Journal of Bioscience and Bioengineering

Genome co-editing technology is effective in breeding filamentous fungi for applications in the fermentation industry, achieving site-directed mutagenesis, the status of non-genetically modified organisms (non-GMOs), and wild-type-like growth phenotype. Prior to this study, thiI gene was found as a selectable marker for such genome co-editing in the filamentous fungus Aspergillus oryzae, while it cannot be reused via marker recycling. Therefore, we aimed to identify another marker gene to knock out another target gene via genome co-editing in A...

In recent years, the demand for beers with a variety of flavors has increased considerably owing to the diversification of consumer preferences. Sour beer is characterized by a sour taste unlike normal beer flavor, and previous studies on sour beer have been primarily focused on addressing issues, such as inconsistent product quality and long production time, and on the associated microorganisms. Scientific knowledge regarding the characteristic flavor of sour beer and flavor components is limited. Therefore, in this study, we aimed to clarify the characteristic sensory attributes of sour beer and the component profiles that explain these attributes...

Antibody drugs play a vital role in diagnostics and therapy. However, producing antibodies from mammalian cells is challenging owing to cellular heterogeneity, which can be addressed by applying droplet-based microfluidic platforms for high-throughput screening (HTS). Here, we designed an integrated system based on disulfide-bonded redox-responsive hydrogel beads (redox-HBs), which were prepared through enzymatic hydrogelation, to compartmentalize, screen, select, retrieve, and recover selected Chinese hamster ovary (CHO) cells secreting high levels of antibodies...

Mucilage is a gelatinous and sticky hydrophilic polysaccharide released from epidermal cells of seed coat after the hydration of mature seeds and is composed primarily of unbranched rhamnogalacturonan I (RG-I). In this study, we produced a recombinant endo-RG-I hydrolase from Aspergillus aculeatus (AaRhgA) in the fission yeast Schizosaccharomyces pombe and examined its substrate preference for pyridylaminated (PA) RG-I with the various degrees of polymerization (DP). Recombinant AaRhgA requires PA-RG-I with a DP of 10 or higher for its hydrolase activity...

Cell culture models that mimic tissue environments are useful for cell and extracellular matrix (ECM) function analysis. Decellularized tissues with tissue-specific ECM are expected to be applied as cell culture scaffolds, however, it is often difficult for seeded cells to permeate their structures. In this study, we evaluated the adhesion and proliferation of mouse fibroblasts seeded onto decellularized bone marrow scaffolds that we fabricated from adult and fetal porcine. Decellularized fetal bone marrow displays more cell attachment and faster cell proliferation than decellularized adult bone marrow...

A new extracellular protease from Bacillus subtilis strain MPK with collagenolytic activity was isolated and purified. Fish skin which otherwise would be treated as waste is used as substrate for the production of protease. Using various techniques such as ammonium sulphate precipitation and ion exchange chromatography, protease was purified and characterized subsequently. Protease of approximately 61 kDa molecular weight was purified by 135.7-fold with 18.42% enzyme recovery. The protease showed effective properties like pH and temperature stability over a broad range with optimum pH 7...

6-(Methylsulfinyl)hexyl isothiocyanate (6-MSITC), a derivative of glucosinolate with a six-carbon chain, is a compound found in wasabi and has diverse health-promoting properties. The biosynthesis of glucosinolates from methionine depends on a crucial step catalyzed methylthioalkylmalate synthases (MAMs), which are responsible for the generation of glucosinolates with varying chain lengths. In this study, our primary focus was the characterization of two methylthioalkyl malate synthases, MAM1-1 and MAM1-2, derived from Eutrema japonicum, commonly referred to as Japanese wasabi...

Unable to move on their own, plants have acquired the ability to produce a wide variety of low molecular weight compounds to survive against various stresses. It is estimated that there are as many as one million different kinds. Plants also have the ability to accumulate high levels of proteins. Although plant-based bioproduction has traditionally relied on classical tissue culture methods, the attraction of bioproduction by plants is increasing with the development of omics and bioinformatics and other various technologies, as well as synthetic biology...

Among different microbial-induced calcium carbonate precipitation (MICCP) mechanisms utilized for biomineralization, ureolysis leads to the greatest yields of calcium carbonate. Unfortunately, it is reported that urea-induced growth inhibition can delay urea hydrolysis but it is not clear how this affects MICCP kinetics. This study investigated the impact of urea addition on the MICCP performance of Lysinibacillus sphaericus MB284 not previously grown on urea (thereafter named bio-agents), compared with those previously cultured in urea-rich media (20 g/L) (hereafter named bio-agents+ or bio-agents-plus)...

Kopyor is a coconut with unique characteristics from Indonesia, one of the largest coconut producers in the world. Kopyor is an edible mature coconut with soft endosperm. Although this fruit is one of the most popular coconuts in the world, there are limited studies on its properties, including its sensory attributes and metabolite profiles. This study investigates the characteristics of kopyor using sensory evaluation, a widely targeted metabolomics approach, and multivariate analysis. The liquid (water) and solid (flesh) endosperms were collected as the samples...

Functional tissue-engineered artificial skeletal muscle tissue has great potential for pharmacological and academic applications. This study demonstrates an in vitro tissue engineering system to construct functional artificial skeletal muscle tissues using self-organization and signal inhibitors. To induce efficient self-organization, we optimized the substrate stiffness and extracellular matrix (ECM) coatings. We modified the tissue morphology to be ring-shaped under optimized self-organization conditions...

Some strains of nonpathogenic Allorhizobium vitis can control crown gall disease in grapevines caused by pathogenic A. vitis and are considered candidates for biocontrol agents. Many plant pathogenic bacteria regulate the expression of their virulence genes via quorum sensing using N-acylhomoserine lactone (AHL) as a signaling compound. The eight nonpathogenic A. vitis strains used in this study showed AHL-degrading activity. The complete genome sequence of A. vitis MAFF 212306 contained three AHL lactonase gene homologs...

The choice of sterilization method for hydrogels used for cell culture influences the ease of preparing the gel. We prepared interpenetrating gelatin/calcium alginate hydrogels containing 1% (w/v) alginate and 1-16% (w/v) gelatin by molding with the mixture of gelatin/sodium alginate solution, followed by the addition of calcium ions by incubation in calcium chloride solution. It is the simplest method to prepare autoclavable gelatin/sodium hydrogel. We measured various properties of the hydrogels including volume, Young's modulus in the compression test, storage modulus, and loss modulus in the dynamic viscoelasticity measurement...

Plant root-associated environments such as the rhizosphere, rhizoplane, and endosphere, are notably different from non-root-associated soil environments. However, the microbial dynamics in these spatially divided compartments remain unexplored. In this study, we propose a combinational analysis of single-cell genomics with 16S rRNA gene sequencing. This method enabled us to understand the entire soil microbiome and individual root-associated microorganisms. We applied this method to soybean microbiomes and revealed that their composition was different between the rhizoplane and rhizosphere in the early growth stages, but became more similar as growth progressed...

Bacteria produce and release small signal molecules, autoinducers, as an indicator of their cell density. The system, called a quorum-sensing (QS) system, is used to control not only virulence factors but also antibiotic production, sporulation, competence, and biofilm formation in bacteria. Different from antibiotics, QS inhibitors are expected to specifically repress the virulence factors in pathogenic bacteria without inhibiting growth or bactericidal effects. Therefore, since QS inhibitors have little risk of antibiotic-resistant bacteria emergence, they have been proposed as promising anti-bacterial agents...

The aim of this study was to evaluate the physiology of 13 yeast strains by assessing their kinetic parameters under anaerobic conditions. They included Saccharomyces cerevisiae CAT-1 and 12 isolated yeasts from different regions in Brazil. The study aimed to enhance understanding of the metabolism of these strains for more effective applications. Measurements included quantification of sugars, ethanol, glycerol, and organic acids. Various kinetic parameters were analyzed, such as specific substrate utilization rate (qS ), maximum specific growth rate (μmax ), doubling time, biomass yield, product yield, maximum cell concentration, ethanol productivity (PEth ), biomass productivity, and CO2 concentration...

Uracil-thymine dehydrogenase (UTDH), which catalyzes the irreversible oxidation of uracil to barbituric acid in oxidative pyrimidine metabolism, was purified from Rhodococcus erythropolis JCM 3132. The finding of unusual stabilizing conditions (pH 11, in the presence of NADP+ or NADPH) enabled the enzyme purification. The purified enzyme was a heteromer consisting of three different subunits. The enzyme catalyzed oxidation of uracil to barbituric acid with artificial electron acceptors such as methylene blue, phenazine methosulfate, benzoquinone, and α-naphthoquinone; however, NAD+ , NADP+ , flavin adenine dinucleotide, and flavin mononucleotide did not serve as electron acceptors...

Monoclonal antibodies (mAbs) represent a significant segment of biopharmaceuticals, with the market for mAb therapeutics expected to reach $200 billion in 2021. Chinese Hamster Ovary (CHO) cells are the industry standard for large-scale mAb production owing to their adaptability and genetic engineering capabilities. However, maintaining consistent product quality is challenging, primarily because of the inherent genetic instability of CHO cells. In this study, we address the need for advanced technologies for quality monitoring of host cells in biopharmaceuticals...

Chinese hamster ovary (CHO) cells are widely used as a host for producing recombinant therapeutic proteins due to advantages such as human-like post-translational modification, correct protein folding, higher productivity, and a proven track record in biopharmaceutical development. Much effort has been made to improve the process of recombinant protein production, in terms of its yield and productivity, using conventional CHO cell lines. However, to the best of our knowledge, no attempts have been made to acquire new CHO cell lines from Chinese hamster ovary...

Hyperthermostable endoglucanases of glycoside hydrolase family 12 from the archaeon Pyrococcus furiosus (EGPf) catalyze the hydrolysis of β-1,4-glucosidic linkages in cellulose and β-glucan structures that contain β-1,3- and β-1,4-mixed linkages. In this study, EGPf was heterologously expressed with Aspergillus niger and the recombinant enzyme was characterized. The successful expression of EGPf resulted as N-glycosylated protein in its secretion into the culture medium. The glycosylation of the recombinant EGPf positively impacted the kinetic characterization of EGPf, thereby enhancing its catalytic efficiency...