Effect of the NF-κB inhibitor pyrrolidine dithiocarbamate on the apoptosis and proliferation of mesangial cells in the rat with anti-thymocyte serum nephritis

AIM: To explore the effect of pyrrolidine dithiocarbamate (PDTC), the specific inhibitor of NF-κB, on anti-thymocyte serum nephritis (ATSN) in rats. METHODS: The rat model of ATSN was reproduced with rabbit anti-thymocyte serum (ATS). The rats were divided into ATSN group, ATSN+PDTC group and control group. The expression of NF-κB p65 and the apoptosis, lysis as well as proliferation of mesangial cells (MC) were examined by immunohistochemical staining, Tdt-mediated X-dUTP nick end labeling (TUNEL), light microscope and electron microscope at 40 minutes, 24 hours and 7 days after injection of ATS or normal serum. RESULTS: The expression of glomerular NF-κB p65 in the ATSN group was observed with significant difference compared to controls at 40 min (P<0.01), it was elevated more at 24 hours, and was significantly increased at day 7, but the expression of NF-κB p65 in ATSN+PDTC group was less than that in ATSN group. The proliferation of glomerular MC and the secretion of extracellular matrix (ECM) in ATSN group were less than those in ATSN+PDTC group on day 7. PDTC had little role in the pathologic changes of rats in ATSN group in early stage (40 min and 24 hours), but affected the MC proliferation. CONCLUSION: PDTC, an inhibitor of NF-κB, suppresses glomerular MC proliferation in rats with ATSN.     

Analysis of glomerular complement C5b-9 deposits and synthesis of NO,TNFα in the model of the rats with anti-thymocyte serum nephritis

AIM: To explore the localization and semi-quantification of the glomerular complement C5b-9 complexes and synthesis of some inflammatory mediators or cytokines such as nitric oxide (NO) and tumor necrosis factor α(TNFα) in the rats with anti-thymocyte serum nephritis(ATSN). METHODS: The animal model of rat ATSN was reproduced by a single intravenous injection of anti-thymocyte serum (ATS). Then, the deposits of glomerular C5b-9 complexes were localized and quantified by immunohistochemical staining and microscopic image scanning separately. And the glomerular mesangial cells (MC) surrounded by C5b-9 complexes were counted under microscope. In addition, the expression of glomerular MC inducible NO synthase(iNOS) mRNA and excretion of urinary NO metabolite (NO^-₂／NO^-₃) and TNF α in the rats with ATSN were detected. RESULTS: The MC in the rats with ATSN emerged necrosis followed by a rapid proliferation. In the early time of MC injury, the C5b-9 complexes were mainly seen in glomerular mesangium and MC surface. But with the progression of ATSN, the MC enclosed by C5b-9 appeared gradual decrease. Moreover, the expression of MC iNOS mRNA in early stage of ATSN obviously increased and the excretion of urinary NO^-₂／NO^-₃ and TNF α also significantly increased. However, the changes of parameters mentioned above in ATSN proliferative stage (after 7 days) alleviated gradually. CONCLUSION: The secondary lysis of MC has relation to the deposition of C5b-9 complexes and synthesis and release of NO and TNF α in rats with ATSN.     

Effect of antiserum against complement C5b-9 complexes on nitric oxide(NO) synthesis and pathologic changes in renal tissue of ATSN rats

AIM: To explore the effect of antiserum against rat complement C5b-9 complexes on nitric oxide synthesis and pathologic changes in renal tissue of rats with mesangioproliferative glomerulonephritis. METHEDS: The rat model of mesangioproliferative glomerulonephritis,namely,anti-thymocyte serum nephritis(ATSN) was established and the rats with ATSN were treated with antiserum against complement C5b-9 complexes. Some parameters related to NO and pathologic changes of the rats were observed.RESULTS: Anti-C5b-9 serum not only reduced the expression of inducible NO synthase(iNOS) mRNA in renal tissue and urinary content of nitrate/nitrite(NO₃^-/ NO₂^-) of rats with ATSN, but also reduced renal pathologic changes. L-N G-nitro arginine methylester (L-NAME) also reduced the contents of urinary NO₃^-/NO₂^- and the renal pathologic changes of rats with ATSN. CONCLUSION: The antiserum against rat complement C5b-9 complexes inhibited glomerular NO synthesis and glomerular mesangial cell proliferation of rats with ATSN.     

基于银杏花芽3个分化时期转录组测序的相关基因筛选与表达分析

鉴定银杏花芽分化调控的关键基因,揭示银杏花芽分化调控的主要分子机制,为缩短银杏童期和选育银杏早花品种提供理论指导。本研究中采用高通量测序技术对银杏花芽分化3个时期（花芽未分化期、花芽分化始期、花芽分化盛期）的样品进行转录组测序,并分析数字表达谱,筛选开花调控相关基因并进行荧光定量PCR（RT-qPCR）表达验证。转录组测序共产生27.52 Gb原始数据,注释到8大功能数据库（GO、COG、KEGG、KOG、NR、Pfam、Swiss-Prot、eggNOG）上的 unigene 总数为35 179个。通过GO分类和KEGG Pathway 富集性分析,将unigene分别归于55个GO类别和126个代谢途径。差异表达基因分析显示,花芽未分化期较花芽分化始期有2 253个基因上调,2 032个基因下调;花芽分化始期较花芽分化盛期有1 770个基因上调,1 901个基因下调;花芽未分化期较花芽分化盛期有1 865 个基因上调,2 042个基因下调。发掘出大量的开花相关的基因涉及5个开花调控途径（光周期途径、春化途径、赤霉素途径、自主途径和年龄途径）。筛选出gene.Gb_17618（GI序列）、gene.Gb_19790（FT/TFL1序列）、gene.Gb_16301（AG序列）、gene.Gb_28337（花发育MADS-box序列）、gene.Gb_01884（SOC1序列）和gene.Gb_41704（CO序列）等6个银杏花芽分化差异表达关键基因序列,荧光定量PCR检测表达水平与转录组结果一致。     

Gene microarray analysis of ovarian serous cystadenocarcinoma-related genes based on TCGA

AIM: To detect the differentially expressed genes associated with ovarian serous cystadenocarcinoma (OV) by microarray and to analyze the participated signaling pathway. METHODS: We analyzed 16 datasets of Affymetrix GeneChip Human Exon 1.0 ST Arrays from The Cancer Genome Atlas (TCGA), including 8 OV and 8 normal ovary samples. The function of differential genes was determined by pathway and gene ontology (GO) analysis. The probable functions of the key genes were predicted according to intergenic signal transduction network. RESULTS: The 1 144 genes were identified as distinctively expressed in OV (P<0.05), 747 of which were up-regulated and 397 were down-regulated. The GO analysis results showed that the altered genes were involved in 362 up-regulated and 160 down-regulated significant functions (P<0.05) related to cell cycle, DNA replication, cell proliferation, cell apoptosis, cell adhesion, etc. The pathways of the different genes were involved in the 59 enrichment-related pathways (P<0.05), 45 of which were up-regulated and 14 were down-regulated. Among the 59 pathways, cell cycle, P53 signaling pathway, DNA replication, pathways in cancer, PI3K-Akt signaling pathway, ECM-receptor signaling pathway, cell adhesion molecules and cell apoptosis were related to tumor genesis, development and metastasis. As a result, 229 genes with significant functions and pathways in GO and pathway analysis were selected to construct signal transduction network (Signal-Net), 4 of which, CDK1, PLK1, MCM3 and PGK1, were found to play key roles in OV signal regulation network. CONCLUSION: The OV shows abundant differentially expressed genes that play key roles in cancer-related signal pathways.     

黄肉苹果转色期前后类胡萝卜素合成相关差异表达基因鉴定

为了了解黄肉苹果种质成熟时富集类胡萝卜素的分子机制,以黄肉种质‘东北黄海棠’为材料,选择转色期前后(盛花后90 d和115 d)两个发育时期的果实进行RNA-seq测序,分析两个样本差异表达基因,并利用实时荧光定量PCR技术验证获得的类胡萝卜素合成相关差异表达基因的表达水平。结果获得两个样本显著差异表达基因共3 056个,与盛花后90 d果实比较,成熟期果实中有1 270个基因上调表达,1 786个基因下调表达。对这些表达差异基因进行了Pathway富集分析,结果显示差异表达基因涉及类胡萝卜素、苯丙氨酸以及类黄酮等代谢途径,其中类胡萝卜素代谢途径基因有3个上调,4个下调。通过对这7个差异表达基因进一步的qRT-PCR及聚类分析,发现一个新的候选基因MdCCD4b,该基因与菊花以及桃等CCD4聚为一类,与其他作物功能已知的CCD4一样,其表达水平与黄肉种质中类胡萝卜素积累呈负相关,推测黄肉种质果实成熟后类胡萝卜素的富集与MdCCD4b基因显著下调有关。     

仁用杏花芽3个发育时期数字基因表达谱分析

以仁用杏‘优一’为试材,运用转录组、数字基因表达谱技术,研究了仁用杏花芽萌动期前后相关基因的表达规律。结果发现,仁用杏花芽在花芽萌动期前后进行着各种旺盛的生物合成和代谢活动,且4个开花调控途径（光周期途径、春化途径、自主途径、GA调控途径）均已启动,光周期途径在花芽萌动时发挥重要作用,涉及到了74条基因,其中有38条差异基因上调表达,29条下调表达;GA途径在花芽萌动期对花芽的生长发育调控表现为抑制作用,涉及到了60条基因,其中有13条差异基因上调,9条差异基因下调;其他两条途径于花芽萌动前作用,其中春化途径涉及到了23个基因,其中有4条差异基因上调,15条差异基因下调;自主途径涉及到了24条基因,其中有3条差异基因上调,11条差异基因下调。本研究通过数字基因表达谱分析,初步了解仁用杏花芽萌动前后的网络途径,为后期对仁用杏花芽相关开花基因的研究、探明仁用杏早花的分子机理及通过分子育种方法培育仁用杏晚花品种提供坚实的理论依据。     

A comparative study on urinary complement C5b-9 complex excretion in four nephritis models of rats

AIM: To explore the significance of measuring urinary complement C5b-9 complex in various types of immune complex (IC) nephritis models of rats. METHODS: The four models of rats, namely, passive Heymann nephritis (PHN), anti-thymocyte serum nephritis(ATSN), anti-glomerular basement membrane nephritis (AGBMN) and chronic serum disease nephritis (CSDN) were reproduced. Then, the contents of complement C5b-9 complex in plasma and urine of the rats were detected with sandwich ELISA. And the deposits of C5b-9 complex in glomeruli of the rats were examined by ABC immunohistochemistry staining. CONCLUSION: Urinary C5b-9 complex excretion could be taken as one of several sensitive immunologic parameters in diagnosing of PHN and in distinguishing PHN from other type of nephritis.     

超表达MdFLS2的拟南芥fls2突变体识别细菌鞭毛蛋白,提高对轮纹病菌的抗性

以红肉苹果‘紫红3号’愈伤组织为试材,克隆了细菌鞭毛蛋白受体基因MdFSL2,研究了其与拟南芥AtFLS2对细菌鞭毛蛋白敏感性差异以及对苹果轮纹病抗性的影响。进化树分析表明,MdFLS2与拟南芥AtFLS2亲缘关系较远,处于不同的进化树分支,与梨PbFLS2的亲缘关系最近。时空表达特异性研究表明,在苹果叶片中MdFLS2表达不随组织衰老而产生差异,能够被外源SA处理诱导,不受IAA、ACC处理影响;在根系中表达量最高,而在花与果实中表达量较低。在拟南芥中异源过表达MdFLS2,显著抑制植株生长,并出现叶片边缘枯死或细胞死亡的表型。在转基因拟南芥中受SA诱导的病程相关基因AtPR1、AtPR2和AtPR5,及衰老相关基因AtORE1和AtNAP的表达水平均显著高于野生型。为研究MdFLS2是否具有感知细菌鞭毛蛋白的能力,进行拟南芥根系生长抑制试验,MdFLS2超表达恢复了细菌鞭毛蛋白N端22个保守氨基酸肽段(flg22)对拟南芥fls2突变体根系生长的抑制作用,但flg22分别处理30和60 min,或20和40 min,flg22诱导的标志性基因表达水平及MAPK激酶活化水平在过表达MdFLS2的fls2突变体中显著低于同样处理的野生型。超表达MdFLS2提高了拟南芥叶片对轮纹病菌的抗性,并增强了拟南芥突变体fls2对假单胞菌DC3000的抗性。研究结果说明苹果MdFLS2是一个有功能的免疫相关基因,MdFLS2与AtFLS2在具体执行功能与作用机制上可能存在差异。     

白榆二倍体及同源四倍体的生理特性及转录组差异分析

为了探究白榆二倍体及其同源四倍体的基因表达谱差异情况,以白榆二倍体及其同源四倍体为材料,比较二者成熟叶片的生理特征并采摘幼嫩叶片进行转录组数据分析。结果显示,与二倍体相比,同源四倍体丙二醛含量、可溶性蛋白含量及叶绿素含量增加,可溶性糖含量降低。转录组测序结果共得到2 407个差异表达基因,其中上调基因为1 076个,下调基因为1 331个。在COG蛋白质的同源注释分析得到918个差异表达基因,主要涉及21个方面。共有1 380个差异表达基因被GO注释,主要与细胞组分、代谢功能、催化活性等相关。通过KEGG通路注释发现,共有930个差异表达基因分布到5大类KEGG通路中,其中以代谢机制中差异表达基因被注释到的最多。叶绿素含量的增加使四倍体的叶片颜色变得更加浓绿,丙二醛、可溶性糖、可溶性蛋白的含量的增加与减少与四倍体植物在植物代谢与生长上有一定关系,经过转录组测序分析,糖酵解途径的基因表达为下调,还原性戊糖磷酸循环与光呼吸等与叶绿体有关的基因为上调。     

利用基因芯片鉴定梨品种自交不亲和基因型

根据东方梨中已鉴定的46个S基因序列和S基因的结构特点,设计了86条寡核苷酸探针并制备成S基因寡核苷酸检测芯片,采用Cy3荧光修饰引物标记被检测品种的PCR产物并与芯片杂交,以检测不同品种的S基因型。结果表明：利用芯片与华梨2号、秀玉和德胜香等已知S基因型的品种杂交,杂交信号显示与各品种已知基因型相符合。利用芯片鉴定了丽江黄酸梨等27个未知S基因型的梨品种,获得了各品种的S基因型,随机选取部分品种进行DNA测序和序列分析,结果与芯片杂交结果完全一致,证明利用S基因寡核苷酸芯片鉴定梨品种S基因型结果准确可靠。     

Effect of nicotine in vitro on expressions of apoptosis-related genes in human lung adenocarcinoma cells by cDNA microarray

AIM: To investigate effect of nicotine on growth of human lung adenocarnoma cells and expressions of apoptosis-related gene. METHODS: Lung adenocarcinoma cell line, SPC-A-1, was cultured in the presence of various concentrations (1-1 000 μg/L) of nicotine for 48 hours. MTT was applied to evaluate effect of nicotine in vitro on growth of SPC-A-1 cell line. After SPC-A-1 cells were treated with 100 μg/L for 48 hours, cDNA expression profile microarray was used to detect the expressions of 451 apoptosis-related genes in SPC-A-1 cell line. RESULTS: Significant proliferation in SPC-A-1 cells treated with nicotine (1-10 μg/L) was observed, but this effect decreased with increase in concentration of nicotine in culture. Growth inhibition rate of 1, 10, 100, 1 000 μg/L of nicotine was 27%, -40%, -40% and -93%. Microarray detection showed that significantly different expressions appeared in 80 of 451 apoptosis-related genes. 29 apoptosis-promoted genes and 26 apoptosis-inhibited genes were up-regulated significantly (CY3/CY5>2.0), and 25 genes were significantly down-regulated (CY3/CY5<0.5). CONCLUSION: Nicotine may promote growth of human lung adenocarcinoma cell through regulating many apoptosis-related gene expressions.     

Influence of ovariectomy and estrogen replacement on gene expression profile of myocardium in rats

AIM:To investigate the influence of ovariectomy and estrogen replacement treatment on profile of gene expression in myocardium by cDNA microarray,and to characterize the targeting genes of estrogen.METHODS:cDNA microarray containing 1 400 rat cDNAs was used to study the genes differentially expressed in myocardium between sham (Ⅰ),ovariectomy (Ⅱ,OVX) and estrogen replacement treatment (Ⅲ,OVX+E2) group.Then down-regulated genes in myocardium of OVX rats were further confirmed by RT-PCR.RESULTS:177 genes were differentially expressed in myocardium between sham and OVX rats,with 91 genes up-regulated and 86 genes down-regulated in OVX rats.164 genes were differentially expressed in myocardium between OVX and OVX+E2 rats,with 113 genes up-regulated and 54 genes down-regulated in OVX rats.There were 54 genes differentially expressed in OVX compared to sham and OVX+E2.They are involved in membrane channels and transporters (18),cell receptors (9),intracellular transducers/effectors/modulator (7) and metabolism (6).Most of the genes (45) were down-regulated in OVX rats and up-regulated in OVX+E2 rats.RT-PCR test confirmed the results of cDNA microarray.CONCLUSIONS:Long-term estrogen replacement may influence the expression of genes involved in membrane channels and transporters,cell receptors,intracellular transducers/effectors/ modulator and metabolism.Long-term estrogen replacement has some beneficial effects on ionic concentration and cardiac function which partially comes from the results of influence of expression on Na+,K+-ATPase and Na+/H+ exchanger.Estrogen has an inhibitory effect on the expression of dopamine receptor,which partially clarify the myocardial protection of estrogen.     

Microarray analysis of tumor metastasis-related gene expression in PSMA-silencing prostate cancer cells

AIM: To investigate the functions of prostate-specific membrane antigen (PSMA) in prostate cancer metastasis. METHODS: Specific siRNA to knock down PSMA expression was designed and transfected into LNCaP cells. The tumor metastasis gene chip was also used to analyze the differential expression of 84 genes related to cancer metastasis. RESULTS: Specific siRNA was successfully designed and constructed and the gene expression of PSMA in LNCaP cells was knocked down. The RNAi efficiency was more than 75% at mRNA level and more than 68% at protein level. The results of the tumor metastasis gene chip indicated that 10 genes were up-regulated (such as CDH6 and CXCL12) and 4 genes were down-regulated (such as CCL7 and MDM2) in the LNCaP cells treated with PSMA siRNA. CONCLUSION: The PSMA is involved in the regulatory pathways in prostate cancer metastasis.     

葡萄活性赤霉素合成关键基因VvGA3ox家族的克隆和表达分析

在植物赤霉素合成代谢中,GA3ox可将几种非活性赤霉素转化为具生理活性的赤霉素。以葡萄有核品种‘黑比诺’和无核品种‘无核白’为材料,克隆葡萄的VvGA3ox基因家族成员,分析基因结构、进行染色体定位和系统发育树构建,检测其组织器官表达特性和在胚珠（幼种子）发育过程的表达变化。结果表明,葡萄基因组VvGA3ox家族有3个成员,cDNA长度分别为1 313、1 225和1 480 bp,都包含2个外显子和1个内含子结构。组织器官特异性表达分析表明,VvGA3ox1在胚珠中的表达很低,在根中高表达;VvGA3ox2和VvGA3ox3在花和胚珠中的表达较高。在受精后胚珠（幼种子）发育过程中,VvGA3ox家族基因的表达趋势存在差异,其中VvGA3ox1在‘黑比诺’与‘无核白’中均是在盛花后30 d时上调之后下降;VvGA3ox2在‘黑比诺’中20 ~ 30 d极速上调之后下降,相应地‘无核白’中是先缓慢下降之后上升;VvGA3ox3在‘黑比诺’中逐渐下降,对应地‘无核白’中是在10 ~ 15 d先上升后在20 ~ 45 d呈下降趋势并逐渐与‘黑比诺’中的表达持平。VvGA3ox在有核和无核葡萄品种中表现较大差异表达,与葡萄无核性状有一定关系。     

Functional analysis of differential microRNA expression profile in mouse fibrotic liver tissues induced by CCl4

AIM:To discover the expression profile of microRNAs (miRNAs) in mouse fibrotic liver tissues induced by carbon tetrachloride (CCl4), and to investigate the functions of these differential miRNAs based on the gene ontology (GO) analysis and KEGG Pathway analysis. METHODS:The mice were randomly divided into normal group and model group. Liver fibrosis was induced by subcutaneous injection of CCl4. miRNA expression profile of the liver tissues was assayed by a mouse miRNA microarray (Agilent 12.0). The differential expression of miRNAs between the normal and model mice was screened, and GO analysis and KEGG Pathway analysis were performed to determine the functions of these differential miRNAs. RESULTS:Thirty-nine miRNAs with differential expression were discovered in the model mice compared with the normal mice, among which 23 were up-regulated and 16 were down-regulated. GO analysis and KEGG Pathway analysis indicated that most pathological processes of liver fibrosis regulated by miRNAs included cell proliferation and activation, cell apoptosis, cell cycle, cell adhesion, inflammatory reaction, cell migration, transforming growth factor β (TGF-β) signaling pathway, Wnt signaling pathway and proteometabolism process. GO analysis revealed that the key up-regulated miRNAs were mmu-miR-322, mmu-miR-15b, mmu-miR-195, mmu-miR-200b and mmu-miR-214, and the key down-regulated miRNAs were mmu-miR-16, mmu-miR-130a, mmu-miR-101b, mmu-miR-30a and mmu-miR-30e. Analyzing the target genes screened out by GO analysis and Pathway analysis simultaneously, we found that the key up-regulated miRNAs included mmu-miR-200b, mmu-miR-322, mmu-miR-106b, mmu-miR-23a and mmu-miR-15b, and the key down-regulated miRNAs included mmu-miR-16, mmu-miR-30e, mmu-miR-30c, mmu-miR-30a and mmu-miR-130a. CONCLUSION: Differential expression of miRNAs is discovered in mouse fibrotic liver tissues induced by CCl4 compared with the normal liver tissues. Most of the pathological processes involved in liver fibrosis may be regulated by miRNA, such as cell proliferation and activation, cell adhesion and apoptosis, cell migration and differentiation, metabolism, TGF-β receptor signaling pathway and so on.     

金枝黄花柳回交子代枝条颜色与转录组研究

为了探究枝条颜色变异的原因，以金枝黄花柳回交子代及其亲本为材料，分析子代枝条性状遗传变异规律及性状与基因表达的关系。结果显示，金枝型回交子代枝条表现为黄色到橙色，普通型回交子代枝条表现为墨绿色至棕色，不同单株个体之间存在颜色差异。枝条转录组共检测到差异表达基因2 499个，其中上调基因984个，下调基因1 515个。功能注释和富集分析发现，卟啉与叶绿素代谢通路(KEGG&ko00860)中与色素合成有关的基因表达量存在差异，其中叶绿素/细菌叶绿素a合成酶(2.5.1.133;2.5.1.62)与叶绿素/细菌叶绿素a还原酶(1.3.1.111)基因表达上调，叶绿素酶(3.1.1.14)基因表达下调。基因差异表达会影响代谢通路，进而影响枝条中叶绿素的含量，导致枝条颜色存在差异。