Search Results (15,547)

Glycosaminoglycans (GAGs) and their degrading enzymes have extensive applications and biotechnology and medicine, and play a crucial role in the recycling of organic matter in oceans. In this study, a potential GAG utilization gene cluster was identified in the genome of a novel marine Bacteroidetes, Roseihalotalea indica gen. nov. sp. nov. TK19036^T, through sole carbon source cultivation and differential proteomic analysis. Multiple GAG-lyases within this locus were purified and characterized. RiPL8 comprises a functionally unknown N-terminal domain and a catalytic C-terminal domain, exhibiting specificity for degrading hyaluronic acid (HA). The activity of RiPL35 is sensitive to Ca²⁺ ion concentration with an optimum at 10 mM. RiPL38 is the first reported member of the PL38 family capable of degrading HA and chondroitin sulfate (CS). In summary, our study reveals Roseihalotalea indica gen. nov. sp. nov. TK19036^T harbors an unpredicted GAG degradation gene cluster, and the encoded GAG-lyases exhibit distinct substrate specificities compared to the host organism. Full article

Cardiovascular disease remains the leading global cause of mortality, largely due to the limited regenerative capacity of adult human myocardium. Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) offer a scalable platform for cardiac repair and disease modeling; however, their persistent metabolic immaturity—characterized by reliance on glycolysis, reduced oxidative phosphorylation (OXPHOS), and structurally underdeveloped mitochondria—limits functional integration and long-term therapeutic efficacy. Recent advances indicate that targeted metabolic reprogramming can enhance mitochondrial biogenesis, increase ATP production, and improve stress resilience in iPSC-CMs. This review examines the complementary integration of CRISPR-based metabolic engineering and extracellular vesicle (EV)-mediated metabolic modulation as a systems-level strategy for cardiac maturation. We discuss CRISPR activation, interference, and epigenome-editing approaches targeting regulators such as PGC-1α, TFAM, and PPARs to promote stable enhancement of mitochondrial networks and respiratory capacity. In parallel, engineered EVs delivering miRNAs, metabolic enzymes, and redox modulators provide non-genomic mechanisms to optimize bioenergetic function and mitigate oxidative stress. By synthesizing mechanistic insights, quantitative bioenergetic metrics, and translational considerations, we propose CRISPR-EV synergy as a precision framework for durable metabolic maturation of iPSC-CMs, with implications for regenerative therapy, pharmacologic screening, and myocardial repair. Full article

This study investigated the genetic regulation of microRNA (miRNA) expression in monocytes and its potential role in musculoskeletal diseases. We mapped expression quantitative trait loci (eQTLs) for miRNAs using data from 281 Caucasian (CAU) and 170 African American (AA) individuals, constructed ancestry-specific models to impute miRNA expression from genotype data, and applied these models to test associations with osteoporosis and sarcopenia. Analysis identified 468 and 2653 independent eQTLs for 61 miRNAs in CAU and 25 in AA, respectively, the majority of which were ancestry-specific. Association analyses identified 22 and 26 miRNAs associated with osteoporosis and sarcopenia, respectively, in the CAU population; corresponding findings in the African American population were 26 and 14 miRNAs. Analysis of their target genes revealed 1238 and 741 genes that were nominally associated with osteoporosis and sarcopenia in CAU; with 524 genes associated with osteoporosis and 891 associated with sarcopenia in AA. Functional enrichment analysis indicated that the target genes of the identified miRNAs are involved in disease-relevant biological processes—cell migration and motility in osteoporosis, and immune/cytokine responses in sarcopenia. This work provides insights into the genetic architecture of miRNA expression and implicates monocyte miRNAs in musculoskeletal diseases, underscoring the importance of including diverse ancestral backgrounds in genomic studies. Full article

The CFEM (Common in Fungal Extracellular Membrane) domain defines a family of cysteine-rich proteins unique to fungi, playing pivotal roles in host–pathogen interactions. However, the repertoire and functions of CFEM proteins in the broad-host-range necrotrophic pathogen Sclerotinia sclerotiorum remain largely unexplored. Through genome-wide bioinformatic analysis, we identified 13 CFEM-containing proteins (SsCFEM1–13) in S. sclerotiorum. Characterization revealed substantial diversity in their physicochemical properties, domain architecture, and predicted subcellular localization. Ten proteins possess a secretion signal, with six predicted to be GPI-anchored and three classified as high-confidence effectors. Members lacking transmembrane domains were predicted to adopt the conserved CFEM “helical-basket” fold. Phylogenetic analysis grouped SsCFEMs into two distinct clades and indicated a complex evolutionary history involving both conserved ancestry and lineage-specific expansion. Transcriptomic profiling showed that most genes were upregulated during early infection of various host plants, with SsCFEM8 exhibiting particularly strong and consistent induction. Crucially, transient expression assays in Nicotiana benthamiana revealed that several SsCFEM proteins, notably SsCFEM4 and SsCFEM9, function as cell death suppressors, validating their predicted effector roles and identifying key virulence candidates. This study provides the first comprehensive catalog and functional prediction of the CFEM protein family in S. sclerotiorum, establishing a foundation for future mechanistic studies on their roles in the pathogenesis of this devastating fungal pathogen. Full article

GWASs have successfully identified numerous genetic variants linked to complex traits, but traditional univariate approaches often fail to capture shared genetic architecture across multiple phenotypes. As the scale of genomic data continues to increase, the demand for more efficient multi-phenotype analysis methods has become particularly critical. In addition, the issue of population structure must also be properly addressed to ensure robust and unbiased results. Multivariate methods for multi-phenotype analysis, such as GAMMA, address this by combining linear mixed models with multivariate distance matrix regression to account for population structure; however, since these methods utilize computationally intensive models, developing efficient implementations is essential for practical analysis. Although GAMMA is a well-designed and effective tool, its original implementation relies on multiple programming environments and requires frequent data exchanges between components. These factors increase computational burden and complicate installation and execution for users unfamiliar with programming, making practical applications, particularly for high-dimensional datasets, challenging. Here, we present GAMMA-RAY, a high-performance C++ implementation that streamlines the computational pipeline, leverages parallel processing, and employs efficient matrix operations to achieve substantial reductions in runtime and memory usage. GAMMA-RAY provides both a user-friendly web-based interface for non-programmers and a standalone version for secure local execution. We further applied GAMMA-RAY to a yeast dataset and identified putative trans-eQTLs, in which several variants overlapped with previously reported cis- and trans-eQTLs. In addition, functional enrichment analysis revealed that the associated trans-eGenes are enriched, a conclusion consistently supported by biological annotation resources and underscoring the biological significance of these results. Full article

PYL proteins are core components of the abscisic acid (ABA) signaling pathway and are involved in plant responses to biotic and abiotic stresses. In this study, a total of 19, four, and eight PYL genes were identified in Saccharum spontaneum, the Saccharum spp. hybrid R570, and Sorghum bicolor, respectively. Phylogenetic analysis classified these PYL genes into three distinct groups. Cis-acting element analysis, Gene Ontology annotation, and Kyoto Encyclopedia of Genes and Genomes pathway enrichment and gene expression profile indicated that members of the PYL gene family are mainly associated with hormone signaling and stress-related biological processes. The ScPYL8 gene (GenBank accession number: OR838856) was isolated from sugarcane cultivar QT3. Expression of the ScPYL8 gene was induced under stresses of cold, PEG, SA, MeJA, ABA, and brown stripe disease (Bipolaris setariae). The gene was expressed in roots, stems and leaves, with the highest expression level in leaves. Subcellular localization analysis showed that the ScPYL8 protein localized to the cytoplasm and nucleus. ScPYL8 overexpression in tobacco activated the reactive oxygen species defense system and regulated the ABA and jasmonic acid signaling pathways, enhancing its resistance against Fusarium solani var. coeruleum. These findings provide insights into the expression, function, and evolutionary characteristics of the PYL gene family in sugarcane, offering valuable genetic resources for future molecular breeding. Full article

Nigrospora musae ST1 is a newly identified pathogen responsible for leaf spot disease in Idesia polycarpa. In order to further advance our understanding of this strain and improve management strategies for the leaf spot disease, the PacBio Sequel II platform was used to perform whole-genome sequencing of N. musae ST1. The assembled genome comprised 42 contigs, with a total length of 49,259,803 bp and an average GC content of 56.23%. Functional annotation identified 12,063 protein-coding genes, including 125 Transporter Classification Database (TCDB)-related genes, 3600 pathogen host interaction (PHI) genes, 2503 Virulence Factor Database (DFVF)-related genes, and 722 genes encoding carbohydrate-active enzymes (CAZymes). Integrated analyses of the secretome, PHI, and DFVF databases revealed six secreted carbohydrate-active enzymes implicated in plant pathogenicity, including three glycoside hydrolases, two pectinate lyases, and one cutinase, potentially playing important roles in pathogenicity. A total of 77 secondary metabolite gene clusters were predicted. Comparative genomic analysis between N. musae ST1 and other Nigrospora species revealed differences in genome rearrangements in Nigrospora fungi. In conclusion, this study has clarified the whole-genome structural characteristics and evolutionary relationships of the newly reported pathogenic fungus, N. musae ST1. It provides a theoretical foundation for future investigations into the pathogenic mechanisms of N. musae ST1 infection in I. polycarpa, as well as potential targets for disease control. Full article

In the context of research aimed at identifying the causes of the progressive decline in cellular and tissue functions characteristic of aging, in recent decades, increasing attention has been devoted to the sirtuin family. Sirtuins are named after the Sir2 protein of Saccharomyces cerevisiae, a product of the SIR gene family, known as “silent information regulator 2”. Sirtuins are NAD⁺-dependent protein deacetylases and deacylases characterized by a conserved catalytic domain of approximately 275 amino acids. The removal of acetyl groups from acetyl-lysine residues on proteins is critical in regulating a wide range of biological functions, including gene silencing, genome stability, longevity, metabolism, and cellular physiology. In humans, the sirtuin family comprises seven isoforms (SIRT1–SIRT7), each with specific substrate preferences and primarily, but not exclusively, localized in the nucleus (SIRT1, SIRT6, and SIRT7), cytoplasm (SIRT2), and mitochondria (SIRT3, SIRT4, and SIRT5). Sirtuins may regulate numerous cellular processes associated with survival and longevity, including transcription and DNA repair, inflammation, glucose and lipid metabolism, oxidative stress, mitochondrial function, apoptosis, autophagy, and stress resistance. Sirtuins’ dependence on NAD⁺ allows them to function as cellular energy sensors, linking metabolic demands to selective lysine deacylation in various subcellular organelles. The aim of this review is to provide an update on this family of molecules, describing their molecular structures, physiological functions, roles in aging processes, and potential to be modulated to serve as a strategy for promoting healthy aging. Full article

TCP transcription factors constitute a key regulatory family in plants, playing crucial roles in plant growth and development. Although this gene family has been extensively studied across diverse plant species, research in Gypsophila paniculata remains limited. Through genome-wide identification and analysis, this study identified 17 GpTCP in G. paniculata. Our analysis revealed that all GpTCP proteins contain a conserved TCP domain, with subcellular localization predictions indicating nuclear localization. Promoter analysis identified multiple cis-regulatory elements associated with plant organ development and growth regulation. Chromosomal synteny studies showed that gene expansion within the G. paniculata TCP gene family occurred after subfamily differentiation. Over-expression of GpTCP10 in Arabidopsis thaliana caused root development inhibition, leaf curling, smaller flowers, and yellowing of flowers. Further studies showed that in two normally growing G. paniculata varieties with different flower sizes, GpTCP10 was specifically expressed in leaf and floral tissues, with significantly higher expression levels in the smaller-flowered G. paniculata. These findings reveal the evolutionary characteristics of the TCP family in G. paniculata, and highlight the role of GpTCP10 in regulating organ growth and development in transgenic Arabidopsis thaliana and floral organ size in G. paniculata. Full article

As sessile organisms, plants must dynamically allocate resources between growth and stress resilience. This review focuses on Ethylene Response Factor (ERF) transcription factors as central regulators of this fundamental balance. We evaluate the molecular basis of ERF function, highlighting their modular structure, dynamic post-translational regulation, and ability to form context-specific protein complexes that integrate diverse signals. While ERF family members show functional redundancy, certain ERF subgroups, such as the ERF-VIIs, exhibit clearer evidence of dual roles in coordinating both developmental programs and adaptive responses to stress. We further elucidate the mechanisms underlying ERF-mediated trade-offs, explaining how these factors direct spatial resource allocation and enable temporal switching between growth and defense states. Finally, we explore how emerging technologies, such as CRISPR-based genome editing and various synthetic biology tools, can harness ERF regulatory networks. These approaches offer promising strategies for engineering crops with precisely tuned adaptive capacity, supporting sustainable agriculture even in changing climate conditions. This synthesis highlights specific ERF subgroups as pivotal integrators and future targets for crop improvement. Full article

Background: The Calcineurin B-like (CBL) and CBL-interacting protein kinase (CIPK) system constitute critical signaling modules mediating plant responses to abiotic stress. Although these families have been studied across various species, their evolutionary dynamics across grasses and the functional plasticity of specific isoforms remain elusive. Methods: A genome-wide analysis of CBL and CIPK families was conducted across five major Poaceae species (Oryza sativa, Triticum aestivum, Zea mays, Sorghum bicolor, and Saccharum spontaneum). Phylogenetic and synteny analyses were analyzed to family expansion and evolution. Cis-regulatory elements analysis in gene promoter regions were examined to predict potential stress-responsive features. Expression profiles of OsCBL and OsCIPK gene families were examined by qRT-PCR under conditions involving PEG-induced osmotic stress, pathogen strain P6 inoculation, and exogenous application of the phytohormones abscisic acid (ABA) and methyl jasmonate (MeJA). Protein–protein interactions between selected CBL (OsCBL4) and CIPK pairs were assessed via Yeast Two-Hybrid (Y2H) and Luciferase Complementation Imaging assays (LCI). Results: Phylogenetic and synteny analyses indicated that segmental duplications have contributed substantially to the expansion of these gene families. Promoter analysis revealed that the majority of CBL and CIPK family members, exemplified by OsCBL4, traditionally characterized as a salt sensor, possesses a cis-element architecture (rich in ABREs and MBS) heavily biased towards dehydration responsiveness. Expression profiling showed that OsCBL4 is significantly hyper-induced by direct osmotic stress (PEG) but exhibits almost no response to exogenous ABA. A subset of kinases genes (e.g., OsCIPK2, 9, 18) displayed PEG-induced expression patterns resembling those of OsCBL4, whereas OsCIPK30 remained transcriptionally unresponsive under the same conditions. Protein interaction assays demonstrated that OsCBL4 physically interacts exclusively with PEG-responsive transcriptionally activated kinases such as OsCIPK9, but failed to interact with the non-responsive OsCIPK30. Conclusions: Our study provides a genomic characterization of CBL and CIPK families across five major Poaceae species. The combined expression and interaction data reveal that OsCBL4-assembles with specific CIPKs into signaling modules during osmotic stress responses in rice, pointing to roles that go beyond salt stress responses. The findings establish a foundation for further functional dissection of CBL-CIPK pathway diversification in abiotic stress adaptation. Full article

Background: Identifying patients most likely to benefit from immune checkpoint inhibitors (ICIs) remains a significant challenge in advanced melanoma. We evaluated the association between tumor somatic mutations and clinical outcomes, focusing on relapse-free survival (RFS) and overall survival (OS) in locoregionally advanced melanoma patients treated with neoadjuvant ipilimumab. Methods: Tumor specimens and matched peripheral blood samples from 22 patients underwent whole-exome sequencing (WES) to identify non-synonymous somatic mutations. Tumor mutational burden (TMB) was quantified, and specific mutations were analyzed for associations with survival outcomes. Results: The analysis revealed a mutational landscape dominated by single-nucleotide missense mutations with a median TMB of 11.4 mutations/MB. BRAF and NRAS mutations were detected in 73% of patients and exhibited mutual exclusivity and concurrence patterns (p < 0.05). Positional clustering identified NRAS and SLC35B4 as key contributors to melanoma (FDR p-value < 0.05). Log-rank analysis indicated that mutations in ODZ1, USP34, CEP192, EML5, KIAA1797, ATAD5, and ANKHD1–EIF4EBP were associated with shorter survival outcomes (RFS or OS). The associations remained significant in both univariate and multivariable Cox regression models adjusted for TMB. These genes can be broadly grouped into functional categories relevant to tumor progression and immune modulation. In applying multiple testing correction, none maintained statistical significance, indicating that these findings should be interpreted as exploratory and require validation in independent cohorts. Conclusions: This study identified tumor genomic alterations associated with clinical outcomes in melanoma patients treated with neoadjuvant ipilimumab, suggesting their potential role in anti-tumor immunity. These findings warrant further investigation in larger cohorts and across other ICIs in melanoma and other malignancies. Full article

Leveraging fungal consortia to degrade heavy oil is an emerging strategy for mitigating/cleaning up environmental pollution. However, many consortia are predominantly evaluated by measuring the biodegradation efficiency of heavy oil, with insufficient attention paid to the mechanistic underpinnings and metabolic pathways. In this study, heavy oil-degrading fungal consortia were developed for potential application in soil bioremediation. Whole-genome sequencing was used to predict the metabolic pathways and interspecific interactions driving heavy oil biodegradation. Three heavy oil-degrading fungal strains, designated Aspergillus corrugatus FH2, Aspergillus terreus FL4, and Alternaria alstroemeriae FW1, were isolated from oil sludge in the Karamay Oilfield in Xinjiang, China. Four consortia were constructed through the combination of two or three strains. The consortium F13 (FH2 + FW1) achieved 72.0% removal of heavy oil in a simulated bioremediation test over 30 days, which was more efficient than other consortia and single strains (59.5–68.5%). Notably, the mean degradation rate of long-chain alkanes (C₂₄–C₂₈) by F13 reached 95.9%. After F13 treatment, the major fractions of heavy oil showed considerable degradation, 87.4% for saturates, 92.0% for aromatics, 69.5% for resins, and 27.3% for asphaltenes. Genome annotation of FH2, FL4, and FW1 revealed the presence of core genes for degradation of n-alkanes and aromatics, e.g., CYP505, frmA, fadB, hmgA, ALDH, and ACSL. These functional genes encoded cross-lineage enzymes, enabling synergistic catabolism of C₁₃–C₂₈ alkanes and aromatics. Our findings indicated that the fungal consortium of A. corrugatus FH2 and Al. alstroemeriae FW1 has remarkable bioremediation potential for heavy oil-contaminated sites. This study provides molecular evidence for the design of targeted interventions to improve soil remediation efficiency with fungal consortia. Full article

Pyroptosis is a pro-inflammatory form of programmed cell death mediated by inflammasomes and caspases and has been implicated in various inflammatory diseases. However, its function and regulatory role in dairy cows with clinical mastitis (CM) remain poorly understood. This study was conducted to investigate the differentially expressed proteins (DEPs) involved in biological processes (BPs) and the Kyoto Encyclopedia of Genes and Genomes pathways related to inflammasome-mediated pyroptosis based on proteomic data and to further explore their potential involvement in mastitis using in vivo and in vitro models. Histopathological analysis revealed morphological features consistent with pyroptosis in the mammary glands of CM-affected cows, including mammary epithelial cell (MEC) membrane disruption, increased reactive oxygen species production, elevated TUNEL–gasdermin D (GSDMD)-positive staining, and inflammatory cell infiltration. Proteomic profiling identified 276 DEPs and 17 BPs, among which NOD-like receptor family pyrin domain-containing 3 (NLRP3) was identified as a key candidate associated with cytokine production, immune defense, and inflammatory responses. Pathway enrichment analysis indicated that NLRP3, caspase-1 (CASP1), and GSDMD were enriched in the NOD-like receptor signaling pathway and were closely associated with mastitis. Immunohistochemical and molecular analyses demonstrated cytoplasmic localization and significant upregulation of NLRP3, CASP1, and GSDMD at both the mRNA and protein levels in CM-affected tissues. In both in vitro and in vivo models, a dose-dependent increase in the expression of pyroptosis-related targets and pro-inflammatory cytokines was observed with the progression of inflammation. Moreover, the pharmacological inhibition of CASP1 attenuated pyroptosis-associated changes and inflammatory responses in BMECs. Collectively, these findings suggest that the NLRP3–CASP1 axis is associated with inflammation-related pyroptosis in bovine mastitis and may represent a potential therapeutic target for clinical mastitis. Full article

Background: Inherited kidney diseases represent a genetically and clinically heterogeneous group of disorders affecting both pediatric and adult populations. Advances in next-generation sequencing (NGS) have improved diagnostic precision; however, genotype–phenotype correlations and diagnostic yield vary substantially across disease entities. Methods:We retrospectively evaluated 165 patients referred for genetic testing due to suspected inherited kidney disease. Patients were classified into three clinical groups: polycystic kidney disease, Alport syndrome, and other syndromic patients with inherited kidney diseases. Genetic analysis was performed using NGS with Human Phenotype Ontology–based gene filtering and included evaluation of both single-nucleotide variants and copy number variations. Results: Overall diagnostic yield differed markedly between groups. A molecular diagnosis was achieved in 71.4% of Alport patients, 41.0% of PKD patients, and 70.2% of patients in the Other syndromic group. In the Alport group, variants were identified exclusively in COL4A3, COL4A4, and COL4A5, with pathogenicity and gene involvement correlating with disease severity and the presence of extrarenal manifestations. The PKD group showed predominant involvement of PKD1, followed by PKHD1 and PKD2, while a substantial proportion of patients remained genetically negative, reflecting technical and biological complexity. The Other group exhibited pronounced genetic heterogeneity, with variants distributed across multiple genes involved in tubular, glomerular, metabolic, and ciliopathy-related pathways. Computational assessments demonstrated that several variants of uncertain significance (VUS) were located in functionally critical domains and were predicted to disrupt protein stability, intermolecular interactions, or conserved structural motifs, thereby supporting the biological plausibility of their potential pathogenic impact. Conclusions: Phenotype-driven NGS enables effective molecular diagnosis across diverse inherited kidney diseases while revealing disease-specific differences in diagnostic yield and genotype–phenotype correlations. Systematic inclusion of variants of uncertain significance and careful integration of genetic and clinical data are essential for accurate interpretation and long-term patient management. Collectively, this study enhances understanding of inherited kidney diseases and underscores the value of integrating comprehensive genomic and computational approaches into routine nephrogenetic practice. Full article