藏羚羊基因组微卫星分析与初步验证

为明确藏羚羊Pantholops hodgsoni核DNA中微卫星分布情况和特征,利用MISA工具对藏羚羊基因组进行微卫星扫描。在全长2 696.89 Mb的藏羚羊基因组中,搜索到723 135个微卫星座位,其中完全型微卫星有675 809个。6种重复类型中,单核苷酸重复最多,有471 142个,占69.72%;其次是二核苷酸、三核苷酸,分别为88 832个和86 658个,占13.14%和12.82%;六核苷酸最少,仅215个,约占0.03%。以藏羚羊基因组DNA为模板对微卫星座位进行验证,在100个微卫星座位中筛选到8个具有多态性的微卫星座位,多态比例约为8%。本研究将为研究藏羚羊微卫星标记、群体遗传多样性、藏羚羊保护生物学提供基础。     

Purification and Characterization of A Human-Specific Esterase From Urine

Abstract

A human-specific esterase was isolated from urine and partially characterized by ammonium sulfate precipitation, starch block electrophoresis, and gel filtration. Its molecular weight was estimated to be 136,000 by polyacrylamide gel electrophoresis in 0.17. SDS. A diffusion coefficient of 8.6 X 10^?7 was determined by the L-plate method. Immunologic identity was shown between the urinary esterase and a human tissue esterase.     

Identification and Characterization of Polymorphisms in piRNA Regions

piRNAs are a class of noncoding RNAs that perform functions in epigenetic regulation and silencing of transposable elements, a mechanism conserved among most mammals. At present, there are more than 30,000 known piRNAs in humans, of which more than 80% are derived from intergenic regions, and approximately 20% are derived from the introns and exons of pre-mRNAs. It was observed that the expression of the piRNA profile is specific in several organs, suggesting that they play functional roles in different tissues. In addition, some studies suggest that changes in regions that encode piRNAs may have an impact on their function. To evaluate the conservation of these regions and explore the existence of a seed region, SNP and INDEL variant rates were investigated in several genomic regions and compared to piRNA region variant rates. Thus, data analysis, data collection, cleaning, treatment, and exploration were implemented using the R programming language with the help of the RStudio platform. We found that piRNA regions are highly conserved after considering INDELs and do not seem to present an identifiable seed region after considering SNPs and INDEL variants. These findings may contribute to future studies attempting to determine how polymorphisms in piRNA regions can impact diseases.     

A Genome-wide Functional Characterization of Arabidopsis Regulatory Calcium Sensors in Pollen Tubes

Calcium, an ubiquitous second messenger, plays an essential and versatile role in cellular signaling. The diverse function of calcium signals is achieved by an excess of calcium sensors. Plants possess large numbers of calcium sensors, most of which have not been functionally characterized. To identify physiologically relevant calcium sensors in a specific cell type, we conducted a genome-wide functional survey in pollen tubes, for which spatiotemporal calcium signals are well-characterized and required for polarized tip growth. Pollen-specific members of calmodulin (CaM), CaM-like (CML), calcium-dependent protein kinase (CDPK) and calcineurin B-like protein (CBL) families were tagged with green fluorescence protein (GFP) and their localization patterns and overexpression phenotypes were characterized in tobacco pollen tubes. We found that several fusion proteins showed distinct overexpression phenotypes and subcellular localization patterns. CDPK24-GFP was localized to the vegetative nucleus and the generative cell/sperms. CDPK32-GFP caused severe growth depolarization. CBL2-GFP and CBL3-GFP exhibited dynamic patterns of subcellular localization, including several endomembrane compartments, the apical plasma membrane (PM), and cytoskeleton-like structures in pollen tubes. Their overexpression also inhibited pollen tube elongation and induced growth depolarization. These putative calcium sensors are excellent candidates for the calcium sensors responsible for the regulation of calcium homeostasis and calcium-dependent tip growth and growth oscillation in pollen tubes.     

毛果杨 NLP 基因家族生物信息学分析与鉴定简

NLP基因家族是一类特殊的转录因子,豆科植物根瘤的形成依赖于该基因家族的存在,在非豆科植物中具有调节植物硝酸盐吸收以及同化的功能。通过对毛果杨（Populus trichocarpa）基因组的生物信息学分析,共鉴定出14个毛果杨NLP基因家族成员,这些成员具有低亲水性的特点,基因结构保守,都含有RWP-RK以及PB1两个保守结构域。通过细胞定位预测,所有成员都定位在细胞核中。直系同源与旁系同源进化分析显示,NLP基因家族成员在漫长的进化过程中经历了严格的选择。染色体定位分析表明,毛果杨NLP基因家族成员坐落在毛果杨9条染色体之上,成员数量的扩增来自于杨柳科染色体自身的扩增事件。芯片数据分析结果显示,NLP基因家族成员在嫩叶,根和雄花中表达,部分基因在木质部以及种子萌发过程之中表达,但所有成员均不在成熟叶片中表达。     

Cloning and Comparative Characterization of the rIGS Regulatory Regions in Human and Pygmy Chimpanzee Pan paniscus

Investigation of randomly cloned genomic and chromosome-specific sequences of ribosomal DNA (rDNA) from different organisms show that different regions of this long repeat unit evolve at different rates. This proves to be true not only with regard to evolutionary variability of transcribed and nontranscribed intergenic (spacer) regions of rDNA. The intergenic spacer (rIGS) of human ribosomal DNA contains both highly variable and more conservative regions with putative regulatory functions. In the present study a comparative analysis of some segments of the rIGS pre-promoter (regulatory) region in human and pygmy chimpanzee (Pan paniscus) was carried out. For these purposes, the corresponding DNA fragments were amplified in PCR with oligonucleotide primers specific to human rIGS and sequenced. Our results show that at the background of substantial structural similarity of these regions in man and chimpanzee, i.e., the presence of highly homologous sequences and similar repetitive units, there are substantial differences between them. These differences are associated with point mutations, insertions, deletions, and complex structural rearrangements.     

Genome-wide Identification and Characterization of a Dehydrin Gene Family in Poplar (Populus trichocarpa)

Dehydrins (DHNs) define a complex group of stress inducible proteins characterized by the presence of one or more lysine-rich motifs. DHNs are present in multiple copies in the genome of plant species. Although genome-wide analysis of DHNs composition and chromosomal distribution has been conducted in herbaceous species, it remains unexplored in woody plants. Here, we report on the identification of ten genes encoding eleven putative DHN polypeptides in Populus. We document that DHN genes occur as duplicated blocks distributed over seven of the 19 poplar chromosomes likely as a result of segmental and tandem duplication events. Based on conserved motifs, poplar DHNs were assigned to four subgroups with the K_n subgroup being the most frequent. One putative DHN polypeptide (PtrDHN-10) with a SKS arrangement could originate from a recombination between SK_n and K_nS genes. In silico analysis of microarray data showed that in unstressed poplar, DHN genes are expressed in all vegetative tissues except for mature leaves. This exhaustive survey of DHN genes in poplar provides important information that will assist future studies on their functional role in poplar.     

Phylogeny of Regulatory Regions of Vertebrate Tyrosinase Genes

Highly homologous DNA elements were found to be shared by the upstream regions of the mouse tyrosinase and tyrosinase related protein (TRP-1) genes. Several nuclear proteins were shown to bind to both of these upstream regions. Shared homologous DNA elements were also found in the 5’ flanking sequences of Japanese quail and snapping turtle tyrosinase genes. Shared homologous nucleotide sequences were found to be scattered like an archipelago in the 5’ upstream regions of mouse and human tyrosinase genes. Comparisons between Japanese quail and snapping turtle tyrosinase genes gave similar results. On the contrary, mammalian (mouse and human) and nonmammalian (quail and snapping turtle) tyrosinase genes did not show significant homology in their 5’ upstream regions. In contrast, coding sequences in the first exons of vertebrate tyrosinase genes and their deduced amino acid sequences were found to be highly conserved except for their putative leader sequence-coding regions.     

血管生成素基因组结合序列的筛选与鉴定

血管生成素（angiogenin,ANG）调控细胞增殖、迁移、分化等生物学过程,但其作用的分子机制尚未完全明了. 目前认为,ANG可结合到rDNA区域促进rRNA转录,也可能与mRNA有结合.为全面鉴定细胞内可结合ANG的基因组序列,我们利用染色质免疫共沉淀结合DNA芯片技术（ChIP-chip）对HeLa细胞的基因组DNA进行了筛选,共获得了1 248个结合片段. 我们进一步分析了这些结合片段附近分布的基因,发现有699个可能受ANG结合调控的基因. 基因注释和聚类分析显示,这些可能受ANG调控的基因主要与肿瘤发生发展有关（特别是结直肠癌和前列腺癌）,并且与TGF-β和Wnt信号通路相关. 最后,我们验证了ANG不仅与WNT6、CCNE1、APC2、FZD8和EGFR基因的启动子区域有直接结合,而且调控其表达.以上研究结果为深入研究ANG的功能机制提供了线索.     

Maximum Number of Fixed Points in Regulatory Boolean Networks

Boolean networks (BNs) have been extensively used as mathematical models of genetic regulatory networks. The number of fixed points of a BN is a key feature of its dynamical behavior. Here, we study the maximum number of fixed points in a particular class of BNs called regulatory Boolean networks, where each interaction between the elements of the network is either an activation or an inhibition. We find relationships between the positive and negative cycles of the interaction graph and the number of fixed points of the network. As our main result, we exhibit an upper bound for the number of fixed points in terms of minimum cardinality of a set of vertices meeting all positive cycles of the network, which can be applied in the design of genetic regulatory networks.     

Genome-wide Identification and Molecular Characterization of Ole_e_I, Allerg_1 and Allerg_2 Domain-containing Pollen-Allergen-like Genes in Oryza sativa

Pollen allergens play important roles in plant development inaddition to their allergenic nature for human. More than 10groups of pollen allergens have been reported. Among them, Pollen_Ole_e_I(Ole), Pollen_allerg_1 (Allerg1) and Pollen_allerg_2 (Allerg2)domain-containing proteins are the majority of allergens. Wehave identified 114 pollen-allergen-like genes in rice genomeby bioinformatics using public databases. Among them, 45 genesencode Ole domain-containing proteins, 62 with Allerg1 and 7with Allerg2. They are distributed on 11 of 12 rice chromosomesexcluding chromosome 11. Comparison analysis of coding regionsfrom both predicted genes and isolated full-length cDNAs showedthat most of predicted genes were correct in the splicing ofexons and introns, and only 7 exhibited wrong predictions. Thefact suggested the applicability of the prediction programsto identify pollen-allergen genes. Phylogenetic analysis revealedthe high diversity within OsOle genes and recent evolutionaryevent in OsAllerg1 genes, and suggested that some of OsOle geneswere new members of the family. Expression analysis by RT–PCRshowed that most of the genes were expressed in all tested tissuesand only eight genes exhibited panicle-specific expression,suggesting that pollen-allergen genes play roles in not onlyproductive but also vegetative development.     

Identification and Functional Characterization of Inhibitor-3, a Regulatory Subunit of Protein Phosphatase 1 in Plants

Protein phosphatase 1 (PP1) is a eukaryotic serine/threonine protein phosphatase, and mediates diverse cellular processes in animal systems via the association of a catalytic subunit (PP1c) with multiple regulatory subunits that determine the catalytic activity, the subcellular localization, and the substrate specificity. However, no regulatory subunit of PP1 has been identified in plants so far. In this study, we identified inhibitor-3 (Inh3) as a regulatory subunit of PP1 and characterized a functional role of Inh3 in Vicia faba and Arabidopsis (Arabidopsis thaliana). We found Inh3 as one of the proteins interacting with PP1c using a yeast two-hybrid system. Biochemical analyses demonstrated that Arabidopsis Inh3 (AtInh3) bound to PP1c via the RVxF motif of AtInh3, a consensus PP1c-binding sequence both in vitro and in vivo. AtInh3 inhibited the PP1c phosphatase activity in the nanomolar range in vitro. AtInh3 was localized in both the nucleus and cytoplasm, and it colocalized with Arabidopsis PP1c in these compartments. Disruption mutants of AtINH3 delayed the progression of early embryogenesis, arrested embryo development at the globular stage, and eventually caused embryo lethality. Furthermore, reduction of AtINH3 expression by RNA interference led to a decrease in fertility. Transformation of the lethal mutant of inh3 with wild-type AtINH3 restored the phenotype, whereas that with the AtINH3 gene having a mutation in the RVxF motif did not. These results define Inh3 as a regulatory subunit of PP1 in plants and suggest that Inh3 plays a crucial role in early embryogenesis in Arabidopsis.     

Interactions of Drosophila Ultrabithorax Regulatory Regions with Native and Foreign Promoters

The Ultrabithorax (Ubx) gene of the Drosophila bithorax complex is required to specify parasegments 5 and 6. Two P-element ``enhancer traps' have been recovered within the locus that contain the bacterial lacZ gene under the control of the P-element promoter. The P insertion that is closer to the Ubx promoter expresses lacZ in a pattern similar to that of the normal Ubx gene, but also in parasegment 4 during embryonic development. Two deletions have been recovered that remove the normal Ubx promoter plus several kilobases on either side, but retain the lacZ reporter gene. The lacZ patterns from the deletion derivatives closely match the normal pattern of Ubx expression in late embryos and imaginal discs. The lacZ genes in the deletion derivatives are also negatively regulated by Ubx and activated in trans by Contrabithorax mutations, again like the normal Ubx gene. Thus, the deleted regions, including several kilobases around the Ubx promoter, are not required for long range interactions with Ubx regulatory regions. The deletion derivatives also stimulate transvection, a pairing-dependent interaction with the Ubx promoter on the homologous chromosome.