串联重复序列在籼粳亚种间的差异及其与栽培稻遗传分化关系的研究

以中籼稻南京11号(N11)和粳稻巴利拉(Balilla)杂交F1代的DH群体为材料，利用荧光原位杂交技术(FISH)结合程氏指数分类，分析2个串联重复序列Os48、45S rDNA在DH群体中的分布，探讨串联重复序列在栽培稻籼、粳亚种间的差异及其与栽培稻遗传分化的关系。结果表明：串联重复序列45S rDNA在DH群体中的分布具有明显的籼、粳特异性；Os48在DH群体中的分布趋势与程氏指数的分类结果一致，而杂交信号为2对的6个DH株系都表现为粳型，利用减数分裂的粗线期染色体进行分析，这6个株系的Os48所在染色体均为第5、6号。从本研究结果可知，串联重复序列Os48、45S rDNA与栽培稻遗传分化有较密切的关系，可作为研究籼、粳分化的标记。     

Unusual immunoglobulin gene rearrangement leads to replacement of recombinational signal sequences

An unexpected immunoglobulin gene rearrangement, signal sequence replacement, was observed in which the recombinational signal sequences of a VH gene segment are fused intact to the 5' end of a DJH element. Nucleotides are not lost from the signal sequences, but they may be lost from the DJH coding sequence. Signal sequence replacement may result from the alternative resolution of an intermediate in VH-to-DJH recombination. This type of rearrangement provides a means to alter the targeting of immunoglobulin gene segments and suggests a mechanism for the occurrence of VH-JH junctions in vivo. Signal sequence replacement may represent an additional pathway for the generation of antibody diversity.     

芥菜型油菜A9染色体黄籽基因区域BAC重叠群的构建

A9染色体是芸薹属植物A基因组最长的染色体(序列约37 Mb),具有控制种子大小、种皮颜色、硫苷合成、油脂合成等重要性状的基因。利用芥菜型油菜A9染色体黄籽性状共分离标记A9-88和A9-32对已经构建的ZBjH BAC文库进行PCR步移筛选,共筛选出BAC 752个,测序395个,得到BAC末端序列674条,利用BAC末端序列设计引物533对,此外利用白菜已经公布的序列设计SSR引物38对、STS引物15对,构建了芥菜型油菜黄籽基因区域估算长约2.2 Mb的BAC重叠群。     

The t(14;18) chromosome translocations involved in B-cell neoplasms result from mistakes in VDJ joining

In this study, the joining sequences between chromosomes 14 and 18 on the 14q+ chromosomes of a patient with pre-B-cell leukemia and four patients with follicular lymphoma carrying a t(14;18) chromosome translocation were analyzed. In each case, the involved segment of chromosome 18 has recombined with the immunoglobulin heavy-chain joining segment (JH) on chromosome 14. The sites of the recombination on chromosome 14 are located close to the 5' end of the involved JH segment, where the diversity (D) regions are rearranged with the JH segments in the production of active heavy-chain genes. As extraneous nucleotides (N regions) were observed at joining sites and specific signal-like sequences were detected on chromosome 18 in close proximity to the breakpoints, it is concluded that the t(14;18) chromosome translocation is the result of a mistake during the process of VDJ joining at the pre-B-cell stage of differentiation. The putative recombinase joins separated DNA segments on two different chromosomes instead of joining separated segments on the same chromosome, causing a t(14;18) chromosome translocation in the involved B cells.     

Chromosomal Localization of the 5S and 45S rDNA Sites and 5S rDNA Sequence Analysis in Nelumbo Species

The physical location of 45S and 5S rDNA sites by double-target fluorescence in situ hybridization (FISH) and 5S rDNA non-transcribed spacer (NTS) sequences was studied in five accessions of Nelumbo nucifera Gaertn. and one accession of N. nucifera subsp. lutea (Willd.). The chromosome number of all tested materials was 2n=16. The loci ofSS rDNA were close to the centromere regions of chromosome 3, and the loci of 45S rDNA were found on chromosomes 7 and 8 in all the six tested accessions, respectively. Similarly, 45S rDNAs were also located on chromosome 4 in four tested aocessions.The 5S rRNA gene sequences were conserved and the NTS sequences were variable among the samples. N. nucifera subsp. Iutea was the longest branch in the phylogenetic tree and clustered with N. nucifera cv. Liangzihu. N. nucifera cv.Heilongjiang and N. nucifera cv. Weishanhu showed a close relationship with each other. N. nucifera cv. Dahe Lian was closer to N. nucifera cv. Nihelu Lian than to other tested accessions. Analysis of the molecular karyotype and the 5S rRNA gene spacer sequence suggested the genetic diversity was limited within Nelumbo species and it seems suitable that American lotus was considered as the subspecies of N. nucifera.     

Human-proto-oncogene nucleotide sequences corresponding to the transforming region of simian sarcoma virus

The nucleotide sequences of the six regions within the normal human cellular locus (c-sis) that correspond to the entire transforming region of the simian sarcoma virus (SSV) genome (v-sis) were determined. The regions are bounded by acceptor and donor splice sites and, except for region 6, resemble exons. Region 6 lacks a 3' donor splice site and terminates -5 base pairs from the 3' v-sis-helper-viral junction. This is consistent with a model proposing that SSV was generated by recombination between proviral DNA of a simian sarcoma associated virus and proto-sis and that introns were spliced out subsequently from a fused viral-sis messenger RNA. This also suggests that the 3' recombination occurred within an exon of the woolly monkey (Lagothrix) genome. The open reading frames predicting the v-sis and c-sis gene products coincide with the stop codon of c-sis located 123 nucleotides into the fifth region of homology. The overall nucleotide homology was 91 percent with substitutions mainly in the third codon positions within the open reading frame and with greatest divergence within the untranslated 3' portion of the sequences. The predicted protein products for v-sis and c-sis are 93 percent homologous. The predicted c-sis gene product is identical in 31 of 31 amino acids to one of the published sequences of platelet-derived growth factor. Thus, c-sis encodes one chain of human platelet-derived growth factor.     

The evolution of resistance gene in plants

Resistance genes enable plants to fight against plant pathogens. Plant resistance genes (R gene) are organized complexly in genome. Some resistance gene sequence data enable an insight into R gene structure and gene evolution. Some sites like Leucine-Rich Repeat (LRR) are of specific interest since homologous recombination can happen. Crossing over, transposon insertion and excision and mutation can produce new specificity. Three models explaining R gene evolution were discussed. More information needed for dissection of R gene evolution though some step can be inferred from genetic and sequence analysis.     

Molecular analysis of the hotspot of recombination in the murine major histocompatibility complex

Biological and serological assays have been used to define four subregions for the I region of the major histocompatibility complex (MHC) in the order I-A, I-B, I-J, and I-E. The I-J subregion presumably encodes the I-J polypeptide of the elusive T-cell suppressor factors. Restriction enzyme site polymorphisms and DNA sequence analyses of the I region from four recombinant mouse strains were used to localize the putative I-B and I-J subregions to a 1.0-kilobase (kb) region within the E beta gene. Sequencing this region from E beta clones derived from the two mouse strains: B10.A(3R), I-Jb and B10.A(5R), I-Jk initially used to define the I-J subregion revealed that these regions are identical, hence the distinct I-Jb and I-Jk molecules cannot be encoded by this DNA. In addition, the DNA sequence data also refute the earlier mapping of the I-B subregion. Analysis of the DNA sequences of three parental and four I region recombinants reveals that the recombinant events in three of the recombinant strains occurred within a 1-kb region of DNA, supporting the proposition that a hotspot for recombination exists in the I region. The only striking feature of this hotspot is a tetramer repeat (AGGC)n that shows 80 percent homology to the minisatellite sequence which may facilitate recombination in human chromosomes.     

Nucleotide sequences of the human and mouse atrial natriuretic factor genes

Mouse and human atrial natriuretic factor (ANF) genes have been cloned and their nucleotide sequences determined. Each ANF gene consists of three coding blocks separated by two intervening sequences. The 5' flanking sequences and those encoding proANF are highly conserved between the two species, while the intervening sequences and 3' untranslated regions are not. The conserved sequences 5' of the gene may play an important role in the regulation of ANF gene expression.     

Polymerase chain reaction with single-sided specificity: analysis of T cell receptor delta chain

In the polymerase chain reaction (PCR), two specific oligonucleotide primers are used to amplify the sequences between them. However, this technique is not suitable for amplifying genes that encode molecules where the 5' portion of the sequences of interest is not known, such as the T cell receptor (TCR) or immunoglobulins. Because of this limitation, a novel technique, anchored polymerase chain reaction (A-PCR), was devised that requires sequence specificity only on the 3' end of the target fragment. It was used to analyze TCR delta chain mRNA's from human peripheral blood gamma delta T cells. Most of these cells had a V delta gene segment not previously described (V delta 3), and the delta chain junctional sequences formed a discrete subpopulation compared with those previously reported.     

濒危红树植物莲叶桐叶绿体基因组及其系统进化

对濒危红树植物莲叶桐的叶绿体基因组及与其近缘物种之间的叶绿体基因组进行比较进化分析。结果表明,莲叶桐叶绿体基因组序列全长157 762 bp,包括1个大的单拷贝区(LSC)86 641 bp,1个小的单拷贝区(SSC)18 603 bp和2个反转重复区(IRs)26 260 bp。叶绿体基因组的GC含量为39.3%,含有133个基因,包括83个蛋白质编码基因、42个tRNA基因和8个rRNA基因。17个基因位于反转重复区,包括6个蛋白编码基因、7个tRNA和4个rRNA。登录号为:MG838431。通过最大似然法对16个双子叶植物（包含5个樟科植物、2个腊梅科植物、3个毛茛科植物、1个小檗科植物、1个报春花科植物、1个蔷薇科植物、1个桑科植物,1个安息香科植物以及莲叶桐）和1个外类群植物水稻的叶绿体基因组序列进行聚类分析,莲叶桐与樟科和腊梅科植物聚为一支。聚类结果将莲叶桐科划入樟目,更支持《中国高等植物图鉴》中分类方式。随后对莲叶桐及其近缘种叶绿体基因组进行了共线性分析,进一步验证了其叶绿体基因组之间具有高度保守性。研究结果为莲叶桐的系统进化提供了新的证据。     

新干特早柚GPAT基因5'端克隆及序列分析

采用5'-RACE技术从新干特早柚(Citrus grandis cv. Xingantezaoyou)叶片中克隆出一条长832 bp的GPAT基因5'端cDNA片段(GenBank 登录号:DQ193970).序列分析结果表明:该cDNA片段序列与其它科属植物的GPAT基因序列的同源性差异较大,除与同类植物--温州蜜柑(Citrus unshiu)的同源性高达98.9%,与红花(Carthamus tinctorius)、拟南芥(Arabidopsis thaliana)、非洲油棕榈(Elaeis guineensis)、豌豆(Pisum sativum)、蚕豆(Vicia faba)的同源性分别为62.5%、54.6%、48.2%、47.4%、46.9%;其所编码的氨基酸序列与红花、拟南芥、非洲油棕榈、豌豆、辣椒的同源性分别为51.6%、60%、45.1%、48%、52.3%,与细菌(Bacillus amyloliquefaciens)的同源性仅为18.9%,说明GPAT基因的氨基酸序列具有种属特异性.     

Derivation of clones close to met by preparative field inversion gel electrophoresis

The molecular analysis of genes identified by mutations is a major problem in mammalian genetics. As a step toward this goal, preparative field inversion gel electrophoresis (FIGE) was used to selectively isolate clones from the environment of genetically linked markers, and to select a subset of these clones containing sequences next to specific restriction sites rare in mammalian DNA. This approach has been used to generate a library highly enriched in sequences closely linked to the cystic fibrosis marker met. One clone derived from the end of a Not I restriction fragment containing the met sequence was analyzed in detail and localized within a long range map to a position 300 kilobase pairs 5' of the metD sequence.     

Identification and Bioinformatics Analysis of SnRK2 and CIPK Family Genes in Sorghum

Through bioinformatic data mining, 10 SnRK2 and 31 CIPK genes were identified from sorghum genome. They are unevenly distributed in the sorghum chromosomes. Most SnRK2 genes have 8 introns, while the CIPK genes have a few （no intron or less than 3 introns） or more than I0 introns. Phylogenetic analysis revealed that SnRK2 genes belong to one cluster and CIPK genes form the other independent cluster. The sorghum SnRK2s are subgrouped into three parts, and CIPK into five parts. More than half SnRK2 and CIPK genes present in homologous pairs, suggesting gene duplication may be due to the amplification of SnRK family genes. The kinase domains of SnRK2 family are highly conserved with 88.40% identity, but those of the CIPK family are less conserved with 63.72% identity. And the identity of sorghum CBLinteracting NAF domains of CIPKs is 61.66%. What＇s more, regarding to the sorghum SnRK2 and CIPK kinases, they are characterized with distinct motifs and their subcellular localization is not necessarily the same, which suggests they may be divergent in functions. Due to less conserved sequences, complex subcellular localization, and more family members, sorghum CIPK genes may play more flexible and multiple biological functions. According to the phylogenetic analysis of SnRK genes and SnRK functional studies in other plants, it is speculated that sorghum SnRK2 and CIPK genes may play important roles in stress response, growth and development.     

黄瓜AQP基因家族的鉴定与生物信息学分析

  目的  深入研究黄瓜Cucumis sativus水通道蛋白(aquaporin, AQP)基因家族(CsAQP)的相关功能。  方法  通过全基因组分析技术鉴定其家族成员,对其蛋白质理化性质、系统进化关系、选择压力、基因结构、保守基序、顺式作用元件、蛋白质互作进行分析。  结果  黄瓜基因组共有33个AQP基因,含有2~5个数量不等的外显子,在染色体上不均匀分布;根据物种进化关系将黄瓜AQP基因家族划分为5个亚家族;基因组重复序列分析表明:5号和6号染色体上各有2~3对基因串联重复;计算这些基因的同义替换(synonymous, K_s)和非同义替换(nonSynonymous, K_a)的比率,结果显示均小于1,表明其进化受纯化选择作用;顺式作用调控元件分析发现,大部分基因启动子区所含元件与激素调节、光响应、胁迫密切相关。  结论  通过黄瓜全基因组扫描,获得黄瓜基因组的33个AQP家族成员,分属于5个亚族,映射于7条染色体上。上游启动子区含逆境相关作用元件,且部分基因参与串联复制,历经纯化选择。图6表4参26