{"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}
Yi Zhang , Jannatul Fardous , Yu Zhou , Lichun Wu , Ryota Doi , Jia Hu , Yuya Hirota , Yasuhiro Ikegami , Shinichi Aishima , Hiroyuki Ijima
{"title":"Topical delivery of gel-in-oil emulsion cocktail with growth factors for the treatment of diabetic pressure ulcers","authors":"Yi Zhang , Jannatul Fardous , Yu Zhou , Lichun Wu , Ryota Doi , Jia Hu , Yuya Hirota , Yasuhiro Ikegami , Shinichi Aishima , Hiroyuki Ijima","doi":"10.1016/j.jbiosc.2024.10.011","DOIUrl":"10.1016/j.jbiosc.2024.10.011","url":null,"abstract":"<div><div>Healing diabetic foot ulcers (DFUs) poses a serious challenge for many individuals with diabetes. The use of biomaterials applied locally for treating DFUs has recently garnered significant attention. Here, we present a gel-in-oil nanogel dispersion (G/O-NGD) capable of local delivery of six different growth factors (GFs) via the topical route, followed by an in-vivo evaluation in mice. Both macroscopic and microscopic changes in skin structure were evidented after topical application of GF-cocktail G/O-NGD, and changes in CD68 and CD31 levels and collagen content were measured. Expression and synthesis of Interleukin-6 (IL-6), transforming GF beta 1 (TGF-β1), and basic fibroblast GF (bFGF) were also analyzed. The results showed that a significant reduction in ulcer area, restoration of skin structure, increase in collagen content, angiogenesis, and suppression of inflammation were possible with GF-cocktail G/O-NGD, indicating that G/O-NGD is a prospective carrier for local delivery of GF, improving wound healing processes.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 2","pages":"Pages 112-122"},"PeriodicalIF":2.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142739786","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":"Protective role of hematin in alcohol oxidase-mediated glycerol oxidation: A kinetic modeling approach","authors":"Adrián Parodi , Agostina Córdoba , Mariano Asteasuain , Ivana Magario","doi":"10.1016/j.jbiosc.2024.12.012","DOIUrl":"10.1016/j.jbiosc.2024.12.012","url":null,"abstract":"<div><div>Mathematical modeling of complex multi-catalytic reaction pathways is a powerful tool not only for determining optimal operational conditions but also for gaining insights into the kinetic behavior of efficient yet product-sensitive enzymes. This approach was applied to the biooxidation of glycerol using oxidases, aided by hematin, a natural mimic of heme peroxidases and catalases, which acts as a scavenger for enzymatically produced H<sub>2</sub>O<sub>2</sub>. The bi-catalytic reaction system was coupled with the formation of a colored imine product from phenol and 4-aminoantipyrine, enabling spectrophotometric monitoring of reaction kinetics. Alcohol oxidase (AOX) from <em>Komagataella pastoris</em> (formerly <em>Pichia pastoris</em>) was submitted to this strategy to overcome some kinetic drawbacks previously observed with galactose oxidase (GAO) from <em>Dactylium dendroides</em>. Although both enzymes exhibited comparable oxidation yields, computer-aided kinetic analyses revealed significant differences in efficiency and sensitivity to H<sub>2</sub>O<sub>2</sub>. AOX demonstrated two orders of magnitude greater efficiency and a similarly higher affinity for glycerol. However, AOX showed a stronger tendency to bind H<sub>2</sub>O<sub>2</sub> compared to hematin or GAO, as suggested by the ratio of the inhibition constant (<em>k</em><sub>inh</sub>) to the activation constant (<em>k</em><sub>1</sub>) for hematin. The kinetic model was also used to simulate optimal conditions for enhancing the stability of AOX and hematin. Reducing glycerol concentration or increasing hematin concentration improved AOX stability, while the addition of phenol helped preserve hematin. The predicted stabilities turn the AOX/hematin/phenol system promising for biosensing or analytical applications.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 4","pages":"Pages 263-270"},"PeriodicalIF":2.3,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143074513","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}