Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species

The chromalveolates form a highly diverse and fascinating assemblage of organisms, ranging from obligatory parasites such as Plasmodium to free-living ciliates and algae such as kelps, diatoms, and dinoflagellates. Many of the species in this monophyletic grouping are of major medical, ecological, and economical importance. Nevertheless, their genome evolution is much less well studied than that of higher plants, animals, or fungi. In the current study, we have analyzed and compared 12 chromalveolate species for which whole-sequence information is available and provide a detailed picture on gene loss and gene gain in the different lineages. As expected, many gene loss and gain events can be directly correlated with the lifestyle and specific adaptations of the organisms studied. For instance, in the obligate intracellular Apicomplexa we observed massive loss of genes that play a role in general basic processes such as amino acid, carbohydrate, and lipid metabolism, reflecting the transition of a free-living to an obligate intracellular lifestyle. In contrast, many gene families show species-specific expansions, such as those in the plant pathogen oomycete Phytophthora that are involved in degrading the plant cell wall polysaccharides to facilitate the pathogen invasion process. In general, chromalveolates show a tremendous difference in genome structure and evolution and in the number of genes they have lost or gained either through duplication or horizontal gene transfer.     

血管紧张素Ⅰ转化酶基因多态和2型糖尿病肾病相关性研究

血管紧张素Ⅰ转化酶（ＡＣＥ）基因多态和２型糖尿病肾病（ＤＮ）的关系。方法用ＰＣＲ技术检测１０２例中国汉族２型糖尿病患者ＡＣＥ基因Ｉ／Ｄ多态基因型。结果ＤＮ组（ｎ＝３６）和无ＤＮ组（ｎ＝４９）相比,Ｄ型等位基因和ＤＤ基因型糖频率升高（分别为５９．７％ｖｓ３８．８％,Ｘ＾２＝７．３０,３３．３％ｖｓ１２．２％,Ｘ＾２＝５．５３）,有显著性差异（Ｐ〈０．０５）,病程≤５年合并ＤＮ组（ｎ＝１１）与病程〉５     

胃癌组织中Survivin、PTEN、P53基因的表达及意义

目的　探讨凋亡抑制基因 Survivin和抑癌基因 PTEN、P53在胃癌组织中的表达及其与胃癌发生发展、临床病理特征之间的关系。方法　应用免疫组织化学链霉亲和素方法 (SABC) ,检测 Survivin、PTEN和 P53基因在 6 5例胃癌、2 6例不典型增生胃黏膜、10例浅表性胃炎和 30例正常胃黏膜组织中的表达。结果　胃癌组织中Survivin、PTEN、突变型 P53基因的阳性表达率分别为 70 %、4 8%、6 5 % ,不典型增生胃黏膜中分别为 4 2 %、85 %、31% ,Survivin和突变型 P53基因在正常胃黏膜和浅表性胃炎组织中不表达 ,PTEN基因在正常胃黏膜和浅表性胃炎组织中全部呈阳性表达。胃癌组织中 PTEN基因的表达与正常胃黏膜组织中的表达差异有显著性 (P<0 .0 5 ) ,胃癌组织、不典型增生胃黏膜以及正常胃黏膜中 Survivin和突变型 P53基因的表达差异均有显著性 (P<0 .0 5 )。随临床分期增加、胃癌分化程度降低、浸润深度加深、淋巴结的转移 ,突变型 P53基因的阳性表达率逐渐上升 (P<0 .0 5 ) ,PTEN基因的阳性表达率逐渐降低 (P<0 .0 5 )。在胃癌组织中 Survivin与突变型 P53基因的表达呈正相关 (P<0 .0 5 ) ,与 PTEN基因的表达呈负相关 (P<0 .0 5 ) ,PTEN基因与突变型 P53基因的表达呈负相关 (P<0 .0 5 )。结论　 Survivin、PTEN和 P53     

Ohno's dilemma: evolution of new genes under continuous selection

New genes with novel functions arise by duplication and divergence, but the process poses a problem. After duplication, an extra gene copy must rise to sufficiently high frequency in the population and remain free of common inactivating lesions long enough to acquire the rare mutations that provide a new selectable function. Maintaining a duplicated gene by selection for the original function would restrict the freedom to diverge. (We refer to this problem as Ohno's dilemma). A model is described by which selection continuously favors both maintenance of the duplicate copy and divergence of that copy from the parent gene. Before duplication, the original gene has a trace side activity (the innovation) in addition to its original function. When an altered ecological niche makes the minor innovation valuable, selection favors increases in its level (the amplification), which is most frequently conferred by increased dosage of the parent gene. Selection for the amplified minor function maintains the extra copies and raises the frequency of the amplification in the population. The same selection favors mutational improvement of any of the extra copies, which are not constrained to maintain their original function (the divergence). The rate of mutations (per genome) that improve the new function is increased by the multiplicity of target copies within a genome. Improvement of some copies relaxes selection on others and allows their loss by mutation (becoming pseudogenes). Ultimately one of the extra copies is able to provide all of the new activity.     

嗜肺军团菌htpA基因的克隆及其原核表达

目的克隆并检测嗜肺军团菌htpA基因在原核系统中表达情况,为进一步研究HtpA蛋白的免疫性能作必要的准备。方法采用聚合酶链反应(PCR)从嗜肺军团菌基因组DNA中扩得军团菌热休克蛋白A基因htpA,并将其定向克隆至原核表达载体pGEX-4T-1,构建原核表达重组质粒pGhtpA,重组子经限制性内切酶分析、聚合酶链式反应及测序鉴定后,转化宿主菌大肠杆菌JM109,IPTG诱导表达,产物进行SDS-PAGE电泳、免疫印迹分析鉴定。结果扩增出了291bp完整的htpA基因,构建了原核表达重组质粒pGhtpA,并检测到约36kDa的GST-htpA融合蛋白质表达条带。结论成功克隆了嗜肺军团菌htpA基因并使HtpA蛋白在原核表达系统中得到了有效的表达,为进一步研究其免疫学特性奠定了基础。     

运动性横纹肌溶解高反应者ACE／CK—MM基因多态性分析

目的探讨中国汉族运动性横纹肌溶解（ERB）高反应者（HR）ACE基因I／D多态性及肌酸肌酶（CK）-MM基因限制性酶切片段多态性的分布特点。方法采用PCR及限制性酶切多态性分析技术,对12例中国汉族ERBHR的ACE、CK-MM基因多态性进行检测、分析。结果本组12例ERBHR的ACE基因频率I为54％、D为46％,D等位基因频率较汉族正常人群高,但无统计学意义（P=0．146）;汉族正常人群与高加索正常人群相比,P〈0．01。本组ERBHR的CK-MM基因频率A为71％、G为29％,G等位基因频率较汉族正常人群高,但无统计学意义（P=0．078）;汉族正常人群与高索ERBHR的该基因频率高度一致（P=0．992）。结论汉族ERBHR人群ACED、CK-MMG等位基因频率均稍高于汉族正常人群。     

福州汉族献血者RHD和RHCE基因的多态性分析

目的：探讨福州市汉族献血者RHD和RHCE基因的多态性。方法：应用PCR-SSP等技术分析206名福州市汉族献血者的RHD和RHCE基因。用Arlequin3.5软件计算RHD、RHCE基因频率,检验Hardy-Weinberg平衡,计算最大可能性RH单倍型频率。结果：206名福州市汉族献血者都携带RhD抗原,都存在所检测的RHD基因第1、3、4、5、6、7、9和10外显子。206名献血者中,RHD、RHd、RHDel、RHCe、RHcE、RHce和RHCE基因频率分别为0.9660、0.0267、0.0073、0.6788、0.1667、0.0857和0.0688;DCe、DcE、Dce、DCE、dCe、dce、DelCe和DelcE单倍型频率分别为0.6580、0.1661、0.0733、0.0685、0.0145、0.0122、0.0065和0.0008。福州市汉族献血者RHD、RHEC各基因座基因频率均符合Hardy-Weinberg平衡定律（P〉0.05）。结论：福州市汉族人群RHD、RHd、RHCe、RHcE、RHce和RHCE等基因和DCe、DcE、Dce、DCE、dCe、dce等单倍型都达到多态水平。在RhD血型阳性中国人中,可能有相当数量的人携带诸如RHd、RHD1227A、RHD207A、RHD710delC等基因。     

Association of low density lipoprotein receptor related protein-associated protein (LRPAP1) gene insertion/deletion polymorphism with gallstone disease

BACKGROUND AND AIM: Gallstones are byproducts of cholesterol supersaturated bile. Various studies have indicated that there might be a genetic predisposition to the disease. Receptor-associated protein (RAP) is a molecular chaperone for low density lipoprotein receptor-related protein (LRP), which plays a key role in cholesterol metabolism. Intron 5 insertion/deletion polymorphism of RAP gene (LRPAP1) has been implicated in other diseases sharing etiology with gallstone disease (GSD). METHODS: To analyze the association of insertion/deletion polymorphism in GSD, 130 gallstone patients and 202 healthy subjects took part in the present study. For genotyping, polymerase chain reaction was followed by 2% agarose gel electrophoresis. RESULTS: The results showed that frequencies of D and I allele were 65.77% and 34.23% in patients, 76.24% and 23.76% in controls, respectively. Frequency of I allele was significantly higher in the patient group than in the control group (P = 0.003). CONCLUSION: In the present study I (insertion) allele was found to be associated with GSD.     

共表达HIV-1的gag-gp120与IL-2的pGPIL-2诱导小鼠产生细胞毒性T细胞的研究

目的 研究HIV-1CN融合基因与IL-2基因共表达基因质粒pGPIL-2诱导产生细胞毒性T细胞（CTL）。方法 脂质体介导共表达中国流行株HIV-1gag-gp120基因与IL-2基因的基因疫苗质粒pGPIL-2转染BHK-21细胞,以间接免疫荧光法鉴定其表达。取pGPIL-2免疫鼠脾细胞,检测pGPIL-2诱导的细胞毒性T细胞杀伤活性。结果 杀伤实验结果证明,经基因免疫获得的 CTL效应细胞,可杀伤 HIV-1CN 融合基因转染的靶细胞。结论 pGPIL-2可有效地诱导 CTL的产生,该研究结果为进一步设计中国流行株HIV-1基因疫苗提供了重要实验依据。     

Fine-scale mergers of chloroplast and mitochondrial genes create functional,transcompartmentally chimeric mitochondrial genes

The mitochondrial genomes of flowering plants possess a promiscuous proclivity for taking up sequences from the chloroplast genome. All characterized chloroplast integrants exist apart from native mitochondrial genes, and only a few, involving chloroplast tRNA genes that have functionally supplanted their mitochondrial counterparts, appear to be of functional consequence. We developed a novel computational approach to search for homologous recombination (gene conversion) in a large number of sequences and applied it to 22 mitochondrial and chloroplast gene pairs, which last shared common ancestry some 2 billion years ago. We found evidence of recurrent conversion of short patches of mitochondrial genes by chloroplast homologs during angiosperm evolution, but no evidence of gene conversion in the opposite direction. All 9 putative conversion events involve the atp1/atpA gene encoding the alpha subunit of ATP synthase, which is unusually well conserved between the 2 organelles and the only shared gene that is widely sequenced across plant mitochondria. Moreover, all conversions were limited to the 2 regions of greatest nucleotide and amino acid conservation of atp1/atpA. These observations probably reflect constraints operating on both the occurrence and fixation of recombination between ancient homologs. These findings indicate that recombination between anciently related sequences is more frequent than previously appreciated and creates functional mitochondrial genes of chimeric origin. These results also have implications for the widespread use of mitochondrial atp1 in phylogeny reconstruction.     

卡介苗ERP基因缺失突变株的构建

目的构建卡介苗ERP基因缺失突变株。方法分别设计两对引物,通过聚合酶链反应（PCR）的方法扩增ERP基因两侧的2个目的片段,分别插入pKO质粒中,构建基因敲除质粒pKO-ERP,电转入至卡介苗菌株细胞内并与BCG基因组中的ERP基因同源交换,筛选出ERP基因敲除菌株。结果通过2次PCR筛选和1次蔗糖反筛选后得到的、并在含潮霉素培养基上不能生长的菌株为ERP基因敲除菌株。结论 pKO质粒可作为基因敲除有用的质粒载体,成功构建了卡介苗ERP基因缺失突变株。     

Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi

A notable characteristic of fungal genomes is that genes involved in successive steps of a metabolic pathway are often physically linked or clustered. To investigate how such clusters of functionally related genes are assembled and maintained, we examined the evolution of gene sequences and order in the galactose utilization (GAL) pathway in whole-genome data from 80 diverse fungi. We found that GAL gene clusters originated independently and by different mechanisms in three unrelated yeast lineages. Specifically, the GAL cluster found in Saccharomyces and Candida yeasts originated through the relocation of native unclustered genes, whereas the GAL cluster of Schizosaccharomyces yeasts was acquired through horizontal gene transfer from a Candida yeast. In contrast, the GAL cluster of Cryptococcus yeasts was assembled independently from the Saccharomyces/Candida and Schizosaccharomyces GAL clusters and coexists in the Cryptococcus genome with unclustered GAL paralogs. These independently evolved GAL clusters represent a striking example of analogy at the genomic level. We also found that species with GAL clusters exhibited significantly higher rates of GAL pathway loss than species with unclustered GAL genes. These results suggest that clustering of metabolic genes might facilitate fungal adaptation to changing environments both through the acquisition and loss of metabolic capacities.     

中国大陆人散发性先天性巨结肠症患者内皮素受体B基因的研究

目的 探讨中国大陆人散发性先天性巨结肠症（sHD）易患基因内皮素受体B（EDNRB）的突变与多态性特征。方法 以92例sHD及其中32例患儿双亲为研究对象，并以60例正常儿为对照。提取受检者外周静脉血DNA，采用聚合酶链反应-单链构象多态性技术（PCR-SSCP）对EDNRB基因外显子-2（exon-2）进行分析，并通过DNA测序检测阳性标本的核苷酸改变方式，与文献报道的其他种族sHD同一基因特征做比较。结果 全部标本EDNRB基因exon-2均未发现突变与多态性位点的存在。结论 中国大陆人sHD患者EDNRB基因的exon-2不存在突变与多态性位点。     

北京地区汉族女性Cbfa1基因多态性与骨密度相关性研究

目的了解北京地区汉族女性核心结合因子α1（core binding factor α1,Cbfa1）基因多态性的分布,并分析其与骨密度的相关性。方法利用异源双链分析技术和直接测序方法,检测北京地区204名无亲缘关系的女性受试者的Cbfa1基因型。受试者中,30—39岁年轻妇女91名（35±3岁）,自然停经1年以上的绝经后妇女113名（63±8岁）。研究对象的骨密度（BMD）采用双能X线骨密度仪（DXA）进行测量。测量部位包括腰椎1-4、股骨颈、Wards三角区及大转子部位。结果（1）北京地区汉族女性Cbfa1基因型分布频率依次为G／G占85．3％,G／A占8．3％,A／A占1．0％,G／11Ala占3．9％,A／11Ala占1．0％,11Ala／11Ala占0．4％。Cbfal等位基因频率为G占94．4％,A占5．6％。（2）校正了年龄、身高、体重和BMI的协方差分析显示,北京地区汉族妇女股骨颈部位和Wards三角区G／A基因型的BMD较G／G基因型高（分别为0．896±0．168比0．823±0．148和0．759±0．236比0．714±0．200g／cm^2;P=0．002,0．036）。独立样本T检验结果显示,股骨颈部位含A等位基因组BMD高于不含A等位基因组（0．901±0．153比0．821±0．148g／cm^2,P=0．023）。资料分为青年妇女组和绝经后妇女组进一步分析,结果提示青年妇女组股骨颈部位和Wards三角区G／A基因型的BMD较G／G基因型高（1．017±0．167比0．924±0．103,0．967±0．172比0．861±0．131g／cm^2;P=0．031,0．046）;而在绝经后妇女组,仅股骨颈部位存在A等位基因的保护作用（0．802±0．097比0．730±0．119g／cm^2,P=0．044）。结论（1）北京地区汉族女性Cbfal基因型,以G等位基因频率为主。（2）北京地区汉族妇女股骨颈部位和Wards三角区骨密度G／A基因型者较G／G基因型者高,A等位基因对BMD具有保护作用,它有利于青年妇女峰值骨量的获得。     

广西汉族妊娠期糖尿病与HLA-DQA1基因相关性研究

目的探讨广西地区汉族妊娠期糖尿病（GDM）与HIA-DQA1等位基因的相关性。方法采用聚合酶链反应-序列特异性引物法检测50例GDM孕妇和50例正常孕妇的HLA．DQAI基因型。结果GDM孕妇与正常孕妇相比较,HLA-DQA1＊0501基因频率明显升高,差异有显著性（P=0．006）。HLA—DQA1＊0101、0104、0201、0601等位基因频率在GDM孕妇中有增高趋势,但差异没有显著性（P均〉0．05）。GDM孕妇中HLA—DQA1＊0102、0103、0301、0302和0401基因频率有降低趋势,差异亦无著性（P均〉0．05）。结论广西地区汉族GDM与HLA—DQA1基因相关,HLA—DQA1％0501基因可能为广西地区汉族GDM的易感基因,未发现与HIA—DQA1相关的GDM保护基因。