• Microbiology and Biotechnology Letters
• /
• v.51 no.3
• /
• pp.325-327
• /
• 2023

This paper presents the complete genome sequence of a novel marine actinomycete, Streptomyces sp. MMBL 11-1. The genome of Streptomyces sp. MMBL 11-1 was obtained through next-generation sequencing using the PacBio Sequel system and Illumina platform provided by Macrogen, Korea. The assembled genome consists of five contigs, with a total length of 8,496,900 bp and a G+C content of 71.6%. The genome harbors multiple biosynthetic gene clusters (BGCs) associated with producing microbial natural products (MNPs). The comprehensive genomic information of this type of strain will serve as a valuable resource for identifying other marine actinomycetes strains.

• Journal of applied mathematics & informatics
• /
• v.42 no.3
• /
• pp.709-723
• /
• 2024

We study the distributions of waiting times in variations of the geometric distribution of order k. Variation imposes length on the runs of successes and failures. We study two types of waiting time random variables. First, we consider the waiting time for a run of k consecutive successes the first time no sequence of consecutive k failures occurs prior, denoted by T^(k). Next, we consider the waiting time for a run of k consecutive failures the first time no sequence of k consecutive successes occurred prior, denoted by J^(k). In addition, we study the distribution of the weighted average. The exact formulae of the probability mass function, mean, and variance of distributions are also obtained.

• Korean Journal of Medicinal Crop Science
• /
• v.12 no.3
• /
• pp.219-225
• /
• 2004

This study was conducted to evaluate growth and yield characteristics and the contribution to the yield according to the emergent sequence of tiller under two planting density $(60{\times}15\;cm,\;60{\times}25\;cm)$ in Coix lachryma-jobi L. var. mayuen Stapf. The average culm length and number of rachillas of $60{\times}25\;cm$ planting density were 20 cm shorter and 4.7 higher, respectively, whereas seed setting position of $60{\times}25\;cm$ planting density was 1.7 nodes lower compared with $60{\times}15\;cm$ planting density. Culm length and culm diameter of each tiller became shorter and thinner as the tiller emerged later. Length of rachillas was longer, number of grains was higher and ripening rate was also higher in $60{\times}25\;cm$ planting density than those of $60{\times}15\;cm$ planting density, whereas 100 grain weight in $60{\times}25\;cm$ planting density was lower by 0.5 g compared with $60{\times}15\;cm$ planting density. Length of rachillas and number of grains according to the emergent sequence of tiller were shown shorter and lower as the tiller emerged later. The highest number of bract was obtained from the main culm in both planting densities. 100 grain weight according to the emergent sequence of tiller became lower as the tiller emerged later in $60{\times}15\;cm$ planting density, but there was no clear tendency in $60{\times}25\;cm$ planting density. Among 8 tillers, 5th tiller and 4th tiller of main culm contributed 84.4% to the yield in $60{\times}15\;cm$ planting density, while it was 84.1% in $60{\times}25\;cm$ planting density. Analysis of path coefficient to grain yield showed that direct effect was the highest in the number of grain per tiller followed by in the 100 grain weight and in ripening rate.

• Parasites, Hosts and Diseases
• /
• v.58 no.1
• /
• pp.73-79
• /
• 2020

Echinostoma revolutum is a zoonotic food-borne intestinal trematode that can cause intestinal bleeding, enteritis, and diarrhea in human and birds. To identify a suspected E. revolutum trematode from a red-crowned crane (Grus japonensis) and to reveal the genetic characteristics of its mitochondrial (mt) genome, the internal transcribed spacer (ITS) and complete mt genome sequence of this trematode were amplified. The results identified the trematode as E. revolutum. Its entire mt genome sequence was 15,714 bp in length, including 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and one non-coding region (NCR), with 61.73% A+T base content and a significant AT preference. The length of the 22 tRNA genes ranged from 59 bp to 70 bp, and their secondary structure showed the typical cloverleaf and D-loop structure. The length of the large subunit of rRNA (rrnL) and the small subunit of rRNA (rrnS) gene was 1,011 bp and 742 bp, respectively. Phylogenetic trees showed that E. revolutum and E. miyagawai clustered together, belonging to Echinostomatidae with Hypoderaeum conoideum. This study may enrich the mitochondrial gene database of Echinostoma trematodes and provide valuable data for studying the molecular identification and phylogeny of some digenean trematodes.

• The Journal of the Korea institute of electronic communication sciences
• /
• v.15 no.2
• /
• pp.319-326
• /
• 2020

PRNGs(Pseudorandom number generators) are essential for generating encryption keys for to secure online communication. A bitstream generated by the PRNG must be generated at high speed to encrypt the big data effectively in a symmetric key cryptosystem and should ensure the randomness of the level to pass through the several statistical tests. CA(Cellular Automata) based PRNGs are known to be easy to implement in hardware and to have better randomness than LFSR based PRNGs. In this paper, we design PRNGs based on PMLCA(Programable Maximum Length CA) that can generate effective key sequences in symmetric key cryptosystem. The proposed PRNGs generate bit streams through nonlinear control method. First, we design a PRNG based on an (m,n)-cell PMLCA ℙ with a single complement vector that produces linear sequences with the long period and analyze the period and the generating polynomial of ℙ. Next, we design an (m,n)-cell PC-MLCA based PRNG with two complement vectors that have the same period as ℙ and generate nonlinear sequences, and analyze the location of outputting the nonlinear sequence.

• Journal of Korea Water Resources Association
• /
• v.54 no.spc1
• /
• pp.1131-1141
• /
• 2021

In this study, the artificial neural network model is applied for real-time dam inflow prediction and then evaluated for the prediction lead times (1, 3, 6 hr) in dam basins in Korea. For the training and testing the model, hourly precipitation and inflow are used as input data according to average annual inflow. The results show that the model performance for up to 6 hour is acceptable because the NSE is 0.57 to 0.79 or higher. Totally, the predictive performance of the model in dry seasons is weaker than the performance in wet seasons, and this difference in performance increases in the larger basin. For the 6 hour prediction lead time, the model performance changes as the sequence length increases. These changes are significant for the dry season with increasing sequence length compared to the wet season. Also, with increasing the sequence length, the prediction performance of the model improved during the dry season. Comparison of observed and predicted hydrographs for flood events showed that although the shape of the prediction hydrograph is similar to the observed hydrograph, the peak flow tends to be underestimated and the peak time is delayed depending on the prediction lead time.

• Research in Plant Disease
• /
• v.18 no.4
• /
• pp.387-390
• /
• 2012

Rice black-streaked dwarf virus (RBSDV) was reported to occur on maize plants in Gochang-gun of Jeonllabuk-do region in 2011. The symptoms typically include stunted and deformed leaves. Virus infected plants usually produce poor or no head. RT-PCR analysis of genomic dsRNA extracted from the plant confirmed the infection. Specific primers for full length genome of segments 8 and 10 were used for RNA amplification. Full-length genomes of S8 and S10 were cloned and sequenced. Sequence analysis revealed that the S8 and S10 sequences of the maize isolate were same with rice isolate in size, 1,936 nt and 1,801 nt, respectively. In comparison with rice RBSDV, S8 and S10 showed 94.9-99.6% and 94.1-98.4% sequence identity, respectively. Phylogenetic analysis showed that RBSDV S8 and S10 of maize plants are categorized into the same group as RBSDV of rice plant.

• Asian-Australasian Journal of Animal Sciences
• /
• v.23 no.1
• /
• pp.116-121
• /
• 2010

Long-chain polyunsaturated fatty acids (LC-PUFA) promote the development of brain and vision of the fetus, relieve inflammation, inhibit oral dysplasia of rumor cell, decrease the incidence of cardiovascular disease and regulate arrhythmia. ${\Delta}-6$ desaturase is the rate-limited enzyme in the desaturation process. This study reports the cloning, characterization and tissue expression of a ${\Delta}-6$ desaturase gene in the chicken. PCR primers were designed based on the predicted sequence of chicken ${\Delta}-6$ desaturase (accession number: XM421053) and used to isolate a cDNA fragment of 1,323 bp from chicken liver. Based on the 1,323 bp fragment an EST (BI390105) was obtained by BLAST. The EST and 5'nd of the 1,323 bp fragment were partially overlapped. Gene specific primers derived from the EST were used for amplification of the 5'nd. Another gene-specific primer derived from the 1,323 bp fragment was used for amplification of the 3'nd by 3'ACE. Then the three overlapping cDNA sequences obtained were assembled with DNAMAN software and a full-length ${\Delta}-6$ desaturase of 2,153 bp was obtained. The full-length cDNA contained an ORF of 1,335 bp with a 5'ntranslated region of 147 nucleotides followed by an ATG initiation codon. Stop codon TGA was at position 1,481-1,483 bp. The deduced amino acids shared an homology above 77% with bovine, mice, orangutan, rat and human. The protein sequence had three histidine-rich regions HDFGH (HisI region), HFQHH (HisII region) and HH (HisIII region), a cytochrome $b_{5}$-like domain containing a heme-binding motif and two transmembrane domains. Sequence analysis of the chicken genomic DNA revealed that the coding sequence of chicken ${\Delta}-6$ desaturase included 12 exons and 11 introns. Semi-quantitative RT-PCR showed that the ${\Delta}-6$ desaturase expression levels were in turn liver, spleen, pancreas, lung, breast muscle, heart, and abdominal fat. The expression of ${\Delta}-6$ desaturase in liver was significantly higher than that in breast muscle (p<0.01). The expression of ${\Delta}-6$ desaturase in lung was significantly higher than that in abdominal fat (p<0.01). This is the first clone of chicken ${\Delta}-6$ desaturase.

• Proceedings of the Microbiological Society of Korea Conference
• /
• 2002.10a
• /
• pp.180-182
• /
• 2002

Substantial genomic diversity has been expected among clinical isolates of H. pylori. We have suggested that the two complete H. pylori genomes already sequenced may be insufficient for providing a discriminatory tool for typing clinical isolates as well as an insight into the genomic diversity, which enable to establish strategy for control of H. pylori infection. In this study, we determine the nucleotide sequence of the entire genome of Korean strain 51 and compare it with two reported genomic sequences to suggest validity for extensive genomic sequencing of H. pylori. The genome of H. pylori 51 consists of a circular chromosome with a size of 1,591,297 bp, which is corresponding to $95.4\%\;and\;96.8\%$ of the 26695 and J99 chromosome length, respectively. We predict that there are 1,454 open reading frames (ORFs) in 51, representing $91.4\%\;and\;97.2\%$ of the reported numbers of ORF of 26695 and J99, respectively. In contrast to 26695 and J99 that have 123 and 65 strain-specific genes, respectively, of the 1,454 genes, only 39 genes are unique to 51. Differences in genomic organization between 51 and each foreign strain were greater than between 2 foreign strains in pair wise entire sequence alignments by BLASTN. Particularly, the extent of genomic rearrangement observed between 51 and 26695 is higher than between 51 and J99. Multiple sequence alignment of orthologous genes among 3 strains showed that 51 is genetically closer to 26695 rather than J99. Phylogenetic analysis of nonsynonymous and synonymous mutation indicated J99 has the longest branch length in the unrooted phylogenetic tree, suggesting that J99 has higher mutation rate than the other 2 strains.

• The Journal of Korean Society of Virology
• /
• v.30 no.1
• /
• pp.71-81
• /
• 2000

We have determined and analyzed the full-length cDNA sequence of a coxsackievirus B3 (CVB3) Korean isolate (CVB3-Korea/97) which has been known as a general human pathogen. The whole genome contains 7,400 nucleotides and has a single large open reading frame with 6,555 nucleotides that encodes a potential polyprotein precursor of 2,185 amino acids. The genome also contains a 5' non-coding region (NCR) of 741 bases and a 3' NCR of 104 bases followed by poly(A) tail. Sequence homologies of nucleotides and deduced amino acids between the CVB3-Korea/97 strain and the prototype (Nancy strain) were 81.7% and 91.5%, respectively. The genes encoding the functional proteins including viral protease and RNA dependent RNA polymerase showed higher homology than those encoding the structural proteins. We have further analyzed the sequences of 5' NCR, VP1 and VP2 of CVB3-Korea/97, which are known as cardiovirulent determining factors at the nucleotide and amino acid levels. Although the CVB 3-Korea/97 strain was isolated from an aseptic meningitis patient without cardiomyopathy, its 234th nucleotide and 165th amino acid were uracil and Asn as same as those of other cardiovirulent strains one. However, the 155th amino acid of VP1, which closely associated with cardiovirulence, was replaced with $Arg^{155}$ by single nucleotide substitution from $A^{2916}$ to $T^{2916}$. Moreover, additional amino acid substitutions were observed in the flanking region of $Asp^{155}$. Taken together, amino acid(s) substitution in VP1 may playa critical role in determining cardiovirulence of the CVB3-Korea/97 strain rather than individual nucleotide replacements in the 5' NCR and/or an amino acid substitution in VP2.