Process Biochemistry最新文献

{"title":"Break through the thermostability of glucose oxidase in extremely thermal environments with a novel dynamic ensemble design protocol","authors":"Tingwei Miao ,&nbsp;Fengdong Zhi ,&nbsp;Xin Yang ,&nbsp;Zhaoting Yuan ,&nbsp;Chuanxi Zhang ,&nbsp;Yinghui Feng ,&nbsp;Hao Wei ,&nbsp;Haiming Jiang ,&nbsp;Bei Gao ,&nbsp;Lujia Zhang","doi":"10.1016/j.procbio.2024.11.019","DOIUrl":"10.1016/j.procbio.2024.11.019","url":null,"abstract":"<div><div>Enhancing the thermostability of glucose oxidase (Gox) is crucial for its industrial applications. However, in traditional design methods based on a single Gox structure, hundreds of or several rounds of variants were predicted and tested, with limited thermostability enhancement under high temperature conditions. Here, we established a method for precisely locating residue by analysing the dynamic conformations of GoxM8 (M8) and further enhancing thermostability while maintaining activity. Our novel dynamic ensemble approach, coupled with FireProt computational analyses, was used to obtain the best mutant, V402F, from diverse conformations of M8. V402F residual activity was six times that of M8 at 80 ℃ for 2 min, with no loss of enzyme activity. Experimental validation and computational analysis of stability mechanisms demonstrated the deficiencies of previous design strategies for flexible enzymes, proving the validity of our approach. Thus, we present a Gox variant with improved thermostability, as well as a more precise and efficient design strategy for Gox and other flexible enzymes.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"148 ","pages":"Pages 55-62"},"PeriodicalIF":3.7,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142706923","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}

{"title":"Recent advances of mesoporous silica-based nanocomposites for photodynamic therapy: A review","authors":"Muhammad Asif ,&nbsp;M. Fakhar-e-Alam ,&nbsp;Iqbal Hussain ,&nbsp;Irsa Amjad ,&nbsp;Ghulam Abbas ,&nbsp;Sara Mahmood","doi":"10.1016/j.procbio.2024.11.013","DOIUrl":"10.1016/j.procbio.2024.11.013","url":null,"abstract":"<div><div>Photodynamic therapy (PDT) has emerged as a promising strategy for treating deep-seated tumors by harnessing the power of reactive oxygen species (ROS) liberation. Current therapy utilizes a photosensitizer (PS) that can be triggered by various external or internal stimuli, such as near-infrared light (NIR) or inner biological/chemical reactions, leading to the production of ROS (e.g., *OH and ¹O₂) within the tumor microenvironment (TME), which leads to cancer killing mechanism. Mesoporous silica nanoparticles (MSNs) and their hybrids forms are promising candidates for PDT due to their exceptional properties, including a high surface area-to-volume ratio, excellent biocompatibility, modifiable surface, pore size, modifiable morphology, high prosperity and biosafety. Herein, the aim of this review to explain the anticancer mechanisms of MSNs-based PDT and multifunctional synergistic therapies. Moreover, we also summarized the up-to-date advances in the design, modification, and applications of MSNs-based PDT. Finally, the current challenges facing MSNs-based PDT are discussed, as well as future prospective for clinical uses of MSNs-based nanocomposites for ROS-activated synergistic therapies.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"148 ","pages":"Pages 79-103"},"PeriodicalIF":3.7,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142706927","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}

{"title":"Use of Rhizomucor miehei fermented babassu cake (an agro-product residue) as efficient biocatalyst for macaúba acid oil deacidification in solvent-free medium: Transforming a non-edible crop product in a favourable biodiesel feedstock","authors":"Elisa D.C. Cavalcanti ,&nbsp;Erika C.G. Aguieiras ,&nbsp;Maria Fernanda S. Mota ,&nbsp;Priscila R. da Silva ,&nbsp;Roberto Fernandez-Lafuente ,&nbsp;Aline M. de Castro ,&nbsp;Denise M.G. Freire","doi":"10.1016/j.procbio.2024.11.018","DOIUrl":"10.1016/j.procbio.2024.11.018","url":null,"abstract":"<div><div>Macaúba, a native South American palm, is used to recover degraded areas in important Brazilian biomes and presents a high oil productivity. Macaúba pulp oil is a sustainable alternative for biodiesel production. However, its high acidity represents a problem for its use. This paper shows an enzymatic process to reduce the acidity of macaúba pulp oil (9.5 wt% acidity) using a low-cost agro-industrial by-product to get a solid-state fermented solid with lipase activity from <em>Rhizomucor miehei</em>. Ethanol, methanol and glycerol were evaluated as acyl acceptors for the esterification of the free fatty acids (FFA) in the oil. Methanol was the best acyl acceptor, with 3.6 and 2.4 times higher deacidification rate than ethanol and glycerol, respectively, for reactions conducted with FFA to alcohol stoichiometric molar ratio. The alcohol stepwise addition strategy gave better results for all tested acyl acceptors. At the best reaction condition (methanol/FFA molar ratio of 6:1, methanol stepwise addition), the desired FFA esterification (acidity of 0.4 wt%, compatible with biodiesel plants requirements) was attained after only 2.5 h. This means the conversion of two no interesting crop products into valuable products.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"148 ","pages":"Pages 176-182"},"PeriodicalIF":3.7,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142707008","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}

{"title":"Adaptive laboratory evolution of Serratia marcescens with enhanced osmotic stress tolerance for prodigiosin synthesis","authors":"Junqing Wang ,&nbsp;Tingting Zhang ,&nbsp;Yang Liu ,&nbsp;Shanshan Wang ,&nbsp;Shuhua Liu ,&nbsp;Yanlei Han ,&nbsp;Hui Xu","doi":"10.1016/j.procbio.2024.11.016","DOIUrl":"10.1016/j.procbio.2024.11.016","url":null,"abstract":"<div><div>Prodigiosin, a valuable intracellular secondary metabolite, is produced by <em>Serratia marcescens</em>. However, synthesis during fermentation is constrained by osmotic pressure. In this study, adaptive laboratory evolution was applied to the strain SDSPY-136 to improve osmotic stress tolerance. After 120 passages, screening and validation yielded a strain with high osmotic pressure resistance, <em>S. marcescens</em> R82. The UV absorption spectrum, HPLC peak time, FTIR functional groups, and ¹H NMR chemical shifts revealed that the pigment generated by the evolved strain was prodigiosin. After batch fermentation in a 5 L bioreactor, the prodigiosin concentration was 11.4 g/L, double the initial strain. Transcriptomic analyses revealed significant enrichment for 830 genes. R82 showed alterations in various pathways, indicating that the regulation of intracellular metabolic pathways promoted the availability of prodigiosin precursors, increasing the capacity for prodigiosin synthesis and extracellular release. This study clarifies the molecular evolution mechanism and presents a novel approach for improving yields in <em>S. marcescens</em>.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"148 ","pages":"Pages 32-42"},"PeriodicalIF":3.7,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142706925","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}

{"title":"Efficient bio-reduction of 3-nitro phthalic acid using engineered nitroreductase and V2O5","authors":"Qin Zhang ,&nbsp;Yahui Feng ,&nbsp;Xiyu Liang ,&nbsp;Shuming Wu ,&nbsp;Fang He ,&nbsp;Yixin Guan ,&nbsp;Zhongqing Wang","doi":"10.1016/j.procbio.2024.11.011","DOIUrl":"10.1016/j.procbio.2024.11.011","url":null,"abstract":"<div><div>In this study, a potent nitroreductase enzyme was successfully identified and engineered, which was then employed in an efficient and environmentally friendly chemo-bio nitroreduction process to synthesize 3-amino phthalic acid from 3-nitro phthalic acid. The wild-type nitroreductase from <em>Azorhizobium caulinodans</em> ORS 571 (<em>Ac</em>NTR) demonstrated robust catalytic activity. Through error-prone PCR mutagenesis, a mutant variant (Q40R/K267R) was generated, which exhibited a 3.1-fold increase in catalytic efficiency. Molecular docking analysis revealed that the mutations at positions R40 and R267 altered the electrostatic properties of the enzyme's surface, modifying the conformation of the active pocket entrance and thereby enhancing catalytic performance. Additionally, when the mutant Q40R/K267R was combined with divanadium pentaoxide (V₂O₅), the accumulation of 3-hydroxyamino phthalic acid during the biotransformation process was effectively prevented. Under optimized reaction conditions, a 90.0 % conversion rate was achieved, transforming 100 g/L of 3-nitro phthalic acid into 3-amino phthalic acid in just 12 h. These findings highlight the significant potential of biocatalytic processes for large-scale synthesis applications.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"148 ","pages":"Pages 157-167"},"PeriodicalIF":3.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142707005","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}

{"title":"Bismuth oxide nanoparticles inhibit HCT116 colorectal cancer cells by inducing apoptosis, cell cycle arrest and ROS production","authors":"Yongjing Hu ,&nbsp;Ying Yin ,&nbsp;Jiayan Shi ,&nbsp;Ali Bahadur ,&nbsp;Kamyar Shameli ,&nbsp;Chenxiao Zheng ,&nbsp;Xiaodong Zhang ,&nbsp;Sin-Yeang Teow","doi":"10.1016/j.procbio.2024.11.017","DOIUrl":"10.1016/j.procbio.2024.11.017","url":null,"abstract":"<div><div>Nanoparticles (NPs) have recently gained traction for anticancer use. Colorectal cancer (CRC) is one of the most common cancer types in the world, but only a few studies have previously reported the anticancer action of Bi₂O₃ NPs towards CRC, and the underlying mechanisms are not well understood. In this study, 1 mg/ml Bi₂O₃ NPs showed 60 % and 8 % inhibition in HCT116 and HT-29 cells, respectively. In the HCT116 spheroid, Bi₂O₃ NPs showed reduced inhibition of 27 % at 1 mg/ml due to the more stringent tissue architecture. Both CRC cells showed successful internalization of Bi₂O₃ NPs through flow cytometry and ICP-MS. The NPs mainly killed HCT116 cells by inducing late-stage apoptosis (∼17 %). In addition, Bi₂O₃ NPs also induced S and G2/M cell cycle arrest (∼4 % and ∼10 %) by targeting CDK2 protein in HCT116 cells. In HT-29 cells, Bi₂O₃ NPs did not trigger apoptosis but induced ∼22 % G2/M cell cycle arrest. Bi₂O₃ NPs also induced ROS production, and potently inhibited the cell migration. 300 μg/ml Bi₂O₃ NPs also exhibited anti-angiogenic action in the angiogenesis assay. In conclusion, the present study highlights the potential anticancer effect of Bi₂O₃ NPs towards CRC, and further investigation is warranted to improve the biocompatibility, targeted selectivity, and tumor-penetrating capacity.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"148 ","pages":"Pages 124-138"},"PeriodicalIF":3.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142706928","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}

{"title":"A review of the Thiopaq process for biological hydrogen sulfide removal from sour gases","authors":"Omar Aboelwafa ,&nbsp;Tamer S. Ahmed ,&nbsp;Mai M. Kamal Fouad ,&nbsp;Amr Abdelghany","doi":"10.1016/j.procbio.2024.11.014","DOIUrl":"10.1016/j.procbio.2024.11.014","url":null,"abstract":"<div><div>Different technologies have been employed for hydrogen sulfide removal from sour gases, whether natural gas, biogas, or other gases, based on market requirements and environmental regulations. Several biological desulfurization technologies have been established for sulfur recovery such as Thiopaq technology. It is considered an ecological, and environmentally sustainable solution that has been studied, developed and commercialized since the end of the past century in different industries especially for biogas desulfurization. In addition, the process offers a decarbonation simultaneously with sulfur recovery. The current work reviews Thiopaq from different aspects that correlate all the technology pillars such as microorganisms, the valuable biosulfur, technology economics, the main operating parameters in addition to a brief description of the sections presented with chemistry of main and side reactions and the technology advantages and disadvantages. Future work should consider deeper research of the viability of technology for decarbonation. In addition, employing mathematical modeling and computation fluid dynamics are crucial for better understanding of bioreactors, the cornerstone of biological desulfurization, in terms of aeration and redox control. Other recommendations are presented.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"148 ","pages":"Pages 63-78"},"PeriodicalIF":3.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142707009","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}

{"title":"A comprehensive analysis of photothermal therapy (PTT) and photodynamic therapy (PDT) for the treatment of cancer","authors":"Nasrin Sultana ,&nbsp;Riya Pathak ,&nbsp;Shibnath Samanta ,&nbsp;Neelotpal Sen Sarma","doi":"10.1016/j.procbio.2024.11.015","DOIUrl":"10.1016/j.procbio.2024.11.015","url":null,"abstract":"<div><div>Photothermal and photodynamic therapies use light to target and eliminate cancer cells by raising the temperature or producing reactive oxygen species. To understand the main effect of both the therapy, studies are going on at the cellular level. Based on the distinct mode of action both photodynamic and photothermal therapy may work synergically according to recent studies. As both therapies are non-toxic, the combination of these two may be more effective for curing cancer. Additionally, a combination of the two therapies is being used to develop nano-platforms that incorporate simultaneously photothermally and photodynamically active drugs. In this review, we have discussed the basic mechanism of both the therapy and different mechanisms such as cell death mechanism, vascular damage, extracellular matrix effect as well as immune effect. Along with that, we have also discussed different factors that can affect photodynamic and photothermal therapy. Additionally, we have also discussed the different types of nanomaterials that can be useful for photodynamic therapy as well as in photothermal therapy.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"148 ","pages":"Pages 17-31"},"PeriodicalIF":3.7,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142660702","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}

{"title":"Growth in traditional fermented soybeans-related research (tempeh, natto, doenjang, chungkookjang, douchi, meju, kinema, oncom, and tauco) from 1928 to 2024, following the omics emergence and trend in functional food","authors":"Andri Frediansyah","doi":"10.1016/j.procbio.2024.11.008","DOIUrl":"10.1016/j.procbio.2024.11.008","url":null,"abstract":"<div><div>Soybean processing has traditionally relied on fermentation. These fermented products have been consumed for decades, particularly in Asian countries. Despite numerous publications on fermented soybeans over the past ninety years, there is a lack of reviews that specifically focus on nine traditional fermented soybean products, namely tempeh, natto, doenjang, chungkookjang, douchi, meju, kinema, oncom, and tauco. Population growth and the need for a healthy diet have prompted researchers to improve soybean-fermented products. The objective of this study was to use reference data to conduct a bibliometric analysis assessing the progress of research on nine traditional fermented soybean products, various uses of these products, and the utilization of advanced technologies to improve research quality. From the scientific database, 2280 documents published between 1928 and 2024 were identified and subjected to bibliometric analysis using the VOSviewer software. Up until recently, article publications and citations increased. South Korea holds the top position in the quantity of publications related to the NTFSP. IPB University is the most productive institution regarding the nine traditional fermented soybean products. <em>In vivo</em> and clinical trials have demonstrated that certain traditional fermented products possess anti-metabolic syndrome properties, including antidiabetic, anti-obesity, antihypertensive effects, cancer, and modulation of bone metabolism. Microbial diversity also provides health benefits to fermented soy products. Furthermore, recent trends include leveraging emerging techniques such as omics, docking, and whole-genome sequencing to advance research on fermented soybeans. However, no references were found for either the <em>in vivo</em> or clinical trials of douchi, meju, kinema, or oncom. Moreover, the use of recent advancement tools has not yet been found in literature related to oncom and tauco. Therefore, using advanced tools, further research on combating metabolic syndrome-related fermented soybean products should be carried out.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"147 ","pages":"Pages 600-624"},"PeriodicalIF":3.7,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142663506","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}

{"title":"Investigating the effect of linker peptides on the fragmentation of Fc-fusion proteins in transient gene expression of mammalian cells","authors":"Eun-Ji Lee ,&nbsp;Hoon-Min Lee ,&nbsp;Hyun-Seung Kim ,&nbsp;So Hui Ryu ,&nbsp;Mi-Jung Kang ,&nbsp;Jungmok You ,&nbsp;Yeon-Gu Kim","doi":"10.1016/j.procbio.2024.11.010","DOIUrl":"10.1016/j.procbio.2024.11.010","url":null,"abstract":"<div><div>Protein fragmentation is a critical quality attribute for Fc-fusion protein production in mammalian cells. In the production of viral non-structural proteins as the form of Fc-fusion protein, fragmentation of Fc-fusion proteins occurred in two transient gene expression (TGE) systems with human embryonic kidney (HEK) 293 and Chinese hamster ovary (CHO) cells. The introduction of a flexible empirical linker reduced fragmentation in HEK293 cells, but not in CHO cells. Additionally, two rigid empirical linkers failed to restore impaired Fc-fusion proteins in CHO cells. <em>In vitro</em> incubation assay using conditioned culture medium and cultures supplemented with protease inhibitor cocktail suggest that fragmentation of Fc-fusion proteins in CHO cells may be due to various host cell proteins released into the culture medium. These findings suggest that the introduction of linker peptides can improve the fragmentation of Fc-fusion proteins in mammalian cells, but exhibit different fragment patterns depending on the cell type.</div></div>","PeriodicalId":20811,"journal":{"name":"Process Biochemistry","volume":"147 ","pages":"Pages 625-629"},"PeriodicalIF":3.7,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142663438","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}