BMC BiotechnologyPub Date : 2026-10-22DOI: 10.1186/s12896-026-01144-y
Marieta Hyde, Michael Cunningham, Xiyun Chai, Mengfei Peng, Hengcheng Alvis Hu, Charles Lu, Aparna Vasanthakumar
{"title":"Evaluating assay performance and freeze-thaw stability in cerebrospinal fluid samples using High-Throughput Proximity Extension Assay Platform.","authors":"Marieta Hyde, Michael Cunningham, Xiyun Chai, Mengfei Peng, Hengcheng Alvis Hu, Charles Lu, Aparna Vasanthakumar","doi":"10.1186/s12896-026-01144-y","DOIUrl":"10.1186/s12896-026-01144-y","url":null,"abstract":"<p><strong>Background: </strong>Analysis of cerebrospinal fluid (CSF) facilitates the understanding of brain-specific molecular changes that may associate with disease progression. Proximity extension assays (PEA) have been deployed in several CSF studies, however the evaluation of the assay and impact of freeze-thaw cycles on the protein signal has not been documented. We sought to (1) assess the technical performance of the PEA platform and (2) evaluate the effect of freeze-thaw cycles on the detectability of analytes on the PEA platform.</p><p><strong>Results: </strong>We have evaluated the PEA with Next Generation Sequencing (NGS) readout assay and report on the detectability and coefficient of variation observed in CSF samples. We have also evaluated proteomic signals with a minimum of 3 and a maximum of 9 freeze thaw cycles and detected very minimal change in signal with increasing cycle number.</p><p><strong>Conclusion: </strong>Our study is the first to evaluate the performance of PEA using NGS readout platform with CSF samples. We report lower protein detection rates and higher variability in the expansion panels compared to the original 4 panels, with acceptable variation above detectability threshold. In addition, our work demonstrates that the proteomic signal is robust and continues to be stable across multiple freeze thaw cycles. This is highly impactful to the processing and analysis of clinical samples and facilitates the investigation of samples with variable pre-analytical conditions.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":"26 1","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13700250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149261801","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}
BMC BiotechnologyPub Date : 2026-09-25DOI: 10.1186/s12896-026-01202-5
Faiza A Shehata, Muhammad A Elsobky, Marwa M Hegazy, Ehab M B Mahdy
{"title":"Biosystematics and molecular characterization of three biotypes of Convolvulus arvensis L. (convolvolaceae) in Marsa Matrouh, Egypt.","authors":"Faiza A Shehata, Muhammad A Elsobky, Marwa M Hegazy, Ehab M B Mahdy","doi":"10.1186/s12896-026-01202-5","DOIUrl":"10.1186/s12896-026-01202-5","url":null,"abstract":"<p><p>The notable characteristic of phenoplasticity in Convolvulus species is flower color polymorphism, with blooms ranging from white to pink. This variation is due to various factors, including genetic drift and natural selection. The primary objective is to conduct a study on the morphoplasticity of eight accessions collected from diverse locations and categorized into three distinct biotypes based on floral pigmentation: Biotype 1 (White; accessions 1, 4, and 7), Biotype 2 (Pale Pink; accessions 2, 5, and 8), and Biotype 3 (Pink; accessions 3 and 6) of Convolvulus arvensis L. Based on the aforementioned characteristics-flower colour, stem outline, leaf shape, pollen features, shape, colpus and pori shapes, epidermal cell shape, and the number of vascular bundles in both stem and petiole-the study employed morphological and anatomical studies, as well as CDDP markers, to evaluate differences among accessions. Leaf tissues are parenchyma above the main vascular bundle, with an angle between the midrib and the wing region. Three distinct biotypes (B1, B2, and B3) have been defined. CDDP marker analysis revealed high polymorphism (74.36%) and Rp (9.50). Samples 7 and 8 (location 3) showed the most informative polymorphism of flower color (white/pale pink/pink). Genetic distances clustered samples primarily by location rather than by color, underscoring the dominant role of location in structuring populations. The interaction between genotype and ecological conditions led to the genetic variation in flower color in C. arvensis.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":"26 1","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13615628/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149057917","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}
BMC BiotechnologyPub Date : 2026-08-10DOI: 10.1186/s12896-026-01209-y
Zahra Abbasi-Malati, Seyed Ghader Azizi, Sahar Balagholi, Ali Akbar Pourfathollah
{"title":"Isolation and in vitro culture of endothelial progenitor cell-like populations from leukoreduction filters.","authors":"Zahra Abbasi-Malati, Seyed Ghader Azizi, Sahar Balagholi, Ali Akbar Pourfathollah","doi":"10.1186/s12896-026-01209-y","DOIUrl":"10.1186/s12896-026-01209-y","url":null,"abstract":"<p><strong>Background: </strong>Leukoreduction filters (LRFs) are routinely used in blood transfusion services and retain substantial numbers of nucleated cells during blood processing. These discarded filters have therefore been explored as a potential source of peripheral blood-derived cells for endothelial progenitor cell (EPC)-like related in vitro studies.</p><p><strong>Methods: </strong>Leukoreduction filters were collected from the Iranian Blood Transfusion Organization (IBTO). Entrapped cells were recovered using a washing-based procedure without the use of magnetic-activated cell sorting (MACS) or endothelial differentiation media. A coating solution containing plasma-derived components, including cryoprecipitate and platelet lysate, was applied to improve early cell adhesion during in vitro culture.</p><p><strong>Results: </strong>Cultured cells were characterized by flow cytometry using CD133 as a surface-associated progenitor marker. Approximately 70% of the cells at passage 3-4 was positive for CD133.</p><p><strong>Conclusion: </strong>Leukoreduction filters may serve as an accessible and cost-effective source of peripheral blood-derived cell populations for EPC-like related in vitro studies. Further studies are required to confirm their endothelial identity and functional properties.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":"26 1","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13737541/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149340506","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":"Predictive comparison and evaluation of ANN and ANFIS as effective tools in modeling prodigiosin production by Serratia marcescens ND93.","authors":"Köksal Erentürk, Neslihan Dikbaş, Sevda Uçar, Şeyma Alım","doi":"10.1186/s12896-026-01210-5","DOIUrl":"10.1186/s12896-026-01210-5","url":null,"abstract":"<p><p>Prodigiosin is a natural red pigment produced by Serratia marcescens that has attracted attention due to its various biological activities and potential for industrial applications. In recent years, research aimed at producing this compound using highly efficient and economically viable bioprocesses has gained increasing importance. In this study, the OD600 value and prodigiosin production of Serratia marcescens isolated from onion were experimentally tested under varying environmental conditions (glycerol, pH, temperature, and time), and artificial neural network (ANN) and ANFIS models were designed to predict prodigiosin production using the obtained data. First, the red pigment extracted with acidified methanol was characterized using a UV-vis spectrophotometer and exhibited maximum absorbance at 535 nm. Next, the modeling phase began, and both the ANN and ANFIS architectures were trained using 80% of the experimental dataset. The reserved 20% of the data served as the testing subset, encompassing input feature vectors including glycerol, pH, temperature, and time alongside their corresponding OD<sub>600</sub> values and prodigiosin amount from the conventional system. Model performance validation was conducted using the Coefficient of Determination R² as the primary metric for assessing predictive accuracy. The ANN model demonstrated superior performance, achieving R² values of 0.9975 and 0.9942 on the training and testing sets, respectively. In contrast, the ANFIS model yielded significantly lower R² metrics of 0.9537 training and 0.9409 testing, respectively. The high R² values associated with the ANN technique signify a strong correlation between the model's predicted outputs and the actual experimental observations. Although the ANFIS R² metrics are lower, they still indicate acceptable predictive error tolerances, particularly considering the constrained size of the experimental dataset. In summary, both ANN and ANFIS models successfully demonstrated efficacy in predicting both OD<sub>600</sub> and prodigiosin amount; however, the ANN model consistently delivered a superior predictive capacity, exhibiting closer agreement with the experimental data. The findings of this study may help to better understand the application of ANN and ANFIS in modeling microbial pigment production and predicting production performance.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":"26 1","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13732988/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149332254","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}
BMC BiotechnologyPub Date : 2026-08-03DOI: 10.1186/s12896-026-01207-0
Deepshikha, Pradeep Verma, Komal Agrawal
{"title":"Valorization of agricultural residue for the production of fructose using fungal inulinase from Talaromyces domesticus ITCC 9483.","authors":"Deepshikha, Pradeep Verma, Komal Agrawal","doi":"10.1186/s12896-026-01207-0","DOIUrl":"10.1186/s12896-026-01207-0","url":null,"abstract":"<p><p>Fungal inulinase hydrolyzes inulin to fructose, a commercially important intermediate with a wide range of applications in various industries. However, its industrial utilization is limited due to high cost of production and processing. Therefore, the present study reports the valorization of low-cost agricultural residues (AR) as an alternative substrate for inulinase production and its application in generation of fructose. In the study, an inulinase producing fungal strain was identified as Talaromyces domesticus ITCC 9483 based on preliminary and secondary screening. Further, various low-cost AR were screened for efficient inulinase production. Amongst these substrates, rice husk (RH) supported the highest enzymatic activity and was utilized as a major component for medium optimization in the presence of inulin as an inducer. It resulted in 2.02-fold increase in inulinase activity from 8.34 ± 1.45 U/mL to 16.86 ± 1.29 U/mL. The inulinase was purified resulting in 5.52-fold purification and a molecular mass of ~ 45-50 kDa. The zymographic analysis confirmed inulinase via distinct red band on native gel. The purified inulinase exhibited maximum stability at pH 5.0 and 50 °C after 24-hours of incubation, with K<sub>m</sub> 0.83 ± 0.19 mM and V<sub>max</sub> 4.58 ± 0.48 µmol/min. The structural characteristics were evaluated using UV spectrum, FTIR and XRD. The optimized inulinase was further employed for valorization of AR generating maximum reducing sugar yield of 2.14, 0.96 and 0.34 mg/mL from WB, SR and wheat straw (WS). The high-performance liquid chromatography (HPLC) confirmed fructose as primary hydrolysis product with concentrations of 47.94, 38.91 and 28.99%. Overall, the study established T. domesticus ITCC 9483 as a potent producer of inulinase capable of valorizing low-cost AR into value-added fructose through enzymatic bioprocessing. The generated fructose can further serve as a significant intermediate for application in biorefinery, food and pharmaceutical industries.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":"26 1","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13721482/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149294324","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":"Enhanced production of ε-Poly-L-lysine through overexpression of LysR involved in interspecies interactions.","authors":"Siying Liao, Zhanyang Zhang, Bingxin Chen, Siyu Tong, Chen Zhang, Huawei Zeng, Deyin Zhao, Mingtao Zhao, Xin Zeng, Bingyue Xin","doi":"10.1186/s12896-026-01208-z","DOIUrl":"https://doi.org/10.1186/s12896-026-01208-z","url":null,"abstract":"<p><strong>Background: </strong>Epsilon-poly-L-lysine (ε-PL), an antimicrobial peptide synthesized by Streptomyces albulus through submerged fermentation, is biosynthesized via multiple metabolic pathways. This suggests that global metabolic regulation and interspecies interactions contribute significantly to enhancing ε-PL yield. Current genetic and metabolic engineering strategies, however, primarily aim at strengthening specific metabolic fluxes, without adequately coordinating the diverse physiological requirements involved in ε-PL production. Previous research has shown that interspecies stress induced by Streptomyces gilvosporeus can elicit a broad enhancement of ε-PL biosynthetic pathways. Building on this finding, the present study seeks to identify key transcriptional regulators that respond to such interspecies stress and are capable of systematically improving metabolic efficiency.</p><p><strong>Results: </strong>Comparative transcriptomic analysis revealed that transcription factors from the RegX3, LysR, and TetR families were significantly upregulated in S. albulus under interspecies stress. Corresponding overexpression strains (OE-RegX3, OE-LysR, OE-TetR1, and OE-TetR2) were constructed using a one-step cloning strategy, all exhibiting altered colony morphology. Among them, OE-LysR showed a 60.9% increase in ε-PL production compared to the wild type in flask cultures. When scaled to a 5-L bioreacter and stimulated with S. gilvosporeus live cells, the ε-PL titer of OE-LysR further rose to 39.6 g/L, marking a 51.1% improvement. Physiological analyses revealed that the enhanced ε-PL production was attributed to the upregulation of key biosynthetic and metabolic pathways.</p><p><strong>Conclusions: </strong>LysR was identified as a key regulator that mediates interspecies stress from S. gilvosporeus to enhance ε-PL biosynthesis in S. albulus. Overexpression of LysR globally activated ε-PL-related metabolic pathways and markedly increased ε-PL production at both flask and fermenter scales, especially when combined with S. gilvosporeus stimulation. These findings offer new strategies for harnessing interspecies stress to enhance antibiotic fermentation efficiency.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":"26 1","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13718126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149294287","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}
BMC BiotechnologyPub Date : 2026-07-29DOI: 10.1186/s12896-026-01205-2
Xuemei Guan, Zhenguang Wei, Liuyan Wang, Dezhi Zhi, Wenhui Chen
{"title":"MGS-HCT enables resistance gene discovery and functional sequence design in forest trees.","authors":"Xuemei Guan, Zhenguang Wei, Liuyan Wang, Dezhi Zhi, Wenhui Chen","doi":"10.1186/s12896-026-01205-2","DOIUrl":"10.1186/s12896-026-01205-2","url":null,"abstract":"<p><p>Resistance gene discovery in forest trees remains challenging because of their large, repeat-rich genomes and the sparse distribution of functional elements, which restrict the direct application of deep learning approaches developed for crop species. While genomic language models have shown promise in crop species, their application to forest trees remains limited. Here, we present MGS-HCT (Multi-scale Gated Sparse Encoder-Hybrid Convolutional Transformer), a deep learning framework tailored for forest tree genomic sequences. The model integrates multi-scale gated units with structure-aware sparse attention for efficient sequence compression, and combines convolutional modules with transformer layers to capture both local motifs and long-range regulatory dependencies. We show that MGS-HCT supports two key applications in forest tree biotechnology: (1) the conditional generation and prioritization of putative NLR candidates for Alnus glutinosa (common alder) and (2) the de novo generation of synthetic DNA sequences containing promoter-like and splice-site-like elements. These results provide a computational foundation for accelerating disease-resistance gene discovery and genomic-assisted breeding in forest tree species, expanding the scope of deep learning from crop plants to forest genomics. By prioritizing candidates supported by multiple computational criteria for subsequent experimental validation, the framework is intended to narrow the experimental search space and help shorten the long breeding cycles of forest trees.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":"26 1","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13700307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149261826","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}
BMC BiotechnologyPub Date : 2026-07-27DOI: 10.1186/s12896-026-01196-0
Ming Xian, Zhangtao Hu, Songmao Guo, Yu Li, Fei Wen, Jianhong Hu
{"title":"Establishment and in vitro validation of a sheep-specific, low-cost TLR7/8 agonist R848-mediated X/Y sperm separation system.","authors":"Ming Xian, Zhangtao Hu, Songmao Guo, Yu Li, Fei Wen, Jianhong Hu","doi":"10.1186/s12896-026-01196-0","DOIUrl":"10.1186/s12896-026-01196-0","url":null,"abstract":"<p><p>Sex control is crucial for maximizing the economic benefits of sheep husbandry: male lambs increase farm income by 30-40% due to superior growth and feed efficiency, while female lambs are essential for fine-wool production and population expansion. However, the only commercialized method (flow cytometry) has critical sheep-specific limitations, including 25-30% flow channel blockage, sperm DNA oxidative damage, and prohibitive cost for large-scale breeding. TLR7/8 agonist R848 has been validated for sperm separation in mice, cattle and goats, but no sheep-specific optimized system has been established due to unique biological characteristics of ovine sperm. In this study, we systematically optimized key parameters of R848-mediated sheep sperm separation, comprehensively evaluated its effects on sperm biological characteristics, and verified separation efficiency at the embryo level via IVF combined with nested PCR sex identification. The optimal R848 concentration was 1 µM: the upper layer was enriched with 90.30% ± 5.21% TLR8-negative Y sperm (validated by 80.20% ± 3.70% male embryos), and the lower layer was enriched with 80.50% ± 4.96% TLR8-positive X sperm (validated by 87.56% ± 9.51% female embryos). R848 specifically inhibited X-sperm motility by reducing ATP production (24.82% decrease, P = 0.006) and mitochondrial membrane potential (29.75% decrease, P = 0.023), without damaging acrosome or plasma membrane integrity. The optimal supporting conditions were determined as 1000 µL elution twice, Y-sperm storage at 17 °C for up to 120 h with stable in vitro performance, and X-sperm use within 24 h after sorting. This study provides a low-cost, sheep-specific sperm separation system with comprehensive in vitro validation, which has significant potential for application in precision sheep breeding after further in vivo validation.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":"26 1","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13688757/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149242680","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}
BMC BiotechnologyPub Date : 2026-07-27DOI: 10.1186/s12896-026-01203-4
Huanglin Huo, Zhenhua Zhou, Rongxiang Guo, Jinyi Zhang, Menghan Li, Huicong Zeng, Dongyu Zhao, Roman P Terekhov, Peng Jiang, Qian Zhou, Bo Li
{"title":"Correction to: Formulation and evaluation of hydrogel based on Brazilian propolis ethanol extract for promoting diabetic wound healing.","authors":"Huanglin Huo, Zhenhua Zhou, Rongxiang Guo, Jinyi Zhang, Menghan Li, Huicong Zeng, Dongyu Zhao, Roman P Terekhov, Peng Jiang, Qian Zhou, Bo Li","doi":"10.1186/s12896-026-01203-4","DOIUrl":"10.1186/s12896-026-01203-4","url":null,"abstract":"","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":"26 1","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13403621/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148598413","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 improvement of specific scFvs interacting with the Neisseria meningitidis factor H-binding protein: a molecular dynamics simulation approach and experimental study.","authors":"Bijan Ghazanfari, Zahra Ebrahimi, Fatemeh Yarian, Arezu Lari, Ali Ghanbariasad, Bahram Kazemi","doi":"10.1186/s12896-026-01204-3","DOIUrl":"10.1186/s12896-026-01204-3","url":null,"abstract":"<p><strong>Background: </strong>In silico approaches are becoming increasingly important for enhancing the affinity of antibodies and antibody fragments, including single-chain variable fragments (scFvs). In this study, we present an in silico affinity-maturation workflow designed to improve the affinity of an scFv directed against Neisseria meningitidis factor H-binding protein (fHbp) by integrating in silico maturation, molecular dynamics (MD) simulations, and experimental validation. Approximately 300 single-point substitutions were designed at scFv residues predicted to interact with fHbp, and the resulting V3 (R99D) scFv-fHbp complexes were analyzed through all-atom MD simulations. Guided by bioinformatic analyses, the top V3 (R99D) variant was cloned and expressed, and its binding activity was validated by ELISA.</p><p><strong>Results: </strong>MD analyses identified five variants, Y35H, L31R, R99D, R99H, and A100K, that exhibited markedly enhanced complex stability. In all variants, the scFv secondary structure remained intact, whereas fHbp showed shrinkage relative to the scFv in the V3 (R99D)-fHbp complexes during the simulations. Hydrogen-bonding patterns and inter-residue distances further supported the improved affinity of the variants relative to the native form. The R99D variant showed the highest binding affinity, with an experimentally measured value of 67.93 × 10⁹ M⁻¹.</p><p><strong>Conclusion: </strong>Collectively, these findings underscore affinity maturation as a powerful strategy for engineering high-affinity antibody fragments.</p>","PeriodicalId":8905,"journal":{"name":"BMC Biotechnology","volume":"26 1","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13685201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149227044","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}