Search Results (3,425)

Post-exertional malaise (PEM) is a defining symptom of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS), yet its molecular underpinnings remain elusive. This study investigated the temporal–longitudinal DNA methylation changes associated with PEM using a structured two-day maximum repeated effort cardiopulmonary exercise testing (CPET) protocol involving pre- and two post-exercise blood samplings from five ME/CFS patients. Cardiopulmonary measurements revealed complex heterogeneous profiles among the patients compared to typical healthy controls, and VO₂ peak indicated all patients had poor normative fitness. The switch to anaerobic metabolism occurred at a lower workload in some patients on Day Two of the test. Reduced Representation Bisulphite Sequencing followed by analysis with Differential Methylation Analysis Package-version 2 (DMAP2) identified differentially methylated fragments (DMFs) present in the DNA genomes of all five ME/CFS patients through the exercise test compared with ‘before exercise’. With further filtering for >10% methylation differences, there were early DMFs (0–24 h after first exercise test) and late DMFs between (24–48 h after the second exercise test), as well as DMFs that changed gradually (between 0 and 48 h). Of these, 98% were ME/CFS-specific, compared with the two healthy controls accompanying the longitudinal study. Principal component analysis illustrated the three distinct clusters at the 0 h, 24 h, and 48 h timepoints, but with heterogeneity among the patients within the clusters, highlighting dynamic methylation responses to exertion in individual patients. There were 24 ME/CFS-specific DMFs at gene promoter fragments that revealed distinct patterns of temporal methylation across the timepoints. Functional enrichment of ME-specific DMFs revealed pathways involved in endothelial function, morphogenesis, inflammation, and immune regulation. These findings uncovered temporally dynamic epigenetic changes in stress/immune functions in ME/CFS during PEM and suggest molecular signatures with potential for diagnosis and of mechanistic significance. Full article

Hyaluronidase is a hydrolytic enzyme that cleaves β-1,4-glycosidic linkages in high-molecular-weight hyaluronic acid, generating low-molecular-weight oligosaccharides with enhanced biological functions. These products exhibit immunomodulatory, antioxidant, and tissue-regenerative properties, making them valuable in pharmaceutical, cosmetic, and functional food applications. However, most commercial hyaluronidases originate from pathogenic bacteria or recombinant hosts, raising concerns over their biosafety and regulatory acceptance, particularly in food-grade applications. In this study, we report the isolation and characterization of a novel non-pathogenic soil bacterium, Paenibacillus residui BSSK58, which produces an extracellular hyaluronidase. Whole-genome sequencing revealed the absence of known virulence factors and antibiotic resistance genes. Phenotypic safety evaluations confirmed that there was no hemolytic activity, biogenic amine production, or cytotoxicity against human intestinal epithelial cell lines (Caco-2 and HT-29). The purified BSSK58 hyaluronidase exhibited a molecular weight of approximately 170 kDa, with optimal activity at pH 8.0–9.0 and 50 °C. The enzyme showed broad substrate specificity toward hyaluronic acid, chondroitin sulfate, and alginate, and its depolymerizing activity was confirmed using gel permeation chromatography. Furthermore, a 13-week oral repeated-dose toxicity study under Good Laboratory Practice conditions demonstrated no adverse effects. These findings support the use of BSSK58 hyaluronidase as a safe, non-recombinant biocatalyst suitable for industrial applications under regulatory-compliant frameworks. Full article

Xylazine abuse is emerging as a global problem, whereas the toxic mechanisms of xylazine poisoning are seldom studied. The present study aims to assess the heart injury in xylazine poisoning and uncover the underlying mechanism. Forty male SD rats were randomly dived into four groups: control (saline), low dose (10 mg/kg xylazine), median dose (20 mg/kg xylazine) and high dose (40 mg/kg xylazine). The rats were injected with the drug intraperitoneally for 28 consecutive days, and then cardiac ultrasound examination was performed and serum and heart tissues were collected. Genomic, proteomic, and metabolic omics analyses were conducted. ELISA, RNA sequencing, histopathology examination, RT-qPCR, and Western blot were performed. Repeated injection of xylazine led to a decrease in the expression of cardiac output (CO), ventricular systole (VS), and ventricular diastole (VD), while concurrently elevating the levels of lactate dehydrogenase (LDH), creatine kinase myocardial band (CK-MB), and cardiac troponin T (c-TNT) in the serum. HE staining analysis showed evidence of contraction band necrosis, interstitial fibrosis, and infiltration by inflammatory cells in animals with xylazine poisoning. The modified genes, proteins, and metabolites were gathered, and the integration of transcriptomic, proteomic, and metabolic networks identified 25 overlapping pathways between the differentially expressed genes and metabolites (DEGs-DEMs) and the differentially expressed proteins and metabolites (DEPs-DEMs) joint pathways. The majority of these pathways pertained to the metabolism of sugars, amino acids, and fats. The proteins associated with fructose and mannose metabolism, as well as cholesterol metabolism, were validated, thereby substantiating their pivotal role in the development of xylazine-induced cardiac injury. Repeated injection of xylazine impaired heart function and the metabolism of fructose and mannose. Cholesterol metabolism pathways were critical in the process of xylazine-induced heart injury. Full article

When complex computations cannot be performed on board a mobile robot, sensory data must be transmitted to a remote station to be processed, and the resulting actions must be sent back to the robot to execute, forming a repeating cycle. This involves stochastic round-trip times in the case of non-deterministic network communications and/or non-hard real-time software. Since robots need to react within strict time constraints, modeling these round-trip times becomes essential for many tasks. Modern approaches for modeling sequences of data are mostly based on time-series forecasting techniques, which impose a computational cost that may be prohibitive for real-time operation, do not consider all the delay sources existing in the sw/hw system, or do not work fully online, i.e., within the time of the current round-trip. Marginal probabilistic models, on the other hand, often have a lower cost, since they discard temporal dependencies between successive measurements of round-trip times, a suitable approximation when regime changes are properly handled given the typically stationary nature of these round-trip times. In this paper we focus on the hypothesis tests needed for marginal modeling of the round-trip times in remotely operated robotic systems with the presence of abrupt changes in regimes. We analyze in depth three common models, namely Log-logistic, Log-normal, and Exponential, and propose some modifications of parameter estimators for them and new thresholds for well-known goodness-of-fit tests, which are aimed at the particularities of our setting. We then evaluate our proposal on a dataset gathered from a variety of networked robot scenarios, both real and simulated; through >2100 h of high-performance computer processing, we assess the statistical robustness and practical suitability of these methods for these kinds of robotic applications. Full article

Chinese pine, Pinus tabuliformis, is one of the most important garden plants in northern China, and the planting of this species is of great significance for the improvement of the ecological environment. In this study, different fungi were isolated and purified from diseased Pinus tabuliformis samples collected in Xi’an city, Shaanxi Province. Of these fungal isolates, only one (isolate AP-3) was pathogenic to the healthy host plant. The pathogenic isolate was identified as Fusarium acuminatum by morphological characteristics and ITS and TEF-1α sequence analyses. The optimal growth conditions for this isolate were further analyzed as follows: Optimal temperature of 25 °C, pH of 11, soluble starch and sodium nitrate as the most preferred carbon and nitrogen sources, respectively. By combining Oxford Nanopore Technologies (ONT) long-read sequencing with Illumina short-read sequencing technologies, we obtained a 41.50 Mb genome assembly for AP-3, with 47.97% GC content and 3.04% repeats. This consisted of 14 contigs with an N50 of 4.64 Mb and a maximum length of 6.45 Mb. The BUSCO completeness of the genome assembly was 98.94% at the fungal level and 97.83% at the Ascomycota level. The genome assembly contained 13,408 protein-coding genes, including 421 carbohydrate-active enzymes (CAZys), 120 cytochrome P450 enzymes (CYPs), 3185 pathogen-host interaction (PHI) genes, and 694 candidate secreted proteins. To our knowledge, this is the first report of F. acuminatum causing needle blight of P. tabuliformis. This study not only uncovered the pathogen responsible for needle blight of P. tabuliformis, but also provided a systematic analysis of its biological characteristics. These findings provide an important theoretical basis for disease control in P. tabuliformis and pave the way for further research into the fungal pathogenicity mechanisms and management strategies. Full article

Callicarpa peichieniana is an important traditional Chinese medicinal plant with pharmacological benefits for digestive system diseases and wounds, as well as high ornamental value. The goal of this study is to establish an effective in vitro regeneration system in order to satisfy the expanding market demand. Extracts from algae can enhance the proliferation and rooting effect of adventitious buds and can improve the survival rate of transplantation. This study developed an in vitro regeneration system using apical bud explants of C. peichieniana associated with Chlorella sorokiniana (an alga species). Inter simple sequence repeat (ISSR) molecular markers confirmed the genetic fidelity of the regenerated plantlets. The highest number of adventitious buds (5.00 buds) was induced from the apical buds with 0.5 mg/L 6-BA in a Murashige and Skoog (MS) medium, and the highest proliferation coefficient (5.83) was achieved with 2.0 mg/L 6-BA. A rooting rate of 100% was achieved by using 0.1 mg/L NAA, MS with 50% macroelements, and 20 g/L sucrose, averaging 6.36 roots per explant and a root length of 1.32 cm. In all micropropagation stages, C. sorokiniana coexisted and proliferated alongside C. peichieniana materials. ISSR showed that the genetic fidelity of C. peichieniana regenerated plants was 95.45%. Coconut coir/perlite = 1∶1 (v/v) was identified as the optimal transplantation substrate, achieving a 100% survival rate. The “C. peichieniana–C. sorokiniana association” in vitro regeneration system established in this study not only enables the mass production of high-quality regenerated plantlets but provides new ideas and demonstrations for culturing multiple species in the same in vitro system. Full article

Fermentation is a crucial stage in the production of washed mild coffees, as it enables the generation of compounds that influence overall quality. The conditions to optimize this process are still unknown. This study evaluated the effects of fermenting coffee fruits and depulped coffee under two conditions: an open tank (semi-anaerobic-SA) and a closed tank (self-induced anaerobic fermentation, SIAF) over 192 h. Samples were taken every 24 h using a sacrificial bioreactor. A randomized complete block design with a factorial arrangement (2 × 2 + 1), plus a standard control, was employed, incorporating two factors: coffee type and fermentation condition. High-throughput sequencing of 16S and ITS amplicons identified an average of 260 ± 71 and 101 ± 24 OTUs, respectively. Weisella was the dominant lactic acid bacteria, followed by Leuconostoc and Lactiplantibacillus. Acetic acid bacteria, mainly Acetobacter, were more abundant under semi-anaerobic conditions. The yeast genera most affected by the fermentation condition were Pichia, Issatchenkia, and Wickerhamomyces. Repeated measures analysis revealed significant differences in pH, glucose consumption, lactic acid production, dry matter content, embryo viability, and the percentage of healthy beans. Principal component analysis was used to develop an index that integrates physical, physiological, and sensory quality variables, thereby clarifying the impact of each treatment. Samples from shorter fermentation times and SIAF conditions scored closest to 1.0, reflecting the most favorable outcomes. Otherwise, samples from longer fermentation times in both depulped and coffee fruits scored 0.497 and 0.369, respectively, on the SA condition. These findings support technically and economically beneficial fermentation strategies. Full article

Suruga fundicola, one of the few known deep-dwelling gobies, is found in Japan, South Korea, and China. Owing to the limited availability of specimens, little is known about its mitogenome characterization, phylogenetic relationship, and adaptive evolution. In this study, we sequenced four complete mitogenomes using the DNBSEQ platform and Sanger sequencing. The mitogenomes in length ranged from 17,138 to 17,352 bp, primarily due to the variation in the number of long tandem repeat (LTR) sequences within variable region 3 (VR3). Although the gene composition and arrangement of the S. fundicola mitogenome are largely consistent with those of other gobies, we identified an expansion of the ND2 gene (78 bp), and an unexpected noncoding region (NC, 35 bp) located between the ND2 and tRNA^trp genes. To further investigate the variation in VR3, we sequenced this region in all nineteen individuals with the Sanger sequencing method. We detected eight distinct LTR types, containing one–three mutation sites, which formed ten different VR3 patterns. Most VR3 patterns (14/19) consisted of a single type of pure LTR, while the remaining five exhibited heterogeneous patterns composed of two different LTRs. Notably, in LTR types T1 and T3, which co-occur in heterogeneous patterns P1 and P9, we found their respective pure patterns (P2–3 and P7). Recombination provides a better, more plausible mechanism for generating the heterogeneity patterns than slipped-strand mispairing, which better explains the homogeneous LTR expansions. These findings provide evidence of recombination in the control region of a vertebrate mitogenome. A phylogenetic analysis confirmed that S. fundicola has a close relationship with Am. hexanema and C. stigmatias. Compared to five shallow-water species of the AcanthogobiusGroup, the deep-dwelling goby S. fundicola was found to be under stronger purifying selection. Within its mitochondrial protein-coding genes (PCGs), ND2 and ND6 genes were subject to stronger purifying selection than the others. Additionally, four genes showed signs of selection sites with high credibility (one in ATP6, ND3, and ND4; eight in ND2). This study provides valuable genomic resources for S. fundicola and enhances our understanding of the phylogenetic relationship, mitogenome recombination, and adaptive evolution of the goby. Full article

Sequencing cyanobacteria from xenic cultures is often challenging when their DNA extracts are confounded by DNA from their heterotrophic microbiome. Using an iterative DNA lysis protocol can fractionate between DNA from the cyanobacterium and the heterotrophic strains. To further demonstrate the utility of this protocol, it was used to sequence another xenic culture of cyanobacteria. This effort led to the assembly of a megabase-length cyanobacterial chromosome; however, repeated ribosomal regions created assembly issues even after adding data from another sequencing run to improve coverage. A separate DNA preparation from a single cell lysis step was also run for comparison but yielded a markedly lower proportion of cyanobacterial reads (<2%). Instead, the circular cyanobacterial chromosome was closed with targeted amplicon sequencing. Phylogenetic analysis assigned this strain to the genus Pseudanabaena. Within the metagenomic assembly were the genomes of six heterotrophic strains, preliminarily assigned as belonging to the genera Acidovorax, Hydrogenophaga, Lysobacter, Novosphingobium, Sediminicoccus, and Tabrizicola. Lysobacter sp. BL-A-41-H3’s chromosome was also assembled as a closed circular contig. This study demonstrates that iterative lysis enriches for cyanobacterial DNA and enables concurrent genome assembly of cohabitating heterotrophs alongside the host cyanobacterium. Full article

Pyrola decorata Andres (P. decorata) is a traditional medicinal plant in China. However, its chloroplast genome and the deep evolutionary relationships among its genus remain unexplored. This study identified the samples as P. decorata using morphological observations from Flora of China (FOC) and ITS sequences. It is the first to analyze the complete chloroplast genome of P. decorata using Illumina and Nanopore sequencing technologies, confirming a typical chloroplast dumbbell structure. The chloroplast DNA (cpDNA) of P. decorata is 179,999 bp in length, consisting of a large single copy (LSC) (62.3% of total length (112,150 bp)), a small single copy (SSC) (6.5% of total length (11,701 bp)), and two inverted repeat regions (IRA and IRB) (31.2% combined (28,074 bp × 2)). Functional annotation revealed 128 genes: 77 conserved coding sequences (CDS) genes, 43 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Phylogenetic analysis placed P. decorata, Pyrola atropurpurea (P. atropurpurea), Pyrola rotundifolia (P. rotundifolia), and Chimaphila japonica within Group I, with P. decorata exhibiting the closest chloroplast genomic affinity to P. atropurpurea. These findings integrate morphological and molecular evidence to facilitate further identification, classification, and evolutionary analysis of this genus. Full article

Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici, represents one of the most threatening biotic stresses of this crop. The cultivated wheat variety ‘Brock’ exhibits resistance not only to rust but also to powdery mildew, making it a valuable resource for exploitation in wheat disease-resistant breeding. This study identified a novel gene in ‘Brock’ distinct from Pm2. In order to identify the disease resistance gene in ‘Brock’, genetic mapping was performed using F₂ and F_2:3 populations derived from the cross ‘Jing411/Brock’. The candidate powdery mildew resistance gene was located within a 6.88 Mb physical interval on chromosome 2D, which harbors a highly expressed gene, TaRPM1-2D. The protein encoded by TaRPM1-2D possesses a typical nucleotide binding, leucine-rich repeat receptor (NLR) domain, and its sequence significantly differs among ‘Jing411’, ‘BJ-1’, and ‘Brock’. Expression of TaRPM1-2D was markedly higher in resistant wheat ‘Brock’ and ‘BJ-1’ compared to the susceptible ‘Jing411’. Both overexpression and gene silencing experiments demonstrated that TaRPM1-2D contributes to enhance resistance against powdery mildew in wheat. These findings reveal the function of TaRPM1-2D in conferring powdery mildew resistance in ‘Brock’ and provide a candidate gene for disease-resistance breeding. Full article

The Naozhou stock of large yellow croakers (Larimichthys crocea) exhibits unique phenotypic traits and high genetic diversity, making it a valuable resource for selective breeding and genetic conservation in aquaculture. Despite its importance, simple sequence repeat (SSR) markers have not been developed for this stock, which limits efforts in genetic evaluation, breeding optimization, and sustainable utilization of this commercially important species. In this study, 195,263 SSRs were identified from the genome of the Naozhou stock of large yellow croaker, covering a total length of 16,578,990 bp with a density of 288 bp/Mb. Dinucleotide repeats were the most common, with the AC motif being the most prevalent. The frequency of SSR markers ranged from 245.63 to 346.60 per Mb. A total of 30 primer pairs were synthesized, of which 28 pairs (93.3%) successfully amplified clear and reproducible bands in PCR assays. Among these, 28 SSR markers exhibited distinct and reproducible bands following gel electrophoresis. For eight SSR loci, the number of alleles (Na) ranged from 4 to 22 (mean = 11.375), while the effective number of alleles (Ne) ranged from 1.5401 to 10.4727 (mean = 5.6475). The assembled mitochondrial genome (mtDNA) was 16,467 bp in length and comprised 37 genes, including 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The total sequence length of the PCGs was 11,431 bp, accounting for 69.4% of the mtDNA. A large portion of the PCGs (5) used incomplete stop codons (e.g., nad2, nad3, cox2), while others used TAA stop codons (e.g., nad6, nad5, TrnT). The mtDNA encoded a total of 3808 codons, with UAA showing the highest relative synonymous codon usage value. The SSR markers and mtDNA data generated in this study provide valuable tools for future genetic breeding and genomic research on the Naozhou stock of large yellow croakers. Full article

Molecular diagnoses of Entamoeba histolytica and Strongyloides stercoralis in human samples are becoming increasingly common. To contribute to the ongoing standardization of molecular diagnostic approaches targeting these parasites, we compared three published E. histolytica- and S. stercoralis-specific real-time PCR assays in test comparisons without a reference standard. Latent class analysis (LCA) was used to calculate diagnostic accuracy estimations for the three compared assays per parameter. The comparison was conducted using stool samples from Ghanaian individuals. In the course of the assessment of 873 stool samples, the number of detected positive PCR results ranged from 10 to 15 for S. stercoralis and from 4 to 54 for E. histolytica depending on the applied assay. Diagnostic accuracy estimates of real-time PCR sensitivity for S. stercoralis and E. histolytica ranged from 89% to 100% and from 75% to 100%, respectively; diagnostic estimates of specificity ranged from 99% to 100% and from 94% to 100%, respectively. Diagnostic accuracy-adjusted prevalence estimates were 1.2% for S. stercoralis and 0.5% for E. histolytica. High cycle threshold values of real-time PCR > 35 showed a particularly reduced likeliness of reproducibility when applying competitor real-time PCR assays. There were no clear-cut differences in terms of diagnostic accuracy favoring either small-subunit ribosomal ribonucleic acid (SSU rRNA) gene sequences or the S. stercoralis dispersed repetitive sequence for S. stercoralis PCR. The same applied to the comparison of real-time PCRs targeting SSU rRNA gene sequences and the SSU rRNA episomal repeat sequence (SREPH) of E. histolytica. In conclusion, interchangeability of the compared real-time PCR assays was higher for the assessed S. stercoralis assays compared with the assessed E. histolytica assays. Regional diagnostic accuracy testing seems advisable before literature-adapted assays for rare tropical pathogens like S. stercoralis and E. histolytica are applied in different study regions. Full article

Background: Indigofera pseudotinctoria, a traditional Chinese forage and medicine widely used in East Asia, holds significant economic and agricultural value. Despite this, genomic information regarding I. pseudotinctoria remains conspicuously lacking. Methods: In this study, we utilized genome survey sequencing to elucidate the complete genome sequence of this species. Results: The genome size of I. pseudotinctoria to be around 637–920 Mb with a heterozygosity rate of 0.98% and a repeat rate of 66.3%. A total of 240,659 simple sequence repeat (SSR) markers were predicted in the genome of I. pseudotinctoria. Substantial differences were observed among nucleotide repeat types, for instance, mononucleotide repeats were found to be predominant (62.47%), whereas pentanucleotide repeats were notably scarce (0.24%). Furthermore, among dinucleotide and trinucleotide repeats, sequence motifs AT/AT (66.57%) and AAT/ATT (54.15%) were found to be particularly abundant. Among the identified unigenes, 58,790 exhibited alignment with known genes in established databases, including 33,218 genes within the Gene Ontology (GO) database and 10,893 genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Conclusions: This study marks the first attempt to both sequence and delineate the genomic landscape of I. pseudotinctoria. Importantly, it will serve as a foundational reference for subsequent comprehensive genome-wide deep sequencing and the development of SSR molecular markers within the scope of I. pseudotinctoria research. Full article

Recent analyses have revealed that orangutan alpha satellite higher-order repeat (HOR) arrays in complete centromeres are composed of three to four distinct HOR blocks, each sharing only 80–90% sequence identity, thus forming a patchwork-quilt pattern of independent HOR expansions. In contrast, using our novel HOR-detection algorithm GRhor, we analyzed the complete Y chromosome centromere in orangutan and identified a highly ordered and complex alpha satellite 58mer superHOR array, comprising 67 HOR copies, including 46 highly identical canonical copies with a remarkably low divergence of only 0.25%. Given that the largest known human alpha satellite HOR is the 34mer on the Y chromosome, this novel 58mer structure qualifies as a superHOR. The canonical 58mer HOR contains only 44 distinct monomer types, with 14 types repeated within the unit, resulting in a unique five-row cascading organization. Such complexity is not detectable using standard HOR-searching tools employed in previous studies. Additionally, we identified a second, less pronounced 45mer cascading superHOR array with 0.81% divergence. For comparative purposes, we also detected a cascading 18mer HOR in gorilla and a Willard-type 28mer HOR in chimpanzee Y centromeres. Notably, preliminary genome-wide analysis in orangutan reveals other superHORs, including 84mer and 53mer arrays in chromosome 5; a 54mer in chromosome 10; a 51mer in chromosome 14; a 53mer in chromosome 15; and a 45mer in chromosome 22. These findings underscore the power of GRMhor in revealing highly structured and species-specific HOR architectures, with potential implications for centromere evolution and primate comparative genomics. Full article