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1.
Nat Immunol ; 24(4): 595-603, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-36941400

RESUMO

Upon detecting pathogens or cell stress, several NOD-like receptors (NLRs) form inflammasome complexes with the adapter ASC and caspase-1, inducing gasdermin D (GSDMD)-dependent cell death and maturation and release of IL-1ß and IL-18. The triggers and activation mechanisms of several inflammasome-forming sensors are not well understood. Here we show that mitochondrial damage activates the NLRP10 inflammasome, leading to ASC speck formation and caspase-1-dependent cytokine release. While the AIM2 inflammasome can also sense mitochondrial demise by detecting mitochondrial DNA (mtDNA) in the cytosol, NLRP10 monitors mitochondrial integrity in an mtDNA-independent manner, suggesting the recognition of distinct molecular entities displayed by the damaged organelles. NLRP10 is highly expressed in differentiated human keratinocytes, in which it can also assemble an inflammasome. Our study shows that this inflammasome surveils mitochondrial integrity. These findings might also lead to a better understanding of mitochondria-linked inflammatory diseases.


Assuntos
Citocinas , Inflamassomos , Humanos , Inflamassomos/metabolismo , Caspase 1/metabolismo , Citocinas/metabolismo , Morte Celular , DNA Mitocondrial/genética , Interleucina-1beta/metabolismo , Proteína 3 que Contém Domínio de Pirina da Família NLR/genética , Proteína 3 que Contém Domínio de Pirina da Família NLR/metabolismo , Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Proteínas Reguladoras de Apoptose/metabolismo
2.
Cell ; 167(1): 187-202.e17, 2016 Sep 22.
Artigo em Inglês | MEDLINE | ID: mdl-27662089

RESUMO

Inflammasome complexes function as key innate immune effectors that trigger inflammation in response to pathogen- and danger-associated signals. Here, we report that germline mutations in the inflammasome sensor NLRP1 cause two overlapping skin disorders: multiple self-healing palmoplantar carcinoma (MSPC) and familial keratosis lichenoides chronica (FKLC). We find that NLRP1 is the most prominent inflammasome sensor in human skin, and all pathogenic NLRP1 mutations are gain-of-function alleles that predispose to inflammasome activation. Mechanistically, NLRP1 mutations lead to increased self-oligomerization by disrupting the PYD and LRR domains, which are essential in maintaining NLRP1 as an inactive monomer. Primary keratinocytes from patients experience spontaneous inflammasome activation and paracrine IL-1 signaling, which is sufficient to cause skin inflammation and epidermal hyperplasia. Our findings establish a group of non-fever inflammasome disorders, uncover an unexpected auto-inhibitory function for the pyrin domain, and provide the first genetic evidence linking NLRP1 to skin inflammatory syndromes and skin cancer predisposition.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal/genética , Proteínas Reguladoras de Apoptose/genética , Carcinoma/genética , Predisposição Genética para Doença , Inflamassomos/metabolismo , Ceratose/genética , Neoplasias Cutâneas/genética , Proteínas Adaptadoras de Transdução de Sinal/química , Sequência de Aminoácidos , Proteínas Reguladoras de Apoptose/química , Carcinoma/patologia , Cromossomos Humanos Par 17/genética , Epiderme/patologia , Mutação em Linhagem Germinativa , Humanos , Hiperplasia/genética , Hiperplasia/patologia , Inflamassomos/genética , Interleucina-1/metabolismo , Ceratose/patologia , Proteínas NLR , Comunicação Parácrina , Linhagem , Domínios Proteicos , Pirina/química , Transdução de Sinais , Neoplasias Cutâneas/patologia , Síndrome
3.
Cell ; 159(6): 1389-403, 2014 Dec 04.
Artigo em Inglês | MEDLINE | ID: mdl-25467444

RESUMO

Telomere maintenance by telomerase is impaired in the stem cell disease dyskeratosis congenita and during human aging. Telomerase depends upon a complex pathway for enzyme assembly, localization in Cajal bodies, and association with telomeres. Here, we identify the chaperonin CCT/TRiC as a critical regulator of telomerase trafficking using a high-content genome-wide siRNA screen in human cells for factors required for Cajal body localization. We find that TRiC is required for folding the telomerase cofactor TCAB1, which controls trafficking of telomerase and small Cajal body RNAs (scaRNAs). Depletion of TRiC causes loss of TCAB1 protein, mislocalization of telomerase and scaRNAs to nucleoli, and failure of telomere elongation. DC patient-derived mutations in TCAB1 impair folding by TRiC, disrupting telomerase function and leading to severe disease. Our findings establish a critical role for TRiC-mediated protein folding in the telomerase pathway and link proteostasis, telomere maintenance, and human disease.


Assuntos
Chaperonina com TCP-1/metabolismo , Telomerase/metabolismo , Telômero/metabolismo , Disceratose Congênita/genética , Disceratose Congênita/patologia , Humanos , Hibridização in Situ Fluorescente , Chaperonas Moleculares , Dobramento de Proteína , Telomerase/química
4.
Cell ; 150(3): 481-94, 2012 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-22863003

RESUMO

Telomere synthesis in cancer cells and stem cells involves trafficking of telomerase to Cajal bodies, and telomerase is thought to be recruited to telomeres through interactions with telomere-binding proteins. Here, we show that the OB-fold domain of the telomere-binding protein TPP1 recruits telomerase to telomeres through an association with the telomerase reverse transcriptase TERT. When tethered away from telomeres and other telomere-binding proteins, the TPP1 OB-fold domain is sufficient to recruit telomerase to a heterologous chromatin locus. Expression of a minimal TPP1 OB-fold inhibits telomere maintenance by blocking access of telomerase to its cognate binding site at telomeres. We identify amino acids required for the TPP1-telomerase interaction, including specific loop residues within the TPP1 OB-fold domain and individual residues within TERT, some of which are mutated in a subset of pulmonary fibrosis patients. These data define a potential interface for telomerase-TPP1 interaction required for telomere maintenance and implicate defective telomerase recruitment in telomerase-related disease.


Assuntos
Telomerase/metabolismo , Proteínas de Ligação a Telômeros/química , Proteínas de Ligação a Telômeros/metabolismo , Telômero/metabolismo , Sequência de Aminoácidos , Linhagem Celular , Linhagem Celular Tumoral , Corpos Enovelados/metabolismo , Humanos , Fibrose Pulmonar Idiopática/genética , Fibrose Pulmonar Idiopática/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Mutação , Estrutura Terciária de Proteína , Saccharomyces cerevisiae/metabolismo , Alinhamento de Sequência , Complexo Shelterina , Telomerase/química , Telomerase/genética , Proteínas de Ligação a Telômeros/genética
5.
PLoS Biol ; 21(4): e3002072, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-37083687

RESUMO

Anti-clustered regularly interspaced short palindromic repeats (CRISPRs) are proteins capable of blocking CRISPR-Cas systems and typically their genes are located on mobile genetic elements. Since their discovery, numerous anti-CRISPR families have been identified. However, little is known about the distribution and sequence diversity of members within a family, nor how these traits influence the anti-CRISPR's function and evolution. Here, we use AcrIF7 to explore the dissemination and molecular evolution of an anti-CRISPR family. We uncovered 5 subclusters and prevalent anti-CRISPR variants within the group. Remarkably, AcrIF7 homologs display high similarity despite their broad geographical, ecological, and temporal distribution. Although mainly associated with Pseudomonas aeruginosa, AcrIF7 was identified in distinct genetic backgrounds indicating horizontal dissemination, primarily by phages. Using mutagenesis, we recreated variation observed in databases but also extended the sequence diversity of the group. Characterisation of the variants identified residues key for the anti-CRISPR function and other contributing to its mutational tolerance. Moreover, molecular docking revealed that variants with affected function lose key interactions with its CRISPR-Cas target. Analysis of publicly available data and the generated variants suggests that the dominant AcrIF7 variant corresponds to the minimal and optimal anti-CRISPR selected in the family. Our study provides a blueprint to investigate the molecular evolution of anti-CRISPR families.


Assuntos
Bacteriófagos , Sistemas CRISPR-Cas , Humanos , Simulação de Acoplamento Molecular , Sistemas CRISPR-Cas/genética , Bacteriófagos/genética , Evolução Molecular , Mutação
6.
Appl Environ Microbiol ; : e0080724, 2024 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-38940562

RESUMO

Enterotoxigenic Escherichia coli (ETEC) is a diverse and poorly characterized E. coli pathotype that causes diarrhea in humans and animals. Phages have been proposed for the veterinary biocontrol of ETEC, but effective solutions require understanding of porcine ETEC diversity that affects phage infection. Here, we sequenced and analyzed the genomes of the PHAGEBio ETEC collection, gathering 79 diverse ETEC strains isolated from European pigs with post-weaning diarrhea (PWD). We identified the virulence factors characterizing the pathotype and several antibiotic resistance genes on plasmids, while phage resistance genes and other virulence factors were mostly chromosome encoded. We experienced that ETEC strains were highly resistant to Enterobacteriaceae phage infection. It was only by enrichment of numerous diverse samples with different media and conditions, using the 41 ETEC strains of our collection as hosts, that we could isolate two lytic phages that could infect a large part of our diverse ETEC collection: vB_EcoP_ETEP21B and vB_EcoS_ETEP102. Based on genome and host range analyses, we discussed the infection strategies of the two phages and identified components of lipopolysaccharides ( LPS) as receptors for the two phages. Our detailed computational structural analysis highlights several loops and pockets in the tail fibers that may allow recognition and binding of ETEC strains, also in the presence of O-antigens. Despite the importance of receptor recognition, the diversity of the ETEC strains remains a significant challenge for isolating ETEC phages and developing sustainable phage-based products to address ETEC-induced PWD.IMPORTANCEEnterotoxigenic Escherichia coli (ETEC)-induced post-weaning diarrhea is a severe disease in piglets that leads to weight loss and potentially death, with high economic and animal welfare costs worldwide. Phage-based approaches have been proposed, but available data are insufficient to ensure efficacy. Genome analysis of an extensive collection of ETEC strains revealed that phage defense mechanisms were mostly chromosome encoded, suggesting a lower chance of spread and selection by phage exposure. The difficulty in isolating lytic phages and the molecular and structural analyses of two ETEC phages point toward a multifactorial resistance of ETEC to phage infection and the importance of extensive phage screenings specifically against clinically relevant strains. The PHAGEBio ETEC collection and these two phages are valuable tools for the scientific community to expand our knowledge on the most studied, but still enigmatic, bacterial species-E. coli.

7.
Transfusion ; 64 Suppl 2: S42-S49, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38361432

RESUMO

BACKGROUND: The Role 2 setting represents the most far-forward military treatment facility with limited surgical and holding capabilities. There are limited data to guide recommendations on blood product utilization at the Role 2. We describe the consumption of blood products in this setting. STUDY DESIGN AND METHODS: We analyzed data from 2007 to 2023 from the Department of Defense Trauma Registry (DODTR) that received care at a Role 2. We used descriptive and inferential statistics to characterize the volumes of blood products consumed in this setting. We also performed a secondary analysis of US military, Coalition, and US contractor personnel. RESULTS: Within our initial cohort analysis of 15,581 encounters, 17% (2636) received at least one unit of PRBCs or whole blood, of which 11% received a submassive transfusion, 4% received a massive transfusion, and 1% received a supermassive transfusion. There were 6402 encounters that met inclusion for our secondary analysis. With this group, 5% received a submassive transfusion, 2% received a massive transfusion, and 1% received a supermassive transfusion. CONCLUSIONS: We described volumes of blood products consumed at the Role 2 during recent conflicts. The maximum number of units consumed among survivors exceeds currently recommended available blood supply. Our findings suggest that rapid resupply and cold-stored chain demands may be higher than anticipated in future conflicts.


Assuntos
Transfusão de Sangue , Militares , Sistema de Registros , Humanos , Estados Unidos , Masculino , Feminino , Adulto , Ferimentos e Lesões/terapia , Ferimentos e Lesões/epidemiologia , United States Department of Defense
8.
Transfusion ; 64 Suppl 2: S85-S92, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38351716

RESUMO

INTRODUCTION: The use of low titer O whole blood (LTOWB) has expanded although it remains unclear how many civilian trauma centers are using LTOWB. METHODS: We analyzed data on civilian LTOWB recipients in the American College of Surgeons Trauma Quality Improvement Program (TQIP) database 2020-2021. Unique facility keys were used to determine the number of centers that used LTOWB in that period. RESULTS: A total of 16,603 patients received LTOWB in the TQIP database between 2020 and 2021; 6600 in 2020, and 10,003 in 2021. The total number of facilities that reported LTOWB use went from 287/779 (37%) in 2020 to 302/795 (38%) in 2021. Between 2020 and 2021, among all level 1-3 designated trauma facilities that report to TQIP LTOWB use increased at level-1 centers (118 to 129), and level-2 centers (81 to 86), but decreased in level-3 facilities (9 to 4). Among pediatric and dual pediatric-adult designated hospitals there was a decrease in the number of pediatric level-1 centers (29 to 28) capable of administering LTOWB. Among centers with either single or dual level-1 trauma center designation with adult centers, the number that administered LTOWB to injured pediatric patients also decreased from 17 to 10, respectively. CONCLUSIONS: There was an increase in the number of facilities transfusing LTOWB between 2020 and 2021. The use of LTOWB is underutilized in children at centers that have it available. These findings inform the expansion of LTOWB use in trauma.


Assuntos
Melhoria de Qualidade , Sistema de Registros , Centros de Traumatologia , Ferimentos e Lesões , Humanos , Ferimentos e Lesões/terapia , Ferimentos e Lesões/sangue , Masculino , Sistema ABO de Grupos Sanguíneos , Transfusão de Sangue/estatística & dados numéricos , Feminino , Inquéritos e Questionários , Adulto
9.
Catheter Cardiovasc Interv ; 103(4): 539-547, 2024 03.
Artigo em Inglês | MEDLINE | ID: mdl-38431912

RESUMO

BACKGROUND: Guide catheter extensions (GCEs) increase support and facilitate equipment delivery, but aggressive instrumentation may be associated with a higher risk of complications. AIM: Our aim was to assess the impact of GCEs on procedural success and complications in patients submitted to chronic total occlusion (CTO) percutaneous coronary intervention (PCI). METHODS: We analyzed data from the multicenter LATAM CTO Registry. Procedural success was defined as <30% residual stenosis and TIMI 3 distal flow. Major adverse cardiac and cerebrovascular events (MACCE) was defined as the composite of all-cause death, myocardial infarction, target vessel revascularization, and stroke. Propensity score matching (PSM) was used to compare outcomes with and without GCE use. RESULTS: From August 2010 to August 2021, 3049 patients were included. GCEs were used in 438 patients (14.5%). In unadjusted analysis, patients in the GCE group were older and had more comorbidities. The median J-CTO score and its components were higher in the GCE group. After PSM, procedural success was higher with GCE use (87.7% vs. 80.5%, p = 0.007). The incidence of coronary perforation (odds ratio [OR]: 1.46, 95% confidence interval [CI]: 0.78-2.71, p = 0.230), bleeding (OR: 1.99, 95% CI: 0.41-2.41, p = 0.986), in-hospital death (OR: 1.39, 95% CI: 0.54-3.62, p = 0.495) and MACCE (OR: 1.07, 95% CI: 0.52-2.19, p = 0.850) were similar in both groups. CONCLUSION: In a contemporary, multicenter cohort of patients undergoing CTO PCI, GCEs were used in older patients, with more comorbidities and complex anatomy. After PSM, GCE use was associated with higher procedural success, and similar incidence of adverse outcomes.


Assuntos
Oclusão Coronária , Intervenção Coronária Percutânea , Idoso , Humanos , Catéteres , Oclusão Coronária/diagnóstico por imagem , Oclusão Coronária/terapia , Oclusão Coronária/etiologia , Mortalidade Hospitalar , Intervenção Coronária Percutânea/efeitos adversos , Resultado do Tratamento
10.
Nucleic Acids Res ; 49(19): 10868-10878, 2021 11 08.
Artigo em Inglês | MEDLINE | ID: mdl-34606606

RESUMO

To provide protection against viral infection and limit the uptake of mobile genetic elements, bacteria and archaea have evolved many diverse defence systems. The discovery and application of CRISPR-Cas adaptive immune systems has spurred recent interest in the identification and classification of new types of defence systems. Many new defence systems have recently been reported but there is a lack of accessible tools available to identify homologs of these systems in different genomes. Here, we report the Prokaryotic Antiviral Defence LOCator (PADLOC), a flexible and scalable open-source tool for defence system identification. With PADLOC, defence system genes are identified using HMM-based homologue searches, followed by validation of system completeness using gene presence/absence and synteny criteria specified by customisable system classifications. We show that PADLOC identifies defence systems with high accuracy and sensitivity. Our modular approach to organising the HMMs and system classifications allows additional defence systems to be easily integrated into the PADLOC database. To demonstrate application of PADLOC to biological questions, we used PADLOC to identify six new subtypes of known defence systems and a putative novel defence system comprised of a helicase, methylase and ATPase. PADLOC is available as a standalone package (https://github.com/padlocbio/padloc) and as a webserver (https://padloc.otago.ac.nz).


Assuntos
Antibiose/genética , Archaea/genética , Proteínas Arqueais/genética , Bactérias/genética , Proteínas de Bactérias/genética , Bacteriófagos/genética , Software , Adenosina Trifosfatases/genética , Adenosina Trifosfatases/metabolismo , Archaea/classificação , Archaea/metabolismo , Archaea/virologia , Proteínas Arqueais/metabolismo , Bactérias/classificação , Bactérias/metabolismo , Bactérias/virologia , Proteínas de Bactérias/metabolismo , Bacteriófagos/crescimento & desenvolvimento , Sistemas CRISPR-Cas , DNA Helicases/genética , DNA Helicases/metabolismo , Metilases de Modificação do DNA/genética , Metilases de Modificação do DNA/metabolismo , Cadeias de Markov , Filogenia , Terminologia como Assunto
11.
Angew Chem Int Ed Engl ; 62(38): e202307995, 2023 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-37549372

RESUMO

Discovering natural product biosynthetic pathways of medicinal plants is challenging and laborious. Capturing the coregulation patterns of pathway enzymes, particularly transcriptomic regulation, has proven an effective method to accelerate pathway identification. In this study, we developed a yeast-based screening method to capture the protein-protein interactions (PPI) between plant enzymes, which is another useful pattern to complement the prevalent approach. Combining this method with plant multiomics analysis, we discovered four enzyme complexes and their organized pathways from kratom, an alkaloid-producing plant. The four pathway branches involved six enzymes, including a strictosidine synthase, a strictosidine ß-D-glucosidase (MsSGD), and four medium-chain dehydrogenase/reductases (MsMDRs). PPI screening selected six MsMDRs interacting with MsSGD from 20 candidates predicted by multiomics analysis. Four of the six MsMDRs were then characterized as functional, indicating the high selectivity of the PPI screening method. This study highlights the opportunity of leveraging post-translational regulation features to discover novel plant natural product biosynthetic pathways.


Assuntos
Antineoplásicos , Produtos Biológicos , Mitragyna , Alcaloides de Triptamina e Secologanina , Saccharomyces cerevisiae/metabolismo , Mitragyna/metabolismo , Plantas/metabolismo , Antineoplásicos/metabolismo , Produtos Biológicos/metabolismo
12.
Nucleic Acids Res ; 48(21): 12074-12084, 2020 12 02.
Artigo em Inglês | MEDLINE | ID: mdl-33219687

RESUMO

CRISPR-Cas systems require discriminating self from non-self DNA during adaptation and interference. Yet, multiple cases have been reported of bacteria containing self-targeting spacers (STS), i.e. CRISPR spacers targeting protospacers on the same genome. STS has been suggested to reflect potential auto-immunity as an unwanted side effect of CRISPR-Cas defense, or a regulatory mechanism for gene expression. Here we investigated the incidence, distribution, and evasion of STS in over 100 000 bacterial genomes. We found STS in all CRISPR-Cas types and in one fifth of all CRISPR-carrying bacteria. Notably, up to 40% of I-B and I-F CRISPR-Cas systems contained STS. We observed that STS-containing genomes almost always carry a prophage and that STS map to prophage regions in more than half of the cases. Despite carrying STS, genetic deterioration of CRISPR-Cas systems appears to be rare, suggesting a level of escape from the potentially deleterious effects of STS by other mechanisms such as anti-CRISPR proteins and CRISPR target mutations. We propose a scenario where it is common to acquire an STS against a prophage, and this may trigger more extensive STS buildup by primed spacer acquisition in type I systems, without detrimental autoimmunity effects as mechanisms of auto-immunity evasion create tolerance to STS-targeted prophages.


Assuntos
Bactérias/genética , Proteínas Associadas a CRISPR/genética , Sistemas CRISPR-Cas/imunologia , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/imunologia , Genoma Bacteriano , Prófagos/genética , Autoimunidade/genética , Bactérias/imunologia , Bactérias/virologia , Sequência de Bases , Proteína 9 Associada à CRISPR/genética , Proteína 9 Associada à CRISPR/imunologia , Proteínas Associadas a CRISPR/imunologia , Mapeamento Cromossômico/estatística & dados numéricos , Software
13.
Proc Natl Acad Sci U S A ; 116(38): 19055-19063, 2019 09 17.
Artigo em Inglês | MEDLINE | ID: mdl-31484767

RESUMO

Juvenile-onset recurrent respiratory papillomatosis (JRRP) is a rare and debilitating childhood disease that presents with recurrent growth of papillomas in the upper airway. Two common human papillomaviruses (HPVs), HPV-6 and -11, are implicated in most cases, but it is still not understood why only a small proportion of children develop JRRP following exposure to these common viruses. We report 2 siblings with a syndromic form of JRRP associated with mild dermatologic abnormalities. Whole-exome sequencing of the patients revealed a private homozygous mutation in NLRP1, encoding Nucleotide-Binding Domain Leucine-Rich Repeat Family Pyrin Domain-Containing 1. We find the NLRP1 mutant allele to be gain of function (GOF) for inflammasome activation, as demonstrated by the induction of inflammasome complex oligomerization and IL-1ß secretion in an overexpression system. Moreover, patient-derived keratinocytes secrete elevated levels of IL-1ß at baseline. Finally, both patients displayed elevated levels of inflammasome-induced cytokines in the serum. Six NLRP1 GOF mutations have previously been described to underlie 3 allelic Mendelian diseases with differing phenotypes and modes of inheritance. Our results demonstrate that an autosomal recessive, syndromic form of JRRP can be associated with an NLRP1 GOF mutation.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal/genética , Proteínas Reguladoras de Apoptose/genética , Mutação com Ganho de Função , Homozigoto , Infecções por Papillomavirus/genética , Infecções por Papillomavirus/patologia , Infecções Respiratórias/genética , Infecções Respiratórias/patologia , Pré-Escolar , Citocinas/metabolismo , Feminino , Humanos , Lactente , Inflamassomos , Queratinócitos/citologia , Queratinócitos/imunologia , Queratinócitos/metabolismo , Masculino , Proteínas NLR , Linhagem , Irmãos , Síndrome
14.
Biophys J ; 120(7): 1198-1209, 2021 04 06.
Artigo em Inglês | MEDLINE | ID: mdl-33617832

RESUMO

The ability to detect specific nucleic acid sequences allows for a wide range of applications such as the identification of pathogens, clinical diagnostics, and genotyping. CRISPR-Cas proteins Cas12a and Cas13a are RNA-guided endonucleases that bind and cleave specific DNA and RNA sequences, respectively. After recognition of a target sequence, both enzymes activate indiscriminate nucleic acid cleavage, which has been exploited for sequence-specific molecular diagnostics of nucleic acids. Here, we present a label-free detection approach that uses a readout based on solution turbidity caused by liquid-liquid phase separation (LLPS). Our approach relies on the fact that the LLPS of oppositely charged polymers requires polymers to be longer than a critical length. This length dependence is predicted by the Voorn-Overbeek model, which we describe in detail and validate experimentally in mixtures of polynucleotides and polycations. We show that the turbidity resulting from LLPS can be used to detect the presence of specific nucleic acid sequences by employing the programmable CRISPR-nucleases Cas12a and Cas13a. Because LLPS of polynucleotides and polycations causes solutions to become turbid, the detection of specific nucleic acid sequences can be observed with the naked eye. We furthermore demonstrate that there is an optimal polynucleotide concentration for detection. Finally, we provide a theoretical prediction that hints towards possible improvements of an LLPS-based detection assay. The deployment of LLPS complements CRISPR-based molecular diagnostic applications and facilitates easy and low-cost nucleotide sequence detection.


Assuntos
Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , RNA , Sistemas CRISPR-Cas , DNA/genética , Endonucleases , RNA/genética
15.
J Virol ; 94(23)2020 11 09.
Artigo em Inglês | MEDLINE | ID: mdl-32938760

RESUMO

The infection of a bacterium by a phage starts with attachment to a receptor molecule on the host cell surface by the phage. Since receptor-phage interactions are crucial to successful infections, they are major determinants of phage host range and, by extension, of the broader effects that phages have on bacterial communities. Many receptor molecules, particularly membrane proteins, are difficult to isolate because their stability is supported by their native membrane environments. Styrene maleic acid lipid particles (SMALPs), a recent advance in membrane protein studies, are the result of membrane solubilizations by styrene maleic acid (SMA) copolymer chains. SMALPs thereby allow for isolation of membrane proteins while maintaining their native environment. Here, we explore SMALPs as a tool to isolate and study phage-receptor interactions. We show that SMALPs produced from taxonomically distant bacterial membranes allow for receptor-specific decrease of viable phage counts of several model phages that span the three largest phage families. After characterizing the effects of incubation time and SMALP concentration on the activity of three distinct phages, we present evidence that the interaction between two model phages and SMALPs is specific to bacterial species and the phage receptor molecule. These interactions additionally lead to DNA ejection by nearly all particles at high phage titers. We conclude that SMALPs are a potentially highly useful tool for phage-host interaction studies.IMPORTANCE Bacteriophages (viruses that infect bacteria or phages) impact every microbial community. All phage infections start with the binding of the viral particle to a specific receptor molecule on the host cell surface. Due to its importance in phage infections, this first step is of interest to many phage-related research and applications. However, many phage receptors are difficult to isolate. Styrene maleic acid lipid particles (SMALPs) are a recently developed approach to isolate membrane proteins in their native environment. In this study, we explore SMALPs as a tool to study phage-receptor interactions. We find that different phage species bind to SMALPs, while maintaining specificity to their receptor. We then characterize the time and concentration dependence of phage-SMALP interactions and furthermore show that they lead to genome ejection by the phage. The results presented here show that SMALPs are a useful tool for future studies of phage-receptor interactions.


Assuntos
Bacteriófagos/fisiologia , Interações Hospedeiro-Patógeno/fisiologia , Gotículas Lipídicas/química , Maleatos/química , Bactérias/virologia , Proteínas da Membrana Bacteriana Externa , Membrana Celular/fisiologia , Proteínas de Membrana/química , Polímeros/química , Poliestirenos , Solubilidade , Vírion
16.
PLoS Comput Biol ; 16(1): e1007314, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31971941

RESUMO

The last decade has witnessed a remarkable increase in our ability to measure genetic information. Advancements of sequencing technologies are challenging the existing methods of data storage and analysis. While methods to cope with the data deluge are progressing, many biologists have lagged behind due to the fast pace of computational advancements and tools available to address their scientific questions. Future generations of biologists must be more computationally aware and capable. This means they should be trained to give them the computational skills to keep pace with technological developments. Here, we propose a model that bridges experimental and bioinformatics concepts using the Oxford Nanopore Technologies (ONT) sequencing platform. We provide both a guide to begin to empower the new generation of educators, scientists, and students in performing long-read assembly of bacterial and bacteriophage genomes and a standalone virtual machine containing all the required software and learning materials for the course.


Assuntos
Biologia Computacional/educação , Sequenciamento por Nanoporos , Humanos , Software
17.
Epidemiol Infect ; 149: e44, 2021 02 10.
Artigo em Inglês | MEDLINE | ID: mdl-33563349

RESUMO

Much of our current understanding about novel coronavirus disease 2019 (COVID-19) comes from hospitalised patients. However, the spectrum of mild and subclinical disease has implications for population-level screening and control. Forty-nine participants were recruited from a group of 99 adults repatriated from a cruise ship with a high incidence of COVID-19. Respiratory and rectal swabs were tested by polymerase chain reaction (PCR) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Sera were tested for anti-SARS-CoV-2 antibodies by enzyme-linked immunosorbent assay (ELISA) and microneutralisation assay. Symptoms, viral shedding and antibody response were examined. Forty-five participants (92%) were considered cases based on either positive PCR or positive ELISA for immunoglobulin G. Forty-two percent of cases were asymptomatic. Only 15% of symptomatic cases reported fever. Serial respiratory and rectal swabs were positive for 10% and 5% of participants respectively about 3 weeks after median symptom onset. Cycle threshold values were high (range 31-45). Attempts to isolate live virus were unsuccessful. The presence of symptoms was not associated with demographics, comorbidities or antibody response. In closed settings, incidence of COVID-19 could be almost double that suggested by symptom-based screening. Serology may be useful in diagnosis of mild disease and in aiding public health investigations.


Assuntos
Anticorpos Antivirais/sangue , COVID-19/epidemiologia , COVID-19/virologia , Navios , Avaliação de Sintomas , Eliminação de Partículas Virais , Adulto , Idoso , Idoso de 80 Anos ou mais , Estudos de Coortes , Ensaio de Imunoadsorção Enzimática , Feminino , Humanos , Incidência , Masculino , Pessoa de Meia-Idade , Testes de Neutralização , SARS-CoV-2/fisiologia , Turismo , Uruguai , Vitória/epidemiologia
18.
Am J Emerg Med ; 41: 104-109, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33421674

RESUMO

INTRODUCTION: Early recognition and management of hemorrhage, damage control resuscitation, and blood product administration have optimized management of severe trauma. Recent data suggest hypocalcemia exacerbates the ensuing effects of coagulopathy in trauma. OBJECTIVE: This narrative review of available literature describes the physiology and role of calcium in trauma resuscitation. Authors did not perform a systematic review or meta-analysis. DISCUSSION: Calcium is a divalent cation found in various physiologic forms, specifically the bound, inactive state and the unbound, physiologically active state. While calcium plays several important physiologic roles in multiple organ systems, the negative hemodynamic effects of hypocalcemia are crucial to address in trauma patients. The negative ramifications of hypocalcemia are intrinsically linked to components of the lethal triad of acidosis, coagulopathy, and hypothermia. Hypocalcemia has direct and indirect effects on each portion of the lethal triad, supporting calcium's potential position as a fourth component in this proposed lethal diamond. Trauma patients often present hypocalcemic in the setting of severe hemorrhage secondary to trauma, which can be worsened by necessary transfusion and resuscitation. The critical consequences of hypocalcemia in the trauma patient have been repeatedly demonstrated with the associated morbidity and mortality. It remains poorly defined when to administer calcium, though current data suggest that earlier administration may be advantageous. CONCLUSIONS: Calcium is a key component of trauma resuscitation and the coagulation cascade. Recent data portray the intricate physiologic reverberations of hypocalcemia in the traumatically injured patient; however, future research is needed to further guide the management of these patients.


Assuntos
Hipocalcemia/etiologia , Ressuscitação , Ferimentos e Lesões/complicações , Ferimentos e Lesões/terapia , Cálcio/fisiologia , Humanos , Ferimentos e Lesões/mortalidade
19.
Nucleic Acids Res ; 47(10): 5223-5230, 2019 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-30937444

RESUMO

Microbes have the unique ability to acquire immunological memories from mobile genetic invaders to protect themselves from predation. To confer CRISPR resistance, new spacers need to be compatible with a targeting requirement in the invader's DNA called the protospacer adjacent motif (PAM). Many CRISPR systems encode Cas4 proteins to ensure new spacers are integrated that meet this targeting prerequisite. Here we report that a gene fusion between cas4 and cas1 from the Geobacter sulfurreducens I-U CRISPR-Cas system is capable of introducing functional spacers carrying interference proficient TTN PAM sequences at much higher frequencies than unfused Cas4 adaptation modules. Mutations of Cas4-domain catalytic residues resulted in dramatically decreased naïve and primed spacer acquisition, and a loss of PAM selectivity showing that the Cas4 domain controls Cas1 activity. We propose the fusion gene evolved to drive the acquisition of only PAM-compatible spacers to optimize CRISPR interference.


Assuntos
Proteínas de Bactérias/genética , Sistemas CRISPR-Cas , Regulação Bacteriana da Expressão Gênica , Geobacter/genética , Mutação , Proteínas de Bactérias/metabolismo , Domínio Catalítico , DNA Bacteriano/metabolismo , Escherichia coli/metabolismo , Fusão Gênica , Genes Bacterianos , Geobacter/metabolismo , Modelos Genéticos , Filogenia , Plasmídeos/genética , Análise de Sequência de DNA
20.
Catheter Cardiovasc Interv ; 96(5): 1046-1055, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-31990453

RESUMO

OBJECTIVES: To report clinical, angiographic characteristics, outcomes, and predictors of unsuccessful procedures in patients who underwent chronic total occlusion (CTO) percutaneous coronary interventions (PCI) in Latin America. BACKGROUND: CTO PCI has been increasingly performed worldwide, but there is a lack of information in this region. METHODS: An international multicenter registry was developed to collect data on CTO PCI performed in centers in Latin America. Patient, angiographic, procedural and outcome data were evaluated. Predictors of unsuccessful procedures were assessed by multivariable analysis. RESULTS: We have included data related to 1,040 CTO PCIs performed in seven countries in Latin America (Argentina, Brazil, Chile, Colombia, Ecuador, Mexico, and Puerto Rico). The mean age was 64 ± 10 years, and CTO PCI was performed mainly for angina control (81%) or treatment of a large ischemic area (30%). Overall technical success rate was 82.5%, and it was achieved with antegrade wire escalation in 81%, antegrade dissection/re-entry in 8% and with retrograde techniques in 11% of the successful procedures. Multivariable analysis identified moderate/severe calcification, a blunt proximal cap and a previous attempt as independent predictors of unsuccessful procedures. In-hospital major adverse cardiovascular events (MACE) occurred in 3.1% of the cases, death in 1% and cardiac tamponade in 0.9% CONCLUSIONS: CTO PCI in Latin America has been performed mainly for ischemia relief. Procedures were associated with a success rate above 80% and low incidence of MACE. Predictors of unsuccessful procedures were similar to those previously reported in the literature.


Assuntos
Oclusão Coronária/terapia , Intervenção Coronária Percutânea , Idoso , Doença Crônica , Angiografia Coronária , Oclusão Coronária/diagnóstico por imagem , Oclusão Coronária/mortalidade , Feminino , Mortalidade Hospitalar , Humanos , América Latina , Masculino , Pessoa de Meia-Idade , Infarto do Miocárdio/mortalidade , Intervenção Coronária Percutânea/efeitos adversos , Intervenção Coronária Percutânea/mortalidade , Sistema de Registros , Medição de Risco , Fatores de Risco , Acidente Vascular Cerebral/mortalidade , Fatores de Tempo , Resultado do Tratamento
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