Search Results (2,759)

Cyanobacteria are increasingly recognised as photosynthetic chassis for sustainable metabolic engineering because oxygenic photosynthesis generates ATP and NADPH via the photosynthetic electron transport chain, which drive CO₂ fixation through the Calvin–Benson–Bassham cycle into carbon intermediates that can be redirected toward engineered heterologous pathways. Their genetic tractability, CO₂-fixing capacity, ecological adaptability, and relatively simple cellular organisation make them attractive platforms for developing low-carbon biotechnological processes. This review explores recent progress in engineering cyanobacteria for heterologous pathway construction, critically evaluating genetic tools including transformation methods, genome integration strategies, promoter systems, and CRISPR-based editing, with specific emphasis on challenges of direct relevance to phototrophic chassis: host–pathway metabolic compatibility, precursor supply, cofactor balancing between photosynthetic output and heterologous pathway demand, and achieving genetic stability in polyploid cyanobacterial genomes. The review also addresses key limitations with mechanistic context: metabolic burden from multi-gene pathway expression reduces growth rate and selects against producing cells; polyploidy delays complete chromosomal segregation of engineered constructs; slow photoautotrophic growth constrains volumetric productivity; native regulatory networks resist carbon flux redirection; and cultivation constraints—including light attenuation in dense cultures and mismatches between photosynthetic ATP/NADPH supply and heterologous pathway demand—further limit achievable yields. Full article

Low-temperature-induced fertility restoration in thermo-sensitive genic male sterile (TGMS) lines severely impairs hybrid seed purity, which is a major bottleneck for two-line hybrid rice production. Most commercial TGMS lines rely on the single tms5 locus, leading to high climatic vulnerability. In this study, we developed a dual-locus strategy by target genome editing of TMS5 and MS1 in indica rice GH89. Adenine base editing at the MS1 locus exhibited a high editing efficiency of 93.5%. Transgene-free homozygous single mutants (GH89-tms5 and GH89-MS1) and double mutant (GH89-tms5 + MS1) were generated for phenotypic analysis. The double mutant GH89-tms5 + MS1 remained completely sterile for 5 and 10 days under controlled low temperature (23.5 °C), with only minimal fertility restoration after 15 days. In the field, it maintained complete sterility for 84 consecutive days and was fully insensitive to short-term low temperature fluctuations, outperforming single mutants and commercial control Y58S. Moreover, the double mutant retained most key yield-related agronomic traits of the wild type with only minor variations. This dual mutation forms a “double-lock” fertility regulatory system, significantly increasing the low-temperature duration threshold for fertility restoration. The GH89-tms5 + MS1 line exhibits promising potential for future rice breeding applications. Full article

Extreme climatic conditions often intensify abiotic stress factors (such as drought, salinity, heat stress, ultraviolet radiation, and soil degradation), and are increasingly limiting crop productivity and threatening global food security. Secondary metabolites (SMs), traditionally viewed as defense compounds, are now recognized as key regulators of plant adaptation to environmental stress. This review synthesizes recent advances in understanding the role of SMs as biochemical targets for improving crop resilience to climate extremes. By integrating evidence from multi-omics studies, artificial-intelligence-driven analyses, and functional genomics, we examine how stress-specific metabolic signatures and regulatory networks can be exploited for crop improvement. We further discuss the application of genome editing, synthetic biology, and metabolomics-assisted breeding to modulate the SM pathways to enhance stress tolerance. Selected case studies highlight the contribution of flavonoids, alkaloids, and terpenoids to stress adaptation in major and underutilized crops grown under salinity, drought, and low-temperature conditions. Despite significant progress, challenges remain, including metabolic trade-offs between stress tolerance and yield, regulatory constraints, and public acceptance of genetically engineered crops. By linking molecular mechanisms with applied strategies, this review provides a conceptual framework for leveraging secondary metabolism in climate-resilient agriculture and identifies key gaps to guide future research and innovation. Full article

Background/Objectives: Immune checkpoints are critical regulatory pathways that maintain peripheral tolerance and prevent autoimmunity. Among these, the programmed death-1/programmed death-ligand 1 (PD-1/PD-L1) axis serves as a major inhibitory pathway that terminates T cell responses. While protein-based checkpoint blockade (ICB) targeting this axis has revolutionized clinical cancer therapy, its clinical efficacy is frequently limited by low response rates, immune-related adverse events (irAEs), and the emergence of adaptive resistance. To break through these bottlenecks, genetic interruption has emerged as a high-precision alternative to modulate the PD-1/PD-L1 pathway at the nucleotide level. Methods: A comprehensive systematic review of literature was performed across major databases (PubMed, Web of Science), with a focus on high quality studies published up to 2026. Results: Direct genomic disruption via CRISPR/Cas9 and post-transcriptional silencing through RNA interference can effectively neutralize inhibitory signaling at its source. Recent advances demonstrate that targeting upstream regulatory nodes—including metabolic checkpoints (e.g., lactate metabolism) and biophysical mechanisms (e.g., liquid–liquid phase separation)—provides superior transcriptional control over PD-L1. Furthermore, engineering CAR-T cells with multiplex gene editing (e.g., TCR/B2M/PD-1 knockout) or localized scFv secretion significantly enhances antitumor potency while reducing systemic toxicity. Innovations in organ-targeted lipid nanoparticles and stimuli-responsive biomimetic carriers further address the delivery barriers in solid tumors. Conclusions: Gene therapy provides a high-precision platform for PD-1/PD-L1 modulation, offering a viable strategy to overcome adaptive resistance. Future clinical application depends on the refinement of safer editing tools, such as base editing, and the standardization of intelligent delivery systems to ensure controllable and scalable cancer immunotherapy. Full article

Mitochondrial DNA (mtDNA) mutations are associated with a diverse spectrum of diseases and pose a significant threat to human health. Despite their importance as therapeutic targets, the unique structural and electrochemical properties of mitochondria—most notably the impermeable inner mitochondrial membrane and the high membrane potential—present formidable challenges for the targeted delivery of therapeutic agents. Currently, there are no approved curative treatments for patients harboring pathogenic mtDNA mutations. In this review, we discuss recent advancements in gene therapy for mitochondrial genome-related disorders, with a particular focus on allotopic expression of mtDNA-encoded genes and mitochondrial genome editing technologies. We conclude that allotopic expression currently stands as the most promising approach for near-term clinical implementation. But we also pay great attention to programmable nucleases and base editors utilizing RNA-independent DNA recognition which are evolving with remarkable speed. Full article

The discovery of various CRISPR–Cas systems has revolutionized genome engineering by enabling precise and programmable nucleic acid targeting. Continued exploration of CRISPR diversity, together with advances in computational modeling and deep learning (DL)-based design, has expanded the potential to manipulate nearly any genomic locus, thereby accelerating both basic research and therapeutic applications. This review systematically provides a structured and up-to-date overview of CRISPR–Cas technologies, including their classification, computational modeling strategies, and the integration of machine learning (ML) and DL approaches to predict guide RNA (gRNA) efficiency and specificity. The emphasis is placed on studies published between 2019 and 2025, which highlight significant progress in modeling Cas–gRNA–DNA interactions, optimizing on/off-target prediction, and developing comprehensive CRISPR-related datasets. By synthesizing recent developments in CRISPR biology, computational simulations, and artificial intelligence, this review underscores the importance of interdisciplinary integration to improve the accuracy, safety, and scalability of next-generation genome-editing systems. Full article

While the cerebellar dopaminergic system is suggested to be implicated in neurodevelopmental disorders, especially autism spectrum disorder (ASD), the details of its disturbances remain unclear. We performed a comparative analysis of human (GTEx) and mouse (GSE144046, GSE144277) transcriptomes, complemented by RT-qPCR in DAT-KO rats, to identify dopaminergic gene associations in the normal cerebellum and neurodevelopmental disorder models. Pairwise dopaminergic gene correlations were generally weak, with a slight increase in interaction complexity in ASD models. However, weighted gene co-expression network analysis identified a robust gene module involving Comt, which was consistently associated with synaptic translation across mouse datasets. These associations reflect regulatory processes in the whole cerebellum, which is commonly represented in rodent studies but absent in human data, which are acquired in studies of cerebellar subregions. ASD modeling exerted contrasting effects: Cul3 haploinsufficiency increased the number of genes involved in the module with a decrease in connectivity, while Mbd5 haploinsufficiency led to module collapse. These findings confirm neurodevelopmental disorders as a heterogeneous condition where divergent backgrounds uniquely rewire cerebellar dopaminergic networks. Considering the cerebellum’s role in ASD and that some ASD medications target the dopamine system, further investigation of these identified trends may support the development of more personalized therapeutic approaches. Full article

Fish represent the most species-rich group within the phylum Chordata, possessing exceptional nutritional and ornamental value. Global aquaculture, particularly finfish farming, is experiencing rapid expansion worldwide, and fish serve as crucial model organisms for vertebrate developmental biology and functional genomics research. However, traditional breeding methods are plagued by limitations such as low precision and lengthy breeding cycles. Currently, gene editing technologies represented by the CRISPR/Cas system, base editing, and prime editing have provided revolutionary tools for dissecting gene function, modeling human diseases, targeted trait improvement, and ecological adaptation studies. This review describes the evolutionary history of gene editing technology, compares gene delivery strategies in fish embryos, and highlights landmark applications in key areas, including gene function research, aquaculture breeding, ornamental fish coloration regulation, and human disease model construction. Finally, we propose that innovation should be pursued while ensuring biosafety and regulatory compliance, to promote the transformation of fish gene editing toward large-scale and safe application. Full article

Tomato (Solanum lycopersicum L.) is a globally important vegetable crop and a major dietary source of bioactive compounds, including lycopene, ascorbic acid, phenolics, and minerals. Modern tomato breeding has substantially improved yield, uniformity, and postharvest performance; however, these gains have often been accompanied by reduced flavor quality, lower nutritional value, and narrowing of the genetic base. This review synthesizes available evidence on Lithuanian tomato germplasm and evaluates its relevance for future breeding strategies aimed at enhancing genetic gain under Northern European conditions. The review integrates published data on genetic diversity, molecular characterization, morphological traits, fruit quality parameters, and yield performance of Lithuanian cultivars and hybrids developed in Lithuania. SSR-based studies indicate moderate genetic diversity, with mean expected heterozygosity of approximately 0.51 and mean PIC values of 0.47 in cultivars and 0.45 in hybrids, while also confirming a relatively narrow breeding pool. Lithuanian cultivars display substantial variation in fruit morphology, dry matter, soluble solids, firmness, lycopene, ascorbic acid, and yield. Traditional cultivars such as ‘Svara’, ‘Milžinai’, ‘Slapukai’, and ‘Balčiai’ show valuable nutritional and technological traits, whereas hybrids such as ‘Auksiai H’, ‘Adas H’, and ‘Ainiai H’ demonstrate improved productivity and firmness. The available evidence suggests persistent yield–quality trade-offs, particularly between productivity, soluble solids content, antioxidant accumulation, and postharvest performance. Although Lithuanian germplasm does not represent exceptionally broad genetic diversity, it contains regionally adapted material with stabilized trait combinations useful for breeding resilience, nutritional quality, and adaptation to temperate environments. Future progress will require broadening the genetic base and integrating traditional breeding with marker-assisted selection, genomic selection, GWAS, genome editing, multi-omics, and pangenomic approaches. Overall, Lithuanian tomato germplasm represents a locally adapted regional resource for translating genetic diversity into genetic gain in modern tomato breeding. Full article

Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn’s disease (CD), is a chronic relapsing inflammatory disorder characterized by epithelial barrier dysfunction, immune dysregulation, microbiota imbalance, and progressive tissue remodeling. Because the pathogenesis of IBD involves complex interactions among genetic, immunological, microbial, and environmental factors, experimental animal models have become indispensable tools for investigating disease mechanisms and evaluating therapeutic strategies. Various experimental colitis models have been developed to reproduce distinct pathological features of human IBD, including chemically induced models, genetically engineered systems, adoptive immune-transfer models, and infectious or microbiota-associated models. Rodent models remain the most widely used experimental platforms because of their accessibility, reproducibility, and well-established genetic manipulation technologies. These systems have significantly contributed to understanding inflammatory signaling pathways, epithelial barrier injury, immune cell dysregulation, and gut microbial crosstalk. However, important species-specific differences in intestinal anatomy, immune responses, microbiota composition, and pharmacokinetics limit direct translation of rodent findings into clinical applications. To overcome these limitations, increasing attention has been directed toward large-animal models, particularly pig and minipig systems, which more closely resemble human gastrointestinal anatomy, digestive physiology, immune regulation, and microbiome-related characteristics. Porcine models additionally support clinically relevant procedures, including repeated colonoscopy, serial biopsy sampling, pharmacokinetic evaluation, and longitudinal therapeutic monitoring. Recent advances in genome-editing technologies and multi-omics approaches have further enhanced the translational utility of porcine IBD models. This review summarizes major experimental colitis animal models, discusses their pathological and translational characteristics, and highlights the growing importance of pig and minipig systems as human-applicable platforms for preclinical therapeutic evaluation and translational IBD research. Full article

Tomato (Solanum lycopersicum) is a globally important horticultural crop, with Asia contributing 60.45% of total production, followed by the Americas at 13.36%. Tomato productivity is increasingly constrained by southern blight, a destructive disease responsible for yield losses ranging from 30 to 90% and annual economic damage of $10–20 million. The causal pathogen, Sclerotium rolfsii, infects the stem base and induces reddish-brown cankers through secretion of oxalic acid (OA) and cell wall-degrading enzymes, which girdle tissues, impair water transport, and result in rapid plant wilting and death. Its persistence in soil via sclerotia, broad host range, and adaptability make the disease difficult to manage. Recent advances in genomics, transcriptomics, proteomics and other multi-omics approaches have substantially improved understanding of pathogen virulence factors, host defense responses and disease epidemiology. These studies have revealed key roles of OA, carbohydrate-active enzymes, effector proteins, and sclerotial melanization in pathogenesis, while highlighting the activation of salicylic acid (SA)-, jasmonic acid (JA)-, and ethylene (ET)-mediated defense pathways in tomato. Although cultural, biological, and chemical measures are available, these measures often provide inconsistent protection when used alone. Promising strategies include the use of biocontrol agents, hypovirulence-inducing mycoviruses, and chemical fungicides such as carboxamides and quinone outside inhibitors (QoIs), though fungicide resistance remains a risk factor. Integrated Disease Management (IDM) approaches, such as combining biocontrol agents with fungicides, demonstrate enhanced efficacy. This review also evaluates progress in resistance breeding, grafting, RNA interference (HIGS and SIGS), CRISPR-based genome editing, and exploitation of wild genotypes for durable resistance. Furthermore, emerging precision agriculture tools, including hyperspectral imaging, machine learning-assisted disease detection and climate-resilient management strategies, were discussed as new components of sustainable disease management. Full article

Global food production systems are increasingly challenged by population growth, climate change, water scarcity, and environmental degradation, necessitating the adoption of sustainable, resource-efficient food production strategies. Aquaponic systems integrate recirculating aquaculture with hydroponic crop cultivation, enabling nutrient recycling and improved water-use efficiency. Simultaneously, CRISPR/Cas9 genome-editing technology has emerged as a powerful tool for precise genetic improvement of economically important aquaculture traits. This review critically evaluates current progress in CRISPR/Cas9 applications in aquaculture, with emphasis on Nile tilapia (Oreochromis niloticus). Evidence from peer-reviewed studies indicates that targeted modification of genes associated with growth regulation, disease resistance, nutrient metabolism, feed efficiency, and stress tolerance can significantly enhance fish productivity and physiological resilience. Genes involved in hypoxia adaptation and nitrogen metabolism may further improve environmental performance in intensive recirculating systems by reducing ammonia accumulation and enhancing nutrient utilization. However, most genome-editing studies have been conducted under laboratory or conventional aquaculture conditions, with limited information available regarding the long-term performance, ecological interactions, microbial dynamics, and biosafety of genome-edited fish in aquaponic environments. Technical limitations including off-target effects, mosaicism, delivery efficiency, regulatory uncertainty, and public acceptance continue to constrain large-scale implementation. In the short term, CRISPR/Cas9 applications are likely to focus on practical trait enhancement under controlled aquaculture systems, whereas longer-term research may explore fish lines specifically optimized for nutrient cycling, environmental resilience, and integrated aquaponic sustainability. Overall, CRISPR/Cas9-mediated genome editing represents a promising but still emerging strategy for improving sustainable aquaculture and aquaponic food production systems. Full article

Corydalis ophiocarpa is a medicinally valuable plant, noted for its abundant alkaloid content. Despite its significance, the mitochondrial (mt) genome of this plant has not been characterized, which impedes both the phylogenetic understanding within the Corydalis genus and the comprehension of its full genetic potential. In this research, we successfully assembled the complete mitogenome of C. ophiocarpa by employing a hybrid method that integrates Oxford Nanopore long reads with Illumina short reads. The assembled genome forms a circular structure of 600,064 bp, with a GC content of 46.49%, and includes 63 genes, comprising 40 unique protein-coding genes (PCGs), 20 tRNAs, and three rRNAs. Through assembly and coverage analysis, we identified a 6383 bp forward repeat associated with a contig having approximately double the depth, indicating a repeat-mediated multipartite structure where the main circle may coexist with two smaller subgenomic forms. We discovered 775 C-to-U RNA editing sites across the 40 PCGs, with 95.4% being non-synonymous and favoring hydrophobic amino acid substitutions, particularly in Complex I subunits. Furthermore, we identified sixteen mt plastid DNA fragments constituting 2.43% of the mitogenome, a proportion more than double that found in the closely related C. saxicola. Phylogenetic analysis confirms that C. ophiocarpa is most closely related to C. saxicola, with C. pauciovulata as another close relative. This study presents the first complete mitogenome of C. ophiocarpa, providing a genomic basis for investigating the relationships between mt genome structure, post-transcriptional regulation, and specialized metabolism in the Corydalis genus. Full article

The lamin proteins are classified into A- and B-types, and together with their associated proteins, they form the nuclear lamina, which governs diverse nuclear structures and functions, including nuclear mechanics, chromatin organization, and gene regulation. Mutations of these proteins give rise to a strikingly diverse group of tissue-specific disorders, the laminopathies, including muscular dystrophies, cardiomyopathies, lipodystrophies, neuropathies, and premature aging syndromes, despite their broad expression. Unraveling the basis of this tissue selectivity has revealed that lamins function not merely as structural elements but as active regulators. While the A-type lamins modulate nuclear stiffness, transcription, and genome integrity, the B-type lamins ensure mechanical resilience and heterochromatin tethering. Pathogenic mutations of these proteins disrupt their functions through convergent mechanisms that manifest according to tissue-specific contexts, leading to impaired nuclear mechanics, aberrant gene regulation, defective DNA repair, and cellular senescence. Advances in patient-derived cellular models and animal systems have illuminated these vulnerabilities and catalyzed therapeutic progress, ranging from farnesyltransferase inhibitors to emerging genome-editing strategies. Collectively, studies of lamin protein function reveal how the nucleus maintains its structures and functions, while studies of laminopathies demonstrate how nuclear dysfunction drives systemic disease and points toward mechanism-based therapies. Full article