A history of research on yeasts 2: Louis Pasteur and his contemporaries, 1850-1880

Exploring future applications of the apiculate yeast Hanseniaspora

As a metaphor, lemons get a bad rap; however the proverb 'if life gives you lemons, make lemonade' is often used in a motivational context. The same could be said of Hanseniaspora in winemaking. Despite its predominance in vineyards and grape must, this lemon-shaped yeast is underappreciated in terms of its contribution to the overall sensory profile of fine wine. Species belonging to this apiculate yeast are known for being common isolates not just on grape berries, but on many other fruits. They play a critical role in the early stages of a fermentation and can influence the quality of the final product. Their deliberate addition within mixed-culture fermentations shows promise in adding to the complexity of a wine and thus provide sensorial benefits. Hanseniaspora species are also key participants in the fermentations of a variety of other foodstuffs ranging from chocolate to apple cider. Outside of their role in fermentation, Hanseniaspora species have attractive biotechnological possibilities as revealed through studies on biocontrol potential, use as a whole-cell biocatalyst and important interactions with Drosophila flies. The growing amount of 'omics data on Hanseniaspora is revealing interesting features of the genus that sets it apart from the other Ascomycetes. This review collates the fields of research conducted on this apiculate yeast genus.

When the microbiome helps the brain-current evidence

The gut microbiota-brain axis has been recognized as a network of connections that provides communication between the gut microflora and both central and autonomic nervous system. The gut microbiota alteration has been targeted for therapy in various neurodegenerative and psychiatric disbalances. Psychobiotics are probiotics that contribute beneficially to the brain function and the host mental health as a result of an interaction with the commensal gut bacteria, although their mechanism of action has not been completely revealed. In this state-of-art review, the findings about the potential therapeutic effects of the psychobiotics alone or in combination with conventional medicine in the treatment of neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease, as well as in some psychiatric diseases like depression, schizophrenia, and bipolar disorder, have been summarized. The evidence of the psychobiotics therapeutic outcomes obtained in preclinical and clinical trials have been given respectively for the observed neurodegenerative and psychiatric disorders.

Development and Characterization of Cultured Buttermilk Fortified with Spirulina plantensis and Its Physico-Chemical and Functional Characteristics

In recent years, there has been an unprecedented increase in the demand for fermented dairy products due to medical recommendations and lifestyle preferences. Cultured buttermilk, as an ancient fermented dairy beverage, is an appropriate product choice in this context. This study presents a novel cultured buttermilk formulated by fortification with high protein microalgae Spirulina platensis, thus making it valuable and attractive because of its antioxidant properties. The fermentation process, nutraceutical properties, and sensory characteristics of developed cultured buttermilk with various concentrations of Spirulina (0.25, 0.5, and 1%) were compared with the control sample (0% Spirulina buttermilk). Different concentrations of Spirulina in buttermilk result in a significant increase in chlorophyll and carotenoid content, boosting its antioxidant properties. The study also evaluated the prebiotic properties of Spirulina, thus, demonstrating its ability to promote a healthy digestive system. It was found that the addition of 0.25% Spirulina was able to ferment the product more quickly and retained the sensory acceptability of the finished product. The protein content, free radical scavenging activity, chlorophyll, carotenoid, and total phenolic content of 0.25% Spirulina-fortified buttermilk was 1.83%, 48.19%, 30.9 mg/g, 8.24 mg/g, and 4.21 mg/g GAE, respectively. Based on the results obtained, it was concluded that cultured buttermilk with a high nutritional value and functional health benefits can be developed by fortification with 0.25% Spirulina as a natural ingredient.

Intestinal fungi and systemic autoimmune diseases

Nearly 20 years of studies have shown that fungi and the human immune system (non-specific immunity and specific immunity) and bacterial--fungal interactions maintain a balance that can't lead to diseases. Fungi--microorganism that lives in human intestine--may play an important role in human health and disease. Population studies and animal models in some diseases have found the changes in the diversity and composition of fungi. The dysregulation of the fungi can disrupt the normal "running" of the immune system and bacteria, which triggers the development of inflammatory diseases. The latest studies of fungi in inflammatory bowel disease, systemic lupus erythematosus, ankylosing spondylitis and type 1 diabetes mellitus were summarized. This review considers how the healthy host protect against the potential harm of intestinal fungi through the immune system and how fungal dysregulation alters host immunity.

The Role of Hypoxia in Brain Tumor Immune Responses

Oxygen is a vital component of living cells. Low levels of oxygen in body tissues, known as hypoxia, can affect multiple cellular functions across a variety of cell types and are a hallmark of brain tumors. In the tumor microenvironment, abnormal vasculature and enhanced oxygen consumption by tumor cells induce broad hypoxia that affects not only tumor cell characteristics but also the antitumor immune system. Although some immune reactions require hypoxia, hypoxia generally negatively affects immunity. Hypoxia induces tumor cell invasion, cellular adaptations to hypoxia, and tumor cell radioresistance. In addition, hypoxia limits the efficacy of immunotherapy and hinders antitumor responses. Therefore, understanding the role of hypoxia in the brain tumor, which usually does not respond to immunotherapy alone is important for the development of effective anti-tumor therapies. In this review, we discuss recent evidence supporting the role of hypoxia in the context of brain tumors.

A Preliminary Study of Yeast Strain Influence on Chemical and Sensory Characteristics of Apple Cider

During the fermentation of apple juice, yeast metabolism creates complex biosynthetic pathways which produce a range of compounds responsible for the organoleptic qualities of cider. In this study, basic cider quality parameters were measured to investigate the influence of six yeast strains on cider made from three apple varieties (‘Pink Lady’, ‘Sturmer’, and ‘Bulmer’s Norman’). Measurement of pH, titratable acidity, and total phenolic content revealed that yeast can influence cider attributes, albeit variety and season dependent. Descriptive sensory analysis using a trained sensory panel was conducted on cider made from ‘Pink Lady’ apples and the same six yeast strains. The sensory panel significantly differentiated the yeast strains on the attributes of ‘fresh apple’, ‘earthy’ and ‘pear’. Identifying the variety specific influence of individual yeast strains on chemical and sensory characteristics of apple cider will provide cider makers with an enhanced understanding when choosing yeast strains.

Probiotics for the Prevention of Antibiotic-Associated Diarrhea

Several communities have started using probiotic-rich fermented foods as therapeutic options with presumed medicinal powers. We now know the importance of microbiome balance and how probiotics can restore imbalances in the microbiome. Probiotics have been tested for a number of clinical uses such as the prevention of antibiotic-associated diarrhea (AAD), the treatment of various diseases such as H. pylori infection, irritable bowel disease, vaginitis, the prevention of allergies, and necrotizing enterocolitis in newborns. AAD has been the most indicated therapeutic use for probiotics. AAD is a common side effect of antibiotic usage, which affects up to 30% of patients. The hypothesis behind using probiotics for AAD is that they help normalize an unbalanced flora. There are many potential mechanisms by which probiotics support intestinal health such as (i) boosting immunity, (ii) increasing gut barrier integrity, (iii) producing antimicrobial substances, (iv) modulating the gut microbiome, (v) increasing water absorption, and (vi) decreasing opportunistic pathogens. Many randomized-controlled trials including the strain-specific trials that use Lactobacillus and Saccharomyces and meta-analyses have shown the benefits of probiotics in addressing AAD. Although adverse events have been reported for probiotics, these are broadly considered to be a safe and inexpensive preventative treatment option for AAD and other gastrointestinal disorders.

Endothelial Cell Metabolism in Vascular Functions

Simple Summary

Recent findings in the field of vascular biology are nourishing the idea that targeting the endothelial cell metabolism may be an alternative strategy to antiangiogenic therapy, as well as a novel therapeutic approach for cardiovascular disease. Deepening the molecular mechanisms regulating how ECs re-adapt their metabolic status in response to the changeable conditions of the tissue microenvironment may be beneficial to develop novel innovative treatments to counteract the aberrant growth of vasculature.

Abstract

The endothelium is the innermost layer of all blood and lymphatic vessels composed of a monolayer of specialized endothelial cells (ECs). It is regarded as a dynamic and multifunctional endocrine organ that takes part in essential processes, such as the control of blood fluidity, the modulation of vascular tone, the regulation of immune response and leukocyte trafficking into perivascular tissues, and angiogenesis. The inability of ECs to perform their normal biological functions, known as endothelial dysfunction, is multi-factorial; for instance, it implicates the failure of ECs to support the normal antithrombotic and anti-inflammatory status, resulting in the onset of unfavorable cardiovascular conditions such as atherosclerosis, coronary artery disease, hypertension, heart problems, and other vascular pathologies. Notably, it is emerging that the ability of ECs to adapt their metabolic status to persistent changes of the tissue microenvironment could be vital for the maintenance of vascular functions and to prevent adverse vascular events. The main purpose of the present article is to shed light on the unique metabolic plasticity of ECs as a prospective therapeutic target; this may lead to the development of novel strategies for cardiovascular diseases and cancer.

Aneuploidy influences the gene expression profiles in Saccharomyces pastorianus group I and II strains during fermentation

The lager yeasts, Saccharomyces pastorianus, are hybrids of Saccharomyces cerevisiae and Saccharomyces eubayanus and are divided into two broad groups, Group I and II. The two groups evolved from at least one common hybridisation event but have subsequently diverged with Group I strains losing many S. cerevisiae chromosomes while the Group II strains retain both sub-genomes. The complex genomes, containing orthologous alleles from the parental chromosomes, pose interesting questions regarding gene regulation and its impact on the fermentation properties of the strains. Superimposed on the presence of orthologous alleles are complexities of gene dosage due to the aneuploid nature of the genomes. We examined the contribution of the S. cerevisiae and S. eubayanus alleles to the gene expression patterns of representative Group I and II strains during fermentation. We show that the relative expression of S. cerevisiae and S. eubayanus orthologues is positively correlated with gene copy number. Despite the reduced S. cerevisiae content in the Group I strain, S. cerevisiae orthologues contribute to biochemical pathways upregulated during fermentation which may explain the retention of specific chromosomes in the strain. Conversely, S. eubayanus genes are significantly overrepresented in the upregulated gene pool in the Group II strain. Comparison of the transcription profiles of the strains during fermentation identified both common and unique gene expression patterns, with gene copy number being a dominant contributory factor. Thus, the aneuploid genomes create complex patterns of gene expression during fermentation with gene dosage playing a crucial role both within and between strains.

Saccharomyces pastorianus are yeasts used for making lager type beers and are natural hybrids of two other yeasts, Saccharomyces cerevisiae and Saccharomyces eubayanus. The hybrids formed just 500–600 years ago, and the combined parental genomes are responsible for the clean crisp flavours associated with lager beers. There are two types of lager yeasts: Group I strains have lost a significant portion of S. cerevisiae chromosomes, while the Group II strains contain the full S. cerevisiae complement. Both contain the full set of S. eubayanus chromosomes. An unusual consequence of the hybridisation is that the genomes of lager yeasts are aneuploid with the copy numbers of chromosomes ranging from 1–6. Aneuploidy is often associated with cancer in humans and therefore an understanding of how aneuploidy contributes to gene expression in lager yeasts may provide insights into its role in tumour cells. Here, we show that gene expression patterns are influenced by chromosomal aneuploidy with transcript levels directly correlated with gene dosage. We also examined the role played by the parental genomes in the gene expression profiles under fermentation conditions and show that while both genomes contribute to the transcript pools, S. eubayanus genes are over-represented during fermentation.

The Ecology and Evolution of the Baker’s Yeast Saccharomyces cerevisiae

The baker’s yeast Saccharomyces cerevisiae has become a powerful model in ecology and evolutionary biology. A global effort on field survey and population genetics and genomics of S. cerevisiae in past decades has shown that the yeast distributes ubiquitously in nature with clearly structured populations. The global genetic diversity of S. cerevisiae is mainly contributed by strains from Far East Asia, and the ancient basal lineages of the species have been found only in China, supporting an ‘out-of-China’ origin hypothesis. The wild and domesticated populations are clearly separated in phylogeny and exhibit hallmark differences in sexuality, heterozygosity, gene copy number variation (CNV), horizontal gene transfer (HGT) and introgression events, and maltose utilization ability. The domesticated strains from different niches generally form distinct lineages and harbor lineage-specific CNVs, HGTs and introgressions, which contribute to their adaptations to specific fermentation environments. However, whether the domesticated lineages originated from a single, or multiple domestication events is still hotly debated and the mechanism causing the diversification of the wild lineages remains to be illuminated. Further worldwide investigations on both wild and domesticated S. cerevisiae, especially in Africa and West Asia, will be helpful for a better understanding of the natural and domestication histories and evolution of S. cerevisiae.

Microbial Communities in Retail Draft Beers and the Biofilms They Produce

In the beer brewing industry, microbial spoilage presents a consistent threat that must be monitored and controlled to ensure the palatability of a finished product. Many of the predominant beer spoilage microbes have been identified and characterized, but the mechanisms of contamination and persistence remain an open area of study. Postproduction, many beers are distributed as kegs that are attached to draft delivery systems in retail settings where ample opportunities for microbial spoilage are present. As such, restaurants and bars can experience substantial costs and downtime for cleaning when beer draft lines become heavily contaminated. Spoilage monitoring on the retail side of the beer industry is often overlooked, yet this arena may represent one of the largest threats to the profitability of a beer if its flavor profile becomes substantially distorted by contaminating microbes. In this study, we sampled and cultured microbial communities found in beers dispensed from a retail draft system to identify the contaminating bacteria and yeasts. We also evaluated their capability to establish new biofilms in a controlled setting. Among four tested beer types, we identified over a hundred different contaminant bacteria and nearly 20 wild yeasts. The culturing experiments demonstrated that most of these microbes were viable and capable of joining new biofilm communities. These data provide an important reference for monitoring specific beer spoilage microbes in draft systems and we provide suggestions for cleaning protocol improvements.

IMPORTANCE Beer production, packaging, and service are each vulnerable to contamination by microbes that metabolize beer chemicals and impart undesirable flavors, which can result in the disposal of entire batches. Therefore, great effort is taken by brewmasters to reduce and monitor contamination during production and packaging. A commonly overlooked quality control stage of a beer supply chain is at the retail service end, where beer kegs supply draft lines in bars and restaurants under nonsterile conditions. We found that retail draft line contamination is rampant and that routine line cleaning methods are insufficient to efficiently suppress beer spoilage. Thus, many customers unknowingly consume spoiled versions of the beers they consume. This study identified the bacteria and yeast that were resident in retail draft beer samples and also investigated their abilities to colonize tubing material as members of biofilm communities.

An Updated Global Species Diversity and Phylogeny in the Genus Wickerhamomyces with Addition of Two New Species from Thailand

Ascomycetous yeast species in the genus Wickerhamomyces (Saccharomycetales, Wickerhamomycetaceae) are isolated from various habitats and distributed throughout the world. Prior to this study, 35 species had been validly published and accepted into this genus. Beneficially, Wickerhamomyces species have been used in a number of biotechnologically applications of environment, food, beverage industries, biofuel, medicine and agriculture. However, in some studies, Wickerhamomyces species have been identified as an opportunistic human pathogen. Through an overview of diversity, taxonomy and recently published literature, we have updated a brief review of Wickerhamomyces. Moreover, two new Wickerhamomyces species were isolated from the soil samples of Assam tea (Camellia sinensis var. assamica) that were collected from plantations in northern Thailand. Herein, we have identified these species as W. lannaensis and W. nanensis. The identification of these species was based on phenotypic (morphological, biochemical and physiological characteristics) and molecular analyses. Phylogenetic analyses of a combination of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit (LSU) of ribosomal DNA genes support that W. lannaensis and W. nanensis are distinct from other species within the genus Wickerhamomyces. A full description, illustrations and a phylogenetic tree showing the position of both new species have been provided. Accordingly, a new combination species, W. myanmarensis has been proposed based on the phylogenetic results. A new key for species identification is provided.

Optogenetic Tools for Control of Public Goods in Saccharomyces cerevisiae

Microorganisms live in dense and diverse communities, with interactions between cells guiding community development and phenotype. The ability to perturb specific intercellular interactions in space and time provides a powerful route to determining the critical interactions and design rules for microbial communities. Approaches using optogenetic tools to modulate these interactions offer promise, as light can be exquisitely controlled in space and time. We report new plasmids for rapid integration of an optogenetic system into Saccharomyces cerevisiae to engineer light control of expression of a gene of interest. In a proof-of-principle study, we demonstrate the ability to control a model cooperative interaction, namely, the expression of the enzyme invertase (SUC2) which allows S. cerevisiae to hydrolyze sucrose and utilize it as a carbon source. We demonstrate that the strength of this cooperative interaction can be tuned in space and time by modulating light intensity and through spatial control of illumination. Spatial control of light allows cooperators and cheaters to be spatially segregated, and we show that the interplay between cooperative and inhibitory interactions in space can lead to pattern formation. Our strategy can be applied to achieve spatiotemporal control of expression of a gene of interest in S. cerevisiae to perturb both intercellular and interspecies interactions.

IMPORTANCE Recent advances in microbial ecology have highlighted the importance of intercellular interactions in controlling the development, composition, and resilience of microbial communities. In order to better understand the role of these interactions in governing community development, it is critical to be able to alter them in a controlled manner. Optogenetically controlled interactions offer advantages over static perturbations or chemically controlled interactions, as light can be manipulated in space and time and does not require the addition of nutrients or antibiotics. Here, we report a system for rapidly achieving light control of a gene of interest in the important model organism Saccharomyces cerevisiae and demonstrate that by controlling expression of the enzyme invertase, we can control cooperative interactions. This approach will be useful for understanding intercellular and interspecies interactions in natural and synthetic microbial consortia containing S. cerevisiae and serves as a proof of principle for implementing this approach in other consortia.

Hanseniaspora vineae and the Concept of Friendly Yeasts to Increase Autochthonous Wine Flavor Diversity

In this perspective, we will explain the concept of “friendly” yeasts for developing wine starters that do not suppress desirable native microbial flora at the initial steps of fermentation, as what usually happens with Saccharomyces strains. Some non-Saccharomyces strains might allow the development of yeast consortia with the native terroir microflora of grapes and its region. The positive contribution of non-Saccharomyces yeasts was underestimated for decades. Avoiding them as spoilage strains and off-flavor producers was the main objective in winemaking. It is understandable, as in our experience after more than 30 years of wine yeast selection, it was shown that no more than 10% of the isolated native strains were positive contributors of superior flavors. Some species that systematically gave desirable flavors during these screening processes were Hanseniaspora vineae and Metschnikowia fructicola. In contrast to the latter, H. vineae is an active fermentative species, and this fact helped to build an improved juice ecosystem, avoiding contaminations of aerobic bacteria and yeasts. Furthermore, this species has a complementary secondary metabolism with S. cerevisiae, increasing flavor complexity with benzenoid and phenylpropanoid synthetic pathways practically inexistent in conventional yeast starters. How does H. vineae share the fermentation niche with other yeast strains? It might be due to the friendly conditions it creates, such as ideal low temperatures and low nitrogen demand during fermentation, reduced synthesis of medium-chain fatty acids, and a rich acetylation capacity of aromatic higher alcohols, well-known inhibitors of many yeasts. We will discuss here how inoculation of H. vineae strains can give the winemaker an opportunity to develop ideal conditions for flavor expression of the microbial terroir without the risk of undesirable strains that can result from spontaneous yeast fermentations.

Endothelial metabolism in pulmonary vascular homeostasis and acute respiratory distress syndrome

Capillary endothelial cells possess a specialized metabolism necessary to adapt to the unique alveolar-capillary environment. Here, we highlight how endothelial metabolism preserves the integrity of the pulmonary circulation by controlling vascular permeability, defending against oxidative stress, facilitating rapid migration and angiogenesis in response to injury, and regulating the epigenetic landscape of endothelial cells. Recent reports on single-cell RNA-sequencing reveal subpopulations of pulmonary capillary endothelial cells with distinctive reparative capacities, which potentially offer new insight into their metabolic signature. Lastly, we discuss broad implications of pulmonary vascular metabolism on acute respiratory distress syndrome, touching on emerging findings of endotheliitis in coronavirus disease 2019 (COVID-19) lungs.

Health-promoting properties of Saccharomyces cerevisiae var. boulardii as a probiotic; characteristics, isolation, and applications in dairy products

Saccharomyces cerevisiae var. boulardii (S. boulardii) has been isolated from lychee (Litchi chinensis), mangosteen fruit, kombucha, and dairy products like kefir. Dairy products containing S. boulardii have been revealed to possess potential probiotic activities owing to their ability to produce organic acids, essential enzymes, vitamins, and other important metabolites such as vanillic acid, phenyl ethyl alcohol, and erythromycin. S. boulardii has a wide spectrum of anti-carcinogenic, antibacterial antiviral, and antioxidant activity, and is known to reduce serum cholesterol levels. However, this yeast has mainly been prescribed for prophylaxis treatment of gastrointestinal infectious diseases, and stimulating the immune system in a number of commercially available products. The present comprehensive review article reviews the properties of S. boulardii related to their use in fermented dairy foods as a probiotic microorganism or starter culture. Technical aspects regarding the integration of this yeast into the dairy foods matrix its health advantages, therapeutic functions, microencapsulation, and viability in harsh conditions, and safety aspects are highlighted.

Packing a punch: understanding how flavours are produced in lager fermentations

Beer is one of the most popular beverages in the world and it has an irreplaceable place in culture. Although invented later than ale, lager beers dominate the current market. Many factors relating to the appearance (colour, clarity and foam stability) and sensory characters (flavour, taste and aroma) of beer, and other psychological determinants affect consumers' perception of the product and defines its drinkability. This review takes a wholistic approach to scrutinise flavour generation in the brewing process, focusing particularly on the contribution of the raw ingredients and the yeasts to the final flavour profiles of lager beers. In addition, we examine current developments to improve lager beer flavour profiles for the modern consumers.

Understanding Human Microbiota Offers Novel and Promising Therapeutic Options against Candida Infections

Human fungal pathogens particularly of Candida species are one of the major causes of hospital acquired infections in immunocompromised patients. The limited arsenal of antifungal drugs to treat Candida infections with concomitant evolution of multidrug resistant strains further complicates the management of these infections. Therefore, deployment of novel strategies to surmount the Candida infections requires immediate attention. The human body is a dynamic ecosystem having microbiota usually involving symbionts that benefit from the host, but in turn may act as commensal organisms or affect positively (mutualism) or negatively (pathogenic) the physiology and nourishment of the host. The composition of human microbiota has garnered a lot of recent attention, and despite the common occurrence of Candida spp. within the microbiota, there is still an incomplete picture of relationships between Candida spp. and other microorganism, as well as how such associations are governed. These relationships could be important to have a more holistic understanding of the human microbiota and its connection to Candida infections. Understanding the mechanisms behind commensalism and pathogenesis is vital for the development of efficient therapeutic strategies for these Candida infections. The concept of host-microbiota crosstalk plays critical roles in human health and microbiota dysbiosis and is responsible for various pathologies. Through this review, we attempted to analyze the types of human microbiota and provide an update on the current understanding in the context of health and Candida infections. The information in this article will help as a resource for development of targeted microbial therapies such as pre-/pro-biotics and microbiota transplant that has gained advantage in recent times over antibiotics and established as novel therapeutic strategy.

History and Domestication of Saccharomyces cerevisiae in Bread Baking

The yeast Saccharomyces cerevisiae has been instrumental in the fermentation of foods and beverages for millennia. In addition to fermentations like wine, beer, cider, sake, and bread, S. cerevisiae has been isolated from environments ranging from soil and trees, to human clinical isolates. Each of these environments has unique selection pressures that S. cerevisiae must adapt to. Bread dough, for example, requires S. cerevisiae to efficiently utilize the complex sugar maltose; tolerate osmotic stress due to the semi-solid state of dough, high salt, and high sugar content of some doughs; withstand various processing conditions, including freezing and drying; and produce desirable aromas and flavors. In this review, we explore the history of bread that gave rise to modern commercial baking yeast, and the genetic and genomic changes that accompanied this. We illustrate the genetic and phenotypic variation that has been documented in baking strains and wild strains, and how this variation might be used for baking strain improvement. While we continue to improve our understanding of how baking strains have adapted to bread dough, we conclude by highlighting some of the remaining open questions in the field.

The Role of Pi, Glutamine and the Essential Amino Acids in Modulating the Metabolism in Diabetes and Cancer

Purpose

Re-examine the current metabolic models.

Methods

Review of literature and gene networks.

Results

Insulin activates Pi uptake, glutamine metabolism to stabilise lipid membranes. Tissue turnover maintains the metabolic health. Current model of intermediary metabolism (IM) suggests glucose is the source of energy, and anaplerotic entry of fatty acids and amino acids into mitochondria increases the oxidative capacity of the TCA cycle to produce the energy (ATP). The reduced cofactors, NADH and FADH2, have different roles in regulating the oxidation of nutrients, membrane potentials and biosynthesis. Trans-hydrogenation of NADH to NADPH activates the biosynthesis. FADH2 sustains the membrane potential during the cell transformations. Glycolytic enzymes assume the non-canonical moonlighting functions, enter the nucleus to remodel the genetic programmes to affect the tissue turnover for efficient use of nutrients. Glycosylation of the CD98 (4F2HC) stabilises the nutrient transporters and regulates the entry of cysteine, glutamine and BCAA into the cells. A reciprocal relationship between the leucine and glutamine entry into cells regulates the cholesterol and fatty acid synthesis and homeostasis in cells. Insulin promotes the Pi transport from the blood to tissues, activates the mitochondrial respiratory activity, and glutamine metabolism, which activates the synthesis of cholesterol and the de novo fatty acids for reorganising and stabilising the lipid membranes for nutrient transport and signal transduction in response to fluctuations in the microenvironmental cues. Fatty acids provide the lipid metabolites, activate the second messengers and protein kinases. Insulin resistance suppresses the lipid raft formation and the mitotic slippage activates the fibrosis and slow death pathways.

Impact of the Physicochemical Composition and Microbial Diversity in Apple Juice Fermentation Process: A Review

Fermented apple beverages are produced all over the world with diverse characteristics associated with each country. Despite the diversifications, cider producers are confronted with similar issues and risks. The nature of the raw material, also known as the fermentation medium, plays a key role in fermentation. A well-defined composition of apples is, therefore, required to produce cider with good quality. In addition, ferment and its metabolism are important factors in the fermentation process. The producers of cider and other alcoholic beverages are looking in general for novel yeast strains or for the use of native strains to produce "authentic" and diversified beverages that are distinct from each other, and that attract more and more consumers. Research articles on cider production are infrequent compared to wine production, especially on the impact of the chemical composition and microbial diversity of apples on fermentation. Even though the processing of fermented beverages is close in terms of microbial interactions and production, the study of the specific properties of apples and the production challenges of cider production is advantageous and meaningful for cider producers. This review summarizes the current knowledge on apple composition and the impact of the must composition on fermentation and yeast growth. In addition, the microbial diversity of cider, activities, and its influence on fermentation are reviewed.

Tumor Hypoxia: Impact on Radiation Therapy and Molecular Pathways

Tumor hypoxia is a common feature of the microenvironment in solid tumors, primarily due to an inadequate, and heterogeneous vascular network. It is associated with resistance to radiotherapy and results in a poorer clinical outcome. The presence of hypoxia in tumors can be identified by various invasive and non-invasive techniques, and there are a number of approaches by which hypoxia can be modified to improve outcome. However, despite these factors and the ongoing extensive pre-clinical studies, the clinical focus on hypoxia is still to a large extent lacking. Hypoxia is a major cellular stress factor and affects a wide range of molecular pathways, and further understanding of the molecular processes involved may lead to greater clinical applicability of hypoxic modifiers. This review is a discussion of the characteristics of tumor hypoxia, hypoxia-related molecular pathways, and the role of hypoxia in treatment resistance. Understanding the molecular aspects of hypoxia will improve our ability to clinically monitor hypoxia and to predict and modify the therapeutic response.

Suitability of the Lebanese “Ace Spur” Apple Variety for Cider Production Using Hanseniaspora sp. Yeast

In the present research work, the physicochemical and fermentative properties of the “Ace spur” apple variety, obtained from a Lebanese farm, and the “Kermerrien” variety, obtained from a French cider industry, were investigated. The pomological properties were first determined for both varieties showing significant differences in the shapes and sizes. Sugar content, titratable acidity, soluble solids, and pH values were then determined. The potential of the “Ace spur” apple juice was then evaluated using the yeast strain Hanseniaspora sp., a major yeast found during the spontaneous fermentation of apples. “Ace spur” apples contained more sugars while the “Kermerrien” cultivar had a highest malic acid and polyphenol concentrations. After 100 h of fermentation, the ethanol percentage (v/v) was around 4% in both ciders. Results obtained in this work revealed the chemical potential of the Lebanese apple juice to produce cider.

Anti-Contamination Strategies for Yeast Fermentations

Yeasts are very useful microorganisms that are used in many industrial fermentation processes such as food and alcohol production. Microbial contamination of such processes is inevitable, since most of the fermentation substrates are not sterile. Contamination can cause a reduction of the final product concentration and render industrial yeast strains unable to be reused. Alternative approaches to controlling contamination, including the use of antibiotics, have been developed and proposed as solutions. However, more efficient and industry-friendly approaches are needed for use in industrial applications. This review covers: (i) general information about industrial uses of yeast fermentation, (ii) microbial contamination and its effects on yeast fermentation, and (iii) currently used and suggested approaches/strategies for controlling microbial contamination at the industrial and/or laboratory scale.

Utility of Feed Enzymes and Yeast Derivatives in Ameliorating Deleterious Effects of Coccidiosis on Intestinal Health and Function in Broiler Chickens

Coccidiosis induced necrotic lesions impair digestive capacity and barrier function in concurrence with increased risks for secondary bacterial infections. The industry has been successful in controlling coccidiosis with anticoccidials and vaccination. However, concerns over Eimeria species resistant to anticoccidials, gaps in vaccination and restriction on antibiotics is stimulating research and application of alternative and/or complimentary strategies for coccidiosis control. The aim of this paper is to appraise literature on the utility of feed enzymes and yeast derivatives in modulating coccidiosis. Feed enzymes can complement endogenous enzymes (protease, amylase, and lipase) that may become insufficient in coccidiosis afflicted birds. Coccidiosis in the upper small intestine creates conditions that enhances efficacy of phytase and there are reports indicating supplemental phytase can mitigate the negative impact of coccidiosis on bone quality. Increase in intestinal short chain fatty acids due supplemental fiber degrading enzymes has been linked with reduced survivability of Eimeria. There is evidence whole yeast (live or dead) and derivatives can modulate coccidiosis. Immunomudulation properties of the yeast derivatives have been shown to enhance cellular and humoral immunity in Eimeria challenge models which is critical for effectiveness of coccidial vaccination. Moreover, yeast nucleotides have been shown to be beneficial in stimulating healing of intestinal mucosal surface. Other novel work has shown that certain yeast cells can produce derivatives with anticoccidial compounds effective in attenuating oocysts shedding. Yeast cell surface has also been shown to be an effective oral Eimeria vaccine delivery vehicle. Overall, while further refinement research is warranted to address inconsistencies in responses and commercial application, there is evidence feed enzymes and yeast derivatives could complement strategies for maintaining intestinal function to bolster growth performance in broilers compromised with coccidiosis. However, broilers receive diets containing several feed additives with distinct mode of actions and yet there is dearth of empirical data on the expected responses.Future evaluations should consider combinations of additives to document animal responses and potential synergies.

A Hands-On Guide to Brewing and Analyzing Beer in the Laboratory

Beer would not exist without microbes. During fermentation, yeast cells convert cereal‐derived sugars into ethanol and CO₂. Yeast also produces a wide array of aroma compounds that influence beer taste and aroma. The complex interaction between all these aroma compounds results in each beer having its own distinctive palette. This article contains all protocols needed to brew beer in a standard lab environment and focuses on the use of yeast in beer brewing. More specifically, it provides protocols for yeast propagation, brewing calculations and, of course, beer brewing. At the end, we have also included protocols for analyses that can be performed on the resulting brew, with a focus on yeast‐derived aroma compounds. © 2019 The Authors.

Free Amino Nitrogen in Brewing

The role of nitrogenous components in malt and wort during the production of beer has long been recognized. The concentration and range of wort amino acids impact on ethanolic fermentation by yeast and on the production of a range of flavour and aroma compounds in the final beer. This review summarizes research on Free Amino Nitrogen (FAN) within brewing, including various methods of analysis.

Mechanisms of Yeast Adaptation to Wine Fermentations

Cells face genetic and/or environmental changes in order to outlast and proliferate. Characterization of changes after stress at different "omics" levels is crucial to understand the adaptation of yeast to changing conditions. Wine fermentation is a stressful situation which yeast cells have to cope with. Genome-wide analyses extend our cellular physiology knowledge by pointing out the mechanisms that contribute to sense the stress caused by these perturbations (temperature, ethanol, sulfites, nitrogen, etc.) and related signaling pathways. The model organism, Saccharomyces cerevisiae, was studied in response to industrial stresses and changes at different cellular levels (transcriptomic, proteomic, and metabolomics), which were followed statically and/or dynamically in the short and long terms. This chapter focuses on the response of yeast cells to the diverse stress situations that occur during wine fermentations, which induce perturbations, including nutritional changes, ethanol stress, temperature stress, oxidative stress, etc.

Environmental potential of the use of CO2 from alcoholic fermentation processes. The CO2-AFP strategy

A novel Carbon Dioxide Utilization (CDU) approach from a relatively minor CO2 emission source, i.e., alcoholic fermentation processes (AFP), is presented. The CO2 produced as a by-product from the AFP is estimated by examining the EtOH consumed per year reported by the World Health Organization in 2014. It is proposed that the extremely pure CO2 from the AFP is captured in NaOH solutions to produce one of the Top 10 commodities in the chemical industry, Na2CO3, as a good example of an atomic economy process. The novel CDU strategy could yield over 30.6Mt of Na2CO3 in oversaturated aqueous solution on using ca. 12.7Mt of captured CO2 and this process would consume less energy than the synthetic methodology (Solvay ammonia soda process) and would not produce low-value by-products. The quantity of Na2CO3 obtained by this strategy could represent ca. 50% of the world Na2CO3 production in one year. In terms of the green economy, the viability of the strategy is discussed according to the recommendations of the CO2Chem network, and an estimation of the CO2negative emission achieved suggests a capture of around 280.0Mt of CO2 from now to 2020 or ca. 1.9Gt from now to 2050. Finally, the results obtained for this new CDU proposal are discussed by considering different scenarios; the CO2 production in a typical winemaking corporation, the CO2 released in the most relevant wine-producing countries, and the use of CO2 from AFP as an alternative for the top Na2CO3-producing countries.

Past and Future of Non-Saccharomyces Yeasts: From Spoilage Microorganisms to Biotechnological Tools for Improving Wine Aroma Complexity

It is well established that non-Saccharomyces wine yeasts, considered in the past as undesired or spoilage yeasts, can enhance the analytical composition, and aroma profile of the wine. The contribution of non-Saccharomyces yeasts, including the ability to secret enzymes and produce secondary metabolites, glycerol and ethanol, release of mannoproteins or contributions to color stability, is species- and strain-specific, pointing out the key importance of a clever strain selection. The use of mixed starters of selected non-Saccharomyces yeasts with strains of Saccharomyces cerevisiae represents an alternative to both spontaneous and inoculated wine fermentations, taking advantage of the potential positive role that non-Saccharomyces wine yeast species play in the organoleptic characteristics of wine. In this context mixed starters can meet the growing demand for new and improved wine yeast strains adapted to different types and styles of wine. With the aim of presenting old and new evidences on the potential of non-Saccharomyces yeasts to address this market trend, we mainly review the studies focused on non-Saccharomyces strain selection and design of mixed starters directed to improve primary and secondary aroma of wines. The ability of non-Saccharomyces wine yeasts to produce enzymes and metabolites of oenological relevance is also discussed.

From yaks to yogurt: the history, development, and current use of probiotics

The development of probiotics, which are living bacteria or yeasts used to confer a health benefit on the host, has paralleled our research in food preservation, microbiologic identification techniques, and our understanding of how the complex interactions in microbiota impact the host's health and recovery from disease. This review briefly describes the history of probiotics, where probiotic strains were originally isolated, and the types of probiotic products currently available on the global market. In addition, the uses or indications for these probiotics are described, along with the types of clinical investigations that have been done. Continuing challenges persist for the proper probiotic strain identification, regulatory pathways, and how healthcare providers can choose a specific strain to recommend to their patients.

Simultaneous Hypoxia and Low Extracellular pH Suppress Overall Metabolic Rate and Protein Synthesis In Vitro

BACKGROUND

The tumor microenvironment is characterized by regions of hypoxia and acidosis which are linked to poor prognosis. This occurs due to an aberrant vasculature as well as high rates of glycolysis and lactate production in tumor cells even in the presence of oxygen (the Warburg effect), which weakens the spatial linkage between hypoxia and acidosis.

METHODS

Five different human squamous cell carcinoma cell lines (SiHa, FaDuDD, UTSCC5, UTSCC14 and UTSCC15) were treated with hypoxia, acidosis (pH 6.3), or a combination, and gene expression analyzed using microarray. SiHa and FaDuDD were chosen for further characterization of cell energetics and protein synthesis. Total cellular ATP turnover and relative glycolytic dependency was determined by simultaneous measurements of oxygen consumption and lactate synthesis rates and total protein synthesis was determined by autoradiographic quantification of the incorporation of 35S-labelled methionine and cysteine into protein.

RESULTS

Microarray analysis allowed differentiation between genes induced at low oxygen only at normal extracellular pH (pHe), genes induced at low oxygen at both normal and low pHe, and genes induced at low pHe independent of oxygen concentration. Several genes were found to be upregulated by acidosis independent of oxygenation. Acidosis resulted in a more wide-scale change in gene expression profiles than hypoxia including upregulation of genes involved in the translation process, for example Eukaryotic translation initiation factor 4A, isoform 2 (EIF4A2), and Ribosomal protein L37 (RPL37). Acidosis suppressed overall ATP turnover and protein synthesis by 50%. Protein synthesis, but not total ATP production, was also suppressed under hypoxic conditions. A dramatic decrease in ATP turnover (SiHa) and protein synthesis (both cell lines) was observed when hypoxia and low pHe were combined.

CONCLUSIONS

We demonstrate here that the influence of hypoxia and acidosis causes different responses, both in gene expression and in de novo protein synthesis, depending on whether the two factors induced alone or overlapping, and as such it is important for in vivo studies to take this into account.

Sucrose utilization in budding yeast as a model for the origin of undifferentiated multicellularity

We use the budding yeast, Saccharomyces cerevisiae, to investigate one model for the initial emergence of multicellularity: the formation of multicellular aggregates as a result of incomplete cell separation. We combine simulations with experiments to show how the use of secreted public goods favors the formation of multicellular aggregates. Yeast cells can cooperate by secreting invertase, an enzyme that digests sucrose into monosaccharides, and many wild isolates are multicellular because cell walls remain attached to each other after the cells divide. We manipulate invertase secretion and cell attachment, and show that multicellular clumps have two advantages over single cells: they grow under conditions where single cells cannot and they compete better against cheaters, cells that do not make invertase. We propose that the prior use of public goods led to selection for the incomplete cell separation that first produced multicellularity.

The evolution of multicellularity is one of the major steps in the history of life and has occurred many times independently. Despite this, we do not understand how and why single-celled organisms first joined together to form multicellular clumps of cells. Here, we show that clumps of cells can cooperate, using secreted enzymes, to collect food from the environment. In nature, the budding yeast Saccharomyces cerevisiae grows as multicellular clumps and secretes invertase, an enzyme that breaks down sucrose into smaller sugars (glucose and fructose) that cells can import. We genetically manipulate both clumping and secretion to show that multicellular clumps of cells can grow when sucrose is scarce, whereas single cells cannot. In addition, we find that clumps of cells have an advantage when competing against “cheating” cells that import sugars but do not make invertase. Since the evolution of secreted enzymes predates the origin of multicellularity, we argue that the social benefits conferred by secreted enzymes were the driving force for the evolution of cell clumps that were the first, primitive form of multicellular life.

The yin and yang of yeast: biodiversity research and systems biology as complementary forces driving innovation in biotechnology

The aim of this article is to review how yeast has contributed to contemporary biotechnology and to seek underlying principles relevant to its future exploitation for human benefit. Recent advances in systems biology combined with new knowledge of genome diversity promise to make yeast the eukaryotic workhorse of choice for production of everything from probiotics and pharmaceuticals to fuels and chemicals. The ability to engineer new capabilities through introduction of controlled diversity based on a complete understanding of genome complexity and metabolic flux is key. Here, we briefly summarise the history that has led to these apparently simple organisms being employed in such a broad range of commercial applications. Subsequently, we discuss the likely consequences of current yeast research for the future of biotechnological innovation.

Improvement of Saccharomyces yeast strains used in brewing, wine making and baking

Yeast was the first microorganism domesticated by mankind. Indeed, the production of bread and alcoholic beverages such as beer and wine dates from antiquity, even though the fact that the origin of alcoholic fermentation is a microorganism was not known until the nineteenth century. The use of starter cultures in yeast industries became a common practice after methods for the isolation of pure yeast strains were developed. Moreover, effort has been undertaken to improve these strains, first by classical genetic methods and later by genetic engineering. In general, yeast strain development has aimed at improving the velocity and efficiency of the respective production process and the quality of the final products. This review highlights the achievements in genetic engineering of Saccharomyces yeast strains applied in food and beverage industry.

Yeast systems biology: modelling the winemaker's art

Yeast research represents an important nexus between fundamental and applied research. Just as fundamental yeast research transitioned from classical, reductionist strategies to whole-genome techniques, whole-genome studies are advancing to the next level of biological research, referred to as systems biology. Industries that rely on high-performing yeast, such as the wine industry, are therefore poised to reap the many benefits that systems biology can provide. This includes the promise of strain development at speeds and costs which are unobtainable using current techniques. This article reviews the current state of whole-genome techniques available to yeast researchers and outlines how these processes can be used to obtain 'systems-level' information to provide insights into winemaking.