Synapse Elimination Triggered by BMP4 Exocytosis and Presynaptic BMP Receptor Activation

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Evolution of Antennapedia-Class Homeobox Genes

Antennapedia (Antp)-class homeobox genes are involved in the determination of pattern formation along the anterior-posterior axis of the animal embryo. A phylogenetic analysis of Antp-class homeodomains of the nematode, Drosophila, amphioxus, mouse, and human indicates that the 13 cognate group genes of this gene family can be divided into two major groups, i.e., groups I and II. Group I genes can further be divided into subgroups A (cognate groups 1-2), B (cognate group 3), and C (cognate groups 4-8), and group II genes can be divided into subgroups D (cognate groups 9-10) and E (cognate groups 11-13), though this classification is somewhat ambiguous. Evolutionary distances among different amino acid sequences suggest that the divergence between group I and group II genes occurred ~1000 million years (MY) ago, and the five different subgroups were formed by ~600 MY ago, probably before the divergence of Pseudocoelomates (e.g., nematodes) and Coelomates (e.g., insects and chordates). Our results show that the genes that are phylogenetically close are also closely located in the chromosome, suggesting that the colinearity between the gene expression and gene arrangement was generated by successive tandem gene duplications and that the gene arrangement has been maintained by some sort of selection.     

Interior-branch and bootstrap tests of phylogenetic trees

We have compared statistical properties of the interior-branch and bootstrap tests of phylogenetic trees when the neighbor-joining tree- building method is used. For each interior branch of a predetermined topology, the interior-branch and bootstrap tests provide the confidence values, PC and PB, respectively, that indicate the extent of statistical support of the sequence cluster generated by the branch. In phylogenetic analysis these two values are often interpreted in the same way, and if PC and PB are high (say, > or = 0.95), the sequence cluster is regarded as reliable. We have shown that PC is in fact the complement of the P-value used in the standard statistical test, but PB is not. Actually, the bootstrap test usually underestimates the extent of statistical support of species clusters. The relationship between the confidence values obtained by the two tests varies with both the topology and expected branch lengths of the true (model) tree. The most conspicuous difference between PC and PB is observed when the true tree is starlike, and there is a tendency for the difference to increase as the number of sequences in the tree increases. The reason for this is that the bootstrap test tends to become progressively more conservative as the number of sequences in the tree increases. Unlike the bootstrap, the interior-branch test has the same statistical properties irrespective of the number of sequences used when a predetermined tree is considered. Therefore, the interior-branch test appears to be preferable to the bootstrap test as long as unbiased estimators of evolutionary distances are used. However, when the interior-branch is applied to a tree estimated from a given data set, PC may give an overestimate of statistical confidence. For this case, we developed a method for computing a modified version (P'C) of the PC value and showed that this P'C tends to give a conservative estimate of statistical confidence, though it is not as conservative as PB. In this paper we have introduced a model in which evolutionary distances between sequences follow a multivariate normal distribution. This model allowed us to study the relationships between the two tests analytically.      

Roles of Ca2+ in hyphal and yeast-form growth inCandida albicans. Growth regulation by altered extracellular and intracellular free Ca2+ concentrations

The dimorphic fungusCandida albicans has both a yeast form and a hyphal form. When yeast-form cells were starved and then transferred to aN-acetylglucosamine medium, the formation of true hyphae from the unbudded yeast-form cells was induced. Removal of Ca²⁺ from the medium with EGTA inhibited hyphal formation by 50%, resulting in only thin and short hyphae. Externally applied excess Ca²⁺ (>10⁻²M) also affected the hyphal formation, resulting in formation of pseudohyphae. This effect required a high concentration of Ca²⁺ but was Ca²⁺-specific. Deprivation of Ca²⁺ also inhibited yeast-form growth. Interestingly, such cells had abnormally wide bud necks and became defective in cell separation. To measure cytosolic free Ca²⁺, fura-2 was introduced into hyphal cells by electroporation. Its normal value was estimated to be about 100 nM. The electroporation caused transient elevation of cytosolic free Ca²⁺ concentration and transient cessation of hyphal growth. There was a close correlation between the timing of recovery of Ca²⁺ concentration and that of the resumption of hyphal growth. Our results demonstrate the importance of extracellular and intracellular free Ca²⁺ for the growth ofC. albicans.     

Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny

The relative efficiencies of different protein-coding genes of the mitochondrial genome and different tree-building methods in recovering a known vertebrate phylogeny (two whale species, cow, rat, mouse, opossum, chicken, frog, and three bony fish species) was evaluated. The tree-building methods examined were the neighbor joining (NJ), minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML), and both nucleotide sequences and deduced amino acid sequences were analyzed. Generally speaking, amino acid sequences were better than nucleotide sequences in obtaining the true tree (topology) or trees close to the true tree. However, when only first and second codon positions data were used, nucleotide sequences produced reasonably good trees. Among the 13 genes examined, Nd5 produced the true tree in all tree-building methods or algorithms for both amino acid and nucleotide sequence data. Genes Cytb and Nd4 also produced the correct tree in most tree-building algorithms when amino acid sequence data were used. By contrast, Co2, Nd1, and Nd41 showed a poor performance. In general, large genes produced better results, and when the entire set of genes was used, all tree-building methods generated the true tree. In each tree-building method, several distance measures or algorithms were used, but all these distance measures or algorithms produced essentially the same results. The ME method, in which many different topologies are examined, was no better than the NJ method, which generates a single final tree. Similarly, an ML method, in which many topologies are examined, was no better than the ML star decomposition algorithm that generates a single final tree. In ML the best substitution model chosen by using the Akaike information criterion produced no better results than simpler substitution models. These results question the utility of the currently used optimization principles in phylogenetic construction. Relatively simple methods such as the NJ and ML star decomposition algorithms seem to produce as good results as those obtained by more sophisticated methods. The efficiencies of the NJ, ME, MP, and ML methods in obtaining the correct tree were nearly the same when amino acid sequence data were used. The most important factor in constructing reliable phylogenetic trees seems to be the number of amino acids or nucleotides used.      

Relative contributions of germline gene variation and somatic mutation to immunoglobulin diversity in the mouse

The relative contributions of germline gene variation and somatic mutation to immunoglobulin diversity were studied by comparing germline gene sequences with their rearranged counterparts for the mouse VH, V kappa, and V lambda genes. The mutation rate at the amino acid level was estimated to be 7.0% in the first and second complementarity- determining regions (CDRs) and 2.0% in the framework regions (FRs). The difference in the mutation rate at the nucleotide level between the CDRs and FRs was of the same order of magnitude as that for the amino acid level. Analysis of amino acid diversity or nucleotide diversity indicated that the contribution of somatic mutation to immunoglobulin diversity is approximately 5%. However, the contribution of somatic mutation to the number of different amino acid sequences of immunoglobulins is much larger than that estimated by the analysis of amino acid diversity, and more than 90% of the different immunoglobulins seem to be generated by somatic mutation. Examination of the pattern of nucleotide substitution has suggested that clonal selection after somatic mutation may not be as strong as generally believed.      

乌尔吉晚更新世动物群和古生态环境

乌尔吉地区晚更新世地层出露广泛,哺乳动物化石常有发现.乌尔吉动物群属于猛犸象—披毛犀动物群,其时代为晚更新世晚期.动物群的生态性质明显反映了当时应为寒温带湿冷草原为主间有疏林和少量灌丛的自然景观.     

Probability of Fixation and Mean Fixation Time of an Overdominant Mutation

The probability of fixation of an overdominant mutation in a finite population depends on the equilibrium gene frequency in an infinite population (m) and the product (A) of population size and selection intensity. If m < 0.5 (disadvantageous overdominant genes), the probability is generally much lower than that of neutral genes; but if m is close to 0.5 and A is relatively small, it becomes higher. If m > 0.5 (advantageous overdominant genes), the probability is largely determined by the fitness of heterozygotes rather than that of mutant homozygotes. Thus, overdominance enhances the probability of fixation of advantageous mutations. The average number of generations until fixation of an overdominant mutation also depends on m and A. This average time is long when m is close to 0.5 but short when m is close to 0 or 1. This dependence on m and A is similar to that of Robertson's retardation factor.