Identification and bioinformatics analysis of pseudogenes from whole genome sequence of Phaeodactylum tricornutum

Pseudogenes share sequence similarities with functional genes, but in general they have lost their protein-coding ability. The identification of pseudogenes is a very important step in genome annotation. Phaeodactylum tricornutum is a marine diatom that is rich in polyunsaturated fatty acids (PUFAs). The genome of P. tricornutum has been completely sequenced. To identify pseudogenes in P. tricornutum, we developed a pipeline to discover and characterize pseudogenes. We identified a total of 1654 ‘true’ processed pseudogenes, 714 duplicated pseudogenes and 4729 pseudogene fragments. The results of the bioinformatics analysis indicated that the genome sequence of P. tricornutum contained many pseudogenes and pseudogene fragments.     

A mouse alpha-globin-related pseudogene lacking intervening sequences

A mouse alpha-globin-related pseudogene (psi alpha 30.5) completely lacks intervening sequences, and could not code for a functional globin poypeptide because of frameshifts. The widespread occurrence of globin pseudogenes in other species suggests that they are not 'dead' genes but may be important in controlling globin expression.     

Structure and organization of the human Ki-ras proto-oncogene and a related processed pseudogene

Analysis of the organization and nucleotide sequence of two human loci related to the transforming gene of Kirsten murine sarcoma virus establishes one as a functional gene and the other as a processed pseudogene. The two final coding exons of the functional gene seem to have arisen by duplication. Differentially spliced mRNAs incorporating one or other of the duplicated exons probably served as the intermediates by which the viral transforming gene and the pseudogene were generated. This suggests that the functional gene may specify either of two related polypeptides depending on the pattern of RNA splicing.     

Can the product of the theta gene be a real globin?

A new member (theta 1, or psi alpha) of the alpha-globin gene family has recently been identified in a number of species. In higher primates the theta 1 gene has all the structural features apparently necessary for expression, and it appears to have long been under strong selective constraints which suggests that it could still be, or recently have been, a functional gene. No corresponding 'globin' has yet been identified, however. In some other species, galago and rabbit for example, the theta 1 and psi alpha genes have accumulated enough inactivating mutations for them to be considered genuine pseudogenes. Horses also have an alpha-like gene (psi alpha), in a 3' position identical to the other species in relation to the functional alpha genes, and this also appears to have the elements required for a functional gene. The predicted amino-acid sequence, however, suggests that any 'globin' product is likely to be non-viable because it has a number of seriously deleterious amino-acid replacements. Some of these amino-acid changes are shared with the rabbit and primate sequences, indicating that they predate the mammalian radiation, and that if indeed any of these genes are still functional, they are unlikely to be making haemoglobin.     

中国人磷酸核糖焦磷酸合成酶-1假基因的克隆与测序

自从第一个假基因被鉴定以后[1] ,有关假基因的性质与发生正在被阐明 .假基因基本上分为两类 :非加工的假基因和被加工的假基因 .被加工的假基因通常与活跃基因序列比较同源性高达 90 %～ 99% ,不含内含子 ,具有ｐｏｌｙ (Ａ)尾巴 ,可以转录 ,但由于在它们内部有许多终止子、插     

<Emphasis Type="Italic">Cis</Emphasis>-regulatory change and expression divergence between duplicate genes formed by genome duplication of <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

As an index of functional divergence, expression divergence between duplicate gene copies has been observed and correlated with protein coding sequence divergence and bias in gene functional classes. However, the changes in the cis-regulatory region of the duplicate genes which is thought to have important role in expression divergence, has not been explored on the genome-wide scale. We analyzed functional genomics data for a large number of duplicated gene pairs formed by ancient polyploidy events in Arabidopsis thaliana. The divergence in cis-regulatory regions between two copies is positively correlated with the magnitude difference of expression. Moreover, we find that highly expressed duplicate gene pairs have a more diverged cis-regulatory region than weakly expressed gene pairs. We also show that the correlation between expression functional constraint and protein functional constraint is different in old and young duplicate pairs. Our results suggest that cis-regulatory sequence divergence contributes to the expression divergence of duplicate genes formed by genome-wide du-plication. Cis-regulatory region diverges faster in highly expressed duplicate pairs. The diversify selection strengths that act on cis-regulatory region and protein coding region are negatively correlated in young duplicate pairs under expression con-straint.     

斜多项式环的一些性质

研究斜多项式环的一些性质,证明了：（1）如果环 R 是一个α-Armendariz 环,则 J（R[x;α]）∩R 是诣零的;（2）如果环 R 是一个α-Armendariz 环,则环 R 是α-Baer 环当且仅当 R[x;α]是-α-Baer 环;（3）如果环 R 是一个α-Armendariz 环且满足 Cα条件,则环 R 是α-拟 Baer 环（分别地,右α-p．q．-Baer 环、右 zip 环）当且仅当 R[x;α]是-α-拟 Baer 环（分别地,右-α-p．q．-Baer 环、右 zip 环）。     

自旋玻璃和可重入磁体的电子自旋共振

本文介绍了非晶(Fe_pNi_(1-p))_(75)P_(16)B_6Al_3在9 GHz上的电子自旋共振实验结果。结果表明在低温区垂直几何和平行几何的情况一样,其共振线宽随温度的降低成指数增加。     

有理数概率下的效用表示定理

Von Neum ann- Morgenstern的期望效用理论假设对所有的抽奖 (c1 ,p;c2 ,1- p) (以概率 p抽得结果 c1 ,以概率 1- p抽得结果 c2 )的偏好序在所有实数 p(0≤ p≤ 1)均有意义 ;而且期望效用理论基于一组公理 ,从而保证效用函数的存在性和正线性变换意义下的唯一性。然而 ,当概率为无理数时 ,对于抽奖就难以给出直观的解释 ,J.C.Shepherdson首先研究了基于有理数概率度量的效用理论。作者提出一组有理数概率下效用函数存在的公理 ,并证明该公理体系下的效用表示定理。     

High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome

Mutations have pivotal functions in the onset of genetic diseases and are the fundamental substrate for evolution. However, present estimates of the spontaneous mutation rate and spectrum are derived from indirect and biased measurements. For instance, mutation rate estimates for Caenorhabditis elegans are extrapolated from observations on a few genetic loci with visible phenotypes and vary over an order of magnitude. Alternative approaches in mammals, relying on phylogenetic comparisons of pseudogene loci and fourfold degenerate codon positions, suffer from uncertainties in the actual number of generations separating the compared species and the inability to exclude biases associated with natural selection. Here we provide a direct and unbiased estimate of the nuclear mutation rate and its molecular spectrum with a set of C. elegans mutation-accumulation lines that reveal a mutation rate about tenfold higher than previous indirect estimates and an excess of insertions over deletions. Because deletions dominate patterns of C. elegans pseudogene variation, our observations indicate that natural selection might be significant in promoting small genome size, and challenge the prevalent assumption that pseudogene divergence accurately reflects the spontaneous mutation spectrum.     

矩阵极分解计算的一个注记

设$p$是大于$1$的偶数,根据方程$x^{-p}-1=0$的Newton求根公式, 给出计算非奇异矩阵酉极因子的数值方法,并证明了它具有二次收敛特性. 数值例子表明该算法是有效的.     

Annexin II light chain regulates sensory neuron-specific sodium channel expression

The tetrodotoxin-resistant sodium channel Na(V)1.8/SNS is expressed exclusively in sensory neurons and appears to have an important role in pain pathways. Unlike other sodium channels, Na(V)1.8 is poorly expressed in cell lines even in the presence of accessory beta-subunits. Here we identify annexin II light chain (p11) as a regulatory factor that facilitates the expression of Na(V)1.8. p11 binds directly to the amino terminus of Na(V)1.8 and promotes the translocation of Na(V)1.8 to the plasma membrane, producing functional channels. The endogenous Na(V)1.8 current in sensory neurons is inhibited by antisense downregulation of p11 expression. Because direct association with p11 is required for functional expression of Na(V)1.8, disrupting this interaction may be a useful new approach to downregulating Na(V)1.8 and effecting analgesia.