Journal of bioscience and bioengineering最新文献_第3页

Data-independent acquisition-based lipidomics reveals lipidome alterations associated with growth of Saccharomyces cerevisiae at low temperature 基于数据独立获取的脂质组学揭示了脂质组改变与酿酒酵母在低温下的生长有关。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-04-16 DOI: 10.1016/j.jbiosc.2025.03.004

Daiki Hara , Nobuyuki Okahashi , Taisuke Seike , Junko Iida , Fumio Matsuda

{"title":"Data-independent acquisition-based lipidomics reveals lipidome alterations associated with growth of Saccharomyces cerevisiae at low temperature","authors":"Daiki Hara , Nobuyuki Okahashi , Taisuke Seike , Junko Iida , Fumio Matsuda","doi":"10.1016/j.jbiosc.2025.03.004","DOIUrl":"10.1016/j.jbiosc.2025.03.004","url":null,"abstract":"<div><div>Budding yeast, <em>Saccharomyces cerevisiae</em>, adapts to low-temperature stress by altering the amounts and proportions of phospholipids, as well as the structures of acyl chains. To better understand this process, a data-independent acquisition-based lipidomics using liquid chromatography–quadrupole time-of-flight mass spectrometry method was developed to quantify acyl chain isomers in glycerolipids and phospholipids. This method distinguished lipid molecular species, such as phosphatidylcholine (PC) 16:1_18:0 and PC16:0_18:1, at the level of acyl chain isomers. These species were previously identified only at the total acyl chain level as PC 34:1 using the conventional data-dependent acquisition (DDA) method. Using this approach, 145 diacyl lipid molecular species were identified in <em>S. cerevisiae</em> at 30 °C, compared to only 101 identified using the conventional DDA method. Analysis of <em>S. cerevisiae</em> at 10 °C revealed 121 phospholipid and diacylglycerol (DG) molecular species and 260 triacylglycerol (TG) features as well as other 51 sphingolipids and sterol lipids. The results demonstrated unique increases in phosphatidylinositol (PI), phosphatidylethanolamine (PE), monomethyl (MM) PE, and TG containing both 16:1 and medium-chain fatty acids (MCFAs). The knockout strains <em>ole1Δ</em> and <em>slc1Δ</em>, lacking the desaturase that produces 16:1 and the acyltransferase favoring MCFAs, respectively, exhibited growth defects exclusively while growing at 10 °C. These findings suggest that <em>S. cerevisiae</em> regulates its lipid profiles to address low-temperature stress.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 6","pages":"Pages 414-423"},"PeriodicalIF":2.3,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143993132","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

Developing a simple activity test to estimate nitrous oxide production from sewage treatment 开发一种简单的活性测试来估计污水处理产生的氧化亚氮。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-04-11 DOI: 10.1016/j.jbiosc.2025.03.003

Shuhei Masuda , Shohei Otomo , Toshimasa Hojo , Akihiko Terada , Hiroshi Yamazaki , Juhyun Kim , Yu-You Li , Fumiaki Takakai , Naoyuki Miyata

引用次数: 0

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

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-04-04 DOI: 10.1016/j.jbiosc.2025.02.010

Mathilde Fénelon, Nicolas Lheureux, Florelle Gindraux

引用次数: 0

Deep-learning-assisted medium optimization improves hyaluronic acid production by Streptococcus zooepidemicus 深度学习辅助培养基优化提高动物流行链球菌透明质酸产量。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-04-03 DOI: 10.1016/j.jbiosc.2025.03.001

Kazuki Watanabe , Yoshizumi Kawai , Tomoko Kagenishi , Tai-Ying Chiou , Masaaki Konishi

{"title":"Deep-learning-assisted medium optimization improves hyaluronic acid production by Streptococcus zooepidemicus","authors":"Kazuki Watanabe , Yoshizumi Kawai , Tomoko Kagenishi , Tai-Ying Chiou , Masaaki Konishi","doi":"10.1016/j.jbiosc.2025.03.001","DOIUrl":"10.1016/j.jbiosc.2025.03.001","url":null,"abstract":"<div><div>To improve the efficiency of hyaluronic acid production by <em>Streptococcus zooepidemicus</em>, the growth medium was optimized with a pipeline involving a deep learning (DL) algorithm. To train the DL model, the initial training dataset (OA01–18) was designed with the L18 orthogonal array, and hyaluronic acid (HA) was produced in small-scale cultures in deepwell plates. The range of HA production was 0.09–1.39 g/L under these conditions. In searching for the optimal medium composition, 54 candidate optimized media (OM01–54) were proposed by the system. According to the confirming culture experiment, the best production of HA (1.66 g/L) was achieved with OM30. During confirmation in a stirred-tank reactor, the volumetric production of HA in OA30 was larger than that in the control medium. In fed batch culture, HA accumulated to 5.13 and 9.96 g/L<sub>initial volume</sub> after 10 and 30 h in culture, respectively. To avoid the suppression of HA production by the high viscosity of the medium conferred by HA, repeated batch culture with OM30 was performed by replacing 90 % of the broth volume approximately every 6 h. As a result, 21.4 g of HA was produced in 46 h, and productivity reached 0.465 g/L<sub>initial volume</sub>/h.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 6","pages":"Pages 429-435"},"PeriodicalIF":2.3,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795553","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

New natural products from Aspergillus candidus NRRL 5214 and their glycosylation by Streptomyces chromofuscus ATCC 49982 白曲霉NRRL 5214的新天然产物及其被色褐链霉菌ATCC 49982糖基化。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-04-03 DOI: 10.1016/j.jbiosc.2025.03.002

Jie Ren , Kyle Jackson , Caleb Don Barton , Hassan Sher , Yu Huang , Jixun Zhan

{"title":"New natural products from Aspergillus candidus NRRL 5214 and their glycosylation by Streptomyces chromofuscus ATCC 49982","authors":"Jie Ren , Kyle Jackson , Caleb Don Barton , Hassan Sher , Yu Huang , Jixun Zhan","doi":"10.1016/j.jbiosc.2025.03.002","DOIUrl":"10.1016/j.jbiosc.2025.03.002","url":null,"abstract":"<div><div>Fungi represent a rich source of bioactive natural products. In this study, we present the isolation and identification of two new diphenyl ethers, named aspergilluscandidus A (<strong>1</strong>) and aspergilluscandidus B (<strong>2</strong>), along with a known compound terphenyllin (<strong>3</strong>), from the fungal strain <em>Aspergillus candidus</em> NRRL 5214. The chemical structures of compounds <strong>1</strong>–<strong>3</strong> were characterized through extensive 1D and 2D NMR analysis. Compounds <strong>1</strong> and <strong>3</strong> were subsequently biotransformed into two new glycosides, namely aspergilluscandidus C (<strong>4</strong>) and terphenyllin-4″-<em>O</em>-β-<span>d</span>-glucuronide (<strong>5</strong>) by the actinomycete strain <em>Streptomyces chromofuscus</em> ATCC 49982. The cytotoxicity assay revealed that the glycosylated products <strong>4</strong> and <strong>5</strong> exhibited significantly improved activity against the glioblastoma 33 cell line compared to their respective substrates, decreasing the IC<sub>50</sub> from 8.15 ± 1.09 μM (<strong>1</strong>) to 5.41 ± 0.30 μM (<strong>4</strong>) and from 88.29 ± 10.54 μM (<strong>3</strong>) to 31.25 ± 4.20 μM (<strong>5</strong>), respectively. Our study emphasizes <em>A. candidus</em> NRRL 5214 as a promising source of new natural products and presents an effective strategy for modifying both diphenyl ether and <em>p</em>-terphenyl compounds using <em>S</em>. <em>chromofuscus</em> ATCC 49982 to enhance their cytotoxicity activity.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 6","pages":"Pages 406-413"},"PeriodicalIF":2.3,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795560","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

Polyvinyl alcohol, N-acetylcysteine, and methyl-β-cyclodextrin exhibit albumin functions in natural killer cell culture 聚乙烯醇、n -乙酰半胱氨酸和甲基β-环糊精在自然杀伤细胞培养中表现出白蛋白功能。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-03-24 DOI: 10.1016/j.jbiosc.2025.02.008

Ruisheng Xu, Guofeng Zhang, Huimin Huang, Yuanyuan Zhao, Wen-Song Tan, Haibo Cai

{"title":"Polyvinyl alcohol, N-acetylcysteine, and methyl-β-cyclodextrin exhibit albumin functions in natural killer cell culture","authors":"Ruisheng Xu, Guofeng Zhang, Huimin Huang, Yuanyuan Zhao, Wen-Song Tan, Haibo Cai","doi":"10.1016/j.jbiosc.2025.02.008","DOIUrl":"10.1016/j.jbiosc.2025.02.008","url":null,"abstract":"<div><div>Albumin is a crucial component of serum-free media, playing a significant role in ex vivo cell culture as a lipid carrier and antioxidant. However, purified albumin contains undefined substances, making it challenging to achieve clinical application standards for effector cell culture. This study used natural killer (NK)-92 cells as a model to investigate the effects of the albumin substitute replacing bovine serum albumin (BSA) on cell expansion and metabolism in an in-house-designed, chemically defined, serum-free medium. We selected polyvinyl alcohol (PVA), <em>N</em>-acetylcysteine (NAC), and methyl-β-cyclodextrin (M-β-CD) as an albumin substitute combination and optimized their concentrations by using response surface methodology. The optimized albumin substitute was named PVA-NAC-M-β-CD (PNM). After 8 days of culture, NK-92 cells cultured with the PNM exhibited phenotype and cytotoxic function comparable to cells cultured with different concentrations of BSA. The expansion fold was 89.22 ± 3.55, significantly higher than the 51.23 ± 6.57 observed in the 0.75 g/L BSA group (<em>p</em> < 0.05). Further verification of functions of PNM showed that intracellular fatty acid levels, cholesterol consumption rates, and the pSTAT5 level in the PNM group were significantly higher than those in the 0.75 g/L BSA group (<em>p</em> < 0.05). Reactive oxygen species levels remained controlled, and mitochondrial membrane potential was similar. These findings suggested that the PNM can effectively replace the functions of BSA as a fatty acid carrier, antioxidant, and, to some extent, a cholesterol carrier. This study provides insights for developing chemically defined media to prepare clinical-grade NK cells efficiently.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 6","pages":"Pages 436-444"},"PeriodicalIF":2.3,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143709905","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

Evaluation of antibody variants using a ribosome display and Brevibacillus choshinensis secretion system 利用核糖体显示和短芽孢杆菌分泌系统评价抗体变异。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-03-22 DOI: 10.1016/j.jbiosc.2025.02.009

Monami Kihara , Rio Okuda , Anri Okada , Teruyo Ojima-Kato , Hideo Nakano

{"title":"Evaluation of antibody variants using a ribosome display and Brevibacillus choshinensis secretion system","authors":"Monami Kihara , Rio Okuda , Anri Okada , Teruyo Ojima-Kato , Hideo Nakano","doi":"10.1016/j.jbiosc.2025.02.009","DOIUrl":"10.1016/j.jbiosc.2025.02.009","url":null,"abstract":"<div><div>In antibody engineering, the development of rapid and efficient strategies for improving affinity is highly necessary. In this study, we aimed to establish a method to efficiently enrich and analyze high-affinity antibody variants by combining protein synthesis using recombinant elements (PURE) ribosome display with next-generation sequencing (NGS) and <em>Brevibacillus choshinensis</em> secretion system using the NZ-1 antibody, which targets the PA tag peptide (GVAMPGAEDDVV) as a model antibody. From the mutated scFab library designed based on the structure, we performed a single-round of PURE ribosome display selection and analyzed the data by NGS to obtain high-affinity scFab candidates with high enrichment factor and high read counts. Subsequently, the most promising candidate was produced as a Fab in the <em>B. choshinensis</em> secretion system, and the purified Fab had an affinity (<em>K</em><sub><em>D</em></sub> = 1.6 × 10<sup>−9</sup> M) similar to the wild type. Overall, this study highlights the potential of the integrated PURE ribosome display with NGS analysis and the <em>B. choshinensis</em> secretion system for the rapid identification and analysis of high-affinity antibody variants.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 6","pages":"Pages 457-464"},"PeriodicalIF":2.3,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692222","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

Overproduction of secondary metabolites in Photorhabdus noenieputensis through rpoB mutations 通过rpoB突变，noenieputensis次生代谢物过量产生。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-03-21 DOI: 10.1016/j.jbiosc.2025.02.004

Yu Imai

{"title":"Overproduction of secondary metabolites in Photorhabdus noenieputensis through rpoB mutations","authors":"Yu Imai","doi":"10.1016/j.jbiosc.2025.02.004","DOIUrl":"10.1016/j.jbiosc.2025.02.004","url":null,"abstract":"<div><div>Specific mutations of the <em>rpoB</em> gene, which encodes the β subunit of bacterial RNA polymerase, can enhance the production of secondary metabolites in bacteria such as actinomycetes. Entomopathogenic bacteria <em>Photorhabdus</em> and <em>Xenorhabdus</em> species produce a variety of secondary metabolites. Recently, these genera have attracted attention as a promising source for novel antibiotics. In this study, the effect of <em>rpoB</em> mutations on secondary metabolite production in <em>Photorhabdus noenieputensis</em> DSM 25462, a known producer of the antituberculosis antibiotic evybactin, was evaluated. Spontaneous rifampicin-resistant mutants, frequently carrying <em>rpoB</em> mutations, were generated by plating cells on agar medium containing four times the minimum inhibitory concentration (MIC) of rifampicin and evaluated their antibacterial production using <em>Escherichia coli</em> WO153 as a test strain. Among 190 spontaneous rifampicin-resistant mutants of <em>P. noenieputensis</em>, strain designated R191, which harbors the <em>rpoB</em> Q148K mutation (C442A), displayed higher antibacterial activity than that of the parental strain DSM 25462. The real-time quantitative RT-PCR analysis of 20 putative secondary metabolite biosynthetic gene clusters (BGCs) identified using antiSMASH revealed that seven of these BGCs were overexpressed in the strain R191. Furthermore, comparative high-pressure liquid chromatography (HPLC) analysis of the metabolite profile indicated that the strain R191 produced several compounds that were not detectable in the DSM 25462 culture. These findings suggest that the introduction of <em>rpoB</em> mutations into <em>Photorhabdus</em> strains is an effective strategy for enhancing secondary metabolite production and may lead to the discovery of novel antibiotics.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 6","pages":"Pages 399-405"},"PeriodicalIF":2.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692225","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

Application of silica monoliths for improved storage stability of metabolites in human plasma 二氧化硅整体石在改善人血浆中代谢物储存稳定性中的应用。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-03-13 DOI: 10.1016/j.jbiosc.2025.02.007

Kazuhiro Kawamura , Eiichiro Fukusaki

{"title":"Application of silica monoliths for improved storage stability of metabolites in human plasma","authors":"Kazuhiro Kawamura , Eiichiro Fukusaki","doi":"10.1016/j.jbiosc.2025.02.007","DOIUrl":"10.1016/j.jbiosc.2025.02.007","url":null,"abstract":"<div><div>In metabolomic studies, sample collection and analysis are typically performed at separate locations, necessitating the transport and storage of samples. However, sample transport and storage conditions are often constrained by the available facilities. Specifically, metabolite levels in biological and food samples can fluctuate due to the activity of endogenous enzymes, depending on the transport and storage conditions. Therefore, in this study, we aimed to achieve metabolite stabilization during storage by sampling human plasma on silica monoliths. Silica monoliths maintained the metabolite samples in a dry state, enabling their transport and storage at high temperatures. Plasmas stored at room temperature and refrigerated were measured using gas chromatography/mass spectrometry (GC/MS), and the fluctuations in metabolites between normal storage and storage on silica monoliths were compared. As a result, fluctuations in several metabolites such as glucose and amino acids were observed during normal storage. However, these were suppressed during storage on silica monoliths. Overall, our findings highlight the efficiency of silica monoliths for sample transport and storage at high temperatures.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 6","pages":"Pages 451-456"},"PeriodicalIF":2.3,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143630501","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

Role of low-level alternating current and impedance for enhancing microalgae biomass and lipid production 低水平交流电流和阻抗对提高微藻生物量和脂质产量的作用。

IF 2.3 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-03-10 DOI: 10.1016/j.jbiosc.2025.02.001

Carine Souza da Silva , Gustavo Miranda Pires Santos , Gabriele Rodrigues Conceição , Ian da Silva Andrade , Alana Nogueira Silva , Rodrigo Miranda Pires Santos , Paulo Fernando de Almeida , Fabio Alexandre Chinalia

{"title":"Role of low-level alternating current and impedance for enhancing microalgae biomass and lipid production","authors":"Carine Souza da Silva , Gustavo Miranda Pires Santos , Gabriele Rodrigues Conceição , Ian da Silva Andrade , Alana Nogueira Silva , Rodrigo Miranda Pires Santos , Paulo Fernando de Almeida , Fabio Alexandre Chinalia","doi":"10.1016/j.jbiosc.2025.02.001","DOIUrl":"10.1016/j.jbiosc.2025.02.001","url":null,"abstract":"<div><div>Microalgae hold significant potential for producing value-added bioproducts in pharmaceutical, cosmetic, food, and biofuel industries, with a global market value estimated at US$ 11.8 billion in 2023. Innovations in culturing systems, such as electric stimulation, aim to enhance growth performance, as it can improve cellular processes, including nutrient uptake and lipid accumulation. This study investigates the effect of low alternating electrical currents (μA) on the growth and lipid production of the halotolerant microalga <em>Dunaliella salina</em> across varying salt concentrations (3.5 % and 8.5 % Conway medium). Applying electric stimulation at 50, 750, and 990 μA for 30 min daily over 15 days resulted in significant enhancements, particularly at 3.5 % salinity, where lipid content increased by 144 %. The findings indicate that electrical stimulation notably reduced the lag phase and increased exponential growth rates, with superior growth coefficients correlating with higher medium impedance rather than direct current levels.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"139 5","pages":"Pages 369-376"},"PeriodicalIF":2.3,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604997","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