Determination of the direct and indirect effects of bend on the urban river ecological heterogeneity.

The ecological heterogeneity created by river bends benefits the diversity of microorganisms, which is vital for the pollutant degradation and overall river health. However, quantitative tools capable of determining the interactions among different trophic levels and species are lacking, and research regarding ecological heterogeneity has been limited to a few species. By integrating the multi-species-based index of biotic integrity (Mt-IBI) and the structure equation model (SEM), an interactions-based prediction modeling framework was established. Based on DNA metabarcoding, a multi-species (i.e., bacteria, protozoans, and metazoans) based index of biotic integrity including 309 candidate metrics was developed. After a three-step screening process, eight core metrics were obtained to assess the ecological heterogeneity, quantitatively. The Mt-IBI value, which ranged from 2.08 to 7.17, was calculated as the sum of each single core metric value. The Mt-IBI revealed that the ecological heterogeneity of concave banks was higher than other sites. According to the result of the SEM, D90 was the controlling factor (r = -0.779) of the ecological heterogeneity under the influence of the river bends. The bend-induced redistribution of sediment particle further influenced the concentrations of carbon, nitrogen, and sulphur. The nitrogen group (r = 0.668) also played an essential role in determining the ecological heterogeneity, follow by carbon group (r = 0.455). Furthermore, the alteration of niches would make a difference on the ecological heterogeneity. This multi-species interactions-based prediction modeling framework proposed a novel method to quantify ecological heterogeneity and provided insight into the enhancement of ecological heterogeneity in river bends.

Cov_FB3D: A De Novo Covalent Drug Design Protocol Integrating the BA-SAMP Strategy and Machine-Learning-Based Synthetic Tractability Evaluation.

De novo drug design actively seeks to use sets of chemical rules for the fast and efficient identification of structurally new chemotypes with the desired set of biological properties. Fragment-based de novo design tools have been successfully applied in the discovery of noncovalent inhibitors. Nevertheless, these tools are rarely applied in the field of covalent inhibitor design. Herein, we present a new protocol, called Cov_FB3D, which involves the in silico assembly of potential novel covalent inhibitors by identifying the active fragments in the covalently binding site of the target protein. In this protocol, we propose a BA-SAMP strategy, which combines the noncovalent moiety score with the X-Score as the molecular mechanism (MM) level, and the covalent candidate score with the PM7 as the QM level. The synthetic accessibility of each suggested compound could be further evaluated with machine-learning-based synthetic complexity evaluation (SCScore). An in-depth test of this protocol against the crystal structures of 15 covalent complexes consisting of BTK inhibitors, KRAS inhibitors, EGFR inhibitors, EphB1 inhibitors, MAGL inhibitors, and MAPK inhibitors revealed that most of these inhibitors could be de novo reproduced from the fragments by Cov_FB3D. The binding modes of most generated reference poses could accurately reproduce the known binding mode of most of the reference covalent adduct in the binding site (RMSD ≤ 2 Å). In particular, most of these inhibitors were ranked in the top 2%, using the BA-SAMP strategy. Notably, the novel human ALDOA inhibitor (T1) with potent inhibitory activity (0.34 ± 0.03 µM) and greater synthetic accessibility was successfully de novo designed by this protocol. The positive results confirm the abilities of Cov_FB3D protocol.

Fabrication and characterization of stable oleofoam based on medium-long chain diacylglycerol and ß-sitosterol.

Oleofoams have emerged as attractive low-calorie aeration systems, but saturated lipids or large amount of surfactants are commonly required. Herein, an innovative strategy was proposed to create oleofoams using medium-long chain diacylglycerol (MLCD) and ß-sitosterol (St). The oleofoams prepared using MLCD and St in ratios of 15:5 and 12:8 exhibited smaller bubble size and much higher stability. MLCD crystals formed rigid Pickering shell, whereby air bubbles acted as "active fillers" leading to enhanced rigidity. Both Pickering and network stabilization for the MLCD-St oleofoam provided a steric hindrance against coalescence. The gelators interacted via hydrogen bonding, causing a condensing effect in improving the gel elasticity. The oleofoams and foam-based emulsions exhibited a favorable capacity in controlling volatile release where the maximum headspace concentrations and partition coefficients showed a significantly decrease. Overall, the oleofoams have shown great potential for development of low-calorie foods and delivery systems with enhanced textural and nutritional features.

How did the bacterial community respond to the level of urbanization along the Yangtze River?

Bacterial communities in the sediment of the Yangtze River influenced by rapid urbanization have thus far been under-investigated despite the importance of microorganisms as mass transporters. Here, the response patterns of the bacterial community along the Yangtze River to different levels of urbanization were generated using 16S rRNA Miseq sequencing. The results reveal that economic aspects have made the largest contribution (41.8%) to the urbanization along the Yangtze River. A clear declining tendency in the abundance of Chloroflexi and Acidobacteria and a significant increase in the abundance of Bacteroidetes were observed with an elevated urbanization level gradient. Bacterial diversity showed a negative relevance (P < 0.01) to the demographic, economic and social urbanization index. Per capita gross domestic product (GDP) (PCGDP) and the GDP of tertiary industry (GDP3) exhibited significantly (P < 0.05) negative correlations with the bacterial diversity, while a positive relationship between the pH and α-diversity (P < 0.05) was observed. Redundancy analysis revealed that PCGDP was significantly correlated (13.9%, P < 0.01) with the overall bacterial compositions, followed by temperature (10.8%, P < 0.01) and GDP3 (8.4%, P < 0.05). Meanwhile, the GDP3 (35.9%), the ratio of total nitrogen and total phosphorus (N/P) (12.9%) and the PCGDP (8.8%) were revealed to be most significantly related to the metabolic bacteria (P < 0.05). The metabolic functions of the bacteria related to the N-cycle and S-cycle were significant in the sediment of the Yangtze River. The variations of the bacterial community and metabolic function responding to the rapid urbanization were related to the economic development via the influence of the 'mass effect'. In brief, the tertiary industry was significantly correlated with the variations in the composition of the metabolic community and the variations in the overall bacteria were both related to the tertiary and secondary industry.

Identifying ecological processes driving vertical and horizontal archaeal community assemblages in a contaminated urban river.

Understanding environmental factors driving ecological processes of archaeal communities in heavily contaminated rivers is crucial for improvements in river ecological monitoring and indication. However, succession mechanisms underlying vertical and horizontal archaeal community assemblages in contaminated rivers remains largely unstudied. Here, to investigate ecological processes controlling archaeal community succession in a contaminated urban river, multivariate statistics approaches were applied to fields samples collected from locations representing vertical and horizontal assemblages of archaeal community. Our results revealed that archaeal community in the river showed distinct vertical and horizontal distribution patterns and the differences between water and sediment samples were most significant. Beta-diversity patterns in the vertical and horizontal assemblages are both almost completely caused by species replacement between sampling points (horizontal ßSIM = 0.60 ± 0.09, ßNES = 0.09 ± 0.05; vertical ßSIM = 0.40 ± 0.07, ßNES = 0.10 ± 0.06). Considering phylogenetic turnover deviation, homogenizing dispersal was the most crucial process dominating archaeal community assemblages in water samples while main ecological process in sediment samples was variable selection. Euryarchaeota and Thaumarchaeota were found to prefer high-nutrients and low-nutrients environments, respectively. Analysis of environmental drivers of archaeal phyla distribution and community assemblages indicated that nutrients played a decisive role in driving the sediment archaeal community. Dissolved oxygen (DO) explained the most variation in phylogenetic turnover deviation within all water archaeal community while oxidation reduction potential (ORP) contributed most for horizontal sediment archaeal community assemblages. These findings help to indicate the pollution situation of the river and provide information to predict how archaeal communities would respond to different environmental variations.

Non-aqueous foams formed by whipping diacylglycerol stabilized oleogel.

Formation of foams is critical for tailoring the texture and mouthfeel of fat-based products. Diacylglycerol (DAG) is regarded as a preferable alternative structurant to hydrogenated lipid. Effect of DAG concentration (2-10 wt%) on the characteristics of oleogels and foams including crystal polymorphisms, size and distribution, rheological and thermodynamic properties was investigated. Oleogel prepared with 10 wt% DAG had comparable whipping and foaming stability to that of 6 wt% fully hydrogenated palm oil (FHPO). DAG formed small plate-crystals which tend to occur at the bubble surface, whereas FHPO showed needle-like crystals that were formed mainly in the continuous phase. For the 2 wt% FHPO-8 wt% DAG-based oil foams, interfacial templating crystallization effect contributed to the smaller bubble size and improved rheological properties whereby less oil drainage and foam breakdown occurred. Hence, the non-aqueous foam formed by DAG has broad application prospect because of the thermoresponsive properties and the desirable health benefits.

Determination of vertical and horizontal assemblage drivers of bacterial community in a heavily polluted urban river.

Identifying vertical and horizontal assemblage drivers of bacterial community is important for improving the efficacies of ecological evaluation and remediation for a huge contaminated river (e.g. black-odor urban river). However, little is known about the effect of stochastic vs. deterministic processes on the reliability of the identification processes. Here, a comprehensive analysis was performed to reveal vertical and horizontal assemblage drivers of bacterial community in a heavily polluted urban river (total area of 4.23 km2 and total length of 9.3 km), considering the relative importance of stochastic and deterministic processes. Heterogeneous bacterial community assemblages were observed in both vertical and horizontal profiles and the differences in the bacterial community between depths were relatively significant at genus level. The higher values for the Simpson dissimilarity index (horizontal ßSIM = 0.59 ±â€¯0.02; vertical ßSIM = 0.48 ±â€¯0.03) compared to the nestedness-resultant dissimilarity index (horizontal ßNES = 0.05 ±â€¯0.02; vertical ßNES = 0.05 ±â€¯0.05) showed that species replacement explained both the vertical and horizontal beta-diversity patterns. Comparison of horizontal and vertical Sørensen dissimilarity indices further indicated that the biodiversity of vertical community deserved more attention due to the shorter geographical distance with similar beta-diversity patterns compared to horizontal assemblages. Various traditional analysis without consideration for phylogenetic turnover revealed that TN, TP, NH4+-N, DO, ORP, Conductivity and CODMn were all the related environmental factors that influenced bacterial community. However, after taking stochastic vs. deterministic processes into account, only NH4+-N and ORP were identified as the main driving forces of trends in the vertical and in the horizontal assembly of bacterial community in the polluted urban river, respectively. This study is helpful for improving ecological assessment methodology and remediation strategy for contaminated urban rivers.