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1.
Nature ; 621(7980): 840-848, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37674084

RESUMO

In both cancer and infections, diseased cells are presented to human Vγ9Vδ2 T cells through an 'inside out' signalling process whereby structurally diverse phosphoantigen (pAg) molecules are sensed by the intracellular domain of butyrophilin BTN3A11-4. Here we show how-in both humans and alpaca-multiple pAgs function as 'molecular glues' to promote heteromeric association between the intracellular domains of BTN3A1 and the structurally similar butyrophilin BTN2A1. X-ray crystallography studies visualized that engagement of BTN3A1 with pAgs forms a composite interface for direct binding to BTN2A1, with various pAg molecules each positioned at the centre of the interface and gluing the butyrophilins with distinct affinities. Our structural insights guided mutagenesis experiments that led to disruption of the intracellular BTN3A1-BTN2A1 association, abolishing pAg-mediated Vγ9Vδ2 T cell activation. Analyses using structure-based molecular-dynamics simulations, 19F-NMR investigations, chimeric receptor engineering and direct measurement of intercellular binding force revealed how pAg-mediated BTN2A1 association drives BTN3A1 intracellular fluctuations outwards in a thermodynamically favourable manner, thereby enabling BTN3A1 to push off from the BTN2A1 ectodomain to initiate T cell receptor-mediated γδ T cell activation. Practically, we harnessed the molecular-glue model for immunotherapeutics design, demonstrating chemical principles for developing both small-molecule activators and inhibitors of human γδ T cell function.


Assuntos
Butirofilinas , Ativação Linfocitária , Fosfoproteínas , Receptores de Antígenos de Linfócitos T gama-delta , Linfócitos T , Animais , Humanos , Antígenos CD/imunologia , Antígenos CD/metabolismo , Butirofilinas/imunologia , Butirofilinas/metabolismo , Camelídeos Americanos/imunologia , Simulação de Dinâmica Molecular , Fosfoproteínas/imunologia , Fosfoproteínas/metabolismo , Receptores de Antígenos de Linfócitos T gama-delta/imunologia , Receptores de Antígenos de Linfócitos T gama-delta/metabolismo , Linfócitos T/citologia , Linfócitos T/imunologia , Linfócitos T/metabolismo , Cristalografia por Raios X , Ressonância Magnética Nuclear Biomolecular , Termodinâmica
2.
EMBO J ; 41(16): e110636, 2022 08 16.
Artigo em Inglês | MEDLINE | ID: mdl-35638332

RESUMO

Activation of the T-cell antigen receptor (TCR)-CD3 complex is critical to induce the anti-tumor response of CD8+ T cells. Here, we found that disulfiram (DSF), an FDA-approved drug previously used to treat alcohol dependency, directly activates TCR signaling. Mechanistically, DSF covalently binds to Cys20/Cys23 residues of lymphocyte-specific protein tyrosine kinase (LCK) and enhances its tyrosine 394 phosphorylation, thereby promoting LCK kinase activity and boosting effector T cell function, interleukin-2 production, metabolic reprogramming, and proliferation. Furthermore, our in vivo data revealed that DSF promotes anti-tumor immunity against both melanoma and colon cancer in mice by activating CD8+ T cells, and this effect was enhanced by anti-PD-1 co-treatment. We conclude that DSF directly activates LCK-mediated TCR signaling to induce strong anti-tumor immunity, providing novel molecular insights into the therapeutic effect of DSF on cancer.


Assuntos
Dissulfiram , Proteína Tirosina Quinase p56(lck) Linfócito-Específica , Animais , Linfócitos T CD8-Positivos , Dissulfiram/farmacologia , Ativação Linfocitária , Proteína Tirosina Quinase p56(lck) Linfócito-Específica/metabolismo , Camundongos , Fosforilação , Receptores de Antígenos de Linfócitos T/metabolismo , Transdução de Sinais
3.
Photodermatol Photoimmunol Photomed ; 39(5): 487-497, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37253092

RESUMO

BACKGROUND: Lysosomal cathepsin D (CTSD) can degrade internalized advanced glycation end products (AGEs) in dermal fibroblasts. CTSD expression is decreased in photoaged fibroblasts, which contributes to intracellular AGEs deposition and further plays a role in AGEs accumulation of photoaged skin. The mechanism under downregulated CTSD expression is unclear. OBJECTIVE: To explore possible mechanism of regulating CTSD expression in photoaged fibroblasts. METHODS: Dermal fibroblasts were induced into photoaging with repetitive ultraviolet A (UVA) irradiation. The competing endogenous RNA (ceRNA) networks were constructed to predict candidate circRNAs or miRNAs related with CTSD expression. AGEs-BSA degradation by fibroblasts was studied with flow cytometry, ELISA, and confocal microscopy. Effects of overexpressing circRNA-406918 via lentiviral transduction on CTSD expression, autophagy, AGE-BSA degradation were analyzed in photoaged fibroblasts. The correlation between circRNA-406918 and CTSD expression or AGEs accumulation in sun-exposed and sun-protected skin was studied. RESULTS: CTSD expression, autophagy, and AGEs-BSA degradation were significantly decreased in photoaged fibroblasts. CircRNA-406918 was identified to regulate CTSD expression, autophagy, and senescence in photoaged fibroblasts. Overexpressing circRNA-406918 potently decreased senescence and increased CTSD expression, autophagic flux, and AGEs-BSA degradation in photoaged fibroblasts. Moreover, circRNA-406918 level was positively correlated with CTSD mRNA expression and negatively associated with AGEs accumulation in photodamaged skin. Further, circRNA-406918 was predicted to mediate CTSD expression through sponging eight miRNAs. CONCLUSION: These findings suggest that circRNA-406918 regulates CTSD expression and AGEs degradation in UVA-induced photoaged fibroblasts and might exert a role in AGEs accumulation in photoaged skin.


Assuntos
MicroRNAs , Envelhecimento da Pele , Humanos , Catepsina D/genética , Catepsina D/metabolismo , Catepsina D/farmacologia , Fibroblastos/metabolismo , Produtos Finais de Glicação Avançada/metabolismo , MicroRNAs/genética , RNA Circular/genética , RNA Circular/metabolismo , RNA Circular/farmacologia , Pele/metabolismo , Envelhecimento da Pele/genética , Raios Ultravioleta/efeitos adversos
4.
Opt Express ; 29(11): 16595-16610, 2021 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-34154219

RESUMO

It is still a challenge to realize the absolute optical path difference (OPD) demodulation of multi-interference systems with a narrow spectral interval and small OPD interval. In this paper, an iterative normalized cross-correlation algorithm is firstly proposed for demodulating the multiple absolute OPDs of a dual-interference system and applied to optical fiber sensing system. By constructing a template function in combined form, the optimal solutions of its components and OPDs are solved iteratively based on the reconstruction matrix method and cross-correlation algorithm, respectively. The simulation and experiment show that the demodulation accuracies near the OPDs of 560 µm and 660 µm are both up to 5 nm in different spectral intervals from 45 to 80 nm. The simulation results show that all demodulation precisions at the spectral interval of 55 nm do not exceed 4 nm when the OPD changes in the range of 650-670 µm. Besides, the experimental verification shows the temperature accuracy (0.125 °C) with 95% confidence of T-distribution is very close to the control accuracy (0.1 °C). The proposed algorithm can improve the multiplexing capability of optical fiber sensor system and reduce its cost.

5.
Physiol Plant ; 173(4): 1841-1849, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34418106

RESUMO

Anthocyanins are common secondary metabolites in plants that impart red coloration to fruits and flowers. The important WRKY transcription factor family plays multifaceted roles in plant growth and development. In this study, we found a WRKY family gene, Pyrus bretschneideri WRKY75, that may be involved in anthocyanin synthesis in pear. Unlike Arabidopsis thaliana WRKY75, PbWRKY75 may be a positive regulator of anthocyanin synthesis. A transient expression assay indicated that PbWRKY75 promoted pear anthocyanin synthesis. The structural genes (PbANS, PbDFR, and PbUFGT) and positive regulators (PbMYB10 and PbMYB10b) of anthocyanin synthesis were significantly upregulated in the fruitlet skins of PbWRKY75-overexpressing "Zaosu" pears. Subsequently, yeast one-hybrid and dual-luciferase assays indicated that PbWRKY75 promoted PbDFR, PbUFGT, and PbMYB10b expression by activating their promoters. These results revealed that PbWRKY75 may promote the expression of both PbMYB10b and anthocyanin late biosynthetic genes (PbDFR and PbUFGT) by activating their promoters, thereby inducing anthocyanin synthesis in pear. This study enhanced our understanding of the mechanism of pear anthocyanin synthesis, which will be beneficial in the improvement of pear peel color.


Assuntos
Pyrus , Antocianinas , Frutas/genética , Frutas/metabolismo , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Pyrus/genética , Pyrus/metabolismo
6.
Int J Mol Sci ; 22(18)2021 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-34576007

RESUMO

Seedless fruit is a feature appreciated by consumers. The ovule abortion process is highly orchestrated and controlled by numerous environmental and endogenous signals. However, the mechanisms underlying ovule abortion in pear remain obscure. Here, we found that gibberellins (GAs) have diverse functions during ovules development between seedless pear '1913' and seeded pear, and that GA4+7 activates a potential programmed cell death process in '1913' ovules. After hormone analyses, strong correlations were determined among jasmonic acid (JA), ethylene and salicylic acid (SA) in seedless and seeded cultivars, and GA4+7 treatments altered the hormone accumulation levels in ovules, resulting in significant correlations between GA and both JA and ethylene. Additionally, SA contributed to ovule abortion in '1913'. Exogenously supplying JA, SA or the ethylene precursor 1-aminocyclopropane-1-carboxylic acid promoted 'Bartlett' seed death. The regulatory mechanism in which ethylene controls ovule death has been demonstrated; therefore, JA's role in regulating '1913' ovule abortion was investigated. A further study identified that the JA signaling receptor MYC2 bound the SENESCENCE-ASSOCIATED 39 promoter and triggered its expression to regulate ovule abortion. Thus, we established ovule abortion-related relationships between GA and the hormones JA, ethylene and SA, and we determined their synergistic functions in regulating ovule death.


Assuntos
Apoptose/efeitos dos fármacos , Ciclopentanos/farmacologia , Etilenos/farmacologia , Giberelinas/farmacologia , Óvulo Vegetal/metabolismo , Oxilipinas/farmacologia , Pyrus/metabolismo , Ciclopentanos/metabolismo , Etilenos/metabolismo , Giberelinas/metabolismo , Oxilipinas/metabolismo
7.
Ecotoxicol Environ Saf ; 194: 110412, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32155482

RESUMO

Hydrogen sulfide (H2S) is a toxic air pollutant that causes immune damage. Recent studies have found that neutrophil extracellular trap (NET) formation is one way in which neutrophils exert immune functions. In addition, the formation of NETs is also related to thrombosis and autoimmune diseases. Recent studies have shown that miRNAs are involved in the regulation of a variety of pathophysiological processes. Here, we investigated the role of H2S in regulating the formation of NETs by affecting miR-16-5p. Our study established an in vitro H2S exposure model for neutrophils using phorbol-myristate-acetate (PMA) to induce NET formation. We observed the morphological changes of cells with scanning electron microscopy and fluorescence microscopy. Then, the content of extracellular DNA and the expression of MPO and NE in each group were detected. The results showed that H2S inhibited the formation of NETs. The expression of miR-16-5p and its target genes PiK3R1 and RAF1 was then measured by qRT-PCR. H2S upregulated miR-16-5p and inhibited expression of the target genes PiK3R1 and RAF1, and it subsequently inhibited the Pi3K/AKT and ERK pathways and decreased respiratory burst levels. Furthermore, H2S attenuated inositol 1,4,5-trisphosphate receptor (IP3R)-mediated endoplasmic reticulum calcium outflow as well as autophagy caused by PMA. This study enriches H2S immunotoxicity research and provides a possible solution for the treatment of NET-related diseases.


Assuntos
Poluentes Atmosféricos/toxicidade , Classe Ia de Fosfatidilinositol 3-Quinase/genética , Armadilhas Extracelulares/efeitos dos fármacos , Sulfeto de Hidrogênio/toxicidade , MicroRNAs/genética , Neutrófilos/efeitos dos fármacos , Proteínas Proto-Oncogênicas c-raf/genética , Animais , Autofagia/efeitos dos fármacos , Galinhas , Armadilhas Extracelulares/metabolismo , Humanos , Sistema de Sinalização das MAP Quinases/efeitos dos fármacos , Modelos Animais , Neutrófilos/metabolismo , Neutrófilos/ultraestrutura , Acetato de Tetradecanoilforbol/farmacologia , Ativação Transcricional/efeitos dos fármacos , Regulação para Cima
8.
Perfusion ; 35(8): 806-813, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32419612

RESUMO

BACKGROUND: Catheter-related thrombosis may lead to catheter infections and failure, further deep venous thrombosis, and pulmonary embolism. Recognizing the risk factors for catheter-related thrombosis is extremely important to inform the development of catheter care guidelines. METHODS: Data were collected from a total of 1,532 patients who had undergone venous catheterization, including indwelling catheterization from 19 March 2019 to 30 March 2019 in the Sun Yat-sen Memorial Hospital. The factors for which data were to be collected included the patients' physical characteristics, catheter-related factors, and catheter care-related factors. Logistic regression analysis, the chi-squared test, Fisher's exact test, and the t-test were used to analyze the data. RESULTS: Of the 1,532 patients studied, 28 developed intraductal thrombi, and of the factors analyzed, malignancy, a catheterization history, a history of thrombophilia, surgery during the week before catheterization, the catheterization duration, and anticoagulant therapy were significant risk factors associated with catheter-related thrombosis (all p < 0.05). There were no significant associations between the catheter brand, the number of lumens, the insertion direction, or the factors associated with catheter care and catheter-related thrombosis (all p > 0.05). CONCLUSION: Our study incorporated clear and systematic risk factors associated with catheter-related thrombosis. Malignancy, history of thrombophilia, history of catheterization, surgery during the week before catheterization, and catheterization duration were associated with increased risks of catheter-related thrombosis. Prophylactic anticoagulation was effective for preventing and treating catheter-related thrombosis.


Assuntos
Cateterismo Venoso Central/efeitos adversos , Trombose/etiologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Cateterismo Venoso Central/métodos , Criança , Pré-Escolar , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , Fatores de Risco , Adulto Jovem
9.
Int J Mol Sci ; 21(4)2020 Feb 24.
Artigo em Inglês | MEDLINE | ID: mdl-32102306

RESUMO

Subgroup 4 R2R3 MYBs play vital roles in the regulation of anthocyanin biosynthesis. However, there is limited knowledge regarding the functions of MYB repressors in pear (Pyrus × bretschneideri). Here, PbMYB120 was identified as a potential regulator of anthocyanin biosynthesis. A phylogenetic analysis revealed that PbMYB120 was clustered into the FaMYB1-like clade of the subgroup 4 R2R3 MYBs. PbMYB120 was expressed higher in red peels than in green peels in five pear cultivars. PbMYB120 expression was positively correlated with anthocyanin accumulation. However, the transient overexpression of PbMYB120 led to the inhibition of anthocyanin accumulation and PbUFGT1 expression. Promoter binding and activation assays indicated that PbMYB120 binds to the promoter of PbUFGT1 and represses the promoter's activity. Thus, the inhibition of anthocyanin accumulation by PbMYB120 may be correlated with the repression of PbUFGT1. Furthermore, during anthocyanin induction, the expression levels of anthocyanin activators and PbMYB120 were upregulated. This study demonstrated that PbMYB120 was highly expressed in pear tissues having higher anthocyanin accumulations but acted as a repressor in the regulation of anthocyanin accumulation. PbMYB120 may work coordinately with anthocyanin activators and serve as a balancer of anthocyanin accumulation.


Assuntos
Antocianinas/metabolismo , Frutas/genética , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética , Pyrus/genética , Fatores de Transcrição/genética , Sequência de Aminoácidos , Cor , Frutas/metabolismo , Perfilação da Expressão Gênica/métodos , Modelos Genéticos , Filogenia , Pigmentação/genética , Proteínas de Plantas/classificação , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas , Pyrus/metabolismo , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Homologia de Sequência de Aminoácidos , Fatores de Transcrição/classificação , Fatores de Transcrição/metabolismo
10.
Biochem Biophys Res Commun ; 518(4): 611-618, 2019 10 22.
Artigo em Inglês | MEDLINE | ID: mdl-31445710

RESUMO

Autophagy has been associated with a variety of diseases especially aging. Human dermal fibroblasts (HDFs) can internalize and then degrade elastin, collagen and advanced glycation end products (AGEs) in lysosomes, which plays prominent roles in extracellular matrix homeostasis and AGEs removal in the dermis. Although autophagy has been reported to be decreased in photoaged fibroblasts, the underlying mechanism and its relevance to photoaging remain elusive. Here, we showed that GFP-LC3 puncta per cell, LC3Ⅰ/Ⅱ conversion and p62 expression were significantly increased, whereas beclin1 expression was not altered in UVA-induced photoaged fibroblasts compared with non-photoaged control. Moreover, autophagic flux was not significantly affected by chloroquine treatment, but was remarkably induced by rapamycin treatment in photoaged fibroblasts, suggesting that UVA-induced photoaging might inhibit autophagy at the degradation stage. Further lysosomal function studies demonstrated that degradation of formed autophagosomes, LC3Ⅱprotein and DQ-Green BSA was all dramatically decreased in photoaged fibroblasts. LysoSensor yellow/blue DND 160 staining and flow cytometry assays demonstrated that photoaging obviously attenuated lysosomal acidification. Also, decreased expression of cathepsin B, L and D was found in photoaged fibroblasts. These data suggest that lowered lysosomal acidity and decreased cathepsins expression might contribute to the inhibition of autophagic degradation, which might be crucial in the development of photoaging through impairing intracellular degradation.


Assuntos
Autofagia/efeitos da radiação , Fibroblastos/efeitos da radiação , Lisossomos/efeitos da radiação , Envelhecimento da Pele/efeitos da radiação , Raios Ultravioleta/efeitos adversos , Autofagossomos/metabolismo , Autofagossomos/efeitos da radiação , Células Cultivadas , Criança , Pré-Escolar , Fibroblastos/citologia , Fibroblastos/metabolismo , Humanos , Lisossomos/metabolismo , Pele/citologia , Pele/metabolismo , Pele/efeitos da radiação
11.
Fish Shellfish Immunol ; 94: 730-738, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31580934

RESUMO

Atrazine (ATR) causes environmental problems and damages the health of fish and aquatic animals. MicroRNAs (miRNAs) play important roles in immune regulation. However, the immunotoxicity mechanism of ATR in fish lymphocytes and the role of miRNA in this process remain unclear. To further study these mechanisms, spleen lymphocytes were exposed to 20, 40 and 60 µg/ml ATR for 18 h. Fluorescence staining and flow cytometry showed that the number of necrotic lymphocytes increased after ATR exposure. Compared with the control group, the mRNA expression of miR-181-5p was inhibited and the mRNA levels of TNF-α and HK2 were increased after ATR exposure. Additionally, the NF-κB inflammatory pathway and the levels of glycometabolism-related genes were upregulated. These results suggest that ATR induces inflammation and elevates glycometabolism in lymphocytes. We further found that the mRNA levels of receptor-interacting serine-threonine kinase 1 (RIP1), receptor-interacting serine-threonine kinase 3 (RIP3), mixed lineage kinase domain-like pseudokinase (MLKL), cylindromatosis (CYLD) and Fas-Associated protein with Death Domain (FADD) and the protein levels of RIP3 and MLKL in the treatment groups were significantly increased compared to those in control group, suggesting that ATR causes lymphocyte necroptosis. We conclude that miR-181-5p plays a key role in necroptosis in carp lymphocytes exposed to ATR by downregulating the expression of HK and TNF-α, which increases the level of glycometabolism and induces the inflammatory response, respectively.


Assuntos
Atrazina/toxicidade , Carpas/imunologia , Doenças dos Peixes/imunologia , Glicólise/imunologia , Inflamação/veterinária , MicroRNAs/metabolismo , Necroptose/imunologia , Animais , Relação Dose-Resposta a Droga , Doenças dos Peixes/induzido quimicamente , Proteínas de Peixes/genética , Proteínas de Peixes/metabolismo , Glicólise/efeitos dos fármacos , Herbicidas/toxicidade , Inflamação/induzido quimicamente , Inflamação/imunologia , Linfócitos/efeitos dos fármacos , Linfócitos/imunologia , Necroptose/efeitos dos fármacos , Baço/efeitos dos fármacos , Baço/imunologia
12.
BMC Med Inform Decis Mak ; 19(Suppl 2): 62, 2019 04 09.
Artigo em Inglês | MEDLINE | ID: mdl-30961595

RESUMO

BACKGROUND: Gender information frequently exists in the eligibility criteria of clinical trial text as essential information for participant population recruitment. Particularly, current eligibility criteria text contains the incompleteness and ambiguity issues in expressing transgender population, leading to difficulties or even failure of transgender population recruitment in clinical trial studies. METHODS: A new gender model is proposed for providing comprehensive transgender requirement specification. In addition, an automated approach is developed to extract and summarize gender requirements from unstructured text in accordance with the gender model. This approach consists of: 1) the feature extraction module, and 2) the feature summarization module. The first module identifies and extracts gender features using heuristic rules and automatically-generated patterns. The second module summarizes gender requirements by relation inference. RESULTS: Based on 100,134 clinical trials from ClinicalTrials.gov , our approach was compared with 20 commonly applied machine learning methods. It achieved a macro-averaged precision of 0.885, a macro-averaged recall of 0.871 and a macro-averaged F1-measure of 0.878. The results illustrated that our approach outperformed all baseline methods in terms of both commonly used metrics and macro-averaged metrics. CONCLUSIONS: This study presented a new gender model aiming for specifying the transgender requirement more precisely. We also proposed an approach for gender information extraction and summarization from unstructured clinical text to enhance transgender-related clinical trial population recruitment. The experiment results demonstrated that the approach was effective in transgender criteria extraction and summarization.


Assuntos
Armazenamento e Recuperação da Informação , Seleção de Pacientes , Pessoas Transgênero , Ensaios Clínicos como Assunto , Heurística , Humanos , Aprendizado de Máquina
13.
BMC Med Inform Decis Mak ; 18(Suppl 5): 119, 2018 12 07.
Artigo em Inglês | MEDLINE | ID: mdl-30526566

RESUMO

BACKGROUND: The Gene Ontology (GO) is a resource that supplies information about gene product function using ontologies to represent biological knowledge. These ontologies cover three domains: Cellular Component (CC), Molecular Function (MF), and Biological Process (BP). GO annotation is a process which assigns gene functional information using GO terms to relevant genes in the literature. It is a common task among the Model Organism Database (MOD) groups. Manual GO annotation relies on human curators assigning gene functional information using GO terms by reading the biomedical literature. This process is very time-consuming and labor-intensive. As a result, many MODs can afford to curate only a fraction of relevant articles. METHODS: GO terms from the CC domain can be essentially divided into two sub-hierarchies: subcellular location terms, and protein complex terms. We cast the task of gene annotation using GO terms from the CC domain as relation extraction between gene and other entities: (1) extract cases where a protein is found to be in a subcellular location, and (2) extract cases where a protein is a subunit of a protein complex. For each relation extraction task, we use an approach based on triggers and syntactic dependencies to extract the desired relations among entities. RESULTS: We tested our approach on the BC4GO test set, a publicly available corpus for GO annotation. Our approach obtains a F1-score of 71%, a precision of 91% and a recall of 58% for predicting GO terms from CC Domain for given genes. CONCLUSIONS: We have described a novel approach of treating gene annotation with GO terms from CC domain as two relation extraction subtasks. Evaluation results show that our approach achieves a F1-score of 71% for predicting GO terms for given genes. Thereby our approach can be used to accelerate the process of GO annotation for the bio-annotators.


Assuntos
Biologia Computacional , Ontologia Genética , Anotação de Sequência Molecular , Processamento de Linguagem Natural , Humanos
14.
BMC Med Inform Decis Mak ; 18(Suppl 1): 22, 2018 03 22.
Artigo em Inglês | MEDLINE | ID: mdl-29589563

RESUMO

BACKGROUND: Temporal expression extraction and normalization is a fundamental and essential step in clinical text processing and analyzing. Though a variety of commonly used NLP tools are available for medical temporal information extraction, few work is satisfactory for multi-lingual heterogeneous clinical texts. METHODS: A novel method called TEER is proposed for both multi-lingual temporal expression extraction and normalization from various types of narrative clinical texts including clinical data requests, clinical notes, and clinical trial summaries. TEER is characterized as temporal feature summarization, heuristic rule generation, and automatic pattern learning. By representing a temporal expression as a triple , TEER identifies temporal mentions M, assigns type attributes A to M, and normalizes the values of M into formal representations N. RESULTS: Based on two heterogeneous clinical text datasets: 400 actual clinical requests in English and 1459 clinical discharge summaries in Chinese. TEER was compared with six state-of-the-art baselines. The results showed that TEER achieved a precision of 0.948 and a recall of 0.877 on the English clinical requests, while a precision of 0.941 and a recall of 0.932 on the Chinese discharge summaries. CONCLUSIONS: An automated method TEER for multi-lingual temporal expression extraction was presented. Based on the two datasets containing heterogeneous clinical texts, the comparison results demonstrated the effectiveness of the TEER method in multi-lingual temporal expression extraction from heterogeneous narrative clinical texts.


Assuntos
Heurística , Armazenamento e Recuperação da Informação , Prontuários Médicos , Processamento de Linguagem Natural , Reconhecimento Automatizado de Padrão , Humanos
15.
BMC Med Inform Decis Mak ; 18(1): 25, 2018 04 13.
Artigo em Inglês | MEDLINE | ID: mdl-29653522

RESUMO

After publication of the original article [1] it was noted that the captions relating to Figs. 2 and 3 had been interchanged.

16.
Mol Cancer ; 13: 95, 2014 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-24775912

RESUMO

BACKGROUND: Grb2 (Growth factor receptor-bound protein 2) is a key adaptor protein in maintaining the ERK activity via linking Sos1 (Son of sevenless homolog 1) or other proteins to activated RTKs, such as EGFR. Currently, little knowledge is available concerning the post-translational modification (PTM) of Grb2 except for its phosphorylation. Since emerging evidences have highlighted the importance of SUMOylation (Small ubiquitin-related modifier), a reversible PTM, in modulating protein functions, we wondered if Grb2 could be SUMOylated and thereby influences its functions especially involved in the Ras/MEK/ERK pathway. METHODS: SUMOylation of Grb2 was analyzed with the in vivo SUMOylation assay using the Ni2+-NTA affinity pulldown and the in vitro E.coli-based SUMOylation assay. To test the ERK activity and cell transformation, the murine fibroblast cell line NIH/3T3 and the murine colon cancer cell line CMT-93 were used for the experiments including Grb2 knockdown, ectopic re-expression, cell transformation and migration. Immunoprecipitation (IP) was employed for seeking proteins that interact with SUMO modified Grb2. Xenograft tumor model in mice was conducted to verify that Grb2 SUMOylation regulated tumorigenesis in vivo. RESULTS: Grb2 can be SUMOylated by SUMO1 at lysine 56 (K56), which is located in the linker region between the N-terminal SH3 domain and the SH2 domain. Knockdown of Grb2 reduced the ERK activity and suppressed cell motility and tumorigenesis in vitro and in vivo, which were all rescued by stable ectopic re-expression of wild-type Grb2 but not the mutant Grb2K56R. Furthermore, Grb2 SUMOylation at K56 increased the formation of Grb2-Sos1 complex, which sequentially leads to the activation of Ras/MEK/MAPK pathway. CONCLUSIONS: Our results provide evidences that Grb2 is SUMOylated in vivo and this modification enhances ERK activities via increasing the formation of Grb2-Sos1 complex, and may consequently promote cell motility, transformation and tumorigenesis.


Assuntos
Neoplasias do Colo/genética , MAP Quinases Reguladas por Sinal Extracelular/genética , Proteína Adaptadora GRB2/genética , Regulação Neoplásica da Expressão Gênica , Processamento de Proteína Pós-Traducional , Proteína SOS1/genética , Sequência de Aminoácidos , Animais , Carcinogênese/genética , Carcinogênese/metabolismo , Carcinogênese/patologia , Linhagem Celular Tumoral , Neoplasias do Colo/metabolismo , Neoplasias do Colo/patologia , MAP Quinases Reguladas por Sinal Extracelular/metabolismo , Proteína Adaptadora GRB2/antagonistas & inibidores , Proteína Adaptadora GRB2/metabolismo , Sistema de Sinalização das MAP Quinases , Masculino , Camundongos , Camundongos Nus , Dados de Sequência Molecular , Células NIH 3T3 , Fosforilação , Ligação Proteica , RNA Interferente Pequeno/genética , RNA Interferente Pequeno/metabolismo , Proteína SOS1/metabolismo , Sumoilação , Ensaios Antitumorais Modelo de Xenoenxerto , Proteínas ras/genética , Proteínas ras/metabolismo
17.
Molecules ; 18(12): 15717-23, 2013 Dec 16.
Artigo em Inglês | MEDLINE | ID: mdl-24352024

RESUMO

A new, simplified method for the synthesis of dimethyl aryl acylsulfonium salts has been developed. A series of dimethyl aryl acylsulfonium bromides were prepared by the reaction of aryl methyl ketones with hydrobromic acid and dimethylsulfoxide (DMSO). This sulfonium salt confirms that bromine production and the bromination reaction take place in the DMSO-HBr oxidation system. What's more, it is also a key intermediate for the synthesis of arylglyoxals.


Assuntos
Brometos/química , Cetonas/química , Brometos/síntese química , Dimetil Sulfóxido/química
18.
Artif Intell Med ; 144: 102667, 2023 10.
Artigo em Inglês | MEDLINE | ID: mdl-37783542

RESUMO

Insufficient training data is a common barrier to effectively learn multimodal information interactions and question semantics in existing medical Visual Question Answering (VQA) models. This paper proposes a new Asymmetric Cross Modal Attention network called ACMA, which constructs an image-guided attention and a question-guided attention to improve multimodal interactions from insufficient data. In addition, a Semantic Understanding Auxiliary (SUA) in the question-guided attention is newly designed to learn rich semantic embeddings for improving model performance on question understanding by integrating word-level and sentence-level information. Moreover, we propose a new data augmentation method called Multimodal Augmented Mixup (MAM) to train the ACMA, denoted as ACMA-MAM. The MAM incorporates various data augmentations and a vanilla mixup strategy to generate more non-repetitive data, which avoids time-consuming artificial data annotations and improves model generalization capability. Our ACMA-MAM outperforms state-of-the-art models on three publicly accessible medical VQA datasets (VQA-Rad, VQA-Slake, and PathVQA) with accuracies of 76.14 %, 83.13 %, and 53.83 % respectively, achieving improvements of 2.00 %, 1.32 %, and 1.59 % accordingly. Moreover, our model achieves F1 scores of 78.33 %, 82.83 %, and 51.86 %, surpassing the state-of-the-art models by 2.80 %, 1.15 %, and 1.37 % respectively.


Assuntos
Aprendizagem , Semântica
19.
Nat Commun ; 14(1): 1645, 2023 03 24.
Artigo em Inglês | MEDLINE | ID: mdl-36964144

RESUMO

Poly(butylene adipate-co-terephthalate) (PBAT), a polyester made of terephthalic acid (TPA), 1,4-butanediol, and adipic acid, is extensively utilized in plastic production and has accumulated globally as environmental waste. Biodegradation is an attractive strategy to manage PBAT, but an effective PBAT-degrading enzyme is required. Here, we demonstrate that cutinases are highly potent enzymes that can completely decompose PBAT films in 48 h. We further show that the engineered cutinases, by applying a double mutation strategy to render a more flexible substrate-binding pocket exhibit higher decomposition rates. Notably, these variants produce TPA as a major end-product, which is beneficial feature for the future recycling economy. The crystal structures of wild type and double mutation of a cutinase from Thermobifida fusca in complex with a substrate analogue are also solved, elucidating their substrate-binding modes. These structural and biochemical analyses enable us to propose the mechanism of cutinase-mediated PBAT degradation.


Assuntos
Adipatos , Poliésteres , Poliésteres/metabolismo
20.
J Invest Dermatol ; 142(10): 2591-2602.e8, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-35421403

RESUMO

Advanced glycation end product (AGE) accumulation is significantly increased in the dermis of photoaged skin and plays crucial roles in photoaging. Although AGEs have been found to contribute to the yellowish discoloration of photoaged skin, their roles in photoaging-associated hyperpigmentation disorders have not been extensively studied. In this study, we observed that AGEs, NLRP3, and IL-18 were increased in the dermis of sun-exposed skin and lesions of melasma and solar lentigo and that dermal deposition of AGE was positively correlated with epidermal melanin levels. In addition, we found that AGE-BSA potently activated NLRP3 inflammasome and promoted IL-18 production and secretion in cultured fibroblasts, which was mediated by receptor for AGE/NF-κB pathway. Moreover, AGE-BSA significantly promoted melanogenesis by increasing tyrosinase activity and expression of microphthalmia-associated transcription factor and tyrosinase, which was dependent on NLRP3 inflammasome activation and IL-18 secretion in fibroblasts. Notably, AGE-collagen could activate NLRP3 inflammasome in fibroblasts and enhance melanogenesis. Furthermore, we found that IL-18 enhanced melanogenesis by binding to its receptor and activating p38 MAPK and extracellular signal‒regulated kinase 1/2 signaling pathways in melanocytes. Importantly, the promelanogenesis of AGE-BSA was verified in ex vivo cultured skin and mouse models. These findings suggest that dermal AGEs stimulate melanogenesis and contribute to the development of photoaging-associated hyperpigmentation disorders.


Assuntos
Inflamassomos , Lentigo , Animais , Fibroblastos/metabolismo , Produtos Finais de Glicação Avançada/metabolismo , Humanos , Inflamassomos/metabolismo , Interleucina-18/metabolismo , Melaninas/metabolismo , Camundongos , Fator de Transcrição Associado à Microftalmia/metabolismo , Proteína Quinase 3 Ativada por Mitógeno/metabolismo , Monofenol Mono-Oxigenase/metabolismo , NF-kappa B/metabolismo , Proteína 3 que Contém Domínio de Pirina da Família NLR/metabolismo , Proteínas Quinases p38 Ativadas por Mitógeno/metabolismo
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