BMC Biotechnology最新文献

{"title":"Metabolic profiling and systems biology analysis of Flammulina filiformis Fv19 extract: an integrated computational and experimental approach for dual anti-cancer and immunomodulatory therapy.","authors":"Heba El-Sayed, Mohamed E Osman, Eslam T Mohamed, Soad Nady, Rehab M Abd El-Hameed","doi":"10.1186/s12896-026-01152-y","DOIUrl":"10.1186/s12896-026-01152-y","url":null,"abstract":"<p><strong>Background: </strong>The increasing demand for multi-target cancer therapies has prompted investigation into the anticancer and immunomodulatory potential of the hot water extract of Flammulina filiformis Fv19, utilizing in vitro cytotoxicity assays, in vivo murine models, and molecular docking analyses.</p><p><strong>Results: </strong>The hot water extraction of mushroom mycelia yielded 11.4 ± 1.2% (w/w). Gas chromatography-mass spectrometry (GC-MS) profiling identified six major metabolites, with the most abundant being cholestan3ol, 2methylene (3α, 5α) (37.47%); spirost8en11one, 3hydroxy (23.24%); and 1Hcycloprop[e]azulen7ol, decahydro1,1,7trimethyl4methylene (12.58%). The extract demonstrated potent inhibition of MCF-7 (IC₅₀ = 5 µg/ml) and Hep-G2 (IC₅₀ = 4 µg/ml) cancer cell lines. In vivo evaluation involved male albino mice receiving oral administration of the extract at a dosage of 200 mg/kg/day for 10 days, employed in both preventive and treatment protocols against the Ehrlich solid tumor model. In vivo oral administration significantly suppressed Ehrlich carcinoma tumor growth with a 99.79% inhibition ratio, achieving complete tumor regression in 66.7% of mice. Additionally, the extract enhanced immune responses by increasing macrophage count by 166%, TNF-α production by 284%, NO release by 71%, and H₂O₂ levels by 55% compared to the tumor-bearing group, while reducing IL-17 production by splenocytes by 27%, indicating immunomodulatory effects. Molecular docking revealed strong interactions with oncogenic and immune-regulatory proteins, including Bcl-2 (-5.015 kcal/mol), EGFR (-4.567 kcal/mol), COX-2 (-4.581 kcal/mol), and iNOS (-5.855 kcal/mol).</p><p><strong>Conclusions: </strong>These findings highlight F. filiformis Fv19 extract as a promising natural anticancer and immunomodulatory agent for multi-target cancer therapy.</p><p><strong>Clinical trial number: </strong>Not applicable.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":"26 1","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13196206/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147986479","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":"Ligand-dependent corepressor suppresses angiogenesis and macrophage infiltration in gliobl astoma microenvironment via MCP-1 down-regulation.","authors":"Shu-Kai Lin, Tai-Qin Li, Xiang-Lan Luo, Yi-Chi Zhang, Jun-Xue Qian, Shi-Lu Huang, Ming Yang, Ke-Gang Linghu, Jun Dong","doi":"10.1186/s12896-026-01166-6","DOIUrl":"10.1186/s12896-026-01166-6","url":null,"abstract":"<p><strong>Background: </strong>Glioblastoma is one of the most aggressive and lethal forms of brain cancer, characterized by rapid angiogenesis and infiltration of tumor-associated macrophages in the tumor microenvironment (TME). Given the limited efficacy of single-targeting tumor cell therapies against glioblastoma, regulating the TME has emerged as a promising strategy to improve therapeutic outcomes.</p><p><strong>Materials and methods: </strong>The Cancer Genome Atlas (TCGA) was used to assess the association between ligand-dependent nuclear receptor corepressor (LCoR) expression and glioblastoma. LCoR expression in patient glioma specimens was examined by qRT‑PCR and Western blot. LCoR was knocked down or overexpressed in glioblastoma cell lines (SF295, SNB19) using lentiviral vectors, followed by functional assays for proliferation, migration, invasion, angiogenesis, chemokine secretion, and monocyte migration. Subcutaneous and orthotopic mouse models were established to evaluate tumor growth, angiogenesis, and macrophage infiltration via immunohistochemistry and immunofluorescence. Transcriptome sequencing was performed on LCoR‑overexpressing cells to explore underlying mechanisms. In addition, mice were treated with the small-molecule compound deoxynyboquinone to assess its therapeutic effect via LCoR‑mediated regulation.</p><p><strong>Results: </strong>TCGA analysis reveals lower LCoR expression in glioblastoma than in normal tissues, correlating with improved patient survival. Clinical samples further confirm reduced LCoR expression in tumor versus peri-tumor tissues. LCoR knockdown significantly enhanced the proliferation, migration, and invasion of glioblastoma cells, whereas LCoR overexpression inhibited these malignant phenotypes. Mechanistically, LCoR suppressed VEGF and HIF-1α expression in tumor cells, thereby reducing angiogenesis and tumor sphere formation. Transcriptome sequencing revealed that LCoR is involved in immune regulation. Further experiments demonstrated that LCoR inhibited chemokine secretion, thereby reducing monocyte migration and macrophage M2 polarization. In subcutaneous and orthotopic glioblastoma mouse models, LCoR overexpression suppressed tumor growth by inhibiting angiogenesis and macrophage M2 polarization. Treatment with the deoxynyboquinone reduced angiogenesis and macrophage infiltration in the TME through LCoR-mediated downregulation of MCP-1, thereby blocking glioblastoma progression.</p><p><strong>Conclusion: </strong>LCoR serves as a potential therapeutic target against glioblastoma. Upregulating LCoR can inhibit glioblastoma development by suppressing angiogenesis and immune evasion within the TME.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":" ","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13371665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147970003","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":"5-Methoxyflavone suppresses nasopharyngeal carcinoma proliferation through regulating p53/SREBP/SCD signaling-mediated lipid synthesis and ferroptosis.","authors":"Yiwen Cui, Yan Zhao, Rong Li, Mingyong Li, Tongyuan Deng, Bo Bao, Yingying Hu","doi":"10.1186/s12896-026-01163-9","DOIUrl":"https://doi.org/10.1186/s12896-026-01163-9","url":null,"abstract":"<p><strong>Background: </strong>Nasopharyngeal carcinoma (NPC) is a highly prevalent malignant epithelial tumor in southern China. Although early-stage NPC patients have a favorable prognosis with concurrent chemoradiotherapy, the limited efficacy of current clinical regimens remains a crucial obstacle in the treatment of advanced NPC patients. 5-Methoxyflavone, a methylated flavonoid, has been reported to exhibit diverse roles in anti-cancer activity and lipid modulation. However, its potential role in NPC remains unclear. This study aims to investigate the effect of 5-Methoxyflavone on NPC proliferation and its underlying mechanism.</p><p><strong>Methods: </strong>MTT, colony formation, EdU assays, and flow cytometry were performed with various concentrations of 5-Methoxyflavone (0, 40, 60, 80 and 100 µM) to investigate its effect on NPC cell proliferation. A HONE1 xenograft model was established for in vivo validation. Immunoprecipitation and dual-luciferase reporter assay were employed to confirm 5-Methoxyflavone's regulatory function on the p53/SREBPs pathway. Lipid synthesis was determined by measuring total cholesterol and triglycerides using ELISA and visualizing lipid droplets via Oil Red O staining. Ferroptosis was evaluated by detecting intracellular ferrous ions, lipid ROS, and glutathione (GSH) levels.</p><p><strong>Results: </strong>5-Methoxyflavone suppressed NPC cell proliferation in a concentration-dependent manner in vitro. In addition, it profoundly inhibited tumor xenograft growth in mice without causing obvious adverse toxicity. Mechanistically, 5-Methoxyflavone deubiquitinated and stabilized p53 via inhibiting MDM2 expression, leading to suppression of SREBPs and their downstream lipid synthesis-related genes, thus inhibiting lipid synthesis in NPC cells. p53 depletion counteracted 5-Methoxyflavone's inhibitory effect, while SREBP1 knockdown restored proliferation in p53-silenced cells. Furthermore, 5-Methoxyflavone-stimulated downregulation of SREBP1/SCD signaling triggered ferroptosis in NPC cells by promoting iron accumulation, lipid peroxidation, and GSH depletion. Overexpression of SCD reversed the ferroptosis-inducing effects of 5-Methoxyflavone.</p><p><strong>Conclusions: </strong>Our findings reveal that 5-Methoxyflavone inhibits NPC proliferation by blocking lipid synthesis and inducing ferroptosis via the p53/SREBPs/SCD signaling pathway, providing evidence for the development of innovative drugs for NPC treatment.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147969981","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":"α-pinene and β-sitosterol co-loaded alginate/gelatin-functionalized niosomes for enhanced antibacterial and anti-biofilm activity against methicillin-resistant Staphylococcus aureus and carbapenem-resistant Klebsiella pneumoniae.","authors":"Hoda Ghoraba, Fatemeh Ashrafi, Rezvan Mousavi Nadushan, Hosein Abbaspour","doi":"10.1186/s12896-026-01132-2","DOIUrl":"10.1186/s12896-026-01132-2","url":null,"abstract":"<p><strong>Background: </strong>The rise of antibiotic resistance in infectious disease, particularly from carbapenem-resistant Klebsiella pneumoniae (CRKP) and methicillin-resistant Staphylococcus aureus (MRSA), poses a significant global health challenge. This study aimed to fabricate and evaluate a novel biocompatible hydrogel scaffold (Nio-PIN/STL@SC) incorporating niosomes loaded with α-pinene (PIN) and β-sitosterol (STL) to enhance antibacterial and anti-biofilm activities against MRSA and CRKP isolates.</p><p><strong>Methods: </strong>Niosomes containing PIN and STL (Nio-PIN/STL) were prepared using the thin-layer hydration method and then incorporated into an alginate/gelatin hydrogel scaffold via a straightforward crosslinking reaction, forming Nio-PIN/STL@SC. The physicochemical properties of the scaffolds were characterized using DLS, SEM, TEM, and FTIR. In vitro assays assessed drug release, swelling, degradation, stability, cytotoxicity, antibacterial efficacy (MIC, disk diffusion, time-kill assay), anti-biofilm activity (CV assay, MBEC), and the expression of biofilm-related genes.</p><p><strong>Results: </strong>The optimized Nio-PIN/STL@SC exhibited an average particle size of 263.5 ± 5.2 nm, Polydispersity Index (PDI) of 0.231 ± 0.011, and entrapment efficiencies (EE%) of 78.2 ± 1.18% (PIN) and 79.7 ± 1.35% (STL). The scaffold demonstrated a sustained biphasic release profile, with only 40.85% of PIN and 43.25% of STL released over 72 h at pH 7.4. Nio-PIN/STL@SC showed markedly enhanced antibacterial activity, with MIC values of 0.97-1.95 µg/mL against MRSA and 0.97-3.9 µg/mL against CRKP, representing at least a 16-fold reduction compared to free drugs. MBEC values revealed a significant reduction in biofilm biomass, decreasing viable MRSA and CRKP cells to approximately 2.0 and 3.5 log10 CFU/mL, respectively. qRT-PCR analysis demonstrated significant downregulation of icaA and icaD in MRSA and mrkA, mrkD, and fimA in CRKP (P < 0.001), alongside upregulation of the biofilm repressor gene icaR.</p><p><strong>Conclusions: </strong>The developed Nio-PIN/STL@SC hydrogel scaffold demonstrates a promising drug delivery system for the synergistic enhancement of antibacterial and anti-biofilm activities against multidrug-resistant pathogens like MRSA and CRKP with reduced cytotoxic effects, suggesting its potential for treating bacterial infections. Further in vivo studies are warranted to validate these findings.</p><p><strong>Clinical trial number: </strong>Not applicable.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":" ","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13425995/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147959749","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":"B3GNT6 suppresses colorectal cancer progression by inhibiting the KRAS/ERK signaling pathway.","authors":"Changwen Jing, Zhuo Wang, Haixia Cao, Yuetong Yu, Bingzhe Li, Rong Ma","doi":"10.1186/s12896-026-01160-y","DOIUrl":"10.1186/s12896-026-01160-y","url":null,"abstract":"<p><strong>Background: </strong>Colorectal cancer (CRC) is one of the most common malignancies with high morbidity and mortality worldwide. B3GNT6 as been predicted to serve as a prognostic indicator for CRC patients, but its biological function and underlying mechanism in CRC remain largely unclear.</p><p><strong>Objective: </strong>Our investigation was designed to clarify the biological function and molecular mechanism of B3GNT6 in CRC progression.</p><p><strong>Methods: </strong>The mRNA and protein expression levels of B3GNT6 in CRC tissues and cell lines were examined using RT-qPCR and western blot assay. CCK-8, flow cytometry, and TUNEL staining were used to evaluate cell proliferation, cell cycle distribution, and apoptosis in vitro and in vivo. The migratory and invasive abilities of cells were determined by Transwell assay. Cell autophagy was analyzed by immunofluorescence staining. The expression of apoptosis-related proteins and key components in the KRAS/ERK signaling pathway was detected using RT-qPCR and western blot analysis.</p><p><strong>Results: </strong>B3GNT6 was significantly downregulated in CRC tissues and cell lines. Functionally, B3GNT6 overexpression inhibited cell proliferation, autophagy, migration, and invasion, induced G2 phase cell cycle arrest and apoptosis, whereas these effects were abolished by KRAS overexpression. In vivo experiments further confirmed that B3GNT6 overexpression suppressed tumor growth and autophagy, and promoted apoptosis. Mechanistically, B3GNT6 overexpression inhibited the activation of the KRAS/ERK signaling pathway, while upregulation of KRAS had the opposite effect.</p><p><strong>Conclusion: </strong>B3GNT6 inhibits colorectal cancer progression by blocking the KRAS/ERK signaling pathway. Thus, B3GNT6 may serve as a promising diagnostic and prognostic biomarker as well as a potential therapeutic target for CRC.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":" ","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13344007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147939624","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":"Affinity enhancement of an anti-VEGF humanized nanobody as a superior candidate to bevacizumab: integrative in silico and in vitro studies.","authors":"Mir Salar Kazemi, Seyed Shahriar Arab, Fatemeh Kazemi-Lomedasht, Reza Ahangari Cohan, Fatemeh Zandi, Alireza Shoari, Mohammad Hosseininejad-Chafi, Golnoosh Mahjoobi, Arghavan Ashja Ardalan, Mozhgan Rezaei Kanavi, Mahdi Behdani","doi":"10.1186/s12896-026-01165-7","DOIUrl":"10.1186/s12896-026-01165-7","url":null,"abstract":"<p><strong>Background: </strong>Although nanobodies have superior characteristics to conventional antibodies, their affinities are often lower because of a single interaction site for antigen binding. Therefore, in the current study, a bioinformatics approach was employed to enhance the affinity of a humanized anti-VEGF nanobody even that of the commercially available antibody, bevacizumab.</p><p><strong>Methods: </strong>The in vitro safe dose and the affinity of the wild and mutated nanobodies were determined and compared to bevacizumab. The best mutated nanobodies (MHNb136 and MHNb256) were selected by implementing umbrella sampling simulation to improve the binding affinity of the wild-type nanobody (WHNb) to VEGF. In vitro safety investigations were performed on nanobodies with doses of 12.5, 25, 50, and 100 µg, equivalent to the dose of bevacizumab as the conventional treatment.</p><p><strong>Results: </strong>Ultimately, umbrella sampling results showed that MHNb136 and MHNb256 bind to VEGF more strongly, with ΔG values of -39.3 and -32.64 kcal/mol, respectively, than WHNb, which has a ΔG value of -19.05 kcal/mol. BIACORE assay results indicated that MHNb136 and MHNb256 bind to VEGF with higher affinity than bevacizumab as a reference.</p><p><strong>Conclusion: </strong>Eventually, MHNb136 and MHNb256 can be subjected for further clinical investigation due to the superiority to bevacizumab.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":" ","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13334927/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147925882","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":"Study on the mesoscopic characteristics of densified forming of shiitake mushroom residue biomass considering particle breakage.","authors":"Hongqiang Wang, Zhen Li, Zhiyu Wang, Yang Han, Zhiwei Geng","doi":"10.1186/s12896-026-01167-5","DOIUrl":"10.1186/s12896-026-01167-5","url":null,"abstract":"<p><p>The development of biomass pellet fuels represents an important pathway for achieving a low-carbon energy transition. Based on the particle breakage behavior of the feedstock, this study investigated the mesoscopic characteristics of the densification process of shiitake mushroom residue (SMR) biomass using piston compression experiments and the discrete element method (DEM). The results indicate that the increase in the relative breakage rate exhibits a negative quadratic relationship with time. After breakage, the particle size distribution is mainly concentrated between the minimum and intermediate values of the original particle size, showing a bimodal tendency with enrichment at both ends and a relatively sparse distribution in the intermediate range. Similarly, the reduction in the voidage of the formed pellets also exhibits a negative quadratic relationship with time. SEM/EDS analyses reveal the presence of hard siliceous nodules and abundant pore structures within the pellets. Due to the combined effects of arching and die-wall friction, the compactness and hardness of the formed pellets gradually decrease along the pressure transmission direction, accompanied by an increase in voidage, and the hardness at the pellet center is significantly lower than that at the edge. After introducing sinusoidal vibration at the bottom of the mold, under the conditions of an amplitude of 1.5 mm and a frequency of 5-7.5 Hz, the axial and circumferential hardness of the pellet became significantly more uniform, indicating a marked improvement in pellet quality. The results of this study can provide valuable references for the theoretical understanding and engineering applications of biomass Pelletizing.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":" ","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13352719/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147925968","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":"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":"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":4.8,"publicationDate":"2026-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326552/pdf/","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":"OA","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":"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":4.8,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13274208/pdf/","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":"OA","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":4.8,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13274054/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}