis cells for reducing Cd(II) as this metal has a more negative redox potential. The BESs were then acclimated to low concentrations of a mixture of metals, followed by more elevated concentrations. This procedure resulted in complete and selective metal reduction at rates of 1.24 ± 0.01 mg/L-h for Cr(VI), 1.07 ± 0.01 mg/L-h for Cu(II), and 0.98 ± 0.01 mg/L-h for Cd(II). These reduction rates were larger than the no adaptive controls by factors of 2.5 for Cr(VI), 2.9 for Cu(II), and 3.6 for Cd(II). This adaptive procedure produced less diverse microbial communities and changes in the microbial communities at the phylum and genus levels. These results demonstrated that bacterial communities can adaptively evolve to utilize solutions containing mixtures of metals, providing a strategy for remediating wastewaters containing Cr(VI), Cu(II), and Cd(II).

Glyphosate, aminomethylphosphonic acid, and glufosinate ammonium in agricultural groundwater and surface water in China from 2017 to 2018: Occurrence, main drivers, and environmental risk assessment.

Glyphosate and glufosinate ammonium are the main herbicides used to control weeds in no-tillage agricultural fields in China. However, their leaching risk to groundwater and ecological risk to aquatic organisms remain unclear. From the agricultural basins among 10 provinces of China, glyphosate, its main metabolite aminomethylphosphonic acid (AMPA), and glufosinate ammonium were detected in 1.01%, 0.86%, 0% of 694 groundwater samples with the maximum concentrations of 2.09, 5.13, and <0.05 µg/L, and were detected in 14.3%, 15.8%, and 2.6% of 196 surface water samples with the maximum levels of 32.49, 10.31 and 13.15 µg/L. Furthermore, to evaluate the main drivers of exposure to the targets in water bodies, the fate models were used. The model simulation indicated that spray drift and overflow runoff were the key factors affecting the exposure to targets in surface water adjacent to rice field, whereas the spray drift deposition, runoff, and erosion induced the exposure to the targets in pond water close to dry land crop fields under different meteorological conditions and soil characteristics. The targets in groundwater posed a low risk to water consumption, while fish embryos might be at unacceptable risk due to glufosinate ammonium exposure in surface water with median risk quotient (RQ) equal to 55.6. The results highlight the spatial and seasonal distribution of glyphosate, AMPA, and glufosinate ammonium in groundwater and surface water in agricultural basins of China, providing the first evidence to the environmental risk of the targets to drinking water consumption and aquatic organism safety in China agriculture system.

Assessment of the dissipation, pre-harvest interval and dietary risk of carbosulfan, dimethoate, and their relevant metabolites in greenhouse cucumber (Cucumis sativus L.).

BACKGROUND: The dissipation behavior, pre-harvest interval and dietary risk of carbosulfan, dimethoate, and their relevant metabolites were investigated in greenhouse cucumber in Tianjin, northern China, to ensure raw consumption safety. RESULTS: Carbosulfan was metabolized to carbofuran, dibutylamine, 3-hydroxycarbofuran and 3-ketocarbofuran, and dimethoate was degraded to omethoate in cucumber fruits and leaves. The dissipation of carbosulfan, carbofuran, 3-hydroxycarbofuran and dimethoate fitted first-order kinetics well, with R2 ranging from 0.912 to 0.992, and their half-lives were 2.6, 2.7, 2.4 and 5.2 days in cucumber fruits and 2.8, 3.0, 4.6 and 2.5 days in leaves, respectively. The estimated daily intakes of the active ingredients and their relevant metabolites were 0.1-4% of the corresponding acceptable daily intakes. Acute oral exposure to carbofuran (a metabolite of carbosulfan) represented 367% of the acute reference dose (ARfD) for 1-6-year-old Chinese children and 227% for the general Chinese population. CONCLUSION: A minimum pre-harvest interval of 12 days for carbosulfan is proposed to ensure safe consumption of cucumber. The slow dissipation rate of omethoate in cucumber reveals that a longer pre-harvest interval (≥ 27 days) is necessary to prevent dietary risk when dimethoate is applied to cucumber. © 2018 Society of Chemical Industry.