Circular RNA circ‐RCCD promotes cardiomyocyte differentiation in mouse embryo development via recruiting YY1 to the promoter of MyD88

Congenital heart disease (CHD) is the most common birth defect, affecting approximately 1% of live births. Genetic and environmental factors are leading factors to CHD, but the mechanism of CHD pathogenesis remains unclear. Circular RNAs (circRNAs) are kinds of endogenous non‐coding RNAs (ncRNAs) involved in a variety of physiological and pathological processes, especially in heart diseases. In this study, three significant differently expressed circRNA between maternal embryonic day (E) E13 and E17 was found by microarray assay. Among them, the content of circ‐RCCD increases with the development of heart and was enriched in primary cardiomyocytes of different species, which arouses our attention. Functional experiments revealed that inhibition of circ‐RCCD dramatically suppressed the formation of beating cell clusters, the fluorescence intensity of cardiac differentiation marker MF20, and the expression of the myocardial‐specific markers CTnT, Mef2c, and GATA4. Next, we found that circ‐RCCD was involved in cardiomyocyte differentiation through negative regulation of MyD88 expression. Further experiments proved that circ‐RCCD inhibited MyD88 levels by recruiting YY1 to the promoter of MyD88; circ‐RCCD inhibited nuclear translocation of YY1. These results reported that circ‐RCCD promoted cardiomyocyte differentiation by recruiting YY1 to the promoter of MyD88. And, this study provided a potential role and molecular mechanism of circ‐RCCD as a target for the treatment of CHD.     

Direct adenylation from 5′-OH-terminated oligonucleotides by a fusion enzyme containing Pfu RNA ligase and T4 polynucleotide kinase

5′-Adenylated oligonucleotides (AppOligos) are widely used for single-stranded DNA/RNA ligation in next-generation sequencing (NGS) applications such as microRNA (miRNA) profiling. The ligation between an AppOligo adapter and target molecules (such as miRNA) no longer requires ATP, thereby minimizing potential self-ligations and simplifying library preparation procedures. AppOligos can be produced by chemical synthesis or enzymatic modification. However, adenylation via chemical synthesis is inefficient and expensive, while enzymatic modification requires pre-phosphorylated substrate and additional purification. Here we cloned and characterized the Pfu RNA ligase encoded by the PF0353 gene in the hyperthermophilic archaea Pyrococcus furiosus. We further engineered fusion enzymes containing both Pfu RNA ligase and T4 polynucleotide kinase. One fusion enzyme, 8H-AP, was thermostable and can directly catalyze 5′-OH-terminated DNA substrates to adenylated products. The newly discovered Pfu RNA ligase and the engineered fusion enzyme may be useful tools for applications using AppOligos.     

Distinct basolateral amygdala excitatory inputs mediate the somatosensory and aversive-affective components of pain

Pain is a multidimensional perception that includes unpleasant somatosensory and affective experiences; however, the underlying neural circuits that mediate different components of pain remain elusive. Although hyperactivity of basolateral amygdala glutamatergic (BLA^Glu) neurons is required for the somatosensory and emotional processing of pain, the precise excitatory inputs to BLA^Glu neurons and their roles in mediating different aspects of pain are unclear. Here, we identified two discrete glutamatergic neuronal circuits in male mice: a projection from the insular cortex glutamatergic (IC^Glu) to BLA^Glu neurons, which modulates both the somatosensory and affective components of pain, and a projection from the mediodorsal thalamic nucleus (MD^Glu) to BLA^Glu neurons, which modulates only the aversive-affective component of pain. Using whole-cell recording and fiber photometry, we found that neurons within the IC→BLA and MD→BLA pathways were activated in mice upon inflammatory pain induced by injection of complete Freund’s adjuvant (CFA) into their paws. Optical inhibition of the IC^Glu→BLA pathway increased the nociceptive threshold and induced behavioral place preference in CFA mice. In contrast, optical inhibition of the MD^Glu→BLA pathway did not affect the nociceptive threshold but still induced place preference in CFA mice. In normal mice, optical activation of the IC^Glu→BLA pathway decreased the nociceptive threshold and induced place aversion, while optical activation of the MD^Glu→BLA pathway only evoked aversion. Taken together, our results demonstrate that discrete IC^Glu→BLA and MD^Glu→BLA pathways are involved in modulating different components of pain, provide insights into its circuit basis, and better our understanding of pain perception.     

Friend or Foe? Implication of the autophagy-lysosome pathway in SARS-CoV-2 infection and COVID-19

There is increasing amount of evidence indicating the close interplays between the replication cycle of SARS-CoV-2 and the autophagy-lysosome pathway in the host cells. While autophagy machinery is known to either assist or inhibit the viral replication process, the reciprocal effects of the SARS-CoV-2 on the autophagy-lysosome pathway have also been increasingly appreciated. More importantly, despite the disappointing results from the clinical trials of chloroquine and hydroxychloroquine in treatment of COVID-19, there is still ongoing effort in discovering new therapeutics targeting the autophagy-lysosome pathway. In this review, we provide an update-to-date summary of the interplays between the autophagy-lysosome pathway in the host cells and the pathogen SARS-CoV-2 at the molecular level, to highlight the prognostic value of autophagy markers in COVID-19 patients and to discuss the potential of developing novel therapeutic strategies for COVID-19 by targeting the autophagy-lysosome pathway. Thus, understanding the nature of such interactions between SARS-CoV-2 and the autophagy-lysosome pathway in the host cells is expected to provide novel strategies in battling against this global pandemic.     

茄子果实相关农艺性状全基因组关联分析研究进展与展望

茄子是重要的园艺作物,也是茄科植物中种植最广泛的蔬菜之一。茄子果实相关农艺性状是一种复杂的数量性状,传统育种选育效率低、周期长。高通量测序技术与生物信息学技术的快速发展,使得全基因组关联分析(genome-wide association study, GWAS)在解析茄子果实相关复杂农艺性状的遗传规律方面展现出巨大的应用前景。本文对全基因组关联分析在茄子的果形、果色等果实相关农艺性状中的研究进展进行了综述;针对茄子数量性状遗传研究中普遍存在的“丢失遗传力”(missing heritability)问题,从4个GWAS策略在茄子果实相关农艺性状研究中的应用热点出发,提出了未来茄子GWAS的发展对策;并结合当前茄子遗传改良的实践需求,展望了GWAS策略在茄子分子育种领域的广阔应用前景。本文为今后利用GWAS解析各种茄子果实相关性状的遗传基础以及选育符合消费者需求的果实材料提供了理论依据和参考。     

生态系统生态学研究的关键问题及趋势——从“整体论与还原论的争论”看

在生态学领域中,存在着生态系统整体论与还原论的争论。Tansley A.G.提出,生态系统是"准有机体"。Odum兄弟提出的"生态系统能量说"被广泛接受,但也受到质疑,称其为"还原论者的整体论"。基于对上述质疑的回应以及对生态系统整体论的追求,Patten B.C.等提出"生态网络理论",运用"网络‘环境子’分析"方法,试图从物理层面分析解决生物层面的"涌现性"问题。不过,这一理论也受到批判,认为其在探究符号化的现象对生态系统的动态影响时,陷入了还原论困境。Jrgensen S.E.等更进一步,提出"系统论"的生态系统生态学,试图从系统科学的角度研究生态系统的"物质-能量-信息-网络"系统。这一理论受到生态学界高度重视,但是也存在着在具体研究过程中如何平衡能量视角和生物地球化学视角的问题。由上述争论可见,生态系统生态学研究的趋势是从"物质实体"到"能量流动",再到"网络信息",最后到"开放系统"层层递进。目前面临的关键问题是:如何在更好地定义生态系统整体性的基础上,采取相应的能够体现生态系统整体性的方法,去获得更多、更好的生态系统整体性的认识。     

链霉菌Streptomyces antibioticus NRRL 8167中Naphthgeranine A生物合成基因簇的分析鉴定

【背景】微生物来源的天然产物是小分子药物或药物先导物的重要来源。对链霉菌Streptomyces antibioticus NRRL 8167的基因组分析显示,其包含多个次级代谢产物的生物合成基因簇,具有产生多种新化合物的潜力。【目的】对链霉菌S. antibioticus NRRL 8167中次级代谢产物进行研究,以期发现结构新颖或生物活性独特的化合物,并对相应产物的生物合成基因簇和生物合成途径进行解析。【方法】利用HPLC图谱结合特征性紫外吸收和LC-MS方法,排除S. antibioticus NRRL 8167产生的已知化合物,确定具有特殊紫外吸收的化合物作为挖掘对象,然后利用正、反相硅胶柱色谱、高效液相色谱等技术对次级代谢产物进行分离纯化,分离化合物。利用质谱及核磁共振光谱技术对化合物结构进行解析和鉴定;提取链霉菌S. antibioticus NRRL 8167基因组DNA,利用PacBio测序平台进行基因组测序;利用生物信息学对基因组进行注释,并对合成该化合物的基因簇进行定位分析,推导其生物合成途径。【结果】确定这个化合物是NaphthgeranineA,属于聚酮类化合物。全基因组序列分析发现S.antibioticusNRRL8167基因组含有28个次级代谢产物生物合成基因簇,其中基因簇20可能负责Naphthgeranine A的生物合成,并对其生物合成途径进行了推导。【结论】基于紫外吸收光谱和质谱特征,从S. antibioticus NRRL 8167菌株的发酵提取物中分离鉴定了一个聚酮类化合物Naphthgeranine A。该菌株的全基因组测序为其生物合成基因簇的鉴定提供了前提,对Naphthgeranine A生物合成基因簇和生物合成途径的推测为进一步研究这个化合物的生物合成机制奠定了基础。