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According to ??molecular connectivity indices?? method, four parameters basing on the locations and occurrence frequencies of four bases (A, C, G, T) in DNA sequences were extracted to characterize the DNA sequences of different species. Similarity analysis among several species was performed basing on Euclidean distance and phylogenetic tree. The results showed that the computation results are in...
The nucleotide imbalance and the nucleotide pair imbalance signals of hominidae mitochondrial nucleotide genomic signals (mtNuGSs) have specific features for the areas encoding the 13 mt proteins, the 22 mt transfer RNAs (mt tRNA), the two mt ribosomal RNAs (mt rRNA), or for the segment(s) corresponding to the D-loop. The nucleotide genomic signal analysis of mt DNA allows identifying such features,...
The specific segment in 3' terminal region of strawberry mild yellow edge virus (SMYEV) genome was amplified by 3' rapid amplification of cDNA ends (RACE). Ten Chinese isolates were sequenced. Sequence analysis of coat protein gene showed nucleotide and deduced amino acid identities ranged from 76.8 to 100% and 86.4 to 100%, respectively. Phylogenetic analysis showed that all isolates of SMYEV fell...
A cladistic analysis of the sequences of five chloroplast and one nuclear (ITS) molecular markers was carried out, both individually and in combination, by distance, parsimony, likelihood, and Bayesian methods. The two families are monophyletic. In Taxus, T. floridana is the first-branching taxon; T. brevifolia and T. globosa cluster together and are sister to T. baccata; the endemic T. yunnanensis...
To elucidate the function of S-allele and the possible molecular mechanism of gametophytic self-incompatibility (GSI) in Chinese white pear (Pyrus bretschneideri Rehd.), full length cDNA encoding S20-RNase was cloned by rapid amplification of cDNA ends (RACE) approach from the cultivar 'Donghuang' (S8S20), and analyzed by bioinformatics method. S20-RNase displayed typical sequence features of pear...
Seven polyacrylamide(PAM)-degrading bacteria were isolated from waste water treated pool of Henan(P.R.China) oil field, six of which were isolated from the sample of sludge, one from the sample of waste water. Sequences and phylogenetic analysis of 16 S rDNA clones of the seven bacteria showed that four were affiliated with Actinobacteria, two with Alphaproteobacteria, one with Bacillus. PCR-DGGE...
Plumcot (Prunus simonii Carr.) is an interspecific hybrid between plum (P. salicina) and apricot (P. armeniaca) that plays an important role in non-timber forestry industry and making medicine. It exhibited S-RNase-based gametophytic self-incompatibility. In this study, four 5-RNase genes were identified and characterized. All of them displayed typical structural features of Prunus S-RNases, i.e....
House dust mites not only live in house dusts but also affect human bodies. Among the many species, D. farinae, D. pteronyssinus, Euroglyphus maynei have been found commonly associated with Ig-E mediated allergic diseases. As a result, there is increasing effort to develop methods for diagnosis and treatment for diseases caused by these species. The present study was to explore the evolutionary relationships...
The wild boar OPN cDNA in size of 909bp was cloned by RT-PCR and analyzed by bioinformatics. The result showed that wild boar OPN contains 1) a potential calcium phosphate apatite binding region of eight consecutive Asp residues beginning at amino acid 86, 2) a cell-attachment Gly-Arg-Gly- Asp-Ser (GRGDS) sequence (residues 153-157), 3) a thrombin RS cleavage site (residues 163 and 164). The phylogenetic...
A strain of denitrifying bacterium DN7, a facultative aerobic bacterim, was isolated from the sea area near the Changhai County of Dalian. Some physiological and biochemical properties were characterized, 16S rDNA gene sequence was amplified by PCR, and its nucleotide sequence was determined. Based on its physiological and biochemical properties, homology and phylogenetic analysis, strain DN7 was...
Strain PSB-01, a bioactive marine photosynthetic bacterium, was isolated from marine sediments of the Bohai Sea Area. Cells are ovoid to short rod-shaped, 0.3-0.5 mum in diameter, and 1.0-1.5 mum in length. Multiply by binary fission, gram-negative and contain internal photosynthetic membrane systems in which the photosynthetic pigments bacteriochlorophylla and carotenoids are located. Researches...
Leaf blight of Camelliaoleifera was one of the major diseases in Hunan's Camellia producing areas. The fungal pathogen infected leaves of the host plants and caused leaves drop, resulting in earlier defoliation and new treetops death. Filamentous fungal strain (No. CSUFT070160A) was isolated from the leaves of Camelliaoleifera with the leaf blight disease. We observed morphological characteristics...
In order to understand the phylogenetic relationships among Vibrio species more rationally , the hemolysin gene partial sequences of 4 Vibrio species (Vibrio alginolyticus, Vibrio harveyi, Vibrio parahaemolyticus, Vibrio minius) were amplifyed and sequenced. We constructed two separate phylogenetic trees by using 16S rRNA and partial hemolysin gene sequences, respectively.The average similarities...
The article introduces the authors'research of an optimum method on the cultivation conditions of a flocculant- producing Strain. Using single factor experiments and orthogonal test, the influence of temperature, PH value and rotational speed on synthesis of microbial flocculants, and optimized culture conditions were studied; 16S gene of the strain was amplified and sequenced.The sequencing was BLAST...
With the increase of sequence information, many methods have been used in detecting sequence similarities. In order to avoid the shortcomings of the traditional method based on sequences alignment such as high time and space complexity, component vector method has been successfully used in the reconstruction of phylogenetic tree using genome (proteome) or conserved molecular sequences. With the aim...
Mitochondria have been known as power sources for energy transduction in eukaryotic cells. Hence, mitochondrial genomes and proteins have been used widely for phylogenetic analysis. However, nuclear-encoded mitochondrial proteins are considered in this study to construct phylogenetic relationship among species. An intuitive yet effective and efficient approach to solving relative positions of species...
Driven by novel biological wet lab techniques such as pyrosequencing there has been an unprecedented molecular data explosion. The growth of biological sequence data has significantly out-paced Moore's law. This development also poses new computational and architectural challenges for the field of phylogenetic inference, i.e., the reconstruction of evolutionary histories (trees) for a set of organisms...
This paper describes a Taverna workflow environment with supporting web services for Single Nucleotide Polymorphisms (SNP) analysis of genes in shrimp. The workflow is used to investigate SNPs advantages for gene development. Our first workflow environment did not give satisfying results for the phylogenetic tree processes because the data flows between the web services would frequently time-out....
Based on the amino acid sequence of bHLH-zip motif in SREBP-1 and SREBP-2 in Landes goose obtained by gene cloning, the sequences of HLH family members in poultry genome were screened in the Protein Databases of NCBI. The classification and evolution of HLH protein family in poultry genome were analyzed. HLH protein family in poultry genome are divided into five groups (A, B, C, D and E) according...
Metagenomics is to study microorganisms by directly extracting and cloning their DNAs from the environment without lab cultivation or isolation of individual genomes. Assembling of metagenomic DNA fragments is very much like the overlap-layout-consensus procedure for assembling isolated genomes, but is augmented by an additional binning step to differentiate scaffolds, contigs and unassembled reads...
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