Search Results (437)

MXenes are a class of two-dimensional materials exhibiting excellent surface-enhanced Raman scattering (SERS) performance. Currently, the SERS studies of MXenes have been primarily focused on those with M₂X and M₃X₂ structural motifs. In order to expand the SERS sensing application based on MXenes, in this paper, a SERS sensor made of Ta₄C₃@AgNP nanocomposite material was fabricated by electrostatic self-assembly. Tests such as different concentrations of R6G probe molecules showed that the minimum detection limit of this SERS sensor was 10⁻⁸ M, demonstrating excellent sensitivity. When different test areas are selected, the relative error of intensity under the same wave number is less than 10.7%, showing good repeatability and consistency. Furthermore, the Ta₄C₃@AgNP nanocomposite SERS sensor was used to detect the pesticide Ziram, and a quantitative model was established. Application detection indicates that this sensor has good sensitivity for the pesticide Ziram, and the minimum detection limit was 10⁻⁶ M, which exceeded national standard requirements. The findings of this study have potential application value in the fields of food safety and environmental protection. Full article

Rice genome encodes ten OsDREB1 proteins that regulate tolerance to abiotic stresses such as cold and drought. OsDREB1s can bind to the C-repeat (CRT) element, dehydration response element (DRE), and GCC-box in gene promoters for transcription regulation. However, the recognition mechanism of OsDREB1s to these DNA elements remains unclear. Here, the structures of OsDREB1s were modelled using AlphaFold 3, which revealed a typical AP2 domain and a disordered KRP/RAGR motif adjacent to AP2 in all OsDREB1s. Structure modeling of OsDREB1A binding to CRT, DRE, and GCC-box showed that four Arg residues and a Glu (E66) from AP2 play important roles in binding to the major groove of DNA, while R40 in the KRP/RAGR motif was predicted to interact with the minor groove. The structure models revealed a few differences in the binding details for CRT, DRE, and GCC-box. Consistent with these predictions, OsDREB1A was evidenced to bind with the three DNA elements in slightly different affinities through EMSA experiments. Mutation analysis verified the key role of R40 and E66 in binding to CRT. Considering the highly conserved structure and sequence of the KRP/RAGR motif and AP2, we speculate that the DNA recognition mechanism found for OsDREB1A may be common for all OsDREB1s. Full article

Sclerotinia sclerotiorum is a globally distributed fungal pathogen responsible for significant agricultural losses across a wide range of crops. This study aimed to develop polymorphic simple sequence repeat (SSR) markers by whole-genome resequencing of three Korean isolates and a public reference genome. A total of 16,885 SSR motifs were identified, of which 368 overlapped with polymorphic insertion–deletion (InDel) sites across the four genomes. From these, 12 SSR markers were selected based on polymorphism information content and amplification quality. Validation across the 28 isolates in Korea revealed high levels of genotypic diversity, suggesting that each isolate is a unique haplotype, although S. sclerotiorum is homothallic and clonally propagated. This multi-genome approach provides robust resources for genotyping, molecular diagnostics, and epidemiological surveillance of S. sclerotiorum. Full article

SGT1 (the suppressor of the G2 allele of Skp1) functions as an adaptor protein that positively regulates plant defense and developmental processes. It comprises three functional domains: the tetratricopeptide repeat (TPR) domain, Chord SGT1 motif (CS), and SGT1-specific motif (SGS). In this study, we resolved the crystal structure of the Oryza sativa OsSGT1-TPR domain at 1.53 Å resolution. Structural analysis showed that the TPR domain adopts a homo-dimeric architecture stabilized by salt bridges (mediated by K52/R79/R109) and hydrophobic interactions (involving F17). Functional validation through gel filtration chromatography revealed that the disruption of the dimerization interface via F17A/K52A/R79A mutations caused complete dissociation into monomers, establishing the essential role of TPR-mediated oligomerization in maintaining the structural stability of full-length OsSGT1. Yeast two-hybrid assays showed that the dimerization disruption of SGT1 mutants retained the interaction with OsHSP81-2 (an HSP90 ortholog) and OsRAR1, indicating that SGT1 oligomerization serves primarily as a structural stabilizer rather than a prerequisite for partner interaction. Evolutionary analysis through the sequence alignment of plant SGT1 proteins revealed the conservation of the dimerization interface residues. This study provides structural insights into the conserved molecular features of SGT1 proteins and highlights the functional significance of their oligomerization state. Full article

Coastal shellfish farming areas in northern China seas face frequent starfish outbreaks, particularly from Asterias amurensis and Patiria pectinifera, leading to significant economic losses. Genomic data are key to understanding the population dynamics and adaptive traits and developing effective control measures for these species. Here, we characterized and compared the genomic information of these two starfish using a whole-genome survey approach. The genome size of A. amurensis is ~477 Mb with 1.52% heterozygosity, 53.60% repetitive sequences, and 39.94% GC content, while P. pectinifera has a ~529 Mb genome, 2.90% heterozygosity, 56.02% repetitive sequences, and 40.63% GC content. Scaffold N50 values were 1823 bp for A. amurensis and 1328 bp for P. pectinifera. We identified 161,786 microsatellite motifs in A. amurensis and 316,245 in P. pectinifera, with mononucleotide repeats being the most common. A total of 171 single-copy homologous genes were found in A. amurensis, with 94 in P. pectinifera. For both species, KEGG annotation showed functional similarities in glycan biosynthesis, translation, metabolism, catabolism, and transport. The Pairwise Sequentially Markovian Coalescent (PSMC) analysis unveiled a bottleneck effect during the Pleistocene glaciation. Additionally, phylogenetic analysis of mitochondrial genomes indicates that P. pectinifera and Patiria miniata of the same genus belong to the same branch in the evolutionary tree as sister groups with the closest genetic relationship, while A. amurensis is most closely related to Astropecten polyacanthus within the class Asteroidea. These findings provide valuable genomic insights for both species. Full article

Introduction: Rice, a cornerstone of global food security, faces escalating demands for enhanced yield and disease resistance. We collected 300 high-quality genomes, representing both cultivated (Oryza sativa indica, O. sativa japonica, and O. sativa aus) and wild species (O. rufipogon, O. glaberrima, and O. barthii). Methods: Leveraging HMMER, NLR-Annotator, and OrthoFinder, we systematically identified 148,077 leucine-rich repeat (LRR) and 143,459 nucleotide-binding leucine-rich repeat (NLR) genes, with LRR receptor-like kinases (LRR-RLKs) dominating immune receptor proportions, followed by coiled-coil domain containing (CNL)-type NLRs and LRR receptor-like proteins (LRR-RLPs). Results: Benchmarking Universal Single-Copy Orthologs (BUSCO) assessments confirmed robust genome quality (average score: 94.78). Strikingly, 454 TIR-NB-LRR (TNL) genes—typically rare in monocots—were detected, challenging prior assumptions. Phylogenetic analysis with Arabidopsis TNLs highlighted five O. glaberrima genes clustering with dicot TNLs; these genes featured truncated PLN03210 motifs fused to nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC) and LRR domains. Conclusions: By bridging structural genomics, evolutionary dynamics, and domestication-driven adaptation, this work provides a foundation for targeted breeding strategies and advances functional studies of plant immunity in rice. Full article

The Himalayan griffon (Gyps himalayensis), an obligate scavenging bird in the Qinghai–Tibet Plateau, provides significant ecological services but is currently listed as near threatened. Despite their importance for conservation, genome-wide screening for microsatellites (or SSRs) in G. himalayensis and the development of corresponding molecular markers have been lacking. This study presents the first in-depth characterization of genome-wide microsatellites in G. himalayensis and the successful development of polymorphic SSR markers. A total of 240,741 microsatellite loci were detected in the G. himalayensis genome, with an average density of 202.2 SSRs per Mb, accounting for 0.44% of the genome. Mononucleotide repeats (53.2%) were the most prevalent among the different microsatellite motif types. Additionally, 100 primer pairs were initially identified, with 17 found to be polymorphic markers. These loci hold significant potential for revealing genotypic diversity in G. himalayensis, thereby laying a foundation for the conservation of this species. Full article

Trypanosoma cruzi GenBank^® M21331 encodes for Antigen 36 (Ag 36), which is a tandemly repeated T. cruzi antigen. GenBank M21331 has a gene sequence similarity to human immune genes IFN-α, IFN-β, and IFN-γ, as well as to human TRIM genes. A BLAST-p search revealed that T. cruzi GenBank M21331 had seven gene sequences homologous to microtubule-associated protein (MAP) genes with a 100% amino acid sequence identity. There are 36 genes in the T. cruzi genome with >94% identity to GenBank M21331, and these genes encode proteins ranging in size from 38 to 2011 amino acids in length, the largest containing 20, 25, and 30 repeats of the Ag 36 thirty-eight-amino-acid-sequence motif. The purpose of this study was to perform a genetic and molecular comparative analysis of T. cruzi GenBank M21331 to determine if this gene sequence is unique to the T. cruzi clade, present in the T. brucei clade, and/or exists in other trypanosomatids. There are seven homologous genes to GenBank M21331 in T. cruzi, but only one homolog found of this gene in T. brucei. The MAP genes in T. cruzi appear to have expanded at least eleven-fold in number compared to similar MAP genes in T. brucei. The DNA sequences and functions of these MAP genes in their respective species and clades will be discussed and are a fascinating area for further scientific study. Full article

m⁶A methylation modification is an important genetic modification involved in biological processes such as sexual maturation, antibacterial, and antiviral in aquatic animals. However, few studies have been conducted in aquatic animals on the relationship between m⁶A methylation modification and autophagy-inflammation induced by lipid metabolism disorders. In the present study, a high-fat (HF) group and HF-MLP group (1 g mulberry leaf polysaccharides (MLPs)/1 kg HF diet) were set up. The mid-hind intestines of Megalobrama amblycephala juveniles from the two groups were collected for MeRIP-seq and RNA-seq after an 8-week feeding trial. The m⁶A peaks in the HF and HF-MLP groups were mainly enriched in the 3′ Untranslated Region (3′UTR), Stop codon, and coding sequence (CDS) region. Compared with the HF group, the m⁶A peaks in the HF-MLP group were shifted toward the 5′UTR region. ‘RRACH’ was the common m⁶A methylation motif in the HF and HF-MLP groups. Methyltransferase mettl14 and wtap expression in the intestines of the HF-MLP group were significantly higher compared with the HF group (p < 0.05). A total of 21 differentially expressed genes(DEGs) with different peaks were screened by the combined MeRIP-seq and RNA-seq analysis. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis enriched BCL2 interacting protein 3 (bnip3) to autophagy–animal and mitophagy–animal signaling pathways, etc., and nucleotide-binding domain leucine-rich repeat protein 1 (nlrp1) was enriched to the Nucleotide-binding oligomerization domain (NOD)-like receptor signaling pathway. Combined MeRIP-seq and RNA-seq analysis indicated that the expression pattern of bnip3 was hyper-up and that of nlrp1 was hyper-down. Gene Set Enrichment Analysis (GSEA) analysis confirmed that the intestinal genes of HF-MLP group positively regulate lysosomal and autophagy–animal signaling pathways. In the present study, we demonstrated that m⁶A methylation modification plays a role in regulating autophagy-inflammatory responses induced by HF diets by MLPs, and further explored the molecular mechanisms by which MLPs work from the epigenetic perspective. Full article

Purple cowpea accumulates abundant anthocyanins in its epidermis, with R2R3-MYB transcription factors serving as potential regulators of anthocyanin accumulation. This study systematically deciphered the genome-wide characteristics of cowpea R2R3-MYB transcription factors, elucidating their critical roles in plant anthocyanin accumulation. Employing a combined strategy of HMMER Hidden Markov Model searches and BLASTP homology alignment, we successfully identified 127 non-redundant VuR2R3-MYB transcription factors. The encoded proteins exhibited remarkable physicochemical diversity: the average length reached 338.8 amino acid residues, with theoretical isoelectric points distributed between 4.79 and 10.91 residues. When performing a phylogenetic analysis with Arabidopsis homologs, 27 distinct subgroups were identified. Among them, the S4–S7 clades showed conserved protein architectures, which might play a role in regulating the phenylpropanoid pathway. An analysis of the gene architecture revealed patterns of intron/exon organization. Specifically, 85 out of 127 loci (66.9%) presented the typical two-intron configuration, whereas 18 genes had no introns. An investigation of the promoters found that, on average, each gene had 52 cis-regulatory elements. These elements were mainly light-responsive motifs and phytohormone-related elements. Chromosomal mapping indicated an uneven distribution of these genes across 11 chromosomes. Duplication analysis further showed 13 tandem repeats and 54 segmentally duplicated pairs. An analysis of evolutionary constraints demonstrated that purifying selection was predominant (Ka/Ks < 0.5) among paralogous pairs. Through comparative transcriptomics of pod color variants, 19 differentially expressed MYB regulators were identified. These included VuR2R3-MYB23 (MYB3 homolog), VuR2R3-MYB95 (MYB4 homolog), VuR2R3-MYB53 (MYB114 homolog), and VuR2R3-MYB92 (MYB5 homolog), which showed a strong correlation with the patterns of anthocyanin accumulation. Our findings are expected to contribute to elucidating the potential regulatory mechanisms through which R2R3-MYB transcription factors mediate anthocyanin biosynthesis and accumulation. Full article

Aquilaria sinensis (Lour.) Spreng. is an economically important tree specie that produces agarwood, a valuable medicinal and aromatic resin, when injured. However, its large-scale cultivation has led to confusion regarding its resources and genetic backgrounds, hindering the conservation and management of A. sinensis accessions. This study systematically developed and validated simple sequence repeat (SSR) molecular markers by using whole-genome resequencing (WGR) data from 60 A. sinensis accessions to elucidate their genetic diversity and population structure. A total of 56,657 SSR sequences (24,430 loci) were identified, which were dominated with dinucleotide repeat motifs (73.59%). After stringent quality control, 46 high-quality SSR loci were obtained, and 93 primer pairs were designed for amplification validation. Ultimately, 20 primer pairs with stable amplification and high polymorphism were selected, of which 11 exhibited high polymorphism (polymorphic information content: 0.554–0.688). These 20 primer pairs identified a total of 121 alleles, with an average of 6 alleles per locus. These primers successfully classified 149 A. sinensis accessions into three subpopulations, achieving a discrimination rate of 95.97%. The analysis of molecular variance revealed that genetic variation within the individuals accounted for 84% of the total variation. This study establishes a rapid and efficient SSR-based method by leveraging resequencing data for large-scale marker discovery in A. sinensis. It further provides a robust technical framework for the conservation and sustainable utilization of this valuable species. Full article

Genomic sequences that form three-stranded triplexes (TPXs) under physiological conditions (called T-flipons) play an important role in defining DNA nucleosome-free regions (NFRs). Within these NFRs, other flipon types can cycle conformations to actuate gene expression. The transcripts read from the NFR form condensates that engage proteins and small RNAs. The helicases bound then trigger RNA polymerase release by dissociating the 7SK ribonucleoprotein. The TPXs formed usually incorporate RNA as the third strand. TPXs made only from DNA arise mostly during DNA replication. Many small RNA types (sRNAs) and long noncoding (lncRNA) can direct TPX formation. TPXs made with circular RNAs have greater stability and specificity than those formed with linear RNAs. LncRNAs can affect local gene expression through TPX formation and transcriptional interference. The condensates seeded by lncRNAs are updated by feedback loops involving proteins and noncoding RNAs from the genes they regulate. Some lncRNAs also target distant loci in a sequence-specific manner. Overall, lncRNAs can rapidly evolve by adding or subtracting sequence motifs that modify the condensates they nucleate. LncRNAs show less sequence conservation than protein-coding sequences. TPXs formed by lncRNAs and sRNAs help place nucleosomes to restrict endogenous retroelement (ERE) expression. The silencing of EREs starts early in embryogenesis and is essential for bootstrapping development. Once the system is set, EREs play a different role, with a notable enrichment of Short Interspersed Nuclear Repeats (SINEs) in Enhancer–Promoter condensates. The highly programmable TPX-dependent processes create a chromaverse capable of many complexities. Full article

Efficient evolution exists before DNA, else the DNA genome itself could not evolve. Current data suggest RNA-membranes for this role. Selected RNAs bind well to phospholipid bilayers; randomized sequences do not. No repeated sequences are evident in selected binding RNAs. This implies small and varied membrane-affinity motifs. Such binding sequences are partially defined. Phospholipid-bound RNAs require divalents like Mg²⁺ and/or Ca²⁺, preferring more ordered bilayers: gel, ripple, or rafted membranes, in that order. RNAs also bind and stabilize bent or sharply deformed bilayers. RNA binding without divalents extends to negatively charged membranes formed from simpler anionic phospholipids and to plausibly prebiotic fatty acid bilayers. RNA-membranes frequently retain RNA solution functions: base pairing, passive transport of tryptophan, specific affinity for arginine side chains, and ribozymic ligase catalysis. Membrane-bound RNAs with several biochemical functions, linked by specific base-pairing, are readily constructed. Given these data, genetic roles seem feasible. RNA activities often require few nucleotides, easily joined in a small RNA. Base-paired groups of such RNAs can also be purposeful, joining related functions. Complex functions can therefore require only replication of short RNAs. RNA-membranes potentially segregate accurately during cell division and quickly evolve through new base pairings. Accordingly, ancient RNA-membranes could act as a protogenome, supporting encoded RNA expression, inheritance, and evolution before the DNA genome: for example, supporting organized biochemistry, coded translation, and a Standard Genetic Code. Full article

Background: The RSPO gene family encodes secreted glycoproteins that are rich in cysteine, which generally serve as activators of the Wnt signaling pathway in animals. Four types of this family have been identified in a few model species. However, the evolution of the family remains unclear. Methods: In this study, we identified a total of 1496 RSPO homologs through an extensive survey of the RSPO genes in 430 animals. Gene family clustering and phylogenetic analysis identified four major subtypes of the family (RSPO1–RSPO4) and clarified their distribution of copy number in different species. Results and Conclusions: Members of the RSPO4 subfamily that were closest to ancestral forms existed in both Deuterostomes and Protostomates, and we speculate that representatives of this subfamily already existed in Urbilatera, the last common ancestor of Deuterostomes. Particularly, in some RSPO3 subtypes of Actinopterygii (ray-finned fishes), an FU repeated motif with three conserved cysteines was identified. Further conservative analysis of amino acids and alignment of tertiary protein structure revealed the potential functional sites for each subgroup. The results provide insight into the phylogenetic relationships and evolutionary patterns of conserved motifs of RSPO family genes in animal kingdoms, which will guide further studies on the biological functions of RSPO in other non-model species. Full article

Inherited neurological disorders, such as spinocerebellar ataxia (SCA) and fragile X (FraX), are frequently caused by short tandem repeat (STR) expansions. The detection and assessment of STRs is important for diagnostics and prognosis. We tested the abilities of nanopore long-read sequencing (LRS) using a custom panel including the nine most common SCA-related genes and FraX and created raw data to report workflow. Using known STR lengths for 23 loci in 12 patients, a pipeline was validated to detect and report STR lengths. In addition, we assessed the capability to detect SNVs, indels, and the methylation status in the same test. For the 23 loci, 22 were concordant with known STR lengths, while for the last, one of three replicates differed, indicating an artefact. All positive control STRs were detected as likely pathogenic, with no additional findings after a visual assessment of repeat motifs. Out of 226 SNV and Indel variants, two were false positive and one false negative (accuracy 98.7%). In all FMR1 controls, a methylation status could be determined. In conclusion, LRS is suitable as a diagnostic workflow for STR analysis in neurological disorders and can be generalized to other diseases. The addition of SNV/Indel and methylation detection promises to allow for a one-test-fits-all workflow. Full article