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1.
Artículo en Inglés | MEDLINE | ID: mdl-37372667

RESUMEN

This study was designed to advance our understanding of how feelings of empowerment in people living with dementia still residing at home can be promoted. We conducted qualitative interviews with 12 participants with mild-to-moderate stages of dementia in Germany and Spain as part of a European study on mindful design for dementia. A qualitative thematic content analysis was performed to elicit the key features of the experience reported by the interviewees. Three overarching categories were identified: the first category 'experiencing changes in personal life and coping with changes in life' covered losses and coping strategies; the second category 'retaining a sense of usefulness' included social participation and the need for activities with others; the third category 'feeling empowered' covered reflections on lifetime achievements, accomplishments in the present life, being in control and self-worth. Participants placed a strong emphasis on continuity and on the importance of making active decisions and meaningful social contributions. Empowerment within the person living with dementia was achieved through their interactions with their social environment, including the significance of communication about their needs and wishes and enabling shared decision-making and interactions with others in reciprocity.


Asunto(s)
Demencia , Medio Social , Humanos , Emociones , Toma de Decisiones , Participación Social , Investigación Cualitativa , Cuidadores
2.
Am J Respir Crit Care Med ; 208(2): 176-187, 2023 07 15.
Artículo en Inglés | MEDLINE | ID: mdl-37141109

RESUMEN

Rationale: Extracellular histones, released into the surrounding environment during extensive cell death, promote inflammation and cell death, and these deleterious roles have been well documented in sepsis. Clusterin (CLU) is a ubiquitous extracellular protein that chaperones misfolded proteins and promotes their removal. Objectives: We investigated whether CLU could protect against the deleterious properties of histones. Methods: We assessed CLU and histone expression in patients with sepsis and evaluated the protective role of CLU against histones in in vitro assays and in vivo models of experimental sepsis. Measurements and Main Results: We show that CLU binds to circulating histones and reduces their inflammatory, thrombotic, and cytotoxic properties. We observed that plasma CLU levels decreased in patients with sepsis and that the decrease was greater and more durable in nonsurvivors than in survivors. Accordingly, CLU deficiency was associated with increased mortality in mouse models of sepsis and endotoxemia. Finally, CLU supplementation improved mouse survival in a sepsis model. Conclusions: This study identifies CLU as a central endogenous histone-neutralizing molecule and suggests that, in pathologies with extensive cell death, CLU supplementation may improve disease tolerance and host survival.


Asunto(s)
Antineoplásicos , Sepsis , Animales , Ratones , Histonas/metabolismo , Clusterina/metabolismo , Inflamación , Muerte Celular , Sepsis/tratamiento farmacológico
3.
Artículo en Inglés | MEDLINE | ID: mdl-37047971

RESUMEN

Many people are keen to be actively involved in social life and activities, but even at an early stage, dementia can have a negative impact on social participation and access to leisure activities. As part of the IDoService project, this study has investigated people's needs and wishes, barriers and facilitators to identify opportunities for improving access to meaningful activities. Individual and focus group interviews were conducted with 5 people living with mild to moderate dementia, 2 familial and 2 professional care partners, as well as 12 people working in the field of dementia and/or community activities. Thematic analysis has highlighted the benefits of participating in meaningful activities, such as empowerment and pride, social contacts, and feeling useful to others. A number of barriers to participation relating to individual and environmental factors were reported. Even where participants praised dementia-friendly activities and facilities, they advocated activities inclusive for all and mentioned that some people might be reluctant to participate in dementia-labelled activities because they may not be suitable for their needs. These results indicate the need for developing tailored opportunities for people with mild to moderate dementia and provide valuable insights for researchers, service providers, policymakers and charities wanting to improve access.


Asunto(s)
Demencia , Humanos , Demencia/terapia , Cuidadores , Participación Social , Grupos Focales , Emociones
4.
J Aging Stud ; 60: 100995, 2022 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-35248311

RESUMEN

Receiving a dementia diagnosis is a difficult experience for most people and often affects their wellbeing negatively. To support people's wellbeing, in a therapeutic context, life-storytelling, reminiscence and mindfulness are used with people with dementia. In an everyday context, traditional games are used as a resource for stimulating memory, cognition and social activity. While an increasing number of creative strategies are available to support people with dementia, the area of board games design and their effect on wellbeing is underexplored. This paper reports on the evaluation of the This is Me (TIM) mindful life-storytelling board game by the European project MinD. Using a co-design methodology, TIM was developed with and for people with mild to moderate dementia to support their wellbeing by enhancing self-empowerment and social engagement. A focus group methodology was used to evaluate TIM with 50 people with dementia and 19 carers across four countries. TIM was evaluated with regard to the usability and experience of the design as well as people's emotional wellbeing, social engagement and agency. The thematic analysis demonstrated that the combination of life-storytelling and mindfulness allowed players to engage in meaningful social interaction and, as a result, they reported enjoyment, learning, more acceptance of the past and present situation, and that they perceived looking forward into the future together with others as helpful. The study demonstrates that design can be a useful means to support people with dementia in aspects of emotional wellbeing, social engagement and a sense of agency.


Asunto(s)
Demencia , Atención Plena , Cuidadores/psicología , Comunicación , Demencia/psicología , Humanos , Participación Social
5.
Rheumatology (Oxford) ; 60(12): 5863-5867, 2021 12 01.
Artículo en Inglés | MEDLINE | ID: mdl-33764396

RESUMEN

OBJECTIVE: To deep sequence the TRIM33 gene in tumours from patients with cancer-associated anti-TIF1γ autoantibody-positive dermatomyositis (DM) as TRIM33 somatic mutations in tumours may trigger this auto-immune disease. METHODS: Next generation sequencing of tumour DNA samples from patients with cancer-associated anti-TIF1γ autoantibody-positive DM. Fourteen tumours from 13 anti-TIF1γ autoantibody-positive DM individuals were sequenced along with two control tumours from non-DM individuals. RESULTS: Fourteen probable somatic variants from four tumours were identified in the TRIM33 gene. CONCLUSION: These results are in accordance with the previous report of Pinal-Fernandez et al. and support the hypothesis of a role of TRIM33 gene mutations in the pathophysiology of anti-TIF1γ autoantibody-positive DM.


Asunto(s)
ADN/genética , Dermatomiositis/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Mutación , Neoplasias/complicaciones , Factores de Transcripción/genética , Anciano , Análisis Mutacional de ADN , Dermatomiositis/etiología , Dermatomiositis/metabolismo , Femenino , Humanos , Masculino , Factores de Transcripción/metabolismo , Dedos de Zinc
6.
Cells ; 10(1)2021 01 05.
Artículo en Inglés | MEDLINE | ID: mdl-33466245

RESUMEN

exDNA is found in various organisms, including plants. However, plant exDNA has thus far received little attention related to its origin and role in the RET (root extracellular trap). In this study, we performed the first high-throughput genomic sequencing of plant exDNA from a Fabaceae with worldwide interest: soybean (Glycine max (L.) Merr.). The origin of this exDNA was first investigated in control condition, and the results show high-coverage on organelles (mitochondria/plastid) DNA relative to nuclear DNA, as well as a mix of coding and non-coding sequences. In the second part of this study, we investigated if exDNA release was modified during an elicitation with PEP-13 (a peptide elicitor from oomycete genus Phytophthora). Our results show that treatment of roots with PEP-13 does not affect the composition of exDNA.


Asunto(s)
ADN de Plantas/metabolismo , Espacio Extracelular/metabolismo , Trampas Extracelulares/metabolismo , Glycine max/metabolismo , Raíces de Plantas/metabolismo , Cromosomas de las Plantas/genética , Orgánulos/metabolismo
7.
Open Res Eur ; 1: 64, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-37645110

RESUMEN

Background: Generalisation of findings is an important aspect of research and essential for evidence-based practice. While generalisation is common in quantitative research, there is a lack of generalisability in qualitative research. This paper presents the experience and challenges faced by the Designing for People with Dementia (MinD) project in meeting the requirements to strengthen the generalisation of findings on the lived experience of people living with dementia and their engagement to co-create designs to empower their everyday living.   Methods: Polit and Beck (2010)'s strategies to generalise qualitative findings were applied: (1) replication in sampling; (2) replication of studies; (3) meta-synthesis of findings; (4) reflexivity and conceptualization; (5) immersion with the data; and (6) thick description. Results: While it is possible to increase the generabilisabilty of qualitative evidence through the replication of the sampling to attain a large, heterogeneous sample in different and multiple contexts and environments; implementation of sound and robust research; conducting in-depth analysis and interpretation collaboratively for emergent themes; and meeting the thick description requirement, there are challenges that the project team faced in implementing some of the Polit and Beck's strategies because of the condition, namely dementia, that our participants are having. Other challenges faced were: the language and cultural diversity in the team; diverse  work and organisational procedures; and the inter-disciplinary differences relating to the methods of enquiry, approaches and techniques to conduct research. These challenges will need to be identified and addressed at the start of the project with a strong leadership to ensure a seamless journey to complete the project successfully. Trust between the researchers and participants, and time to build this trust are critical to recruitment and participation in the study; these factors are of utmost important in research involving participants with condition such as dementia.

8.
J Med Genet ; 58(12): 796-805, 2021 12.
Artículo en Inglés | MEDLINE | ID: mdl-33051313

RESUMEN

BACKGROUND: The interpretation of germline TP53 variants is critical to ensure appropriate medical management of patients with cancer and follow-up of variant carriers. This interpretation remains complex and is becoming a growing challenge considering the exponential increase in TP53 tests. We developed a functional assay directly performed on patients' blood. METHODS: Peripheral blood mononuclear cells were cultured, activated, exposed to doxorubicin and the p53-mediated transcriptional response was quantified using reverse transcription-multiplex ligation probe amplification and RT-QMPSF assays, including 10 p53 targets selected from transcriptome analysis, and two amplicons to measure p53 mRNA levels. We applied this blood functional assay to 77 patients addressed for TP53 analysis. RESULTS: In 51 wild-type TP53 individuals, the mean p53 functionality score was 12.7 (range 7.5-22.8). Among eight individuals harbouring likely pathogenic or pathogenic variants, the scores were reduced (mean 4.8, range 3.1-7.1), and p53 mRNA levels were reduced in patients harbouring truncating variants. We tested 14 rare unclassified variants (p.(Pro72His), p.(Gly105Asp), p.(Arg110His), p.(Phe134Leu), p.(Arg158Cys), p.(Pro191Arg), p.(Pro278Arg), p.(Arg283Cys), p.(Leu348Ser), p.(Asp352Tyr), p.(Gly108_Phe109delinsVal), p.(Asn131del), p.(Leu265del), c.-117G>T) and 12 yielded functionally abnormal scores. Remarkably, the assay revealed that the c.*1175A>C polymorphic variant within TP53 poly-adenylation site can impact p53 function with the same magnitude as a null variant, when present on both alleles, and may act as a modifying factor in pathogenic variant carriers. CONCLUSION: This blood p53 assay should therefore be a useful tool for the rapid clinical classification of germline TP53 variants and detection of non-coding functional variants.


Asunto(s)
Análisis Mutacional de ADN/métodos , Predisposición Genética a la Enfermedad/genética , Mutación de Línea Germinal , Neoplasias/genética , Proteína p53 Supresora de Tumor/genética , Adolescente , Adulto , Anciano , Niño , Preescolar , Femenino , Genotipo , Humanos , Leucocitos Mononucleares/metabolismo , Masculino , Persona de Mediana Edad , Neoplasias/patología , Polimorfismo de Nucleótido Simple , Reproducibilidad de los Resultados , Proteína p53 Supresora de Tumor/sangre , Adulto Joven
9.
Eur J Hum Genet ; 29(1): 99-109, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-32591635

RESUMEN

The detection of copy-number variations (CNVs) from NGS data is underexploited as chip-based or targeted techniques are still commonly used. We assessed the performances of a workflow centered on CANOES, a bioinformatics tool based on read depth information. We applied our workflow to gene panel (GP) and whole-exome sequencing (WES) data, and compared CNV calls to quantitative multiplex PCR of short fluorescent fragments (QMSPF) or array comparative genomic hybridization (aCGH) results. From GP data of 3776 samples, we reached an overall positive predictive value (PPV) of 87.8%. This dataset included a complete comprehensive QMPSF comparison of four genes (60 exons) on which we obtained 100% sensitivity and specificity. From WES data, we first compared 137 samples with aCGH and filtered comparable events (exonic CNVs encompassing enough aCGH probes) and obtained an 87.25% sensitivity. The overall PPV was 86.4% following the targeted confirmation of candidate CNVs from 1056 additional WES. In addition, our CANOES-centered workflow on WES data allowed the detection of CNVs with a resolution of single exons, allowing the detection of CNVs that were missed by aCGH. Overall, switching to an NGS-only approach should be cost-effective as it allows a reduction in overall costs together with likely stable diagnostic yields. Our bioinformatics pipeline is available at: https://gitlab.bioinfo-diag.fr/nc4gpm/canoes-centered-workflow .


Asunto(s)
Variaciones en el Número de Copia de ADN , Secuenciación del Exoma/normas , Pruebas Genéticas/normas , Secuenciación de Nucleótidos de Alto Rendimiento/normas , Hibridación Genómica Comparativa/normas , Humanos , Reacción en Cadena de la Polimerasa Multiplex/normas , Sensibilidad y Especificidad , Flujo de Trabajo
10.
World J Biol Psychiatry ; 22(7): 516-525, 2021 09.
Artículo en Inglés | MEDLINE | ID: mdl-33143529

RESUMEN

PURPOSE: The current COVID-19 pandemic confronts psychiatric patients and mental health services with unique and severe challenges. METHODS: In order to identify these trans-national challenges across Europe, an ad-hoc survey was conducted among 23 experts, each answering for one European or aligned country. RESULTS: A number of important themes and issues were raised for the impact of COVID-19 on mental health and mental health services, barriers to service provision and future consequences. A number of key issues were reported by colleagues across several jurisdictions, even though these were at different stages of their national epidemics. CONCLUSIONS: Based on these findings, we articulate some important learnings from the early stages of the COVID-19 European pandemic, and highlight key considerations for all countries' mental health services as the current pandemic develops and for future pandemics.


Asunto(s)
COVID-19 , Servicios de Salud Mental , Europa (Continente) , Humanos , Pandemias , SARS-CoV-2
11.
BMC Genomics ; 21(1): 86, 2020 Jan 28.
Artículo en Inglés | MEDLINE | ID: mdl-31992191

RESUMEN

BACKGROUND: Branch points (BPs) map within short motifs upstream of acceptor splice sites (3'ss) and are essential for splicing of pre-mature mRNA. Several BP-dedicated bioinformatics tools, including HSF, SVM-BPfinder, BPP, Branchpointer, LaBranchoR and RNABPS were developed during the last decade. Here, we evaluated their capability to detect the position of BPs, and also to predict the impact on splicing of variants occurring upstream of 3'ss. RESULTS: We used a large set of constitutive and alternative human 3'ss collected from Ensembl (n = 264,787 3'ss) and from in-house RNAseq experiments (n = 51,986 3'ss). We also gathered an unprecedented collection of functional splicing data for 120 variants (62 unpublished) occurring in BP areas of disease-causing genes. Branchpointer showed the best performance to detect the relevant BPs upstream of constitutive and alternative 3'ss (99.48 and 65.84% accuracies, respectively). For variants occurring in a BP area, BPP emerged as having the best performance to predict effects on mRNA splicing, with an accuracy of 89.17%. CONCLUSIONS: Our investigations revealed that Branchpointer was optimal to detect BPs upstream of 3'ss, and that BPP was most relevant to predict splicing alteration due to variants in the BP area.


Asunto(s)
Intrones , Precursores del ARN , Sitios de Empalme de ARN , Empalme del ARN , Empalme Alternativo , Biología Computacional/métodos , Humanos , Motivos de Nucleótidos , Posición Específica de Matrices de Puntuación , Procesamiento Postranscripcional del ARN , Curva ROC , Reproducibilidad de los Resultados
12.
Front Microbiol ; 10: 2479, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31736914

RESUMEN

Staphylococcus lugdunensis is a commensal bacterium of human skin that has emerged as a virulent Coagulase-Negative Staphylococcus in both community-acquired and healthcare associated infections. Genotyping methods have shown a clonal population structure of this pathogen but failed to identify hypervirulent lineages. Here, complete genomes of three pathogenic and three carriage S. lugdunensis strains were obtained by Single-Molecule sequencing (PacBio) and compared to 15 complete genomes available in GenBank database. The aim was to identify (i) genetic determinants specific to pathogenic or carriage strains or specific to clonal complexes (CCs) defined by MultiLocus Sequence Typing, and (ii) antibiotic resistance genes and new putative virulence factors encoded or not by mobile genetic elements (MGE). Comparative genomic analysis did not show a strict correlation between gene content and the ability of the six strains to cause infections in humans and in a Galleria mellonella infection model. However, this study identified new MGEs (five prophages, two genomic islands and one plasmid) and genetic variations of some putative virulence-associated loci, especially in CC3 strains. For a clonal population, high variability and eight CC-dependent genetic organizations were observed for the ess locus, which encodes a putative type VII secretion system (T7SS) homologous to that of S. aureus. Further phenotypic and functional studies are needed to characterize this particular CC3 and to evaluate the role of T7SS in the virulence of S. lugdunensis.

13.
Maturitas ; 128: 10-16, 2019 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-31561816

RESUMEN

Dementia is generally considered to be one of the most pressing societal issues now and in the years to come. Although insights from different disciplines have contributed to a better understanding of dementia and the development of interventions targeting dementia symptoms, there is a lack of integration of insights from these different perspectives for the purposes of design for dementia. The aim of this paper is to show how insights from environmental psychology and advances in technology can inform a user-centred multidisciplinary design approach. To this end, first a brief meta-review of (systematic) reviews from the fields of assistive technology for dementia care and healing environments research is presented, after which gaps and opportunities for a multidisciplinary design approach are identified. To illustrate what such an approach could look like, two exploratory case studies are presented in which technology-enhanced prototypes of an experience handrail (aimed at facilitating wayfinding by providing meaningful sensory experiences) and a virtual nature installation (aimed at providing relaxation and stimulating social engagement) were implemented at a Dutch care centre for people with dementia. Preliminary evaluations indicate that these designs contribute to the wellbeing of people with dementia and confirm the fruitfulness of the design approach presented in this paper. Furthermore, this approach may not only provide a means to optimize existing environments and enhance ease of living, but may also lead to novel solutions to the challenges people with dementia face on a day-to-day basis, and improve their quality of life.


Asunto(s)
Demencia/terapia , Planificación Ambiental , Casas de Salud , Calidad de Vida , Dispositivos de Autoayuda , Demencia/psicología , Humanos
14.
J Med Chem ; 62(18): 8365-8391, 2019 09 26.
Artículo en Inglés | MEDLINE | ID: mdl-30964283

RESUMEN

Malaria still affects around 200 million people and is responsible for more than 400,000 deaths per year, mostly children in subequatorial areas. This disease is caused by parasites of the Plasmodium genus. Only a few WHO-recommended treatments are available to prevent or cure plasmodial infections, but genetic mutations in the causal parasites have led to onset of resistance against all commercial antimalarial drugs. New drugs and targets are being investigated to cope with this emerging problem, including enzymes belonging to the main metabolic pathways, while nucleoside and nucleotide analogues are also a promising class of potential drugs. This review highlights the main metabolic pathways targeted for the development of potential antiplasmodial therapies based on nucleos(t)ide analogues, as well as the different series of purine-containing nucleoside and nucleotide derivatives designed to inhibit Plasmodium falciparum purine metabolism.


Asunto(s)
Antimaláricos/farmacología , Nucleósidos/metabolismo , Nucleótidos/metabolismo , Plasmodium falciparum/efectos de los fármacos , Purinas/metabolismo , Transporte Biológico , Diseño de Fármacos , Eritrocitos/parasitología , Humanos , Concentración 50 Inhibidora , Malaria/tratamiento farmacológico , Malaria/parasitología , Plasmodium falciparum/metabolismo , Pirimidinas/metabolismo
15.
Acta Neuropathol Commun ; 6(1): 109, 2018 10 19.
Artículo en Inglés | MEDLINE | ID: mdl-30340542

RESUMEN

Extreme microcephaly and rhombencephalosynapsis represent unusual pathological conditions, each of which occurs in isolation or in association with various other cerebral and or extracerebral anomalies. Unlike microcephaly for which several disease-causing genes have been identified with different modes of inheritance, the molecular bases of rhombencephalosynapsis remain unknown and rhombencephalosynapsis presents mainly as a sporadic condition consistent with de novo dominant variations. We report for the first time the association of extreme microcephaly with almost no sulcation and rhombencephalosynapsis in a fœtus for which comparative patient-parent exome sequencing strategy revealed a heterozygous de novo missense variant in the ADGRL2 gene. ADGRL2 encodes latrophilin 2, an adhesion G-protein-coupled receptor whose exogenous ligand is α-latrotoxin. Adgrl2 immunohistochemistry and in situ hybridization revealed expression in the telencephalon, mesencephalon and rhombencephalon of mouse and chicken embryos. In human brain embryos and fœtuses, Adgrl2 immunoreactivity was observed in the hemispheric and cerebellar germinal zones, the cortical plate, basal ganglia, pons and cerebellar cortex. Microfluorimetry experiments evaluating intracellular calcium release in response to α-latrotoxin binding showed significantly reduced cytosolic calcium release in the fœtus amniocytes vs amniocytes from age-matched control fœtuses and in HeLa cells transfected with mutant ADGRL2 cDNA vs wild-type construct. Embryonic lethality was also observed in constitutive Adgrl2-/- mice. In Adgrl2+/- mice, MRI studies revealed microcephaly and vermis hypoplasia. Cell adhesion and wound healing assays demonstrated that the variation increased cell adhesion properties and reduced cell motility. Furthermore, HeLa cells overexpressing mutant ADGRL2 displayed a highly developed cytoplasmic F-actin network related to cytoskeletal dynamic modulation. ADGRL2 is the first gene identified as being responsible for extreme microcephaly with rhombencephalosynapsis. Increased cell adhesion, reduced cell motility and cytoskeletal dynamic alterations induced by the variant therefore represent a new mechanism responsible for microcephaly.


Asunto(s)
Microcefalia/genética , Microcefalia/patología , Mutación/genética , Receptores Acoplados a Proteínas G/genética , Receptores Acoplados a Proteínas G/metabolismo , Rombencéfalo/patología , Adulto , Animales , Ciclo Celular/genética , Células Cultivadas , Embrión de Pollo , Análisis Mutacional de ADN , Embrión de Mamíferos , Femenino , Feto , Regulación del Desarrollo de la Expresión Génica/genética , Edad Gestacional , Humanos , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Transgénicos , Microcefalia/complicaciones , Microcefalia/diagnóstico por imagen , Persona de Mediana Edad , Neuroglía/metabolismo , Neuroglía/patología , Rombencéfalo/diagnóstico por imagen
16.
Sci Rep ; 8(1): 14340, 2018 09 25.
Artículo en Inglés | MEDLINE | ID: mdl-30254372

RESUMEN

Phaeodactylum tricornutum is the most studied diatom encountered principally in coastal unstable environments. It has been hypothesized that the great adaptability of P. tricornutum is probably due to its pleomorphism. Indeed, P. tricornutum is an atypical diatom since it can display three morphotypes: fusiform, triradiate and oval. Currently, little information is available regarding the physiological significance of this morphogenesis. In this study, we adapted P. tricornutum Pt3 strain to obtain algal culture particularly enriched in one dominant morphotype: fusiform, triradiate or oval. These cultures were used to run high-throughput RNA-Sequencing. The whole mRNA transcriptome of each morphotype was determined. Pairwise comparisons highlighted biological processes and molecular functions which are up- and down-regulated. Finally, intersection analysis allowed us to identify the specific features from the oval morphotype which is of particular interest as it is often described to be more resistant to stresses. This study represent the first transcriptome wide characterization of the three morphotypes from P. tricornutum performed on cultures specifically enriched issued from the same Pt3 strain. This work represents an important step for the understanding of the morphogenesis in P. tricornutum and highlights the particular features of the oval morphotype.


Asunto(s)
Diatomeas/genética , Fenotipo , Análisis de Secuencia de ARN , Diatomeas/fisiología , Perfilación de la Expresión Génica , Estrés Fisiológico
17.
Eur J Hum Genet ; 26(11): 1597-1602, 2018 11.
Artículo en Inglés | MEDLINE | ID: mdl-29967336

RESUMEN

We have developed and validated for the diagnosis of inherited colorectal cancer (CRC) a massive parallel sequencing strategy based on: (i) fast capture of exonic and intronic sequences from ten genes involved in Mendelian forms of CRC (MLH1, MSH2, MSH6, PMS2, APC, MUTYH, STK11, SMAD4, BMPR1A and PTEN); (ii) sequencing on MiSeq and NextSeq 500 Illumina platforms; (iii) a bioinformatic pipeline that includes BWA-Picard-GATK (Broad Institute) and CASAVA (Illumina) in parallel for mapping and variant calling, Alamut Batch (Interactive BioSoftware) for annotation, CANOES for CNV detection and finally, chimeric reads analysis for the detection of other types of structural variants (SVs). Analysis of 1644 new index cases allowed the identification of 323 patients with class 4 or 5 variants, corresponding to a 20% disease-causing variant detection rate. This rate reached 37% in patients with Lynch syndrome, suspected on the basis of tumour analyses. Thanks to this strategy, we detected overlapping phenotypes (e.g., MUTYH biallelic mutations mimicking Lynch syndrome), mosaic alterations and complex SVs such as a genomic deletion involving the last BMPR1A exons and PTEN, an Alu insertion within MSH2 exon 8 and a mosaic deletion of STK11 exons 3-10. This strategy allows, in a single step, detection of all types of CRC gene alterations including SVs and provides a high disease-causing variant detection rate, thus optimizing the diagnosis of inherited CRC.


Asunto(s)
Neoplasias Colorrectales/genética , Pruebas Genéticas/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Análisis de Secuencia de ADN/métodos , Adulto , Neoplasias Colorrectales/diagnóstico , Exones , Femenino , Pruebas Genéticas/normas , Secuenciación de Nucleótidos de Alto Rendimiento/normas , Humanos , Intrones , Masculino , Persona de Mediana Edad , Reproducibilidad de los Resultados , Sensibilidad y Especificidad , Análisis de Secuencia de ADN/normas
18.
J Lipid Res ; 59(8): 1461-1471, 2018 08.
Artículo en Inglés | MEDLINE | ID: mdl-29853527

RESUMEN

The malaria parasite, Plasmodium falciparum, develops and multiplies in the human erythrocyte. It needs to synthesize considerable amounts of phospholipids (PLs), principally phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylserine (PS). Several metabolic pathways coexist for their de novo biosynthesis, involving a dozen enzymes. Given the importance of these PLs for the survival of the parasite, we sought to determine their sources and to understand the connections and dependencies between the multiple pathways. We used three deuterated precursors (choline-d9, ethanolamine-d4, and serine-d3) to follow and quantify simultaneously their incorporations in the intermediate metabolites and the final PLs by LC/MS/MS. We show that PC is mainly derived from choline, itself provided by lysophosphatidylcholine contained in the serum. In the absence of choline, the parasite is able to use both other precursors, ethanolamine and serine. PE is almost equally synthesized from ethanolamine and serine, with both precursors being able to compensate for each other. Serine incorporated in PS is mainly derived from the degradation of host cell hemoglobin by the parasite. P. falciparum thus shows an unexpected adaptability of its PL synthesis pathways in response to different disturbances. These data provide new information by mapping the importance of the PL metabolic pathways of the malaria parasite and could be used to design future therapeutic approaches.


Asunto(s)
Malaria Falciparum/parasitología , Fosfolípidos/metabolismo , Plasmodium falciparum/metabolismo , Redes y Vías Metabólicas , Fosfolípidos/biosíntesis , Plasmodium falciparum/fisiología
19.
Virulence ; 9(1): 923-929, 2018 12 31.
Artículo en Inglés | MEDLINE | ID: mdl-29638173

RESUMEN

Carriage and invasion balance in the pathogenesis of Neisseria meningitidis was analyzed during a recent clonal outbreak of meningococcal B in Normandy, France, that offered the opportunity to compare six isolates undistinguable by conventional typing (B:14:P1.7,16:F3-3/ST-32) isolated from invasive disease or pharyngeal asymptomatic carriage. Data from animal model (transgenic mice rendered susceptible to N. meningitidis infection) showed an absence of virulence for two non-capsulated carriage isolates, an intermediate virulence for two capsulated carriage isolates and a marked virulence for two capsulated invasive isolates. This differential pathogenesis well correlated with whole genome sequencing analysis that clustered both isolates of each group together, forming their own arm within the Norman cluster. Gene-by-gene analysis specified that genes involved in iron acquisition were among the elements differentially represented in cluster of invasive isolates compared to cluster of capsulated carriage isolates. The hemoglobin receptor encoding gene hmbR was in an ON-phase in the capsulated invasive isolates while carriage capsulated isolates were in an OFF-phase. An ON-phase variant of a capsulated carriage isolate showed enhanced virulence. These data underline the role of phase variation (ON/OFF) of HmbR in the balance between disease isolates/carriage isolates.


Asunto(s)
Cápsulas Bacterianas/metabolismo , Proteínas Bacterianas/metabolismo , Portador Sano/microbiología , Hemoglobinas/metabolismo , Infecciones Meningocócicas/metabolismo , Neisseria meningitidis/metabolismo , Neisseria meningitidis/patogenicidad , Receptores de Superficie Celular/metabolismo , Cápsulas Bacterianas/genética , Proteínas Bacterianas/genética , Portador Sano/metabolismo , Humanos , Infecciones Meningocócicas/microbiología , Neisseria meningitidis/genética , Neisseria meningitidis/aislamiento & purificación , Unión Proteica , Receptores de Superficie Celular/genética , Virulencia
20.
Clin Chim Acta ; 481: 1-8, 2018 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-29476731

RESUMEN

PURPOSES: Hydrops fetalis is a life-threatening fetal condition, and 85% of all cases are classified as nonimmune hydrops fetalis (NIHF). Up to 15% of NIHF cases may be due to inborn errors of metabolism (IEM), but a large proportion of cases linked to metabolic disorders remains undiagnosed. This lack of diagnosis may be related to the limitations of conventional biological procedures, which involve sequential investigations and require multiple samples and steps. In addition, this approach is time consuming. We have developed a next-generation sequencing (NGS) panel to investigate metabolic causes of NIHF, ascites, and polyhydramnios associated to another fetal abnormality. METHODS: The hydrops fetalis (HydFet) panel was designed to cover the coding regions and flanking intronic sequences of 41 genes. A retrospective study of amniotic fluid samples from 40 subjects was conducted. A prospective study was subsequently initiated, and six samples were analyzed using the NGS panel. RESULTS: Five IEM diagnoses were made using the HydFet panel (Niemann-Pick type C (NPC), Barth syndrome, HNF1Β deficiency, GM1 gangliosidosis, and Gaucher disease). This analysis also allowed the identification of 8p sequence triplication in an additional case. CONCLUSION: NGS combined with robust bioinformatics analyses is a useful tool for identifying the causative variants of NIHF. Subsequent functional characterization of the protein encoded by the altered gene and morphological studies may confirm the diagnosis. This paradigm shift allows a significant improvement of IEM diagnosis in NIHF.


Asunto(s)
Hidropesía Fetal/genética , Hidropesía Fetal/metabolismo , Errores Innatos del Metabolismo/genética , Errores Innatos del Metabolismo/metabolismo , Adulto , Biología Computacional , Femenino , Humanos , Hidropesía Fetal/diagnóstico , Errores Innatos del Metabolismo/diagnóstico , Embarazo , Estudios Retrospectivos , Análisis de Secuencia de ADN , Adulto Joven
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