BMC Biotechnology最新文献

{"title":"PAM-flexible SpCas9 variants expand the targeting scope for porcine genome editing and cellular disease modeling.","authors":"Zhiwei Peng, Wenxin Duan, Yuhang Fan, Qiang Yang, Yu Ye, Yuyun Xing","doi":"10.1186/s12896-026-01164-8","DOIUrl":"https://doi.org/10.1186/s12896-026-01164-8","url":null,"abstract":"<p><strong>Background: </strong>CRISPR-Cas-mediated gene editing has revolutionized life sciences, yet the targeting scope of the widely used SpCas9 is limited by its strict requirement for the NGG protospacer adjacent motif (PAM). To overcome this limitation, PAM-flexible SpCas9 variants have been developed and characterized in multiple species; however, their potential in pigs (an important biomedical model for humans) remains unexplored. Here, we systematically evaluated the editing performance of three PAM-flexible SpCas9 variants (SpRY, SpG, and SpCas9-NG) and their derived base editors in porcine fetal fibroblasts (PFFs).</p><p><strong>Results: </strong>Profiling across 228 target sites revealed that SpRY exhibits nearly PAM-less activity, with significantly higher editing efficiency at NRN (15.82%, R = A/G) than at NYN PAMs (5.75%, Y = C/T). SpG and SpCas9-NG preferentially targeted NGN PAMs, achieving mean efficiencies of 14.81% and 16.33%, respectively. PAM‑flexible cytosine base editors (CBEs) mediated efficient C:G‑to‑T:A conversion, with mean efficiencies of 12.01% for SpRY‑BE4max (NNN PAMs), 15.43% for SpG‑BE4max (NGN PAMs), and 18.39% for SpCas9‑NG‑BE4max (NGN PAMs). Similarly, PAM‑flexible adenine base editors (ABEs) mediated efficient A:T‑to‑G:C conversion, with mean efficiencies of 15.66% for SpRY‑ABE8e (NNN PAMs), 24.16% for SpG‑ABE8e (NGN PAMs), and 20.50% for SpCas9‑NG‑ABE8e (NGN PAMs). By exploiting this expanded targeting scope, we successfully introduced 16 pathogenic single‑nucleotide variants (SNVs) at NRN PAM sites in the porcine genome, with editing efficiencies reaching up to 40.68% for CBEs and 61.76% for ABEs.</p><p><strong>Conclusions: </strong>PAM-flexible SpCas9 variants and their derived base editors greatly expand the targeting scope for porcine genome engineering, thereby substantially broadening the applicability potential of CRISPR-Cas-mediated genome editing tools in porcine genetic improvement and disease model generation.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147863226","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":"Machine learning optimized callogenesis in Justicia gendarussa Burm. f. and phytochemical profiling of in vitro derived callus and leaf extracts.","authors":"Nikita Purohit, Deepa Sankar Parasurama","doi":"10.1186/s12896-026-01156-8","DOIUrl":"https://doi.org/10.1186/s12896-026-01156-8","url":null,"abstract":"<p><strong>Background: </strong>In vitro callus culture systems have been well documented to increase the production of bioactive metabolites. However, optimization of culture conditions through traditional methods consumes time and resources. In the current study, we utilized Machine Learning (ML) tools to improve callus formation conventions. The resultant callus and the leaf tissues of the mother plant were analyzed for their phytochemical profiles to gain insights into the altered synthesis of metabolites.</p><p><strong>Methods: </strong>Leaf explants were grown in the dark on Murashige & Skoog medium (MS) with 28 altered plant growth regulator combinations. The parameters of callogenesis were measured and analyzed using a generalized regression neural network (GRNN) to predict optimal hormone concentrations. Predicted concentrations were validated through in vitro experiments. Metabolite quantification assays and profiling were carried out through liquid chromatography-mass spectrometry (LC-MS).</p><p><strong>Results: </strong>The mean earliest callus initiation was calculated as 14.9 days in MS media fortified with 3 mg/L 2,4-D and 0.5 mg/L BAP. The maximum callus mean fresh weight was recorded as 2.948 g in MS media with 2.5 mg/L 2,4-D and 1.0 mg/L BAP. The data obtained through experimentation were fed into a machine learning model to predict the optimal concentrations for callus initiation and maximum callus fresh weight. Machine learning predicted the earliest callus initiation as the 14th day if grown in MS media with 2.92 mg/L 2,4-D, 0.35 mg/L Kin, and 0.17 mg/L BAP, which closely aligns with validated experimental results showing 15.1 days. The predicted callus fresh weight of 2.954 g in MS media with 2.5 mg/L 2,4-D, 0.11 mg/L Kin, and 0.91 mg/L BAP on validation was in sync with the experimental results, amounting to 3.004 ± 0.098 g, and hence was used for subculturing. Phytochemical analysis indicated notable increases in phenolic (1.22-fold) and flavonoid (1.27-fold) contents in callus extracts compared to mother plant leaves, whereas terpenoid levels were lower.</p><p><strong>Conclusion: </strong>The current study demonstrates the effective incorporation of ML in optimal callogenesis. It highlights the improved accumulation of phenolics and flavonoids in calli obtained from ML optimized conditions, emphasizing its precise prediction in maximizing output. These findings can contribute to the development of efficient biotechnological strategies for the production of pharmaceutically important phytochemicals.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810447","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":"Gas vesicle-expressing human pluripotent stem cells enable multimodal ultrasound and optical coherence tomographic imaging.","authors":"John Kim, Alessandro R Howells, Sumin Park, Xueding Wang, Chengzhi Shi, Xiaojun Lance Lian","doi":"10.1186/s12896-026-01161-x","DOIUrl":"10.1186/s12896-026-01161-x","url":null,"abstract":"<p><p>Genetically encoded imaging reporters are critical tools for tracking cell fate and function in regenerative medicine. Gas vesicles (GVs), air-filled protein nanostructures derived from bacteria, offer unique advantages for noninvasive imaging due to their acoustic and optical properties. In this study, we engineered human pluripotent stem cells (hPSCs) to express GVs using a doxycycline (Dox)-inducible system. Stable GV expression was achieved by TALEN-mediated knock-in of the GvpNtoV cassette at the GAPDH locus together with PiggyBac GvpA integration driven by transposase, followed by antibiotic selection to isolate correctly modified clones. Upon Dox treatment, GVs formed intracellularly and enabled enhanced contrast in both ultrasound and optical coherence tomography (OCT) imaging. Dynamic ultrasound imaging revealed pressure-dependent GV buckling and harmonic signal generation, while OCT imaging confirmed high sensitivity and depth-resolved detection in both in vitro and ex vivo retinal models. Our work establishes a multimodal GV-based reporter platform compatible with human stem cells and clinically relevant imaging modalities. This approach offers a powerful and versatile tool for noninvasively visualizing and tracking therapeutic cells in real time, advancing the development and monitoring of cell-based therapies.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810473","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":"Recapitulation of clinical and molecular hallmarks of lipid-induced hepatic insulin resistance in a zonated, vascularized human liver acinus microphysiological system during metabolic dysfunction-associated steatotic liver disease (MASLD) progression.","authors":"Julio Aleman, Lawrence Vernetti, Mark E Schurdak, Richard DeBiasio, Greg LaRocca, Vijay K Yechoor, D Lansing Taylor, Andrew M Stern, Mark T Miedel","doi":"10.1186/s12896-026-01158-6","DOIUrl":"10.1186/s12896-026-01158-6","url":null,"abstract":"<p><p>Metabolic dysfunction-associated steatotic liver disease (MASLD) impacts ca. 30% of the global population and is very heterogeneous, making it a challenge to develop therapeutics. The heterogeneity arises from genetics, co-morbidities, the microbiome, and lifestyle. To help address this challenge, we have refined the human vascularized liver acinus microphysiological system (vLAMPS), which provides an all-human platform for drug development, satisfying recently updated federal requirements for the use of New Approach Methodologies (NAMs). By introducing clinically relevant media perturbations and employing several diverse and reproducible in situ and systemic measurements, we show that the vLAMPS can recapitulate key structural and functional aspects of normal physiology, acinus zonation, and all stages of MASLD progression including stellate cell activation and fibrosis. Importantly, in this study we also demonstrate that several hallmarks of lipid-induced hepatic insulin resistance paralleled MASLD progression. These included reduction of insulin receptor substrate 2 (IRS2) protein, compromised insulin receptor mediated insulin clearance, enhanced pericentral lipid accumulation, increased Very-low-density lipoprotein (VLDL) secretion, and enhanced hepatic glucose output mediated by increased periportal nuclear translocation of Forkhead box protein O1 (FOXO1). These results suggest that the mechanisms underlying MASLD progression in vLAMPS are clinically relevant and support the tenable hypothesis that the hepatic insulin resistant state plays both a causal and consequential role in a vicious cycle driving disease progression.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810467","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":"An assessment of curcumin, curcumin spanlastics nanoparticles, and curcumin nanocrystals as possible drug delivery systems with antimicrobial, antioxidant, and antitumor activities.","authors":"Jawza A Almutairi, Thanaa A El-Masry, Maisra M El-Bouseary, Enas I El Zahaby, Eman Wahsh, Noha A Mohamed, Heba M Hashem, Nancy M Abdel-Kareem, Naifa Alenazi, Maysa M F El-Nagar","doi":"10.1186/s12896-026-01153-x","DOIUrl":"https://doi.org/10.1186/s12896-026-01153-x","url":null,"abstract":"","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":"26 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13123162/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antibacterial and antibiofilm activities of curcumin-mediated green-synthesised silver nanoparticles against Methicillin-resistant Staphylococcus aureus and Pseudomonas aeruginosa.","authors":"Raha Zare Shahraki, Leili Shokoohizadeh, Zahra Chegini, Esmaeel Sharifi, Mohammad Reza Arabestani","doi":"10.1186/s12896-026-01138-w","DOIUrl":"https://doi.org/10.1186/s12896-026-01138-w","url":null,"abstract":"","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760989","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":"Propolis-functionalized acellular fish skin scaffolds as biotechnological platforms for antimicrobial activity and regenerative wound healing.","authors":"Sima Bakhtazad, Sepehr Mehdizadeh, Nosratollah Zarghami, Ali Akbar Shabani, Mehdi Dadashpour, Younes Pilehvar","doi":"10.1186/s12896-026-01155-9","DOIUrl":"https://doi.org/10.1186/s12896-026-01155-9","url":null,"abstract":"","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147761039","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":"Sustained-release enteric formulations of Lactiplantibacillus plantarum based on granulation technology: preparation and therapeutic evaluation in acute colitis.","authors":"Xiwei Zhang, Jianfeng Wan, Xile Wang, Xiaocan Zhang, Miaomiao Jiang, Shuang Liang, Hongqing Zhang, Guangzhou Zhou","doi":"10.1186/s12896-026-01157-7","DOIUrl":"https://doi.org/10.1186/s12896-026-01157-7","url":null,"abstract":"","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760976","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":"Mechanistic insights into how cichoriin inhibits P2Y₁₄R to suppress MSU-induced gouty inflammation.","authors":"Xue Wu, Shanshan Liu, Li Leng, Zhengqi Liu","doi":"10.1186/s12896-026-01151-z","DOIUrl":"https://doi.org/10.1186/s12896-026-01151-z","url":null,"abstract":"<p><strong>Background: </strong>Gout is a prevalent, chronic inflammatory joint diseases, and its global prevalence and incidence are continue to rise. Currently, the adverse side effects of anti-gout drugs underscore the urgent need for safer and more effective anti-gout agents.</p><p><strong>Objective: </strong>Cichoriin is a kind of coumarin, which exhibits diversity of biological activities. The current investigation aimed to explore the mechanism of the inhibition of MSU-induced gouty inflammation by cichoriin.</p><p><strong>Methods: </strong>The enzyme inhibitory assay of P2Y₁₄R, cell viability detection, ELISA, immunofluorescence staining, and flow cytometry were used to explore the molecular mechanism of cichoriin in the inhibition of MSU-induced gouty inflammation. The molecular level details of inhibitory effects of chchoriin against P2Y₁₄R were obtained by molecular dynamics simulation.</p><p><strong>Results: </strong>The in vitro experiments revealed that cichoriin could inhibit the activity of P2Y₁₄R, up-regulate the expressions of NLRP3, Caspase-1, GSDMD and ASC, increase IL-1β and IL-18 levels, and decrease the percentage of Caspase-1/PI double-positive cells. The computational calculations revealed that cichoriin and P2Y₁₄R could form a stable and rigid complex. Free energy landscape exhibited that cichoriin stabilized the global conformations of P2Y₁₄R to the minimum global energy. MM-PBSA provided evidence for cichoriin's stability inside the binding pocket of P2Y₁₄R with a binding free energy of -35.13 kcal/mol. The decomposition of binding energy showed the pivotal amino acids residues responsible for the stability of cichoriin's interaction with P2Y₁₄R by forming hydrogen bonds and hydrophobic interactions.</p><p><strong>Conclusions: </strong>This work highlighted the potential roles of cichoriin in attenuating MSU-induced gouty inflammation.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147687931","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 novel cell-penetrating peptide supports hair follicle growth through anti-inflammatory and growth factor-associated mechanisms in preclinical models.","authors":"Young In Lee, Wooram Kim, Hyojin Roh, Ahlim Min, Jinyoung Jung, Hosung Choi, Jewan Kaiser Hwang, Ngoc Ha Nguyen, Jae Hyun Park, Inhee Jung, Ju Hee Lee","doi":"10.1186/s12896-026-01130-4","DOIUrl":"https://doi.org/10.1186/s12896-026-01130-4","url":null,"abstract":"","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147670143","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}