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1.
Medicina (Kaunas) ; 60(1)2024 Jan 03.
Artículo en Inglés | MEDLINE | ID: mdl-38256354

RESUMEN

Background and Objectives: Cardiac patients are particularly at risk of herpes zoster (HZ), which is associated with a higher risk of major cardiovascular events. This research aimed to analyze the knowledge, attitudes and practices towards recombinant zoster vaccine (RZV) among cardiac healthcare professionals (HPs). Materials and Methods: A cross-sectional survey was conducted in a cardiological hospital in Italy. Multivariate regression models were built to identify factors associated with the outcomes of interest. Results: The response rate was 78.2% (154/197). Overall, age > 50 years and immunosuppression were recognized as risk factors for HZ by 38.3% and 75.3% of respondents, respectively. Regarding RZV, 29.1% of the HPs correctly responded about its schedule and 57.6% about the possibility of administration in immunocompromised individuals. This knowledge was significantly higher in HPs with a higher educational level (odds ratio (OR) = 4.42; 95%CI 1.70-11.47), in those who knew that HZ could cause postherpetic neuralgia (OR = 2.56; 95%CI 1.05-6.25) or major cardiovascular events (OR = 4.23; 95%CI 1.50-11.91), in those who had participated in professional updates on vaccinations (OR = 3.86; 95%CI 1.51-9.87) and in those who stated the need for further information about the RZV (OR = 6.43; 95%CI 1.42-29.98). Younger HPs (coefficient (ß) = -0.02; 95%CI -0.04--0.01), those with a positive attitude toward RZV safety (ß = 2.92; 95%CI 2.49-3.36) and those who had previously cared for patients with HZ (ß = 0.45; 95%CI 0.03-0.88) reported a more positive attitude toward RZV effectiveness. The practice of recommending vaccination was more prevalent in younger HPs (OR = 0.94; 95%CI 0.89-0.99), in those who had a master's degree or higher education (OR = 7.21; 95%CI 1.44-36.08), in those with more positive attitudes toward RZV effectiveness (OR = 7.17; 95%CI 1.71-30.03) and in HPs who had already recommended the vaccine to patients in the past (OR = 4.03; 95%CI 1.08-14.96). Conclusions: Despite being a single-center study, our research brings attention to factors that currently impact cardiac HPs' approaches to RZV. The findings indicate potential measures to enhance HPs' awareness and practices, ultimately aiming to improve vaccination adherence and reduce the burden associated with HZ.


Asunto(s)
Cardiólogos , Enfermedades Cardiovasculares , Vacuna contra el Herpes Zóster , Herpes Zóster , Humanos , Persona de Mediana Edad , Vacuna contra el Herpes Zóster/uso terapéutico , Estudios Transversales , Conocimientos, Actitudes y Práctica en Salud , Herpes Zóster/prevención & control , Vacunas Sintéticas , Italia/epidemiología , Encuestas y Cuestionarios , Enfermedades Cardiovasculares/prevención & control
2.
Vet Pathol ; 60(5): 560-577, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-37458195

RESUMEN

Disease outbreaks in several ecologically or commercially important invertebrate marine species have been reported in recent years all over the world. Mass mortality events (MMEs) have affected the noble pen shell (Pinna nobilis), causing its near extinction. Our knowledge of the dynamics of diseases affecting this species is still unclear. Early studies investigating the causative etiological agent focused on a novel protozoan parasite, Haplosporidium pinnae, although further investigations suggested that concurrent polymicrobial infections could have been pivotal in some MMEs, even in the absence of H. pinnae. Indeed, moribund specimens collected during MMEs in Italy, Greece, and Spain demonstrated the presence of a bacteria from within the Mycobacterium simiae complex and, in some cases, species similar to Vibrio mediterranei. The diagnostic processes used for investigation of MMEs are still not standardized and require the expertise of veterinary and para-veterinary pathologists, who could simultaneously evaluate a variety of factors, from clinical signs to environmental conditions. Here, we review the available literature on mortality events in P. nobilis and discuss approaches to define MMEs in P. nobilis. The proposed consensus approach should form the basis for establishing a foundation for future studies aimed at preserving populations in the wild.


Asunto(s)
Bivalvos , Haplosporidios , Mycobacterium , Animales , Bivalvos/microbiología , Bivalvos/parasitología , Italia , Brotes de Enfermedades
3.
Int J Mol Sci ; 23(18)2022 Sep 12.
Artículo en Inglés | MEDLINE | ID: mdl-36142485

RESUMEN

The present work proposes the use of a fast analytical platform for the mass spectrometric (MS) profiling of canine mammary tissues in their native form for the building of a predictive statistical model. The latter could be used as a novel diagnostic tool for the real-time identification of different cellular alterations in order to improve tissue resection during veterinary surgery, as previously validated in human oncology. Specifically, Rapid Evaporative Ionization Mass Spectrometry (REIMS) coupled with surgical electrocautery (intelligent knife-iKnife) was used to collect MS data from histologically processed mammary samples, classified into healthy, hyperplastic/dysplastic, mastitis and tumors. Differences in the lipid composition enabled tissue discrimination with an accuracy greater than 90%. The recognition capability of REIMS was tested on unknown mammary samples, and all of them were correctly identified with a correctness score of 98-100%. Triglyceride identification was increased in healthy mammary tissues, while the abundance of phospholipids was observed in altered tissues, reflecting morpho-functional changes in cell membranes, and oxidized species were also tentatively identified as discriminant features. The obtained lipidomic profiles represented unique fingerprints of the samples, suggesting that the iKnife technique is capable of differentiating mammary tissues following chemical changes in cellular metabolism.


Asunto(s)
Mama , Lipidómica , Animales , Perros , Femenino , Humanos , Espectrometría de Masas/métodos , Fosfolípidos/química , Triglicéridos
4.
Mol Cell Proteomics ; 17(3): 533-548, 2018 03.
Artículo en Inglés | MEDLINE | ID: mdl-29242379

RESUMEN

Comprehensive knowledge of the human leukocyte antigen (HLA) class-I and class-II peptides presented to T-cells is crucial for designing innovative therapeutics against cancer and other diseases. However methodologies for their purification for mass-spectrometry analysis have been a major limitation. We designed a novel high-throughput, reproducible and sensitive method for sequential immuno-affinity purification of HLA-I and -II peptides from up to 96 samples in a plate format, suitable for both cell lines and tissues. Our methodology drastically reduces sample-handling and can be completed within five hours. We challenged our methodology by extracting HLA peptides from multiple replicates of tissues (n = 7) and cell lines (n = 21, 108 cells per replicate), which resulted in unprecedented depth, sensitivity and high reproducibility (Pearson correlations up to 0.98 and 0.97 for HLA-I and HLA-II). Because of the method's achieved sensitivity, even single measurements of peptides purified from 107 B-cells resulted in the identification of more than 1700 HLA-I and 2200 HLA-II peptides. We demonstrate the feasibility of performing drug-screening by using ovarian cancer cells treated with interferon gamma (IFNγ). Our analysis revealed an augmented presentation of chymotryptic-like and longer ligands associated with IFNγ induced changes of the antigen processing and presentation machinery. This straightforward method is applicable for basic and clinical applications.


Asunto(s)
Antígenos de Histocompatibilidad Clase II/metabolismo , Antígenos de Histocompatibilidad Clase I/metabolismo , Interferón gamma/farmacología , Péptidos/metabolismo , Linfocitos B/metabolismo , Línea Celular , Humanos , Ligandos , Neoplasias/metabolismo , Proteómica/métodos , Linfocitos T/metabolismo
5.
Nucleic Acids Res ; 46(D1): D1237-D1247, 2018 01 04.
Artículo en Inglés | MEDLINE | ID: mdl-28985418

RESUMEN

Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility complex (MHC) molecules. The broad clinical relevance of MHC-associated peptides, e.g. in precision medicine, provides a strong rationale for the large-scale generation of immunopeptidomic datasets and recent developments in MS-based peptide analysis technologies now support the generation of the required data. Importantly, the availability of diverse immunopeptidomic datasets has resulted in an increasing need to standardize, store and exchange this type of data to enable better collaborations among researchers, to advance the field more efficiently and to establish quality measures required for the meaningful comparison of datasets. Here we present the SysteMHC Atlas (https://systemhcatlas.org), a public database that aims at collecting, organizing, sharing, visualizing and exploring immunopeptidomic data generated by MS. The Atlas includes raw mass spectrometer output files collected from several laboratories around the globe, a catalog of context-specific datasets of MHC class I and class II peptides, standardized MHC allele-specific peptide spectral libraries consisting of consensus spectra calculated from repeat measurements of the same peptide sequence, and links to other proteomics and immunology databases. The SysteMHC Atlas project was created and will be further expanded using a uniform and open computational pipeline that controls the quality of peptide identifications and peptide annotations. Thus, the SysteMHC Atlas disseminates quality controlled immunopeptidomic information to the public domain and serves as a community resource toward the generation of a high-quality comprehensive map of the human immunopeptidome and the support of consistent measurement of immunopeptidomic sample cohorts.


Asunto(s)
Bases de Datos Factuales , Antígenos HLA , Antígenos de Histocompatibilidad , Espectrometría de Masas , Alelos , Antígenos HLA/química , Antígenos HLA/inmunología , Antígenos de Histocompatibilidad/química , Antígenos de Histocompatibilidad/inmunología , Humanos , Internet , Espectrometría de Masas en Tándem , Interfaz Usuario-Computador
6.
BMC Vet Res ; 15(1): 186, 2019 Jun 04.
Artículo en Inglés | MEDLINE | ID: mdl-31164162

RESUMEN

BACKGROUND: Melanosis of lymph nodes in black pigs has generally been related to regression of congenital melanoma and, occasionally, to ingestion of acorns. The aim of this manuscript is to confirm the hypothesis of a possible acquired acorn-related pseudomelanosis in the Nero Calabrese pig, a swine breed belonging to the group of Italian native breeds and whose coverage area corresponds to the region of Calabria, southern Italy. This pig is characterized by slow-growing subjects, producing, however, high quality meat suitable for the production of sausages and fine hams. The study was carried out on 142 normally slaughtered pigs. All organs were examined. Lymph nodes and intestine (jejunum) were sampled. Histochemistry was performed on deparaffinized histological sections to identify the cell types involved and to characterize the pigment stored. To further confirm the pigmentation disorder, immunohistochemistry was carried out. Total phenolic substances were identified in acorns through the use of a biochemical reaction. RESULTS: Lymph node pigmentation appears directly related to acorn ingestion, with a higher incidence in the group which was 70% natural fed (acorn of Quercus virgiliana). Moreover, findings obtained revealed how different amounts of phenolic substrates present in Q. virgiliana and Q. ilex acorns can influence the incidence of such exogenous pigmentation. CONCLUSION: The findings obtained in this study confirm the acquired nature of the melanin-like pigmentation detected in lymph nodes from acorn-fed swine. Acquired pigmentation must be differentiated from true melanosis as well as from melanosis related to tumor regression of congenital melanoma. This thesaurismosis can be proposed as a marker of wellbeing and quality, confirming that the pigs have been bred and fed in natural conditions.


Asunto(s)
Alimentación Animal , Hiperpigmentación/veterinaria , Enfermedades Linfáticas/veterinaria , Quercus , Semillas , Enfermedades de los Porcinos/etiología , Animales , Femenino , Hiperpigmentación/etiología , Hiperpigmentación/patología , Ganglios Linfáticos/patología , Enfermedades Linfáticas/etiología , Enfermedades Linfáticas/patología , Masculino , Porcinos , Enfermedades de los Porcinos/patología
7.
Mol Cell Proteomics ; 16(2): 181-193, 2017 02.
Artículo en Inglés | MEDLINE | ID: mdl-27920218

RESUMEN

As aberrant protein phosphorylation is a hallmark of tumor cells, the display of tumor-specific phosphopeptides by Human Leukocyte Antigen (HLA) class I molecules can be exploited in the treatment of cancer by T-cell-based immunotherapy. Yet, the characterization and prediction of HLA-I phospholigands is challenging as the molecular determinants of the presentation of such post-translationally modified peptides are not fully understood. Here, we employed a peptidomic workflow to identify 256 unique phosphorylated ligands associated with HLA-B*40, -B*27, -B*39, or -B*07. Remarkably, these phosphopeptides showed similar molecular features. Besides the specific anchor motifs imposed by the binding groove of each allotype, the predominance of phosphorylation at peptide position 4 (P4) became strikingly evident, as was the enrichment of basic residues at P1. To determine the structural basis of this observation, we carried out a series of peptide binding assays and solved the crystal structures of HLA-B*40 in complex with a phosphorylated ligand or its nonphosphorylated counterpart. Overall, our data provide a clear explanation to the common motif found in the phosphopeptidomes associated to different HLA-B molecules. The high prevalence of phosphorylation at P4 is dictated by the presence of the conserved residue Arg62 in the heavy chain, a structural feature shared by most HLA-B alleles. In contrast, the preference for basic residues at P1 is allotype-dependent and might be linked to the structure of the A pocket. This molecular understanding of the presentation of phosphopeptides by HLA-B molecules provides a base for the improved prediction and identification of phosphorylated neo-antigens, as potentially used for cancer immunotherapy.


Asunto(s)
Antígenos HLA-B/química , Antígenos HLA-B/metabolismo , Péptidos/química , Proteómica/métodos , Secuencias de Aminoácidos , Línea Celular , Cristalografía por Rayos X , Antígeno HLA-B40/química , Antígeno HLA-B40/metabolismo , Humanos , Modelos Moleculares , Péptidos/análisis , Fosforilación , Unión Proteica
8.
Proteomics ; 18(12): e1800041, 2018 06.
Artículo en Inglés | MEDLINE | ID: mdl-29513933

RESUMEN

Mass spectrometry (MS)-based immunopeptidomics has developed as one of the leading methodologies for comprehensive characterization of in vivo presented human leukocyte antigen (HLA)-bound peptides. Unveiling the identity of HLA-bound peptides derived from diseased cells is crucial to gain knowledge on the constitution of efficient disease-specific T cell responses. The HLA-presented peptidome reflects the status of the cellular proteome, hence disease-related aberrations of posttranslational modifications (PTMs) might lead to presentation of peptides harboring PTMs. Therefore, characterization of HLA-bound PTM peptides could shed light on their relevance in immune and disease processes. In this issue, Ramarathinam et al. investigate the presentation of HIV envelope (HIVenv) peptides bound to the HLA-B*57:01 allele. Among these peptides, the authors specifically focused on a kynurenine-modified peptide. To this end, they characterize the possible origin of the kynurenine modification, its effect on HLA binding affinity, stability, conformation within the complex, and its immunogenicity compared to the native counterpart.


Asunto(s)
Presentación de Antígeno , Antígenos VIH , Epítopos , VIH , Antígenos HLA-B , Humanos
9.
Proteomics ; 18(12): e1800110, 2018 06.
Artículo en Inglés | MEDLINE | ID: mdl-29791771

RESUMEN

Minimal information about an immuno-peptidomics experiment (MIAIPE) is an initiative of the members of the Human Immuno-Peptidome Project (HIPP), an international program organized by the Human Proteome Organization (HUPO). The aim of the MIAIPE guidelines is to deliver technical guidelines representing the minimal information required to sufficiently support the evaluation and interpretation of immunopeptidomics experiments. The MIAIPE document has been designed to report essential information about sample preparation, mass spectrometric measurement, and associated mass spectrometry (MS)-related bioinformatics aspects that are unique to immunopeptidomics and may not be covered by the general proteomics MIAPE (minimal information about a proteomics experiment) guidelines.


Asunto(s)
Biología Computacional/normas , Antígenos de Histocompatibilidad Clase II/metabolismo , Antígenos de Histocompatibilidad Clase I/metabolismo , Fragmentos de Péptidos/metabolismo , Proteómica/normas , Programas Informáticos , Manejo de Especímenes/normas , Bases de Datos de Proteínas , Antígenos de Histocompatibilidad Clase I/análisis , Antígenos de Histocompatibilidad Clase I/inmunología , Antígenos de Histocompatibilidad Clase II/análisis , Antígenos de Histocompatibilidad Clase II/inmunología , Humanos , Fragmentos de Péptidos/análisis , Fragmentos de Péptidos/inmunología
10.
Mol Cell Proteomics ; 15(4): 1412-23, 2016 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-26764012

RESUMEN

Comprehensive analysis of the complex nature of the Human Leukocyte Antigen (HLA) class II ligandome is of utmost importance to understand the basis for CD4(+)T cell mediated immunity and tolerance. Here, we implemented important improvements in the analysis of the repertoire of HLA-DR-presented peptides, using hybrid mass spectrometry-based peptide fragmentation techniques on a ligandome sample isolated from matured human monocyte-derived dendritic cells (DC). The reported data set constitutes nearly 14 thousand unique high-confident peptides,i.e.the largest single inventory of human DC derived HLA-DR ligands to date. From a technical viewpoint the most prominent finding is that no single peptide fragmentation technique could elucidate the majority of HLA-DR ligands, because of the wide range of physical chemical properties displayed by the HLA-DR ligandome. Our in-depth profiling allowed us to reveal a strikingly poor correlation between the source proteins identified in the HLA class II ligandome and the DC cellular proteome. Important selective sieving from the sampled proteome to the ligandome was evidenced by specificity in the sequences of the core regions both at their N- and C- termini, hence not only reflecting binding motifs but also dominant protease activity associated to the endolysosomal compartments. Moreover, we demonstrate that the HLA-DR ligandome reflects a surface representation of cell-compartments specific for biological events linked to the maturation of monocytes into antigen presenting cells. Our results present new perspectives into the complex nature of the HLA class II system and will aid future immunological studies in characterizing the full breadth of potential CD4(+)T cell epitopes relevant in health and disease.


Asunto(s)
Antígenos HLA-DR/metabolismo , Péptidos/metabolismo , Proteoma/metabolismo , Presentación de Antígeno , Células Cultivadas , Células Dendríticas/metabolismo , Humanos , Ligandos , Espectrometría de Masas
11.
J Proteome Res ; 16(1): 34-44, 2017 01 06.
Artículo en Inglés | MEDLINE | ID: mdl-27503676

RESUMEN

Alterations in protein post-translational modification (PTM) are recognized hallmarks of diseases. These modifications potentially provide a unique source of disease-related human leukocyte antigen (HLA) class I-presented peptides that can elicit specific immune responses. While phosphorylated HLA peptides have already received attention, arginine methylated HLA class I peptide presentation has not been characterized in detail. In a human B-cell line we detected 149 HLA class I peptides harboring mono- and/or dimethylated arginine residues by mass spectrometry. A striking preference was observed in the presentation of arginine (di)methylated peptides for HLA-B*07 molecules, likely because the binding motifs of this allele resemble consensus sequences recognized by arginine methyl-transferases. Moreover, HLA-B*07-bound peptides preferentially harbored dimethylated groups at the P3 position, thus consecutively to the proline anchor residue. Such a proline-arginine sequence has been associated with the arginine methyl-transferases CARM1 and PRMT5. Making use of the specific neutral losses in fragmentation spectra, we found most of the peptides to be asymmetrically dimethylated, most likely by CARM1. These data expand our knowledge of the processing and presentation of arginine (di)methylated HLA class I peptides and demonstrate that these types of modified peptides can be presented for recognition by T-cells. HLA class I peptides with mono- and dimethylated arginine residues may therefore offer a novel target for immunotherapy.


Asunto(s)
Presentación de Antígeno , Arginina/metabolismo , Linfocitos B/metabolismo , Proteínas Adaptadoras de Señalización CARD/genética , Guanilato Ciclasa/genética , Péptidos/química , Procesamiento Proteico-Postraduccional , Secuencia de Aminoácidos , Arginina/inmunología , Linfocitos B/citología , Linfocitos B/inmunología , Sitios de Unión , Proteínas Adaptadoras de Señalización CARD/inmunología , Línea Celular , Expresión Génica , Guanilato Ciclasa/inmunología , Antígeno HLA-B7 , Humanos , Metilación , Mapeo Peptídico , Péptidos/genética , Péptidos/inmunología , Prolina/inmunología , Prolina/metabolismo , Unión Proteica , Proteína-Arginina N-Metiltransferasas/genética , Proteína-Arginina N-Metiltransferasas/inmunología
12.
Anal Chem ; 89(6): 3318-3325, 2017 03 21.
Artículo en Inglés | MEDLINE | ID: mdl-28233997

RESUMEN

Mass spectrometry (MS)-based proteomics workflows can crudely be classified into two distinct regimes, targeting either relatively small peptides (i.e., 0.7 kDa < Mw < 3.0 kDa) or small to medium sized intact proteins (i.e., 10 kDa < Mw < 30 kDa), respectively, termed bottom-up and top-down proteomics. Recently, a niche has started to be explored covering the analysis of middle-range peptides (i.e., 3.0 kDa < Mw < 10 kDa), aptly termed middle-down proteomics. Although middle-down proteomics can follow, in principle, a modular workflow similar to that of bottom-up proteomics, we hypothesized that each of these modules would benefit from targeted optimization to improve its overall performance in the analysis of middle-range sized peptides. Hence, to generate middle-range sized peptides from cellular lysates, we explored the use of the proteases Asp-N and Glu-C and a nonenzymatic acid induced cleavage. To increase the depth of the proteome, a strong cation exchange (SCX) separation, carefully tuned to improve the separation of longer peptides, combined with reversed phase-liquid chromatography (RP-LC) using columns packed with material possessing a larger pore size, was used. Finally, after evaluating the combination of potentially beneficial MS settings, we also assessed the peptide fragmentation techniques, including higher-energy collision dissociation (HCD), electron-transfer dissociation (ETD), and electron-transfer combined with higher-energy collision dissociation (EThcD), for characterization of middle-range sized peptides. These combined improvements clearly improve the detection and sequence coverage of middle-range peptides and should guide researchers to explore further how middle-down proteomics may lead to an improved proteome coverage, beneficial for, among other things, the enhanced analysis of (co-occurring) post-translational modifications.


Asunto(s)
Péptido Hidrolasas/metabolismo , Péptidos/análisis , Proteómica , Células HeLa , Humanos , Espectrometría de Masas , Tamaño de la Partícula , Péptidos/metabolismo
13.
Anal Chem ; 88(4): 2303-10, 2016 Feb 16.
Artículo en Inglés | MEDLINE | ID: mdl-26760441

RESUMEN

Proteomics applications performed on the popular benchtop Q Exactive Orbitrap mass spectrometer have so far relied exclusively on higher collision-energy dissociation (HCD) fragmentation for peptide sequencing. While this fragmentation technique is applicable to a wide range of biological questions, it also has limitations, and all questions cannot be addressed equally well. Here, we demonstrate that the fragmentation capabilities of the Q Exactive mass spectrometer can be extended with ultraviolet photodissociation (UVPD) fragmentation, complete with synchronization triggering to make it compatible with liquid chromatography (LC)/tandem mass spectrometry (MS/MS) workflows. We show that UVPD not only is directly compatible with LC/MS workflows but also, when combined with these workflows, can result in higher database scores and increased identification rates for complex samples as compared to HCD methods. UVPD as a fragmentation technique offers prompt, high-energy fragmentation, which can potentially lead to improved analyses of labile post-translational modifications. Techniques like HCD result in substantial amounts of modification losses, competing with fragmentation pathways that provide information-rich ion fragments. We investigate here the utility of UVPD for identification of phosphorylated peptides and find that UVPD fragmentation reduces the extent of labile modification loss by up to ∼60%. Collectively, when integrated into a complete workflow on the Q Exactive Orbitrap, UVPD provides distinct advantages to the analysis of post-translational modifications and is a powerful and complementary addition to the proteomic toolbox.


Asunto(s)
Fosfoproteínas/análisis , Fosfoproteínas/efectos de la radiación , Fotólisis/efectos de la radiación , Proteómica/instrumentación , Espectrometría de Masas en Tándem/instrumentación , Rayos Ultravioleta , Cromatografía Liquida/instrumentación
14.
J Proteome Res ; 14(2): 977-85, 2015 Feb 06.
Artículo en Inglés | MEDLINE | ID: mdl-25485597

RESUMEN

Here, we explore applications of a LC system using disposable solid-phase extraction (SPE) cartridges and very short LC-MS/MS gradients that allows for rapid analyses in less than 10 min analysis time. The setup consists of an autosampler harboring two sets of 96 STAGE tips that function as precolumns and a short RP analytical column running 6.5 min gradients. This system combines efficiently with several proteomics workflows such as offline prefractionation methods, including 1D gel electrophoresis and strong-cation exchange chromatography. It also enables the analysis of interactomes obtained by affinity purification with an analysis time of approximately 1 h. In a typical shotgun proteomics experiment involving 36 SCX fractions of an AspN digested cell lysate, we detected over 3600 protein groups with an analysis time of less than 5.5 h. This innovative fast LC system reduces proteome analysis time while maintaining sufficient proteomic detail. This has particular relevance for the use of proteomics within a clinical environment, where large sample numbers and fast turnover times are essential.


Asunto(s)
Cromatografía Líquida de Alta Presión/métodos , Proteoma/análisis , Proteómica/métodos , Extracción en Fase Sólida/métodos , Espectrometría de Masas en Tándem/métodos , Cromatografía por Intercambio Iónico , Células HeLa , Humanos , Células Jurkat , Fragmentos de Péptidos/análisis , Fragmentos de Péptidos/química , Mapeo de Interacción de Proteínas , Proteoma/química
15.
J Am Chem Soc ; 137(34): 10922-10925, 2015 Sep 02.
Artículo en Inglés | MEDLINE | ID: mdl-26280087

RESUMEN

We report unexpected mass spectrometric observations of glycosylated human leukocyte antigen (HLA) class I-bound peptides. Complemented by molecular modeling, in vitro enzymatic assays, and oxonium ion patterns, we propose that the observed O-linked glycans carrying up to five monosaccharides are extended O-GlcNAc's rather than GalNAc-initiated O-glycans. A cytosolic O-GlcNAc modification is normally terminal and does not extend to produce a polysaccharide, but O-GlcNAc on an HLA peptide presents a special case because the loaded HLA class I complex traffics through the endoplasmic reticulum and Golgi apparatus on its way to the cell membrane and is hence exposed to glycosyltransferases. We also report for the first time natural HLA class I presentation of O- and N-linked glycopeptides derived from membrane proteins. HLA class I peptides with centrally located oligosaccharides have been shown to be immunogenic and may thus be important targets for immune surveillance.


Asunto(s)
Acetilglucosamina/química , Antígenos de Histocompatibilidad Clase I/química , Péptidos/química , Antígenos de Histocompatibilidad Clase I/metabolismo , Humanos , Modelos Moleculares , Péptidos/metabolismo
16.
Analyst ; 139(24): 6520-8, 2014 Dec 21.
Artículo en Inglés | MEDLINE | ID: mdl-25346955

RESUMEN

Ultra-high pressure liquid chromatography (UHPLC) systems combined with state-of-the-art mass spectrometers have pushed the limit of deep proteome sequencing to new heights making it possible to identify thousands of proteins in a single LC-MS experiment within a few hours. The recently released EASY-spray technology allows one to implement nano-UHPLC with straightforwardness. In this work we initially characterized the EASY-spray containing a 50 cm column containing <2 µm particles and found that the system allowed 3000 proteins to be identified in 90 minutes. We then asked the question whether a fast and sensitive online 2D SCX-RP UHPLC-MS/MS workflow could compete with 1D long gradient analyses, using total analysis time versus proteome coverage and sample usage as benchmark parameters. The 2D LC-MS strategy consisted of the EASY-spray system that had been augmented by the addition of an SCX column. The conversion was made facile since no additional valves were required and by the use of components containing viper fittings. We benchmarked the system using a human cell lysate digest (<10 µg). The 2D SCX-RP UHPLC-MS/MS workflow allowed the identification of almost 37,000 unique peptides and 6000 proteins in a total analysis time of ~7 hours. On the same system a 1D RP UHPLC-MS/MS workflow plateaued at only 20,000 peptides and 4400 unique proteins and required approx. 8 hours of analysis time. Furthermore, the 2D workflow could continue to increase the proteome coverage with longer analysis times, in fact with a 21 hour analysis we identified 56,600 unique peptides and >7500 proteins. We report, here, that with this fast online SCX-RP UHPLC-MS/MS workflow, the proteome coverage can be substantially extended without significantly compromising the analysis time and sample usage.


Asunto(s)
Cromatografía Líquida de Alta Presión/instrumentación , Proteoma/análisis , Proteómica/instrumentación , Diseño de Equipo , Células HEK293 , Humanos , Proteoma/aislamiento & purificación , Espectrometría de Masas en Tándem
17.
ScientificWorldJournal ; 2014: 384165, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-25180198

RESUMEN

The radiological differences between the urinary tract of Dicentrarchus labrax, Sparus aurata, Tinca tinca, and Cyprinus carpio are shown. In fresh water teleosts the urinary bladder is sigmoid and a short urethra leads to the urinary pore. Genital and anal pores are present. In Sparus aurata the urinary bladder has a globoid shape. In Dicentrarchus labrax the urinary bladder is smaller and elongate. In both marine teleosts a single urogenital pore is visible. Positive contrast was used to survey the urogenital system and evaluate shape and size of the bladder, urethra, ureter, and gonadal ducts. Results demonstrate the morphological variability of the urinary bladder and the craniodorsal entry of the ureters into the bladder. It is envisaged that this work will provide baseline information for further imaging studies for investigating the urogenital morphology and can be applied to identify disorders in fishes. Furthermore, the main interest of this study is that it demonstrates the morphological variability of the lower urinary system that exists between different species of fishes.


Asunto(s)
Cyprinidae/anatomía & histología , Perciformes/anatomía & histología , Animales , Sistema Urogenital/anatomía & histología , Urografía
18.
Angew Chem Int Ed Engl ; 53(36): 9660-4, 2014 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-25044833

RESUMEN

Protein phosphorylation is a widespread process forming the mechanistic basis of cellular signaling. Up to now, different aspects, for example, site-specificity, kinetics, role of co-factors, and structure-function relationships have been typically investigated by multiple techniques that are incompatible with one another. The approach introduced here maximizes the amount of information gained on protein (complex) phosphorylation while minimizing sample handling. Using high-resolution native mass spectrometry on intact protein (assemblies) up to 150 kDa we track the sequential incorporation of phosphate groups and map their localization by peptide LC-MS/MS. On two model systems, the protein kinase G and the interplay between Aurora kinase A and Bora, we demonstrate the simultaneous monitoring of various aspects of the phosphorylation process, namely the effect of different cofactors on PKG autophosphorylation and the interaction of AurA and Bora as both an enzyme-substrate pair and physical binding partners.


Asunto(s)
Fosforilación/fisiología , Proteínas/metabolismo , Animales , Aurora Quinasa A/metabolismo , Proteínas Quinasas Dependientes de GMP Cíclico/metabolismo , Humanos , Cinética , Espectrometría de Masas , Especificidad por Sustrato
19.
Infect Dis Rep ; 16(1): 128-141, 2024 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-38391588

RESUMEN

As respiratory syncytial virus (RSV) vaccine distribution gains traction in Europe and Italy, healthcare workers (HCWs) can strategize about vaccine promotion to increase uptake among patients at risk of RSV consequences, such cardiac patients. This cross-sectional survey investigated the knowledge about and attitude towards RSV and RSV vaccines, and the intention to recommend vaccination within a cardiological hospital in Italy. To explore factors associated with the outcomes of interest, multivariate logistic regression analyses were conducted. Of 197 invited HCWs, 78.2% returned the survey. The knowledge about market authorisation for new RSV vaccines for older adults (present in 46.9% of respondents) was significantly associated with the HCWs' age, education, and previous update on vaccinations. HCWs with a higher educational level and those with a positive attitude towards RSV vaccines safety reported a higher attitude towards the importance of vaccinating people at risk. The willingness of recommending RSV vaccination to patients (70.5% of respondents) was more likely in HCWs who were knowledgeable about market authorisation for RSV vaccines and in physicians. This tempestive research sheds light on current factors influencing the strategies of cardiac HCWs regarding RSV vaccination. The results suggest the need for training events on the protective role of RSV vaccination in cardiac patients.

20.
J Proteome Res ; 12(5): 2214-24, 2013 May 03.
Artículo en Inglés | MEDLINE | ID: mdl-23510141

RESUMEN

In order to understand cellular signaling, a clear understanding of kinase-substrate relationships is essential. Some of these relationships are defined by consensus recognition motifs present in substrates making them amendable for phosphorylation by designated kinases. Here, we explore a method that is based on two sequential steps of strong cation exchange chromatography combined with differential stable isotope labeling, to define kinase consensus motifs with high accuracy. We demonstrate the value of our method by evaluating the motifs of two very distinct kinases: cAMP regulated protein kinase A (PKA) and human monopolar spindle 1 (Mps1) kinase, also known as TTK. PKA is a well-studied basophilic kinase with a relatively well-defined motif and numerous known substrates in vitro and in vivo. Mps1, a kinase involved in chromosome segregation, has been less well characterized. Its substrate specificity is unclear and here we show that Mps1 is an acidophilic kinase with a striking tendency for phosphorylation of threonines. The final outcomes of our work are high-definition kinase consensus motifs for PKA and Mps1. Our generic method, which makes use of proteolytic cell lysates as a source for peptide-substrate libraries, can be implemented for any kinase present in the kinome.


Asunto(s)
Proteínas de Ciclo Celular/metabolismo , Proteínas Quinasas Dependientes de AMP Cíclico/metabolismo , Pruebas de Enzimas , Proteínas Serina-Treonina Quinasas/metabolismo , Proteínas Tirosina Quinasas/metabolismo , Secuencias de Aminoácidos , Sitios de Unión , Proteínas de Ciclo Celular/química , Cromatografía por Intercambio Iónico , Secuencia de Consenso , Proteínas Quinasas Dependientes de AMP Cíclico/química , Células HEK293 , Células HeLa , Humanos , Marcaje Isotópico/métodos , Metilación , Datos de Secuencia Molecular , Fosfoproteínas/química , Fosfoproteínas/metabolismo , Fosforilación , Procesamiento Proteico-Postraduccional , Proteínas Serina-Treonina Quinasas/química , Proteínas Tirosina Quinasas/química , Proteómica , Especificidad por Sustrato , Espectrometría de Masas en Tándem
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