Molecular Biotechnology最新文献

{"title":"Enhanced SELEX Platforms for Aptamer Selection with Improved Characteristics: A Review.","authors":"Reza Didarian, Hatice K Ozbek, Veli C Ozalp, Ozcan Erel, Nimet Yildirim-Tirgil","doi":"10.1007/s12033-024-01256-w","DOIUrl":"10.1007/s12033-024-01256-w","url":null,"abstract":"<p><p>This review delves into the advancements in molecular recognition through enhanced SELEX (Systematic Evolution of Ligands by Exponential Enrichment) platforms and post-aptamer modifications. Aptamers, with their superior specificity and affinity compared to antibodies, are central to this discussion. Despite the advantages of the SELEX process-encompassing stages like ssDNA library preparation, incubation, separation, and PCR amplification-it faces challenges, such as nuclease susceptibility. To address these issues and propel aptamer technology forward, we examine next-generation SELEX platforms, including microfluidic-based SELEX, capillary electrophoresis SELEX, cell-based aptamer selection, counter-SELEX, in vivo SELEX, and high-throughput sequencing SELEX, highlighting their respective merits and innovations. Furthermore, this article underscores the significance of post-aptamer modifications, particularly chemical strategies that enhance aptamer stability, reduce renal filtration, and expand their target range, thereby broadening their utility in diagnostics, therapeutics, and nanotechnology. By synthesizing these advanced SELEX platforms and modifications, this review illuminates the dynamic progress in aptamer research and outlines the ongoing efforts to surmount existing challenges and enhance their clinical applicability, charting a path for future breakthroughs in this evolving field.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"2962-2977"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141996149","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":"Unraveling the Interaction Mechanism of the Compounds From Cladophora sp to Recognize Prospective Larvicidal and Bactericidal Activities: In vitro and In Silico Approaches.","authors":"K T Nachammai, S Amaradeepa, S Raageshwari, A V Swathilakshmi, M Poonkothai, K Langeswaran","doi":"10.1007/s12033-023-00902-z","DOIUrl":"10.1007/s12033-023-00902-z","url":null,"abstract":"<p><p>The present investigation aims to validate the larvicidal and antibacterial potential of Cladophora sp through in vitro and in silico approaches. The presence of phytoconstituents, functional groups and the compounds responsible for antibacterial and larvicidal activity were assessed through FT-IR and GC-MS analyses which unveiled the existence of active secondary metabolites, hydroxyl, alkane and carbonyl groups. The larvicidal and antibacterial activity of algal extract were examined and revealed complete mortality and substantial zone of inhibition was observed against Culex quinquefasciatus and E. coli. To support the in vitro investigation in silico studies were performed. Molecular docking investigations of the selected compounds from GC-MS which exhibited favorable agreement with drug likeness and ADMET properties indicated robust interactions with the larvicidal and bacterial proteins showcasing considerable binding affinities. Notably, 1,2,4-Oxadiazole, 3-(1,3-benzodioxol-5-yl)-5-[(4-iodo-1H-pyrazol-1-yl) methyl]- exhibited strong interactions with the target proteins. Density Functional Theory revealed that the energy gap of the lead compound was reduced and substantiates the occurrence of intermolecular charge transfer. Molecular Dynamic simulations confirms the stability and flexibility of the lead compound. Hence, this investigation offers computational perspectives on the molecular interactions of Cladophora sp, suggesting its suitability as a promising biocontrol agent.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3154-3174"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41236910","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":"Cellulose Degradation Enzymes in Filamentous Fungi, A Bioprocessing Approach Towards Biorefinery.","authors":"Abdulmoseen Segun Giwa, Nasir Ali, Mohammed Salim Akhter","doi":"10.1007/s12033-023-00900-1","DOIUrl":"10.1007/s12033-023-00900-1","url":null,"abstract":"<p><p>The economic exploration of renewable energy resources has hot fundamentals among the countries besides dwindling energy resources and increasing public pressure. Cellulose accumulation is a major bio-natural resource from agricultural waste. Cellulases are the most potential enzymes that systematically degrade cellulosic biomass into monomers which could be further processed into several efficient value-added products via chemical and biological reactions including useful biomaterial for human benefits. This could lower the environmental risks problems followed by an energy crisis. Cellulases are mainly synthesized by special fungal genotypes. The strain Trichoderma orientalis could highly express cellulases and was regarded as an ideal strain for further research, as the genetic tools have found compatibility for cellulose breakdown by producing effective cellulose-degrading enzymes. This strain has found a cellulase production of about 35 g/L that needs further studies for advancement. The enzyme activity of strain Trichoderma orientalis needed to be further improved from a molecular level which is one of the important methods. Considering synthetic biological approaches to unveil the genetic tools will boost the knowledge about commercial cellulases bioproduction. Several genetic transformation methods were significantly cited in this study. The transformation approaches that are currently researchers are exploring is transcription regulatory factors that are deeply explained in this study, that are considered essential regulators of gene expression.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"2931-2945"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41236830","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":"Fermentative Biohydrogen and Biomethane Production from High-Strength Industrial Food Waste Hydrolysate Using Suspended Cell Techniques.","authors":"Onjira Kongthong, Pannipha Dokmaingam, Chen-Yeon Chu","doi":"10.1007/s12033-023-00939-0","DOIUrl":"10.1007/s12033-023-00939-0","url":null,"abstract":"<p><p>The food waste was very difficult to treat in a proper way since its high-organic matter. The novel biohythane (H₂ + CH₄) production from high-strength industry food waste hydrolysate in two steps anaerobic well mixed batch bioreactor was carried out in this study using cultivated microflora. The temperature was controlled at 37 °C and initial substrate concentration of industrial food waste hydrolysate varied from 60, 80, 100, and 120 g COD/L, respectively. The pH, TS, VS, and SCOD were analyzed from the influent and effluent samples. These analytical parameters showed the correlations between the biogas production rates and yields in the batch fermentation system. This study was the first time to use the industry food waste hydrolysate which was collected from the subcritical water hydrolysis process. In this study, the optimal biohydrogen and biomethane yield production by using suspended cells were 0.65 mL H₂/g COD and 203.72 mL CH₄/g COD where the initial substrate concentrations of total COD and SCOD were 60 g/L and 39.80 g/L, respectively. The optimal of the biohydrogen and biomethane yields production by using suspended cells were 0.65 mL H₂/g COD and 203.72 mL CH₄/g COD where the initial substrate concentrations of total COD and SCOD were 60 g/L and 39.80 g/L, respectively. The results of this study supported that the cultivation of inoculum in a suspended cell type can have a higher tolerance for the biohydrogen and biomethane production in a high-strength initial substrate concentration of 60 g COD/L.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3186-3193"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71483789","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":"Identification of Pyroptosis-Related Molecular Subtypes and Diagnostic Model development in Major Depressive Disorder.","authors":"Lin Feng, Jiabo Yuan, Li Li, Junze Tang","doi":"10.1007/s12033-024-01252-0","DOIUrl":"10.1007/s12033-024-01252-0","url":null,"abstract":"<p><p>Major depressive disorder (MDD) is a prevalent psychological disorder associated with inflammation, with complex pathological mechanisms. Pyroptosis has been suggested to contribute to inflammation in central nervous system diseases. Little research, however, has examined what role pyroptosis played in MDD. In the present study, the differential expression pyroptosis-related genes (DE-PRGs) in MDD were identified from the GEO database (GSE98793 and GSE19738). Then, consensus clustering analysis was used to evaluate differences in MDD molecular subtypes characteristics based on PRGs. The characteristic diagnostic biomarkers for MDD were identified by Weighted Correlation Network Analysis (WGCNA) and multiple machine learning algorithms. Three intersection genes (GZMA, AKR1C3, and CD52) were obtained, which are expected to become potential biomarkers for MDD with excellent reliability and accuracy. Subsequently, the immune infiltration characteristics result indicated that the development of MDD is mediated by immune-related function, where three DE-PRGs were strongly related to the immune infiltration landscape of MDD. The biological experiments in vitro further proved that three unique PRGs are emerging as important players in MDD diagnosis. Our research aimed to provide novel ideas and biomarkers targeting MDD.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3281-3295"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142036429","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":"Antioxidant, In Vitro Cytotoxicity, and Anti-diabetic Attributes of a Drug-Free Guar Gum Nanoformulation as a Novel Candidate for Diabetic Wound Healing.","authors":"Debojyoti Mandal, Jayanta K Sarmah, Vancha Harish, Jeena Gupta","doi":"10.1007/s12033-024-01261-z","DOIUrl":"10.1007/s12033-024-01261-z","url":null,"abstract":"<p><p>The escalating intersection of diabetes and impaired wound healing poses a substantial societal burden, marked by an increasing prevalence of chronic wounds. Diabetic individuals struggle with hindered recovery, attributed to compromised blood circulation and diminished immune function, resulting in prolonged healing periods and elevated healthcare expenditures. To address this challenge, we report here a drug-free novel guar gum (GG)-based nano-formulation which is effective against diabetic wound healing. Nanoparticles with an average particle size of 32.4 nm display stability with negative zeta potential. Differential scanning calorimetry (DSC) and Fourier transform infrared (FTIR) analysis reveal alterations in thermal properties and molecular structures induced by the nano-particulation process. In vitro studies highlight the antioxidant potential of GGNP through concentration-dependent free radical scavenging activity in DPPH and ABTS assays. The nanoformulation also exhibits inhibitory effects on α-glucosidase and α-amylase enzymes. Cell viability studies have indicated moderate cytotoxicity in L929 cells and significant proliferation and migration in HaCaT cells, suggesting a positive impact on skin cells. In vitro enzymatic activity assessments under hyperglycaemic conditions reveal the potential of GGNP to modulate glutathione-S-transferase (GST), superoxide dismutase (SOD), and catalase activities as well as decreasing lipid peroxidation (LPO) levels, showcasing an antioxidant response. These results suggest GGNP as a promising candidate in diabetic wound healing.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3330-3344"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142109623","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":"Ultrasound-Assisted Lipid Extraction from Chlorella sp.: Taguchi Design and Life Cycle Assessment.","authors":"Tam Minh Phan, Biet Van Huynh, Susilo Nur Aji Cokro Darsono, Thanh-Luu Pham, Ha Manh Bui","doi":"10.1007/s12033-023-00836-6","DOIUrl":"10.1007/s12033-023-00836-6","url":null,"abstract":"<p><p>The present study delved into the enhancement of essential oil (EO) extraction process from Chlorella sp. through the implementation of ultrasound-assisted extraction. The Taguchi method was instrumental in determining the ideal parameters for the extraction process, which encompassed ultrasonic amplitude, reaction duration, hexane/ethanol (HE/EtOH) ratio, and processing temperature. The empirical findings indicated that optimal EO yield was realized at an ultrasonic amplitude of 80%, a reaction timeframe of 15 min, a HE/EtOH proportion of 3:1, and a temperature setting of 40 °C. These optimal conditions were further substantiated through additional experimentation, resulting in an EO yield of 18.8 ± 0.2%. A fatty acid profile analysis disclosed that the extracted EO predominantly consisted of long-chain fatty acids (C14-C20), with Palmitic, Heptadecanoic, Oleic, and Linoleic acids featuring as the main components. Nevertheless, a high unsaturation rate of 37.9% in the EO could potentially render it vulnerable to oxidative deterioration during storage, consequently affecting the quality of the ensuing biodiesel. A life cycle assessment of the sonication technique utilized for biodiesel production from Chlorella sp. highlighted that lipid extraction was the principal contributor to global warming and ecotoxicity, as per the CML and TRACI methods. Hence, the ultrasound-assisted extraction of EO from Chlorella sp. appears to be a promising and ecologically viable substitute to conventional techniques employed for biodiesel production.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3097-3108"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9918680","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":"Water Quality Index Assessment of River Ganga at Haridwar Stretch Using Multivariate Statistical Technique.","authors":"Abdul Gani, Shray Pathak, Athar Hussain, Salman Ahmed, Rajesh Singh, Abhishek Khevariya, Abhishek Banerjee, Ramamoorthy Ayyamperumal, Ali Bahadur","doi":"10.1007/s12033-023-00864-2","DOIUrl":"10.1007/s12033-023-00864-2","url":null,"abstract":"<p><p>The Ganges (Ganga) river contributes significant water resources for the ecology and economy, but it frequently encounters severe deterioration due to cumulative impact from upstream natural and anthropogenic variables. Knowledge and understanding of the dynamic behavior of such networks remain a significant challenge, particularly in the context of rising environmental pressures, such as climate change and industrialization, as well as constraints in both process and data understanding across geographies. An interdisciplinary approach is required to be developed to investigate the hydrogeochemical dynamics and anthropogenic sources influencing water quality in major river systems. The present study has been carried out to evaluate the characterization of river water quality in terms of the physico-chemical & bacteriological parameters. Also, the development of a water quality index (WQI) for Domestic (drinking) and Spiritual (bathing) usage is a part of the study. The water quality index has been developed using the Canadian Council of Ministers of the Environmental Water Quality Index (CCME WQI). The river's water quality index score in the present study lies in the range of 38.32 to 79.82, indicating the quality of water from fair to poor for drinking purposes. The highest water quality index value of 79.82 has been observed at Guru Kashnik Ghat, while the lowest WQI value of 38.32 has been observed at Har ki Pauri for drinking purposes. However, the water quality score for bathing purposes ranged from 71.04 to 91.22 thus signifying the quality of the water from fair to good for bathing purposes. The highest water quality index value of 91.22 has been assessed at Guru Kashnik Ghat, while the lowest WQI value of 71.04 has been assessed at Bhimgoda Barrage. The developed water indices assessment in the present study will be beneficial for society to provide a benchmark for the control of water pollution in River Ganga. These findings will support policymakers and stakeholders in addressing water quality issues in a more efficient and effective manner. The study also emphasizes the requirement for ongoing water quality monitoring and evaluation in order to guarantee the long-term well-being of the river and its ecosystems.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3130-3153"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41138900","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":"Role of Small Non-Coding RNA in Gram-Negative Bacteria: New Insights and Comprehensive Review of Mechanisms, Functions, and Potential Applications.","authors":"Mansoor Khaledi, Mehrdad Khatami, Jaber Hemmati, Shahriar Bakhti, Seyedeh Asal Hoseini, Hossein Ghahramanpour","doi":"10.1007/s12033-024-01248-w","DOIUrl":"10.1007/s12033-024-01248-w","url":null,"abstract":"<p><p>Small non-coding RNAs (sRNAs) are a key part of gene expression regulation in bacteria. Many physiologic activities like adaptation to environmental stresses, antibiotic resistance, quorum sensing, and modulation of the host immune response are regulated directly or indirectly by sRNAs in Gram-negative bacteria. Therefore, sRNAs can be considered as potentially useful therapeutic options. They have opened promising perspectives in the field of diagnosis of pathogens and treatment of infections caused by antibiotic-resistant organisms. Identification of sRNAs can be executed by sequence and expression-based methods. Despite the valuable progress in the last two decades, and discovery of new sRNAs, their exact role in biological pathways especially in co-operation with other biomolecules involved in gene expression regulation such as RNA-binding proteins (RBPs), riboswitches, and other sRNAs needs further investigation. Although the numerous RNA databases are available, including 59 databases used by RNAcentral, there remains a significant gap in the absence of a comprehensive and professional database that categorizes experimentally validated sRNAs in Gram-negative pathogens. Here, we review the present knowledge about most recent and important sRNAs and their regulatory mechanism, strengths and weaknesses of current methods of sRNAs identification. Also, we try to demonstrate the potential applications and new insights of sRNAs for future studies.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"2978-2996"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141996150","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":"Anoikis-Related Genes Impact Prognosis and Tumor Microenvironment in Bladder Cancer.","authors":"Tao Zhang, Shaojun Chen, Shanna Qu, Longsheng Wang","doi":"10.1007/s12033-024-01255-x","DOIUrl":"10.1007/s12033-024-01255-x","url":null,"abstract":"<p><p>Anoikis tolerance is an important biological process of tumor colonization and metastasis outside the primary tumor. Recent research has progressively elucidated the function and underlying mechanisms of anoikis in the metastasis of various solid tumors. Nevertheless, the specific mechanisms of anoikis in bladder cancer and its consequent effects on the tumor immune microenvironment remain ambiguous. In this study, we developed an anoikis score based on five genes (ETV7, NGF, SCD, LAMC1, and CASP6) and categorized subjects into high and low-risk groups using the median score from the TCGA database. Our findings indicate that SCD enhances the proliferation of bladder cancer cells in vitro. Furthermore, integrating the anoikis score with clinicopathological features to construct a prognostic nomogram demonstrated precision in assessing patient outcomes. Immune cell analysis revealed elevated infiltration levels of Treg cells and M2 macrophages in the high anoikis score group, whereas CD8⁺ T cell levels were reduced. This study highlights the importance of anoikis score in predicting patient prognosis, immune cell infiltration, and drug response, which may provide a treatment modality worth exploring in depth for the study of bladder cancer.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3268-3280"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142018022","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}