Journal of bioscience and bioengineering最新文献

Efficient selection of pyruvate decarboxylase sequences from database for high ethanol productivity in Synechocystis sp. PCC 6803. 聚囊藻PCC 6803丙酮酸脱羧酶序列的高效筛选。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-06-19 DOI: 10.1016/j.jbiosc.2025.05.011

Hiroki Nishiguchi, Teppei Niide, Yoshihiro Toya, Hiroshi Shimizu

{"title":"Efficient selection of pyruvate decarboxylase sequences from database for high ethanol productivity in Synechocystis sp. PCC 6803.","authors":"Hiroki Nishiguchi, Teppei Niide, Yoshihiro Toya, Hiroshi Shimizu","doi":"10.1016/j.jbiosc.2025.05.011","DOIUrl":"https://doi.org/10.1016/j.jbiosc.2025.05.011","url":null,"abstract":"Ethanol production using the model cyanobacterium Synechocystis sp. PCC 6803 (PCC6803) has garnered considerable attention. A heterologous pyruvate decarboxylase (PDC) is essential for synthesizing ethanol in PCC6803. Although many organisms possess PDCs, no systematic search for suitable PDCs has been reported. This study employed a two-step approach to identify promising PDCs. First, nine diverse natural PDCs with confirmed activity in BRENDA were evaluated for ethanol production in PCC6803. Ethanol production was observed only with PDCs from Zymomonas mobilis (Zm PDC) and Gluconobacter diazotrophicus, suggesting that bacterial PDCs are suitable. In the second step, the search focused on bacterial PDCs, not only natural PDCs but also artificial sequences designed via the Protein Repair One-Stop Shop or ancestral sequence reconstruction. A PDC from Gluconobacter oxydans showed higher ethanol productivity (88.9 mg/L/5 days) than Zm PDC. Although productivity did not surpass that of Zm PDC, ethanol production was achieved with previously unconfirmed or engineered PDCs, expanding the range of useable sequences. This stepwise strategy demonstrates a robust approach for identifying and designing useful enzymes across sequence spaces.","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144336533","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}

引用次数: 0

Effects of vascular endothelial cells on the neurite outgrowth of nerve cells. 血管内皮细胞对神经细胞突突生长的影响。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-06-16 DOI: 10.1016/j.jbiosc.2025.05.010

Tomoki Asaba, Tatsuya Osaki, Koki Murayama, Sayuri Hamano, Tatsuto Kageyama, Junji Fukuda

引用次数: 0

Role of the Pho regulon and genetic reconstruction of a phosphite-dependent Escherichia coli. Pho调控子的作用和亚磷酸依赖大肠杆菌的基因重建。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-06-16 DOI: 10.1016/j.jbiosc.2025.05.012

Naoki Momokawa, Takeshi Ikeda, Takenori Ishida, Kaori Nimura-Matsune, Hisakage Funabashi, Satoru Watanabe, Akio Kuroda, Ryuichi Hirota

{"title":"Role of the Pho regulon and genetic reconstruction of a phosphite-dependent Escherichia coli.","authors":"Naoki Momokawa, Takeshi Ikeda, Takenori Ishida, Kaori Nimura-Matsune, Hisakage Funabashi, Satoru Watanabe, Akio Kuroda, Ryuichi Hirota","doi":"10.1016/j.jbiosc.2025.05.012","DOIUrl":"https://doi.org/10.1016/j.jbiosc.2025.05.012","url":null,"abstract":"A phosphite (Pt)-dependent biological containment strategy, achieved by introducing a Pt-metabolic pathway and disrupting endogenous phosphate transporters, renders Escherichia coli growth strictly dependent on Pt, a compound rarely detected in natural environments, thereby preventing unintended environmental spread. In this study, we demonstrated that expression of phosphate regulon (Pho regulon) genes was markedly upregulated in a Pt-dependent E. coli strain due to the elimination of phoU, a negative regulator of the Pho regulon, along with the high-affinity phosphate transporter pstSCAB. However, further genetic modification of this strain for detailed analysis was hindered by the presence of multiple antibiotic resistance markers. To overcome this limitation, we reconstructed a Pt-dependent E. coli strain using CRISPR-Cas12a-mediated genome editing, enabling the removal of the antibiotic resistance markers and facilitating subsequent genetic manipulation. Using this strain, we disrupted the PhoBR two-component regulatory genes and found that deletion of phoBR alleviated the constitutive overexpression of Pho regulon genes and partially restored growth of the Pt-dependent strain. These findings provide mechanistic insights and technical advances for the refinement and practical application of Pt-dependent biocontainment strategy.","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144317019","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}

引用次数: 0

Design of a thermostable bilirubin oxidase from Myrotheciumverrucaria. 一种耐热性胆红素氧化酶的设计。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-06-11 DOI: 10.1016/j.jbiosc.2025.05.006

Haruka Kado Horiguchi, Shohei Yamada, Hironori Semba, Hirokazu Tsuboi, Takayuki Bogaki, Akio Koda, Kazuhiko Ishikawa, Yutaro Mori, Chiaki Ogino, Masahiro Takagi, Yoshio Tsujino

{"title":"Design of a thermostable bilirubin oxidase from Myrotheciumverrucaria.","authors":"Haruka Kado Horiguchi, Shohei Yamada, Hironori Semba, Hirokazu Tsuboi, Takayuki Bogaki, Akio Koda, Kazuhiko Ishikawa, Yutaro Mori, Chiaki Ogino, Masahiro Takagi, Yoshio Tsujino","doi":"10.1016/j.jbiosc.2025.05.006","DOIUrl":"https://doi.org/10.1016/j.jbiosc.2025.05.006","url":null,"abstract":"Bilirubin oxidase (BOD), identified as a multicopper oxidase produced by Myrothecium verrucaria, plays a critical role in the oxidation of bilirubin to biliverdin, which is pivotal in various biochemical processes. To construct a highly thermostable BOD, we have used three protein engineering methods: (i) stabilization of the main chain (proline substitution), (ii) design of salt bridges, and (iii) improvement of hydrophobic interactions. Significant enhancement of thermostability was achieved through stabilization of the main chain (L476P, A496P), introduction of a salt bridge (Q495R), and improvement of hydrophobic interactions (A264V). Furthermore, the combination of these point mutations, which contributed to structural stabilization, resulted in a novel thermostable mutant. Utilizing the cumulative effect of point mutations based on the three strategies, we were able to obtain a thermostable enzyme that exhibited approximately 3.9-fold higher residual activity than wild-type BOD (WT) even after incubation at 60 °C for 1 h and nearly 10 °C higher optimum temperature than that of WT. Importantly, these mutations did not affect its 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) oxidation activity. This approach provides a valuable strategy for improving the thermostability of multivalent copper oxidases and offers promising prospects for industrial applications.","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144284503","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}

引用次数: 0

Response to the letter to the editor on "Evaluation methods for decellularized tissues: A focus on human amniotic membrane". 回复“脱细胞组织的评价方法：以人羊膜为重点”致编辑的信。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-06-10 DOI: 10.1016/j.jbiosc.2025.05.007

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

引用次数: 0

Establishment of a nitrate-reductase promoter-driven inducible expression system for metabolic engineering in the marine diatom Fistulifera solaris. 硝酸还原酶启动子驱动海洋硅藻代谢工程诱导表达系统的建立。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-06-07 DOI: 10.1016/j.jbiosc.2025.05.009

Tomoki Yamanaka, Takashi Yabuuchi, Maeda Yoshiaki, Tomoko Yoshino, Kosuke Kataoka, Tsuyoshi Tanaka

{"title":"Establishment of a nitrate-reductase promoter-driven inducible expression system for metabolic engineering in the marine diatom Fistulifera solaris.","authors":"Tomoki Yamanaka, Takashi Yabuuchi, Maeda Yoshiaki, Tomoko Yoshino, Kosuke Kataoka, Tsuyoshi Tanaka","doi":"10.1016/j.jbiosc.2025.05.009","DOIUrl":"https://doi.org/10.1016/j.jbiosc.2025.05.009","url":null,"abstract":"Microalgae have emerged as promising hosts for producing valuable compounds, including lipids and recombinant proteins. The oleaginous diatom Fistulifera solaris has shown potential for industrial applications. However, the constitutive expression of proteins often causes cellular toxicity, necessitating a controlled gene expression system to enhance productivity. In this study, we characterized the endogenous promoter of the nitrate reductase (NR) gene as an inducible expression system. The promoter was activated by nitrate and suppressed by ammonium. We also established a nitrate-spike method for controlled promoter activation by adding NaNO3 at specific time points, which achieved strong induction without compromising the cellular lipid content. This study provides the first characterization of the NR promoter in an oleaginous diatom and demonstrates its use for controlled compound production. The inducible expression system developed in this study represents fundamental technology for enhancing the productivity of F. solaris.","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144248068","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}

引用次数: 0

Recovery of hyaluronic acid using thermosensitive polymer-salt aqueous biphasic system with polymer recycling. 热敏聚合物-盐双水相体系回收透明质酸的研究。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-06-06 DOI: 10.1016/j.jbiosc.2025.04.007

Nagaraju Marimuthu, Yin Hui Chow, Phei Er Kee, John Chi-Wei Lan, Zee Wei Lai, Li Wan Yoon, Yew Joon Tam

{"title":"Recovery of hyaluronic acid using thermosensitive polymer-salt aqueous biphasic system with polymer recycling.","authors":"Nagaraju Marimuthu, Yin Hui Chow, Phei Er Kee, John Chi-Wei Lan, Zee Wei Lai, Li Wan Yoon, Yew Joon Tam","doi":"10.1016/j.jbiosc.2025.04.007","DOIUrl":"https://doi.org/10.1016/j.jbiosc.2025.04.007","url":null,"abstract":"Microbial fermentation emerges as a viable alternative to animal tissue-based extraction for industrial hyaluronic acid (HA) production. However, microbial HA requires rigorous separation and purification processes to meet high purity standards for cosmeceutical use. Aqueous biphasic system (ABS) presents a promising strategy for HA recovery due to its cost-effectiveness, high yield, purity and eco-friendly nature. Thermosensitive polymer, specifically ethylene oxide-propylene oxide (EOPO)-salt ABS, was proposed in the present study to recover microbial HA from Streptococcus zooepidemicus fermentation broth. The effects of molecular weight (MW) of EOPO, types of salt, phase composition, and the amount of crude extract on the efficiency of ABS for HA recovery were studied. Furthermore, the recovery efficiency of ABS formed using recycled EOPO was investigated. HA exhibited a preference for the salt-rich bottom phase of ABS because of its hydrophilic surface features. Highest partition coefficient of 11.41 ± 0.00 and yield of 93.42 % ± 0.00 % were achieved in ABS containing 14 % (w/w) EOPO2500, 12 % (w/w) sodium citrate at pH 8.2 and 15 % (w/w) crude extract. More than 70 % of EOPO2500 was recovered through the thermo-separation process, and the 1st recycling of EOPO2500 maintained a recovery yield of HA above 80 % in ABS. Moreover, Fourier transform infrared spectroscopy validated that HA retained its structure after the recovery process. In conclusion, this study demonstrates the effectiveness of EOPO-salt ABS for microbial HA recovery, achieving high recovery yield. The recycling of EOPO enhances the economic viability and environmental sustainability of the system. These findings pave the way for greener, scalable HA production practices while maintaining product integrity.","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144248069","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}

引用次数: 0

Discovery and affinity maturation of antibody fragments from an unfavorably enriched phage display selection by deep sequencing and machine learning. 通过深度测序和机器学习从不利富集的噬菌体展示选择中发现抗体片段并进行亲和成熟。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-06-04 DOI: 10.1016/j.jbiosc.2025.05.004

Sakiya Kawada, Yoichi Kurumida, Tomoyuki Ito, Thuy Duong Nguyen, Hafumi Nishi, Hikaru Nakazawa, Yutaka Saito, Tomoshi Kameda, Koji Tsuda, Mitsuo Umetsu

{"title":"Discovery and affinity maturation of antibody fragments from an unfavorably enriched phage display selection by deep sequencing and machine learning.","authors":"Sakiya Kawada, Yoichi Kurumida, Tomoyuki Ito, Thuy Duong Nguyen, Hafumi Nishi, Hikaru Nakazawa, Yutaka Saito, Tomoshi Kameda, Koji Tsuda, Mitsuo Umetsu","doi":"10.1016/j.jbiosc.2025.05.004","DOIUrl":"https://doi.org/10.1016/j.jbiosc.2025.05.004","url":null,"abstract":"Phage display selection has been used for directed evolution of antibody fragments. However, variants with binding affinity cannot be always identified due to undesirable enrichment of target-unrelated variants in the biopanning process. Here, our goal was to obtain functional variants by deep sequencing and machine learning from a phage display library where functional variants were not appropriately enriched. Deep sequencing of the previously biopanned pools revealed that amplification bias might have prevented the enrichment of target-binding phages. We performed a sequence similarity search based on the deep sequencing analysis so that the influence of bias was decreased, leading to discovery of a variant with binding affinity, which could not be discovered by a conventional screening method alone. We applied machine learning to the deep sequencing data; the machine learning proposed effective mutations for increasing affinity, allowing us to identify a variant with improved affinity (EC50 = 3.46 μM). In summary, we present the possibility of obtaining functional variants even from unfavorably enriched phage libraries by using deep sequencing and machine learning.","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234236","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}

引用次数: 0

Preparation of minicircle DNA vectors for gene knock-in to mammalian cells. 哺乳动物细胞基因敲入用小环DNA载体的制备。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-05-29 DOI: 10.1016/j.jbiosc.2025.05.005

Yoshinori Kawabe, Makoto Hamaoka, Akio Kuno, Yusaku Yoshimura, Masamichi Kamihira

{"title":"Preparation of minicircle DNA vectors for gene knock-in to mammalian cells.","authors":"Yoshinori Kawabe, Makoto Hamaoka, Akio Kuno, Yusaku Yoshimura, Masamichi Kamihira","doi":"10.1016/j.jbiosc.2025.05.005","DOIUrl":"https://doi.org/10.1016/j.jbiosc.2025.05.005","url":null,"abstract":"Minicircle DNA vectors (MCs) are gene carriers with favorable characteristics for gene therapy and the production of recombinant cells using animal cells as hosts. Typically, MCs are prepared by inserting target gene fragments as an expression unit into a standard plasmid vector, followed by the removal of bacterial sequences. In this study, we report a method for MC preparation utilizing the Cre-loxP recombination system. By inserting the target gene fragments between two loxP sites introduced into the plasmid vector, the plasmid backbone can be removed through the action of Cre recombinase. We explored optimal reaction conditions for MC generation using Cre. Furthermore, site-specific knock-ins into the CHO cell genome were performed using the remaining loxP sequence in the generated MCs via the Cre-loxP reaction. When MCs were used as gene donors, significant improvements in gene integration efficiency and enhanced gene expression in CHO cells were observed compared with conventional plasmids. The MC preparation and gene knock-in techniques developed in this study are highly useful for CHO cell engineering.","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144187060","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}

引用次数: 0

Construction of contractile human iPSC-derived skeletal muscle tissues on 96-well scale microdevices. 在96孔级微设备上构建可收缩的人类ipsc衍生骨骼肌组织。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-05-28 DOI: 10.1016/j.jbiosc.2025.05.003

Seitaro Nakamura, Yuhei Kamei, Ayumu Matsushima, Kazuki Yamamoto, Hirokazu Akiyama, Muhammad Irfanur Rashid, Yohei Okada, Tomoya Uchimura, Hidetoshi Sakurai, Hiroyuki Honda, Kazunori Shimizu

{"title":"Construction of contractile human iPSC-derived skeletal muscle tissues on 96-well scale microdevices.","authors":"Seitaro Nakamura, Yuhei Kamei, Ayumu Matsushima, Kazuki Yamamoto, Hirokazu Akiyama, Muhammad Irfanur Rashid, Yohei Okada, Tomoya Uchimura, Hidetoshi Sakurai, Hiroyuki Honda, Kazunori Shimizu","doi":"10.1016/j.jbiosc.2025.05.003","DOIUrl":"https://doi.org/10.1016/j.jbiosc.2025.05.003","url":null,"abstract":"Tissue-engineered three-dimensional (3D) skeletal muscles can be potentially used in contractile force-based phenotypic screening to elucidate the mechanisms of skeletal muscle dysfunction and develop preventive and therapeutic strategies. Human induced pluripotent stem cells (hiPSCs) expressing tetracycline-inducible myogenic differentiation 1 (MYOD1) are a promising cell source for construction of tissue-engineered skeletal muscles. Although we successfully constructed contractile tissues using these hiPSCs in a previous study, further improvements are required because of their weak contractile force and inefficient screening capabilities. In this study, we aimed to construct iPSC-derived muscle tissues with high contractile force using a 96-well scale microdevice that we had previously developed. To increase the contractile force, we optimized the time of supplementation of the transforming growth factor-β (TGF-β) inhibitor, SB431542 (SB), to identify culture conditions that enhance contractile force. The maximum contractile force with addition of SB was approximately five times greater than that without SB (58.45 ± 20.14 μN with SB compared to 11.64 ± 4.86 μN without SB). Various analyses, including immunostaining, transmission electron microscopy, gene expression analysis, and proteomics, revealed enhanced myotube differentiation and muscle tissue maturation in the presence of SB. Experiments using inhibitors indicated that TGFβ1, not myostatin, is partially involved in these effects. Furthermore, we confirmed that tissues constructed from iPSCs derived from patients with Duchenne muscular dystrophy also showed improved contractility following addition of SB. Therefore, iPSC-derived muscle tissues cultured with SB on the 96-well microdevice provide a promising platform for screening compounds that can ameliorate disease pathology.","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144181801","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}

引用次数: 0