Articles Online (Volume 3, Issue 3)

Editoral

How to Push Forward Science and Technology in China —About Research, Development, and Technological Innovation

Dah-You Maa

It is out of question that China has achieved consid- erable advancements in science and technology. The worldwide spread of “Made in China” that gets on the western countries’ nerves is a good illustration. How- ever, although comparatively better than some other developing countries, we have to face the situation that science and technology in such a great nation as China is still seriously lagged behind, lacking great breakthroughs and top-ranking masters and leaders. That’s why we feel uneasy in front of international colleagues.
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Page 129-131


Review Article

Proteome Analysis of Rice Root Proteins Regulated by Gibberellin

Setsuko Komatsu,Hirosato Konishi

To gain an enhanced understanding of the mechanism by which gibberellins (GAs) regulate the growth and development of plants, it is necessary to identify proteins regulated by GA. Proteome analysis techniques have been applied as a direct, effective, and reliable tool in differential protein expressions. In previous studies, sixteen proteins showed differences in accumulation levels as a result of treatment with GA3, uniconazole, or abscisic acid (ABA), and/or the differences between the GA-deficient semi-dwarf mutant, Tan-ginbozu, and normal cultivars. Among these proteins, aldolase increased in roots treated with GA3, was present at low levels in Tan-ginbozu roots, and decreased in roots treated with uniconazole or ABA. In a root elongation assay, the growth of aldolase-antisense transgenic rice was half of that of vector control transgenic rice. These results indicate that increases in aldolase activity stimulate the glycolytic pathway and may play an important role in the GA-induced growth of roots. In this review, we discuss the relationship among GA, aldolase, and root growth.
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Page 132-142


Special Report

Preliminary DNA Identification for the Tsunami Victims in Thai- land

Yajun Deng,Yuan-Zhe Li,Xiao-Guang Yu,Li Li,Dongying Wu,Jun Zhou,Tian-You Man,Guang Yang,Jiangwei Yan,Daqing Cai,Jian Wang,Huan-Ming Yang,Shengbin Li,Jun Yu

The 2004 Southeast Asia Tsunami killed nearly 5,400 people in Southern Thailand, including foreign tourists and local residents. To recover DNA evidence as much as possible from the seriously decomposed bodies, we explored procedures of sample preparation from both bone and tooth samples as well as both mitochondrial and nuclear markers. Despite having failed to recover enough DNA for nuclear marker typing, we succeeded in obtaining fully informative results for mitochondrial mark- ers (HV1 and HV2) from 258 tooth samples with a success rate of 51% (258/507). Using an organic DNA extraction method coupled with an ultrafiltration step, we obtained 16 STR (including 13 CODIS loci, one sex discrimination locus, and two Identifiler loci) profiles for 834 samples with a success rate of 79% (834/1,062). In addition, by comparing the allelic frequencies between the typed samples as a group and other index populations, we conclude that the Thai tsunami victims are a combined group of several populations. Our results provide valuable evidence and protocols for the future forensic practice.
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Page 143-157


Research Article

Neighboring-Nucleotide Effects on the Mutation Patterns of the Rice Genome

Hui Zhao,Qizhai Li,Changqing Zeng,Huan-Ming Yang,Jun Yu

DNA composition dynamics across genomes of diverse taxonomy is a major sub- ject of genome analyses. DNA composition changes are characteristics of both replication and repair machineries. We investigated 3,611,007 single nucleotide polymorphisms (SNPs) generated by comparing two sequenced rice genomes from distant inbred lines (subspecies), including those from 242,811 introns and 45,462 protein-coding sequences (CDSs). Neighboring-nucleotide effects (NNEs) of these SNPs are diverse, depending on structural content-based classifications (genome- wide, intronic, and CDS) and sequence context-based categories (A/C, A/G, A/T, C/G, C/T, and G/T substitutions) of the analyzed SNPs. Strong and evident NNEs and nucleotide proportion biases surrounding the analyzed SNPs were ob- served in 1–3 bp sequences on both sides of an SNP. Strong biases were observed around neighboring nucleotides of protein-coding SNPs, which exhibit a periodicity of three in nucleotide content, constrained by a combined effect of codon-related rules and DNA repair mechanisms. Unlike a previous finding in the human genome, we found negative correlation between GC contents of chromosomes and the mag- nitude of corresponding bias of nucleotide C at −1 site and G at +1 site. These results will further our understanding of the mutation mechanism in rice as well as its evolutionary implications.
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Page 158-168


Research Article

Non-destructive Analysis of the Nuclei of Transgenic Living Cells Using Laser Tweezers and Near-infrared Raman Spectroscopic Technique

Wei Tang,Ronald J. Newton,Chang-an Xie,Yongqing Li,Nicki Whitley

Transgenic cell lines of loblolly pine (Pinus taeda L.) were analyzed by a compact laser-tweezers-Raman-spectroscopy (LTRS) system in this investigation. A low power diode laser at 785 nm was used for both laser optical trapping of single transgenic cells and excitation for near-infrared Raman spectroscopy of the nuclei of synchronized cells, which were treated as single organic particles, at the S-phase of the cell cycle. Transgenic living cells with gfp and uidA genes were used as biological samples to test this LTRS technique. As expected, different Raman spectra were observed from the tested biological samples. This technique provides a high sensitivity and enables real-time spectroscopic measurements of transgenic cell lines. It could be a valuable tool for the study of the fundamental cell and molecular biological process by trapping single nucleus and by providing a wealth of molecular information about the nuclei of cells.
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Page 169-178


Method

A Comprehensive Software Suite for the Analysis of cDNAs

Kazuharu Arakawa,Haruo Suzuki,Kosuke Fujishima,Kenji Fujimoto,Sho Ueda,Motomu Matsui,Masaru Tomita

We have developed a comprehensive software suite for bioinformatics research of cDNAs; it is aimed at rapid characterization of the features of genes and the pro- teins they code. Methods implemented include the detection of translation initia- tion and termination signals, statistical analysis of codon usage, comparative study of amino acid composition, comparative modeling of the structures of product pro- teins, prediction of alternative splice forms, and metabolic pathway reconstruction. The software package is freely available under the GNU General Public License at http://www.g-language.org/data/cdna/.
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Page 179-188


Method

An Improved Biclustering Algorithm and Its Application to Gene Expression Spectrum Analysis

Hua Qu,Liupu Wang,Yanchun Liang,Chunguo Wu

Cheng and Church algorithm is an important approach in biclustering algorithms. In this paper, the process of the extended space in the second stage of Cheng and Church algorithm is improved and the selections of two important parameters are discussed. The results of the improved algorithm used in the gene expression spectrum analysis show that, compared with Cheng and Church algorithm, the quality of clustering results is enhanced obviously, the mining expression models are better, and the data possess a strong consistency with fluctuation on the condition while the computational time does not increase significantly.
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Page 189-193


Meeting Report

Systems Biology Brings Life Sciences Closer —Report on the China-UK Systems Biology Workshop 2005

Ming Chen

The China-UK Systems Biology Workshop 2005 was held during June 20–21 in the National Science Park of Zhejiang University, Hangzhou, China. It was or- ganized by the Institute of Bioinformatics, Zhejiang University, and was initiated by Prof. Dr. Jun Zhu (Zhejiang University) and Prof. Dr. John Findlay (University of Leeds, UK). The workshop was part of the program called UK-China Partners in Science, a one-year campaign that was initiated by the British government to explore more collaborations between UK and China on science and technology. It was at- tended also by a representative of this program, Mr. Frank Yuan, senior science & innovation officer. The idea of the workshop was to bring together experts with specialists in systems biology in order to promote the “natural partnership” between scientists from the two countries. The most important items of systems biology considered at the workshop were: (1) New technologies and advances in systems biology; (2) Re- search developments in genomics and proteomics; (3) New methodologies and software in computational bi- ology; (4) Research collaboration on systems biology between China and UK.
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Page 194-196