Up until now, we have identified 17 exotic species of Mollusca in Korea. These include Achatina (... more Up until now, we have identified 17 exotic species of Mollusca in Korea. These include Achatina (Lissachatina)
The availability of fast and inexpensive sequencing technology has enabled researchers around the... more The availability of fast and inexpensive sequencing technology has enabled researchers around the world to conduct many genome sequencing and expressed sequence tag (EST) projects of diverse organisms. In recent years, whole genome projects have been undertaken to sequence ten species from the phylum Mollusca. These include Aplysia californica, Lottia gigantea, Crassostrea virginica, Spisula solidissima, Mytilus californianus, Biomphalaria glabrata, Crepidula fornicata, Elysia chlorotica, Lottia scutum and Radix balthica. Additionally, complete mitochondrial genomes of 91 mollusks have been reported. In Korea, EST projects have been conducted in nine mollusk species that include Nesiohelix samarangae, Pisidium (Neopisidium) coreanum, Physa acuta, Incilaria fruhstorferi, Meretrix lusoria, Ruditapes philippinarum, Nordotis gigantea, Crassostrea gigas and Laternula elliptica. Finally, the mitochondrial genome projects from the Pacific Oyster (Crassostrea gigas) and the rock shell (Thais clavigera) have been conducted and reported. However, no systemic mollusk genome project has so far been conducted in Korea. In this report, the current status and research trends in mollusk genome study in Korea will be discussed.
Myogenic satellite cells (MSCs) are mononuclear, multipotent progenitors of adult skeletal muscle... more Myogenic satellite cells (MSCs) are mononuclear, multipotent progenitors of adult skeletal muscle possessing a capacity of forming adipocyte-like cells (ALC). To identify the skeletal muscle type-specific myogenic and adipogenic genes during MSCs differentiation, total RNA was extracted from bovine MSCs, myotube-formed cell (MFC), and ALC from each of Beef shank, Longissimus dorsi, Deep pectoral, and Semitendinosus. DNA microarray analysis (24,000 oligo chip) comparing MSCs with MFC and ALC, respectively, revealed 135 differentially expressed genes (> 4 fold) among four cuts. Real-time PCR confirmed expression of 29 genes. Furthermore, the whole tissue sample RNAs analysis showed 6 differentially expressed genes in Beef shank. Among which, 1 gene in MSCs, 4 in MFC, and 1 in ALCs were highly expressed. This study will provide an insight for better understanding the molecular mechanism of differentiation of skeletal muscle type-specific MSCs. The identified genes may be used as marker to distinguish skeletal muscle types.
The genus Acanthamoeba can cause severe infections such as granulomatous amebic encephalitis and ... more The genus Acanthamoeba can cause severe infections such as granulomatous amebic encephalitis and amebic keratitis in humans. However, little genomic information of Acanthamoeba has been reported. Here, we constructed Acanthamoeba expressed sequence tags (EST) database (Acanthamoeba EST DB) derived from our 4 kinds of Acanthamoeba cDNA library. The Acanthamoeba EST DB contains 3,897 EST generated from amebae under various conditions of long term in vitro culture, mouse brain passage, or encystation, and downloaded data of Acanthamoeba from National Center for Biotechnology Information (NCBI) and Taxonomically Broad EST Database (TBestDB). The almost reported cDNA/genomic sequences of Acanthamoeba provide stand alone BLAST system with nucleotide (BLAST NT) and amino acid (BLAST AA) sequence database. In BLAST results, each gene links for the significant information including sequence data, gene orthology annotations, relevant references, and a BlastX result. This is the first attempt ...
Asian-Australasian Journal of Animal Sciences, 2007
In this study, we have investigated sequence variants in the PRNP gene of 20 individuals belongin... more In this study, we have investigated sequence variants in the PRNP gene of 20 individuals belonging to the Korean cattle, and have analyzed and compared genetic features between varieties of other cattle breeds. Of the 73 sequence variants identified in Korean cattle, 27 were identified for the first time in this study, whereas 46 of these polymorphisms had previously been isolated. We discovered a 2.6 kb SNP hot spot region localized on the putative promoter region of the PRNP gene. Furthermore, the copy numbers of the octapeptide repeat (24 bp indel) which is detected on the coding sequence (CDS) of the PRNP exhibited a completely homozygous 6/6 genotype which is dominant in other cattle breeds. We also characterized a new 19 bp/10 bp allele located on the putative promoter region of the PRNP gene, which represented 0.71 in allele frequency. To the best of our knowledge, this report is the first to address polymorphisms of the PRNP gene structure in Korean cattle in which BSE has yet to be discovered. Therefore, our findings may prove useful with regard to our current understanding of allelic diversity in bovine species, and may also provide new insights into the genetic factors associated with susceptibility or resistance to BSE.
Asian-Australasian Journal of Animal Sciences, 2007
As an initial step toward a better understanding of the genome structure of Korean cattle (Hanwoo... more As an initial step toward a better understanding of the genome structure of Korean cattle (Hanwoo breed) and initiation of the framework for genomic research in this bovine, the bacterial artificial chromosome (BAC) end sequencing of 21,024 clones was recently completed. Among these clones, BAC End Sequences (BESs) of 20,158 clones with high quality sequences (Phred score >20, average BES equaled 620 bp and totaled 23,585,814 bp), after editing sequencing results by eliminating vector sequences, were used initially to compare sequence homology with the known bovine chromosomal DNA sequence by using BLASTN analysis. Blast analysis of the BESs against the NCBI Genome database for Bos taurus (Build 2.1) indicated that the BESs from 13,201 clones matched bovine contig sequences with significant blast hits (E<e-40), including 7,075 single-end hits and 6,126 paired-end hits. Finally, a total of 5,105 clones of the Korean cattle BAC clones with paired-end hits, including 4,053 clones from the primary analysis and 1,052 clones from the secondary analysis, were mapped to the bovine chromosome with very high accuracy. (Key Words : Korean Cattle (Hanwoo), BAC End Sequence (BES), Chromosomal Map) MATERIALS AND METHODS BAC end sequencing Single BAC colonies were transferred into 1 ml of Terrific Broth (TB) medium supplemented with antibiotic (chloramphenicol at 12.5 卩 g/ml) using a 96-deep well plate and incubated at 37°C overnight with gentle rotation (550 rpm; HT-MegaGrow shaking incubator, Bioneer, Daejeon, Korea). The BAC DNA was extracted and purified using a Montage BAC96 miniprep kit (Millipore, Bedford, MA, USA), or modification of an alkaline lysis method commonly used for isolating plasmid DNA from bacteria (Birnboim et al., 1979; Kelley et al., 1999) designed to optimize DNA yield. BAC end sequencing was performed according to the manufacturer's instructions with a BigDye Terminator Cycle Sequencing Kit (ver. 3.1, Applied Bio systems, Foster City, CA, USA). Cycle sequencing reaction was performed with 600 ng of BAC DNA, 3 pmoles of primer, 0.87 |il of 5x buffer, 1.38 |il of distilled water and 0.5 pl of BigDye, using a GeneAmp PCR System 9700 (Applied Biosystems). The universal sequences of primers used for the forward primer was T7 and the reverse primer were slightly modified RP2 or M13R. Amplification was conducted at 96OC for 2 min and 80 cycles of denaturation at 96OC for 15 sec, annealing at 50OC for 10 sec, and extension at 60OC for 2.5 min. PCR products were purified by ethanol precipitation and resolved on an ABI 3730XL DNA Analyzer (Applied Biosystems). Sequence analysis Sequence chromatograms were processed automatically using sequencing analysis software (Sequencing analysis; ver. 3.7, Applied Biosystems). The trace files were trimmed with trim-alt 0.05 (P-score >20) using Phred program (Ewing and Green, 1998; Ewing et al., 1998) and the sequence below 100 bp was removed. In addition, vector trimming was conducted using cross-match software (http://www.phrap.org). Repetitive elements were identified with the RepeatMasker program (Jurka et al., 2005) to determine the relative content of interspersed repeats, small RNAs, satellites, simple repeats and low complexity sequences in the nucleotide sequences. Finally cleaned multi-fasta formatted data with the RepeatMasker program and Repbase database (ver 2006.2) were analyzed with NCBI local BLAST (Altschul et al., 1990) and sequences were searched against the NCBI Bos taurus genome data (build 2.1 based on Btau 2.0). 5M 10M 15M 20M 25M
Rodent malaria parasites, such as Plasmodium berghei, are practical and useful model organisms fo... more Rodent malaria parasites, such as Plasmodium berghei, are practical and useful model organisms for human malaria research because of their analogies to the human malaria in terms of structure, physiology, and life cycle. Exploit ing the available genetic sequence information, we constructed a cDNA library from the erythrocytic stages of P. berghei and analyzed the expressed sequence tag (EST). A total of 10,040 ESTs were generated and assembled into 2,462 clus ters. These EST clusters were compared against public protein databases and 48 putative new transcripts, most of which were hypothetical proteins with unknown function, were identified. Genes encoding ribosomal or membrane proteins and purine nucleotide phosphorylases were highly abundant clusters in P. berghei. Protein domain analyses and the Gene On tology functional categorization revealed translation/protein folding, metabolism, protein degradation, and multiple family of variant antigens to be mainly prevalent. The presentlycollected ESTs and its bioinformatic analysis will be useful re sources to identify for drug target and vaccine candidates and validate gene predictions of P. berghei.
Genomic analysis of Feldmannia sp. virus 158, the second phaeovirus to be sequenced in its entire... more Genomic analysis of Feldmannia sp. virus 158, the second phaeovirus to be sequenced in its entirety, provides further evidence that large double-stranded DNA viruses share similar evolutionary pressures as cellular organisms. Reductive evolution is clearly evident within the phaeoviruses which occurred via several routes: the loss of genes from an ancestral virus core genome most likely through genetic drift; and as a result of relatively large recombination events that caused wholesale loss of genes. The entire genome is 154,641 bp in length and has 150 predicted coding sequences of which 87% have amino acid sequence similarities to other algal virus coding sequences within the family Phycodnaviridae. Significant similarities were found, for thirty eight coding sequences (25%), to genes in gene databanks that are known to be involved in processes that include DNA replication, DNA methylation, signal transduction, viral integration and transposition, and protein-protein interactions. Unsurprisingly, the greatest similarity was observed between the two known viruses that infect Feldmannia, indicating the taxonomic linkage of these two viruses with their hosts. Moreover, comparative analysis of phycodnaviral genomic sequences revealed the smallest set of core genes (10 out of a possible 31) required to make a functional nucleocytoplasmic large dsDNA virus.
We report a systematic study of gene expression during myogenesis and transdifferentiation in fou... more We report a systematic study of gene expression during myogenesis and transdifferentiation in four bovine muscle tissues and of adipogenesis in three bovine fat tissues using DNA microarray analysis. One hundred hybridizations were performed and 7245 genes of known and unknown function were identified as being differentially expressed. Supervised hierarchical cluster analysis of gene expression patterns revealed the tissue specificity of genes. A close relationship in global gene expression observed for adipocyte-like cells derived from muscle and adipocytes derived from intramuscular fat suggests a common origin for these cells. The role of transthyretin in myogenesis is a novel finding. Different genes were highly induced during the transdifferentiation of myogenic satellite cells and in the adipogenesis of preadipocytes, indicating the involvement of different molecular mechanisms in these processes. Induction of CD36 and FABP4 expression in adipocyte-like cells and adipocytes may share a common pathway.
ABSTRACTPhage display of single-chain variable fragment (scFv) antibodies is a powerful tool for ... more ABSTRACTPhage display of single-chain variable fragment (scFv) antibodies is a powerful tool for selecting important, useful, and specific human antibodies. We constructed a library from three patients infected withPlasmodium vivax. Panning on recombinant PvRII enriched a population of scFvs that recognized region II of theP. vivaxDuffy binding protein (DBP). Three clones of scFvs that reacted with PvRII were selected, and their biological functions were analyzed. These scFvs inhibited erythrocyte binding to DBP. Clone SFDBII92 had the greatest affinity (dissociation constant = 3.62 × 10−8M) and the greatest inhibition activity (50% inhibitory concentration ≈ 2.9 μg/ml) to DBP. Thus, we demonstrated that human neutralizing antibody could be made from malaria patients using phage display and that these neutralizing scFvs should prove valuable for developing both passive and active immunization strategies based on DBP.
Anisakis simplex is one of the parasitic nematodes, and has a complex life cycle in crustaceans, ... more Anisakis simplex is one of the parasitic nematodes, and has a complex life cycle in crustaceans, fish, squid or whale. When people eat under-processed or raw fish, it causes anisakidosis and also plays a critical role in inducing serious allergic reactions in humans. However, no web-based database on A. simplex at the level of DNA or protein has been so far reported. In this context, we constructed a web-based database for Anisakis research. To build up the web-based database for Anisakis research, we proceeded with the following measures: First, sequences of order Ascaridida were downloaded and translated into the multifasta format which was stored as database for stand-alone BLAST. Second, all of the nucleotide and EST sequences were clustered and assembled. And EST sequences were translated into amino acid sequences for Nuclear Localization Signal prediction. In addition, we added the vector, E. coli, and repeat sequences into the database to confirm a potential contamination. The web-based database gave us several advantages. Only data that agrees with the nucleotide sequences directly related with the order Ascaridida can be found and retrieved when searching BLAST. It is also very convenient to confirm contamination when making the cDNA or genomic library from Anisakis. Furthermore, BLAST results on the Anisakis sequence information can be quickly accessed. Taken together, the Web-based database on A. simplex will be valuable in developing species specific PCR markers and in studying SNP in A. simplex-related researches in the future.
Recently, the 2 nd generation genome map of the Korean cattle (Hanwoo) has been constructed by co... more Recently, the 2 nd generation genome map of the Korean cattle (Hanwoo) has been constructed by comparison of the nucleotide sequence of the Korean cattle BAC clones with whole genome sequence of the bovine database (B_tau 2.1 build). The objective of this study was to update the 2 nd generation genome map of the Korean cattle using the similar approach. The nucleotide sequence of the Korean cattle BAC clones utilized in the construction of the 2 nd generation map was compared with the newly released bovine database (B_tau 3.1 build) to generate the 3 rd generation map. While, 5,105 BAC clones were localized on bovine chromosome in the 2 nd generation map, a total of 9,595 BAC clones, which spans about 37.27% of the bovine chromosome after eliminating the overlapping sequence among the clones, have been mapped on the bovine chromosome in the 3 rd generation map. Further analysis of the nucleotide sequence of the BAC clones will allow us to develop map and facilitate to pinpoint the genes that are important for the improvement of the performance in this cattle breed.
Up until now, we have identified 17 exotic species of Mollusca in Korea. These include Achatina (... more Up until now, we have identified 17 exotic species of Mollusca in Korea. These include Achatina (Lissachatina)
The availability of fast and inexpensive sequencing technology has enabled researchers around the... more The availability of fast and inexpensive sequencing technology has enabled researchers around the world to conduct many genome sequencing and expressed sequence tag (EST) projects of diverse organisms. In recent years, whole genome projects have been undertaken to sequence ten species from the phylum Mollusca. These include Aplysia californica, Lottia gigantea, Crassostrea virginica, Spisula solidissima, Mytilus californianus, Biomphalaria glabrata, Crepidula fornicata, Elysia chlorotica, Lottia scutum and Radix balthica. Additionally, complete mitochondrial genomes of 91 mollusks have been reported. In Korea, EST projects have been conducted in nine mollusk species that include Nesiohelix samarangae, Pisidium (Neopisidium) coreanum, Physa acuta, Incilaria fruhstorferi, Meretrix lusoria, Ruditapes philippinarum, Nordotis gigantea, Crassostrea gigas and Laternula elliptica. Finally, the mitochondrial genome projects from the Pacific Oyster (Crassostrea gigas) and the rock shell (Thais clavigera) have been conducted and reported. However, no systemic mollusk genome project has so far been conducted in Korea. In this report, the current status and research trends in mollusk genome study in Korea will be discussed.
Myogenic satellite cells (MSCs) are mononuclear, multipotent progenitors of adult skeletal muscle... more Myogenic satellite cells (MSCs) are mononuclear, multipotent progenitors of adult skeletal muscle possessing a capacity of forming adipocyte-like cells (ALC). To identify the skeletal muscle type-specific myogenic and adipogenic genes during MSCs differentiation, total RNA was extracted from bovine MSCs, myotube-formed cell (MFC), and ALC from each of Beef shank, Longissimus dorsi, Deep pectoral, and Semitendinosus. DNA microarray analysis (24,000 oligo chip) comparing MSCs with MFC and ALC, respectively, revealed 135 differentially expressed genes (> 4 fold) among four cuts. Real-time PCR confirmed expression of 29 genes. Furthermore, the whole tissue sample RNAs analysis showed 6 differentially expressed genes in Beef shank. Among which, 1 gene in MSCs, 4 in MFC, and 1 in ALCs were highly expressed. This study will provide an insight for better understanding the molecular mechanism of differentiation of skeletal muscle type-specific MSCs. The identified genes may be used as marker to distinguish skeletal muscle types.
The genus Acanthamoeba can cause severe infections such as granulomatous amebic encephalitis and ... more The genus Acanthamoeba can cause severe infections such as granulomatous amebic encephalitis and amebic keratitis in humans. However, little genomic information of Acanthamoeba has been reported. Here, we constructed Acanthamoeba expressed sequence tags (EST) database (Acanthamoeba EST DB) derived from our 4 kinds of Acanthamoeba cDNA library. The Acanthamoeba EST DB contains 3,897 EST generated from amebae under various conditions of long term in vitro culture, mouse brain passage, or encystation, and downloaded data of Acanthamoeba from National Center for Biotechnology Information (NCBI) and Taxonomically Broad EST Database (TBestDB). The almost reported cDNA/genomic sequences of Acanthamoeba provide stand alone BLAST system with nucleotide (BLAST NT) and amino acid (BLAST AA) sequence database. In BLAST results, each gene links for the significant information including sequence data, gene orthology annotations, relevant references, and a BlastX result. This is the first attempt ...
Asian-Australasian Journal of Animal Sciences, 2007
In this study, we have investigated sequence variants in the PRNP gene of 20 individuals belongin... more In this study, we have investigated sequence variants in the PRNP gene of 20 individuals belonging to the Korean cattle, and have analyzed and compared genetic features between varieties of other cattle breeds. Of the 73 sequence variants identified in Korean cattle, 27 were identified for the first time in this study, whereas 46 of these polymorphisms had previously been isolated. We discovered a 2.6 kb SNP hot spot region localized on the putative promoter region of the PRNP gene. Furthermore, the copy numbers of the octapeptide repeat (24 bp indel) which is detected on the coding sequence (CDS) of the PRNP exhibited a completely homozygous 6/6 genotype which is dominant in other cattle breeds. We also characterized a new 19 bp/10 bp allele located on the putative promoter region of the PRNP gene, which represented 0.71 in allele frequency. To the best of our knowledge, this report is the first to address polymorphisms of the PRNP gene structure in Korean cattle in which BSE has yet to be discovered. Therefore, our findings may prove useful with regard to our current understanding of allelic diversity in bovine species, and may also provide new insights into the genetic factors associated with susceptibility or resistance to BSE.
Asian-Australasian Journal of Animal Sciences, 2007
As an initial step toward a better understanding of the genome structure of Korean cattle (Hanwoo... more As an initial step toward a better understanding of the genome structure of Korean cattle (Hanwoo breed) and initiation of the framework for genomic research in this bovine, the bacterial artificial chromosome (BAC) end sequencing of 21,024 clones was recently completed. Among these clones, BAC End Sequences (BESs) of 20,158 clones with high quality sequences (Phred score >20, average BES equaled 620 bp and totaled 23,585,814 bp), after editing sequencing results by eliminating vector sequences, were used initially to compare sequence homology with the known bovine chromosomal DNA sequence by using BLASTN analysis. Blast analysis of the BESs against the NCBI Genome database for Bos taurus (Build 2.1) indicated that the BESs from 13,201 clones matched bovine contig sequences with significant blast hits (E<e-40), including 7,075 single-end hits and 6,126 paired-end hits. Finally, a total of 5,105 clones of the Korean cattle BAC clones with paired-end hits, including 4,053 clones from the primary analysis and 1,052 clones from the secondary analysis, were mapped to the bovine chromosome with very high accuracy. (Key Words : Korean Cattle (Hanwoo), BAC End Sequence (BES), Chromosomal Map) MATERIALS AND METHODS BAC end sequencing Single BAC colonies were transferred into 1 ml of Terrific Broth (TB) medium supplemented with antibiotic (chloramphenicol at 12.5 卩 g/ml) using a 96-deep well plate and incubated at 37°C overnight with gentle rotation (550 rpm; HT-MegaGrow shaking incubator, Bioneer, Daejeon, Korea). The BAC DNA was extracted and purified using a Montage BAC96 miniprep kit (Millipore, Bedford, MA, USA), or modification of an alkaline lysis method commonly used for isolating plasmid DNA from bacteria (Birnboim et al., 1979; Kelley et al., 1999) designed to optimize DNA yield. BAC end sequencing was performed according to the manufacturer's instructions with a BigDye Terminator Cycle Sequencing Kit (ver. 3.1, Applied Bio systems, Foster City, CA, USA). Cycle sequencing reaction was performed with 600 ng of BAC DNA, 3 pmoles of primer, 0.87 |il of 5x buffer, 1.38 |il of distilled water and 0.5 pl of BigDye, using a GeneAmp PCR System 9700 (Applied Biosystems). The universal sequences of primers used for the forward primer was T7 and the reverse primer were slightly modified RP2 or M13R. Amplification was conducted at 96OC for 2 min and 80 cycles of denaturation at 96OC for 15 sec, annealing at 50OC for 10 sec, and extension at 60OC for 2.5 min. PCR products were purified by ethanol precipitation and resolved on an ABI 3730XL DNA Analyzer (Applied Biosystems). Sequence analysis Sequence chromatograms were processed automatically using sequencing analysis software (Sequencing analysis; ver. 3.7, Applied Biosystems). The trace files were trimmed with trim-alt 0.05 (P-score >20) using Phred program (Ewing and Green, 1998; Ewing et al., 1998) and the sequence below 100 bp was removed. In addition, vector trimming was conducted using cross-match software (http://www.phrap.org). Repetitive elements were identified with the RepeatMasker program (Jurka et al., 2005) to determine the relative content of interspersed repeats, small RNAs, satellites, simple repeats and low complexity sequences in the nucleotide sequences. Finally cleaned multi-fasta formatted data with the RepeatMasker program and Repbase database (ver 2006.2) were analyzed with NCBI local BLAST (Altschul et al., 1990) and sequences were searched against the NCBI Bos taurus genome data (build 2.1 based on Btau 2.0). 5M 10M 15M 20M 25M
Rodent malaria parasites, such as Plasmodium berghei, are practical and useful model organisms fo... more Rodent malaria parasites, such as Plasmodium berghei, are practical and useful model organisms for human malaria research because of their analogies to the human malaria in terms of structure, physiology, and life cycle. Exploit ing the available genetic sequence information, we constructed a cDNA library from the erythrocytic stages of P. berghei and analyzed the expressed sequence tag (EST). A total of 10,040 ESTs were generated and assembled into 2,462 clus ters. These EST clusters were compared against public protein databases and 48 putative new transcripts, most of which were hypothetical proteins with unknown function, were identified. Genes encoding ribosomal or membrane proteins and purine nucleotide phosphorylases were highly abundant clusters in P. berghei. Protein domain analyses and the Gene On tology functional categorization revealed translation/protein folding, metabolism, protein degradation, and multiple family of variant antigens to be mainly prevalent. The presentlycollected ESTs and its bioinformatic analysis will be useful re sources to identify for drug target and vaccine candidates and validate gene predictions of P. berghei.
Genomic analysis of Feldmannia sp. virus 158, the second phaeovirus to be sequenced in its entire... more Genomic analysis of Feldmannia sp. virus 158, the second phaeovirus to be sequenced in its entirety, provides further evidence that large double-stranded DNA viruses share similar evolutionary pressures as cellular organisms. Reductive evolution is clearly evident within the phaeoviruses which occurred via several routes: the loss of genes from an ancestral virus core genome most likely through genetic drift; and as a result of relatively large recombination events that caused wholesale loss of genes. The entire genome is 154,641 bp in length and has 150 predicted coding sequences of which 87% have amino acid sequence similarities to other algal virus coding sequences within the family Phycodnaviridae. Significant similarities were found, for thirty eight coding sequences (25%), to genes in gene databanks that are known to be involved in processes that include DNA replication, DNA methylation, signal transduction, viral integration and transposition, and protein-protein interactions. Unsurprisingly, the greatest similarity was observed between the two known viruses that infect Feldmannia, indicating the taxonomic linkage of these two viruses with their hosts. Moreover, comparative analysis of phycodnaviral genomic sequences revealed the smallest set of core genes (10 out of a possible 31) required to make a functional nucleocytoplasmic large dsDNA virus.
We report a systematic study of gene expression during myogenesis and transdifferentiation in fou... more We report a systematic study of gene expression during myogenesis and transdifferentiation in four bovine muscle tissues and of adipogenesis in three bovine fat tissues using DNA microarray analysis. One hundred hybridizations were performed and 7245 genes of known and unknown function were identified as being differentially expressed. Supervised hierarchical cluster analysis of gene expression patterns revealed the tissue specificity of genes. A close relationship in global gene expression observed for adipocyte-like cells derived from muscle and adipocytes derived from intramuscular fat suggests a common origin for these cells. The role of transthyretin in myogenesis is a novel finding. Different genes were highly induced during the transdifferentiation of myogenic satellite cells and in the adipogenesis of preadipocytes, indicating the involvement of different molecular mechanisms in these processes. Induction of CD36 and FABP4 expression in adipocyte-like cells and adipocytes may share a common pathway.
ABSTRACTPhage display of single-chain variable fragment (scFv) antibodies is a powerful tool for ... more ABSTRACTPhage display of single-chain variable fragment (scFv) antibodies is a powerful tool for selecting important, useful, and specific human antibodies. We constructed a library from three patients infected withPlasmodium vivax. Panning on recombinant PvRII enriched a population of scFvs that recognized region II of theP. vivaxDuffy binding protein (DBP). Three clones of scFvs that reacted with PvRII were selected, and their biological functions were analyzed. These scFvs inhibited erythrocyte binding to DBP. Clone SFDBII92 had the greatest affinity (dissociation constant = 3.62 × 10−8M) and the greatest inhibition activity (50% inhibitory concentration ≈ 2.9 μg/ml) to DBP. Thus, we demonstrated that human neutralizing antibody could be made from malaria patients using phage display and that these neutralizing scFvs should prove valuable for developing both passive and active immunization strategies based on DBP.
Anisakis simplex is one of the parasitic nematodes, and has a complex life cycle in crustaceans, ... more Anisakis simplex is one of the parasitic nematodes, and has a complex life cycle in crustaceans, fish, squid or whale. When people eat under-processed or raw fish, it causes anisakidosis and also plays a critical role in inducing serious allergic reactions in humans. However, no web-based database on A. simplex at the level of DNA or protein has been so far reported. In this context, we constructed a web-based database for Anisakis research. To build up the web-based database for Anisakis research, we proceeded with the following measures: First, sequences of order Ascaridida were downloaded and translated into the multifasta format which was stored as database for stand-alone BLAST. Second, all of the nucleotide and EST sequences were clustered and assembled. And EST sequences were translated into amino acid sequences for Nuclear Localization Signal prediction. In addition, we added the vector, E. coli, and repeat sequences into the database to confirm a potential contamination. The web-based database gave us several advantages. Only data that agrees with the nucleotide sequences directly related with the order Ascaridida can be found and retrieved when searching BLAST. It is also very convenient to confirm contamination when making the cDNA or genomic library from Anisakis. Furthermore, BLAST results on the Anisakis sequence information can be quickly accessed. Taken together, the Web-based database on A. simplex will be valuable in developing species specific PCR markers and in studying SNP in A. simplex-related researches in the future.
Recently, the 2 nd generation genome map of the Korean cattle (Hanwoo) has been constructed by co... more Recently, the 2 nd generation genome map of the Korean cattle (Hanwoo) has been constructed by comparison of the nucleotide sequence of the Korean cattle BAC clones with whole genome sequence of the bovine database (B_tau 2.1 build). The objective of this study was to update the 2 nd generation genome map of the Korean cattle using the similar approach. The nucleotide sequence of the Korean cattle BAC clones utilized in the construction of the 2 nd generation map was compared with the newly released bovine database (B_tau 3.1 build) to generate the 3 rd generation map. While, 5,105 BAC clones were localized on bovine chromosome in the 2 nd generation map, a total of 9,595 BAC clones, which spans about 37.27% of the bovine chromosome after eliminating the overlapping sequence among the clones, have been mapped on the bovine chromosome in the 3 rd generation map. Further analysis of the nucleotide sequence of the BAC clones will allow us to develop map and facilitate to pinpoint the genes that are important for the improvement of the performance in this cattle breed.
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Papers by YONGSEOK LEE