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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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Journal DOI :
Korean Society for Biochemistry and Molecular Biology
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Volume & Issues
Volume 37, Issue 6 - Nov 2004
Volume 37, Issue 5 - Sep 2004
Volume 37, Issue 4 - Jul 2004
Volume 37, Issue 3 - May 2004
Volume 37, Issue 2 - Mar 2004
Volume 37, Issue 1 - Jan 2004
Selecting the target year
Quantitative Analysis of Nucleic Acids - the Last Few Years of Progress
Ding, Chunming ; Cantor, Charles R. ;
BMB Reports , volume 37, issue 1, 2004, Pages 1~10
DOI : 10.5483/BMBRep.2004.37.1.001
DNA and RNA quantifications are widely used in biological and biomedical research. In the last ten years, many technologies have been developed to enable automated and high-throughput analyses. In this review, we first give a brief overview of how DNA and RNA quantifications are carried out. Then, five technologies (microarrays, SAGE, differential display, real time PCR and real competitive PCR) are introduced, with an emphasis on how these technologies can be applied and what their limitations are. The technologies are also evaluated in terms of a few key aspects of nucleic acids quantification such as accuracy, sensitivity, specificity, cost and throughput.
Global Genetic Analysis
Elahi, Elahe ; Kumm, Jochen ; Ronaghi, Mostafa ;
BMB Reports , volume 37, issue 1, 2004, Pages 11~27
DOI : 10.5483/BMBRep.2004.37.1.011
The introduction of molecular markers in genetic analysis has revolutionized medicine. These molecular markers are genetic variations associated with a predisposition to common diseases and individual variations in drug responses. Identification and genotyping a vast number of genetic polymorphisms in large populations are increasingly important for disease gene identification, pharmacogenetics and population-based studies. Among variations being analyzed, single nucleotide polymorphisms seem to be most useful in large-scale genetic analysis. This review discusses approaches for genetic analysis, use of different markers, and emerging technologies for large-scale genetic analysis where millions of genotyping need to be performed.
Structure-based Functional Discovery of Proteins: Structural Proteomics
Jung, Jin-Won ; Lee, Weon-Tae ;
BMB Reports , volume 37, issue 1, 2004, Pages 28~34
DOI : 10.5483/BMBRep.2004.37.1.028
The discovery of biochemical and cellular functions of unannotated gene products begins with a database search of proteins with structure/sequence homologues based on known genes. Very recently, a number of frontier groups in structural biology proposed a new paradigm to predict biological functions of an unknown protein on the basis of its three-dimensional structure on a genomic scale. Structural proteomics (genomics), a research area for structure-based functional discovery, aims to complete the protein-folding universe of all gene products in a cell. It would lead us to a complete understanding of a living organism from protein structure. Two major complementary experimental techniques, X-ray crystallography and NMR spectroscopy, combined with recently developed high throughput methods have played a central role in structural proteomics research; however, an integration of these methodologies together with comparative modeling and electron microscopy would speed up the goal for completing a full dictionary of protein folding space in the near future.
Post-translational Modifications and Their Biological Functions: Proteomic Analysis and Systematic Approaches
Seo, Ja-Won ; Lee, Kong-Joo ;
BMB Reports , volume 37, issue 1, 2004, Pages 35~44
DOI : 10.5483/BMBRep.2004.37.1.035
Recently produced information on post-translational modifications makes it possible to interpret their biological regulation with new insights. Various protein modifications finely tune the cellular functions of each protein. Understanding the relationship between post-translational modifications and functional changes ("post-translatomics") is another enormous project, not unlike the human genome project. Proteomics, combined with separation technology and mass spectrometry, makes it possible to dissect and characterize the individual parts of post-translational modifications and provide a systemic analysis. Systemic analysis of post-translational modifications in various signaling pathways has been applied to illustrate the kinetics of modifications. Availability will advance new technologies that improve sensitivity and peptide coverage. The progress of "post-translatomics", novel analytical technologies that are rapidly emerging, offer a great potential for determining the details of the modification sites.
Protein-protein Interaction Networks: from Interactions to Networks
Cho, Sa-Yeon ; Park, Sung-Goo ; Lee, Do-Hee ; Park, Byoung-Chul ;
BMB Reports , volume 37, issue 1, 2004, Pages 45~52
DOI : 10.5483/BMBRep.2004.37.1.045
The goal of interaction proteomics that studies the protein-protein interactions of all expressed proteins is to understand biological processes that are strictly regulated by these interactions. The availability of entire genome sequences of many organisms and high-throughput analysis tools has led scientists to study the entire proteome (Pandey and Mann, 2000). There are various high-throughput methods for detecting protein interactions such as yeast two-hybrid approach and mass spectrometry to produce vast amounts of data that can be utilized to decipher protein functions in complicated biological networks. In this review, we discuss recent developments in analytical methods for large-scale protein interactions and the future direction of interaction proteomics.
Chemical Genomics and Medicinal Systems Biology: Chemical Control of Genomic Networks in Human Systems Biology for Innovative Medicine
Kim, Tae-Kook ;
BMB Reports , volume 37, issue 1, 2004, Pages 53~58
DOI : 10.5483/BMBRep.2004.37.1.053
With advances in determining the entire DNA sequence of the human genome, it is now critical to systematically identify the function of a number of genes in the human genome. These biological challenges, especially those in human diseases, should be addressed in human cells in which conventional (e.g. genetic) approaches have been extremely difficult to implement. To overcome this, several approaches have been initiated. This review will focus on the development of a novel 'chemical genetic/genomic approach' that uses small molecules to 'probe and identify' the function of genes in specific biological processes or pathways in human cells. Due to the close relationship of small molecules with drugs, these systematic and integrative studies will lead to the 'medicinal systems biology approach' which is critical to 'formulate and modulate' complex biological (disease) networks by small molecules (drugs) in human bio-systems.
Nutriproteomics: Identifying the Molecular Targets of Nutritive and Non-nutritive Components of the Diet
Barnes, Stephen ; Kim, Helen ;
BMB Reports , volume 37, issue 1, 2004, Pages 59~74
DOI : 10.5483/BMBRep.2004.37.1.059
The study of whole patterns of changes in protein expression and their modifications, or proteomics, presents both technological advances as well as formidable challenges to biological researchers. Nutrition research and the food sciences in general will be strongly influenced by the new knowledge generated by the proteomics approach. This review examines the different aspects of proteomics technologies, while emphasizing the value of consideration of "traditional" aspects of protein separation. These include the choice of the cell, the subcellular fraction, and the isolation and purification of the relevant protein fraction (if known) by protein chromatographic procedures. Qualitative and quantitative analyses of proteins and their peptides formed by proteolytic hydrolysis have been substantially enhanced by the development of mass spectrometry technologies in combination with nanoscale fluidics analysis. These are described, as are the pros and cons of each method in current use.
Bioinformatics in the Post-genome Era
Yu, Ung-Sik ; Lee, Sung-Hoon ; Kim, Young-Joo ; Kim, Sang-Soo ;
BMB Reports , volume 37, issue 1, 2004, Pages 75~82
DOI : 10.5483/BMBRep.2004.37.1.075
Recent years saw a dramatic increase in genomic and proteomic data in public archives. Now with the complete genome sequences of human and other species in hand, detailed analyses of the genome sequences will undoubtedly improve our understanding of biological systems and at the same time require sophisticated bioinformatic tools. Here we review what computational challenges are ahead and what are the new exciting developments in this exciting field.
From the Sequence to Cell Modeling: Comprehensive Functional Genomics in Escherichia coli
Mori, Hirotada ;
BMB Reports , volume 37, issue 1, 2004, Pages 83~92
DOI : 10.5483/BMBRep.2004.37.1.083
As a result of the enormous amount of information that has been collected with E. coli over the past half century (e.g. genome sequence, mutant phenotypes, metabolic and regulatory networks, etc.), we now have detailed knowledge about gene regulation, protein activity, several hundred enzyme reactions, metabolic pathways, macromolecular machines, and regulatory interactions for this model organism. However, understanding how all these processes interact to form a living cell will require further characterization, quantification, data integration, and mathematical modeling, systems biology. No organism can rival E. coli with respect to the amount of available basic information and experimental tractability for the technologies needed for this undertaking. A focused, systematic effort to understand the E. coli cell will accelerate the development of new post-genomic technologies, including both experimental and computational tools. It will also lead to new technologies that will be applicable to other organisms, from microbes to plants, animals, and humans. E. coli is not only the best studied free-living model organism, but is also an extensively used microbe for industrial applications, especially for the production of small molecules of interest. It is an excellent representative of Gram-negative commensal bacteria. E. coli may represent a perfect model organism for systems biology that is aimed at elucidating both its free-living and commensal life-styles, which should open the door to whole-cell modeling and simulation.
Yeast as a Touchstone in Post-genomic Research: Strategies for Integrative Analysis in Functional Genomics
Castrillo, Juan I. ; Oliver, Stephen G. ;
BMB Reports , volume 37, issue 1, 2004, Pages 93~106
DOI : 10.5483/BMBRep.2004.37.1.093
The new complexity arising from the genome sequencing projects requires new comprehensive post-genomic strategies: advanced studies in regulatory mechanisms, application of new high-throughput technologies at a genome-wide scale, at the different levels of cellular complexity (genome, transcriptome, proteome and metabolome), efficient analysis of the results, and application of new bioinformatic methods in an integrative or systems biology perspective. This can be accomplished in studies with model organisms under controlled conditions. In this review a perspective of the favourable characteristics of yeast as a touchstone model in post-genomic research is presented. The state-of-the art, latest advances in the field and bottlenecks, new strategies, new regulatory mechanisms, applications (patents) and high-throughput technologies, most of them being developed and validated in yeast, are presented. The optimal characteristics of yeast as a well-defined system for comprehensive studies under controlled conditions makes it a perfect model to be used in integrative, 'systems biology' studies to get new insights into the mechanisms of regulation (regulatory networks) responsible of specific phenotypes under particular environmental conditions, to be applied to more complex organisms (e.g. plants, human).
Functional Genomic Approaches Using the Nematode Caenorhabditis elegans as a Model System
Lee, Jun-Ho ; Nam, Seung-Hee ; Hwang, Soon-Baek ; Hong, Min-Gi ; Kwon, Jae-Young ; Joeng, Kyu-Sang ; Im, Seol-Hee ; Shim, Ji-Won ; Park, Moon-Cheol ;
BMB Reports , volume 37, issue 1, 2004, Pages 107~113
DOI : 10.5483/BMBRep.2004.37.1.107
Since the completion of the genome project of the nematode C. elegans in 1998, functional genomic approaches have been applied to elucidate the gene and protein networks in this model organism. The recent completion of the whole genome of C. briggsae, a close sister species of C. elegans, now makes it possible to employ the comparative genomic approaches for identifying regulatory mechanisms that are conserved in these species and to make more precise annotation of the predicted genes. RNA interference (RNAi) screenings in C. elegans have been performed to screen the whole genome for the genes whose mutations give rise to specific phenotypes of interest. RNAi screens can also be used to identify genes that act genetically together with a gene of interest. Microarray experiments have been very useful in identifying genes that exhibit co-regulated expression profiles in given genetic or environmental conditions. Proteomic approaches also can be applied to the nematode, just as in other species whose genomes are known. With all these functional genomic tools, genetics will still remain an important tool for gene function studies in the post genome era. New breakthroughs in C. elegans biology, such as establishing a feasible gene knockout method, immortalized cell lines, or identifying viruses that can be used as vectors for introducing exogenous gene constructs into the worms, will augment the usage of this small organism for genome-wide biology.
Transient Receptor Potential Ion Channels and Animal Sensation: Lessons from Drosophila Functional Research
Kim, Chang-Soo ;
BMB Reports , volume 37, issue 1, 2004, Pages 114~121
DOI : 10.5483/BMBRep.2004.37.1.114
Ion channels of the transient receptor potential (TRP) superfamily are non-selective cationic channels with six transmembrane domains. The TRP channel made its first debut as a light-gated
channel in Drosophila. Recently, research on animal sensation in Drosophila disclosed other members of the TRP family that are required for touch sensation and hearing as well as the sensation of painful stimuli.
Functional Genomics Approach Using Mice
Sung, Young-Hoon ; Song, Jae-Whan ; Lee, Han-Woong ;
BMB Reports , volume 37, issue 1, 2004, Pages 122~132
DOI : 10.5483/BMBRep.2004.37.1.122
The rapid development and characterization of the mouse genome sequence, coupled with comparative sequence analysis of human, has been paralleled by a reinforced enthusiasm for mouse functional genomics. The way to uncover the in vivo function of genes is to analyze the phenotypes of the mutant animals. From this standpoint, the mouse is a suitable and valuable model organism in the studies of functional genomics. Therefore, there have been enormous efforts to enrich the list of the mutant mice. Such a trend emphasizes the random mutagenesis, including ENU mutagenesis and gene-trap mutagenesis, to obtain a large stock of mutant mice. However, since various mutant alleles are needed to precisely characterize the role of a gene in vivo, mutations should be designed. The simplicity and utility of transgenic technology can satisfy this demand. The combination of RNA interference with transgenic technology will provide more opportunities for researchers. Nevertheless, gene targeting can solely define the in vivo function of a gene without a doubt. Thus, transgenesis and gene targeting will be the major strategies in the field of functional genomics.
Proteomic Studies in Plants
Park, Ohk-Mae K. ;
BMB Reports , volume 37, issue 1, 2004, Pages 133~138
DOI : 10.5483/BMBRep.2004.37.1.133
Proteomics is a leading technology for the high-throughput analysis of proteins on a genome-wide scale. With the completion of genome sequencing projects and the development of analytical methods for protein characterization, proteomics has become a major field of functional genomics. The initial objective of proteomics was the large-scale identification of all protein species in a cell or tissue. The applications are currently being extended to analyze various functional aspects of proteins such as post-translational modifications, protein-protein interactions, activities and structures. Whereas the proteomics research is quite advanced in animals and yeast as well as Escherichia coli, plant proteomics is only at the initial phase. Major studies of plant proteomics have been reported on subcellular proteomes and protein complexes (e.g. proteins in the plasma membranes, chloroplasts, mitochondria and nuclei). Here several plant proteomics studies will be presented, followed by a recent work using multidimensional protein identification technology (MudPIT).