High-quality de novo assembly of the Eucommia ulmoides haploid genome provides new insights into evolution and rubber biosynthesis

We report the acquisition of a high-quality haploid chromosome-scale genome assembly for the first time in a tree species, Eucommia ulmoides, which is known for its rubber biosynthesis and medicinal applications. The assembly was obtained by applying PacBio and Hi–C technologies to a haploid that we specifically generated. Compared to the initial genome release, this one has significantly improved assembly quality. The scaffold N50 (53.15 MB) increased 28-fold, and the repetitive sequence content (520 Mb) increased by 158.24 Mb, whereas the number of gaps decreased from 104,772 to 128. A total of 92.87% of the 26,001 predicted protein-coding genes identified with multiple strategies were anchored to the 17 chromosomes. A new whole-genome duplication event was superimposed on the earlier γ paleohexaploidization event, and the expansion of long terminal repeats contributed greatly to the evolution of the genome. The more primitive rubber biosynthesis of this species, as opposed to that in Hevea brasiliensis, relies on the methylerythritol-phosphate pathway rather than the mevalonate pathway to synthesize isoprenyl diphosphate, as the MEP pathway operates predominantly in trans-polyisoprene-containing leaves and central peels. Chlorogenic acid biosynthesis pathway enzymes were preferentially expressed in leaves rather than in bark. This assembly with higher sequence contiguity can foster not only studies on genome structure and evolution, gene mapping, epigenetic analysis and functional genomics but also efforts to improve E. ulmoides for industrial and medical uses through genetic engineering

Applicability assessment and uncertainty analysis of multi-precipitation datasets for the simulation of hydrologic models

Hydrologic models are essential tools for understanding hydrologic processes, such as precipitation, which is a fundamental component of the water cycle. For an improved understanding and the evaluation of different precipitation datasets, especially their applicability for hydrologic modelling, three kinds of precipitation products, CMADS, TMPA-3B42V7 and gauge-interpolated datasets, are compared. Two hydrologic models (IHACRES and Sacramento) are applied to study the accuracy of the three types of precipitation products on the daily streamflow of the Lijiang River, which is located in southern China. The models are calibrated separately with different precipitation products, with the results showing that the CMADS product performs best based on the Nash-Sutcliffe efficiency, including a much better accuracy and better skill in capturing the streamflow peaks than the other precipitation products. The TMPA-3B42V7 product shows a small improvement on the gauge-interpolated product. Compared to TMPA-3B42V7, CMADS shows better agreement with the ground-observation data through a pixel-to-point comparison. The comparison of the two hydrologic models shows that both the IHACRES and Sacramento models perform well. The IHACRES model however displays less uncertainty and a higher applicability than the Sacramento model in the Lijiang River basin

Comparative Water Environment Simulation Study of Two Typical Models with BMPs in a Karst Basin

Carbonate rocks are widely distributed in southwest China, forming a unique karst landscape. The Lijiang River Basin provides a typical example of an area with concentrated karst. Research on the laws of hydrology and water quality migration in the Lijiang River Basin is important for the management of the water resources of Guilin City and similar areas. In this study, we combined three meteorological data with the soil and water assessment tool (SWAT) model and the hydrological simulation program-Fortran (HSPF) model to simulate the hydrological and water quality processes in the Lijiang River Basin separately. We chose the Nash–Sutcliffe efficiency (NSE) coefficient, coefficient of determination (R2), root mean square error-observations standard deviation ratio (RSR), and mean absolute error (MAE) as the metrics used to evaluate the models. The results, combined with the time-series process lines, indicated that the SWAT model provides a more accurate performance than the HSPF model in streamflow, ammonia nitrogen (NH3-N), and dissolved oxygen (DO) simulations. In addition, we divided the karst and non-karst areas, and we analyzed the differences between them in water balance, sediment transport, and pollution load. We further identified the key source areas of pollution load in the Lijiang River Basin, evaluated the pollution reduction effect of best management practices (BMPs) on surface source pollution, and proposed some pollution control countermeasures. Each scenario, especially returning farmland to forest and creating vegetation buffer zones, reduces the NH3-N and DO pollution load

Spatial and Temporal Distribution Characteristics of Nutrient Elements and Heavy Metals in Surface Water of Tibet, China and Their Pollution Assessment

In the context of global climate change, the ecological environment of Tibet has been gaining attention given its unique geographical and fragile nature. In this study, to understand the pollution status of the surface water of Tibet, China, we collected monthly data of 12 indicators from 41 cross-sectional monitoring sites in 2021 and analyzed the spatial and temporal variations of nutrients and heavy metal elements, water quality conditions, and pollutant sources in surface water. All 12 polluting elements, except lead (Pb), had significant seasonal variations, but the magnitude of the differences was very small. Spatially, nutrient elements were relatively concentrated in the agricultural and pastoral development areas in central and northern Tibet. In general, the water quality in most parts of Tibet was found to be good, and the water quality of 41 monitoring sections belonged to Class I water standard as per the entropy method–fuzzy evaluation method. The study used a multivariate statistical method to analyze the sources of pollution factors. The principal component analysis method identified four principal components. The results of this study can provide a scientific basis for pollution prevention and control in the Tibet Autonomous Region, and contribute to further research on water ecology

Retrieval and Evaluation of Chlorophyll-a Concentration in Reservoirs with Main Water Supply Function in Beijing, China, Based on Landsat Satellite Images

Remote sensing retrieval is an important technology for studying water eutrophication. In this study, Guanting Reservoir with the main water supply function of Beijing was selected as the research object. Based on the measured data in 2016, 2017, and 2019, and Landsat-8 remote sensing images, the concentration and distribution of chlorophyll-a in the Guanting Reservoir were inversed. We analyzed the changes in chlorophyll-a concentration of the reservoir in Beijing and the reasons and effects. Although the concentration of chlorophyll-a in the Guanting Reservoir decreased gradually, it may still increase. The amount and stability of water storage, chlorophyll-a concentration of the supply water, and nitrogen and phosphorus concentration change are important factors affecting the chlorophyll-a concentration of the reservoir. We also found a strong correlation between the pixel values of adjacent reservoirs in the same image, so the chlorophyll-a estimation model can be applied to each other

Percutaneous endoscopic interlaminar discectomy of L5–S1 disc herniation: a comparison between intermittent endoscopy technique and full endoscopy technique

Abstract Background Percutaneous endoscopic laminar discectomy is a typical minimally invasive discectomy operation that is classified into the percutaneous endoscopic transforaminal discectomy and the percutaneous endoscopic interlaminar discectomy. Based on whether the surgeon chooses to deal with the ligamentum flavum under endoscope guidance, percutaneous endoscopic discectomy by the interlaminar approach can be performed with a full endoscope technique with the intermittent endoscope technique. To our knowledge, there is no study comparing these two techniques in regard to their surgical effects and advantages. Therefore, we conducted this study to compare the cost, safety, and efficacy between the intermittent endoscopy technique and full endoscopy technique of endoscopic interlaminar lumbar discectomy at the L5–S1 level. Methods From September 2014 to March 2015, a total of 126 patients with radiculopathy due to L5–S1 disc herniation who were treated by a full endoscopy technique (65 patients) or intermittent endoscopy technique (61 patients) were included. Relevant data, such as duration time of the operation, hospitalization expenses, postoperative bed rest time, length of hospitalization, and complication rates, were recorded. Clinical outcomes were assessed by the visual analog scale score, modified MacNab criteria, and Oswestry disability index. Results In the full endoscope (FE) group, the mean duration time of surgery was 75.0 ± 11.9 min. The postoperative bed rest time was 6.5 ± 1.1 h, length of hospitalization was 3.8 ± 1.1 days, and complication rate was 7.69%. In the intermittent endoscopy (IE) group, the mean duration time of surgery was 43.0 ± 16.4 min. The postoperative bed rest time was 5.0 ± 1.1 h, length of hospitalization was 3.6 ± 1.2 days, and complication rate was 6.60%. The average hospitalization expenses of the FE group and IE group, respectively, were 32,069 ± 1086 RMB and 22,665 ± 899 RMB. There were significant differences in the surgical duration and hospitalization expenses (P  0.05). The postoperative Oswestry disability index and VAS were clearly improved in both groups compared with those of preoperation (P  0.05). Conclusions Both the full endoscopy technique and intermittent endoscopy technique achieved good outcomes, whereas the intermittent endoscopy technique is a more effective option for a shorter duration surgery and lower hospitalization expenses

Characterization of bla AFM-1-positive carbapenem-resistant strains isolated in Guangzhou, China

Abstract Background Carbapenemase-producing makes a great contribution to carbapenem resistance in Gram-negative bacilli. Bla AFM-1 gene was first discovered by us in Alcaligenes faecalis AN70 strain isolated in Guangzhou of China and, was submitted to NCBI on 16 November 2018. Methods Antimicrobial susceptibility testing was performed by broth microdilution assay using BD Phoenix 100. The phylogenetic tree of AFM and other B1 metallo-β-lactamases was visualized by MEGA7.0. Whole-genome sequencing technology was used to sequence carbapenem-resistant strains including the bla AFM-1 gene. Cloning and expressing of bla AFM-1 were designed to verify the function of AFM-1 to hydrolyze carbapenems and common β-lactamase substrates. Carba NP and Etest experiments were conducted to evaluate the activity of carbapenemase. Homology modeling was applied to predict the spatial structure of AFM-1. A conjugation assay was performed to test the ability of horizontal transfer of AFM-1 enzyme. The genetic context of bla AFM-1 was performed by Blast alignment. Results Alcaligenes faecalis strain AN70, Comamonas testosteroni strain NFYY023, Bordetella trematum strain E202, and Stenotrophomonas maltophilia strain NCTC10498 were identified as carrying the bla AFM-1 gene. All of these four strains were carbapenem-resistant strains. Phylogenetic analysis revealed that AFM-1 shares little nucleotide and amino acid identity with other class B carbapenemases (the highest identity (86%) with NDM-1 at the amino acid sequence level). The spatial structure of the AFM-1 enzyme was predicted to be αβ/βα sandwich structure, with two zinc atoms at its active site structure. Cloning and expressing of bla AFM-1 verified AFM-1 could hydrolyze carbapenems and common β-lactamase substrates. Carba NP test presented that the AFM-1 enzyme possesses carbapenemase activity. The successful transfer of pAN70-1(plasmid of AN70) to E.coli J53 suggested that the bla AFM-1 gene could be disseminated by the plasmid. The genetic context of bla AFM indicated that the downstream of the bla AFM gene was always adjacent to trpF and ble MBL. Comparative genome analysis revealed that bla AFM appeared to have been mobilized by an ISCR27-related mediated event. Conclusions The bla AFM-1 gene is derived from chromosome and plasmid, and the bla AFM-1 gene derived from the pAN70-1 plasmid can transfer carbapenem resistance to susceptible strains through horizontal transfer. Several bla AFM-1 -positive species have been isolated from feces in Guangzhou, China

Assessment of multiple precipitation interpolation methods and uncertainty analysis of hydrological models in Chaohe River basin, China

Precipitation interpolation is widely used to generate continuous rainfall surfaces for hydrological simulations. However, increasing the precision of values at the unknown points generated by different spatial interpolation methods is challenging. This study used the Chaohe River Basin, which is an important source of Beijing’s drinking water, as a research area to comprehensively evaluate several precipitation interpolation methods (Thiessen polygon, inverse distance weighting, ordinary kriging and ANUSPLIN) for inputs in hydrological simulations. This research showed that the precipitation time-series surface generated using the ANUSPLIN interpolation method had higher accuracy and reliability. Using this precipitation input to drive the hydrological models, we explored the parameter uncertainties of four typical hydrological models (GR4J, IHACRES, Sacramento and MIKE SHE) based on the multi-objective generalized likelihood uncertainty estimation (GLUE) method. The GLUE method was used to study the parameter sensitivity and uncertainty of the model. Results showed that the ANUSPLIN precipitation interpolation surface combined with the Sacramento model performed best. The multi-objective GLUE method had obvious advantages in parameter uncertainty analysis in hydrological models. Simultaneously exploring the convex line and point density distributions of the behavioural parameters with multi-objective functions determined their distribution and sensitivity more effectively

phoH-carrying virus communities responded to multiple factors and their correlation network with prokaryotes in sediments along Bohai Sea, Yellow Sea, and East China Sea in China

Viruses carrying phoH genes are an important functional group that may boost phosphate metabolism of their prokaryote hosts and affect phosphorus cycle in the ocean. However, at present, very little is known about the phoH-carrying viruses' community structure and diversity in marine sediments, as well as their correlation network with prokaryotes and environment. Here, via a large spatial scale investigation along the Bohai Sea, Yellow Sea, and East China Sea, for the first time, diverse unknown benthic phoH-carrying viruses were uncovered, which were mainly affiliated to three clusters. Interestingly, these viruses presented a very distinct community structure compared to those in seawaters. Correlation network analysis implied that these viruses might mainly infect the prokaryotes of Gamm-/Delta-proteobacteria, Thaumarchaeota, and Cyanobacteria in sediments. Distinct virus-prokaryote correlation network modules were shown in different sea areas. These modules' highly nested feature implied their coevolution with prokaryotes during long-term arms race. Their distribution in sediments was influenced by multiple factors including geographic separation and the key environmental variables of total organic carbon and total phosphorus, and responded to terrestrial inputs and coastal aquaculture activities. The results of this study provide novel insights into the benthic virus communities potentially participating in phosphorus cycling in the ocean