Search Results (368)

Antirestriction proteins protect mobile genetic elements from the host’s restriction-modification systems. Here, we investigated the ability of ArdA and ArdB antirestriction proteins to regulate gene expression in an engineered E. coli K-12 MG1655-based biosensor strain. This biosensor strain harbors a lux-based reporter system controlled by the AllR-repressed promoter. Although structurally similar, DNA-mimic ArdA proteins interact with AllR differently. Recently described small sArdC and well-known ArdA from the conjugative plasmid R64 appear to bind AllR and open the promoter, while the other tested antirestriction proteins (small sArdN protein and various full-sized ArdA proteins from different sources) have no effect on gene expression under AllR-controlled promoter. Direct binding between ArdA and AllR was experimentally confirmed using pull-down assays with His-tagged ArdA. Our study opens up prospects for the specific use of antirestriction proteins for the regulation of gene expression. Surprisingly, ArdB, a non-DNA-mimic antirestriction protein used initially as a control, was also able to open the promoter, apparently through nonspecific interaction with DNA. We verified this effect with a distant ArdB homolog from a rhizobacterium, which was also able to open the promoter. Full article

Chimeric antigen receptor (CAR)-T cell therapy has achieved remarkable success in hematologic malignancies, and its development is being actively pursued across a broad range of cancer types. However, current CAR-T cell therapies rely on ex vivo engineering, which presents significant logistical, temporal, and biological limitations. In vivo CAR-T cell engineering is emerging as a new paradigm that may overcome these challenges by enabling the direct reprogramming of immune cells within the patient through the administration of CAR-encoding vectors. This approach represents an off-the-shelf form of autologous immune therapy. Advances in viral engineering and nanotechnology have enabled the development of diverse CAR delivery platforms that not only deliver CAR constructs but also facilitate the delivery of gene-editing components, such as Cas9, allowing for more sophisticated in vivo genetic modifications. Some of these approaches have already entered clinical evaluation and have shown promising early results in hematologic malignancies, with clinical trials in solid tumors now underway. However, the application of in vivo-engineered CAR-T cell therapies to malignant glioma remains largely unexplored, reflecting challenges distinct from those encountered in hematologic malignancies. In this review, we discuss these challenges and potential strategies to address them, while highlighting recent progress in in vivo CAR-T cell engineering. Full article

Exosomes are small vesicles released by cells that have attracted growing interest as drug delivery vehicles, particularly for brain diseases, where getting therapeutics across the BBB remains a fundamental problem. While conventional platforms such as liposomes, polymeric nanoparticles, and viral vectors often suffer from immune clearance and poor brain accumulation, engineered exosomes leverage natural cellular transport mechanisms to cross the BBB, protect cargo from degradation, and enable biocompatible interactions with target cells. This review takes a mechanistic and translational look at how exosomes are being engineered for CNS disorders, with a particular focus on glioblastoma. We cover exosome biogenesis through ESCRT-dependent and ESCRT-independent pathways, and how the competition between Rab27-driven secretion and Rab7-driven lysosomal degradation determines how many exosomes a cell releases, which has direct consequences for therapeutic production. We then discuss cargo loading strategies, from genetic approaches where donor cells are engineered to package specific molecules during biogenesis to physical methods like electroporation and sonication applied to isolated vesicles, alongside surface modification techniques for directing exosomes toward specific cell types. In glioblastoma, engineered exosomes have shown real promise for delivering chemotherapeutics across the BBB, targeting glioma stem cells, enabling CRISPR-based gene editing, and functioning as combined treatment and imaging tools. Applications in stroke and neurodegenerative diseases, where engineered exosomes carrying microRNAs and neuroprotective cargo have produced encouraging preclinical results, are also discussed. Scalable manufacturing and consistent targeting remain the hardest unsolved problems, and we outline emerging approaches including bioreactor-based production, programmable cargo loading, and patient-specific exosome design that are beginning to address these gaps. Overall, the progress reviewed here suggests that engineered exosomes are moving from an interesting biological concept toward a practically viable platform for CNS drug delivery. Full article

Extracellular vesicles (EVs), naturally secreted by cells as nanoscale lipid bilayer structures, have become a research hotspot in biomedicine owing to their excellent biocompatibility, low immunogenicity, and inherent ability to cross biological barriers. This review systematically summarizes recent advances in EVs as natural nanomaterials. The biogenesis mechanisms of EVs are outlined, followed by a comparative analysis of the advantages and limitations of mainstream isolation and purification methods, including ultracentrifugation, size-exclusion chromatography, and microfluidic technologies. The core guiding role of the MISEV 2023 guidelines in standardizing EV characterization is highlighted. Engineering strategies to enhance EV therapeutic efficacy—including parental cell modification, post-isolation physicochemical tailoring, and hybrid vesicle construction—are then reviewed, followed by a comparative analysis of mainstream isolation technologies, emphasizing the trade-offs between purity and yield. Distinct from conventional descriptive reviews, this article establishes a strong biomimetic framework to scrutinize engineering strategies, including parental cell genetic modification, post-isolation physicochemical tailoring, and the fabrication of hybrid bio-synthetic vesicles. The design principles governing targeted delivery, drug-loading physics, and in vivo pharmacokinetic stability are critically evaluated through the lens of biomimetic nanotechnology. Furthermore, we identify critical research gaps and technical bottlenecks impeding clinical translation, offering a forward-looking perspective on the evolution of EVs from natural messengers into standardized precision medicine platforms. Full article

Bacterial outer membrane vesicles (OMVs) are spherical structures made up of a double layer, they are each nanostructured (20–300 nm), and they are released from all populations of Gram-negative bacteria. The purpose of this review is to synthesize a comprehensive summary of the current state of knowledge about OMV biogenesis, function in biology, and application to biomedical engineering. Using these three known biogenesis mechanisms as a basis for this review, we discuss the mechanisms of OMV biogenesis that have been described as conserved: (1) disruption of outer membrane–peptidoglycan links. (2) periplasmic stress-driven adaptive release is associated with bilayer lipid asymmetry and the use of signaling molecules. OMVs are considered to be “public goods” for the microbe, allowing for nutrient acquisition, resistance to antibiotics, and the potential for horizontal gene transfer between microbes. OMVs exhibit a different duality at the interface of the pathogen host, where the pathogenic OMV is the delivery vehicle for virulence factors and pathogen-associated molecular patterns (PAMPs) leading to host immune response, while the symbiotic OMV (e.g., those produced by Bacteroides fragilis (Bact. fragilis)) promote regulatory T cell differentiation and mucosal tolerance. The review also addresses the various techniques currently available to isolate OMVs (e.g., ultracentrifugation and size-exclusion chromatographic techniques) and presents engineered/alloying strategies (e.g., genetic modifications to tolR/msbB and surface functionalization) to enhance the viability, safety, and specificity of OMVs for biomedical delivery. Finally, the review addresses significant obstacles related to standardization, batch variation, and in vivo safety associated with synthetic or personalized therapeutics based on OMVs, providing some recommendations for future research in this area. Full article

Perilla frutescens (L.) Britt., a medicinal and edible herb, is valued for its diverse leaf coloration, attributed to varying levels of anthocyanin accumulation. The primary anthocyanins in P. frutescens are acylated cyanidin glycosides; however, the enzymes facilitating the acylation process have yet to be characterized. BAHD acyltransferases, known to catalyze such modifications, remain uncharacterized in P. frutescens. To systematically identify potential genes that may be associated with this function, we performed a comprehensive genome-wide analysis of the BAHD acyltransferase family in P. frutescens. Our study identified 134 PfBAHD genes, which were subsequently analyzed for their physicochemical properties, phylogenetic relationships, conserved domains, motif compositions, and promoter cis-elements. Phylogenetic analysis categorized the PfBAHD genes into six clades, with Clade I being the primary candidate for anthocyanin-related activity due to its enrichment with members known to acylate flavonoids in other species. Promoter analysis indicated a significant presence of cis-elements associated with light, phytohormones, and stress responses. By integrating tissue-specific metabolomic and transcriptomic data, we established correlations between anthocyanin accumulation patterns and PfBAHD gene expression. Through the integration of multi-omics data, six candidate genes were prioritized, with PfBAHD05, PfBAHD77, and PfBAHD112 emerging as the most promising candidates. These genes demonstrated predominant expression in leaves, were induced under conditions of high light exposure, and were predicted to be localized in the cytoplasm. To further explore their potential functions, molecular docking analyses were conducted, suggesting that PfBAHD77 may have a preference for highly glycosylated anthocyanins, whereas PfBAHD05 and PfBAHD112 may favor substrates with lower levels of glycosylation. Collectively, these findings provide a preliminary foundation for understanding anthocyanin acylation in P. frutescens and identify several BAHD candidate genes that could be potentially targeted in future metabolic engineering efforts pending further biochemical and genetic validation. Full article

Plant diseases remain a major constraint to crop productivity and global food security. Conventional breeding has long been used to develop resistant cultivars through the introgression of resistance traits from wild relatives and the selection of favorable phenotypes. However, this process is often slow and limited by linkage drag, known genetic diversity, intrinsic genetic limitations, and the rapid evolution of pathogen populations. Molecular breeding strategies, including marker-assisted selection and genomic selection, have improved the precision of resistance breeding but still rely on existing genetic variation. Recent advances in genome editing technologies are transforming plant breeding by enabling precise modification of gene targets. CRISPR-based systems allow targeted gene knockouts, promoter editing, allelic replacement, and multiplex editing to rapidly generate resistance traits. Many studies have demonstrated that editing susceptibility genes or regulatory regions can enhance resistance to diverse pathogens. Recent research shows that resistance can also be improved by targeting non-classical genes involved in plant immunity, including transcription factors, membrane transporters, heat shock proteins, cell wall-related genes, metabolic enzymes, and epigenetic regulators. Emerging tools such as base editing, prime editing, regulatory tools, and transposon-associated genome engineering systems are further expanding the precision and versatility of plant genome editing. Despite these advances, challenges related to delivery systems, editing efficiency, regulatory frameworks, and field validation remain. Continued technological progress and improved knowledge of plant immune networks will be essential to fully integrate genome editing into crop improvement programs. Full article

As food demand increases, agricultural practices have evolved, prompting increased exploration of sustainable ecological techniques and utilization of plant-associated microorganisms. In this context, plant fitness has been enhanced by plant growth-promoting microorganisms (PGPM), which stimulate growth through direct mechanisms, such as improved nutrient availability and phytohormone production, as well as indirect mechanisms, including protection against phytopathogens and suppression of soil-borne diseases. However, these innate capabilities of PGPM can be further improved through genomic modification or editing. This article reviews advances in the genomic engineering of plant-beneficial microorganisms as tools to enhance their positive effects on crop performance and environmental remediation. The genetic modification strategies analyzed here include random mutagenesis, targeted genome editing (such as CRISPR-Cas), gene over-expression, genome shuffling, RNA interference, metabolic pathway engineering, and synthetic biology approaches. These tools have enabled the optimization of functions, such as nitrogen fixation, phosphate solubilization, secondary metabolite production, biocontrol, stress tolerance, and bioremediation. However, we propose expanding the discussion of their regulation and use in various countries. Additionally, these modifications must be efficient and safe for the beneficial microbiota associated with the target crop, as well as for humans, animals, and the environment, all of which depend on sustainable agricultural practices. Full article

This review summarizes mechanisms regulating mRNA translation under cellular stress and highlights design strategies to improve translation efficiency and stability in the gene therapy of human diseases. mRNA-based therapeutics are emerging as a versatile gene therapy platform enabling transient and controllable expression of therapeutic proteins for the treatment of cancer, genetic disorders, and inflammatory diseases. The efficacy of mRNA-based gene therapy is strongly influenced by sequence design, chemical modifications, and structural features. Evidence shows that rational mRNA engineering can significantly enhance translation efficiency even under stress conditions that impair canonical protein synthesis, as observed in many pathological states. Cellular stress activates regulatory pathways that suppress global translation; however, optimized mRNA constructs can partially bypass these inhibitory mechanisms, enabling sustained protein expression. By improving mRNA stability and resistance to stress-responsive translational control, robust therapeutic protein production can be achieved even in challenging cellular environments. This article was prepared as a narrative review focused on translational regulation mechanisms relevant to therapeutic mRNA design under cellular stress conditions. Literature was collected from PubMed, Google Scholar, and Web of Science using keywords including “mRNA therapeutics,” “cellular stress,” “translation regulation,” “UTR engineering,” and “cap-independent translation.” Studies published mainly between 2010 and 2025 were considered. Original articles and reviews related to stress-responsive translation and therapeutic mRNA optimization were included, while studies outside the scope of translational control and mRNA engineering were excluded. Priority was given to recent and mechanistically relevant publications. Full article

Cell-based immunotherapies require noninvasive tools that can quantify the migration, biodistribution, and persistence of administered immune cells. This review focuses primarily on oncologic immune cell therapy, while also considering selected inflammatory disease models in which immune-cell trafficking is biologically relevant. We critically compare direct radionuclide labeling, sodium iodide symporter (NIS)-based reporter gene imaging, radionuclide-integrated nanoplatforms, and Cerenkov-based hybrid optical conversion strategies. Direct labeling with agents such as [⁸⁹Zr]Zr-oxine, [¹¹¹In]In-oxine, and [⁹⁹ᵐTc]Tc-HMPAO enables early positron emission tomography (PET)/single-photon emission computed tomography (SPECT) biodistribution assessment, usually within hours to several days after cell administration. NIS reporter imaging with [¹²⁴I]NaI, [¹²³I]NaI, [⁹⁹ᵐTc]TcO₄⁻, or [¹⁸F]TFB supports repeated viability-dependent imaging, because signal generation depends on active transporter expression in living engineered cells. Radionuclide-integrated gold nanoplatforms can improve intracellular retention and offer theranostic potential through combined imaging, photothermal, radiotherapeutic, or immunomodulatory functions. We further discuss PET/SPECT balance, radiopharmaceutical nomenclature, nanoparticle stabilization, ethical aspects of genetic modification, tumor-on-a-chip systems for preclinical testing, and limitations of narrative evidence synthesis. Together, these platforms provide complementary strategies for image-guided immune cell therapy, with translational relevance for patient selection, treatment optimization, safety monitoring, and oncology practice. In conclusion, NIS-centered nuclear imaging and radionuclide-integrated nanoplatforms represent complementary, clinically actionable tools for quantitative immune-cell tracking, therapeutic optimization, and safety monitoring in translational oncology and inflammatory disease research. Full article

Primary biliary cholangitis (PBC) is an autoimmune-mediated cholestatic liver disease characterized by the progressive destruction of intrahepatic bile ducts, which ultimately leads to hepatic fibrosis and cirrhosis. The current first-line therapy, ursodeoxycholic acid, is associated with a high rate of non-response. Moreover, second-line treatments are constrained by variable efficacy and safety concerns. Mesenchymal stem cells (MSCs), owing to their potent immunomodulatory and tissue-repairing capabilities, represent a promising new therapeutic strategy for PBC patients with poor response to conventional therapies. This review systematically outlines the pathogenesis of PBC, focusing on factors including genetics, environment, and immune dysregulation. Furthermore, it examines recent evidence on the mechanisms by which MSCs and their derivatives, such as exosomes, may intervene in PBC progression through immunomodulation, anti-fibrotic effects, and potential hepatic differentiation. This paper also reviews the current status and challenges of the clinical translation of MSCs therapy, and proposes that engineered modification and standardized preparation are the key directions to promote its application. In conclusion, this review provides a theoretical foundation and future directions for deepening the understanding of PBC pathogenesis and developing novel MSC-based therapeutic strategies. Full article

Chronic cutaneous wounds and traumatic skin injuries remain a major clinical challenge, characterized by dysregulated healing phases, high susceptibility to microbial infection, and suboptimal response to conventional therapies. Stem cell-derived exosomes (SC-Exos) have emerged as a paradigm-shifting, cell-free nanotherapeutic platform that harnesses the paracrine secretome of stem cells while avoiding the immunological and proliferative complications inherent to direct cell transplantation. Exosomes derived from diverse stem cell sources orchestrate multifactorial wound repair by modulating key cellular signaling cascades and transcriptomic programs that collectively regulate inflammation, angiogenesis, re-epithelialization, extracellular matrix (ECM) remodeling, and scar formation. Beyond their intrinsic regenerative capacity, SC Exos can be engineered using direct strategies (cargo loading, surface modification, biomaterial integration, and conjugation) and indirect approaches (genetic engineering, pretreatment, and preconditioning of parental cells), thereby enabling spatially controlled and temporally sustained exosome release at wound sites with enhanced bioavailability and therapeutic efficacy. In parallel, biomaterial-assisted delivery platforms, including hydrogels, scaffolds, and nanofibers, enhance exosome retention, stability, and controlled-release profiles within the wound microenvironment, thereby further potentiating tissue repair. This review provides a comprehensive overview of recent advances in SC Exos for wound healing and skin regeneration. We first summarize exosome biogenesis, molecular composition, and the distinctive characteristics of exosomes derived from different stem cell sources, along with preclinical evidence supporting their efficacy in cutaneous repair. We then critically examine exosome engineering strategies and biomaterial-integrated delivery systems that augment and fine-tune therapeutic outcomes. Finally, we discuss the current status of clinical trials of SC Exo-based therapies, key manufacturing and regulatory challenges, and future directions for translating these nanoscale, cell-free therapeutics into advanced, personalized wound management. Full article

Medicinal plants have long served as a primary source of bioactive compounds with essential therapeutic applications. Recent advances in functional genomics and plant biotechnology now enable precise manipulation of metabolic pathways to enhance the production of specialized metabolites with medicinal value. However, an integrative understanding of how genomic discovery can be linked with pathway engineering, scalable production systems, and healthcare applications remains insufficiently developed. This knowledge gap limits the effective translation of molecular insights into the sustainable production of medicinally important compounds. The novelty of this review lies in its integrated framework linking functional genomic discovery with pathway engineering, synthetic biology, artificial intelligence-assisted prediction, and scalable production systems for medicinal plant-derived therapeutics. This review aims to provide a comprehensive overview of cutting-edge approaches in medicinal plant research, emphasizing high-throughput RNA sequencing, CRISPR/Cas9 gene editing, synthetic biology, and metabolic engineering for optimizing the production of key bioactive compounds, including artemisinin, cannabinoids, ginsenosides, and taxol. It further examines how these tools collectively support metabolite discovery, pathway elucidation, yield improvement, and biotechnological production in major medicinal plant systems. We explore the application of genomic and biotechnological approaches in plants such as Artemisia annua, Cannabis sativa, Panax ginseng, and Taxus baccata to enhance metabolite yields and promote sustainable production. The review highlights case studies that demonstrate how genetic modification, metabolic engineering, and synthetic pathway design have been successfully employed to increase the synthesis of key medicinal compounds. Moreover, we discuss the integration of artificial intelligence and machine learning to predict gene–metabolite relationships, support personalized phytochemical therapies, and facilitate sustainable, large-scale production. Finally, the review addresses the implications of these innovations for the pharmaceutical industry, healthcare, and agriculture, while also highlighting sustainable and scalable directions for future medicinal plant biotechnology. Full article

Aiming to reduce synthetic fertilizer dependence and enhance soil fertility, this study isolated and characterized nitrogen-fixing bacteria from the maize rhizosphere. Nitrogen-free selective media were used for bacterial isolation, followed by detection of the nifH gene and nitrogenase activity. Phylogenetic identification was conducted via 16S rRNA sequencing. Growth-promoting traits, stress tolerance, and pot-based plant inoculation effects were assessed. Genetic modification of strain GN8811 was performed to improve nitrogen fixation and growth promotion. Seven isolates that carried the nifH gene and exhibited nitrogenase activity were closely related to four genera. Several isolates showed phosphate solubilization, iron chelation, IAA production, or potassium solubilization, with GN2003 and GN8811 tolerating high salinity and variable pH. Inoculation with GN8811 promoted maize growth comparable to nitrogen fertilization, and its genetically modified derivative (ΔnifL:PrpoD) showed further improvement even under high nitrogen conditions. These findings highlight the potential of combining microbial screening with genetic engineering to develop efficient bioinoculants for sustainable maize cultivation. Full article

The CRISPR-Cas systems, identified initially as adaptive immune mechanisms in bacteria and archaea against viral threats, have rapidly evolved into transformative tools in genetic engineering and biotechnology. These RNA-guided systems are broadly classified into Class 1, comprising multi-subunit complexes, and Class 2, characterized by compact single-effector protein, such as Cas9, Cas12, and Cas13. Their remarkable structural and functional diversity enables microorganisms to adapt to diverse ecological niches, offering a vast repertoire of genome-editing strategies. Beyond their natural role in maintaining genome integrity and defense, CRISPR-Cas systems have been extensively repurposed for precise genome modification, transcriptional regulation, epigenetic editing, and nucleic acid detection. Recent advances in computational mining of microbial genomes and metagenomes have uncovered a broad range of novel CRISPR effectors with unique properties, distinct protospacer adjacent motif (PAM) requirements, RNA-targeting capabilities, miniature architectures, and promiscuous cleavage activities that significantly expand the molecular biology toolkit. The development of CRISPR-based technologies such as base editing, prime editing, gene knock-in/out, and live-cell DNA/RNA imaging exemplifies the versatility of these systems. Despite the challenges associated with delivering complex Class 1 systems, both classes are now being actively harnessed across diverse microbial platforms. Concurrently, the CRISPR-Cas research, particularly for guide RNA (gRNA) design and activity prediction, has revolutionized target specificity and editing efficiency. This review presents a comprehensive overview of CRISPR-Cas system diversity, their genomic landscape in microorganisms, and their cutting-edge biotechnological applications. It also emphasizes the transformative potential of CRISPR in synthetic biology, therapeutics, diagnostics, environmental remediation, and agriculture, while also addressing the ethical and biosafety considerations surrounding its deployment. As CRISPR-Cas systems continue to evolve, they stand at the forefront of innovations that bridge natural microbial immunity with engineered precision tools for next-generation biotechnology. Full article