RESUMO
Structural variation (SV) is an important form of genomic variation that influences gene function and expression by altering the structure of the genome. Although long-read data have been proven to better characterize SVs, SVs detected from noisy long-read data still include a considerable portion of false-positive calls. To accurately detect SVs in long-read data, we present SVDF, a method that employs a learning-based noise filtering strategy and an SV signature-adaptive clustering algorithm, for effectively reducing the likelihood of false-positive events. Benchmarking results from multiple orthogonal experiments demonstrate that, across different sequencing platforms and depths, SVDF achieves higher calling accuracy for each sample compared to several existing general SV calling tools. We believe that, with its meticulous and sensitive SV detection capability, SVDF can bring new opportunities and advancements to cutting-edge genomic research.
Assuntos
Algoritmos , Humanos , Análise de Sequência de DNA/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Genômica/métodos , Variação Estrutural do Genoma , SoftwareRESUMO
OBJECTIVES: This study investigated the potential effects of perfluoroalkyl substance (PFAS) in serum on MAFLD, NAFLD, and liver fibrosis. METHODS: Our sample included 696 participants (≥ 18 years) from the 2017-2018 NHANES study with available serum PFASs, covariates, and outcomes. Using the first quartile of PFAS as the reference group, we used weighted binary logistic regression and multiple ordered logistic regression used to analyze the relationship between PFAS and MAFLD, NAFLD, and liver fibrosis and multiple ordinal logistic regression to investigate the relationship between PFAS and MAFLD, NAFLD, and liver fibrosis and calculated the odds ratio (OR) and 95% confidence interval for each chemical. Finally, stratified analysis and sensitivity analysis were performed according to gender, age, BMI, and serum cotinine concentration. RESULTS: A total of 696 study subjects were included, including 212 NAFLD patients (weighted 27.03%) and 253 MAFLD patients (weighted 32.65%). The quartile 2 of serum PFOA was positively correlated with MAFLD and NAFLD (MAFLD, OR 2.29, 95% CI 1.05-4.98; NAFLD, OR 2.37, 95% CI 1.03-5.47). PFAS were not significantly associated with liver fibrosis after adjusting for potential confounders in MAFLD and NAFLD. Stratified analysis showed that PFOA was strongly associated with MAFLD, NAFLD, and liver fibrosis in males and obese subjects. In women over 60 years old, PFHxS was also correlated with MAFLD, NAFLD, and liver fibrosis. CONCLUSION: The serum PFOA was positively associated with MAFLD and NAFLD in US adults. After stratified analysis, the serum PFHxS was correlated with MFALD, NAFLD, and liver fibrosis.
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Flag leaf angle impacts the photosynthetic capacity of densely grown plants and is thus an important agronomic breeding trait for crop architecture and yield. The hormone auxin plays a key role in regulating this trait, yet the underlying molecular and cellular mechanisms remain unclear. Here, we report that two rice (Oryza sativa) auxin response factors (ARFs), OsARF6 and OsARF17, which are highly expressed in lamina joint tissues, control flag leaf angle in response to auxin. Loss-of-function double osarf6 osarf17 mutants displayed reduced secondary cell wall levels of lamina joint sclerenchymatous cells (Scs), resulting in an exaggerated flag leaf angle and decreased grain yield under dense planting conditions. Mechanical measurements indicated that the mutant lamina joint tissues were too weak to support the weight of the flag leaf blade, resembling the phenotype of the rice increased leaf angle1 (ila1) mutant. We demonstrate that OsARF6 and OsARF17 directly bind to the ILA1 promoter independently and synergistically to activate its expression. In addition, auxin-induced ILA1 expression was dependent on OsARF6 and OsARF17. Collectively, our study reveals a mechanism that integrates auxin signaling with the secondary cell wall composition to determine flag leaf angle, providing breeding targets in rice, and potentially other cereals, for this key trait.
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Oryza/genética , Folhas de Planta/crescimento & desenvolvimento , Proteínas de Plantas/genética , Fatores de Transcrição/genética , Parede Celular/metabolismo , Oryza/crescimento & desenvolvimento , Oryza/metabolismo , Proteínas de Plantas/metabolismo , Fatores de Transcrição/metabolismoRESUMO
Prompt reperfusion after cerebral ischemia is important to maintain neuronal survival and reduce permanent disability and death. However, the resupply of blood can induce oxidative stress, inflammatory response and apoptosis, further leading to tissue damage. Here, we report the versatile biological roles of transcript-induced in spermiogenesis 40 (Tisp40) in ischemic stroke. We found that the expression of Tisp40 was upregulated in ischemia/reperfusion-induced brain tissues and oxygen glucose deprivation/returned -stimulated neurons. Tisp40 deficiency increased the infarct size and neurological deficit score, and promoted inflammation and apoptosis. Tisp40 overexpression played the opposite role. In vitro, the oxygen glucose deprivation/returned model was established in Tisp40 knockdown and overexpression primary cultured cortical neurons. Tisp40 knockdown can aggravate the process of inflammation and apoptosis, and Tisp40 overexpression ameliorated the aforementioned processes. Mechanistically, Tisp40 protected against ischemic stroke via activating the AKT signaling pathway. Tisp40 may be a new therapeutic target in brain ischemia/reperfusion injury.
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Isquemia Encefálica , Traumatismo por Reperfusão , Animais , Traumatismo por Reperfusão/metabolismo , Masculino , Isquemia Encefálica/metabolismo , Apoptose/fisiologia , Neurônios/metabolismo , Neurônios/patologia , Camundongos Endogâmicos C57BL , AVC Isquêmico/metabolismo , Células Cultivadas , Camundongos , Proteínas Proto-Oncogênicas c-akt/metabolismoRESUMO
BACKGROUND: Endothelial-mesenchymal transition (EndMT) induced by low shear stress plays an important role in the development of atherosclerosis. However, little is known about the correlation between hydrogen sulfide (H2S), a protective gaseous mediator in atherosclerosis and the process of EndMT. METHODS: We constructed a stable low-shear-stress-induced(2 dyn/cm2) EndMT model, acombined with the pretreatment method of hydrogen sulfide slow release agent(GYY4137). The level of MEST was detected in the common carotid artery of ApoE-/- mice with local carotid artery ligation. The effect of MEST on atherosclerosis development in vivo was verified using ApoE-/- mice were given tail-vein injection of endothelial-specific overexpressed and knock-down MEST adeno-associated virus (AAV). RESULTS: These findings confirmed that MEST is up-regulated in low-shear-stress-induced EndMT and atherosclerosis. In vivo experiments showed that MEST gene overexpression significantly promoted EndMT and aggravated the development of atherosclerotic plaques and MEST gene knockdown significantly inhibited EndMT and delayed the process of atherosclerosis. In vitro, H2S inhibits the expression of MEST and EndMT induced by low shear stress and inhibits EndMT induced by MEST overexpression. Knockdown of NFIL3 inhibit the up regulation of MEST and EndMT induced by low shear stress in HUVECs. CHIP-qPCR assay and Luciferase Reporter assay confirmed that NFIL3 binds to MEST DNA, increases its transcription and H2S inhibits the binding of NFIL3 and MEST DNA, weakening NFIL3's transcriptional promotion of MEST. Mechanistically, H2S increased the sulfhydrylation level of NFIL3, an important upstream transcription factors of MEST. In part, transcription factor NFIL3 restrain its binding to MEST DNA by sulfhydration. CONCLUSIONS: H2S negatively regulate the expression of MEST by sulfhydrylation of NFIL3, thereby inhibiting low-shear-stress-induced EndMT and atherosclerosis.
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Aterosclerose , Sulfeto de Hidrogênio , Camundongos , Animais , Humanos , Sulfeto de Hidrogênio/farmacologia , Sulfeto de Hidrogênio/metabolismo , Transição Endotélio-Mesênquima , Aterosclerose/genética , Aterosclerose/metabolismo , Endotélio/metabolismo , DNA/metabolismo , Apolipoproteínas E/metabolismo , Células Endoteliais da Veia Umbilical Humana/metabolismo , Transição Epitelial-MesenquimalRESUMO
Ions serve as essential nutrients in higher plants and can also act as signaling molecules. Little is known about how plants sense changes in soil nutrient concentrations. Previous studies showed that T101-phosphorylated CHL1 is a high-affinity nitrate transporter, whereas T101-dephosphorylated CHL1 is a low-affinity transporter. In this study, analysis of an uptake- and sensing-decoupled mutant showed that the nitrate transporter CHL1 functions as a nitrate sensor. Primary nitrate responses in CHL1T101D and CHLT101A transgenic plants showed that phosphorylated and dephosphorylated CHL1 lead to a low- and high-level response, respectively. In vitro and in vivo studies showed that, in response to low nitrate concentrations, protein kinase CIPK23 can phosphorylate T101 of CHL1 to maintain a low-level primary response. Thus, CHL1 uses dual-affinity binding and a phosphorylation switch to sense a wide range of nitrate concentrations in the soil, thereby functioning as an ion sensor in higher plants. For a video summary of this article, see the PaperFlick file with the Supplemental Data available online.
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Proteínas de Transporte de Ânions/metabolismo , Arabidopsis/metabolismo , Nitratos/metabolismo , Proteínas de Plantas/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Regulação da Expressão Gênica de Plantas , Fosforilação , Proteínas Serina-Treonina Quinases/genética , Proteínas Serina-Treonina Quinases/metabolismoRESUMO
Objective: This study aimed to investigate the effects of stevioside (STE) on pulmonary fibrosis (PF) and the potential mechanisms. Methods: In this study, a mouse model of PF was established by a single intratracheal injection of bleomycin (BLM, 3 mg/kg). The experiment consisted of four groups: control group, BLM group, and STE treatment groups (STE 50 and 100 mg/kg). ELISA and biochemical tests were conducted to determine the levels of TNF-α, IL-1ß, IL-6, NO, hydroxyproline (HYP), SOD, GSH, and MDA. Histopathological changes and collagen deposition in lung tissues were observed by HE and Masson staining. Immunohistochemistry was performed to determine the levels of collagen I-, collagen III-, TGF-ß1- and p-Smad2/3-positive cells. Western blot analysis was used to measure the expression of epithelial-mesenchymal transition (EMT) markers, including α-SMA, vimentin, E-cadherin, and ZO-1, as well as proteins related to the nuclear factor erythroid 2-related factor 2 (Nrf2) pathway, nuclear transcription factor-κB (NF-κB) pathway, and TGF-ß1/Smad2/3 pathway in lung tissues. Results: STE significantly alleviated BLM-induced body weight loss and lung injury in mice, decreased HYP levels, and reduced the levels of collagen I- and collagen III-positive cells, thereby decreasing extracellular matrix (ECM) deposition. Moreover, STE markedly improved oxidative stress (MDA levels were decreased, while SOD and GSH activity were enhanced), the inflammatory response (the levels of TNF-α, IL-1ß, IL-6, and NO were reduced), and EMT (the expression of α-SMA and vimentin was downregulated, and the expression of E-cadherin and ZO-1 was upregulated). Further mechanistic analysis revealed that STE could activate the Nrf2 pathway and inhibit the NF-κB and TGF-ß1/Smad2/3 pathways. Conclusion: STE may alleviate oxidative stress by activating the Nrf2 pathway, suppress the inflammatory response by downregulating the NF-κB pathway, and inhibit EMT progression by blocking the TGF-ß1/Smad2/3 pathway, thereby improving BLM-induced PF.
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Fibrose Pulmonar , Camundongos , Animais , Fibrose Pulmonar/induzido quimicamente , Fibrose Pulmonar/tratamento farmacológico , Fibrose Pulmonar/metabolismo , NF-kappa B , Fator de Crescimento Transformador beta1/metabolismo , Bleomicina/efeitos adversos , Vimentina , Fator 2 Relacionado a NF-E2 , Fator de Necrose Tumoral alfa , Interleucina-6 , Colágeno/metabolismo , Colágeno Tipo I/metabolismo , Caderinas , Superóxido DismutaseRESUMO
BACKGROUND AND AIMS: NAFLD is the most prevalent chronic liver disease worldwide, but no effective pharmacological therapeutics are available for clinical use. NASH is the more severe stage of NAFLD. During this progress, dysregulation of endoplasmic reticulum (ER)-related pathways and proteins is one of the predominant hallmarks. We aimed to reveal the role of ring finger protein 5 (RNF5), an ER-localized E3 ubiquitin-protein ligase, in NASH and to explore its underlying mechanism. APPROACH AND RESULTS: We first inspected the expression level of RNF5 and found that it was markedly decreased in livers with NASH in multiple species including humans. We then introduced adenoviruses for Rnf5 overexpression or knockdown into primary mouse hepatocytes and found that palmitic acid/oleic acid (PAOA)-induced lipid accumulation and inflammation in hepatocytes were markedly attenuated by Rnf5 overexpression but exacerbated by Rnf5 gene silencing. Hepatocyte-specific Rnf5 knockout significantly exacerbated hepatic steatosis, inflammatory response, and fibrosis in mice challenged with diet-induced NASH. Mechanistically, we identified 3-hydroxy-3-methylglutaryl CoA reductase degradation protein 1 (HRD1) as a binding partner of RNF5 by systematic interactomics analysis. RNF5 directly bound to HRD1 and promoted its lysine 48 (K48)-linked and K33-linked ubiquitination and subsequent proteasomal degradation. Furthermore, Hrd1 overexpression significantly exacerbated PAOA-induced lipid accumulation and inflammation, and short hairpin RNA-mediated Hrd1 knockdown exerted the opposite effects. Notably, Hrd1 knockdown significantly diminished PAOA-induced lipid deposition, and up-regulation of related genes resulted from Rnf5 ablation in hepatocytes. CONCLUSIONS: These data indicate that RNF5 inhibits NASH progression by targeting HRD1 in the ubiquitin-mediated proteasomal pathway. Targeting the RNF5-HRD1 axis may provide insights into the pathogenesis of NASH and pave the way for developing strategies for NASH prevention and treatment.
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Proteínas de Ligação a DNA/metabolismo , Proteínas de Membrana/metabolismo , Hepatopatia Gordurosa não Alcoólica/patologia , Ubiquitina-Proteína Ligases/metabolismo , Animais , Biópsia , Proteínas de Ligação a DNA/análise , Dieta Hiperlipídica/efeitos adversos , Modelos Animais de Doenças , Regulação para Baixo , Feminino , Técnicas de Silenciamento de Genes , Células HEK293 , Hepatócitos , Humanos , Fígado/patologia , Masculino , Proteínas de Membrana/análise , Camundongos , Cultura Primária de Células , Mapeamento de Interação de Proteínas , Proteólise , RNA-Seq , Ubiquitina-Proteína Ligases/análise , Ubiquitina-Proteína Ligases/genética , UbiquitinaçãoRESUMO
Computation offloading for wireless sensor devices is critical to improve energy efficiency and maintain service delay requirements. However, simultaneous offloadings may cause high interferences to decrease the upload rate and cause additional transmission delay. It is thus intuitive to distribute wireless sensor devices in different channels, but the problem of multi-channel computation offloading is NP-hard. In order to solve this problem efficiently, we formulate the computation offloading decision problem as a decision-making game. Then, we apply the game theory to address the problem of allowing wireless sensor devices to make offloading decisions based on their own interests. In the game theory, not only are the data size of wireless sensor devices and their computation capability considered but the channel gain of each wireless sensor device is also included to improve the transmission rate. The consideration could evenly distribute wireless sensor devices to different channels. We prove that the proposed offloading game is a potential game, where the Nash equilibrium exists in each game after all device states converge. Finally, we extensively evaluate the performance of the proposed algorithm based on simulations. The simulation results demonstrate that our algorithm can reduce the number of iterations to achieve Nash equilibrium by 16%. Moreover, it improves the utilization of each channel to effectively increase the number of successful offloadings and lower the energy consumption of wireless sensor devices.
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Hepatopatia Gordurosa não Alcoólica , Humanos , Teoria dos Jogos , Simulação por Computador , Algoritmos , Fenômenos FísicosRESUMO
AIM: Atrial fibrillation (AF) is a common clinical arrhythmia and can cause a variety of complications. To study the therapeutic effect of H2S in atrial fibrosis and explore the important role of miR-133a, in vitro experiments in human atrial fibroblasts (HAFs) were conducted. METHODS: The fibrosis in HAFs was induced by Ang II. The expression levels of miR-133a and CTGF in HAFs were examined by qRT-PCR. The proliferation and migration of HAFs were detected by CCK-8 and cell scratch assays. The protein expressions of CTGF, collagen I, collagen III and α-SMA were detected by western blotting. The dual-luciferase reporter gene was used to detect the interaction between miR-133a and CTGF. RESULTS: The proliferation and migration of HAFs stimulated by Ang II were enhanced, the expression of miR-133a was reduced, and the levels of CTGF and fibrosis markers (collagen I, collagen III and α-SMA) were increased. Furthermore, H2S reduced fibrosis, proliferation and migration of HAFs induced by Ang II. Accordingly, overexpression of miR-133a inhibited the proliferation and migration ability on Ang II-induced HAFs, and decreased the protein expressions of related fibrosis markers and CTGF. Meanwhile, miR-133a inhibitor could reverse the inhibition effect of H2S on proliferation and migration in HAFs by Ang II-induced. By targeting CTGF, miR-133a inhibited the expression of CTGF. CONCLUSION: H2S improved myocardial cell fibrosis by significantly increasing the expression of miR-133a, and CTGF might be a potential target for miR-133a to play an important role in myocardial fibrosis.
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Fibrilação Atrial/tratamento farmacológico , Fibrilação Atrial/genética , Fator de Crescimento do Tecido Conjuntivo/metabolismo , Átrios do Coração/patologia , Sulfeto de Hidrogênio/uso terapêutico , MicroRNAs/metabolismo , Angiotensina II , Sequência de Bases , Fibroblastos/efeitos dos fármacos , Fibroblastos/metabolismo , Fibroblastos/patologia , Fibrose , Humanos , Sulfeto de Hidrogênio/farmacologia , MicroRNAs/genéticaRESUMO
PURPOSE: Therapeutic strategies to treat ischemic stroke are limited due to the heterogeneity of cerebral ischemic injury and the mechanisms that contribute to the cell death. Since oxidative stress is one of the primary mechanisms that cause brain injury post-stroke, we hypothesized that therapeutic targets that modulate mitochondrial function could protect against reperfusion-injury after cerebral ischemia, with the focus here on a mitochondrial protein, mitoNEET, that modulates cellular bioenergetics. METHOD: In this study, we evaluated the pharmacology of the mitoNEET ligand NL-1 in an in vivo therapeutic role for NL-1 in a C57Bl/6 murine model of ischemic stroke. RESULTS: NL-1 decreased hydrogen peroxide production with an IC50 of 5.95 µM in neuronal cells (N2A). The in vivo activity of NL-1 was evaluated in a murine 1 h transient middle cerebral artery occlusion (t-MCAO) model of ischemic stroke. We found that mice treated with NL-1 (10 mg/kg, i.p.) at time of reperfusion and allowed to recover for 24 h showed a 43% reduction in infarct volume and 68% reduction in edema compared to sham-injured mice. Additionally, we found that when NL-1 was administered 15 min post-t-MCAO, the ischemia volume was reduced by 41%, and stroke-associated edema by 63%. CONCLUSION: As support of our hypothesis, as expected, NL-1 failed to reduce stroke infarct in a permanent photothrombotic occlusion model of stroke. This report demonstrates the potential therapeutic benefits of using mitoNEET ligands like NL-1 as novel mitoceuticals for treating reperfusion-injury with cerebral stroke.
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Moléculas de Adesão Celular Neuronais/farmacologia , Infarto da Artéria Cerebral Média/tratamento farmacológico , Ataque Isquêmico Transitório/tratamento farmacológico , Mitocôndrias/efeitos dos fármacos , Animais , Moléculas de Adesão Celular Neuronais/uso terapêutico , Modelos Animais de Doenças , Metabolismo Energético/efeitos dos fármacos , Humanos , Injeções Intraperitoneais , Proteínas de Ligação ao Ferro/metabolismo , Masculino , Potencial da Membrana Mitocondrial/efeitos dos fármacos , Proteínas de Membrana/metabolismo , Camundongos , Camundongos Endogâmicos C57BL , Mitocôndrias/metabolismo , Estresse Oxidativo/efeitos dos fármacosRESUMO
This study aimed to compare the efficacy of two commonly used therapeutic pressures, 2.0 atmospheres absolute (ATA) versus 2.2 ATA, applied in hyperbaric oxygen (HBO2) therapy for sudden sensorineural hearing loss (SSNHL). We retrospectively reviewed the clinical records of 160 SSNHL patients treated by typical therapy or additional HBO2 therapy with pressure 2.0 or 2.2 ATA at Yijishan Hospital, the First Affiliated Hospital of Wannan Medical College, from February 2018 to May 2020. The pure-tone threshold audiometry results pre- and post-treatment were compared across three groups. In the range of frequencies 250-500 Hz, P2.0 (20.92±26.11 dB, p=0.047) and P2.2 group (20.47±±21.54 dB, p=0.012) both acquired higher hearing gain compared to the control group (11.94±23.32 dB). While in the range of frequencies 1,000-2,000 Hz, only the P2.2 group showed significant improvement of the hearing gain compared to the control group (19.70±21.13 dB vs.10.56±25.24 dB, p=0.015). In the range of frequencies 4,000-8,000, both the P2.0 and P2.2 groups failed to reach the desired effect. Our results suggest that the therapeutic effect is associated with HBO2 therapeutic pressure when applying HBO2 treatment combined with standard medical therapy. Within the range of appropriate pressure, the higher pressure, which means higher partial pressure of oxygen, has better therapeutic efficacy for SSNHL.
Assuntos
Perda Auditiva Neurossensorial , Perda Auditiva Súbita , Audiometria de Tons Puros , Perda Auditiva Neurossensorial/terapia , Perda Auditiva Súbita/terapia , Humanos , Oxigênio , Estudos Retrospectivos , Resultado do TratamentoRESUMO
Atrial fibrillation (AF) is associated with metabolic stress and induces myocardial fibrosis reconstruction by increasing glycolysis. One goal in the treatment of paroxysmal AF (p-AF) is to improve myocardial fibrosis reconstruction and myocardial metabolic stress caused by the Warburg effect. Adopted male canine that rapid right atrial pacing (RAP) for 6 days to establish a p-AF model. The canines were pre-treated with phenylephrine (PE) or dichloroacetic acid (DCA) before exposure to p-AF or non-p-AF. P-wave duration (Pmax), minimum P-wave duration (Pmin), P wave dispersion (PWD), atrial effective refractory period (AERP) and AERP dispersion (AERPd) were measured in canine atrial cardiomyocytes. Pyruvate dehydrogenase kinase-1 (PDK-1), PDK-4, lactate dehydrogenase A (LDHA), pyruvate dehydrogenase (PDH), citrate synthase (CS), isocitrate dehydrogenase (IDH), and matrix metalloproteinase 9 (MMP-9) were evaluated by western blotting and reverse transcription polymerase chain reaction (RT-PCR), content of adenosine monophosphate (AMP), adenosine triphosphate (ATP), lactic acid and glycogen, and activity of LDHA, PDK-1 and PDK-4 were evaluated by enzyme-linked immunosorbent assay (ELISA), myocardial tissue glycogen content was evaluated by PAS, myocardial fibrosis remodeling was evaluated by hematoxylin and eosin (H&E) and Masson staining. Our findings demonstrated that p-AF increases the Warburg effect-related metabolic stress and myocardial fibrosis remodeling by increasing the expression and activity of PDK-1, PDK-4, and LDHA, content of AMP and lactic acid, and the ratio of AMP/ATP and decreasing the expression of PDH, CS, and IDH, and glycogen content. In addition, p-AF can induce cardiomyocyte fibrosis remodeling and increase MMP-9 expression, and p-AF also increases atrial intracardiac waveform activity by prolonging Pmax, Pmin, PWD, and AERPd and shortening AERP. PDK isoforms agonists (PE) produce a similar p-AF pathological effect and can produce synergistic effects with p-AF, further increasing Warburg effect-related metabolic stress, myocardial fibrosis remodeling, and atrial intracardiac waveform activity. In contrast, the use of PDK-specific inhibitors (DCA) completely reverses these pathophysiological changes induced by p-AF. We demonstrate that p-AF can induce the Warburg effect in canine atrial cardiomyocytes and significantly improve p-AF-induced metabolic stress, myocardial fibrosis remodeling, and atrial intracardiac waveform activity by inhibiting the Warburg effect.
Assuntos
Fibrilação Atrial/metabolismo , Glicólise/fisiologia , Sistema de Condução Cardíaco/metabolismo , Miocárdio/metabolismo , Estresse Fisiológico/fisiologia , Animais , Fibrilação Atrial/genética , Fibrilação Atrial/fisiopatologia , Estimulação Cardíaca Artificial , Ácido Dicloroacético/farmacologia , Cães , Fibrose , Regulação Enzimológica da Expressão Gênica/efeitos dos fármacos , Glicogênio/metabolismo , Glicólise/efeitos dos fármacos , Glicólise/genética , Sistema de Condução Cardíaco/efeitos dos fármacos , Sistema de Condução Cardíaco/fisiopatologia , Lactato Desidrogenase 5/genética , Lactato Desidrogenase 5/metabolismo , Masculino , Miocárdio/patologia , Miócitos Cardíacos/efeitos dos fármacos , Miócitos Cardíacos/metabolismo , Fenilefrina/farmacologia , Piruvato Desidrogenase Quinase de Transferência de Acetil/genética , Piruvato Desidrogenase Quinase de Transferência de Acetil/metabolismoRESUMO
BACKGROUND: Short read DNA sequencing technologies have revolutionized genome assembly by providing high accuracy and throughput data at low cost. But it remains challenging to assemble short read data, particularly for large, complex and polyploid genomes. The linked read strategy has the potential to enhance the value of short reads for genome assembly because all reads originating from a single long molecule of DNA share a common barcode. However, the majority of studies to date that have employed linked reads were focused on human haplotype phasing and genome assembly. RESULTS: Here we describe a de novo maize B73 genome assembly generated via linked read technology which contains ~ 172,000 scaffolds with an N50 of 89 kb that cover 50% of the genome. Based on comparisons to the B73 reference genome, 91% of linked read contigs are accurately assembled. Because it was possible to identify errors with > 76% accuracy using machine learning, it may be possible to identify and potentially correct systematic errors. Complex polyploids represent one of the last grand challenges in genome assembly. Linked read technology was able to successfully resolve the two subgenomes of the recent allopolyploid, proso millet (Panicum miliaceum). Our assembly covers ~ 83% of the 1 Gb genome and consists of 30,819 scaffolds with an N50 of 912 kb. CONCLUSIONS: Our analysis provides a framework for future de novo genome assemblies using linked reads, and we suggest computational strategies that if implemented have the potential to further improve linked read assemblies, particularly for repetitive genomes.
Assuntos
Genoma de Planta , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Folhas de Planta/genética , Poliploidia , Análise de Sequência de DNA/métodos , Zea mays/genéticaRESUMO
Polyurethane coatings containing nanopools of a grafted lubricating liquid ingredient for dewetting enablement (NP-GLIDE) are prepared by curing a commercial polyol P0, a hexamethylene diisocyanate trimer, and P1- g-PDMS, which is a graft copolymer consisting of a polyol backbone P1 bearing poly(dimethylsiloxane) (PDMS) side chains. These materials are known as NP-GLIDE because most test liquids have no problem to cleanly glide off them and because segregated nanopools of the grafted lubricating ingredient (PDMS) for dewetting enablement are dispersed throughout the coating matrix. To optimize the dewetting performance of the NP-GLIDE coatings, the molecular weights of the PDMS side chains in the P1- g-PDMS samples were increased from 1.0 kDa (1k) to 5.0 kDa (5k) and 10.0 kDa (10k). A comparative study of the coatings containing three different P1- g-PDMS samples at a constant PDMS mass fraction of either 6.0 or 2.00% (m/m) showed that P1- g-PDMS5k-based coatings exhibited the best dewetting properties. These properties included the lowest sliding angles for test liquids that were incompatible with PDMS and the fastest and most effective contraction of marker ink traces and a paint. Coatings containing 0.50 and 1.00% (m/m) of PDMS5k were also prepared from P1- g-PDMS5k and compared with those containing 2.00 and 6.0% (m/m) of PDMS5k. The coatings were shown to retain their dewetting properties with the PDMS contents as low as 1.00% (m/m). Although the results of this study provided valuable insight into the design of future practical NP-GLIDE coatings, a model has also been proposed for the surface structure of the coatings to justify our observations.
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Chronic cerebrovascular hypoperfusion results in vascular dementia and increases predisposition to lacunar infarcts. However, there are no suitable animal models. In this study, we developed a novel model for chronic irreversible cerebral hypoperfusion in mice. Briefly, an ameroid constrictor was placed on the right carotid artery to gradually occlude the vessel, while a microcoil was placed on the left carotid artery to prevent compensation of the blood flow. This procedure resulted in a gradual hypoperfusion developing over a period of 34 days with no cerebral blood flow recovery. Histological analysis of the brain revealed neuronal and axonal degeneration as well as necrotic lesions. The most severely affected regions were located in the hippocampus and the corpus callosum. Overall, our paradigm is a viable model to study brain pathology resulting from gradual cerebrovascular hypoperfusion.
Assuntos
Artéria Carótida Primitiva/patologia , Estenose das Carótidas/patologia , Circulação Cerebrovascular/fisiologia , Demência Vascular/patologia , Modelos Animais de Doenças , Animais , Artéria Carótida Primitiva/fisiopatologia , Estenose das Carótidas/complicações , Estenose das Carótidas/fisiopatologia , Demência Vascular/etiologia , Demência Vascular/fisiopatologia , Masculino , Camundongos , Camundongos Endogâmicos C57BLRESUMO
We report a 17-km free-space quantum key distribution (QKD) experiment using an engineering model of the space-bound optical transmitter and a ground station for satellite-ground QKD. The final key rate of ~ 0.5 kbps is achieved in this experiment with the quantum bit error rate (QBER) of ~ 3.4%. An efficient error correction algorithm, Turbo Code, is employed. Compared with the current error correction algorithm of Cascade, a high-efficiency error correction is realized by Turbo Code with only one-time data exchange. For a low QBER, with only one-time data exchange, the final key rates based on Turbo code are similar with Cascade. As the QBER increases, Turbo Code gives higher final key rates than Cascade. Our results experimentally demonstrate the feasibility of satellite-ground QKD and show that the efficient error correction based on Turbo Code is potentially useful for the satellite-ground quantum communication.
RESUMO
Cardiovascular disease is a growing major global public health problem. Oxidative stress is regarded as one of the key regulators of pathological physiology, which eventually leads to cardiovascular disease. However, mechanisms by which FGF-2 rescues cells from oxidative stress damage in cardiovascular disease is not fully elucidated. Herein this study was designed to investigate the protective effects of FGF-2 in H2O2-induced apoptosis of H9c2 cardiomyocytes, as well as the possible signaling pathway involved. Apoptosis of H9c2 cardiomyocytes was induced by H2O2 and assessed using methyl thiazolyl tetrazolium assay, Hoechst, and TUNEL staining. Cells were pretreated with PI3K/Akt inhibitor LY294002 to investigate the possible PI3K/Akt pathways involved in the protection of FGF-2. The levels of p-Akt, p-FoxO3a, and Bim were detected by immunoblotting. Stimulation with H2O2 decreased the phosphorylation of Akt and FoxO3a, and induced nuclear localization of FoxO3a and apoptosis of H9c2 cells. These effects of H2O2 were abrogated by pretreatment with FGF-2. Furthermore, the protective effects of FGF-2 were abolished by PI3K/Akt inhibitor LY294002. In conclusion, our data suggest that FGF-2 protects against H2O2-induced apoptosis of H9c2 cardiomyocytes via activation of the PI3K/Akt/FoxO3a pathway.
Assuntos
Apoptose/efeitos dos fármacos , Fator 2 de Crescimento de Fibroblastos/fisiologia , Proteína Forkhead Box O3/metabolismo , Peróxido de Hidrogênio/toxicidade , Miócitos Cardíacos/metabolismo , Fosfatidilinositol 3-Quinases/metabolismo , Proteínas Proto-Oncogênicas c-akt/metabolismo , Animais , Proteína 11 Semelhante a Bcl-2/metabolismo , Linhagem Celular , Fosforilação , Transporte Proteico , RatosRESUMO
It is generally accepted that gestational xenobiotic exposures result in systemic consequences in the adult F1 generation. However, data on detailed behavioral and cognitive consequences remain limited. Using our whole-body nanoparticle inhalation facility, pregnant Sprague-Dawley rats (gestational day [GD] 7) were exposed 4 d/wk to either filtered air (control) or nano-titanium dioxide aerosols (nano-TiO2; count median aerodynamic diameter of 170.9 ± 6.4 nm, 10.4 ± 0.4 mg/m(3), 5 h/d) for 7.8 ± 0.5 d of the remaining gestational period. All rats received their final exposure on GD 20 prior to delivery. The calculated daily maternal deposition was 13.9 ± 0.5 µg. Subsequently, at 5 mo of age, behavior and cognitive functions of these pups were evaluated employing a standard battery of locomotion, learning, and anxiety tests. These assessments revealed significant working impairments, especially under maximal mnemonic challenge, and possible deficits in initial motivation in male F1 adults. Evidence indicates that maternal engineered nanomaterial exposure during gestation produces psychological deficits that persist into adulthood in male rats.
Assuntos
Cognição/efeitos dos fármacos , Nanopartículas Metálicas/toxicidade , Atividade Motora/efeitos dos fármacos , Efeitos Tardios da Exposição Pré-Natal/induzido quimicamente , Titânio/toxicidade , Animais , Feminino , Masculino , Exposição Materna , Gravidez , Ratos , Ratos Sprague-DawleyRESUMO
BACKGROUND AND PURPOSE: The blood-brain barrier (BBB) is a selectively permeable cerebrovascular endothelial barrier that maintains homeostasis between the periphery and the central nervous system. BBB disruption is a consequence of ischemic stroke and BBB permeability can be altered by infection/inflammation, but the complex cellular and molecular changes that result in this BBB alteration need to be elucidated to determine mechanisms. METHODS: Infection mimic (lipopolysaccharide) challenge on infarct volume, BBB permeability, infiltrated neutrophils, and functional outcomes after murine transient middle cerebral artery occlusion in vivo; mitochondrial evaluation of cerebrovascular endothelial cells challenged by lipopolysaccharide in vitro; pharmacological inhibition of mitochondria on BBB permeability in vitro and in vivo; the effects of mitochondrial inhibitor on BBB permeability, infarct volume, and functional outcomes after transient middle cerebral artery occlusion. RESULTS: We report here that lipopolysaccharide worsens ischemic stroke outcome and increases BBB permeability after transient middle cerebral artery occlusion in mice. Furthermore, we elucidate a novel mechanism that compromised mitochondrial function accounts for increased BBB permeability as evidenced by: lipopolysaccharide-induced reductions in oxidative phosphorylation and subunit expression of respiratory chain complexes in cerebrovascular endothelial cells, a compromised BBB permeability induced by pharmacological inhibition of mitochondrial function in cerebrovascular endothelial cells in vitro and in an in vivo animal model, and worsened stroke outcomes in transient middle cerebral artery occlusion mice after inhibition of mitochondrial function. CONCLUSIONS: We concluded that mitochondria are key players in BBB permeability. These novel findings suggest a potential new therapeutic strategy for ischemic stroke by endothelial cell mitochondrial regulation.