Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Decontamination and Ecological Restoration Performance of a Bioretention Cell-Microbial Fuel Cell under Multiple-Antibiotics Stress

Antibiotics are refractory pollutants that have been widely found in various environmental media such as soil and surface water. Existing sewage treatments perform poorly at preventing antibiotics in urban sewage from polluting natural environments. In this study, we designed a bioelectrically enhanced bioretention cell system (bioretention cell-microbial fuel cell, BRC-MFC) that utilizes the unique structure of the BRC system to improve the removal of sewage antibiotics. This new system can efficiently remove antibiotics by using a synergy of plant absorption, filler adsorption, filler filtration and microbial degradation. To study the influences of multiple-antibiotics stress on the decontamination performance of BRC-MFC, ofloxacin (OFLX) and tetracycline (TC) were selected as target antibiotics, and five BRC-MFCs were built to treat sewage containing antibiotics of different concentrations. The concentrations of pollutant in the influent and effluent were measured and the pollutant removal performance of BRC-MFC was studied. The diversity of rhizosphere microorganisms and the abundance of denitrifying functional genes were analyzed. Experimental results showed that over 90% of OFLX and TC in each BRC-MFC were removed, with the removal rates positively correlating with the concentration of antibiotics. In addition, the removal rates of chemical oxygen demand (COD) in BRC-MFC were both over 90%, while the removal rate of total nitrogen (TN) was around 70%. Meanwhile, antibiotics could significantly improve the removal of ammonia nitrogen (NH4+-N, p < 0.01). The microbial richness decreased, and we found that combined antibiotic stress on microorganisms was stronger than single antibiotic stress. The abundance of denitrifying functional genes was reduced by antibiotic stress. The results of this study provide reference values for other projects focusing on removing various antibiotics from domestic sewage using BRC-MFC

Insights into Allosteric Mechanisms of the Lung-Enriched p53 Mutants V157F and R158L

Lung cancer is a leading fatal malignancy in humans. p53 mutants exhibit not only loss of tumor suppressor capability but also oncogenic gain-of-function, contributing to lung cancer initiation, progression and therapeutic resistance. Research shows that p53 mutants V157F and R158L occur with high frequency in lung squamous cell carcinomas. Revealing their conformational dynamics is critical for developing novel lung therapies. Here, we used all-atom molecular dynamics (MD) simulations to investigate the effect of V157F and R158L substitutions on the structural properties of the p53 core domain (p53C). Compared to wild-type (WT) p53C, both V157F and R158L mutants display slightly lesser &beta;-sheet structure, larger radius of gyration, larger volume and larger exposed surface area, showing aggregation-prone structural characteristics. The aggregation-prone fragments (residues 249&ndash;267 and 268&ndash;282) of two mutants are more exposed to water solution than that of WT p53C. V157F and R158L mutation sites can affect the conformation switch of loop 1 through long-range associations. Simulations also reveal that the local structure and conformation around the V157F and R158L mutation sites are in a dynamic equilibrium between the misfolded and properly folded conformations. These results provide molecular mechanistic insights into allosteric mechanisms of the lung-enriched p53 mutants

Characteristics and Driving Factors of Nitrogen-Use Efficiency in Chinese Greenhouse Tomato Cultivation

Excessive nitrogen fertilizer application in greenhouses could cause a significant variation in the nitrogen-use efficiency at the regional scale. This study aims to quantify agronomic nitrogen-use efficiency (AEN) and identify its driving factors across Chinese greenhouse tomato cultivation. Three hundred and forty-eight AEN values were obtained from 64 papers, including mineral nitrogen (MN) and mineral combined with organic nitrogen (MON) treatments. The average AEN values for the MN and MON treatments were 56.6 ± 7.0 kg kg−1 and 34.6 ± 3.5 kg kg−1, respectively. The AEN of the MN treatment was higher than that of the MON treatment for cultivation using soil with an organic matter content of less than 10 g kg−1 and the drip fertigation method. The AENs of the MN and MON treatments were divided into two segments according to the nitrogen application rate. The inflection points of the nitrogen application rate were 290 and 1100 kg N ha−1 for the MN and MON treatments, respectively. When the ratio of organic nitrogen to total nitrogen was less than 0.4, it was beneficial for improving the AEN. The soil organic matter content and the nitrogen application rate were the most critical factors determining the AEN. These results suggest that rationally reducing the nitrogen input and partially substituting mineral nitrogen with organic nitrogen can help improve the nitrogen-use efficiency

Characteristics and Driving Factors of Nitrogen-Use Efficiency in Chinese Greenhouse Tomato Cultivation

Excessive nitrogen fertilizer application in greenhouses could cause a significant variation in the nitrogen-use efficiency at the regional scale. This study aims to quantify agronomic nitrogen-use efficiency (AEN) and identify its driving factors across Chinese greenhouse tomato cultivation. Three hundred and forty-eight AEN values were obtained from 64 papers, including mineral nitrogen (MN) and mineral combined with organic nitrogen (MON) treatments. The average AEN values for the MN and MON treatments were 56.6 &plusmn; 7.0 kg kg&minus;1 and 34.6 &plusmn; 3.5 kg kg&minus;1, respectively. The AEN of the MN treatment was higher than that of the MON treatment for cultivation using soil with an organic matter content of less than 10 g kg&minus;1 and the drip fertigation method. The AENs of the MN and MON treatments were divided into two segments according to the nitrogen application rate. The inflection points of the nitrogen application rate were 290 and 1100 kg N ha&minus;1 for the MN and MON treatments, respectively. When the ratio of organic nitrogen to total nitrogen was less than 0.4, it was beneficial for improving the AEN. The soil organic matter content and the nitrogen application rate were the most critical factors determining the AEN. These results suggest that rationally reducing the nitrogen input and partially substituting mineral nitrogen with organic nitrogen can help improve the nitrogen-use efficiency

Reply to Simpson et al. : Short-term no tillage reduces soil carbon stocks but longer duration can alleviate the initial decline

Peer reviewedPublisher PD

Magnitude, direction, and drivers of rhizosphere effect on soil nitrogen and phosphorus in global agroecosystem

The rhizosphere is the most active soil area for material transformation and energy flow of soil, root, and microorganism, which plays an important role in soil biochemical cycling. Although the rhizospheric nitrogen (N) and phosphorous (P) were easily disturbed in the agroecosystem, the effects of rhizosphere on the dynamics of soil N and P cycling have not yet been systematically quantified globally. We summarized the magnitude, direction, and driving forces of rhizosphere effects on agroecosystem's N and P dynamics by 1063 observations and 15 variables from 122 literature. Rhizosphere effects increased available N (AN, 9%), available P (AP, 11%), and total P (TP, 5%), and decreased nitrate N (NO3–N, 18%) and ammonia N (NH4–N, 16%). The effect of rhizosphere on total N (TN) was not significant. These effects improved AN in tropical (12%) and subtropical (14%) regions. The effect of rhizosphere on TP was greater under subtropical conditions than in other climates. The most substantial effects of the rhizosphere on TP and AP were observed under humid conditions. Rhizosphere effects increased AN and AP in vegetables more than in other crop systems. Application of N > 300 kg ha−1 had the most significant and positive rhizosphere effects on TN and AN. P application of 100–150 kg ha−1 had the greatest rhizosphere effects on TP and AP. These effects also improved the microbial (biomass N and P) and enzymatic aspects (urease, acid phosphatase, and alkaline phosphatase) of soil P and N cycling. Structural equation modeling suggested that aridity indices, fertilizer application rate, soil pH, microbial biomass, and soil enzymes strongly influence the magnitude and direction of the rhizosphere's effect on the P and N cycles. Overall, these findings are critical for improving soil nutrient utilization efficiency and modeling nutrient cycling in the rhizosphere for agricultural systems

Serum uric acid level is correlated with the clinical, pathological progression and prognosis of IgA nephropathy: an observational retrospective pilot-study

Objectives This study was aimed to assess the relationship between serum uric acid (SUA) level and the clinical, pathological phenotype of IgA nephropathy (IgAN), and to determine the role of SUA level in the progression and prognosis of IgAN. Methods A total of 208 patients with IgAN were included in this study, and were classified into the normo-uricemia group and hyperuricemia group according to the SUA level. The clinical data at baseline, IgAN Oxford classification scores (MEST-C scoring system), and other pathological features were collected and further analyzed. All patients were followed up and the prognosis was assessed using Kaplan-Meier survival curves. GraphPad Prism 7.0 and SPSS 23.0 were used for statistical analyses. Results In clinical indicators, patients with hyperuricemia had the significantly higher proportion of males to females, mean arterial pressure, the levels of total cholesterol, triglyceride, Scr, BUN, 24 hour-urine protein, C3, and C4, the lower levels of high-density lipoprotein cholesterol and eGFR than those without (p  0.05). As for the depositions of immune complexes deposition in IgAN, the hyperuricemia group had less deposition of immunoglobulin G and FRA than the normo-uricemia group (p < 0.05), while the deposition of immunoglobulin A, immunoglobulin M, and complement C3 in the two groups showed no statistical difference. The survival curve suggested that patients in the hyperuricemia group have significantly poorer renal outcome than those in the normo-uricemia group (p = 0.0147). Results also revealed that the SUA level is a valuable predictor of renal outcome in patients with IgAN. The optimal cutoff value was 361.1 µmol/L (AUC = 0.76 ± 0.08167) and 614 µmol/L (AUC = 0.5728 ± 0.2029) for female and male, respectively. Conclusions The level of SUA is associated with renal function level and pathological severity of IgAN, and maybe a prognostic indicator of IgAN