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Database : the Journal of Biological... Jun 2024We launched the initial version of FishTEDB in 2018, which aimed to establish an open-source, user-friendly, data-rich transposable element (TE) database. Over the past...
We launched the initial version of FishTEDB in 2018, which aimed to establish an open-source, user-friendly, data-rich transposable element (TE) database. Over the past 5 years, FishTEDB 1.0 has gained approximately 10 000 users, accumulating more than 450 000 interactions. With the unveiling of extensive fish genome data and the increasing emphasis on TE research, FishTEDB needs to extend the richness of data and functions. To achieve the above goals, we introduced 33 new fish species to FishTEDB 2.0, encompassing a wide array of fish belonging to 48 orders. To make the updated database more functional, we added a genome browser to visualize the positional relationship between TEs and genes and the estimated TE insertion time in different species. In conclusion, we released a new version of the fish TE database, FishTEDB 2.0, designed to assist researchers in the future study of TE functions and promote the progress of biological theories related to TEs. Database URL: https://www.fishtedb.com/.
Topics: DNA Transposable Elements; Animals; Fishes; Databases, Genetic; Databases, Nucleic Acid
PubMed: 38829853
DOI: 10.1093/database/baae044 -
ACS Sensors Jun 2024The development of new or improved single fluorescent protein (FP)-based biosensors (SFPBs), particularly those with excitation and emission at near-infrared...
The development of new or improved single fluorescent protein (FP)-based biosensors (SFPBs), particularly those with excitation and emission at near-infrared wavelengths, is important for the continued advancement of biological imaging applications. In an effort to accelerate the development of new SFPBs, we report modified transposons for the transposase-based creation of libraries of FPs randomly inserted into analyte binding domains, or vice versa. These modified transposons feature ends that are optimized to minimize the length of the linkers that connect the FP to the analyte binding domain. We rationalized that shorter linkers between the domains should result in more effective allosteric coupling between the analyte binding-dependent conformational change in the binding domain and the fluorescence modulation of the chromophore of the FP domain. As a proof of concept, we employed end-modified Mu transposons for the discovery of SFPB prototypes based on the insertion of two circularly permuted red FPs (mApple and FusionRed) into binding proteins for l-lactate and spermidine. Using an analogous approach, we discovered calcium ion (Ca)-specific SFPBs by random insertion of calmodulin (CaM)-RS20 into miRFP680, a particularly bright near-infrared (NIR) FP based on a biliverdin (BV)-binding fluorescent protein. Starting from an miRFP680-based Ca biosensor prototype, we performed extensive directed evolution, including under BV-deficient conditions, to create highly optimized biosensors designated the NIR-GECO3 series. We have extensively characterized the NIR-GECO3 series and explored their utility for biological Ca imaging. The methods described in this work will serve to accelerate SFPB development and open avenues for further exploration and optimization of SFPBs across a spectrum of biological applications.
Topics: Biosensing Techniques; Calcium; DNA Transposable Elements; Luminescent Proteins; Humans; Calmodulin
PubMed: 38822813
DOI: 10.1021/acssensors.4c00727 -
The New Phytologist Jul 2024In the early 1900s, Erwin Baur established Antirrhinum majus as a model system, identifying and characterising numerous flower colour variants. This included...
In the early 1900s, Erwin Baur established Antirrhinum majus as a model system, identifying and characterising numerous flower colour variants. This included Picturatum/Eluta, which restricts the accumulation of magenta anthocyanin pigments, forming bullseye markings on the flower face. We identified the gene underlying the Eluta locus by transposon-tagging, using an Antirrhinum line that spontaneously lost the nonsuppressive el phenotype. A candidate MYB repressor gene at this locus contained a CACTA transposable element. We subsequently identified plants where this element excised, reverting to a suppressive Eluta phenotype. El alleles inhibit expression of anthocyanin biosynthetic genes, confirming it to be a regulatory locus. The modes of action of Eluta were investigated by generating stable transgenic tobacco lines, biolistic transformation of Antirrhinum petals and promoter activation/repression assays. Eluta competes with MYB activators for promoter cis-elements, and also by titrating essential cofactors (bHLH proteins) to reduce transcription of target genes. Eluta restricts the pigmentation established by the R2R3-MYB factors, Rosea and Venosa, with the greatest repression on those parts of the petals where Eluta is most highly expressed. Baur questioned the origin of heredity units determining flower colour variation in cultivated A. majus. Our findings support introgression from wild species into cultivated varieties.
Topics: Antirrhinum; Flowers; Pigmentation; Plant Proteins; Gene Expression Regulation, Plant; Anthocyanins; Phenotype; Plants, Genetically Modified; Genes, Plant; Nicotiana; Promoter Regions, Genetic; DNA Transposable Elements; Alleles
PubMed: 38822654
DOI: 10.1111/nph.19866 -
Journal of Water and Health May 2024Hospital wastewater has been identified as a hotspot for the emergence and transmission of multidrug-resistant (MDR) pathogens that present a serious threat to public...
Hospital wastewater has been identified as a hotspot for the emergence and transmission of multidrug-resistant (MDR) pathogens that present a serious threat to public health. Therefore, we investigated the current status of antibiotic resistance as well as the phenotypic and genotypic basis of biofilm formation in from hospital wastewater in Dhaka, Bangladesh. The disc diffusion method and the crystal violet assay were performed to characterize antimicrobial resistance and biofilm formation, respectively. Biofilm and integron-associated genes were amplified by the polymerase chain reaction. Isolates exhibited varying degrees of resistance to different antibiotics, in which >80% of isolates showed sensitivity to meropenem, amikacin, and gentamicin. The results indicated that 93.82% of isolates were MDR and 71 out of 76 MDR isolates showed biofilm formation activities. We observed the high prevalence of biofilm-related genes, in which (82.7%) was found to be the prevalent biofilm genotypic pattern. Sixteen isolates (19.75%) possessed class 1 integron () genes. However, statistical analysis revealed no significant association between biofilm formation and multidrug resistance ( = 0.35, = 0.55). Taken together, hospital wastewater in Dhaka city may act as a reservoir for MDR and biofilm-forming , and therefore, the adequate treatment of wastewater is recommended to reduce the occurrence of outbreaks.
Topics: Biofilms; Pseudomonas aeruginosa; Wastewater; Bangladesh; Drug Resistance, Multiple, Bacterial; Hospitals; Anti-Bacterial Agents; Integrons; Microbial Sensitivity Tests
PubMed: 38822462
DOI: 10.2166/wh.2024.294 -
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 -
International Journal of Food... Aug 2024Peanut-based products have been associated with Salmonella foodborne outbreaks and/or recalls worldwide. The ability of Salmonella to persist for a long time in a low...
Peanut-based products have been associated with Salmonella foodborne outbreaks and/or recalls worldwide. The ability of Salmonella to persist for a long time in a low moisture environment can contribute to this kind of contamination. The objective of this study was to analyse the genome of five S. enterica enterica strains isolated from the peanut supply chain in Brazil, as well as to identify genetic determinants for survival under desiccation and validate these findings by phenotypic test of desiccation stress. The strains were in silico serotyped using the platform SeqSero2 as Miami (M2851), Javiana (M2973), Oranienburg (M2976), Muenster (M624), and Glostrup/Chomedey (M7864); with phylogenomic analysis support. Based on Multilocus Sequence Typing (MLST) the strains were assigned to STs 140, 1674, 321, 174, and 2519. In addition, eight pathogenicity islands were found in all the genomes using the SPIFinder 2.0 (SPI-1, SPI-2, SPI-3, SPI-5, SPI-9, SPI-13, SPI-14). The absence of a SPI-4 may indicate a loss of this island in the surveyed genomes. For the pangenomic analysis, 49 S. enterica genomes were input into the Roary pipeline. The majority of the stress related genes were considered as soft-core genes and were located on the chromosome. A desiccation stress phenotypic test was performed in trypticase soy broth (TSB) with four different water activity (a) values. M2976 and M7864, both isolated from the peanut samples with the lowest a, showed the highest OD in TSB a 0.964 and were statistically different (p < 0.05) from the strain isolated from the peanut sample with the highest a (0.997). In conclusion, genome analyses have revealed signatures of desiccation adaptation in Salmonella strains, but phenotypic analyses suggested the environment influences the adaptive ability of Salmonella to overcome desiccation stress.
Topics: Arachis; Brazil; Salmonella enterica; Genome, Bacterial; Phylogeny; Multilocus Sequence Typing; Food Microbiology; Genomic Islands; Desiccation; Genomics
PubMed: 38820989
DOI: 10.1016/j.ijfoodmicro.2024.110767 -
Methods in Molecular Biology (Clifton,... 2024The data generated in nearly 30 years of bacterial genome sequencing has revealed the abundance of transposable elements (TE) and their importance in genome and...
The data generated in nearly 30 years of bacterial genome sequencing has revealed the abundance of transposable elements (TE) and their importance in genome and transcript remodeling through the mediation of DNA insertions and deletions, structural rearrangements, and regulation of gene expression. Furthermore, what we have learned from studying transposition mechanisms and their regulation in bacterial TE is fundamental to our current understanding of TE in other organisms because much of what has been observed in bacteria is conserved in all domains of life. However, unlike eukaryotic TE, prokaryotic TE sequester and transmit important classes of genes that impact host fitness, such as resistance to antibiotics and heavy metals and virulence factors affecting animals and plants, among other acquired traits. This provides dynamism and plasticity to bacteria, which would otherwise be propagated clonally. The insertion sequences (IS), the simplest form of prokaryotic TE, are autonomous and compact mobile genetic elements. These can be organized into compound transposons, in which two similar IS can flank any DNA segment and render it transposable. Other more complex structures, called unit transposons, can be grouped into four major families (Tn3, Tn7, Tn402, Tn554) with specific genetic characteristics. This chapter will revisit the prominent structural features of these elements, focusing on a genomic annotation framework and comparative analysis. Relevant aspects of TE will also be presented, stressing their key position in genome impact and evolution, especially in the emergence of antimicrobial resistance and other adaptive traits.
Topics: DNA Transposable Elements; Genomics; Molecular Sequence Annotation; Genome, Bacterial; Bacteria; Evolution, Molecular; Prokaryotic Cells
PubMed: 38819561
DOI: 10.1007/978-1-0716-3838-5_8 -
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