Yeast Biotechnology 2.0

Yeasts are truly fascinating microorganisms. Due to their diverse and dynamic activities, they have been used for the production of many interesting products, such as beer, wine, bread, biofuels, and biopharmaceuticals. Saccharomyces cerevisiae (brewers’ or bakers’ yeast) is the yeast species that is surely the most exploited by humans. Saccharomyces is a top-choice organism for industrial applications, although its use for producing beer dates back to at least the 6th millennium BC. Bakers’ yeast has been a cornerstone of modern biotechnology, enabling the development of efficient production processes. Today, diverse yeast species are explored for industrial applications. This Special Issue “Yeast Biotechnology 2.0” is a continuation of the first Special Issue, “Yeast Biotechnology” (https://www.mdpi.com/books/pdfview/book/324). It compiles the current state-of-the-art of research and technology in the area of “yeast biotechnology” and highlights prominent current research directions in the fields of yeast synthetic biology and strain engineering, new developments in efficient biomolecule production, fermented beverages (beer, wine, and honey fermentation), and yeast nanobiotechnology.

Machine learning method for the classification of the state of living organisms’ oscillations

The World Health Organization highlights the urgent need to address the global threat posed by antibiotic-resistant bacteria. Efficient and rapid detection of bacterial response to antibiotics and their virulence state is crucial for the effective treatment of bacterial infections. However, current methods for investigating bacterial antibiotic response and metabolic state are time-consuming and lack accuracy. To address these limitations, we propose a novel method for classifying bacterial virulence based on statistical analysis of nanomotion recordings. We demonstrated the method by classifying living Bordetella pertussis bacteria in the virulent or avirulence phase, and dead bacteria, based on their cellular nanomotion signal. Our method offers significant advantages over current approaches, as it is faster and more accurate. Additionally, its versatility allows for the analysis of cellular nanomotion in various applications beyond bacterial virulence classification

Modulation of the nanoscale motion rate of Candida albicans by X-rays

IntroductionPatients undergoing cancer treatment by radiation therapy commonly develop Candida albicans infections (candidiasis). Such infections are generally treated by antifungals that unfortunately also induce numerous secondary effects in the patient. Additional to the effect on the immune system, ionizing radiation influences the vital activity of C. albicans cells themselves; however, the reaction of C. albicans to ionizing radiation acting simultaneously with antifungals is much less well documented. In this study, we explored the effects of ionizing radiation and an antifungal drug and their combined effect on C. albicans.MethodsThe study essentially relied on a novel technique, referred to as optical nanomotion detection (ONMD) that monitors the viability and metabolic activity of the yeast cells in a label and attachment-free manner.Results and discussionOur findings demonstrate that after exposure to X-ray radiation alone or in combination with fluconazole, low-frequency nanoscale oscillations of whole cells are suppressed and the nanomotion rate depends on the phase of the cell cycle, absorbed dose, fluconazole concentration, and post-irradiation period. In a further development, the ONMD method can help in rapidly determining the sensitivity of C. albicans to antifungals and the individual concentration of antifungals in cancer patients undergoing radiation therapy

DNA‐Interacting characteristics of the archaeal Rudiviral protein SIRV2_Gp1

Whereas the infection cycles of many bacterial and eukaryotic viruses have been characterized in detail, those of archaeal viruses remain largely unexplored. Recently, studies on a few model archaeal viruses such as SIRV2 (Sulfolobus islandicus rod‐shaped virus) have revealed an unusual lysis mechanism that involves the formation of pyramidal egress structures on the host cell surface. To expand understanding of the infection cycle of SIRV2, we aimed to functionally characterize gp1, which is a SIRV2 gene with unknown function. The SIRV2_Gp1 protein is highly expressed during early stages of infection and it is the only protein that is encoded twice on the viral genome. It harbours a helix‐turn‐helix motif and was therefore hypothesized to bind DNA. The DNA‐binding behavior of SIRV2_Gp1 was characterized with electrophoretic mobility shift assays and atomic force microscopy. We provide evidence that the protein interacts with DNA and that it forms large aggregates, thereby causing extreme condensation of the DNA. Furthermore, the N‐terminal domain of the protein mediates toxicity to the viral host Sulfolobus. Our findings may lead to biotechnological applications, such as the development of a toxic peptide for the containment of pathogenic bacteria, and add to our understanding of the Rudiviral infection cycle.Publisher PDFPeer reviewe

A universal fixation method based on quaternary ammonium salts (RNAlater) for omics-technologies: Saccharomyces cerevisiae as a case study

Abstract Genomics, transcriptomics, proteomics and fluxomics are powerful omics-technologies that play a major role in today's research. For each of these techniques good sample quality is crucial. Major factors contributing to the quality of a sample is the actual sampling procedure itself and the way the sample is stored directly after sampling. It has already been described that RNAlater can be used to store tissues and cells in a way that the RNA quality and quantity are preserved. In this paper, we demonstrate that quaternary ammonium salts (RNAlater) are also suitable to preserve and store samples from Saccharomyces cerevisiae for later use with the four major omics-technologies. Moreover, it is shown that RNAlater also preserves the cell morphology and the potential to recover growth, permitting microscopic analysis and yeast cell culturing at a later stage

Adhesins of Yeasts: Protein Structure and Interactions

The ability of yeast cells to adhere to other cells or substrates is crucial for many yeasts. The budding yeast Saccharomyces cerevisiae can switch from a unicellular lifestyle to a multicellular one. A crucial step in multicellular lifestyle adaptation is self-recognition, self-interaction, and adhesion to abiotic surfaces. Infectious yeast diseases such as candidiasis are initiated by the adhesion of the yeast cells to host cells. Adhesion is accomplished by adhesin proteins that are attached to the cell wall and stick out to interact with other cells or substrates. Protein structures give detailed insights into the molecular mechanism of adhesin-ligand interaction. Currently, only the structures of a very limited number of N-terminal adhesion domains of adhesins have been solved. Therefore, this review focuses on these adhesin protein families. The protein architectures, protein structures, and ligand interactions of the flocculation protein family of S. cerevisiae; the epithelial adhesion family of C. glabrata; and the agglutinin-like sequence protein family of C. albicans are reviewed and discussed

Yeast Biotechnology 4.0

This Special Issue is a continuation of the first, second, and third “Yeast Biotechnology” Special Issue series of the journal Fermentation (MDPI) [...

Micro- and Nanoscale Approaches in Antifungal Drug Discovery

Clinical needs for novel antifungal agents have increased due to the increase of people with a compromised immune system, the appearance of resistant fungi, and infections by unusual yeasts. The search for new molecular targets for antifungals has generated considerable research, especially using modern omics methods (genomics, genome-wide collections of mutants, and proteomics) and bioinformatics approaches. Recently, micro- and nanoscale approaches have been introduced in antifungal drug discovery. Microfluidic platforms have been developed, since they have a number of advantages compared to traditional multiwell-plate screening, such as low reagent consumption, the manipulation of a large number of cells simultaneously and independently, and ease of integrating numerous analytical standard operations and large-scale integration. Automated high-throughput antifungal drug screening is achievable by massive parallel processing. Various microfluidic antimicrobial susceptibility testing (AST) methods have been developed, since they can provide the result in a short time-frame, which is necessary for personalized medicine in the clinic. New nanosensors, based on detecting the nanomotions of cells, have been developed to further decrease the time to test antifungal susceptibility to a few minutes. Finally, nanoparticles (especially, silver nanoparticles) that demonstrated antifungal activity are reviewed

Yeast Biotechnology

Yeasts are truly fascinating microorganisms. Due to their diverse and dynamic activities, they have been used for the production of many interesting products, such as beer, wine, bread, biofuels, and biopharmaceuticals. Saccharomyces cerevisiae (brewers’ or bakers’ yeast) is the yeast species that is surely the most exploited by man. Saccharomyces is a top choice organism for industrial applications, although its use for producing beer dates back to at least the 6th millennium BC. Bakers’ yeast has been a cornerstone of modern biotechnology, enabling the development of efficient production processes. Today, diverse yeast species are explored for industrial applications. This Special Issue is focused on some recent developments of yeast biotechnology, i.e., bioethanol, wine and beer, and enzyme production. Additionally, the new field of yeast nanobiotechnology is introduced and reviewed

Yeast Biotechnology 2.0

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