Soyfoods and soybean products: from traditional use to modern applications

Soybean products (soyfoods), reported as potential functional foods, are implicated in several health-enhancing properties, such as easing the symptoms of postmenopausal women, reducing the risk of osteoporosis, preventing cardiovascular disease, and antimutagenic effects. Isoflavone, for example, is one of the most important compounds abundantly found in soybean, mainly accounting for the health-enhancing properties as mentioned earlier. However, most biological activities of isoflavones are mainly attributed to their aglycone forms. It has also been demonstrated that isoflavone aglycones are absorbed faster and in greater amount than their glycosides in human intestines. Fortunately, deglycosylation of isoflavones can be achieved during fermentation process by several strains such as lactic acid bacteria, basidiomycetes, filamentous fungus, and Bacillus subtilis with their β-glucosidase activity. This article presents an overview of soybean's chemistry, application, state-of-the-art advances in soybean fermentation processing and products as well as their applications in food and pharmaceutical industries. Different compounds, such as isoflavone, dietary fibers, and proteins which exhibit significant bioactivities, are summarized. The roles of different microorganisms in bioconversion and enhancement of bioactivities of fermented soybean are also discussed.     

Putting microbes to work: dairy fermentation, cell factories and bioactive peptides. Part I: overview

A variety of milk-derived biologically active peptides have been shown to exert both functional and physiological roles in vitro and in vivo, and because of this are of particular interest for food science and nutrition applications. Biological activities associated with such peptides include immunomodulatory, antibacterial, anti-hypertensive and opioid-like properties. Milk proteins are recognized as a primary source of bioactive peptides, which can be encrypted within the amino acid sequence of dairy proteins, requiring proteolysis for release and activation. Fermentation of milk proteins using the proteolytic systems of lactic acid bacteria (LAB) is an attractive approach for generation of functional foods enriched in bioactive peptides given the low cost and positive nutritional image associated with fermented milk drinks and yoghurt. In this review, we discuss the exploitation of such fermentation towards the development of functional foods conferring specific health benefits to the consumer beyond basic nutrition. In particular, in Part I, we focus on the release of encrypted bioactive peptides from a range of food protein sources, as well as the use of LAB as cell factories for the de novo generation of bioactivities.     

A review of fish-derived antioxidant and antimicrobial peptides: their production, assessment, and applications

Fishes are rich sources of structurally diverse bioactive compounds. In recent years, much attention has been paid to the existence of peptides with biological activities and proteins derived from foods that might have beneficial effects for humans. Antioxidant and antimicrobial peptides isolated from fish sources may be used as functional ingredients in food formulations to promote consumer health and improve the shelf life of food products. This paper presents an overview of the antioxidant and antimicrobial peptides derived from various fishes. In addition, we discuss the extraction of fish proteins, enzymatic production, and the techniques used to isolate and characterize these compounds. Furthermore, we review the methods used to assay the bioactivities and their applications in food and nutraceuticals.     

Comprehensive approaches to molecular biomarker discovery for detection and identification of Cronobacter spp. (Enterobacter sakazakii) and Salmonella spp

Cronobacter spp. (formerly Enterobacter sakazakii) and Salmonella spp. are increasingly implicated internationally as important microbiological contaminants in low-moisture food products, including powdered infant formula. Estimates indicate that 40 to 80% of infants infected with Cronobacter sakazakii and/or Salmonella in the United States may not survive the illness. A systematic approach, combining literature-based data mining, comparative genome analysis, and the direct sequencing of PCR products of specific biomarker genes, was used to construct an initial collection of genes to be targeted. These targeted genes, particularly genes encoding virulence factors and genes responsible for unique phenotypes, have the potential to function as biomarker genes for the identification and differentiation of Cronobacter spp. and Salmonella from other food-borne pathogens in low-moisture food products. In this paper, a total of 58 unique Salmonella gene clusters and 126 unique potential Cronobacter biomarkers and putative virulence factors were identified. A chitinase gene, a well-studied virulence factor in fungi, plants, and bacteria, was used to confirm this approach. We found that the chitinase gene has very low sequence variability and/or polymorphism among Cronobacter, Citrobacter, and Salmonella, while differing significantly in other food-borne pathogens, either by sequence blasting or experimental testing, including PCR amplification and direct sequencing. This computational analysis for Cronobacter and Salmonella biomarker identification and the preliminary laboratory studies are only a starting point; thus, PCR and array-based biomarker verification studies of these and other food-borne pathogens are currently being conducted.     

Inconvenient truth: Cancer biomarker development by using proteomics

A biomarker is a crucial tool for measuring the progress of disease and the effects of treatment for better clinical outcomes in cancer patients. Diagnostic, predictive, and prognostic biomarkers are required in various clinical settings. The proteome, a functional translation of the genome, is considered a rich source of biomarkers; therefore, sizable time and funding have been spent in proteomics to develop biomarkers. Although significant progress has been made in technologies toward comprehensive protein expression profiling, and many biomarker candidates published, none of the reported biomarkers have proven to be beneficial for cancer patients. The present deceleration in biomarker research can be attributed to technical limitations. Additional efforts are required to further technical progress; however, there are many examples demonstrating that problems in biomarker research are not so much with the technology but in the study design. In the study of biomarkers for early diagnosis, candidates are screened and validated by comparing cases and controls of similar sample size, and the low prevalence of disease is often ignored. Although it is reasonable to take advantage of multiple rather than single biomarkers when studying diverse disease mechanisms, the annotation of individual components of reported multiple biomarkers does not often explain the variety of molecular events underlying the clinical observations. In tissue biomarker studies, the heterogeneity of disease tissues and pathological observations are often not considered, and tissues are homogenized as a whole for protein extraction. In addition to the challenge of technical limitations, the fundamental aspects of biomarker development in a disease study need to be addressed. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.     

Differential proteomic analysis of late-stage and recurrent breast cancer from formalin-fixed paraffin-embedded tissues

The heterogeneity of breast cancer requires the discovery of more incisive molecular tools that better define disease progression and prognosis. Proteomic analysis of homogeneous tumor cell populations derived by laser microdissection from formalin-fixed, paraffin-embedded (FFPE) tissues has proven to be a robust strategy for conducting retrospective cancer biomarker investigations. We describe an MS-based analysis of laser microdissected cancerous epithelial cells derived from twenty-five breast cancer patients at defined clinical disease stages with the goal of identifying protein abundance characteristics indicative of disease progression and recurrence. Comparative analysis of stage 0 and stage III patients revealed 113 proteins that significantly differentiated these groups and included known factors associated with disease pathogenesis, such as CDH1 and CTNNB1, as well as those previously implicated in breast cancer, such as TSP-1. Similar analyses of patients presenting with stage II disease that did or did not exhibit recurrence two years postdiagnosis revealed 42 proteins that significantly differentiated these subgroups and included IRS-1 and PARK7. These data provide evidence supporting the utility of FFPE tissues for functional proteomic analyses and protein biomarker discovery and yielded protein candidates indicative of disease stage and recurrence in breast cancer that warrant further investigation for diagnostic utility and biological relevance.     

槲皮素的生物活性机制及药动学特点

近年来,许多文献报道了槲皮素发挥生物活性的机制,发现槲皮素并不只是通过抗氧化机制发挥活性。细胞因子及细胞信号转导在槲皮素发挥生物活性的过程中也起到了重要作用。另一方面,有研究表明,口服生物利用度不高、首关效应强是阻碍食物中槲皮素充分发挥生物活性的重要原因。然而,槲皮素的体内分布和代谢特征又给予它发挥在体活性的潜力。因此,槲皮素很有研究价值。本文主要介绍槲皮素的作用机制,并阐述其药动学特点,为人们对槲皮素的进一步研究提供参考。     

Functional relevance and health benefits of soymilk fermented by lactic acid bacteria

The growing interest of consumers towards nutritionally enriched, and health promoting foods, provoke interest in the eventual development of fermented functional foods. Soymilk is a growing trend that can serve as a low-cost non-dairy alternative with improved functional and nutritional properties. Soymilk acts as a good nutrition media for the growth and proliferation of the micro-organism as well as for their bioactivities. The bioactive compounds produced by fermentation of soymilk with lactic acid bacteria (LAB) exhibit enhanced nutritional values, and several improved health benefits including antihypertensive, antioxidant, antidiabetic, anticancer and hypocholesterolaemic effects. The fermented soymilk is acquiring a significant position in the functional food industry due to its increased techno-functional qualities as well as ensuring the survivability of probiotic bacteria producing diverse metabolites. This review covers the important benefits conferred by the consumption of soymilk fermented by LAB producing bioactive compounds. It provides a holistic approach to obtain existing knowledge on the biofunctional attributes of fermented soymilk, with a focus on the functionality of soymilk fermented by LAB.     

Beneficial and preventive effect of chitin nanofibrils in a dextran sulfate sodium-induced acute ulcerative colitis model

Chitin nanofibrils, which are prepared from dried crab shells by a grinding method, are newly developed natural materials with uniform widths of approximately 10-20 nm. The bioactivities of chitin nanofibrils have not been investigated. In this study, we examined the preventive effects of chitin nanofibrils in a mouse model of dextran sulfate sodium (DSS)-induced acute ulcerative colitis. The results indicated that chitin nanofibrils improved clinical symptoms and suppressed ulcerative colitis. Furthermore, chitin nanofibrils suppressed myeloperoxidase activation in the colon and decreased serum interleukin-6 concentrations. Conversely, chitin powder did not suppress DSS-induced acute ulcerative colitis. Our results suggested that chitin nanofibrils have potential as a functional substance for inflammatory bowel disease patients.     

Validation of biomarkers of food intake—critical assessment of candidate biomarkers

Biomarkers of food intake (BFIs) are a promising tool for limiting misclassification in nutrition research where more subjective dietary assessment instruments are used. They may also be used to assess compliance to dietary guidelines or to a dietary intervention. Biomarkers therefore hold promise for direct and objective measurement of food intake. However, the number of comprehensively validated biomarkers of food intake is limited to just a few. Many new candidate biomarkers emerge from metabolic profiling studies and from advances in food chemistry. Furthermore, candidate food intake biomarkers may also be identified based on extensive literature reviews such as described in the guidelines for Biomarker of Food Intake Reviews (BFIRev). To systematically and critically assess the validity of candidate biomarkers of food intake, it is necessary to outline and streamline an optimal and reproducible validation process. A consensus-based procedure was used to provide and evaluate a set of the most important criteria for systematic validation of BFIs. As a result, a validation procedure was developed including eight criteria, plausibility, dose-response, time-response, robustness, reliability, stability, analytical performance, and inter-laboratory reproducibility. The validation has a dual purpose: (1) to estimate the current level of validation of candidate biomarkers of food intake based on an objective and systematic approach and (2) to pinpoint which additional studies are needed to provide full validation of each candidate biomarker of food intake. This position paper on biomarker of food intake validation outlines the second step of the BFIRev procedure but may also be used as such for validation of new candidate biomarkers identified, e.g., in food metabolomic studies.     

食管鳞癌的蛋白质组学

大部分食管鳞癌（esophageal squamous cell carcinoma, ESCC）确诊时已发展至中晚期,临床治疗效果差,是导致我国华北地区ESCC死亡率居高不下的主要原因之一.因此,亟需筛查ESCC特异性、敏感性的生物标志物,以期用于ESCC早期诊断、个体化分子靶向治疗和预后评价. 与相对稳定、携带遗传信息的基因组不同,蛋白质组具有时空变化特性,由此构成生命活动复杂性的物质基础.在病理情况下,蛋白质组能够精确反映患病组织器官的功能状态,因此为疾病的监测提供了窗口.本文总结了ESCC蛋白质组研究现状及差异表达的蛋白质谱,并探讨了ESCC候选分子标志物的潜在临床应用价值.     

尿液作为新型生物标志物来源的探索

机体各种变化是生物标志物研究的核心内容.因为机体固有的稳态调控机制,在血液中早期产生的变化容易被清除.而在尿液中不存在稳态调控机制,允许容纳更多的变化因素存在.尤其在疾病发生的早期阶段,从尿液中更有可能发现新型的早期生物标志物.在尿液生物标志物研究中,亦应当考虑药物的影响.使用尿液生物标志物研究路线图,能够有效规避各种影响因素对于尿液生物标志物研究的干扰;同时,结合膜处理新技术,有利于经济、高效地大规模收集尿液样本,促进尿液生物标志物的大规模研究.另外,本文介绍了最容易在尿液中体现出变化的肾脏疾病生物标志物的研究进展.尿液生物标志物的研究,将赋予人类在疾病预防、诊断、治疗及预后监测等诸多方面实现更多进步的可能性.     

尿液蛋白质组作为下一代生物标志物的潜力

生物标志物是与机体生理及病理生理状态相关的可监测到变化的生化指标,尿液不属于内环境,没有稳态机制,能够积累并反映机体生理状态的早期变化,有潜力辅助疾病的早期诊断和预后监测。得益于非侵入性的收集方式,尿液可以被连续、大量、重复收集并便捷、稳定地保存,且组分相对简单,易于分析,是理想的标志物研究样本。但临床尿液样本蛋白质组可能会受到生活习惯、用药情况等多种混杂因素的影响,而动物模型方便控制变量,可以最大程度减少混杂因素的干扰,并使得在疾病发生、发展极早期采集样本成为可能;此外,患者的疾病分期、分型、用药情况等信息不能被忽视,现有样本策略和分析方式有待优化,例如,对同一个人不同时期、不同状态(例如患病前后)的尿液样本进行前后对照是一种理想的分析方式,这种方式能够消除个体间差异性的影响,符合个性化、精准化医疗的趋势;在无自身对照样本的情况下,一对多的分析方法能够更好地体现个体与健康群体的差别,辅助未知疾病的诊断和鉴别。尿液大分子的膜保存方式使得临床样本的保存更加简单经济。尿液生物标志物领域研究的进步需要政策和伦理的支持、资金和人力长期持续的投入以及大样本、大数据的辅助。本文综述了尿液生物标志物...     

Time‐dependent classification accuracy curve under marker‐dependent sampling

Evaluating the classification accuracy of a candidate biomarker signaling the onset of disease or disease status is essential for medical decision making. A good biomarker would accurately identify the patients who are likely to progress or die at a particular time in the future or who are in urgent need for active treatments. To assess the performance of a candidate biomarker, the receiver operating characteristic (ROC) curve and the area under the ROC curve (AUC) are commonly used. In many cases, the standard simple random sampling (SRS) design used for biomarker validation studies is costly and inefficient. In order to improve the efficiency and reduce the cost of biomarker validation, marker‐dependent sampling (MDS) may be used. In a MDS design, the selection of patients to assess true survival time is dependent on the result of a biomarker assay. In this article, we introduce a nonparametric estimator for time‐dependent AUC under a MDS design. The consistency and the asymptotic normality of the proposed estimator is established. Simulation shows the unbiasedness of the proposed estimator and a significant efficiency gain of the MDS design over the SRS design.     

Biologically functional molecules from mushroom-forming fungi*

Fungi including mushrooms have been proved to be an important biosource of numerous metabolites having a huge variety of chemical structures and diverse bioactivities. Metabolites of mushrooms are of remarkable importance as new lead compounds for medicine and agrochemicals. This review presents some of our studies on biologically functional molecules purified from mushroom-forming fungi; (1) endoplasmic reticulum stress suppressor, (2) osteoclast-forming suppressing compounds, (3) plant growth regulators.     

Neutral lipid fatty acid composition as trait and constraint in Collembola evolution

Functional traits determine the occurrence of species along environmental gradients and their coexistence with other species. Understanding how traits evolved among coexisting species helps to infer community assembly processes. We propose fatty acid composition in consumer tissue as a functional trait related to both food resources and physiological functions of species. We measured phylogenetic signal in fatty acid profiles of 13 field‐sampled Collembola (springtail) species and then combined the data with published fatty acid profiles of another 24 species. Collembola fatty acid profiles generally showed phylogenetic signal, with related species resembling each other. Long‐chain polyunsaturated fatty acids, related to physiological functions, demonstrated phylogenetic signal. In contrast, most food resource biomarker fatty acids and the ratios between bacterial, fungal, and plant biomarker fatty acids exhibited no phylogenetic signal. Presumably, fatty acids related to physiological functions have been constrained during Collembola evolutionary history: Species with close phylogenetic affinity experienced similar environments during divergence, while niche partitioning in food resources among closely related species favored species coexistence. Measuring phylogenetic signal in ecologically relevant traits of coexisting species provides an evolutionary perspective to contemporary assembly processes of ecological communities. Integrating phylogenetic comparative methods with community phylogenetic and trait‐based approaches may compensate for the limitations of each method when used alone and improve understanding of processes driving and maintaining assembly patterns.     

Polyphenols and health: Update and perspectives

Current issues in research on health effects by polyphenols are addressed. As to the cardiovascular system, flow-mediated dilation (FMD), a functional biomarker, can be used as surrogate marker for cardiovascular risk. Acute short-term effects peaking at 2 h after ingestion of polyphenol-rich food items are distinguished from longer-term effects over days and weeks. The role of polyphenol metabolites as bioactives is presented, underlining that specific target enzymes such as NADPH oxidases or lipoxygenases provide a basis for molecular action of polyphenols, rather than unspecific direct antioxidant effects. Cautionary words are given for the use of non-compositional assays of ‘total antioxidant capacity’ (TAC) in blood plasma. Enhanced interest emerges for polyphenols in the gastrointestinal tract. Recommendations for health professionals and the public are summarized, as well as prospects and challenges for future research.