• The Korean Journal of Applied Statistics
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• v.33 no.6
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• pp.683-696
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• 2020

The aim of this research is to find an optimal gene set that provides highly accurate multi-class classification with a minimum number of genes. A two-stage procedure is proposed: Based on minimum redundancy and maximum relevance (mRMR) framework, several statistics to rank differential expression genes and K-means clustering to reduce redundancy between genes are used for data filtering procedure. And a particle swarm optimization is modified to select a small subset of informative genes. Two well known multi-class microarray data sets, ALL and SRBCT, are analyzed to indicate the effectiveness of this hybrid method.

• International Journal of Industrial Entomology and Biomaterials
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• v.2 no.1
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• pp.79-81
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• 2001

A study was conducted to establish the degree of genetic divergence between different hybrid forms and rearing conditions through estimation of the minimum number of genes (allelic pairs) differentiating parents in terms of specific quantitative traits. It was established that the minimum gene numbers differentiating parental lines in the inheritance of cocoon was 1, of cocoon shell weight- between 1 and 2, and of silk filament length- between 2 and 3. The variability in the specific genetic parameter could be explained by the reliability of the statistical-and-genetic method used and the expression of genes affecting the formation of each of the characters tested. Gene expression, in its turns is conditioned both by the gene interaction within the genotypes and the different genotype response to environmental change. To go deep in the problem, experiments should be conducted under strictly controlled conditions, reducing the mathematical-and-genetic analysis to a physiological levels and hence to analyse the genetic nature of the specific quantitative character formation and its genetic control.

• ALGAE
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• v.26 no.3
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• pp.229-235
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• 2011

Spliced leader (SL) trans-splicing is a mRNA processing mechanism in dinoflagellate nuclear genes. Although studies have identified a short, conserved dinoflagellate SL (dinoSL) sequence (22-nt) in their nuclear-encoded transcripts, whether the majority of nuclear-coded transcripts in dinoflagellates have the dinoSL sequence remains doubtful. In this study, we investigated dinoSL-containing gene transcripts using 454 pyrosequencing data (Cochlodinium polykrikoides, 93 K sequence reads, 31 Mb; Prorocentrum minimum, 773 K sequence reads, 291 Mb). After making comparisons and performing local BLAST searches, we identified dinoSL for one C. polykrikoides gene transcript and eight P. minimum gene transcripts. This showed transcripts containing the dinoSL sequence were markedly fewer in number than the total expressed sequence tag (EST) transcripts. In addition, we found no direct evidence to prove that most dinoflagellate nuclear-coded transcripts have this dinoSL sequence.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2005.06a
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• pp.230-232
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• 2005

The formation of insoluble aggregation of the recombinant kringle fragment of human apolipoprotein(a), rhLK8, in endoplasmic reticulum was identified as the rate-limiting step in the rhLK8 secretion in Saccharomyces cerevisiae. To analyze the protein secretion pathway, some of yeast genes closely related to protein secretion was rationally selected and their oligomer DNA were arrayed on the chip. The expression profiling of these genes during the induction of rhLK8 in fermentor fed-batch cultures revealed that several foldases including pdi1 gene were up-regulated in the early induction phase, whereas protein transport-related genes were up-regulated in the late induction phase. The coexpression of pdi1 gene increased rhLK8-folding capacity. Hence, the secretion efficiency of rhLK8 in the strain overexpressing pdi1 gene increased by 2-fold comparing in its parental strain. The oligomer DNA chip arrayed with minimum number of the genes selected in this study could be generally applicable to the monitoring system for the heterologous protein secretion and expression in Saccharomyces cerevisiae. With the optimization of fed-batch culture conditions and the alteration of genetic background of host, we obtained extracellular rhLK8 at higher yields than with Pichia pastoris systems, which was a 25-fold increased secretion level of rhLK8 compared to the secretion level at the initiation of this study.

• Korean journal of applied entomology
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• v.34 no.1
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• pp.20-32
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• 1995

Adult diapause in insects is characterized by suppression of reproductive development. It is induced by environmental cues such as photoperiod, temperature, food availability, and other conditions Diapause-inducing environment is recognized and analyzed by the brain of the insects. The interpreted information is conveyed via endocrine system to target tissues such as ovaries, fat body, and other tissues. From this signal hierarchy of a brain-endocrine-target tissue axis, several factors are involved to express a diapause trait in a quantitative mode, even though the insects show a binomial phenotye between being in diapause or not. Recent works estimated that the number of the factors is relatively small by a series of crossing trials between high and low diapause lines. Heritability of the diapause is quite high (ca. 70%) in some species. Epistasis, sex-linkage, pleiotropism, and other nongenetic components also affect diapause inheritance. Most physiological studies have been focused on control mechanisms of the juvenile hormone (JH) synthesis in corpora allata (CA) because JH level in hemolymph of teneral adults is critical to decide a later developmental mode. Allatostatin, an antagonizer of JH synthesis, has been believed to be a potent brain message to CA for adult diapause induction.

• Journal of Internet Computing and Services
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• v.18 no.5
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• pp.47-53
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• 2017

In past few years, high-throughput sequencing, big-data generation, cloud computing, and computational biology are revolutionary. RNA sequencing is emerging as an attractive alternative to DNA microarrays. And the methods for constructing Gene Regulatory Network (GRN) from RNA-Seq are extremely lacking and urgently required. Because GRN has obtained substantial observation from genomics and bioinformatics, an elementary requirement of the GRN has been to maximize distinguishable genes. Despite of RNA sequencing techniques to generate a big amount of data, there are few computational methods to exploit the huge amount of the big data. Therefore, we have suggested a novel gene selection algorithm combining Support Vector Machines and Intensity-dependent normalization, which uses log differential expression ratio in RNAseq. It is an extended variation of support vector machine recursive feature elimination (SVM-RFE) algorithm. This algorithm accomplishes minimum relevancy with subsets of Big-Data, such as NCBI-GEO. The proposed algorithm was compared to the existing one which uses gene expression profiling DNA microarrays. It finds that the proposed algorithm have provided as convenient and quick method than previous because it uses all functions in R package and have more improvement with regard to the classification accuracy based on gene ontology and time consuming in terms of Big-Data. The comparison was performed based on the number of genes selected in RNAseq Big-Data.

• Journal of Life Science
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• v.26 no.6
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• pp.711-720
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• 2016

To determine the degree of common genes and the phylogenetic relationships among genome-sequenced 680 prokaryotes, the similarities among 4,631 clusters of orthologous groups of protein (COGs)’ presence/ absence and gene content trees were analyzed. The number of COGs was in the range of 103–2,199 (mean 1377.1) among 680 prokaryotes. Candidatus Nasuia deltocephalinicola str. NAS-ALF, an obligate symbiont with insects, showed the minimum COG, while Pseudomonas aeruginosa PAO1, an opportunistic pathogen, represented the maximum COG. The similarities between two prokaryotes were 49.30–99.78 % (mean 72.65%). Methanocaldococcus jannaschii DSM 2661 (hyperthermophilic and autotrophic, Euryarchaeota phylum) and Mesorhizobium loti MAFF303099 (mesophilic and symbiotic, alpha-Proteobacteria class) had the minimum amount of similarities. As gene content may represent the potential for an organism to adapt to each habitat, this may represent the history of prokaryotic evolution or the range of prokaryotic habitats at present on earth. COG content trees represented the following. First, two members of Chloroflexi phylum (Dehalogenimonas lykanthroporepellens BL-DC-9 and Dehalococcoides mccartyi 195) showed a greater relationship with Archaea than other Eubacteria. Second, members of the same phylum or class in the 16S rRNA gene were separated in the COG content tree. Finally, delta- and epsilon-Proteobacteria were in different lineages with other Proteobacteria classes in neighbor-joining (NJ) and maximum likelihood (ML) trees. The results of this study would be valuable to identifying the origins of organisms, functional relationships, and useful genes.

• 한국균학회소식:학술대회논문집
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• 2014.05a
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• pp.27-28
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• 2014

Beauveria bassiana (Cordycipitaceae, Hypocreales, Ascomycota) is an anamorphic fungus having a potential to be used as a biological control agent because it parasitizes a wide range of arthropod hosts including termites, aphids, beetles and many other insects. A number of bioactive secondary metabolites (SMs) have been isolated from B. bassiana and functionally verified. Among them, beauvericin and bassianolide are cyclic depsipeptides with antibiotic and insecticidal effects belonging to the enniatin family. Non-ribosomal peptide synthetases (NRPSs) play a crucial role in the synthesis of these secondary metabolites. NRPSs are modularly organized multienzyme complexes in which each module is responsible for the elongation of proteinogenic and non-protein amino acids, as well as carboxyl and hydroxyacids. A minimum of three domains are necessary for one NRPS elongation module: an adenylation (A) domain for substrate recognition and activation; a tholation (T) domain that tethers the growing peptide chain and the incoming aminoacyl unit; and a condensation (C) domain to catalyze peptide bond formation. Some of the optional domains include epimerization (E), heterocyclization (Cy) and oxidation (Ox) domains, which may modify the enzyme-bound precursors or intermediates. In the present study, we analyzed genomes of B. bassiana and its allied species in Hypocreales to verify the distribution of NRPS-encoding genes involving biosynthesis of beauvericin and bassianolide, and to unveil the evolutionary processes of the gene clusters. Initially, we retrieved completely or partially assembled genomic sequences of fungal species belonging to Hypocreales from public databases. SM biosynthesizing genes were predicted from the selected genomes using antiSMASH program. Adenylation (A) domains were extracted from the predicted NRPS, NRPS-like and NRPS-PKS hybrid genes, and used them to construct a phylogenetic tree. Based on the preliminary results of SM biosynthetic gene prediction in B. bassiana, we analyzed the conserved gene orders of beauvericin and bassianolide biosynthetic gene clusters among the hypocrealean fungi. Reciprocal best blast hit (RBH) approach was performed to identify the regions orthologous to the biosynthetic gene cluster in the selected fungal genomes. A clear recombination pattern was recognized in the inferred A-domain tree in which A-domains in the 1st and 2nd modules of beauvericin and bassianolide synthetases were grouped in CYCLO and EAS clades, respectively, suggesting that two modules of each synthetase have evolved independently. In addition, inferred topologies were congruent with the species phylogeny of Cordycipitaceae, indicating that the gene fusion event have occurred before the species divergence. Beauvericin and bassianolide synthetases turned out to possess identical domain organization as C-A-T-C-A-NM-T-T-C. We also predicted precursors of beauvericin and bassianolide synthetases based on the extracted signature residues in A-domain core motifs. The result showed that the A-domains in the 1st module of both synthetases select D-2-hydroxyisovalerate (D-Hiv), while A-domains in the 2nd modules specifically activate L-phenylalanine (Phe) in beauvericin synthetase and leucine (Leu) in bassianolide synthetase. antiSMASH ver. 2.0 predicted 15 genes in the beauvericin biosynthetic gene cluster of the B. bassiana genome dispersed across a total length of approximately 50kb. The beauvericin biosynthetic gene cluster contains beauvericin synthetase as well as kivr gene encoding NADPH-dependent ketoisovalerate reductase which is necessary to convert 2-ketoisovalarate to D-Hiv and a gene encoding a putative Gal4-like transcriptional regulator. Our syntenic comparison showed that species in Cordycipitaceae have almost conserved beauvericin biosynthetic gene cluster although the gene order and direction were sometimes variable. It is intriguing that there is no region orthologous to beauvericin synthetase gene in Cordyceps militaris genome. It is likely that beauvericin synthetase was present in common ancestor of Cordycipitaceae but selective gene loss has occurred in several species including C. militaris. Putative bassianolide biosynthetic gene cluster consisted of 16 genes including bassianolide synthetase, cytochrome P450 monooxygenase, and putative Gal4-like transcriptional regulator genes. Our synteny analysis found that only B. bassiana possessed a bassianolide synthetase gene among the studied fungi. This result is consistent with the groupings in A-domain tree in which bassianolide synthetase gene found in B. bassiana was not grouped with NRPS genes predicted in other species. We hypothesized that bassianolide biosynthesizing cluster genes in B. bassiana are possibly acquired by horizontal gene transfer (HGT) from distantly related fungi. The present study showed that B. bassiana is the only species capable of producing both beauvericin and bassianolide. This property led to B. bassiana infect multiple hosts and to be a potential biological control agent against agricultural pests.

• Microbiology and Biotechnology Letters
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• v.31 no.4
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• pp.322-328
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• 2003

The Transformation-Associated Recombination (TAR) cloning technique allows selective isolation of chromosomal regions and genes from complex genomes. The procedure requires knowledge of relatively small genomic sequences that reside adjacent to the chromosomal region of interest. This technique involves homologous recombination during yeast spheroplast transformation between genomic DNA and a TAR vector that has 5'and 3' gene targeting sequences. In this study, we examined the minimum size of specific hooks required for a single-copy gene isolation and compared the utility of different TAR vectors, radial and unique vectors, by cloning the same single-copy gene. The efficiency of TAR cloning of the hHPRT gene was same using hooks varying from 750 to 63 bp. The number of transformants decreased approximately 20-fold when the TAR vector contained two unique hooks versus using a radial vector, but the percentage of positive recombinants increased over 2-fold when a unique TAR vector was used. Therefore, we suggest that the two-unique TAR vector is suitable for general TAR cloning given its high selectivity, and the radial TAR vector is more suitable when genomic DNA is in limited quantity, for example, DNA isolated from pathological specimens. Moreover, we confirm the minimal length of a unique sequence in a TAR vector is approximately 60 bp for a single-copy gene isolation.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.10
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• pp.1-43
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• 1971

Experiment I: The objective of this study was to know variation in some selected agronomic characters of sweet sorghum when planted in several growing seasons. The 17 different sweet sorghum varieties having various maturities, and plant, syrup and sugar types were used in this study which had been carried out for the period of two years from 1968 to 1969 at Industrial Crops Division of Crop Experiment Station in Suwon. These varieties were planted at an interval of 20 days from April 5 to August 25 both in 1968 and 1969. The experimental results could be summarized as follows: 1. As planting was made early, the number of days from sowing to germination was getting prolonged while germination took place early when planted at the later date of which air temperature was relatively higher. However, such a tendency was not observed beyond the planting on August 25. In general, a significant negative correlation was found between the number of days from sowing to germination and the average daily temperature but a positive correlation was found between the former and the total accumulated average temperature during the growth period. 2. The period from sowing to heading was generally shortened as planting was getting delayed. The average varietal difference in number of days from sowing to heading was as much as 30.2 days. All the varieties were grouped into early-, medium and late-maturing groups based upon a difference of 10 days in heading. The average number of days from sowing to heading was 78.5$\pm$4.5 days in the early-maturing varieties, 88.5$\pm$4.5 days in the medium varieties and 98.5$\pm$4.5 days in the late-maturing varieties, respectively. The early-maturing varieties had the shortest period to heading when planted from July 15 to August 5, the medium varieties did when planted before July 15 and the late-maturing varieties did when planted before June 5. 3. The relationship between the sowing date (x) and number of days from sowing to heading could be expressed in an equation of y=a+bx. A highly positive correlation was found between the coefficient of the equation(shortening rate in heading time) and the average number of days from sowing to heading. 4. The number of days from sowing to heading was shortened as the daily average temperature during the growth period was getting higher. Early-maturing varieties had the shortest period to heading at a temperature of 24.2$^{\circ}C$, medium varieties at 23.8$^{\circ}C$ and late-maturing varieties at 22.9$^{\circ}C$, respectively. In other words, the number of days from sowing to heading was shortened rapidly in case that the average temperature for 30 days before heading was 22$^{\circ}C$ to $25^{\circ}C$. It prolonged relatively when the temperature was lower than 21$^{\circ}C$. 5. There was a little difference in plant height among varieties. In case of early planting, no noticeable difference in the height was observed. The plant height shortened generally as planting season was delayed. Elongation of plant height was remarkably accelerated as planting was delayed. This tendency was more pronounced in case of early-maturing varieties rather than late-maturing varieties. As a result, the difference in plant height between the maximum and the minimum was greater in late-maturing varieties than in early-maturing varieties. 6. Diameter of the stalk was getting thicker as planted earlier in late-maturing varieties. On the other hand, medium or early-maturing varieties had he thickest diameter when they were planted on April 25. 7. In general, a higher stalk yield was obtained when planted from April 25 to May 15. However, the planting time for the maximum stalk yield varied from one variety to another depending upon maturity of variety. Ear]y-maturing varieties produced the maximum yield when planted about April 25, medium varieties from April 25 to May 15 and late-maturing varieties did when planted from April 5 to May 15 respectively. The yield decreased linearly when they were planted later than the above dates. 8. A varietal difference in Brix % was also observed. The Brix % decreased linearly when the varieties were planted later than May 15. Therefore, a highly negative relationship between planting date(x) and Brix %(y) was detected. 9. The Brix % during 40 to 45 days after leading was the highest at the 1st to the 3rd internodes from the top while it decreased gradually from the 4th internode. It increased again somewhat at the 2nd internode from the ground level. However, it showed a reverse relationship between the Brix % and position of internode before heading. 10. Sugar content in stalk decreased gradually as planting was getting delayed though one variety differed from another. It seemed that sweet sorghum which planted later than June had no value as a sugar crop at all. 11. The Brix % and sugar content in stalk increased from heading and reached the maximum 40 to 45 days after heading. The percentage of purity showed the same tendency as the mentioned characters. Accordingly, a highly positive correlation was observed between. percentage of purity and Brix % or sugar content in stalk. 12. The highest refinable sugar yield was obtained from the planting on April 25 in late-maturing varieties and from that on May 15 in early-maturing varieties. The yield rapidly decreased when planted later than those dates. Such a negative correlation between planting date(x) and refinable sugar yield(y) was highly significant at 1% level. 13. Negative correlations or linear regressions between delayed planting and the number of days from sowing to germination. accumulated temperature during germination period, number of days to heading, accumulated temperature to heading, plant height, stem diameter, stalk weight, Brix %. sugar content, refinable sugar yield or Purity % were obtained. On the other hand, highly positive correlations between the number of days from sowing to heading(x) and Brix %, sugar content, purity %, refinable sugar yield, plant height or stalk yield, between Brix %(x) and purity %, refinable sugar yield or stalk yield, between sugar content(x) and purity% or refinable sugar yield(y), between purity %(x) and refinable sugar yield and between daylength at heading(x) and Brix %. number of days from sowing to heading, sugar content, purity % or refinable sugar yield (y), were found, respectively. Experiment II: The 11 varieties were selected out of the varieties used in Experiment I from ecological and genetic viewpoints. Complete diallel cross were made among them and the heading date, stalk length, stalk yield, Brix %, syrup yield, combining ability and genetic behavior of F$_1$ plants and their parental varieties were investigated. The results could be summarized as follows: 1. In general, number of days to heading showed a partial dominance over earliness or late maturity or had a mid-value, though there were some specific combinations showing a complete dominance or transgressive segregation in maturity. Some combinations showed relatively high general or specific combining abilities in maturity. Therefore, a 50 to 50 segregation ratio in heading date could be estimated in this study and it might be positive to have a selection in early generation since heritability of the character was relatively high. 2. A vigorous hybrid vigor was observed in stalk length. A complete or partial dominant effect of long stalk was obtained. The general combining ability and specific combining ability of stalk length were generally high. Long and short stalks segregated in a ratio of 50:50 and its heritability was relatively low. 3. Except for several specific combinations, high stalk yield seemed to be partial dominant over the low yield. Some varieties demonstrated relatively high general as well as specific combining abilities. It was assumed that several recessive genes were involved in expression of this character. The interaction among regulating recessive genes was also obtained. Accordingly, the heritability of stalk yield seemed to be rather low. 4. The Brix % of hybrid plants located around mid-parental value though some of them showed much higher or lower percentage. It could be explained by the fact that such behavior might be due to partial dominance of Brix %. The varieties with, relatively higher Brix % were high both in general. and specific combining abilities. Therefore, it could be recommended to use the varieties having higher sugar content in order to develop higher-sugar varieties. 5. The syrup yield seemed to be transgressively segregated or completely dominant over low yield. Hybrid vigor of syrup yield was relatively high. No-consistent relationship between general combining ability and specific combining ability was observed. However, some cases demonstrated that the varieties with relatively higher general combining ability had relatively lower specific combining ability. It was assumed that the frequencies of dominant and recessive alleles were almost same.