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1.
Proc Natl Acad Sci U S A ; 121(5): e2318718121, 2024 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-38252820

RESUMO

Several compounds have been used for atherosclerosis treatment, including clinical trials; however, no anti-atherosclerotic drugs based on hemodynamic force-mediated atherogenesis have been discovered. Our previous studies demonstrated that "small mothers against decapentaplegic homolog 1/5" (Smad1/5) is a convergent signaling molecule for chemical [e.g., bone morphogenetic proteins (BMPs)] and mechanical (e.g., disturbed flow) stimulations and hence may serve as a promising hemodynamic-based target for anti-atherosclerosis drug development. The goal of this study was to develop a high-throughput screening (HTS) platform to identify potential compounds that can inhibit disturbed flow- and BMP-induced Smad1/5 activation and atherosclerosis. Through HTS using a Smad1/5 downstream target inhibitor of DNA binding 1 (Id-1) as a luciferase reporter, we demonstrated that KU-55933 and Apicidin suppressed Id-1 expression in AD-293 cells. KU-55933 (10 µM), Apicidin (10 µM), and the combination of half doses of each [1/2(K + A)] inhibited disturbed flow- and BMP4-induced Smad1/5 activation in human vascular endothelial cells (ECs). KU-55933, Apicidin, and 1/2(K + A) treatments caused 50.6%, 47.4%, and 73.3% inhibitions of EC proliferation induced by disturbed flow, respectively, whereas EC inflammation was only suppressed by KU-55933 and 1/2(K + A), but not Apicidin alone. Administrations of KU-55933 and 1/2(K + A) to apolipoprotein E-deficient mice inhibited Smad1/5 activation in ECs in athero-susceptible regions, thereby suppressing endothelial proliferation and inflammation, with the attenuation of atherosclerotic lesions in these mice. A unique drug screening platform has been developed to demonstrate that KU-55933 and its combination with Apicidin are promising therapeutic compounds for atherosclerosis based on hemodynamic considerations.


Assuntos
Aterosclerose , Células Endoteliais , Morfolinas , Pironas , Humanos , Animais , Camundongos , Avaliação Pré-Clínica de Medicamentos , Ensaios de Triagem em Larga Escala , Aterosclerose/tratamento farmacológico , Hemodinâmica , Inflamação
2.
Nature ; 565(7737): 49-55, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30479383

RESUMO

The proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is responsible for selective protein degradation in eukaryotic cells. Here we present cryo-electron microscopy structures of the substrate-engaged human proteasome in seven conformational states at 2.8-3.6 Å resolution, captured during breakdown of a polyubiquitylated protein. These structures illuminate a spatiotemporal continuum of dynamic substrate-proteasome interactions from ubiquitin recognition to substrate translocation, during which ATP hydrolysis sequentially navigates through all six ATPases. There are three principal modes of coordinated hydrolysis, featuring hydrolytic events in two oppositely positioned ATPases, in two adjacent ATPases and in one ATPase at a time. These hydrolytic modes regulate deubiquitylation, initiation of translocation and processive unfolding of substrates, respectively. Hydrolysis of ATP powers a hinge-like motion in each ATPase that regulates its substrate interaction. Synchronization of ATP binding, ADP release and ATP hydrolysis in three adjacent ATPases drives rigid-body rotations of substrate-bound ATPases that are propagated unidirectionally in the ATPase ring and unfold the substrate.


Assuntos
Microscopia Crioeletrônica , Complexo de Endopeptidases do Proteassoma/metabolismo , Complexo de Endopeptidases do Proteassoma/ultraestrutura , Adenosina Trifosfatases/metabolismo , Trifosfato de Adenosina/metabolismo , Regulação Alostérica , Holoenzimas/química , Holoenzimas/metabolismo , Holoenzimas/ultraestrutura , Humanos , Hidrólise , Modelos Moleculares , Complexo de Endopeptidases do Proteassoma/química , Conformação Proteica , Estrutura Quaternária de Proteína , Desdobramento de Proteína , Especificidade por Substrato , Ubiquitinação
3.
Nature ; 570(7761): 338-343, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31189953

RESUMO

The NLRP3 inflammasome can be activated by stimuli that include nigericin, uric acid crystals, amyloid-ß fibrils and extracellular ATP. The mitotic kinase NEK7 licenses the assembly and activation of the NLRP3 inflammasome in interphase. Here we report a cryo-electron microscopy structure of inactive human NLRP3 in complex with NEK7, at a resolution of 3.8 Å. The earring-shaped NLRP3 consists of curved leucine-rich-repeat and globular NACHT domains, and the C-terminal lobe of NEK7 nestles against both NLRP3 domains. Structural recognition between NLRP3 and NEK7 is confirmed by mutagenesis both in vitro and in cells. Modelling of an active NLRP3-NEK7 conformation based on the NLRC4 inflammasome predicts an additional contact between an NLRP3-bound NEK7 and a neighbouring NLRP3. Mutations to this interface abolish the ability of NEK7 or NLRP3 to rescue NLRP3 activation in NEK7-knockout or NLRP3-knockout cells. These data suggest that NEK7 bridges adjacent NLRP3 subunits with bipartite interactions to mediate the activation of the NLRP3 inflammasome.


Assuntos
Microscopia Crioeletrônica , Inflamassomos/metabolismo , Inflamassomos/ultraestrutura , Quinases Relacionadas a NIMA/metabolismo , Quinases Relacionadas a NIMA/ultraestrutura , Proteína 3 que Contém Domínio de Pirina da Família NLR/metabolismo , Proteína 3 que Contém Domínio de Pirina da Família NLR/ultraestrutura , Ligação Competitiva , Humanos , Inflamassomos/química , Inflamassomos/genética , Modelos Moleculares , Mutação , Quinases Relacionadas a NIMA/química , Quinases Relacionadas a NIMA/deficiência , Proteína 3 que Contém Domínio de Pirina da Família NLR/química , Proteína 3 que Contém Domínio de Pirina da Família NLR/deficiência , Ligação Proteica , Domínios Proteicos , Multimerização Proteica , Estrutura Quaternária de Proteína
4.
Anal Chem ; 96(17): 6550-6557, 2024 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-38642045

RESUMO

There is growing interest in developing a high-performance self-supervised denoising algorithm for real-time chemical hyperspectral imaging. With a good understanding of the working function of the zero-shot Noise2Noise-based denoising algorithm, we developed a self-supervised Signal2Signal (S2S) algorithm for real-time denoising with a single chemical hyperspectral image. Owing to the accurate distinction and capture of the weak signal from the random fluctuating noise, S2S displays excellent denoising performance, even for the hyperspectral image with a spectral signal-to-noise ratio (SNR) as low as 1.12. Under this condition, both the image clarity and the spatial resolution could be significantly improved and present an almost identical pattern with a spectral SNR of 7.87. The feasibility of real-time denoising during imaging was well demonstrated, and S2S was applied to monitor the photoinduced exfoliation of transition metal dichalcogenide, which is hard to accomplish by confocal Raman spectroscopy. In general, the real-time denoising capability of S2S offers an easy way toward in situ/in vivo/operando research with much improved spatial and temporal resolution. S2S is open-source at https://github.com/3331822w/Signal2signal and will be accessible online at https://ramancloud.xmu.edu.cn/tutorial.

5.
Eur Heart J ; 44(4): 304-318, 2023 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-36380599

RESUMO

BACKGROUND AND AIMS: Atherosclerosis preferentially develops in arterial branches and curvatures where vascular endothelium is exposed to disturbed flow. In this study, the effects of disturbed flow on the regulation of vascular endothelial phosphoproteins and their contribution to therapeutic application in atherogenesis were elucidated. METHODS: Porcine models, large-scale phosphoproteomics, transgenic mice, and clinical specimens were used to discover novel site-specific phosphorylation alterations induced by disturbed flow in endothelial cells (ECs). RESULTS: A large-scale phosphoproteomics analysis of native endothelium from disturbed (athero-susceptible) vs. pulsatile flow (athero-resistant) regions of porcine aortas led to the identification of a novel atherosclerosis-related phosphoprotein vinculin (VCL) with disturbed flow-induced phosphorylation at serine 721 (VCLS721p). The induction of VCLS721p was mediated by G-protein-coupled receptor kinase 2 (GRK2)S29p and resulted in an inactive form of VCL with a closed conformation, leading to the VE-cadherin/catenin complex disruption to enhance endothelial permeability and atherogenesis. The generation of novel apolipoprotein E-deficient (ApoE-/-) mice overexpressing S721-non-phosphorylatable VCL mutant in ECs confirmed the critical role of VCLS721p in promoting atherosclerosis. The administration of a GRK2 inhibitor to ApoE-/- mice suppressed plaque formation by inhibiting endothelial VCLS721p. Studies on clinical specimens from patients with coronary artery disease (CAD) revealed that endothelial VCLS721p is a critical clinicopathological biomarker for atherosclerosis progression and that serum VCLS721p level is a promising biomarker for CAD diagnosis. CONCLUSIONS: The findings of this study indicate that endothelial VCLS721p is a valuable hemodynamic-based target for clinical assessment and treatment of vascular disorders resulting from atherosclerosis.


Assuntos
Aterosclerose , Células Endoteliais , Vinculina , Animais , Camundongos , Aterosclerose/patologia , Células Endoteliais/patologia , Endotélio Vascular/patologia , Camundongos Knockout para ApoE , Fosforilação , Suínos , Humanos
6.
Circ Res ; 129(12): 1158-1174, 2021 12 03.
Artigo em Inglês | MEDLINE | ID: mdl-34747636

RESUMO

RATIONALE: Disturbed flow occurring in arterial branches and curvatures induces vascular endothelial cell (EC) dysfunction and atherosclerosis. We postulated that disturbed flow plays important role in modulating phosphoprotein expression profiles to regulate endothelial functions and atherogenesis. OBJECTIVE: The goal of this study is to discover novel site-specific phosphorylation alterations induced by disturbed flow in ECs to contribute to atherosclerosis. METHODS AND RESULTS: Quantitative phosphoproteomics analysis of ECs exposed to disturbed flow with low and oscillatory shear stress (0.5±4 dynes/cm2) versus pulsatile shear stress (12±4 dynes/cm2) revealed that oscillatory shear stress induces phospho-YY1S118 (serine [S]118 phosphorylation of Yin Yang 1) in ECs. Elevated phospho-YY1S118 level in ECs was further confirmed to be present in the disturbed flow regions in experimental animals and human atherosclerotic arteries. This disturbed flow-induced EC phospho-YY1S118 is mediated by CK2α (casein kinase 2α) through its direct interaction with YY1. Yeast 2-hybrid library screening and in situ proximity ligation assays demonstrate that phospho-YY1S118 directly binds ZKSCAN4 (zinc finger with KRAB [krüppel-associated box] and SCAN [SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA] domains 4) to induce promoter activity and gene expression of HDM2 (human double minute 2), which consequently induces EC proliferation through downregulation of p53 and p21CIP1. Administration of apoE-deficient (ApoE-/-) mice with CK2-specific inhibitor tetrabromocinnamic acid or atorvastatin inhibits atherosclerosis formation through downregulations of EC phospho-YY1S118 and HDM2. Generation of novel transgenic mice bearing EC-specific overexpression of S118-nonphosphorylatable mutant of YY1 in ApoE-/- mice confirms the critical role of phospho-YY1S118 in promoting atherosclerosis through EC HDM2. CONCLUSIONS: Our findings provide new insights into the mechanisms by which disturbed flow induces endothelial phospho-YY1S118 to promote atherosclerosis, thus indicating phospho-YY1S118 as a potential molecular target for atherosclerosis treatment.


Assuntos
Aterosclerose/metabolismo , Células Endoteliais/metabolismo , Fator de Transcrição YY1/metabolismo , Animais , Aterosclerose/fisiopatologia , Sítios de Ligação , Circulação Sanguínea , Caseína Quinase II/metabolismo , Linhagem Celular , Endotélio Vascular/citologia , Endotélio Vascular/metabolismo , Endotélio Vascular/patologia , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Fosforilação , Ligação Proteica , Proteínas Proto-Oncogênicas c-mdm2/genética , Proteínas Proto-Oncogênicas c-mdm2/metabolismo , Ratos , Ratos Sprague-Dawley , Fator de Transcrição YY1/química , Fator de Transcrição YY1/genética , Dedos de Zinco
7.
Psychogeriatrics ; 23(4): 701-712, 2023 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-37248166

RESUMO

BACKGROUND: Magic-based programs have been utilised to enhance well-being across various health aspects. However, there is a lack of studies on whether performing magic tricks can provide mental health benefits for older adults living in the community. Therefore, this study aims to investigate the effects of a magic-based intervention program on self-esteem, depressive symptoms, and quality of life (QOL), and to examine the relationship between these factors in older adults. METHODS: Thirty-eight participants, aged 60-90 years, were randomly assigned to either a magic intervention group or a control group. The magic intervention program, tailored for older adults, was conducted for 90 min, twice weekly, over 6 weeks. The Rosenberg Self-Esteem Scale (RSE), the 15-item Geriatric Depression Scale (GDS-15), and the World Health Organization Quality of Life-BREF scores were measured and analyzed in both groups before and after the intervention. RESULTS: The magic-based intervention significantly increased self-esteem and reduced depressive symptoms in older adults, with large effect sizes. However, no significant impact on QOL was observed. Additionally, no significant correlation was found between the improvement in self-esteem and the reduction in depressive levels. Despite this, a moderate but significant negative correlation was detected between the post-intervention scores of RSE and GDS-15 in the magic intervention group. CONCLUSIONS: The study demonstrated that the magic intervention program was beneficial in promoting mental health in community-dwelling older adults. Implementing magic programs in communities appears to be an effective approach to enhance self-esteem and alleviate depressive symptoms in the older population.


Assuntos
Depressão , Vida Independente , Humanos , Idoso , Depressão/psicologia , Qualidade de Vida/psicologia , Saúde Mental , Autoimagem
8.
Anal Chem ; 94(28): 10151-10158, 2022 07 19.
Artigo em Inglês | MEDLINE | ID: mdl-35794045

RESUMO

Surface-enhanced Raman spectroscopy (SERS), providing near-single-molecule-level fingerprint information, is a powerful tool for the trace analysis of a target in a complicated matrix and is especially facilitated by the development of modern machine learning algorithms. However, both the high demand of mass data and the low interpretability of the mysterious black-box operation significantly limit the well-trained model to real systems in practical applications. Aiming at these two issues, we constructed a novel machine learning algorithm-based framework (Vis-CAD), integrating visual random forest, characteristic amplifier, and data augmentation. The introduction of data augmentation significantly reduced the requirement of mass data, and the visualization of the random forest clearly presented the captured features, by which one was able to determine the reliability of the algorithm. Taking the trace analysis of individual polycyclic aromatic hydrocarbons in a mixture as an example, a trustworthy accuracy no less than 99% was realized under the optimized condition. The visualization of the algorithm framework distinctly demonstrated that the captured feature was well correlated to the characteristic Raman peaks of each individual. Furthermore, the sensitivity toward the trace individual could be improved by least 1 order of magnitude as compared to that with the naked eye. The proposed algorithm distinguished by the lesser demand of mass data and the visualization of the operation process offers a new way for the indestructible application of machine learning algorithms, which would bring push-to-the-limit sensitivity toward the qualitative and quantitative analysis of trace targets, not only in the field of SERS, but also in the much wider spectroscopy world. It is implemented in the Python programming language and is open-source at https://github.com/3331822w/Vis-CAD.


Assuntos
Aprendizado de Máquina , Hidrocarbonetos Policíclicos Aromáticos , Algoritmos , Reprodutibilidade dos Testes , Análise Espectral Raman/métodos
9.
J Virol ; 95(24): e0052921, 2021 11 23.
Artigo em Inglês | MEDLINE | ID: mdl-34549974

RESUMO

The functional human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer [(gp120/gp41)3] is produced by cleavage of a conformationally flexible gp160 precursor. gp160 cleavage or the binding of BMS-806, an entry inhibitor, stabilizes the pretriggered, "closed" (state 1) conformation recognized by rarely elicited broadly neutralizing antibodies. Poorly neutralizing antibodies (pNAbs) elicited at high titers during natural infection recognize more "open" Env conformations (states 2 and 3) induced by binding the receptor, CD4. We found that BMS-806 treatment and cross-linking decreased the exposure of pNAb epitopes on cell surface gp160; however, after detergent solubilization, cross-linked and BMS-806-treated gp160 sampled non-state-1 conformations that could be recognized by pNAbs. Cryo-electron microscopy of the purified BMS-806-bound gp160 revealed two hitherto unknown asymmetric trimer conformations, providing insights into the allosteric coupling between trimer opening and structural variation in the gp41 HR1N region. The individual protomer structures in the asymmetric gp160 trimers resemble those of other genetically modified or antibody-bound cleaved HIV-1 Env trimers, which have been suggested to assume state-2-like conformations. Asymmetry of the uncleaved Env potentially exposes surfaces of the trimer to pNAbs. To evaluate the effect of stabilizing a state-1-like conformation of the membrane Env precursor, we treated cells expressing wild-type HIV-1 Env with BMS-806. BMS-806 treatment decreased both gp160 cleavage and the addition of complex glycans, implying that gp160 conformational flexibility contributes to the efficiency of these processes. Selective pressure to maintain flexibility in the precursor of functional Env allows the uncleaved Env to sample asymmetric conformations that potentially skew host antibody responses toward pNAbs. IMPORTANCE The envelope glycoprotein (Env) trimers on the surface of human immunodeficiency virus (HIV-1) mediate the entry of the virus into host cells and serve as targets for neutralizing antibodies. The functional Env trimer is produced by cleavage of the gp160 precursor in the infected cell. We found that the HIV-1 Env precursor is highly plastic, allowing it to assume different asymmetric shapes. This conformational plasticity is potentially important for Env cleavage and proper modification by sugars. Having a flexible, asymmetric Env precursor that can misdirect host antibody responses without compromising virus infectivity would be an advantage for a persistent virus like HIV-1.


Assuntos
Proteína gp120 do Envelope de HIV/imunologia , Proteína gp41 do Envelope de HIV/química , HIV-1/química , Animais , Anticorpos Neutralizantes/imunologia , Células CHO , Cricetulus , Microscopia Crioeletrônica/métodos , Infecções por HIV/virologia , HIV-1/imunologia , Humanos , Ligação Proteica , Conformação Proteica , Multimerização Proteica , Produtos do Gene env do Vírus da Imunodeficiência Humana/imunologia
10.
Org Biomol Chem ; 20(28): 5566-5574, 2022 07 20.
Artigo em Inglês | MEDLINE | ID: mdl-35792054

RESUMO

A concise manganese(III)-promoted stereoselective ß-phosphorylation of acyclic tertiary enamides and diverse H-phosphine oxides was achieved. This reaction proceeds with absolute E-selectivity in contrast to Z-selectivity obtained in other previous works and affords various E-selective ß-phosphorylated tertiary enamides in high efficiency. To the best of our knowledge, this is the first case of E-selective ß-phosphorylation of tertiary enamides through C-H functionalization. In addition, the method features broad substrate scope, good functional group compatibility and efficient scale-up.


Assuntos
Amidas , Manganês , Humanos , Estrutura Molecular , Fosforilação , Estereoisomerismo
11.
Geriatr Nurs ; 48: 169-176, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36257222

RESUMO

OBJECTIVES: To evaluate a magic recreation program to reduce depressive symptoms in institutionalized older adults. METHODS: We conducted a pilot randomized controlled trial in which participants were assigned to either a magic group (n = 6) or a control group with usual activities (n = 6). The magic group received a 6-week magic recreation program. The data were analyzed by generalized estimating equations in terms of intention-to-treat analysis. A sensitivity analysis was conducted by examining the complete case analysis. RESULTS: The magic recreation program significantly improved the scores of Patient Health Questionnaire-9 in the magic group (Wald χ 2 = 8.816, p = 0.004, Cohen's  d  = 1.51, power = 0.9968). The results of the sensitivity analysis were consistent with the results of primary analysis. CONCLUSIONS: The 6-week magic recreation program reduced depressive symptoms among institutionalized older adults with minor depressive symptoms.


Assuntos
Depressão , Assistência de Longa Duração , Humanos , Idoso , Depressão/diagnóstico , Projetos Piloto
12.
Org Biomol Chem ; 19(37): 8086-8095, 2021 09 29.
Artigo em Inglês | MEDLINE | ID: mdl-34476428

RESUMO

An exquisite metal-free cascade cyclization reaction of 2-acylbenzoic acids with amines was developed, which provided a powerful method for the one-pot synthesis of diverse isoindoloisoquinoline and benzoindolizinoindole derivatives. This protocol avoided the use of metal catalysts, proceeded with high efficiency and had broad substrate scope. These resulting products could be transformed into tertiary amines under the reduction of LiAlH4/AlCl3, followed by the Hofmann elimination offering lots of nitrogen-containing nine-membered ring compounds in excellent yields. All synthesized products containing fused N-polycyclic skeletons were difficult to be constructed using traditional methods and they have a wide range of applications in the pharmaceutical area.


Assuntos
Aminas
13.
BMC Psychiatry ; 20(1): 195, 2020 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-32357858

RESUMO

BACKGROUND: To examine the effectiveness and safety of yoga of women with sleep problems by performing a systematic review and meta-analysis. METHODS: Medline/PubMed, ClinicalKey, ScienceDirect, Embase, PsycINFO, and the Cochrane Library were searched throughout the month of June, 2019. Randomized controlled trials comparing yoga groups with control groups in women with sleep problems were included. Two reviewers independently evaluated risk of bias by using the risk of bias tool suggested by the Cochrane Collaboration for programming and conducting systematic reviews and meta-analyses. The main outcome measure was sleep quality or the severity of insomnia, which was measured using subjective instruments, such as the Pittsburgh Sleep Quality Index (PSQI), Insomnia Severity Index (ISI), or objective instruments such as polysomnography, actigraphy, and safety of the intervention. For each outcome, a standardized mean difference (SMD) and confidence intervals (CIs) of 95% were determined. RESULTS: Nineteen studies in this systematic review included 1832 participants. The meta-analysis of the combined data conducted according to Comprehensive Meta-Analysis showed a significant improvement in sleep (SMD = - 0.327, 95% CI = - 0.506 to - 0.148, P < 0.001). Meta-analyses revealed positive effects of yoga using PSQI scores in 16 randomized control trials (RCTs), compared with the control group in improving sleep quality among women using PSQI (SMD = - 0.54; 95% CI = - 0.89 to - 0.19; P = 0.003). However, three RCTs revealed no effects of yoga compared to the control group in reducing insomnia among women using ISI (SMD = - 0.13; 95% CI = - 0.74 to 0.48; P = 0.69). Seven RCTs revealed no evidence for effects of yoga compared with the control group in improving sleep quality for women with breast cancer using PSQI (SMD = - 0.15; 95% CI = - 0.31 to 0.01; P = 0.5). Four RCTs revealed no evidence for the effects of yoga compared with the control group in improving the sleep quality for peri/postmenopausal women using PSQI (SMD = - 0.31; 95% CI = - 0.95 to 0.33; P = 0.34). Yoga was not associated with any serious adverse events. DISCUSSION: This systematic review and meta-analysis demonstrated that yoga intervention in women can be beneficial when compared to non-active control conditions in term of managing sleep problems. The moderator analyses suggest that participants in the non-breast cancer subgroup and participants in the non-peri/postmenopausal subgroup were associated with greater benefits, with a direct correlation of total class time with quality of sleep among other related benefits.


Assuntos
Qualidade de Vida/psicologia , Distúrbios do Início e da Manutenção do Sono/terapia , Sono/fisiologia , Yoga , Feminino , Humanos , Recreação , Distúrbios do Início e da Manutenção do Sono/psicologia
14.
Proc Natl Acad Sci U S A ; 114(28): 7367-7372, 2017 07 11.
Artigo em Inglês | MEDLINE | ID: mdl-28652322

RESUMO

DNA-dependent protein kinase (DNA-PK) is a large protein complex central to the nonhomologous end joining (NHEJ) DNA-repair pathway. It comprises the DNA-PK catalytic subunit (DNA-PKcs) and the heterodimer of DNA-binding proteins Ku70 and Ku80. Here, we report the cryo-electron microscopy (cryo-EM) structures of human DNA-PKcs at 4.4-Å resolution and the DNA-PK holoenzyme at 5.8-Å resolution. The DNA-PKcs structure contains three distinct segments: the N-terminal region with an arm and a bridge, the circular cradle, and the head that includes the kinase domain. Two perpendicular apertures exist in the structure, which are sufficiently large for the passage of dsDNA. The DNA-PK holoenzyme cryo-EM map reveals density for the C-terminal globular domain of Ku80 that interacts with the arm of DNA-PKcs. The Ku80-binding site is adjacent to the previously identified density for the DNA-binding region of the Ku70/Ku80 complex, suggesting concerted DNA interaction by DNA-PKcs and the Ku complex.


Assuntos
Microscopia Crioeletrônica , Proteína Quinase Ativada por DNA/química , Proteínas Nucleares/química , Catálise , Domínio Catalítico , Cristalografia por Raios X , Quebras de DNA de Cadeia Dupla , Reparo do DNA , Proteína Quinase Ativada por DNA/genética , Células HeLa , Humanos , Autoantígeno Ku/química , Proteínas Nucleares/genética , Ligação Proteica
15.
BMC Bioinformatics ; 20(1): 169, 2019 Apr 03.
Artigo em Inglês | MEDLINE | ID: mdl-30943890

RESUMO

BACKGROUND: The detection of weak signals and selection of single particles from low-contrast micrographs of frozen hydrated biomolecules by cryo-electron microscopy (cryo-EM) represents a major practical bottleneck in cryo-EM data analysis. Template-based particle picking by an objective function using fast local correlation (FLC) allows computational extraction of a large number of candidate particles from micrographs. Another independent objective function based on maximum likelihood estimates (MLE) can be used to align the images and verify the presence of a signal in the selected particles. Despite the widespread applications of the two objective functions, an optimal combination of their utilities has not been exploited. Here we propose a bi-objective function (BOF) approach that combines both FLC and MLE and explore the potential advantages and limitations of BOF in signal detection from cryo-EM data. RESULTS: The robustness of the BOF strategy in particle selection and verification was systematically examined with both simulated and experimental cryo-EM data. We investigated how the performance of the BOF approach is quantitatively affected by the signal-to-noise ratio (SNR) of cryo-EM data and by the choice of initialization for FLC and MLE. We quantitatively pinpointed the critical SNR (~ 0.005), at which the BOF approach starts losing its ability to select and verify particles reliably. We found that the use of a Gaussian model to initialize the MLE suppresses the adverse effects of reference dependency in the FLC function used for template-matching. CONCLUSION: The BOF approach, which combines two distinct objective functions, provides a sensitive way to verify particles for downstream cryo-EM structure analysis. Importantly, reference dependency of the FLC does not necessarily transfer to the MLE, enabling the robust detection of weak signals. Our insights into the numerical behavior of the BOF approach can be used to improve automation efficiency in the cryo-EM data processing pipeline for high-resolution structural determination.


Assuntos
Microscopia Crioeletrônica/métodos , Processamento de Imagem Assistida por Computador , Funções Verossimilhança , Razão Sinal-Ruído
16.
J Biomed Sci ; 25(1): 1, 2018 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-29295709

RESUMO

BACKGROUND: Atherosclerosis occurs in arterial curvatures and branches, where the flow is disturbed with low and oscillatory shear stress (OSS). The remodeling and alterations of extracellular matrices (ECMs) and their composition is the critical step in atherogenesis. In this study, we investigated the effects of different ECM proteins on the regulation of mechanotransduction in vascular endothelial cells (ECs) in response to OSS. METHODS: Through the experiments ranging from in vitro cell culture studies on effects of OSS on molecular signaling to in vivo examinations on clinical specimens from patients with coronary artery disease (CAD), we elucidated the roles of integrins and different ECMs, i.e., fibronectin (FN) and laminin (LM), in transforming growth factor (TGF)-ß receptor (TßR)-mediated Smad2 activation and nuclear factor-κB (NF-κB) signaling in ECs in response to OSS and hence atherogenesis. RESULTS: OSS at 0.5±12 dynes/cm2 induces sustained increases in the association of types I and II TßRs with ß1 and ß3 integrins in ECs grown on FN, but it only transient increases in ECs grown on LM. OSS induces a sustained activation of Smad2 in ECs on FN, but only a transient activation of Smad2 in ECs on LM. OSS-activation of Smad2 in ECs on FN regulates downstream NF-κB signaling and pro-inflammatory gene expression through the activation of ß1 integrin and its association with TßRs. In contrast, OSS induces transient activations of ß1 and ß3 integrins in ECs on LM, which associate with type I TßR to regulate Smad2 phosphorylation, resulting in transient induction of NF-κB and pro-inflammatory gene expression. In vivo investigations on diseased human coronary arteries from CAD patients revealed that Smad2 is highly activated in ECs of atherosclerotic lesions, which is accompanied by the concomitant increase of FN rather than LM in the EC layer and neointimal region of atherosclerotic lesions. CONCLUSIONS: Our findings provide new insights into the mechanisms of how OSS regulates Smad2 signaling and pro-inflammatory genes through the complex signaling networks of integrins, TßRs, and ECMs, thus illustrating the molecular basis of regional pro-inflammatory activation within disturbed flow regions in the arterial tree.


Assuntos
Células Endoteliais/fisiologia , Mecanotransdução Celular , Proteína Smad2/genética , Fenômenos Biomecânicos , Células Cultivadas , Proteínas da Matriz Extracelular/genética , Proteínas da Matriz Extracelular/metabolismo , Fibronectinas/genética , Fibronectinas/metabolismo , Humanos , Laminina/genética , Laminina/metabolismo , Proteína Smad2/metabolismo , Estresse Mecânico
17.
Foodborne Pathog Dis ; 15(9): 544-547, 2018 09.
Artigo em Inglês | MEDLINE | ID: mdl-29782189

RESUMO

Currently, there is no information available on the detection of Toxoplasma gondii and Neospora caninum in the tissues of Tolai hares in China. This study aimed to investigate the prevalence of these protozoan parasites in Tolai hares obtained from Shandong province, eastern China, between January 2016 and June 2017. Serum and brain tissue samples of 358 Tolai hares were obtained and detected for the presence of antibody and parasite DNAs by serodiagnosis and polymerase chain reaction (PCR), respectively. The seroprevalence of T. gondii and N. caninum infection in Tolai hares was 8.10% (29/358) and 0.84% (3/358), respectively. However, all the 358 tested Tolai hares were negative for N. caninum by PCR and T. gondii DNA was detected in 23 Tolai hares (6.42%, 23/358). The positive T. gondii DNA was genotyped at 11 genetic markers using multilocus PCR-restriction fragment length polymorphism technology. Of the 23 positive samples, only 2 of them produced complete genotyping results, and were identified as ToxoDB Genotype #9. This is the first report to detect T. gondii in the tissues of Tolai hares from China and the first study to focus on N. caninum in Tolai hares from China.


Assuntos
Lebres/parasitologia , Neospora/genética , Toxoplasma/genética , Toxoplasmose Animal/epidemiologia , Animais , Anticorpos Antiprotozoários/sangue , China/epidemiologia , Coccidiose/parasitologia , DNA de Protozoário/análise , Feminino , Inocuidade dos Alimentos , Genótipo , Lebres/sangue , Masculino , Reação em Cadeia da Polimerase , Polimorfismo de Fragmento de Restrição
18.
Circ Res ; 116(7): 1157-69, 2015 Mar 27.
Artigo em Inglês | MEDLINE | ID: mdl-25623956

RESUMO

RATIONALE: In atherosclerotic lesions, synthetic smooth muscle cells (sSMCs) induce aberrant microRNA (miR) profiles in endothelial cells (ECs) under flow stagnation. Increase in shear stress induces favorable miR modulation to mitigate sSMC-induced inflammation. OBJECTIVE: To address the role of miRs in sSMC-induced EC inflammation and its inhibition by shear stress. METHODS AND RESULTS: Coculturing ECs with sSMCs under static condition causes initial increases of 4 anti-inflammatory miRs (146a/708/451/98) in ECs followed by decreases below basal levels at 7 days; the increases for miR-146a/708 peaked at 24 hours and those for miR-451/98 lasted for only 6 to 12 hours. Shear stress (12 dynes/cm(2)) to cocultured ECs for 24 hours augments these 4 miR expressions. In vivo, these 4 miRs are highly expressed in neointimal ECs in injured arteries under physiological levels of flow, but not expressed under flow stagnation. MiR-146a, miR-708, miR-451, and miR-98 target interleukin-1 receptor-associated kinase, inhibitor of nuclear factor-κB kinase subunit-γ, interleukin-6 receptor, and conserved helix-loop-helix ubiquitous kinase, respectively, to inhibit nuclear factor-κB signaling, which exerts negative feedback control on the biogenesis of these miRs. Nuclear factor-E2-related factor (Nrf)-2 is critical for shear-induction of miR-146a in cocultured ECs. Silencing either Nrf-2 or miR-146a led to increased neointima formation of injured rat carotid artery under physiological levels of flow. Overexpressing miR-146a inhibits neointima formation of rat or mouse carotid artery induced by injury or flow cessation. CONCLUSIONS: Nrf-2-mediated miR-146a expression is augmented by atheroprotective shear stress in ECs adjacent to sSMCs to inhibit neointima formation of injured arteries.


Assuntos
Aterosclerose/prevenção & controle , Citocinas/biossíntese , Células Endoteliais/fisiologia , Endotélio Vascular/fisiopatologia , Hemorreologia , Inflamação/genética , MicroRNAs/fisiologia , Músculo Liso Vascular/fisiopatologia , Miócitos de Músculo Liso/fisiologia , Neointima/genética , Interferência de RNA , Animais , Aorta , Aterosclerose/genética , Lesões das Artérias Carótidas/genética , Lesões das Artérias Carótidas/patologia , Comunicação Celular , Células Cultivadas , Técnicas de Cocultura , Cricetinae , Citocinas/genética , Feminino , Regulação da Expressão Gênica , Integrinas/fisiologia , Masculino , Camundongos , Camundongos Endogâmicos , Fator 2 Relacionado a NF-E2/fisiologia , NF-kappa B/metabolismo , Neointima/metabolismo , Ratos , Ratos Sprague-Dawley
19.
Fish Shellfish Immunol ; 68: 500-508, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28774846

RESUMO

Energy metabolism plays important roles in stress resistance and immunity in mammals, however, such functions have not been established in fish. In the present study, Nile tilapia (Oreochromis niloticus) was fed with mildronate, an inhibitor of mitochondrial fatty acid (FA) ß-oxidation, for six weeks subsequently challenged with Aeromonas hydrophila and ammonia nitrogen exposure. Mildronate treatment reduced significantly l-carnitine concentration and mitochondrial FA ß-oxidation efficiency, while it increased lipid accumulation in liver. The fish with inhibited hepatic FA catabolism had lower survival rate when exposed to Aeromonas hydrophila and ammonia nitrogen. Moreover, fish fed mildronate supplemented diet had lower immune enzymes activities and anti-inflammatory cytokine genes expressions, but had higher pro-inflammatory cytokine genes expressions. However, the oxidative stress-related biochemical indexes were not significantly affected by mildronate treatment. Taken together, inhibited mitochondrial FA ß-oxidation impaired stress resistance ability in Nile tilapia mainly through inhibiting immune functions and triggering inflammation. This is the first study showing the regulatory effects of lipid catabolism on stress resistance and immune functions in fish.


Assuntos
Ciclídeos , Ácidos Graxos/metabolismo , Doenças dos Peixes/imunologia , Infecções por Bactérias Gram-Negativas/veterinária , Metilidrazinas/farmacologia , Estresse Fisiológico/efeitos dos fármacos , Aeromonas hydrophila/fisiologia , Amônia/metabolismo , Ração Animal , Animais , Carnitina/metabolismo , Ciclídeos/metabolismo , Dieta , Suplementos Nutricionais , Doenças dos Peixes/microbiologia , Infecções por Bactérias Gram-Negativas/imunologia , Infecções por Bactérias Gram-Negativas/microbiologia , Mitocôndrias/efeitos dos fármacos , Nitrogênio/metabolismo , Oxirredução/efeitos dos fármacos , Distribuição Aleatória
20.
J Med Virol ; 87(9): 1573-7, 2015 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25940435

RESUMO

Hepatitis E virus (HEV) infection is an important public health concern worldwide, especially in developing countries, causing waterborne outbreaks as well as sporadic autochthonous hepatitis. China is usually considered to be a HEV-endemic area, but the prevalence of HEV infection in children in mainland China remains unclear. Between May 2013 and July 2014, a cross-sectional study was conducted to estimate the seroprevalence and potential risk factors associated with the acquisition of HEV infection by children in China. A total of 1,500 healthy children (range 1-18; 942 and 558 from urban and rural areas, respectively) were recruited to examine for the presence of anti-HEV IgG and IgM antibodies by enzyme-linked immunosorbent assay. Socio-demographic and behavioral characteristics from the examined children were obtained. The overall seroprevalence of HEV in the examined children was 14.93%. Of these, 174 (11.60%) were positive for only anti-HEV IgG antibodies, 50 (3.33%) were IgM positive and IgG negative, and 44 (2.93%) were positive for both anti-HEV IgG and IgM antibodies. Age, type of residence area, contact with pigs, and source of drinking water were found to be associated with HEV infection. These findings demonstrated the high prevalence of HEV and the considerable potential for the transmission of HEV infection in children in China.


Assuntos
Anticorpos Anti-Hepatite/sangue , Vírus da Hepatite E/imunologia , Hepatite E/epidemiologia , Estudos Soroepidemiológicos , Adolescente , Animais , Criança , Pré-Escolar , China/epidemiologia , Estudos Transversais , Demografia , Ensaio de Imunoadsorção Enzimática , Feminino , Hepatite E/transmissão , Humanos , Imunoglobulina G/sangue , Imunoglobulina M/sangue , Lactente , Masculino , Fatores de Risco , Suínos
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