RESUMO
BACKGROUND: Alport syndrome (AS) is an inherited nephropathy caused by mutations in the type IV collagen genes. It is clinically characterized by damage to the eyes, ears and kidneys. Diagnosis of AS is hampered by its atypical clinical picture, particularly when the typical features, include persistent hematuria and microscopic changes in the glomerular basement membrane (GBM), are the only clinical manifestations in the patient. METHODS: We screened 10 families with suspected AS using whole exome sequencing (WES) and analyzed the harmfulness, conservation, and protein structure changes of mutated genes. In further, we performed in vitro functional analysis of two missense mutations in the COL4A5 gene (c.2359G > C, p.G787R and c.2605G > A, p.G869R). RESULTS: We identified 11 pathogenic variants in the type IV collagen genes (COL4A3, COL4A4 and COL4A5). These pathogenic variants include eight missense mutations, two nonsense mutations and one frameshift mutation. Notably, Family 2 had digenic mutations in the COL4A3 (p.G1170A) and UMOD genes (p.M229K). Family 3 had a digenic missense mutation (p.G997E) in COL4A3 and a frameshift mutation (p.P502L fs*151) in COL4A4. To our knowledge, four of the 11 mutations are novel mutations. In addition, we found that COL4A5 mutation relation mRNA levels were significantly decreased in HEK 293 T cell compared to control, while the cellular localization remained the same. CONCLUSIONS: Our research expands the spectrum of COL4A3-5 pathogenic variants, which is helpful for clinical and scientific research.
Assuntos
Autoantígenos , Colágeno Tipo IV , Nefrite Hereditária , Linhagem , Humanos , Nefrite Hereditária/genética , Nefrite Hereditária/patologia , Colágeno Tipo IV/genética , Autoantígenos/genética , Feminino , Masculino , Adulto , Mutação , Sequenciamento do Exoma , Pessoa de Meia-Idade , Mutação de Sentido Incorreto , Células HEK293RESUMO
BACKGROUND: Microbial adaptation to salinity has been a classic inquiry in the field of microbiology. It has been demonstrated that microorganisms can endure salinity stress via either the "salt-in" strategy, involving inorganic ion uptake, or the "salt-out" strategy, relying on compatible solutes. While these insights are mostly based on laboratory-cultured isolates, exploring the adaptive mechanisms of microorganisms within natural salinity gradient is crucial for gaining a deeper understanding of microbial adaptation in the estuarine ecosystem. RESULTS: Here, we conducted metagenomic analyses on filtered surface water samples collected from a typical subtropical short residence-time estuary and categorized them by salinity into low-, intermediate-, and high-salinity metagenomes. Our findings highlighted salinity-driven variations in microbial community composition and function, as revealed through taxonomic and Clusters of Orthologous Group (COG) functional annotations. Through metagenomic binning, 127 bacterial and archaeal metagenome-assembled genomes (MAGs) were reconstructed. These MAGs were categorized as stenohaline-specific to low-, intermediate-, or high-salinity-based on the average relative abundance in one salinity category significantly exceeding those in the other two categories by an order of magnitude. Those that did not meet this criterion were classified as euryhaline, indicating a broader range of salinity tolerance. Applying the Boruta algorithm, a machine learning-based feature selection method, we discerned important genomic features from the stenohaline bacterial MAGs. Of the total 12,162 COGs obtained, 40 were identified as important features, with the "inorganic ion transport and metabolism" COG category emerging as the most prominent. Furthermore, eight COGs were implicated in microbial osmoregulation, of which four were related to the "salt-in" strategy, three to the "salt-out" strategy, and one to the regulation of water channel activity. COG0168, annotated as the Trk-type K+ transporter related to the "salt-in" strategy, was ranked as the most important feature. The relative abundance of COG0168 was observed to increase with rising salinity across metagenomes, the stenohaline strains, and the dominant Actinobacteriota and Proteobacteria phyla. CONCLUSIONS: We demonstrated that salinity exerts influences on both the taxonomic and functional profiles of the microbial communities inhabiting the estuarine ecosystem. Our findings shed light on diverse salinity adaptation strategies employed by the estuarine microbial communities, highlighting the crucial role of the "salt-in" strategy mediated by Trk-type K+ transporters for microorganisms thriving under osmotic stress in the short residence-time estuary. Video Abstract.
Assuntos
Archaea , Bactérias , Estuários , Metagenoma , Metagenômica , Salinidade , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Bactérias/isolamento & purificação , Archaea/genética , Archaea/classificação , Archaea/metabolismo , Adaptação Fisiológica , Microbiota/genética , Água do Mar/microbiologia , Microbiologia da ÁguaRESUMO
The horizontal transfer of plasmids has been recognized as one of the key drivers for the worldwide spread of antimicrobial resistance (AMR) across bacterial pathogens. However, knowledge remain limited about the contribution made by environmental stress on the evolution of bacterial AMR by modulating horizontal acquisition of AMR plasmids and other mobile genetic elements. Here we combined experimental evolution, whole genome sequencing, reverse genetic engineering, and transcriptomics to examine if the evolution of chromosomal AMR to triclosan (TCS) disinfectant has correlated effects on modulating bacterial pathogen (Klebsiella pneumoniae) permissiveness to AMR plasmids and phage susceptibility. Herein, we show that TCS exposure increases the evolvability of K. pneumoniae to evolve TCS-resistant mutants (TRMs) by acquiring mutations and altered expression of several genes previously associated with TCS and antibiotic resistance. Notably, nsrR deletion increases conjugation permissiveness of K. pneumoniae to four AMR plasmids, and enhances susceptibility to various Klebsiella-specific phages through the downregulation of several bacterial defense systems and changes in membrane potential with altered reactive oxygen species response. Our findings suggest that unrestricted use of TCS disinfectant imposes a dual impact on bacterial antibiotic resistance by augmenting both chromosomally and horizontally acquired AMR mechanisms.
Assuntos
Bacteriófagos , Klebsiella pneumoniae , Plasmídeos , Triclosan , Triclosan/farmacologia , Plasmídeos/genética , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/virologia , Bacteriófagos/genética , Bacteriófagos/fisiologia , Farmacorresistência Bacteriana Múltipla/genética , Mutação , Transferência Genética Horizontal , Sequenciamento Completo do Genoma , Evolução Molecular , Antibacterianos/farmacologiaRESUMO
As a synthetic androgen, 17α-methyltestosterone (MT) is widely used in aquaculture to induce sex reversal and may pose a potential risk to aquatic organisms. This ecological risk has attracted the attention of many scholars, but it is not comprehensive enough. Thus, the adverse effects of MT on zebrafish (Danio rerio) were comprehensively evaluated from gonadal histology, as well as the mRNA expression levels of 47 genes related to hypothalamic-pituitary-gonadal (HPG) axis, germ cell differentiation, sex determination, and hypothalamus-pituitary-thyroid (HPT) axis. Adult zebrafish with a female/male ratio of 5:7 were exposed to a solvent control (0.001% dimethyl sulfoxide) and three measured concentrations of MT (5, 51 and 583 ng/L) for 50 days. The results showed that MT had no significant histological effects on the ovaries of females, but the frequency of late-mature oocytes (LMO) showed a downward trend, indicating that MT could induce ovarian suppression to a certain extent. The transcriptional expression of activating transcription factor 4b1 (atf4b1), activating transcription factor 4b2 (atf4b2), calcium/calmodulin-dependent protein kinase II delta 1 (camk2d1), calcium/calmodulin-dependent protein kinase II delta 2 (camk2d2) and calcium/calmodulin-dependent protein kinase II inhibitor 2 (camk2n2) genes in the brain of females increased significantly at all treatment groups of MT, and the mRNA expression of forkhead box L2a (foxl2) and ovarian cytochrome P450 aromatase (cyp19a1a) genes in the ovaries were down-regulated by 5 and 583 ng/L group, which would translate into inhibition of oocyte development. As compared to females, MT had relatively little effects on the reproductive system of males, and only the transcriptional alterations of synaptonemal complex protein 3 (sycp3) and 17-alpha-hydroxylase/17,20-lyase (cyp17) genes were observed in the testes, not enough to affect testicular histology. In addition, MT at all treatments strongly increased corticotropin-releasing hormone (crh) transcript in the brain of females, as well as deiodinase 2 (dio2) transcript in the brain of males. The paired box protein 8 (pax8) gene was significantly decreased at 51 or 583 ng/L of MT in both female and male brains. The above results suggest that MT can pose potential adverse effects on the reproductive and thyroid endocrine system of fish.
Assuntos
Poluentes Químicos da Água , Peixe-Zebra , Animais , Masculino , Feminino , Peixe-Zebra/metabolismo , Metiltestosterona/metabolismo , Metiltestosterona/farmacologia , Eixo Hipotalâmico-Hipofisário-Gonadal , Glândula Tireoide/metabolismo , Cálcio/metabolismo , Proteína Quinase Tipo 2 Dependente de Cálcio-Calmodulina/genética , Proteína Quinase Tipo 2 Dependente de Cálcio-Calmodulina/metabolismo , Proteína Quinase Tipo 2 Dependente de Cálcio-Calmodulina/farmacologia , Gônadas , Expressão Gênica , Células Germinativas , RNA Mensageiro/metabolismo , Fatores Ativadores da Transcrição/genética , Fatores Ativadores da Transcrição/metabolismo , Fatores Ativadores da Transcrição/farmacologia , Poluentes Químicos da Água/metabolismoRESUMO
IMPORTANCE: Reactive oxygen species (ROS), including superoxide anion, is a series of substances that cause oxidative stress for all organisms. Marine group II (MGII) archaea are mainly live in the surface seawater and exposed to considerable ROS. Therefore, it is important to understand the antioxidant capacity of MGII. Our research found that Fe/Mn- superoxide dismutase (Fe/MnSOD) may be more suitable for MGII to resist oxidative damage, and the changes in oxygen concentrations and SOD metallic cofactors play an important role in the selection of SOD by the 17 clades of MGII, which in turn affects the species differentiation of MGII. Overall, this study provides insight into the co-evolutionary history of these uncultivated marine archaea with the earth system.
Assuntos
Archaea , Oxigênio , Archaea/genética , Espécies Reativas de Oxigênio , Superóxido Dismutase/genética , SuperóxidosRESUMO
BACKGROUND: The global spread of plasmid-borne carbapenem resistance is an ongoing public health challenge; however, the nature of such horizontal gene transfer events among complex bacterial communities remains poorly understood. We examined the in-situ transfer of the globally dominant New Delhi metallo-ß-lactamase (NDM)-5-positive IncX3 plasmid (denoted pX3_NDM-5) in hospital wastewater to simulate a real-world, One Health antimicrobial resistance context. METHODS: For this transmission study, we tagged pX3_NDM-5 with the green fluorescent protein gene, gfp, using a CRISPR-based method and transferred the plasmid to a donor Escherichia coli strain. Bacteria were extracted from a hospital wastewater treatment plant (Fujian Provincial Maternity and Children's Hospital, Fuzhou, China) as the bacterial recipient community. We mixed this recipient community with the E coli donor strain carrying the gfp-tagged plasmid, both with and without sodium hypochlorite (NaClO) as an environmental stressor, and conducted several culture-based and culture-independent conjugation assays. The conjugation events were observed microscopically and quantified by fluorescence-activated cell sorting. We analysed the taxonomic composition of the sorted transconjugal pool by 16S rRNA gene amplicon sequencing and assessed the stability of the plasmid in the isolated transconjugants and its ability to transfer back to E coli. FINDINGS: We show that the plasmid pX3_NDM-5 has a broad host range and can transfer across various bacterial phyla, including between Gram-negative and Gram-positive bacteria. Although environmental stress with NaClO did not affect the overall plasmid transfer frequency, it reduced the breadth of the transconjugant pool. The taxonomic composition of the transconjugal pool was distinct from that of the recipient communities, and environmental stress modulated the permissiveness of some operational taxonomic units towards the acquisition of pX3_NDM-5. Notably, pX3_NDM-5 transconjugants included the Gram-positive pathogen Enterococcus faecalis, and the plasmid could subsequently be reconjugated back to E coli. These findings suggest that E faecalis could act as a natural shuttle vector for the wide dissemination of pX3_NDM-5 plasmids. INTERPRETATION: Our culture-independent conjugation model simulates natural environmental conditions and challenges the established theory that Gram-negative and Gram-positive bacteria rarely exchange clinically important plasmids. The data show that plasmids disseminate more widely across genera and phyla than previously thought. These findings have substantial implications when considering the spread of antimicrobial resistance across One Health sectors. FUNDING: The Laboratory of Lingnan Modern Agriculture Project, the National Natural Science Foundation of China, the Natural Science Foundation of Fujian Province of China, and the Outstanding Young Research Talents Program of Fujian Agriculture and Forestry University.
Assuntos
Anti-Infecciosos , Escherichia coli , Feminino , Gravidez , Criança , Humanos , Escherichia coli/genética , Águas Residuárias , RNA Ribossômico 16S/genética , Plasmídeos/genética , Bactérias/genética , HospitaisRESUMO
Thaumarchaeota account for a large portion of microbial symbionts in deep-sea sponges and are even dominant in some cases. In this study, we investigated three new sponge-associated Thaumarchaeota from the deep West Pacific Ocean. Thaumarchaeota were found to be the most dominant phylum in this sponge by both prokaryotic 16S rRNA amplicons and metagenomic sequencing. Fifty-seven published Thaumarchaeota genomes from sponges and other habitats were included for genomic comparison. Similar to shallow sponge-associated Thaumarchaeota, those Thaumarchaeota in deep-sea sponges have extended genome sizes and lower coding density compared with their free-living lineages. Thaumarchaeota in deep-sea sponges were specifically enriched in genes related to stress adapting, symbiotic adhesion and stability, host-microbe interaction and protein transportation. The genes involved in defense mechanisms, such as the restriction-modification system, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system, and toxin-antitoxin system were commonly enriched in both shallow and deep sponge-associated Thaumarchaeota. Our study demonstrates the significant effects of both depth and symbiosis on forming genomic characteristics of Thaumarchaeota, and provides novel insights into their niche adaptation in deep-sea sponges.
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A dynamic epigenome is critical for appropriate gene expression in development and health1-5. Central to this is the intricate process of transcription6-11, which integrates cellular signaling with chromatin changes, transcriptional machinery and modifications to messenger RNA, such as N6-methyladenosine (m6A), which is co-transcriptionally incorporated. The integration of these aspects of the dynamic epigenome, however, is not well understood mechanistically. Here we show that the repressive histone mark H3K9me2 is specifically removed by the induction of m6A-modified transcripts. We demonstrate that the methyltransferase METTL3/METTL14 regulates H3K9me2 modification. We observe a genome-wide correlation between m6A and occupancy by the H3K9me2 demethylase KDM3B, and we find that the m6A reader YTHDC1 physically interacts with and recruits KDM3B to m6A-associated chromatin regions, promoting H3K9me2 demethylation and gene expression. This study establishes a direct link between m6A and dynamic chromatin modification and provides mechanistic insight into the co-transcriptional interplay between RNA modifications and histone modifications.
Assuntos
Adenosina/análogos & derivados , Histonas/genética , Adenosina/genética , Linhagem Celular , Cromatina/genética , Expressão Gênica/genética , Células HEK293 , Humanos , Metilação , Metiltransferases/genética , RNA Mensageiro/genética , Transcrição Gênica/genéticaRESUMO
Terrestrial organic matter occupies an important position in the oceanic organic carbon pool. Some terrestrial proxies, like the Branched and Isoprenoid Tetraether (BIT) index, have been applied successfully to indicate the relative abundance of terrestrial organic matter in marine sediments. A new terrestrial proxy derived from sediment pore water fluorescent dissolved matter (fluorescent dissolved organic matter (FDOM)) was developed in this study. Surface sediment samples were collected from forty-two sites in the coastal region of the East China Sea (ECS) to examine the distributional patterns of FDOM. Three protein-like components (C1, C4 and C5) and two humic-like components (C2 and C3) of FDOM were identified using fluorescence excitation-emission matrices parallel factor analysis (EEMs-PARAFAC). Spatially, the intensity of these five components generally increased from the coast to the ocean with protein-like components showing a more obvious trend, which suggested that all five components had autochthonous contribution. However, the C2 and C3 proportions, especially C2 that mainly corresponds to the proportion of peak A in fluorescence excitation-emission matrices, significantly decreased from the coast to the ocean and significantly correlated with the BIT index from corresponding solid fractions. We posit that part of the humic-like components from terrestrial organic matter in sediments are released into the C2 and C3 pools in pore waters, which may be constrained by specific environmental conditions. Thus, the FDOM from pore waters can be integrated with BIT index to validate the nature of FDOM and use it as a biomarker to reflect the terrestrial input of organic matter mediated by different biogeochemical processes in coastal oceans. The proportion of peak A responsible for the fluorescence of C2 was suggest as a new terrestrial derived from FDOM.
Assuntos
Corantes , China , Análise Fatorial , Oceanos e Mares , Espectrometria de FluorescênciaRESUMO
PURPOSE: To introduce an alternative method for the reinsertion of pigtail catheter for collapsed nephrostomy tract. MATERIALS AND METHODS: Between January 2013 and October 2016, a total of ten patients with collapsed nephros-tomy tract underwent ureteroscope-aided reinsertion of the pigtail catheter after the failure of manual reinsertion by guidewire. Under local anesthesia, the ureteroscope was inserted through a percutaneous nephrostomy (PCN) opening. The access path was obtained by careful tracing for prior placement of pigtail catheter. The clinical features of these ten patients, including operation time, success rate and complications, were evaluated by retro-spective chart review. The Clavien classification was applied to define the grade of complications after one-month follow-up. RESULTS: Among the ten cases of difficult PCN revision, eight underwent the procedure within 24 hours of the dislodgement. The remaining two patients underwent the procedure within 2 days and 8 days. The period of pigtail tube dwelling ranged from 2 weeks to 10.5 months. The procedure was successful in nine cases and the operation time ranged from 10 to 30 minutes. No fluoroscope was used in any patient. All of the nine patients had a good drainage function after tube reinsertion. Complications occurred only in one patient who had postoperative fever classified as Clavien grade 2. CONCLUSION: Reinserting the dislodged pigtail nephrostomy tube with the aid of an ureteroscope is an alternative method that may decrease the necessity of new tract creation.
Assuntos
Catéteres , Nefrostomia Percutânea/instrumentação , Complicações Pós-Operatórias/cirurgia , Ureteroscópios , Idoso , Idoso de 80 Anos ou mais , Falha de Equipamento , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Complicações Pós-Operatórias/etiologia , Reoperação , Estudos RetrospectivosRESUMO
Two cDNAs encoding putative type 1 acyl-CoA: diacylglycerol acyltransferases (DGAT1, EC 2.3.1.20), were cloned from Tetraena mongolica, an extreme xerophyte with high oil content in the stems. The 1 488-bp and 1 485-bp of the open reading frame (ORF) of the two cDNAs, designated as TmDGAT1a and TmDGAT1b, were both predicted to encode proteins of 495 and 494 amino acids, respectively. Southern blot analysis revealed that TmDGAT1a and TmDGAT1b both had low copy numbers in the T. mongolica genome. In addition to ubiquitous expression with different intensity in different tissues, including stems, leaves and roots, TmDGAT1a and TmDGAT1b, were found to be strongly induced by high salinity, drought and osmotic stress, resulting in a remarkable increase of triacylglycerol (TAG) accumulation in T. mongolica plantlets. TmDGAT1a and TmDGAT1b activities were confirmed in the yeast H1246 quadruple mutant (DGA1, LRO1, ARE1, ARE2) by restoring DGAT activity of the mutant host to produce TAG. Overexpression of TmDGAT1a and TmDGAT1b in soybean hairy roots as well as in T. mongolica calli both resulted in an increase in oil content (ranging from 37% to 108%), accompanied by altered fatty acid profiles.
Assuntos
Diacilglicerol O-Aciltransferase/metabolismo , Proteínas de Plantas/metabolismo , Zygophyllaceae/enzimologia , Diacilglicerol O-Aciltransferase/genética , Ácidos Graxos/metabolismo , Proteínas de Plantas/genética , Raízes de Plantas/enzimologia , Raízes de Plantas/genética , Raízes de Plantas/metabolismo , Plantas Geneticamente Modificadas/enzimologia , Plantas Geneticamente Modificadas/genética , Plantas Geneticamente Modificadas/metabolismo , Triglicerídeos/metabolismo , Zygophyllaceae/genética , Zygophyllaceae/metabolismoRESUMO
Monogalactosyldiacylglycerol (MGDG) is the most abundant lipid component of the thylakoid membrane. Although MGDG is believed to be important in sustaining the structure and function of the photosynthetic membrane, its exact role in photosynthesis in vivo requires further investigation. In this study, the transgenic tobacco plant M18, which has an MGDG deficiency of approximately 53%, and which contains many fewer thylakoid membranes and exhibits retarded growth and a chlorotic phenotype, was used to investigate the role of MGDG. Chlorophyll fluorescence analysis of the M18 line revealed that PSII activity was inhibited when the plants were exposed to light. The inactive linear electron transport found in M18 plants was mainly attributed to a block in the intersystem electron transport process that was revealed by P700 redox kinetics and PSI light response analysis. Immunoblotting and Blue Native SDS-PAGE analysis suggested that a reduction in the accumulation of cytochrome b6f in M18 plants is a direct structural effect of MGDG deficiency, and this is likely to be responsible for the inefficiency observed in intersystem electron transport. Although drastic impairments of PSII subunits were detected in M18 plants grown under normal conditions, further investigations of low-light-grown M18 plants indicated that the impairments are not direct structural effects. Instead, they are likely to result from the cumulative photodamage that occurs due to impaired photostability under long-term exposure to relatively high light levels. The study suggests that MGDG plays important roles in maintaining both the linear electron transport process and the photostability of the PSII apparatus.