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

Functionalized peptide hydrogel to generate human insulin-producing cells in vitro 功能化肽水凝胶体外生成人胰岛素生成细胞。

IF 2.9 4区生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of bioscience and bioengineering

Pub Date : 2025-12-23 DOI: 10.1016/j.jbiosc.2025.11.007

Brandhon F. Flores-Ibarra , Andrea I. Enríquez-Rodríguez , Kimberly P. Robles-Pablos , Beatriz A. Rodas-Junco , Waldo M. Argüelles-Monal , Luisa L. Silva-Gutiérrez , Refugio Pérez-González , Olga A. Patrón-Soberano , Carmen S. Rochín-Wong , Luis A. Castillo-Díaz

Type I diabetes is a chronic disease that affects people worldwide. When insulin administration is no longer effective, transplantation of pancreatic islets represents an alternative for diabetics. However, islet grafting carries limitations, which include poor availability of donors, surgery risks, and lifelong immunosuppressive therapy. To address this, novel approaches, such as the use of soft hydrogels as vehicles of cells are being developed for tissue grafting applications. Self-assembling peptide hydrogels (SAPHs) are biocompatible and versatile materials widely used for both, three-dimensional (3D) cell culture and regenerative medicine applications. Therefore, in this study, we explored the effect of the functionalization of the SAPH FEFEFKFKK (FEK9) with extracellular matrix (ECM) motifs, RGD, GFOGER and IKVAV, to support the directed differentiation of human dental pulp stem cells (hDPSCs) into insulin-producing cells (IPCs). The resulting ECM-functionalized FEK9 hydrogel was formed under mildly acidic conditions (pH 5–6). Infrared spectroscopy confirmed that ECM-FEK9 adopts a β-sheet secondary structure and forms a dense nanofibrillar network, while rheological measurements demonstrated the formation of a soft hydrogel. hDPSC cultured in hydrogel displayed steady viability and metabolism. Moreover, under directed induction, cells in ECM-FEK9 expressed β-cell markers, such as PDX-1 and Glut-2, as well as synthetized insulin within 10 days of 3D culture in vitro, as evidenced through fluorescence confocal microscopy and spectrophotometry evaluations, respectively. Therefore, ECM-FEK9 could be a promising candidate to support the culture of hDPSCs and the generation of IPCs after refinement of directed induction under 3D cell culture conditions.

1型糖尿病是一种影响全世界人民的慢性疾病。当胰岛素治疗不再有效时，胰岛移植是糖尿病患者的另一种选择。然而，胰岛移植有其局限性，包括供体缺乏、手术风险和终身免疫抑制治疗。为了解决这个问题，新的方法，如使用软水凝胶作为细胞载体，正在开发用于组织移植应用。自组装肽水凝胶（SAPHs）是一种生物相容性和多功能材料，广泛用于三维（3D）细胞培养和再生医学应用。因此，在本研究中，我们探索了SAPH FEFEFKFKK （FEK9）与细胞外基质（ECM）基序- RGD， GFOGER和IKVAV -功能化的作用，以支持人牙髓干细胞（hDPSCs）向胰岛素生成细胞（IPCs）的定向分化。得到的ecm功能化FEK9水凝胶在温和的酸性条件下（pH 5-6）形成。红外光谱证实ECM-FEK9采用β-片二级结构，形成致密的纳米纤维网络，而流变学测量表明形成了柔软的水凝胶。水凝胶培养的hDPSC表现出稳定的活力和代谢。此外，在定向诱导下，ECM-FEK9细胞在体外3D培养10天内分别通过荧光共聚焦显微镜和分光光度法评估，表达β细胞标记物，如PDX-1和Glut-2，并合成胰岛素。因此，ECM-FEK9可能是支持hdpsc培养和在3D细胞培养条件下定向诱导后生成IPCs的有希望的候选者。

{"title":"Functionalized peptide hydrogel to generate human insulin-producing cells in vitro","authors":"Brandhon F. Flores-Ibarra , Andrea I. Enríquez-Rodríguez , Kimberly P. Robles-Pablos , Beatriz A. Rodas-Junco , Waldo M. Argüelles-Monal , Luisa L. Silva-Gutiérrez , Refugio Pérez-González , Olga A. Patrón-Soberano , Carmen S. Rochín-Wong , Luis A. Castillo-Díaz","doi":"10.1016/j.jbiosc.2025.11.007","DOIUrl":"10.1016/j.jbiosc.2025.11.007","url":null,"abstract":"<div><div>Type I diabetes is a chronic disease that affects people worldwide. When insulin administration is no longer effective, transplantation of pancreatic islets represents an alternative for diabetics. However, islet grafting carries limitations, which include poor availability of donors, surgery risks, and lifelong immunosuppressive therapy. To address this, novel approaches, such as the use of soft hydrogels as vehicles of cells are being developed for tissue grafting applications. Self-assembling peptide hydrogels (SAPHs) are biocompatible and versatile materials widely used for both, three-dimensional (3D) cell culture and regenerative medicine applications. Therefore, in this study, we explored the effect of the functionalization of the SAPH FEFEFKFKK (FEK9) with extracellular matrix (ECM) motifs, RGD, GFOGER and IKVAV, to support the directed differentiation of human dental pulp stem cells (hDPSCs) into insulin-producing cells (IPCs). The resulting ECM-functionalized FEK9 hydrogel was formed under mildly acidic conditions (pH 5–6). Infrared spectroscopy confirmed that ECM-FEK9 adopts a β-sheet secondary structure and forms a dense nanofibrillar network, while rheological measurements demonstrated the formation of a soft hydrogel. hDPSC cultured in hydrogel displayed steady viability and metabolism. Moreover, under directed induction, cells in ECM-FEK9 expressed β-cell markers, such as PDX-1 and Glut-2, as well as synthetized insulin within 10 days of 3D culture <em>in vitro</em>, as evidenced through fluorescence confocal microscopy and spectrophotometry evaluations, respectively. Therefore, ECM-FEK9 could be a promising candidate to support the culture of hDPSCs and the generation of IPCs after refinement of directed induction under 3D cell culture conditions.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 3","pages":"Pages 185-193"},"PeriodicalIF":2.9,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145819421","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

Production and characterization of norovirus virus-like particles vaccine candidates in a genetically modified Ogataea minuta system 诺如病毒样颗粒候选疫苗在转基因欧加藤系统中的生产和特性研究。

IF 2.9 4区生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of bioscience and bioengineering

Pub Date : 2025-12-20 DOI: 10.1016/j.jbiosc.2025.11.008

Masashi Tsuda , Yuki Nakatani , Satoshi Baba , Kumi Yoshida , Kazuhiko Someya , Yoshikuni Onodera , Koichi Nonaka , Yasunori Chiba

The development of an effective vaccine against noroviruses remains a major public health priority. Norovirus GII.4 capsid protein VP1 as a promising vaccine candidate was produced by the methylotrophic yeast Ogataea minuta production system. It was intracellularly expressed and subsequently purified by immobilized metal affinity chromatography and anion exchange chromatography, yielding 13.4 mg of highly purified VP1 protein from 50 mL of culture supernatant. The formation of VP1-based virus-like particles (VLPs) that retained their structure even after freeze-thawing was confirmed by transmission electron microscopy. The VP1 protein purified in the form of VLPs displayed strong antigenicity and specific, dose-dependent binding to histo-blood group antigens, as determined by the enzyme-linked immunosorbent assay (ELISA). Immunogenicity studies in BALB/c mice demonstrated that intramuscular administration induced robust serum IgG responses across all tested doses, with no significant dose-dependent differences. Furthermore, mucosal administration intranasally or sublingually induced systemic IgG, systemic IgA, and mucosal IgA responses. These responses were significantly enhanced by the lipid A adjuvant. These findings showed that the O. minuta production system is capable of producing immunogenic Norovirus VLPs as a vaccine candidate.

研制诺如病毒的有效疫苗仍然是一项主要的公共卫生优先事项。利用甲基营养酵母（Ogataea minuta）生产系统生产诺如病毒GII.4衣壳蛋白VP1。通过细胞内表达，固定化金属亲和层析和阴离子交换层析纯化，从50 mL培养上清中得到13.4 mg高纯度VP1蛋白。基于vp1的病毒样颗粒（vlp）的形成，即使在冻融后仍保持其结构，这是通过透射电子显微镜证实的。通过酶联免疫吸附试验（ELISA）确定，以VLPs形式纯化的VP1蛋白表现出很强的抗原性和特异性，与组织血型抗原的剂量依赖性结合。BALB/c小鼠的免疫原性研究表明，在所有测试剂量中，肌肉注射诱导了强大的血清IgG反应，没有显著的剂量依赖性差异。此外，鼻内或舌下粘膜给药可诱导全身IgG、全身IgA和粘膜IgA反应。脂质A佐剂显著增强了这些反应。这些发现表明，O. minuta生产系统能够生产免疫原性诺如病毒VLPs作为候选疫苗。

{"title":"Production and characterization of norovirus virus-like particles vaccine candidates in a genetically modified Ogataea minuta system","authors":"Masashi Tsuda , Yuki Nakatani , Satoshi Baba , Kumi Yoshida , Kazuhiko Someya , Yoshikuni Onodera , Koichi Nonaka , Yasunori Chiba","doi":"10.1016/j.jbiosc.2025.11.008","DOIUrl":"10.1016/j.jbiosc.2025.11.008","url":null,"abstract":"<div><div>The development of an effective vaccine against noroviruses remains a major public health priority. Norovirus GII.4 capsid protein VP1 as a promising vaccine candidate was produced by the methylotrophic yeast <em>Ogataea minuta</em> production system. It was intracellularly expressed and subsequently purified by immobilized metal affinity chromatography and anion exchange chromatography, yielding 13.4 mg of highly purified VP1 protein from 50 mL of culture supernatant. The formation of VP1-based virus-like particles (VLPs) that retained their structure even after freeze-thawing was confirmed by transmission electron microscopy. The VP1 protein purified in the form of VLPs displayed strong antigenicity and specific, dose-dependent binding to histo-blood group antigens, as determined by the enzyme-linked immunosorbent assay (ELISA). Immunogenicity studies in BALB/c mice demonstrated that intramuscular administration induced robust serum IgG responses across all tested doses, with no significant dose-dependent differences. Furthermore, mucosal administration intranasally or sublingually induced systemic IgG, systemic IgA, and mucosal IgA responses. These responses were significantly enhanced by the lipid A adjuvant. These findings showed that the <em>O. minuta</em> production system is capable of producing immunogenic Norovirus VLPs as a vaccine candidate.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 3","pages":"Pages 165-171"},"PeriodicalIF":2.9,"publicationDate":"2025-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145804660","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

Spheroid size-induced apoptosis enhances osteogenic differentiation of iPS cells 球体大小诱导的细胞凋亡促进iPS细胞成骨分化。

IF 2.9 4区生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of bioscience and bioengineering

Pub Date : 2025-12-20 DOI: 10.1016/j.jbiosc.2025.11.010

Hideto Tatsumi , Hiroko Okawa , Naruephorn Vinaikosol , Akihito Moribayashi , Hiroki Kayashima , Hirofumi Yatani , Hiroshi Egusa

Induced pluripotent stem cells (iPSCs) have significant potential for regenerative medicine, particularly for bone tissue engineering. While three-dimensional spheroid cultures enhance iPSC differentiation by better mimicking physiological conditions, spheroid size critically affects cell viability and differentiation ability. Microwell plates enable large-scale production of uniform spheroids and would be especially useful for regenerative medicine and tissue engineering. Here, we investigated the effect of spheroid size on the osteogenic differentiation of iPSCs using microwell plates to generate spheroids under the following conditions: Elp200 (microwell plate with 200/100 μm diameter/depth) and Elp900 (microwell plate with 900/700 μm). We observed that larger Elp900 spheroids promoted mesodermal differentiation more effectively, likely due to enhanced cell–cell interactions and altered internal microenvironments. However, Elp900 spheroids exhibited increased apoptosis in their core regions, evidenced by viability staining, transmission electron microscopy, and TUNEL staining. Upon dissociation and adherent culture, Elp900-derived cells demonstrated significantly higher expression of osteogenic markers (Runx2, Ibsp) and mineralization compared to Elp200-derived cells. Proteomic analysis revealed that apoptosis- and extracellular matrix (ECM)-related proteins, such as SERPINH1 and COL4A1, were upregulated in Elp900 cultures. These findings suggest that controlled apoptosis within larger spheroids may activate stress-related pathways, promote ECM formation, and enhance osteogenic differentiation by activating the TGF-β signaling pathway. Our findings highlight optimal spheroid sizing as a key factor for maximizing the efficiency and reproducibility of osteogenic differentiation of iPSCs, providing a foundation for improved strategies in iPSC-based bone tissue regeneration.

诱导多能干细胞（iPSCs）在再生医学，特别是骨组织工程方面具有巨大的潜力。虽然三维球形培养物通过更好地模拟生理条件来促进iPSC的分化，但球形大小对细胞的活力和分化能力有重要影响。微孔板使均匀球体的大规模生产成为可能，对再生医学和组织工程尤其有用。本研究采用Elp200（直径/深度为200/100 μm的微孔板）和Elp900（直径/深度为900/700 μm的微孔板）制备球形细胞，研究了球形细胞大小对iPSCs成骨分化的影响。我们观察到较大的Elp900球体更有效地促进了中胚层分化，可能是由于细胞间相互作用增强和内部微环境改变。然而，活力染色、透射电镜和TUNEL染色表明，Elp900球体的核心区域细胞凋亡增加。在分离和贴壁培养后，与elp200来源的细胞相比，elp900来源的细胞表现出明显更高的成骨标志物（Runx2, Ibsp）和矿化表达。蛋白质组学分析显示，凋亡和细胞外基质（ECM）相关蛋白，如SERPINH1和COL4A1，在Elp900培养中上调。这些研究结果表明，大球体内的受控凋亡可能通过激活TGF-β信号通路激活应激相关通路，促进ECM形成，并增强成骨分化。我们的研究结果强调了最佳球体大小是最大限度地提高ipsc成骨分化效率和可重复性的关键因素，为改进基于ipsc的骨组织再生策略提供了基础。

{"title":"Spheroid size-induced apoptosis enhances osteogenic differentiation of iPS cells","authors":"Hideto Tatsumi , Hiroko Okawa , Naruephorn Vinaikosol , Akihito Moribayashi , Hiroki Kayashima , Hirofumi Yatani , Hiroshi Egusa","doi":"10.1016/j.jbiosc.2025.11.010","DOIUrl":"10.1016/j.jbiosc.2025.11.010","url":null,"abstract":"<div><div>Induced pluripotent stem cells (iPSCs) have significant potential for regenerative medicine, particularly for bone tissue engineering. While three-dimensional spheroid cultures enhance iPSC differentiation by better mimicking physiological conditions, spheroid size critically affects cell viability and differentiation ability. Microwell plates enable large-scale production of uniform spheroids and would be especially useful for regenerative medicine and tissue engineering. Here, we investigated the effect of spheroid size on the osteogenic differentiation of iPSCs using microwell plates to generate spheroids under the following conditions: Elp200 (microwell plate with 200/100 μm diameter/depth) and Elp900 (microwell plate with 900/700 μm). We observed that larger Elp900 spheroids promoted mesodermal differentiation more effectively, likely due to enhanced cell–cell interactions and altered internal microenvironments. However, Elp900 spheroids exhibited increased apoptosis in their core regions, evidenced by viability staining, transmission electron microscopy, and TUNEL staining. Upon dissociation and adherent culture, Elp900-derived cells demonstrated significantly higher expression of osteogenic markers (<em>Runx2</em>, <em>Ibsp</em>) and mineralization compared to Elp200-derived cells. Proteomic analysis revealed that apoptosis- and extracellular matrix (ECM)-related proteins, such as SERPINH1 and COL4A1, were upregulated in Elp900 cultures. These findings suggest that controlled apoptosis within larger spheroids may activate stress-related pathways, promote ECM formation, and enhance osteogenic differentiation by activating the TGF-β signaling pathway. Our findings highlight optimal spheroid sizing as a key factor for maximizing the efficiency and reproducibility of osteogenic differentiation of iPSCs, providing a foundation for improved strategies in iPSC-based bone tissue regeneration.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 3","pages":"Pages 203-209"},"PeriodicalIF":2.9,"publicationDate":"2025-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145804722","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

Establishment of a simple and novel method for contact-dependent intercellular interaction analysis using extracellular vesicles 利用细胞外囊泡建立一种简单而新颖的接触依赖性细胞间相互作用分析方法。

IF 2.9 4区生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of bioscience and bioengineering

Pub Date : 2025-12-16 DOI: 10.1016/j.jbiosc.2025.11.009

Rina Sakamaki , Takao Matsuba , Yasuyuki Kurihara

Extracellular vesicles (EVs), including exosomes, microvesicles, and apoptotic bodies, are membrane-bound vesicles secreted by cells. They play essential roles in intercellular communications and are involved in numerous physiological processes. Given their functional importance, EVs have emerged as promising tools for diagnosing and treating various diseases. In this study, we focused on the utility of EVs and explored their application in the analysis of contact-dependent cell–cell interactions, which are essential for the control of cell differentiation and induction of immune responses. Although several methods have been developed to evaluate these interactions, they often require complex procedures and advanced optimization, limiting their broad applicability. To overcome these limitations, we developed a novel method utilizing EVs to present membrane proteins in their native conformations. Our strategy involved producing fluorescently labeled EVs with target antigens and quantitatively assessing their binding to target cells via flow cytometry. Using fluorescently labeled EVs presenting with either an N-terminal pro-brain natriuretic peptide or interleukin-2 receptor, we successfully detected specific interactions with corresponding hybridoma B cell receptors. This simpler method requires no advanced optimization and effectively analyzes cell–cell interactions under physiological conditions in a high-throughput and quantitative manner. Our findings highlight the potential of this EV-based system as a valuable tool for studying membrane protein-mediated cell–cell interactions in bioscience research.

细胞外囊泡（EVs）是由细胞分泌的膜结合囊泡，包括外泌体、微囊泡和凋亡小体。它们在细胞间通讯中起着至关重要的作用，并参与许多生理过程。鉴于其功能的重要性，电动汽车已成为诊断和治疗各种疾病的有前途的工具。在这项研究中，我们重点关注了ev的应用，并探讨了它们在分析接触依赖的细胞-细胞相互作用中的应用，这是控制细胞分化和诱导免疫反应所必需的。虽然已经开发了几种方法来评估这些相互作用，但它们通常需要复杂的程序和高级优化，限制了它们的广泛适用性。为了克服这些限制，我们开发了一种利用ev以其天然构象呈现膜蛋白的新方法。我们的策略包括生产带有靶抗原的荧光标记ev，并通过流式细胞术定量评估其与靶细胞的结合。利用荧光标记的ev，我们成功地检测了其与相应的杂交瘤B细胞受体的特异性相互作用，这些ev要么呈n端前脑利钠肽，要么呈白介素-2受体。这种简单的方法不需要高级优化，可以高通量和定量地有效分析生理条件下细胞-细胞相互作用。我们的研究结果强调了这种基于ev的系统在生物科学研究中作为研究膜蛋白介导的细胞-细胞相互作用的有价值工具的潜力。

{"title":"Establishment of a simple and novel method for contact-dependent intercellular interaction analysis using extracellular vesicles","authors":"Rina Sakamaki , Takao Matsuba , Yasuyuki Kurihara","doi":"10.1016/j.jbiosc.2025.11.009","DOIUrl":"10.1016/j.jbiosc.2025.11.009","url":null,"abstract":"<div><div>Extracellular vesicles (EVs), including exosomes, microvesicles, and apoptotic bodies, are membrane-bound vesicles secreted by cells. They play essential roles in intercellular communications and are involved in numerous physiological processes. Given their functional importance, EVs have emerged as promising tools for diagnosing and treating various diseases. In this study, we focused on the utility of EVs and explored their application in the analysis of contact-dependent cell–cell interactions, which are essential for the control of cell differentiation and induction of immune responses. Although several methods have been developed to evaluate these interactions, they often require complex procedures and advanced optimization, limiting their broad applicability. To overcome these limitations, we developed a novel method utilizing EVs to present membrane proteins in their native conformations. Our strategy involved producing fluorescently labeled EVs with target antigens and quantitatively assessing their binding to target cells via flow cytometry. Using fluorescently labeled EVs presenting with either an N-terminal pro-brain natriuretic peptide or interleukin-2 receptor, we successfully detected specific interactions with corresponding hybridoma B cell receptors. This simpler method requires no advanced optimization and effectively analyzes cell–cell interactions under physiological conditions in a high-throughput and quantitative manner. Our findings highlight the potential of this EV-based system as a valuable tool for studying membrane protein-mediated cell–cell interactions in bioscience research.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 3","pages":"Pages 194-202"},"PeriodicalIF":2.9,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145774699","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

Adaptive laboratory evolution optimizes an engineered phosphite utilization pathway in Synechococcus elongatus PCC 7942 适应性实验室进化优化了长聚球菌PCC 7942的工程亚磷酸酯利用途径。

IF 2.9 4区生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of bioscience and bioengineering

Pub Date : 2025-12-13 DOI: 10.1016/j.jbiosc.2025.11.006

Hiroki Murakami , Naoki Momokawa , Kei Motomura , Akio Kuroda , Ryuichi Hirota

Synthetic biology approaches enable the creation of promising chassis for practical application in various fields, though engineering of microbial metabolism often imposes a metabolic burden, potentially driving adaptive evolution during long-term cultivation. A previously established phosphite (Pt)-dependent metabolic system has proven to be an effective strategy for the containment of genetically engineered microorganisms, although its implementation accompanied a slight growth retardation. Here, we investigated the effect of long-term serial passaging cultivation on the Pt-dependent strain of Synechococcus elongatus PCC 7942, RH714. Compared with the originally constructed RH714, the passaged population of RH714 exhibited improved growth and a higher rate of Pt consumption in culture medium. Sequence analysis revealed point mutations within the introduced htxBCDE transporter genes, which are required for selective incorporation of Pt as a phosphorus nutrition. Introduction of the mutated gene cluster into S. elongatus PCC 7942 reproduced the traits of the passaged RH714 population, suggesting that these genetic changes enhance Pt transport activity and account for the observed phenotypes. Disruption of endogenous phosphate (Pi) transporter genes in the strains expressing the mutated htxBCDE-ptxD cluster abolished growth in Pi-containing medium, suggesting that the mutations in the transporter genes did not alter substrate specificity toward Pi. These results indicated that long-term passage cultivation developed an optimized mutant capable of efficient proliferation under the Pt metabolizing conditions without compromising its biocontainment capability.

尽管微生物代谢工程通常会带来代谢负担，但合成生物学方法能够为各种领域的实际应用创造有前途的基础，在长期培养过程中可能会推动适应性进化。先前建立的亚磷酸酯（Pt）依赖代谢系统已被证明是遏制基因工程微生物的有效策略，尽管其实施伴随着轻微的生长迟缓。本实验研究了长聚球菌（PCC） 7942， RH714对pt依赖菌株的长期连续传代培养的影响。与原构建的RH714相比，RH714的传代群体表现出更好的生长和更高的培养基Pt消耗率。序列分析显示，引入的htxBCDE转运体基因发生了点突变，这是Pt作为磷营养物选择性结合所必需的。将突变基因簇导入S. elongatus PCC 7942，可以再现传代的RH714群体的性状，表明这些遗传变化增强了Pt转运活性，并解释了所观察到的表型。在表达突变的htxBCDE-ptxD簇的菌株中，内源性磷酸盐（Pi）转运蛋白基因的破坏使其在含Pi的培养基中生长中断，这表明转运蛋白基因的突变并未改变对Pi的底物特异性。这些结果表明，长期传代培养产生了一个优化的突变体，能够在Pt代谢条件下高效增殖，而不影响其生物抑制能力。

{"title":"Adaptive laboratory evolution optimizes an engineered phosphite utilization pathway in Synechococcus elongatus PCC 7942","authors":"Hiroki Murakami , Naoki Momokawa , Kei Motomura , Akio Kuroda , Ryuichi Hirota","doi":"10.1016/j.jbiosc.2025.11.006","DOIUrl":"10.1016/j.jbiosc.2025.11.006","url":null,"abstract":"<div><div>Synthetic biology approaches enable the creation of promising chassis for practical application in various fields, though engineering of microbial metabolism often imposes a metabolic burden, potentially driving adaptive evolution during long-term cultivation. A previously established phosphite (Pt)-dependent metabolic system has proven to be an effective strategy for the containment of genetically engineered microorganisms, although its implementation accompanied a slight growth retardation. Here, we investigated the effect of long-term serial passaging cultivation on the Pt-dependent strain of <em>Synechococcus elongatus</em> PCC 7942, RH714. Compared with the originally constructed RH714, the passaged population of RH714 exhibited improved growth and a higher rate of Pt consumption in culture medium. Sequence analysis revealed point mutations within the introduced <em>htxBCDE</em> transporter genes, which are required for selective incorporation of Pt as a phosphorus nutrition. Introduction of the mutated gene cluster into <em>S. elongatus</em> PCC 7942 reproduced the traits of the passaged RH714 population, suggesting that these genetic changes enhance Pt transport activity and account for the observed phenotypes. Disruption of endogenous phosphate (Pi) transporter genes in the strains expressing the mutated <em>htxBCDE-ptxD</em> cluster abolished growth in Pi-containing medium, suggesting that the mutations in the transporter genes did not alter substrate specificity toward Pi. These results indicated that long-term passage cultivation developed an optimized mutant capable of efficient proliferation under the Pt metabolizing conditions without compromising its biocontainment capability.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 3","pages":"Pages 152-157"},"PeriodicalIF":2.9,"publicationDate":"2025-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145751920","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

Development of dectin-1-binding peptides targeting dendritic cells for antigen delivery via ribosome display 通过核糖体展示靶向树突状细胞抗原递送的dectin-1结合肽的开发。

IF 2.9 4区生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of bioscience and bioengineering

Pub Date : 2025-12-07 DOI: 10.1016/j.jbiosc.2025.11.005

Yoshirou Kawaguchi , Md Shahin Sarker , Mina Yokoyama , Misuzu Nakaya , Takanatsu Hosokawa , Noriho Kamiya , Masahiro Goto

Dendritic cells (DCs) are professional antigen-presenting cells that play a central role in initiating and shaping adaptive immune responses. Targeting antigens to DCs has emerged as a promising strategy to enhance vaccine efficacy and tailor desired immune responses. While antibodies are well established as targeting molecules for DCs, the use of peptides remains underexplored despite their favorable tissue penetration and their ability to offer design flexibility. Here, we report the identification of dectin-1-binding peptides using a ribosome display-based in vitro directed evolution system. Dectin-1 is a C-type lectin receptor expressed on murine CD11b⁺ and human CD1c⁺ DCs, which plays a key role in antigen uptake and in directing immune responses toward specific pathways, particularly the Th17 pathway. Using recombinant murine dectin-1 as bait, we performed four rounds of ribosome display selection and obtained peptides with high affinity. Selected peptides fused to enhanced green fluorescent protein showed binding to recombinant dectin-1 and native dectin-1-expressing cells, including bone marrow-derived DCs. These results demonstrated the feasibility of peptide-based molecular targeting toward dectin-1⁺ DCs, which would not only provide a versatile platform for the development of next-generation vaccines and immunotherapies, but also a valuable tool for dissecting the functional roles of dectin-1⁺ DCs in immune regulation.

树突状细胞（dc）是一种专业的抗原呈递细胞，在启动和形成适应性免疫反应中起着核心作用。将抗原靶向dc已成为提高疫苗效力和定制所需免疫反应的一种有希望的策略。虽然抗体作为树突状细胞的靶向分子已经很好地建立起来，但尽管肽具有良好的组织穿透性和设计灵活性，但其使用仍未得到充分的探索。在这里，我们报告了使用基于核糖体显示的体外定向进化系统鉴定检测素-1结合肽。Dectin-1是一种c型凝集素受体，在小鼠CD11b+和人CD1c+ dc上表达，在抗原摄取和引导免疫反应向特定途径，特别是Th17途径中起关键作用。我们以重组小鼠dectin-1为诱饵，进行了四轮核糖体展示选择，获得了高亲和力的多肽。与增强绿色荧光蛋白融合的选定肽显示与重组dectin-1和天然表达dectin-1的细胞结合，包括骨髓来源的dc。这些结果证明了基于肽的分子靶向dectin-1+ dc的可行性，这不仅为下一代疫苗和免疫疗法的开发提供了一个通用的平台，而且为解剖dectin-1+ dc在免疫调节中的功能作用提供了有价值的工具。

{"title":"Development of dectin-1-binding peptides targeting dendritic cells for antigen delivery via ribosome display","authors":"Yoshirou Kawaguchi , Md Shahin Sarker , Mina Yokoyama , Misuzu Nakaya , Takanatsu Hosokawa , Noriho Kamiya , Masahiro Goto","doi":"10.1016/j.jbiosc.2025.11.005","DOIUrl":"10.1016/j.jbiosc.2025.11.005","url":null,"abstract":"<div><div>Dendritic cells (DCs) are professional antigen-presenting cells that play a central role in initiating and shaping adaptive immune responses. Targeting antigens to DCs has emerged as a promising strategy to enhance vaccine efficacy and tailor desired immune responses. While antibodies are well established as targeting molecules for DCs, the use of peptides remains underexplored despite their favorable tissue penetration and their ability to offer design flexibility. Here, we report the identification of dectin-1-binding peptides using a ribosome display-based in vitro directed evolution system. Dectin-1 is a C-type lectin receptor expressed on murine CD11b<sup>+</sup> and human CD1c<sup>+</sup> DCs, which plays a key role in antigen uptake and in directing immune responses toward specific pathways, particularly the Th17 pathway. Using recombinant murine dectin-1 as bait, we performed four rounds of ribosome display selection and obtained peptides with high affinity. Selected peptides fused to enhanced green fluorescent protein showed binding to recombinant dectin-1 and native dectin-1-expressing cells, including bone marrow-derived DCs. These results demonstrated the feasibility of peptide-based molecular targeting toward dectin-1<sup>+</sup> DCs, which would not only provide a versatile platform for the development of next-generation vaccines and immunotherapies, but also a valuable tool for dissecting the functional roles of dectin-1<sup>+</sup> DCs in immune regulation.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 3","pages":"Pages 158-164"},"PeriodicalIF":2.9,"publicationDate":"2025-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145701096","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

Recovering genomes from uncultured fungi with single-cell genomics 用单细胞基因组学从未培养的真菌中恢复基因组。

IF 2.9 4区生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of bioscience and bioengineering

Pub Date : 2025-12-05 DOI: 10.1016/j.jbiosc.2025.11.004

Nevin McCone , Masahito Hosokawa

Single-cell genomics (SCG) complements culture-independent metagenomics for accessing fungal genomes, particularly from lineages that remain uncultured. We contrast metagenomics, which excels when profiling community composition and metabolic potential but often underrepresents low-abundance fungi, with SCG, which first isolates individual cells or nuclei to generate single-amplified genomes (SAGs) and can recover rare or microdiverse taxa. We then organize existing fungal SCG applications into three subgroups: spore-level sequencing from host-enriched or environmental material; single-nucleus genomics for multinucleate fungi; and single-spore sequencing of haploid progeny for diploid linkage and chromosome phasing. Across studies, pooling and co-assembly of cognate cells improves completeness; key hurdles persist in wall lysis, whole-genome amplification bias, and contamination control. Practical advances include shallow sequencing for QC triage, nuclei pooling with normalized co-assembly, and hybrid long- and short-read assembly. SCG adds unique value where strain resolution and genotypic context matter, including host-to-mobile-element linkage, recovery of large biosynthetic gene clusters, and karyotype validation against telomere-to-telomere references. Used alongside metagenomics, SCG enables a strain-resolved view of fungal biodiversity and function, with incremental improvements across the SCG pipeline promising routine access to genomes from early-diverging and other environmentally embedded fungi.

单细胞基因组学（SCG）补充了独立于培养的宏基因组学，用于获取真菌基因组，特别是来自未培养的谱系。宏基因组学在分析群落组成和代谢潜力方面表现出色，但通常不代表低丰度真菌，而SCG则首先分离单个细胞或细胞核产生单扩增基因组（sag），并可以恢复稀有或微多样性的分类群。然后，我们将现有的真菌SCG应用分为三个亚组：从宿主富集或环境材料中进行孢子水平测序；多核真菌的单核基因组学研究单倍体后代的单孢子测序，用于二倍体连锁和染色体分期。在整个研究中，同源细胞的汇集和共同组装提高了完整性；关键的障碍仍然存在于细胞壁裂解、全基因组扩增偏倚和污染控制。实际的进展包括浅测序的QC分流，核池与标准化的共组装，和混合长和短读组装。SCG在菌株分辨率和基因型背景重要的情况下增加了独特的价值，包括宿主-移动元件链接，大型生物合成基因簇的恢复，以及针对端粒-端粒参考的核型验证。与宏基因组学一起使用，SCG可以实现真菌生物多样性和功能的菌株解析视图，随着SCG管道的逐步改进，有望常规获取早期分化和其他环境嵌入真菌的基因组。

{"title":"Recovering genomes from uncultured fungi with single-cell genomics","authors":"Nevin McCone , Masahito Hosokawa","doi":"10.1016/j.jbiosc.2025.11.004","DOIUrl":"10.1016/j.jbiosc.2025.11.004","url":null,"abstract":"<div><div>Single-cell genomics (SCG) complements culture-independent metagenomics for accessing fungal genomes, particularly from lineages that remain uncultured. We contrast metagenomics, which excels when profiling community composition and metabolic potential but often underrepresents low-abundance fungi, with SCG, which first isolates individual cells or nuclei to generate single-amplified genomes (SAGs) and can recover rare or microdiverse taxa. We then organize existing fungal SCG applications into three subgroups: spore-level sequencing from host-enriched or environmental material; single-nucleus genomics for multinucleate fungi; and single-spore sequencing of haploid progeny for diploid linkage and chromosome phasing. Across studies, pooling and co-assembly of cognate cells improves completeness; key hurdles persist in wall lysis, whole-genome amplification bias, and contamination control. Practical advances include shallow sequencing for QC triage, nuclei pooling with normalized co-assembly, and hybrid long- and short-read assembly. SCG adds unique value where strain resolution and genotypic context matter, including host-to-mobile-element linkage, recovery of large biosynthetic gene clusters, and karyotype validation against telomere-to-telomere references. Used alongside metagenomics, SCG enables a strain-resolved view of fungal biodiversity and function, with incremental improvements across the SCG pipeline promising routine access to genomes from early-diverging and other environmentally embedded fungi.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 3","pages":"Pages 143-151"},"PeriodicalIF":2.9,"publicationDate":"2025-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145695859","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

Zein/Fucoidan microcarriers promote myogenic differentiation via topographical cues and hydrodynamic modulation 玉米蛋白/岩藻聚糖微载体通过地形线索和流体动力学调节促进肌源性分化。

IF 2.9 4区生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of bioscience and bioengineering

Pub Date : 2025-12-04 DOI: 10.1016/j.jbiosc.2025.11.003

Wanli Xiong, Chengxin Ge, Botao Zhang, Ziying Chen, Yuzhe Guo, Qiaohui Lu, Wen-song Tan, Yan Zhou

Microcarrier surface topography and fluid shear stress (FSS) critically regulate cellular behavior. An edible zein/fucoidan microcarrier with 200 μm grooves was designed for this study. Computational fluid dynamics (CFD) simulations and experiments were combined to analyze surface microfluidic characteristics during dynamic culture and their cellular effects. The research demonstrates controlled myogenic differentiation through groove topography and FSS modulation for scalable cultured meat production. The results demonstrated that the grooved microcarriers exhibited excellent cell attachment and proliferation capacity in spinner flask dynamic culture, achieving a maximum cell density of 1.16 × 10⁶ cells/mL, comparable to commercial Cultispher-S microcarriers. The groove structure promoted cell alignment through contact guidance, significantly enhancing the gene expression of myogenic differentiation markers (myogenic differentiation 1, MyoD1; α-actinin; myosin heavy chain, MHC) and cell fusion (myomaker, MYMK). CFD simulations revealed that the grooves created a low-shear microenvironment (minimum average FSS: 3.93 × 10⁻² Pa, maximum: 1.18 × 10⁻¹ Pa), which effectively avoided high FSS-induced damage while maintaining mechanical stimulation. This optimal mechanical microenvironment further activated the expression of key genes involved in early-stage (MyoD1; myogenin, MyoG; myocyte enhancer factor 2C, MEF2C) and late-stage (α-actinin; myosin heavy chain 2, Myh2) myogenic differentiation. Flat and spherical microcarriers showed lower myogenic differentiation efficiency. This study elucidates the synergistic mechanism between groove structures and the low FSS microenvironment within grooves, providing a novel scaffold design rationale that combines biomimetic topology with fluid dynamics compatibility for large-scale cultured meat production.

微载体表面形貌和流体剪切应力（FSS）对细胞行为起着关键的调节作用。设计了一种具有200 μm凹槽的玉米蛋白/岩藻聚糖微载体。采用计算流体力学（CFD）模拟与实验相结合的方法，分析了动态培养过程中表面微流体的特性及其细胞效应。研究表明，通过沟槽地形和FSS调节控制的肌源性分化可用于规模化养殖肉生产。结果表明，微载体在旋转瓶动态培养中表现出良好的细胞附着和增殖能力，最大细胞密度为1.16 × 106个细胞/mL，与市售cultisper - s微载体相当。凹槽结构通过接触引导促进细胞排列，显著增强了成肌分化标志物（myogenic differentiation 1, MyoD1; α- actitin; myosin heavy chain， MHC）的基因表达和细胞融合（myomaker， MYMK）。CFD模拟表明，沟槽创造了一个低剪切微环境（最小平均FSS: 3.93 × 10-2 Pa，最大值：1.18 × 10-1 Pa），有效避免了高FSS引起的损伤，同时保持了机械刺激。这种优化的机械微环境进一步激活了参与早期（MyoD1; myogenin, MyoG; myocyte enhancer factor 2C, MEF2C）和晚期（α- actitin； myosin重链2，Myh2）成肌分化的关键基因的表达。扁平微载体和球形微载体的成肌分化效率较低。本研究阐明了沟槽结构与沟槽内低FSS微环境之间的协同机制，为大规模养殖肉类生产提供了一种结合仿生拓扑和流体动力学兼容性的新型支架设计原理。

{"title":"Zein/Fucoidan microcarriers promote myogenic differentiation via topographical cues and hydrodynamic modulation","authors":"Wanli Xiong, Chengxin Ge, Botao Zhang, Ziying Chen, Yuzhe Guo, Qiaohui Lu, Wen-song Tan, Yan Zhou","doi":"10.1016/j.jbiosc.2025.11.003","DOIUrl":"10.1016/j.jbiosc.2025.11.003","url":null,"abstract":"<div><div>Microcarrier surface topography and fluid shear stress (FSS) critically regulate cellular behavior. An edible zein/fucoidan microcarrier with 200 μm grooves was designed for this study. Computational fluid dynamics (CFD) simulations and experiments were combined to analyze surface microfluidic characteristics during dynamic culture and their cellular effects. The research demonstrates controlled myogenic differentiation through groove topography and FSS modulation for scalable cultured meat production. The results demonstrated that the grooved microcarriers exhibited excellent cell attachment and proliferation capacity in spinner flask dynamic culture, achieving a maximum cell density of 1.16 × 10<sup>6</sup> cells/mL, comparable to commercial Cultispher-S microcarriers. The groove structure promoted cell alignment through contact guidance, significantly enhancing the gene expression of myogenic differentiation markers (myogenic differentiation 1, MyoD1; α-actinin; myosin heavy chain, MHC) and cell fusion (myomaker, MYMK). CFD simulations revealed that the grooves created a low-shear microenvironment (minimum average FSS: 3.93 × 10<sup>−2</sup> Pa, maximum: 1.18 × 10<sup>−1</sup> Pa), which effectively avoided high FSS-induced damage while maintaining mechanical stimulation. This optimal mechanical microenvironment further activated the expression of key genes involved in early-stage (MyoD1; myogenin, MyoG; myocyte enhancer factor 2C, MEF2C) and late-stage (α-actinin; myosin heavy chain 2, Myh2) myogenic differentiation. Flat and spherical microcarriers showed lower myogenic differentiation efficiency. This study elucidates the synergistic mechanism between groove structures and the low FSS microenvironment within grooves, providing a novel scaffold design rationale that combines biomimetic topology with fluid dynamics compatibility for large-scale cultured meat production.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 3","pages":"Pages 172-184"},"PeriodicalIF":2.9,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145687478","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

Spatial, temporal, and biotic changes in the natural abundances of stable carbon and nitrogen isotopes in a biological treatment reactor 生物处理反应器中稳定碳和氮同位素自然丰度的时空和生物变化。

IF 2.9 4区生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of bioscience and bioengineering

Pub Date : 2025-11-25 DOI: 10.1016/j.jbiosc.2025.11.002

Takashi Onodera , Kengo Kubota , Akinori Iguchi , Akihiro Nagamachi , Tadashi Tagawa , Gen Kanaya , Ayato Kohzu , Kazuaki Syutsubo

The natural abundances of stable isotopes were used to determine prey–predator relationships and material flows in a biological treatment reactor for municipal wastewater. The reactor used in this study was a down-flow hanging sponge (DHS), which is an alternative trickling filter that uses sponge as the packing material. The sponge retained sludge containing a wide variety of organisms, including microfauna. Stable isotope analysis revealed spatial, temporal, and biotic variations in the carbon and nitrogen stable isotope ratios (δ¹³C and δ¹⁵N) of the retained sludge and microfauna (water mites and fly larvae). In addition, adult flies and spiders were present and analyzed. The δ¹³C and δ¹⁵N in sludge were temporally and spatially similar along the reactor. The isotopic signature was associated with treatment characteristics such as a low nitrification efficiency in the DHS reactor. The δ¹³C and δ¹⁵N of sympatric fly larvae differed from those of water mites, which indicated dietary differences between the taxa. Interestingly, the water mites had higher δ¹³C and δ¹⁵N than the retained sludge, which indicated that they were in a higher trophic position in the food web. In addition, the δ¹³C and δ¹⁵N values of spiders were approximately 1 ‰–3‰ higher than those of adult flies. This strongly suggested that a prey–predator relationship existed between adult flies and spiders.

稳定同位素的天然丰度用于确定城市污水生物处理反应器中的捕食关系和物质流动。本研究采用的反应器为下流式悬挂海绵反应器（DHS），是一种以海绵为填料的替代性滴滤器。海绵保留的污泥中含有各种各样的生物，包括微型动物。稳定同位素分析揭示了滞留污泥和微动物（水螨和蝇幼虫）碳氮稳定同位素比值（δ13C和δ15N）的时空和生物变化。此外，还发现并分析了成虫蝇和蜘蛛。污泥中的δ13C和δ15N在时间和空间上沿反应器方向相似。同位素特征与处理特性有关，如DHS反应器的低硝化效率。同域蝇幼虫的δ13C和δ15N与水螨幼虫的δ13C和δ15N存在差异，说明不同类群间存在差异。有趣的是，水螨的δ13C和δ15N高于残留污泥，这表明它们在食物网中处于更高的营养地位。此外，蜘蛛的δ13C和δ15N值比成蝇高约1‰~ 3‰。这有力地表明，成年苍蝇和蜘蛛之间存在一种捕食关系。

{"title":"Spatial, temporal, and biotic changes in the natural abundances of stable carbon and nitrogen isotopes in a biological treatment reactor","authors":"Takashi Onodera , Kengo Kubota , Akinori Iguchi , Akihiro Nagamachi , Tadashi Tagawa , Gen Kanaya , Ayato Kohzu , Kazuaki Syutsubo","doi":"10.1016/j.jbiosc.2025.11.002","DOIUrl":"10.1016/j.jbiosc.2025.11.002","url":null,"abstract":"<div><div>The natural abundances of stable isotopes were used to determine prey–predator relationships and material flows in a biological treatment reactor for municipal wastewater. The reactor used in this study was a down-flow hanging sponge (DHS), which is an alternative trickling filter that uses sponge as the packing material. The sponge retained sludge containing a wide variety of organisms, including microfauna. Stable isotope analysis revealed spatial, temporal, and biotic variations in the carbon and nitrogen stable isotope ratios (<em>δ</em><sup>13</sup>C and <em>δ</em><sup>15</sup>N) of the retained sludge and microfauna (water mites and fly larvae). In addition, adult flies and spiders were present and analyzed. The <em>δ</em><sup>13</sup>C and <em>δ</em><sup>15</sup>N in sludge were temporally and spatially similar along the reactor. The isotopic signature was associated with treatment characteristics such as a low nitrification efficiency in the DHS reactor. The <em>δ</em><sup>13</sup>C and <em>δ</em><sup>15</sup>N of sympatric fly larvae differed from those of water mites, which indicated dietary differences between the taxa. Interestingly, the water mites had higher <em>δ</em><sup>13</sup>C and <em>δ</em><sup>15</sup>N than the retained sludge, which indicated that they were in a higher trophic position in the food web. In addition, the <em>δ</em><sup>13</sup>C and <em>δ</em><sup>15</sup>N values of spiders were approximately 1 ‰–3‰ higher than those of adult flies. This strongly suggested that a prey–predator relationship existed between adult flies and spiders.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 2","pages":"Pages 135-141"},"PeriodicalIF":2.9,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145633959","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

Using pure oxygen aeration to increase recombinant protein production by an Aspergillus oryzae hyphal dispersion strain 利用纯氧曝气提高米曲霉菌丝分散菌株重组蛋白的产量。

IF 2.9 4区生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of bioscience and bioengineering

Pub Date : 2025-11-24 DOI: 10.1016/j.jbiosc.2025.10.011

Satoshi Ishibashi , Shunya Susukida , Kiyoaki Muto , Ken Miyazawa , Silai Zhang , Akira Yoshimi , Eiji Tabata , Keietsu Abe

A high growth rate is essential for increasing protein production efficiency in liquid fermentation of filamentous fungi, such as Aspergillus oryzae. However, the increase in culture viscosity due to fungal growth constrains the overall yield. We have demonstrated that culture viscosity is lower in A. oryzae AGΔ-GAGΔ strains, which are deficient in the cell surface polysaccharides α-1,3-glucan (AG) and galactosaminogalactan (GAG), than in the wild-type (WT) strains. Nevertheless, even in aerated fermentation, an increase in AGΔ-GAGΔ viscosity results in oxygen depletion, which limits fungal growth and enzyme production. In this study, we investigated viscosity dynamics and protein production during high-cell-density fermentation of AGΔ-GAGΔ under pure oxygen aeration. Fed-batch cultivation of the WT and AGΔ-GAGΔ strains, expressing recombinant xylanase (XynF1), was used to compare the effects of air and pure oxygen aeration at the same flow rate. At 60 h, AGΔ-GAGΔ under pure oxygen aeration showed higher cell density (1.2× WT under pure oxygen aeration, 2.1× AGΔ-GAGΔ under air aeration) and XynF1 activity (1.8× WT under pure oxygen aeration, 2.3× AGΔ-GAGΔ under air aeration). Under pure oxygen aeration, AGΔ-GAGΔ showed lower viscosity (0.32×) and mixing time (0.50×) than WT. At 60 h, fine mycelial pellets (micropellets; 200–700 μm) were clearly observed in AGΔ-GAGΔ under pure oxygen but not under air aeration. These findings suggest that oxygen enrichment during AGΔ-GAGΔ cultivation mitigated the increase in viscosity, thereby promoting higher cell density and protein production. The formation of micropellets in AGΔ-GAGΔ likely contributed to a reduction in culture viscosity.

在米曲霉等丝状真菌的液体发酵过程中，提高蛋白质的生产效率需要较高的生长速率。然而，由于真菌生长而增加的培养粘度限制了总体产量。我们已经证明，与野生型（WT）菌株相比，缺乏细胞表面多糖α-1,3-葡聚糖（AG）和半乳糖半乳聚糖（GAG）的米芽孢杆菌AGΔ-GAGΔ菌株的培养粘度较低。然而，即使在曝气发酵中，AGΔ-GAGΔ粘度的增加也会导致氧气消耗，从而限制真菌的生长和酶的产生。在这项研究中，我们研究了在纯氧曝气下AGΔ-GAGΔ高密度发酵过程中的粘度动力学和蛋白质产量。对WT和AGΔ-GAGΔ菌株进行补料分批培养，表达重组木聚糖酶（XynF1），比较相同流速下空气和纯氧曝气的效果。60 h时，纯氧曝气AGΔ-GAGΔ的细胞密度更高（纯氧曝气1.2× WT，空气曝气2.1× AGΔ-GAGΔ）， XynF1活性更高（纯氧曝气1.8× WT，空气曝气2.3× AGΔ-GAGΔ）。在纯氧曝气条件下，AGΔ-GAGΔ的黏度（0.32×）和混合时间（0.50×）均低于WT。60 h时，AGΔ-GAGΔ在纯氧条件下明显可见到细小的菌丝球（微球；200-700 μm），而在空气曝气条件下则没有。这些发现表明，AGΔ-GAGΔ培养过程中的氧富集减轻了黏度的增加，从而促进了更高的细胞密度和蛋白质的产生。AGΔ-GAGΔ中微球的形成可能有助于降低培养粘度。

{"title":"Using pure oxygen aeration to increase recombinant protein production by an Aspergillus oryzae hyphal dispersion strain","authors":"Satoshi Ishibashi , Shunya Susukida , Kiyoaki Muto , Ken Miyazawa , Silai Zhang , Akira Yoshimi , Eiji Tabata , Keietsu Abe","doi":"10.1016/j.jbiosc.2025.10.011","DOIUrl":"10.1016/j.jbiosc.2025.10.011","url":null,"abstract":"<div><div>A high growth rate is essential for increasing protein production efficiency in liquid fermentation of filamentous fungi, such as <em>Aspergillus oryzae</em>. However, the increase in culture viscosity due to fungal growth constrains the overall yield. We have demonstrated that culture viscosity is lower in <em>A. oryzae</em> AGΔ-GAGΔ strains, which are deficient in the cell surface polysaccharides α-1,3-glucan (AG) and galactosaminogalactan (GAG), than in the wild-type (WT) strains. Nevertheless, even in aerated fermentation, an increase in AGΔ-GAGΔ viscosity results in oxygen depletion, which limits fungal growth and enzyme production. In this study, we investigated viscosity dynamics and protein production during high-cell-density fermentation of AGΔ-GAGΔ under pure oxygen aeration. Fed-batch cultivation of the WT and AGΔ-GAGΔ strains, expressing recombinant xylanase (XynF1), was used to compare the effects of air and pure oxygen aeration at the same flow rate. At 60 h, AGΔ-GAGΔ under pure oxygen aeration showed higher cell density (1.2× WT under pure oxygen aeration, 2.1× AGΔ-GAGΔ under air aeration) and XynF1 activity (1.8× WT under pure oxygen aeration, 2.3× AGΔ-GAGΔ under air aeration). Under pure oxygen aeration, AGΔ-GAGΔ showed lower viscosity (0.32×) and mixing time (0.50×) than WT. At 60 h, fine mycelial pellets (micropellets; 200–700 μm) were clearly observed in AGΔ-GAGΔ under pure oxygen but not under air aeration. These findings suggest that oxygen enrichment during AGΔ-GAGΔ cultivation mitigated the increase in viscosity, thereby promoting higher cell density and protein production. The formation of micropellets in AGΔ-GAGΔ likely contributed to a reduction in culture viscosity.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 2","pages":"Pages 98-107"},"PeriodicalIF":2.9,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145604529","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