Structural Properties of CXCL4L1 and Its Recognition of the CXCR3 N-Terminus.

Chemokine CXCL4L1, a homologue of CXCL4, is a more potent antiangiogenic ligand. Its structural property is correlated with the downstream receptor binding. The two chemokines execute their functions by binding the receptors of CXCR3A and CXCR3B. The receptors differ by an extra 51-residue extension in the CXCR3B N-terminus. To understand the binding specificity, a GB1 protein scaffold was used to carry different CXCR3 extracellular elements, and artificial CXCL4 and CXCL4L1 monomers were engineered for the binding assay. We first characterized the molten globule property of CXCL4L1. The structural property causes the CXCL4L1 tetramer to dissociate into monomers in low concentrations, but native CXCL4 adopts a stable tetramer structure in solution. In the titration experiments, the combination of the CXCR3A N-terminus and receptor extracellular loop 2 provided moderate and comparable binding affinities to CXCL4 and CXCL4L1, while sulfation on the CXCR3A N-terminal tyrosine residues provided binding specificity. However, the CXCR3B N-terminal extension did not show significant enhancement in the binding of CXCL4 or CXCL4L1. This result indicates that the tendency to form a chemokine monomer and the binding affinity together contribute the high antiangiogenic activity of CXCL4L1.

Exploration of the Catalytic Cycle Dynamics of Vigna Radiata H+-Translocating Pyrophosphatases Through Hydrogen-Deuterium Exchange Mass Spectrometry.

Vigna radiata H+-translocating pyrophosphatases (VrH+-PPases, EC 3.6.1.1) are present in various endomembranes of plants, bacteria, archaea, and certain protozoa. They transport H+ into the lumen by hydrolyzing pyrophosphate, which is a by-product of many essential anabolic reactions. Although the crystal structure of H+-PPases has been elucidated, the H+ translocation mechanism of H+-PPases in the solution state remains unclear. In this study, we used hydrogen-deuterium exchange (HDX) coupled with mass spectrometry (MS) to investigate the dynamics of H+-PPases between the previously proposed R state (resting state, Apo form), I state (intermediate state, bound to a substrate analog), and T state (transient state, bound to inorganic phosphate). When hydrogen was replaced by proteins in deuterium oxide solution, the backbone hydrogen atoms, which were exchanged with deuterium, were identified through MS. Accordingly, we used deuterium uptake to examine the structural dynamics and conformational changes of H+-PPases in solution. In the highly conserved substrate binding and proton exit regions, HDX-MS revealed the existence of a compact conformation with deuterium exchange when H+-PPases were bound with a substrate analog and product. Thus, a novel working model was developed to elucidate the in situ catalytic mechanism of pyrophosphate hydrolysis and proton transport. In this model, a proton is released in the I state, and the TM5 inner wall serves as a proton piston.

Intra-block pyramid cross-scale network for thermal radiation effect correction of uncooled infrared images.

Thermal radiation effects can greatly degrade the image quality of uncooled infrared focal plane array detection systems. In this paper, we propose a thermal radiation effect correction network based on intra-block pyramid cross-scale feature extraction and fusion. First, an intra-block pyramid residual attention module is introduced to obtain fine-grained features from long-range IR images by extracting cross-scale local features within the residual block. Second, we propose a cross-scale gated fusion module to efficiently integrate the shallow and abstract features at multiple scales of the encoder and decoder through gated linear units. Finally, to ensure accurate correction of thermal radiation effects, we add double-loss constraints in the spatial-frequency domain and construct a single-input, multi-output network with multiple supervised constraints. The experimental results demonstrate that our proposed method outperforms state-of-the-art correction methods in terms of both visual quality and quantitative evaluation metrics.

The evolutionary origin and domestication history of goldfish (Carassius auratus).

Goldfish have been subjected to over 1,000 y of intensive domestication and selective breeding. In this report, we describe a high-quality goldfish genome (2n = 100), anchoring 95.75% of contigs into 50 pseudochromosomes. Comparative genomics enabled us to disentangle the two subgenomes that resulted from an ancient hybridization event. Resequencing 185 representative goldfish variants and 16 wild crucian carp revealed the origin of goldfish and identified genomic regions that have been shaped by selective sweeps linked to its domestication. Our comprehensive collection of goldfish varieties enabled us to associate genetic variations with a number of well-known anatomical features, including features that distinguish traditional goldfish clades. Additionally, we identified a tyrosine-protein kinase receptor as a candidate causal gene for the first well-known case of Mendelian inheritance in goldfish-the transparent mutant. The goldfish genome and diversity data offer unique resources to make goldfish a promising model for functional genomics, as well as domestication.

Upconversion NaYF4:Yb/Er-TiO2-Ti3C2 Heterostructure-Based Near-Infrared Light-Driven Photoelectrochemical Biosensor for Highly Sensitive and Selective d-Serine Detection.

A near-infrared (NIR) light-driven NaYF4:Yb/Er-TiO2-Ti3C2 (NYF-TiO2-Ti3C2) heterostructure-based photoelectrochemical (PEC) biosensing platform was constructed for highly sensitive d-serine (d-ser) detection. Accurate d-ser detection depends on the model biocatalyst, d-amino acid oxidase (DAAO), which converts d-ser into hydroxypyruvate and an equimolar concentration of hydrogen peroxide (H2O2) via an enzymatic reaction. The TiO2-Ti3C2 semiconductor and NaYF4:Yb/Er optical transducer formed a Schottky junction that provided an irreversible channel for electron transfer. Infrared light was converted into absorbable multiemission light, thereby effectively increasing light absorption. Simultaneously, the generated H2O2 rapidly scavenged photogenerated holes to separate electron-hole pairs, which amplified the photocurrent signal. Under optimal conditions, the NIR light-driven PEC biosensor exhibited an excellent PEC performance for d-ser detection, with a wide linear range of 2-1650 µmol L-1 and detection limit as low as 0.286 µmol L-1. Importantly, high detection reproducibility and accuracy were achieved using this strategy for analyzing human serum and rat cerebrospinal fluid (CSF) specimens. The admirable applicability of the NYF-TiO2-Ti3C2-based PEC biosensor for detecting d-ser may lead to further opportunities for detecting other disease-related biomarkers.

Composite hydrolytic acidification - aerobic MBBR process for treating traditional Chinese medicine wastewater.

Traditional Chinese medicine (TCM) wastewater is characterized by high organic content, unstable water quality and quantity and low biodegradability. In this paper, the hydrolytic acidification reactor-aerobic moving bed biofilm (MBBR) process was used to degrade TCM wastewater. Besides, a small pilot study was conducted. The appropriate operating parameters: hydraulic retention time (HRT) of the hydrolytic reactor was 16 h, HRT of MBBR was 30 h, dissolved oxygen of MBBR was 6 mg/L, sludge return ratio of MBBR was 100%. The hydrolytic reactor was started for 25 days. MBBR was run in series with the hydrolytic reactor after 24 days of separate operation. The start-up of the composite reactor was completed after another 26 days. The average removal efficiencies of chemical oxygen demand and ammonia nitrogen were 92% and 70%. The hydrolytic reactor was effective in decomposing macromolecules and MBBR had a strong ability to degrade pollutants through the excitation-emission-matrix spectra. The evolution pattern of the dominant bacterial genera and the surface morphology of sludge were studied by scanning electron microscopy and high-throughput sequencing analysis. It could be seen that the surface morphology of the biological filler was suitable for the growth and reproduction of microorganisms.

BRM: a statistical method for QTL mapping based on bulked segregant analysis by deep sequencing.

MOTIVATION: Bulked segregant analysis by deep sequencing (BSA-seq) has been widely used for quantitative trait locus (QTL) mapping in recent years. A number of different statistical methods for BSA-seq have been proposed. However, determination of significance threshold, the key point for QTL identification, remains to be a problem that has not been well solved due to the difficulty of multiple testing correction. In addition, estimation of the confidence interval is also a problem to be solved. RESULTS: In this paper, we propose a new statistical method for BSA-seq, named Block Regression Mapping (BRM). BRM is robust to sequencing noise and is applicable to the case of low sequencing depth. Significance threshold can be reasonably determined by taking multiple testing correction into account. Meanwhile, the confidence interval of QTL position can also be estimated. AVAILABILITY AND IMPLEMENTATION: The R scripts of our method are open source under GPLv3 license at https://github.com/huanglikun/BRM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Bulked Segregant Analysis Coupled with Whole-Genome Sequencing (BSA-Seq) Mapping Identifies a Novel pi21 Haplotype Conferring Basal Resistance to Rice Blast Disease.

Basal or partial resistance has been considered race-non-specific and broad-spectrum. Therefore, the identification of genes or quantitative trait loci (QTLs) conferring basal resistance and germplasm containing them is of significance in breeding crops with durable resistance. In this study, we performed a bulked segregant analysis coupled with whole-genome sequencing (BSA-seq) to identify QTLs controlling basal resistance to blast disease in an F2 population derived from two rice varieties, 02428 and LiXinGeng (LXG), which differ significantly in basal resistance to rice blast. Four candidate QTLs, qBBR-4, qBBR-7, qBBR-8, and qBBR-11, were mapped on chromosomes 4, 7, 8, and 11, respectively. Allelic and genotypic association analyses identified a novel haplotype of the durable blast resistance gene pi21 carrying double deletions of 30 bp and 33 bp in 02428 (pi21-2428) as a candidate gene of qBBR-4. We further assessed haplotypes of Pi21 in 325 rice accessions, and identified 11 haplotypes among the accessions, of which eight were novel types. While the resistant pi21 gene was found only in japonica before, three Chinese indica varieties, ShuHui881, Yong4, and ZhengDa4Hao, were detected carrying the resistant pi21-2428 allele. The pi21-2428 allele and pi21-2428-containing rice germplasm, thus, provide valuable resources for breeding rice varieties, especially indica rice varieties, with durable resistance to blast disease. Our results also lay the foundation for further identification and functional characterization of the other three QTLs to better understand the molecular mechanisms underlying rice basal resistance to blast disease.

Potassium Stimulation of IAA Transport Mediated by the Arabidopsis Importer AUX1 Investigated in a Heterologous Yeast System.

Auxin regulates diverse processes involved in plant growth and development. AUX1 is the first identified and most widely investigated auxin importer, and plays an important role in root gravitropism and the development of lateral root and root hair. However, the regulation of auxin transport by AUX1 is still not well understood. In this study, we examined the effect of metal ions on AUX1 transport function and found that the activity could be specifically stimulated four times by K+. Further experiments revealed the preference of KF on the enhancement of transport activity of AUX1 over KCl, KBr, and KI. In addition, the interaction between K+ and AUX1 confers AUX1 more resistant to thermal stress but more vulnerable to proteolysis. Conventional chemical modification indicated that the extracellular acidic amino acids of AUX1 play a key role in the K+ stimulation. Site-specific mutagenesis showed that the replacement of Asp166, Asp293, and Asp312 of AUX1 to alanine deteriorated the K+-stimulated auxin transport. By contrast, when these residues were mutated to glutamate, lysine, or asparagine, only the D312E variant restored the IAA transport activity to the wild-type level. It is thus convinced that D312 is presumably the most promising residue for the K+ stimulation on AUX1.

Estimation of QTL heritability based on pooled sequencing data.

Motivation: Bulked segregant analysis combined with next generation sequencing has proven to be a simple and efficient approach for fast mapping of quantitative trait loci (QTLs). However, how to estimate the proportion of phenotypic variance explained by a QTL (or termed QTL heritability) in such pooled QTL mapping is an unsolved problem. Results: In this paper, we propose a method called PQHE to estimate QTL heritability using pooled sequencing data obtained under different experimental designs. Simulation studies indicated that our method is correct and feasible. Four practical examples from rice and yeast are demonstrated, each representing a different situation. Availability and implementation: The R scripts of our method are open source under GPLv3 license at http://genetics.fafu.edu.cn/PQHE or https://github.com/biotangweiqi/PQHE. The R scripts require the R package rootSolve. Contact: wuwr@fafu.edu.cn. Supplementary information: Supplementary data are available at Bioinformatics online.

Regulation of H+-pyrophosphatase by 14-3-3 Proteins from Arabidopsis thaliana.

Plant vacuolar H+-transporting inorganic pyrophosphatase (V-PPase; EC 3.6.1.1) is a crucial enzyme that exists on the tonoplast to maintain pH homeostasis across the vacuolar membrane. This enzyme generates proton gradient between cytosol and vacuolar lumen by hydrolysis of a metabolic byproduct, pyrophosphate (PP i ). The regulation of V-PPase at protein level has drawn attentions of many workers for decades, but its mechanism is still unclear. In this work, we show that AVP1, the V-PPase from Arabidopsis thaliana, is a target protein for regulatory 14-3-3 proteins at the vacuolar membrane, and all twelve 14-3-3 isoforms were analyzed for their association with AVP1. In the presence of 14-3-3ν, -µ, -ο, and -ι, both enzymatic activities and its associated proton pumping of AVP1 were increased. Among these 14-3-3 proteins, 14-3-3 µ shows the highest stimulation on coupling efficiency. Furthermore, 14-3-3ν, -µ, -ο, and -ι exerted protection of AVP1 against the inhibition of suicidal substrate PP i at high concentration. Moreover, the thermal profile revealed the presence of 14-3-3ο improves the structural stability of AVP1 against high temperature deterioration. Additionally, the 14-3-3 proteins mitigate the inhibition of Na+ to AVP1. Besides, the binding sites/motifs of AVP1 were identified for each 14-3-3 protein. Taken together, a working model was proposed to elucidate the association of 14-3-3 proteins with AVP1 for stimulation of its enzymatic activity.

Microbial characteristics of landfill leachate disposed by aerobic moving bed biofilm reactor.

An aerobic moving bed biofilm reactor (MBBR) was applied to treat landfill leachate generated from a domestic waste incineration plant. Pollutant removal efficiency of this reactor under stable operating condition was studied. The biomass, bacteria species, and microbial metabolism in this reactor were investigated. These results showed that the average removal efficiency of chemical oxygen demand (COD) and ammonia nitrogen in the aerobic MBBR achieved 64% and 97% in the optimum conditions, respectively. The three-dimensional fluorescence spectrum revealed that the content of soluble microbial byproducts from extracellular polymeric substances extraction in suspended sludge was much higher than that on biofilm, and the types of pollutants were various in different regions of the reactor. It also indicated that the MBBR system had a stable, rich and regular microorganism community, including large amounts of nitrifying bacteria and denitrifying bacteria. Scanning electron microscopy suggested that biofilm attached to the packing provided a good anoxic-aerobic micro environment system to achieve a high metabolic activity, which favored COD and ammonia removal.

Method for RNA extraction and cDNA library construction from microbes in crop rhizosphere soil.

Techniques to analyze the transcriptome of the soil rhizosphere are essential to reveal the interactions and communications between plants and microorganisms in the soil ecosystem. In this study, different volumes of Al2(SO4)3 were added to rhizosphere soil samples to precipitate humic substances, which interfere with most procedures of RNA and DNA analyses. After humic substances were precipitated, cells of soil microorganisms were broken by vortexing with glass beads, and then DNA and RNA were recovered using Tris-HCl buffer with LiCl, SDS, and EDTA. The crude extract was precipitated and dissolved in RNAse-free water, and then separated by agarose gel electrophoresis. We determined the optimum volume of Al2(SO4)3 for treating rhizosphere soil of rice, tobacco, sugarcane, Rehmannia glutinosa, and Pseudostellaria heterophylla. The crude nucleic acids extract from rice soil was treated with DNase I and then RNA was purified using a gel filtration column. The purified RNA was reverse-transcribed into single-strand cDNA and then ligated with an adaptor at each end before amplifying ds cDNA. The ds cDNA was sub-cloned for subsequent gene sequence analysis. We conducted qPCR to amplify 16S ribosomal DNA and observed highly efficient amplification. These results show that the extraction method can be optimized to isolate and obtain high-quality nucleic acids from microbes in different rhizosphere soils, suitable for genomic and post-genomic analyses.

Chemical characteristics and source apportionment of atmospheric particles during heating period in Harbin, China.

Atmospheric particles (total suspended particles (TSPs); particulate matter (PM) with particle size below 10 µm, PM10; particulate matter with particle size below 2.5 µm, PM(2.5)) were collected and analyzed during heating and non-heating periods in Harbin. The sources of PM10 and PM(2.5) were identified by the chemical mass balance (CMB) receptor model. Results indicated that PM(2.5)/TSP was the most prevalent and PM(2.5) was the main component of PM(10), while the presence of PM(10-100) was relatively weak. SO(4)(2-) and NO(3)(-) concentrations were more significant than other ions during the heating period. As compared with the non-heating period, Mn, Ni, Pb, S, Si, Ti, Zn, As, Ba, Cd, Cr, Fe and K were relatively higher during the heating period. In particular, Mn, Ni, S, Si, Ti, Zn and As in PM(2.5) were obviously higher during the heating period. Organic carbon (OC) in the heating period was 2-5 times higher than in the non-heating period. Elemental carbon (EC) did not change much. OC/EC ratios were 8-11 during the heating period, which was much higher than in other Chinese cities (OC/EC: 4-6). Results from the CMB indicated that 11 pollution sources were identified, of which traffic, coal combustion, secondary sulfate, secondary nitrate, and secondary organic carbon made the greatest contribution. Before the heating period, dust and petrochemical industry made a larger contribution. In the heating period, coal combustion and secondary sulfate were higher. After the heating period, dust and petrochemical industry were higher. Some hazardous components in PM(2.5) were higher than in PM(10), because PM(2.5) has a higher ability to absorb toxic substances. Thus PM(2.5) pollution is more significant regarding human health effects in the heating period.

Activated carbon fibers functionalized with superhydrophilic coated pDA/TiO2/SiO2 with photoluminescent self-cleaning properties for efficient oil-water separation.

The adhesion of high-viscosity oil contamination poses limitations on three-dimensional (3D) materials' practical use in treating oilfield-produced water (OPW). In this study, we developed a hybrid pDA/TiO2/SiO2 coating (PTS) on the surface of hydrophilic activated carbon (ACF1) through a combination of dopamine (DA) polymerization, ethyl orthosilicate (TEOS) hydrolysis, and the condensation of TiO2 nanoparticles (NPs) with SiO2 NPs. This coating was designed for gravity-based oil-water separation. The inherent porosity and generous pore size of ACF1-PTS conferred it an ultra-high permeation flux (pure water flux of 3.72 × 105 L∙m-2∙h-1), allowing it to effectively separate simulated oil-water mixtures and oil-water emulsions while maintaining exceptional permeation flux and oil rejection efficiency. When compared to cleaning methods involving ethanol aqueous solutions and NaClO, ultraviolet (UV) illumination cleaning proved superior, enabling oil-contaminated ACF1-PTS to exhibit remarkable flux recovery efficiency and oil-removal capabilities during cyclic separation of actual OPW. Furthermore, the ACF1-PTS material demonstrated impressive stability and durability when exposed to acidic environments (acid, alkali, and salt), robust hydraulic washout conditions, and 25-cycle tests. This study offers valuable insights and research avenues for the development of highly efficient and environmentally friendly 3D oil-water separation materials for the actual treatment of OPW.

Efficient degradation of cellulosic ethanol wastewater by perovskite activation of Sr element A-site doped lanthanide copper chalcogenide materials.

The degradation of cellulosic ethanol wastewater by peroxymonosulfate (PMS) is one of the important methods to solve the environmental problems caused by it. In order to improve the degradation efficiency of cellulosic ethanol wastewater, the design of more catalytically active and stable chalcogenide catalysts has become a problem that needs to be solved nowadays. The application of foreign cations to replace the A- or B-site to increase the oxygen vacancy of the chalcocite catalyst to improve the efficiency of chalcocite catalytic degradation of wastewater has received much attention. In this work, the perovskite material LaCuO3 was synthesized using a citric acid-sol-gel method, and the novel material La1-xSrxCuO3 was prepared by doping of Sr element at the A position. In order to prepare catalytic materials with better performance, this study carried out performance-optimized degradation experiments on the prepared materials and determined that the catalytic efficiency of La0.5Sr0.5CuO3 prepared under the conditions of the complexing agent dosage of 1:2, the gel temperature of 80 °C, and the calcination temperature of 700 °C was better than that of the catalytic materials prepared under other conditions. The prepared material has good recycling function; after four times recycling, the removal rate of pollutant COD is still more than 85%. This work provides a new synthesis method of perovskite material with good recycling function and high catalytic efficiency for the degradation technology of cellulosic ethanol wastewater.

A review of the development in shale oil and gas wastewater desalination.

The development of the shale oil and gas extraction industry has heightened concerns about shale oil and gas wastewater (SOGW). This review comprehensively summarizes, analyzes, and evaluates multiple issues in SOGW desalination. The detailed analysis of SOGW water quality and various disposal strategies with different water quality standards reveals the water quality characteristics and disposal status of SOGW, clarifying the necessity of desalination for the rational management of SOGW. Subsequently, potential and implemented technologies for SOGW desalination are reviewed, mainly including membrane-based, thermal-based, and adsorption-based desalination technologies, as well as bioelectrochemical desalination systems, and the research progress of these technologies in desalinating SOGW are highlighted. In addition, various pretreatment methods for SOGW desalination are comprehensively reviewed, and the synergistic effects on SOGW desalination that can be achieved by combining different desalination technologies are summarized. Renewable energy sources and waste heat are also discussed, which can be used to replace traditional fossil energy to drive SOGW desalination and reduce the negative impact of shale oil and gas exploitation on the environment. Moreover, real project cases for SOGW desalination are presented, and the full-scale or pilot-scale on-site treatment devices for SOGW desalination are summarized. In order to compare different desalination processes clearly, operational parameters and performance data of varying desalination processes, including feed salinity, water flux, salt removal rate, water recovery, energy consumption, and cost, are collected and analyzed, and the applicability of different desalination technologies in desalinating SOGW is qualitatively evaluated. Finally, the recovery of valuable inorganic resources in SOGW is discussed, which is a meaningful research direction for SOGW desalination. At present, the development of SOGW desalination has not reached a satisfactory level, and investing enough energy in SOGW desalination in the future is still necessary to achieve the optimal management of SOGW.

Ternary Heterojunction Graphitic Carbon Nitride/Cupric Sulfide/Titanium Dioxide Photoelectrochemical Sensor for Sesamol Quantification and Antioxidant Synergism.

Sesamol (SM) is a potent natural antioxidant that can quench free radicals and modulate the cholinergic system in the brain, thereby ameliorating memory and cognitive impairment in Alzheimer's disease patients. Moreover, the total antioxidant capacity can be amplified by synergistic interactions between different antioxidants. Here, we constructed a ternary heterojunction graphitic carbon nitride/cupric sulfide/titanium dioxide (g-C3N4/CuS/TiO2) photoelectrochemical (PEC) sensor for the quantification of SM and its synergistic interactions with other antioxidants. Crucially, the Schottky barrier in ternary semiconductors considerably enhances electron transfer. The PEC sensor showed a wide linear range for SM detection, ranging from 2 to 1277 µmol L-1, and had a limit of detection of 1.8 µmol L-1. Remarkably, this sensing platform could evaluate the synergism between SM and five typical lipid-soluble antioxidants: tert-butyl hydroquinone, vitamin E, butyl hydroxyanisole, propyl gallate, and butylated hydroxytoluene. Owing to its low redox potential, SM could reduce antioxidant radicals and promote their regeneration, which increased the overall antioxidant performance. The g-C3N4/CuS/TiO2 PEC sensor exhibited high sensitivity, satisfactory selectivity, and stability, and was successfully applied for SM determination in both soybean and peanut oils. The findings of this study provide guidance for the development of nutritional foods, nutrition analysis, and the treatment of diseases caused by free radicals.