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1.
Brief Bioinform ; 25(2)2024 Jan 22.
Artículo en Inglés | MEDLINE | ID: mdl-38385873

RESUMEN

Lysine lactylation (Kla) is a newly discovered posttranslational modification that is involved in important life activities, such as glycolysis-related cell function, macrophage polarization and nervous system regulation, and has received widespread attention due to the Warburg effect in tumor cells. In this work, we first design a natural language processing method to automatically extract the 3D structural features of Kla sites, avoiding potential biases caused by manually designed structural features. Then, we establish two Kla prediction frameworks, Attention-based feature fusion Kla model (ABFF-Kla) and EBFF-Kla, to integrate the sequence features and the structure features based on the attention layer and embedding layer, respectively. The results indicate that ABFF-Kla and Embedding-based feature fusion Kla model (EBFF-Kla), which fuse features from protein sequences and spatial structures, have better predictive performance than that of models that use only sequence features. Our work provides an approach for the automatic extraction of protein structural features, as well as a flexible framework for Kla prediction. The source code and the training data of the ABFF-Kla and the EBFF-Kla are publicly deposited at: https://github.com/ispotato/Lactylation_model.


Asunto(s)
Lisina , Procesamiento de Lenguaje Natural , Secuencia de Aminoácidos , Dominios Proteicos , Procesamiento Proteico-Postraduccional
2.
Mol Cell Proteomics ; 23(6): 100770, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38641226

RESUMEN

Inhalation of crystalline silica dust induces incurable lung damage, silicosis, and pulmonary fibrosis. However, the mechanisms of the lung injury remain poorly understood, with limited therapeutic options aside from lung transplantation. Posttranslational modifications can regulate the function of proteins and play an important role in studying disease mechanisms. To investigate changes in posttranslational modifications of proteins in silicosis, combined quantitative proteome, acetylome, and succinylome analyses were performed with lung tissues from silica-injured and healthy mice using liquid chromatography-mass spectrometry. Combined analysis was applied to the three omics datasets to construct a protein landscape. The acetylation and succinylation of the key transcription factor STAT1 were found to play important roles in the silica-induced pathophysiological changes. Modulating the acetylation level of STAT1 with geranylgeranylacetone effectively inhibited the progression of silicosis. This report revealed a comprehensive landscape of posttranslational modifications in silica-injured mouse and presented a novel therapeutic strategy targeting the posttranslational level for silica-induced lung diseases.


Asunto(s)
Lisina , Procesamiento Proteico-Postraduccional , Proteoma , Factor de Transcripción STAT1 , Silicosis , Animales , Silicosis/metabolismo , Silicosis/tratamiento farmacológico , Silicosis/patología , Factor de Transcripción STAT1/metabolismo , Proteoma/metabolismo , Lisina/metabolismo , Acetilación/efectos de los fármacos , Ratones , Dióxido de Silicio , Pulmón/metabolismo , Pulmón/efectos de los fármacos , Pulmón/patología , Ratones Endogámicos C57BL , Proteómica/métodos , Masculino , Ácido Succínico/metabolismo
3.
Proteomics ; 24(1-2): e2300185, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-37847886

RESUMEN

Lactylation, as a novel posttranslational modification, is essential for studying the functions and regulation of proteins in physiological and pathological processes, as well as for gaining in-depth knowledge on the occurrence and development of many diseases, including tumors. However, few studies have examined the protein lactylation of one whole organism. Thus, we studied the lactylation of global proteins in Caenorhabditis elegans to obtain an in vivo lactylome. Using an MS-based platform, we identified 1836 Class I (localization probabilities > 0.75) lactylated sites in 487 proteins. Bioinformatics analysis showed that lactylated proteins were mainly located in the cytoplasm and involved in the tricarboxylic acid cycle (TCA cycle) and other metabolic pathways. Then, we evaluated the conservation of lactylation in different organisms. In total, 41 C. elegans proteins were lactylated and homologous to lactylated proteins in humans and rats. Moreover, lactylation on H4K80 was conserved in three species. An additional 238 lactylated proteins were identified in C. elegans for the first time. This study establishes the first lactylome database in C. elegans and provides a basis for studying the role of lactylation.


Asunto(s)
Proteínas de Caenorhabditis elegans , Caenorhabditis elegans , Humanos , Animales , Ratas , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/metabolismo , Ciclo del Ácido Cítrico , Redes y Vías Metabólicas , Proteoma/metabolismo
4.
Mol Cancer ; 23(1): 127, 2024 Jun 17.
Artículo en Inglés | MEDLINE | ID: mdl-38880903

RESUMEN

The clinical heterogeneity of early-stage endometrial cancer (EC) is worthy of further study to identify high-quality prognostic markers and their potential role in aggressive tumor behavior. Mutation of TP53 was considered as an important primary triage in modified molecular typing for EC, it still cannot precisely predict the prognosis of EC. After proteomic analysis of cancer and para-cancerous tissues from 24 early-stage endometrioid EC patients with different survival outcomes, 13 differentially expressed proteins were screen out while 2 proteins enriched in p53 signaling pathway were further identified by single-cell transcriptome (scRNA-seq). Interestingly, tumor necrosis factor type-1 receptor-associated protein (TRAP1) and calmodulin-regulated spectrin-associated protein family member 3 (CAMSAP3) were found to be significantly downregulated in the specific cell cluster. Expectedly, the signature genes of TRAP1low/CAMSAP3low cluster included classical oncogenes. Moreover, close cellular interactions were observed between myeloid cells and the TRAP1low/CAMSAP3low cluster after systematically elucidating their relationship with tumor microenvironment (TME). The expression of TRAP1 and CAMSAP3 was verified by immunohistochemistry. Thus, a novel prediction model combining TRAP1, CAMSAP3 and TP53 was construct by multi-omics. Compared with the area under the curve, it demonstrated a significantly improvemrnt in the diagnostic efficacy in EC patients from TCGA bank. In conclusion, this work improved the current knowledge regarding the prognosis of early-stage EC through proteomics and scRNA-seq. These findings may lead to improvements in precise risk stratification of early-stage EC patients.


Asunto(s)
Biomarcadores de Tumor , Neoplasias Endometriales , Regulación Neoplásica de la Expresión Génica , Estadificación de Neoplasias , Proteómica , Humanos , Femenino , Neoplasias Endometriales/genética , Neoplasias Endometriales/patología , Neoplasias Endometriales/metabolismo , Neoplasias Endometriales/mortalidad , Pronóstico , Biomarcadores de Tumor/genética , Proteómica/métodos , Microambiente Tumoral/genética , Perfilación de la Expresión Génica , Persona de Mediana Edad , Transcriptoma , Multiómica , Proteínas HSP90 de Choque Térmico
5.
Zhongguo Yi Xue Ke Xue Yuan Xue Bao ; 46(2): 147-153, 2024 Apr.
Artículo en Zh | MEDLINE | ID: mdl-38686709

RESUMEN

Objective To screen out the biomarkers linked to prognosis of breast invasive carcinoma based on the analysis of transcriptome data by random forest (RF),extreme gradient boosting (XGBoost),light gradient boosting machine (LightGBM),and categorical boosting (CatBoost). Methods We obtained the expression data of breast invasive carcinoma from The Cancer Genome Atlas and employed DESeq2,t-test,and Cox univariate analysis to identify the differentially expressed protein-coding genes associated with survival prognosis in human breast invasive carcinoma samples.Furthermore,RF,XGBoost,LightGBM,and CatBoost models were established to mine the protein-coding gene markers related to the prognosis of breast invasive cancer and the model performance was compared.The expression data of breast cancer from the Gene Expression Omnibus was used for validation. Results A total of 151 differentially expressed protein-coding genes related to survival prognosis were screened out.The machine learning model established with C3orf80,UGP2,and SPC25 demonstrated the best performance. Conclusions Three protein-coding genes (UGP2,C3orf80,and SPC25) were screened out to identify breast invasive carcinoma.This study provides a new direction for the treatment and diagnosis of breast invasive carcinoma.


Asunto(s)
Biomarcadores de Tumor , Neoplasias de la Mama , Aprendizaje Automático , Humanos , Neoplasias de la Mama/genética , Femenino , Biomarcadores de Tumor/genética , Pronóstico , Perfilación de la Expresión Génica
6.
Proteomics ; 23(15): e2200437, 2023 08.
Artículo en Inglés | MEDLINE | ID: mdl-37170646

RESUMEN

Lactate is closely related to various cellular processes, such as angiogenesis, responses to hypoxia, and macrophage polarization, while regulating natural immune signaling pathways and promoting neurogenesis and cognitive function. Lysine lactylation (Kla) is a novel posttranslational modification, the examination of which may lead to new understanding of the nonmetabolic functions of lactate and the various physiological and pathological processes in which lactate is involved, such as infection, tumorigenesis and tumor development. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), researchers have identified lactylation in human gastric cancer cells and some other species, but no research on lactylation in human lungs has been reported. In this study, we performed global profiling of lactylation in human lungs under normal physiological conditions, and 724 Kla sites in 451 proteins were identified. After comparing the identified proteins with those reported in human lactylation datasets, 141 proteins that undergo lactylation were identified for the first time in this study. Our work expands the database on human lactylation and helps advance the study on lactylation function and regulation under physiological and pathological conditions.


Asunto(s)
Lisina , Espectrometría de Masas en Tándem , Humanos , Cromatografía Liquida , Ácido Láctico , Pulmón
7.
Proteomics ; 23(16): e2300096, 2023 08.
Artículo en Inglés | MEDLINE | ID: mdl-37309728

RESUMEN

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected hundreds of millions of people all over the world and thus threatens human life. Clinical evidence shows that SARS-CoV-2 infection can cause several neurological consequences, but the existing antiviral drugs and vaccines have failed to stop its spread. Therefore, an understanding of the response to SARS-CoV-2 infection of hosts is vital to find a resultful therapy. Here, we employed a K18-hACE2 mouse infection model and LC-MS/MS to systematically evaluate the acetylomes of brain cortexes in the presence and absence of SARS-CoV-2 infection. Using a label-free strategy, 3829 lysine acetylation (Kac) sites in 1735 histone and nonhistone proteins were identified. Bioinformatics analyses indicated that SARS-CoV-2 infection might lead to neurological consequences via acetylation or deacetylation of important proteins. According to a previous study, we found 26 SARS-CoV-2 proteins interacted with 61 differentially expressed acetylated proteins with high confidence and identified one acetylated SARS-CoV-2 protein nucleocapsid phosphoprotein. We greatly expanded the known set of acetylated proteins and provide the first report of the brain cortex acetylome in this model and thus a theoretical basis for future research on the pathological mechanisms and therapies of neurological consequences after SARS-CoV-2 infection.


Asunto(s)
COVID-19 , SARS-CoV-2 , Ratones , Humanos , Animales , SARS-CoV-2/metabolismo , COVID-19/patología , Lisina/metabolismo , Acetilación , Cromatografía Liquida , Peptidil-Dipeptidasa A/metabolismo , Enzima Convertidora de Angiotensina 2/metabolismo , Espectrometría de Masas en Tándem , Encéfalo/metabolismo , Ratones Transgénicos , Modelos Animales de Enfermedad
8.
Zhongguo Yi Xue Ke Xue Yuan Xue Bao ; 45(6): 867-885, 2023 Dec 30.
Artículo en Zh | MEDLINE | ID: mdl-38173097

RESUMEN

Objective To investigate the role and mechanism of eukaryotic translation elongation factor 1(EEF1) family members (EEF1D,EEF1A1,and EEF1A2) in lung adenocarcinoma (LUAD) based on public databases.Methods We examined EEF1 member expression levels in human LUAD samples via The Cancer Genome Atlas in the UCSC Xena browser and the Clinical Proteomic Tumor Analysis Consortium.We analyzed the mRNA and protein levels of EEF1D,EEF1A1,and EEF1A2 and their correlations with pathological variables via the Mann-Whitney U test.The Kaplan-Meier curves were established to assess the prognostic values of EEF1D,EEF1A1,and EEF1A2.The single-sample gene set enrichment analysis algorithm was employed to explore the relationship between the expression levels of EEF1 members and tumor immune cell infiltration.Spearman and Pearson correlation analyses were performed to examine the relationship between the expression levels of EEF1 members and those of the genes in the phosphatidylinositol 3-kinase/protein kinase B signaling pathway.The immunohistochemical assay was employed to determine the expression levels of EEF1D,EEF1A1,and EEF1A2 in the LUAD tissue (n=75) and paracancer tissue (n=75) samples.Results The mRNA and protein levels of EEF1D,EEF1A1,and EEF1A2 showed significant differences between tumor and paracancer tissues (all P<0.001).The patients with high protein levels of EEF1A1 showed bad prognosis in terms of overall survival (P=0.039),and those with high protein levels of EEF1A2 showed good prognosis in terms of overall survival (P=0.012).The influence of the mRNA level of EEF1D on prognosis was associated with pathological characteristics.The expression levels of EEF1 members were significantly associated with the infiltration of various immune cells and the expression of key molecules in the phosphatidylinositol 3-kinase/protein kinase B signaling pathway.Conclusion EEF1D,EEF1A1,and EEF1A2 are associated with the progression of LUAD,serving as the candidate prognostic markers for LUAD.


Asunto(s)
Adenocarcinoma del Pulmón , Neoplasias Pulmonares , Humanos , Factor 1 de Elongación Peptídica/química , Factor 1 de Elongación Peptídica/genética , Factor 1 de Elongación Peptídica/metabolismo , Proteómica , Proteínas Proto-Oncogénicas c-akt/metabolismo , Carcinogénesis , ARN Mensajero/genética , Fosfatidilinositol 3-Quinasas , Pronóstico
9.
Proteomics ; 22(17): e2100381, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-35644922

RESUMEN

The lysine succinylation (Ksucc) is involved in many core energy metabolism pathways and affects the metabolic process in mitochondria, making this modification highly valuable for studying diseases related to mitochondrial disorders. In this paper, we used liquid chromatography with tandem mass spectrometry (LC-MS/MS) to perform the first global profiling of succinylation in human lungs under normal physiological conditions. Using an MS-based platform, we identified 1485 Ksucc sites in 568 proteins. We then compared these sites with those previously identified in human succinylome studies to investigate specific succinylated proteins and identify their possible functions in the lung and to explore the substrate preferences of succinylation modifiers in different cell lines and at different subcellular localizations. Our work expands the succinylation database and supplementary materials on the human succinylome and will thus help in further study of the function of Ksucc and regulation under related physiological and pathological conditions.


Asunto(s)
Lisina , Espectrometría de Masas en Tándem , Cromatografía Liquida , Humanos , Pulmón/metabolismo , Lisina/metabolismo , Procesamiento Proteico-Postraduccional , Proteoma/metabolismo
10.
Proteome Sci ; 20(1): 12, 2022 Aug 05.
Artículo en Inglés | MEDLINE | ID: mdl-35932011

RESUMEN

BACKGROUND: Aging is a complex biological process accompanied by a time-dependent functional decline that affects most living organisms. Omics studies help to comprehensively understand the mechanism of aging and discover potential intervention methods. Old mice are frequently obese with a fatty liver. METHODS: We applied mass spectrometry-based phosphoproteomics to obtain a global phosphorylation profile of the liver in mice aged 2 or 18 months. MaxQuant was used for quantitative analysis and PCA was used for unsupervised clustering. RESULTS: Through phosphoproteome analysis, a total of 5,685 phosphosites in 2,335 proteins were filtered for quantitative analysis. PCA analysis of both the phosphoproteome and transcriptome data could distinguish young and old mice. However, from kinase prediction, kinase-substrate interaction analysis, and KEGG functional enrichment analysis done with phosphoproteome data, we observed high phosphorylation of fatty acid biosynthesis, ß-oxidation, and potential secretory processes, together with low phosphorylation of the Egfr-Sos1-Araf/Braf-Map2k1-Mapk1 pathway and Ctnnb1 during aging. Proteins with differentially expressed phosphosites seemed more directly related to the aging-associated fatty liver phenotype than the differentially expressed transcripts. The phosphoproteome may reveal distinctive biological functions that are lost in the transcriptome. CONCLUSIONS: In summary, we constructed a phosphorylation-associated network in the mouse liver during normal aging, which may help to discover novel antiaging strategies.

11.
Cerebrovasc Dis ; 51(2): 138-148, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35288494

RESUMEN

BACKGROUND AND PURPOSE: Delayed cerebral ischemia is a major cause of morbidity and mortality in patients with aneurysmal subarachnoid hemorrhage (aSAH). Cilostazol, a selective inhibitor of phosphodiesterase 3, was reported to reduce cerebral vasospasm and improve outcomes. We aimed to conduct an updated systematic review and meta-analysis of the efficacy and safety of cilostazol in aSAH. METHODS: We systematically searched PubMed, Embase, MEDLINE, and the Cochrane Library for articles published in English with the latest publishing time in August 2020. Articles reporting favorable outcome as the primary outcome and reporting severe angiographic vasospasm (aVS), symptomatic vasospasm (sVS), new cerebral infarction, or mortality as the secondary outcome were included in this review. Furthermore, we examined whether clinical outcomes were associated with the dosage of cilostazol (300 mg/day vs. 100-200 mg/day). RESULTS: Data from 405 patients in 4 randomized controlled trials (RCTs) and 461 patients in 4 observational studies (OSs) were included. In RCT studies, cilostazol was associated with significant favorable outcomes at discharge or 1 month (risk ratio [RR] 1.41, 95% confidence interval [CI] 1.01-1.97, p = 0.04) or 3 or 6 months (RR 1.16, 95% CI 1.05-1.28, p = 0.002). However, in OSs, no significant difference was indicated in favorable outcomes at discharge or 1 month (RR 1.22, 95% CI 0.94-1.60, p = 0.14) nor 3 or 6 months (RR 1.29, 95% CI 0.92-1.81, p = 0.14). The analyses found that cilostazol significantly reduced the incidences of severe aVS (RCT: RR 0.64, 95% CI 0.41-1.01, p = 0.05; OS: RR 0.61, 95% CI 0.43-0.88, p = 0.007), sVS (RCT: RR 0.46, 95% CI 0.31-0.70, p = 0.0002; OS: RR 0.38, 95% CI 0.21-0.68, p = 0.001), and new cerebral infarction (RCT: RR 0.40, 95% CI 0.24-0.67, p = 0.0005; OS: RR 0.38, 95% CI 0.23-0.64, p = 0.0002). However, no significant difference in mortality (RCT: RR 0.86, 95% CI 0.23-3.21, p = 0.82; OS: RR 0.16, 95% CI 0.02-1.24, p = 0.08) was found. In 3 OSs which reported different doses of cilostazol (300 mg/day vs. 100-200 mg/day) for aSAH, the 300-mg/day cilostazol groups showed decreased delayed cerebral infarction (RR 0.27, 95% CI 0.09-0.81, p = 0.02) but no significant difference in shunt-dependent hydrocephalus (RR 0.92, 95% CI 0.33-2.60, p = 0.88) or functional outcomes (RR 1.14, 95% CI 0.74-1.75, p = 0.56) compared with the 100-200 mg/day cilostazol groups. CONCLUSIONS: The meta-analyses suggest the credible efficacy and safety of cilostazol in treating aSAH. Furthermore, 300-mg/day cilostazol treatment appeared to be more effective than 100-200 mg/day treatment.


Asunto(s)
Hemorragia Subaracnoidea , Vasoespasmo Intracraneal , Infarto Cerebral/complicaciones , Cilostazol/efectos adversos , Humanos , Hemorragia Subaracnoidea/diagnóstico por imagen , Hemorragia Subaracnoidea/tratamiento farmacológico , Resultado del Tratamiento
12.
BMC Musculoskelet Disord ; 22(1): 944, 2021 Nov 11.
Artículo en Inglés | MEDLINE | ID: mdl-34763682

RESUMEN

BACKGROUND: Poor osseointegration is the key reason for implant failure after arthroplasty,whether under osteoporotic or normal bone conditions. To date, osseointegration remains a major challenge. Recent studies have shown that deferoxamine (DFO) can accelerate osteogenesis by activating the hypoxia signaling pathway. The purpose of this study was to test the following hypothesis: after knee replacement, intra-articular injection of DFO will promote osteogenesis and osseointegration with a 3D printed titanium prosthesis in the bones of osteoporotic rats. MATERIALS AND METHODS: Ninety female Sprague-Dawley rats were used for the experiment. Ten rats were used to confirm the successful establishment of the osteoporosis model: five rats in the sham operation group and five rats in the ovariectomy group. After ovariectomy and knee arthroplasty were performed, the remaining 80 rats were randomly divided into DFO and control groups (n = 40 per group). The two groups were treated by intraarticular injection of DFO and saline respectively. After 2 weeks, polymerase chain reaction (PCR) and immunohistochemistry were used to evaluate the levels of HIF-1a, VEGF, and CD31. HIF-1a and VEGF have been shown to promote angiogenesis and bone regeneration, and CD31 is an important marker of angiogenesis. After 12 weeks, the specimens were examined by micro-computed tomography (micro-CT), biomechanics, and histopathology to evaluate osteogenesis and osseointegration. RESULTS: The results of PCR showed that the mRNA levels of VEGF and CD31 in the DFO group were significantly higher than those in the control group. The immunohistochemistry results indicated that positive cell expression of HIF-1a, VEGF, and CD31 in the DFO group was also higher. Compared with the control group, the micro-CT parameters of BMD, BV/TV, TB. N, and TB. Th were significantly higher. The maximal pull-out force and the bone-to-implant contact value were also higher. CONCLUSIONS: The local administration of DFO, which is used to activate the HIF-1a signaling pathway, can promote osteogenesis and osseointegration with a prosthesis in osteoporotic bone.


Asunto(s)
Miembros Artificiales , Titanio , Animales , Femenino , Humanos , Hipoxia , Oseointegración , Ovariectomía , Ratas , Ratas Sprague-Dawley , Microtomografía por Rayos X
13.
Zhongguo Yi Xue Ke Xue Yuan Xue Bao ; 43(4): 536-544, 2021 Aug.
Artículo en Zh | MEDLINE | ID: mdl-34494523

RESUMEN

Objective To obtain the metabolome profiles in liver and serum of mice during normal aging. Methods The liver and serum samples of ten 2-month-old mice and ten 18-month-old C57BL/6J mice under physiological conditions were collected.Metabolites were identified and quantified by liquid chromatography-tandem mass spectrometry.The overall assessment,differential screening,and functional analysis were performed with the filtered high-quality data. Results In the negative-ion mode and positive-ion mode,242 and 399 metabolites were identified in the liver and 265 and 230 in serum,respectively.The difference of metabolome between young and old mice was moderate.The upregulated metabolites identified in aging liver were related to the metabolism of riboflavin,glucose,and arachidonic acid,while the downregulated ones were associated with the metabolism of pyrimidine,purine,glycerophospholipid,glutathione,and nicotinamide.Altered metabolites in serum during aging were involved in a variety of nucleic acid metabolism-related pathways,such as pyrimidine metabolism,purine metabolism,one carbon pool by folate,and amino sugar and nucleotide sugar metabolism. Conclusions The metabolome profiles of mouse liver and serum both revealed dysregulated nucleic acid metabolism pathways during normal aging.This study provides metabolome data for further research on aging-associated mechanism and may support the discovery of intervention methods for aging.


Asunto(s)
Metaboloma , Metabolómica , Envejecimiento , Animales , Hígado , Ratones , Ratones Endogámicos C57BL
14.
Zhongguo Yi Xue Ke Xue Yuan Xue Bao ; 43(5): 696-705, 2021 Oct.
Artículo en Zh | MEDLINE | ID: mdl-34728030

RESUMEN

Objective To obtain the proteome and acetylome profiles of livers in mice during normal aging.Methods We applied tandem mass tag labeling and liquid chromatography tandem mass spectrometry and achieved proteome and acetylome data in C57BL/6J male mice aged 2 and 18 months under physiological conditions.Results A total of 4712 proteins were quantified by proteome profiling,and 4818 acetylated sites in 1367 proteins by acetylome profiling.The proteome and acetylome revealed moderate differences in the livers of young and old mice.There were 195 differentially expressed proteins in the proteome and 113 differentially expressed acetylated sites corresponding to 76 proteins in the acetylome.Functional enrichment analysis for the proteome showed that aging-associated upregulated proteins were mainly involved in fatty acid metabolism,epoxygenase P450 pathway,drug catabolic process,organic hydroxy compound metabolic process,and arachidonic acid metabolic process,while the downregulated proteins were related to regulation of gene silencing,nucleosome assembly,protein heterotetramerization,response to interferon,protein-DNA complex assembly and other processes.For the acetylome,the proteins with aging-associated upregulated acetylated sites mainly participated in cofactor metabolism,small molecule catabolic process,ribose phosphate metabolic process,ribonucleotide metabolic process,and purine-containing compound metabolic process,while the proteins with downregulated acetylated sites were associated with sulfur compound metabolic process,response to unfolded protein,and amino acid metabolic process.Conclusion We profiled the proteome and acetylome of livers in mice during normal aging and generated datasets for further research on aging.


Asunto(s)
Lisina , Proteoma , Acetilación , Envejecimiento , Animales , Hígado , Lisina/metabolismo , Masculino , Ratones , Ratones Endogámicos C57BL , Proteoma/metabolismo
15.
Proteomics ; 20(19-20): e2000049, 2020 10.
Artículo en Inglés | MEDLINE | ID: mdl-32864800

RESUMEN

Lysine crotonylation (Kcr) is a recently discovered post-translational modification that potentially regulates multiple biological processes. With an objective to expand the available crotonylation datasets, LC-MS/MS is performed using mouse liver samples under normal physiological conditions to obtain in vivo crotonylome. A label-free strategy is used and 10 034 Class I (localization probabilities > 0.75) crotonylated sites are identified in 2245 proteins. The KcrE, KcrD, and EKcr motifs are significantly enriched in the crotonylated peptides. The identified crotonylated proteins are mostly enzymes and primarily located in the cytoplasm and nucleus. Functional enrichment analysis based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes shows that the crotonylated proteins are closely related to the purine-containing compound metabolic process, ribose phosphate metabolic process, carbon metabolism pathway, ribosome pathway, and a series of metabolism-associated biological processes. To the best of the authors' knowledge, this research provides the first report on the mouse liver crotonylome. Furthermore, it offers additional evidence that crotonylation exists in non-histone proteins, and is likely involved in various biological processes. The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium with the dataset identifiers PXD019145.


Asunto(s)
Lisina , Proteoma , Animales , Cromatografía Liquida , Hígado/metabolismo , Lisina/metabolismo , Ratones , Procesamiento Proteico-Postraduccional , Proteoma/metabolismo , Espectrometría de Masas en Tándem
16.
BMC Vet Res ; 16(1): 404, 2020 Oct 27.
Artículo en Inglés | MEDLINE | ID: mdl-33109179

RESUMEN

BACKGROUND: Disease prevention and control is a significant part in the ex-situ conservation of the endangered red panda (Ailurus fulgens), being bacterial infection is one of the most important health threats to the captive population. To date, studies about the infection caused by Escherichia coli in the red panda are scarce. This study was conducted to determine the cause of death of a captive red panda through clinical symptoms, complete blood count, biochemical analysis, pathological diagnosis and bacterial whole genome sequencing. CASE PRESENTATION: The following report describes a case of a 1.5 year old captive red panda (Ailurus fulgens) that was found lethargic and anorectic. She was moved to the quarantine area for daily treatment with 50 mg of Cefpodoxime Proxetil. During the three-day treatment, she did not eat or defecate, and then died. Clinical hematology revealed the values of neutrophils, alanine aminotransferase (ALT), aspartate aminotransferase (AST) and blood urea nitrogen (BUN) were significantly higher. Histological analysis demonstrated major pathological damage in the kidneys, liver and lungs, characterized by hyperemia, parenchymal cell degeneration and necrosis and inflammatory cell infiltration which were predominantly neutrophilic. A bacterial strain confirmed as Escherichia coli was isolated post mortem. Whole genome sequencing of the E. coli showed the complete genome size was 4.99 Mbp. PapA, PapC, OmpA, OmpU and other virulence factors which specific to Uropathogenic Escherichia coli (UPEC) were found in the isolate. Among the virulence factors, P pili, type I pili and related factors of the iron uptake system were associated with nephrotoxicity. CONCLUSION: The red panda died of bacterial infection caused by an uropathogenic strain of Escherichia coli. The pathogenic mechanisms of the strain are closely related to the expression of specific virulence genes.


Asunto(s)
Ailuridae , Infecciones por Escherichia coli/veterinaria , Escherichia coli Uropatógena/aislamiento & purificación , Animales , Antibacterianos/uso terapéutico , Ceftizoxima/análogos & derivados , Ceftizoxima/uso terapéutico , Infecciones por Escherichia coli/tratamiento farmacológico , Infecciones por Escherichia coli/microbiología , Femenino , Genoma Bacteriano , Escherichia coli Uropatógena/genética , Escherichia coli Uropatógena/patogenicidad , Factores de Virulencia/genética , Secuenciación Completa del Genoma/veterinaria , Cefpodoxima Proxetilo
18.
Phys Chem Chem Phys ; 21(27): 15206-15214, 2019 Jul 10.
Artículo en Inglés | MEDLINE | ID: mdl-31250869

RESUMEN

Thiophene/benzene-fused π-conjugated systems are normally employed as the core units of two- and three-dimensionally expanded small molecule hole-transporting materials (HTMs) to improve their electronic and charge transport properties, whereas comparison studies between two-dimensional and three-dimensional core conformations are less reported. To further find useful clues for the design of highly-efficient small molecule HTMs and to find new core units, in this work, four HTM molecules are designed by employing triphenylene, benzotrithiophene, triptycene, and thiophenetriptycene as the core units, and simulated with density functional theory combined with the Marcus hopping model. Our results show that all the considered HTMs display appropriate molecular energy levels, less optical absorption in the visible light region and large Stokes shifts, and high hole mobilities (9.80 × 10-2 cm2 V-1 s-1). Compared with the two-dimensional core structures, the three-dimensional cores exhibit evident superiorities with the same chemical components. Meanwhile, we also find that the quasi-degenerate HOMO energy levels will be helpful to enlarge the transfer integrals between adjacent molecules, and further to promote the hole transport in HTMs. By considering the various elements simultaneously, these investigated HTMs (S-1-S-4) with thiophene- and benzene-fused cores can be expected as potential promising candidates to help create more efficient solar cells.

19.
Kidney Int ; 92(6): 1404-1418, 2017 12.
Artículo en Inglés | MEDLINE | ID: mdl-28709639

RESUMEN

Autosomal dominant polycystic kidney disease (ADPKD) is a common monogenetic disease characterized by the progressive development of renal cysts with further need for effective therapy. Here our aim was to investigate the effect of Ganoderma triterpenes (GT) on the development of kidney cysts. Importantly, GT attenuated cyst development in two mouse models of ADPKD with phenotypes of severe cystic kidney disease. Assays for tubulogenesis showed that GT promoted epithelial tubule formation in MDCK cells, suggesting a possible effect on epithelial cell differentiation. The role of GT in regulating key signaling pathways involved in the pathogenesis of PKD was further investigated by immune blotting. This showed that GT specifically downregulated the activation of the Ras/MAPK signaling pathway both in vitro and in vivo without detectable effect on the mTOR pathway. This mechanism may be involved in GT downregulating intracellular cAMP levels. Screening of 15 monomers purified from GT for their effects on cyst development indicated that CBLZ-7 (ethyl ganoderate C2) had a potent inhibitory effect on cyst development in vitro. Additionally, like GT, CBLZ-7 was able to downregulate forskolin-induced activation of the Ras/MAPK pathway. Thus, GT and its purified monomer CBLZ-7 may be potential therapeutic regents for treating ADPKD.


Asunto(s)
Diferenciación Celular/efectos de los fármacos , Ganoderma/química , Sistema de Señalización de MAP Quinasas/efectos de los fármacos , Riñón Poliquístico Autosómico Dominante/tratamiento farmacológico , Triterpenos/farmacología , 8-Bromo Monofosfato de Adenosina Cíclica/análogos & derivados , Animales , Línea Celular , Proliferación Celular/efectos de los fármacos , Colforsina/farmacología , Quistes/tratamiento farmacológico , Modelos Animales de Enfermedad , Regulación hacia Abajo , Células Epiteliales/efectos de los fármacos , Humanos , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Riñón Poliquístico Autosómico Dominante/genética , Transducción de Señal , Serina-Treonina Quinasas TOR/metabolismo , Canales Catiónicos TRPP/genética , Triterpenos/aislamiento & purificación , Triterpenos/uso terapéutico , Proteínas ras/metabolismo
20.
Chemistry ; 23(72): 18140-18145, 2017 Dec 22.
Artículo en Inglés | MEDLINE | ID: mdl-29139155

RESUMEN

To reduce intrinsic defect density in perovskite films, various additives are often added into the precursor solution. In this paper, a novel solution, in which isopropanol (IPA) was added into the precursor solution, was developed for the preparation of normal planar perovskite solar cells (PSCs). A champion power conversion efficiency (PCE) of 19.70 % was achieved with this approach. By adding IPA into the precursor solution, CH3 NH3 PbI3 perovskite showed better crystallization and stability, indicating improved film quality. Because of the improved morphology of perovskite crystal, the PCE of PSCs increased. In addition, the unencapsulated PSCs retained high output for up to 40 days in air at room temperature, indicating the stability of PSCs. These results may provide a new avenue for manufacturing high efficiency and high stability PSCs.

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