Search Results (1,209)

Bark beetles depend on detoxifying enzymes to counteract the defensive terpenoids produced by host trees. Insect ABC transporters play a critical role in the detoxification of insecticides and plant secondary metabolites. However, the specific functions of ABC genes in the metabolism of host allelochemicals remain unclear in D. armandi. In this study, we observed that verapamil significantly enhanced the mortality of host allelochemicals in beetles, indicating that ABC transporter genes are involved in the metabolism of monoterpenes by D. armandi. We then sequenced and characterized the full-length cDNAs of three ABCH subfamily genes (DaABCH1–DaABCH3) from D. armandi. Spatiotemporal expression profiling revealed that all three genes were upregulated during developmental transitions (egg to larva and pupa to adult) and tissue-specific enrichment in detoxification-related organs (Malpighian tubules, fat body, and midgut). Additionally, DaABCH3 expression was detected in the hindgut and brain. Furthermore, DaABCH1 and DaABCH2 were significantly induced by treatment with α-pinene and limonene, whereas DaABCH3 was induced by β-pinene and limonene. Importantly, silencing DaABCH1 significantly increased mortality in adults fumigated with α-pinene and limonene. These results strongly suggest that DaABCH1 acts as a key regulator modulating D. armandi’s sensitivity to host plant allelochemicals. This finding provides a conceptual basis for developing novel control strategies against this economically significant forest pest. Full article

The One Health approach is used to assess health-associated risks resulting from human exposure to antibiotic-resistant bacteria (ARB) that pose a significant public health risk. In this approach, wastewater treatment plants (WWTPs) play an important role in reducing bacteria and antibiotic-resistant genes (ARGs) in the environment. The ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) are of significant concern due to their ability to evade the effects of multiple antibiotics, including last-resort treatments such as carbapenems and glycopeptides. This study aimed to investigate the environmental surveillance of ESKAPE bacteria in wastewater and their adjacent receiving water bodies in Limpopo Province, South Africa. Methodology: Over a period of 6 months, all isolates were identified phenotypically, and genomic DNA was extracted using the QIAamp 96 DNA QIAcube^® HT Kit. Species-specific PCR was performed, followed by Sanger sequencing. The relevant sequences were compared to NCBI GenBank references using BLAST for confirmation and to assess the potential human health-associated risks. Results: ESKAPE organisms identified phenotypically were confirmed using PCR in both WWTP samples. Bacteria such as Acinetobacter baumannii and Enterobacter spp. were not detected in upstream or downstream river samples, particularly during August and September. In December and January, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa were not detected in effluent samples at both sites. Phylogenetic analysis revealed a diverse range of clinically significant genera, including Pseudomonas, Klebsiella, Enterobacter, and Staphylococcus, with strains closely related to global clinical isolates. Many of the isolates were associated with resistance to carbapenems, fluoroquinolones, and aminoglycosides. In addition, some strains clustered with both methicillin-sensitive and methicillin-resistant lineages. Conclusions: The findings emphasise the urgent need for increased genomic surveillance in environmental settings affected by wastewater discharge and highlight the importance of integrated antimicrobial resistance monitoring that connects clinical and environmental health sectors. Full article

α-Linolenic acid (ALA) is an important essential omega-3 (ω-3) polyunsaturated fatty acid for the maintenance of human health. Although ALA has traditionally been obtained from plant sources, microbial fermentation has emerged as a promising alternative for its sustainable and cost-effective production. However, most of the present approaches rely on genetically modified organisms, which present regulatory and consumer-acceptance concerns. In this study, we aimed to develop a high-ALA-producing strain of Aspergillus oryzae, a Generally Recognized As Safe (GRAS) microorganism widely used in food production in Japan, through self-cloning, a form of genetic engineering that utilizes only the host’s own DNA. To achieve this, an endogenous ω-3 desaturase gene (fad3), which catalyzes the conversion of linoleic acid to ALA, was identified via BLASTP analysis. Subsequently, a multicopy A. oryzae strain (Aofad3-MC) overexpressing fad3 was constructed. This strain increased ALA production, with ALA comprising 30.7% of the total lipids. Furthermore, k-mer analysis confirmed the absence of foreign vector sequences, verifying that Aofad3-MC was constructed through self-cloning. In addition to the identification of the A. oryzae ω-3 desaturase gene, this study provides a microbial platform for the sustainable production of ALA, with potential applications across the food, feed, and related industries. Full article

Eurasian griffon vultures (Gyps fulvus) are endangered scavenger birds. Haemosporidian parasites infect the blood cells and organs of many avian species globally, using blood-sucking insect vectors, and they negatively affect health of birds and subsequently wildlife biodiversity. Fifty-nine vultures were admitted to the Greek wildlife rehabilitation center “ANIMA” and included in this study. Blood samples were collected, and the microscopy of stained blood smears was performed. Moreover, DNA was extracted, samples were screened for Leucocytozoon, Haemoproteus, and Plasmodium spp. following nested PCR protocols, and positive samples were sequenced. The detected haemosporidians are reported for the first time in Eurasian griffon vultures globally. The overall prevalence was 11.9% (Leucocytozoon spp. 5.1%, Haemoproteus spp. 5.1%, Plasmodium spp. 3.4%); this further corroborates the statement that the vultures’ immunity protects them from blood parasites. Notably, new genetic lineages of Leucocytozoon (GYPFUL02), Haemoproteus (GYPFUL01), and Plasmodium (GYPFUL03) species were recorded for the first time. Furthermore, it was the first molecular isolation of Haemoproteus in Old World vultures and Haemoproteus brachiatus was isolated for the first time from a vulture species. Moreover, this demonstrates the first record of Parahaemoproteus genetic lineages in vultures. Results highlight the genetic diversity of haemosporidians in griffon vultures and the need for additional studies. Full article

DNA binding proteins play a crucial role in regulating gene expression, DNA replication, and chromatin organization. While many DNA-binding proteins have been identified, many unique DNA-binding proteins in non-model organisms and recently evolved lineage- or species-specific proteins remain uncharacterized or often lack experimental validation. In addition, genetic variants may alter previously known DNA-binding proteins, leading to loss of binding ability. To address this gap, various computational tools have been developed to predict DNA-binding proteins from protein sequences or structures. Yet, their real-world utility in biological research remains uncertain. To evaluate their effectiveness, we assessed the availability and predictive performance of existing tools using five real-world case studies. We found that most tools were web-based, offering accessibility to researchers without computational expertise. However, many suffered from poor maintenance, including frequent server connection problems, input errors, and long processing times. Among the ten tools that were functional and practical, we found that prediction scores often failed to reflect incorrect outputs, and multiple methods frequently produced the same erroneous predictions. Overall, even a small number of misclassifications can significantly distort biological interpretation, indicating that current DNA-binding prediction tools are not yet sufficiently reliable for empirical research. Full article

The Bacillus anthracis pXO1 plasmid, encoding ~143 proteins, presents a compact model for exploring protein function and evolutionary patterns using protein language models. Due to the organism’s slow evolutionary rate, its limited amino acid variation enhances detection of physiologically relevant patterns in plasmid protein composition. In this study, we applied embedding-based analyses and machine learning methods to characterize pXO1 protein modules across diverse B. anthracis lineages. We generated protein sequence embeddings, constructed phylogenies, and compared plasmid content with whole genome variation. While whole genome and plasmid-based phylogenies diverge, the composition of proteins encoded along the pXO1 plasmid revealed lineage specific structure. Association rule mining combined with decision tree classification produced plasmid-encoded targets for assessing anthrax sublineage, which yielded functionally redundant protein modules that reflected geographic and phylogenetic patterns. A conserved DNA replication module exhibited both shared and B. anthracis lineage specific features. These results show that pXO1 plasmid protein modules contain biologically meaningful and evolutionarily informative signatures, exemplifying their value in phylogeographic characterizations of bacterial pathogens. This framework can be extended to study additional virulence plasmids across Bacillus and other environmental pathogens using scalable protein language model tools. Full article

Taeniasis and neurocysticercosis (NCC), caused by Taenia solium, are significant public health concerns recognised by the World Health Organization (WHO) in developing countries across the Americas, Asia, and Africa. Taeniasis occurs in humans after consuming undercooked pork containing the larval stage (Cysticerci), which matures into the adult reproductive form in the intestine, releasing eggs through faeces. Accidental ingestion of these eggs by humans is the primary cause of NCC, a principal contributor to acquired epilepsy in endemic regions. Interrupting this transmission cycle is crucial to reducing the incidence of human NCC and porcine cysticercosis, thereby underscoring the need for accurate diagnosis and timely treatment of taeniasis. Current diagnostic tests for taeniasis, including microscopy, serology, copro-DNA, and coproantigen assays, exhibit variability in sensitivity, reproducibility, cross-reactivity, and accessibility. To overcome these limitations, bioinformatics tools were integrated with recombinant DNA technology to identify protein sequences with immunological potential. These sequences were evaluated in silico and used to construct an expression system. Subsequently, the antigens were expressed in a eukaryotic system, yielding two purified recombinant protein variants of 21 and 30 kDa. Their purification validated via Western blotting of the molecular tag, paves the way for the development of a direct immunological assay for the specific detection of Taenia solium carriers. Full article

Dichlorvos (DDVP) has been used in the management of agricultural pests for a long time. DDVP can cause DNA damage in mammals, and its residues in the environment and food have attracted attention. In this study, we reported a DDVP-degrading strain, Stenotrophomonas acidaminiphila G1, which could degrade DDVP to 20 mg/L with a DT₅₀ of 3.81 min at 37 °C, a pH of 7.0, and a concentration of 1.18 × 10¹⁰ colony-forming units (CFUs)/mL. Strain G1’s DDVP degradation products were determined by comparison with standard substances and UPLC-MS/MS analysis. The results showed that dimethyl phosphate (DMPP) was the main metabolite of DDVP, and its toxicity to non-target organisms was significantly lower than that of the parent compound. Furthermore, the key genes for the degradation of DDVP by strain G1 were analyzed using whole-genome sequencing. A methyl parathion hydrolase gene, mpd, was identified, and its activity was verified through prokaryotic expression and enzyme kinetics. The purified enzyme MPD could entirely degrade 20 mg/L DDVP within 1 min. These results not only provide biological resources for the rapid degradation of organophosphorus pesticides but also offer a theoretical basis for the efficient remediation of pesticide residues. Full article

Grifola frondosa polysaccharides (GFP), which possess antitumor properties, can counteract intestinal injury induced by cyclophosphamide (CTX). The objective of this research was to evaluate the efficacy of GFP in protecting the intestinal barrier of mice and investigate the mechanisms behind this effect. Using a CTX-induced intestinal barrier injury model, we found that GFP treatment significantly alleviated body weight loss and organ atrophy, while enhancing serum IgG and IgM levels. Histological analysis showed that GFP effectively repaired the intestinal mucosal structure, increased goblet cell numbers, and led to an upregulation in the gene expression of ZO-1, Occludin, and MUC2. GFP modulated cytokine expression, including IFN-γ, IL-4, IL-10, and IL-22. According to 16S rDNA sequencing results, GFP enhanced the abundance of unclassified_Muribaculaceae while reducing the prevalence of Escherichia_Shigella. Furthermore, GFP elevated the concentrations of several metabolites, including SCFAs and pyridoxal, which are closely related to intestinal barrier protection and mucosal immunity. Overall, this study demonstrated that GFP has strong potential as an immune-enhancing adjuvant and may represent a promising intervention strategy to mitigate chemotherapy-induced intestinal injury. Full article

Cellular organisms store heritable information in two forms, genetic and epigenetic, the latter being largely dependent on cytosine methylation (5mC). Chargaff’s Second Parity Rule (CSPR) describes the nucleotide composition of cellular genomes in terms of intra-strand DNA symmetry. However, it remains unknown whether DNA methylation patterns display intra-strand DNA symmetry. Computational analysis was conducted of the DNA methylation patterns observed in human cell lines and in tissue samples from healthy donors. Analysis of 5mC marks in mutually reverse-complementary pairs of short oligomers, containing CpG dinucleotide in the middle, revealed deviations from CSPR and methylation asymmetry that can be observed for two non-overlapping mirror groups defined by CpG methylation values. Deviations from CSPR, together with combinatorial probabilities of pattern distributions and computer simulations, highlight the non-random nature of methylation processes and enabled us to identify specific cell types as outliers. Further analysis revealed a compensatory methylation asymmetry that reduces deviations from intra-strand symmetry and implies the existence of strand-specific methylation during cell differentiation. Among six pairs of reverse-complementary tetranucleotides, four pairs with specific sequence motifs display pronounced methylation asymmetry. This mirror asymmetry may be associated with chromosome folding and the formation of a complex three-dimensional landscape. Full article

K-mer analysis is a powerful tool for understanding genome structure and evolution. A “k-mer” refers to a short DNA sequence made up of k nucleotides (where k is a specific integer), while an “m-mer” is a similar concept but with a shorter sequence length. The functional mechanisms of CG-containing k-mers, as well as their potential role in evolutionary processes, remain unclear. To explore this issue, we analyzed 8-mers in several species with varying genomic complexities and evolutionary divergences: Homo sapiens, Saccharomyces cerevisiae, Bombyx mori, Ciona intestinalis, Danio rerio, and Caenorhabditis elegans, which were grouped by CG dinucleotide content (0CG, 1CG, and 2CG). We examined the relative frequencies of shorter m-mers (with m = 3 and 4) within each CG-defined group, using information-theoretic, distance-based, and angular metrics. Our results show that 0CG motifs follow random patterns, while 1CG and 2CG motifs display significant deviations, likely due to functional constraints such as nucleosome-binding and CpG island association. The observed unimodal distribution of 8-mers arises from the convergence of the three CG-defined groups. Among them, the 2CG group shows the highest divergence in m-mer composition, followed by 1CG, reflecting varying degrees of selective pressure. Furthermore, species-specific differences in CG-classified 8-mer patterns could provide valuable insights into phylogenetic relationships. Through extensive comparison, we explore how CG content and sequence composition influence genomic organization and contribute to evolutionary divergence across different taxa. These findings deepen our understanding of short motif functions, genome organization, and sequence evolution. Full article

The Fukushima nuclear accident in 2011 caused adverse phenotypic changes in wild organisms in radioactively polluted areas. However, few studies have investigated genetic changes after the accident. Here, we analyzed the nuclear DNA sequences of internal transcribed spacer 2 (ITS2) from the pale grass blue butterfly Zizeeria maha collected in 2011–2014 (n = 389). We detected 29 haplotypes, but the most frequent haplotype (H1) represented 86% of alleles examined. The haplotype H22 from Takahagi phylogenetically had the latest sequence, suggesting that it may be a novel mutant produced by the accident or just a minor existing haplotype. In Fukushima Prefecture, the H1 percentage oscillated; it peaked in Fall 2011 and decreased in Spring 2012 but peaked again in Fall 2012. Haplotype diversity and nucleotide diversity were low in Spring 2012 and Fall 2012 and then increased. The ratio of H1 to nonH1 was significantly different between the early and late periods of our field surveys. These results suggest that genetic diversity in Fukushima Prefecture initially decreased through a selection process in response to the Fukushima nuclear accident but was recovered by Fall 2014, probably due to immigrants and emerging mutants, which is consistent with previous morphological abnormality data. Full article

2,2′,4,4′-Tetrabromodiphenyl ether (BDE-47) is a refractory organic pollutant that is characterized by its persistence, toxicity and potential for bioaccumulation. As a typical biocontrol bacteria, Pseudomonas protegens has not been reported to degrade organic pollutants in the environment. A single strain of Pseudomonas protegens was isolated and acclimated from municipal sludge, and its ability to degrade BDE-47 was investigated. The enhancing effects of different carbon sources and inducers on Pseudomonas protegens were also examined. Through the reinforcement of bacterial enhancers, Pseudomonas protegens was applied to remediate soil and water contaminated with BDE-47. Based on colony characteristics, physiological and biochemical properties, and 16S rDNA gene sequence homology analysis, the strain was identified as Pseudomonas protegens and named YP1. This marks the first discovery of Pseudomonas protegens being capable of degrading BDE-47. Strain YP1 utilized BDE-47 as a carbon source and achieved a degradation rate of 69.57% after 75 h of incubation under conditions of 37 °C, pH 7, and constant temperature in a dark shaking incubator. After comparing the actual enhancement effects, glucose was selected as the carbon source and 2,4-dichlorophenol as the inducer to improve the environmental remediation capability of Pseudomonas protegens. After 14 days of remediation, the degradation rates of BDE-47 in contaminated soil and water reached 48.26% and 52.60%, respectively. The Pseudomonas protegens strain obtained from municipal sludge through screening, acclimation, and enhancement processes exhibits excellent environmental remediation capabilities and promising practical application prospects. Full article

The Order Polycladida comprises a diverse yet understudied group of free-living flatworms, traditionally divided into Cotylea and Acotylea based on the presence or absence of a ventral adhesive organ known as a cotyl. Species identification, particularly within Acotylea, is often challenging due to the need for histological examination of reproductive structures and the scarcity of molecular data. The Tropical Western Atlantic, especially the Caribbean Sea, hosts high polyclad diversity but remains poorly surveyed. This study updates the checklist of Acotylea from the Colombian Caribbean, combining new collections from Santa Marta with the literature records. Field work yielded 22 acotylean species from 14 genera and 10 families, with DNA sequences (28S rDNA and/or COI mtDNA) obtained for 20 species. 11 species are new records for Colombia, and five for the Caribbean Sea: Latocestus brasiliensis Hyman, 1953, Notocomplana martae (Marcus, 1948), Interplana evelinae (Marcus, 1952), Triadomma curvum Marcus, 1949, and Adenoplana evelinae Marcus, 1950. In total, 29 species are now documented from the region. We provide photographs of live specimens, whole mounts, and histological sections; DNA barcodes for most species; and the first dichotomous key for Colombian Caribbean acotyleans, based primarily on external traits, providing a practical tool to support further taxonomic, ecological, and biodiversity research. Full article

Cysticercosis in wild and domestic ungulates, caused by the larval metacestode stages of Taenia hydatigena and Taenia multiceps (formerly known as Cysticercus tenuicollis and Coenurus cerebralis, respectively), is a widespread parasitic disease and poses a significant concern worldwide, particularly in endemic regions. Although Taenia species have been extensively studied globally, their epidemiology and genetic diversity in Kazakhstan remain poorly understood. In this study, wild (roe deer, red deer, moose) and domestic (cattle, sheep) ungulates, serving as intermediate hosts for Taenia spp., were examined for cysticerci in muscle tissues and internal organs. Phylogenetic analysis and pairwise nucleotide variation assessments of the cox1 and nad1 genes were conducted. An overall prevalence of 5.2% was recorded among 1370 ruminant carcasses (cattle = 773, sheep = 563, roe deer = 25, moose = 9), with infection rates of 0.6% in cattle, 1.1% in sheep, 8.0% in roe deer, and 11.1% in moose. Cattle, sheep, and moose were infected with T. hydatigena, while roe deer were infected with T. multiceps. DNA sequence analysis of all isolates revealed four nad1 gene haplotypes for T. hydatigena, with Hap_3 being the most common (10 isolates). Phylogenetic analysis showed that T. multiceps isolates from roe deer clustered within the clade defined by the reference sequences for this species. This study provides important baseline data on the prevalence and genetic variation in T. hydatigena and T. multiceps in Kazakhstan and lays the groundwork for future research on the epidemiology and population genetics of Taenia species in the region. Full article