Articles Online (Volume 3, Issue 1)

Editoral

What Are You Going to Conquer with the Spear?

Jun Yu

Almost everyone in China knows this story, even ele- mentary school pupils: Once upon a time, there was a weapon salesman claiming with confidence to one crowd that all his spears were capable of piercing ev- ery shield that existed in the world, then he turned around and told the other crowd mysteriously that all his shields were not penetrable. A bystander who heard both claims asked him, “How about stabbing your shields with your spears?” It was indeed an un- expected question that made the eloquent salesman mute right on the spot. Since then, the Chinese peo- ple have called contradiction as ”mao-dun”, which lit- erally means “the spear (pronounced as “mao”) and shield (pronounced as “dun”)”.
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Page 1-2


Brief Report

Genome Biology: The Second Modern Synthesis

Jun Yu,Gane Ka-Shu Wong

A scientific dream proposed some 20 years ago has been realized—the completion of the DNA sequence for the Human Genome Project (HGP) in 2004. As a result, an entirely new field of biological research has arisen: genome biology or genomics is celebrated for its unprecedented scale, intrinsically digital out- put, and systematic approach to getting all the data. Its sequel, the HapMap Project, will reach fruition later this year. These projects established new prece- dents for international collaborations and open data access. Chinese scientists contributed to 1% of the HGP and 10% of the HapMap. They also initiated and completed several projects of their own, includ- ing the Chinese Superhybrid Rice Genome Project, the Silkworm Genome Project, the Chicken Genome Polymorphism Project, and a Genome Survey of the Porcine Genome. These projects will benefit fields as diverse as agriculture, medicine, and the economy in general.
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Research Article

A Mitochondrial Genome Sequence of the Tibetan Antelope (Pantholops hodgsonii)

Shu-qing Xu,Ying-zhong Yang,Jun Zhou,Guo-En Jin,Yun-Tian Chen,Jun Wang,Huan-Ming Yang,Jian Wang,Jun Yu,Xiao-Guang Zheng,Ri-Li Ge

To investigate genetic mechanisms of high altitude adaptations of native mammals on the Tibetan Plateau, we compared mitochondrial sequences of the endangered Pantholops hodgsonii with its lowland distant relatives Ovis aries and Capra hir- cus, as well as other mammals. The complete mitochondrial genome of P. hodgsonii (16,498 bp) revealed a similar gene order as of other mammals. Because of tandem duplications, the control region of P. hodgsonii mitochondrial genome is shorter than those of O. aries and C. hircus, but longer than those of Bos species. Phy- logenetic analysis based on alignments of the entire cytochrome b genes suggested that P. hodgsonii is more closely related to O. aries and C. hircus, rather than to species of the Antilopinae subfamily. The estimated divergence time between P. hodgsonii and O. aries is about 2.25 million years ago. Further analysis on natu- ral selection indicated that the COXI (cytochrome c oxidase subunit I) gene was under positive selection in P. hodgsonii and Bos grunniens. Considering the same climates and environments shared by these two mammalian species, we proposed that the mitochondrial COXI gene is probably relevant for these native mammals to adapt the high altitude environment unique to the Tibetan Plateau.
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Page 4-17


Research Article

SARS-CoV Genome Polymorphism: A Bioinformatics Study

Gordana M.Pavlovic-Lazetic,Nenad S. Mitic,Andrija M. Tomovic,Mirjana D. Pavlovic,Milos V. Beljanski

A dataset of 103 SARS-CoV isolates (101 human patients and 2 palm civets) was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide variations (SNVs) and inser- tions and deletions, with respect to a “profile”, were determined and discussed (“profile” being a sequence containing the most represented letter per position). Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was de- termined, along with amino acid (a.a.) property changes. Similar analysis was performed for the spike (S) protein in all the isolates (55 of them being predicted for the first time). The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and geno- types. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes: TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes. Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time.
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Page 18-35


Research Article

Clustering Gene Expression Data Based on Predicted Differential Effects of G V Interaction

Haiyan Pan,Jun Zhu,Danfu Han

Microarray has become a popular biotechnology in biological and medical research. However, systematic and stochastic variabilities in microarray data are expected and unavoidable, resulting in the problem that the raw measurements have in- herent “noise” within microarray experiments. Currently, logarithmic ratios are usually analyzed by various clustering methods directly, which may introduce bias interpretation in identifying groups of genes or samples. In this paper, a statistical method based on mixed model approaches was proposed for microarray data clus- ter analysis. The underlying rationale of this method is to partition the observed total gene expression level into various variations caused by different factors using an ANOVA model, and to predict the differential effects of GV (gene by variety) interaction using the adjusted unbiased prediction (AUP) method. The predicted GV interaction effects can then be used as the inputs of cluster analysis. We illus- trated the application of our method with a gene expression dataset and elucidated the utility of our approach using an external validation.
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Letter

Phylogeny of the Insect Homeobox Gene (Hox) Cluster

Sangeeta Dhawan,K. P. Gopinathan

The homeobox (Hox) genes form an evolutionarily conserved family encoding tran- scription factors that play major roles in segmental identity and organ specification across species. The canonical grouping of Hox genes present in the HOM-C cluster of Drosophila or related clusters in other organisms includes eight “typical” genes, which are localized in the order labial (lab), proboscipedia (pb), Deformed (Dfd), Sex combs reduced (Scr), Antennapedia (Antp), Ultrabithorax (Ubx), abdominalA (abdA), and AbdominalB (AbdB). The members of Hox cluster are expressed in a distinct anterior to posterior order in the embryo. Analysis of the relatedness of different members of the Hox gene cluster to each other in four evolutionarily di- verse insect taxa revealed that the loci pb/Dfd and AbdB, which are farthest apart in linkage, had a high degree of evolutionary relatedness, indicating that pb/Dfd type anterior genes and AbdB are closest to the ancestral anterior and posterior Hox genes, respectively. The greater relatedness of other posterior genes Ubx and abdA to the more anterior genes such as Antp and Scr suggested that they arose by gene duplications in the more anterior members rather than the posterior AbdB.
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Letter

Electrochemical Detection of Single A-G Mismatch Using Biosens- ing Surface Based on Gold Nanoparticles

Ren-Yun Zhang,Xue-Mei Wang,Sheng-Jin Gong,Nong-Yue He

The study of small drug molecules interacting with nucleic acids is an area of intense research that has particular relevance in our understanding of relative mechanism in chemotherapeutic applications and the association between genetics (including sequence variation) and drug response. In this contribution, we demonstrate how the sequence-specific binding of an anticancer drug Dacarbazine (DTIC) to single base (A-G) mismatch could be sensitively detected by combining electrochemical detection with biosensing surface based on gold nanoparticles.
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Letter

DCCP and DICP: Construction and Analyses of Databases for Copper- and Iron-Chelating Proteins

Hao Wu,Yan Yang,Sheng-Juan Jiang,Ling-Ling Chen,Hai-Xia Gao,Qing-Shan Fu,Feng Li,Bin-Guang Ma,Hong-Yu Zhang

Copper and iron play important roles in a variety of biological processes, especially when being chelated with proteins. The proteins involved in the metal binding, transporting and metabolism have aroused much interest. To facilitate the study on this topic, we constructed two databases (DCCP and DICP) containing the known copper- and iron-chelating proteins, which are freely available from the website http://sdbi.sdut.edu.cn/en. Users can conveniently search and browse all of the entries in the databases. Based on the two databases, bioinformatic analyses were performed, which provided some novel insights into metalloproteins.
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Application

PoInTree: A Polar and Interactive Phylogenetic Tree

Carreras Marco,Gianti Eleonora,Sartori Luca,Plyte Simon Edward,Isacchi Antonella,Bosotti Roberta

PoInTree (Polar and Interactive Tree) is an application that allows to build, visu- alize, and customize phylogenetic trees in a polar, interactive, and highly flexible view. It takes as input a FASTA file or multiple alignment formats. Phylogenetic tree calculation is based on a sequence distance method and utilizes the Neighbor Joining (NJ) algorithm. It also allows displaying precalculated trees of the major protein families based on Pfam classification. In PoInTree, nodes can be dynami- cally opened and closed and distances between genes are graphically represented. Tree root can be centered on a selected leaf. Text search mechanism, color-coding and labeling display are integrated. The visualizer can be connected to an Oracle database containing information on sequences and other biological data, helping to guide their interpretation within a given protein family across multiple species. The application is written in Borland Delphi and based on VCL Teechart Pro 6 graphical component (Steema software).
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