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1.
Mol Cell Proteomics ; 21(7): 100252, 2022 07.
Artículo en Inglés | MEDLINE | ID: mdl-35636728

RESUMEN

Changes in the abundance of individual proteins in the proteome can be elicited by modulation of protein synthesis (the rate of input of newly synthesized proteins into the protein pool) or degradation (the rate of removal of protein molecules from the pool). A full understanding of proteome changes therefore requires a definition of the roles of these two processes in proteostasis, collectively known as protein turnover. Because protein turnover occurs even in the absence of overt changes in pool abundance, turnover measurements necessitate monitoring the flux of stable isotope-labeled precursors through the protein pool such as labeled amino acids or metabolic precursors such as ammonium chloride or heavy water. In cells in culture, the ability to manipulate precursor pools by rapid medium changes is simple, but for more complex systems such as intact animals, the approach becomes more convoluted. Individual methods bring specific complications, and the suitability of different methods has not been comprehensively explored. In this study, we compare the turnover rates of proteins across four mouse tissues, obtained from the same inbred mouse strain maintained under identical husbandry conditions, measured using either [13C6]lysine or [2H2]O as the labeling precursor. We show that for long-lived proteins, the two approaches yield essentially identical measures of the first-order rate constant for degradation. For short-lived proteins, there is a need to compensate for the slower equilibration of lysine through the precursor pools. We evaluate different approaches to provide that compensation. We conclude that both labels are suitable, but careful determination of precursor enrichment kinetics in amino acid labeling is critical and has a considerable influence on the numerical values of the derived protein turnover rates.


Asunto(s)
Lisina , Proteoma , Aminoácidos/metabolismo , Animales , Marcaje Isotópico/métodos , Lisina/metabolismo , Ratones , Proteolisis , Proteoma/metabolismo
2.
Int J Mol Sci ; 24(23)2023 Nov 28.
Artículo en Inglés | MEDLINE | ID: mdl-38069171

RESUMEN

Micro-environmental factors, including stromal and immune cells, cytokines, and circulating hormones are well recognized to determine cancer progression. Melanoma cell growth was recently shown to be suppressed by cholecystokinin/gastrin (CCK) receptor antagonists, and our preliminary data suggested that melanoma patients with Helicobacter gastritis (which is associated with elevated serum gastrin) might have an increased risk of cancer progression. Therefore, in the present study, we examined how gastrin may act on melanoma cells. In 89 melanoma patients, we found a statistically significant association between circulating gastrin concentrations and melanoma thickness and metastasis, which are known risk factors of melanoma progression and prognosis. Immunocytochemistry using a validated antibody confirmed weak to moderate CCK2R expression in both primary malignant melanoma cells and the melanoma cell lines SK-MEL-2 and G361. Furthermore, among the 219 tumors in the Skin Cutaneous Melanoma TCGA Pan-Cancer dataset showing gastrin receptor (CCKBR) expression, significantly higher CCKBR mRNA levels were linked to stage III-IV than stage I-II melanomas. In both cell lines, gastrin increased intracellular calcium levels and stimulated cell migration and invasion through mechanisms inhibited by a CCK2 receptor antagonist. Proteomic studies identified increased MMP-2 and reduced TIMP-3 levels in response to gastrin that were likely to contribute to the increased migration of both cell lines. However, the effects of gastrin on tumor cell invasion were relatively weak in the presence of the extracellular matrix. Nevertheless, dermal fibroblasts/myofibroblasts, known also to express CCK2R, increased gastrin-induced cancer cell invasion. Our data suggest that in a subset of melanoma patients, an elevated serum gastrin concentration is a risk factor for melanoma tumor progression, and that gastrin may act on both melanoma and adjacent stromal cells through CCK2 receptors to promote mechanisms of tumor migration and invasion.


Asunto(s)
Melanoma , Neoplasias Cutáneas , Humanos , Melanoma/metabolismo , Gastrinas/farmacología , Gastrinas/metabolismo , Proteómica , Receptores de Colecistoquinina , Receptor de Colecistoquinina B/genética , Receptor de Colecistoquinina B/metabolismo
3.
Scand J Med Sci Sports ; 31(11): 2033-2043, 2021 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-34271594

RESUMEN

Injuries to the intra-articular anterior cruciate ligament (ACL) and the extra-articular medial collateral ligament (MCL) result in significant knee joint instability, pain, and immobility. Moderate endurance-type exercise can increase ligament strength but little is known on the effect of short-term regular bouts of high-intensity exercise on the extracellular matrix (ECM) structure of knee ligaments. Therefore, this study aimed to identify the effect of short-term regular bouts high exercise on the proteome of the rat ACL and MCL using mass spectrometry. Sprague-Dawley male rats (n = 6) were split into control and exercise groups, and subjected to high-intensity training for four 4 weeks followed by proteomic analyses of the ACL and MCL. Knee joint health status was assessed using OARSI and a validated histological scoring system. Histopathological analyses demonstrated no significant changes in either in cruciate, collateral ligaments, or cartilage between the control and exercised knee joints. However, significant proteins were found to be more abundant in the exercised ACL compared to ACL control group but not between the exercised MCL and control MCL groups. The significant abundant proteins in ACL exercise groups were mostly cytoskeletal, ribosomal and enzymes with several abundant matrisomal proteins such as collagen proteins and proteoglycans being found in this group. In conclusion, our results indicate that short-term regular bouts of high-intensity exercise have an impact on the intra-articular ACL but not extra-articular MCL ECM protein expression.


Asunto(s)
Articulación de la Rodilla/metabolismo , Ligamentos Articulares/metabolismo , Condicionamiento Físico Animal/métodos , Proteómica/métodos , Animales , Masculino , Ratas , Ratas Sprague-Dawley
4.
Cell Microbiol ; 21(1): e12969, 2019 01.
Artículo en Inglés | MEDLINE | ID: mdl-30370674

RESUMEN

The protozoan parasites Theileria annulata and Theileria parva are unique amongst intracellular eukaryotic pathogens as they induce a transformation-like phenotype in their bovine host cell. T. annulata causes tropical theileriosis, which is frequently fatal, with infected leukocytes becoming metastatic and forming foci in multiple organs resulting in destruction of the lymphoid system. Exosomes, a subset of extracellular vesicles (EV), are critical in metastatic progression in many cancers. Here, we characterised the cargo of EV from a control bovine lymphosarcoma cell line (BL20) and BL20 infected with T. annulata (TBL20) by comparative mass spectrometry and microRNA (miRNA) profiling (data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively). Ingenuity pathway analysis that many infection-associated proteins essential to migration and extracellular matrix digestion were upregulated in EV from TBL20 cells compared with BL20 controls. An altered repertoire of host miRNA, many with known roles in tumour and/or infection biology, was also observed. Focusing on the tumour suppressor miRNA, bta-miR-181a and bta-miR-181b, we identified putative messenger RNA targets and confirmed the interaction of bta-miR181a with ICAM-1. We propose that EV and their miRNA cargo play an important role in the manipulation of the host cell phenotype and the pathobiology of Theileria infection.


Asunto(s)
Vesículas Extracelulares/química , Vesículas Extracelulares/metabolismo , Leucocitos/metabolismo , Leucocitos/parasitología , MicroARNs/análisis , Proteínas/análisis , Theileria annulata/crecimiento & desarrollo , Animales , Bovinos , Línea Celular
5.
Mol Cell Proteomics ; 17(9): 1837-1849, 2018 09.
Artículo en Inglés | MEDLINE | ID: mdl-29915148

RESUMEN

Analysis of secretomes critically underpins the capacity to understand the mechanisms determining interactions between cells and between cells and their environment. In the context of cancer cell micro-environments, the relevant interactions are recognized to be an important determinant of tumor progression. Global proteomic analyses of secretomes are often performed at a single time point and frequently identify both classical secreted proteins (possessing an N-terminal signal sequence), as well as many intracellular proteins, the release of which is of uncertain biological significance. Here, we describe a mass spectrometry-based method for stable isotope dynamic labeling of secretomes (SIDLS) that, by dynamic SILAC, discriminates the secretion kinetics of classical secretory proteins and intracellular proteins released from cancer and stromal cells in culture. SIDLS is a robust classifier of the different cellular origins of proteins within the secretome and should be broadly applicable to nonproliferating cells and cells grown in short term culture.


Asunto(s)
Marcaje Isotópico/métodos , Neoplasias/metabolismo , Proteoma/metabolismo , Línea Celular Tumoral , Ontología de Genes , Humanos , Espacio Intracelular/metabolismo , Cinética , Reproducibilidad de los Resultados , Transducción de Señal , Células del Estroma/metabolismo , Factores de Tiempo
6.
J Proteome Res ; 18(3): 1328-1339, 2019 03 01.
Artículo en Inglés | MEDLINE | ID: mdl-30667229

RESUMEN

Ligaments are prone to injury and degeneration in humans and animals, however the healing potential of ligament is poor and current treatment options ineffective. Stem cell-based therapies hold potential for treatment of ligament injuries. This study aimed to characterize a ligament progenitor cell (LPC) population and to identify specific niche components which could promote the survival and function of LPCs. LPCs were isolated from canine cranial cruciate ligament and characterized for clonogenicity, multipotency and marker expression. The extracellular matrix (ECM) composition was characterized by the novel application of a metabolic labeling and mass spectrometry technique. LPCs demonstrated clonogenicity, multipotency, and stem cell marker expression. A number of different collagens, glycoproteins, and proteoglycans were identified in the LPC niche using proteomics. Metabolic labeling of cells demonstrated unique turnover profiles for distinct ECM protein groups, indicating the importance of certain niche components for LPC survival and function. The newly synthesized niche components identified in this study could be exploited to aid identification of LPCs and to promote their survival and function for potential ligament repair strategies.


Asunto(s)
Ligamento Cruzado Anterior/citología , Proteínas de la Matriz Extracelular/genética , Nicho de Células Madre/genética , Células Madre/citología , Animales , Ligamento Cruzado Anterior/trasplante , Linaje de la Célula/genética , Colágeno/genética , Colágeno/metabolismo , Ensayo de Unidades Formadoras de Colonias , Perros , Matriz Extracelular/genética , Proteínas de la Matriz Extracelular/aislamiento & purificación , Proteínas de la Matriz Extracelular/metabolismo , Regulación del Desarrollo de la Expresión Génica/genética , Humanos , Hígado/metabolismo , Proteoglicanos/genética , Células Madre/metabolismo
7.
J Neurosci Res ; 97(11): 1378-1392, 2019 11.
Artículo en Inglés | MEDLINE | ID: mdl-31090233

RESUMEN

Antiepileptogenic agents that prevent the development of epilepsy following a brain insult remain the holy grail of epilepsy therapeutics. We have employed a label-free proteomic approach that allows quantification of large numbers of brain-expressed proteins in a single analysis in the mouse (male C57BL/6J) kainate (KA) model of epileptogenesis. In addition, we have incorporated two putative antiepileptogenic drugs, postsynaptic density protein-95 blocking peptide (PSD95BP or Tat-NR2B9c) and a highly selective inducible nitric oxide synthase inhibitor, 1400W, to give an insight into how such agents might ameliorate epileptogenesis. The test drugs were administered after the induction of status epilepticus (SE) and the animals were euthanized at 7 days, their hippocampi removed, and subjected to LC-MS/MS analysis. A total of 2,579 proteins were identified; their normalized abundance was compared between treatment groups using ANOVA, with correction for multiple testing by false discovery rate. Significantly altered proteins were subjected to gene ontology and KEGG pathway enrichment analyses. KA-induced SE was most robustly associated with an alteration in the abundance of proteins involved in neuroinflammation, including heat shock protein beta-1 (HSP27), glial fibrillary acidic protein, and CD44 antigen. Treatment with PSD95BP or 1400W moderated the abundance of several of these proteins plus that of secretogranin and Src substrate cortactin. Pathway analysis identified the glutamatergic synapse as a key target for both drugs. Our observations require validation in a larger-scale investigation, with candidate proteins explored in more detail. Nevertheless, this study has identified several mechanisms by which epilepsy might develop and several targets for novel drug development. OPEN PRACTICES: This article has been awarded Open Data. All materials and data are publicly accessible as supporting information. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki.


Asunto(s)
Amidinas/administración & dosificación , Anticonvulsivantes/administración & dosificación , Bencilaminas/administración & dosificación , Epilepsia/metabolismo , Hipocampo/efectos de los fármacos , Hipocampo/metabolismo , Óxido Nítrico Sintasa de Tipo II/antagonistas & inhibidores , Péptidos/administración & dosificación , Animales , Epilepsia/inducido químicamente , Ácido Kaínico/administración & dosificación , Masculino , Ratones Endogámicos C57BL , Proteómica , Estado Epiléptico/inducido químicamente , Estado Epiléptico/metabolismo
8.
J Biol Chem ; 292(20): 8381-8389, 2017 05 19.
Artículo en Inglés | MEDLINE | ID: mdl-28364041

RESUMEN

The galactoside-binding protein galectin-3 is increasingly recognized as an important player in cancer development, progression, and metastasis via its interactions with various galactoside-terminated glycans. We have shown previously that circulating galectin-3, which is increased up to 30-fold in cancer patients, promotes blood-borne metastasis in an animal cancer model. This effect is partly attributable to the interaction of galectin-3 with unknown receptor(s) on vascular endothelial cells and causes endothelial secretion of several metastasis-promoting cytokines. Here we sought to identify the galectin-3-binding molecule(s) on the endothelial cell surface responsible for the galectin-3-mediated cytokine secretion. Using two different galectin-3 affinity purification processes, we extracted four cell membrane glycoproteins, CD146/melanoma cell adhesion molecule (MCAM)/MUC18, CD31/platelet endothelial cell adhesion molecule-1 (PECAM-1), CD144/VE-cadherin, and CD106/Endoglin, from vascular endothelial cells. CD146 was the major galectin-3-binding ligand and strongly co-localized with galectin-3 on endothelial cell surfaces treated with exogenous galectin-3. Moreover, galectin-3 bound to N-linked glycans on CD146 and induced CD146 dimerization and subsequent activation of AKT signaling. siRNA-mediated suppression of CD146 expression completely abolished the galectin-3-induced secretion of IL-6 and G-CSF cytokines from the endothelial cells. Thus, CD146/MCAM is the functional galectin-3-binding ligand on endothelial cell surfaces responsible for galectin-3-induced secretion of metastasis-promoting cytokines. We conclude that CD146/MCAM interactions with circulating galectin-3 may have an important influence on cancer progression and metastasis.


Asunto(s)
Galectina 3/metabolismo , Factor Estimulante de Colonias de Granulocitos/metabolismo , Células Endoteliales de la Vena Umbilical Humana/metabolismo , Interleucina-6/metabolismo , Multimerización de Proteína , Antígenos CD/genética , Antígenos CD/metabolismo , Proteínas Sanguíneas , Antígeno CD146/genética , Antígeno CD146/metabolismo , Cadherinas/genética , Cadherinas/metabolismo , Galectina 3/genética , Galectinas , Factor Estimulante de Colonias de Granulocitos/genética , Células Endoteliales de la Vena Umbilical Humana/patología , Humanos , Interleucina-6/genética , Metástasis de la Neoplasia , Neoplasias/genética , Neoplasias/metabolismo , Neoplasias/patología , Molécula-1 de Adhesión Celular Endotelial de Plaqueta/genética , Molécula-1 de Adhesión Celular Endotelial de Plaqueta/metabolismo
9.
Acta Neuropathol ; 135(5): 757-777, 2018 05.
Artículo en Inglés | MEDLINE | ID: mdl-29541918

RESUMEN

Adamantinomatous craniopharyngiomas (ACPs) are clinically challenging tumours, the majority of which have activating mutations in CTNNB1. They are histologically complex, showing cystic and solid components, the latter comprised of different morphological cell types (e.g. ß-catenin-accumulating cluster cells and palisading epithelium), surrounded by a florid glial reaction with immune cells. Here, we have carried out RNA sequencing on 18 ACP samples and integrated these data with an existing ACP transcriptomic dataset. No studies so far have examined the patterns of gene expression within the different cellular compartments of the tumour. To achieve this goal, we have combined laser capture microdissection with computational analyses to reveal groups of genes that are associated with either epithelial tumour cells (clusters and palisading epithelium), glial tissue or immune infiltrate. We use these human ACP molecular signatures and RNA-Seq data from two ACP mouse models to reveal that cell clusters are molecularly analogous to the enamel knot, a critical signalling centre controlling normal tooth morphogenesis. Supporting this finding, we show that human cluster cells express high levels of several members of the FGF, TGFB and BMP families of secreted factors, which signal to neighbouring cells as evidenced by immunostaining against the phosphorylated proteins pERK1/2, pSMAD3 and pSMAD1/5/9 in both human and mouse ACP. We reveal that inhibiting the MAPK/ERK pathway with trametinib, a clinically approved MEK inhibitor, results in reduced proliferation and increased apoptosis in explant cultures of human and mouse ACP. Finally, we analyse a prominent molecular signature in the glial reactive tissue to characterise the inflammatory microenvironment and uncover the activation of inflammasomes in human ACP. We validate these results by immunostaining against immune cell markers, cytokine ELISA and proteome analysis in both solid tumour and cystic fluid from ACP patients. Our data support a new molecular paradigm for understanding ACP tumorigenesis as an aberrant mimic of natural tooth development and opens new therapeutic opportunities by revealing the activation of the MAPK/ERK and inflammasome pathways in human ACP.


Asunto(s)
Craneofaringioma/metabolismo , Sistema de Señalización de MAP Quinasas , Neoplasias Hipofisarias/metabolismo , Transcriptoma , Microambiente Tumoral/fisiología , Animales , Biología Computacional , Craneofaringioma/patología , Craneofaringioma/terapia , Citocinas/metabolismo , Modelos Animales de Enfermedad , Humanos , Inflamación/metabolismo , Inflamación/terapia , Captura por Microdisección con Láser , Ratones , Neuroglía/metabolismo , Odontogénesis/fisiología , Hipófisis/embriología , Hipófisis/patología , Neoplasias Hipofisarias/patología , Neoplasias Hipofisarias/terapia , Análisis de Secuencia de ARN , Técnicas de Cultivo de Tejidos
10.
Mol Cell Proteomics ; 15(4): 1204-19, 2016 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-26839000

RESUMEN

Understanding the role of protein turnover in the maintenance of proteostasis requires accurate measurements of the rates of replacement of proteins in complex systems, such as intact animals. Moreover, any investigation of allometric scaling of protein turnover is likely to include species for which fully annotated proteomes are not available. We have used dietary administration of stable isotope labeled lysine to assess protein turnover rates for proteins from four tissues in the bank vole,Myodes glareolus The annotated genome for this species is not available, so protein identification was attained through cross-species matching to the mouse. For proteins for which confident identifications were derived, the pattern of lysine incorporation over 40 days was used to define the rate of synthesis of individual proteins in the four tissues. The data were heavily filtered to retain a very high quality dataset of turnover rates for 1088 proteins. Comparative analysis of the four tissues revealed different median rates of degradation (kidney: 0.099 days(-1); liver 0.136 days(-1); heart, 0.054 days(-1), and skeletal muscle, 0.035 days(-1)). These data were compared with protein degradation rates from other studies on intact animals or from cells in culture and indicate that both cell type and analytical methodology may contribute to variance in turnover data between different studies. These differences were not only due to tissue-specific proteins but were reflected in gene products common to all tissues. All data are available via ProteomeXchange with identifier PXD002054.


Asunto(s)
Arvicolinae/metabolismo , Riñón/metabolismo , Hígado/metabolismo , Lisina/farmacocinética , Músculo Esquelético/metabolismo , Miocardio/metabolismo , Proteoma/metabolismo , Animales , Marcaje Isotópico , Cinética , Lisina/administración & dosificación , Ratones , Especificidad de Órganos , Proteolisis , Proteómica/métodos , Distribución Tisular
11.
Afr J AIDS Res ; 17(2): 175-182, 2018 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-30003846

RESUMEN

This article investigates an assertion by faith-based organisations (FBO) that spirituality is the defining feature of their HIV and AIDS interventions. It is based on interviews with 24 people working on the issue of HIV and AIDS in churches or church organisations in Johannesburg, Rustenburg, Pretoria, Durban, Pietermaritzburg, and Cape Town. The article critically assesses the perceived difference between faith-based responses to HIV and AIDS and secular responses, including government programmes, in relation to the research literature on spirituality. After introducing the article, the argument begins with an exploration of the literature on churches and HIV and AIDS, outlining a gap which the article seeks to fill. The article then discusses the methods used for interviewing and analysing interview material. This is followed by religious leaders' own comments on how faith-based responses to HIV and AIDS differ from secular responses. The article concludes with a discussion which brings the literature to bear on the interview excerpts and then outlines the implications of decreased international funding for the HIV and AIDS programmes operated by the Anglican and Catholic churches, for example, a likely reduction in the accompaniment and monitoring of those who are HIV-positive.


Asunto(s)
Síndrome de Inmunodeficiencia Adquirida/psicología , Síndrome de Inmunodeficiencia Adquirida/terapia , Adaptación Psicológica , Religión y Medicina , Recolección de Datos , VIH , Humanos , Masculino , Sudáfrica
12.
Med Teach ; 38(2): 141-9, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-26398270

RESUMEN

Medical education fellowship programs (MEFPs) are a form of faculty development contributing to an organization's educational mission and participants' career development. Building an MEFP requires a systematic design, implementation, and evaluation approach which aligns institutional and individual faculty goals. Implementing an MEFP requires a team of committed individuals who provide expertise, guidance, and mentoring. Qualified MEFP directors should utilize instructional methods that promote individual and institutional short and long term growth. Directors must balance the use of traditional design, implementation, and evaluation methodologies with advancing trends that may support or threaten the acceptability and sustainability of the program. Drawing on the expertise of 28 MEFP directors, we provide twelve tips as a guide to those implementing, sustaining, and/or growing a successful MEFP whose value is demonstrated by its impacts on participants, learners, patients, teaching faculty, institutions, the greater medical education community, and the population's health.


Asunto(s)
Educación Médica , Becas/normas , Desarrollo de Programa/métodos , Docentes Médicos , Guías como Asunto , Humanos , Desarrollo de Personal
13.
WMJ ; 115(2): 81-5, 2016 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-27197341

RESUMEN

INTRODUCTION: Patient care transitions are prevalent in health care, and faulty transition-related communications are associated with 80% of serious medical errors. While medical student curricula on care transitions are increasing, there are limited evaluation reports and little guidance on primary care transition training. METHODS: The Medical College of Wisconsin initiated an annual 2-hour patient care transition intersession for third-year medical students. The intersession used a critical incident report, where students wrote about a recent, de-identified patient transition they witnessed that evoked in them "a strong emotional reaction." Next, intersession training included a novel, structured communication handoff mnemonic. At the intersession conclusion, students wrote what they would do differently if their critical incident transition occured in the future. Evaluations (2010-2014) consisted of students' post-session reactions and learning. Authors completed a detailed, qualitative analysis of students' critical incident reports from the 2010 intersession. RESULTS: Students reacted positively to all intersession elements, especially clinician-led, small-group discussions. Student reports revealed that over 90% of their critical incident evoked negative emotional reactions (eg, frustrated, disappointed, helpless). Post-intersession, 86% of students reported intentions to adopt new strategies to improve future care transitions, and 38% referenced components of the learned mnemonic. CONCLUSION: Medical students reacted positively to this intersession, especially small-group discussions. Students revealed mostly negative emotions from their critical incident on patient handoffs, but they gained effective strategies for future handoff communications. Authors recommend continued use of the handoff mnemonic, with greater attention to training environments that emphasize patient and learner safety.


Asunto(s)
Continuidad de la Atención al Paciente/normas , Educación de Pregrado en Medicina/organización & administración , Errores Médicos/prevención & control , Seguridad del Paciente , Adulto , Comunicación , Curriculum , Evaluación Educacional , Femenino , Humanos , Masculino , Gestión de Riesgos , Wisconsin , Escritura
14.
Proteomics ; 15(18): 3152-62, 2015 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-26037908

RESUMEN

The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML-based format, capable of representing data about two-dimensional features from LC-MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java-based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)-level quantification values from peptide-level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC-MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in-built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq-lib/.


Asunto(s)
Sistemas de Administración de Bases de Datos , Bases de Datos de Proteínas/normas , Proteómica/métodos , Proteómica/normas , Programas Informáticos
15.
Acad Psychiatry ; 39(3): 275-9, 2015 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-25037248

RESUMEN

OBJECTIVE: The aim of this study was to determine if communication skills differ for medical students entering person or technique-oriented specialties. METHODS: Communication ratings by clerkship preceptors on an institutionally required end of clerkship medical student performance evaluation (SPE) form were compiled for 2011/2012 academic year (Class of 2013). M3 clerkships and the Class of 2013 match appointments were categorized as person or technique-oriented clerkships/specialties. Mean differences in SPE communication scores were determined by analyses of variance (ANOVA) and independent t tests. Score associations were determined by Pearson correlations. Inter-item reliability was reported with Cronbach alpha. RESULTS: The Class of 2013 match appointments were as follows: person-oriented (N = 91) and technique-oriented (N = 91) residency specialties. There was no significant difference in mean communication scores for medical students who entered person-oriented (mean 7.8, SD 0.4) versus technique-oriented (mean 7.9, SD 0.4) specialties (p = 0.258) or for person-oriented clerkship (mean 7.8, SD 0.4) versus technique-oriented clerkship (mean 7.9, SD 0.6) ratings for medical students who matched into person-oriented specialties (p = 0.124). Medical students who matched into technique-oriented specialties (mean 8.1, SD 0.5) received significantly higher (p = 0.001) communication ratings as compared with those matching into person-oriented specialties (mean 7.8, SD 0.5) from technique-oriented clerkships. CONCLUSIONS: Communication with patients and families is a complex constellation of specific abilities that appear to be influenced by the rater's specialty. Further study is needed to determine if technique-oriented specialties communication skill rating criteria differ from those used by raters from person-oriented specialties.


Asunto(s)
Selección de Profesión , Comunicación , Relaciones Profesional-Paciente , Estudiantes de Medicina/psicología , Adulto , Prácticas Clínicas , Evaluación del Rendimiento de Empleados , Femenino , Humanos , Masculino , Adulto Joven
16.
Carcinogenesis ; 35(8): 1798-806, 2014 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-24710625

RESUMEN

Stromal cells influence cancer progression. Myofibroblasts are an important stromal cell type, which influence the tumour microenvironment by release of extracellular matrix (ECM) proteins, proteases, cytokines and chemokines. The mechanisms of secretion are poorly understood. Here, we describe the secretion of marker proteins in gastric cancer and control myofibroblasts in response to insulin-like growth factor (IGF) stimulation and, using functional genomic approaches, we identify proteins influencing the secretory response. IGF rapidly increased myofibroblast secretion of an ECM protein, TGFßig-h3. The secretory response was not blocked by inhibition of protein synthesis and was partially mediated by increased intracellular calcium (Ca(2+)). The capacity for evoked secretion was associated with the presence of dense-core secretory vesicles and was lost in cells from patients with advanced gastric cancer. In cells responding to IGF-II, the expression of neuroendocrine marker proteins, including secretogranin-II and proenkephalin, was identified by gene array and LC-MS/MS respectively, and verified experimentally. The expression of proenkephalin was decreased in cancers from patients with advanced disease. Inhibition of secretogranin-II expression decreased the secretory response to IGF, and its over-expression recovered the secretory response consistent with a role in secretory vesicle biogenesis. We conclude that normal and some gastric cancer myofibroblasts have a neuroendocrine-like phenotype characterized by Ca(2+)-dependent regulated secretion, dense-core secretory vesicles and expression of neuroendocrine marker proteins; loss of the phenotype is associated with advanced cancer. A failure to regulate myofibroblast protein secretion may contribute to cancer progression.


Asunto(s)
Factor II del Crecimiento Similar a la Insulina/metabolismo , Miofibroblastos/patología , Sistemas Neurosecretores/patología , Secretogranina II/metabolismo , Neoplasias Gástricas/patología , Western Blotting , Estudios de Casos y Controles , Células Cultivadas , Progresión de la Enfermedad , Exocitosis/fisiología , Mucosa Gástrica/metabolismo , Humanos , Técnicas para Inmunoenzimas , Marcaje Isotópico , Miofibroblastos/metabolismo , Sistemas Neurosecretores/metabolismo , Fenotipo , ARN Interferente Pequeño/genética , Secretogranina II/antagonistas & inhibidores , Secretogranina II/genética , Neoplasias Gástricas/metabolismo , Espectrometría de Masas en Tándem
17.
Biochem Soc Trans ; 42(4): 837-45, 2014 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-25109966

RESUMEN

The high degree of protein sequence similarity in the MUPs (major urinary proteins) poses considerable challenges for their individual differentiation, analysis and quantification. In the present review, we discuss MS approaches for MUP quantification, at either the protein or the peptide level. In particular, we describe an approach to multiplexed quantification based on the design and synthesis of novel proteins (QconCATs) that are concatamers of quantification standards, providing a simple route to the generation of a set of stable-isotope-labelled peptide standards. The MUPs pose a particular challenge to QconCAT design, because of their sequence similarity and the limited number of peptides that can be used to construct the standards. Such difficulties can be overcome by careful attention to the analytical workflow.


Asunto(s)
Espectrometría de Masas/métodos , Proteínas/análisis , Proteínas/metabolismo , Animales , Marcaje Isotópico , Proteómica
18.
Mol Cell Proteomics ; 10(12): M111.007633, 2011 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-21931151

RESUMEN

The availability of label-free data derived from yeast cells (based on the summed intensity of the three strongest, isoform-specific peptides) permitted a preliminary assessment of protein abundances for glycolytic proteins. Following this analysis, we demonstrate successful application of the QconCAT technology, which uses recombinant DNA techniques to generate artificial concatamers of large numbers of internal standard peptides, to the quantification of enzymes of the glycolysis pathway in the yeast Saccharomyces cerevisiae. A QconCAT of 88 kDa (59 tryptic peptides) corresponding to 27 isoenzymes was designed and built to encode two or three analyte peptides per protein, and after stable isotope labeling of the standard in vivo, protein levels were determined by LC-MS, using ultra high performance liquid chromatography-coupled mass spectrometry. We were able to determine absolute protein concentrations between 14,000 and 10 million molecules/cell. Issues such as efficiency of extraction and completeness of proteolysis are addressed, as well as generic factors such as optimal quantotypic peptide selection and expression. In addition, the same proteins were quantified by intensity-based label-free analysis, and both sets of data were compared with other quantification methods.


Asunto(s)
Glucólisis , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/enzimología , Secuencia de Aminoácidos , Expresión Génica , Isoenzimas/química , Isoenzimas/genética , Isoenzimas/metabolismo , Datos de Secuencia Molecular , Fragmentos de Péptidos/química , Fragmentos de Péptidos/normas , Procesamiento Proteico-Postraduccional , Proteolisis , Proteómica , Estándares de Referencia , Reproducibilidad de los Resultados , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genética , Espectrometría de Masas en Tándem/normas
19.
Vet Dermatol ; 24(6): 598-601, e143-4, 2013 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-24118463

RESUMEN

BACKGROUND: Prednisone doses of up to 8 mg/kg/day have been used to treat feline pemphigus foliaceus (PF). Oral prednisolone has more favourable pharmacokinetics in cats than prednisone; therefore, lower doses of prednisolone may be effective in treating feline PF. HYPOTHESIS/OBJECTIVES: To assess the dose of prednisolone required to induce and maintain remission of PF in cats. ANIMALS: Thirty-seven client-owned cats with a diagnosis of PF treated with prednisolone monotherapy for induction of remission. METHODS: A retrospective analysis of records of a veterinary dermatology referral practice between the years of 1995 and 2013 was carried out. History, clinical signs, cytological and/or histopathological findings, lack of response to antimicrobials, absence of fungal hyphae on periodic acid Schiff staining and/or negative fungal culture and positive response to immunosuppressive therapy were used to confirm the diagnosis. Cats were included in the study if prednisolone was used as the monotherapy induction protocol. RESULTS: Complete remission was achieved within 8 weeks in 97% of cats with a median induction dose of 2 mg/kg prednisolone daily. In cats requiring ongoing treatment, 67% were maintained in remission with prednisolone monotherapy. The median maintenance dose was 1.2 mg/kg/week. In 14% of cats, medication was eventually discontinued. CONCLUSIONS AND CLINICAL IMPORTANCE: Daily prednisolone at 2 mg/kg is an effective dose for inducing remission of PF in cats. Adverse effects were uncommon with this dose. In a small population, permanent remission may be induced. Secondary bacterial overgrowth and exudate in claw folds resolved in all cases with immunosuppressive therapy; therefore, antimicrobial therapy may be unnecessary.


Asunto(s)
Enfermedades de los Gatos/tratamiento farmacológico , Glucocorticoides/uso terapéutico , Pénfigo/veterinaria , Prednisolona/uso terapéutico , Animales , Gatos , Glucocorticoides/administración & dosificación , Pénfigo/tratamiento farmacológico , Prednisolona/administración & dosificación , Estudios Retrospectivos
20.
Vet Dermatol ; 24(5): 552-e132, 2013 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-23931071

RESUMEN

BACKGROUND: Pyoderma gangrenosum (PG) is a rare disease, which, to the best of the authors' knowledge, has been the subject of only one case report in the peer-reviewed veterinary literature. HYPOTHESIS/OBJECTIVES: To describe the history, clinical signs, diagnostic findings and treatment outcome in two cases of canine PG. ANIMALS: Two client-owned dogs presented to a private veterinary referral practice between 2008 and 2010 who received a diagnosis of PG by specialist veterinary dermatologists. METHODS: Medical records were analysed to retrieve relevant information. RESULTS: Both dogs were treated with prednisolone; this was combined with ciclosporin in case 1 and azathioprine in case 2. Case 2 had a more complete response of lesions to treatment and a longer survival time after diagnosis (763 days) than case 1 (81 days). CONCLUSIONS AND CLINICAL IMPORTANCE: Pyoderma gangrenosum is a rare disease distinguished by rapid progression of painful, necrolytic, cutaneous ulcers with irregular, violaceous undermined borders. Azathioprine with glucocorticoids may lead to a better outcome than ciclosporin and glucocorticoids (currently the first-line treatment in humans and the only reported treatment in dogs).


Asunto(s)
Enfermedades de los Perros/patología , Piodermia Gangrenosa/veterinaria , Animales , Antibacterianos/uso terapéutico , Antiinflamatorios/administración & dosificación , Antiinflamatorios/uso terapéutico , Enfermedades de los Perros/diagnóstico , Perros , Masculino , Prednisolona/administración & dosificación , Prednisolona/uso terapéutico , Piodermia Gangrenosa/diagnóstico , Piodermia Gangrenosa/patología , Sulfasalazina/administración & dosificación , Sulfasalazina/uso terapéutico
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