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1.
Brief Bioinform ; 22(2): 1038-1052, 2021 03 22.
Artigo em Inglês | MEDLINE | ID: mdl-33458747

RESUMO

The current genomics era is bringing an unprecedented growth in the amount of gene expression data, only comparable to the exponential growth of sequences in databases during the last decades. This data allow the design of secondary analyses that take advantage of this information to create new knowledge. One of these feasible analyses is the evaluation of the expression level for a gene through a series of different conditions or cell types. Based on this idea, we have developed Automatic and Serial Analysis of CO-expression, which performs expression profiles for a given gene along hundreds of heterogeneous and normalized transcriptomics experiments and discover other genes that show either a similar or an inverse behavior. It might help to discover co-regulated genes, and common transcriptional regulators in any biological model. The present severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is an opportunity to test this novel approach due to the wealth of data that are being generated, which could be used for validating results. Thus, we have identified 35 host factors in the literature putatively involved in the infectious cycle of SARS-CoV viruses and searched for genes tightly co-expressed with them. We have found 1899 co-expressed genes whose assigned functions are strongly related to viral cycles. Moreover, this set of genes heavily overlaps with those identified by former laboratory high-throughput screenings (with P-value near 0). Our results reveal a series of common regulators, involved in immune and inflammatory responses that might be key virus targets to induce the coordinated expression of SARS-CoV-2 host factors.


Assuntos
Ensaios de Triagem em Larga Escala/métodos , SARS-CoV-2/metabolismo , Algoritmos , COVID-19/virologia , Biologia Computacional , Regulação Viral da Expressão Gênica/fisiologia , Humanos , Interferons/fisiologia , SARS-CoV-2/genética
2.
Microb Ecol ; 86(4): 2320-2329, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-37222805

RESUMO

Staphylococcus aureus is one of the most prevalent pathogens causing bovine mastitis in the world, in part because of its ease of adaptation to various hosts and the environment. This study aimed to determine the prevalence of S. aureus in Colombian dairy farms and its relationship with the causal network of subclinical mastitis. From thirteen dairy farms enrolled, 1288 quarter milk samples (QMS) and 330 teat samples were taken from cows with positive (70.1%) and negative California Mastitis Test (CMT). In addition, 126 samples from the milking parlor environment and 40 from workers (nasal) were collected. On each dairy farm, a survey was conducted, and the milking process was monitored on the day of sampling. S. aureus was identified in 176 samples, i.e., 138 QMS, 20 from teats, 8 from the milking parlor environment, and 10 from workers' nasal swabs. Isolates identified as S. aureus underwent proteomics (clustering of mass spectrum) and molecular (tuf, coa, spa Ig, clfA, and eno genes) analysis. Regarding proteomics results, isolates were distributed into three clusters, each with members from all sources and all farms. Concerning molecular analysis, the virulence-related genes clfA and eno were identified in 41.3% and 37.8% of S. aureus isolates, respectively. We provide evidence on the circulation of S. aureus strains with limited variability among animals, humans, and the environment. The parameters with the lowest compliance in the farms which may be implicated in the transmission of S. aureus are the lack of handwashing and abnormal milk handling.


Assuntos
Mastite Bovina , Infecções Estafilocócicas , Animais , Bovinos , Humanos , Feminino , Staphylococcus aureus/genética , Fazendas , Colômbia/epidemiologia , Proteômica , Mastite Bovina/epidemiologia , Infecções Estafilocócicas/epidemiologia , Infecções Estafilocócicas/veterinária , Leite
3.
J Antimicrob Chemother ; 77(3): 585-597, 2022 02 23.
Artigo em Inglês | MEDLINE | ID: mdl-34893830

RESUMO

BACKGROUND: Echinocandin resistance represents a great concern, as these drugs are recommended as first-line therapy for invasive candidiasis. Echinocandin resistance is conferred by mutations in FKS genes. Nevertheless, pathways are crucial for enabling tolerance, evolution, and maintenance of resistance. Therefore, understanding the biological processes and proteins involved in the response to caspofungin may provide clues indicating new therapeutic targets. OBJECTIVES: We determined the resistance mechanism and assessed the proteome response to caspofungin exposure. We then evaluated the phenotypic impact of calcineurin inhibition by FK506 and cephalosporine A (CsA) on caspofungin-resistant Candida glabrata isolates. METHODS: Twenty-five genes associated with caspofungin resistance were analysed by NGS, followed by studies of the quantitative proteomic response to caspofungin exposure. Then, susceptibility testing of caspofungin in presence of FK506 and CsA was performed. The effects of calcineurin inhibitor/caspofungin combinations on heat stress (40°C), oxidative stress (0.2 and 0.4 mM menadione) and on biofilm formation (polyurethane catheter) were analysed. Finally, a Galleria mellonella model using blastospores (1 × 109 cfu/mL) was developed to evaluate the impact of the combinations on larval survival. RESULTS: F659-del was found in the FKS2 gene of resistant strains. Proteomics data showed some up-regulated proteins are involved in cell-wall biosynthesis, response to stress and pathogenesis, some of them being members of calmodulin-calcineurin pathway. Therefore, the impact of calmodulin inhibition was explored. Calmodulin inhibition restored caspofungin susceptibility, decreased capacity to respond to stress conditions, and reduced biofilm formation and in vivo pathogenicity. CONCLUSIONS: Our findings confirm that calmodulin-calcineurin-Crz1 could provide a relevant target in life-threatening invasive candidiasis.


Assuntos
Candidíase Invasiva , Equinocandinas , Antifúngicos/farmacologia , Antifúngicos/uso terapêutico , Inibidores de Calcineurina/farmacologia , Inibidores de Calcineurina/uso terapêutico , Candida glabrata , Candidíase Invasiva/tratamento farmacológico , Caspofungina/farmacologia , Caspofungina/uso terapêutico , Farmacorresistência Fúngica/genética , Equinocandinas/farmacologia , Equinocandinas/uso terapêutico , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Testes de Sensibilidade Microbiana , Proteômica
4.
Appl Environ Microbiol ; 88(4): e0221321, 2022 02 22.
Artigo em Inglês | MEDLINE | ID: mdl-34910561

RESUMO

Killer yeasts and their toxins have many potential applications in environmental, medical, and industrial biotechnology. The killer phenotype in Saccharomyces cerevisiae relies on the cytoplasmic persistence of two dsRNA viruses, L-A and M. M encodes the toxin, and L-A provides proteins for expression, replication, and capsids for both viruses. Yeast screening and characterization of this trait are usually performed phenotypically based on their toxin production and immunity. In this study, we describe a simple and specific reverse transcription (RT) multiplex PCR assay for direct diagnosis of the dsRNA totivirus genomes associated with the killer trait in the S. cerevisiae yeast. This method obviates RNA purification steps and primer addition to the RT reaction. Using a mixture of specific primers at the PCR step, this multiplex RT-PCR protocol provided an accurate diagnosis of both L-A and M totivirus in all its known variants, L-A-1/M1, L-A-2/M2, L-A-28/M28, and L-A-lus/Mlus, found in infected killer yeasts. Using this method, the expected L-A-2/M2 totivirus associations in natural wine yeasts cells were identified but, importantly, asymptomatic L-A-2/M2 infected cells were found in addition to unexpected L-A-lus/M2 totiviral associations. IMPORTANCE The killer phenomenon in S. cerevisiae yeast cells provides the opportunity to study host-virus interactions in a eukaryotic model. Therefore, the development of simple methods for their detection significantly facilitates their study. The simplified multiplex RT-PCR protocol described here provides a useful and accurate tool for the genotypic characterization of yeast totiviruses in killer yeast cells. The killer trait depended on two dsRNA totiviruses, L-A and M. Each M dsRNA depends on a specific helper L-A virus. Thus, direct genotyping by the described method also provided valuable insights into L-A/M viral associations and their coadaptational events in nature.


Assuntos
Saccharomyces cerevisiae/virologia , Totivirus , Fatores Matadores de Levedura/genética , Reação em Cadeia da Polimerase Multiplex , RNA de Cadeia Dupla/metabolismo , RNA Viral/genética , Transcrição Reversa , Totivirus/genética , Totivirus/isolamento & purificação , Vinho/microbiologia
5.
J Antimicrob Chemother ; 75(5): 1187-1193, 2020 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-32011702

RESUMO

BACKGROUND: In recent decades, Candida glabrata has emerged as a frequent cause of life-threatening fungal infection. In C. glabrata, echinocandin resistance is associated with mutations in FKS1/FKS2 (ß-1,3-glucan synthase). The calmodulin/calcineurin pathway is implicated in response to antifungal stress and calcineurin gene disruption specifically reverses Fks2-mediated resistance of clinical isolates. OBJECTIVES: We evaluated the impact of calmodulin inhibition by fluphenazine in two caspofungin-resistant C. glabrata isolates. METHODS: C. glabrata isolates were identified by ITS1/ITS4 (where ITS stands for internal transcribed spacer) sequencing and the echinocandin target FKS1/FKS2 genes were sequenced. Susceptibility testing of caspofungin in the presence of fluphenazine was performed by a modified CLSI microbroth dilution method. The effect of the fluphenazine/caspofungin combination on heat stress (37°C or 40°C), oxidative stress (0.2 and 0.4 mM menadione) and biofilm formation (polyurethane catheter) was analysed. A Galleria mellonella model using blastospores (1 × 109 cfu/mL) was developed to evaluate the impact of this combination on larval survival. RESULTS: F659del was found in the FKS2 gene of both resistant strains. In these clinical isolates, fluphenazine increased susceptibility to caspofungin and reduced their thermotolerance. Furthermore, the fluphenazine/caspofungin combination significantly impaired biofilm formation in an in vitro polyurethane catheter model. All these features participated in the increasing survival of infected G. mellonella after combination treatment in comparison with caspofungin alone. CONCLUSIONS: In a repurposing strategy, our findings confirm that calmodulin could provide a relevant target in life-threatening fungal infectious diseases.


Assuntos
Candida glabrata , Flufenazina , Antifúngicos/farmacologia , Antifúngicos/uso terapêutico , Biofilmes , Calmodulina/genética , Candida glabrata/genética , Caspofungina , Farmacorresistência Fúngica , Equinocandinas/farmacologia , Flufenazina/farmacologia , Testes de Sensibilidade Microbiana , Virulência
6.
BMC Microbiol ; 19(1): 106, 2019 05 23.
Artigo em Inglês | MEDLINE | ID: mdl-31122184

RESUMO

BACKGROUND: The introduction of MALDI-TOF MS in the clinical microbiology laboratory has modified the approaches for the identification of fungi. Thanks to this tool, it is possible to identify cryptic species, which possess critical susceptibility patterns. Clinical strains were identified using the MicroScan and MALDI-TOF MS systems. Discrepant results from both methods were investigated using ITS rDNA barcoding. Finally, these isolates were also tested for in vitro susceptibility. RESULTS: The percentage of agreement between both methods to 498 yeast isolates was of 93.6% (32 discrepant isolates). The concordance of ITS sequencing with MALDI-TOF MS was higher (99%) than that of MicroScan (94%). Several of these discordant yeasts displayed high MICs for antifungal agents. CONCLUSIONS: Our study highlights the need of the MS and molecular approaches such as MALDI-TOF MS and ITS rDNA barcoding for the correct identification of emerging or cryptic yeast species; besides, some of these could be multidrug resistant. This work was the first experience in the implementation of the MALDI-TOF MS technology in Colombia. We found the first uncommon yeasts including Candida auris and we could identify Trichosporon faecalis. Our work highlights a clear necessity of an accurate yeast identification as a much more pertinent technique than the susceptibility profiles, because the most unusual yeasts exhibit resistance profiles to the few available antifungals.


Assuntos
DNA Ribossômico/genética , Farmacorresistência Fúngica Múltipla , Micoses/microbiologia , Leveduras/isolamento & purificação , Antifúngicos/farmacologia , Colômbia , DNA Fúngico/genética , Humanos , Testes de Sensibilidade Microbiana , Filogenia , Análise de Sequência de DNA , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Atenção Terciária à Saúde , Leveduras/classificação , Leveduras/efeitos dos fármacos , Leveduras/genética
8.
Avian Pathol ; 45(1): 73-81, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-26610321

RESUMO

Highly virulent fowl aviadenoviruses (genus: Aviadenovirus) represent a significant risk in poultry farming that may contribute to increased mortality rates and may adversely affect the growth performance of poultry flocks. In this study, we performed the clinicopathological characterization of a FAdV strain SHP95 isolated from a commercial farm and its whole genome sequencing. The study revealed that the isolated strain is a highly virulent serotype 4 FAdV that can cause 100% mortality in day-old specific pathogen free (SPF) chickens with a dose of 2.5 × 10(5) TCID50. At a lower viral dose (1.5 × 10(4) TCID50), the infection in day-old SPF chickens caused 40% mortality and lesions characteristic for Hepatitis-hydropericardium syndrome (HHS). The viral strain was detectable by real time PCR in chicken organs, including the lymphoid organs until day 28 after infection. The whole genome assembly of strain SHP95 revealed a size of 45,641 bp, which encodes for 42 viral open reading frame (ORF). The comparative analysis in the genome shows 98.1% similarity between strain SHP95 and other FAdV-4 genomes reported. The major differences in the genome sequence between pathogenic and non-pathogenic fowl Adenovirus were identified in the right arm of the genome.


Assuntos
Infecções por Adenoviridae/veterinária , Aviadenovirus/genética , Galinhas/virologia , Genoma Viral/genética , Doenças das Aves Domésticas/virologia , Infecções por Adenoviridae/mortalidade , Infecções por Adenoviridae/virologia , Animais , Aviadenovirus/isolamento & purificação , Fígado/patologia , Fígado/virologia , Fases de Leitura Aberta/genética , Doenças das Aves Domésticas/mortalidade , Análise de Sequência de DNA/veterinária , Sorogrupo , Organismos Livres de Patógenos Específicos
9.
J Chem Phys ; 144(15): 154902, 2016 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-27389235

RESUMO

The effect of fluorine substitution on the molecular structure, crystal packing, and n-type semiconducting properties of a set of poly(arylene-ethynylene) polymers based on alternating thiadiazole and phenyl units linked through ethynylene groups has been studied by means of Density Functional Theory. As a result, an enlargement in the interplanar distance between cofacial polymer chains, as well as a decrease of the electronic coupling and electron mobility is predicted. On the other hand, fluorination could facilitate electron injection into the material. A polymer containing both alkoxy pendant chains and fluorine atoms is proposed as a compromise solution between efficiency of electron injection and charge transport within the material.

10.
J Bacteriol ; 196(2): 257-64, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24163342

RESUMO

The histidine autokinase CheA functions as the central processing unit in the Escherichia coli chemotaxis signaling machinery. CheA receives autophosphorylation control inputs from chemoreceptors and in turn regulates the flux of signaling phosphates to the CheY and CheB response regulator proteins. Phospho-CheY changes the direction of flagellar rotation; phospho-CheB covalently modifies receptor molecules during sensory adaptation. The CheA phosphorylation site, His-48, lies in the N-terminal P1 domain, which must engage the CheA ATP-binding domain, P4, to initiate an autophosphorylation reaction cycle. The docking determinants for the P1-P4 interaction have not been experimentally identified. We devised mutant screens to isolate P1 domains with impaired autophosphorylation or phosphotransfer activities. One set of P1 mutants identified amino acid replacements at surface-exposed residues distal to His-48. These lesions reduced the rate of P1 transphosphorylation by P4. However, once phosphorylated, the mutant P1 domains transferred phosphate to CheY at the wild-type rate. Thus, these P1 mutants appear to define interaction determinants for P1-P4 docking during the CheA autophosphorylation reaction.


Assuntos
Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Quimiotaxia , Escherichia coli/fisiologia , Proteínas de Membrana/genética , Proteínas de Membrana/metabolismo , Transdução de Sinais , Análise Mutacional de DNA , Escherichia coli/genética , Proteínas de Escherichia coli , Histidina Quinase , Proteínas Quimiotáticas Aceptoras de Metil , Modelos Biológicos , Fosforilação , Proteínas Quinases/genética , Proteínas Quinases/metabolismo , Estrutura Terciária de Proteína/genética
11.
Virus Genes ; 49(2): 233-6, 2014 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-24845060

RESUMO

Newcastle disease virus with velogenic characteristics circulates in the poultry industry in Mexico and various other American countries. In Mexico, vaccine efficacy testing to obtain commercial registration is reliant on a challenge with a velogenic strain known colloquially as Chimalhuacan due to the site where it was isolated. In this paper, we performed a full genome sequencing of the Chimalhuacan strain. The strain belongs to Class II of APMV, particularly genotype V. The viral RNA genome is 15,192 nt in size and contains six genes: 3' NP-P-M-F-HN-L 5'. The 3' leader sequence is 55 nt in size and the 5' trailer sequence 113 nt. The deduced amino acid sequence confirms a velogenic genotype with four basic amino acids at the cleavage site: (112)RRQKR(↓)F(117). In addition, evolutionary relatedness based on the gene sequence of the fusion protein indicates that this strain is the ancestor of the strains currently circulating in Mexico.


Assuntos
Evolução Molecular , Variação Genética , Genoma Viral , Vírus da Doença de Newcastle/classificação , Vírus da Doença de Newcastle/genética , Aves Domésticas/virologia , RNA Viral/genética , Regiões 3' não Traduzidas , Regiões 5' não Traduzidas , Sequência de Aminoácidos , Animais , Análise por Conglomerados , Genótipo , México , Dados de Sequência Molecular , Vírus da Doença de Newcastle/isolamento & purificação , Filogenia , Análise de Sequência de DNA
12.
J Chem Phys ; 140(4): 044908, 2014 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-25669584

RESUMO

Aimed to optimize the ratio accuracy/computational cost, in this work we study the performance of three different theoretical methodologies in the calculation of the optical bandgap for a test set made of a number of poly(aryl-ethynylene)s related polymers. Infinite, ideal polymer chains were first optimized by means of periodic calculations. Different length oligomers were afterward generated by direct replication of the corresponding periodic structure and their optical bandgaps were calculated by means of different time dependent-density functional theory (TD-DFT) methodologies. These results were fitted to an exponential function for each oligomer family in order to get a theoretical estimation of the optical bandgap for each polymer to be compared to the experimental reported values. The best result was obtained for TD-M06-2X yielding an average deviation of 3.4% with respect to the experimental values.


Assuntos
Modelos Teóricos , Polímeros/química , Estrutura Molecular
13.
Virus Res ; 340: 199293, 2024 02.
Artigo em Inglês | MEDLINE | ID: mdl-38101578

RESUMO

Although next-generation sequencing technologies are advancing rapidly, many research topics often require selective sequencing of genomic regions of interest. In addition, sequencing low-titre viruses is challenging, especially for coronaviruses, which are the largest RNA viruses. Prior to sequencing, enrichment of viral particles can help to significantly increase target sequence information as well as avoid large sequencing efforts and, consequently, can increase sensitivity and reduce sequencing costs. Targeting nucleic acids using capture by hybridization is another efficient method that can be performed by applying complementary probes (DNA or RNA baits) to directly enrich genetic information of interest while removing background non-target material. In studies where sequence capture by hybridization has been applied to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, most authors agree that this technique is useful to easily access sequence targets in complex samples. Furthermore, this approach allows for complete or near-complete sequencing of the viral genome, even in samples with low viral load or poor nucleic acid integrity. In addition, this strategy is highly efficient at discovering new variants by facilitating downstream investigations, such as phylogenetics, epidemiology, and evolution. Commercial kits, as well as in-house protocols, have been developed for enrichment of viral sequences. However, these kits have multiple variations in procedure, with differences in performance. This review compiles and describes studies in which hybridization capture has been applied to SARS-CoV-2 variant genomes.


Assuntos
COVID-19 , Vírus , Humanos , SARS-CoV-2/genética , Vírus/genética , Hibridização de Ácido Nucleico , Genoma Viral
14.
Brief Funct Genomics ; 23(4): 484-494, 2024 Jul 19.
Artigo em Inglês | MEDLINE | ID: mdl-38422352

RESUMO

Massive gene expression analyses are widely used to find differentially expressed genes under specific conditions. The results of these experiments are often available in public databases that are undergoing a growth similar to that of molecular sequence databases in the past. This now allows novel secondary computational tools to emerge that use such information to gain new knowledge. If several genes have a similar expression profile across heterogeneous transcriptomics experiments, they could be functionally related. These associations are usually useful for the annotation of uncharacterized genes. In addition, the search for genes with opposite expression profiles is useful for finding negative regulators and proposing inhibitory compounds in drug repurposing projects. Here we present a new web application, Automatic and Serial Analysis of CO-expression (ASACO), which has the potential to discover positive and negative correlator genes to a given query gene, based on thousands of public transcriptomics experiments. In addition, examples of use are presented, comparing with previous contrasted knowledge. The results obtained propose ASACO as a useful tool to improve knowledge about genes associated with human diseases and noncoding genes. ASACO is available at http://www.bioinfocabd.upo.es/asaco/.


Assuntos
Reposicionamento de Medicamentos , Reposicionamento de Medicamentos/métodos , Humanos , Software , Perfilação da Expressão Gênica/métodos , Biologia Computacional/métodos , Bases de Dados Genéticas , Transcriptoma/genética
15.
J Chem Phys ; 138(15): 154902, 2013 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-23614443

RESUMO

In the present study, a series of crystalline poly(arylene-ethynylene) copolymers containing phenylethynylene and 2,5-dialkoxy-phenylethynylene units together with 1,3,4-thiadiazole rings has been modeled by means of periodic calculations. Optimized three-dimensional polymeric structures show interchain distances that are consistent with the experimental values reported for a related polymer. It has also been observed that the presence of pendant alkoxy chains brings on both a further flattening and a separation of the coplanar chains. This fact is linked to a decrease of the interchain cofacial distance. The electron transport character of the polymer crystal structures was assessed through Marcus theory. Electronic coupling between neighboring polymer chains is most influenced by the presence of alkoxy chains giving rise to an expectable enhancement of the electron hopping mobility.

16.
Antibiotics (Basel) ; 12(11)2023 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-37998777

RESUMO

Staphylococcus is a very prevalent etiologic agent of bovine mastitis, and antibiotic resistance contributes to the successful colonization and dissemination of these bacteria in different environments and hosts on dairy farms. This study aimed to identify the antimicrobial resistance (AMR) genotypes and phenotypes of Staphylococcus spp. isolates from different sources on dairy farms and their relationship with the use of antibiotics. An antimicrobial susceptibility test was performed on 349 Staphylococcus strains (S. aureus, n = 152; non-aureus staphylococci (NAS), n = 197) isolated from quarter milk samples (QMSs) from cows with subclinical mastitis (176), the teats of cows (116), the milking parlor environment (32), and the nasal cavities of milk workers (25). Resistance and multidrug resistance percentages found for S. aureus and NAS were (S. aureus = 63.2%, NAS = 55.8%) and (S. aureus = 4.6%, NAS = 11.7%), respectively. S. aureus and NAS isolates showed resistance mainly to penicillin (10 IU) (54.1% and 32.4%) and ampicillin (10 mg) (50.3% and 27.0%) drugs. The prevalence of AMR Staphylococcus was higher in environmental samples (81.3%) compared to other sources (52.6-76.0%). In S. aureus isolates, the identification of the blaZ (83.9%), aacAaphD (48.6%), ermC (23.5%), tetK (12.9%), and mecA (12.1%) genes did not entirely agree with the AMR phenotype. We conclude that the use of ß-lactam antibiotics influences the expression of AMR in Staphylococcus circulating on dairy farms and that S. aureus isolates from the environment and humans may be reservoirs of AMR for other bacteria on dairy farms.

17.
Sci Adv ; 9(12): eadd8911, 2023 03 24.
Artigo em Inglês | MEDLINE | ID: mdl-36961900

RESUMO

CRISPR-Cas systems are prokaryotic acquired immunity mechanisms, which are found in 40% of bacterial genomes. They prevent viral infections through small DNA fragments called spacers. However, the vast majority of these spacers have not yet been associated with the virus they recognize, and it has been named CRISPR dark matter. By analyzing the spacers of tens of thousands of genomes from six bacterial species, we have been able to reduce the CRISPR dark matter from 80% to as low as 15% in some of the species. In addition, we have observed that, when a genome presents CRISPR-Cas systems, this is accompanied by particular sets of membrane proteins. Our results suggest that when bacteria present membrane proteins that make it compete better in its environment and these proteins are, in turn, receptors for specific phages, they would be forced to acquire CRISPR-Cas.


Assuntos
Bacteriófagos , Sistemas CRISPR-Cas , Sistemas CRISPR-Cas/genética , Bactérias/genética , Genoma Bacteriano , Bacteriófagos/genética
18.
Front Cell Infect Microbiol ; 13: 1136217, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37026059

RESUMO

Methods: Over a four-year period, 123 Candida bloodstream isolates were collected at a quaternary care hospital. The isolates were identified by MALDI-TOF MS and their fluconazole (FLC) susceptibility patterns were assessed according to CLSI guidelines. Subsequently, sequencing of ERG11, TAC1 or MRR1, and efflux pump activity were performed for resistant isolates. Results: Out of 123 clinical strains,C. albicans accounted for 37.4%, followed by C. tropicalis 26.8%, C. parapsilosis 19.5%, C. auris 8.1%, C. glabrata 4.1%, C. krusei 2.4% and C. lusitaniae 1.6%. Resistance to FLC reached 18%; in addition, a high proportion of isolates were cross-resistant to voriconazole. Erg11 amino acid substitutions associated with FLC-resistance (Y132F, K143R, or T220L) were found in 11/19 (58%) of FLCresistant isolates. Furthermore, novel mutations were found in all genes evaluated. Regarding efflux pumps, 8/19 (42%) of FLC-resistant Candida spp strains showed significant efflux activity. Finally, 6/19 (31%) of FLC-resistant isolates neither harbored resistance-associated mutations nor showed efflux pump activity. Among FLC-resistant species, C. auris 7/10 (70%) and C. parapsilosis 6/24 (25%) displayed the highest percentages of resistance (C. albicans 6/46, 13%). Discussion: Overall, 68% of FLC-resistant isolates exhibited a mechanism that could explain their phenotype (e.g. mutations, efflux pump activity, or both). We provide evidence that isolates from patients admitted to a Colombian hospital harbor amino acid substitutions related to resistance to one of the most commonly used molecules in the hospital setting, with Y132F being the most frequently detected.


Assuntos
Antifúngicos , Azóis , Azóis/farmacologia , Antifúngicos/farmacologia , Antifúngicos/uso terapêutico , Candida albicans/genética , Candida parapsilosis/genética , Colômbia , Fluconazol/farmacologia , Candida , Candida tropicalis , Testes de Sensibilidade Microbiana , Farmacorresistência Fúngica
19.
J Fungi (Basel) ; 9(4)2023 Mar 31.
Artigo em Inglês | MEDLINE | ID: mdl-37108885

RESUMO

Candida auris has become a major health threat due to its transmissibility, multidrug resistance and severe outcomes. In a case-control design, 74 hospitalised patients with candidemia were enrolled. In total, 22 cases (29.7%) and 52 controls (C. albicans, 21.6%; C. parapsilosis, 21.6%; C. tropicalis, 21.6%; C. glabrata, 1.4%) were included and analysed in this study. Risk factors, clinical and microbiological characteristics and outcomes of patients with C. auris and non-auris Candida species (NACS) candidemia were compared. Previous fluconazole exposure was significantly higher in C. auris candidemia patients (OR 3.3; 1.15-9.5). Most C. auris isolates were resistant to fluconazole (86.3%) and amphotericin B (59%) whilst NACS isolates were generally susceptible. No isolates resistant to echinocandins were detected. The average time to start antifungal therapy was 3.6 days. Sixty-three (85.1%) patients received adequate antifungal therapy, without significant differences between the two groups. The crude mortality at 30 and 90 days of candidemia was up to 37.8% and 40.5%, respectively. However, there was no difference in mortality both at 30 and 90 days between the group with candidemia by C. auris (31.8%) and by NACS (42.3%) (OR 0.6; 95% IC 0.24-1.97) and 36.4% and 42.3% (0.77; 0.27-2.1), respectively. In this study, mortality due to candidemia between C. auris and NACS was similar. Appropriate antifungal therapy in both groups may have contributed to finding no differences in outcomes.

20.
Curr Genet ; 58(4): 191-203, 2012 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-22543982

RESUMO

In Schizosaccharomyces pombe, cytokinesis occurs by ordered recruitment of actomyosin components at the division site, followed by lateral condensation to produce a ring-like structure early in anaphase, which eventually matures and contracts at the end of mitosis. We found that in temperature-sensitive hsp90-w1 mutant cells, encoding an Hsp90 mutant protein, ring components were recruited to form a cortical network at the division site, but this network failed to condense into a compact ring, suggesting a role for Hsp90 in this particular step. hsp90-w1 mutant shows strong genetic interaction with specific mutant alleles of the fission yeast cdc2, such as cdc2-33. Interestingly, actomyosin ring defects in hsp90-w1 cdc2-33 mutant cells resembled that of hsp90-w1 single mutant at restrictive temperature. Noteworthy, similar genetic interaction was found with a mutant allele of polo-like kinase, plo1-ts4, suggesting that Hsp90 collaborates with Cdc2 and Plo1 cell cycle kinases to condense medial ring components. In vitro analyses suggested that Cdc2 and Plo1 physically interact with Hsp90. Association of Cdc2 to Hsp90 was ATP independent, while Plo1 binds to this chaperone in an ATP-dependent manner, indicating that these two kinases interact with different Hsp90 complexes. Overall, our analyses of hsp90-w1 reveal a possible role for this chaperone in medial ring condensation in association with Cdc2 and Plo1 kinases.


Assuntos
Actomiosina/metabolismo , Proteína Quinase CDC2/metabolismo , Proteínas de Choque Térmico HSP90/metabolismo , Proteínas Serina-Treonina Quinases/metabolismo , Proteínas de Schizosaccharomyces pombe/metabolismo , Schizosaccharomyces/metabolismo , Proteína Quinase CDC2/genética , Proteínas de Choque Térmico HSP90/genética , Isoenzimas/genética , Isoenzimas/metabolismo , Mitose , Mutação , Ligação Proteica , Proteínas Serina-Treonina Quinases/genética , Schizosaccharomyces/citologia , Schizosaccharomyces/genética , Proteínas de Schizosaccharomyces pombe/genética
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