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J Neurovirol ; 2019 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-31654372


This case report presents a 1-year-old boy from China, with sudden onset of fever, convulsion, and sleepiness, screened for viral DNA in blood and cerebrospinal fluid (CSF) sample using next-generation sequencing (NGS) to diagnose herpes simplex virus type 1 (HSV-1) encephalitis, further validated by PCR. After acyclovir treatment, the patient's symptom disappeared and HSV-1 DNA unique reads decreased from 4290 to zero in CSF, and from 23 to zero in blood detected by NGS. The clinical presentation and outcome were consistent with the pathogenic diagnostic results of NGS. NGS of CSF samples can be used as a diagnostic assay for HSV-1 encephalitis and also might be a semi-quantitative method for evaluation of treatment effect.

Anal Biochem ; 583: 113364, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31323206


Long non-coding RNA (lncRNA) plays an important role in cells through the interaction with RNA-binding proteins (RBPs). Finding the RBPs binding sites on the lncRNA chains can help to understand the post-transcriptional regulatory mechanism, exploring the pathogenesis of cancers and possible roles in other diseases. Although many genome-wide RBP experimental techniques can identify the RNA-protein interactions and detect the binding sites on RNA chains, they are still time-consuming, labor-intensive and cost-heavy. Thus, many computational methods have been developed to predict the RBPs sites by integrating the RNA sequence, structure and domain specific features, etc. However, current approaches that focus on predicting the RBPs binding sites on RNA chains lack a consideration of the dependencies among nucleotides. In this work, we propose a higher-order nucleotide encoding convolutional neural network-based method (namely HOCNNLB) to predict the RBPs binding sites on lncRNA chains. HOCNNLB first employs a high-order one-hot encoding strategy to encode the lncRNA sequences by considering the dependence among nucleotides, then the encoded lncRNA sequences are fed into the convolutional neural network (CNN) to predict the RBP binding sites. We evaluate HOCNNLB on 31 experimental datasets of 12 lncRNA binding proteins. The average AUC of HOCNNLB achieves 0.953, which is 0.247, 0.175 higher than that of iDeepS and DeepBind, respectively. The average accuracy is 90.2%, which is 26.8%, 19.5% higher than that of iDeepS and DeepBind, respectively. These results demonstrate that HOCNNLB can reliably predict the RBP binding sites on lncRNA chains and outperforms the state-of-the-art methods. The source code of HOCNNLB and the datasets used in this work are available at for academic users.

BMC Infect Dis ; 19(1): 495, 2019 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-31164085


BACKGROUND: There is currently no research on the diagnostic value of metagenomic next-generation sequencing (mNGS) for a single pathogens in CSF. The aim of this study was to analyse the value of mNGS for identifying Streptococcus pneumoniae (S. pneumoniae) in paediatric bacterial meningitis. METHODS: Bacterial meningitis (BM) cases from October 23, 2014, to December 31, 2016, and December 1, 2017, to July 31, 2018 at Beijing Children's Hospital were reviewed. Clinical features and pathogens were analysed. RESULTS: We diagnosed 135 patients with BM in this study. A total of 43 S. pneumoniae were identified by combination methods. 26/135 (19.3%) patients had positive results in S. pneumoniae by blood and/or cerebrospinal fluid (CSF) culture. Alere BinaxNow®Streptococcus pneumoniae Antigen test was positive in 35/135(25.9%) cases. 32/135 (23.7%) S. pneumoniae were identified by mNGS. Six CSF samples were identified as S. pneumoniae only by mNGS technology. Taking culture as the gold standard, the sensitivity and specificity of mNGS for diagnosing S. pneumoniae meningitis were 73.1 and 88.1%, respectively. The positive predictive value (PPV) and negative predictive value (NPV) of diagnosing S. pneumoniae meningitis by mNGS were 59.4 and 93.2%, respectively. When comparison between mNGS and combined tests (culture and Alere BinaxNow®Streptococcus pneumoniae Antigen test), the sensitivity and specificity of mNGS for S. pneumoniae identification were 70.3 and 93.9%, the PPV and NPV in the identification of S. pneumoniae by mNGS were 81.4 and 89.3%, respectively. The difference in number of unique reads of S. pneumoniaein from CSF sample (< 14 days onset) and CSF sample (> 14 days from onset) was statistically significant (170.5 VS. 13, P = 0.019). The difference in the collected time of CSF for culture and mNGS was statistically significant (4 days VS. 14 days, P < 0.001). CONCLUSIONS: mNGS has high sensitivity and specificity for S. pneumoniae identification. The pathogen load (number of unique reads) of S. pneumonia is related to the CSF collection time. mNGS was less affected than culture by the use of antibiotics before CSF collection.

Sequenciamento de Nucleotídeos em Larga Escala , Meningites Bacterianas/diagnóstico , Metagenômica/métodos , Streptococcus pneumoniae/genética , Streptococcus pneumoniae/isolamento & purificação , Adolescente , Fatores Etários , Antígenos de Bactérias/análise , Antígenos de Bactérias/sangue , Antígenos de Bactérias/líquido cefalorraquidiano , Antígenos de Bactérias/genética , Criança , Pré-Escolar , Testes Diagnósticos de Rotina , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Meningites Bacterianas/sangue , Meningites Bacterianas/líquido cefalorraquidiano , Meningites Bacterianas/microbiologia , Pediatria/métodos , Reação em Cadeia da Polimerase/métodos , Valor Preditivo dos Testes , Sensibilidade e Especificidade
Cancer Lett ; 459: 100-111, 2019 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-31158430


The mixed lineage kinase domain-like protein (MLKL) has emerged as a critical mediator of necroptosis, which results in the release of cellular damage-associated molecular patterns (DAMPs). However, its physiological role in regulating inflammation is not fully understood. We herein showed that Mlkl-/- mice were highly susceptible to colitis and colitis-associated tumorigenesis (CAT), which was associated with massive leukocyte infiltration and increased inflammatory responses. Moreover, we used bone marrow transplantation to reveal that MLKL in inflammatory cells is crucial for its role on colitis. Intestinal mucosal tissue and polyps isolated from Mlkl-/- mice exhibited increased ERK activation and elevated expression of genes associated with inflammation and cancer. Mechanistically, enhanced inflammation in Mlkl-/- mice was due to MEK/ERK activation particularly in dendritic cells (DCs). Our results demonstrate the role of MLKL in maintaining intestinal homeostasis and protecting against colitis and tumorigenesis.

Ying Yong Sheng Tai Xue Bao ; 29(12): 3949-3958, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30584721


To understand the mechanism underlying responses of stomatal traits, gas exchange parameters, and biomass of tomato plants to salt stress, two tomato cultivars (Shed and Alam) were treated by salt stress by adding NaCl (0.1 mol·L-1) to nutrition medium in environmental growth chambers for 90 days. Our results showed that salt stress substantially decreased the stomatal density, stomatal width, stomatal area, and stomatal area index of Shed by 32%, 45%, 25%, and 49%, respectively. The stomatal traits of Alam were not affected by NaCl treatment. The spatial scales of the regular stomatal distribution pattern of Shed and Alam were significantly decreased by 30% and 43%, and the nearest neighbor distance Lhat (d) of shed cultivar was increased by 20% under salt stress. NaCl stress resulted in marginal declines in the net photosynthetic rates (Pn), stomatal conductance (gs), transpiration rates (Tr) of both cultivars. The decrease of the photosynthetic rate of Shed under salt stress resulted from stomatal limitation, whereas the Pn of Alam was subjected to non-stomatal constraints. NaCl stress substantially decreased the seedling biomass of both cultivars, and the decline of belowground biomass was higher than that of aboveground biomass. Overall, our results suggested that the Alam cultivar is more salt-tolerant than Shed.

Biomassa , Lycopersicon esculentum/fisiologia , Folhas de Planta/fisiologia , Estresse Salino/fisiologia , Cloreto de Sódio/toxicidade , Clorofila , Fotossíntese , Estômatos de Plantas/anatomia & histologia , Estômatos de Plantas/fisiologia
Cell Rep ; 19(4): 798-808, 2017 04 25.
Artigo em Inglês | MEDLINE | ID: mdl-28445730


RIPK3 mediates cell death and regulates inflammatory responses. Although genetic studies have suggested that RIPK3-MLKL-mediated necroptosis leads to embryonic lethality in Fadd or Caspase-8-deficient mice, the exact mechanisms are not fully understood. Here, we generated Ripk3 mutant mice by altering the RIPK3 kinase domain (Ripk3Δ/Δ mice), thus abolishing its kinase activity. Ripk3Δ/Δ cells were resistant to necroptosis stimulation in vitro, and Ripk3Δ/Δ mice were protected from necroptotic diseases. Although the Ripk3Δ/Δ mutation rescued embryonic lethality in Fadd-/- embryos, Fadd-/-Ripk3Δ/Δ mice died within 1 day after birth due to massive inflammation. These results indicate that Ripk3 ablation rescues embryonic lethality in Fadd-deficient mice by suppressing two RIPK3-mediating processes: necroptosis during embryogenesis and inflammation during postnatal development in Fadd-/- mice.

Apoptose , Proteína de Domínio de Morte Associada a Fas/genética , Proteína Serina-Treonina Quinases de Interação com Receptores/metabolismo , Animais , Apoptose/efeitos dos fármacos , Caspase 8/genética , Caspase 8/metabolismo , Ceruletídeo/toxicidade , Quimiocinas/metabolismo , Citocinas/análise , Citocinas/metabolismo , Embrião de Mamíferos/metabolismo , Desenvolvimento Embrionário/efeitos dos fármacos , Proteína de Domínio de Morte Associada a Fas/deficiência , Células HEK293 , Humanos , Inflamação , Lipopolissacarídeos/toxicidade , Macrófagos/citologia , Macrófagos/efeitos dos fármacos , Macrófagos/metabolismo , Camundongos , Camundongos Knockout , Mutagênese , Necrose , Oligopeptídeos/farmacologia , Pancreatite/induzido quimicamente , Pancreatite/patologia , Fosforilação , Proteínas Quinases/metabolismo , Proteína Serina-Treonina Quinases de Interação com Receptores/genética