Comparative Study on Biological Activities and Chemical Profiling of Mushroom (Pleurotus pulmonarius (Fr.) Quel.) Cultured on Lignocellulosic Agro Wastes

The relevance of the lignocellulosic substrate in the cultivation of mushrooms has lent support to the exploration of several lignocellulosic agro wastes. This study was, thus, aimed at the evaluation of durian peel as an alternative substrate for more sustainable mushroom cultivation and climate change mitigation. The secondary metabolites and biological activities of both aqueous and organic mushroom (Pleurotus pulmonarius (Fr.) Quel.) extract cultured on durian peel and rubberwood sawdust substrate were compared using GCMS, LCMS as well as various biological assays (cytotoxicity, antimicrobial and antioxidant activities). Mushroom extracts from durian peel substrates possess remarkable biological activities. The results showed that the aqueous extracts had poor antimicrobial activities. The organic extracts were more active against cancer cells than the aqueous extracts, while the aqueous extracts were more potent as antioxidants than the organic extracts. Overall, the mushroom extract from the durian substrate was the most effective except against A549 and SW948, while the aqueous extract from the durian substrate was the most effective against the A549 cancer cell lines with 29.53±2.39 % inhibition. On the other hand, the organic mushroom extract from the sawdust substrate was the most effective against SW948 with 60.24±2.45 % inhibition. Further studies, however, are needed to elucidate the molecular mechanism of action of P. pulmonarius extracts against cancer cell proliferation and the effect of the substrates on the nutritional composition, secondary metabolites, and other biological activities of P. pulmonarius extracts.     

Simultaneous Purification of Murine Mammary Tumor Virus Structural Proteins: Analysis of Antigenic Reactivities of Native gp34 by Radioimmunocompetition Assays

All the structural proteins (gp47, gp34, p27, p23, p16, and p12) of the murine mammary tumor virus (MuMTV) were simultaneously purified utilizing alkylagarose chromatography as the initial fractionation step. Least-hydrophobic MuMTV polypeptides (p23, p16) and the slightly hydrophobic p27 were separated from moderately hydrophobic proteins gp47 and p12 by passage through octylimino (C(8))-agarose; the gp47 and p12 could be removed from the matrix by elution with ethylene glycol, whereas the most hydrophobic MuMTV protein, gp34, was eluted using nonionic detergent together with ethylene glycol. Subsequent purification steps involved ion-exchange or gel filtration chromatography. The resulting protein preparations appeared near-homogeneous on analysis by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. Recoveries of MuMTV proteins, based on their approximate individual contribution to total virus protein, ranged from about 20% for gp47 to greater than 100% for the minor structural component p23, the major phosphoprotein of MuMTV. Antiserum against purified C3H MuMTV gp34, together with purified, radioiodinated gp34, was used to develop a radioimmunoassay which showed that from 13 to 14% of total MuMTV protein by weight is gp34. Using this assay system, the group-specific antigenic reactivity of gp34 was also demonstrated. When solubilized preparations of C3H, RIII, and GR MuMTV's were used as competing antigens in gp34 radioimmunoassays with anti-C3H MuMTV serum, both group- and type-specific differences in antigenic reactivity were found.     

Evaluation of healing following frenectomy

Aberrant frenum attachment would cause plaque accumulation and malalignment of teeth. It can be managed by frenotomy or frenectomy methods, through a conventional surgical technique or laser technique. Therefore, it is of interest to compare frenectomy healing surgical and laser techniques. Data from 51 outpatients and post-operative healing of frenectomy was assessed by Landry’s healing score index using 3 weeks postoperative photographs followed by statistical analysis. Based on the healing score index, the laser technique showed better outcomes than the surgical technique. Moreover, the association between the management of high frenal attachment and the healing score index was found to be statistically significant.     

Modeling protein-protein,protein-peptide,and protein-oligosaccharide complexes: CAPRI 7th edition

We present the seventh report on the performance of methods for predicting the atomic resolution structures of protein complexes offered as targets to the community-wide initiative on the Critical Assessment of Predicted Interactions. Performance was evaluated on the basis of 36 114 models of protein complexes submitted by 57 groups—including 13 automatic servers—in prediction rounds held during the years 2016 to 2019 for eight protein-protein, three protein-peptide, and five protein-oligosaccharide targets with different length ligands. Six of the protein-protein targets represented challenging hetero-complexes, due to factors such as availability of distantly related templates for the individual subunits, or for the full complex, inter-domain flexibility, conformational adjustments at the binding region, or the multi-component nature of the complex. The main challenge for the protein-peptide and protein-oligosaccharide complexes was to accurately model the ligand conformation and its interactions at the interface. Encouragingly, models of acceptable quality, or better, were obtained for a total of six protein-protein complexes, which included four of the challenging hetero-complexes and a homo-decamer. But fewer of these targets were predicted with medium or higher accuracy. High accuracy models were obtained for two of the three protein-peptide targets, and for one of the protein-oligosaccharide targets. The remaining protein-sugar targets were predicted with medium accuracy. Our analysis indicates that progress in predicting increasingly challenging and diverse types of targets is due to closer integration of template-based modeling techniques with docking, scoring, and model refinement procedures, and to significant incremental improvements in the underlying methodologies.     

A Hybrid One-Way ANOVA Approach for the Robust and Efficient Estimation of Differential Gene Expression with Multiple Patterns

Background

Identifying genes that are differentially expressed (DE) between two or more conditions with multiple patterns of expression is one of the primary objectives of gene expression data analysis. Several statistical approaches, including one-way analysis of variance (ANOVA), are used to identify DE genes. However, most of these methods provide misleading results for two or more conditions with multiple patterns of expression in the presence of outlying genes. In this paper, an attempt is made to develop a hybrid one-way ANOVA approach that unifies the robustness and efficiency of estimation using the minimum β-divergence method to overcome some problems that arise in the existing robust methods for both small- and large-sample cases with multiple patterns of expression.

Results

The proposed method relies on a β-weight function, which produces values between 0 and 1. The β-weight function with β = 0.2 is used as a measure of outlier detection. It assigns smaller weights (≥ 0) to outlying expressions and larger weights (≤ 1) to typical expressions. The distribution of the β-weights is used to calculate the cut-off point, which is compared to the observed β-weight of an expression to determine whether that gene expression is an outlier. This weight function plays a key role in unifying the robustness and efficiency of estimation in one-way ANOVA.

Conclusion

Analyses of simulated gene expression profiles revealed that all eight methods (ANOVA, SAM, LIMMA, EBarrays, eLNN, KW, robust BetaEB and proposed) perform almost identically for m = 2 conditions in the absence of outliers. However, the robust BetaEB method and the proposed method exhibited considerably better performance than the other six methods in the presence of outliers. In this case, the BetaEB method exhibited slightly better performance than the proposed method for the small-sample cases, but the the proposed method exhibited much better performance than the BetaEB method for both the small- and large-sample cases in the presence of more than 50% outlying genes. The proposed method also exhibited better performance than the other methods for m > 2 conditions with multiple patterns of expression, where the BetaEB was not extended for this condition. Therefore, the proposed approach would be more suitable and reliable on average for the identification of DE genes between two or more conditions with multiple patterns of expression.     

Triarylmethane Dye Decolorization by Pellets of Pycnoporus sanguineus: Statistical Optimization and Effects of Novel Impeller Geometry

A study was carried out to optimize selected parameters for decolorization of a triarylmethane dye, such as crystal violet by white rot fungus, Pycnoporus sanguineus, pellets. The parameters studied were initial dye concentration (ppm), agitation speed (rpm), and process time (days) and were optimized using response surface methodology (RSM). It is shown that process time, agitation speed, and their interactions have significant effects on the decolorization process. Following the optimization, the decolorization study was extended to a stirred tank reactor (STR) process. Effects of different geometry of impellers on the decolorization process and power consumption were studied. Novel impeller geometries, such as 180° curved blade and 60° angled blade impellers, were used in the STR. The application of 180° curved blade impeller resulted in higher percentage of decolorization at a relatively less power consumption as compared with 60° angled blade impeller.     

Synthesis and cytotoxic activity of organotin(IV) diallyldithiocarbamate compounds as anticancer agent towards colon adenocarcinoma cells (HT-29)

ContextDiphenyltin(IV) diallyldithiocarbamate compound (Compound 1) and triphenyltin(IV) diallyldithiocarbamate compound (Compound 2) are two newly synthesised compounds of organotin(IV) with diallyldithiocarbamate ligands.ObjectiveTo assess the cytotoxic effects of two synthesised compounds against HT-29 human colon adenocarcinoma cells and human CCD-18Co normal colon cells.Materials and methodsTwo successfully synthesised compounds were characterised using elemental (carbon, hydrogen, nitrogen, and sulphur) analysis, Fourier-Transform Infrared (FTIR), and ¹H, ¹³C ¹¹⁹Sn Nucleus Magnetic Resonance (NMR) spectroscopies. The single-crystal structure of both compounds was determined by X-ray single-crystal analysis. The cytotoxicity of the compounds was assessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazholium bromide (MTT) assay upon 24 h of treatment. While the mode of cell death was determined based on the externalisation of phosphatidylserine using a flow cytometer.ResultsThe elemental analysis data of the two compounds showed an agreement with the suggested formula of (C₆H₅)₂Sn[S₂CN(C₃H₅)₂]₂ for Compound 1 and (C₆H₅)₃Sn[S₂CN(C₃H₅)₂] for Compound 2. The two major peaks of infrared absorbance, i.e., ν(C = N) and ν(C = S) were detected at the range of 1475–1479 cm⁻¹ and 972–977 cm⁻¹, respectively. The chemical shift of carbon in NCS₂ group for Compound 1 and 2 were found at 200.82 and 197.79 ppm. The crystal structure of Compound 1 showed that it is six coordinated and crystallised in monoclinic, P2₁/c space group. While the crystal structure of Compound 2 is five coordinated and crystallised in monoclinic, P2₁/c space group. The cytotoxicity (IC₅₀) of the two compounds against HT-29 cell were 2.36 μM and 0.39 μM. Meanwhile, the percentage of cell death modes between 60% and 75% for compound 1 and compound 2 were mainly due to apoptosis, suggesting that both compounds induced growth arrest.ConclusionOur study concluded that the synthesised compounds showed potent cytotoxicity towards HT-29 cell, with the triphenyltin(IV) compound showing the highest effect compared to diphenyltin(IV).     

In silico investigation of potential inhibitors to main protease and spike protein of SARS-CoV-2 in propolis

Docking analysis of propolis's natural compound was successfully performed against SARS-CoV-2 main protease (Mpro) and spike protein subunit 2 (S2). Initially, the propolis's protein was screened using chromatography analysis and successfully identified 22 compounds in the propolis. Four compounds were further investigated, i.e., neoblavaisoflavone, methylophiopogonone A, 3′-Methoxydaidzin, and genistin. The binding affinity of 3′-Methoxydaidzin was ?7.7 kcal/mol, which is similar to nelfinavir (control), while the others were ?7.6 kcal/mol. However, we found the key residue of Glu A:166 in the methylophiopogonone A and genistin, even though the predicted binding energy slightly higher than nelfinavir. In contrast, the predicted binding affinity of neoblavaisoflavone, methylophiopogonone A, 3′-Methoxydaidzin, and genistin against S2 were ?8.1, ?8.2, ?8.3, and ?8.3 kcal/mol, respectively, which is far below of the control (pravastatin, ?7.3 kcal/mol). Instead of conventional hydrogen bonding, the π bonding influenced the binding affinity against S2. The results reveal that this is the first report about methylophiopogonone A, 3′-Methoxydaidzin, and genistin as candidates for anti-viral agents. Those compounds can then be further explored and used as a parent backbone molecule to develop a new supplementation for preventing SARS-CoV-2 infections during COVID-19 outbreaks.     

鸡肠道微生物菌群的建立发育、分布和生理学意义

鸡的胃肠道具有复杂的微生物菌群,该微生物菌群与宿主的肠道和整体健康密切相关,为了全面揭示鸡肠道微生物菌群的组成及其功能,本文对鸡肠道微生物菌群的建立发育、各肠段群落的分布及其生理学意义进行综述,从而为鸡肠道功能菌株的分离及有效利用,合理调控微生物菌群-宿主相互作用,提高饲料转化率和改善肠道健康提供理论依据。