Molecular Biotechnology最新文献

{"title":"Triamcinolone Acetonide Produced by Bacillus velezensis YEBBR6 Exerts Antagonistic Activity Against Fusarium oxysporum f. sp. Cubense: A Computational Analysis.","authors":"R U Krishna Nayana, S Nakkeeran, N Saranya, R Saravanan, K Mahendra, Suhail Ashraf, Kahkashan Perveen, Najla A Alshaikh, R Z Sayyed, Pau Loke Show","doi":"10.1007/s12033-023-00797-w","DOIUrl":"10.1007/s12033-023-00797-w","url":null,"abstract":"<p><p>Fusarium oxysporum f. sp. cubense is one of the most severe and threatening pathogens of bananas, causing \"Panama wilt\" worldwide. Confrontation assay of Foc antagonistic bacterial endophyte, Bacillus velezensis YEBBR6, with the Foc and GC-MS profiling of excised agar from the zone of inhibition, led to the unveiling of secondary metabolites produced by the endophyte. To refine the probable antifungal compounds among the numerous biomolecules formed during their di-trophic interaction with the pathogen, fungal protein targets were modeled, and docking studies (AutoDock Vina module of the PyRx 0.8 server) were done with all the compounds. Triamcinolone acetonide exhibited the most excellent affinity for the protein targets among the compounds studied. It had a maximum binding affinity of 11.2 kcal/mol for XRN2 (5' → 3'). Further, the protein-ligand complex formation kinetics was done through Molecular Dynamic Simulation studies. Graphs for the RMSD, RMSF, Rg, potential energy, and SASA were generated, and the values during the simulation period suggested the stability of the biomolecule as a complex with the protein. This indicated Triamcinolone acetonide's potential ability to act as a functional disrupter of the target protein and likely an antifungal molecule. Further, the biomolecule was tested for its activity against Foc by screening in the wet lab through the poisoned plate technique, and it was found to be fully inhibitory to the growth of the pathogen at 1000 ppm.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3436-3454"},"PeriodicalIF":3.2,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9961174","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":"Research Advances in Multi-tissue Organoid Models Based on PBMCs.","authors":"Dongyang He, Yicheng Feng, Xiao An","doi":"10.1007/s12033-026-01573-2","DOIUrl":"10.1007/s12033-026-01573-2","url":null,"abstract":"<p><p>Organoids, as three-dimensional in vitro culture models, closely recapitulate the architectural, cellular, and functional characteristics of their in vivo counterparts. Consequently, they play a pivotal role in diverse biomedical fields, including disease modeling, drug screening, and regenerative medicine. However, conventional organoid models often lack a complex native microenvironment, specifically the tumor microenvironment (TME), which limits their utility in studying immune-related pathologies and evaluating immunotherapeutic strategies. Peripheral blood mononuclear cells (PBMCs) offer distinct advantages, including accessibility, a heterogeneous composition of immune cells, and the capacity to mirror a patient's specific immune status. As a result, PBMCs have emerged as a predominant source of immune cells for engineering immune-integrated organoid models. This article reviews recent advancements in integrating PBMCs into various tissue organoid systems. It summarizes the key biological properties of PBMCs and their applications across multiple models, including cerebral, renal, pulmonary, and hepatic organoids. Furthermore, this study compares the advantages and limitations of current modeling methodologies and discusses future research directions and persistent challenges in leveraging PBMC-integrated organoids for personalized medicine and the elucidation of disease mechanisms.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3314-3322"},"PeriodicalIF":3.2,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776832","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":"DNA-Based Boolean Logic Gates for Molecular Computation and Biosensing: A Critical Review.","authors":"Abinaya Srinivasan, Hema Kesavan, Umamaheswari Rajendran, Tejashree Palayam, Senthil Bakthavatchalam, Ramachandran Vinayagam","doi":"10.1007/s12033-026-01582-1","DOIUrl":"10.1007/s12033-026-01582-1","url":null,"abstract":"<p><p>DNA-based Boolean logic gates represent a transformative platform in molecular computation, providing a bridge between biological processes. The field has advanced toward sophisticated designs incorporating spatiotemporal control. Distinguished by features such as massive parallelism, biocompatibility, energy efficiency, and programmability, DNA computing enables operations beyond the scope of silicon-based technologies. These qualities have enabled applications in biomedical diagnostics, autonomous biosensing, and therapeutic regulation. Furthermore, multi-layered circuit architectures, including neural network like designs, highlight the transition from basic proofs of concept to practical, application-oriented technologies. Key challenges remain particularly signal leakage, gate stability, scalability, and NOT gate constraints. Emerging solutions, such as photocaging for precise activation, enzyme-mediated processing for higher fidelity, and cost-effective array-based DNA synthesis, have improved reliability and scalability. Integration with artificial intelligence, machine learning, and bioelectronics is further advancing hybrid molecular electronic systems capable of coupling biological recognition with robust digital processing. Future progress depends on standardization, reproducibility, and economic scalability. The development of automated design frameworks, rigorous validation, and cost reduction strategies will be central to driving adoption. With immediate potential in diagnostics and environmental monitoring, DNA logic gates are shaping the foundation of molecular intelligence platforms.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3344-3371"},"PeriodicalIF":3.2,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148138635","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":"An Intensive Study on Algal Diversity in the Ancient Man-Made Aquatic Ecosystem of Tiruvallur, South India: Exploration for Sustainable Development.","authors":"Keerthivarman G Subramanian, Manikandavelu Dhanushkodi, Aruna Satyapriyan, Muralidharan Nagarajan, P Muthuvinayagam, Moulitharan Nallathambi, Elangovan Prabu, Dhinesh Rajendiran, Govarthanan Muthusamy","doi":"10.1007/s12033-023-00817-9","DOIUrl":"10.1007/s12033-023-00817-9","url":null,"abstract":"<p><p>Eco-friendly and beneficial nature algae make it prominent in our earth as well as for human life. In recent decades, microalgal applications is sought in varied fields from the remediation of wastes to the production of pharmaceutical products. Still, more extensive research on bioprospecting should to conducted to get the genus-specific or species-specific applications of microalgae with high efficiency. This inquiry was carried out (October 2021 to September 2022) for the effectual understanding of microalgal composition structure along with seasonal physicochemical variations in the age-old holy tank at Tiruvallur, southeast India. This inquiry also acts as the source data and makes the bioprospecting process easier. It also ignites the researchers to address the microalgae seasonal composition structure of peculiar wet environments. A total of 41 microalgae species were recorded, in which six major algal groups were in order of, Chlorophyceae > Bacillariophyceae > Cyanophyceae > Euglenophyceae > Zygnematophyceae > Trebouxiophyceae. Mean seasonal abundance was highest in the summer season (351 cells/L) and lowest in the monsoon (113 cells/L). One-way ANOVA showed seasonal variations of physicochemical parameters, in which the majority of them attained their peak during summer. Mean values of water temperature, pH, salinity, total dissolved solids, total solids, electrical conductivity, chemical oxygen demand, total hardness, total alkalinity, ammonia, nitrite-nitrogen, and nitrate-nitrogen for the summer were 31.43 °C, 8.53, 0.56 ppt, 383 mg/L, 525 mg/L, 0.85 mS/cm, 46.27 mg/L, 300 ppm, 251.67 ppm, 1.51 mg/L, 0.62 mg/L, and 0.70 mg/L, respectively. Karl Pearson's correlation revealed a most significant relationship between water quality factors and algal density. The Shannon's diversity index (2.78-3.39) indicated moderately rich microalgal diversity in the study area. Palmer's pollution index stated that the temple tank was organically polluted all over the study period except November.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3398-3408"},"PeriodicalIF":3.2,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10214624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Retraction Note: Advances of Predicting Allosteric Mechanisms Through Protein Contact in New Technologies and Their Application.","authors":"Sayed Haidar Abbas Raza, Ruimin Zhong, Xiaoting Yu, Gang Zhao, Xiaoqun Wei, Hongtao Lei","doi":"10.1007/s12033-026-01571-4","DOIUrl":"10.1007/s12033-026-01571-4","url":null,"abstract":"","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3471"},"PeriodicalIF":3.2,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147481017","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":"RETRACTED ARTICLE: Physiological and Molecular Role of Strigolactones as Plant Growth Regulators: A Review.","authors":"Varsha Rani, R S Sengar, Sanjay Kumar Garg, Pragati Mishra, Pradeep Kumar Shukla","doi":"10.1007/s12033-023-00694-2","DOIUrl":"10.1007/s12033-023-00694-2","url":null,"abstract":"","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3381"},"PeriodicalIF":3.2,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10753002","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":"Heterologous Systems in the Functional Characterization of Proteins from Phytopathogenic Fungi: A Systematic Review.","authors":"Hermanna Vanesca Viana de Oliveira, Darília Christane Bomfim de Rezende, Joel Augusto Moura Porto, Eric Roberto Guimarães Rocha Aguiar, Diogo Pereira Silva de Novais, Irma Yuliana Mora-Ocampo, Ariana Silva Santos, Carlos Priminho Pirovani","doi":"10.1007/s12033-026-01592-z","DOIUrl":"https://doi.org/10.1007/s12033-026-01592-z","url":null,"abstract":"<p><p>Fungal-host coevolution, intensified by climate change, is attracting greater efforts to characterize new virulence proteins to enable the protection of agricultural crops. Under PRISMA guidelines, in this systematic review we analyzed 122 experimental studies from the Scopus, PubMed, ScienceDirect, and Web of Science databases, mapping heterologous expression systems for fungal phytopathogen proteins from crops such as wheat, maize, rice, and apple, among other agricultural commodities. The results reveal the predominance of Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris, Nicotiana benthamiana, and filamentous fungi in structural and functional validation, both in vitro and in vivo. Although these heterologous hosts elucidate relevant pathogenicity mechanisms and immune suppression, gaps persist, such as the restricted use of filamentous fungi as models and the absence of standardized workflows for the integrated characterization of proteins across multiple hosts. By systematizing bibliometric trends and methodological approaches, this study reveals different strategies used to accelerate the analysis of fungal proteins, contributing to the advancement of molecular phytopathology and global food security.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148579448","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":"An R2R3-MYB Gene GhMYBPA of Gossypium hirsutum Promotes Proanthocyanidin Accumulation and Improves Heat Tolerance in Arabidopsis.","authors":"Yemin Xu, Wumeng Gong, Shiying Yu, Qingyuan Gu, Jun Mei, Meng Miao","doi":"10.1007/s12033-026-01600-2","DOIUrl":"https://doi.org/10.1007/s12033-026-01600-2","url":null,"abstract":"<p><p>R2R3-MYB transcription factors are typical members of the MYB transcription factor family and have been extensively investigated as key regulatory factors in the flavonoid metabolic pathway of model plants. Nonetheless, research on the functional characterization of R2R3-MYB genes remains limited in cotton. Here, we identified an R2R3-MYB gene GhMYBPA, which demonstrates predominant expression in the leaves of the Gossypium hirsutum cultivar XinCai20 (XC20). The coding sequence of the GhMYBPA is 765 bp. It contains two conserved MYB domains and demonstrates a close evolutionary relationship with other characterized proanthocyanidin metabolic regulators. The GhMYBPA-GFP fusion protein is enriched in the nucleus, and GhMYBPA exhibits significant transcriptional activation properties. Downregulation of GhMYBPA led to a significant decrease in proanthocyanidin levels in cotton leaves, whereas upregulation of GhMYBPA in Arabidopsis produced the opposite phenotype. Additionally, Arabidopsis lines overexpressing GhMYBPA exhibited enhanced tolerance to heat stress, with a significant upregulation of stress-responsive genes. The findings lay a foundation for investigating the function of GhMYBPA in Gossypium hirsutum, particularly regarding its involvement in proanthocyanidin accumulation and heat stress response.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148497717","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":"Mechanistic Insights into Effector-Mediated Modulation of Rice Mitochondrial Proteins by Magnaporthe oryzae.","authors":"Bharati Pandey, Chetna Tyagi","doi":"10.1007/s12033-026-01594-x","DOIUrl":"https://doi.org/10.1007/s12033-026-01594-x","url":null,"abstract":"<p><p>Mitochondria are crucial for the plant and animal immunity. The effector protein MoCDIP4 reduces rice immunity by targeting the mitochondria-associated OsDjA9-OsDRP1E protein complex. The present study is focussed on how Magnaporthe oryzae, the fungus that causes rice blast disease, affects mitochondrial dynamics and inhibits innate immune responses in rice plants using molecular modelling, molecular dynamics simulations and free energy-based binding analysis. The protein structure prediction of the effector protein MoCDIP4 and the targets was carried out using artificial intelligence-based tool, AlphaFold. The MD simulation analysis of the effector protein showed significant changes in the secondary structure especially at its C-terminal. The protein-protein complex conformations for OsDjA9-OsDRP1E and OsDjA9-MoCDIP4 were predicted using ab initio molecular methods and energy minimised for enhanced sampling (accelerated) molecular dynamics (MD) simulations. We found that MoCDIP4 targets and binds to the same N-terminal \"fork-like\" binding site on OsDjA9 which is required for OsDjA9-OsDRP1E complex formation, thereby, resulting in accumulation of OsDRP1E in the mitochondria. Moreover, OsDjA9 was found to undergo large conformational globular folding when bound to OsDRP1E as shown by increased root-mean-square deviation (RMSD) values and overall structural compactness. The binding free energy was calculated by Molecular Mechanics with Generalised Born and Surface Area Solvation (MM/GBSA) model where the OsDjA9-OsDRP1E complexes were scored at - 83.79 kcal/mol and the OsDjA9-MoCDIP4 scored at - 49.24 kcal/mol. The study also highlighted the key residues involved in the interaction of the effector protein as well as from the mitochondria-associated OsDjA9-OsDRP1E protein complex which would pave the path for studying the plant-pathogen interaction.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148471955","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":"Haplotype Analysis of the Wx and SSIIa Genes and Their Association with Starch Physicochemical Properties in Diverse Rice Germplasm.","authors":"Daud Ali Shah, Hakim Zamir, Hussam Ahmad, Fawad Rauf, Shahrukh Khan, Zameer Hussain Jamali, Usman Zulfiqar, Mohammed S Alotaibi, Bakhrom Jobborov, Shakal Khan Korai","doi":"10.1007/s12033-026-01596-9","DOIUrl":"https://doi.org/10.1007/s12033-026-01596-9","url":null,"abstract":"<p><p>Starch physicochemical properties are key determinants of rice (Oryza sativa L.) grain quality, influencing cooking performance, texture, nutritional value, and industrial functionality. Among the genes regulating starch biosynthesis, Wx (encoding granule-bound starch synthase I, GBSSI) and SSIIa (starch synthase IIa) are major-effect loci controlling amylose content and amylopectin chain length distribution, respectively. Although classical studies identified major functional polymorphisms within these genes, recent genomic analyses reveal extensive haplotypic diversity that better explains quantitative variation in starch traits across diverse rice germplasm. This review synthesizes current knowledge on the molecular structure, regulation, and allelic diversity of Wx and SSIIa, highlighting the importance of haplotype-based approaches for interpreting starch physicochemical behavior. Wx haplotypes primarily modulate amylose accumulation and associated properties such as gel consistency, pasting characteristics, and resistant starch formation, whereas SSIIa haplotypes largely determine gelatinization temperature and amylopectin structural organization. Evidence from association mapping and population genomic studies further demonstrates that combined Wx-SSIIa haplotypes exert additive and epistatic effects on starch thermal properties, pasting profiles, and eating quality traits. Environmental factors, particularly temperature during grain filling, also influence gene expression and starch structure, generating important genotype × environment interactions. Integration of haplotype information into molecular breeding, genomic prediction, and genome editing strategies provides powerful opportunities to develop rice varieties with tailored starch functionality and improved quality under changing climatic conditions.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148448210","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}