Search Results (4,377)

Fruit anthocyanins are primary determinants of color, sensory quality, and nutritional value in grapes; however, their endogenous biosynthesis is governed by complex interactions among genetic, environmental, agronomic, and postharvest factors. This review elaborates recent advances in physiology and molecular biology to clarify the biosynthetic mechanisms in grapes, including the coordinated action of structural enzymes, MYB–bHLH–WD40 regulatory complexes, hormone-mediated signaling pathways, and vacuolar transport processes. Key environmental factors, such as temperature fluctuations, light exposure, water availability, and soil properties, regulate these networks, contributing to significant variation in pigmentation profiles across cultivars and growing regions. Strategic agronomic practices, including canopy management, regulated deficit irrigation, balanced nutrient management, and temperature-mitigation techniques, further influence pigmentation by modifying the microclimate of the fruit zone during development. Based on these mechanistic insights, this review evaluates targeted strategies for enhancing anthocyanin accumulation, highlighting recent progress in genetic improvement through CRISPR/Cas genome editing, transgenic approaches, and marker-assisted selection (MAS), which enable precise modulation of biosynthetic and regulatory genes. Complementary postharvest interventions, such as optimized cold storage, modified-atmosphere packaging, hormonal elicitors, and controlled oxidative technologies, provide additional opportunities to maintain or enhance pigment stability after harvest. Collectively, these advances establish a comprehensive framework linking molecular regulation with practical vineyard, breeding, and postharvest strategies, offering an integrated pathway to improve anthocyanin consistency, berry quality, and the phenolic characteristics of grape-derived products. Full article

Aphids are major agricultural pests worldwide, causing crop damage both through direct piercing-sucking feeding and the transmission of plant viruses. Their multistage life cycle, unique developmental physiology, plasticity in developing pesticide resistance, and multifaceted interactions with host plants and bacterial endosymbionts make effective control particularly challenging. In this review, we summarize the current toolbox available for aphid control across major crop systems, including chemical pesticides, biological agents, plant resistance, cultural practices, biorational control, and emerging strategies such as RNA interference (RNAi) and symbiosis-targeted approaches. Rather than providing an exhaustive survey of the literature, we draw on conceptual and illustrative studies to critically evaluate the strengths and limitations of each control strategy. Finally, we outline future directions for aphid control, highlighting the potential of modern technologies, such as artificial intelligence (AI), synthetic biology, data-driven analytics, and CRISPR-based genome editing, to expand and improve existing control options. Full article

The life sciences are currently undergoing a serious transition from the reductive biochemical analysis of dissociated tissues to non-destructive “spatial forensics”. In addition to discovering new molecules, we are moving towards finding out their precise tissue localization and performing in situ interrogation to uncover a biological logic within preserved cellular “neighborhoods”. Our perspective is focused on exploring the spatial imperative, including the structural logic and “neighborhood effects” of the tissue microenvironment, which is a prerequisite to understanding cellular function in normal and in pathological conditions. Beginning with a historical foundation of the origins of histochemistry, dating back to the 19th century with pioneer botanist François-Vincent Raspail, we emphasize the technological metamorphosis, transitioning from classical immunohistochemistry to modern multi- and high-plex spatial multi-omics. A critical evaluation of the current operational landscape has been made, addressing the engineering strategies behind multiplexed immunofluorescence (mIF), the challenges of experimental design in spatial transcriptomics, and the functional symbiosis between targeted and unbiased spatial proteomics. There are many layers of genomic and proteomic information we have to consider in order to unravel the mechanisms underlying body function. If we learn how to combine all this information together, we will be able to better understand how cells communicate with each other and what disrupts their communication, leading to cancer and many other pathologies. It is obvious that by implementing spatial biology tools, it becomes possible to develop new medicines and treat diseases in the most efficient ways. At the same time, we realize that there is an urgent need to learn how to put data pieces together so that they blend seamlessly into a meaningful output, further transitioning spatial biology over time into a routine tool to cure for both common and rare diseases and improve our lives and health. Full article

Genotyping is a key step in molecular breeding. Due to its cost-effectiveness, accuracy, and flexibility, genotyping by target sequencing (GBTS) has become a preferred technology for medium-density genotyping. In this study, a new GBTS array for fresh edible maize was developed using resequencing data from 477 lines. The array contains 5759 SNPs evenly distributed across the maize genome, with average minor allele frequency (MAF) and polymorphism information content (PIC) values of 0.40 and 0.36, respectively. These SNPs are closely associated with 1566 functional genes. Cluster analysis of 198 maize lines based on the GBTS array was consistent with their pedigree relationships. Furthermore, 277 fresh waxy maize lines were genotyped and used for genomic selection analyses of hundred-kernel weight, kernel length, and kernel width. Comparative evaluation of different models indicated that Ridge Regression Best Linear Unbiased Prediction (rrBLUP) was the optimal model, with prediction accuracies of 0.33, 0.64, and 0.36, respectively. Additional analyses using different marker densities based on the rrBLUP model showed that prediction accuracy did not increase when the number of markers exceeded 2000, indicating that this array provides sufficient marker density for genetic analysis and genomic selection. Overall, this array provides a useful tool for genetic studies of fresh edible maize and facilitates the application of genomic selection in breeding programs. Full article

Duchenne muscular dystrophy (DMD) is a fatal X-linked neuromuscular disorder caused by mutations in the dystrophin gene. Prime editing is a versatile genome editing technology capable of introducing precise nucleotide changes without generating double-strand DNA breaks, making it a promising approach for correcting pathogenic point mutations. In this study, we applied prime editing to modify mdx-4cv and mdx-5cv mutation-equivalent sites in mouse C2C12 myoblasts in vitro. Initial editing efficiencies were unexpectedly low and were associated with the presence of a 5′-TTCT-3′ motif within engineered prime editing guide RNAs (epegRNAs). epegRNA designs containing this motif exhibited reduced prime editing efficiency, whereas silent substitution eliminating the motif significantly improved editing outcomes, indicating that specific sequence features within epegRNAs can influence editing performance. Rational redesign of epegRNAs to remove this motif substantially enhanced editing efficiency, achieving up to 20% modification at the 4cv target site using an NGG PAM and 21% editing at the 5cv locus using an NGAG PAM. These findings highlight an important sequence-dependent constraint in epegRNA design and provide practical guidance for optimizing prime editing strategies targeting Dmd mutations in vitro. Full article

High-quality genomic DNA extraction remains a major bottleneck for fungal genomics, particularly for worldwide aerobic and non-photosynthetic mushroom species that rely on their rigid cell walls, interference between metabolites, polysaccharides, etc., and complex genomes. This study systematically compares five DNA extraction protocols involving four distinct sample preparation procedures (fresh (A), filtered (B), frozen (C) and cryogenic mycelium (D)) across mycelial cultures of eight Tunisian fungal strains representing Ascomycota and Basidiomycota to identify the optimal combination for genomic DNA extraction from mycelium. The eight phylogenetically diverse fungal species were analyzed using short-read (MiSeq and NextSeq550) and/or long-read (MinION Mk1C) sequencing technologies, giving a depth coverage between 3.7× and 83×. The generation and quality of the assemblies were assessed within the Galaxy platform, which revealed a gap percentage of 0–0.509%. Taxonomic characterization and phylogenetic inference were performed with SANGER technology using the Internal Transcribed Spacer (ITS) and D1/D2 region of the 26S rRNA gene, assigning the species to our eight different strains: Clitopilus baronii (BS6), Porostereum spadiceum (BS200), Trametes versicolor (BS22-9), Schizophyllum commune (BS23-13), Gloeophyllum abietinum (BS23-14), Irpex laceratus (BS100), Trichoderma asperellum (GC9) and Trichoderma harzianum (S3). The optimized DNeasy Plant Pro Kit protocol with cryogenic biomass treatment presents a safe and cost-effective method for fungal genome sequencing and taxonomic resolution. This integrated comparative evaluation of extraction for sequencing identifies an optimal Qiagen-based extraction strategy combined with cryogenic treatment for eight diverse Tunisian fungal species, guiding method selection based on specific cell wall characteristics rather than proposing a universal protocol limited by unequal replication and strain numbers. Full article

Microorganisms represent the Earth’s most abundant biomass and a vast reservoir of genetic diversity. However, traditional agar plate methods fail to recover the vast majority of these species, leaving a “microbial dark matter” that holds immense potential for the discovery of novel antibiotics and bioactive compounds. While conventional techniques such as selective media and enrichment culture remain foundational, they are inherently limited by community biases and the inability to support low-abundance, oligotrophic species. To address these bottlenecks, a diverse array of innovative isolation strategies has emerged. This review systematically categorizes and evaluates these methodologies, ranging from in situ cultivation to high-resolution single-cell manipulation. We first examine membrane diffusion-based cultivation (e.g., iChip), which mimics natural microenvironments to resuscitate recalcitrant microbes. Subsequently, we explore high-throughput single-cell technologies, including microfluidics for physicochemical separation, optical tweezers for precise manipulation, and fluorescence-activated cell sorting (FACS). Special attention is given to Raman-activated cell sorting (RACS) as a label-free functional screening tool and reverse genomics for targeted capture. By synthesizing the strengths and limitations of these approaches, we propose integrated workflows designed to accelerate the mining of untapped microbial resources. Full article

Background: Cognitive and psychiatric disorders are caused by a complex interplay between genetic predisposition, environmental exposures, and dynamic molecular regulation in the brain. Animal models provide a controlled environment for examining these mechanisms, and advances in transcriptome and epigenomic technologies have greatly expanded our knowledge of disease-relevant pathways. Objective: This scoping review systematically maps and synthesizes the epigenetic and transcriptomic findings from the established animal models of four neuropsychiatric conditions—autism spectrum disorder (ASD), schizophrenia, depression, and Rett syndrome—drawing on a PRISMA-ScR-guided literature search. The review characterizes the breadth of evidence, identifies convergent and divergent molecular pathways, and highlights the translational gaps and therapeutic implications. Methods: Research employing chromatin accessibility testing, genome-wide DNA methylation mapping, single-cell and bulk RNA sequencing, histone modification profiling, and multi-omics integration in mouse and other validated animal models was thoroughly reviewed. A quality appraisal of the primary experimental studies (n = 63) was performed using a modified CAMARADES checklist. Results: Beyond generalized cellular stress responses, multi-omics analysis emphasizes the cell-type- and context-dependent nature of epigenetic changes in animal models, including isoform-specific histone modifications and model-dependent binding of HDAC/MeCP2 complexes to genes involved in synaptic plasticity. Single-cell RNA sequencing analyses have uniformly shown transcriptional changes in parvalbumin-positive (PV+) interneurons. Conclusions: The specific convergence of epigenetic disruptions in neural circuits involved in synaptic structure and inhibitory function could play a role in the generation of neuropsychiatric phenotypes in animal models, highlighting the importance of circuit- and cell-type-specific epigenetics while pointing to potential therapeutic avenues. Full article

Mosses (Bryophyta) comprises a group of terrestrial plants that colonized land more than 450 million years ago that play fundamental ecological and evolutionary roles, particularly in polar and peatland ecosystems. The sequencing of Physcomitrium patens marked a milestone in bryophyte genomics, establishing mosses as model organisms for evolutionary and functional studies. However, the recent advent of next-generation sequencing technologies has broadened genomic exploration beyond P. patens, unveiling the genetic diversity of additional bryophyte species. Notably, the genomes of Sphagnum fallax, Sphagnum magellanicum, the liverwort Marchantia polymorpha and hornworts from Athoceros genus have provided new insights into carbon fixation mechanisms, ecological adaptations, and lineage-specific evolutionary traits. These advances have enabled large-scale comparative analyses and expanded the understanding of conserved and divergent genomic features among bryophytes. The integration of these datasets into public databases such as Phytozome and NCBI Genome has created a robust framework for investigating plant genome evolution and biotechnological potential. Altogether, the expanding genomic landscape of bryophytes reveals their remarkable evolutionary plasticity and underscores their importance as key models for studying adaptation, metabolism, and genomic innovation in terrestrial plants. Full article

CRISPR technologies are transforming cardiovascular therapy development by creating an increasingly seamless pipeline from potential target discovery to clinical translation. What began as a genome-editing tool has evolved into a versatile platform that enables researchers to precisely interrogate and modulate cardiac biology with tools such as base- and prime-editors, and CRISPR inhibition and activation. In this review, we follow the use of CRISPR across the stages of biomedical research through to bench-to-bedside application. This review begins by addressing how genome-wide and focused CRISPR screens discover developmental regulators, disease drivers, and drug-response pathways, making the first steps in identifying therapeutic targets. We then explore how CRISPR engineering creates progressively more relevant disease model systems to validate mechanisms of disease and test interventions, helping bridge the translational gaps between the lab and the clinic. Finally, we consider how CRISPR technologies are beginning to enter cardiovascular clinical trials, while highlighting the key challenges that still limit this translation. By linking the latest advances of modern CRISPR platforms to the stages of therapeutic development, this review highlights how CRISPR technology is reshaping the pipeline from molecular insight to clinical innovation in cardiac disease. Full article

Plant metabolism is essential for coordinating growth, development, and defense under changing environmental conditions. Plants continuously adjust their metabolic pathways to balance resource allocation between growth and immune responses. Under stress, metabolic reprogramming redirects energy and resources toward the production of defense compounds and activation of immune signaling pathways. These changes involve complex interactions among primary metabolism, specialised metabolites, and regulatory networks, including calcium signaling, reactive oxygen species, and phytohormones. Advances in metabolomics and multi-omics technologies have improved understanding of the metabolic control of plant immunity; however, knowledge remains fragmented, and an integrated framework linking metabolism, development, and defense is still emerging. This review examines plant immunometabolism by highlighting the dynamic relationships between metabolic networks and immune functions during development and stress. It discusses pathways that influence growth, stress-induced metabolic shifts linked to defense, and how signaling interacts with metabolism. Progress in metabolomics, transcriptomics, proteomics, and computational modeling that supports systems-level analysis of plant metabolism is also summarized. In addition, potential applications in agriculture and biotechnology, including metabolic engineering, genome editing, and metabolomics-based breeding, are considered in relation to crop resilience. By integrating metabolism, signaling, and systems biology, this review provides a broad perspective on how metabolic reprogramming shapes the growth–defense trade-off in plants and outlines future directions for developing climate-resilient crops. Full article

Single-cell RNA-sequencing (scRNA-seq) studies over the past several years have provided unprecedented resolution into the transcriptomic landscape of both major and minor salivary glands. This technology enables the identification of diverse and functionally specialized cell populations that underlie glandular architecture and physiology. Increasingly, scRNA-seq has become an integral component of experimental design, used not only to validate prior observations but also to uncover novel cell types, pathways, and molecular regulatory mechanisms. As a result, a growing number of publicly available datasets now encompass a wide spectrum of biological contexts including homeostasis, disease, and regeneration. However, inconsistencies in data processing and incomplete reporting of experimental methods pose challenges for reproducibility and limit the ability to distinguish high-quality datasets. As single-cell technologies continue to evolve and become more accessible, their application in salivary gland research is expected to expand, offering deeper insight into both basic biology and clinical translation. This review compiles and summarizes findings from a growing body of scRNA-seq studies of the salivary glands, highlights current limitations, provides methodological considerations, and expounds on key cellular and genomic discoveries to help guide future investigations. Full article

Bacillus and Paenibacillus species are common and widely distributed microorganisms in food systems, often implicated in food spoilage and quality issues. Bacillus subtilis, in particular, has been associated with gas production and package bulging in seasoned foods. In this study, we developed a rapid and visual detection method for Bacillus subtilis by integrating (Recombinase Polymerase Amplification) RPA with (Clustered Regularly Interspaced Short Palindromic Repeats) CRISPR/Cas12a technology (designated as RPA-CRISPR/Cas12a). Specific RPA primers and probes were designed based on the conserved gyrB gene of Bacillus subtilis. Two sets of crRNA were designed according to the number of T-rich PAM sites on the RPA-amplified target sequence, and the reaction conditions were optimized in combination with the CRISPR/Cas12a trans-cleavage detection technology. Under optimized conditions, the crRNA3 guide (with a TT-rich PAM site) demonstrated superior cleavage efficiency compared to crRNA2 (TTT-rich PAM), while crRNA1 (TTTT-rich PAM) showed no activity. The assay achieved a detection limit of 150 pg/μL for genomic DNA and 5.5 CFU/mL for bacterial suspensions within 10 min at 37 °C. The method exhibited high specificity and sensitivity, providing a robust tool for early and on-site detection of Bacillus subtilis in food products. Full article

Sweet–waxy maize is a highly valuable specialty maize type with an increasing market demand, but conventional breeding methods for producing sweet–waxy maize are restricted by severe bottlenecks, such as long breeding cycles and linkage drag. This study was conducted to rapidly create sweet–waxy maize germplasm using CRISPR/Cas9 genome-editing technology. We used a CRISPR/Cas9 system to target maize Sh2 (regulating the super-sweet kernel trait) and Wx (controlling the waxy kernel trait), which are two key genes in the starch biosynthesis pathway. Two small-guide RNAs (sgRNAs) designed for each gene were incorporated into CRISPR/Cas9 vectors, which were then introduced into maize via Agrobacterium-mediated transformation. We obtained Cas9-free T₃ homozygous sh2 and wx mutant lines with significant increases in kernel soluble sugar and amylopectin contents, respectively, but no adverse changes to major agronomic traits. Using these Cas9-free lines, we developed a new type of sweet–waxy maize germplasm, in which waxy and sweet kernels on the same ear segregated at a 3:1 ratio. Our results indicate that CRISPR/Cas9-mediated editing of Sh2 and Wx can efficiently generate sweet–waxy maize germplasm with no detectable linkage drag. The study methods would be useful for optimizing the molecular breeding of novel and innovative maize germplasm. Full article

Quercus oxyphylla (E. H. Wilson) Hand.-Mazz. is a threatened evergreen subalpine tree species with fragmented habitats native to China. Here, we present a de novo chromosome-level genome assembly of this oak species by integrating PacBio long-read high-fidelity (HiFi) sequencing and Hi-C mapping technologies. The assembled genome size of Q. oxyphylla in this study is 824.15 megabases (Mb) in length with 12 putative chromosomes. Genome annotation of this oak species identified 514.09 Mb of repeat sequences, 53,730 protein-coding genes and 1048 non-coding RNA sequences. Genomic analyses of whole-genome duplication (WGD) and long terminal repeat retrotransposon (LTR-RT) insertion events in Q. oxyphylla revealed no species-specific WGD and recent accumulation of LTR-RTs in the genome within the last seven million years. A phylogenomic analysis with eight oak representatives confirmed the framework phylogeny of genus Quercus and indicated that Q. oxyphylla possibly split with the ancestor of Cerris oaks about 20.4 million years ago. We identified 2074 expanded and 903 contracted gene families across the genome assembly of Q. oxyphylla, while the significantly expanded gene families had notable disease resistance-related genes that were mainly enriched in plant–pathogen interaction pathways. The high-quality genome assembly of Q. oxyphylla generated in this study provides a valuable genome resource for the genetic conservation and management of Q. oxyphylla, and may facilitate our understanding of genome evolution and species adaptation of the oak lineage. Full article