Otterlace软件在猪全基因组序列人工注释分析中的应用

2009年11月,美、英等国科学家宣布首次绘制出家猪的基因组草图。近两年,随着全基因组序列陆续释放,越来越多的测序片段得到正确拼接组装,从全基因组水平上对猪功能基因进行注释分析显得尤为迫切。文章以丝切蛋白1(Cofilin 1,CFL1)基因的注释过程为例,介绍了运用Sanger研究所开发的Otterlace软件对猪全基因组的免疫基因序列进行人工分析与注释。通过详细说明Zmap、Blixem和Dotter 3个注释工具的使用方法,并给出了注释过程的主要步骤,以期对Otterlace的应用起一个抛砖引玉的作用。运用Otterlace软件对243个免疫相关基因进行分析,其中180个基因得到完整或部分注释,这为后续深入开展这些基因的功能研究奠定了基础。     

The G protein coupled receptor 3 is involved in cAMP and cGMP signaling and maintenance of meiotic arrest in porcine oocytes

The arrest of meiotic prophase in mammalian oocytes within fully grown follicles is dependent on cyclic adenosine monophosphate (cAMP) regulation. A large part of cAMP is produced by the Gs-linked G-protein-coupled receptor (GPR) pathway. In the present study, we examined whether GPR3 is involved in the maintenance of meiotic arrest in porcine oocytes. Expression and distribution of GPR3 were examined by western blot and immunofluorescence microscopy, respectively. The results showed that GPR3 was expressed at various stages during porcine oocyte maturation. At the germinal vesicle (GV) stage, GPR3 displayed a maximal expression level, and its expression remained stable from pro-metaphase I (MI) to metaphase II (MII). Immunofluorescence staining showed that GPR3 was mainly distributed at the nuclear envelope during the GV stage and localized to the plasma membrane at pro-MI, MI and MII stages. RNA interference (RNAi) was used to knock down the GPR3 expression within oocytes. Injection of small interfering double-stranded RNA (siRNA) targeting GPR3 stimulated meiotic resumption of oocytes. On the other hand, overexpression of GPR3 inhibited meiotic maturation of porcine oocytes, which was caused by increase of cGMP and cAMP levels and inhibition of cyclin B accumulation. Furthermore, incubation of porcine oocytes with the GPR3 ligand sphingosylphosphorylcholine (SPC) inhibited oocyte maturation. We propose that GPR3 is required for maintenance of meiotic arrest in porcine oocytes through pathways involved in the regulation of cAMP and cGMP.     

Cytotoxicity, apoptosis, cellular uptake, cell cycle distribution, and DNA-binding investigation of ruthenium complexes

Three new ruthenium(II) polypyridyl complexes [Ru(bpy)(2)(BHIP)](2+) 1, [Ru(phen)(2)(BHIP)](2+) 2, and [Ru(dip)(2)(BHIP)](2+) 3 were synthesized and characterized. The cytotoxicity of the three complexes was evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The apoptosis induced by the complexes was studied by cell morphology and flow cytometry. The results showed that the percentage of apoptotic cells is 7.19%, 75.58%, and 3.51% in the presence of complexes 1, 2, and 3, respectively. The cellular uptakes were also performed and the results indicated that complexes 1, 2, and 3 can enter into the cytoplasm and also into the nucleus. The studies on antiproliferative mechanism showed the induction of S-phase arrest by complexes 1, 2, and 3. DNA-binding constants of these complexes with calf thymus DNA (CT-DNA) were determined to be 1.07 (± 0.47) × 10(5) M(-1) (s = 2.04), 1.21 (± 0.32) × 10(5) M(-1) (s = 1.88), and 2.75 (± 0.27) × 10(5) M(-1) (s = 2.17), respectively. Upon irradiation at 365 nm, complexes 1, 2, and 3 can induce cleavage of pBR322 DNA.     

Prediction of Disease-Related Interactions between MicroRNAs and Environmental Factors Based on a Semi-Supervised Classifier

Accumulated evidence has shown that microRNAs (miRNAs) can functionally interact with a number of environmental factors (EFs) and their interactions critically affect phenotypes and diseases. Therefore, in-silico inference of disease-related miRNA-EF interactions is becoming crucial not only for the understanding of the mechanisms by which miRNAs and EFs contribute to disease, but also for disease diagnosis, treatment, and prognosis. In this paper, we analyzed the human miRNA-EF interaction data and revealed that miRNAs (EFs) with similar functions tend to interact with similar EFs (miRNAs) in the context of a given disease, which suggests a potential way to expand the current relation space of miRNAs, EFs, and diseases. Based on this observation, we further proposed a semi-supervised classifier based method (miREFScan) to predict novel disease-related interactions between miRNAs and EFs. As a result, the leave-one-out cross validation has shown that miREFScan obtained an AUC of 0.9564, indicating that miREFScan has a reliable performance. Moreover, we applied miREFScan to predict acute promyelocytic leukemia-related miRNA-EF interactions. The result shows that forty-nine of the top 1% predictions have been confirmed by experimental literature. In addition, using miREFScan we predicted and publicly released novel miRNA-EF interactions for 97 human diseases. Finally, we believe that miREFScan would be a useful bioinformatic resource for the research about the relationships among miRNAs, EFs, and human diseases.     

不同生态区云南黄连居群的染色体核型比较

采用根尖压片和卡宝品红染色法,对分布于高黎贡山的东、西坡不同生态带的8个云南黄连居群进行染色体核型比较分析。结果表明,8个居群染色体数目均为2n=2x=18,核型基本一致,除东坡一个居群为3A型外,其余均为2A型;总体上同一生态区域内各居群的核型表现出较大的相似性,但不同生态区域的居群间却存在较大的差异,主要为近端部和端部着丝点染色体的有无及数目在东西坡居群间存在较大变化;东坡居群的不对称程度均较西坡高。     

全反式维甲酸通过γ-氨基丁酸途径促进小鼠胚胎腭板间充质细胞的凋亡

维甲酸(RA)是一种能够诱导腭裂发生的致畸物．研究显示γ-氨基丁酸(GABA)在腭板的发育过程中发挥重要作用．而GABA是否参与了RA诱导的腭裂发生还不清楚．本研究以小鼠胚胎腭板间充质细胞(MEPM)为研究对象,观察全反式维甲酸(atRA)(0.2、0.67、2.0和 6.7 μmol/L)对MEPM细胞增殖和凋亡的影响,并探讨GABA信号通路在其中的可能作用．结果显示,atRA(2.0 μmol/L和6.7 μmol/L)显著性抑制了MEPM的增殖,并促进了细胞凋亡．atRA(0.67、2.0和 6.7 μmol/L)显著性降低了GABA合成的关键酶谷氨酸脱羧酶(GAD67)mRNA和蛋白质的表达,但对γ-氨基丁酸A型受体-β3(GABAAR-β3)mRNA和蛋白质的表达没有影响．1.0 μmol/L的GABA逆转了atRA(6.7 μmol/L)对MEPM细胞增殖和凋亡的影响．以上结果表明,atRA通过下调GAD67的表达,减少GABA的产生,抑制MEPM的增殖和促进MEPM的凋亡,从而可能影响腭板的发育,诱导腭裂形成．     

山楂酸减少L02细胞脂质累积作用的研究(英文)

非酒精性脂肪性肝在发达国家和发展中国家中是一种常见的肝脏疾病。引起非酒精性脂肪性肝病的最常见原因有肥胖、糖尿病和高胆固醇。尽管非酒精性脂肪性肝病的发病率日益升高,事实上至今尚未发现可以用于治疗的药物。山楂酸是一种五环三萜化合物,已报道具有多种药理特性,包括抗炎、抗氧化以及免疫调节作用。我们的前期研究表明,山楂酸能够抑制高脂饲料诱导大鼠非酒精性脂肪性肝病的生成。本研究中,我们将探讨山楂酸体外对肝细胞(LO2)脂质累积的抑制作用。结果表明,山楂酸可抑制游离脂肪酸(FFA)诱导的LO2细胞脂质累积,进一步研究表明,山楂酸可抑制LO2细胞的SCAP mRNA水平和蛋白水平的表达。     

高粱种质材料幼苗期耐盐碱性评价

采用Hoagland营养液砂培法,以NaCl和Na2CO3组成的混合盐碱对高粱幼苗进行胁迫处理,建立高粱幼苗期耐盐碱评价方法,并评价了66份高粱种质材料的耐盐碱性.结果表明:盐浓度在8.0～12.5 g·L-1时,高粱耐盐碱品种‘TS-185’与盐碱敏感品种‘Tx-622B’在幼苗期的耐盐碱性差异明显,表明进行高粱幼苗期耐盐碱性评价时适宜的盐浓度范围为8.0～12.5 g· L-1.在10.0和12.5 g·L-12个盐浓度下,66份高粱种质材料的相对存活率、相对地上部鲜质量和相对株高的差异均达显著水平,表明不同品种的耐盐碱性不同.其中,‘三尺三’为高度耐盐碱品种,‘MN-2735’等16个品种为耐盐碱品种,‘EARLY HONEY’等32个品种为中等耐盐碱品种,‘Tx-622B’等16个品种为盐碱敏感品种,‘MN-4588’为高度盐碱敏感品种.苏丹草类型高粱一般具有较高的耐盐碱性,而保持系对盐碱较为敏感.     

Transient bioheat simulation of the laser-tissue interaction in human skin using hybrid finite element formulation

This paper presents a hybrid finite element model for describing quantitatively the thermal responses of skin tissue under laser irradiation. The model is based on the boundary integral-based finite element method and the Pennes bioheat transfer equation. In this study, temporal discretization of the bioheat system is first performed and leads to the well-known modified Helmholtz equation. A radial basis function approach and the boundary integral based finite element method are employed to obtain particular and homogeneous solutions of the laser-tissue interaction problem. In the boundary integral based finite element formulation, two independent fields are assumed: intra-element field and frame field. The intra-element field is approximated through a linear combination of fundamental solutions at a number of source points outside the element domain. The frame temperature field is expressed in terms of nodal temperature and the corresponding shape function. Numerical examples are considered to verify and assess the proposed numerical model. Sensitivity analysis is performed to explore the thermal effects of various control parameters on tissue temperature and to identify the degree of burn injury due to laser heating.