Abstract:自噬是细胞的一个重要生物学功能。细胞通过对自噬底物的识别、自噬囊泡的形成，再经过与溶酶体的融合，清除老化细胞器以及降解长周期蛋白和异常积聚蛋白。因此，自噬在蛋白质的代谢、细胞器更新以及组织发育中有着重要作用，其功能调控直接参与了机体对细胞稳态的维持和对疾病的抵抗。目前已有大量研究表明，自噬与疾病的发生密切相关，如心血管病、肿瘤、炎症和免疫以及神经退行性疾病等。近年来，自噬研究得到了国内外科学家的广泛重视，研究论文的数量直线上升。科技部和国家自然科学基金委均已资助相关课题，这进一步促进了我国在自噬研究领域的发展。我国科学家在自噬的机制和疾病关系研究中也取得了重大进展，许多研究成果已经走在世界前沿。本刊对自噬这一研究领域一直十分关注，为促进对该领域现状及发展的了解，本期汇集了6 篇述评和1 篇研究论文，作为自噬研究专题发表，以飨读者。
本专题主要对自噬与一些相关疾病关系的现状和发展进行了评述，并对自噬研究方法学和基本机制也进行了综述，同时报道了在果蝇脊髓小脑变性3型动物模型中开展的关于自噬与Sir2发挥神经保护作用相关性的研究，反映了目前自噬研究的一个侧面。马泰等主要综述了目前自噬研究的技术和方法进展，评价了自噬的评估指标和这些自噬方法学的应用，提供了一个自噬方法学上的基础交流。吴葩等介绍了PI3K复合物中各组分蛋白与细胞自噬的关系，详细阐述了该通路在细胞自噬调节中的最新研究进展，为这一信号通路研究提供了信息。何云凌等很好地总结了低氧环境诱导线粒体自噬发生的相关分子机制，对参与调节线粒体自噬的重要蛋白进行了系统的描述，为目前人们普遍关注的线粒体自噬与疾病的关系提供了前沿资料。谢凤等对心脏疾病状态下细胞自噬的发生、发展及其对心脏疾病的影响进行了详细的论述，有助于研究者从自噬的角度来探讨心脏疾病的发生发展及其机制。林小龙等围绕当前热点问题对自噬与血管内皮细胞的关系作了描述，介绍了血管内皮细胞在各种药物刺激以及相关蛋白质过表达情况下对于自噬的反应以及所引起的下游应答，探讨了自噬与血管疾病发病的相互关系。向波等介绍了细胞自噬与肿瘤的发生发展的关系，描述了炎症-自噬-肿瘤的相关性以及自噬可能的抑瘤机制。曾爱源等利用果蝇的遗传性脊髓小脑变性3 型模型，研究了Sir2在自噬存在情况下对转基因果蝇的神经保护作用，并发现在自噬抑制后Sir2的保护作用明显减弱，揭示了Sir2通过自噬保护神经元、减缓神经变性蛋白损伤的作用机制。
本刊欢迎和期待更多、更好的有关自噬研究的来稿，以更广泛和深入地促进我国自噬研究领域的发展和学术交流。

Abstract:Autophagy extensively participate in physiological and pathological processes, and has been focused by contemporary biomedicine scientists in recent years. Transmission electron microscopy, immunofluorescence and immunoblotting techniques were common used in detection of autophagy. Deeper research needs more accurate detection of autophagy. Dysfunction of autophagy involves formation and degeneration of autophosome, accordingly, accurate and comprehensive evaluation of autophagy includes autophosome detection, as well as the fluency of autophagic degeneration, i.e. autophagic flux assay. Additionally, artificial up- or down-regulation of autophagy by drugs or gene interferences in in vitro or in vivo models has also been considered as important part of autophagy analysis. Any method currently used alone may not been as evidence of autophagy. More careful attention should be paid on results of any assays of autophagy, especially DO NOT interpret "increase or decrease of autophosome" (also "up- or down-expression of autophagy-related proteins") as "enhancement or attenuation of autophagic function".

Abstract:Class Ⅲ phosphoinositide 3-kinase (class Ⅲ PI3K), which specifically phosphorylate PtdIns to generate PtdIns3P, plays a vital role in autophagy and vacuolar sorting pathways by forming Class Ⅲ PI3K(PI3KC3) complexes with a variety of regulatory proteins. Proteins that compose PI3KC3 complex, namely, PI3K, p150, Beclin 1, ATG14L, UVRAG, Bif-1 and Rubicon are conserved in evolution. In addition, neurodevelopment, situs inversus totalis and development of tumor are found to closely related to these members.

Abstract:Hypoxia is a representative stress environment, under which cell energy and oxidative metabolism change a lot. Among the product of metabolism, reactive oxygen species (ROS) which generate from mitochondria under hypoxia seriously threaten cell survive. Mitophagy was recently found as an adaptive metabolic response to hypoxia. Cell induces mitophagy by the pathway mediated by BNIP3/BNIP3L and Beclin-1 that are activated by up-regulation of HIF-1 under hypoxia, then reduces the production of ROS, and ultimately promotes cell survival. This process leads to the adaptation of organism to hypoxia. In this paper, we will overview the role and the mechanism of mitophagy in adaptation to hypoxia.

Abstract:Autophagy is a process in which damaged, modified or aging proteins and organelles are transported to the lysosome/vacuole for degradation. Autophagy is not only a widespread normal physiological process, but also a cell defense mechanism to adverse environment, involved in the pathological process of diseases. The normal level of autophagy can protect cells from environmental stimuli, however, continued excessive or insufficient autophagy could lead to disease. In the heart, myocardial autophagy plays a vital role to maintain myocardial function, but dysfunctional autophagy contributes to a diverse set of heart diseases, such as Danon disease. Multiple forms of cardiovascular stress can increase autophagic activity in cardiomyocytes, including chronic ischemia, reperfusion injury and Chronic hypoxia. The function of autophagy in these conditions is poorly understood: Does it serve a pro-survival function or contribute to disease pathogenesis, cell death, or both? Heart disease is the abnormal myocardia function when to produce a variety of pathological state. In the state of disease, cardiac autophagy degree will change, related to the occurrence and development of disease. As in Hypertrophic cardiomyopathy process, cell autophagy is reduced and aggravate myocardial hypertrophy. In heart failure process, autophagy increases can lead to cell death; And in myocardial infarction process, autophagy is enhanced and reduce the infarction area. But the real role of autophagy in the myocardium depending on the level of autophagic activation and the context in which it is induced. Currently, more and more people begin to pay close attention to the relationship between drugs and autophagy regulation, particularly on antitumor drugs and cardiovascular drugs. In addition, there are reports of estrogen receptor antagonists tamoxifen and vitamins also has a regulatory role for autophagy. To research of the relationship between autophagy and heart disease, and drugs on the regulation of autophagy will benefit for the occurrence and development of heart disease, and explore a new mechanism of drug treatment from the autophagy perspectives.

Abstract:Autophagy plays critical role in maintaining the cell homeostasis, organelle turnover and nutrient recycling in physiological condition. Autophagy is consist in the body's physiological and pathological process. It has protection and repairing role at basic autophagy level, but over-autophagy would lead to injury and apoptosis. In the past years, major studies are focussing on cancer cell autophagy, and only a few studies concerning about normal cells. Vascular endothelial cells as one of the most active cells in the human body, many cardioascular disease were bound up with vascular endothelial cells (VECs) function change. This review summarizes influence factors on vascular endothelial cells autophagy.

Abstract:Autophagy is an evolutionarily conserved catabolic process crucial for development, differentiation, survival, and homeostasis. However, if it proceeds to completion, autophagy can lead to cell death. Changes in macroautophagy activity have been described in cancer cells and in solid tumors, and inhibition of macroautophagy promotes tumorigenesis. The review focuses on the importance of autophagy in tumour development and cancer therapy. We summarize what is currently known about autophagy, and discuss its role in cell death and survival. We discuss possible mechanisms underlying the anti-tumor activity of autophagy. We also discuss the effect of autophagy modulation in cancer therapy.

Abstract:To confer the influence of Sir2 on pathogenesis of SCA3/MJD. GMR-GAL4 and Nrv2-GAL4 system SCA3/MJD transgenic Drosophila models were constructed by using the promoter GMR-GAL4 and Nrv2-GAL4 which drive target selective gene expression in cells of the developing eyes and motor neurons, respectively. Then, Sir2 protein was overexpressed in SCA3/MJD transgenic Drosophila models by genetic methods with or without in a background of RNAi knockdown of Atg7. Overexpression of endogenous Drosophila Sir2 not only notably suppresses the neurotoxicity of MJDtr-Q78 protein, but also significantly improves the movement ability of flies. Moreover, RNAi knockdown of Atg7 significantly Sir2's protection against SCA3/MJD Drosophila. We confirmed that overexpression of Sir2 could protect SCA3/MJD Drosophila models, and the protection role of Sir2 on SCA3/MJD Drosophila models is autophagy-dependent.

Abstract:Cellular senescence is a process that leads to a growth arrest. Some of these cells are cleared after being in a state of alive but lose the ability to divided long time, while some cells (named senescent cell) accumulate in aging tissues, secrete agents that stimulate the immune system and cause low-level inflammation, which may disrupt nearby tissue structure and function even promote cancer progression. A recent report in Nature by Baker et al. introduced a method of delaying aging process by clearing senescent cells in mice. The findings raise the prospect that any therapy that rids the body of senescent cells would protect it from the ravages of aging.

Abstract:Retinoic acid (RA) is a teratogen which can induce cleft palate. Recent studies suggested that gamma amino butyric acid (GABA) was involved in the development of palate. If the GABA signal pathway participates the cleft palate induced by RA remains to be elucidated. In the present study, we investigated the effect of all-trans retinoic acid (atRA) (0.2, 0.67, 2.0 and 6.7 μmol/L) on cell proliferation and apoptosis, and then examined the role of gamma amino butyric acid (GABA) signaling pathway in regulation of cell proliferation and apoptosis by atRA in murine embryonic palate mesenchymal (MEPM) cells. Results showed that atRA (2 μmol/L and 6.7 μmol/L) significantly inhibited cell proliferation and increased apoptosis. The mRNA and protein expression of glutamic acid decarboxylase 67 (GAD 67) which was a key enzyme in synthesis of GABA were significantly down regulated by atRA (0.67, 2.0 μmol/L and 6.7 μmol/L). But the mRNA and protein expression of GABAAR-β3 were shown no obvious change compared with the control group. When GABA (1.0 μmol/L) was added to cell culture system, the effect of atRA (6.7 μmol/L) on the proliferation and apoptosis of MEPM cells was reversed. In conclusion, all-trans retinoic acid inhibits cell proliferation and promotes cell apoptosis through gamma amino butyric acid pathway in murine embryonic palate mesenchymal cells.

Abstract:Pantoea agglomerans YS19 is an endophytic diazotrophic bacterium isolated from rice (Oryza sativa cv. Yuefu) grown in temperate climatic regions in west Beijing (China). The bacterium forms aggregate structures called "symplasmata", in which several (at least two) to hundreds of individual cells tightly bind together. Our previous study revealed that there were two growth stages for YS19, including the single cell stage existing before exponential growth phase and the symplasmata forming stage starting at the end of the exponential growth phase in liquid LB medium. More strikingly, the symplasmata structures contribute to bacterial stress (e.g., dehydration, heavy metal toxicity, and osmotic shock) resistance and are especially significant for bacterial surviving strategy in suiting an adaptive life to hostile environments. In this research, YS19 was cultivated in LB medium, and the whole cellular protein expression of the cultures sampled at different times (0～12 h) was analyzed by SDS-PAGE. Here, a novel protein differentially expressed at the symplasmata forming stage was captured. The protein was purified and digested by trypsin. The digests were analyzed by MALDI-TOF mass spectrometry and the peptide mass fingerprint of this protein was successfully obtained. Then, database searching with Mascot in the SWISS-Prot database was performed using the recorded peptide mass fingerprint data. It is found that among 53 peptides, there are 14 peptide masses matching to MalE from Enterobacter aerogenes, which is a protein belonging to the periplasmic maltose-binding protein family of the ATP-binding cassette transporters. Then the gene of the MalE protein was cloned from YS19, expressed in the E. coli BL21(DE3), and the recombinant protein was purified to homogeneity. Under stress (acid) treatments, the recombinant protein showed strong anti-aggregation ability, and even exhibited chaperone-like activity. This assay was achieved by comparing the quantity of the substrate proteins remaining in the supernatant under various denaturing acid conditions, where the aggregation of the substrate protein was effectively suppressed in the presence of the recombinant MalE protein. Far-UV circular dichroism spectroscopy examination on the purified MalE proteins under different pHs indicated that the global structures exhibited a sudden transition from a highly ordered conformation to a less ordered one. However, MalE was still capable of maintaining most of its secondary structures under these extreme acidic conditions (pH1～2).Finally, the Bis-ANS fluorescent probe technique was used to explore the effect of acid condition on the hydrophobic surfaces exposing of the protein. It is found that with the decrease of the pH value, the fluorescence intensity of the samples increased gradually, suggesting the MalE protein exposed the hydrophobic surfaces of the molecule to bind the substrates, implying the protein performed its chaperone activity via exposing its hydrophobic surfaces under acidic condition. MalE protein, originally found as a periplasmic maltose-binding protein of the ATP-binding cassette transporters, whose expression in YS19, however, far exceeds the amount being needed for transmembrane transports, is most likely a moonlighting protein for its alternative biological functions as a chaperone protein as revealed by this study. This research provided valuable information on the life styles and survival strategies of microorganisms that forms multicellular aggregates at specific growth stages and also explained the protein basis adopted by YS19 symplasmata-forming cells in surviving the stress conditions.

Abstract:RNA editing is a widespread post-transcriptional modification mechanism that alters genetic information at the RNA level by nucleotide insertions, deletions or substitutions, which can contribute to the diversification of the transcriptome and proteome. Although tens of thousands of A-to-I RNA editing events have been found in humans, there is limited knowledge of RNA editing in other nonhuman primates. For exploring the mechanism as well as potential functions of the RNA editing events in chimpanzee, we identified RNA editing sites based on chimpanzee RNA-Seq data here. By aligning between RNA-Seq data and chimpanzee genome sequences with TopHat software, all RNA-DNA mismatch sites were regarded as a candidate set. Low quality sites were filtered out by using both genome and transcriptome sequencing quality scores. The other filters containing uncertainty of sequencing at 3'-terminial positions, read coverage, SNP sites and estimated editing level were also applied on the candidate set. Statistical tests based on the Binomial distribution and Bonferroni multiple testing correction were performed on each candidate site to remove random errors between genome and transcriptome. Then, we detected tissue- and sex-specific RNA editing sites using bioinformatics approaches based on the Fisher's exact test and the Bonferroni multiple testing correction. The Two Sample Logo software was used to analyze the feature of the sequences surrounding the RNA editing site. A total of 8 334 RNA editing sites were identified in chimpanzee transcriptome and all 12 possible categories of discordances were observed. The top four distributions were A-to-G, U-to-C, G-to-A and C-to-U editing sites, which contained 1 995, 1 452, 1 293 and 1 101 sites, respectively. Forty-one editing sites alter amino acid residues, one of them creates a new stop codon which may shorten the KRT31 protein and affect its activity. Three editing sites damage the binding of microRNA potentially. Six hundred and forty and eight hundred and seventy-two RNA editing sites were identified to be tissue-specific and sex-specific respectively. The analysis of base frequencies indicated that all substitution editings have preferences for certain neighbouring nucleotides. RNA editing is widespread in chimpanzee and has important biology function. Our findings paved the way for further exploration of the mechanism of RNA editing in primates.