Process Biochemistry最新文献

英文中文

Enhancing polymeric nano-composite ceramic membrane performance and sustainable recovery for palm oil mill effluent (POME) wastewater treatment using advanced chemometric algorithms

IF 3.7 3区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Process Biochemistry

Pub Date : 2025-01-26 DOI: 10.1016/j.procbio.2025.01.022

Jamilu Usman , Yusuf Olabode Raji , Sani. I. Abba , A.G. Usman , Lukka Thuyavan Yogarathinam , Fahad Jibrin Abdu , Mohd Hafiz Dzarfan Othman , Isam H. Aljundi

This study investigates the enhancement of emulsified oily wastewater treatment using high-performance poly (diallyldimethylammonium chloride) PDADMAC ultrafiltration membranes through a multi-model machine learning (ML) approach. The study was based on experimental scenarios and more emphasis on computational learning applications. In this context, kernel Gaussian Process Regression (GPR), Linear Regression (LR), Stepwise Regression (SWR), and Multiple Linear Regression (MLR) were employed to predict water flux (WF) and oil rejection (OR). Subsequently, traditional Response Surface Methodology (RSM) was developed for predictive comparison. The predictive skills were evaluated and visualized using statistical indicators and 2-dimensional diagrams. GPR achieved the highest predictive accuracy for OR, with an NSE of 99.32 %, zero bias (PBIAS 0.0000), and the lowest MAE (0.0010). For WF, the RSM-W) model outperformed others with an NSE of 82.03 %, the lowest MAE (0.0051), and a slight underestimation bias (PBIAS −0.0587). These models significantly outperformed RLR, SWR, and MLR, which showed moderate accuracy and higher prediction errors. The environmental implications align with the goals of the Environmental Protection Agency (EPA) and the United Nations Sustainable Development Goals (SDGs). Enhanced treatment processes contribute to cleaner water bodies, protect marine ecosystems, and promote sustainable industrial practices. Future research should focus on field trials to validate these models under real-world conditions, integration with real-time monitoring systems for dynamic adjustments, and life cycle assessments to evaluate long-term sustainability.

{"title":"Enhancing polymeric nano-composite ceramic membrane performance and sustainable recovery for palm oil mill effluent (POME) wastewater treatment using advanced chemometric algorithms","authors":"Jamilu Usman , Yusuf Olabode Raji , Sani. I. Abba , A.G. Usman , Lukka Thuyavan Yogarathinam , Fahad Jibrin Abdu , Mohd Hafiz Dzarfan Othman , Isam H. Aljundi","doi":"10.1016/j.procbio.2025.01.022","DOIUrl":"10.1016/j.procbio.2025.01.022","url":null,"abstract":"<div><div>This study investigates the enhancement of emulsified oily wastewater treatment using high-performance poly (diallyldimethylammonium chloride) PDADMAC ultrafiltration membranes through a multi-model machine learning (ML) approach. The study was based on experimental scenarios and more emphasis on computational learning applications. In this context, kernel Gaussian Process Regression (GPR), Linear Regression (LR), Stepwise Regression (SWR), and Multiple Linear Regression (MLR) were employed to predict water flux (WF) and oil rejection (OR). Subsequently, traditional Response Surface Methodology (RSM) was developed for predictive comparison. The predictive skills were evaluated and visualized using statistical indicators and 2-dimensional diagrams. GPR achieved the highest predictive accuracy for OR, with an NSE of 99.32 %, zero bias (PBIAS 0.0000), and the lowest MAE (0.0010). For WF, the RSM-W) model outperformed others with an NSE of 82.03 %, the lowest MAE (0.0051), and a slight underestimation bias (PBIAS −0.0587). These models significantly outperformed RLR, SWR, and MLR, which showed moderate accuracy and higher prediction errors. The environmental implications align with the goals of the Environmental Protection Agency (EPA) and the United Nations Sustainable Development Goals (SDGs). Enhanced treatment processes contribute to cleaner water bodies, protect marine ecosystems, and promote sustainable industrial practices. Future research should focus on field trials to validate these models under real-world conditions, integration with real-time monitoring systems for dynamic adjustments, and life cycle assessments to evaluate long-term sustainability.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"150 ","pages":"Pages 306-317"},"PeriodicalIF":3.7,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143099602","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}

引用次数: 0

Biosynthesis and modification strategies of novel cyclic lipopeptide secreted by Bacillus spp.: Research progress

IF 3.7 3区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Process Biochemistry

Pub Date : 2025-01-26 DOI: 10.1016/j.procbio.2025.01.023

Zhengjun Pang , Wenshuo Zhang , Bo Zhang , Shiza Navaz , Fenghuan Wang , Yonghong Liao

Cyclic lipopeptides, as a novel and green biosurfactant, has crucial biological functions, including antiviral, anti-inflammatory, anti-cancer, and environmental healing. However, the complex regulatory systems, need for a stringent synthetic pathway, mixing of multiple congeners, and low yield have hampered the development and excavation of cyclic lipopeptide forming strains. In this paper, the fundamental structure and catalytic mechanism of non-ribosomal peptide synthetases, and cyclic lipopeptide biosynthesis routes, are subsequently addressed. Then, the targeted modification strategies for the synthesis of cyclic lipopeptides are described systematically. Finally, the current status and measures of developing novel cyclic peptides are analyzed, and the deficiencies, solutions and prospects of cyclic lipopeptides are discussed and prospected, aiming to improve application of cyclic lipopeptides in terms of both "quantity" and "diversity".

引用次数: 0

Toward sustainable bioplastics: The potential of algal biomass in PHA production and biocomposites fabrication

IF 3.7 3区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Process Biochemistry

Pub Date : 2025-01-24 DOI: 10.1016/j.procbio.2025.01.019

Raul E. Martínez-Herrera , Georgia M. González-Meza , Edgar R. Meléndez-Sánchez

This review hypothesizes that algal biomass, an underexplored and promising raw material, offers significant potential for polyhydroxyalkanoate (PHA) production within sustainable bioprocess frameworks. The increasing urgency to find alternative, eco-friendly solutions to traditional plastic production is driven by growing environmental concerns over plastic pollution. The review highlights novel interdisciplinary connections between algal biomass utilization, bioremediation, and PHA biosynthesis, revealing new pathways that optimize renewable resource use and enhance waste valorization. These hybrid processes, combining microalgal and cyanobacterial biomass after bioactive compound extraction, have not been sufficiently explored, presenting significant environmental and economic opportunities for the bioplastics industry. Additionally, the integration of artificial intelligence (AI) in the development of PHA + algal biomass biocomposites, with desirable properties for industrial and medical applications, presents a breakthrough opportunity. Future research should focus on advancing pretreatment methods to improve fermentable carbohydrate availability, scaling up production, and addressing challenges related to energy efficiency, cost-effectiveness, and the commercial viability of these biocomposites in the bioplastics market.

{"title":"Toward sustainable bioplastics: The potential of algal biomass in PHA production and biocomposites fabrication","authors":"Raul E. Martínez-Herrera , Georgia M. González-Meza , Edgar R. Meléndez-Sánchez","doi":"10.1016/j.procbio.2025.01.019","DOIUrl":"10.1016/j.procbio.2025.01.019","url":null,"abstract":"<div><div>This review hypothesizes that algal biomass, an underexplored and promising raw material, offers significant potential for polyhydroxyalkanoate (PHA) production within sustainable bioprocess frameworks. The increasing urgency to find alternative, eco-friendly solutions to traditional plastic production is driven by growing environmental concerns over plastic pollution. The review highlights novel interdisciplinary connections between algal biomass utilization, bioremediation, and PHA biosynthesis, revealing new pathways that optimize renewable resource use and enhance waste valorization. These hybrid processes, combining microalgal and cyanobacterial biomass after bioactive compound extraction, have not been sufficiently explored, presenting significant environmental and economic opportunities for the bioplastics industry. Additionally, the integration of artificial intelligence (AI) in the development of PHA + algal biomass biocomposites, with desirable properties for industrial and medical applications, presents a breakthrough opportunity. Future research should focus on advancing pretreatment methods to improve fermentable carbohydrate availability, scaling up production, and addressing challenges related to energy efficiency, cost-effectiveness, and the commercial viability of these biocomposites in the bioplastics market.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"150 ","pages":"Pages 276-287"},"PeriodicalIF":3.7,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143099603","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}

引用次数: 0

A review on biodesulfurization of crude oil using different microorganisms: Reaction mechanisms, effective factors, and removal efficiency of organic sulfur compounds

IF 3.7 3区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Process Biochemistry

Pub Date : 2025-01-23 DOI: 10.1016/j.procbio.2025.01.018

Sajad Tamjidi , Hossein Esmaeili

Thiophene, benzothiophene and dibenzothiophene are the main organic sulfur compounds in crude oil, which reduce the quality of crude oil. Previous studies have shown that biodesulfurization (BDS) is the most efficient method for the separation of complex organic sulfur compounds from crude oil. BDS is performed at ambient pressure and temperature with excellent selectivity, leading to reduced energy cost, low emissions of CO₂ and lack of production of unfavorable by-products. In this review study, the advantages and disadvantages of BDS compared to other processes, the performance of various microorganisms in the removal of complex sulfur compounds, environmental impacts, and biodesulfurization kinetics were thoroughly discussed. Also, different mechanisms of biodesulfurization process and their pathways in removing sulfur compounds were investigated. Moreover, the utilization of genetic engineering to improve biodesulfurization efficiency was studied. According to previous studies, the Bintulu oil field in Malaysia and the Boscan oil field in Venezuela have the lowest (0.03 %) and the highest sulfur content (5.7 %), respectively. Also, some microorganisms such as Mycobacterium goodie X7B, Rhodococcus erythropolis XP, Rhodococcus sp. ECRD-1, and Gordonia alkanivorans have shown significant biodesulfurization efficiency. In general, the integration of BDS and hydrodesulfurization processes is recommended as an efficient and environmentally friendly process in removing complex sulfur compounds.

{"title":"A review on biodesulfurization of crude oil using different microorganisms: Reaction mechanisms, effective factors, and removal efficiency of organic sulfur compounds","authors":"Sajad Tamjidi , Hossein Esmaeili","doi":"10.1016/j.procbio.2025.01.018","DOIUrl":"10.1016/j.procbio.2025.01.018","url":null,"abstract":"<div><div>Thiophene, benzothiophene and dibenzothiophene are the main organic sulfur compounds in crude oil, which reduce the quality of crude oil. Previous studies have shown that biodesulfurization (BDS) is the most efficient method for the separation of complex organic sulfur compounds from crude oil. BDS is performed at ambient pressure and temperature with excellent selectivity, leading to reduced energy cost, low emissions of CO<sub>2</sub> and lack of production of unfavorable by-products. In this review study, the advantages and disadvantages of BDS compared to other processes, the performance of various microorganisms in the removal of complex sulfur compounds, environmental impacts, and biodesulfurization kinetics were thoroughly discussed. Also, different mechanisms of biodesulfurization process and their pathways in removing sulfur compounds were investigated. Moreover, the utilization of genetic engineering to improve biodesulfurization efficiency was studied. According to previous studies, the Bintulu oil field in Malaysia and the Boscan oil field in Venezuela have the lowest (0.03 %) and the highest sulfur content (5.7 %), respectively. Also, some microorganisms such as <em>Mycobacterium goodie</em> X7B, <em>Rhodococcus erythropolis</em> XP, <em>Rhodococcus sp</em>. ECRD-1, and <em>Gordonia alkanivorans</em> have shown significant biodesulfurization efficiency. In general, the integration of BDS and hydrodesulfurization processes is recommended as an efficient and environmentally friendly process in removing complex sulfur compounds.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"150 ","pages":"Pages 288-305"},"PeriodicalIF":3.7,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143099612","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}

引用次数: 0

Oxygen uptake rate (OUR) guided nitrogen control strategy for improving nemadectin production by Streptomyces cyaneogriseus ssp. noncyanogenus

IF 3.7 3区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Process Biochemistry

Pub Date : 2025-01-20 DOI: 10.1016/j.procbio.2025.01.017

Xiaoqing Song , Zishu Zhang , Junxiong Yu , Yun Zhang , Jiayun Xue , Yuanxin Guo , Jianguang Liang , Min Ren , Qingyun Ling , Ali Mohsin , Jiangchao Qian , Zejian Wang , Yonghong Wang

Oxygen supply and oxygen uptake rate (OUR) significantly influences both the physiological state of cells and nemadectin biosynthesis by Streptomyces cyaneogriseus ssp. noncyanogenus. In this study, a real-time monitoring approach for nemadectin fermentation was developed for the first time by an online OUR control strategy. The effect of OUR levels during the mycelium differentiation phase on nemadectin biosynthesis was studied and optimized by adjusting feeding rates of (NH₄)₂SO₄. Results showed that controlling the OUR at approximately 17.5 mmol·L⁻¹·h⁻¹ during the mycelium differentiation phase effectively enhanced nemadectin production, reaching 2805.1 μg·mL⁻¹, making a 129.5 % increase compared to the control. This OUR control strategy was successfully scaled-up to a 500 L pilot scale, achieving the highest ever nemadectin production of 2867.3 μg·mL⁻¹. These findings demonstrate that this OUR control strategy provides an effective and scalable approach for industrial nemadectin production.

{"title":"Oxygen uptake rate (OUR) guided nitrogen control strategy for improving nemadectin production by Streptomyces cyaneogriseus ssp. noncyanogenus","authors":"Xiaoqing Song , Zishu Zhang , Junxiong Yu , Yun Zhang , Jiayun Xue , Yuanxin Guo , Jianguang Liang , Min Ren , Qingyun Ling , Ali Mohsin , Jiangchao Qian , Zejian Wang , Yonghong Wang","doi":"10.1016/j.procbio.2025.01.017","DOIUrl":"10.1016/j.procbio.2025.01.017","url":null,"abstract":"<div><div>Oxygen supply and oxygen uptake rate (OUR) significantly influences both the physiological state of cells and nemadectin biosynthesis by <em>Streptomyces cyaneogriseus ssp. noncyanogenus.</em> In this study, a real-time monitoring approach for nemadectin fermentation was developed for the first time by an online OUR control strategy. The effect of OUR levels during the mycelium differentiation phase on nemadectin biosynthesis was studied and optimized by adjusting feeding rates of (NH<sub>4</sub>)<sub>2</sub>SO<sub>4</sub>. Results showed that controlling the OUR at approximately 17.5 mmol·L<sup>−1</sup>·h<sup>−1</sup> during the mycelium differentiation phase effectively enhanced nemadectin production, reaching 2805.1 μg·mL<sup>−1</sup>, making a 129.5 % increase compared to the control. This OUR control strategy was successfully scaled-up to a 500 L pilot scale, achieving the highest ever nemadectin production of 2867.3 μg·mL<sup>−1</sup>. These findings demonstrate that this OUR control strategy provides an effective and scalable approach for industrial nemadectin production.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"150 ","pages":"Pages 248-256"},"PeriodicalIF":3.7,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143094486","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}

引用次数: 0

Mathematical prediction of COD removal using interrelation of operating variables of the aerobic inverse fluidized bed biofilm reactor (AIFBBR)

IF 3.7 3区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Process Biochemistry

Pub Date : 2025-01-20 DOI: 10.1016/j.procbio.2025.01.014

Mallikarjuna Challa, Rajesh Roshan Dash

The present study aimed to develop a mathematical model for predicting COD removal using the interrelation of operating variables. The model for predicting COD removal is named the dimensionless number for COD removal (DNC). The DNC was formulated based on the critical variables of the AIFBBR process for the rice mill wastewater treatment. HRT, OLR, and biomass concentration (M_b) are considered for the generation of DNC for the AIFBBR system. In the present attempt of framing such a dimensionless number DNC, many experimental runs were conducted by varying the COD strength of 0.8–3.2 kg/m³, OLR of 0.80–6.40 kg/m³.d, and M_b of 0.90–7.43 kg/m³. The developed DNC was subjected to sensitivity analysis, and biomass concentration in the system was observed to be the most sensitive among other parameters incorporated in the model. In addition, from the sensitivity analysis, it was also revealed that the removal efficiencies were observed to increase with the increase in DNC values in the COD range of 0.8–3.2 kg/m³. In addition, the plot between the reported removals from the literature on biofilm processes for wastewater treatment and DNC values yielded an R² value of 0.79.

{"title":"Mathematical prediction of COD removal using interrelation of operating variables of the aerobic inverse fluidized bed biofilm reactor (AIFBBR)","authors":"Mallikarjuna Challa, Rajesh Roshan Dash","doi":"10.1016/j.procbio.2025.01.014","DOIUrl":"10.1016/j.procbio.2025.01.014","url":null,"abstract":"<div><div>The present study aimed to develop a mathematical model for predicting COD removal using the interrelation of operating variables. The model for predicting COD removal is named the dimensionless number for COD removal (DNC). The DNC was formulated based on the critical variables of the AIFBBR process for the rice mill wastewater treatment. HRT, OLR, and biomass concentration (M<sub>b</sub>) are considered for the generation of DNC for the AIFBBR system. In the present attempt of framing such a dimensionless number DNC, many experimental runs were conducted by varying the COD strength of 0.8–3.2 kg/m<sup>3</sup>, OLR of 0.80–6.40 kg/m<sup>3</sup>.d, and M<sub>b</sub> of 0.90–7.43 kg/m<sup>3</sup>. The developed DNC was subjected to sensitivity analysis, and biomass concentration in the system was observed to be the most sensitive among other parameters incorporated in the model. In addition, from the sensitivity analysis, it was also revealed that the removal efficiencies were observed to increase with the increase in DNC values in the COD range of 0.8–3.2 kg/m<sup>3</sup>. In addition, the plot between the reported removals from the literature on biofilm processes for wastewater treatment and DNC values yielded an <em>R</em><sup><em>2</em></sup> value of 0.79.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"150 ","pages":"Pages 257-264"},"PeriodicalIF":3.7,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143094489","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}

引用次数: 0

RSM-based optimization and scale-up production of hIL-2 in Escherichia coli

IF 3.7 3区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Process Biochemistry

Pub Date : 2025-01-20 DOI: 10.1016/j.procbio.2025.01.015

Yuxiao Liu, Mingfang Zhang, Yueying Xu, Lin Yang, Fei Wang, Yuming Fang, Jiayu Wang, Xiaoran Jing, Junjun Jiang

Human interleukin 2 (hIL-2) has become a pivotal molecule widely used in the treatment of various diseases. The development of a robust and highly productive high cell density cultivation process for producing hIL-2 from inclusion bodies represents a promising and attractive strategy for its commercial production. In this study, a 12-bioreactor 250 mL DASbox mini bioreactor system was employed to develop a model using Response Surface Methodology (RSM) aimed at understanding the impacts of cultivation parameters on cell growth and product yiled as well as maximizing hIL-2 production. The optimized process was further validated in a 5-L stirred tank bioreactor: an induction temperature of 31.3°C, an isopropyl β-D-1-thiogalactopyranoside (IPTG) concentration of 1.0 mM, a post-induction feeding rate of 103.80 mL/h, and an induction OD₆₀₀ of 150.0. The maximum hIL-2 titer achieved 4.90 g/L, which correlated well with the predicted range. Subsequent solubilization and in vitro refolding process resulted in hIL-2 purity exceeding 99 %, and a the bioactivity of 0.88 × 10⁷ U/mL, comparable to that of commercial products. This study demonstrates the effectiveness of optimizing cultivation parameters to enhance hIL-2 yield and highlights the value of employing statistical methods as a powerful tool to guide manufacturing operations in recombinant protein production.

{"title":"RSM-based optimization and scale-up production of hIL-2 in Escherichia coli","authors":"Yuxiao Liu, Mingfang Zhang, Yueying Xu, Lin Yang, Fei Wang, Yuming Fang, Jiayu Wang, Xiaoran Jing, Junjun Jiang","doi":"10.1016/j.procbio.2025.01.015","DOIUrl":"10.1016/j.procbio.2025.01.015","url":null,"abstract":"<div><div>Human interleukin 2 (hIL-2) has become a pivotal molecule widely used in the treatment of various diseases. The development of a robust and highly productive high cell density cultivation process for producing hIL-2 from inclusion bodies represents a promising and attractive strategy for its commercial production. In this study, a 12-bioreactor 250 mL DASbox mini bioreactor system was employed to develop a model using Response Surface Methodology (RSM) aimed at understanding the impacts of cultivation parameters on cell growth and product yiled as well as maximizing hIL-2 production. The optimized process was further validated in a 5-L stirred tank bioreactor: an induction temperature of 31.3°C, an isopropyl β-D-1-thiogalactopyranoside (IPTG) concentration of 1.0 mM, a post-induction feeding rate of 103.80 mL/h, and an induction OD<sub>600</sub> of 150.0. The maximum hIL-2 titer achieved 4.90 g/L, which correlated well with the predicted range. Subsequent solubilization and in vitro refolding process resulted in hIL-2 purity exceeding 99 %, and a the bioactivity of 0.88 × 10<sup>7</sup> U/mL, comparable to that of commercial products. This study demonstrates the effectiveness of optimizing cultivation parameters to enhance hIL-2 yield and highlights the value of employing statistical methods as a powerful tool to guide manufacturing operations in recombinant protein production.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"150 ","pages":"Pages 265-275"},"PeriodicalIF":3.7,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143094479","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}

引用次数: 0

Optimized nitrogen removal in low-carbon settings via sequencing batch reactors with vermiculite-enveloped layered double hydroxides bio-fillers

IF 3.7 3区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Process Biochemistry

Pub Date : 2025-01-19 DOI: 10.1016/j.procbio.2025.01.016

Lv Xi, Zhang Peng, Zhang Qiwu, He Xiaoman

This study assesses Mg-Al-LDHs (Layered Double Hydroxides) /VMT (Vermiculite) and Zn-Al-LDHs/VMT as bioreactor packing materials in Sequencing Batch Reactor (SBR) systems for nitrogen removal. The materials were synthesized using a ball milling-hydrothermal method and tested under low-carbon conditions. The study achieved rapid start-up within 24 days, with ammonia nitrogen conversion rates of 77.9 % and 77.3 % for Mg-Al-LDHs/VMT and Zn-Al-LDHs/VMT, respectively, compared to less than 40 % in the control group. The VMT-LDHs bio-filler facilitated the formation of a dynamic film, enhancing biological adherence and adsorption of ammonia nitrogen and dissolved oxygen. This significantly improved the nitrification and denitrification processes. These findings highlight the potential of Mg-Al-LDHs/VMT and Zn-Al-LDHs/VMT to enhance nitrogen removal efficiency in wastewater treatment.

引用次数: 0

Improving eicosapentaenoic acid yield by constructing an enzyme-constrained model of Schizochytrium

IF 3.7 3区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Process Biochemistry

Pub Date : 2025-01-17 DOI: 10.1016/j.procbio.2025.01.010

Zijian Hu , Dechun Kong , Tianjun Gan , Yuhong Xin , Yuetong Wang , Tianqiong Shi , Chao Ye

Eicosapentaenoic acid (EPA), an essential omega-3 polyunsaturated fatty acid (PUFA), cannot be produced by the human body. It finds applications in various fields, including health foods, pharmaceuticals, and animal feed. Schizochytrium sp., an oleaginous microorganism rich in PUFAs, holds promise for EPA production. However, its complex metabolic network limits its full potential. To address this challenge, we constructed a detailed enzyme-constrained model eciCY1170_DHA of Schizochytrium's metabolism. This model incorporated 1083 genes, 5236 reactions, and 2989 metabolites. We then used this model to simulate fermentation conditions and validated our predictions through experiments. Our research results indicate that the optimal nitrogen source absorption rate is 0.7692 mmol/gDW/h, and the optimal oxygen absorption rate is 3.41 mmol/gDW/h. When both absorption rates are higher or lower than the optimal values, they will hinder EPA production. Conclusions drawn from simulations and experiments show that by adjusting the nitrogen source concentration, Ventilation volume, and agitation speed, the maximum yield of EPA reached 1.09 g/L in a 5 L fermenter. By analyzing protein requirements, we identified 20 potential targets predicted to enhance EPA production. This study provides new ideas for the optimization of medium composition and strain modification for the industrial production of EPA using Schizochytrium.

{"title":"Improving eicosapentaenoic acid yield by constructing an enzyme-constrained model of Schizochytrium","authors":"Zijian Hu , Dechun Kong , Tianjun Gan , Yuhong Xin , Yuetong Wang , Tianqiong Shi , Chao Ye","doi":"10.1016/j.procbio.2025.01.010","DOIUrl":"10.1016/j.procbio.2025.01.010","url":null,"abstract":"<div><div>Eicosapentaenoic acid (EPA), an essential omega-3 polyunsaturated fatty acid (PUFA), cannot be produced by the human body. It finds applications in various fields, including health foods, pharmaceuticals, and animal feed. <em>Schizochytrium</em> sp., an oleaginous microorganism rich in PUFAs, holds promise for EPA production. However, its complex metabolic network limits its full potential. To address this challenge, we constructed a detailed enzyme-constrained model eciCY1170_DHA of <em>Schizochytrium</em>'s metabolism. This model incorporated 1083 genes, 5236 reactions, and 2989 metabolites. We then used this model to simulate fermentation conditions and validated our predictions through experiments. Our research results indicate that the optimal nitrogen source absorption rate is 0.7692 mmol/gDW/h, and the optimal oxygen absorption rate is 3.41 mmol/gDW/h. When both absorption rates are higher or lower than the optimal values, they will hinder EPA production. Conclusions drawn from simulations and experiments show that by adjusting the nitrogen source concentration, Ventilation volume, and agitation speed, the maximum yield of EPA reached 1.09 g/L in a 5 L fermenter. By analyzing protein requirements, we identified 20 potential targets predicted to enhance EPA production. This study provides new ideas for the optimization of medium composition and strain modification for the industrial production of EPA using <em>Schizochytrium</em>.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"150 ","pages":"Pages 238-247"},"PeriodicalIF":3.7,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143099622","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}

引用次数: 0

De novo carbon monoxide dehydrogenase and carbonic anhydrase using molecular dynamics and deep generative model

IF 3.7 3区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Process Biochemistry

Pub Date : 2025-01-16 DOI: 10.1016/j.procbio.2025.01.013

Ruei-En Hu , Chang-Chun Chang , Tzu-Hao Chen , Ching-Ping Chang , Chi-Hua Yu , I-Son Ng

Carbon monoxide dehydrogenase (CODH) and carbonic anhydrase (CA) play crucial roles in cellular metabolism by catalyzing the interconversion of carbon monoxide, carbon dioxide, and bicarbonate. However, the diversity of both enzymes remains unclear. This study integrates deep generative models and molecular dynamics simulations to streamline the design of novel CODH and CA variants. Using highly active enzymes from Carboxydothermus hydrogenoformans (PDB: 1SU8) and human carbonic anhydrase II (PDB:1HEB) as templates, we engineered de novo protein structures with enzymatic activities. Deep generative models including RFdiffusion, ProteinMPNN, CLEAN, and AlphaFold3 were employed to design novel CODH variants. Among all candidates, CODH2206 showed superior stability and activity in simulations but protein expressed as inclusion bodies in E. coli BL21(DE3) and improved in C43(DE3). Further characterization revealed that CODH2206 exhibited higher activity at pH 8. To resolve the quality and quantity of de novo enzymes, we applied SoDoPe solubility and trRosetta structure prediction for pixel-to-protein creation. Finally, hCAd3 activity increased 5-folds when chaperones and rare codons were involved in the system. This pipeline has high potential to generate diverse enzymes, advancing protein engineering for the creation of biocatalysts in the future.

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