基于卷积神经网络的大肠杆菌启动子预测

目的 基于位点特异性打分矩阵（position-specific scoring matrices,PSSM）的预测模型已经取得了良好的效果,基于PSSM的各种优化方法也在不断发展,但准确率相对较低,为了进一步提高预测准确率,本文基于卷积神经网络（convolutional neural networks,CNN）算法做了进一步研究。方法 采用PSSM将启动子序列处理成数值矩阵,通过CNN算法进行分类。大肠杆菌K-12（Escherichia coli K-12,E.coli K-12,下文简称大肠杆菌）的Sigma38、Sigma54和Sigma70 3种启动子序列被作为正集,编码（Coding）区和非编码（Non-coding）区的序列为负集。结果 在预测大肠杆菌启动子的二分类中,准确率达到99%,启动子预测的成功率接近100%;在对Sigma38、Sigma54、Sigma70 3种启动子的三分类中,预测准确率为98%,并且针对每一种序列的预测准确率均可以达到98%以上。最后,本文以Sigma38、Sigma54、Sigma70 3种启动子分别和Coding区或者Non-coding区序列做四分类,预测得到的准确性为0.98,对3种Sigma启动子均衡样本的十交叉检验预测精度均可以达到0.95以上,海明距离为0.016,Kappa系数为0.97。结论 相较于支持向量机（support vector machine,SVM）等其他分类算法,CNN分类算法更具优势,并且基于CNN的分类优势,编码方式亦可以得到简化。     

温度对取食玉米籽粒桃蛀螟生长发育、存活和生殖的影响

为了明确不同温度对取食玉米籽粒桃蛀螟生长发育、存活和生殖的影响,本研究依据年龄-龄期两性生命表理论计算了在21、24、27和30 ℃下取食玉米籽粒的桃蛀螟种群的生命表参数,并基于这些参数预测了未来80 d的种群动态。结果表明: 在21、24、27和30 ℃下桃蛀螟均能完成1个世代,随着温度升高,各阶段的发育历期缩短,且温度间差异显著。24 ℃下的平均单雌产卵量最高(116.7粒),成虫前期存活率最高(84.7%),雌虫占比最高(0.46),均显著高于其他温度。24、27、30 ℃下种群的内禀增长率分别为0.1059、0.1101、0.1045 d^-1,周限增长率分别为1.1117、1.1164、1.1102 d^-1,处理间差异不显著,但均显著高于21 ℃处理。21、24、27和30 ℃下的净增殖率(R₀)分别为17.3、53.7、36.9、19.8个后代个体,其中24 ℃时的R₀最高且显著高于其他温度处理。表明桃蛀螟种群在24～27 ℃下的存活率高、繁殖力大、雌性占比较高,是其生长发育、生存和繁殖的适合温度。     

Timing of establishment of paternal methylation imprints in the mouse

Imprinted genes are characterized by predominant expression from one parental allele and differential DNA methylation. Few imprinted genes have been found to acquire a methylation mark in the male germ line, however, and only one of these, H19, has been studied in detail. We examined methylation of the Rasgrf1 and Gtl2 differentially methylated regions (DMR) to determine whether methylation is erased in male germ cells at e12.5 and when the paternal allele acquires methylation. We also compared their methylation dynamics with those of H19 and the maternally methylated gene Snrpn. Our results show that methylation is erased on Rasgrf1, H19, and Snrpn at e12.5, but that Gtl2 retains substantial methylation at this stage. Erasure of methylation marks on Gtl2 appears to occur later in female germ cells to give the unmethylated profile seen in mature MII oocytes. In the male germ line, de novo methylation of Rasgrf1, Gtl2, and H19 occurs in parallel between e12.5 and e17.5, but the DMR are not completely methylated until the mature sperm stage, suggesting a methylation dynamic different from that of IAP, L1, and minor satellite sequences, which have been shown to become fully methylated by e17.5 in male germ cells. This study also indicates important differences between different imprinted DMR in timing and extent of methylation in the germ cells.     

血管紧张素Ⅱ在小鼠卵泡闭锁中的作用

应用幼年小鼠经孕马血清促性腺激素（pregnant mares serum gonadotropin,PMSG)处理的动物模型,研究了卵泡从发育到闭锁动态变化过程中血管紧张素Ⅱ（AngⅡ）的作用。结果表明：（1）24日龄小鼠给予PMSG（10IU/只）后6d时,卵巢中出现大量闭锁卵泡,颗粒细胞DNA琼脂糖电泳显示了梯形条带;（2）随卵泡闭锁发生,卵巢AngⅡ含量增加;（3）AngⅡ显著拮抗FSH刺激颗粒细胞雌二醇生成的作用。我们认为,AngⅡ参与了对小鼠卵泡闭锁的调节。     

基因操作技术在药物代谢酶系研究中的应用

采用基因敲除与转基因技术,可制备具有人类CYP450药物氧化代谢种属特性的“人源化”整体动物模型,在外源性化学物质与肿瘤发生的易感性研究等方面,具有重要的药理学和毒理学意义,也可为新药的研制与开发提供新的更为可靠的评价手段。     

肝靶向配体半乳糖基白蛋白和多聚谷氨酸

化学合成两类去唾液酸糖蛋白受体(ASGPR)的人工配体——半乳糖基白蛋白(Gal_nHSA)和半乳糖基多聚-L-谷氨酸(Gal_nPLGA), 并以 ¹²⁵I标记的去唾液酸胎球蛋白(ASF)为标准配体,测定了合成配体抑制 ¹²⁵I-ASF与大鼠肝细胞膜ASGPR结合的IC₅₀值. 结果表明,Gal₁₂HSA、Gal₁₅HSA、Gal₂₆HSA、Gal₃₀HSA和Gal₃₄PLGA均能够有效地抑制 ¹²⁵I-ASF与ASGPR的结合,且前者与ASGPR的亲和力随半乳糖基化程度的增加而增加. 这些合成配体来源丰富、制备简单,适合于作为药物或基因肝靶向运送的导向配体.     

Local chromatin microenvironment determines DNMT activity: from DNA methyltransferase to DNA demethylase or DNA dehydroxymethylase

Insights on active DNA demethylation disproved the original assumption that DNA methylation is a stable epigenetic modification. Interestingly, mammalian DNA methyltransferases 3A and 3B (DNMT-3A and -3B) have also been reported to induce active DNA demethylation, in addition to their well-known function in catalyzing methylation. In situations of extremely low levels of S-adenosyl methionine (SAM), DNMT-3A and -3B might demethylate C-5 methyl cytosine (5mC) via deamination to thymine, which is subsequently replaced by an unmodified cytosine through the base excision repair (BER) pathway. Alternatively, 5mC when converted to 5- hydroxymethylcytosine (5hmC) by TET enzymes, might be further modified to an unmodified cytosine by DNMT-3A and -3B under oxidized redox conditions, although exact pathways are yet to be elucidated. Interestingly, even direct conversion of 5mC to cytosine might be catalyzed by DNMTs. Here, we summarize the evidence on the DNA dehydroxymethylase and demethylase activity of DNMT-3A and -3B. Although physiological relevance needs to be demonstrated, the current indications on the 5mC- and 5hmC-modifying activities of de novo DNA C-5 methyltransferases shed a new light on these enzymes. Despite the extreme circumstances required for such unexpected reactions to occur, we here put forward that the chromatin microenvironment can be locally exposed to extreme conditions, and hypothesize that such waves of extremes allow enzymes to act in differential ways.     

Deficiency in a Glutamine-Specific Methyltransferase for Release Factor Causes Mouse Embryonic Lethality

Biological methylation is a fundamental enzymatic reaction for a variety of substrates in multiple cellular processes. Mammalian N6amt1 was thought to be a homologue of bacterial N⁶-adenine DNA methyltransferases, but its substrate specificity and physiological importance remain elusive. Here, we demonstrate that N6amt1 functions as a protein methyltransferase for the translation termination factor eRF1 in mammalian cells both in vitro and in vivo. Mass spectrometry analysis indicated that about 70% of the endogenous eRF1 is methylated at the glutamine residue of the conserved GGQ motif. To address the physiological significance of eRF1 methylation, we disrupted the N6amt1 gene in the mouse. Loss of N6amt1 led to early embryonic lethality. The postimplantation development of mutant embryos was impaired, resulting in degeneration around embryonic day 6.5. This is in contrast to what occurs in Escherichia coli and Saccharomyces cerevisiae, which can survive without the N6amt1 homologues. Thus, N6amt1 is the first glutamine-specific protein methyltransferase characterized in vivo in mammals and methylation of eRF1 by N6amt1 might be essential for the viability of early embryos.Nucleic acids, proteins, carbohydrates, and lipids, as well as a body of small molecules, are subject to methylation in a wide variety of biological contexts (3). The majority of methylation reactions are catalyzed by S-adenosylmethionine (AdoMet)-dependent methyltransferases (MTases). These enzymes ubiquitously exist in species from all three domains of life.Methylation of DNA occurs on one of two bases: cytosine or adenine (19). In prokaryotes, adenine methylation is as widespread as cytosine methylation. In contrast, eukaryotic genomes are devoid of adenine methylation or this type of methylation is too rare to be detected (23, 26). Intriguingly, two putative N⁶-adenine DNA MTases, named N6amt1 and N6amt2, are encoded in the mouse and human genomes. In addition to the conserved AdoMet-binding signature motif GXGXG and other sequence elements, they possess the NPPY motif characteristic of the N⁶-adenine or N⁴-cytosine DNA MTases in bacteria (6, 14). N6amt1 was thus proposed as an AdoMet-dependent DNA MTase, although no evidence had been provided that N6amt1 could methylate DNA (23).No functional clue for N6amt1 existed until two groups independently identified Escherichia coli HemK, distantly related to N6amt1, as a protein MTase for polypeptide release factors RF1 and RF2 (8, 17). The HemK gene was initially discovered in a genetic screen for heme biosynthesis mutants (18), although subsequent studies revealed no direct involvement in heme metabolism. The presence of an NPPY motif, thought to be restricted to members of the adenine and cytosine amino methyltransferases, led to the suggestion that HemK could be an AdoMet-dependent DNA MTase (2). However, a series of genetic and biochemical experiments finally revealed that HemK methylates the side-chain amide group of a glutamine residue in the universally conserved tripeptide motif GGQ of the two release factors in E. coli (8, 17). Methylation of the release factors ensures efficient translation termination and release of newly synthesized peptide from the ribosome (16). Similarly, the yeast HemK homologue, YDR140w (Mtq2p), was confirmed to methylate the eukaryotic release factor eRF1 on a corresponding glutamine residue (9, 22). More recently, the human homologue N6amt1 (HemK2) was reported to methylate release factor 1 (eRF1) in vitro (5).We initially sought to characterize the function of N6amt1 as a potential DNA adenine MTase. Interestingly, the human N6amt1 gene is located on chromosome 21q21.3, a critical region for Down syndrome (1, 20). In this study, we report the identification of murine N6amt1 as a glutamine-specific MTase of eRF1 both in vitro and in vivo. Mammalian eRF1, the only mammalian release factor, is indeed methylated at the glutamine residue of the GGQ motif. Inactivation of the N6amt1 gene by targeted disruption led to embryonic lethality in the mouse. These data confirm that N6amt1 functions as a protein MTase in mammals and indicate that modulation of the eRF1 activity by N6amt1-mediated glutamine methylation might be essential for embryo viability.     

Reducing Pectobacterium virulence by expression of an N-acyl homoserine lactonase gene Plpp-aiiA in Lysobacter enzymogenes strain OH11

An N-acyl homoserine lactonase gene aiiA, transcribed by a strong and constitutive Escherichia coli promoter P_lpp (Accession No. EU723847), was transformed into Lysobacter enzymogenes strain OH11, creating strain OH11A. The N-acyl-homoserine lactone (AHL)-degradation assay showed that transformant OH11A acquired the ability to degrade AHL molecules produced by Agrobacterium tumefaciens, Pectobacterium carotovorum, Pseudomonas syringae pv. tomato strain DC3000 and Acidovorax avenae subsp. citrulli. Pathogenicity tests showed that while the parental strain OH11 did not reduce P. carotovorum infection, the transformant OH11A caused a strong reduction of Pectobacterium virulence on Chinese cabbage and cactus, whereas strain OH11A did not seem to interfere with the normal growth of this pathogen in cabbages. In antimicrobial activity assays, strain OH11A and OH11 showed similar antimicrobial activity against Phytophthora capsici and Sclerotinia sclerotiorum. This work provided a new strategy for developing genetically engineered multi-functional L. enzymogenes strains that possessed the ability to biologically control fungal pathogens and reduce bacterial pathogenicity.     

非体外循环与并行循环不停跳冠脉搭桥术炎性因子的比较

目的:通过对比非体外循环与并行循环下不停跳冠脉搭桥术炎性因子的变化,观察不同方法对机体全身炎性反应程度的影响.方法:选择2009年6月～2010年1月在我院行冠脉搭桥术患者30例,其中选取采用并行循环下不停跳冠脉搭桥术(OnP-BH CABG)和非体外循环冠脉搭桥术(OPCABG)患者各15例,即A组和B组.检测T1(术前)、T2(手术结束时)、T3(术后6小时)、T4(术后12小时)、T5(术后24小时)不同时间点血浆肿瘤坏死因子-α(TNF-α)、白介素-6(IL-6)、白介素-8(IL-8)、肌钙蛋白I(cTnI)含量,并记录桥血管数量、精神状况、引流量及ICU入住时间.结果:两组血浆TNF-α、IL-6、IL-8、cTnI舍量T1时无统计学意义(P>0.05),T2、T3、T4、T5均呈升高趋势.A组较B组T2、T3、T4、T5各时间点TNF-α、IL-6、IL-8指标升高差异显著(P<0.01);cTnI升高幅度略缓,T4、T5差异无统计学意义.比较患者术后精神状况及ICU入住时间,B组均优于A组(P>0.05).术中搭桥血管支数无统计学差异、A组引流量较B组多,有统计学意义(p=0.02).结论:并行循环下不停跳冠脉搭桥术与非体外循环冠脉搭桥术相比,心肌损伤略重;体外循环可加重机体全身炎性反应程度.

Abstract：

Objective: The aim of this study was to compare the differences of inflammatory cytokines level and inflammatory reaction in patients between on-pump beating heart CABG and off-pump CABG. Methods: Select the patients from June 2009 to Jan 2010 who underwent the CABG in our hospital with on-pump beating heart CABG and off-pump CABG and each group was 15 patients. That was named Group A and group B. Serial blood samples were collected at the following intervals respectively: before operation and Oh, 6h, 12h, 24h after the operation to evaluate the concentration of TNF-α , IL-6, IL-8 and cTn I. Recorded and compared the grafts, mental status、bleeding and the time of intensive care unit. Results: There was no significant difference between two groups in plasma TNF -α , IL - 6, IL - 8 and cTn I level at T1. The level of TNF -α , IL - 6 and IL - 8 was significantly increased at T2 - T5 compared with that before operation (T1) in both groups. However, the plasma concentrations of TNF -α , IL - 6, IL - 8 were significantly lower in group B than group A. The level of cTnI was significantly increased at T2-T3 compared with T1, and no significantly difference at T4, T5. The general condition of the patients in group B was better than group A. The bleeding was significantly fewer in groups B. Conclusions: Myocardial injury was slightly heavier in patients with on pump beating heart CABG than off pump CABG. Cardiopulmonary bypass can aggravate inflammatory reaction.