{"title":"New glycerol glycosides in sake formed by Aspergillus oryzae α-glucosidase A","authors":"Yui Akiyama , Kou Yoshizawa , Asuka Yamada , Izumi Kobayashi , Masafumi Tokuoka , Shigenori Kumazawa , Chihiro Honda","doi":"10.1016/j.jbiosc.2025.01.002","DOIUrl":"10.1016/j.jbiosc.2025.01.002","url":null,"abstract":"<div><div>Sake contains unique glycosides produced by the transglycosylation action of α-glucosidase from <em>Aspergillus oryzae</em>. Besides influencing the taste of sake, some transglycosylation products in sake exhibit beneficial biological activities. In this study, we searched for new transglycosylation products in sake. Liquid chromatography–mass spectrometry (LC–MS) revealed that peaks with <em>m/z</em> values corresponding to the glycosides, diglucopyranosylglycerol, triglucopyranosylglycerol, and tetraglucopyranosylglycerol, are present in sake. The presence of glycosides containing up to four polymerized glucose units is the first observation in sake. The peaks of the compounds were not observed in the sake that was brewed with a rice-koji made by α-glucosidase A (AgdA) gene disruption <em>A</em>. <em>oryzae</em> strain. The <em>in vitro</em> transglycosylation experiment using maltose, glycerol and a recombinant AgdA suggested that the compounds in sake were transglycosylation products composed of glycerol and one to four units of glucose. Nuclear magnetic resonance (NMR) analysis revealed that one of the major products of <em>in vitro</em> synthesis was α-isomaltosylglycerol (α-iMG). α-iMG was detected in commercial sake as a common component at an average of 1095 ppm (mg/L). This is the first study to report the presence of α-iMG in foods and beverages.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 4","pages":"Pages 296-301"},"PeriodicalIF":2.3,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143255584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Yeast diversity during the spontaneous fermentation of wine in a winery and in a laboratory using sterilized equipment","authors":"Hideaki Shimizu , Aya Kamada , Takeshi Akao , Yoshiya Kanno , Kazuya Koyama , Kazuhiro Iwashita , Nami Goto-Yamamoto","doi":"10.1016/j.jbiosc.2024.11.001","DOIUrl":"10.1016/j.jbiosc.2024.11.001","url":null,"abstract":"<div><div>A recent trend in some wineries is the return to using spontaneous fermentation, but it is not clear whether winery flora or vineyard microorganisms drive fermentation. We compared fungal communities during the spontaneous fermentation of wine produced in a winery and in a laboratory with sterilized equipment using three grape cultivars (Chardonnay, Merlot, and Muscat Bailey A) obtained from the same harvest. High-throughput sequencing analysis based on the ITS1 region showed that <em>Saccharomyces cerevisiae</em> was the dominant species in winery batches at the end of fermentation, but it was not always dominant in laboratory batches. The number of laboratory batches where <em>S. cerevisiae</em> reached more than 50% at the end of fermentation was only 10 of 26. Consistent with this, in the grape juice/must before fermentation, <em>S. cerevisiae</em> accounted for 1.71% of fungal species identified in winery batches and 0.04% in laboratory batches. In addition, in laboratory-based winemaking, juice clarification of Chardonnay and cold maceration of Merlot influenced the microbial communities observed during fermentation. Our findings suggest that <em>S. cerevisiae</em> present in the winery environment participates at an early stage of fermentation, leading to its dominance at the end in wine produced by spontaneous fermentation in a winery.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 2","pages":"Pages 106-111"},"PeriodicalIF":2.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"COP II-mediated ER-to-Golgi transport is a bottleneck for IgNAR-Fc production in the Chinese hamster ovary cell expression system","authors":"Xiaofang Lyu , Noriko Yamano-Adachi , Yuichi Koga , Takeshi Omasa","doi":"10.1016/j.jbiosc.2024.10.012","DOIUrl":"10.1016/j.jbiosc.2024.10.012","url":null,"abstract":"<div><div>The novel heavy-chain antibody known as immunoglobulin new antigen receptor (IgNAR) is derived from cartilaginous fishes such as sharks. IgNAR, which binds to antigens with the high specificity and affinity of a conventional IgG antibody and exhibits high resistance to denaturation, has potential as a next-generation antibody in biopharmaceutical and biotechnological applications. High-level expression of recombinant IgNAR in animal cells has been challenging. In our previous study, IgNAR was expressed as a fusion protein with a human IgG Fc region (IgNAR-Fc) in Chinese hamster ovary (CHO) cells, but did not meet the production level required for further research and application. In this study, we sought to identify the production bottleneck in CHO cells as a first step toward achieving abundant production of IgNAR. Using an established IgG high-production CHO cell line as a comparator, we found that the amounts of intracellular dimeric IgNAR-Fc produced in CHO cells were similar to those of intracellular dimeric IgG. Furthermore, the majority of intracellular IgNAR-Fc was retained in the endoplasmic reticulum (ER) and strongly colocalized to ERGIC-53, the cargo receptor for coat protein complex II (COP II)-coated vesicles. These findings suggest that COP II-mediated ER-to-Golgi transport may represent a bottleneck for IgNAR-Fc production in the CHO cell expression system.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 2","pages":"Pages 133-140"},"PeriodicalIF":2.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142716202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Miriam Guadalupe Salgado García , Néstor Fabián Díaz , Guadalupe García López , Ikuri Álvarez Maya , Claudia Hernández Jimenez , Yvonne Roman Maldonado , David José Mendoza Aguayo , Néstor Emmanuel Díaz Martínez
{"title":"Evaluation methods for decellularized tissues: A focus on human amniotic membrane","authors":"Miriam Guadalupe Salgado García , Néstor Fabián Díaz , Guadalupe García López , Ikuri Álvarez Maya , Claudia Hernández Jimenez , Yvonne Roman Maldonado , David José Mendoza Aguayo , Néstor Emmanuel Díaz Martínez","doi":"10.1016/j.jbiosc.2024.10.009","DOIUrl":"10.1016/j.jbiosc.2024.10.009","url":null,"abstract":"<div><div>Tissue engineering, a multidisciplinary research field aiming to revolutionize regenerative medicine, relies on scaffolds for optimal cell cultures and organ development. Decellularized tissue extracellular matrices (dECM) scaffolds, particularly from human amniotic membrane (hAM), show promise in clinical applications. This review discusses the significance of scaffolds, emphasizing dECM-based hAM scaffolds, delving into ECM complexities, decellularization processes, and evaluation methods. Raman spectroscopy emerges as a non-destructive tool for evaluating ECM preservation, presenting potential for quantifying ECM components in hAM before and after decellularization. The review explores the role of hAM as a biomaterial, detailing its composition and characteristics and emphasizes the importance of evaluating ultrastructural components and suggests Raman spectroscopy as a valuable technique for this purpose.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 2","pages":"Pages 85-94"},"PeriodicalIF":2.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142728952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Metagenomic profiling of antibiotic resistance genes and their associations with the bacterial community along the Kanda River, an urban river in Japan","authors":"Chang Xiao , Keigo Ide , Hiroko Matsunaga , Masato Kogawa , Ryota Wagatsuma , Haruko Takeyama","doi":"10.1016/j.jbiosc.2024.09.006","DOIUrl":"10.1016/j.jbiosc.2024.09.006","url":null,"abstract":"<div><div>Antibiotic resistance genes (ARGs) present in urban rivers have the potential to disseminate antibiotic-resistant bacteria into other environments, posing significant threats to both ecological and public health. Although metagenomic analyses have been widely employed to detect ARGs in rivers, our understanding of their dynamics across different seasons in diverse watersheds remains limited. In this study, we performed a comprehensive genomic analysis of the Kanda River in Japan at 11 sites from upstream to estuary throughout the year to assess the spread of ARGs and their associations with bacterial communities. Analysis of 110 water samples using the 16S rRNA gene revealed variations in bacterial composition corresponding to seasonal changes in environmental parameters along the river. Shotgun metagenomics-based profiling of ARGs in 44 water samples indicated higher ARG abundance downstream, particularly during the summer. Weighted gene co-expression network analysis (WGCNA) linking bacterial lineages and ARGs revealed that 12 ARG subtypes co-occurred with 128 amplicon sequence variants (ASVs). WGCNA suggested potential hosts for <em>ErmB</em>, <em>ErmF</em>, <em>ErmG</em>, <em>tetQ</em>, <em>tet (W/N/W)</em>, <em>aadA2</em>, and <em>adeF</em>, including gut-associated bacteria (e.g., <em>Prevotella</em>, <em>Bacteroides</em>, <em>Arcobacter</em>) and indigenous aquatic microbes (e.g., <em>Limnohabitans</em> and <em>C39</em>). In addition, <em>Pseudarcobacter</em> (a later synonym of <em>Arcobater</em>) was identified as a host for <em>adeF</em>, which was also confirmed by single cell genomics. This study shows that ARG distribution in urban rivers is affected by seasonal and geographical factors and demonstrates the importance of monitoring rivers using multiple types of genome sequencing, including 16S rRNA gene sequencing, metagenomics, and single cell genomics.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 2","pages":"Pages 147-155"},"PeriodicalIF":2.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142564516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Identification and characterization of a circular bacteriocin, garvicin SC, a novel garvicin ML variant, produced by Lactococcus garvieae ABG0038","authors":"Yumi Komori , Naoya Ozawa , Hiroshi Kuwahara , Takeshi Zendo , Mikio Aoki","doi":"10.1016/j.jbiosc.2024.10.008","DOIUrl":"10.1016/j.jbiosc.2024.10.008","url":null,"abstract":"<div><div>We have identified and characterized a circular bacteriocin, termed garvicin SC (GarSC), produced by <em>Lactococcus garvieae</em> ABG0038 isolated from pine cones. Genome analysis of <em>L. garvieae</em> ABG0038 revealed that GarSC was a variant of the circular bacteriocin, garvicin ML (GarML), caused by an amino acid substitution, and predicted that GarSC was produced through a biosynthetic mechanism very similar to that of GarML. The two circular bacteriocins were purified and characterized for activity, and several differences were observed in pH stability, enzyme sensitivity, and antimicrobial activity. In particular, GarSC showed excellent stability in the basic pH range, which might extend the range of garvicin’s application to one broader than that of GarML.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 2","pages":"Pages 95-99"},"PeriodicalIF":2.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142639182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shan Tu , Tatsuto Kageyama , Jieun Seo , Yinghui Zhou , Junji Fukuda
{"title":"Development of in vitro hair pigmentation model using hair follicle organoids","authors":"Shan Tu , Tatsuto Kageyama , Jieun Seo , Yinghui Zhou , Junji Fukuda","doi":"10.1016/j.jbiosc.2024.11.003","DOIUrl":"10.1016/j.jbiosc.2024.11.003","url":null,"abstract":"<div><div>Hair color is formed through a series of processes such as melanin synthesis and storage in melanosomes, transfer from melanocytes, and reception by hair matrix cells in the hair bulb. Because gray hair is caused by the deterioration of a single or multiple of these processes, understanding the mechanisms responsible for these processes is crucial for developing therapeutic strategies. Recently, a robust approach for preparing hair follicle organoids (HFOs) was reported, in which hair follicle morphogenesis, including hair shaft elongation, was tracked <em>in vitro</em>. Here, we investigated whether HFOs could be used to assess genes involved in hair pigmentation. HFOs generated hair follicles and pigmented shafts during the <em>in vitro</em> culturing process. The knockdown of genes associated with melanosome production (<em>Bcl2</em> and <em>Mitf</em>) and transport (<em>MyoX</em>, <em>PAR2</em>, and <em>Rab11b</em>) significantly increased the number of gray hairs in HFOs. This organoid model may be a promising platform for better understanding hair pigmentation and screening drugs for gray hair.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 2","pages":"Pages 141-146"},"PeriodicalIF":2.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Eriko Numao, Kumi Yanagisawa, Yuki Yagi, Daisuke Tsuchida, Katsuyoshi Yamazaki
{"title":"Comparison of a new peak detection function for selecting a phase-appropriate multi-attribute method system","authors":"Eriko Numao, Kumi Yanagisawa, Yuki Yagi, Daisuke Tsuchida, Katsuyoshi Yamazaki","doi":"10.1016/j.jbiosc.2024.10.005","DOIUrl":"10.1016/j.jbiosc.2024.10.005","url":null,"abstract":"<div><div>The multi-attribute method (MAM) has been recognized as an optimal tool for quality control in biotherapeutics. New peak detection (NPD) is one of the functions of MAM for detecting unexpected differences in samples and is an essential feature required for replacing conventional methods with MAM. Not only used for release and stability testing, NPD is also considered valuable for evaluating comparability and identifying product quality attributes in the research phase. Although many researchers consider the processing parameter the key to NPD, the details of the decision-making process are unclear. Besides specific instruments and software packages has been used almost exclusively, yet the differences in NPD function between other choices have not been confirmed. Thus, this research aimed to confirm the applicability of our original decision-making approach for NPD processing parameters using two different systems. After optimization for each, under a condition that detected crucial differences and did not return false positives, they differed in the reproducibility of the results. To our knowledge, this was the first time the comparison of NPD results of different systems has been published, and the eligibility of processing methods was evaluated in light of the equivalency of conventional methods' detectability. The findings suggested that the capability of NPD is determined not only by the instrument's resolution but also by the software's capability. Our approach for optimizing the NPD processing parameter is deemed widely applicable and practical in developing therapeutic proteins. The revealed difference will help us select the fit-for-purpose system.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 2","pages":"Pages 156-163"},"PeriodicalIF":2.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"In-situ collagen mineralization modulates metastatic properties of breast cancer cells","authors":"Jaya Thilakan , Sudhir Kumar Goel , Neha Arya","doi":"10.1016/j.jbiosc.2024.07.010","DOIUrl":"10.1016/j.jbiosc.2024.07.010","url":null,"abstract":"<div><div>Bone metastasis is the leading cause of morbidity and mortality in advanced-stage breast cancer patients. While most studies focus on the cellular and genetic factors associated with breast cancer metastasis, the role of the extracellular matrix (ECM) of bone in breast cancer metastasis remains elusive. In this study, we recapitulated the bone microenvironment using <em>in-situ</em> mineralized collagen type-I hydrogels and utilized them to understand breast cancer metastasis. Our results indicated successful mineralization of collagen type-I based hydrogels in the presence of serum proteins, which increased as a function of time. There was no difference in the adhesion of breast cancer cells seeded on collagen and mineralized collagen surfaces. However, there was a marked reduction in cell proliferation, down-regulation of various metastatic markers, and decreased migratory phenotype with a concomitant increase in cleaved caspase-3 on mineralized collagen compared to collagen hydrogels. In conclusion, our results suggest an inverse relationship between bone mineralization and the metastatic propensity of breast cancer cells. We further speculate the role of other factors in the skeletal ecosystem for mediating preferential homing of breast cancer cells to the bone microenvironment.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 2","pages":"Pages 123-132"},"PeriodicalIF":2.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Efficient yeast breeding using a sake metabolome analysis for a strain evaluation","authors":"Risako Kinoshita , Muneyoshi Kanai , Kaoru Takegawa , Kazuhiro Iwashita","doi":"10.1016/j.jbiosc.2024.10.010","DOIUrl":"10.1016/j.jbiosc.2024.10.010","url":null,"abstract":"<div><div>Breeding sake yeast typically involves generating several gene mutants through UV irradiation or mutagen treatment and selecting those with desired traits based on indicators such as analog resistance. However, this approach often alters traits beyond the target trait due to the random and numerous mutations introduced. To address this issue, we used a previously established metabolome analysis, a sake metabolome analysis, to evaluate the selected yeast strain. After screening for target traits, 110 sake yeast candidates were cultured in yeastnitrogen-based liquid medium using test tubes. The contents were extracted and subjected to comprehensive metabolite analysis through sake metabolome analysis. A phylogenetic tree was then constructed using the metabolome analysis data, enabling the selection of candidate yeasts with only the target traits modified and other traits similar to the parental strain. Selected 21 candidate strains underwent fermentation tests, and the resulting sakes were analyzed using liquid chromatography quadrupole/time-of-flight mass spectrometry (LC-Q/TOF-MS). The findings suggested that the metabolomic data of yeast extracts obtained by simple small-scale culture was similar to the data of resulting sake in the larger-scale fermentation tests. This underscores the utility of metabolome analysis data of yeast extracts in the yeast breeding process, marking the first report proposing the use of the sake metabolome analysis method for yeast breeding.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 2","pages":"Pages 100-105"},"PeriodicalIF":2.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142791816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}