Articles Online (Volume 1, Issue 4)

Editoral

The Difference in Cognition Consistency Between the Sciences and Humanities

Jianzhang Zhou

It is reasonable that the strict sciences represented by mathematics, physics and chemistry have nearly been a kind of substitutional belief of humans after"the Death of God". To conclude theoretically, the significant attraction or the extremely great power of science is, in a word, the validity of thinking and action. From the viewpoint of human action or practice, science is the only really effective means we have to deal with nature (the other) that speaks the language of power. Being a creature that maybe has no competitive advantage in biological sense except the brain, men could not live in the world without power, and the subjective human power represented and embodied in science can be considered as the only secret by whic h we could stand above all the other beings on the earth.
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Page 243-246


Review Article

Molecular Advances in Severe Acute Respiratory Syndrome-associated Coronavirus (SARS-CoV)

Ken Yan Ching Chow,Chung Chau Hon,Raymond Kin Hi Hui,Raymond Tsz Yeung Wong,Chi Wai Yip,Fanya Zeng,Frederick Chi Ching Leung

The sudden outbreak of severe acute respiratory syndrome (SARS) in 2002 prompted the establishment of a global scientific network subsuming most of the traditional rivalries in the competitive field of virology. Within months of the SARS outbreak, collaborative work revealed the identity of the disastrous pathogen as SARS-associated coronavirus (SARS-CoV). However, although the rapid identifi- cation of the agent represented an important breakthrough, our understanding of the deadly virus remains limited. Detailed biological knowledge is crucial for the development of effective countermeasures, diagnostic tests, vaccines and antiviral drugs against the SARS-CoV. This article reviews the present state of molecular knowledge about SARS-CoV, from the aspects of comparative genomics, molecular biology of viral genes, evolution, and epidemiology, and describes the diagnostic tests and the anti-viral drugs derived so far based on the available molecular infor- mation.
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Page 247-262


Review Article

Functional Genomics of Wood Quality and Properties

Wei Tang,Xiaoyan Luo,Aaron Nelson,Hilary Collver,Katherine Kinken

Genomics promises to enrich the investigations of biology and biochemistry. Current advancements in genomics have major implications for genetic improvement in animals, plants, and microorganisms, and for our understanding of cell growth, development, differentiation, and communication. Significant progress has been made in the understanding of plant genomics in recent years, and the area continues to progress rapidly. Functional genomics offers enormous potential to tree improvement and the understanding of gene expression in this area of science worldwide.In this review we focus on functional genomics of wood quality and properties in trees, mainly based on progresses made in genomics study of Pinus and Populus.The aims of this review are to summarize the current status of functional genomics including: (1) Gene discovery; (2) EST and genomic sequencing; (3) From EST to functional genomics; (4) Approaches to functional analysis; (5) Engineering lignin biosynthesis; (6) Modification of cell wall biogenesis; and (7) Molecular modelling.Functional genomics has been greatly invested worldwide and will be important in identifying candidate genes whose function is critical to all aspects of plant growth, development, differentiation, and defense. Forest biotechnology industry will significantly benefit from the advent of functional genomics of wood quality and properties.
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Page 263-278


Research Article

Genetic Algorithms Applied to Multi-Class Clustering for Gene Ex- pression Data

Haiyan Pan,Jun Zhu,Danfu Han

A hybrid GA (genetic algorithm)-based clustering (HGACLUS) schema, combin- ing merits of the Simulated Annealing, was described for finding an optimal or near-optimal set of medoids. This schema maximized the clustering success by achieving internal cluster cohesion and external cluster isolation. The performance of HGACLUS and other methods was compared by using simulated data and open microarray gene-expression datasets. HGACLUS was generally found to be more accurate and robust than other methods discussed in this paper by the exact vali- dation strategy and the explicit cluster number.
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Page 279-287


Research Article

Bioinformatics-Based Identification of Chemosensory Proteins in African Malaria Mosquito, Anopheles gambiae

Zhengxi Li,Zuorui Shen,Jingjiang Zhou,Lin Field

Chemosensory proteins (CSPs) are identifiable by four spatially conserved Cys- teine residues in their primary structure or by two disulfide bridges in their ter- tiary structure according to the previously identified olfactory specific-D related proteins. A genomics- and bioinformatics-based approach is taken in the present study to identify the putative CSPs in the malaria-carrying mosquito, Anopheles gambiae. The results show that five out of the nine annotated candidates are the most possible Anopheles CSPs of A. gambiae. This study lays the foundation for further functional identification of Anopheles CSPs, though all of these candidates need additional experimental verification.
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Page 288-298


Letter

Bioinformatics Data Distribution and Integration via Web Services and XML

Xiao Li,Yizheng Zhang

It is widely recognized that exchange, distribution, and integration of biological data are the keys to improve bioinformatics and genome biology in post-genomic era. However, the problem of exchanging and integrating biological data is not solved satisfactorily. The eXtensible Markup Language (XML) is rapidly spreading as an emerging standard for structuring documents to exchange and integrate data on the World Wide Web (WWW). Web service is the next generation of WWW and is founded upon the open standards of W3C (World Wide Web Consortium) and IETF (Internet Engineering Task Force). This paper presents XML and Web Services technologies and their use for an appropriate solution to the problem of bioinformatics data exchange and integration .
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Page 299-303


Letter

HLA-A Gene Polymorphism Defined by High-Resolution Sequence- Based Typing in 161 Northern Chinese Han People

Chunxia Yan,Ruiling Wang,Jingxiang Li,Yajun Deng,Dongying Wu,Hongbo Zhang,Hongxing Zhang,Lidong Wang,Chunrong Zhang,Haiyan Sun,Xiuqing Zhang,Jian Wang,Huan-Ming Yang,Shengbin Li

Human leukocyte antigen (HLA) system is the most polymorphic region known in the human genome. In the present study, we analyzed for the first time the HLA-A gene polymorphisms defined by the high-resolution typing methods— sequence-based typing (SBT) in 161 Northern Chinese Han people. A total of 74 different HLA-A gene types and 36 alleles were detected. The most frequent alleles were A*110101 (GF=0.2360), A*24020101 (GF=0.1646), and A*020101 (GF=0.1553); followed by A*3303 (GF=0.1180), A*3001 (GF=0.0590), and A*310102 (GF=0.0404). The frequencies of following alleles, A*0203, A*0205, A*0206, A*0207, A*030101, A*2423, A*2601, A*3201, and A*3301, are all higher than 0.0093. The homozygous alleles include A*020101, A*110101, A*24020101 and A*310102. Heterozygosity (H), polymorphism information content (PIC), dis- crimination power (DP) and probability of paternity exclusion (PPE) of HLA-A in the samples were calculated and their values were 0.8705, 0.8491, 0.6014, and 0.9475, respectively. These results by SBT analysis of HLA-A polymorphism in Northern Chinese Han population, especially the allele subtypes character, will be of great interest for clinical transplantation, disease-associated study and forensic identification. Implementation of high-resolution typing methods allows a signifi- cantly wider spectrum of HLA variation including rare alleles. This spectrum will further be extensively utilized in many fields.
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Page 304-309


Letter

Molecular Phylogenetics and Functional Evolution of Major RNA Recognition Domains of Recently Cloned and Characterized Au- toimmune RNA-Binding Particle

Erhan Suleymanoglu

Heterogeneous nuclear ribonucleoproteins (hnRNPs) are spliceosomal macromole- cular assemblages and thus actively participate in pre-mRNA metabolism. They are composed of evolutionarily conserved and tandemly repeated motifs, where both RNA-binding and protein-protein recognition occur to achieve cellular activ- ities. By yet unknown mechanisms, these ribonucleoprotein (RNP) particles are targeted by autoantibodies and hence play significant role in a variety of human systemic autoimmune diseases. This feature makes them important prognostic markers in terms of molecular epidemiology and pathogenesis of autoimmunity. Since RNP domain is one of the most conserved and widespread scaffolds, evo- lutionary analyses of these RNA-binding domains can provide further clues on disease-specific epitope formation. The study presented herein represents a se- quence comparison of RNA-recognition regions of recently cloned and character- ized human hnRNP A3 with those of other relevant hnRNP A/B-type proteins. Their implications in human autoimmunity are particularly emphasized.
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Page 310-320