SAMP: Identifying Antimicrobial Peptides by an Ensemble Learning Model Based on Proportionalized Split Amino Acid Composition.

It is projected that 10 million deaths could be attributed to drug-resistant bacteria infections in 2050. To address this concern, identifying new-generation antibiotics is an effective way. Antimicrobial peptides (AMPs), a class of innate immune effectors, have received significant attention for their capacity to eliminate drug-resistant pathogens, including viruses, bacteria, and fungi. Recent years have witnessed widespread applications of computational methods especially machine learning (ML) and deep learning (DL) for discovering AMPs. However, existing methods only use features including compositional, physiochemical, and structural properties of peptides, which cannot fully capture sequence information from AMPs. Here, we present SAMP, an ensemble random projection (RP) based computational model that leverages a new type of features called Proportionalized Split Amino Acid Composition (PSAAC) in addition to conventional sequence-based features for AMP prediction. With this new feature set, SAMP captures the residue patterns like sorting signals at around both the N-terminus and the C-terminus, while also retaining the sequence order information from the middle peptide fragments. Benchmarking tests on different balanced and imbalanced datasets demonstrate that SAMP consistently outperforms existing state-of-the-art methods, such as iAMPpred and AMPScanner V2, in terms of accuracy, MCC, G-measure and F1-score. In addition, by leveraging an ensemble RP architecture, SAMP is scalable to processing large-scale AMP identification with further performance improvement, compared to those models without RP. To facilitate the use of SAMP, we have developed a Python package freely available at https://github.com/wan-mlab/SAMP.

Identification of key astringent compounds in aronia berry juice.

Aronia berry has extremely strong and unpleasant astringent mouthfeel. However, detailed information on the key astringent compounds is still limited. To fill this gap, astringent compounds were firstly separated from aronia juice. Following sensory evaluation, phenolic profile determination, validation by in-vitro models, and thiolytic degradation, key astringent compounds were identified. Results showed when most proanthocyanidins (PAs) were removed while other phenolic compounds remained, the astringency intensity of aronia juice was significantly decreased. In-vitro models, including saliva precipitation index and mucin turbidity, validated PAs rather than anthocyanins as the key astringent compounds. The protein-precipitated PAs from aronia juice were identified as polymers, linked by B-type bonds, with (-)-epicatechin as the extension unit and predominantly as the terminal unit, having a 69.56 mean degree of polymerization (mDP), far higher than the 35.38 mDP of PAs separated directly from juice. These findings would be valuable to the development of targeted astringency mitigation approaches.

High pressure processing (HPP) improved safety and quality of emerging aronia berry juice: a pilot scale shelf-life study.

The effect of high pressure processing (HPP, 600 MPa, 5 min) and thermal treatment (85 °C, 15 min) on aronia berry juice in a pilot scale was studied. The maximal shelf-life of treated samples at room temperature (RT, approximately 25 °C) or refrigerated storage (RS, 4 °C) was also investigated. Microbial counts, physicochemical properties, enzymes activities, phenolic compounds, and antioxidant activities of these juices were determined and compared. Results indicated that HPP treatment improved the microbial shelf-life of the aronia juice by at least 10-times at RT and 5-times at RS. Although thermal treatment was equally effective in extending the shelf-life, the high temperature resulted in a quicker degradation of polyphenols in aronia juice, which was decreased by 36.6% during RT storage (5 weeks) and 43.3% at RS storage (24 weeks). Therefore, HPP was more efficient in maintaining the safety and quality of aronia juice. The study also indicated HPP treated aronia juice could be stored at RT for at least one month that could be of benefit to the non-cold chain process which is targeting for a low-energy input while still retaining a minimal effect on the nutritional properties of food products.

The application of machine-learning and Raman spectroscopy for the rapid detection of edible oils type and adulteration.

Raman spectroscopy is an emerging technique for the rapid detection of oil qualities. But the spectral analysis is time-consuming and low-throughput, which has limited the broad adoption. To address this issue, nine supervised machine learning (ML) algorithms were integrated into a Raman spectroscopy protocol for achieving the rapid analysis. Raman spectra were obtained for ten commercial edible oils from a variety of brands and the resulting spectral dataset was analyzed with supervised ML algorithms and compared against a principal component analysis (PCA) model. A ML-derived model obtained an accuracy of 96.7% in detecting oil type and an adulteration prediction of 0.984 (R2). Several ML algorithms also were superior than PCA in classifying edible oils based on fatty acid compositions by gas chromatography, with a faster readout and 100% accuracy. This study provided an exemplar for combining conventional Raman spectroscopy or gas chromatography with ML for the rapid food analysis.

An overview of the perception and mitigation of astringency associated with phenolic compounds.

Astringency, as a kind of puckering, drying, or rough sensation, is widely perceived from natural foods, especially plants rich in phenolic compounds. Although the interaction and precipitation of salivary proteins by phenolic compounds was often believed as the major mechanism of astringency, a definitive theory about astringency is still lacking due to the complex oral sensations. The interaction with oral epithelial cells and the activation of trigeminal chemoreceptors and mechanoreceptors also shed light on some of the phenolic astringency mechanisms, which complement the insufficient mechanism of interaction with salivary proteins. Since phenolic compounds with different types and structures show different astringency thresholds in a certain regularity, there might be some relationships between the phenolic structures and perceived astringency. On the other hand, novel approaches to reducing the unfavorable perception of phenolic astringency have been increasingly emerging; however, the according summary is still sparse. Therefore, this review aims to: (a) illustrate the possible mechanisms of astringency elicited by phenolic compounds, (b) reveal the possible relationships between phenolic structures and perception of astringency, and (c) summarize the emerging mitigation approaches to astringency triggered by phenolic compounds. This comprehensive review would be of great value to both the understanding of phenolic astringency and the finding of appropriate mitigation approaches to phenolic astringency in future research.

Comparison of wheat, soybean, rice, and pea protein properties for effective applications in food products.

Pea and rice proteins are promising to substitute allergenic proteins, and increasingly, play important roles in the food industry because of their hypoallergenic characteristics and nutritional value. However, manufacturers generally provide limited functionality information on these proteins. Therefore, this study comprehensively compared functional properties of wheat, soybean, rice, and pea proteins for their industrial applications and illustrated correlation among various functionalities. Results showed that protein solubility (PS) was highly related to its water absorption (WA) capacity, emulsifying activity index (EAI), and emulsion stability index (ESI). The overall functionality of pea protein was close to that of soybean protein while rice protein cannot match with all other proteins. sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis indicated the composition of each protein was unique. While the deconvolution of the amide I band of the Raman spectra indicated soybean and pea proteins that shared similar features, but they were different from that of wheat and rice proteins. PRACTICAL APPLICATIONS: Due to the allergenicity of wheat and soybean proteins, food manufacturers are looking for alternative protein sources. Rice and Pea proteins are promising substitutes because of their "allergen-friendly" as well as their emergence in the food market. This study provided a comprehensive comparison of the functionality of commercially available wheat, soybean, rice, and pea proteins. The information presented in this study would be helpful to food scientists, scholars, or engineers when they develop appropriate application of various proteins in food products.

Evaluation of phenolic compounds, antioxidant and antiproliferative activities of 31 grape cultivars with different genotypes.

This study evaluated the total phenolic content, phenolic composition, antioxidant and in vitro antiproliferative properties of seeds and skins of 31 different grape cultivars. These properties of seeds and skins varied greatly among grape cultivars. European grapes had the highest values of phenolic compounds, antioxidant properties in seeds followed by Muscadine > American grapes > Oriental grapes. European grape seed extracts also were the strongest in inhibiting the growth of HepG2 cell, followed by American grapes > Muscadine > Oriental grapes. While these values of the Euro-Asian or Euro-American hybrids fell between the parents. However, the differences of these values in skin extracts among different grape cultivars were not significant. The antiproliferative activities were significantly correlated to the three antioxidant assays and the main phenolic compounds. PRACTICAL APPLICATIONS: This study presents phenolic compounds, antioxidant, and in vitro antiproliferative properties of seeds and skins of 31 different grape cultivars. The information is highly relevant to the ever-increasing need for natural sources of antioxidants or nutraceuticals among consumers. The study also provides information for grape geneticists to breed cultivars with higher nutritional value, and for food scientists to exploit the natural polyphenol antioxidants in various grape pomace.

Phytochemical profiles, and antimicrobial and antioxidant activities of greater galangal [Alpinia galanga (Linn.) Swartz.] flowers.

Previous studies of galangal (Alpinia galanga) have focussed mostly on rhizomes but seldom on flowers. A comprehensive look at galangal flowers could reveal additional benefits. The chemical composition of galangal flowers was significantly (p < 0.05) different from that of galangal rhizome. Pentadecane and α-humulene were identified as major compounds of galangal flower essential oil. 1'-acetoxyeugenol acetate was identified as the highest compound in flowers and exhibited the strongest antimicrobial activity among all fractions, with MIC50 values of 34 µg/ml against Staphylococcus aureus and 68 µg/ml against Listeria monocytogenes. Galangal flowers had a 3-fold higher total phenols content than had rhizomes (10.5 vs. 3.33 mg GAE/g powder). The antioxidant activities of different flower fractions varied from 2 to 4.45 mmol  trolox/g phenolics. These findings suggest that antimicrobial and antioxidant agents extracted from galangal flowers could potentially be utilized as natural food preservatives or as therapeutic agents.

The growing season impacts the accumulation and composition of flavonoids in grape skins in two-crop-a-year viticulture.

The influence of growing season (winter vs. summer) on the flavonoid accumulation and composition was studied in the skins of three grape cultivars for two consecutive years under a two-crop-a-year viticulture practice in Southwest China. The total anthocyanin, flavonol and flavan-3-ol contents in winter berry skins were significantly higher than those in summer berry skins for 'Kyoho' and 'Muscat Hamburg'. Reversely, the content of anthocyanin in 'NW196' winter berry was lower than summer berry. However, the percentage of diglycosylated, trihydroxylated, methylated, and acylated anthocyanins, trihydroxylated and methylated flavonols, and flavan-3-ol polymers were higher in the summer berry skins than the winter berry skins among all the three grape cultivars. Winter climatic conditions were favorable to flavonoid accumulation for the non native grapes 'Kyoho' and 'Muscat Hamburg', while the summer climatic conditions were beneficial to anthocyanin accumulation for 'NW196' that has 50% genetic background from a local wild grape species Vitis quinquangularis. These seasonal variations of flavonoid accumulations and compositions in the grape skins were primarily contributed by different climatic factors, such as temperature, solar radiation, and rainfall.

Profile of Polyphenol Compounds of Five Muscadine Grapes Cultivated in the United States and in Newly Adapted Locations in China.

Polyphenol compositions and concentrations in skins and seeds of five muscadine grapes (cv. "Noble", "Alachua", "Carlos", "Fry", and "Granny Val") cultivated in the United States (Tallahassee-Florida, TA-FL) and South China (Nanning-Guangxi, NN-GX and Pu'er-Yunnan, PE-YN) were investigated, using ultra performance liquid chromatography tandem triple quadrupole time-of-flight mass spectrometry (UPLC Triple TOF MS/MS). Fourteen ellagitannins were newly identified in these muscadine grapes. The grapes grown in NN-GX accumulated higher levels of ellagic acid, methyl brevifolin carboxylate, and ellagic acid glucoside in skins, and penta-O-galloyl-glucose in seeds. In PE-YN, more flavonols were detected in skins, and higher contents of flavan-3-ols, ellagic acid, and methyl gallate were identified in seeds. Abundant seed gallic acid and flavonols were found among the grapes grown in TA-FL. Based on principal component analysis (PCA) of 54 evaluation parameters, various cultivars grown in different locations could be grouped together and vice versa for the same cultivar cultivated in different regions. This is the result of the interaction between genotype and environmental conditions, which apparently influences the polyphenol synthesis and accumulation.

Fruit quality, nutraceutical and antimicrobial properties of 58 muscadine grape varieties (Vitis rotundifolia Michx.) grown in United States.

Fifty-eight muscadine grape varieties were evaluated for their fruit quality, nutraceutical, and antimicrobial properties during two growing seasons (2012 vs. 2013). Fruit quality was significantly different among muscadine grape varieties, with weight ranged from 2.93 to 22.32g, pH from 3.01 to 3.84, titratable acidity from 0.27% to 0.83%, and °Brix from 10.92 to 23.91. Total phenols for different muscadine juices varied from 0.26 to 1.28mgGA/mL, skins from 10.13 to 30.02mgGA/g DM, and seeds from 22.47 to 72.01mgGA/g DM. Accordingly, the antioxidant activity of grape juices varied from 0.97 to 6.78mmolTrolox/mL, skins from 83.59 to 221.20µmolTrolox/g DM, and seeds from 178.22 to 619.73µmolTrolox/g DM. Study demonstratedgrape seed polyphenols (MIC 54.8-60.1µg/ml) showed stronger antimicrobial activity against S. aureus than skin polyphenols (MIC 70.7-80.2µg/ml). This information could be a valuable asset in the research and extension of muscadine grapes.

Muscadine grape seed oil as a novel source of tocotrienols to reduce adipogenesis and adipocyte inflammation.

Tocotrienols are unsaturated forms of vitamin E previously shown to reduce adipogenesis and adipose inflammation. In this study, muscadine grape seed oil (MGSO) was identified as a novel source of tocotrienols containing significant amounts of α- and γ-tocotrienol (T3) with minor seasonal changes. The aim of this study was to assess the anti-adipogenic and anti-inflammatory potential of MGSO by using primary human adipose-derived stem cells (hASCs). Differentiating hASCs were treated with MGSO and compared with rice bran and olive oil. Accumulation of triglyceride was significantly lower in MGSO-treated hASCs than rice bran and olive oils. A tocotrienol rich fraction (TRF) from MGSO was prepared by solid phase extraction and eluted with 15% 1,4-dioxane in hexane. The MGSO-derived TRF treatment significantly reduced mRNA and protein expression that are crucial to adipogenesis (e.g., PPARγ and aP2) in hASCs. Furthermore, TRF from MGSO markedly reduced LPS-induced proinflammatory gene expression in human adipocytes and cytokine secretion to the medium (IL-6 and IL-8). Collectively, our work suggests that MGSO is a stable and reliable natural source of T3 and MGSO may constitute a new dietary strategy to attenuate obesity and its associated adipose inflammation.

Application of muscadine grape (Vitis rotundifolia Michx.) pomace extract to reduce carcinogenic acrylamide.

Acrylamide is a byproduct of the Maillard reaction and is formed in a variety of heat-treated commercial starchy foods. It is known to be toxic and potentially carcinogenic to humans. Muscadine grape polyphenols and standard phenolic compounds were examined on the reduction of acrylamide in an equimolar asparagine/glucose chemical model, a potato chip model, and a simulated physiological system. Polyphenols were found to significantly reduce acrylamide in the chemical model, with reduced rates higher than 90% at 100 µg/ml. In the potato chip model, grape polyphenols reduced the acrylamide level by 60.3% as concentration was increased to 0.1%. However, polyphenols exhibited no acrylamide reduction in the simulated physiological system. Results also indicated no significant correlation between the antioxidant activities of polyphenols and their acrylamide inhibition. This study demonstrated muscadine grape extract can mitigate acrylamide formation in the Maillard reaction, which provides a new value-added application for winery pomace waste.

Antioxidant, antibacterial, and antibiofilm properties of polyphenols from muscadine grape (Vitis rotundifolia Michx.) pomace against selected foodborne pathogens.

Polyphenols are predominantly secondary metabolites in muscadine grapes, playing an important role in the species' strong resistance to pests and diseases. This study examined the above property by evaluating the antioxidant, antibacterial, and antibiofilm activities of muscadine polyphenols against selected foodborne pathogens. Results showed that antioxidant activity for different polyphenols varied greatly, ranging from 5 to 11.1 mmol Trolox/g. Antioxidant and antibacterial activities for polyphenols showed a positive correlation. Muscadine polyphenols exhibited a broad spectrum of antibacterial activity against tested foodborne pathogens, especially Staphylococcus aureus (MIC = 67-152 mg/L). Muscadine polyphenols at 4 × MIC caused nearly a 5 log10 CFU/mL drop in cell viability for S. aureus in 6 h with lysis, whereas at 0.5 × MIC they inhibited its biofilm formation and at 16 × MIC they eradicated biofilms. Muscadine polyphenols showed synergy with antibiotics and maximally caused a 6.2 log10 CFU/mL drop in cell viability at subinhibitory concentration.

Enzyme release of phenolics from muscadine grape (Vitis rotundifolia Michx.) skins and seeds.

Enzyme degradation of plant cell wall polysaccharides can potentially enhance the release of bioactive phenolics. The aim of this study was to evaluate various combinations of solvent and enzyme, enzyme type (cellulase, pectinase, ß-glucosidase), and hydrolysis time (1, 4, 8, 24 h) on the release of muscadine grape skin and seed phenolics, and their antioxidant activities. Results showed that pre-treated muscadine skins and seeds with enzymes decreased total phenolic yield compared with solvent (50% ethanol) alone. Enzyme release of phenolics from skins of different muscadine varieties was significantly different while release from seeds was similar. Enzyme hydrolysis was found to shorten extraction time. Most importantly, enzyme hydrolysis modified the galloylated form of polyphenols to low molecular weight phenolics, releasing phenolic acids (especially gallic acid), and enhancing antioxidant activity.

[Application value of diffusion-weighted imaging in ischemic-type biliary lesions after liver transplantation].

OBJECTIVE: To discuss the application values of DWI (diffusion-weighted imaging) and ADC (apparent diffusion coefficient) on ischemic-type biliary lesions (ITBL) after orthotopic liver transplantation. METHODS: According to whether there was ITBL after liver transplantation or not, 46 cases of liver transplantation were selected and divided into 2 groups on the basis of PTC (percutaneous transhepatic cholangiography) or ERCP (endoscopic retrograde cholangiopancreatography) examination, pathology or clinical follow-up data: ITBL group (n = 29) and no ITBL group (C group, n = 17). The ADC value was measured for right lobe of graft liver parenchyma (b value = 600 s/mm(2)). And the signal of biliary system of graft on DWI and biliary tract on MRCP were analyzed. RESULTS: (1) The ADC values of liver graft were (1.456 ± 0.286) × 10(-3) mm(2)/s and (1.716 ± 0.391) × 10(-3) mm(2)/s in ITBL and C groups respectively. The difference in ADC value was significant between two groups (P = 0.015); (2) the incidence of increased signal of bile duct on DWI was 82.8% (24/29) and 5.9% (1/17) for ITBL and C groups respectively. The lesion was located in porta hepatis and intrahepatic small bile duct was seen in 17 of 24 patients (70.8%) in ITBL group. The difference was significant in signal of bile ducts between ITBL and C groups (P < 0.001). Twenty-one cases with sludge on DWI in ITBL group had hyperintensity, isointensity or hypointensity. There was no abnormal signal in the lumen of bile duct in C group. CONCLUSION: The major sign of ITBL is a hyperintensity of porta hepatis and small bile ducts on DWI. And the ADC value of graft liver parenchyma decreases. These reflect the pathological changes to an extent and may be an effective and sensitive monitoring tool of early ITBL. DWI is a novel, non-invasive, simple and practical method in the diagnosis and differential diagnosis of ITBL after liver transplantation.

Influence of growing season on phenolic compounds and antioxidant properties of grape berries from vines grown in subtropical climate.

The influence of growing season (winter vs summer) on the synthesis and accumulation of phenolic compounds and antioxidant properties was studied in five grape cultivars for three consecutive years. Four phenolic compound parameters (total phenols, flavonoids, flavan-3-ols, and anthocyanins) and three antioxidant property parameters [2,2-diphenyl-1-picrylhydrazyl radical scavenging, 2,2-azinobis(3-ethylbenzothiazolinesulfonic acid) radical scavenging, and ferric reducing antioxidant power] were investigated. Results showed that both phenolic compounds and antioxidant properties in the seed and skin of winter berries were significantly (p < 0.05) higher than those of summer berries for all of the cultivars investigated. The anthocyanin profiles of berry skins appeared to be extremely consistent in different years for the same crop, whereas they varied greatly between the two crops within the same year (winter vs summer). Winter berries contained richer glucosides of delphinidin, cyanidin, peonidin, and malvidin than summer berries. These seasonal variations of phenolic compounds and antioxidant properties on grape berries were largely contributed by climatic factors such as temperature, solar radiation, rainfall, and hydrothermic coefficient between different growing seasons.