On preprocessing and antisymmetry in de novo peptide sequencing: improving efficiency and accuracy

Peptide sequencing plays a fundamental role in proteomics. Tandem mass spectrometry, being sensitive and efficient, is one of the most commonly used techniques in peptide sequencing. Many computational models and algorithms have been developed for peptide sequencing using tandem mass spectrometry. In this paper, we investigate general issues in de novo sequencing, and present results that can be used to improve current de novo sequencing algorithms. We propose a general preprocessing scheme that performs binning, pseudo-peak introduction, and noise removal, and present theoretical and experimental analyses on each of the components. Then, we study the antisymmetry problem and current assumptions related to it, and propose a more realistic way to handle the antisymmetry problem based on analysis of some datasets. We integrate our findings on preprocessing and the antisymmetry problem with some current models for peptide sequencing. Experimental results show that our findings help to improve accuracies for de novo sequencing.     

ART患者早期流产组织染色体异常及相关因素分析

目的:分析ART患者早期流产组织染色体异常及其相关影响因素。方法:回顾性分析2013-2017年ART患者行早期流产组织染色体检查的409例样本,分析胚胎染色体非整倍性发生及其与女方年龄、不孕年限、不孕因素、促排卵指标之间的关系。结果:ART流产患者中,流产组织染色体非整倍性发生率为57.46%,发生频次以16三体占比最高(23.95%),其次是22三体(13.45%)及Turner(9.24%)。流产组织染色体非整倍性患者平均年龄高于染色体整倍性患者(P0.001)。16三体组患者年龄低于22三体(P0.01)及Turner组(P0.05)。16三体组患者平均Gn使用量低于22三体组(P0.05)。16三体组患者移植15天血HCG值低于22三体(P0.05)及Turner组(P0.01)。结论:ART患者流产组织染色体非整倍性与女方年龄正相关,但16三体及Turner的发生与女方年龄相关性不大,且16三体更容易引发早期流产。     

Emperipolesis mediated by CD8+ T cells correlates with biliary epithelia cell injury in primary biliary cholangitis

Primary biliary cholangitis (PBC) is an autoimmune disease characterized by chronic destruction of the bile ducts. A major unanswered question regarding the pathogenesis of PBC is the precise mechanisms of small bile duct injury. Emperipolesis is one of cell‐in‐cell structures that is a potential histological hallmark associated with chronic hepatitis B. This study aimed to clarify the pathogenesis and characteristics of emperipolesis in PBC liver injury. Sixty‐six PBC patients, diagnosed by liver biopsy combined with laboratory test, were divided into early‐stage PBC (stages I and II, n = 39) and late‐stage PBC (stages III and IV, n = 27). Emperipolesis was measured in liver sections stained with haematoxylin‐eosin. The expressions of CK19, CD3, CD4, CD8, CD20, Ki67 and apoptosis of BECs were evaluated by immunohistochemistry or immunofluorescence double labelling. Emperipolesis was observed in 62.1% of patients with PBC, and BECs were predominantly host cells. The number of infiltrating CD3⁺ and CD8⁺ T cells correlated with the advancement of emperipolesis (R² = 0.318, P < .001; R² = 0.060, P < .05). The cell numbers of TUNEL‐positive BECs and double staining for CK19 and Ki67 showed a significant positive correlation with emperipolesis degree (R² = 0.236, P < .001; R² = 0.267, P < .001). We conclude that emperipolesis mediated by CD8⁺ T cells appears to be relevant to apoptosis of BEC and thus may aggravate the further injury of interlobular bile ducts.     

植物TOR激酶响应上游信号的研究进展

雷帕霉素靶蛋白(TOR)是真核生物中高度保守的丝氨酸/苏氨酸蛋白激酶, 能整合营养、能量、生长因子及环境信号, 协调细胞增殖、生长和代谢等过程, 是真核生物生长发育的核心调控因子。近年来, 随着相关研究系统的建立, 植物TOR的功能和机制研究取得了众多突破, 发现其进化上保守的生物学功能及植物中特有的信号通路。该文概述了TOR蛋白复合体的构成, 以及植物TOR响应糖、营养元素(氮、磷和硫)、激素及逆境胁迫信号来调控下游基因转录、蛋白翻译、代谢、细胞自噬和胁迫应答等生物学过程的分子机制, 并提出了植物TOR领域一些亟待解决的科学问题, 以期为全面揭示植物TOR的生物学功能提供参考。     

秸秆、氮肥和食细菌线虫交互作用对土壤活性碳氮和温室气体排放的影响

采用3因素2水平交互设计室内恒温培养试验,通过调控秸秆施用、氮肥用量及食细菌线虫,探讨三者对土壤微生物生物量碳氮(C_mic和N_mic)、可溶性碳氮(DOC、DON)、矿质氮(NH₄⁺-N和NO₃^--N)及温室气体排放(CO₂、N₂O和CH₄)的交互影响.结果表明： 施用秸秆显著增加了食细菌线虫数量、C_mic和N_mic,而随着氮肥用量增加,C_mic和N_mic降低,食细菌线虫对C_mic和N_mic的影响则依赖于秸秆和氮肥用量.秸秆、氮肥和食细菌线虫对可溶性碳氮和矿质氮表现出强烈的交互作用,其中秸秆和氮肥均增加了DOC、NH₄⁺ -N和NO₃^--N;食细菌线虫对DOC的抑制作用和对矿质氮的促进作用达到显著水平.秸秆处理对CO₂、N₂O的促进及对CH₄的抑制均达到显著水平,而线虫和氮肥的影响则更多表现出交互作用.在培养第56天,有秸秆时,低量氮肥下食细菌线虫显著促进了CO₂的排放,而高量氮肥下则表现出对CO₂和N₂O显著的抑制作用.总之,土壤生态功能的发挥不可忽视土壤动物的作用.     

T-614, a novel immunomodulator, attenuates joint inflammation and articular damage in collagen-induced arthritis

Introduction

T-614 is a novel oral antirheumatic agent for the treatment of rheumatoid arthritis. Whether it has immunomodulatory or disease-modifying properties and its mechanism of action are largely undetermined.

Methods

Rats with collagen-induced arthritis (CIA) were treated with T-614 (5 and 20 mg/kg) daily. Animals receiving methotrexate (1 mg/kg every 3 days) and the nonsteroidal anti-inflammatory agent nimesulide (10 mg/kg per day) were used as controls. A combination therapy group was treated with both T-614(10 mg/kg per day) and methotrexate (1 mg/kg every 3 days). Hind paw swelling was evaluated and radiographic scores calculated. Serum cytokine levels were assessed by Bio-plex analysis. Quantitative PCR was used to evaluate expression of mRNA for interferon-γ, IL-4 and IL-17. Serum IL-17 and anti-type II collagen antibodies (total IgG, IgG₁, IgG_2a, IgG_2b and IgM) were measured using ELISA.

Results

Oral T-614 inhibited paw swelling and offered significant protection against arthritis-induced cartilage and bone erosion, comparable to the effects of methotrexate. CIA rats treated with T-614 exhibited decreases in both mRNA expression of IL-17 in peripheral blood mononuclear cells and lymph node cells, and circulating IL-17 in a dose-dependent manner. T-614 also reduced serum levels of tumor necrosis factor-α, IL-1β and IL-6. A synergistic effect was observed for the combination of methotrexate and T-614. In addition, T-614 (20 mg/kg per day) depressed production of anti-type II collagen antibodies and differentially affected levels of IgG_2a subclasses in vivo, whereas IgM level was decreased without any change in the IgG₁ level. Together, the findings presented here indicate that the novel agent T-614 has disease-modifying effects against experimental arthritis, as opposed to nimesulide.

Conclusions

Our data suggested that T-614 is an effective disease-modifying agent that can prevent bone/cartilage destruction and inflammation in in CIA rats. Combination with methotrexate markedly enhances the therapeutic effect of T-614.     

南京老山秤锤树空间分布格局及种间关联性

以南京老山1 hm 2样地秤锤树(Sinojackia xylocarpa)天然种群为研究对象,运用成对g(r)函数,选择完全随机模型、异质泊松模型与先决条件零模型,分析秤锤树种群结构和空间分布格局及其空间关联性,从空间格局角度来深入认识其种群结构和分布格局及形成该格局可能存在的机制并提出保护建议。结果表明:(1)秤锤树天然种群中小径个体数量占优,属于增长型种群。(2)种内空间分布研究中,基于完全随机模型分析,秤锤树种群在尺度0~26 m时为聚集分布,尺度29~30 m时为均匀分布;基于异质泊松模型分析,秤锤树种群在0~23 m时为聚集分布,尺度27~30 m时为均匀分布。秤锤树空间分布表现为由聚集分布向均匀分布变化。(3)主要种间关联性研究中,秤锤树与朴树(Celtis sinensis)的种间关联性表现为小尺度下负关联,随着空间尺度的增加变为正关联。秤锤树与黄连木(Pistacia chinensis)和秤锤树与三角槭(Acer buergerianum)的种间关联性大致相同,基本为大尺度下正关联,偶尔出现负关联和无关联。上述结果表明,秤锤树种群更新状况良好,种群空间分布以聚集分布为主,其主要受种间竞争、扩散限制与密度制约的影响。基于种群现状开展就地保护与适当干扰其生存群落,是濒危物种秤锤树的科学有效的保护措施。     

Protective Effect of Phosphatidylcholine on Restoration of Ethanol-Injured Hepatocytes Related with Caveolin-1

The absorption of phospholipid may improve the fluidity of membrane and enzyme activities. Phospholipids also play a role in promoting Caveolae formation and membrane synthesis. Caveolin-1 has a significant effect on signaling pathways involved in regulating cell proliferation and stress responsiveness. Thus, we can speculate that Caveolin-1 could affect the sense of environmental stress. We use Chang liver cell line to investigate the ability of Caveolin-1 to modulate the cellular response to ethanol injury. Caveolin-1 downregulate cells (Cav-1^?/?) were established by stable transfecting with psiRNA-CAV1 plasmids, which were more sensitive to toxic effects of ethanol than the untransfected parental cells (WT). Releasing of ALT and electric conductivity were changed significantly in Cav-1^?/? cells compared with WT. Caveolin-1 gene silencing could obviously down-regulate the activities of protein kinase C-α (PKC-α) and phospho-p42/44 MAP kinase, indicating cell proliferation and self-repairing abilities were inhibited. However, the levels of Caveolin-1 and PKC-α were increased by phosphatidylcholine administration. The results indicated that the inhibition of lipid peroxidation by phosphatidylcholine could lead to the prevention of membrane disruption, which closely correlated with the level of Caveolin-1. Since the protective effects of phosphatidylcholine against ethanol-induced lipid peroxidation might be regulated by phospholipid-PKC-α signaling pathway, related with Caveolin-1, the potential effects of phosphatidylcholine on membranes need to be verified.     

On the interaction of colicin E3 with the ribosome

Colicin E3 is a protein that kills Escherichia coli cells by a process that involves binding to a surface receptor, entering the cell and inactivating its protein biosynthetic machinery. Colicin E3 kills cells by a catalytic mechanism of a specific ribonucleolytic cleavage in 16S rRNA at the ribosomal decoding A-site between A1493 and G1494 (E. coli numbering system). The breaking of this single phosphodiester bond results in a complete cessation of protein biosynthesis and cell death. The inactive E517Q mutant of the catalytic domain of colicin E3 binds to 30S ribosomal subunits of Thermus thermophilus, as demonstrated by an immunoblotting assay. A model structure of the complex of the ribosomal subunit 30S and colicin E3, obtained via docking, explains the role of the catalytic residues, suggests a catalytic mechanism and provides insight into the specificity of the reaction. Furthermore, the model structure suggests that the inhibitory action of bound immunity is due to charge repulsion of this acidic protein by the negatively charged rRNA backbone