Kyungtaek Lim

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Ribosomal RNA (rRNA) genes, essential to all forms of life, have been viewed as highly conserved and evolutionarily stable, partly because very little is known about their natural variations. Here, we explored large-scale variations of rRNA genes through bioinformatic analyses of available complete bacterial genomic sequences with an emphasis on formation(More)
Enterococcus isolates (1500) obtained from the feces of 48 humans, 209 domesticated food animals, and 155 wild geese in South Korea were characterized with respect to species status by PCR analyses and resistance to antibiotics. Of the 1500 strains examined, the majority (n=577) were Enterococcus faecalis from 224 (54.4%) of the samples feces, while 299(More)
Myeloid-derived suppressor cells (MDSCs) actively suppress immune cells and have been considered as an impediment to successful cancer immunotherapy. Many approaches have been made to overcome such immunosuppressive factors and to exert effective anti-tumor effects, but the possibility of using medicinal plants for this purpose has been overlooked. Korean(More)
Background In prokaryotes, the Shine-Dalgarno (SD) sequence in the 5’ untranslated region (UTR) of mRNA forms a duplex with the anti-Shine-Dalgarno (anti-SD) sequence to initiate translation [1]. The mechanism has been regarded as universal, as the core of the anti-SD sequence (5’-CCTCC3’, anti-SD motif) is completely conserved in every prokaryote genome(More)
Protein database search for public databases is a fundamental step in the target selection of proteins in structural and functional genomics and also for inferring protein structure, function, and evolution. Most database search methods employ amino acid substitution matrices to score amino acid pairs. The choice of substitution matrix strongly affects(More)
PSI-BLAST, an extremely popular tool for sequence similarity search, features the utilization of Position-Specific Scoring Matrix (PSSM) constructed from a multiple sequence alignment (MSA). PSSM allows the detection of more distant homologs than a general amino acid substitution matrix does. An accurate estimation of the weights for sequences in an MSA is(More)
Translation initiation depends on the recognition of mRNA by a ribosome. For this to occur, prokaryotes primarily use the Shine-Dalgarno (SD) interaction, where the 3'-tail of small subunit rRNA (core motif: 3'CCUCC) forms base pairs with a complementary signal sequence in the 5'-untranslated region of mRNA. Here, we examined what happened to SD(More)
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