Ryota Goto , Shinji Sakai , Cédric Delattre , Emmanuel Petit , Redouan El Boutachfaiti , Masaki Nakahata
{"title":"Enzymatically cross-linkable sulfated bacterial polyglucuronic acid as an affinity-based carrier of FGF-2 for therapeutic angiogenesis","authors":"Ryota Goto , Shinji Sakai , Cédric Delattre , Emmanuel Petit , Redouan El Boutachfaiti , Masaki Nakahata","doi":"10.1016/j.jbiosc.2024.08.011","DOIUrl":"10.1016/j.jbiosc.2024.08.011","url":null,"abstract":"<div><div>The fibroblast growth factor-2 (FGF-2) is a critical protein for biological processes such as angiogenesis and tissue regeneration. Recently, hydrogels based on semi-synthetic sulfated polysaccharides have been developed for the controlled delivery of FGF-2. These affinity-based FGF-2 carriers utilizing hydrogels based on sulfated polysaccharides enable sustained delivery of FGF-2, yet choice of materials is limited. Here, we demonstrate a novel synthetic sulfated polysaccharide-based hydrogel based on bacterial polyglucuronic acid (PGU). We synthesized phenol-grafted sulfated PGU (PGUS-Ph), an enzymatically cross-linkable PGU derivative that exhibited an enhanced affinity for FGF-2. The aqueous solution of PGUS-Ph, when combined with FGF-2, could be injected into affected sites and form a hydrogel in a minimally invasive manner. The FGF-2 released from the PGUS-Ph hydrogel induced blood vessel formation, as proven by a chick embryo-based angiogenesis assay. Our results indicate that the PGUS-Ph has the potential as an enzymatically cross-linkable and minimally invasively injectable affinity-based FGF-2 delivery system.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"138 6","pages":"Pages 541-547"},"PeriodicalIF":2.3,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142347276","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":"Elucidation of d-allulose recognition mechanism in ketose 3-epimerase","authors":"Masahiro Watanabe , Yusuke Nakamichi , Shohei Mine","doi":"10.1016/j.jbiosc.2024.08.010","DOIUrl":"10.1016/j.jbiosc.2024.08.010","url":null,"abstract":"<div><div><span>d</span>-Allulose is a low-calorie sweetener with multiple nutritional functions that can be produced through <span>d</span>-fructose isomerization by ketose 3-epimerase (KEase). <span>l</span>-Ribulose 3-epimerase from <em>Arthrobacter</em> <em>globiformis</em> (AgLRE) is one of the most important enzymes that produce <span>d</span>-allulose; however, its substrate recognition mechanism is unknown. In this study, the crystal structures of AgLRE and its complex with <span>d</span>-allulose and <span>d</span>-fructose were determined. Upon substrate binding, the hydrophobic residues around the active-site entrance move toward the bound substrate. A comparison of AgLRE and other KEase structures revealed that the substrate-binding residues are not the main factors responsible for its marked specificity for <span>d</span>-allulose and <span>d</span>-fructose, but the hydrophobicity of the active site pocket influences substrate recognition. Particularly, the two hydrophobic regions at the active site entrance are the regulatory elements that modulate substrate recognition by AgLRE. This study provides useful information for designing AgLRE to increase its affinity for <span>d</span>-allulose and <span>d</span>-fructose.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"138 6","pages":"Pages 488-494"},"PeriodicalIF":2.3,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142347275","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":"Rapid one-pot human single nucleotide polymorphism genotyping platform with Cas13a nuclease","authors":"Rui Lei , Xi-Peng Liu","doi":"10.1016/j.jbiosc.2024.08.003","DOIUrl":"10.1016/j.jbiosc.2024.08.003","url":null,"abstract":"<div><div>Single nucleotide polymorphism (SNP), as one of the key components of the genetic factors, is important for disease detection and early screening of hereditary diseases. Current SNP genotyping methods require laboratory instruments or long operating times. To facilitate the diagnosis of hereditary diseases, we developed a new method referred to as the LwaCas13a-based SNP genotyping platform (Cas13a platform), which is useful for detecting disease-related SNPs. We report a CRISPR/Cas13a-based SNP genotyping platform that couples recombinase-aided amplification (RAA), T7 transcription, and <em>Leptotrichia wadei</em> Cas13a (LwaCas13a) detection for simple and fast genotyping of human disease-related SNPs. We used this Cas13a platform to identify 17 disease-related SNPs, demonstrating that position 2 in gRNA is suitable for the introduction of additional mismatches to achieve high discrimination in genotyping across a wide range of SNP targets. The discrimination specificity of 17 SNPs was improved 3.0–35.1-fold after introducing additional mismatches at position 2 from the 5′-end. We developed a method, which has a lower risk of cross-contamination and operational complexity, for genotyping SNPs using human saliva samples in an one-pot testing that delivers results within 60 min. Compared to TaqMan probe qPCR, RFLP, AS-PCR and other SNP genotyping methods, the Cas13a platform is simple, rapid and reliable, expanding the applications of the CRISPR/Cas system in nucleic acid detection and SNP genotyping.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"138 6","pages":"Pages 469-477"},"PeriodicalIF":2.3,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142288070","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":"Dynamics of the microbiome and volatile organic compounds during fermentation and aging of soy sauce","authors":"Yuichi Mizuno , Takashi Yoshimura , Kazutaka Sawada , Keisuke Tsuge , Yukio Nagano , Yumiko Yoshizaki , Masatoshi Goto , Genta Kobayashi","doi":"10.1016/j.jbiosc.2024.08.009","DOIUrl":"10.1016/j.jbiosc.2024.08.009","url":null,"abstract":"<div><div>A comprehensive analysis of the microbiome and volatile organic compounds (VOC) in the <em>moromi</em> of soy sauce during fermentation and aging was conducted under industrial production. Microbiome analysis using next-generation sequencing revealed the presence and dynamics of microorganisms other than <em>Aspergillus</em>, <em>Tetragenococcus</em>, <em>Zygosaccharomyces</em>, and <em>Wickerhamiella</em>, which were used as starters. The bacterial community of the <em>moromi</em> on the first day of this process was rich in diversity. <em>Staphylococcus</em>, <em>Bacillus</em>, <em>Kurthia</em>, <em>Acinetobacter</em>, <em>Enterococcus</em>, and <em>Macrococcus</em> that grew during <em>koji</em> making were relatively dominant. However, as the fermentation progressed, only <em>Tetragenococcus</em> became dominant in the bacterial communities. In contrast, the fungal community was simple at the beginning of fermentation and aging, with <em>Aspergillus</em> present almost exclusively. After adding <em>Zygosaccharomyces rouxii</em> on day 42, the fungal community changed significantly. At the end of fermentation and aging, the fungal community diversified, with <em>Millerozyma</em>, <em>Wickerhamiella</em>, <em>Yamadazyma</em>, and <em>Saccharomycopsis</em> becoming dominant. The analysis of VOC showed that the VOC profile changed during fermentation and aging, and that the VOC profile changed significantly after adding <em>Z. rouxii</em>. The correlation analysis between the microbiome and VOC showed that <em>Wickerhamiella</em>, <em>Millerozyma</em>, <em>Debaryomyces</em>, <em>Yamadazyma</em>, and <em>Candida</em> had a significant positive correlation with alcohols, esters, and phenols produced in the later stage of fermentation and aging, indicating that not only <em>Z. rouxii</em> but also various fungi may contribute to the formation of the complex aroma profile of soy sauce.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"138 6","pages":"Pages 522-532"},"PeriodicalIF":2.3,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142288069","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":"Developing a plant microbial fuel cell by planting water spinach in a hanging-submerged plant pot system","authors":"Yi-Hsuan Chen, Shiue-Lin Li, Ching-Ya Hung, Pei-Ching Wu, Yue-Xiang Hong, Wen-Jing Chen, Shu-yi Chang, Yu-Ya Hsu, Wei-Yi Chao, Kai-Jhih Tsai, You-Chen Chen, Ji-Teng Chen, Chia-Le Hsu, Yun-Ju Lu, Li-Ming Fang, Ming-Han Yang, I-Ting Tan, Ying-Chuan Hsu, Hong-Yu Yang, Rui-Hong Jiang","doi":"10.1016/j.jbiosc.2024.08.007","DOIUrl":"10.1016/j.jbiosc.2024.08.007","url":null,"abstract":"<div><div>To plant crops (especially dry crops such as water spinach) with concomitant electricity recovery, a hanging-submerged-plant-pot system (HSPP) is developed. The HSPP consists of a soil pot (anodic) partially submerged under the water surface of a cathode tank. The microbial communities changed with conditions were also investigated. It was found that with chemical fertilizers the closed-circuit voltage (CCV, with 1 kΩ) was stable (approximately 250 mV) within 28 d; however, without fertilizer, the water spinach could adjust to the environment to obtain a better power output (approximately 3 mW m<sup>−2</sup>) at day 28. The microbial-community analyses revealed that the <em>Pseudomonas</em> sp. was the only exoeletrogens found in the anode pots. Using a secondary design of HSPP, for a better water-level adjustment, the maximum power output of each plant was found to be approximately 27.1 mW m<sup>−2</sup>. During operation, high temperature resulted in low oxygen solubility, and low CCV as well. At this time, it is yet to be concluded whether the submerged water level significantly affects electricity generation.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"138 6","pages":"Pages 533-540"},"PeriodicalIF":2.3,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142248091","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":"Blending of selected yeast extract and peptone for inducible and constitutive protein production in Escherichia coli using the pET system","authors":"Mikiko Nakamura , Rinji Akada","doi":"10.1016/j.jbiosc.2024.08.008","DOIUrl":"10.1016/j.jbiosc.2024.08.008","url":null,"abstract":"<div><div>pET vectors allow inducible expression of recombinant proteins in <em>Escherichia coli</em>. In this system, isopropyl β-<span>d</span>-1-thiogalactopyranoside (IPTG) drives <em>lac</em>UV5 promoter to produce T7 RNA polymerase, simultaneously releasing the suppression of T7<em>lac</em> promoter. T7 RNA polymerase then strongly transcribes the target gene. A lac repressor encoded by <em>lacI</em> in the vector represses the promoters. Despite stringent repression and inducible expression achieved with the pET system, unexpected leaky expression can occur without IPTG induction. Here, by evaluating leaky expression in recombinant cells cultured in various Luria–Bertani (LB) media, prepared using yeast extract and peptone from different suppliers, as well as in five commercial premix-LB media, we confirmed the presence of unknown <em>lac</em> inducers in LB. To explore these inducers, we examined <em>E. coli</em> growth in media comprising yeast extract or peptone. At 4% concentration, five commercial yeast extract and six peptone samples individually allowed <em>E. coli</em> growth equivalent to that in LB medium. We determined the luciferase activity of the <em>luxCDABE</em> operon in the pET vector under these conditions. The presence of different concentrations of inducers was detected in both the yeast extract and peptone. Furthermore, we blended yeast extract and peptone with low or high concentrations of <em>lac</em> inducers. The low-expression blend, used as a basal medium before IPTG addition, allowed leak-free, tightly controlled expression. The high-expression blend was used for constitutive high-expression and pET induction with the basal medium, in lieu of IPTG. These blended media can be used for well-controlled inducible and constitutive expression using the pET system.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"138 6","pages":"Pages 548-556"},"PeriodicalIF":2.3,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142217177","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":"Improved fermentative gamma-aminobutyric acid production from glucose by the inactivation of respiratory chain components NDH-I and Cytbo₃ in Escherichia coli","authors":"Hiroki Wakahara , Takuya Mizokoshi , Kotaro Yamagami , Satoru Fukiya , Atsushi Yokota , Tomoya Maeda","doi":"10.1016/j.jbiosc.2024.08.004","DOIUrl":"10.1016/j.jbiosc.2024.08.004","url":null,"abstract":"<div><div>Gamma-aminobutyric acid (GABA), which is synthesized from <span>l</span>-glutamic acid via glutamate decarboxylase (Gad), is used as food, supplements, and biodegradable plastics. Our previous study demonstrated an <em>Escherichia coli</em> mutant (ΔΔ) strain, lacking type I NADH dehydrogenase (NDH-I) and cytochrome <em>bo</em><sub>3</sub> oxidase (Cyt<em>bo</em><sub>3</sub>), produced 7 g/L glutamic acid on MS1 glucose-minimal medium. In this study, the ΔΔ strain was used for improving GABA production. A plasmid (pMBL19-<em>gadB</em>′) expressing a mutated <em>E. coli</em> GadB (Glu89Gln/Δ452-466), retaining activity at neutral pH, was introduced into the ΔΔ strain and its parent strain (W1485). The ΔΔ strain carrying pMBL19-<em>gadB</em>′ exhibited a twofold increase in GABA production compared to the W1485 strain carrying pMBL19-<em>gadB</em>′. Deleting the C-terminal (Δ471–511) of GadC antiporter in the ΔΔ strain further improved GABA yield to 1.5 g/L when cultured in MS1 glucose-minimal medium. On the other hand, a large amount of glutamic acid produced by the ΔΔ strain was not fully converted to GABA, likely due to the inhibition of GadB activity by the accumulation of acetic acid. Although there is room for improvement, these results indicate the efficacy of the ΔNDH-IΔCyt<em>bo</em><sub>3</sub> double mutation in augmenting GABA production.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"138 6","pages":"Pages 501-506"},"PeriodicalIF":2.3,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154190","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":"Generation of a plasmid series for rapid sub-cloning and use in various Enterobacteriaceae","authors":"Hannah Gertrude Braun , Nabeela Kanwal , Luisa Fernanda Rivera Lopez , Jenny-Lee Thomassin","doi":"10.1016/j.jbiosc.2024.08.006","DOIUrl":"10.1016/j.jbiosc.2024.08.006","url":null,"abstract":"<div><div>Plasmids are molecular genetic tools used for trans-complementation and gene expression in bacteria. Challenges faced by researchers include limited repertoire of antibiotic resistance of plasmids, issues related to plasmid compatibility and restricted or incompatible multiple cloning sites when needing to change plasmid copy number to tune production of their protein of interest. In this study, a series of plasmids were generated with compatible multiple cloning sites and homologous DNA regions to allow for modular cloning for rapid exchange of antibiotic resistance and plasmid origin. Plasmids generated in this series have options for high, mid, and low plasmid copy number, and have either an integrated FLAG epitope in the multiple cloning site or possess an uninterrupted multiple cloning site with the option of using the common LacZ-based blue/white screening method. Low copy plasmids also have one of five antibiotic selection markers. To demonstrate functionality of these plasmids, a representative FLAG tagged protein and mCherry were cloned into the low copy plasmids and expressed in various bacteria belonging to the <em>Enterobacteriaceae</em> family. In conclusion, by creating a new plasmid series, we have expanded the toolkit of available molecular biology tools for bacterial work.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"138 6","pages":"Pages 478-487"},"PeriodicalIF":2.3,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145722","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":"Characterization of the membrane vesicle fraction from Acetobacter sp. WSS15","authors":"Atsushi Kurata , Kota Aimatsu , Yuki Kimura , Hinako Hashiguchi , Asami Maeda , Tomoya Imai , Shino Yamasaki-Yashiki , Kensaku Hamada , Yuki Fujimoto , Akira Fujii , Koichi Uegaki","doi":"10.1016/j.jbiosc.2024.07.017","DOIUrl":"10.1016/j.jbiosc.2024.07.017","url":null,"abstract":"<div><div>A bacterium that produces membrane vesicles (MVs), strain WSS15, was isolated from a traditional vinegar in Japan called Kurozu. A phylogenetic analysis of 16S rRNA gene sequences indicated that this bacterium belongs to the genus <em>Acetobacter</em>. MVs and peptidoglycan-associated lipoprotein (Pal) were detected in the MV fraction of strain WSS15. In the presence of the WSS15 MV fraction, murine macrophages produced the pro-inflammatory cytokine interleukin-6 (IL-6) via the recognition by superficial Toll-like receptor 2 (TLR2). WSS15 MVs adhered to the cell surface of macrophages. The macrophages secreted IL-6 through the TLR2 recognition of an acylated N-terminal peptide of Pal. We elucidated the mode of action of WSS15 MVs on immune cells and identified the Pal peptide from strain WSS15 as an agonist of TLR2.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"138 6","pages":"Pages 495-500"},"PeriodicalIF":2.3,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145721","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":"Novel sampling and gas-phase derivatization strategy: Proof-of-concept by profiling ionic polar metabolites using gas chromatography-mass spectrometry","authors":"Kazuhiro Kawamura , Eiichiro Fukusaki","doi":"10.1016/j.jbiosc.2024.07.019","DOIUrl":"10.1016/j.jbiosc.2024.07.019","url":null,"abstract":"<div><div>Metabolomic research involves the comprehensive analysis of metabolites in biological samples and has many applications. Gas chromatography-mass spectrometry (GC-MS) is an established and widely used approach for metabolic profiling. However, sample preparation and metabolite derivatization are time-consuming, and derivatization options are limited. We propose gas–solid phase derivatization (GSPD) as a novel sampling and derivatization method that uses a silica monolith substrate and gaseous derivatization reagents for metabolomics using GC-MS. We developed a method to measure the organic acids and sugar phosphates responsible for glycolysis and the tricarboxylic acid (TCA) cycle. GSPD simplifies the sample preparation and can be applied to derivatization reactions that are difficult to perform in solution owing to solvent limitations. The developed method was applied to human plasma and tomato pulp and was shown to have a higher detection performance than the conventional method. This study provides a strategy to simplify sample preparation and expand derivatization options for GC-MS-based metabolomics.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"138 5","pages":"Pages 462-468"},"PeriodicalIF":2.3,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132788","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}