Biotechnology and applied biochemistry最新文献

{"title":"Alchemy of Fungi and AI: Response Surface Methodology and Artificial Neural Network-Based Optimization of Echinocandin B Production in Aspergillus nidulans.","authors":"Shaurya Prakash, Nageswar Sahu, Anita Choudhary, Hemlata Kumari, Minakshi, Biswanath Mahanty, Antresh Kumar","doi":"10.1002/bab.2787","DOIUrl":"https://doi.org/10.1002/bab.2787","url":null,"abstract":"<p><p>Echinocandin B (ECB) is the precursor of a first-line antifungal, anidulafungin, widely used to treat systemic and invasive fungal infections in nosocomial and community-acquired settings. This potent antifungal is naturally synthesized in Aspergillus nidulans in trace amounts, which can be improved by optimizing growth and physiological conditions. The current study is focused on optimizing the fermentation medium by employing statistical and artificial neural network (ANN)-based model to improve ECB activity in fermentation broth. In the present study, the most significant parameters for ECB activity (i.e., molasses, dextrose, casein, and pH) were identified through the Plackett-Burman design and were further optimized using different statistical models based on central composite design experiments. Process optimization with a reduced quadratic (RQ) model and ANN model (architecture: 4-6-2-1) suggested a 3.64- and 3.03-fold increase in ECB activity, respectively. However, prediction from the RQ model (R²: 0.93) could be unreliable when compared to the ANN model (R²: 0.99), effectively capturing the complex relationships. The study concludes that the ANN-based predicted model displayed more accuracy and provided optimum levels of the analyzed factors for a 3-fold increase in ECB activity.</p>","PeriodicalId":9274,"journal":{"name":"Biotechnology and applied biochemistry","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144141348","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":"Cryptic Mutation in the Genome of Salmonella enterica to Acquire AMR Genes With Alteration of Amino Acid Sequences: A Pathogenomics Study.","authors":"Smaranika Pattnaik","doi":"10.1002/bab.2785","DOIUrl":"https://doi.org/10.1002/bab.2785","url":null,"abstract":"<p><p>The Mahanadi river is a freshwater sink of Odisha which has taken its course through the Western Odisha and finally end in the Bay of Bengal. However, the river water is receiving pathogenic bacterial strains due to anthropogenic activities and therefore health of the common man is severely affected with regular outbreaks. This present pursuit had aimed to carry out pathogenomics of a bacterial isolate perpetuating in the said river water near a local tertiary care hospital, Burla, Odisha, India. Relevant procedures and experiments were carried out, and a strain of Salmonella enterica was identified. The whole genome of said isolate was sequenced using NGS approaches. It was observed that there was alteration of amino acids leading genome with acquire of AMR genes. There was a change in nucleotide codon from CTA reversed back to CTA, amino acid from I > P, position in contig, 143183-146332 at node 15, and the eluted gene was acrB with identity 99.97%. In addition, AGC reversed back to ACC amino acid from T > S at node 17 position in contig, with elution of genes, pmrA (109013-10968) and pmrB (109691-110761) in contig. It was further observed that there was depiction of nucleotide codon change from ATG to ACG, GTC to GCC, GGC to AGC, GTA to ATA, ATT to GTT, and GCG to ACG. As a result of which, methionine to threonine (M > T), valine to alanine (V > A), glycine to serine (G > S), valine to isoleucine (V > I), isoleucine to valine (I > V), and alanine to threonine (A > T) were changed without any change in respect to AMR gene consociation.</p>","PeriodicalId":9274,"journal":{"name":"Biotechnology and applied biochemistry","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109472","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":"Enhanced DNA Extraction From Dimorphic Fungi: Exploring the Advantages of Blastospores Versus Mycelia.","authors":"Ahmad El Khatib, Dalal Sabbagh, Sarah Dimassi, Hadi Akl, Karen El Khoury, Jimmy Bou Saba, Mariline Al Kazzi, Hani Dimassi, Sima Tokajian, Nabil Nemer, Charbel Al Khoury","doi":"10.1002/bab.2786","DOIUrl":"https://doi.org/10.1002/bab.2786","url":null,"abstract":"<p><p>The extraction of high-quality DNA from fungi remains a significant challenge due to the structural complexity and resilience of fungal cell walls. This study presents the first comprehensive comparison of DNA extraction efficiency between blastospores (BS) and mycelial cells (MCs) in dimorphic fungi. We evaluated six DNA extraction procedures and two pre-treatment methods to determine their effectiveness in extracting DNA of high quality and yield from both forms. DNA quantification was performed using absolute RT-qPCR targeting the single-copy γ-Actin gene, with specificity and efficiency validated through standardized protocols. Our results showed that BS consistently yielded higher DNA quantity and quality across all conditions, with a mean antilog DNA copy concentration of 5.03 ± 0.20, compared to 2.51 ± 0.20 for MC. DNA quality was superior in BS, as indicated by significantly better 260/280 and 260/230 ratios (31.5% vs. 7.4% for MC, p value = 0.002). Additionally, BS produced higher molecular weight DNA (10,770.5 base pairs vs. 8139.0 base pairs for MC, p value < 0.001) and exhibited greater long-term stability at both 4°C and -20°C. The results demonstrate that BS serve as a more reliable source of high-quality DNA compared to MC. This finding enhances current methodologies in molecular biology and supports more accurate analyses, particularly in studies involving dimorphic fungi.</p>","PeriodicalId":9274,"journal":{"name":"Biotechnology and applied biochemistry","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109604","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":"Electro-Sensing Analysis for Parkinson's Disease Biomarker on Dual-Electrode Surface: Complemented by Molecular Docking.","authors":"Hussaini Adam, Subash C B Gopinath, Thirumananseri Kumarevel, Thanganadar Ashokkumar, Tijjani Adam, M K Md Arshad, Mohammed Mohammed, Chun Hong Voon, Muhammad Mahyiddin Ramli, M N A Uda, Makram A Fakhri, Evan T Salim","doi":"10.1002/bab.2775","DOIUrl":"https://doi.org/10.1002/bab.2775","url":null,"abstract":"<p><p>This study was designed to improve the sensitivity, specificity, and selectivity of the electrochemical method of detecting Parkinson's disease by identifying alpha-synuclein as a biomarker using gold interdigitated electrodes (AuIDEs with and without surface modified with zinc oxide (ZnO). AuIDE modified with zinc oxide and AuIDE without zinc oxide were characterized using a scanning electron microscope, 3D profilometers, and a high-power microscope. Current-voltage measurements were performed for antigen-antibody interaction and targeted detection using a Keithley 6482 Picoammeter. The linear range was from 1 fM to 1 pM. The limit of detections for AuIDE modified with zinc oxide and AuIDE without zinc oxide were calculated using the signal-to-noise ratio (S/N) = 3 formula. Linear regression analysis of the AuIDE without zinc oxide was R² of 0.9779. The linear regression analysis for AuIDE with zinc oxide was R² = 0.9809. Regression analysis thus yielded a better result in the modified AuIDE. For the determination of selectivity, alpha-synuclein and tau were tested on the surface-modified AuIDE. Tau was used as a control variable. However, only alpha-synuclein produced significant current change, while the control protein yielded no significant changes. Hence, the inclusion of the ZnO layer improved the sensor's performance and the sensor was reproducible and stable after repeated testing.</p>","PeriodicalId":9274,"journal":{"name":"Biotechnology and applied biochemistry","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092671","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":"Aquaporin 9: Exacerbation of Vulnerable Carotid Plaque Formation.","authors":"Bin Xu, Yifei Zheng, Yi Wang, Jie Sun, Dehai Lang, Qiyang Xu","doi":"10.1002/bab.2776","DOIUrl":"https://doi.org/10.1002/bab.2776","url":null,"abstract":"<p><p>Aquaporin 9 (AQP9) expression is significantly elevated in vulnerable carotid plaque (VCP). Hence, we probed the mechanism of AQP9 in VCP formation. The VCP model was established in ApoE^-/- C57BL/6 mice. Dataset GSE163154 was analyzed by R software. Human aortic endothelial cells (HAECs) were incubated with 50 µg/mL oxidized low-density lipoprotein (ox-LDL) and 20 mM l-(+)-lactic acid for 24 h. Mice (AQP9 overexpression plasmid) and HAECs (AQP9 overexpression/dynamin-related protein 1 [DRP1] silencing plasmids) were infected by lentivirus. Mouse plasma lipid level was estimated. The histopathological condition of model mice was observed by oil red lipid staining, hematoxylin-eosin (H&E) staining, and Masson staining. Levels of AQP9 and DRP1 in model mice and HAECs were quantified by quantitative real-time polymerase chain reaction (qRT-PCR). Levels of AQP9, DRP1, and mitochondrial fission-/endothelium-mesenchymal transition (EndMT)-related factors in model mice and HAECs were assayed by western blot. Lactate level in model mice was detected. Promoter histone lactylation level of DRP1 was measured by chromatin immunoprecipitation (ChIP). Behaviors of HAECs were tested by cell counting kit-8 (CCK-8), colony formation test, and scratch test. AQP9 was highly expressed in intraplaque hemorrhage patients. AQP9 overexpression promoted levels of DRP1, lactate, histone lactylation, mitochondrial fission factor, vimentin, and N-cadherin, while inhibiting vascular endothelial (VE)-cadherin level and plaque stability in model mice and facilitating viability, proliferation, and migration of HAECs. DRP1 silencing reversed the impacts of AQP9 overexpression on cell viability, proliferation, migration, and levels of mitochondrial fission-/EndMT-related factors in HAECs. AQP9 enhances DRP1-mediated mitochondrial fission by lactate and thus promotes EndMT to exacerbate the VCP formation.</p>","PeriodicalId":9274,"journal":{"name":"Biotechnology and applied biochemistry","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143980365","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: Design and Characterization of a Chimeric Multiepitope Construct Containing CfaB, Heat-Stable Toxoid, CssA, CssB, and Heat-Labile Toxin Subunit B of Enterotoxigenic Escherichia Coli: A Bioinformatic Approach.","authors":"","doi":"10.1002/bab.2774","DOIUrl":"https://doi.org/10.1002/bab.2774","url":null,"abstract":"","PeriodicalId":9274,"journal":{"name":"Biotechnology and applied biochemistry","volume":" ","pages":"e2774"},"PeriodicalIF":3.2,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143989490","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":"Mathematical Correlation of Yield Coefficients Based on Individual Reaction of Cell and Product Formation and Total Metabolic Reaction in Biological Reaction Kinetic Modeling.","authors":"Swatika Juhana, Fitri Nur Kayati, Aris Sudomo, Arini Wresta","doi":"10.1002/bab.2773","DOIUrl":"10.1002/bab.2773","url":null,"abstract":"<p><p>Kinetic models are important tools required in designing biological reactors and can be developed through mass balance equations arrangement based on kinetic data of microorganism metabolic reactions. Yield coefficients are an important parameter in the arrangement of mass balance equations as they can quantitatively link substrate consumption to cell and product formation. We know two forms of yield coefficients of cell and product formation that have different uses. The first coefficients are derived from the stoichiometric equation of overall metabolic reaction and the second are derived from the parallel reactions of cell formation, product formation, and maintenance. Since these types of yield coefficients are usually written in the similar pattern, these coefficients are frequently misused. A previous researcher has defined and differentiated the use of these two types of yield coefficients to avoid inappropriate uses that can cause an error in the calculation results. To complete and clarify the definition, this communication discusses the mathematical correlation between these two types of yield coefficients using the latest thermodynamic approach for stoichiometric coefficients estimation of metabolic reaction.</p>","PeriodicalId":9274,"journal":{"name":"Biotechnology and applied biochemistry","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143980366","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":"Revealing the Taxonomic Profile of a Wild Edible Mushroom From Tribal Cuisine and Its Pharmacological Significance.","authors":"Gouri Basak, Niranjan Roy, Arun Kumar Dutta, Krishnendu Acharya","doi":"10.1002/bab.2779","DOIUrl":"https://doi.org/10.1002/bab.2779","url":null,"abstract":"<p><p>The historical use of wild mushrooms as food and medicine has been documented in several countries, including India. The Indian macrofungal flora consists of a diverse range of distinct species that have long been valued by various tribal groups for their medicinal and culinary qualities. During the process of documenting indigenous mushroom species, one unique edible Russula sp. was collected from the Pinus-dominated forest of the East Khasi Hills district of Meghalaya. Following a thorough assessment of the morphological traits and molecular phylogenetic analysis, this distinct species has been identified as Russula pseudojaponica, a new record from India. In order to investigate its therapeutic potential, a methanolic fraction was prepared and characterized for myco-chemicals. A substantial quantity of different secondary metabolites like carotenoids, ascorbic acid, and phenolics has been detected. The methanolic fraction also had notable antioxidant activity, displaying strong capabilities in scavenging DPPH and ABTS radicals, possessing high reducing power, and chelating capacity. In addition, the extract demonstrated the capacity to hinder the growth of Listeria monocytogenes, Bacillus subtilis, Pseudomonas aeruginosa, Escherichia coli, Salmonella typhi, and Staphylococcus aureus, as seen in the broth microdilution experiment. Furthermore, it induced morphological changes in bacterial cells, which were seen by scanning electron microscopy. Moreover, the extract demonstrated the ability to inhibit the proliferation, clonogenicity, and migratory potential of lung carcinoma cells, suggesting its potential as an anticancer agent. The extract successfully arrested the cell cycle progression in the S phase of cell division. Involvement of the intrinsic mitochondrial pathway of apoptosis was also observed after extract treatment. Hence, based on the findings of this study, this exceptional fungus has the capacity to function as an organic reservoir for the creation of novel medications to counteract illnesses associated with oxidative stress, bacterial ailments, and cancer.</p>","PeriodicalId":9274,"journal":{"name":"Biotechnology and applied biochemistry","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143954760","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":"A Novel Therapeutic Strategy for Ameliorating Hyperglycemia-Induced Liver Injury via Overexpression of the Carboxyl Terminus of HSP70-Interacting Protein in Wharton's Jelly Mesenchymal Stem Cells.","authors":"Shun-An Kan, Ayaz Ali, Shih-Wen Kao, Bruce Chi-Kang Tsai, Yueh-Min Lin, Dennis Jine-Yuan Hsieh, Chia-Hua Kuo, Wei-Wen Kuo, Shinn-Zong Lin, Chih-Yang Huang","doi":"10.1002/bab.2771","DOIUrl":"https://doi.org/10.1002/bab.2771","url":null,"abstract":"<p><p>Diabetes is a widespread metabolic disorder that significantly affects modern society. The liver plays a vital role in metabolism; however, hyperglycemia can induce liver damage and disrupt its normal functions. Wharton's jelly mesenchymal stem cells (WJMSCs) engineered to express the carboxyl terminus of HSP70-interacting protein (CHIP) have demonstrated protective effects against hyperglycemia-induced damage in various organs. Nonetheless, the potential hepatoprotective effects and underlying mechanisms of these modified stem cells in diabetic livers remain unclear. Therefore, this study aimed to evaluate the efficacy of CHIP-transfected WJMSCs in mitigating hyperglycemia-induced hepatic injury in diabetic rats and to elucidate the associated protective mechanisms. Diabetic rats received tail vein injections of WJMSCs either overexpressing or silenced for CHIP. Seven weeks post-transplantation, all rats were sacrificed, and liver tissues were harvested for histological staining and Western blot analysis. The findings indicated that CHIP-overexpressing WJMSCs significantly reversed hyperglycemia-induced liver damage, reducing tissue injury, fibrosis, and glycogen deposition. These cells also alleviated hepatic inflammation and apoptosis. Moreover, they regulated oxidative stress pathways by lowering gp91-phox, Rac1, and phosphorylated PKCζ levels, while enhancing phosphorylated Nrf2 and SOD-2 expression. Additionally, the modified WJMSCs suppressed STAT3 activation and downregulated FOXO3a, suggesting a role in attenuating fibrosis and triglyceride accumulation in diabetic livers. Overall, CHIP-overexpressing WJMSCs reversed hyperglycemia-induced hepatic alterations by mitigating inflammation and oxidative stress while also modulating pathways related to fibrosis and lipid metabolism. These results highlight the therapeutic potential of CHIP-modified WJMSCs in managing diabetic liver complications and offer promising avenues for future treatment strategies.</p>","PeriodicalId":9274,"journal":{"name":"Biotechnology and applied biochemistry","volume":" ","pages":"e2771"},"PeriodicalIF":3.2,"publicationDate":"2025-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143966239","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":"Engineering of Ruthenium-Based Anticancer Drug RAPTA-C and Carvacrol Incorporated Hyaluronic Acid-Altered Liposome Formulation for Ovarian Cells and Its Apoptosis Induction.","authors":"Xin Huang","doi":"10.1002/bab.2770","DOIUrl":"https://doi.org/10.1002/bab.2770","url":null,"abstract":"<p><p>Ovarian cancer (OC) is the fifth most common cancer in women, resulting in more deaths than any other female reproductive system disease. This investigation presents hyaluronic acid (HA)-altered liposome encapsulating 1,3,5-triaza-7-phosphaadamantane compound (RAP) and carvacrol (CAR) (RAP-HA@Lipo/CAR) for targeted delivery to enhance antitumor and antimetastatic efficacy in OC. The co-delivered liposomes enhanced anticancer and synergic activity in A2780 OC cells. Further, the apoptotic potential of RAP-HA@Lipo/CAR was assessed by acridine orange (AO)/propidium iodide (PI) and 4,6-diamidino-2-phenylindole dihydrochloride (DAPI)/PI staining techniques. The antimetastatic potential of RAP-HA@Lipo/CAR was evaluated using wound healing and migration assays. Our findings indicated that HA alteration enhanced the cell uptake of the developed RAP-HA@Lipo/CAR in A2780 cell lines. This study demonstrates a tumor-targeting RAP-HA@Lipo/CAR delivery promising to treat OC cells.</p>","PeriodicalId":9274,"journal":{"name":"Biotechnology and applied biochemistry","volume":" ","pages":"e2770"},"PeriodicalIF":3.2,"publicationDate":"2025-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143967657","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}