To describe the fractal feature of CGR (Chaos-game representation) graph of genomes sequences, a multifractal theory is presented in the analysis. By studying the effect of three probability sets on the scale invariance range, the probability set with the best scale invariance is chosen, and then the smooth general dimension spectrum and multifractal spectrum are calculated. The experimental result shows that the probability set composed of the relative probability has the best scale-invariance performance. The scale invariance has three different variance regions, which indicate that genomes sequence segments with different lengths have different distribution rules. It is concluded that the multifractal method is effective for describing the fractal feature of CGR graph of genomes sequences.
Algorithms ; Base Sequence ; Computer Simulation ; Game Theory ; Genome ; Humans ; Mathematical Computing ; Sequence Analysis, DNA ; statistics & numerical data

Biosequence analysis is the primary research field of bioinformatics. In this field, useful information can be extracted by comparison analysis methods. Among them, sequence alignment is the most common comparison method. However the sequence comparison by alignment, which assumes conservation of contiguity between homologous segments, is at odds with genetic recombination. Especially for the multisequence alignment, there exists the difficulty in the complexity of calculation. Therefore, alignment-free sequence comparison methods are required. In this paper, two main categories of alignment-free sequence comparison methods are reviewed. The first one is based on the word (oligomer) frequency and its distribution. The sequences are compared using the distances defined in a Cartesian space by the frequency vectors. In the second category, sequences are compared using Kolmogorov complexity and chaos theory.
Algorithms ; Computational Biology ; Sequence Alignment ; Sequence Analysis ; methods

OBJECTIVETo detect the mutation sites of exons 2, 20, 11A and 11B in Chinese patients with breast cancer.

METHODSA total of 86 patients with breast cancer without blood relationship were randomly selected. Polymerase chain reaction (PCR) and double-strand DNA direct sequencing were applied.

RESULTSNo mutations, especially deletions were found in exons 2, 20 and 11 with carefully checking the sequencing results, although they were reported frequently in Europe populations with breast cancer. We found one polymorphism in exon 11, with high frequency, and in the test of chi-square, the frequencies of two alleles had no significant difference between the patients and controls.

CONCLUSIONThe above results suggest this SNP may not be associated with the breast cancer in Chinese population, and indicates that the gene sequence of what we have studied doesn't account much for occurrence of the breast cancer in the population of China.

Asian Continental Ancestry Group ; genetics ; BRCA1 Protein ; genetics ; Breast Neoplasms ; genetics ; Exons ; Female ; Gene Frequency ; Humans ; Mutation ; Polymorphism, Genetic

Retroviral vectors are wildly used as vehicles for gene transfer into hematopoietic cells based on its potency for efficient gene delivery and integration of transgene in host genome. The development of better transduction protocols depends on gene markers that allow a rapid detection and effective selection of genetically transduced cells. In this study, the enhanced green fluorescent protein (EGFP), a gene that is optimized for detection and expression in mammalian cells, was firstly amplified and cloned by high-fidelity PCR. The vector LGSN carrying EGFP gene was then constructed and the retroviral producer cell lines that yield high titers of LGSN vector in supernatants were developed by liposome-mediated transfection in combination with cross infection. Both GP + envAm12 murine fibroblasts and K562 leukemic cells transduced with EGFP virus demonstrated a stable green fluorescence signal readily detectable by flow cytometry or fluorescence microscopy in up to 97% and 86% of examined cells, respectively. The integration of LGSN provirus in transduced cells was confirmed by PCR analysis. These results indicate EGFP is a suitable reporter molecule for gene transfer and expression in hematopoietic cells. Therefore, the bright and long-term expression of EGFP in living cells will advance the study of gene therapy in vitro and in vivo, particularly for human applications.

Malus floribunda Siebold. (Malus) is widely cultivated all over the world, which is of high ornamental value and breeding significance. Comparative analysis of the chloroplast genome can help enrich the phylogenetic relationship and facilitate germplasm utilization of Malus. Based on the whole genome sequencing data, a complete chloroplast genome (M. floribunda) with tetrad structure was assembled. The chloroplast genome (160 037 bp) was composed of a large single-copy (LSC) region (88 142 bp), inverted repeat (IR) B (26 353 bp), a small single-copy (SSC) region (19 189 bp), and IRA (26 353 bp). A total of 111 genes were annotated: 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. In addition, a large number of repeat sequences were identified in the genome, which was slightly different from that of M. sieboldii and M. toringoides. As for the relative synonymous codon usage, 30 high-frequency codons were found, and the codons tended to end with A/T. The results of interspecific sequence alignment and boundary analysis suggested the sequence variation of the LSC region was large, and the expansion and contraction of the SC region and IR region of the eight Malus species were generally similar. According to the phylogenetic analysis of chloroplast genome sequences, M. floribunda, M. hupehensis, and M. toringoides were grouped into one clade. The findings in this study can provide data support for the development of genetic markers and utilization of germplasm resources in the future.
Genome, Chloroplast ; Malus ; Phylogeny ; Plant Breeding ; Codon