Protein-protein interaction and site prediction using transfer learning.

The advanced language models have enabled us to recognize protein-protein interactions (PPIs) and interaction sites using protein sequences or structures. Here, we trained the MindSpore ProteinBERT (MP-BERT) model, a Bidirectional Encoder Representation from Transformers, using protein pairs as inputs, making it suitable for identifying PPIs and their respective interaction sites. The pretrained model (MP-BERT) was fine-tuned as MPB-PPI (MP-BERT on PPI) and demonstrated its superiority over the state-of-the-art models on diverse benchmark datasets for predicting PPIs. Moreover, the model's capability to recognize PPIs among various organisms was evaluated on multiple organisms. An amalgamated organism model was designed, exhibiting a high level of generalization across the majority of organisms and attaining an accuracy of 92.65%. The model was also customized to predict interaction site propensity by fine-tuning it with PPI site data as MPB-PPISP. Our method facilitates the prediction of both PPIs and their interaction sites, thereby illustrating the potency of transfer learning in dealing with the protein pair task.

Determination of Four PAHs and Formaldehyde in Traditionally Smoked Chicken Products.

The present study was conducted to analyze the level of four priority polycyclic aromatic hydrocarbons (PAHs), including benzo[a]pyrene (BaP), chrysene (Chr), benzo[a]anthracene (BaA), and benzo[b]fluoranthene (BbF), in traditionally smoked chicken products marketed in China. The results show that the amount of Æ©PAH4 (the sum of four different PAHs: BaP, Chr, BaA, and BbF) was 30.43-225.17 and 18.75-129.54 µg/kg in the skin and meat of smoked chicken products, respectively. The content of Æ©PAH4 in the smoked skin was significantly higher as compared to the smoked meat (p < 0.05). The calculation of MOE (margin of exposure) results suggested the possibilities of ingestion risk associated with the consumption of smoked chicken skin. Furthermore, the formaldehyde content in the skin of smoked chicken was 2.17-6.84 mg/kg and 0.86-2.95 mg/kg in the smoked meat. These results indicate that optimization or alternative methods for food processing should be developed to reduce the high level of harmful substances formed during processing to ensure the safety of smoked chicken products. Moreover, along with harmful substances, the moisture content and color of traditionally smoked chicken were analyzed to provide a practical reference for healthy, safe and green processing technology for smoked chicken.

Oxytropis glabra DC. Inhibits Biofilm Formation of Staphylococcus epidermidis by Down-Regulating ica Operon Expression.

Staphylococcus epidermidis is one of the main causes of medical device-related infections and bovine mastitis owing to its biofilm-forming abilities. Oxytropis glabra DC. is one of the most widespread Fabaceae species and used as a Chinese herbal formulation in Western China. Our research investigated the effects of O. glabra on the biofilm formation of S. epidermidis and the possible inhibiting mechanism. The biofilm-forming reference strain, S. epidermidis SE-1 (ATCC 35,984), was employed as a model and semi-quantitative biofilm assay was performed to evaluate the antibiofilm activity of O. glabra. The exopolysaccharides (EPS) production and expression of ica operon were studied to explore the possible antibiofilm mechanism using thin-layer chromatography and quantitative real-time PCR assay, respectively. The results obtained indicated that O. glabra decoction at 7.5 mg mL-1 significantly inhibited biofilm formation by about 95% without affecting cell growth of S. epidermidis. Two hydrolysis productions of EPS were significantly decreased by 64% and 54% with the addition of 7.5 mg mL-1O. glabra and the expression of icaR was significantly up-regulated 2.2-times, whereas icaB was significantly down-regulated more than 50% by 7.5 mg mL-1O. glabra. These findings suggest a potential application for O. glabra as a promising candidate for the exploration of new drugs against S. epidermidis biofilm-associated infections.

Isorhamnetin, Hispidulin, and Cirsimaritin Identified in Tamarix ramosissima Barks from Southern Xinjiang and Their Antioxidant and Antimicrobial Activities.

As a natural potential resource, Tamarix ramosissima has been widely used as barbecue skewers for a good taste and unique flavor. The polyphenolics in the branch bark play a key role in the quality improvement. The purposes of the present work were to explore the polyphenolic composition of T. ramosissima bark extract and assess their potential antioxidant and antimicrobial activities. Hispidulin and cirsimaritin from T. ramosissima bark extract were first identified in the Tamarix genus reported with UPLC-MS analysis. Isorhamnetin (36.91 µg/mg extract), hispidulin (28.79 µg/mg extract) and cirsimaritin (13.35 µg/mg extract) are rich in the bark extract. The extract exhibited promising antioxidant activity with IC50 values of 117.05 µg/mL for 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 151.57 µg/mL for hydroxyl radical scavenging activities, as well as excellent reducing power with an EC50 of 93.77 µg/mL. The bark extract showed appreciable antibacterial properties against foodborne pathogens. Listeria monocytogenes was the most sensitive microorganism with the lowest minimum inhibitory concentration (MIC) value of 5 mg/mL and minimum bactericidal concentration (MBC) value of 10 mg/mL followed by S. castellani and S. aureus among the tested bacteria. The T. ramosissima bark extract showed significantly stronger inhibitory activity against Gram-positive than Gram-negative bacteria. Nevertheless, this extract failed to show any activity against tested fungi. Overall, these results suggested that T. ramosissima shows potential in improving food quality due to its highly efficacious antioxidant and antibacterial properties.

Enterococcus Xinjiangensis sp. nov., Isolated from Yogurt of Xinjiang, China.

A Gram-strain-positive bacterial strain 48(T) was isolated from traditional yogurt in Xinjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, polymerase α subunit (rpoA) gene sequence analysis, determination of DNA G+C content, DNA-DNA hybridization with the type strain of Enterococcus ratti and analysis of phenotypic features. Strain 48(T) accounted for 96.1, 95.8, 95.8, and 95.7 % with Enterococcus faecium CGMCC 1.2136(T), Enterococcus hirae ATCC 9790(T), Enterococcus durans CECT 411(T), and E. ratti ATCC 700914(T) in the 16S rRNA gene sequence similarities, respectively. The sequence of rpoA gene showed similarities of 99.0, 96.0, 96.0, and 96 % with that of E. faecium ATCC 19434(T), Enterococcus villorum LMG12287, E. hirae ATCC 9790(T), and E. durans ATCC 19432(T), respectively. Based upon of polyphasic characterization data obtained in the study, a novel species, Enterococcus xinjiangensis sp. nov., was proposed and the type strain was 48(T)(=CCTCC AB 2014041(T) = JCM 30200(T)).

Effects of basic amino acids on heterocyclic amines and quality characteristics of fried beef patties at low NaCl level.

The impact of basic amino acids (Lysine, Arginine, Histidine) on the formation of total heterocyclic amines (HAs) was investigated in fried beef patties at 1% NaCl level. Different levels of basic amino acids (0.1%, 0.5%, 1%) significantly inhibited the formation of the total and individual HAs at 1% NaCl, and the inhibitory effect was more effective than 3% NaCl (6.19 ng/g, 26.93% inhibition) (P < 0.05). Lys at 1% reduced total HAs the most (2.46 ng/g, 70.88% inhibition), followed by 1% His (2.79 ng/g, 67.03% inhibition) and 1% Arg (3.43 ng/g, 59.51% inhibition). Compared to the 3% NaCl, the quality characteristics (moisture content, frying loss, texture profile, and color) of the fried beef patties were significantly improved when basic amino acids were added at 1% NaCl (P < 0.05). The lipid oxidation of fried beef patties was significantly inhibited by 1% Arg and 1% Lys at 1% NaCl level (P < 0.05). The results indicated that basic amino acids could inhibit the formation of total HAs while maintaining the quality of meat products at low NaCl condition.

Exploring the Characteristic Aroma Components of Traditional Fermented Koumiss of Kazakh Ethnicity in Different Regions of Xinjiang by Combining Modern Instrumental Detection Technology with Multivariate Statistical Analysis Methods for Odor Activity Value and Sensory Analysis.

To investigate the characteristic aromatic compounds, present in the traditional fermented koumiss of the Kazakh ethnic group in different regions of Xinjiang, GC-IMS, and GC-MS were used to analyze the volatile compounds in koumiss from four regions. A total of 87 volatile substances were detected, and esters, acids, and alcohols were found to be the main aroma compounds in koumiss. While the types of aroma compounds in koumiss were similar across different regions, the differences in their concentrations were significant and displayed clear regional characteristics. The fingerprint spectrum of GC-IMS, combined with PLS-DA analysis, indicates that eight distinctive volatile compounds, including ethyl butyrate, can be utilized to distinguish between different origins. Additionally, we analyzed the OVA value and sensory quantification of koumiss in different regions. We found that aroma components such as ethyl caprylate and ethyl caprate, which exhibit buttery and milky characteristics, were prominent in the YL and TC regions. In contrast, aroma components such as phenylethanol, which feature a floral fragrance, were more prominent in the ALTe region. The aroma profiles of koumiss from the four regions were defined. These studies provide theoretical guidance for the industrial production of Kazakh koumiss products.

Inhibitory Effect of Tamarix ramosissima Extract on the Formation of Heterocyclic Amines in Roast Lamb Patties by Retarding the Consumption of Precursors and Preventing Free Radicals.

Tamarix ramosissima has been widely used as barbecue skewers for the good taste and unique flavor it gives to the meat, but the effects of T. ramosissima on heterocyclic amine (HA) formation in roast lamb are unknown. The influence of T. ramosissima extract (TRE) on HA formation, precursors' consumption, and free radicals' generation in roast lamb patties were elucidated by UPLC-MS, HPLC, and electron spin resonance (ESR) analysis, respectively. Six HAs were identified and compared with the control group; the total and polar HAs decreased by 30.51% and 56.92% with TRE addition at 0.30 g/kg. The highest inhibitory effect was found against 2-amino-1-methyl-6-phenylimidazo[4,5-f]pyridine (PhIP) formation (70.83%) at 0.45 g/kg. The addition of TRE retarded the consumption of HA precursors, resulting in fewer HAs formed. The typical signal intensity of free radicals in roast lamb patties significantly decreased with TRE addition versus the control group (p < 0.05), and the higher the levels of the TRE, the greater the decrease in signal intensity. We propose that the inhibitory effects of TRE on HA formation, especially on polar HAs, were probably achieved by retarding the consumption of precursors and preventing free radicals from being generated in roast lamb patties. These findings provide valuable information concerning TRE's effectiveness in preventing HA formation through both the precursor consumption and free radical scavenging mechanisms.

Formation and Inhibition of Lipid Alkyl Radicals in Roasted Meat.

Free radicals are ubiquitous in roasted foods. In this work, lipid-derived carbon-centered alkyl radical formation was first studied in roasted meat by electron spin resonance (ESR). The influence of antioxidants on the inhibition of free radicals was investigated. The results showed that the high temperature, high heat transfer rate, and high polyunsaturated fatty acid (PUFA) content resulted in high radical content in roasted meat, while the high water content in meat retarded radical formation. The 0.03% addition of tea polyphenols (TPP) significantly reduced radical formation during roasting (p < 0.05), whereas the 0.03% rosemary extract (RE) had no significant inhibitory effect (p > 0.05). These results suggested that water retention and the addition of TPP would decrease radical generation during the roasting of meat.

Emulsification of oil-in-water emulsions with eggplant (Solanum melongena L.).

HYPOTHESIS: Eggplant is rich in polysaccharides. The mechanically homogenized eggplant flesh pulp (EFP) is expected to emulsify and stabilize o/w emulsions. The adsorption and network structure of the polysaccharides are hypothesized to contribute to the stability of emulsions. EXPERIMENTS: Creaming index (CI) and droplet size distribution were observed to evaluate the stabilities of EFP emulsions at different EFP concentrations (0.50, 0.75, 1.00, 1.25 and 1.50% w/v). Optical and fluorescence microscopy, confocal laser scanning microscopy and cryogenic scanning electron microscopy were conducted to observe the emulsification properties of the EFP-stabilized emulsions. In addition, rheological measurements were performed to reveal the EFP emulsions' rheological behaviours. FINDINGS: The prepared oil-in-water emulsion emulsified by EFP remained stable at an EFP concentration of 1.50%. Rheological analysis illustrated that the emulsions had typical shear-thinning property and gel-like nature. The emulsification mechanisms were explained by the formation of an interfacial film adhered to the oil droplets and the coherent three-dimensional network formed by filament and sheet-like polysaccharide strands in the continuous phase. This finding may define a new kind of natural and dietary emulsifier for emulsion-based food, beverage, and pharmaceutical products.

Isorhamnetin and Hispidulin from Tamarix ramosissima Inhibit 2-Amino-1-Methyl-6-Phenylimidazo[4,5-b]Pyridine (PhIP) Formation by Trapping Phenylacetaldehyde as a Key Mechanism.

Tamarix has been widely used as barbecue skewers to obtain a good taste and a unique flavor of roast lamb in China. Many flavonoids have been identified from Tamarix, which is an important strategy employed to reduce the formation of heterocyclic amines (HAs) in roast meat. Isorhamnetin, hispidulin, and cirsimaritin from Tamarix ramosissima bark extract (TRE) effectively inhibit the formation of 2-amino-1-methyl-6-phenylimidazo[4,5-b] pyridine (PhIP), the most abundant HAs in foods, both in roast lamb patties and in chemical models. According to the results of the GC-MS analysis, TRE and the three flavonoids significantly reduced the contents of phenylacetaldehyde, an important intermediate involved in PhIP formation at three levels. A subsequent ultra performance liquid chromatography-mass spectrometry (UPLC-MS) analysis revealed that these flavonoids trapped phenylacetaldehyde by forming interaction adducts. The formation of three postulated adducts, 8-C-(E-phenylethenyl)isorhamnetin, 6-C-(E-phenylethenyl)isorhamnetin and 8-C-(E-phenylethenyl)hispidulin, in the chemical models and roast lamb patties was further confirmed by a TOF-MS/MS analysis. Our results demonstrate that TRE and the corresponding flavonoids trap phenylacetaldehyde to form adducts and thus inhibit PhIP formation, suggesting their great potential beneficial effects on human health.

Interconverting flavonostilbenes with antibacterial activity from Sophora alopecuroides.

Five flavonostilbenes (alopecurones H, I, J, K and L) and five known ones were isolated from roots of Sophora alopecuroides, in addition to ten other phenolic compounds. A non-enzymatic interconversion of the lavandulyl-substituted flavonostilbenes was observed among alopecurones A, H, I, and K through a Wessely-Moser rearrangement reaction; this was proven by 1D and 2D NMR, HPLC-CD-PDA and HRMS analyses. Bioassay results suggested that flavonostilbenes exhibit significant antibacterial and anti-biofilm formation activities against Staphylococcus epidermidis with MIC values ranging from 3.1 to 12.5µg/mL.