Applied Biochemistry and Biotechnology最新文献

{"title":"Exploring CRISPR/Cas9-Mediated Gene Editing Advances in Conventional and Non-conventional Yeast Species.","authors":"Sumedha Arora Kapoor, Poonam Choudhary, Ramesh Chand Kasana","doi":"10.1007/s12010-025-05382-2","DOIUrl":"https://doi.org/10.1007/s12010-025-05382-2","url":null,"abstract":"<p><p>In recent years, using modern technologies, researchers have harnessed the potential of yeast species for various industrial uses, such as the bioproduction of biopharmaceuticals, food additives, industrial biocatalysts, and biofuels. To improve the efficiency and potential of yeast species for industrial uses, genetic modification is carried out. Various genome engineering techniques, including Cre-loxP, homing endonucleases, zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9), have been employed by different research groups for the genetic manipulation of yeast species. Among different genome engineering techniques, CRISPR/Cas9 has become popular because of its precise editing at targeted loci with increased efficiency. The ease of use, effectiveness, and adaptability of CRISPR/Cas9 make multiplexing possible for simultaneously targeting multiple genes, which was earlier very challenging through traditional methods. Moreover, the ability to perform marker-free editing is the significant advantage offered by CRISPR/Cas9. This review focuses on the applications of the CRISPR/Cas9 system in both conventional and non-conventional yeast species. Further, we discussed the advancements of CRISPR/Cas9, including the regulation of gene transcription-activation/repression and other genome engineering aspects. Additionally, innovations in CRISPR/Cas9, such as cloning-free CRISPR/Cas9 assembly, CRISPR-targeted in vivo editing (ACtive), CRISPR/Cas9-induced gene conversion, and selective ploidy ablation (CRI-SPA) are also discussed for enhancing the potential applications of CRISPR/Cas9 in diverse yeast species.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Retraction Note: Evaluation of Antibiofilm and Antiquorum Sensing Activities of Fucoidan Characterized from Padina boryana against Nosocomial Pathogens.","authors":"Geetha Mani, Ishwarya Rajendran, Tharani Jayakumar, Arunkumar Mani, Rajalakshmi Govindaraju, Sangeetha Dhayalan","doi":"10.1007/s12010-025-05383-1","DOIUrl":"https://doi.org/10.1007/s12010-025-05383-1","url":null,"abstract":"","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances in Microalgal Biomass Harvesting: Sustainable Approaches for Biofuel and Biorefinery Applications.","authors":"Salam S Alsharari","doi":"10.1007/s12010-025-05358-2","DOIUrl":"https://doi.org/10.1007/s12010-025-05358-2","url":null,"abstract":"<p><p>As a sustainable energy source and potential petroleum-free fuel, microalgae biomass is gaining popularity. The varied metabolic activities of microalgae species allow the extraction of bioproducts for animal feed, food, nutraceuticals, cosmetics, and biopharmaceuticals. Concentrating and measuring microalgal biomass biochemicals requires a lot of raw materials due to the low biomass-to-liquid ratio. This makes sustainable energy equilibrium in microalgae processing difficult. Thus, microalgae collection is a difficult field that needs more research. This paper presents the latest chemical/physical flocculation, bioflocculation, and electrical-based microalgal biomass harvesting methods. Physical flocculation needs energy and equipment, which may make microalgal biomass collection expensive. However, chemical flocculation, which uses inorganic and organic flocculants, is becoming more successful. This review also discusses biomolecule separation using low-liquefying ionic liquids or salts. This approach allows varied biorefinery theories to value microalgal biomass while maintaining biomolecule structural integrity and activity. The article uses comprehensive methods to examine scale up, industrial application, life cycle analysis problems, and future research prospects in microalgae collection for sustainable biofuel generation.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ginsenoside Rc Targets ROCK2 to Inhibit NF-κB Activation and Alleviate Cognitive Dysfunction in Septic Encephalopathy in vitro and in vivo.","authors":"Wei Wang, Lv-Yue Wang, Yan-Yan Zhao","doi":"10.1007/s12010-025-05372-4","DOIUrl":"https://doi.org/10.1007/s12010-025-05372-4","url":null,"abstract":"<p><p>Septic encephalopathy (SE), a severe complication of systemic inflammatory response syndrome, continues to lack effective therapeutic options due to its complex pathophysiology. Ginsenoside Rc (GRc), a principal bioactive component in several medicinal herbs, has demonstrated neuroprotective and anti-tumor properties. However, its potential role in the pathogenesis of SE and the identification of its molecular targets remain unclear. Rho-associated kinase (ROCK) has been implicated in the onset and progression of sepsis, although its precise mechanism of action is not fully understood. In this study, we demonstrated that GRc significantly alleviated cognitive impairment in a murine model of SE, as assessed by the Morris water maze and open-field tests. To explore the ROCK-mediated mechanisms underlying SE and the anti-septic effects of GRc, we examined changes in ROCK2 protein expression in LPS-induced SE mice and identified NF-κBp65 as a downstream phosphorylation target. GRc treatment effectively reduced ROCK2 expression and suppressed the secretion of inflammatory cytokines. These findings elucidate the pathological role of the ROCK2/NF-κBp65 signaling axis in SE and provide compelling evidence that GRc mitigates SE, at least in part, by directly binding to ROCK2 and inhibiting NF-κBp65 phosphorylation.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Linoleic Acid Production Platform via Mortierellaceae Strains: Bioprospection, Molecular Characterization, Cultivation Optimization, and Respirometric Analysis.","authors":"Rafaela B Oliveira, Juliane Machado da Silveira, Maria Manuela C Feltes, Diogo Robl, Jaciane L Ienczak","doi":"10.1007/s12010-025-05369-z","DOIUrl":"https://doi.org/10.1007/s12010-025-05369-z","url":null,"abstract":"<p><p>Polyunsaturated fatty acids (PUFAs) are essential dietary lipids, vital for health and cellular integrity, with growing applications in biofuel, food, and pharmaceuticals. In this sense, this work investigated the production of single cell oil (SCO) from newly isolated Mortierellaceae strains from Antarctica. These strains were identified through ITS region sequencing and one of them (Linnemannia sp. ACF038) was selected for scaling up studies. The study of the physiological characterization of the selected strain was made by assessing various parameters including pH, temperature, nitrogen sources, and concentrations through solid and flask cultures. Based on these results, it was possible to scale up and optimize the culture conditions for SCO production using bench-scale bioreactors with submerged cultures. This process involved the use of two different culture media and an in-depth kinetic study to identify the most effective strategy for SCO production. The study also examined the volumetric oxygen transfer coefficient and oxygen consumption rate. The results showed that the culture medium with high initial glucose content and sodium nitrate significantly increased lipid production, reaching 65% of lipid content. Linoleic acid (LA) comprised 42% of the lipids, indicating strong potential for large-scale LA production. Linnemannia sp. ACF038 proved to be a promising candidate for sustainable industrial LA production, meeting the rising demand for PUFAs.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145038822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Electrical Vagus Nerve Stimulation Ameliorates Cardiac Ischemia and Reperfusion Injury by Improving Mitochondrial Biogenesis Through the SIRT1/PGC-1α Pathway.","authors":"Yingqiang Guo, Yu Zhang, Jinzhou Zhang, Xingwan Bai, Wei Kang, Yujie Guo, Xianming Zeng","doi":"10.1007/s12010-025-05359-1","DOIUrl":"https://doi.org/10.1007/s12010-025-05359-1","url":null,"abstract":"<p><p>Vagus nerve stimulation (VNS) has demonstrated cardioprotective effects in a variety of cardiovascular diseases, including cardiac ischemia and reperfusion (IR) injury. However, the mechanisms responsible for these effects have not been completely understood. The present work aimed to uncover the potential mechanisms through which VNS confers protection against cardiac IR injury. Rats subjected to cardiac IR injury received electrical VNS through the right cervical vagus nerve. This intervention led to a notable reduction in cardiac dysfunction and injury, as well as decreased cardiac apoptosis, oxidative stress, and inflammation. Moreover, VNS treatment improved mitochondrial biogenesis by upregulating estrogen-related receptor α (ERRα), nuclear respiratory factor 1 (NRF-1), and transcriptional factor A mitochondrial (TFAM). In addition, VNS treatment not only increased the copy number of mitochondrial DNA (mtDNA) and the content of adenosine triphosphate (ATP), but also effectively reduced mitochondrial damage. VNS also upregulated the expression of silent information regulator 1 (SIRT1) and peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) in IR-injured hearts. Inhibition of either SIRT1 or PGC-1α significantly reversed the effects of VNS on mitochondrial biogenesis and abolished its cardioprotective benefits. Notably, VNS increased the level of acetylcholine (ACh) in IR-injured hearts. Administration of atropine, a muscarinic ACh receptor (mAChR) antagonist, counteracted the effects of VNS on the SIRT1/PGC-1α pathway, mitochondrial biogenesis, and the associated cardioprotective outcomes. These findings suggest that VNS protects against cardiac I/R injury by enhancing mitochondrial biogenesis. This beneficial effect of VNS on mitochondrial biogenesis is attributed to activation of the SIRT1/PGC-1α pathway through the ACh/mAChR axis. Therefore, this research offers fresh perspectives on the mechanisms underlying the cardioprotective effects of VNS.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biodiversity to Breakthroughs: The Promise of Saudi Arabian Medicinal Plants in Antiviral Research.","authors":"Hamdoon A Moohammed, Riaz A Khan","doi":"10.1007/s12010-025-05380-4","DOIUrl":"https://doi.org/10.1007/s12010-025-05380-4","url":null,"abstract":"<p><p>Viruses are minuscule entities that cannot survive independently without a Living host. Pathogenic viruses pose a significant threat to global health, resulting annually in the deaths of thousands of people. Recent studies indicate that medicinal plants may serve as an effective source of sustainable natural antiviral agents. Saudi Arabia exhibits diverse climates, resulting in a variety of ecosystems and environmental setups with a diverse array of plant species. Diversified flora thriving in various climatic conditions produces a wide spectrum of phytochemical constituents, many of which possess antiviral and other pharmacological properties. Saudi Arabia, home to approximately 2285 distinct plant species, renders an advantageous situation for the development of novel chemopreventive and therapeutic agents for combating infectious diseases. This review seeks to secure information regarding the antiviral properties of medicinal plants and their constituent phytochemicals from Saudi Arabia. The review provides a Listing of the phytoconstituents responsible for antiviral effects, their mechanistic workings, and pathways associated with the activity. Data mined from PubMed, Scopus, ScienceDirect, Google Scholar, EMBASE, and ChemSpider are included. The findings indicate that under 5% of these plant species have been investigated for their antiviral potential, thereby highlighting a significant gap in the information source. Investigating the antiviral potential of these unexplored plant species, in all probability, may result in the identification of novel compounds for the treatment of viral infections.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"NSUN6 Promotes Gastric Cancer Progression by Stabilizing CEBPZ mRNA in a m⁵C-Dependent Manner.","authors":"Jianqiang Guo, BingXiang Wu, Sijing Wang, Dechao Huang, Yingying Hu","doi":"10.1007/s12010-025-05367-1","DOIUrl":"https://doi.org/10.1007/s12010-025-05367-1","url":null,"abstract":"<p><p>Gastric cancer (GC) is a malignant tumor originating from the epithelial cells of the gastric mucosa. The 5-methylcytosine (m⁵C) modification refers to the addition of a methyl group to the fifth carbon atom of cytosine in RNA molecules. This study aimed to investigate the role of NOL1/NOP2/SUN domain (NSUN)6 in GC and its underlying molecular mechanisms. Human gastric mucosa cells and gastric cancer cells were used for in vitro experiments. m⁵C level was quantified using dot blot analysis. Cell viability and proliferation were evaluated via cell counting kit-8 and colony formation assays. Apoptosis rates were analyzed by flow cytometry. Autophagy-related protein expression was detected through Western blot analysis. The interaction between NSUN6 and CCAAT/Enhancer Binding Protein Zeta (CEBPZ) was validated by RNA immunoprecipitation. Results demonstrated that NSUN6 functioned as an oncogene in GC. Furthermore, NSUN6 inhibition suppressed GC cell proliferation while promoting apoptosis and autophagy. CEBPZ was identified as a target gene of NSUN6 in GC through bioinformatic analysis. Mechanistically, NSUN6 enhanced CEBPZ mRNA stability via m⁵C methylation. Subsequent rescue experiments revealed that CEBPZ overexpression increased cell proliferation and reduced apoptosis and autophagy in GC. Additionally, NSUN6-mediated m⁵C methylation of CEBPZ suppressed autophagy by activating the p53/mTOR pathway. In conclusion, NSUN6 promoted GC progression by stabilizing CEBPZ mRNA in an m⁵C-dependent manner. However, further in vivo and clinical studies are warranted to validate these findings and explore their translational potential.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization and Development of Salt-Resistant Aspergillus oryzae for Marine-Derived Enzyme Expression.","authors":"Bei Han, Qianqian Shao, Yilun Zhang, Qi Liu, Menghao Cai","doi":"10.1007/s12010-025-05374-2","DOIUrl":"https://doi.org/10.1007/s12010-025-05374-2","url":null,"abstract":"<p><p>Marine-derived enzymes often show distinct physiological properties and great potential for industrial use. Salt ions may improve the stability and expression efficiency of marine enzymes, which requires salt-resistant host based expression platform. Aspergillus oryzae of good protein expression and secretion was evaluated and explored for this purpose. Growth, sporulation, secreted extracellular proteins and transcriptome-based metabolic characteristics under artificial seawater condition were analyzed. Also, genetic manipulation system was developed and compared in various strains. Finally, A. oryzae AS 3.487 was recognized as a dominant chassis host. Efficient constitutive and artificial seawater-inducible promoters were screened from the transcriptomic data, which were further evaluated using marine alginate lyase AlgI as the reporter. Medium and condition optimizations improved enzyme production subsequently. Multicopy expression strategy further achieved a maximum enzyme production of 797 U/mL in flask culture. This study provides new references for the heterologous expression of marine-derived enzymes under high-salinity culture conditions.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploration of Comprehensive Structural and Functional Potential of Recombinant Proteins Using Cutting-Edge Bioinformatics Tools.","authors":"Mohsin Shad, Ayesha Liaqat, Arshia Nazir, Naveed Hussain, Khadija Yaqoob, Muhammad Waheed Akhtar, Muhammad Sajjad","doi":"10.1007/s12010-025-05366-2","DOIUrl":"https://doi.org/10.1007/s12010-025-05366-2","url":null,"abstract":"<p><p>Recombinant DNA technology is widely used to produce industrially and pharmaceutically important proteins. In silico analysis, performed before executing wet lab experiments has been greatly helpful in this connection. A shift in protein analysis has been observed over the past decade, driven by advancements in bioinformatics databases, tools, software, and web servers. Several bioinformatics tools and resources are available for predicting a protein's structural and functional relationship. Insights into the proteins' structure and function are important for drug discovery, development, and enhancing the suitability of the recombinant enzymes/proteins for industrial applications. This review compares and discusses various computational tools that provide structural and functional insights into recombinant proteins, including genome mining, sequence alignment, topological arrangement, physicochemical properties, including solubility and stability, site-directed mutagenesis, protein design and engineering, ligand binding interactions through molecular docking, and molecular dynamics simulation. This comparative study explores the utilisation of different computational tools, software, and web servers with their principles, algorithms, and outcomes. This document would be a milestone for the scientists to select suitable computational approaches to plan and improve the outcome for achieving the desired targets.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}