Improving key gene expression and di-n-butyl phthalate (DBP) degrading ability in a novel Pseudochrobactrum sp. XF203 by ribosome engineering.

Di-n-butyl phthalate (DBP) is one of the important phthalates detected commonly in soils and crops, posing serious threat to human health. Pseudochrobactrum sp. XF203 (XF203), a new strain related with DBP biodegradation, was first identified from a natural habitat lacking human disturbance. Genomic analysis coupled with gene expression comparison assay revealed this strain harbors the key aromatic ring-cleaving gene catE203 (encoding catechol 2,3-dioxygenase/C23O) involved DBP biodegradation. Following intermediates identification and enzymatic analysis also indicated a C23O dependent DBP lysis pathway in XF203. The gene directed ribosome engineering was operated and to generate a desirable mutant strain XF203R with highest catE203 gene expression level and strong DBP degrading ability. The X203R removed DBP in soil jointly by reassembling bacterial community. These results demonstrate a great value of XF203R for the practical DBP bioremediation application, highlighting the important role of the key gene-directed ribosome engineering in mining multi-pollutants degrading bacteria from natural habitats where various functional genes are well conserved.

Deciphering the Cofilin Oligomers via Intermolecular Disulfide Bond Formation: A Coarse-Grained Molecular Dynamics Approach to Understanding Cofilin's Regulation on Actin Filaments.

Cofilin, a key actin-binding protein, orchestrates the dynamics of the actomyosin network through its actin-severing activity and by promoting the recycling of actin monomers. Recent experiments suggest that cofilin forms functionally distinct oligomers via thiol post-translational modifications (PTMs) that promote actin nucleation and assembly. Despite these advances, the structural conformations of cofilin oligomers that modulate actin activity remain elusive because there are combinatorial ways to oxidize thiols in cysteines to form disulfide bonds rapidly. This study employs molecular dynamics simulations to investigate human cofilin 1 as a case study for exploring cofilin dimers via disulfide bond formation. Utilizing a biasing scheme in simulations, we focus on analyzing dimer conformations conducive to disulfide bond formation. Additionally, we explore potential PTMs arising from the examined conformational ensemble. Using the free energy profiling, our simulations unveil a range of probable cofilin dimer structures not represented in current Protein Data Bank entries. These candidate dimers are characterized by their distinct population distributions and relative free energies. Of particular note is a dimer featuring an interface between cysteines 139 and 147 residues, which demonstrates stable free energy characteristics and intriguingly symmetrical geometry. In contrast, the experimentally proposed dimer structure exhibits a less stable free energy profile. We also evaluate frustration quantification based on the energy landscape theory in the protein-protein interactions at the dimer interfaces. Notably, the 39-39 dimer configuration emerges as a promising candidate for forming cofilin tetramers, as substantiated by frustration analysis. Additionally, docking simulations with actin filaments further evaluate the stability of these cofilin dimer-actin complexes. Our findings thus offer a computational framework for understanding the role of thiol PTM of cofilin proteins in regulating oligomerization, and the subsequent cofilin-mediated actin dynamics in the actomyosin network.

Spatial distributions and environmentally-mediated factors of dimethylsulfoxide off the northern Antarctic Peninsula in summer.

Spatial distributions of dissolved and particulate dimethylsulfoxide (DMSOd and DMSOp) were investigated off the northern Antarctic Peninsula during the austral summer of 2018, an ecologically and climatically important region of the world. In the upper waters, DMSOd was concentrated in the ice-melt zone because DMSO functions physiologically as an intracellular osmolyte and cryoprotectant. DMSOd concentrations had a weak positive correlation with temperature but a negative correlation with nutrients. This highlighted the importance of temperature-dependent biological activities and photolysis in DMSOd production and the important role of the intracellular antioxidation system in phytoplankton cells. The decrease of average DMSOp:Chl-a ratios in upper waters from west to east, along with decreasing temperatures and increasing diatoms proportions in the phytoplankton, illustrates how seawater DMSO production capacities depend on ambient temperatures and the composition of phytoplankton assemblages. DMSOp were accumulated in deep waters through bio-debris accumulation and microbial activity.

Quorum sensing bacteria in microplastics epiphytic biofilms and their biological characteristics which potentially impact marine ecosystem.

Microplastics (MPs) have been shown to be a new type of pollutant in the oceans, with complex biofilms attached to their surfaces. Bacteria with quorum sensing (QS) systems are important participants in biofilms. Such bacteria can secrete and detect signal molecules. When a signal molecule reaches its threshold level, bacteria with QS systems can perform several biological functions, such as biofilm formation and antibiotic metabolite production. However, the ecological effects of QS bacteria in biofilm as MPs distribute globally with ocean currents are not to be elucidate yet. In this study, polypropylene and polyvinyl chloride were selected for on-site enrichment to acquire microplastics with biofilms. Eight culturable QS bacteria in the resulting biofilm were isolated by using biosensor assays, and their biodiversity was analyzed. The profiles of the N-acyl-homoserine lactones (AHLs) produced by these bacteria were analyzed by using thin-layer chromatography (TLC)-bioautography and gas chromatography and mass spectrometry (GC-MS). Biofilm-forming properties and several biological characteristics, such as bacteriostasis, algal inhibition, and dimethylsulfoniopropionate (DMSP) degradation, were explored along with QS quenching. Results showed that QS bacteria were mainly affiliated with class Alphaproteobacteria, particularly Rhodobacteraceae, followed by class Gammaproteobacteria. TLC-bioautography and GC-MS analyses revealed that seven AHLs, namely, C6-HSL, C8-HSL, 3-oxo-C6-HSL, 3-oxo-C8-HSL, 3-oxo-C10-HSL, and two unidentified AHLs were produced. The QS system equipped bacteria with strong biofilm-forming capacity and may contribute to the keystone roles of Rhodobacteraceae. In addition, QS bacteria may exacerbate the adverse environmental effects of MPs, such as inducing the misfeeding of planktons on MPs. This study elucidated the diversity of QS bacteria in MP-associated biofilms and provided a new perspective of the effect of key membrane-forming bacteria on the marine ecological environment.

Effects of cactus Opuntia dillenii polysaccharide-based coatings loaded with glutathione on the preservation of freshly cut Chinese water chestnut.

This study explored the effects of coatings based on glutathione-loaded cactus Opuntia dillenii polysaccharide (ODP) on the preservation of freshly cut Chinese water chestnut. Freshly cut Chinese water chestnut samples were treated with one of the three dipping solutions, namely, distilled water (control), 0.4 % glutathione (treatment-1) or 1 % ODP + 0.4 % glutathione (treatment-2) and stored at 3 °C for 10 days. All treatments suppressed respiration rate, weight loss and decreases in firmness and browning and increased soluble solid content and likeness score compared with the control (P < 0.05). In terms of sensory quality, treatment-2 extended the shelf life of the freshly cut Chinese water chestnut at least by 6 days compared with the control group. Results verified that treatment with ODP-based coatings incorporated with glutathione may be a promising method for preserving freshly cut Chinese water chestnut.

Dietary chitosan modulates the growth performance, body composition and nonspecific immunity of juvenile yellow catfish (Pelteobagrus fulvidraco).

This study investigated the effects of feeding different concentrations of chitosan on the growth performance, body composition and non-specific immune function of juvenile yellow catfish (Pelteobagrus fulvidraco). Four kinds of experimental diets were respectively prepared by adding 0 (control group), 5, 10 and 15 g/kg of chitosan to the basal feed and fed to juvenile yellow catfish for 8 weeks. Results show that the body weight gain rate, specific growth rate, survival rate, body protein content, serum superoxide dismutase activity, catalase activity, glutathione peroxidise activity, lysozyme activity and disease resistance ability against Aeromonas hydrophila of the experimental group with chitosan added to its diet were significantly higher than those of the control group optimally by 36.22 %, 14.37 %, 9.46 %, 8.97 %, 50.89 %, 33.15 %, 21.52 %, 40.80 %, 41.09 %, and 79.71 %, respectively (P < 0.05). No significant differences in feed efficiency among all groups (P > 0.05) were observed. The optimum dose of dietary chitosan required for the maximum growth of juvenile yellow catfish was 8.95 g/kg. Therefore, adding an appropriate amount of chitosan (8.95 g/kg) to the feed of yellow catfish can significantly improve its growth performance, ameliorate body composition and enhance its non-specific immunity.

Diversity and functions of quorum sensing bacteria in the root environment of the Suaeda glauca and Phragmites australis coastal wetlands.

The quorum sensing (QS) system plays a significant role in the bacteria-bacteria or plant-bacteria relationships through signal molecules. However, little is known about the distribution and functional diversity of QS bacteria in the root environment of Suaeda glauca and Phragmites australis in coastal wetlands. We explored the bacterial community by amplicon sequencing and isolated 1050 strains from the rhizosphere soil and root tissues of S. glauca and P. australis in northern China to investigate the bacterial community and AHL producers. AHL activity was found in 76 isolates, and 22 distinct strains were confirmed by 16S rRNA gene sequencing. A substantial number of AHL producers clustered in rhizobiales and sphingomonadale, which derived from the root tissues. AHL producers in the rhizosphere soil mostly belonged to rhodobacterales. The different taxa of AHL producers in the rhizosphere soil and root tissues resulted in a variation of AHL profiles that C6-HSL dominated the AHL profiles in root bacteria compared to the C8-HSL in rhizobacteria, implying different ecological roles for AHL producers in the rhizosphere soil and root tissues. Many AHL producers may form biofilms, and some can degrade DMSP and oil, demonstrating that QS bacteria in the root environment have a wide ecological roles. In our study, for one of the first times here, we explore the distribution and functional variety of AHL producers in the root environment of S. glauca-P. australis. This study expands current knowledge of the relationship between QS bacteria and coastal plants (S. glauca and P. australis), and vital roles of QS bacterial in maintaining the health of coastal wetlands.

Comprehensive Evaluation of 17 Qualities of 84 Types of Rice Based on Principal Component Analysis.

Rice quality is a complex indicator, and people are paying more and more attention to the quality of rice. Therefore, we used seven rice varieties for twelve nitrogen fertilizer treatments and obtained eighty-four rice types with seventeen qualities. It was found that 17 quality traits had different coefficients of variation. Among them, the coefficient of variation of chalkiness and protein content was the largest, 44.60% and 17.89% respectively. The cluster analysis method was used to define four categories of different rice qualities. The principal component analysis method was used to comprehensively evaluate 17 qualities of 84 rice. It was found that rice quality was better under low nitrogen conditions, Huanghuazhan and Lvyinzhan were easier to obtain better comprehensive rice quality during cultivation. Future rice research should focus on reducing protein content and increasing peak viscosity.

Forecasting Avalanches in Branched Actomyosin Networks with Network Science and Machine Learning.

We explored the dynamic and structural effects of actin-related proteins 2/3 (Arp2/3) on actomyosin networks using mechanochemical simulations of active matter networks. On the nanoscale, the Arp2/3 complex alters the topology of actomyosin by nucleating a daughter filament at an angle with respect to a mother filament. At a subcellular scale, they orchestrate the formation of a branched actomyosin network. Using a coarse-grained approach, we sought to understand how an actomyosin network temporally and spatially reorganizes itself by varying the concentration of the Arp2/3 complexes. Driven by motor dynamics, the network stalls at a high concentration of Arp2/3 and contracts at a low Arp2/3 concentration. At an intermediate Arp2/3 concentration, however, the actomyosin network is formed by loosely connected clusters that may collapse suddenly when driven by motors. This physical phenomenon is called an "avalanche" largely due to the marginal instability inherent to the morphology of a branched actomyosin network when the Arp2/3 complex is present. While embracing the data science approaches, we unveiled the higher-order patterns in the branched actomyosin networks and discovered a sudden change in the "social" network topology of actomyosin, which is a new type of avalanche in addition to the two types of avalanches associated with a sudden change in the size or shape of the whole actomyosin network, as shown in a previous investigation. Our new finding promotes the importance of using network theory and machine learning models to forecast avalanches in actomyosin networks. The mechanisms of the Arp2/3 complexes in shaping the architecture of branched actomyosin networks obtained in this paper will help us better understand the emergent reorganization of the topology in dense actomyosin networks that are difficult to detect in experiments.

Occurrence, distribution, and sea-air fluxes of volatile halocarbons in the upper ocean off the northern Antarctic Peninsula in summer.

We studied the spatial variations of six volatile halocarbons (VHCs), namely, iodomethane (CH3I), chloroform (CHCl3), tetrachloroethylene (C2Cl4), bromodichloromethane (CHBrCl2), dibromomethane (CH2Br2), and carbon tetrachloride (CCl4), and the environmental influencing factors involved in the cycling of VHCs in the upper ocean (0-500 m) off the Northern Antarctic Peninsula (NAP) during the summer of 2018. About 5%-10% of the total biogenic VHCs in the upper ocean were accumulated in the assemblage layer (AL) with high chlorophyll a. However, higher VHCs levels were observed in the dicothermal layer (DL) compared with the AL because of the preservation from winter and production from dinoflagellates and chlorophytes. Owing to the co-existence occurrence of sharp seasonal pycnocline and thick permanent pycnocline, DL could be an important VHCs reservoir in the upper water column during summer. In response to melting of sea ice and glacier, decreased salinity was responsible for ca. 50% of the variation in the CH2Br2 and CCl4 concentrations, which corresponded with increased CH2Br2 and CCl4 concentrations in the less saline water mass. Anthropogenic CCl4 was found with an average concentration of 44.9 pmol/L, and there was a strong positive relationship between CCl4 and CHCl3 in the upper water, indicating their similar source of pollutant transport caused by anthropogenic activities. Calculated sea-to-air fluxes of CCl4, C2Cl4, CHBrCl2, and CH2Br2 averaged 478.7, 93.7, 33.7, and 61.8 nmol/(m2·d) in summer, respectively, indicating that the waters off the NAP are important sources of VHCs for the atmosphere and exert potentially adverse impacts on the Antarctica ozone depletion.

Use of Protein Content, Amylose Content, and RVA Parameters to Evaluate the Taste Quality of Rice.

Taste quality of rice is the key to its value. However, it is greatly affected by rice types and the environment. It is a complex but necessary factor to accurately evaluate the taste quality of various types of rice in different environments. In this study, 7 different types of rice with different taste values were used as materials, and 12 nitrogen fertilizer treatments were applied to obtain 84 different rice taste values. We used protein content, amylose content, and RVA to evaluate changes in the taste value of rice. Rice with high taste value tended to have higher amylose content, peak viscosity, hold viscosity, final viscosity, and breakdown, as well as lower protein content, pasting temperature, and peak time. Protein and amylose contents affected the taste value of rice by affecting the RVA profiles except for setback. For high and low taste-value rice types, protein content could explain 66.8 and 42.9% of the variation in taste value, respectively. In the case of medium taste-value type, protein content was not enough to evaluate the taste quality of rice. Stickiness could explain 59.6% of the variation in taste value. When the protein content of rice was less than 6.61% or greater than 9.34%, it could be used to reflect the taste quality of rice. When the protein content was in between the two, protein content was not enough to reflect the taste quality of rice. Our results suggested that protein content could better reflect the taste quality change for rice, which provided a theoretical and technical basis for the accurate evaluation of the taste value of various types of rice.

An Estimation Approach for the Effective Elastic Modulus of Lightweight Bulk Filling Material with Compressible Inclusions and Imperfect Interfaces.

In this study, an approach is developed to estimate the density and effective elastic modulus of a lightweight bulk filling material made up of expanded polystyrene (EPS) and cement-reinforced clay (matrix). First, a representative volume element (RVE) is composed of cell A (an EPS and matrix) and cell B (matrix only). Then, an elastic interface is introduced to describe the discontinuity of displacement at the interface between EPS beads and matrix. Third, an Eshelby compliance tensor is modified in cell A to include the effects of imperfect interface and the compressibility of EPS beads. Finally, the approach for the density and effective elastic modulus of the EPS beads mixed cement-reinforced clay is verified with experimental data. The compressibility ratio of lightweight clay is compared under different confining pressures and curing times. It is found that the imperfect interface has salient impacts on the effective elastic modulus with the increase of volume fraction of inclusions. The interface parameters (α and ß) vary with curing time and confining pressure. At the same curing time, the parameter α is almost constant regardless of confining pressure but the parameter ß changes with confining pressure. The compressibility ratio is smaller for longer curing time if the confining pressure is constant.

Imaging with intracardiac echocardiography compared to transesophageal echocardiography during left atrial appendage occlusion.

We performed a meta-analysis comparing the procedural and outcomes data and related to left atrial appendage occlusion guided by intracardiac echocardiography (ICE) and transesophageal echocardiography (TEE) in nonvalvular atrial fibrillation patients. Technical success with ICE was significantly similar to that of TEE (odds ratio [OR] 1.38, 95% CI [0.62, 3.09], I2 = 0%, P = 0.43). The peri-procedural complications showed no significant difference between the two groups (OR 0.84, 95% CI [0.57, 1.23], I2 = 0%, P = 0.37). Mortality was similar in procedures using ICE vs TEE (OR 0.89, 95% CI [0.51, 1.57], I2 = 0%, P = 0.69). Landing zones, procedural time and fluoroscopic times between ICE and TEE showed no significant differences (MD 1.96, 95% CI [-0.01, 3.94], I2 = 90%, P = 0.05; MD -1.64, 95% CI [-13.45, 10.17], I2 =95%, P =0.79; and MD 0.49, 95% CI [-2.18, 3.16], I2 = 87%, P = 0.72, respectively). Imaging with ICE or TEE is associated with similar outcomes in left atrial appendage occlusion procedures.

Overexpression of miR-27b-3p Targeting Wnt3a Regulates the Signaling Pathway of Wnt/ß-Catenin and Attenuates Atrial Fibrosis in Rats with Atrial Fibrillation.

MicroRNAs (miRNAs) are regarded as a potential method for the treatment of atrial fibrillation (AF) although its molecular mechanism remains unknown. We found in our previous study that the level of peripheral blood miR-27b-3p and the expression of atrial tissue CX43 were both significantly downregulated in AF patients. In the present study, we propose and test this hypothesis that overexpression of miR-27b-3p attenuates atrial fibrosis, increases CX43 expression, and regulates the signaling pathway of Wnt/ß-Catenin by targeting Wnt3a. miR-27b-3p overexpression was induced by rat tail vein injection of adeno-associated virus. Two weeks after transfection of adeno-associated virus, the rat AF model was established by tail vein injection of acetylcholine- (ACh-) CaCl2 for 7 days, and 1 ml/kg was injected daily. The incidence and duration of AF were recorded with an electrocardiogram. Cardiac function was monitored by cardiac ultrasound. Serum cardiac enzyme was detected by ELISA. The expression of atrial miR-27b-3 and Wnt3a was assayed by quantitative RT-PCR. Atrial fibrosis was determined by Masson's trichrome staining. Expression of atrial Collagen-I and Collagen-III was tested by the immunohistochemical method. Expression of CX43 was measured by immunofluorescence. The expression of Collagen-I, a-SMA, Collagen-III, TGF-ß1, CX43, Wnt3a, ß-Catenin, and p-ß-Catenin was assayed by western blot. Our results showed that miR-27b-3p overexpression could reduce the incidence and duration of AF, alleviate atrial fibrosis, increase atrial CX43 expression, and decrease the expression of Collagen-I, a-SMA, Collagen-III, TGF-ß1, Wnt3a, and p-ß-Catenin. In addition, the results of luciferase activity assay showed that Wnt3a is a validated miR-27b-3p target in HEK 293T cells. Our results provide a new evidence that miR-27b-3p regulates the signaling pathway of Wnt/ß-Catenin by targeting Wnt3a, which may play an important role in the development of atrial fibrosis and AF.

Hydrochemical properties and chemocline of the Sansha Yongle Blue Hole in the South China Sea.

Blue holes can provide valuable information regarding paleoclimate, climate change, karst processes, marine ecology, and carbonate geochemistry. The Sansha Yongle Blue Hole, located on Yongle Atoll in the Paracel Islands in the South China Sea, is the deepest blue hole in the world. A comprehensive investigation of the blue hole was conducted to determine the hydrochemical properties and associated redox processes active in the water column. Results indicate the presence of two thermoclines, one at 13-20 m and a second at 70-150 m, dividing the water column into five stratified water layers. Based on redox state, the water column can be divided into three layers: an oxic layer in the top 70 m, a chemocline at 70-100 m, which acts as a redox boundary, and an anoxic deep layer. In the oxic layer, photosynthesis in the oxic layer above the seasonal thermocline, results in nutrient uptake, transformation of inorganic carbon to organic carbon in the top mixed layer above the seasonal thermocline; Below the seasonal thermocline, organic matter degradation and nitrification, which are the main biological process at depths around 30 m and 50-70 m, lead to the accumulation of nitrate and a decrease in dissolved oxygen and pH; whereas photosynthesis is dominant at depths of 30-50 m, leading to increase in dissolved oxygen and pH. Within the chemocline, organic matter decays via a variety of reactions (e.g. aerobic mineralization, denitrification and anammox), leading to sharp decreases in the oxidizing chemical species (e.g., dissolved oxygen and nitrate) and corresponding increases in the reduced species (e.g., ammonium and sulfide). Within this layer, about 60% of the nitrogen is lost and chemoautotrophic/photoautotrophic production may contribute significantly to particulate organic carbon. Within the deep anoxic layer, sulfate reduction and degradation of organic matter result in accumulations of sulfide, dissolved inorganic carbon, and nutrients.