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1.
Article in English | MEDLINE | ID: mdl-38929024

ABSTRACT

Duchenne muscular dystrophy (DMD) is a disease that primarily affects males and causes a gradual loss of muscle strength. This results in a deterioration of motor skills and functional mobility, which can impact the performance of various occupations. Individuals with DMD often rely heavily on caregivers to assist with daily activities, which can lead to caregiver burden. A case study was conducted to explore and describe potential variations in the performance of a young adult diagnosed with DMD and his caregivers resulting from the integration of smart speakers (SS)-controlled Internet of Things (IoT) devices in the home environment. The study also examined the potential of SS as an environment control unit (ECU) and analysed variations in caregiver burden. Smart devices and SS were installed in the most frequently used spaces, namely, the bedroom and living room. The study employed WebQDA software to perform content analysis and Microsoft Excel to calculate the scores of the structured instruments. The implementation of the IoT-assisted environment compensated for previously physical tasks, resulting in a slight increase in independent performance and reduced demands on caregivers.


Subject(s)
Muscular Dystrophy, Duchenne , Muscular Dystrophy, Duchenne/physiopathology , Humans , Male , Young Adult , Activities of Daily Living , Adult , Caregivers
2.
Water Res ; 258: 121784, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38761599

ABSTRACT

The present study aims to characterize the bacterial community, resistome and integron abundance of a municipal wastewater treatment plant (WWTP) over the course of 12 months and evaluate the year-long performance of integron-related genes as potential indicators of antibiotic resistance mechanisms in influents and effluents. For that, total DNA was extracted and subjected to 16S rRNA-targeted metabarcoding, high-throughput (HT) qPCR (48 targets) and standard qPCR (5 targets). Targets included integrase genes, antibiotic resistance genes (ARGs) and putative pathogenic groups. A total of 16 physicochemical parameters determined in the wastewater samples were also considered. Results revealed that the WWTP treatment significantly impacted the bacterial community, as well as the content in ARGs and integrase genes. Indeed, there was a relative enrichment from influent to effluent of 13 pathogenic groups (e.g., Legionella and Mycobacterium) and genes conferring resistance to sulphonamides, aminoglycosides and disinfectants. Effluent samples (n = 25) also presented seasonal differences, with an increase of the total ARGs' concentration in summer, and differences between winter and summer on relative abundance of sulphonamide and disinfectant resistance mechanisms. From the eight putative integron-related genes selected, all were positively correlated with the total ARGs' content in wastewater and the relative abundance of resistance to most of the specific antibiotic classes. The genes intI1, blaGES and qacE∆1 were the most strongly correlated with the total concentration of ARGs. Genes blaGES and blaVIM, were better correlated to resistance to beta-lactams, aminoglycosides and tetracyclines. This study supports the use of integron-related genes as powerful indicators of antibiotic resistance in wastewater, being robust despite the variability caused by wastewater treatment and seasonality.


Subject(s)
Drug Resistance, Microbial , Integrons , Seasons , Wastewater , Integrons/genetics , Drug Resistance, Microbial/genetics , Waste Disposal, Fluid , RNA, Ribosomal, 16S/genetics , Genes, Bacterial , Anti-Bacterial Agents/pharmacology , Bacteria/genetics , Bacteria/drug effects
3.
Proc Natl Acad Sci U S A ; 121(7): e2320240121, 2024 Feb 13.
Article in English | MEDLINE | ID: mdl-38315865

ABSTRACT

DNA structure can regulate genome function. Four-stranded DNA G-quadruplex (G4) structures have been implicated in transcriptional regulation; however, previous studies have not directly addressed the role of an individual G4 within its endogenous cellular context. Using CRISPR to genetically abrogate endogenous G4 structure folding, we directly interrogate the G4 found within the upstream regulatory region of the critical human MYC oncogene. G4 loss leads to suppression of MYC transcription from the P1 promoter that is mediated by the deposition of a de novo nucleosome alongside alterations in RNA polymerase recruitment. We also show that replacement of the endogenous MYC G4 with a different G4 structure from the KRAS oncogene restores G4 folding and MYC transcription. Moreover, we demonstrate that the MYC G4 structure itself, rather than its sequence, recruits transcription factors and histone modifiers. Overall, our work establishes that G4 structures are important features of transcriptional regulation that coordinate recruitment of key chromatin proteins and the transcriptional machinery through interactions with DNA secondary structure, rather than primary sequence.


Subject(s)
G-Quadruplexes , Proto-Oncogene Proteins c-myc , Humans , DNA/metabolism , Gene Expression Regulation , Promoter Regions, Genetic/genetics , Transcription Factors/metabolism , Proto-Oncogene Proteins c-myc/genetics
4.
J Mol Biol ; 435(22): 168299, 2023 11 15.
Article in English | MEDLINE | ID: mdl-37802215

ABSTRACT

Chemical modifications are essential regulatory elements that modulate the behavior and function of cellular RNAs. Despite recent advances in sequencing-based RNA modification mapping, methods combining accuracy and speed are still lacking. Here, we introduce MRT-ModSeq for rapid, simultaneous detection of multiple RNA modifications using MarathonRT. MRT-ModSeq employs distinct divalent cofactors to generate 2-D mutational profiles that are highly dependent on nucleotide identity and modification type. As a proof of concept, we use the MRT fingerprints of well-studied rRNAs to implement a general workflow for detecting RNA modifications. MRT-ModSeq rapidly detects positions of diverse modifications across a RNA transcript, enabling assignment of m1acp3Y, m1A, m3U, m7G and 2'-OMe locations through mutation-rate filtering and machine learning. m1A sites in sparsely modified targets, such as MALAT1 and PRUNE1 could also be detected. MRT-ModSeq can be trained on natural and synthetic transcripts to expedite detection of diverse RNA modification subtypes across targets of interest.


Subject(s)
RNA Processing, Post-Transcriptional , RNA, Ribosomal , Mutation , RNA, Ribosomal/chemistry , RNA, Ribosomal/genetics , Sequence Analysis, RNA/methods , Humans
5.
bioRxiv ; 2023 May 25.
Article in English | MEDLINE | ID: mdl-37292902

ABSTRACT

Chemical modifications are essential regulatory elements that modulate the behavior and function of cellular RNAs. Despite recent advances in sequencing-based RNA modification mapping, methods combining accuracy and speed are still lacking. Here, we introduce MRT- ModSeq for rapid, simultaneous detection of multiple RNA modifications using MarathonRT. MRT-ModSeq employs distinct divalent cofactors to generate 2-D mutational profiles that are highly dependent on nucleotide identity and modification type. As a proof of concept, we use the MRT fingerprints of well-studied rRNAs to implement a general workflow for detecting RNA modifications. MRT-ModSeq rapidly detects positions of diverse modifications across a RNA transcript, enabling assignment of m1acp3Y, m1A, m3U, m7G and 2'-OMe locations through mutation-rate filtering and machine learning. m1A sites in sparsely modified targets, such as MALAT1 and PRUNE1 could also be detected. MRT-ModSeq can be trained on natural and synthetic transcripts to expedite detection of diverse RNA modification subtypes across targets of interest.

6.
Bioinformatics ; 39(3)2023 03 01.
Article in English | MEDLINE | ID: mdl-36857576

ABSTRACT

MOTIVATION: The increasing availability of RNA structural information that spans many kilobases of transcript sequence imposes a need for tools that can rapidly screen, identify, and prioritize structural modules of interest. RESULTS: We describe RNA Structural Content Scanner (RSCanner), an automated tool that scans RNA transcripts for regions that contain high levels of secondary structure and then classifies each region for its relative propensity to adopt stable or dynamic structures. RSCanner then generates an intuitive heatmap enabling users to rapidly pinpoint regions likely to contain a high or low density of discrete RNA structures, thereby informing downstream functional or structural investigation. AVAILABILITY AND IMPLEMENTATION: RSCanner is freely available as both R script and R Markdown files, along with full documentation and test data (https://github.com/pylelab/RSCanner).


Subject(s)
RNA , Software , Protein Structure, Secondary , Documentation , Sequence Analysis, RNA
7.
Polymers (Basel) ; 15(3)2023 Jan 18.
Article in English | MEDLINE | ID: mdl-36771817

ABSTRACT

Bioplastics are one of the possible alternative solutions to the polymers of petrochemical origins. Bioplastics have several advantages over traditional plastics in terms of low carbon footprint, energy efficiency, biodegradability and versatility. Although they have numerous benefits and are revolutionizing many application fields, they also have several weaknesses, such as brittleness, high-water absorption, low crystallization ability and low thermal degradation temperature. These drawbacks can be a limiting factor that prevents their use in many applications. Nonetheless, reinforcements and plasticizers can be added to bioplastic production as a way to overcome such limitations. Bioplastics materials are not yet studied in depth, but it is with great optimism that their industrial use and market scenarios are increasing; such growth can be a positive driver for more research in this field. National and international investments in the bioplastics industry can also promote the green transition. International projects, such as EcoPlast and Animpol, aim to study and develop new polymeric materials made from alternative sources. One of their biggest problems is their waste management; there is no separation process yet to recycle the nonbiodegradable bioplastics, and they are considered contaminants when mixed with other polymers. Some materials use additives, and their impact on the microplastics they leave after breaking apart is subject to debate. For this reason, it is important to consider their life cycle analysis and assess their environmental viability. These are materials that can possibly be processed in various ways, including conventional processes used for petrochemical ones. Those include injection moulding and extrusion, as well as digital manufacturing. This and the possibility to use these materials in several applications is one of their greatest strengths. All these aspects will be discussed in this review.

8.
PLoS One ; 17(12): e0264879, 2022.
Article in English | MEDLINE | ID: mdl-36525407

ABSTRACT

Defining demographically independent units and understanding patterns of gene flow between them is essential for managing and conserving exploited populations. The critically endangered scalloped hammerhead shark, Sphyrna lewini, is a coastal semi-oceanic species found worldwide in tropical and subtropical waters. Pregnant females give birth in shallow coastal estuarine habitats that serve as nursery grounds for neonates and small juveniles, whereas adults move offshore and become highly migratory. We evaluated the population structure and connectivity of S. lewini in coastal areas and one oceanic island (Cocos Island) across the Eastern Tropical Pacific (ETP) using both sequences of the mitochondrial DNA control region (mtCR) and 9 nuclear-encoded microsatellite loci. The mtCR defined two genetically discrete groups: one in the Mexican Pacific and another one in the central-southern Eastern Tropical Pacific (Guatemala, Costa Rica, Panama, and Colombia). Overall, the mtCR data showed low levels of haplotype diversity ranging from 0.000 to 0.608, while nucleotide diversity ranged from 0.000 to 0.0015. More fine-grade population structure was detected using microsatellite loci where Guatemala, Costa Rica, and Panama differed significantly. Relatedness analysis revealed that individuals within nursery areas were more closely related than expected by chance, suggesting that S. lewini may exhibit reproductive philopatric behaviour within the ETP. Findings of at least two different management units, and evidence of philopatric behaviour call for intensive conservation actions for this highly threatened species in the ETP.


Subject(s)
Sharks , Female , Animals , Sharks/genetics , Endangered Species , Microsatellite Repeats/genetics , Genetics, Population , DNA, Mitochondrial/genetics , Birds/genetics
9.
Microorganisms ; 10(11)2022 Nov 12.
Article in English | MEDLINE | ID: mdl-36422313

ABSTRACT

BACKGROUND: New Delhi metallo-beta-lactamase (NDM) has been spreading across the globe, but the causes of its success are poorly understood. We characterized a blaNDM-5-positive Escherichia coli strain from a Portuguese hospital and conducted comparative genomic analyses to understand the role of clonal background and horizontal gene transfer in blaNDM-5 dissemination. METHODS: After blaNDM PCR screening and genome sequencing, Ec355340 was subjected to mating, transformation, and plasmid curing assays and MICs determination for several antibiotics. Comparison with data compiled from public databases was performed. RESULTS: blaNDM-5 was in a complex integron co-located in a FIB-FII plasmid (pEc355340_NDM-5). The mating assays were unsuccessful, but plasmid transformation into a susceptible host led to resistance to all beta-lactams and to sulfamethoxazole-trimethoprim. The profile of virulence genes (n = 73) was compatible with extraintestinal pathogenesis. An analysis of genomes from public databases suggested that blaNDM-5 has rarely been associated with ST156 strains (such as Ec355340), while is has frequently been found on strains of the ST10 clonal complex. However, ST156 may play a role in the co-spreading of blaNDM and mcr genes. Regardless, comparative genomics confirmed the presence of blaNDM in similar complex integrons in plasmids (48/100 plasmids most similar to pEc355340_NDM-5) and ST156 genomes (20/41 blaNDM-positive genomes). CONCLUSIONS: blaNDM-5 and other blaNDM variants were more frequently associated to complex integrons than previously reported and, therefore, these platforms may be important drivers in their dissemination. The identification of blaNDM-5 for the first time in Portugal could be a game-changer in the current Portuguese antibiotic resistance scenario, as this gene encodes a higher-level resistance phenotype, and its spread may be facilitated due to the association with complex integrons.

10.
Front Plant Sci ; 13: 868027, 2022.
Article in English | MEDLINE | ID: mdl-35712599

ABSTRACT

The prokaryote-derived Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas mediated gene editing tools have revolutionized our ability to precisely manipulate specific genome sequences in plants and animals. The simplicity, precision, affordability, and robustness of this technology have allowed a myriad of genomes from a diverse group of plant species to be successfully edited. Even though CRISPR/Cas, base editing, and prime editing technologies have been rapidly adopted and implemented in plants, their editing efficiency rate and specificity varies greatly. In this review, we provide a critical overview of the recent advances in CRISPR/Cas9-derived technologies and their implications on enhancing editing efficiency. We highlight the major efforts of engineering Cas9, Cas12a, Cas12b, and Cas12f proteins aiming to improve their efficiencies. We also provide a perspective on the global future of agriculturally based products using DNA-free CRISPR/Cas techniques. The improvement of CRISPR-based technologies efficiency will enable the implementation of genome editing tools in a variety of crop plants, as well as accelerate progress in basic research and molecular breeding.

11.
Eval Program Plann ; 89: 101984, 2021 12.
Article in English | MEDLINE | ID: mdl-34461349

ABSTRACT

The evaluation of Higher Education Institutions (HEIs) is a challenging task, due to the complexity inherent in the context in which they are inserted, the different institutional profiles, the variety of resources used and the results offered in the performance of their mission. In this way, the present study proposes an evaluative approach that aims to measure efficiency taking into account the diverse activities characteristic of university institutions. To this end, a data envelopment analysis (DEA) approach, known as Network DEA, is used, which encompasses the different processes and subprocesses that take place within these institutions. In all, the evaluation considers eleven variables organized in three distinct stages, which reflect the performance of the HEIs in different perspectives: financial, undergraduate level and graduate level (student training and scientific production and innovation). Finally, the model was applied at 45 Brazilian federal universities. This case study allows a comprehensive efficiency analysis to be carried out for the set of institutions considered, from each perspective taken into account in the approach.


Subject(s)
Schools , Universities , Brazil , Humans , Program Evaluation , Students
12.
Science ; 372(6547): 1176-1181, 2021 06 11.
Article in English | MEDLINE | ID: mdl-34112688

ABSTRACT

How eukaryotic cells assess and maintain sizes specific for their species and cell type remains unclear. We show that in the Arabidopsis shoot stem cell niche, cell size variability caused by asymmetric divisions is corrected by adjusting the growth period before DNA synthesis. KIP-related protein 4 (KRP4) inhibits progression to DNA synthesis and associates with mitotic chromosomes. The F BOX-LIKE 17 (FBL17) protein removes excess KRP4. Consequently, daughter cells are born with comparable amounts of KRP4. Inhibitor dilution models predicted that KRP4 inherited through chromatin would robustly regulate size, whereas inheritance of excess free KRP4 would disrupt size homeostasis, as confirmed by mutant analyses. We propose that a cell cycle regulator, stabilized by association with mitotic chromosomes, reads DNA content as a cell size-independent scale.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/cytology , Cyclin-Dependent Kinase Inhibitor Proteins/metabolism , DNA, Plant/metabolism , Meristem/cytology , Plant Cells/physiology , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Asymmetric Cell Division , Cell Cycle , Cell Cycle Checkpoints , Cell Division , Cell Size , Chromatin/metabolism , Chromosomes, Plant/metabolism , Cyclin-Dependent Kinase Inhibitor Proteins/genetics , DNA Replication , F-Box Proteins/metabolism , G1 Phase , Mitosis , Models, Biological , Mutation , S Phase
13.
Proc Natl Acad Sci U S A ; 118(17)2021 04 27.
Article in English | MEDLINE | ID: mdl-33888582

ABSTRACT

The diversity and environmental plasticity of plant growth results from variations of repetitive modules, such as the basic shoot units made of a leaf, axillary bud, and internode. Internode elongation is regulated both developmentally and in response to environmental conditions, such as light quality, but the integration of internal and environmental signals is poorly understood. Here, we show that the compressed rosette growth habit of Arabidopsis is maintained by the convergent activities of the organ boundary gene ARABIDOPSIS THALIANA HOMEOBOX GENE 1 (ATH1) and of the gibberellin-signaling DELLA genes. Combined loss of ATH1 and DELLA function activated stem development during the vegetative phase and changed the growth habit from rosette to caulescent. Chromatin immunoprecipitation high-throughput sequencing and genetic analysis indicated that ATH1 and the DELLA gene REPRESSOR OF GA1-3 (RGA) converge on the regulation of light responses, including the PHYTOCHROME INTERACTING FACTORS (PIF) pathway, and showed that the ATH1 input is mediated in part by direct activation of BLADE ON PETIOLE (BOP1 and BOP2) genes, whose products destabilize PIF proteins. We conclude that an organ-patterning gene converges with hormone signaling to spatially restrict environmental responses and establish a widespread type of plant architecture.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/growth & development , Homeodomain Proteins/metabolism , Transcription Factors/metabolism , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Environment , Gene Expression/genetics , Gene Expression Regulation, Plant/genetics , Genes, Homeobox/genetics , Genes, Plant/genetics , Gibberellins/metabolism , Homeodomain Proteins/genetics , Plant Development/genetics , Plant Growth Regulators/metabolism , Plant Leaves/metabolism , Plants, Genetically Modified/genetics , Signal Transduction/genetics , Stress, Physiological/physiology , Transcription Factors/genetics
14.
Front Plant Sci ; 12: 630587, 2021.
Article in English | MEDLINE | ID: mdl-33659017

ABSTRACT

High crop yields are generally associated with high nitrogen (N) fertilizer rates. A growing tendency that is urgently demanding the adoption of precision technologies that manage N more efficiently, combined with the advances of crop genetics to meet the needs of sustainable farm systems. Among the plant traits, stem architecture has been of paramount importance to enhance harvest index in the cereal crops. Nonetheless, the reduced stature also brought undesirable effect, such as poor N-uptake, which has led to the overuse of N fertilizer. Therefore, a better understanding of how N signals modulate the initial and late stages of stem development might uncover novel semi-dwarf alleles without pleiotropic effects. Our attempt here is to review the most recent advances on this topic.

15.
Mol Cell ; 81(3): 584-598.e5, 2021 02 04.
Article in English | MEDLINE | ID: mdl-33444546

ABSTRACT

Severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2) is the positive-sense RNA virus that causes coronavirus disease 2019 (COVID-19). The genome of SARS-CoV-2 is unique among viral RNAs in its vast potential to form RNA structures, yet as much as 97% of its 30 kilobases have not been structurally explored. Here, we apply a novel long amplicon strategy to determine the secondary structure of the SARS-CoV-2 RNA genome at single-nucleotide resolution in infected cells. Our in-depth structural analysis reveals networks of well-folded RNA structures throughout Orf1ab and reveals aspects of SARS-CoV-2 genome architecture that distinguish it from other RNA viruses. Evolutionary analysis shows that several features of the SARS-CoV-2 genomic structure are conserved across ß-coronaviruses, and we pinpoint regions of well-folded RNA structure that merit downstream functional analysis. The native, secondary structure of SARS-CoV-2 presented here is a roadmap that will facilitate focused studies on the viral life cycle, facilitate primer design, and guide the identification of RNA drug targets against COVID-19.


Subject(s)
COVID-19 , Genome, Viral , Nucleic Acid Conformation , RNA, Viral , Response Elements , SARS-CoV-2 , COVID-19/genetics , COVID-19/metabolism , Cell Line, Tumor , Humans , RNA, Viral/genetics , RNA, Viral/metabolism , SARS-CoV-2/genetics , SARS-CoV-2/metabolism
16.
J Virol ; 95(5)2021 03 01.
Article in English | MEDLINE | ID: mdl-33268519

ABSTRACT

SARS-CoV-2 is the causative viral agent of COVID-19, the disease at the center of the current global pandemic. While knowledge of highly structured regions is integral for mechanistic insights into the viral infection cycle, very little is known about the location and folding stability of functional elements within the massive, ∼30kb SARS-CoV-2 RNA genome. In this study, we analyze the folding stability of this RNA genome relative to the structural landscape of other well-known viral RNAs. We present an in-silico pipeline to predict regions of high base pair content across long genomes and to pinpoint hotspots of well-defined RNA structures, a method that allows for direct comparisons of RNA structural complexity within the several domains in SARS-CoV-2 genome. We report that the SARS-CoV-2 genomic propensity for stable RNA folding is exceptional among RNA viruses, superseding even that of HCV, one of the most structured viral RNAs in nature. Furthermore, our analysis suggests varying levels of RNA structure across genomic functional regions, with accessory and structural ORFs containing the highest structural density in the viral genome. Finally, we take a step further to examine how individual RNA structures formed by these ORFs are affected by the differences in genomic and subgenomic contexts, which given the technical difficulty of experimentally separating cellular mixtures of sgRNA from gRNA, is a unique advantage of our in-silico pipeline. The resulting findings provide a useful roadmap for planning focused empirical studies of SARS-CoV-2 RNA biology, and a preliminary guide for exploring potential SARS-CoV-2 RNA drug targets.Importance The RNA genome of SARS-CoV-2 is among the largest and most complex viral genomes, and yet its RNA structural features remain relatively unexplored. Since RNA elements guide function in most RNA viruses, and they represent potential drug targets, it is essential to chart the architectural features of SARS-CoV-2 and pinpoint regions that merit focused study. Here we show that RNA folding stability of SARS-CoV-2 genome is exceptional among viral genomes and we develop a method to directly compare levels of predicted secondary structure across SARS-CoV-2 domains. Remarkably, we find that coding regions display the highest structural propensity in the genome, forming motifs that differ between the genomic and subgenomic contexts. Our approach provides an attractive strategy to rapidly screen for candidate structured regions based on base pairing potential and provides a readily interpretable roadmap to guide functional studies of RNA viruses and other pharmacologically relevant RNA transcripts.

17.
Water Res ; 184: 116079, 2020 Oct 01.
Article in English | MEDLINE | ID: mdl-32717492

ABSTRACT

Wastewater treatment plants (WWTPs) are relevant sources of antibiotic resistance into aquatic environments. Disinfection of WWTPs' effluents (e.g. by UV-C irradiation) may attenuate this problem, though some clinically relevant bacteria have been shown to survive disinfection. In this study we characterized 25 CTX-M-producing Escherichia coli strains isolated from a WWTP's UV-C-irradiated effluent, aiming to identify putative human health hazards associated with such effluents. Molecular typing indicated that the strains belong to the phylogroups A, B2 and C and clustered into 9 multilocus sequence types (STs), namely B2:ST131 (n = 7), A:ST58 (n = 1), A:ST155 (n = 4), C:ST410 (n = 2), A:ST453 (n = 2), A:ST617 (n = 2), A:ST744 (n = 1), A:ST1284 (n = 3) and a putative novel ST (n = 3). PCR-screening identified 9 of the 20 antibiotic resistance genes investigated [i.e. sul1, sul2, sul3, tet(A), tet(B), blaOXA-1-like, aacA4, aacA4-cr and qnrS1]. The more prevalent were sul1, sul2 (n = 15 isolates) and tet(A) (n = 14 isolates). Plasmid restriction analysis indicated diverse plasmid content among strains (14 distinct profiles) and mating assays yielded cefotaxime-resistant transconjugants for 8 strains. Two of the transconjugants displayed a multi-drug resistance (MDR) phenotype. All strains were classified as cytotoxic to Vero cells (9 significantly more cytotoxic than the positive control) and 10 of 21 strains were invasive towards this cell line (including all B2:ST131 strains). The 10 strains tested against G. mellonella larvae exhibited a virulent behaviour. Twenty-four and 7 of the 25 strains produced siderophores and haemolysins, respectively. Approximately 66% of the strains formed biofilms. Genome analysis of 6 selected strains identified several virulence genes encoding toxins, siderophores, and colonizing, adhesion and invasion factors. Freshwater microcosms assays showed that after 28 days of incubation 3 out of 6 strains were still detected by cultivation and 4 strains by qPCR. Resistance phenotypes of these strains remained unaltered. Overall, we confirmed WWTP's UV-C-treated outflow as a source of MDR and/or virulent E. coli strains, some probably capable of persisting in freshwater, and that carry conjugative antibiotic resistance plasmids. Hence, disinfected wastewater may still represent a risk for human health. More detailed evaluation of strains isolated from wastewater effluents is urgent, to design treatments that can mitigate the release of such bacteria.


Subject(s)
Escherichia coli Infections , Escherichia coli , Animals , Anti-Bacterial Agents/pharmacology , Chlorocebus aethiops , Drug Resistance, Multiple, Bacterial , Escherichia coli/genetics , Humans , Microbial Sensitivity Tests , Phenotype , Plasmids , Vero Cells , Wastewater/analysis , beta-Lactamases/genetics
18.
bioRxiv ; 2020 Jul 10.
Article in English | MEDLINE | ID: mdl-32676598

ABSTRACT

SARS-CoV-2 is the positive-sense RNA virus that causes COVID-19, a disease that has triggered a major human health and economic crisis. The genome of SARS-CoV-2 is unique among viral RNAs in its vast potential to form stable RNA structures and yet, as much as 97% of its 30 kilobases have not been structurally explored in the context of a viral infection. Our limited knowledge of SARS-CoV-2 genomic architecture is a fundamental limitation to both our mechanistic understanding of coronavirus life cycle and the development of COVID-19 RNA-based therapeutics. Here, we apply a novel long amplicon strategy to determine for the first time the secondary structure of the SARS-CoV-2 RNA genome probed in infected cells. In addition to the conserved structural motifs at the viral termini, we report new structural features like a conformationally flexible programmed ribosomal frameshifting pseudoknot, and a host of novel RNA structures, each of which highlights the importance of studying viral structures in their native genomic context. Our in-depth structural analysis reveals extensive networks of well-folded RNA structures throughout Orf1ab and reveals new aspects of SARS-CoV-2 genome architecture that distinguish it from other single-stranded, positive-sense RNA viruses. Evolutionary analysis of RNA structures in SARS-CoV-2 shows that several features of its genomic structure are conserved across beta coronaviruses and we pinpoint individual regions of well-folded RNA structure that merit downstream functional analysis. The native, complete secondary structure of SAR-CoV-2 presented here is a roadmap that will facilitate focused studies on mechanisms of replication, translation and packaging, and guide the identification of new RNA drug targets against COVID-19.

19.
Mar Pollut Bull ; 157: 111302, 2020 Aug.
Article in English | MEDLINE | ID: mdl-32658670

ABSTRACT

Concentration of bacterial species indicative of fecal contamination in the gut of mangrove oysters (Crassostrea gasar) is a major concern for public health and food surveillance. Our work aimed to determine the occurrence, antibiotic-resistance, phylogenetic profile and virulence of Escherichia coli strains isolated from C. gasar farmed in four estuaries of Amazonia. Santo Antônio de Urindeua was the sampling point with the highest number of E. coli cells in oyster samples (104 per 100 g of sample). Twenty-four isolates (52.2%) showed resistance to cephalotin and 18 to amoxicillin (39.1%). Eighteen clonal populations were determined by rep-PCR and were mainly affiliated to the pathogenic and commensal phylo-groups B1 and D. The presence of elt genes suggests that 10 of these clones belong to the Enterotoxigenic Escherichia coli pathotype. Plasmids, mostly of the F incompatibility group, were detected in the majority of the strains. All isolates were susceptible to last-resort antibiotics.


Subject(s)
Crassostrea , Escherichia coli , Animals , Anti-Bacterial Agents , Brazil , Estuaries , Phylogeny , Virulence
20.
Rev Col Bras Cir ; 47: e20202398, 2020.
Article in Portuguese, English | MEDLINE | ID: mdl-32555962

ABSTRACT

OBJECTIVE: The purpose of this study was to assess the quality of life of patients who had undergone bilateral thoracic sympathectomy from R5 to R8 as a treatment for severe and debilitating compensatory hyperhidrosis (CH). METHODS: Twelve patients with severe and debilitating compensatory hyperhidrosis underwent extended sympathectomy (R5-R8) from September 2016 to May 2019 at the Hospital das Clínicas, Federal University of Pernambuco, Brazil. Outcomes such as the level of patient satisfaction with the operation, quality of life scores as well as postoperative complications were assessed. RESULTS: There has been a substantial improvement in the quality of life score of 66% of the sample. In all four domains, a statistical significant difference was seen, regarding the relief of compensatory hyperhidrosis symptoms. CONCLUSIONS: Extended sympathectomy from R5 to R8 was shown to be quite effective in most cases, leading us to believe that this approach could be a therapeutic option for severe compensatory hyperhidrosis.


OBJETIVO: Avaliar a qualidade de vida de pacientes submetidos a simpatectomia torácica bilateral de R5 a R8 como forma de tratamento da hiperidrose compensatória (HC) grave e debilitante em pacientes que foram previamente submetidos a simpatectomia torácica bilateral para tratamento da hiperidrose localizada. MÉTODOS: Doze pacientes com hiperidrose compensatória grave e debilitante foram submetidos a simpatectomia estendida no Hospital das Clínicas da Universidade Federal de Pernambuco, Brasil, entre setembro de 2016 e maio de 2019. Os seguintes desfechos foram estudados: nível de satisfação com a operação, escore de qualidade de vida e as possíveis complicações cirúrgicas. RESULTADOS: Houve significativa melhora na qualidade de vida em 66% da amostra. Em todas as esferas de função, foi evidenciada relevância estatística no que se refere ao alívio dos sintomas relacionados à hiperidrose compensatória. CONCLUSÕES: A simpatectomia estendida de R5 a R8 mostrou-se efetiva na maioria dos casos operados, caracterizando este procedimento como promissor, podendo, após estudos futuros, ser incluído como uma opção terapêutica para a hiperidrose compensatória.


Subject(s)
Hyperhidrosis/surgery , Patient Satisfaction/statistics & numerical data , Quality of Life/psychology , Sympathectomy/methods , Humans , Hyperhidrosis/psychology , Severity of Illness Index , Sympathectomy/psychology , Treatment Outcome
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