Cross-view contrastive representation learning approach to predicting DTIs via integrating multi-source information.

Drug-target interaction (DTI) prediction serves as the foundation of new drug findings and drug repositioning. For drugs/targets, the sequence data contains the biological structural information, while the heterogeneous network contains the biochemical functional information. These two types of information describe different aspects of drugs and targets. Due to the complexity of DTI machinery, it is necessary to learn the representation from multiple perspectives. We hereby try to design a way to leverage information from multi-source data to the maximum extent and find a strategy to fuse them. To address the above challenges, we propose a model, named MOVE (short for integrating multi-source information for predicting DTI via cross-view contrastive learning), for learning comprehensive representations of each drug and target from multi-source data. MOVE extracts information from the sequence view and the network view, then utilizes a fusion module with auxiliary contrastive learning to facilitate the fusion of representations. Experimental results on the benchmark dataset demonstrate that MOVE is effective in DTI prediction.

Graph convolutional network approach to discovering disease-related circRNA-miRNA-mRNA axes.

Non-coding RNAs are gaining prominence in biology and medicine, as they play major roles in cellular homeostasis among which the circRNA-miRNA-mRNA axes are involved in a series of disease-related pathways, such as apoptosis, cell invasion and metastasis. Recently, many computational methods have been developed for the prediction of the relationship between ncRNAs and diseases, which can alleviate the time-consuming and labor-intensive exploration involved with biological experiments. However, these methods handle ncRNAs separately, ignoring the impact of the interactions among ncRNAs on the diseases. In this paper we present a novel approach to discovering disease-related circRNA-miRNA-mRNA axes from the disease-RNA information network. Our method, using graph convolutional network, learns the characteristic representation of each biological entity by propagating and aggregating local neighbor information based on the global structure of the network. The approach is evaluated using the real-world datasets and the results show that it outperforms other state-of-the-art baselines on most of the metrics.

Diagnostic ion filtering targeted screening and isolation of anti-inflammatory iridoid glycosides from Hedyotis diffusa.

Efficient and targeted screening and isolation of bioactive compounds from complex natural products is still a challenging work. Herein, diagnostic ion filtering based high-performance liquid chromatography-quadrupole time-of-flight-tandem mass spectrometry was firstly developed to screen six main iridoid glycosides from Hedyotis diffusa. Then, online extraction-high-speed counter current chromatography was proposed for targeted enrichment and preparative isolation using ethyl acetate/n-butanol/water (4.5:0.5:5, v/v/v) as solvent system. After that, Sephadex LH-20 column chromatography using methanol as solvent system was selected for further purification of six iridoid glycosides with purities over 98%. They were finally identified as monotropein, desacetylasperuloside acid, asperuloside, 6-O-(Z)-p-coumaroyl scandoside methyl ester, 6-O-(Z)-feruloyl scandoside methyl ester, and 6-O-(E)-p-coumaroyl scandoside methyl ester. And their anti-inflammatory activities were evaluated and confirmed by lipopolysaccharide activated RAW 264.7 macrophages. Obviously, the results provide a scientific basis for the potential applications of H. diffusa, and the developed methodology is efficient and reliable for targeted screening and isolation of bioactive compounds from natural products.

Growth and nutrient removal of three macrophytes in response to concentrations and ratios of N and P.

Wastewater from different sources shows great differences in concentrations and ratios of N and P. In order to choose suitable plant species to remove excess N and/or P from polluted waters, it is important to know the performances of these plants under different N and P concentrations. In this study, we investigated the growth and N and P removal rate of three macrophytes, Coix lacryma-jobi, Iris wilsonii, and Arundo donax under six N and P combination treatments. C. lacryma-jobi preferred higher N and P concentrations (16 mg N L-1 and 3.2 mg P L-1), and increasing N supply could increase its P removal rate. I. wilsonii exhibited a growth preference at a combination of moderate N and P concentrations (8 mg N L-1 and 0.8 mg P L-1). A. donax could grow well at all combinations of N and P and had significantly higher relative growth rate and N and P removal rates than the other two species. These results showed A. donax is a promising species to treat various polluted waters and the other two species can be used specifically to treat certain types of wastewater.

Effects of stirring speed ladder on the acid-promoted refolding of rice glutelin.

The effects of stirring speed (0, 250, 500, 750, 1000, 1250, and 1500 rpm) on the rice glutelin hydrocolloids (1 %, w/v) during the acidified process were investigated. As the stirring speed was increased to 750 rpm, the hydration diameter of the rice glutelin was significantly decreased, but higher stirring speeds had no significant effect on size. The highest and lowest solubility were recorded for the samples treated at 750 and 0 rpm stirring speeds, respectively. The surface hydrophobicity and molecular weight increased first and then decreased, both the minimum value was recorded at 750 rpm sample. The principal component analysis (PCA) was employed to detect patterns between changes in various properties (solubility, particle size, ß-sheet content, surface hydrophobicity, and ζ-potential) and stirring treatment. To conclude, the various properties of rice glutelin refold during acidification are drastically affected by employing different stirring speeds. Choosing a suitable stirring speed is important for quality control in protein hydrocolloid production.

Mining Similar Aspects for Gene Similarity Explanation Based on Gene Information Network.

Analysis of gene similarity not only can provide information on the understanding of the biological roles and functions of a gene, but may also reveal the relationships among various genes. In this paper, we introduce a novel idea of mining similar aspects from a gene information network, i.e., for a given gene pair, we want to know in which aspects (meta paths) they are most similar from the perspective of the gene information network. We defined a similarity metric based on the set of meta paths connecting the query genes in the gene information network and used the rank of similarity of a gene pair in a meta path set to measure the similarity significance in that aspect. A minimal set of gene meta paths where the query gene pair ranks the highest is a similar aspect, and the similar aspect of a query gene pair is far from trivial. We proposed a novel method, SCENARIO, to investigate minimal similar aspects. Our empirical study on the gene information network, constructed from six public gene-related databases, verified that our proposed method is effective, efficient, and useful.

Plant-protein-enabled biodegradable triboelectric nanogenerator for sustainable agriculture.

As the use of triboelectric nanogenerators (TENGs) increases, the generation of related electronic waste has been a major challenge. Therefore, the development of environmentally friendly, biodegradable, and low-cost TENGs must be prioritized. Having discovered that plant proteins, by-products of grain processing, possess excellent triboelectric properties, we explore these properties by evaluating the protein structure. The proteins are recycled to fabricate triboelectric layers, and the triboelectric series according to electrical properties is determined for the first time. Using a special structure design, we construct a plant-protein-enabled biodegradable TENG by integrating a polylactic acid film, which is used as a new type of mulch film to construct a growth-promoting system that generates space electric fields for agriculture. Thus, from the plant protein to the crop, a sustainable recycling loop is implemented. Using bean seedlings as a model to confirm the feasibility of the mulch film, we further use it in the cultivation of greenhouse vegetables. Experimental results demonstrate the applicability of the proposed plant-protein-enabled biodegradable TENG in sustainable agriculture.

Effect of microbial transglutaminase on the structural and rheological characteristics and in vitro digestion of rice glutelin-casein blends.

The effect of microbial transglutaminase (MTGase) in cross-linking and modifying of rice glutelin-casein blends was investigated in this work. The maximum MTGase activity on rice glutelin-casein blends were found when its addition was 15 U/g of protein. Compared with the blends without MTGase, the appropriate addition of MTGase significantly affected the microstructure of the cross-linked proteins, resulting in the gradual 'burying' of Trp residue; while the space for hydrogen bonding was more abundant. Secondary structure changes, denoted by the disappearance of the α-helix and the decrement of the ß-sheet structure, was due to the formation of the large loop and random coil structures. The MTGase-catalyzed reaction improves the protease resistance of the blends but not promote the conversion of free sulfhydryl groups (-SH) to disulfide groups (S-S). All the samples evaluated exhibited Bingham flow behavior instead of shear-thinning behavior, and thermally stable fluid properties dominated by elasticity, regardless of MTGase concentration used. Both the storage modulus (G') and loss modulus (G'') gradually decreased with the addition of MTGase. In short, this work demonstrated how the structure, rheology, digestibility of rice glutelin-casein blends are influenced by MTGase concentration.

[Effects of Eucalyptus Branches Biochar Application on Soil Physicochemical Properties of Acidified Soil in a Eucalyptus plantation in Northern Guangxi].

This study aims to explore the effects of different biochar applications on soil physical and chemical properties in a Eucalyptus plantation in Northern Guangxi, find the best biochar application amount, and provide scientific guidance for the efficient utilization of forest residue and soil improvement. The soil of a four-year Eucalyptus plantation at the Huangmian forest farm in Northern Guangxi was selected as the study area, and six treatments including 0 (CK), 0.5% (T1), 1.0% (T2), 2% (T3), 4% (T4), and 6% (T5) were set through a field-positioning experiment to analyze the changes in soil physical and chemical properties under different application rates. Compared with the 0-30 cm soil layer of the control treatment, biochar application decreased the mean soil bulk by 3.82%-33.55%, while it increased the soil natural water content, capillary porosity, and total capillary porosity by 7.67%-31.75%, 8.95%-33.19%, and 9.28%-35.86%, respectively. The contents of exchangeable acid, exchangeable aluminum, exchangeable hydrogen, and exchangeable sodium in the soil decreased by 8.28%-70.03%, 5.55%-70.34%, 5.10%-21.78%, and 12.81%-49.27%. Biochar application increased the cation exchange capacity, electrical conductivity, exchangeable magnesium, and exchangeable calcium by 27.08%-160.39%, 117.00%-546.64%, 17.10%-66.14%, and 17.38%-71.38%, respectively. Soil pH increased by 0.17-1.29 after biochar addition. Similarly, the contents of soil organic carbon, total phosphorus, total potassium, available nitrogen, available phosphorus, and available potassium increased by 10.94%-51.37%, 14.29%-59.45%, 6.48%-59.57%, 6.28%-29.41%, 4.79%-19.81%, and 7.72%-75.87%. There was a positive correlation among the main physical and chemical factors. The physical and chemical properties reached their maximum values in the T4 or T5 treatment (4% or 6%). Biochar application provided considerable relief from soil acidification in the Eucalyptus plantation and had a positive effect on soil physicochemical properties. The addition 4%-6% of ripe Eucalyptus biochar produced the optimum results. The results show that biochar can improve the physical and chemical properties of soil, increase soil fertility, and enhance the soil's ability to retain water and fertilizer after twelve months. The findings of this study can be used as a reference in practical applications for soil improvement and sustainable management of Eucalyptus plantations.

Formation of fibrils derived from whey protein isolate: structural characteristics and protease resistance.

The formation of lactoglobulin (ß-lg) fibrils from its native globular form has been investigated hitherto with pure lactoglobulin conditions. For commercially feasible production of ß-lg fibrils for food and therapeutic applications, the effect of impurities (albeit at very small fractions) found in industrial grade lactoglobulin proteins will need to be considered. In this work, food grade whey protein isolate (WPI), with its associated trace globulin and other impurities, was used to study the ß-lg fibril formation process. SDS-PAGE analysis supported by Thioflavin T measurement showed that the WPI fibril formation accompanied by hydrolysis limited the formation reaction rate; further analysis indicated that main impurities especially for α-lactalbumin may affect the intermolecular contacts among ß-lg. The increase of ß-sheet and α-helix conformation analyzed by circular dichroism revealed that the ß strand axis with an α-helix stabilized the linear structure of fibrils. The WPI fibrils exhibited a significant variation in lengths and differences in morphology when compared to some other protein fibrils reported in the literature. Two-stage pepsin followed by pancreatin digestion analysis revealed that the WPI fibrils produced will have the potential as a medium for active compound delivery to the intestinal environment.

[Research on optimization system on tissue culture and rapid propagation of Pueraria mirifica].

OBJECTIVE: To study the tissue culture and rapid-proliferation techniques of Pueraria mirifica. METHOD: The tender branch were used as explants and cultivated in different media. The optimum media for inducing buds, proliferation and rooting were selected by adjusting the kinds and doses of plant hormones and special compounds. RESULT: The medium of MS + IBA 0.05 mg L(-1) + BA 0.5 mg L(-1) was suitable for buds inducing and could be used in the first generation cultivation; MS + IBA 0. 02 mg L(-1) + BA 0.2 mg L(-1) and MS +BA 0.1 mg L(-1) were employed by turns in subculture, 25 days propagation coefficient was 3.0; and the medium of 1/2MS + IBA 0.1 mg L(-1) + IAA 0.2 mg L(-1) + C (special compound) 10 mg L(-1) was used for roots inducing, the rooting rate was 76.9%. Rooting plantlets were transplanted in spring and summer; the surviving rate was 81.0%. CONCLUSION: This technique system could be employed for rapid propagation of P. mirifica.

Leaf economics of evergreen and deciduous tree species along an elevational gradient in a subtropical mountain.

The ecophysiological mechanisms underlying the pattern of bimodal elevational distribution of evergreen tree species remain incompletely understood. Here we used leaf economics spectrum (LES) theory to explain such patterns. We measured leaf economic traits and constructed an LES for the co-existing 19 evergreen and 15 deciduous species growing in evergreen broad-leaved forest at low elevation, beech-mixed forest at middle elevation and hemlock-mixed forest at high elevation in Mao'er Mountain, Guangxi, Southern China (25°50'N, 110°49'E). Leaf economic traits presented low but significant phylogenetic signal, suggesting trait similarity between closely related species. After considering the effects of phylogenetic history, deciduous species in general showed a more acquisitive leaf strategy with a higher ratio of leaf water to dry mass, higher leaf nitrogen and phosphorous contents, higher photosynthetic and respiratory rates and greater photosynthetic nitrogen-use efficiency. In contrast, evergreen species exhibited a more conservative leaf strategy with higher leaf mass per area, greater construction costs and longer leaf life span. With the elevation-induced decreases of temperature and soil fertility, both evergreen and deciduous species showed greater resource conservation, suggesting the increasing importance of environmental filtering to community assembly with increasing elevation. We found close inter-specific correlations between leaf economic traits, suggesting that there are strong genetic constraints limiting the independent evolution of LES traits. Phylogenetic signal increased with decreasing evolutionary rate across leaf economic traits, suggesting that genetic constraints are important for the process of trait evolution. We found a significantly positive relationship between primary axis species score (PASS) distance and phylogenetic distance across species pairs and an increasing average PASS distance between evergreen and deciduous species with increasing elevation, implying that the frequency of distantly related evergreen and deciduous pairs with wide spreading of leaf economic values increases with increasing elevation. Our findings thus suggest that elevation acts as an environmental filter to both select the locally adapted evergreen and deciduous species with sufficient phylogenetic variation and regulate their distribution along the elevational gradient based on their coordinated spreading of phylogenetic divergence and leaf economic variation.

[Seasonal variation of Cyclobalanopsis glauca whole-tree transpiration in karst region].

By using Granier's sap-flow method, the variations of sap flux density and whole-tree transpiration of Cyclobalanopsis glauca (syn. Quercus glauca) on a hilly slope in the karst region of South China were studied, with their driving factors analyzed. The sap flux density (Js) of C. glauca varied randomly with the diameter of breast height of individual trees, and its maximum occurred at 13:30-14:30. In a seasonal course, the daily Js was the maximum (56.00 g H2O x m(-2) x s(-1)) in summer, and the minimum (35.86 g H2O x m(-2) x s(-1)) in spring. The daily whole-tree transpiration had a greater change with weather condition, representing a power functional relationship with vapor pressure deficit (VPD) and photosynthesically active radiation (PAR) (R = 0.97, P < 0.01). The average daily whole-tree transpiration tended to be high in summer and low in winter and spring, and decreased with the decrease of soil moisture content in autumn (drought season). However, comparing with that of the tree species in other regions, the daily whole-tree transpiration amount of C. glauca in study region was still higher, even though the weather was dry and the soil was thin. It was presumed that in the dry season in karst region, the water supply for C. glauca could be mainly depended on the water-rich epikarst.

[Effect of ecological organic fertilizer on tomato bacterial wilt and soil microbial diversities].

The effects of ecological organic fertilizer (EOF) on tomato bacterial wilt and soil microbial community were studied through field trial and fatty acid methyl esters (FAMEs) analysis. The results showed that the incidence rate of tomato bacterial wilt was 100% in continuous cropped soil, and significantly reduced to 39% and 50% when applying EOF at 1.0 kg.m-2 and 0.5 kg.m-2, respectively. There was no significant difference between two fertilization treatments. The fatty acid fingerprints of soil microbial community were greatly changed, and the relative contents of cyc17:0 cited as biomarker for GN bacteria, c18:2 w6 as biomarker for fungi and c16:1 11c as biomarker for arbuscular mycorrhizal (AM) fungi all increased when applying EOF. The minimum distance of cluster analysis was 1.08 between control and treatments of applying ecological organic fertilizer, and 0.70 between different fertilization treatments. Applying EOF could adjust soil microbial community structure, benefit for soil beneficial microbes, and develop stability and disease suppression of soil ecological system, and hence, improve soil quality.

[Utilization of sugar cane bagasse hydrolysates for xylitol production by yeast].

The effects of the concentration of sulfuric acid and the ratio of liquid to solid on xylose yield from sugar cane bagasse in its hemicellulose hydrolysis process were studied with the Quadratic Rotary Combination Design. Regression analysis showed that there was a marked regression relationship between the two factors and xylose yield. As the result of optimizing the hydrolysis conditions by regression equation, xylose yield of 24 g/100 g sugar cane bagasse was obtained when sulfuric acid concentration was 2.4 g/L and liquid to solid ratio was 6.2 under the conditions of stream pressure of 2.5 x 10(4) Pa and hydrolysis time of 2.5 h. The macroporous resin adsorption was proved to be a good method to reduce the concentration of yeast cell growth inhibitor in sugar cane bagasse hemicellulose hydrolysate and to enhance the hydrolysate fermentability. The hydrolysate treated with macroporous resin adsorption under pH2 was used as the substrate for xylitol production by a xylitol-producting yeast, Candida tropicalis AS2.1776. At an initial xylose concentration of 200 g/L, all xylose was consumed within 110 h with a xylitol production rate of 1.15 g/L.h, and a xylitol yield of 0.64 g/g xylose.