The optimization conditions of establishing an H9c2 cardiomyocyte hypoxia/reoxygenation injury model based on an AnaeroPack System

Ischemia–reperfusion (I/R) injury is a major cause of cardiomyocyte apoptosis after vascular recanalization, which was mimicked by a hypoxia/reoxygenation (H/R) injury model of cardiomyocytes in vitro. In this study, we explored an optimal H/R duration procedure using the AnaeroPack System. To study the H/R procedure, cardiomyocytes were exposed to the AnaeroPack System with sugar and serum-free medium, followed by reoxygenation under normal conditions. Cell injury was detected through lactate dehydrogenase (LDH) and cardiac troponin (c-Tn) release, morphological changes, cell apoptosis, and expression of apoptosis-related proteins. The results showed that the damage to H9c2 cells increased with prolonged hypoxia time, as demonstrated by increased apoptosis rate, LDH and c-Tn release, HIF-1α expression, as well as decreased expression of Bcl-2. Furthermore, hypoxia for 10 h and reoxygenation for 6 h exhibited the highest apoptosis rate and damage and cytokine release; in addition, cells were deformed, small, and visibly round. After 12 h of hypoxia, the majority of the cells were dead. Taken together, this study showed that subjecting H9c2 cells to the AnaeroPack System for 10 h and reoxygenation for 6 h can achieve a practicable and repeatable H/R injury model.     

Scoparone alleviates Ang II-induced pathological myocardial hypertrophy in mice by inhibiting oxidative stress

Long-term poorly controlled myocardial hypertrophy often leads to heart failure and sudden death. Activation of ras-related C3 botulinum toxin substrate 1 (RAC1) by angiotensin II (Ang II) plays a pivotal role in myocardial hypertrophy. Previous studies have demonstrated that scoparone (SCO) has beneficial effects on hypertension and extracellular matrix remodelling. However, the function of SCO on Ang II-mediated myocardial hypertrophy remains unknown. In our study, a mouse model of myocardial hypertrophy was established by Ang II infusion (2 mg/kg/day) for 4 weeks, and SCO (60 mg/kg bodyweight) was administered by gavage daily. In vitro experiments were also performed. Our results showed that SCO could alleviate Ang II infusion-induced cardiac hypertrophy and fibrosis in mice. In vitro, SCO treatment blocks Ang II-induced cardiomyocyte hypertrophy, cardiac fibroblast collagen synthesis and differentiation to myofibroblasts. Meanwhile, we found that SCO treatment blocked Ang II-induced oxidative stress in cardiomyocytes and cardiac fibroblasts by inhibiting RAC1-GTP and total RAC1 in vivo and in vitro. Furthermore, reactive oxygen species (ROS) burst by overexpression of RAC1 completely abolished SCO-mediated protection in cardiomyocytes and cardiac fibroblasts in vitro. In conclusion, SCO, an antioxidant, may attenuate Ang II-induced myocardial hypertrophy by suppressing of RAC1 mediated oxidative stress.     

CRISPR/Cas9-mediated mutagenesis at microhomologous regions of human mitochondrial genome

Genetic manipulation of mitochondrial DNA(mtDNA) could be harnessed for deciphering the gene function of mitochondria; it also acts as a promising approach for the therapeutic correction of pathogenic mutation in mtDNA. However, there is still a lack of direct evidence showing the edited mutagenesis within human mtDNA by clustered regularly interspaced short palindromic repeats-associated protein 9(CRISPR/Cas9). Here, using engineered CRISPR/Cas9, we observed numerous insertion/deletion(InDel) events at several mtDNA microhomologous regions, which were triggered specifically by double-strand break(DSB)lesions within mtDNA. InDel mutagenesis was significantly improved by sgRNA multiplexing and a DSB repair inhibitor,iniparib, demonstrating the evidence of rewiring DSB repair status to manipulate mtDNA using CRISPR/Cas9. These findings would provide novel insights into mtDNA mutagenesis and mitochondrial gene therapy for diseases involving pathogenic mtDNA.     

A taxonomic and phylogenetic perspective on plant community assembly along an elevational gradient in subtropical forests

亚热带森林植物群落沿海拔梯度的分类与系统发育研究 生物多样性沿海拔梯度的分布格局已受到广泛关注。然而,生物多样性格局沿海拔梯度的变异及其潜在机制尚不清楚。整合生物多样性的多维度信息为理解群落构建机制提供了新思路。本研究在我国东部亚热带森林沿海拔270–1470 m的梯度上设置了17个木本植物固定样地,分析了沿海拔梯度植物群落 构建的生态和进化驱动力。基于样地内物种出现(0–1数据)和多度信息,计算群落内被子植物的物种和系统发育alpha和beta多样性、系统发育结构等,并量化多样性指标与微气候和地形之间的关系。研究发现,不论多度加权与否,物种alpha多样性均沿海拔升高而增加,物种和系统发育的相似性随海拔距离的增加而呈衰减趋势。然而,多度加权与否会形成不同的系统发育alpha多样性格局。对于系统发育结构而言,沿海拔增加并无明显趋势。地形和微气候是多样性格局和系统发育结构的主要驱动力。与未考虑物种多度的多样性指标相比,多度加权的指标与坡度和胸高断面积相关性更高。这些结果表明,由局域物种多度介导的确定性过程对沿海拔梯度的植物群落构建具有一定影响。     

CPT2 down-regulation promotes tumor growth and metastasis through inducing ROS/NFκB pathway in ovarian cancer

BackgroundCarnitine palmitoyltransferase 2 (CPT2) is a rate-limiting enzyme involved in fatty acid β-oxidation (FAO) regulation. Recently, it has been increasingly recognized that lipid metabolism dysregulation is closely implicated in tumorigenesis. However, the involvement of CPT2 in the progression of cancer is still largely unclear, especially in ovarian cancer (OC).MethodsIn the present study, CPT2 expression and its clinical significance were determined in OC tissues and cells. The biological functions and molecular mechanisms of CPT2 in OC growth and metastasis were determined by in vitro and in vivo assays.FindingsWe found that CPT2 was frequently down-regulated in primary ovarian serous carcinomas, which is significantly correlated with poor survival of ovarian cancer patients. Functional experiments revealed that CPT2 inhibited OC cell growth and metastasis via suppression of G1/S cell cycle transition and epithelial to mesenchymal transition (EMT), as well as induction of cell apoptosis. Mechanistically, suppression of ROS/NFκB signaling pathway by increasing fatty acid oxidation-derived NADPH production was involved in the anti-tumorigenic functions of CPT2 in OC cells.InterpretationAltogether, our findings demonstrate that CPT2 functions as a potential tumor suppressor in OC progression. CPT2 may serve as a novel prognostic marker and therapeutic target in OC.     

A novel network-based method for measuring the functional relationship between gene sets

MOTIVATION: In the functional genomic era, a large number of gene sets have been identified via high-throughput genomic and proteomic technologies. These gene sets of interest are often related to the same or similar disorders or phenotypes, and are commonly presented as differentially expressed gene lists, co-expressed gene modules, protein complexes or signaling pathways. However, biologists are still faced by the challenge of comparing gene sets and interpreting the functional relationships between gene sets into an understanding of the underlying biological mechanisms. RESULTS: We introduce a novel network-based method, designated corrected cumulative rank score (CCRS), which analyzes the functional communication and physical interaction between genes, and presents an easy-to-use web-based toolkit called GsNetCom to quantify the functional relationship between two gene sets. To evaluate the performance of our method in assessing the functional similarity between two gene sets, we analyzed the functional coherence of complexes in functional catalog and identified protein complexes in the same functional catalog. The results suggested that CCRS can offer a significant advance in addressing the functional relationship between different gene sets compared with several other available tools or algorithms with similar functionality. We also conducted the case study based on our method, and succeeded in prioritizing candidate leukemia-associated protein complexes and expanding the prioritization and analysis of cancer-related complexes to other cancer types. In addition, GsNetCom provides a new insight into the communication between gene modules, such as exploring gene sets from the perspective of well-annotated protein complexes. Availability and Implementation: GsNetCom is a freely available web accessible toolkit at http://bioinfo.hrbmu.edu.cn/GsNetCom.     

Molecular characterization of erm(B)- and mef(E)-mediated erythromycin-resistant Streptococcus pneumoniae in China and complete DNA sequence of Tn2010

Aims: To characterize the erm(B)‐ and mef(E)‐mediated erythromycin‐resistant Streptococcus pneumoniae clinical isolates obtained from ten hospitals located different cities in China. Methods and Results: Totally 83 S. pneumoniae were collected, and eighteen representative strains of 66 strains that exhibited erythromycin resistance were used for further characterization by antibiograms, serotyping, PFGE, MLST, DNA sequencing of the macrolide‐resistance elements and mapping of the elements on the chromosome. Twelve isolates showed a high‐level resistance to erythromycin, and six other isolates showed a low‐level resistance to erythromycin. Thirteen isolates harboured a Tn2010 transposon (26·4 kbp) encoding the erm(B), tet(M) and mef(E) genes and were classified into three types by Tn2010 structures. The remaining five isolates harboured a Tn6002 transposon (20·9 kbp) encoding the erm(B) and tet(M) genes and were classified into three types by Tn6002 locations on the chromosome. Three of the Tn6002 elements were located within the Tn5252‐like element, implying that these composed a large mobile element. The MLST analyses showed that several clones had been disseminated and that the CC271 strains carrying the Tn2010 element expressing the high‐level resistance to erythromycin were predominant in China. Four new MLST strains, which were designated as ST3262, ST3263, ST3397 and ST3398 were also identified. Conclusions: The erythromycin resistance determinant of S. pneumoniae that had been isolated in China was located in Tn2010 or the Tn6002 element and several clones had been disseminated, and the CC271 strains carrying the Tn2010 element expressing the high‐level resistance to erythromycin were predominant in China. Significance and Impact of the Study: This is the first molecular analysis of erythromycin‐resistant Streptococcus pneumoniae clinical isolates in China, and the first report of the complete nucleotide sequence of Tn2010 (26 390 bp).     

Co-transfection and tandem transfection of HEK293A cells for overexpression and RNAi experiments

pIRES2-EGFP was employed and a non-target shRNA expressing plasmid was constructed to simulate overexpression and RNAi (RNA interference) experiments. Transfection of pIRES2-EGFP into HEK293A cells by cationic lipids VigoFect demonstrated that transfection efficiency increased in a dose-dependent manner with amount of DNA plasmid used, and optimal transfection time and cell density should be identified to reach a compromise of higher transfection efficiency and lower toxicity. Co-transfection experiments indicated that the two co-transfected plasmids were equivalently delivered into the same cells, and the co-transfection efficiency was rarely affected by cell density and proportion of the two plasmids. However, plasmid-receipted cells seemed indisposed to accept plasmid again during the second transfection, and very low co-transfection efficiency was observed in tandem transfection.