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The SARS-CoV-2 Omicron variant with increased fitness is spreading rapidly worldwide. Analysis of cryo-EM structures of the spike (S) from Omicron reveals amino acid substitutions forging interactions that stably maintain an active conformation for receptor recognition. The relatively more compact domain organization confers improved stability and enhances attachment but compromises the efficiency of the viral fusion step. Alterations in local conformation, charge, and hydrophobic microenvironments underpin the modulation of the epitopes such that they are not recognized by most NTD- and RBD-antibodies, facilitating viral immune escape. Structure of the Omicron S bound with human ACE2, together with the analysis of sequence conservation in ACE2 binding region of 25 sarbecovirus members, as well as heatmaps of the immunogenic sites and their corresponding mutational frequencies, sheds light on conserved and structurally restrained regions that can be used for the development of broad-spectrum vaccines and therapeutics.
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Evasão da Resposta Imune/fisiologia , SARS-CoV-2/fisiologia , Glicoproteína da Espícula de Coronavírus/química , Enzima de Conversão de Angiotensina 2/química , Enzima de Conversão de Angiotensina 2/metabolismo , Anticorpos Antivirais/imunologia , Sítios de Ligação , COVID-19/imunologia , COVID-19/patologia , COVID-19/virologia , Microscopia Crioeletrônica , Humanos , Mutagênese Sítio-Dirigida , Testes de Neutralização , Ligação Proteica , Domínios Proteicos/imunologia , Estrutura Quaternária de Proteína , SARS-CoV-2/isolamento & purificação , Glicoproteína da Espícula de Coronavírus/genética , Glicoproteína da Espícula de Coronavírus/metabolismo , Ressonância de Plasmônio de Superfície , Ligação ViralRESUMO
Omicron (B.1.1.529), the most heavily mutated SARS-CoV-2 variant so far, is highly resistant to neutralizing antibodies, raising concerns about the effectiveness of antibody therapies and vaccines1,2. Here we examined whether sera from individuals who received two or three doses of inactivated SARS-CoV-2 vaccine could neutralize authentic Omicron. The seroconversion rates of neutralizing antibodies were 3.3% (2 out of 60) and 95% (57 out of 60) for individuals who had received 2 and 3 doses of vaccine, respectively. For recipients of three vaccine doses, the geometric mean neutralization antibody titre for Omicron was 16.5-fold lower than for the ancestral virus (254). We isolated 323 human monoclonal antibodies derived from memory B cells in triple vaccinees, half of which recognized the receptor-binding domain, and showed that a subset (24 out of 163) potently neutralized all SARS-CoV-2 variants of concern, including Omicron. Therapeutic treatments with representative broadly neutralizing monoclonal antibodies were highly protective against infection of mice with SARS-CoV-2 Beta (B.1.351) and Omicron. Atomic structures of the Omicron spike protein in complex with three classes of antibodies that were active against all five variants of concern defined the binding and neutralizing determinants and revealed a key antibody escape site, G446S, that confers greater resistance to a class of antibodies that bind on the right shoulder of the receptor-binding domain by altering local conformation at the binding interface. Our results rationalize the use of three-dose immunization regimens and suggest that the fundamental epitopes revealed by these broadly ultrapotent antibodies are rational targets for a universal sarbecovirus vaccine.
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Vacinas contra COVID-19 , COVID-19 , Células B de Memória , SARS-CoV-2 , Animais , Anticorpos Monoclonais/imunologia , Anticorpos Monoclonais/isolamento & purificação , Anticorpos Monoclonais/uso terapêutico , Anticorpos Neutralizantes/imunologia , Anticorpos Neutralizantes/isolamento & purificação , Anticorpos Neutralizantes/uso terapêutico , Anticorpos Antivirais/imunologia , Anticorpos Antivirais/isolamento & purificação , Anticorpos Antivirais/uso terapêutico , COVID-19/imunologia , COVID-19/prevenção & controle , COVID-19/virologia , Vacinas contra COVID-19/administração & dosagem , Vacinas contra COVID-19/imunologia , Modelos Animais de Doenças , Humanos , Células B de Memória/imunologia , Camundongos , Testes de Neutralização , SARS-CoV-2/classificação , SARS-CoV-2/genética , SARS-CoV-2/imunologia , Glicoproteína da Espícula de Coronavírus/imunologiaRESUMO
Exosomes (EXOs) have been proven as biomarkers for disease diagnosis and agents for therapeutics. Great challenge remains in the separation of EXOs with high-purity and low-damage from complex biological media, which is critical for the downstream applications. Herein, we report a DNA-based hydrogel to realize the specific and nondestructive separation of EXOs from complex biological media. The separated EXOs were directly utilized in the detection of human breast cancer in clinical samples, as well as applied in the therapeutics of myocardial infarction in rat models. The materials chemistry basis of this strategy involved the synthesis of ultralong DNA chains via an enzymatic amplification, and the formation of DNA hydrogels through complementary base-pairing. These ultralong DNA chains that contained polyvalent aptamers were able to recognize and bind with the receptors on EXOs, and the specific and efficient binding ensured the selective separation of EXOs from media into the further formed networked DNA hydrogel. Based on this DNA hydrogel, rationally designed optical modules were introduced for the detection of exosomal pathogenic microRNA, which achieved the classification of breast cancer patients versus healthy donors with 100% precision. Furthermore, the DNA hydrogel that contained mesenchymal stem cell-derived EXOs was proved with significant therapeutic efficacy in repairing infarcted myocardium of rat models. We envision that this DNA hydrogel-based bioseparation system is promising as a powerful biotechnology, which will promote the development of extracellular vesicles in nanobiomedicine.
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Exossomos , Células-Tronco Mesenquimais , MicroRNAs , Humanos , Ratos , Animais , Exossomos/genética , Exossomos/metabolismo , Hidrogéis/metabolismo , MicroRNAs/genética , MicroRNAs/metabolismo , Células-Tronco Mesenquimais/metabolismoRESUMO
Patients with Hutchinson-Gilford progeria syndrome (HGPS) present with a number of premature aging phenotypes, including DNA damage accumulation, and many of them die of cardiovascular complications. Although vascular pathologies have been reported, whether HGPS patients exhibit cardiac dysfunction and its underlying mechanism is unclear, rendering limited options for treating HGPS-related cardiomyopathy. In this study, we reported a cardiac atrophy phenotype in the LmnaG609G/G609G mice (hereafter, HGPS mice). Using a GFP-based reporter system, we demonstrated that the efficiency of nonhomologous end joining (NHEJ) declined by 50% in HGPS cardiomyocytes in vivo, due to the attenuated interaction between γH2AX and Progerin, the causative factor of HGPS. As a result, genomic instability in cardiomyocytes led to an increase of CHK2 protein level, promoting the LKB1-AMPKα interaction and AMPKα phosphorylation, which further led to the activation of FOXO3A-mediated transcription of atrophy-related genes. Moreover, inhibiting AMPK enlarged cardiomyocyte sizes both in vitro and in vivo. Most importantly, our proof-of-concept study indicated that isoproterenol treatment significantly reduced AMPKα and FOXO3A phosphorylation in the heart, attenuated the atrophy phenotype, and extended the mean lifespan of HGPS mice by ~21%, implying that targeting cardiac atrophy may be an approach to HGPS treatment.
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Senilidade Prematura , Progéria , Humanos , Camundongos , Animais , Progéria/metabolismo , Coração , Dano ao DNA , Instabilidade Genômica , Proteínas Quinases Ativadas por AMP/genética , Lamina Tipo A/genética , Lamina Tipo A/metabolismoRESUMO
MOTIVATION: Cell-type-specific gene expression is maintained in large part by transcription factors (TFs) selectively binding to distinct sets of sites in different cell types. Recent research works have provided evidence that such cell-type-specific binding is determined by TF's intrinsic sequence preferences, cooperative interactions with co-factors, cell-type-specific chromatin landscapes and 3D chromatin interactions. However, computational prediction and characterization of cell-type-specific and shared binding sites is rarely studied. RESULTS: In this article, we propose two computational approaches for predicting and characterizing cell-type-specific and shared binding sites by integrating multiple types of features, in which one is based on XGBoost and another is based on convolutional neural network (CNN). To validate the performance of our proposed approaches, ChIP-seq datasets of 10 binding factors were collected from the GM12878 (lymphoblastoid) and K562 (erythroleukemic) human hematopoietic cell lines, each of which was further categorized into cell-type-specific (GM12878- and K562-specific) and shared binding sites. Then, multiple types of features for these binding sites were integrated to train the XGBoost- and CNN-based models. Experimental results show that our proposed approaches significantly outperform other competing methods on three classification tasks. Moreover, we identified independent feature contributions for cell-type-specific and shared sites through SHAP values and explored the ability of the CNN-based model to predict cell-type-specific and shared binding sites by excluding or including DNase signals. Furthermore, we investigated the generalization ability of our proposed approaches to different binding factors in the same cellular environment. AVAILABILITY AND IMPLEMENTATION: The source code is available at: https://github.com/turningpoint1988/CSSBS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Cromatina , Fatores de Transcrição , Humanos , Ligação Proteica/genética , Sítios de Ligação/genética , Fatores de Transcrição/metabolismo , Sequenciamento de Cromatina por Imunoprecipitação , Biologia Computacional/métodosRESUMO
Adsorption-desorption performance, electronic properties, and sensitivity of O-defective g-ZnO (ODZO) gas sensors for volatile organic compounds (VOCs) are calculated using density functional theory and nonequilibrium Green's formalism. The VOCs are CH2O, CH4, C2H4O, CH4O, and C2H6. The intrinsic g-ZnO (IZO) and ODZO exhibit strong adsorption capabilities for C2H4O and CH4O. The IZO (0.118 e) and ODZO (0.059 e), which act as electron donors, exhibit the highest charge transfer to CH2O, indicating a strong interaction. The VOCs adsorption on the IZO and ODZO systems maintain nonmagnetic semiconductor characteristics. Additionally, the introduction of an O-defect causes the adsorption energy and charge transfer amount of ODZO to show an overall decrease, indicating better desorption ability. Notably, the sensitivity results show that the ODZO gas sensors exhibit high sensitivity to CH2O (39.3%), C2H4O (29.0%), and CH4O (19.6%) at a voltage of 2.6 V, consistent with the adsorption-desorption performance and electronic properties.
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The g-ZnO/Si9C15 heterojunction is designed, and its stability, electronic properties and photo-electro catalytic properties, and the impact of biaxial strain on the electronic and photocatalytic properties are investigated. The g-ZnO/Si9C15 heterojunction has a staggered (type-II) band structure (band gap is 1.770 eV), following the S-scheme mechanism. A high electron mobility of 5.113 × 103 cm2 V-1 s-1 and hole mobility of 3.324 × 104 cm2 V-1 s-1 are obtained in the zigzag and armchair directions, respectively. Suitable oxidation and reduction potentials are obtained such that photocatalytic water decomposition can occur at pH = 0-14, and the corrected solar to hydrogen (STH) efficiency is up to 35.4%. The absorption of visible light is enhanced, and the power conversion efficiency (PCE) is 15.1%. The electro-catalytic hydrogen evolution reaction (HER) is more likely to occur at the Si9C15 interface with a low over-voltage of 0.190 V. Under biaxial strain, due to the controllable band structure, the corrected STH efficiency and PCE increase to 42.7% and 16.7%, respectively. The heterojunction shows potential value in the field of high-efficiency solar devices and catalytic materials for water splitting.
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INTRODUCTION: Surgery remains the primary treatment modality for thymic carcinoma, with adjuvant radiotherapy being recommended to effectively mitigate local recurrence and metastasis rates subsequent to incomplete or complete resection. Chemoradiotherapy has the potential to induce coronary artery occlusion, thereby potentially impacting patients' long-term survival rates. The existing literature currently lacks comprehensive research on the lesion characteristics of coronary artery injury resulting from chemoradiotherapy. CASE PRESENTATION: The male patient, aged 55, was admitted to the hospital due to recurrent chest tightness and pain persisting for one week. Notably, the patient had previously undergone curative resection surgery for thymic carcinoma seven years ago. After the surgical procedure, the patient underwent a course of adjuvant chemotherapy comprising docetaxel and platinum. 11 months later, imaging examination diagnosed tumor recurrence, and concurrent chemoradiotherapy was administered at a total dose of 62 Gy/31F for planning gross target volume (PGTV) and 54 Gy/31F for planning target volume (PTV) with 2 cycles of paclitaxel and cisplatin. Re-admission of the patient occurred after a 7-year interval subsequent to the completion of concurrent chemoradiotherapy, leading to a subsequent diagnosis of acute non-ST segment elevation myocardial infarction. Following administration of antiplatelet, anticoagulant, and anti-myocardial ischemia therapy, coronary angiography revealed the presence of a bifurcation lesion at the distal end of the left main trunk. Intravascular ultrasound (IVUS) examination demonstrated significant negative remodeling of both the main trunk and its branches at the bifurcation site, characterized by minimal atherosclerotic plaque components. CONCLUSIONS: Chemoradiotherapy may induce damage to endothelial cells, resulting in an inflammatory response. Negative remodeling of blood vessels is likely to occur, primarily characterized by vasoconstriction but with less atherosclerotic plaque burden. Routine stent implantation in negatively remodeled areas may lead to vascular rupture, necessitating intravascular imaging examination.
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Timoma , Neoplasias do Timo , Humanos , Masculino , Neoplasias do Timo/terapia , Neoplasias do Timo/diagnóstico por imagem , Pessoa de Meia-Idade , Resultado do Tratamento , Fatores de Tempo , Timoma/terapia , Timoma/diagnóstico por imagem , Angiografia Coronária , Lesões do Sistema Vascular/etiologia , Lesões do Sistema Vascular/diagnóstico por imagem , Lesões do Sistema Vascular/terapia , Vasos Coronários/diagnóstico por imagem , Vasos Coronários/lesões , Vasos Coronários/efeitos dos fármacos , Quimiorradioterapia/efeitos adversosRESUMO
Establishment of a new method for improved shoot tip cryopreservation is crucial to facilitate the long-term preservation of plant germplasm as well as the use of cryotherapy for pathogen eradication. The present study reported a vitrification (V) cryo-foil method for shoot tip cryopreservation and virus eradication in apple. Shoot tip regrowth levels after cryopreservation were comparable among V cryo-foil (53 %), V cryo-plate (46 %) and conventional droplet vitrification (Dr-vi, 48 %). The V cryo-foil is more efficient to perform than Dr-vi as more shoot tips can be cryopreserved by one person. In the histological study applying an image-overlaying strategy, shoot tips cryopreserved by V cryo-foil showed a higher survival chance in the youngest leaf primordia than in the apical dome. When V cryo-foil was tested for virus eradication, fifty-five percent (55 %) of cryo-derived shoots were free of the apple stem pitting virus (ASPV), while none and less than 10 % were free of the apple stem grooving virus (ASGV) and the apple chlorotic leaf spot virus (ACLSV), respectively. Thus, these two viruses were efficiently preserved by V cryo-foil cryopreservation. Noticeably, although the shoot regrowth level was reduced to 27 %, a higher frequency (81 %) of ASPV eradication was achieved when a reduced duration of cryoprotectant exposure was applied in V cryo-foil, supporting the use of insufficient cryoprotection for improved virus eradication.
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Environmental pollution, virus infection, allergens, and other factors may cause respiratory disease, which could be improved by dietary therapy. Allium species are common daily food seasoning and have high nutritional and medical value. Diallyl disulfide (DADS) is the major volatile oil compound of Allium species. The present study aims to explore the preventive effect and potential mechanism of DADS on pulmonary fibrosis. C57BL/6J mice were intratracheally injected with bleomycin (BLM) to establish pulmonary fibrosis and then administrated with DADS. Primary lung fibroblasts or A549 were stimulated with BLM, followed by DADS, farnesoid X receptor (FXR) agonist (GW4064), yes-associated protein 1 (YAP1) inhibitor (verteporfin), or silencing of FXR and YAP1. In BLM-stimulated mice, DADS significantly ameliorated histopathological changes and interleukin-1ß levels in bronchoalveolar lavage fluid. DADS decreased fibrosis markers, HIF-1α, inflammatory cytokines, and epithelial-mesenchymal transition in pulmonary mice and activated fibroblasts. DADS significantly enhanced FXR expression and inhibited YAP1 activation, which functions as GW4064 and verteporfin. A deficiency of FXR or YAP1 could result in the increase of these two protein expressions, respectively. DADS ameliorated extracellular matrix deposition, hypoxia, epithelial-mesenchymal transition, and inflammation in FXR or YAP1 knockdown A549. Taken together, targeting the crosstalk of FXR and YAP1 might be the potential mechanism for DADS against pulmonary fibrosis. DADS can serve as a potential candidate or dietary nutraceutical supplement for the treatment of pulmonary fibrosis.
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Compostos Alílicos , Dissulfetos , Camundongos Endogâmicos C57BL , Fibrose Pulmonar , Receptores Citoplasmáticos e Nucleares , Transdução de Sinais , Proteínas de Sinalização YAP , Animais , Fibrose Pulmonar/tratamento farmacológico , Fibrose Pulmonar/induzido quimicamente , Camundongos , Dissulfetos/farmacologia , Humanos , Receptores Citoplasmáticos e Nucleares/metabolismo , Transdução de Sinais/efeitos dos fármacos , Compostos Alílicos/farmacologia , Células A549 , Masculino , Allium/química , Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Bleomicina , Pulmão/efeitos dos fármacos , Pulmão/patologia , Fibroblastos/efeitos dos fármacos , Fibroblastos/metabolismoRESUMO
The endoperoxide group of artemisinins is universally accepted an essential group for their anti-cancer effects. In this study, a series of D-ring-contracted artemisinin derivatives were constructed by combining ring-contracted artemisinin core with fragments of functional heterocyclic molecules or classical CDK4/6 inhibitors to identify more efficacious breast cancer treatment agents. Twenty-six novel hybridized molecules were synthesized and characterized by HRMS, IR, 1H-NMR and 13Câ NMR. In antiproliferative activities and kinase inhibitory effects assays, we found that the antiproliferative effects of B01 were close to those of the positive control Palbociclib, with GI50 values of 4.87±0.23â µM and 9.97±1.44â µM towards T47D cells and MDA-MB-436 cells respectively. In addition, the results showed that B01 was the most potent compound against CDK6/cyclin D3 kinase, with an IC50 value of 0.135±0.041â µM, and its activity was approximately 1/3 of the positive control Palbociclib.
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Antineoplásicos , Artemisininas , Neoplasias da Mama , Proliferação de Células , Quinase 4 Dependente de Ciclina , Quinase 6 Dependente de Ciclina , Ensaios de Seleção de Medicamentos Antitumorais , Inibidores de Proteínas Quinases , Humanos , Quinase 6 Dependente de Ciclina/antagonistas & inibidores , Quinase 6 Dependente de Ciclina/metabolismo , Artemisininas/farmacologia , Artemisininas/química , Artemisininas/síntese química , Quinase 4 Dependente de Ciclina/antagonistas & inibidores , Quinase 4 Dependente de Ciclina/metabolismo , Antineoplásicos/farmacologia , Antineoplásicos/síntese química , Antineoplásicos/química , Inibidores de Proteínas Quinases/farmacologia , Inibidores de Proteínas Quinases/síntese química , Inibidores de Proteínas Quinases/química , Proliferação de Células/efeitos dos fármacos , Neoplasias da Mama/tratamento farmacológico , Neoplasias da Mama/patologia , Neoplasias da Mama/metabolismo , Relação Estrutura-Atividade , Linhagem Celular Tumoral , Estrutura Molecular , Feminino , Relação Dose-Resposta a Droga , Simulação de Acoplamento MolecularRESUMO
The gas sensitivity of the W defect in WS2 (VW/WS2) to five toxic gases-HCHO, CH4, CH3HO, CH3OH, and CH3CH3-has been examined in this article. These five gases were adsorbed on the VW/WS2 surface, and the band, density of state (DOS), charge density difference (CDD), work function (W), current-voltage (I-V) characteristic, and sensitivity of adsorption systems were determined. Interestingly, for HCHO-VW/WS2, the energy level contribution of HCHO is closer to the Fermi level, the charge transfer (B) is the largest (0.104 e), the increase in W is more obvious than other adsorption systems, the slope of the I-V characteristic changes more obviously, and the calculated sensitivity is the highest. To sum up, VW/WS2 is more sensitive to HCHO. In conclusion, VW/WS2 has a great deal of promise for producing HCHO chemical sensors due to its high sensitivity and selectivity for HCHO, which can aid in the precise and efficient detection of toxic gases.
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To evaluate the efficacy of cognitive behavioural therapy (CBT) as a psychological intervention for elderly patients with extensive burns, focusing on its impact on emotional well-being, self-efficacy and quality of life. A prospective, randomized study involving 200 elderly burn patients was conducted from November 2021 to January 2023. The patients were randomly assigned to receive either standard care (control group) or burn care based on cognitive behavioural therapy (CBT-B) (study group), with 100 patients in each group. Outcome measures included the Visual Analog Scale (VAS) for pain assessment, 36-item Short Form Survey (SF-36) for quality of life, General Self-Efficacy Scale (GSES) and Rosenberg Self-Esteem Scale (RSES). The study revealed that CBT-based intervention significantly reduced anxiety and depression scores compared with standard care (p < 0.05). Additionally, patients in the CBT group exhibited improved self-efficacy, self-esteem and quality of life (p < 0.05). CBT proves to be a valuable intervention for elderly burn patients, effectively addressing emotional distress and enhancing their psychological well-being. By modifying negative cognitive patterns, providing coping mechanisms and fostering problem-solving skills, CBT-based care contributes to a more positive recovery experience and improved quality of life.
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Terapia Cognitivo-Comportamental , Qualidade de Vida , Humanos , Idoso , Estudos Prospectivos , Intervenção Psicossocial , Ansiedade/terapiaRESUMO
This analysis systematically reviewed the efficacy of evidence-based care on diabetic foot ulcers. A computerised literature search was conducted for randomised controlled studies (RCTs) of evidence-based care interventions for the treatment of diabetic foot ulcers using the PubMed, Embase, Cochrane Library, Web of Science, China National Knowledge Infrastructure (CNKI), China Biomedical Literature Database (CBM) and Wanfang databases from the date of inception of each database to June 2023. The articles were independently screened, data were extracted by two researchers, and the quality of each study was assessed using the Cochrane bias assessment tool. Meta-analysis of the data was performed using RevMan 5.4 software. Twenty-five RCTs with a total of 2272 patients were included. Meta-analysis showed that, compared with other care methods, evidence-based care significantly improved the treatment efficacy of diabetic foot ulcers (odds ratio: 3.91, 95% confidence interval [CI]: 2.76 to 5.53, p < 0.001) and significantly reduced their fasting plasma glucose (mean difference [MD]: -1.10, 95% CI: -1.24 to -0.96, p < 0.001), 2-h postprandial glucose (2hPG) (MD: -1.69, 95% CI: -2.07 to -1.31, p < 0.001) and glycated haemoglobin (HbA1c) (MD: -0.71, 95% CI: -0.94 to -0.48, p < 0.001). Evidence-based care intervention is effective at reducing FPG, 2hPG and HbA1c levels and improving treatment efficacy in patients with diabetic foot ulcers.
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Diabetes Mellitus , Pé Diabético , Humanos , Pé Diabético/terapia , Medicina Baseada em Evidências , Hemoglobinas Glicadas , Resultado do Tratamento , ChinaRESUMO
Sesquiterpene synthases (STPSs) catalyze carbocation-driven cyclization reactions that can generate structurally diverse hydrocarbons. The deprotonation-reprotonation process is widely used in STPSs to promote structural diversity, largely attributable to the distinct regio/stereoselective reprotonations. However, the molecular basis for reprotonation regioselectivity remains largely understudied. Herein, we analyzed two highly paralogous STPSs, Artabotrys hexapetalus (-)-cyperene synthase (AhCS) and ishwarane synthase (AhIS), which catalyze reactions that are distinct from the regioselective protonation of germacrene A (GA), resulting in distinct skeletons of 5/5/6 tricyclic (-)-cyperene and 6/6/5/3 tetracyclic ishwarane, respectively. Isotopic labeling experiments demonstrated that these protonations occur at C3 and C6 of GA in AhCS and AhIS, respectively. The cryo-electron microscopy-derived AhCS complex structure provided the structural basis for identifying different key active site residues that may govern their functional disparity. The structure-guided mutagenesis of these residues resulted in successful functional interconversion between AhCS and AhIS, thus targeting the three active site residues [L311-S419-C458]/[M311-V419-A458] that may act as a C3/C6 reprotonation switch for GA. These findings facilitate the rational design or directed evolution of STPSs with structurally diverse skeletons.
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Alquil e Aril Transferases , Sesquiterpenos , Microscopia Crioeletrônica , Sesquiterpenos/química , Catálise , Domínio Catalítico , Alquil e Aril Transferases/genéticaRESUMO
Transcription factors (TFs) play an important role in regulating gene expression, thus the identification of the sites bound by them has become a fundamental step for molecular and cellular biology. In this paper, we developed a deep learning framework leveraging existing fully convolutional neural networks (FCN) to predict TF-DNA binding signals at the base-resolution level (named as FCNsignal). The proposed FCNsignal can simultaneously achieve the following tasks: (i) modeling the base-resolution signals of binding regions; (ii) discriminating binding or non-binding regions; (iii) locating TF-DNA binding regions; (iv) predicting binding motifs. Besides, FCNsignal can also be used to predict opening regions across the whole genome. The experimental results on 53 TF ChIP-seq datasets and 6 chromatin accessibility ATAC-seq datasets show that our proposed framework outperforms some existing state-of-the-art methods. In addition, we explored to use the trained FCNsignal to locate all potential TF-DNA binding regions on a whole chromosome and predict DNA sequences of arbitrary length, and the results show that our framework can find most of the known binding regions and accept sequences of arbitrary length. Furthermore, we demonstrated the potential ability of our framework in discovering causal disease-associated single-nucleotide polymorphisms (SNPs) through a series of experiments.
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Aprendizado Profundo , Sítios de Ligação , Sequenciamento de Cromatina por Imunoprecipitação , Ligação Proteica , Fatores de Transcrição/metabolismoRESUMO
In recent years, major advances have been made in various chromosome conformation capture technologies to further satisfy the needs of researchers for high-quality, high-resolution contact interactions. Discriminating the loops from genome-wide contact interactions is crucial for dissecting three-dimensional(3D) genome structure and function. Here, we present a deep learning method to predict genome-wide chromatin loops, called DLoopCaller, by combining accessible chromatin landscapes and raw Hi-C contact maps. Some available orthogonal data ChIA-PET/HiChIP and Capture Hi-C were used to generate positive samples with a wider contact matrix which provides the possibility to find more potential genome-wide chromatin loops. The experimental results demonstrate that DLoopCaller effectively improves the accuracy of predicting genome-wide chromatin loops compared to the state-of-the-art method Peakachu. Moreover, compared to two of most popular loop callers, such as HiCCUPS and Fit-Hi-C, DLoopCaller identifies some unique interactions. We conclude that a combination of chromatin landscapes on the one-dimensional genome contributes to understanding the 3D genome organization, and the identified chromatin loops reveal cell-type specificity and transcription factor motif co-enrichment across different cell lines and species.
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Cromatina , Aprendizado Profundo , Cromatina/genética , Genoma/genética , Cromossomos , Fatores de Transcrição/genéticaRESUMO
Aeromonas salmonicida is the typical pathogen causing furunculosis, reported widely in salmonids. Because of multiple serotypes, the control of A. salmonicida-caused disease has increasingly received much attention. Recently, A. salmonicida infection was reported in non-salmonid fish species. Here, a pathogenic A. salmonicida, named as As-s, was isolated from cultured snakehead (Channa argus) in a local fish farm in Shandong, China. As-s displayed clear hemolysis, amylase, and positive catalase activities, and grew at a wide range of temperatures (10-37 °C) and pH values (5.5-8.5). As-s was highly sensitive to cefuroxime sodium, ceftriaxone, ceftazidime, piperacillin, and cefoperazone and also apparently sensitive to chloramphenicol, erythromycin, and 25% cinnamaldehyde. The Virulence array protein gene cloning' results suggested that As-s has this gene compared with the other two vapA-containing strains, despite a close relationship of these strains via phylogenetic analysis. Severe ulcers on skin, muscle, and abnormal liver, and hemorrhage in pectoral/ventral fins and anal region were observed, and exophthalmos were also noticed in infected juvenile snakehead, as well as necrosis and infiltration of blood cells emerged in the internal organs using pathological section. In addition, As-s caused high mortality in snakehead, consistently with its immune gene response. This study reports the first isolation of vapA-absent A. salmonicida in snakehead.
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OBJECTIVES: We applied a fully automated pixel-wise post-processing framework to evaluate fully quantitative cardiovascular magnetic resonance myocardial perfusion imaging (CMR-MPI). In addition, we aimed to evaluate the additive value of coronary magnetic resonance angiography (CMRA) to the diagnostic performance of fully automated pixel-wise quantitative CMR-MPI for detecting hemodynamically significant coronary artery disease (CAD). METHODS: A total of 109 patients with suspected CAD were prospectively enrolled and underwent stress and rest CMR-MPI, CMRA, invasive coronary angiography (ICA), and fractional flow reserve (FFR). CMRA was acquired between stress and rest CMR-MPI acquisition, without any additional contrast agent. Finally, CMR-MPI quantification was analyzed by a fully automated pixel-wise post-processing framework. RESULTS: Of the 109 patients, 42 patients had hemodynamically significant CAD (FFR ≤ 0.80 or luminal stenosis ≥ 90% on ICA) and 67 patients had hemodynamically non-significant CAD (FFR Ë 0.80 or luminal stenosis < 30% on ICA) were enrolled. On the per-territory analysis, patients with hemodynamically significant CAD had higher myocardial blood flow (MBF) at rest, lower MBF under stress, and lower myocardial perfusion reserve (MPR) than patients with hemodynamically non-significant CAD (p < 0.001). The area under the receiver operating characteristic curve of MPR (0.93) was significantly larger than those of stress and rest MBF, visual assessment of CMR-MPI, and CMRA (p < 0.05), but similar to that of the integration of CMR-MPI with CMRA (0.90). CONCLUSIONS: Fully automated pixel-wise quantitative CMR-MPI can accurately detect hemodynamically significant CAD, but the integration of CMRA obtained between stress and rest CMR-MPI acquisition did not provide significantly additive value. KEY POINTS: ⢠Full quantification of stress and rest cardiovascular magnetic resonance myocardial perfusion imaging can be postprocessed fully automatically, generating pixel-wise myocardial blood flow (MBF) and myocardial perfusion reserve (MPR) maps. ⢠Fully quantitative MPR provided higher diagnostic performance for detecting hemodynamically significant coronary artery disease, compared with stress and rest MBF, qualitative assessment, and coronary magnetic resonance angiography (CMRA). ⢠The integration of CMRA and MPR did not significantly improve the diagnostic performance of MPR alone.
Assuntos
Doença da Artéria Coronariana , Estenose Coronária , Reserva Fracionada de Fluxo Miocárdico , Imagem de Perfusão do Miocárdio , Humanos , Doença da Artéria Coronariana/diagnóstico , Angiografia Coronária/métodos , Reserva Fracionada de Fluxo Miocárdico/fisiologia , Constrição Patológica , Valor Preditivo dos Testes , Perfusão , Imagem de Perfusão do Miocárdio/métodosRESUMO
BACKGROUND: Vitamin B6 is an essential water-soluble vitamin for humans. It is often used to prevent a variety of neuropathies, relieve vomiting, and relieve symptoms such as hand and foot neuritis. AIM: To evaluate whether vitamin B6 can alleviate the adverse reactions caused by the quadruple anti-Helicobacter pylori treatment regimen containing minocycline and metronidazole. METHODS: In this randomized controlled trial, 280 patients with H. pylori infection were randomly placed into one of two treatment groups-the conventional treatment group and the vitamin B6 supplement treatment group-for 2 weeks. The primary endpoint was the total incidence of adverse reactions up to 2 weeks after treatment initiation. The study was designed according to CONSORT Medicinal Interventions. And it was registered with Chinese Clinical Trial Registry under the number ChiCTR2100053833. RESULTS: In terms of efficacy, vitamin B6 does not affect the efficacy of conventional regimen. In the vitamin B6 supplement treatment group, the incidence of adverse reactions was 56.92%, which was significantly lower than the 74.62% observed in the conventional treatment group. In addition, the severity of adverse reactions was also significantly reduced. The proportion of moderate to severe central nervous system symptoms decreased from 58.7 to 14.63%. And, the proportion of moderate to severe gastrointestinal reactions decreased from 33.33 to 0%. We speculate that the mechanism of vitamin B6 of reducing adverse reaction may be related to the production of GABA in the brain. CONCLUSIONS: Vitamin B6 can alleviate adverse reactions of the quadruple anti-H. pylori regimen containing minocycline and metronidazole.