Search Results (2,137)

Dendrobium is an orchid genus with high economic and ecological importance, but its taxonomy based on morphology remains controversial. Dendrobium linawianum, a critically endangered species with both ornamental and medicinal value, represents a key taxon within this genus. However, its phylogenetic relationship has long been unplaced due to similar morphological traits. Despite its conservation and taxonomic importance, its complete chloroplast genome has not been previously characterized. Here, we newly sequenced and assembled the complete chloroplast genome of D. linawianum. The 150,497 bp genome exhibits a typical quadripartite structure, encoding 119 genes. A total of 161 simple sequence repeats (SSRs) were identified, predominantly mononucleotide and dinucleotide motifs. Condon usage analysis revealed leucine as the most abundant amino acid. Phylogenetic analysis based on complete chloroplast genome sequences strongly supported the close relationship of D. linawianum with D. hercoglossum, D. thyrsiflorum, and D. moniliforme, resolving its taxonomic position within the genus. The complete chloroplast genomes successfully resolved the phylogenetic relationships among 35 Dendrobium species, demonstrating their efficacy as powerful molecular markers for resolving taxonomic ambiguities within this morphologically complex genus. Our findings provide a genomic foundation for precise species identification and molecular breeding of D. linawianum, and enhance understanding of phylogenetic relationships in this taxonomically challenging group. Full article

Snakes are model animals to study energy balance, but studies on the gut microbiota of the animals are rather scarce. To fill the gap, we used metagenome sequencing to investigate the microbial community composition and adaptability in the stomach, small intestine, and large intestine of Big-eyed Bamboo Snake. The results showed that there was no significant differences in α-diversity among different gastrointestinal segments. Pseudomonadota, Bacteroidota, and Bacillota were the most abundant phyla. The dominant genera in the stomach and small intestine were similar, while those in the large intestine were distinct. The abundance of Bacteroides, Citrobacter and Clostridium was significantly higher in the large intestine than in the small intestine. The LEfSe analysis revealed that the small intestine had the most characteristic bacteria, with a total of 20 species, while the stomach and large intestine each had two species. Additionally, in the current study, we also focused on the impact of the microbial community structure on functions through functional annotations in the KEGG and CAZy. There were significant differences in the KEGG level 2 between the stomach and the small intestine. The LEfSe analysis revealed the differences in the CAZy level 2 between the large intestine and the small intestine. Overall, our study provided a comparative and contrastive analysis of the gut microbiota in different gastrointestinal segments of Big-eyed Bamboo Snake, offering valuable insights for the co-evolution mechanism of the host and the gut microbiota. Full article

Monitoring freshwater resources is crucial to drinking water quality. The Ismailia Canal supplies most freshwater to the Suez Canal area in Egypt. However, information on the freshwater microbiome is limited in this region. A total of 59 freshwater samples were collected. Along with determining the physicochemical properties of the samples, we used conventional methods to identify indicator bacteria. To overcome limitations of conventional culture, we employed high-throughput 16S rRNA gene sequencing, taxonomy profiling, and functional prediction to study uncultivated microbial communities. Total and fecal coliforms prevailed in 100% and 80% of samples, respectively. Predominant contaminants included E. coli, fecal streptococci, Pseudomonas aeruginosa, and Staphylococcus aureus. Taxonomic profiling revealed dominance of Proteobacteria and Actinobacteriota. Proteobacteria showed a positive correlation with Bacteroidetes and a negative correlation with Actinobacteria. Most samples had similar bacterial community structures, despite location-driven variability. Elevated bacterial loads were notable at the Qassasin district, which exhibited the highest relative abundance of genes associated with bacterial infections. This study provides key insights into the impact of freshwater microbiome on public health. Full article

The family Flaviviridae is divided into flaviviruses, hepaciviruses and pestiviruses. Its members infect a wide range of organisms, from insects to humans, and share a similar genome organization where proteins require sequential cleavage from a single translated polyprotein. Despite decades of study, the structures of some non-structural (NS) membrane proteins, or details of their protein–protein interactions (PPIs), are still unclear. Since AlphaFold (AF) can be used to predict interactions between protein domains using Predicted Alignment Error (PAE) score plots, we hypothesized that AF-predicted interactions between domains of complete viral polyproteins can represent PPIs if these interactions are retained once the different proteins are sequentially cleaved. We complemented this approach using AF predictions involving all independent separate protein sequences, instead of using a single polyprotein. We found that most of these PPIs have already been reported experimentally, which validates the use of AF in this context, but not all of these PPIs have been characterized from a structural perspective. Thus, we propose that AF provides testable hypotheses regarding residues involved in these PPIs, and that comparison of the three genera in this family may provide much needed clues to the function of these proteins during the viral life cycle. Full article

Non-coding RNAs (ncRNAs) are involved in many biological processes, making their identification and functional characterization a priority. Among them, long non-coding RNAs (lncRNAs) have been shown to regulate diverse cellular processes, such as cell development, stress response, and transcriptional regulation. The continued identification of new lncRNAs highlights the demand for reliable methods for their detection, with structural analysis offering insightful information. Currently, lncRNAs are identified using tools such as LncFinder, whose database has a large collection of lncRNAs from humans, mice, and chickens, among others. In this work, we present a graph-based algorithm to represent and compare RNA secondary structures. Rooted tree graphs were used to compare two groups of Saccharomyces cerevisiae RNA sequences, lncRNAs and not lncRNAs, by searching for structural similarities between each group. When applied to a novel candidate sequence dataset, the algorithm evaluated whether characteristic structures identified in known lncRNAs recurred. If so, the sequences were classified as likely lncRNAs. These results indicate that graph-based structural analysis offers a complementary methodology for identifying lncRNAs and may complement existing sequence-based tools such as lncFinder or PreLnc. Recent studies have shown that tumor cells can secrete lncRNAs into human biological fluids forming circulating lncRNAs which can be used as biomarkers for cancer. Our algorithm could be applied to identify novel lncRNAs with structural similarities to those associated with tumor malignancy. Full article

Microbial communities that develop within biofilms on electrodes are necessary for the proper functioning of the microbial electrochemical system. However, the mechanism through which an exogenous exoelectrogen influences the population dynamics and electrochemical performance of biofilms remains unclear. In this study, we explored the community structure dynamics and electrochemical characteristics of iron mine soil biofilm co-cultured with Shewanella oneidensis MR-1, with the anode as the electron acceptor, and compared the results with those of iron mine soil biofilms alone on the anode. Shewanella oneidensis MR-1 improved the electrochemical activity of microbial biofilms, resulting in a higher maximum power density of 195 ± 8 mW/m² compared with that of iron mine soil (175 ± 7 mW/m²) and Shewanella (88 ± 8 mW/m²) biofilms individually. The co-cultured biofilms could perform near the highest power density for a longer duration than the iron mine soil biofilms could. High-throughput 16S rRNA gene sequencing of the biofilms on the anode indicated that the relative abundance of Pelobacteraceae in the co-culture system was significantly (p = 0.02) increased, while that of Rhodocyclaceae was significantly (p = 0.008) decreased, compared with that in iron mine soil biofilms. After continuing the experiment for two months, the presence of Shewanella oneidensis MR-1 changed the predominant bacteria of the microbial community in the biofilms, and the relative abundance of Shewanella was significantly (p = 0.02) decreased to a level similar to that in iron mine soil. These results demonstrate that Shewanella oneidensis MR-1 could improve the performance of iron mine soil biofilms in electrochemical systems by altering the composition of the functional microbial communities. Full article

The Thracian Sea, a semi-enclosed coastal basin in the northeastern Aegean Sea, represents a dynamic marine environment influenced by freshwater inputs, stratification, and seasonal variability. Here, we investigated the spatiotemporal dynamics of microbial and ichthyofaunal communities using environmental DNA (eDNA) and high-throughput sequencing across various stations in the vicinity of the Thracian Sea, in consecutive months (through spring and summer). Seawater samples were collected from the surface and thermocline layers, and environmental parameters were recorded to examine their influence on biodiversity patterns. Microbial communities exhibited strong seasonal and depth-related structuring. Alpha diversity was highest in spring and declined during summer, while beta diversity analyses revealed clear clustering by month and depth. Dominant taxa included Alphaproteobacteria (SAR11), Cyanobacteria (Synechococcus, Prochlorococcus), with distinct core microbiomes. Fish communities, identified via CytB metabarcoding, displayed marked temporal turnover but limited spatial segregation. While alpha diversity metrics did not differ significantly, beta diversity analyses showed seasonal shifts with dominant taxa such as Raja spp., Engraulis spp., and Diplodus sargus. Multivariate and co-structure analyses (Mantel, Procrustes) revealed moderate but significant concordance between microbial and fish communities and support the existence of similar biodiversity responses to environmental parameters across temporal and spatial variability. Co-occurrence networks further present depth-specific associations, with surface communities being more cooperative and phototrophic, while thermocline networks showed modularity and potential ecological specialization. This study highlights the value of integrated eDNA-based monitoring in revealing seasonal biodiversity dynamics and ecological interactions in coastal marine ecosystems, supporting future spatial planning and conservation strategies in the Thracian Sea. Full article

Background/Objectives: Ginsenosides, one of the most pharmaceutically valuable chemical compounds in Panax ginseng, are synthesized with several enzymes, including UGTs. UGTs determine absorbability and physiological function upon consumption. Thus, understanding the functional residues of ginsenoside biosynthesis-associated UGTs is crucial for enhancing the production of valuable ginsenoside varieties. Methods: We collected the UGT homologs of high sequence similarity from two rate-limiting steps of the biosynthetic pathway. The 3D structures of these proteins were predicted using the AlphaFold3 model. The ligand-binding interactions of these UGTs were examined using SwissDock and CB-Dock2. Enzyme kinetics were analyzed with MPEK. Using these tools, we performed in silico mutagenic analyses to identify the functional residues of UGTs in detail. Results: We elucidated the molecular mechanisms of experimentally verified functional residues in UGTs, many of which were associated with optimal ligand interaction angles that expose target carbons. We also identified putatively important amino acid residues that mediate ligand interactions and modulate reaction kinetics by more than 25%. In this study, residues at positions 62, 224, 397, and 398 were shown to significantly influence enzyme kinetics. Conclusions: Our study provides the first structural analysis of the functional residues of ginsenoside biosynthetic UGTs based on their 3D structures. We identified several key amino acid residues essential for proper ginsenoside biosynthesis: (1) residues determining ligand interactions, (2) residues modulating ligand binding angles, and (3) residues affecting reaction kinetics. Our findings demonstrate an effective approach to identifying functional residues in plant enzymes and present valuable UGT candidates for future experimental validation. Full article

Amaranthus palmeri is an aggressive, highly invasive weed that thrives across a wide range of adverse environments worldwide; nevertheless, the mechanisms underlying its rapid expansion remain largely unstudied. Glutathione peroxidase (GPX) is a crucial enzyme within the antioxidant defense system, belonging to the phylogenetic conserved family of oxidoreductases present in all living organisms. Despite its significance, the role of GPX in A. palmeri has not been reported. This study identified eight GPX genes (ApGPXs) in A. palmeri through comprehensive bioinformatics and gene expression analyses. The research examined the characteristics, evolutionary relationships, chromosomal mapping, gene structure, subcellular localization, conserved motifs, and cis-acting elements of these genes, as well as their evolutionary conserved functions in relation to Arabidopsis thaliana GPXs and RT-qPCR analysis under various stress conditions. The ApGPXs were distributed across scaffolds (2, 4, and 12) of the A. palmeri genome. Phylogenetic analysis grouped GPX genes into four subgroups, and conserved motifs were found within certain phylogenetic subgroups. We identified Actin8 as the most stable internal reference gene for A. palmeri under diverse stress conditions. Gene expression analysis revealed that ApGPXs participate in both early and late regulatory responses to oxidative stress induced by NaCl, high temperature, osmotic pressure, and glufosinate ammonium. The Arabidopsis GPX mutant (AT4G31870) exhibited a stronger flg22-induced oxidative burst than the wild type, and qPCR confirmed that AtGPXs contribute significantly to glufosinate ammonium stress responses. Evolutionary analysis found high sequence similarity between ApGPX4 and AT1G63460, as well as ApGPX3 and AT4G11600. Also, ApGPX3 and AT4G11600 shared similar expression patterns under glufosinate ammonium stress. This research presents the first gene family study in A. palmeri and provides foundational insights for future studies in this economically critical species. Our findings establish a framework for mitigating A. palmeri’s impact on crop production and exploring ApGPXs in developing herbicide- and stress-tolerant cultivars. Full article

This study presents a machine learning-based framework for classifying five embroidered stitch patterns—straight, zigzag, joining, satin, and wave—under 10% tensile strain, aiming to enhance their utility in smart textile circuits. Electrical conductivity was derived from resistance data and standardized using Z-score normalization. Conductivity sequences were first analyzed with PCA and Random Forest classifiers, then classified using a structural artificial neural network model. The model employed a structurally informed filter design, reflecting stitch-wise signal periodicity to capture time-varying electrical patterns under cyclic strain. It achieved a test accuracy of 97.33%, with F1-scores above 0.83 for all classes and perfect scores in three. Partial confusion between wave and zigzag patterns was observed due to their similar curved geometry and signal profiles. These results validate the discriminative power of conductivity-based features and demonstrate the potential of structure-aware neural networks for identifying dynamic stitched circuits in smart textiles. Full article

SHORT INTERNODE (SHI)-Related Sequence (SRS) transcription factors play crucial roles in plant growth, development, and stress responses and have been extensively studied in various plant species. However, the molecular functions and regulatory mechanisms of SRS genes in the economically important tropical fruit crop pitaya (Hylocereus undatus) remain poorly understood. This study identified 9 HuSRS genes in pitaya via bioinformatics analysis, with subcellular localization predicting nuclear distributions for all. Gene structure analysis showed 1–4 exons, and conserved motifs (RING-type zinc finger and IXGH domains) were shared across subclasses. Phylogenetic analysis classified the HuSRS genes into three subfamilies. Subfamily I (HuSRS1–HuSRS4) is closely related to poplar and tomato homologs and subfamily III (HuSRS6–HuSRS8) contains a recently duplicated paralogous pair (HuSRS7/HuSRS8) and shows affinity to rice SRS genes. Protein structure prediction revealed dominance of random coils, α-helices, and extended strands, with spatial similarity correlating to subfamily classification. Interaction networks showed HuSRS1, HuSRS2, HuSRS7 and HuSRS8 interact with functional proteins in transcription and hormone signaling. Promoter analysis identified abundant light/hormone/stress-responsive elements, with HuSRS5 harboring the most motifs. Transcriptome and qPCR analyses revealed spatiotemporal expression patterns: HuSRS4, HuSRS5, and HuSRS7 exhibited significantly higher expression levels in callus (WG), which may be associated with dedifferentiation capacity. In seedlings, HuSRS9 exhibited extremely high transcriptional accumulation in stem segments, while HuSRS1, HuSRS5, HuSRS7 and HuSRS8 were highly active in cotyledons. This study systematically analyzed the characteristics of the SRS gene family in pitaya, revealing its evolutionary conservation and spatio-temporal expression differences. The research results have laid a foundation for in-depth exploration of the function of the SRS gene in the tissue culture and molecular breeding of pitaya. Full article

Bisphenol A (BPA) and its substitutes have been identified as endocrine-disrupting chemicals (EDCs). However, little information is available on their reproductive endocrine disruptive effects in mollusks. This study cloned the full-length sequence (2434 bp) of the estrogen-related receptor (ERR) gene in the freshwater bivalve Corbicula fluminea and performed a bioinformatics analysis and tissue-specific expression analysis. We further examined the expression of the CfERR gene after exposure to E2, BPA, and their substitutes (BPS, BPF, and BPAF) at 1, 10, and 100 μg/L for 0, 1, 7, 14, 21, and 28 days. The results showed that CfERR is a nuclear protein with a typical structure. Phylogenetic analysis indicated a high degree of similarity among bivalve species. The high expression of CfERR in the gonad suggested its important role in reproductive regulation. The exposure experiment confirmed that CfERR showed a time- and dose-dependent upregulation in response to all pollutants, with BPS and BPAF exhibiting stronger estrogenic interference effects. This study facilitates a better understanding of the reproductive regulation of bivalves and provides data to support the toxicity evaluation of BPA and its substitutes. Full article

Background/Objectives: The global dissemination of tet(X) variants critically threatens tigecycline efficacy as a last-resort antibiotic. The aim of this study was to characterize a tet(X6)-carrying integrative and conjugative element (ICE) in a multidrug-resistant Chryseobacterium lecithinasegens strain, SHZ29, isolated from Shanghai, China. Methods: Minimum inhibitory concentrations (MICs) were determined by broth microdilution for SHZ29. Whole genomic sequencing and bioinformatic analysis were performed to depict the structure of the novel tet(X6)-carrying ICE. Inverse PCR and conjugation experiments were conducted to investigate the transfer ability of the ICE. Results: We depicted a novel tet(X6)-carrying ICE, named ICECleSHZ29, which is 74,906 bp in size and inserted into the 3′ end of tRNA-Met-CAT gene of the C. lecithinasegens strain SHZ29, with 17 bp direct repeats (5′-tcccgtcttcgctacaa-3′). This ICE possesses a 38 kb conserved backbone and four variable regions (VR1-4), with VR3 aggregating multiple resistance genes, including tet(X6), tet(X2), erm(F), ere(D), floR, catB, sul2, ant(6)-I and bla_OXA-1327. NCBI database searching identified 13 additional ICEs sharing a similar backbone to ICECleSHZ29. These ICECleSHZ29-like ICEs could be classified into two types based on their distinct insertion sites: Type I, inserted at the tRNA-Met-CAT gene; and Type II, inserted at the tRNA-Glu-TTC gene. Phylogenetic analysis indicated that differences in integrases may result in differences in the insertion site among these ICEs. A circular intermediate form of ICECleSHZ29 was detected by inverse PCR. However, the conjugation experiments using Escherichia coli EC600 as recipients failed. Conclusions: To our knowledge, this study provides the first report of tet(X6) in C. lecithinasegens and characterizes its carrier, a novel ICE: ICECleSHZ29. Full article

The SETD6 protein lysine methyltransferase monomethylates specific lysine residues in a diverse set of substrates which contain the target lysine residue in a highly variable amino acid sequence context. To investigate the mechanism underlying this multispecificity, we analyzed SETD6 substrate recognition using AlphaFold 3 docking and peptide SPOT array methylation experiments. Structural modeling of the SETD6–E2F1 complex suggested that substrate binding alone is insufficient to restrict SETD6 activity to only one lysine residue, pointing to additional sequence readout at the target site. Methylation of mutational scanning peptide SPOT arrays derived from four different SETD6 substrates (E2F1 K117, H2A.Z K7, RELA K310, and H4 K12) revealed sequence preferences of SETD6 at positions −1, +2, and +3 relative to the target lysine. Notably, glycine or large aliphatic residues were favored at −1, isoleucine/valine at +2, and lysine at +3. These preferences, however, were sequence context dependent and variably exploited among different substrates, indicating conformational variability of the enzyme–substrate interface. Mutation of SETD6 residue L260, which forms a contact with the +2 site in the available SETD6-RELA structure, further demonstrated substrate-specific differences in recognition at the +2/+3 sites. Together, these findings reveal a versatile mode of peptide recognition in which the readout of each substrate position depends on the overall substrate peptide sequence. These findings can explain the multispecificity of SETD6 and similar mechanisms may underlie substrate selection in other protein methyltransferases. Full article

Bacteriophages have been widely investigated as a promising treatment of food, medical equipment, and humans colonized by antibiotic-resistant bacteria. Phages pose particular interest in combating those bacteria which form biofilms, such as the medically important human pathogen Pseudomonas aeruginosa and several plant pathogens, including P. syringae. In an undergraduate lab course, P. putida was used as the host to isolate novel anti-pseudomonal bacteriophages. Environmental samples of soil and water were collected, and purified phage isolates were obtained. After Illumina sequencing, genomes of these phages were assembled de novo and annotated. Assembled genomes were compared with known genomes in the literature and GenBank to identify taxonomic relations and to refine their functional annotations. The thirteen phages described are sipho-, myo-, and podoviruses in several families of Caudoviricetes, spanning several novel genera, with genomes ranging from 40,000 to 96,000 bp. One phage (DDSR119) is unique and is the first reported P. putida siphovirus. The remaining 12 can be clustered into four distinct groups. Six are highly related to each other and to previously described Autotranscriptaviridae phages: Waldo5, PlaquesPlease, and Laces98 all belong to the Waldovirus genus, whereas Stalingrad, Bosely, and Stamos belong to the Troedvirus genus. Zuri was previously classified as the founding member of a new genus Zurivirus within the family Schitoviridae. Ebordelon and Holyagarpour each represent different species within Zurivirus, whereas Meara is a more distantly related member of the Schitoviridae. Dolphis and Jeremy are similar enough to form a genus but have only a few distant relatives among sequenced phages and are notable for being temperate. We identified the lysis cassettes in all 13 phages, compared tail spike structures, and found auxiliary metabolic genes in several. Studies like these, which isolate and characterize infectious virions, enable the identification of novel proteins and molecular systems and also provide the raw materials for further study, evaluation, and manipulation of phage proteins and their hosts. Full article