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1.
Small ; 20(21): e2309626, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38098431

RESUMO

Floating gate memory (FGM), composed of van der Waals (vdW) junctions with an atomically thin floating layer for charge storage, is widely employed to develop logic-in memories and in-sensor computing devices. Most research efforts of FGM are spent on achieving long-term charge storage and fast reading/writing for flash and random-access memory. However, dynamic modulation of memory time via a tunneling barrier and vdW interfaces, which is critical for synaptic computing and machine vision, is still lacking. Here, a van der Waals short-term memory with tunable memory windows and retention times from milliseconds to thousands of seconds is reported, which is approximately exponentially proportional to the thickness h-BN (hexagonal boron nitride) barrier. The specific h-BN barrier with fruitful gap states provides charge release channels for trapped charges, making the vdW device switchable between positive photoconductance and negative photoconductance with a broadband light from IR to UV range. The dynamic short-term memory with tunable photo response highlights the design strategy of novel vdW memory vis interface engineering for further intelligent information storage and optoelectronic detection.

2.
Exp Cell Res ; 430(1): 113685, 2023 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-37330182

RESUMO

Acute lung injury (ALI), a common clinical type of critical illness, is an acute hypoxic respiratory insufficiency caused by the damage of alveolar epithelial cells and capillary endothelial cells. In a previous study, we reported a novel lncRNA, lncRNA PFI, which could protect against pulmonary fibrosis in pulmonary fibroblasts. The present study demonstrated that lncRNA PFI was downregulated in alveolar epithelial cell of mice injury lung tissues, and further investigated the role of lncRNA PFI in regulating inflammation-induced alveolar epithelial cell apoptosis. Overexpression of lncRNA PFI could partially abrogated bleomycin induced type II AECs injured. Subsequently, bioinformatic prediction revealed that lncRNA PFI might directly bind to miR-328-3p, and further AGO-2 RNA binding protein immunoprecipitation (RIP) assay confirmed their binding relationship. Furthermore, miR-328-3p promoted apoptosis in MLE-12 cells by limiting the activation of the Creb1, a protein correlated with cell apoptosis, whereas AMO-328-3p ablated the pro-apoptosis effect of silencing lncRNA PFI in MLE-12 cells. While miR-328-3p could also ablate the function of lncRNA PFI in bleomycin treated human lung epithelial cells. Enhanced expression of lncRNA PFI reversed the LPS-induced lung injury in mice. Overall, these data reveal that lncRNA PFI mitigated acute lung injury through miR-328-3p/Creb1 pathway in alveolar epithelial cells.


Assuntos
Lesão Pulmonar Aguda , MicroRNAs , RNA Longo não Codificante , Síndrome do Desconforto Respiratório , Humanos , Camundongos , Animais , Células Epiteliais Alveolares/metabolismo , MicroRNAs/metabolismo , RNA Longo não Codificante/genética , RNA Longo não Codificante/metabolismo , Células Endoteliais/metabolismo , Lesão Pulmonar Aguda/induzido quimicamente , Lesão Pulmonar Aguda/genética , Lesão Pulmonar Aguda/metabolismo , Apoptose/genética , Síndrome do Desconforto Respiratório/metabolismo , Lipopolissacarídeos/efeitos adversos , Bleomicina/farmacologia
3.
Nucleic Acids Res ; 50(W1): W312-W321, 2022 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-35639516

RESUMO

In the era of life-omics, huge amounts of multi-omics data have been generated and widely used in biomedical research. It is challenging for biologists with limited programming skills to obtain biological insights from multi-omics data. Thus, a biologist-oriented platform containing visualization functions is needed to make complex omics data digestible. Here, we propose an easy-to-use, interactive web server named ExpressVis. In ExpressVis, users can prepare datasets; perform differential expression analysis, clustering analysis, and survival analysis; and integrate expression data with protein-protein interaction networks and pathway maps. These analyses are organized into six modules. Users can use each module independently or use several modules interactively. ExpressVis displays analysis results in interactive figures and tables, and provides comprehensive interactive operations in each figure and table, between figures or tables in each module, and among different modules. It is freely accessible at https://omicsmining.ncpsb.org.cn/ExpressVis and does not require login. To test the performance of ExpressVis for multi-omics studies of clinical cohorts, we re-analyzed a published hepatocellular carcinoma dataset and reproduced their main findings, suggesting that ExpressVis is convenient enough to analyze multi-omics data. Based on its complete analysis processes and unique interactive operations, ExpressVis provides an easy-to-use solution for exploring multi-omics data.


Assuntos
Multiômica , Software , Computadores , Mapas de Interação de Proteínas , Internet
4.
Genomics ; 114(1): 292-304, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34915127

RESUMO

Mycobacterium tuberculosis (MTB) is a severe causing agent of tuberculosis (TB). Although H37Rv, the type strain of M. tuberculosis was sequenced in 1998, annotation errors of encoding genes have been frequently reported in hundreds of papers. This phenomenon is particularly severe at the 5' end of the genes. Here, we applied a TMPP [(N-Succinimidyloxycarbonylmethyl) tris (2,4,6-trimethoxyphenyl) phosphonium bromide] labeling combined with StageTip separating strategy on M. tuberculosis H37Rv to characterize the N-terminal start sites of its annotated encoding genes. Totally, 1047 proteins were identified with 2058 TMPP labeled N-terminal peptides from all the 2625 mass spectrometer (MS) sequenced proteins. Comparative genomics analysis allowed the re-annotation of 43 proteins' N-termini in H37Rv and 762 proteins in Mycobacteriaceae. All revised N-termini start sites were distributed in 5'-UTR of annotated genes due to over-annotation of previous N-terminal initiation codon, especially the ATG. In addition, we identified and verified a novel gene Rv1078A in +3 frame different from the annotated gene Rv1078 in +2 frame. Altogether, our findings contribute to the better understanding of N-terminal of H37Rv and other species from Mycobacteriaceae that can assist future studies on biological study.


Assuntos
Mycobacterium tuberculosis , Tuberculose , Humanos , Espectrometria de Massas , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/metabolismo , Peptídeos/química , Proteínas/metabolismo
5.
BMC Microbiol ; 22(1): 264, 2022 Nov 04.
Artigo em Inglês | MEDLINE | ID: mdl-36333788

RESUMO

BACKGROUND: Deinococcus radiodurans (D. radiodurans) is best known for its extreme resistance to diverse environmental stress factors, including ionizing radiation (IR), ultraviolet (UV) irradiation, oxidative stress, and high temperatures. Robust DNA repair system and antioxidant system have been demonstrated to contribute to extreme resistance in D. radiodurans. However, practically all studies on the mechanism underlying D. radiodurans's extraordinary resistance relied on the treated strain during the post-treatment recovery lag phase to identify the key elements involved. The direct gene or protein changes of D. radiodurans after stress have not yet been characterized. RESULTS: In this study, we performed a proteomics profiling on D. radiodurans right after the heavy ion irradiation treatment, to discover the altered proteins that were quickly responsive to IR in D. radiodurans. Our study found that D. radiodurans shown exceptional resistance to 12C6+ heavy ion irradiation, in contrast to Escherichia coli (E.coli) strains. By using iTRAQ (Isobaric Tags for Relative and Absolute Quantitation)-based quantitative mass spectrometry analysis, the kinetics of proteome changes induced by various dosages of 12C6+ heavy ion irradiation were mapped. The results revealed that 452 proteins were differentially expressed under heavy ion irradiation, with the majority of proteins being upregulated, indicating the upregulation of functional categories of translation, TCA cycle (Tricarboxylic Acid cycle), and antioxidation regulation under heavy ion irradiation. CONCLUSIONS: This study shows how D. radiodurans reacts to exposure to 12C6+ heavy ion irradiation in terms of its overall protein expression profile. Most importantly, comparing the proteome profiling of D. radiodurans directly after heavy ion irradiation with research on the post-irradiation recovery phase would potentially provide a better understanding of mechanisms underlying the extreme radioresistance in D. radiodurans.


Assuntos
Deinococcus , Íons Pesados , Deinococcus/genética , Deinococcus/metabolismo , Deinococcus/efeitos da radiação , Proteoma/metabolismo , Proteômica , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Escherichia coli/genética , Antioxidantes/metabolismo
6.
Toxicol Appl Pharmacol ; 449: 116110, 2022 08 15.
Artigo em Inglês | MEDLINE | ID: mdl-35688186

RESUMO

Protein phosphorylation is the most common type of post-translational modification where serine, threonine or tyrosine are reversibly bound to the phosphate group of ATP in a reaction catalyzed by protein kinases. Phosphorylation plays an important role in regulation of cell homeostasis, including but not limited to signal perception and transduction, gene expression and function of proteins. Protein phosphorylation happens on a fast time scale and represents an energy-efficient way for the cell to adapt to exposure to chemical stressors. To understand the cascade of cellular signaling induced by exposure to chemicals, we have exposed HepG2 cells to three chemicals with different modes of action, namely, caffeine, coumarin, and quercetin in a concentration and time response manner. Significantly upregulated and downregulated phosphosites were screened to analyze the activation/deactivation of signaling pathways by protein kinases. In total, 69, 44 and 12 signaling pathways were found enriched in caffeine, coumarin and quercetin treated cells, respectively, of which 9 pathways were co-enriched with 11 jointly responded kinases. Among identified co-responded kinases, CDK1, MAPK1 and MAPK3 play important roles in cell cycle and insulin signaling pathways. Quantitative phosphoproteomics can sensitively distinguish the effects of different chemicals on cells, allowing the assessment of chemical safety through changes in substrates and metabolic pathways at the cellular level, which is important for the development of non-animal approaches for chemical safety assessment.


Assuntos
Cafeína , Cumarínicos , Quercetina , Cafeína/farmacologia , Cumarínicos/farmacologia , Células Hep G2 , Humanos , Fosforilação , Proteínas Quinases/metabolismo , Proteômica , Quercetina/farmacologia
7.
Int J Mol Sci ; 23(14)2022 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-35887401

RESUMO

Vitis vinifera plants are disease-susceptible while Vitis pseudoreticulata plants are disease-resistant; however, the molecular mechanism remains unclear. In this study, the single-stranded DNA- and RNA-binding protein gene Whirly (VvWhy1 and VpWhy1) were cloned from V. vinifera "Cabernet Sauvignon" and V. pseudoreticulata "HD1". VvWhy1 and VpWhy1 promoter sequences (pVv and pVp) were also isolated; however, the identity of the promoter sequences was far lower than that between the Why1 coding sequences (CDSs). Both Why1 gene sequences had seven exons and six introns, and they had a C-terminal Whirly conserved domain and N-terminal chloroplast transit peptide, which was then verified to be chloroplast localization. Transcriptional expression showed that VpWhy1 was strongly induced by Plasmopara viticola, while VvWhy1 showed a low expression level. Further, the GUS activity indicated pVp had high activity involved in response to Phytophthora capsici infection. In addition, Nicotiana benthamiana transiently expressing pVp::VvWhy1 and pVp::VpWhy1 enhanced the P. capsici resistance. Moreover, Why1, PR1 and PR10 were upregulated in pVp transgenic N. benthamiana leaves. This research presented a novel insight into disease resistance mechanism that pVp promoted the transcription of Why1, which subsequently regulated the expression of PR1 and PR10, further enhancing the resistance to P. capsici.


Assuntos
Phytophthora , Vitis , DNA de Cadeia Simples/metabolismo , Resistência à Doença/genética , Regulação da Expressão Gênica de Plantas , Phytophthora/metabolismo , Doenças das Plantas/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Vitis/genética , Vitis/metabolismo
8.
J Proteome Res ; 20(2): 1328-1340, 2021 02 05.
Artigo em Inglês | MEDLINE | ID: mdl-33443437

RESUMO

Proteomics approaches designed to catalogue all open reading frames (ORFs) under a defined set of growth conditions of an organism have flourished in recent years. However, no proteome has been sequenced completely so far. Here, we generate the largest yeast proteome data set, including 5610 identified proteins, using a strategy based on optimized sample preparation and high-resolution mass spectrometry. Among the 5610 identified proteins, 94.1% are core proteins, which achieves near-complete coverage of the yeast ORFs. Comprehensive analysis of missing proteins showed that proteins are missed mainly due to physical properties. A review of protein abundance shows that our proteome encompasses a uniquely broad dynamic range. Additionally, these values highly correlate with mRNA abundance, implying a high level of accuracy, sensitivity, and precision. We present examples of how the data could be used, including reannotating gene localization, providing expression evidence of pseudogenes. Our near-complete yeast proteome data set will be a useful and important resource for further systematic studies.


Assuntos
Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae , Espectrometria de Massas , Proteoma/genética , Proteômica , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética
9.
J Proteome Res ; 20(6): 3290-3304, 2021 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-34008989

RESUMO

Blastobotrys adeninivorans plays an essential role in pile-fermenting of Pu-erh tea. Its ability to assimilate various carbon and nitrogen sources makes it available for application in a wide range of industry sectors. The genome of B. adeninivorans TMCC 70007 isolated from pile-fermented Pu-erh tea was sequenced and assembled. Proteomics analysis indicated that 4900 proteins in TMCC 70007 were expressed under various culture conditions. Proteogenomics mapping revealed 48 previously unknown genes and corrected 118 gene models predicted by GeneMark-ES. Ortho-proteogenomics analysis identified 17 previously unidentified genes in B. adeninivorans LS3, the first strain with a sequenced genome among the genus Blastobotrys as well. More importantly, five species specific genes were identified from TMCC 70007, which could serve as a barcode for strain typing and were applicable for fermentation process protection of this industrial species. The datasets generated from tea aqueous extract culture not only increased the proteome coverage and accuracy but also contributed to the identification of proteins related to polyphenols and caffeine, which were considered to change greatly during the microbial fermentation of Pu-erh tea. This study provides a proteome perspective on TMCC 70007, which was considered to be an important strain in the production of Pu-erh tea. The systematic proteogenomics analysis not only made a better annotation on the genome of B. adeninivorans TMCC 70007 as previous proteogenomics study but also provided solution for fermentation process protection on valuable industrial species with species specific genes uniquely identified from proteogenomics study.


Assuntos
Proteogenômica , Chá , Carbolinas , Fermentação , Saccharomyces cerevisiae , Saccharomycetales
10.
FASEB J ; 34(6): 8416-8427, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32350948

RESUMO

During human erythroid maturation, Hsp70 translocates into the nucleus and protects GATA-1 from caspase-3 cleavage. Failure of Hsp70 to localize to the nucleus was found in Myelodysplastic syndrome (MDS) erythroblasts and can induce dyserythropoiesis, with arrest of maturation and death of erythroblasts. However, the mechanism of the nuclear trafficking of Hsp70 in erythroblasts remains unknown. Here, we found the hematopoietic transcriptional regulator, EDAG, to be a novel binding partner of Hsp70 that forms a protein complex with Hsp70 and GATA-1 during human normal erythroid differentiation. EDAG overexpression blocked the cytoplasmic translocation of Hsp70 induced by EPO deprivation, inhibited GATA-1 degradation, thereby promoting erythroid maturation in an Hsp70-dependent manner. Furthermore, in myelodysplastic syndrome (MDS) patients with dyserythropoiesis, EDAG is dramatically down-regulated, and forced expression of EDAG has been found to restore the localization of Hsp70 in the nucleus and elevate the protein level of GATA-1 to a significant extent. In addition, EDAG rescued the dyserythropoiesis of MDS patients by increasing erythroid differentiation and decreasing cell apoptosis. This study demonstrates the molecular mechanism of Hsp70 nuclear sustaining during erythroid maturation and establishes that EDAG might be a suitable therapeutic target for dyserythropoiesis in MDS patients.


Assuntos
Núcleo Celular/metabolismo , Eritroblastos/metabolismo , Eritropoese/fisiologia , Proteínas de Choque Térmico HSP70/metabolismo , Síndromes Mielodisplásicas/metabolismo , Proteínas Nucleares/metabolismo , Apoptose/fisiologia , Caspase 3/metabolismo , Diferenciação Celular/fisiologia , Células Cultivadas , Citoplasma/metabolismo , Regulação da Expressão Gênica/fisiologia , Doenças Hematológicas/metabolismo , Humanos
11.
Environ Sci Technol ; 54(21): 14046-14056, 2020 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-33064470

RESUMO

Recently, the sulfate radical (SO4•-) has been found to exhibit broad application prospects in various research fields such as chemical, biomedical, and environmental sciences. It has been suggested that SO4•- could be transformed into a more reactive hydroxyl radical (•OH); however, no direct and unequivocal experimental evidence has been reported yet. In this study, using an electron spin resonance (ESR) secondary radical spin-trapping method coupled with the classic spin-trapping agent 5,5-dimethyl-1-pyrroline N-oxide (DMPO) and the typical •OH-scavenging agent dimethyl sulfoxide (DMSO), we found that •OH can be produced from three SO4•--generating systems from weakly acidic (pH = 5.5) to alkaline conditions (optimal at pH = 13.0), while SO4•- is the predominant radical species at pH < 5.5. A comparative study with three typical •OH-generating systems strongly supports the above conclusion. This is the first direct and unequivocal ESR spin-trapping evidence for •OH formation from SO4•- over a wide pH range, which is of great significance to understand and study the mechanism of many SO4•--related reactions and processes. This study also provides an effective and direct method for unequivocally distinguishing •OH from SO4•-.


Assuntos
Óxidos N-Cíclicos , Radical Hidroxila , Espectroscopia de Ressonância de Spin Eletrônica , Radicais Livres , Concentração de Íons de Hidrogênio , Marcadores de Spin , Sulfatos
12.
J Biomed Inform ; 106: 103437, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32360987

RESUMO

Adverse reactions caused by drugs are one of the most important public health problems. Social media has encouraged more patients to share their drug use experiences and has become a major source for the detection of professionally unreported adverse drug reactions (ADRs). Since a large number of user posts do not mention any ADR, accurate detection of the presence of ADRs in each user post is necessary before further research can be conducted. Previous feature-based methods focus on extracting more shallow linguistic features that are unable to capture deep and subtle information in the context, ultimately failing to provide satisfactory accuracy. To overcome the limitations of previous studies, this paper proposes a novel method that can extract deep linguistic features and then combine them with shallow linguistic features for ADR detection. We first extract predicate-ADR pairs under the guidance of extended syntactic dependencies and ADR lexicon. Then, we extract semantic and part-of-speech (POS) features for each pair and pool the features of different pairs to generate a holistic representation of deep linguistic features. Finally, we use the collection of deep features and several shallow features to train the predictive models. A series of experiments are performed on data sets collected from DailyStrength and Twitter. Our approach can achieve AUCs of 94.44% and 88.97% on the two data sets, respectively, outperforming other state-of-the-art methods. The results demonstrate the potential benefits of deep linguistic features for ADR detection on social data. This method can be applied to multiple other healthcare and text analysis tasks and can be used to support pharmacovigilance research.


Assuntos
Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos , Mídias Sociais , Sistemas de Notificação de Reações Adversas a Medicamentos , Humanos , Farmacovigilância , Saúde Pública , Semântica
13.
J Nerv Ment Dis ; 207(8): 693-699, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31356409

RESUMO

Postoperative cognitive dysfunction is a severe outcome after lung transplantation, especially in the elderly lung transplant recipients. Home-based computerized cognitive training (CCT) is a widely used intervention for cognition improvement, but its efficacy has not been validated in this population. A randomized controlled trial was conducted to analyze the effect of CCT on elderly lung transplant recipients. The participants received either an 8-week CCT intervention or usual care. The changes of cognitive function were assessed between preintervention (T1), postintervention (T2), and 12 weeks postintervention (T3). Among the 46 participants, 91.3% completed the interventions. The CCT group performed better than the control group on Digit-Span Forward Test (T3: p = 0.0044) and Verbal Fluency Test (T3: p = 0.0331), indicating the efficacy of CCT on verbal memory in the elderly lung transplant recipients. Although varied impacts were observed on different cognitive domains, it seems promising to use CCT on the elderly population after lung transplantation.


Assuntos
Remediação Cognitiva , Transplante de Pulmão/efeitos adversos , Complicações Cognitivas Pós-Operatórias/terapia , Terapia Assistida por Computador , Idoso , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Avaliação de Resultados em Cuidados de Saúde
14.
J Proteome Res ; 17(12): 4178-4185, 2018 12 07.
Artigo em Inglês | MEDLINE | ID: mdl-30277781

RESUMO

In 2012, the Chromosome-centric Human Proteome Project (C-HPP) launched an investigation for missing proteins (MPs) to complete the Human Proteome Project (HPP). The majority of the MPs were distributed in low-molecular-weight (LMW) ranges, especially from 0 to 40 kDa. LMW protein identification is challenging, owing to their short length, low abundance, and hydrophobicity. Furthermore, many sequences from trypsin digestion are unlikely to yield detectable peptides or a reasonable quality of MS2 spectrum. Therefore, we focused on small MPs by combining LMW protein enrichment and a pair of complementary proteases strategy with trypsin and LysargiNase for human testis samples. In-depth testis LMW protein profiling resulted in the identification of 4063 proteins, of which 2565 were LMW proteins and 1130 had pairs of peptides generated from both trypsin and LysargiNase. This provided additional mass spectral evidence of further verification of small MPs. Finally, two MPs were verified from the seven MP candidates. One of them, Q8N688 , was verified with two series of continuous and complementary b/y-product ions from the pairs of spectra for tryptic and LysargiNase digested peptides after the "mirror spectrum" matching. This make the confident identification of the representative peptides for the target MPs. On the contrary, the two verified peptides for Q86WR6 were identified with the same strategy from the gel-separation and gel-elution samples, respectively. Although the other five MP candidates showed high-quality spectra, they could not be sufficiently distinguished as PE1s and require further verification. All MS data sets have been deposited in the ProteomeXchange with identifier PXD010093.


Assuntos
Peptídeos/análise , Testículo/química , Humanos , Masculino , Espectrometria de Massas/métodos , Peso Molecular , Peptídeo Hidrolases/metabolismo
15.
Clin Exp Rheumatol ; 36 Suppl 112(3): 234-236, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29745886

RESUMO

Bone marrow fibrosis has been found to be associated with autoimmune disorders, and autoimmune myelofibrosis (AIMF) has been defined. Primary myelofibrosis (PMF), a clonal myeloproliferative disorder, should be distinguished from AIMF which has a good response to steroids, as the former has a high mortality and very bad response to conventional treatment. This case report describes a rare case of PMF accompanied with Sjögren's syndrome (SJS) and primary biliary cirrhosis (PBC), in a patient with trisomy 8 mosaic. Careful clinical assessment, gene mutation screening, and bone marrow evaluation can lead to an accurate diagnosis.


Assuntos
Medula Óssea/patologia , Cirrose Hepática Biliar/complicações , Mielofibrose Primária/complicações , Síndrome de Sjogren/complicações , Trissomia/genética , Dissomia Uniparental/genética , Idoso , Antibacterianos/uso terapêutico , Biópsia , Medula Óssea/efeitos dos fármacos , Exame de Medula Óssea , Colagogos e Coleréticos/uso terapêutico , Cromossomos Humanos Par 8/genética , Diagnóstico Diferencial , Evolução Fatal , Feminino , Glucocorticoides/uso terapêutico , Humanos , Imunossupressores/uso terapêutico , Cariotipagem , Cirrose Hepática Biliar/diagnóstico , Cirrose Hepática Biliar/tratamento farmacológico , Cirrose Hepática Biliar/imunologia , Mosaicismo , Valor Preditivo dos Testes , Mielofibrose Primária/tratamento farmacológico , Mielofibrose Primária/imunologia , Mielofibrose Primária/patologia , Síndrome de Sjogren/diagnóstico , Síndrome de Sjogren/tratamento farmacológico , Síndrome de Sjogren/imunologia , Trissomia/diagnóstico , Dissomia Uniparental/diagnóstico
16.
Mol Cell Proteomics ; 15(4): 1381-96, 2016 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-27037361

RESUMO

Ubiquitination is one of the most common post-translational modifications, regulating protein stability and function. However, the proteome-wide profiling of ubiquitinated proteins remains challenging due to their low abundance in cells. In this study, we systematically evaluated the affinity of ubiquitin-binding domains (UBDs) to different types of ubiquitin chains. By selecting UBDs with high affinity and evaluating various UBD combinations with different lengths and types, we constructed two artificial tandem hybrid UBDs (ThUBDs), including four UBDs made of DSK2p-derived ubiquitin-associated (UBA) and ubiquilin 2-derived UBA (ThUDQ2) and of DSK2p-derived UBA and RABGEF1-derived A20-ZnF (ThUDA20). ThUBD binds to ubiquitinated proteins, with markedly higher affinity than naturally occurring UBDs. Furthermore, it displays almost unbiased high affinity to all seven lysine-linked chains. Using ThUBD-based profiling with mass spectrometry, we identified 1092 and 7487 putative ubiquitinated proteins from yeast and mammalian cells, respectively, of which 362 and 1125 proteins had ubiquitin-modified sites. These results demonstrate that ThUBD is a refined and promising approach for enriching the ubiquitinated proteome while circumventing the need to overexpress tagged ubiquitin variants and use antibodies to recognize ubiquitin remnants, thus providing a readily accessible tool for the protein ubiquitination research community.


Assuntos
Proteômica/métodos , Saccharomyces cerevisiae/metabolismo , Ubiquitina/metabolismo , Proteínas Ubiquitinadas/isolamento & purificação , Animais , Sítios de Ligação , Humanos , Espectrometria de Massas/métodos , Ligação Proteica , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/isolamento & purificação , Proteínas Ubiquitinadas/química
17.
J Org Chem ; 82(24): 13084-13092, 2017 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-29096055

RESUMO

Pyridinium aldoximes, which are best-known as therapeutic antidotes for organophosphorus chemical warfare nerve-agents and pesticides, have been found to markedly detoxify polyhalogenated quinones, which are a class of carcinogenic intermediates and recently identified disinfection byproducts in drinking water. However, the exact chemical mechanism underlying this detoxication remains unclear. Here we demonstrate that pralidoxime can remarkably facilitate the dechlorination/hydroxylation of the highly toxic tetrachloro-1,4-benzoquinone in two-consecutive steps to generate the much less toxic 2,5-dichloro-3,6-dihydroxy-1,4-benzoquonine, with rate enhancements of up to 180 000-times. On the contrary, no accelerating effect was noticed with O-methylated pralidoxime. The major reaction product from pralidoxime was identified as its corresponding nitrile (2-cyano-1-methylpyridinium chloride). Along with oxygen-18 isotope-labeling studies, a reaction mechanism was proposed in which nucleophilic substitution coupled with an unprecedented double Beckmann fragmentation reaction was responsible for the dramatic enhancement in the detoxification process. This represents the first report of an unusually mild and facile Beckmann-type fragmentation that can occur under normal physiological conditions in two-consecutive steps. The study may have broad biomedical and environmental significance for future investigations of aldoxime therapeutic agents and carcinogenic polyhalogenated quinones.


Assuntos
Desintoxicação Metabólica Fase I , Compostos de Pralidoxima/química , Estrutura Molecular
18.
Environ Sci Technol ; 51(5): 2934-2943, 2017 03 07.
Artigo em Inglês | MEDLINE | ID: mdl-28128926

RESUMO

We found recently that intrinsic chemiluminescence (CL) could be produced by all 19 chlorophenolic persistent organic pollutants during environmentally friendly advanced oxidation processes. However, the underlying mechanism for the structure-activity relationship (SAR, i.e., the chemical structures and the CL generation) remains unclear. In this study, we found that, for all 19 chlorophenol congeners tested, the CL increased with an increasing number of chlorine atoms in general; and for chlorophenol isomers (such as the 6 trichlorophenols), the CL decreased in the order of meta- > ortho-/para-Cl-substituents with respect to the -OH group of chlorophenols. Further studies showed that not only chlorinated quinoid intermediates but also, more interestingly, chlorinated semiquinone radicals were produced during the degradation of trichlorophenols by the Fenton reagent; and the type and yield of which were determined by the directing effects, hydrogen bonding, and steric hindrance effect of the OH- and/or Cl-substitution groups. More importantly, a good correlation was observed between the formation of these quinoid intermediates and CL generation, which could fully explain the above SAR findings. This represents the first report on the structure-activity relationship study and the critical role of quinoid and semiquinone radical intermediates, which may have broad chemical and environmental implications for future studies on remediation of other halogenated persistent organic pollutants by advanced oxidation processes.


Assuntos
Luminescência , Fenóis/química , Clorofenóis/química , Oxirredução , Relação Estrutura-Atividade
19.
J Environ Sci (China) ; 62: 68-83, 2017 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-29289294

RESUMO

The ubiquitous distribution of halogenated aromatic compounds (XAr) coupled with their carcinogenicity has raised public concerns on their potential risks to both human health and the ecosystem. Recently, advanced oxidation processes (AOPs) have been considered as an "environmentally-friendly" technology for the remediation and destruction of such recalcitrant and highly toxic XAr. During our study on the mechanism of metal-independent production of hydroxyl radicals (OH) by halogenated quinones and H2O2, we found, unexpectedly, that an unprecedented OH-dependent two-step intrinsic chemiluminescene (CL) can be produced by H2O2 and tetrachloro-p-benzoquinone, the major carcinogenic metabolite of the widely used wood preservative pentachlorophenol. Further investigations showed that, in all OH-generating systems, CL can also be produced not only by pentachlorophenol and all other halogenated phenols, but also by all XAr tested. A systematic structure-activity relationship study for all 19 chlorophenolic congeners showed that the CL increased with an increasing number of Cl-substitution in general. More importantly, a relatively good correlation was observed between the formation of quinoid/semiquinone radical intermediates and CL generation. Based on these results, we propose that OH-dependent formation of quinoid intermediates and electronically excited carbonyl species is responsible for this unusual CL production; and a rapid, sensitive, simple, and effective CL method was developed not only to detect and quantify trace amount of XAr, but also to provide useful information for predicting the toxicity or monitoring real-time degradation kinetics of XAr. These findings may have broad chemical, environmental and biological implications for future studies on halogenated aromatic persistent organic pollutants.


Assuntos
Hidrocarbonetos Halogenados/química , Modelos Químicos , Benzoquinonas/química , Peróxido de Hidrogênio/química , Radical Hidroxila/química , Luminescência , Oxirredução , Pentaclorofenol/química , Relação Estrutura-Atividade
20.
Environ Sci Technol ; 49(13): 7940-7, 2015 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-26009932

RESUMO

The ubiquitous distribution coupled with their carcinogenicity has raised public concerns on the potential risks to both human health and the ecosystem posed by the halogenated aromatic compounds (XAr). Recently, advanced oxidation processes (AOPs) have been increasingly favored as an "environmentally-green" technology for the remediation of such recalcitrant and highly toxic XAr. Here, we show that AOPs-mediated degradation of the priority pollutant pentachlorophenol and all other XAr produces an intrinsic chemiluminescence that directly depends on the generation of the extremely reactive hydroxyl radicals. We propose that the hydroxyl radical-dependent formation of quinoid intermediates and electronically excited carbonyl species is responsible for this unusual chemiluminescence production. A rapid, sensitive, simple, and effective chemiluminescence method was developed to quantify trace amounts of XAr and monitor their real-time degradation kinetics. These findings may have broad biological and environmental implications for future research on this important class of halogenated persistent organic pollutants.


Assuntos
Carcinógenos/química , Hidrocarbonetos Aromáticos/análise , Hidrocarbonetos Halogenados/análise , Luminescência , Ácido Edético/química , Meio Ambiente , Peróxido de Hidrogênio/química , Radical Hidroxila/química , Ferro/química , Cinética , Oxirredução , Ozônio/química , Pentaclorofenol/química
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