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1.
Mol Cell ; 83(19): 3533-3545.e5, 2023 Oct 05.
Artículo en Inglés | MEDLINE | ID: mdl-37802026

RESUMEN

CRISPR-Cas9 is a powerful gene-editing technology; however, off-target activity remains an important consideration for therapeutic applications. We have previously shown that force-stretching DNA induces off-target activity and hypothesized that distortions of the DNA topology in vivo, such as negative DNA supercoiling, could reduce Cas9 specificity. Using single-molecule optical-tweezers, we demonstrate that negative supercoiling λ-DNA induces sequence-specific Cas9 off-target binding at multiple sites, even at low forces. Using an adapted CIRCLE-seq approach, we detect over 10,000 negative-supercoiling-induced Cas9 off-target double-strand breaks genome-wide caused by increased mismatch tolerance. We further demonstrate in vivo that directed local DNA distortion increases off-target activity in cells and that induced off-target events can be detected during Cas9 genome editing. These data demonstrate that Cas9 off-target activity is regulated by DNA topology in vitro and in vivo, suggesting that cellular processes, such as transcription and replication, could induce off-target activity at previously overlooked sites.


Asunto(s)
Sistemas CRISPR-Cas , Edición Génica , Genoma , ADN/genética , Pinzas Ópticas
2.
Phys Chem Chem Phys ; 23(47): 26640-26644, 2021 Dec 08.
Artículo en Inglés | MEDLINE | ID: mdl-34494640

RESUMEN

Using optical tweezers, we investigate target search and cleavage by CRISPR-Cas12a on force-stretched λ-DNA. Cas12a uses fast, one-dimensional hopping to locate its target. Binding and cleavage occur rapidly and specifically at low forces (≤5 pN), with a 1.8 nm rate-limiting conformational change. Mechanical distortion slows diffusion, increases off-target binding but hinders cleavage.


Asunto(s)
Proteínas Bacterianas/química , Proteínas Asociadas a CRISPR/química , ADN/química , Endodesoxirribonucleasas/química , Sistemas CRISPR-Cas , Modelos Moleculares , Pinzas Ópticas
3.
Eur J Public Health ; 29(5): 966-971, 2019 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-31329846

RESUMEN

BACKGROUND: A large outbreak of measles has spread across Italy over the year 2017. Its impact on emergency department (ED) of a tertiary-care teaching hospital and the related critical issues in public health were evaluated. METHODS: Medical records of adults discharged from January to December 2017 with diagnosis of 'measles' or 'measles suspicion' were collected and analyzed. RESULTS: From a total of 58 579 admissions, 218 medical records matched enrollment criteria. Measles infection was confirmed in 55.3% of patients, excluded in 26.2%, and judged as possible or probable in 18.3% of cases. Considered that the vaccination status was unknown in 89.2% of patients, the mean time spent in temporary isolation rooms (TIRs) waiting serological results was 1.7 ± 0.8 days. Measles-free patients spent a mean of 1.9 ± 0.9 days in TIRs, meaning a cumulative unnecessary time of isolation of 106.4 days. Despite most of patients were pauci-simptomatic and with a low burden of comorbidities, only 28.6% of them reported a previous out-of-hospital medical contact. Moreover an assessment of moderately critical conditions was assigned to 89.6% of cases, representing an over-valuation of the severity of the cases. Antibiotic therapy had been prescribed in 69.0% of cases and 57.7% of patients were hospitalized. We found no differences in terms of median time spent in TIRs, rate of hospitalization and antibiotic prescription between measles cases and measles-free patients. CONCLUSION: A preventable high-infective disease outbreak can lead to a misapply of ED facilities in terms of unjustified admissions, time spent in TIRs, antibiotic prescription and in hospitalization rate.


Asunto(s)
Brotes de Enfermedades/estadística & datos numéricos , Servicios Médicos de Urgencia/estadística & datos numéricos , Hospitales de Enseñanza/estadística & datos numéricos , Sarampión/epidemiología , Centros de Atención Terciaria/estadística & datos numéricos , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Femenino , Hospitalización/estadística & datos numéricos , Humanos , Italia/epidemiología , Masculino , Sarampión/diagnóstico , Sarampión/terapia , Persona de Mediana Edad , Estudios Retrospectivos , Adulto Joven
4.
BMC Biol ; 16(1): 150, 2018 12 28.
Artículo en Inglés | MEDLINE | ID: mdl-30593278

RESUMEN

BACKGROUND: Base Editing is a precise genome editing method that uses a deaminase-Cas9 fusion protein to mutate cytidine to thymidine in target DNA in situ without the generation of a double-strand break. However, the efficient enrichment of genetically modified cells using this technique is limited by the ability to detect such events. RESULTS: We have developed a Base Editing FLuorescent Activity REporter (BE-FLARE), which allows for the enrichment of cells that have undergone editing of target loci based on a fluorescence shift from BFP to GFP. We used BE-FLARE to evaluate the editing efficiency of APOBEC3A and APOBEC3B family members as alternatives deaminase domains to the rat APOBEC1 domain used in base editor 3 (BE3). We identified human APOBEC3A and APOBEC3B as highly efficient cytidine deaminases for base editing applications with unique properties. CONCLUSIONS: Using BE-FLARE to report on the efficiency and precision of editing events, we outline workflows for the accelerated generation of genetically engineered cell models and the discovery of alternative base editors.


Asunto(s)
Desaminasas APOBEC-1/genética , Citidina Desaminasa/genética , Edición Génica/métodos , Ingeniería Genética/métodos , Antígenos de Histocompatibilidad Menor/genética , Proteínas/genética , Animales , Humanos , Ratas
5.
J Infect Chemother ; 23(11): 763-768, 2017 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-28899610

RESUMEN

Toxinogenic Clostridium difficile infection (CDI) is a leading cause of infectious diarrhea. In this retrospective cohort study the molecular epidemiology of hospital-acquired and community-associated CDI was investigated in patients admitted to a tertiary care hospital. CD in stools samples was revealed by a two steps diagnostic algorithm, firstly screening for positivity to GDH antigen and thereafter RT-PCR analysis. Increased CDI incidence was observed ranging from 1.70episodes/10000patient-days in the 1st year, to 2.62 in the 2nd year, mostly hospitalized in the medicine wards, followed by outpatients (5.74 and 5.12episodes/10.000patient-days respectively). CDI positive were older than CDI negative patients and presented increased trend of diarrhea episodes as the patients' age increased. RT-PCR positive patients (n° = 314) were classified according to the CD toxin producing genes in three groups (1-3, carrying tcdB, both tcdB and cdt, and the two genes plus the deletion Δ117 of tcdC, respectively). The incidence of the group 2 and 3 increased statistically with the age of the patients showing correlation with the gender. Higher frequency of patients belonging to group 1 and group 3 was observed in the medical wards. Of note was the high incidence of group 3 in outpatients. Interestingly, patients with previous health care contacts had higher risk (RR = 1.88) of being infected by CD strains with higher toxicity than community patients. Recurrence rate was 15.9%. In conclusion the knowledge of the toxigenic profiles and of their relationships to gender, age and wards distribution may help the clinicians in the clinical management of the disease.


Asunto(s)
Centros Médicos Académicos/estadística & datos numéricos , Toxinas Bacterianas/aislamiento & purificación , Clostridioides difficile/aislamiento & purificación , Infección Hospitalaria/epidemiología , Diarrea/epidemiología , Enterocolitis Seudomembranosa/epidemiología , Adulto , Factores de Edad , Anciano , Anciano de 80 o más Años , Antígenos Bacterianos/aislamiento & purificación , Infección Hospitalaria/microbiología , Diarrea/microbiología , Enterocolitis Seudomembranosa/microbiología , Heces/microbiología , Femenino , Hospitalización/estadística & datos numéricos , Humanos , Incidencia , Italia/epidemiología , Masculino , Persona de Mediana Edad , Epidemiología Molecular , Recurrencia , Estudios Retrospectivos , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Centros de Atención Terciaria/estadística & datos numéricos
6.
SLAS Discov ; 29(2): 100136, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38104659

RESUMEN

Molecular glues are small molecules, typically smaller than PROTACs, and usually with improved physicochemical properties that aim to stabilise the interaction between two proteins. Most often this approach is used to improve or induce an interaction between the target and an E3 ligase, but other interactions which stabilise interactions to increase activity or to inhibit binding to a natural effector have also been demonstrated. This review will describe the effects of induced proximity, discuss current methods used to identify molecular glues and introduce approaches that could be adapted for molecular glue screening.


Asunto(s)
Proteínas , Ubiquitina-Proteína Ligasas , Proteolisis , Ubiquitina-Proteína Ligasas/metabolismo , Proteínas/metabolismo
7.
Environ Int ; 190: 108839, 2024 Jun 22.
Artículo en Inglés | MEDLINE | ID: mdl-38943925

RESUMEN

The presence in seawater of low-molecular-weight polyethylene (PE) and polydimethylsiloxane (PDMS), synthetic polymers with high chemical resistance, has been demonstrated in this study for the first time by developing a novel methodology for their recovery and quantification from surface seawater. These synthetic polymer debris (SPD) with very low molecular weights and sizes in the nano- and micro-metre range have escaped conventional analytical methods. SPD have been easily recovered from water samples (2 L) through filtration with a nitrocellulose membrane filter with a pore size of 0.45 µm. Dissolving the filter in acetone allowed the isolation of the particulates by centrifugation followed by drying. The isolated SPD were analysed by 1H nuclear magnetic resonance spectroscopy (1H NMR), identifying PE and PDMS. These polymers are thus persisting on seawater because of their low density and the ponderal concentrations were quantified in mg/m3. This method was used in an actual case study in which 120 surface seawater samples were collected during two sampling campaigns in the Mediterranean Sea (from the Gulf of Salerno to the Gulf of Policastro in South Italy). The developed analytical protocol allowed achieving unprecedented simplicity, rapidity and sensitivity. The 1H and 13C NMR structural analysis of the PE debris indicates the presence of oxidised polymer chains with very low molecular weights. Additionally, the origin of those low molecular weight polymers was investigated by analysing influents and effluents from a wastewater treatment plant (WWTP) in Salerno as a hot spot for the release of SPD: the analysis indicates the presence of low molecular weight polymers compatible with wax-PE, widely used for coating applications, food industry, cosmetics and detergents. Moreover, the origin of PDMS debris found in surface seawater can be ascribed to silicone-based antifoamers and emulsifiers.

8.
Clin Cancer Res ; 2024 Apr 17.
Artículo en Inglés | MEDLINE | ID: mdl-38630555

RESUMEN

PURPOSE: Osimertinib is an epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) indicated for the treatment of EGFR mutated (EGFRm)-driven lung adenocarcinomas. Osimertinib significantly improves progression-free survival in first-line treated patients with EGFRm advanced NSCLC. Despite the durable disease control, the majority of patients receiving osimertinib eventually develop disease progression. EXPERIMENTAL DESIGN: ctDNA profiling analysis on-progression plasma samples from patients treated with osimertinib in both first (Phase 3, FLAURA trial) and second-line trials (Phase 3, AURA3 trial) revealed a high prevalence of PIK3CA/AKT/PTEN alterations. In vitro and in vivo evidence using CRISPR engineered NSCLC cell lines and PXD models support a functional role for PIK3CA and PTEN mutations in the development of osimertinib resistance. RESULTS: These alterations are functionally relevant as EGFRm NSCLC cells with engineered PIK3CA/AKT/PTEN alterations develop resistance to osimertinib and can be re-sensitized by treatment with the combination of osimertinib and the AKT inhibitor capivasertib. Moreover, xenograft and PDX in vivo models with PIK3CA/AKT/PTEN alterations display limited sensitivity to osimertinib relative to models without alteration, and in these double mutant models capivasertib and osimertinib combination elicits an improved anti-tumor effect versus osimertinib alone. CONCLUSIONS: Together, this approach offers a potential treatment strategy for patients with EGFRm-driven NSCLC that have a sub-optimal response, or develop resistance, to osimertinib through PIK3CA/AKT/PTEN alterations.

9.
Oncogene ; 43(17): 1263-1273, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38433256

RESUMEN

DNA double-strand breaks (DSBs) contribute to genome instability, a key feature of cancer. DSBs are mainly repaired by homologous recombination (HR) and non-homologous end-joining (NHEJ). We investigated the role of an isoform of the multifunctional cyclin-dependent kinase 9, CDK9-55, in DNA repair, by generating CDK9-55-knockout HeLa clones (through CRISPR-Cas9), which showed potential HR dysfunction. A phosphoproteomic screening in these clones treated with camptothecin revealed that CDC23 (cell division cycle 23), a component of the E3-ubiquitin ligase APC/C (anaphase-promoting complex/cyclosome), is a new substrate of CDK9-55, with S588 being its putative phosphorylation site. Mutated non-phosphorylatable CDC23(S588A) affected the repair pathway choice by impairing HR and favouring error-prone NHEJ. This CDK9 role should be considered when designing CDK-inhibitor-based cancer therapies.

10.
Front Oncol ; 13: 1117262, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37409248

RESUMEN

Introduction: DNA double-strand breaks are the most toxic lesions repaired through the non-homologous and joining (NHEJ) or the homologous recombination (HR), which is dependent on the generation of single-strand tails, by the DNA end resection mechanism. The resolution of the HR intermediates leads to error-free repair (Gene Conversion) or the mutagenic pathways (Single Strand Annealing and Alternative End-Joining); the regulation of processes leading to the resolution of the HR intermediates is not fully understood. Methods: Here, we used a hydrophilic extract of a new tomato genotype (named DHO) in order to modulate the Camptothecin (CPT) DNA damage response. Results: We demonstrated increased phosphorylation of Replication Protein A 32 Serine 4/8 (RPA32 S4/8) protein in HeLa cells treated with the CPT in combination with DHO extract with respect to CPT alone. Moreover, we pointed out a change in HR intermediates resolution from Gene Conversion to Single Strand Annealing through the modified DNA repair protein RAD52 homolog (RAD52), DNA excision repair protein ERCC-1 (ERCC1) chromatin loading in response to DHO extract, and CPT co-treatment, with respect to the vehicle. Finally, we showed an increased sensitivity of HeLa cell lines to DHO extract and CPT co-treatment suggesting a possible mechanism for increasing the efficiency of cancer therapy. Discussion: We described the potential role of DHO extract in the modulation of DNA repair, in response to Camptothecin treatment (CPT), favoring an increased sensitivity of HeLa cell lines to topoisomerase inhibitor therapy.

11.
J Biol Chem ; 286(11): 9713-25, 2011 Mar 18.
Artículo en Inglés | MEDLINE | ID: mdl-21233209

RESUMEN

Cyclin/cyclin-dependent kinase (CDK) complexes are critical regulators of cellular proliferation. A complex network of regulatory mechanisms has evolved to control their activity, including activating and inactivating phosphorylation of the catalytic CDK subunit and inhibition through specific regulatory proteins. Primate herpesviruses, including the oncogenic Kaposi sarcoma herpesvirus, encode cyclin D homologues. Viral cyclins have diverged from their cellular progenitor in that they elicit holoenzyme activity independent of activating phosphorylation by the CDK-activating kinase and resistant to inhibition by CDK inhibitors. Using sequence comparison and site-directed mutagenesis, we performed molecular analysis of the cellular cyclin D and the Kaposi sarcoma herpesvirus-cyclin to delineate the molecular mechanisms behind their different behavior. This provides evidence that a surface recognized for its involvement in the docking of CIP/KIP inhibitors is required and sufficient to modulate cyclin-CDK response to a range of regulatory cues, including INK4 sensitivity and CDK-activating kinase dependence. Importantly, amino acids in this region are critically linked to substrate selection, suggesting that a mutational drift in this surface simultaneously affects function and regulation. Together our work provides novel insight into the molecular mechanisms governing cyclin-CDK function and regulation and defines the biological forces that may have driven evolution of viral cyclins.


Asunto(s)
Ciclina D/metabolismo , Proteínas Inhibidoras de las Quinasas Dependientes de la Ciclina/metabolismo , Quinasas Ciclina-Dependientes/metabolismo , Evolución Molecular , Herpesvirus Humano 8/enzimología , Proteínas Virales/metabolismo , Animales , Línea Celular , Ciclina D/química , Ciclina D/genética , Proteínas Inhibidoras de las Quinasas Dependientes de la Ciclina/química , Proteínas Inhibidoras de las Quinasas Dependientes de la Ciclina/genética , Quinasas Ciclina-Dependientes/química , Quinasas Ciclina-Dependientes/genética , Humanos , Modelos Biológicos , Modelos Moleculares , Mutagénesis Sitio-Dirigida , Fosforilación , Análisis de Secuencia de Proteína , Proteínas Virales/química , Proteínas Virales/genética
12.
Methods Mol Biol ; 2478: 349-378, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36063327

RESUMEN

The discovery of CRISPR/Cas9 as an easily programmable endonuclease heralds a new era of genetic manipulation. With this comes the prospect of novel gene therapy approaches, and the potential to cure previously untreatable genetic diseases. However, reports of spurious off-target editing by CRISPR/Cas9 pose a significant hurdle to realizing this potential. A deeper understanding of the factors that affect Cas9 specificity is vital for development of safe and efficient therapeutics. Here, we describe methods for the use of optical tweezers combined with confocal fluorescence microscopy and microfluidics for the analysis of on- and off-target activity of Cas9 activity.


Asunto(s)
Sistemas CRISPR-Cas , Edición Génica , Sistemas CRISPR-Cas/genética , Endonucleasas/genética , Edición Génica/métodos , Terapia Genética/métodos , Imagen Individual de Molécula
13.
Front Public Health ; 10: 840996, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35444987

RESUMEN

The aim of the present study is to assess saliva as a reliable specimen for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by real-time reverse transcription-PCR (RT-PCR), especially in community mass screening programs. The performance analysis considered 1,221 total samples [nasopharyngeal (NP) swabs and corresponding saliva], tested by means of a reference diagnostic real-time RT-PCR assay. Conflicting results were further investigated with a second, more sensitive, reference assay. Analysis of agreement showed a good concordance (95.82%), with a k coefficient value of.74 (p < 0.001); moreover, a follow-up analysis revealed the presence of viral gene targets in saliva samples at the time point the corresponding NP swabs turned negative. Data obtained prove the reliability of this alternative biofluid for SARS-CoV-2 detection in real-time RT-PCR. Considering the role of saliva in the coronavirus disease 2019 (COVID-19) transmission and pathogenesis, and the advantages in the use of salivary diagnostics, the present validation supports the use of saliva as an optimal choice in large-scale population screening and monitoring of the SARS-CoV-2 virus.


Asunto(s)
COVID-19 , COVID-19/diagnóstico , Humanos , Nasofaringe , Reproducibilidad de los Resultados , SARS-CoV-2 , Saliva , Manejo de Especímenes/métodos
14.
Artículo en Inglés | MEDLINE | ID: mdl-35055765

RESUMEN

Bivalve shellfish are readily contaminated by human pathogens present in waters impacted by municipal sewage, and the detection of SARS-CoV-2 in feces of infected patients and in wastewater has drawn attention to the possible presence of the virus in bivalves. The aim of this study was to collect data on SARS-CoV-2 prevalence in bivalve mollusks from harvesting areas of Campania region. A total of 179 samples were collected between September 2019 and April 2021 and were tested using droplet digital RT-PCR (dd RT-PCR) and real-time RT-PCR. Combining results obtained with different assays, SARS-CoV-2 presence was detected in 27/179 (15.1%) of samples. A median viral concentration of 1.1 × 102 and 1.4 × 102 g.c./g was obtained using either Orf1b nsp14 or RdRp/gene E, respectively. Positive results were unevenly distributed among harvesting areas and over time, positive samples being more frequent after January 2021. Partial sequencing of the spike region was achieved for five samples, one of which displaying mutations characteristic of the Alpha variant (lineage B.1.1.7). This study confirms that bivalve mollusks may bioaccumulate SARS-CoV-2 to detectable levels and that they may represent a valuable approach to track SARS-CoV-2 in water bodies and to monitor outbreak trends and viral diversity.


Asunto(s)
Bivalvos , COVID-19 , Animales , Humanos , ARN Viral , Reacción en Cadena en Tiempo Real de la Polimerasa , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , SARS-CoV-2 , Aguas Residuales
15.
J Virol Methods ; 300: 114420, 2022 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-34902456

RESUMEN

The emergence and spread of SARS-CoV-2 has led to a compelling request for accurate diagnostic tests. The aim of this study was assessing the performance of a real-time RT-qPCR (rt RT-qPCR) assay and of a droplet digital RT-PCR (dd RT-PCR) targeting the nsp14 genome region for the detection of SARS-CoV-2 in nasopharyngeal swabs. A total of 258 nasopharyngeal swabs were analyzed with the nsp14 assays and, for comparison, with a reference assay targeting the RdRp and E genes. Conflicting results were further investigated by two additional protocols, the Centers for Disease Control and Prevention (CDC) real-time targeting N1/N2, and a nested RT-PCR for the spike region. Agreement of results was achieved on 226 samples (156 positive and 70 negative), 8 samples were positive in the reference assay and in the nsp14 rt RT-qPCR but negative with the dd RT-PCR, and 24 samples provided different combinations of results with the three assays. Sensitivity, specificity and accuracy (95 %C.I.) of the nsp14 assays were: 100.0 % (97.4-100.0), 98.7 % (92.1-100.0), and 99.6 % (97.5-100.0) for the rt RT-qPCR; 92.4 % (87.4-95.6), 100.0 % (94.2-100.0), and 94.7 % (91.1-97.0) for the dd RT-PCR. The results of the study support the use of the nsp14 real-time RT-qPCR and ddPCR for the detection of SARS-CoV-2 in nasopharyngeal swabs.


Asunto(s)
COVID-19 , Reacción en Cadena en Tiempo Real de la Polimerasa , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , SARS-CoV-2 , COVID-19/diagnóstico , Exonucleasas , Humanos , Nasofaringe/virología , ARN Viral/genética , SARS-CoV-2/aislamiento & purificación , Sensibilidad y Especificidad
16.
Genome Med ; 14(1): 90, 2022 08 12.
Artículo en Inglés | MEDLINE | ID: mdl-35962405

RESUMEN

BACKGROUND: Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the only approach to rapidly monitor and tackle emerging variants of concern (VOC) of the COVID-19 pandemic. Such scrutiny is crucial to limit the spread of VOC that might escape the immune protection conferred by vaccination strategies or previous virus exposure. It is also becoming clear now that efficient genomic surveillance would require monitoring of the host gene expression to identify prognostic biomarkers of treatment efficacy and disease progression. Here we propose an integrative workflow to both generate thousands of SARS-CoV-2 genome sequences per week and analyze host gene expression upon infection. METHODS: In this study we applied an integrated workflow for RNA extracted from nasal swabs to obtain in parallel the full genome of SARS-CoV-2 and transcriptome of host respiratory epithelium. The RNA extracted from each sample was reverse transcribed and the viral genome was specifically enriched through an amplicon-based approach. The very same RNA was then used for patient transcriptome analysis. Samples were collected in the Campania region, Italy, for viral genome sequencing. Patient transcriptome analysis was performed on about 700 samples divided into two cohorts of patients, depending on the viral variant detected (B.1 or delta). RESULTS: We sequenced over 20,000 viral genomes since the beginning of the pandemic, producing the highest number of sequences in Italy. We thus reconstructed the pandemic dynamics in the regional territory from March 2020 to December 2021. In addition, we have matured and applied novel proof-of-principle approaches to prioritize possible gain-of-function mutations by leveraging patients' metadata and isolated patient-specific signatures of SARS-CoV-2 infection. This allowed us to (i) identify three new viral variants that specifically originated in the Campania region, (ii) map SARS-CoV-2 intrahost variability during long-term infections and in one case identify an increase in the number of mutations in the viral genome, and (iii) identify host gene expression signatures correlated with viral load in upper respiratory ways. CONCLUSION: In conclusion, we have successfully generated an optimized and cost-effective strategy to monitor SARS-CoV-2 genetic variability, without the need of automation. Thus, our approach is suitable for any lab with a benchtop sequencer and a limited budget, allowing an integrated genomic surveillance on premises. Finally, we have also identified a gene expression signature defining SARS-CoV-2 infection in real-world patients' upper respiratory ways.


Asunto(s)
COVID-19 , SARS-CoV-2 , COVID-19/genética , Genoma Viral , Humanos , Pandemias , ARN , SARS-CoV-2/genética
17.
Future Sci OA ; 7(7): FSO711, 2021 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-34254029

RESUMEN

SARS-CoV-2, the causative agent of the COVID-19 pandemic, has rarely been associated with transmission from humans to animals (reverse zoonotic transmission). In this retrospective study, the authors reviewed data obtained from 236 animals, including buffaloes, goats/sheep, horses, carrier pigeons, rabbits, hens, snakes, pigs and cows that were screened for SARS-CoV-2 infection because they had been in contact with their SARS-CoV-2-positive breeder for at least 2 weeks. None of the tested animals were found to be positive. The authors' findings suggest that the risk of reverse zoonotic transmission among bred animals and SARS-CoV-2-positive breeders is very low or nonexistent. Additional studies are warranted.

18.
Front Public Health ; 9: 649781, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33996728

RESUMEN

The onset of the new SARS-CoV-2 coronavirus encouraged the development of new serologic tests that could be additional and complementary to real-time RT-PCR-based assays. In such a context, the study of performances of available tests is urgently needed, as their use has just been initiated for seroprevalence assessment. The aim of this study was to compare four chemiluminescence immunoassays and one immunochromatography test for SARS-Cov-2 antibodies for the evaluation of the degree of diffusion of SARS-CoV-2 infection in Salerno Province (Campania Region, Italy). A total of 3,185 specimens from citizens were tested for anti-SARS-CoV-2 antibodies as part of a screening program. Four automated immunoassays (Abbott and Liaison SARS-CoV-2 CLIA IgG and Roche and Siemens SARS-CoV-2 CLIA IgM/IgG/IgA assays) and one lateral flow immunoassay (LFIA Technogenetics IgG-IgM COVID-19) were used. Seroprevalence in the entire cohort was 2.41, 2.10, 1.82, and 1.85% according to the Liaison IgG, Abbott IgG, Siemens, and Roche total Ig tests, respectively. When we explored the agreement among the rapid tests and the serologic assays, we reported good agreement for Abbott, Siemens, and Roche (Cohen's Kappa coefficient 0.69, 0.67, and 0.67, respectively), whereas we found moderate agreement for Liaison (Cohen's kappa coefficient 0.58). Our study showed that Abbott and Liaison SARS-CoV-2 CLIA IgG, Roche and Siemens SARS-CoV-2 CLIA IgM/IgG/IgA assays, and LFIA Technogenetics IgG-IgM COVID-19 have good agreement in seroprevalence assessment. In addition, our findings indicate that the prevalence of IgG and total Ig antibodies against SARS-CoV-2 at the time of the study was as low as around 3%, likely explaining the amplitude of the current second wave.


Asunto(s)
COVID-19 , SARS-CoV-2 , Humanos , Inmunoensayo , Inmunoglobulina M , Italia , Luminiscencia , Sensibilidad y Especificidad , Estudios Seroepidemiológicos
19.
Nat Commun ; 11(1): 4132, 2020 08 17.
Artículo en Inglés | MEDLINE | ID: mdl-32807781

RESUMEN

Precise genome editing using CRISPR-Cas9 is a promising therapeutic avenue for genetic diseases, although off-target editing remains a significant safety concern. Guide RNAs shorter than 16 nucleotides in length effectively recruit Cas9 to complementary sites in the genome but do not permit Cas9 nuclease activity. Here we describe CRISPR Guide RNA Assisted Reduction of Damage (CRISPR GUARD) as a method for protecting off-targets sites by co-delivery of short guide RNAs directed against off-target loci by competition with the on-target guide RNA. CRISPR GUARD reduces off-target mutagenesis while retaining on-target editing efficiencies with Cas9 and base editor. However, we discover that short guide RNAs can also support base editing if they contain cytosines within the deaminase activity window. We explore design rules and the universality of this method through in vitro studies and high-throughput screening, revealing CRISPR GUARD as a rapidly implementable strategy to improve the specificity of genome editing for most genomic loci. Finally, we create an online tool for CRISPR GUARD design.


Asunto(s)
Edición Génica/métodos , ARN Guía de Kinetoplastida/metabolismo , Sistemas CRISPR-Cas/genética , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas/genética , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas/fisiología , Humanos , Mutagénesis/genética , Mutagénesis/fisiología , ARN Guía de Kinetoplastida/genética
20.
Pharmaceuticals (Basel) ; 13(8)2020 Jul 29.
Artículo en Inglés | MEDLINE | ID: mdl-32751396

RESUMEN

Three Ru(II)-based CO-releasing molecules featuring bidentate benzimidazole and terpyridine derivatives as ligands were investigated for their ability to modulate the aggregation process of the second helix of the C-terminal domain of nucleophosmin 1, namely nucleophosmin 1 (NPM1)264-277, a model amyloidogenic system, before and after irradiation at 365 nm. Thioflavin T (ThT) binding assays and UV/Vis absorption spectra indicate that binding of the compounds to the peptide inhibits its aggregation and that the inhibitory effect increases upon irradiation (half maximal effective concentration (EC50) values in the high micromolar range). Electrospray ionization mass spectrometry data of the peptide in the presence of one of these compounds confirm that the modulation of amyloid aggregation relies on the formation of adducts obtained when the Ru compounds react with the peptide upon releasing of labile ligands, like chloride and carbon monoxide. This mechanism of action explains the subtle different behavior of the three compounds observed in ThT experiments. Overall, data support the hypothesis that metal-based CO releasing molecules can be used to develop metal-based drugs with potential application as anti-amyloidogenic agents.

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