• Journal of Life Science
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• v.11 no.2
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• pp.74-80
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• 2001

The nucleotide sequences of the internal transcribed spacer regions (ITS1 and ITS2) of ribosomal DNA (rDNA), and the 5.85 rRNA gene, have been determined for 13 strains of dinoflagellates in order to analyze the phylo-genetic relationship. The DNA sequences contained considerable variation in the ITS regions, but little in the 5.85 rDNA. In addition, the ITS1 was more variable than the ITS2 in all species examined. The nucleotide length of this region varied from 519 bp to 596 bp depending on the taxa. The investigated taxa were divided into three large groups based on the ITS length, i. e., a group with short ITS region (A. fraterculus and Alexandrium sp.), a with ITS region group (P. micans, P. minimum and P. triestinum) and a with ITS region group (G. impudicum, C. polykrikoides, G. sanguineum, G. catenatum and H. triquetra). The relationship between nucleotide length of ITS1 and that of ITS2 was negative, whereas G+C content and nucleotide length showed positive correlation. In phylogenetic analyses producing NJ trees, the topology was similar cluster and clearly divided the taxa into three groups based on 5.8S rDNA that were similar to those based on morphological characteristics. In particular, G. impudicum was more closely related to G. catenatum than to C. polykrikoides using phylogenetic analysis. From this study, we chew that the length of ITS region contributes to discriminate Korean harmful algal species and ITS analysis is a useful method for resolving the systematic relationships of dinoflagellates.

• Journal of Life Science
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• v.8 no.3
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• pp.279-284
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• 1998

The nucleotide sequences of the 5'-untraslated region(5'-UTR) of Hepatitis G virus(HGV) from sera of Korean patients were determines. When compared to the previously reported isolates, the Korean isolates have higher sequence homology with the Japanese isolates indicating the geographic distribution of HGV variants. Interestingly, three discrete regions which are highly conserved among HGV isolates from the same geographical area, thus could be applied to distinguish HGV isolates from the different areas were noticed in the 5'-UTR. Based on the sequences of these group-specific regions, twenty four different HGV isolates could be classified into 5 groups. By using the group-specific regions, inconsistency in HGV typing when based on the different regions of HGV could be solved.

• Journal of the Korean Society for Industrial and Applied Mathematics
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• v.11 no.2
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• pp.9-14
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• 2007

A signed 3-partite graph is a 3-partite graph in which each edge is assigned a positive or a negative sign. Let G(U, V, W) be a signed 3-partite graph with $U\;=\;\{u_1,\;u_2,\;{\cdots},\;u_p\},\;V\;=\;\{v_1,\;v_2,\;{\cdots},\;v_q\}\;and\;W\;=\;\{w_1,\;w_2,\;{\cdots},\;w_r\}$. Then, signed degree of $u_i(v_j\;and\;w_k)$ is $sdeg(u_i)\;=\;d_i\;=\;d^+_i\;-\;d^-_i,\;1\;{\leq}\;i\;{\leq}\;p\;(sdeg(v_j)\;=\;e_j\;=\;e^+_j\;-\;e^-_j,\;1\;{\leq}\;j\;{\leq}q$ and $sdeg(w_k)\;=\;f_k\;=\;f^+_k\;-\;f^-_k,\;1\;{\leq}\;k\;{\leq}\;r)$ where $d^+_i(e^+_j\;and\;f^+_k)$ is the number of positive edges incident with $u_i(v_j\;and\;w_k)$ and $d^-_i(e^-_j\;and\;f^-_k)$ is the number of negative edges incident with $u_i(v_j\;and\;w_k)$. The sequences ${\alpha}\;=\;[d_1,\;d_2,\;{\cdots},\;d_p],\;{\beta}\;=\;[e_1,\;e_2,\;{\cdots},\;e_q]$ and ${\gamma}\;=\;[f_1,\;f_2,\;{\cdots},\;f_r]$ are called the signed degree sequences of G(U, V, W). In this paper, we characterize the signed degree sequences of signed 3-partite graphs.

• Journal of KIISE:Computing Practices and Letters
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• v.16 no.3
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• pp.275-280
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• 2010

A local alignment algorithm finds a substring pair of given two strings where two substrings of the pair are similar to each other. A DNA sequence can consist of not only A, C, G, and T but also N and X where N and X are used when the original bases lose their information for various reasons. In this paper, we present an efficient local alignment algorithm for two DNA sequences including N and X using the affine gap penalty metric. Our algorithm is an extended version of the Kim-Park algorithm and can be extended in case of including other characters which have similar properties to N and X.

• BMB Reports
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• v.34 no.1
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• pp.51-58
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• 2001

Attempts using in vitro and in vivo selection procedures have been made to search for hammerhead ribozymes that have higher activities than the wild-type ribozyme and also to determine whether other sequences might be possible in the catalytic core of the hammerhead ribozyme. Active sequences selected in the past conformed broadly to the consensus core sequence except at A9, and no sequences were associated with higher activity than that of the hammerhead with the consensus core, an indication that the consensus sequence derived from viruses and virusoids is probably the optimal sequence [Vaish et al. (1997) Biochemistry 36, 6495-6501]. Recently, during construction of ribozyme expression vectors, we isolated a mutant hammerhead ribozyme, with an insertion of G between A9 and G10.1, that appeared to show significant activity [Kawasaki et al. (1996) Nucleic Acids Res. 24, 3010-3016; Kawasaki et al. (1998) Nature 393, 284-289]. We, therefore, characterized kinetic properties of the G-inserted mutant ribozymes in terms of the NUX rule. We demonstrate that the NUX rule is basically applicable to the G-inserted ribozymes and, more importantly, one type of G-inserted ribozyme was very active with $k_{cat}$, value of $6.4\;min^{-1}$ in 50 mM Tris-HCl (pH 8.0) and 10 mM $MgCl_2$ at $37^{\circ}C$.

• Food Science and Biotechnology
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• v.17 no.6
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• pp.1285-1288
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• 2008

The purpose of this study was to characterize and investigate the immune activity of CpG oligodeoxynucleotides (ODNs) from Bifidobacterium longum. Bacterial CpG motifs have attracted considerable interests because of their immunomodulatory activities. Genomic DNA from B. longum was prepared and amplified for 4 different 180-188-mer double-stranded ODNs (BLODN1-BLODN4). When immune cells (RAW 264.7 murine macrophages and JAWS II dendritic cells) with these ODNs were treated, BLODN4 induced the highest immune activity. To assess the effectiveness of the CpG sequences within BLODN4, single-stranded 40-mer ODNs containing CpG sequences (sBLODN4-1, sBLODN4-2) were synthesized. sBLODN4-1 induced higher level of cytokines such as interleukin (IL)-12p40 and tumor necrosis factor (TNF)-$\alpha$ by macrophage and IL-6 and TNF-$\alpha$ by dendritic cells than did sBLODN4-2. The results suggest that CpG ODNs-enriched components of B. longum might be useful as an immunomodulatory functional food ingredient.

• Journal of applied mathematics & informatics
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• v.20 no.1_2
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• pp.171-180
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• 2006

Two infinite classes of special finite groups considered (The group G is special, if G' and Z(G) coincide). Using certain sequences of numbers we give explicit formulas for the Fibonacci lenghts of these classes which involve the well-known Wall numbers k(n).

• Phonetics and Speech Sciences
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• v.5 no.1
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• pp.109-121
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• 2013

This study examined several kinematic properties of the primary articulator (the tongue dorsum) and the supplementary articulator (the jaw) in the articulation of the voiceless velar stop (/k/) within nonassimilating contexts. We examined in particular the spatiotemporal properties (constriction duration and constriction maxima) from the constriction onset to the constriction offset by analyzing a velar (/k/) followed by the coronal fricative (/s/), the coronal stop (/t/), and the labial (/p/) in across-word boundary conditions (/k#s/, /k#t/, and /k#p/). Along with these measurements, we investigated intergestural temporal coordination between C1 and C2 and the jaw articulator in relation to its coordination with the articulation of consonant sequences. The articulatory movement data was collected by means of electromagnetic midsagittal articulometry (EMMA). Four native speakers of Seoul Korean participated in the laboratory experiment. The results showed several characteristics. First, a velar (/k/) in C1 was not categorically reduced. Constriction duration and constriction degree of the velar (/k/) were similar within nonassimilating contexts (/k#s/=/k#t/=/k#p/). This might mean that spatiotemporal attributes during constriction duration were stable and consistent across different contexts, which might be subsequently associated with the nontarget status of the velar in place assimilation. Second, the gestural overlap could be represented as the order of /k#s/ (less) < /k#p/ (intermediate) < /k#t/ (more) as we measured the onset-to-onset lag (a longer lag indicated shorter gestural overlap.). This indicates a gestural overlap within nonassimilating contexts may not be constrained by any of the several constraints including the perceptual recoverability constraint (e.g., more overlap in Front-to-Back sequences compared to the reverse order (Back-to-Front) since perceptual cues in C1 can be recovered anytime during C2 articulation), the low-level speech motor constraint (e.g., more overlap in lingual-nonlingual sequences as compared to the lingual-lingual sequences), or phonological contexts effects (e.g., similarity in gestural overlap within nonassimilating contexts). As one possible account for more overlap in /k#t/ sequences as compared to /k#p/, we suspect speakers' knowledge may be receptive to extreme encroachment on C1 by the gestural overlap of the coronal in C2 since it does not obscure the perceptual cue of C1 as much as the labial in C2. Third, actual jaw position during C2 was higher in coronals (/s/, /t/) than in the labial (/p/). However, within the coronals, there was no manner-dependent jaw height difference in C2 (/s/=/t/). Vertical jaw position of C1 and C2 was seen as inter-dependent as higher jaw position in C1 was closely associated with C2. Lastly, a greater gap in jaw height was associated with longer intergestural timing (e.g., less overlap), but was confined to the cluster type (/kp/) with the lingual-nonlingual sequence. This study showed that Korean jaw articulation was independent from coordinating primary articulators in gestural overlap in some cluster types (/k#s/, /k#t/) while not in others (e.g., /k#p/). Overall, the results coherently indicate the velar stop (/k/) in C1 was robust in articulation, which may have subsequently contributed to the nontarget status of the velar (/k/) in place assimilation processes.

• Journal of the Korean Society of Tobacco Science
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• v.28 no.2
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• pp.94-99
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• 2006

AFLP(Amplified Fragment Length Polymorphism) analysis was conducted to cultivars of tobacco, Nicotiana tabacum in order to select the cultivar-specific markers. AFLP results using 12 primer sets revealed genetic diversity among 12 field grown tobacco cultivars. Polymorphic fragments amplified by PCR was purified and cloned to identify their nucleotide sequences. From the sequences of them, 40 primer sets were designed to select cultivar-specific markers. When genomic DNA isolated from tobacco were used as PCR template, a set of primers, BrSF/BrSR showed Burley-specific band patterns. The results indicate that AFLP technique used in this experiments is useful for identifying tobacco cultivars in a rapid manner.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.3
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• pp.1151-1157
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• 2015

Human papillomavirus (HPV) is responsible for one of the most frequent sexually transmitted infections. The first phylogenetic analysis was based on a LCR region fragment. Nowadays, 4 variants are known: African (Af-1, Af-2), Asian-American (AA) and European (E). However the existence of sub-lineages of the European variant havs been proposed, specific mutations in the E6 and LCR sequences being possibly related to persistent viral infections. The aim of this study was a phylogenetic study of HPV16 sequences of endocervical samples from C${\acute{o}}$rdoba, in order to detect the circulating lineages and analyze the presence of mutations that could be correlated with malignant disease. The phylogenetic analysis determined that 86% of the samples belonged to the E variant, 7% to AF-1 and the remaining 7% to AF-2. The most frequent mutation in LCR sequences was G7521A, in 80% of the analyzed samples; it affects the binding site of a transcription factor that could contribute to carcinogenesis. In the E6 sequences, the most common mutation was T350G (L83V), detected in 67% of the samples, associated with increased risk of persistent infection. The high detection rate of the European lineage correlated with patterns of human migration. This study emphasizes the importance of recognizing circulating lineages, as well as the detection of mutations associated with high-grade neoplastic lesions that could be correlated to the development of carcinogenic lesions.