杧果LEAFY同源基因的分离及序列分析

分析在植物开花过程中起重要作用的LEAFY(LFY)基因的保守区序列,设计1对长度均为23bp的PCR引物,以杧果基因组DNA为模板,采用PCR方法扩增出长为822bp的DNA片段,克隆入pGEM-T Easy载体。测序和序列分析表明,获得了杧果LFY同源基因(miLFY)3’端的1个片段,该片段有1个415bp的内含子,编码区共编码135个氨基酸,其序列已经在GenBank中登记(登录号AY189684)。在GenBank中进行同源性检索,发现其氨基酸序列与其它植物LFY同源基因的氨基酸序列同源性高达74%~97%,推测它们具有相似的功能。     

应用PCR技术对DMD患者进行缺失检测与产前基因诊断

运用聚合酶链式反应(polymerasechainreaction,PCR)技术对3个Duchenne型肌营养不良症(DMD)家系中的患者进行dystrophin基因内9个外显子缺失检测,在2个家系中检测到外显子45、48、51缺失,同时运用PCR技术扩增位于dystrophin基因内内含子短串联重复序列,对非缺失型DMD家系进行了产前诊断,胎儿为正常女性.dystrophin基因外显子缺失检测方法快速、敏感、准确,可在临床推广中应用;短串联重复序列(STR)多态性分析方法可用于DMD家系的产前基因诊断和携带者检出.     

马铃薯StPSKRs基因的克隆及其亚细胞定位分析

该研究采用同源克隆与PCR扩增方法,从马铃薯品种‘Desiree’中克隆植物磺肽素受体基因StPSKR1和StPSKR2的全长cDNA,并对其进行生物信息学分析及亚细胞定位分析,为深入研究StPSKR1和StPSKR2基因在马铃薯生长发育和生物胁迫中的作用提供理论依据。结果发现:(1)通过同源克隆与PCR扩增获得StPSKR1和StPSKR2的全长cDNA片段,并将其克隆到pGWB5-GFP载体;测序结果显示这2个基因编码的蛋白质与数据库给定的蛋白质序列保持一致,表明成功克隆到StPSKR1和StPSKR2基因。(2)StPSKR1位于马铃薯1号染色体上,cDNA全长3 042 bp,编码1 013个氨基酸,预测蛋白相对分子质量为112.16 kD,理论等电点6.27;StPSKR2位于7号染色体,cDNA全长3 135 bp,编码1 044个氨基酸,相对分子量为114.99 kD,理论等电点6.19。(3)生物信息学分析显示,StPSKR1和StPSKR2都属于跨膜蛋白。(4)亚细胞定位结果显示,StPSKR1和StPSKR2均定位于细胞膜上。     

青鳉p53基因克隆、结构分析及同源重组载体构建

应用“Long PCR”技术 ,用 6对 p5 3引物从青胚胎干细胞基因组DNA中扩增出 6个相互重叠的片段 ,其中最大的片段长达 4 5kb ,这 6个PCR片段覆盖了整个 p5 3基因。序列分析表明青p5 3基因长约 8 7kb ,由 11个外显子和 10个内含子组成。结构比较表明 ,青 p5 3基因在大小上与人和小鼠 p5 3基因存在较大差异。青p5 3基因的内含子 1仅为 0 85kb ,而人和小鼠p5 3基因的内含子 1则分别长达 10kb和 6kb ;青 p5 3基因的外显子 3(86bp)明显大于人和小鼠 p5 3基因的外显子 3(2 2bp) ;外显子 4 (170bp)比人 (2 80bp)和小鼠 (2 6 0bp)的外显子 4小 ;内含子 10 (3 5kb)则比人和小鼠内含子 10 (0 7kb和 0 9kb)大得多。用SVTK neo基因作正选择标记基因 ,用SVTK tk基因作负选择标记基因 ,用青 p5 3基因组片段作同源序列 ,构建了鱼类 p5 3基因同源重组载体。将此载体转染青胚胎干细胞 ,并经G4 18和Ganc药物选择后证明上述正、负选择标记基因在干细胞中能够有效表达 ,并提供对G4 18的抗性和对Ganc的敏感性。     

7-木糖紫杉烷糖基水解酶Lxyl—pl-2基因突变库与高通量筛选体系的构建

对7－木糖紫杉烷糖基水解酶Lxyl－p1－2基因进行定向进化的初步研究，确定易错PCR条件、优化克隆连接方法、建立基于48微孔板高通量筛选模型。利用易错PCR技术对Lxyl－pl－2基因进行随机突变，比较不同浓度M聋’进行易错PCR，每组随机挑取10个克隆进行测序。序列分析表明：在M聋’浓度为7mmol／L条件下，碱基平均突变率为0．12％，即对于Lxyl－p1－2基因（2．4kb）来说，每个基因序列平均有3个碱基突变，达到构建突变文库的频率要求，选择该条件作为易错PCR条件。利用in-fusion技术将Lxyl－p1－2突变基因克隆到pPIC3．5K载体中，获得大量重组突变质粒。该研究优化了in-fusion连接反应中基因片段和载体片段的摩尔比，并探讨了基因片段与载体片段问同源序列长度对in—fusion连接效率的影响。试验结果表明：基因片段与载体片段的摩尔比最佳梯度为5：1；同源序列长度的选择成为影响in—fusion连接效率的关键因素之一。当同源序列长度为100bp时连接效率达到最大值，且显著高于同源序列长度为15～50bp的连接效率，此时阳性重组率提高至90％左右。与常规酶切一连接法相比，in-fusion法具有明显优势，同时将克隆周期由3～4d缩短为1～2d。挑取单菌落，在48微孔培养板上进行培养、诱导表达2d后，取菌液进行酶活测定（底物PNP-Xyl）。以野生型为例，β-木糖苷酶的酶活013405均数μ=3．415，其数据组标准差为δ=±0．078，数值符合正态分布的原理，建立统计学野生型均数分布范围和48微孔板高通量筛选，为后续突变体筛选提供基础。     

牛α—s1酪蛋白基因5’端及上游区的克隆鉴定和部分序列分析

本文以PcR法克隆得到牛α—s1酪蛋白基因5’端800bp片段,并以该片段为探针,筛选了以EMBL3为载体构建的牛基因组文库,得到一个阳性克隆。酶切该克隆,并以牛α—s1酪蛋白基因5’端800bp片段及该基因cDNA为探针杂交,鉴定了该插人片段的方向,亚克隆了各相应酶切片段,制作了较为详细的限制酶图谱,并分析了该基因转录起始点前后部分序列。与该基因现有的资料比较,酶切图谱存在部分位点的差异,序列存在少量突变和缺失,在5’上游区均发现有内含子及外显子部分,且缺失均发生于有重复序列的部位。     

'黄金桃'PpAG基因克隆及其相似片段序列分析

以桃品种黄金桃为材料,通过同源克隆法获得了AGAMOUS基因的同源基因,命名为PpAG.序列分析表明:该基因全长为6 372 bp,含有8个外显子,大小为42~231 bp;7个内含子,大小为88~3 889 bp.Southern杂交结果表明,该基因在桃基因组中为单拷贝.此外,还获得了与PpAG基因5′端序列近似的一段序列,但该序列缺失了PpAG基因表达的关键序列.推测在桃基因组中PpAG基因只存在单拷贝,但可能存在着不能正常表达的基因或基因片段,从而影响雌蕊与雄蕊的形成和发育.     

乙肝病毒突变核心蛋白基因的克隆及序列分析

目的克隆发生长片段缺失的乙肝病毒核心蛋白基因（HBV-C）,并对其进行DNA序列和蛋白质结构分析。方法通过PCR从1株乙型肝炎病毒中扩增得到发生长片段缺失的HBV-C基因,利用TA克隆将PCR产物克隆人pUCm—T载体并进行测序、同源性比较和蛋白质结构分析。结果PCR扩增出的HBV-C基因经序列分析表明长度为454bp,其核苷酸序列缺失了220—317bp之间的98个碱基,造成从74个氨基酸起发生移码突变。结论成功克隆发生长片段缺失的HBV-C基因,为表达及功能研究奠定了基础。     

东北地区抗肌营养不良蛋白基因缺失的研究及应用

为了解东北地区Duchenne／Becker型肌营养不良症患者基因缺失的分布及进行产前基因诊断,用12对引物以多重PCR法检测120例DMD／BMD患者,并分析缺失型患者dystrophin基因的断裂点分布及各引物优化组合,并将高危男性胎儿行缺失检测。结果表明,缺失检出率为49．2％,66．4％的断裂点位于内含子44～52内,以内含子50为最多(14．8％),4对外显子引物的优化组合为外显子48、51、45和8,总检出率为41．7％;29例高危胎儿中9例男性胎儿为缺失型,缺失位点与先证者相同。通过首次对我国东北地区DMD／BMD患者筛查缺失发现dystrophin基因缺失主要分布于两个热区内,与国内其他地区比较外显子8附近区域可能是该地区缺失断裂的高发区;内含子44～52高度不稳定,其中内含子44的稳定性要高于中央缺失热区的稳定性,内含子50的不稳定性存在地区及种族差异;引物优化组合为检测患者及产前基因诊断提供了捷径,尤其是对散发家系是可行的并且有其优越性。     

小鼠锌指蛋白基因ZF-12的克隆与基因结构以及5′端启动子活性的分析

人类锌指蛋白ZNF191为类krueppel转录因子,其可能与神经精神病、心血管疾病和肝癌等疾病的发生或发展有关,为了采用基因敲除模型来探讨它的生理功能,克隆和定位其在模式生物（小鼠）中的同源基因,并阐明其结构特征是必需的。通过筛选小鼠λ噬菌体基因组文库,获得了它在小鼠中的同源基因ZF－12基因组全长片段。序列分析表明：该基因含有4个外显子和3个内含子,内含子都遵循GT／AG的剪接模式;第91密码子处存在单核苷酸多态性;可能存在2种大小不同的3′端的非翻译区（3′－UTR）;与锌指蛋白基因Zfp-35相连锁,可将其定位于18号染色体的B3－C带上或附近;5′端上游存在1个约250bp高度富含GC的启动子序列。ZF－12基因的5′端系列缺失荧光素酶基因报告载体的瞬时转染实验表明:其上游序列（-762～ 70bp）具有启动子转录活性,在更上游的序列（－824～-762bp)上可能存在负调控元件。这项研究结果为进一步的基因敲除研究奠定了基础。     

Organization of the sex-linked late-feathering haplotype in chickens

Nucleotide sequence analysis of polymerase chain reaction products confirmed that ev 21 integrated into one of two large homologous elements on the Z chromosome of late-feathering (LF) White Leghorn chickens. Southern blots of Not I-, Nae I-, Ksp I- and Bam HI-digested DNA from early-feathering (EF) and LF White Leghorns, that had been hybridized with a probe that flanks ev 21, indicated a 180 kb duplication of an unoccupied repeat in the LF genotype of White Leghorns. A Ksp I fragment that carries ev 21 was about 32 kb smaller than the Ksp I fragment found in EF DNA. In the evolution of LF, retroviral insertion into one of two large repeats and a 32 kb deletion may have generated LF.     

Breakpoint Junction of Interstitial Homozygous Deletion at Chromosome 2q33 in a Small Cell Lung Carcinoma

We have characterized the breakpoint junction of the homozygousdeletion at chromosome 2q33 in a small cell lung carcinoma cellline. Cloning and sequencing of the genomic regions surroundingthe breakpoint junction of the deletion revealed that the homozygousdeletion was caused by a simple interstitial deletion of a 220-kbsegment. An AT-dinucleotide of contributing germline sequenceswas overlapped at the junction. Since there were one or twonucleotide overlaps of germline sequences at breakpoint junctionsin all four cases of interstitial deletions analyzed to date,this may reflect a common mechanism underlying the occurrenceof chromosomal interstitial deletion.     

Molecular cytogenetic characterization of two independent karyotypic anomalies in a patient with severe mental retardation and juvenile idiopathic arthritis

We report on a patient with severe mental retardation, dysmorphic features as well as juvenile idiopathic arthritis. G-banding indicated two independent karyotypic anomalies in this patient: an interstitial deletion del(X)(p21p22.3) and a rearrangement involving chromosomes 1 and 7, which represents a direct insertion, ins(7;1)(q36;p13.2p31.2). Non-random inactivation of the paternally derived del(X) chromosome was observed in blood lymphocytes and fibroblasts. High resolution analysis of the rearrangement involving chromosomes 1 and 7 subsequently revealed the additional submicroscopic deletion of at least 5 Mb at the 1p13.2 breakpoint. The deletion occurred on the paternal chromosome and encompasses the PTPN22 gene, already known to be associated with juvenile idiopathic arthritis. Our findings underline the importance of closely investigating the breakpoint regions of apparently balanced rearrangements in patients with abnormal phenotypes since complex chromosomal rearrangements (CCRs) may turn out to be unbalanced. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A new approach to assessing the validity of indels in algorithmic pair alignments

Analysis of the structure of indels in algorithmic versus evolutionary alignments based on a set of inequalities confirms the conclusions from numerical modeling. For the more divergent sequences (PAM > 60), the tested aligning algorithm (SW) tends to increase the mean length of indels and decrease their number.     

毕赤酵母重组菌株直接基因缺失方法的研究

毕赤酵母重组菌在表达外源蛋白时往往存在比较严重的蛋白降解现象,一种可供选择的解决办法就是将其中起作用的某种蛋白酶基因缺失,但目前国内外研究主要集中于非重组毕赤酵母的基因缺失,直接对重组菌进行基因缺失的研究较少。以现有的毕赤酵母基因重组菌(GS115Hir)为宿主菌,分别采用有标记的插入替换方法和无标记的Pop-In/Pop-Out方法直接缺失其PRC1蛋白酶基因和KEX1蛋白酶基因。缺失菌株经测序分析,结果显示发生了理论的基因缺失。在此基础上本文比较了这两种方法的各自优缺点,探讨了它们的不同的用途,为直接在毕赤酵母重组菌中进行基因缺失提供了有益的参考。     

Latour system精简酿酒酵母染色体方法的建立及应用

酿酒酵母是第一个完成全基因组测序的真核生物,具有广泛的科研应用价值。利用酿酒酵母的全基因组序列可以进行精确的基因定位及敲除,从而达到对其基因组进行精简的目的,为合成生物学最小基因组的研究工作打下基础。根据Latour system 设计敲除所需引物,构建敲除盒,筛选重组体和缺失体,成功敲除酿酒酵母a型单倍体染色体XIII中339301-352281 nt包含的8个基因,为酿酒酵母染色体精简奠定基础,同时证明了Latour system 可以应用于酿酒酵母大片段敲除。     

Use of NotI microarrays in analysis of epigenetic and structural changes in epithelial tumor genomes by the example of human chromosome 3

A new comparative genome hybridization technology using NotI microarrays is described (Karolinska Institute International Patent WO02/086163). The method is based on comparative genome hybridization of NotI-enriched probes from tumor and normal genomic DNA with radically new NotI microarrays. A total of 181 NotI-binding loci of human chromosome 3 were assayed in 200 human malignant tissue samples from various organs: kidney, lung, breast, ovary, cervix, and prostate. The most significant portion (above 30%) of aberrations (deletions and methylation) were detected in NotI sites located in the MINT24, BHLHB2, RPL15, RARbeta1, ITGA9, RBSP3, VHL, and ZIC4 genes. This indicates that they may be associated with cancer development. Methylation of these genomic loci was confirmed by methylation-specific PCR and bisulfite sequencing. The results confirm that the proposed method can contribute to cancer genomics.     

Effects of N-Terminal Deletion Mutation on Rabbit Muscle Lactate Dehydrogenase

Deletion mutants of rabbit muscle lactate dehydrogenase (LDH) were constructed using polymerase chain reaction (PCR) to study the roles of N-terminal residues. The coding sequences of the first 5 (LD5) and 10 (LD10) amino acids of the N-terminus were deleted and the gene was inserted into the prokaryotic expression vector pET21b. The mutant enzymes were expressed in E. coli BL21/DE3 and were purified. Then their characteristics and stabilities were studied. The results showed LDH was completely inactivated when the first 10 N-terminal amino acid residues were removed, but the mutant (LD10) could have partially restored activity in the presence of structure-making ions. The removal of the first 5 and 10 N-terminal amino acid residues did not affect the aggregation state of the enzyme, that is, LD5 and LD10 were still tetramers. The stabilities of recombinant wild-type LDH (RW-LD), LD5, and LD10 were compared by incubating them at low pH, elevated temperature, and high GuHCl. The results showed that the N-terminal deletion mutants were more sensitive to denaturing environments; they were easily inactivated and unfolded. Their instability increased and their ability to refold decreased with the increased number of amino acid residues removed from the N-terminus of LDH. These results confirm that the N-terminus of LDH plays a crucial role in stabilizing the structure and in maintaining the function of the enzyme.     

Gene deletion, a mechanism of induced mutation by arabinosyl nucleosides

9-β- -Arabinofuranosyl-2-fluoroadenine (F-ara-A) and 9-β- -arabinofuranosyladenine (ara-A) are purine nucleoside analogues which are incorporated into nucleic acids. This study demonstrates the mutagenic properties of F-ara-A and ara-A and provides evidence for mechanisms by which the arabinosyl nucleosides induce mutation. At the drug dosages that evoked exponential cell killing, F-ara-A and ara-A caused a significant increase in the number of 6-thioguanine-resistant mutants in Chinese hamster ovary cells. Southern analyses showed that 15 of 16 drug-induced mutants had lost all or part of the HPRT gene, whereas no loss of the gene was found in 4 spontaneous mutants. We conclude that both F-ara-A and ara-A induced mutation predominantly by causing deletion of genetic method. The remarkable frequency of gene deletion among these drug-induced mutations is discussed with respect to possible mechanisms of action of arabinosyl nucleosides in mutational studies.