Pub Date : 2024-11-23DOI: 10.1016/j.bej.2024.109590
Ryan M. Delaney, Katherine A. Lamb, Olivia M. Irvin, Zachary T. Baumer, Timothy A. Whitehead
T7 RNA polymerase (T7 RNAP) biosensors, in which T7 RNAP transcribes some reporter gene or signal in response to external stimuli, have wide applications in synthetic biology and metabolic engineering. We adapted a biochemical reaction network model and used an in vitro transcription assay to determine network parameters for different T7 RNAP constructs. Under conditions where template DNA is limiting, the EC50 values of native and engineered T7 RNAPs ranged from 33 nM (29–37 95 % c.i.) to 570 nM (258–714 95 % c.i.) (wild-type T7 RNAP). The measured EC50 values were largely insensitive to free magnesium, pH, or other buffer conditions. Many biosensor configurations use a split RNAP construct, where the C-terminal (CT7) and N-terminal T7 (NT7) are fused to proximity induced dimerization modules. We used proteolysis and ion exchange chromatography to prepare a CT7 (80 kDa) product. The impact of free CT7 on T7 RNAP transcriptional activity was well described by a competitive inhibition model, with an inhibitory constant KI = 23 nM (18–28 95 % c.i.) of the sensor. These model parameters will be useful for forward modeling and design of T7 RNAP-based genetic circuits.
{"title":"in vitro analysis of a competitive inhibition model for T7 RNA polymerase biosensors","authors":"Ryan M. Delaney, Katherine A. Lamb, Olivia M. Irvin, Zachary T. Baumer, Timothy A. Whitehead","doi":"10.1016/j.bej.2024.109590","DOIUrl":"10.1016/j.bej.2024.109590","url":null,"abstract":"<div><div>T7 RNA polymerase (T7 RNAP) biosensors, in which T7 RNAP transcribes some reporter gene or signal in response to external stimuli, have wide applications in synthetic biology and metabolic engineering. We adapted a biochemical reaction network model and used an <em>in vitro</em> transcription assay to determine network parameters for different T7 RNAP constructs. Under conditions where template DNA is limiting, the EC<sub>50</sub> values of native and engineered T7 RNAPs ranged from 33 nM (29–37 95 % c.i.) to 570 nM (258–714 95 % c.i.) (wild-type T7 RNAP). The measured EC<sub>50</sub> values were largely insensitive to free magnesium, pH, or other buffer conditions. Many biosensor configurations use a split RNAP construct, where the C-terminal (CT7) and N-terminal T7 (NT7) are fused to proximity induced dimerization modules. We used proteolysis and ion exchange chromatography to prepare a CT7 (80 kDa) product. The impact of free CT7 on T7 RNAP transcriptional activity was well described by a competitive inhibition model, with an inhibitory constant K<sub>I</sub> = 23 nM (18–28 95 % c.i.) of the sensor. These model parameters will be useful for forward modeling and design of T7 RNAP-based genetic circuits.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"215 ","pages":"Article 109590"},"PeriodicalIF":3.7,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142722156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-23DOI: 10.1016/j.bej.2024.109591
Yuki Ozawa, Takamasa Hashizume, Bei-Wen Ying
Cell culture media are critical for cell propagation and bioproduction to be as efficient as possible to meet medical and pharmaceutical requirements. However, optimizing medium composition to achieve optimal cell culture remains a significant challenge due to the complexity of living cells and their required media. This study, which is a significant contribution to the field, addresses the need for data-driven techniques in cell culture technologies by integrating active machine learning (ML) to reformulate a widely used base medium for mammalian cell culture. The optimization process was facilitated by developing various ML models, which accounted for experimental data processing and time consumption. It provided a detailed methodology and essential knowledge for utilizing ML in medium development. Growth determinative medium components were identified through data mining and scale-up culture. In addition, RNA sequencing analysis indicated that active learning finetuned the media for the changes in gene expression for improved cell culture. This study offers new insights and methodologies to be applied to cell culture for future medical purposes.
细胞培养基对于尽可能高效地进行细胞繁殖和生物生产以满足医疗和制药要求至关重要。然而，由于活细胞及其所需培养基的复杂性，优化培养基成分以实现最佳细胞培养仍是一项重大挑战。本研究通过整合主动机器学习（ML）来重新配置一种广泛应用于哺乳动物细胞培养的基础培养基，满足了细胞培养技术中对数据驱动技术的需求，是对该领域的重大贡献。通过开发各种 ML 模型，考虑到实验数据处理和时间消耗，促进了优化过程。它为在培养基开发中利用 ML 提供了详细的方法和基本知识。通过数据挖掘和放大培养，确定了决定生长的培养基成分。此外，RNA 测序分析表明，主动学习可根据基因表达的变化对培养基进行微调，从而改进细胞培养。这项研究提供了新的见解和方法，可应用于未来医学目的的细胞培养。
{"title":"A data-driven approach for cell culture medium optimization","authors":"Yuki Ozawa, Takamasa Hashizume, Bei-Wen Ying","doi":"10.1016/j.bej.2024.109591","DOIUrl":"10.1016/j.bej.2024.109591","url":null,"abstract":"<div><div>Cell culture media are critical for cell propagation and bioproduction to be as efficient as possible to meet medical and pharmaceutical requirements. However, optimizing medium composition to achieve optimal cell culture remains a significant challenge due to the complexity of living cells and their required media. This study, which is a significant contribution to the field, addresses the need for data-driven techniques in cell culture technologies by integrating active machine learning (ML) to reformulate a widely used base medium for mammalian cell culture. The optimization process was facilitated by developing various ML models, which accounted for experimental data processing and time consumption. It provided a detailed methodology and essential knowledge for utilizing ML in medium development. Growth determinative medium components were identified through data mining and scale-up culture. In addition, RNA sequencing analysis indicated that active learning finetuned the media for the changes in gene expression for improved cell culture. This study offers new insights and methodologies to be applied to cell culture for future medical purposes.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"214 ","pages":"Article 109591"},"PeriodicalIF":3.7,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142704579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-22DOI: 10.1016/j.bej.2024.109589
Tadej Markuš , Mladen Soldat , Vasilka Magdevska , Jaka Horvat , Martin Kavšček , Gregor Kosec , Štefan Fujs , Uroš Petrovič
Yarrowia lipolytica, a non-conventional oleaginous yeast, holds great promise for a wide range of metabolic engineering applications. Strains of this species are renowned for their capacity to accommodate high carbon flux through acetyl-CoA and are, therefore, being extensively studied for producing chemicals derived from this precursor molecule. We investigated the effects of the pyruvate bypass, phosphoketolase bypass, and the carnitine shuttle on Y. lipolytica’s central carbon metabolism by monitoring the production of lipids and β-carotene. We constructed a set of parental strains derived from the Y. lipolytica YB-392 wild-type strain, introduced the metabolic bypasses, and subjected the constructed strains to a series of fermentation experiments. We discovered that upon introducing the modifications to central carbon metabolism, carbon is preferentially directed through the lipid biosynthesis pathway, making such engineering an effective strategy for increasing lipid production. The highest lipid content of 0.61 glipids/gDCW was recorded after introducing the carnitine shuttle-associated gene YlCAT2. Meanwhile, the highest increase in production efficiency, 78.2 %, was recorded for a combination of genes associated with the pyruvate bypass (YlPDC1, YlALD3, YlACS1).
{"title":"Engineering central metabolism in Yarrowia lipolytica increases lipid accumulation","authors":"Tadej Markuš , Mladen Soldat , Vasilka Magdevska , Jaka Horvat , Martin Kavšček , Gregor Kosec , Štefan Fujs , Uroš Petrovič","doi":"10.1016/j.bej.2024.109589","DOIUrl":"10.1016/j.bej.2024.109589","url":null,"abstract":"<div><div><em>Yarrowia lipolytica</em>, a non-conventional oleaginous yeast, holds great promise for a wide range of metabolic engineering applications. Strains of this species are renowned for their capacity to accommodate high carbon flux through acetyl-CoA and are, therefore, being extensively studied for producing chemicals derived from this precursor molecule. We investigated the effects of the pyruvate bypass, phosphoketolase bypass, and the carnitine shuttle on <em>Y. lipolytica</em>’s central carbon metabolism by monitoring the production of lipids and β-carotene. We constructed a set of parental strains derived from the <em>Y. lipolytica</em> YB-392 wild-type strain, introduced the metabolic bypasses, and subjected the constructed strains to a series of fermentation experiments. We discovered that upon introducing the modifications to central carbon metabolism, carbon is preferentially directed through the lipid biosynthesis pathway, making such engineering an effective strategy for increasing lipid production. The highest lipid content of 0.61 g<sub>lipids</sub>/g<sub>DCW</sub> was recorded after introducing the carnitine shuttle-associated gene <em>YlCAT2</em>. Meanwhile, the highest increase in production efficiency, 78.2 %, was recorded for a combination of genes associated with the pyruvate bypass (<em>YlPDC1</em>, <em>YlALD3</em>, <em>YlACS1</em>).</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"215 ","pages":"Article 109589"},"PeriodicalIF":3.7,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142722154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-22DOI: 10.1016/j.bej.2024.109575
Baoshan Wang , Xingxiang Zhang , Zhilong Dong , Xiaojie Chen , Chengcheng Wen , Zhiyuan Wang , Yingming Liu , Enli Liu
Electron donor-mediated biological denitrification, the most extensively employed method for the treatment of nitrate nitrogen (NO3−-N), involves NO3−-N directly or indirectly by acquiring electrons provided by electron donors and converting them into N2. Currently, the most widely researched electron donors are gaseous, liquid, and solid forms. Owing to the difficulties in storing and transporting gaseous and liquid electron donors, and their potential for causing secondary pollution, solid-phase electron donors (SPEDs), which can be slowly utilized by microorganisms, have gradually gained attention. SPEDs not only serve as a carrier for microbial attachment, but most SPEDs are also low-cost and readily available, making them advantageous for practical applications. In this review, the different types of SPEDs are classified and their microbial utilization mechanisms in the biological denitrification process discussed based on their classification. Their denitrification performance, influencing factors, practical applications, and existing issues are summarized. This review provides a reference for future research on SPED and its applications. It also provides an outlook on SPED-mediated mixotrophic denitrification and SPED-coupled electrochemical technology for enhanced nitrogen removal processes, in view of this hot direction in SPED research.
{"title":"Research progress on solid-phase electron donors for the denitrification of wastewater: A review","authors":"Baoshan Wang , Xingxiang Zhang , Zhilong Dong , Xiaojie Chen , Chengcheng Wen , Zhiyuan Wang , Yingming Liu , Enli Liu","doi":"10.1016/j.bej.2024.109575","DOIUrl":"10.1016/j.bej.2024.109575","url":null,"abstract":"<div><div>Electron donor-mediated biological denitrification, the most extensively employed method for the treatment of nitrate nitrogen (NO<sub>3</sub><sup>−</sup>-N), involves NO<sub>3</sub><sup>−</sup>-N directly or indirectly by acquiring electrons provided by electron donors and converting them into N<sub>2</sub>. Currently, the most widely researched electron donors are gaseous, liquid, and solid forms. Owing to the difficulties in storing and transporting gaseous and liquid electron donors, and their potential for causing secondary pollution, solid-phase electron donors (SPEDs), which can be slowly utilized by microorganisms, have gradually gained attention. SPEDs not only serve as a carrier for microbial attachment, but most SPEDs are also low-cost and readily available, making them advantageous for practical applications. In this review, the different types of SPEDs are classified and their microbial utilization mechanisms in the biological denitrification process discussed based on their classification. Their denitrification performance, influencing factors, practical applications, and existing issues are summarized. This review provides a reference for future research on SPED and its applications. It also provides an outlook on SPED-mediated mixotrophic denitrification and SPED-coupled electrochemical technology for enhanced nitrogen removal processes, in view of this hot direction in SPED research.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"214 ","pages":"Article 109575"},"PeriodicalIF":3.7,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142704605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-21DOI: 10.1016/j.bej.2024.109588
Fengman Han , Xianglong Li , Yu Tan , Qingyu Zhou
The recombinant spider silk proteins (spidroins) are promising biomaterials for the use as drug delivery system (DDS) because of their non-cytotoxicity, low immunogenicity and customizable properties. However, most reported spidroin-based materials as DDS derive from the repetitive domain of dragline silk protein, limiting us to take advantage of their desirable properties for medical and industrial innovation. Here, we produced the recombinant aciniform silk protein (rAcSp2) that contains only the N-terminal domain and formulated it into nanoparticles for use as a DDS. We demonstrated that antitumor peptide drugs such as ChMAP-28 can be loaded onto rAcSp2 particles via electrostatic interaction, with a high loading capacity of up to 45 % (w/w) and nearly 100 % loading efficiency. In addition, the release of ChMAP-28 depends on the pH and ionic strength of the release buffer. In the meantime, rAcSp2 particles not only effectively reduce the toxicity of ChMAP-28 to normal cells, but also significantly enhance its anti-tumor activity. Therefore, our rAcSp2 particles are a promising novel particulate drug carrier system for the delivery of peptide drugs with anti-tumor activity.
{"title":"Particles made of a novel recombinant spider silk protein rAcSp2 as delivery system for peptide drugs with anti-tumor activity","authors":"Fengman Han , Xianglong Li , Yu Tan , Qingyu Zhou","doi":"10.1016/j.bej.2024.109588","DOIUrl":"10.1016/j.bej.2024.109588","url":null,"abstract":"<div><div>The recombinant spider silk proteins (spidroins) are promising biomaterials for the use as drug delivery system (DDS) because of their non-cytotoxicity, low immunogenicity and customizable properties. However, most reported spidroin-based materials as DDS derive from the repetitive domain of dragline silk protein, limiting us to take advantage of their desirable properties for medical and industrial innovation. Here, we produced the recombinant aciniform silk protein (rAcSp2) that contains only the N-terminal domain and formulated it into nanoparticles for use as a DDS. We demonstrated that antitumor peptide drugs such as ChMAP-28 can be loaded onto rAcSp2 particles via electrostatic interaction, with a high loading capacity of up to 45 % (w/w) and nearly 100 % loading efficiency. In addition, the release of ChMAP-28 depends on the pH and ionic strength of the release buffer. In the meantime, rAcSp2 particles not only effectively reduce the toxicity of ChMAP-28 to normal cells, but also significantly enhance its anti-tumor activity. Therefore, our rAcSp2 particles are a promising novel particulate drug carrier system for the delivery of peptide drugs with anti-tumor activity.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"214 ","pages":"Article 109588"},"PeriodicalIF":3.7,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142704604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-21DOI: 10.1016/j.bej.2024.109587
Ning Xu , Haiyan Gao , Yanran Wang , Chenxuan Liu , Lei Hu , Aiyong He , Wankui Jiang , Fengxue Xin
In order to achieve the sustainable development of society and reduce environmental footprint of chemical industry, some cleaner and greener production methods are still needed. Microbial fermentation has shown great potentials for sustainable production of chemicals, which can convert renewable resources into different products under mild conditions. Particularly, organic acids production has become a highly competitive and rapidly developed field, as they show broad applications in food, cosmetic and medical areas. Especially, yeasts have shown many advantages in organic acids production especially at high osmotic pressure or low pH. Accordingly, this review will discuss the latest progress of engineered yeasts as cell factories for organic acids production. Different strategies for improvement of organic acids production will be introduced, and future perspectives will also be proposed.
{"title":"Recent advances in bio-based production of organic acids by genetically engineered yeasts","authors":"Ning Xu , Haiyan Gao , Yanran Wang , Chenxuan Liu , Lei Hu , Aiyong He , Wankui Jiang , Fengxue Xin","doi":"10.1016/j.bej.2024.109587","DOIUrl":"10.1016/j.bej.2024.109587","url":null,"abstract":"<div><div>In order to achieve the sustainable development of society and reduce environmental footprint of chemical industry, some cleaner and greener production methods are still needed. Microbial fermentation has shown great potentials for sustainable production of chemicals, which can convert renewable resources into different products under mild conditions. Particularly, organic acids production has become a highly competitive and rapidly developed field, as they show broad applications in food, cosmetic and medical areas. Especially, yeasts have shown many advantages in organic acids production especially at high osmotic pressure or low pH. Accordingly, this review will discuss the latest progress of engineered yeasts as cell factories for organic acids production. Different strategies for improvement of organic acids production will be introduced, and future perspectives will also be proposed.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"215 ","pages":"Article 109587"},"PeriodicalIF":3.7,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142745162","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-20DOI: 10.1016/j.bej.2024.109586
X. Li , XY Wang , M. Li , QW Zhan , WY Dong
Recycled hardened concrete powder (RHCP) was used as a raw material, and microorganisms were introduced to accelerate carbonization to enhance its activity. The carbonation ability of RHCP was investigated by altering the solid-liquid ratio during carbonation. The results indicated that the carbon sequestration amount of RHCP after 7 days of carbonation at room temperature and pressure initially increased and then decreased with the rise of the solid-liquid ratio. When the solid-liquid ratio was 1:0.8, the carbon sequestration amount of RHCP was the highest, reaching 208.65 g/kg. The carbonized RHCP (C-RHCP) and RHCP were then used to partially replace cement to investigate their effects on the workability, mechanical, and durability properties of the mixtures. The results showed that when the replacement amount of C-RHCP was 30 %, all the properties were relatively good. The water demand and setting time were not significantly different. After 28 days of curing, the compressive strength of the 30 % C-RHCP specimen reached over 70 % of that of the pure cement group. However, its carbonation resistance was significantly lower than that of pure cement, while its resistance to chloride ion penetration and drying shrinkage was similar.
{"title":"Study on activation and performance of recycled hardened concrete powder based on microbial accelerated carbonization","authors":"X. Li , XY Wang , M. Li , QW Zhan , WY Dong","doi":"10.1016/j.bej.2024.109586","DOIUrl":"10.1016/j.bej.2024.109586","url":null,"abstract":"<div><div>Recycled hardened concrete powder (RHCP) was used as a raw material, and microorganisms were introduced to accelerate carbonization to enhance its activity. The carbonation ability of RHCP was investigated by altering the solid-liquid ratio during carbonation. The results indicated that the carbon sequestration amount of RHCP after 7 days of carbonation at room temperature and pressure initially increased and then decreased with the rise of the solid-liquid ratio. When the solid-liquid ratio was 1:0.8, the carbon sequestration amount of RHCP was the highest, reaching 208.65 g/kg. The carbonized RHCP (C-RHCP) and RHCP were then used to partially replace cement to investigate their effects on the workability, mechanical, and durability properties of the mixtures. The results showed that when the replacement amount of C-RHCP was 30 %, all the properties were relatively good. The water demand and setting time were not significantly different. After 28 days of curing, the compressive strength of the 30 % C-RHCP specimen reached over 70 % of that of the pure cement group. However, its carbonation resistance was significantly lower than that of pure cement, while its resistance to chloride ion penetration and drying shrinkage was similar.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"214 ","pages":"Article 109586"},"PeriodicalIF":3.7,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142704602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-19DOI: 10.1016/j.bej.2024.109574
Paola A. Palacios , Mads U. Sieborg , Simon B. Kuipers , Simon Fruergaard , Michael V.W. Kofoed
Ex situ biomethanation is a promising technology that combines the concepts of Power-to-X and carbon capture and utilization (CCU) by employing microorganisms to convert hydrogen (H2) and carbon dioxide (CO2) into biomethane (CH4). Mesophilic (37°C) and thermophilic (50°C) ex situ biomethanation processes in continuous stirred tank reactors (CSTRs), were evaluated for the first time under a high continuous H2/CO2 supply. Each process was evaluated with and without the addition of minerals and vitamins. In all thermophilic reactors, methanogenesis was favored, achieving stable methane yields of 110 ± 8 %. Additionally, the addition of minerals resulted in a 67 % increase in H2 consumption rates. In contrast, mesophilic reactors showed low CH4 yields (7.5 %) and acetogenesis as the dominant pathway, with acetate concentrations reaching up to 7.6 ± 2 g L−1. The effect of free acetic acid (FAA), a rarely considered concept based on the correlation between pH and acetic acid concentration, was also tested on thermophilic ex situ CSTRs. A clear negative correlation was demonstrated between FAA concentration and the CH4 productivity, with a 50 % inhibition of CH4 productivity at 0.062 g L−1 of FAA.
{"title":"Temperature tactics: Targeting acetate or methane production in autotrophic H2/CO2 conversion with mixed cultures","authors":"Paola A. Palacios , Mads U. Sieborg , Simon B. Kuipers , Simon Fruergaard , Michael V.W. Kofoed","doi":"10.1016/j.bej.2024.109574","DOIUrl":"10.1016/j.bej.2024.109574","url":null,"abstract":"<div><div><em>Ex situ</em> biomethanation is a promising technology that combines the concepts of Power-to-X and carbon capture and utilization (CCU) by employing microorganisms to convert hydrogen (H<sub>2</sub>) and carbon dioxide (CO<sub>2</sub>) into biomethane (CH<sub>4</sub>). Mesophilic (37°C) and thermophilic (50°C) <em>ex situ</em> biomethanation processes in continuous stirred tank reactors (CSTRs), were evaluated for the first time under a high continuous H<sub>2</sub>/CO<sub>2</sub> supply. Each process was evaluated with and without the addition of minerals and vitamins. In all thermophilic reactors, methanogenesis was favored, achieving stable methane yields of 110 ± 8 %. Additionally, the addition of minerals resulted in a 67 % increase in H<sub>2</sub> consumption rates. In contrast, mesophilic reactors showed low CH<sub>4</sub> yields (7.5 %) and acetogenesis as the dominant pathway, with acetate concentrations reaching up to 7.6 ± 2 g L<sup>−1</sup>. The effect of free acetic acid (FAA), a rarely considered concept based on the correlation between pH and acetic acid concentration, was also tested on thermophilic <em>ex situ</em> CSTRs. A clear negative correlation was demonstrated between FAA concentration and the CH<sub>4</sub> productivity, with a 50 % inhibition of CH<sub>4</sub> productivity at 0.062 g L<sup>−1</sup> of FAA.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"214 ","pages":"Article 109574"},"PeriodicalIF":3.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142704606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-19DOI: 10.1016/j.bej.2024.109585
Bovinille Anye Cho , George Mbella Teke , Godfrey K. Gakingo , Robert William McClelland Pott , Dongda Zhang
High-throughput systems using miniaturised stirred bioreactors accelerate bioprocess development due to their simplicity and low cost. However, fluctuating hydrodynamics pose numerical challenges for coupling (bio)reaction kinetics, critical for optimisation and scale-up/down in chemical and bioprocess industries. To address this, hydrodynamic convergence was achieved by time-averaging instantaneous RANS solutions of the transitional SST model over a sufficiently long period to achieve statistical significance in step one. Subsequently, photo-bioreaction transport models, accounting for the photobioreactor’s directional illumination and curvature, were solved based on these converged fields, overcoming two-step coupling challenges in an approach not previously reported. Applied to a 0.7 L Schott bottle photobioreactor mechanically mixed by a magnetic stirrer (100–500 rpm), the model accurately predicted swirly vortex fields at 500 rpm, with a 7 % error margin for simulated tracer diffusion, and aligned biomass growth profiles with literature data on Rhodopseudomonas palustris. However, parallel computing efficiency did not scale linearly with processor count, making time-averaging computationally expensive. Also, improved bioreactor mixing enhanced biomass productivity, but rpms over 300 required increased incident light intensity (>100 Wm−2) due to observed light limitation. Hence, this model facilitates optimising stirring speeds and refining operational parameters for scale-up and scale-down processes.
{"title":"CFD predictive simulations of miniature bioreactor mixing dynamics coupled with photo-bioreaction kinetics in transitional flow regime","authors":"Bovinille Anye Cho , George Mbella Teke , Godfrey K. Gakingo , Robert William McClelland Pott , Dongda Zhang","doi":"10.1016/j.bej.2024.109585","DOIUrl":"10.1016/j.bej.2024.109585","url":null,"abstract":"<div><div>High-throughput systems using miniaturised stirred bioreactors accelerate bioprocess development due to their simplicity and low cost. However, fluctuating hydrodynamics pose numerical challenges for coupling (bio)reaction kinetics, critical for optimisation and scale-up/down in chemical and bioprocess industries. To address this, hydrodynamic convergence was achieved by time-averaging instantaneous RANS solutions of the <em>transitional</em> SST model over a sufficiently long period to achieve statistical significance in step one. Subsequently, photo-bioreaction transport models, accounting for the photobioreactor’s directional illumination and curvature, were solved based on these converged fields, overcoming two-step coupling challenges in an approach not previously reported. Applied to a 0.7 L Schott bottle photobioreactor mechanically mixed by a magnetic stirrer (100–500 rpm), the model accurately predicted swirly vortex fields at 500 rpm, with a 7 % error margin for simulated tracer diffusion, and aligned biomass growth profiles with literature data on <em>Rhodopseudomonas palustris</em>. However, parallel computing efficiency did not scale linearly with processor count, making time-averaging computationally expensive. Also, improved bioreactor mixing enhanced biomass productivity, but rpms over 300 required increased incident light intensity (>100 Wm<sup>−2</sup>) due to observed light limitation. Hence, this model facilitates optimising stirring speeds and refining operational parameters for scale-up and scale-down processes.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"214 ","pages":"Article 109585"},"PeriodicalIF":3.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142704603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Herein, glucose oxidase was immobilized into bimetallic (Cu2+, Zn2+) hybrid magnetic nanoflowers (GOx-mcNFs) to perform as a more stable glucose biosensor and antibacterial material. Morphological characterizations of GOx-mcNFs verified the construction of nanoflowers through metal ions-GOx coordination. The encapsulation yield was obtained as 93.5 %, where the activity recovery was 650.3 %. Magnetic nanoparticles also enhanced the peroxidase-like activity of metal-phosphates and caused GOx-mcNFs to show excellent peroxidase-like properties with the apparent Km values of 0.19 mM and 0.267 mM for H2O2 and TMB, respectively. Thermodynamic studies revealed a 16.5 kJ mol−1 higher activation energy of denaturation for GOx-mcNFs over the free GOx. The reusability of GOx-mcNF was confirmed by maintaining 70.5 % of its initial activity until the eighth cycle. A limit of detection as 0.7 µM with a wide linear range (0–1000 µM) and the recovery rate of human serum glucose as 97.02–105.9 % were attained. Furthermore, GOx-mcNFs displayed an antibacterial effect due to the generation of ROS by peroxidase-like nanozymes. In vitro antibacterial assays displayed inactivation rates of 99.6 % and 98.8 % against S.aureus and E.coli with 75 μg mL−1 and 750 μg mL−1 of GOx-mcNFs, respectively. Consequently, bi-functional GOx-mcNF provides a promising strategy for glucose biosensing and antibacterial applications.
{"title":"Synthesis and characterization of glucose oxidase bimetallic hybrid magnetic nanoflowers for a sensitive glucose biosensor and an effective antibacterial agent","authors":"Samira Iranmanesh, Arastoo Badoei-Dalfard, Zahra Karami","doi":"10.1016/j.bej.2024.109583","DOIUrl":"10.1016/j.bej.2024.109583","url":null,"abstract":"<div><div>Herein, glucose oxidase was immobilized into bimetallic (Cu<sup>2+</sup>, Zn<sup>2+</sup>) hybrid magnetic nanoflowers (GOx-mcNFs) to perform as a more stable glucose biosensor and antibacterial material. Morphological characterizations of GOx-mcNFs verified the construction of nanoflowers through metal ions-GOx coordination. The encapsulation yield was obtained as 93.5 %, where the activity recovery was 650.3 %. Magnetic nanoparticles also enhanced the peroxidase-like activity of metal-phosphates and caused GOx-mcNFs to show excellent peroxidase-like properties with the apparent <em>K</em><sub><em>m</em></sub> values of 0.19 mM and 0.267 mM for H2O2 and TMB, respectively. Thermodynamic studies revealed a 16.5 kJ mol<sup>−1</sup> higher activation energy of denaturation for GOx-mcNFs over the free GOx. The reusability of GOx-mcNF was confirmed by maintaining 70.5 % of its initial activity until the eighth cycle. A limit of detection as 0.7 µM with a wide linear range (0–1000 µM) and the recovery rate of human serum glucose as 97.02–105.9 % were attained. Furthermore, GOx-mcNFs displayed an antibacterial effect due to the generation of ROS by peroxidase-like nanozymes. <em>In vitro</em> antibacterial assays displayed inactivation rates of 99.6 % and 98.8 % against <em>S.aureus</em> and <em>E.coli</em> with 75 μg mL<sup>−1</sup> and 750 μg mL<sup>−1</sup> of GOx-mcNFs, respectively. Consequently, bi-functional GOx-mcNF provides a promising strategy for glucose biosensing and antibacterial applications.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"214 ","pages":"Article 109583"},"PeriodicalIF":3.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142704601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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