Hereditary spastic paraplegia (HSP) is a neurodegenerative disease characterized by lower-limb spasticity, hyperreflexia, progressive spastic gait abnormalities, and an extensor-plantar response. It is genetically very heterogeneous, with 28 Human Genome Organisation (HUGO)-approved IDs in the database (last search: August 8, 2004). Following the identification of the SPG6 gene, NIPA1, we have identified two novel mutations, c.316G>C and c.316G>A, in two independent Chinese families linked to the SPG6 locus. These two mutations would cause a p.G106R substitution, and cosegregated with the disease. Structural predictions suggest that p.G106 is located in the third transmembrane domain of the protein, and that the mutant p.G106R disrupts this structure, causing the intramembrane loop to descend into the cytoplasm. Our results identify two novel mutations responsible for HSP and suggest that c.316 of theNIPA1 gene may be a mutational hotspot.
We perform an exhaustive, taxon by taxon, comparison of the branchings in the composition vector trees (CVTrees) inferred from 432 prokaryotic genomes available on 31 December 2006, with the bacteriologists' taxonomy--primarily the latest online Outline of the Bergey's Manual of Systematic Bacteriology. The CVTree phylogeny agrees very well with the Bergey's taxonomy in majority of fine branchings and overall structures. At the same time most of the differences between the trees and the Manual have been known to biologists to some extent and may hint at taxonomic revisions. Instead of demonstrating the overwhelming agreement this paper puts emphasis on the biological implications of the differences.
The newly proposed alignment-free and parameter-free composition vector (CVtree) method has been successfully applied to infer phylogenetic relationship of viruses, chloroplasts, bacteria, and fungi from their whole-genome data. In this study we pay special attention to the phylogenetic positions of 56 Archaea genomes among which 7 species have not been listed either in Bergey's Manual of Systematic Bacteriology or in Taxonomic Outline of Bacteria and Archaea (TOBA). By inspecting the stable monophyletic branchings in CVTrees reconstructed from a total of 861 genomes (56 Archaea plus 797 Bacteria, using 8 Eukarya as outgroups) definite taxonomic assignments were proposed for these not-fully-classified species. Further development of Archaea taxonomy may verify the predicted phylogenetic results of the CVTree approach.Archaea, phylogeny, taxonomy, composition vector, alignment-free, CVTree, 16S rRNA analysis Citation:Sun J D, Xu Z, Hao B L. Whole-genome based Archaea phylogeny and taxonomy: A composition vector approach.
Recent advances have shown that the majority of the nucleotide variation in human genome is single nucleotide polymorphisms (SNPs). Using SNPs each chromosome can be divided into different haplotype blocks, and there are limited common haplotypes in each block. This provides a powerful approach for whole genome scan for disease-associated genes/variants. However, most data available today are based on the large-scale genomic analyses, data concerning individual genes for fine mapping with high density SNPs are relatively lacking. We have sequenced 7 genes and their flanking regions, identified 34 novel SNPs, constructed high density SNP haplotypes and haplotype blocks in 5 genes in the centromeric region of chromosome 15 in 100 Chinese Han subjects. Our results show that there is a great heterogeneity in the haplotypes and haplotype block structures within and between these genes, which are in close physical proximity. Data obtained in this study provide a useful tool for candidate gene approach at the fine scale for identifying disease contributing variants in the genes/regions.
Hippodonta fujiannensis sp. nov., a new small-sized species of Hippodonta (Bacillariophyceae), was described from the low intertidal zone, Fujian Province, China. The morphology and ultrastructure were investigated by light and scanning electron microscopy, which revealed the following results: 1) valves asymmetrical, elliptic-lanceolate to rhombic-lanceolate with non-protracted apices; 2) raphe filiform, with teardrop-shaped and closely spaced central endings; 3) striae uniseriate, evenly spaced throughout the whole valve; 4) single row of lineolae around the valve apices. In particular, this new species is characterized by its dissymmetrical valves with one special column of lineolae which is close to the raphe and positioned perpendicular to the remaining lineolae of the striae, on only one side of the valves. Hippodonta fujiannensis is epipsammic and inhabits the marine environment. Conventional morphometric analyses were employed to elucidate the differences between this new species and several taxa similar in valve morphology, and the results are discussed.
Based on the light and scanning electron microscopy observations, we present a detailed description of a new brackish diatom Navicula amoyensis sp. nov. Samples were collected from an intertidal sand flat in the Jiulong River estuary, Southern China. The key diagnostic features of this species include the simple terminal raphe endings, broad terminal area, two rows of perpendicular apical pores, a wide contracted girdle region with pectinate margin and internal proximal raphe endings with a raised siliceous rib and accessory rib. Furthermore, the main taxonomic features of N. amoyensis sp. nov. and the genera Hippodonta and Navicula are also discussed in detail.
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