Sensitive fluorescence detection of nucleic acids based on isothermal circular strand-displacement polymerization reaction

Here we have developed a sensitive DNA amplified detection method based on isothermal strand-displacement polymerization reaction. This method takes advantage of both the hybridization property of DNA and the strand-displacement property of polymerase. Importantly, we demonstrate that our method produces a circular polymerization reaction activated by the target, which essentially allows it to self-detect. Functionally, this DNA system consists of a hairpin fluorescence probe, a short primer and polymerase. Upon recognition and hybridization with the target ssDNA, the stem of the hairpin probe is opened, after which the opened probe anneals with the primer and triggers the polymerization reaction. During this process of the polymerization reaction, a complementary DNA is synthesized and the hybridized target is displaced. Finally, the displaced target recognizes and hybridizes with another probe, triggering the next round of polymerization reaction, reaching a target detection limit of 6.4 × 10−15 M

A comparative study on the three calculation methods for reproduction numbers of COVID-19

ObjectiveThis study uses four COVID-19 outbreaks as examples to calculate and compare merits and demerits, as well as applicational scenarios, of three methods for calculating reproduction numbers.MethodThe epidemiological characteristics of the COVID-19 outbreaks are described. Through the definition method, the next-generation matrix-based method, and the epidemic curve and serial interval (SI)-based method, corresponding reproduction numbers were obtained and compared.ResultsReproduction numbers (Reff), obtained by the definition method of the four regions, are 1.20, 1.14, 1.66, and 1.12. Through the next generation matrix method, in region H Reff = 4.30, 0.44; region P Reff = 6.5, 1.39, 0; region X Reff = 6.82, 1.39, 0; and region Z Reff = 2.99, 0.65. Time-varying reproduction numbers (Rt), which are attained by SI of onset dates, are decreasing with time. Region H reached its highest Rt = 2.8 on July 29 and decreased to Rt < 1 after August 4; region P reached its highest Rt = 5.8 on September 9 and dropped to Rt < 1 by September 14; region X had a fluctuation in the Rt and Rt < 1 after September 22; Rt in region Z reached a maximum of 1.8 on September 15 and decreased continuously to Rt < 1 on September 19.ConclusionThe reproduction number obtained by the definition method is optimal in the early stage of epidemics with a small number of cases that have clear transmission chains to predict the trend of epidemics accurately. The effective reproduction number Reff, calculated by the next generation matrix, could assess the scale of the epidemic and be used to evaluate the effectiveness of prevention and control measures used in epidemics with a large number of cases. Time-varying reproduction number Rt, obtained via epidemic curve and SI, can give a clear picture of the change in transmissibility over time, but the conditions of use are more rigorous, requiring a greater sample size and clear transmission chains to perform the calculation. The rational use of the three methods for reproduction numbers plays a role in the further study of the transmissibility of COVID-19

Land use change and climate variation in the Three Gorges Reservoir Catchment from 2000 to 2015 based on the Google Earth Engine

Possible environmental change and ecosystem degradation have received increasing attention since the construction of Three Gorges Reservoir Catchment (TGRC) in China. The advanced Google Earth Engine (GEE) cloud-based platform and the large number of Geosciences and Remote Sensing datasets archived in GEE were used to analyze the land use and land cover change (LULCC) and climate variation in TGRC. GlobeLand30 data were used to evaluate the spatial land dynamics from 2000 to 2010 and Landsat 8 Operational Land Imager (OLI) images were applied for land use in 2015. The interannual variations in the Land Surface Temperature (LST) and seasonally integrated normalized difference vegetation index (SINDVI) were estimated using Moderate Resolution Imaging Spectroradiometer (MODIS) products. The climate factors including air temperature, precipitation and evapotranspiration were investigated based on the data from the Global Land Data Assimilation System (GLDAS). The results indicated that from 2000 to 2015, the cultivated land and grassland decreased by 2.05% and 6.02%, while the forest, wetland, artificial surface, shrub land and waterbody increased by 3.64%, 0.94%, 0.87%, 1.17% and 1.45%, respectively. The SINDVI increased by 3.209 in the period of 2000-2015, while the LST decreased by 0.253 °C from 2001 to 2015. The LST showed an increasing trend primarily in urbanized area, with a decreasing trend mainly in forest area. In particular, Chongqing City had the highest LST during the research period. A marked decrease in SINDVI occurred primarily in urbanized areas. Good vegetation areas were primarily located in the eastern part of the TGRC, such as Wuxi County, Wushan County, and Xingshan County. During the 2000–2015 period, the air temperature, precipitation and evapotranspiration rose by 0.0678 °C/a, 1.0844 mm/a, and 0.4105 mm/a, respectively. The climate change in the TGRC was influenced by LULCC, but the effect was limited. What is more, the climate change was affected by regional climate change in Southwest China. Marked changes in land use have occurred in the TGRC, and they have resulted in changes in the LST and SINDVI. There was a significantly negative relationship between LST and SINDVI in most parts of the TGRC, especially in expanding urban areas and growing forest areas. Our study highlighted the importance of environmental protection, particularly proper management of land use, for sustainable development in the catchment

Correction-Efficiency-Coefficient-Based Trajectory Optimization for Two-Dimensional Trajectory Correction Projectile

Based on the lift-to-drag ratio of a two-dimensional trajectory correction projectile, in this paper, a novel correction efficiency coefficient model has been proposed for the trajectory optimization of a two-dimensional trajectory correction projectile, and research on the influence a correction efficiency coefficient has on the flight parameters of correction trajectory is carried out. A series of results are obtained through theoretical analysis and simulation calculations, indicating that, the smaller the value of the correction efficiency coefficient is, the stronger the correction ability of the projectile reserves. The trajectory and canard geometry of the correction section of the two-dimensional trajectory correction projectile are optimized by the Gauss pseudo-spectral method and correction efficiency coefficient, and, after taking the correction efficiency coefficient into account, the projectile can accurately hit the target and effectively eliminate the swing phenomenon of the projectile’s lateral trajectory. Meanwhile, a stable roll control command is obtained. When the diameter aspect ratio of the canard is 0.4, both the flight state quantity of the optimized projectile and the roll control command are more stable, and, when the canard shape is trapezoidal, the correction efficiency coefficient is smaller, the result of trajectory optimization is more stable, and the stability of the output roll control command is better. The research results of this paper can provide certain references for both the designs of the two-dimensional trajectory correction projectile’s trajectory and the canard geometry

Dietary proline supplementation alters colonic luminal microbiota and bacterial metabolite composition between days 45 and 70 of pregnancy in Huanjiang mini-pigs

Abstract Background Pregnancy is associated with important changes in gut microbiota composition. Dietary factors may affect the diversity, composition, and metabolic activity of the intestinal microbiota. Among amino acids, proline is known to play important roles in protein metabolism and structure, cell differentiation, conceptus growth and development, and gut microbiota re-equilibration in case of dysbiosis. Results Dietary supplementation with 1% proline decreased (P < 0.05) the amounts of Klebsiella pneumoniae, Peptostreptococcus productus, Pseudomonas, and Veillonella spp. in distal colonic contents than that in the control group. The colonic contents of Butyrivibrio fibrisolvens, Bifidobacterium sp., Clostridium coccoides, Clostridium coccoides-Eubacterium rectale, Clostridium leptum subgroup, Escherichia coli, Faecalibacterium prausnitzii, Fusobacterium prausnitzii, and Prevotella increased (P < 0.05) on d 70 of pregnancy as compared with those on d 45 of pregnancy. The colonic concentrations of acetate, total straight-chain fatty acid, and total short-chain fatty acids (SCFA) in the proline-supplemented group were lower (P < 0.05), and butyrate level (P = 0.06) decreased as compared with the control group. Almost all of the SCFA displayed higher (P < 0.05) concentrations in proximal colonic contents on d 70 of pregnancy than those on d 45 of pregnancy. The concentrations of 1,7-heptyl diamine (P = 0.09) and phenylethylamine (P < 0.05) in proximal colonic contents were higher, while those of spermidine (P = 0.05) and total bioamine (P = 0.06) tended to be lower in the proline-supplemented group than those in the control group. The concentrations of spermidine, spermine, and total bioamine in colonic contents were higher (P < 0.05) on d 70 of pregnancy than those measured on d 45 of pregnancy. In contrast, the concentration of phenylethylamine was lower (P < 0.05) on d 70 than on d 45 of pregnancy. Conclusion These findings indicate that L-proline supplementation modifies both the colonic microbiota composition and the luminal concentrations of several bacterial metabolites. Furthermore, our data show that both the microbiota composition and the concentrations of bacterial metabolites are evolving in the course of pregnancy. These results are discussed in terms of possible implication in terms of luminal environment and consequences for gut physiology and health

Impact of Fiscal Expenditure on Farmers’ Livelihood Capital in the Ethnic Minority Mountainous Region of Sichuan, China

Poverty alleviation is the first battle to realize the rural revitalization strategy in China, and research on the sustainable livelihood of rural households is of great significance to solving the problem of rural poverty. Based on the sustainable livelihood framework, the reasonable scale and structure of fiscal expenditure is an inevitable requirement in producing sustainable livelihood capital toward this aim. In this study, the system Gaussian mixed model was used to analyze the impact of fiscal expenditure on farmers’ livelihoods. Representative survey data uses panel data from 48 counties across Liangshan Prefecture, Ganzi Prefecture, and Aba Prefecture in Sichuan, China. The results are as follows: (1) The average stock of human capital in 2010 to 2015 was the highest in the composition of farmers’ livelihood capital; (2) natural capital and physical capital were positively affected by the total scale of fiscal expenditure, agriculture, forestry, and water expenditure, and the former was negatively affected by general public service expenditure, education expenditure, social security and employment expenditure, and medical expenditure; (3) financial capital and the total amount of livelihood capital were positively affected by the total scale of fiscal expenditure, agriculture, forestry and water expenditure, education expenditure, social security and employment expenditure, and medical expenditure, and negatively affected by general public service expenditure; (4) human capital was positively affected by the total scale of fiscal expenditure, education expenditure, social security and employment expenditure, and medical expenditure; and (5) social capital was positively affected by agriculture, forestry and water expenditure, and education expenditure

Simple method for direct crown base height estimation of individual conifer trees using airborne LiDAR data

Crown base height (CBH) is an essential tree biophysical parameter for many applications in forest management, forest fuel treatment, wildfire modeling, ecosystem modeling and global climate change studies. Accurate and automatic estimation of CBH for individual trees is still a challenging task. Airborne light detection and ranging (LiDAR) provides reliable and promising data for estimating CBH. Various methods have been developed to calculate CBH indirectly using regression-based means from airborne LiDAR data and field measurements. However, little attention has been paid to directly calculate CBH at the individual tree scale in mixed-species forests without field measurements. In this study, we propose a new method for directly estimating individual-tree CBH from airborne LiDAR data. Our method involves two main strategies: 1) removing noise and understory vegetation for each tree; and 2) estimating CBH by generating percentile ranking profile for each tree and using a spline curve to identify its inflection points. These two strategies lend our method the advantages of no requirement of field measurements and being efficient and effective in mixed-species forests. The proposed method was applied to a mixed conifer forest in the Sierra Nevada, California and was validated by field measurements. The results showed that our method can directly estimate CBH at individual tree level with a root-mean-squared error of 1.62 m a coefficient of determination of 0.88 and a relative bias of 3.36%. Furthermore, we systematically analyzed the accuracies among different height groups and tree species by comparing with field measurements. Our results implied that taller trees had relatively higher uncertainties than shorter trees. Our findings also show that the accuracy for CBH estimation was the highest for black oak trees, with an RMSE of 0.52 m. The conifer species results were also good with uniformly high R-2 ranging from 0.82 to 0.93. In general, our method has demonstrated high accuracy for individual tree CBH estimation and strong potential for applications in mixed species over large areas. (C) 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreemen

Changes in carcass traits, meat quality, muscle fiber characteristics and liver function of finishing pigs fed high level of fish oil

The study was aimed to investigate the changes in carcass traits, meat quality, muscle fiber characteristics, and liver function in pigs fed with high levels of fresh fish oil and oxidized fish oil. About 30 piglets were randomly assigned to receive basal diet plus 2% fish oil (LFO), basal diet plus 8% fish oil (HFO), or basal diet plus 8% oxidized fish oil (OFO) for 120 d. Pigs of the HFO and OFO group showed reduced carcass weight, dressing percentage, loin eye area, and increased yellowness of the longissimus dorsi muscle compared with LFO group (P < 0.05). Dietary HFO and OFO suppressed the relative expression levels of myosin heavy chain (MyHC) isoform (I and II a), glutathione peroxidase 4, and NAD(P)H: quinone oxidoreductase-1 and mitochondrial biogenesis in longissimus dorsi muscle (P < 0.05). Dietary HFO or OFO increased the serum aspartates aminotransferase, alanine aminotransferase, total bilirubin, direct bilirubin, oxidized low-density lipoprotein, liver index, and concentration of malondialdehyde (MDA) in liver (P < 0.05). In conclusion, high levels of fresh fish oil and oxidized fish oil have adverse effects on carcass traits, muscle fiber characteristics, and liver function, which may be partly due to the mitochondrial dysfunction and impaired antioxidative capacity.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author