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Chemosphere Aug 2024Plastic polymers were largely added with chemical substances to be utilized in the items and product manufacturing. The leachability of these substances is a matter of...
Plastic polymers were largely added with chemical substances to be utilized in the items and product manufacturing. The leachability of these substances is a matter of concern given the wide amount of plastic waste, particularly in terrestrial environments, where soil represents a sink for these novel contaminants and a possible pathway of human health risk. In this study, we integrated genetic, molecular, and behavioral approaches to comparatively evaluate toxicological effects of plastic leachates, virgin and oxodegradable polypropylene (PP) and polyethylene (PE), in Drosophila melanogaster, a novel in vivo model organism for environmental monitoring studies and (eco)toxicological research. The results of this study revealed that while conventional toxicological endpoints such as developmental times and longevity remain largely unaffected, exposure to plastic leachates induces chromosomal abnormalities and transposable element (TE) activation in neural tissues. The combined effects of DNA damage and TE mobilization contribute to genome instability and increase the likelihood of LOH events, thus potentiating tumor growth and metastatic behavior ofRas clones. Collectively, these findings indicate that plastic leachates exert genotoxic effects in Drosophila thus highlighting potential risks associated with leachate-related plastic pollution and their implications for ecosystems and human health.
Topics: Animals; Drosophila melanogaster; DNA Damage; Plastics; Polypropylenes; Polyethylene; Chromosome Aberrations; Environmental Monitoring; Mutagens; DNA Transposable Elements; Mutagenicity Tests
PubMed: 38821133
DOI: 10.1016/j.chemosphere.2024.142440 -
BMC Ecology and Evolution May 2024Ctenoluciidae is a Neotropical freshwater fish family composed of two genera, Ctenolucius (C. beani and C. hujeta) and Boulengerella (B. cuvieri, B. lateristriga, B....
Ctenoluciidae is a Neotropical freshwater fish family composed of two genera, Ctenolucius (C. beani and C. hujeta) and Boulengerella (B. cuvieri, B. lateristriga, B. lucius, B. maculata, and B. xyrekes), which present diploid number conservation of 36 chromosomes and a strong association of telomeric sequences with ribosomal DNAs. In the present study, we performed chromosomal mapping of microsatellites and transposable elements (TEs) in Boulengerella species and Ctenolucius hujeta. We aim to understand how those sequences are distributed in these organisms' genomes and their influence on the chromosomal evolution of the group. Our results indicate that repetitive sequences may had an active role in the karyotypic diversification of this family, especially in the formation of chromosomal hotspots that are traceable in the diversification processes of Ctenoluciidae karyotypes. We demonstrate that (GATA)n sequences also accumulate in the secondary constriction formed by the 18 S rDNA site, which shows consistent size heteromorphism between males and females in all Boulengerella species, suggesting an initial process of sex chromosome differentiation.
Topics: Animals; Characiformes; Male; Chromosome Mapping; Female; Retroelements; Repetitive Sequences, Nucleic Acid; Evolution, Molecular; Microsatellite Repeats; Karyotype; Chromosomes
PubMed: 38816840
DOI: 10.1186/s12862-024-02262-x -
Nature Communications May 2024Parental or ancestral environments can induce heritable phenotypic changes, but whether such environment-induced heritable changes are a common phenomenon remains...
Parental or ancestral environments can induce heritable phenotypic changes, but whether such environment-induced heritable changes are a common phenomenon remains unexplored. Here, we subject 14 genotypes of Arabidopsis thaliana to 10 different environmental treatments and observe phenotypic and genome-wide gene expression changes over four successive generations. We find that all treatments caused heritable phenotypic and gene expression changes, with a substantial proportion stably transmitted over all observed generations. Intriguingly, the susceptibility of a genotype to environmental inductions could be predicted based on the transposon abundance in the genome. Our study thus challenges the classic view that the environment only participates in the selection of heritable variation and suggests that the environment can play a significant role in generating of heritable variations.
Topics: Arabidopsis; Phenotype; Gene Expression Regulation, Plant; DNA Transposable Elements; Genotype; Genetic Variation; Genome, Plant; Environment; Gene-Environment Interaction
PubMed: 38816460
DOI: 10.1038/s41467-024-49024-3 -
Scientific Data May 2024The cold-water species Ophiura sarsii, a brittle star, is a key echinoderm in the Arctic continental shelf region, highly sensitive to climate change. However, the...
The cold-water species Ophiura sarsii, a brittle star, is a key echinoderm in the Arctic continental shelf region, highly sensitive to climate change. However, the absence of a high-quality genome has hindered a thorough understanding of its adaptive evolution. In this study, we reported the first chromosome-level genome assembly of O. sarsii. The genome assembly totalled 1.57 Gb, encompassing 19 chromosomes with a GC content of 37.11% and a scaffold N50 length of 78.03 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment yielded a completeness estimate of 93.5% for this assembly. We predicted a total of 27,099 protein-coding genes, with 25,079 functionally annotated. The genome was comprised of 58.09% transposable elements. This chromosome-level genome of O. sarsii contributes to our understanding of the origin and evolution of marine organisms.
Topics: Animals; Genome; Chromosomes; Echinodermata; Molecular Sequence Annotation; Base Composition; DNA Transposable Elements
PubMed: 38816401
DOI: 10.1038/s41597-024-03412-y -
Microbial Genomics May 2024is an emerging human enteric pathogen. However, the genomic features and virulence genes of strains from human gastroenteritis and other sources have not been fully...
Analysis of global genomes revealed that strains carrying T6SS are more common in human gastroenteritis than in environmental sources and are often phylogenetically related.
is an emerging human enteric pathogen. However, the genomic features and virulence genes of strains from human gastroenteritis and other sources have not been fully elucidated. Here, we conducted a genomic analysis of 565 global strains isolated from different sources, including 261 strains isolated from faecal samples of gastroenteritis patients, of which 18 genomes were sequenced in this study. The presence of bacterial virulence genes and secretion systems in strains from different sources was compared, and the phylogenetic relationship of strains was assessed based on the core genome. The complete genome of strain A20-9 isolated from a gastroenteritis patient was obtained in this study, from which 300 putative virulence factors and a T4SS-encoding plasmid, pAC, were identified. Genes encoding T4SS were also identified in a novel genomic island, ACI-1, from other T4SS-positive strains. The prevalence of T4SS was significantly lower in strains from gastroenteritis patients than in environmental strains (3 %, <0.0001 vs 14 %, <0.01). Conversely, the prevalence of T6SS was significantly higher in strains isolated from gastroenteritis patients than in environmental strains (25 %, <0.05 vs 13 %, <0.01). Four phylogenetic clusters were formed based on the core genome of 565 . strains, and strains carrying T6SS often showed close phylogenetic relationships. T3SS, aerolysin and thermostable cytotonic enterotoxin were absent in all 565 . strains. Our findings provide novel information on the genomic features of and suggest that T6SS may play a role in -induced human gastroenteritis.
Topics: Gastroenteritis; Humans; Phylogeny; Genome, Bacterial; Aeromonas caviae; Virulence Factors; Type VI Secretion Systems; Feces; Gram-Negative Bacterial Infections; Genomic Islands; Plasmids
PubMed: 38814176
DOI: 10.1099/mgen.0.001258 -
Nature Communications May 2024Bacterial pathogens carrying multidrug resistance (MDR) plasmids are a major threat to human health. The acquisition of antibiotic resistance genes (ARGs) in plasmids is...
Bacterial pathogens carrying multidrug resistance (MDR) plasmids are a major threat to human health. The acquisition of antibiotic resistance genes (ARGs) in plasmids is often facilitated by mobile genetic elements that copy or translocate ARGs between DNA molecules. The agglomeration of mobile elements in plasmids generates resistance islands comprising multiple ARGs. However, whether the emergence of resistance islands is restricted to specific MDR plasmid lineages remains understudied. Here we show that the agglomeration of ARGs in resistance islands is biased towards specific large plasmid lineages. Analyzing 6784 plasmids in 2441 Escherichia, Salmonella, and Klebsiella isolates, we quantify that 84% of the ARGs in MDR plasmids are found in resistance islands. We furthermore observe rapid evolution of ARG combinations in resistance islands. Most regions identified as resistance islands are shared among closely related plasmids but rarely among distantly related plasmids. Our results suggest the presence of barriers for the dissemination of ARGs between plasmid lineages, which are related to plasmid genetic properties, host range and the plasmid evolutionary history. The agglomeration of ARGs in plasmids is attributed to the workings of mobile genetic elements that operate within the framework of existing plasmid lineages.
Topics: Plasmids; Evolution, Molecular; Salmonella; Anti-Bacterial Agents; Humans; Drug Resistance, Multiple, Bacterial; Klebsiella; Genomic Islands; Escherichia coli; Interspersed Repetitive Sequences
PubMed: 38811529
DOI: 10.1038/s41467-024-48352-8 -
Polish Journal of Microbiology Jun 2024is a non-fermentative Gram-negative bacterium that can cause nosocomial infections in critically ill patients. Carbapenem-resistant (CRAB) has spread rapidly in...
is a non-fermentative Gram-negative bacterium that can cause nosocomial infections in critically ill patients. Carbapenem-resistant (CRAB) has spread rapidly in clinical settings and has become a key concern. The main objective of this study was to identify the distribution of integrons and biofilm-formation-related virulence genes in CRAB isolates. A total of 269 isolates (219 isolates of CRAB and 50 isolates of carbapenem-sensitive (CSAB)) were collected. Carbapenemase genes ( , , , , and ) and biofilm-formation-related virulence genes (, , , and ) were screened with PCR. Class 1 integron was screened with PCR, and common promoters and gene cassette arrays were determined with restriction pattern analysis combined with primer walking sequencing. Whole-genome sequencing was conducted, and data were analyzed for a -negative isolate. All 219 CRAB isolates were negative for , , , and , while was detected in 218 isolates. The detection rates for , , , and in 219 CRAB were 93.15%, 63.93%, 88.13%, and 77.63%, respectively. Class 1 integron was detected in 75 CRAB (34.25%) and in 3 CSAB. The single gene cassette array with relatively strong PcH2 promoter was detected in class 1 integrons. The -negative CRAB isolate was revealed to be a new sequence type (Oxford 3272, Pasteur 2520) carrying , , and . In conclusion, was the main reason for CRAB's resistance to carbapenems. A new (Oxford 3272, Pasteur 2520) CRAB sequence type carrying the , , and was reported.
Topics: Acinetobacter baumannii; beta-Lactamases; Integrons; Biofilms; Bacterial Proteins; Acinetobacter Infections; Humans; Anti-Bacterial Agents; Carbapenems; Microbial Sensitivity Tests
PubMed: 38808771
DOI: 10.33073/pjm-2024-017 -
Virulence Dec 2024() is a bacterial pathogen responsible for a range of infections in humans and various animal hosts, causing significant economic losses in farming. Integrative and...
() is a bacterial pathogen responsible for a range of infections in humans and various animal hosts, causing significant economic losses in farming. Integrative and conjugative elements (ICEs) are important horizontal gene transfer elements, potentially enabling host bacteria to enhance adaptability by acquiring multiple functional genes. However, the understanding of ICEs in and their impact on the transmission of this pathogen remains limited. In this study, 42 poultry-sourced genomes obtained by high-throughput sequencing together with 393 publicly available genomes were used to analyse the horizontal transfer of ICEs. Eighty-two ICEs were identified in , including SXT/R391 and Tn916 subtypes, as well as three subtypes of ICE1056 family, with the latter being widely prevalent in and carrying multiple resistance genes. The correlations between insertion sequences and resistant genes in ICEs were also identified, and some ICEs introduced the carbapenem gene and the bleomycin gene to . Phylogenetic and collinearity analyses of these bioinformatics found that ICEs in were transmitted vertically and horizontally and have evolved with host specialization. These findings provide insight into the transmission and evolution mode of ICEs in and highlight the importance of understanding these elements for controlling the spread of antibiotic resistance.
Topics: Pasteurella multocida; Gene Transfer, Horizontal; Animals; Phylogeny; Pasteurella Infections; Genome, Bacterial; DNA Transposable Elements; Conjugation, Genetic; Evolution, Molecular; Poultry; Prevalence; High-Throughput Nucleotide Sequencing
PubMed: 38808732
DOI: 10.1080/21505594.2024.2359467 -
Scientific Reports May 2024Salmonella enterica is a pathogenic bacterium known for causing severe typhoid fever in humans, making it important to study due to its potential health risks and...
Salmonella enterica is a pathogenic bacterium known for causing severe typhoid fever in humans, making it important to study due to its potential health risks and significant impact on public health. This study provides evolutionary classification of proteins from Salmonella enterica pangenome. We classified 17,238 domains from 13,147 proteins from 79,758 Salmonella enterica strains and studied in detail domains of 272 proteins from 14 characterized Salmonella pathogenicity islands (SPIs). Among SPIs-related proteins, 90 proteins function in the secretion machinery. 41% domains of SPI proteins have no previous sequence annotation. By comparing clinical and environmental isolates, we identified 3682 proteins that are overrepresented in clinical group that we consider as potentially pathogenic. Among domains of potentially pathogenic proteins only 50% domains were annotated by sequence methods previously. Moreover, 36% (1330 out of 3682) of potentially pathogenic proteins cannot be classified into Evolutionary Classification of Protein Domains database (ECOD). Among classified domains of potentially pathogenic proteins the most populated homology groups include helix-turn-helix (HTH), Immunoglobulin-related, and P-loop domains-related. Functional analysis revealed overrepresentation of these protein in biological processes related to viral entry into host cell, antibiotic biosynthesis, DNA metabolism and conformation change, and underrepresentation in translational processes. Analysis of the potentially pathogenic proteins indicates that they form 119 clusters or novel potential pathogenicity islands (NPPIs) within the Salmonella genome, suggesting their potential contribution to the bacterium's virulence. One of the NPPIs revealed significant overrepresentation of potentially pathogenic proteins. Overall, our analysis revealed that identified potentially pathogenic proteins are poorly studied.
Topics: Genomic Islands; Salmonella enterica; Bacterial Proteins; Genome, Bacterial; Humans; Protein Domains
PubMed: 38806511
DOI: 10.1038/s41598-024-60991-x -
Genomics Jul 2024Cassava, a crucial tropical crop, faces challenges from cold stress, necessitating an exploration of its molecular response. Here, we investigated the role of DNA...
Cassava, a crucial tropical crop, faces challenges from cold stress, necessitating an exploration of its molecular response. Here, we investigated the role of DNA methylation in moderating the response to moderate cold stress (10 °C) in cassava. Using whole-genome bisulfite sequencing, we examined DNA methylation patterns in leaf blades and petioles under control conditions, 5 h, and 48 h of cold stress. Tissue-specific responses were observed, with leaf blades exhibiting subtle changes, while petioles displayed a pronounced decrease in methylation levels under cold stress. We identified cold stress-induced differentially methylated regions (DMRs) that demonstrated both tissue and treatment specificity. Importantly, these DMRs were enriched in genes with altered expression, implying functional relevance. The cold-response transcription factor ERF105 associated with DMRs emerged as a significant and conserved regulator across tissues and treatments. Furthermore, we investigated DNA methylation dynamics in transposable elements, emphasizing the sensitivity of MITEs with bHLH binding motifs to cold stress. These findings provide insights into the epigenetic regulation of response to cold stress in cassava, contributing to an understanding of the molecular mechanisms underlying stress adaptation in this tropical plant.
Topics: Manihot; DNA Methylation; Cold-Shock Response; Plant Proteins; Gene Expression Regulation, Plant; Epigenesis, Genetic; Plant Leaves; DNA Transposable Elements; Transcription Factors
PubMed: 38806102
DOI: 10.1016/j.ygeno.2024.110871