Biochemical Engineering Journal最新文献_第4页

Molecularly-imprinted polymer based on graphene oxide functionalized pencil graphite electrode for cholesterol detection 基于氧化石墨烯功能化铅笔石墨电极的分子印迹聚合物用于胆固醇检测

IF 3.7 3区生物学

Biochemical Engineering Journal Pub Date : 2025-05-16 DOI: 10.1016/j.bej.2025.109769

Fera Ayu Dianovita , Elly Septia Yulianti , Siti Hanafiah , Siti Fauziyah Rahman

{"title":"Molecularly-imprinted polymer based on graphene oxide functionalized pencil graphite electrode for cholesterol detection","authors":"Fera Ayu Dianovita , Elly Septia Yulianti , Siti Hanafiah , Siti Fauziyah Rahman","doi":"10.1016/j.bej.2025.109769","DOIUrl":"10.1016/j.bej.2025.109769","url":null,"abstract":"<div><div>Cholesterol plays a vital role in biological functions that must be maintained at a normal level of < 5.2 mmol/L to prevent hypercholesterolemia, leading to cardiovascular diseases. This research examines a molecularly-imprinted polymer (MIP) based biosensor using a pencil graphite electrode (PGE) modified graphene oxide (GO) for the sensitive, selective, and stable detection of cholesterol with a simple approach using the electropolymerization process. The imprinted poly[2-(dimethylamino) ethyl methacrylate] (poly[DMAEMA]) layers on PGE/GO surface exhibit strong electrochemical responses during cholesterol detection through the formation of cholesterol-specific recognition cavities that were formed to mimic the cholesterol’s structures, allowing non-enzymatic detection. Through the optimization of the parameters during electropolymerization, including the ratio of template molecule concentration to monomer, polymerization and template removal cycles, scan rate, rebinding duration, and pH, the sensor demonstrated satisfactory performance. With the limit of detection (LOD) of 0.85 mM, limit of quantification (LOQ) of 2.85 mM, a linear range of 1–6 mM, and sensitivity of 40.52 μA.μM⁻¹ .cm⁻², the sensor offered good electrochemical performance and selectivity towards cholesterol, despite the presence of other interference molecules. The current stability percentage on the tenth day was 85.52 %, which indicates good stability of the sensor modification and indicates potential for repeated cholesterol sensing for further point-of-care testing (POCT) application.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"221 ","pages":"Article 109769"},"PeriodicalIF":3.7,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144106669","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

Spatiotemporal dynamics of algal-microbial interactions in a membrane photobioreactor for integrated nutrient remediation and microalgal resource recovery from shrimp aquaculture wastewater 膜光生物反应器中藻类与微生物相互作用的时空动态研究——用于对虾养殖废水营养物综合修复和微藻资源回收

IF 3.7 3区生物学

Biochemical Engineering Journal Pub Date : 2025-05-16 DOI: 10.1016/j.bej.2025.109793

Tianyi Ye , Miaoxin Li , Derek M. Ayittey , Yuanyuan Qi , Zheng Sun , Zhijuan Jiang , Guoqi Zhang , Yun Ling

{"title":"Spatiotemporal dynamics of algal-microbial interactions in a membrane photobioreactor for integrated nutrient remediation and microalgal resource recovery from shrimp aquaculture wastewater","authors":"Tianyi Ye , Miaoxin Li , Derek M. Ayittey , Yuanyuan Qi , Zheng Sun , Zhijuan Jiang , Guoqi Zhang , Yun Ling","doi":"10.1016/j.bej.2025.109793","DOIUrl":"10.1016/j.bej.2025.109793","url":null,"abstract":"<div><div>The projected rise of global aquaculture to 106 million tons by 2030 has amplified concerns over nutrient-rich wastewater, demanding sustainable treatment solutions. This study developed an aerated membrane photobioreactor (MPBR) to simultaneously assess nutrient removal, biomass productivity, and algal–microbial community dynamics. High-throughput sequencing identified a dominant, stable consortium featuring the nitrogen-fixing <em>Azospirillum</em> (20.81 %) and the eukaryotic alga <em>Halochlorella</em> (53.19 %). Membrane surface analysis revealed a diverse biofilm community including <em>Limnothrix</em> (12.36 %) and <em>Scenedesmus</em> (28.70 %), suggesting synergistic microbial interactions. Isolated dominant species achieved total nitrogen (TN) removal of 58.36 %–65.50 %, total phosphate (TP) removal of 97.68 %–100 %, and ammonium (NH₄⁺-N) removal of 97.37 %–100 % at a 10-hour hydraulic retention time. These findings underscore the MPBR's dual functionality in effective nutrient remediation and microalgal biomass valorization, offering an informed strategy for resource recovery and environmentally sustainable aquaculture wastewater management.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"221 ","pages":"Article 109793"},"PeriodicalIF":3.7,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144154903","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

Factors influencing the removal of extracellular resistance genes in activated sludge process 活性污泥法去除胞外抗性基因的影响因素

IF 3.7 3区生物学

Biochemical Engineering Journal Pub Date : 2025-05-15 DOI: 10.1016/j.bej.2025.109791

Jinyuan Xue , Mengqi Zhang , Anji Chen , Yuhan Li , Chenke Zhong , Chaoqi Chen

{"title":"Factors influencing the removal of extracellular resistance genes in activated sludge process","authors":"Jinyuan Xue , Mengqi Zhang , Anji Chen , Yuhan Li , Chenke Zhong , Chaoqi Chen","doi":"10.1016/j.bej.2025.109791","DOIUrl":"10.1016/j.bej.2025.109791","url":null,"abstract":"<div><div>Extracellular antibiotic resistance genes (eARGs) contribute to antimicrobial resistance spread in the environment, yet their removal mechanisms in activated sludge remain poorly understood. Here, an artificial resistant plasmid (PUC57-<em>sul</em>1) and its corresponding <em>sul</em>1 amplicon were treated in aerobic reactors under varying conditions. The removal of eARGs was significantly affected by sludge disinfection, biomass concentrations, aeration rate, and temperature. The results indicated that the influencing factors for eARGs are similar to those for small-molecular-organic compounds. At optimal conditions (5 g/L biomass concentration, 400 mL/min aeration rate, and 30°C), the removal efficiency at 12-h was 88.7 % for the amplicon and 67.4 % for the plasmid, respectively, indicating that eARG removal was largely affected by size and conformation. A transient increase of eARGs was observed when actual hospital wastewater was treated, likely due to the lysis of ARG-carrying bacteria. In undiluted hospital wastewater, the concentration of <em>sul</em>1 was reduced by 15.3 % relative to its peak concentration, even under the optimized conditions. In contrast, when the wastewater was 10-fold diluted, the concentration of <em>sul</em>1 was reduced by 81.3 %, confirming the effectiveness of the activated sludge process when toxicity was reduced. Microbial inhibition may be the key factor limiting eARG removal. These findings contribute to a better understanding of factors facilitating the degradation of eARGs, potentially guiding future strategies for improving wastewater treatment practices.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"221 ","pages":"Article 109791"},"PeriodicalIF":3.7,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144070389","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

Enhancing fatty acid production from waste activated sludge through low-temperature heat treatment and biostimulant pretreatment: Performance and mechanism analysis 通过低温热处理和生物刺激素预处理提高废活性污泥脂肪酸产量：性能及机理分析

IF 3.7 3区生物学

Biochemical Engineering Journal Pub Date : 2025-05-12 DOI: 10.1016/j.bej.2025.109789

Yuan Shan , Yanyan Wang , Jing Zhang , Yihan Gong , Tiantian Yao , Yihao Wang , Guanghui Chen , Deshuang Yu

{"title":"Enhancing fatty acid production from waste activated sludge through low-temperature heat treatment and biostimulant pretreatment: Performance and mechanism analysis","authors":"Yuan Shan , Yanyan Wang , Jing Zhang , Yihan Gong , Tiantian Yao , Yihao Wang , Guanghui Chen , Deshuang Yu","doi":"10.1016/j.bej.2025.109789","DOIUrl":"10.1016/j.bej.2025.109789","url":null,"abstract":"<div><div>Anaerobic fermentation of sludge is constrained by low short-chain fatty acids (SCFAs) yields and limited solubilization of organic matter. This study presents a novel approach that integrates low-temperature heat treatment with biostimulant pretreatment to enhance the recovery of SCFAs from waste activated sludge. Experimental results indicate that applying 90 °C heat treatment and 1.2 g/g TSS D-limonene without pH adjustment led to an SCFAs yield of 2664 mg/L, representing a 2.3-fold increase over the control group. Furthermore, under conditions with initial pH set to 12, the SCFAs yield peaked at 2977 mg/L by the seventh day. Mechanistic analysis revealed that the combined pretreatment effectively disrupted extracellular polymeric substances and cell walls, facilitating SCFAs production. Microbial community analysis demonstrated an enrichment of Proteobacteria, Actinobacteria, and chain-elongating bacteria, enhancing the conversion of low-value organic matter into high-value products. The results offer new perspectives for optimizing anaerobic fermentation processes to enhance organic matter recovery from sludge.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"221 ","pages":"Article 109789"},"PeriodicalIF":3.7,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143947154","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

Expressing and functionally evaluating anticancer bispecific antibody fragments using cyanobacterium Synechocystis sp. PCC6803 for sustainable production 利用聚胞蓝藻PCC6803表达抗癌双特异性抗体片段并对其进行功能评价

IF 3.7 3区生物学

Biochemical Engineering Journal Pub Date : 2025-05-11 DOI: 10.1016/j.bej.2025.109776

Gota Kasai , Sayumi Shioya , Miku Kobe , Shunichi Kobayashi , Shouhei Takamatsu , Koki Makabe , Izumi Kumagai , Koji Sode , Ryutaro Asano

{"title":"Expressing and functionally evaluating anticancer bispecific antibody fragments using cyanobacterium Synechocystis sp. PCC6803 for sustainable production","authors":"Gota Kasai , Sayumi Shioya , Miku Kobe , Shunichi Kobayashi , Shouhei Takamatsu , Koki Makabe , Izumi Kumagai , Koji Sode , Ryutaro Asano","doi":"10.1016/j.bej.2025.109776","DOIUrl":"10.1016/j.bej.2025.109776","url":null,"abstract":"<div><div>Anticancer bispecific antibody (BsAb) fragments are effective therapeutic agents because of their high tissue penetration and cytotoxic effects, which can be produced in cost-effective bacterial hosts. We used the cyanobacterium <em>Synechocystis</em> sp. PCC6803 (PCC6803) as an alternative host for sustainably producing BsAb fragments from CO<sub>2</sub>. Cyanobacteria are sustainable and independent of external carbon sources such as glucose, because of producing substances via photosynthesis. Cyanobacteria can be cultured using wastewater or seawater, reducing freshwater consumption and the environmental impact of the process, suggesting that cyanobacteria can be used as a sustainable BsAb production platform. We examined the production of various antibody fragments, namely, single-chain bispecific diabody (scBsDb), single-chain fragment variable (scFv), variable domains of the heavy-chain antibody VHH, and bispecific tandem VHH (BsVHH), using PCC6803. scBsDb showed partial antigen-binding ability and no cytotoxic effects. In contrast, all scFvs and VHH had binding abilities and we prepared BsVHH up to 2.4 mg/L culture. BsVHH showed binding activity with the targets and cytotoxic effects against carcinoma, unlike scBsDb. Our results highlight the suitability of VHH and VHH-based engineered antibody fragments for using PCC6803 and indicate their potential for producing other therapeutic proteins. We report producing functional BsAb fragments using cyanobacteria. Our findings contribute to developing cyanobacterial bioprocesses for producing therapeutic BsAb fragments, expanding the possibilities for sustainably producing valuable materials from CO<sub>2</sub>.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"221 ","pages":"Article 109776"},"PeriodicalIF":3.7,"publicationDate":"2025-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143941236","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

Enhanced biodesulfurization of recalcitrant organosulfur compounds by a newly identified Gordonia alkanivorans JT-2 in the presence of mycolic acid 在霉菌酸存在下，新鉴定的烷化戈登菌JT-2增强了难固定性有机硫化合物的生物脱硫作用

IF 3.7 3区生物学

Biochemical Engineering Journal Pub Date : 2025-05-11 DOI: 10.1016/j.bej.2025.109779

Maosheng Yin , Shuiquan Chen , Meng Zang , Lin Li , Chaocheng Zhao , Xiuxia Zhang

{"title":"Enhanced biodesulfurization of recalcitrant organosulfur compounds by a newly identified Gordonia alkanivorans JT-2 in the presence of mycolic acid","authors":"Maosheng Yin , Shuiquan Chen , Meng Zang , Lin Li , Chaocheng Zhao , Xiuxia Zhang","doi":"10.1016/j.bej.2025.109779","DOIUrl":"10.1016/j.bej.2025.109779","url":null,"abstract":"<div><div>With the increasing stringency of global regulations on the sulfur content of petroleum products, the development of efficient desulfurization technologies has become imperative. While biodesulfurization offers an eco-friendly alternative to hydrodesulfurization, its industrial adoption remains hindered by (i) poor degradation of alkylated DBTs/BTs and (ii) inefficient oil-water phase mass transfer. In this study, we identified a novel strain, <em>Gordonia alkanivorans JT-2</em>, demonstrating enhanced biodesulfurization performance, attributed to its production of mycolic acid, which improves hydrophobicity and mass transfer efficiency. Genomic analysis revealed key desulfurization genes (<em>dszA</em>, <em>dszB</em>, <em>dszC</em>, and <em>dszD</em>) and mycolic acid biosynthesis genes (<em>fas</em>, <em>pks13</em>, <em>kasAB</em>, <em>fabD</em>, and <em>fadD32</em>). Biodesulfurization experiments showed significant sulfur removal, reducing sulfur content in model oil to 35.7 ± 5.9 mg/L (DBT), 55.2 ± 7.9 mg/L (4-MDBT), 63.1 ± 5.7 mg/L (3-MBT), and 73.7 ± 3.8 mg/L (4,6-DMDBT) within 5 days. Protein interaction network analysis further illustrated the interplay between lipid biosynthesis and sulfur metabolism, underscoring the metabolic adaptability of strain JT-2. This work addresses a critical limitation in existing biodesulfurization technologies by improving mass transfer efficiency and broadening substrate range, positioning <em>G. alkanivorans</em> JT-2 as a promising candidate for industrial biodesulfurization applications.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"221 ","pages":"Article 109779"},"PeriodicalIF":3.7,"publicationDate":"2025-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143935120","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

Degradation of malachite green by a novel salt-tolerant Vibrio natriegens: Optimal degradation conditions, mechanisms, and safety assessment 一种新型耐盐营养弧菌降解孔雀石绿：最佳降解条件、机制和安全性评估

IF 3.7 3区生物学

Biochemical Engineering Journal Pub Date : 2025-05-11 DOI: 10.1016/j.bej.2025.109775

Ruihong Sun , Qingzhong Wang , Shuqin Shao , Shanshan Zhang , Ying Wang

{"title":"Degradation of malachite green by a novel salt-tolerant Vibrio natriegens: Optimal degradation conditions, mechanisms, and safety assessment","authors":"Ruihong Sun , Qingzhong Wang , Shuqin Shao , Shanshan Zhang , Ying Wang","doi":"10.1016/j.bej.2025.109775","DOIUrl":"10.1016/j.bej.2025.109775","url":null,"abstract":"<div><div>Synthetic dyes, such as malachite green (MG), are widely used in the textile industry but pose significant environmental risks due to their toxicity. In this study, a highly efficient salt-tolerant bacterial strain, <em>Vibrio natriegens</em> SWS5, was isolated and identified through morphological, physiological, biochemical, and 16S rRNA gene sequence analyses. Systematic investigations were conducted to optimize degradation conditions, analyze enzyme activities, elucidate degradation pathways, and assess detoxification effects. The optimal degradation conditions were determined as follows: peptone 7.5 g/L, NaCl 20 g/L, Fe²⁺ 0.04 g/L, pH 7, temperature 30 °C, and shaking speed 220 rpm. Under these conditions, SWS5 achieved 97.88 % degradation of MG (100 mg/L) within 168 hours. After MG added, enzyme activity assays revealed in dye-decolorizing peroxidase (823 U/L), laccase (358 U/L), and manganese peroxidase (0.204 U/L) activities. HPLC-MS analysis identified key intermediates, enabling the proposal of two potential MG degradation pathways. Toxicity assessments using microbial tests and zebrafish models demonstrated a significant reduction in the toxicity of degradation products. Transcriptome sequencing provided novel insights into the regulatory pathways of MG degradation, offering a theoretical foundation for the bioremediation of MG contaminated wastewater. <em>Vibrio natriegens</em> was demonstrated for the first time to degrade triphenylmethane dyes, especially MG, in high-salinity environments. This study highlights the potential of <em>Vibrio natriegens</em> SWS5 as an efficient and eco-friendly solution for dye wastewater treatment.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"221 ","pages":"Article 109775"},"PeriodicalIF":3.7,"publicationDate":"2025-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143941237","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

Impacts of the combined application of digestate-based compost and biochar on the heavy metal Cd distribution and stress in the plant-soil system 沼液堆肥与生物炭配施对植物-土壤系统重金属Cd分布及胁迫的影响

IF 3.7 3区生物学

Biochemical Engineering Journal Pub Date : 2025-05-08 DOI: 10.1016/j.bej.2025.109773

Feng Zhen , Hengbing Zhou , Linpei Han , Yifan Zhang , Yuwan Pang , Tao Xing , Lei Li

{"title":"Impacts of the combined application of digestate-based compost and biochar on the heavy metal Cd distribution and stress in the plant-soil system","authors":"Feng Zhen , Hengbing Zhou , Linpei Han , Yifan Zhang , Yuwan Pang , Tao Xing , Lei Li","doi":"10.1016/j.bej.2025.109773","DOIUrl":"10.1016/j.bej.2025.109773","url":null,"abstract":"<div><div>In this study, a pot experiment was conducted to evaluate the effects of digestate-based compost, chemical fertilizer, and their combination with biochar on heavy metal distribution, plant growth, and soil microbial communities. The experimental results demonstrated that the combined application of digestate-based compost and biochar (OFB group) promoted heavy metal immobilization in soil and enhanced plant growth, while reducing the accumulation of heavy metals in plants. Oxidizable and residual Cd levels in the OFB group increased by 14.90 % and 17.60 % compared to the control group. The biomass of Chinese cabbage was 384 % higher than that of the control group, and its Cd content decreased by 57.90 % compared to the control group. The addition of digestate-based compost to the soil increased soil organic matter, total nitrogen, total phosphorus, total potassium, and electrical conductivity (p < 0.05), along with the relative abundance of beneficial microorganisms such as <em>Bacillus</em>, <em>norank_f__norank_o__Actinomarinales</em>, <em>Chryseolinea</em>, <em>Saccharomonospora</em>, <em>Pseudomonas,</em> and <em>norank_f__BIrii41</em>. Biochar played a significant role in minimizing the migration of heavy metals to plants. The study demonstrated that the combined application of digestate-based compost and biochar reduces heavy metal stress, enhances soil fertility, and promotes biomass growth, offering potential solutions for the sustainable management of cadmium-contaminated soil and the application of digestate-based compost.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"221 ","pages":"Article 109773"},"PeriodicalIF":3.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143927751","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 constructive bottom-up approach for the elaboration of metabolic networks: Case study of photosynthetic cyanobacteria Arthrospira spirulina platensis PCC 8005

IF 3.7 3区生物学

Biochemical Engineering Journal Pub Date : 2025-05-08 DOI: 10.1016/j.bej.2025.109770

Maxime Maton , Baptiste Leroy , Alain Vande Wouwer

{"title":"A constructive bottom-up approach for the elaboration of metabolic networks: Case study of photosynthetic cyanobacteria Arthrospira spirulina platensis PCC 8005","authors":"Maxime Maton , Baptiste Leroy , Alain Vande Wouwer","doi":"10.1016/j.bej.2025.109770","DOIUrl":"10.1016/j.bej.2025.109770","url":null,"abstract":"<div><div>Mathematical modeling has proven to be a highly effective tool for understanding microbial metabolism for which in-silico and experimental studies help to quantify intracellular mechanisms and pave the way for optimizing the production of molecules of interest. In that context, the development of metabolic networks turns out to be particularly interesting despite the challenges underlying their reconstruction. While the elaboration of genome-scale networks is computationally costly, small networks are often oversimplified and important biological mechanisms might be omitted, which limits their use in industrial applications. For this purpose, this study proposes a constructive bottom-up approach for the identification of metabolic networks of intermediate size, typically comprised of a couple of hundred reactions. It combines basic biological knowledge and a series of constraint-based methods in an iterative strategy, enabling the refinement of the network definition. The network is first validated using in-silico data, and subsequently refined using experimental data to enhance its biological relevance. Several case studies have been addressed to assess the efficiency of the methodology, and this paper focuses on the modeling of photosynthetic cyanobacteria <em>Arthrospira</em> sp. PCC 8005. The procedure is effective and provides promising results and metabolic analyses show consistent predictive capabilities of the network, in concordance with existing studies.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"221 ","pages":"Article 109770"},"PeriodicalIF":3.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143941238","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

Corrigendum to: “Responses of nitrogen removal, microbial community and antibiotic resistance genes to biodegradable microplastics during biological wastewater treatment” [Biochem. Eng. J. 219 (2025) 109732] 《废水生物处理过程中氮去除、微生物群落和抗生素耐药基因对可生物降解微塑料的反应》[生物化学]。Eng。J. 219 (2025) 109732]

IF 3.7 3区生物学

Biochemical Engineering Journal Pub Date : 2025-05-08 DOI: 10.1016/j.bej.2025.109774

Yiwei Zhou , Shaochen Bian , Hua Wang , Yixuan Chu , Lei Zheng , Yali Song , Chengran Fang

引用次数: 0