• Journal of the Korean Chemical Society
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• v.39 no.9
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• pp.734-740
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• 1995

The primary and secondary structures of Xanthomonas palargonii 5S rRNA were determined. The higher order structure of the 5S rRNA was also analysed using several ribonucleases and chemical probes, such as ethylnitrourea, Pb2+, dimethylsulfate and diethyl pyrocarbonate. Ethylnitrourea was used for probing the phosphate groups involved in the tertiary interactions in the 5S rRNA. Nucleotides G72, A73, G75, A78, G98, G100 and A101 in unstable helical region d, nucleotides C36, C37, A39, and C41 in loop c, nucleotides A29 and G33 in stem C became resistant to ethylnitrourea modification in the presence of Mg2+. On the basis of findings from chemical and enzymatic studies, and also Pb2+-induced cleavages, it was concluded that region b-C and unstable helical region d may act as hinges in the folding of 5S rRNA.

• The Korea Journal of Herbology
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• v.28 no.3
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• pp.75-84
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• 2013

Objectives : The origin of Breeae Herba (So-gye) and Cirsii Herba (Dae-gye) is differently prescribed in Korean and Chinese modern pharmacopoeia. Since the similar morphological characteristics and chaotic plant names, moreover, the aerial part of Carduus crispus have been used as the Cirsii Herba. To develop a reliable method for correct identification of these herbal medicines and to evaluate the genetic relationship of these closely related plant species, we analyzed sequences of DNA barcode regions. Methods : Thirty-one samples of 6 medicinal plants (B. segeta, B. setosa, C. japonicum var. maackii, C. setidens, C. chanroenicum, and C. crispus) were collected from different habitate and nucleotide sequences of DNA barcode regions (rDNA-ITS, matK, and rbcL) were analyzed after amplification using appropriate primers reported in previous studies. The nucleotides of species-specific authentic marker and phylogenetic relations were estimated based on the entire sequences of DNA barcodes by the analysis of ClastalW and UPGMA, respectively. Results : In comparative analysis of DNA barcode sequences, we obtained specific nucleotides to discriminate the medicinal plant of Breeae/Cirsii Herba in species level and evaluated the phylogenetic relationship of these species. Futhermore, we identified distinct marker nucleotides enough to authenticate respective species. These sequence differences at corresponding positions were avaliable genetic markers to determine the botanical origins of Breeae Herbal as well as Cirsii Herba. Conclusions : These marker nucleotides would be useful to identify the official herbal medicines by providing of definitive information that can identify each plant species and distinguish from unauthentic adulterants and substitutes.

• The Plant Pathology Journal
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• v.15 no.5
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• pp.270-279
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• 1999

cDNAs complementary to the 3'-terminal regions of two potyvirus genomes were cloned and sequenced. The clone G7 contains one open reading frame (ORF) of 1,338 nucleotides and a 3' untranslated region (3'-UTR) of 403 nucleotides at the 3'-end excluding the 3'end poly(A) tail. The putative viral coat protein (CP) shows 55%-92% amino acid sequence homology to those of Allium potyviruses. The genome size of the virus was analyzed to be about 9.0 kb by Northern blot analysis. Five cDNA clones were screened out using GPV2 oligonucleotide as a probe. One of these clones, DEA72, which has a longest cDNA insert, contains one ORF of 1,459 nucleotides and a 3'-UTR of 590 nucleotides at the 3'-end excluding the 3'-end poly(A) tail. The putative viral CP shows 57%-88% amino acid sequence homologies to those of Allium potyviruses. The genome size of the virus was analyzed to be about 9.6 kb by Northern blot analysis. The results of immunoblot and Northern blot analyses suggest that almost all of the tested garlic plants showing mosaic or streak symptoms are infected with DEA72-potyvirus in variable degrees but rarely infected with G7-potyvirus in variable degrees but rarely infected with DEA72-potyvirus in variable degrees but rarely infected with G7-potyvirus. Immunoelectron microscopy using anti-DEA72 CP antibody shows that this potyvirus is about 750 nm long and flexuous rod shaped.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.4 no.1
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• pp.31-41
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• 1971

The present study was directed to define the degradation pattern of the nucleotides and their related compounds in the muscle of anchovy during drying. Three kinds of samples, fresh, sun dried and boiled-and-dried anchovy, were prepared and the contents of nucleotides and related compounds of samples were determined by ion exchange chromatography. The results obtained are summarized as follows: Almost all of ATP disappeared in both muscle of sun dried and boiled-and-dried anchovy, although the initial content of ATP in fresh muscle was very low ($1.8{\mu}moles/g$, dry basis). But the remainning amount of ADP was considerably high while the other nucleotide almost entirely disappeared. This suggested that the residual ADP is responsible to the 'bound nucleotide' of myofibrils. In general, AMP content was comparatively lower than that of other nucleotides. Among three samples, the boiled-and-dried sample showed relatively higher AMP value than others. The amount of IMP remained in muscle remarkably varied between the boiled-and-dried anchovy and sun dried anchovy, the former's value being sixteen times higher than that of latter. In the contents of inosine and hypoxanthine, the sun dried anchovy marked an exceedingly high value equivalent to 2.7 times of the boiled-and-dried anchovy. In comparison of the ratio of inosine and hypoxanthine, hypoxanthine was accumulating in boiled-and-dried anchovy whereas inosine was in the sun-dried anchovy. Eighty three percent of total nucleotides in the fresh anchovy retained in the boiled-and-dried anchovy and IMP ratio in total nucleotides was $73\%$. On the contrary, the sun dried anchovy showed barely $10\%$ of retention rate and IMP ratio was only $38\%$. Considered from the flavor quality of dried anchovy, so far as concerned IMP content, it may be said that the boiled-and-drying method is more favorable process for dried product of anchovy than the sun-drying method.

• Korean journal of food and cookery science
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• v.17 no.6
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• pp.589-597
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• 2001

This study was conducted to develop a standardized Korean cold noodle stock recipe which can be used in food service establishments. The qualities of three kinds of stock made of beef rib only(B group), beef rib added with chicken(BC group), and beef rib added with chicken and vegetable(BCV group) were investigated by using sensory evaluation and instrumental analyses for free amino acids and nucleotides during heating (2, 3, 4, and 6 hr) at 90$\pm$ 5$\^{C}$ The highest amino acid contained in B, BCV, and BCV groups was arginine followed by alanine, glycine, and glutamic acid. B and BC groups was extracted to the best contents of amino acids by heating for 4 hours but BCV group for 3 hours. Nucleotides were extracted from B and BC group between 3 and 4 hours of heating but in BCV group between 2 and 3 hours. In sensory evaluation, BCV group obtained the highest score for overall preference. In the measurement of color difference, BCV group was the lowest in L value(lightness) but the highest in b value(yellowness).

• The Korean Journal of Physiology and Pharmacology
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• v.4 no.4
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• pp.311-318
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• 2000

We cultured the rabbit inner medullary collecting duct (IMCD) cells as monolayers on collagen-coated membrane filters, and investigated distribution of the P2Y receptors by analyzing nucleotide-induced short circuit current $(I_{sc})$ responses. Exposure to different nucleotides of either the apical or basolateral surface of cell monolayers stimulated $I_{sc}.$ Dose-response relationship and cross-desensitization studies suggested that at least 3 distinct P2Y receptors are expressed asymmetrically on the apical and basolateral membranes. A $P2Y_2-like$ receptor, which responds to UTP and ATP, is expressed on both the apical and basolateral membranes. In addition, a uracil nucleotide receptor, which responds to UDP and UTP, but not ATP, is expressed predominantly on the apical membrane. In contrast, a $P2Y_1-like$ receptor, which responds to ADP and 2-methylthio-ATP, is expressed predominantly on the basolateral membrane. These nucleotides stimulated intracellular cAMP production with an asymmetrical profile, which was comparable to that in the stimulation of $I_{sc}.$ Our results suggest that the adenine and uracil nucleotides can interact with different P2Y nucleotide receptors that are expressed asymmetrically on the apical and basolateral membranes of the rabbit IMCD cells, and that both cAMP- and $Ca^{2+}-dependent$ signaling mechanisms underlie the stimulation of $I_{sc}$.

• BMB Reports
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• v.35 no.4
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• pp.403-408
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• 2002

A hypothetical 21.0 kDa protein (ORF O197) from Escherichia coli K-12 was cloned, purified, and characterized. The protein sequence of ORF O197(termed EcO197) shares a 33.5% identity with that of a novel NTPase from Methanococcus jannaschii. The EcO197 protein was purified using Ni-NTA affinity chromatography, protease digestion, and gel filtration column. It hydrolyzed nucleoside triphosphates with an O6 atom-containing purine base to nucleoside monophosphate and pyrophosphate. The EcO197 protein had a strong preference for deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP), while it had little activity in the standard nucleoside triphosphates (dATP, dCTP, dGTP, and dTTP). These aberrant nucleotides can be produced by oxidative deamination from purine nucleotides in cells; they are potentially mutagenic. The mutation protection mechanisms are caused by the incorporation into DNA of unwelcome nucleotides that are formed spontaneously. The EcO197 protein may function to eliminate specifically damaged purine nucleotide that contains the 6-keto group. This protein appears to be the first eubacterial dITP-and XTP-hydrolyzing enzyme that has been identified.

• Journal of Plant Biology
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• v.34 no.4
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• pp.331-339
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• 1991

To elucidate the regulatory mechanism of virE operon from vir regions (virA, virB, virC, virD, virG, virE) of pTiA6 which have been known to be essential for efficient crown gall tumorigenesis in plants, the activity of the truncated virE, promoter was analyzed. pSM358cd, a recombinant plasmid in which virE :: Tn3-HoHo1 (Tn3-promoterless lacZ) was cloned into SalI site of pVK102, was digested with SalI, and virE :: Tn3-HoHo1 was seperated from pVK102. To construct the truncted virE recombinant plasmids (pJS031, pJS051, pJS102, pJS201, pJS301), 5'-end of vireE promoter was deleted with BAL31 and cloned into pVK102 and then transferred into a. tumefaciens A348(pTiA6). According to the activity of the truncated virE promoter in recombinant plasmids, they were classified into two groups, pJS031, pJS051, pJS101 and pJS201 belong to a functional group and pJS301 is a non-functional. The size of deleted nucleotides of pJS201 and pJS301 seemed to be about 130 nucleotides and about 250 nucleotides from 5'-end of virE promoter, respectively. Hence it was thought that the essential site of the virE promoter was located between about 130th nucleotide and 250th nucleotide from 5'-end of the virE promoter.

• Journal of the Korean Society of Food Science and Nutrition
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• v.17 no.1
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• pp.69-72
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• 1988

The free amino acids, nucleotides and their related compounds in soypaste made from native and improved meju and soypaste product purchased from the market were investigated by amino acid autoanalzer and HPLC, respectively. The glutamic acid contents in each soypaste were great in order of improved) native ) products. The total free amino acid contents in soypaste made from improved meju showed the highest level and those of the soypaste made from native meju showed the lowest level. GMP content in those made from native and improved me was greatest among the nucleotides and their related compounds.

• Proceedings of the Korea Information Processing Society Conference
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• 2005.11a
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• pp.15-18
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• 2005

A ribonucleic acid (RNA) is one of the two types of nucleic acids found in living organisms. An RNA molecule represents a long chain of monomers called nucleotides. The sequence of nucleotides of an RNA molecule constitutes its primary structure, and the pattern of pairing between nucleotides determines the secondary structure of an RNA. Non-coding RNA genes produce transcripts that exert their function without ever producing proteins. Predicting the secondary structure of non-coding RNAs is very important for understanding their functions. We focus on Nussinov's algorithm as useful techniques for predicting RNA secondary structures. We introduce a new traceback matrix and scoring table to improve above algorithm. And the improved prediction algorithm provides better levels of performance than the originals.