• Genomics & Informatics
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• v.21 no.1
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• pp.3.1-3.10
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• 2023

Characterization as well as prediction of the secondary and tertiary structure of hypothetical proteins from their amino acid sequences uploaded in databases by in silico approach are the critical issues in computational biology. Severe acute respiratory syndrome-associated coronavirus (SARS-CoV), which is responsible for pneumonia alike diseases, possesses a wide range of proteins of which many are still uncharacterized. The current study was conducted to reveal the physicochemical characteristics and structures of an uncharacterized protein Q6S8D9_SARS of SARS-CoV. Following the common flowchart of characterizing a hypothetical protein, several sophisticated computerized tools e.g., ExPASy Protparam, CD Search, SOPMA, PSIPRED, HHpred, etc. were employed to discover the functions and structures of Q6S8D9_SARS. After delineating the secondary and tertiary structures of the protein, some quality evaluating tools e.g., PROCHECK, ProSA-web etc. were performed to assess the structures and later the active site was identified also by CASTp v.3.0. The protein contains more negatively charged residues than positively charged residues and a high aliphatic index value which make the protein more stable. The 2D and 3D structures modeled by several bioinformatics tools ensured that the proteins had domain in it which indicated it was functional protein having the ability to trouble host antiviral inflammatory cytokine and interferon production pathways. Moreover, active site was found in the protein where ligand could bind. The study was aimed to unveil the features and structures of an uncharacterized protein of SARS-CoV which can be a therapeutic target for development of vaccines against the virus. Further research are needed to accomplish the task.

• Journal of Microbiology and Biotechnology
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• v.33 no.9
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• pp.1238-1249
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• 2023

In this study, we sought to investigate the production and optimization of biosurfactants by soil fungi isolated from petroleum oil-contaminated soil in Saudi Arabia. Forty-four fungal isolates were isolated from ten petroleum oil-contaminated soil samples. All isolates were identified using the internal transcribed spacer (ITS) region, and biosurfactant screening showed that thirty-nine of the isolates were positive. Aspergillus niger SA1 was the highest biosurfactant producer, demonstrating surface tension, drop collapsing, oil displacement, and an emulsification index (E₂₄) of 35.8 mN/m, 0.55 cm, 6.7 cm, and 70%, respectively. This isolate was therefore selected for biosurfactant optimization using the Fit Group model. The biosurfactant yield was increased 1.22 times higher than in the nonoptimized medium (8.02 g/l) under conditions of pH 6, temperature 35℃, waste frying oil (5.5 g), agitation rate of 200 rpm, and an incubation period of 7 days. Model significance and fitness analysis had an RMSE score of 0.852 and a p-value of 0.0016. The biosurfactant activities were surface tension (35.8 mN/m), drop collapsing (0.7 cm), oil displacement (4.5 cm), and E₂₄ (65.0%). The time course of biosurfactant production was a growth-associated phase. The main outputs of the mathematical model for biomass yield were Yx/s (1.18), and µ_max (0.0306) for biosurfactant yield was Y_p/s (1.87) and Y_p/x (2.51); for waste frying oil consumption the So was 55 g/l, and Ke was 2.56. To verify the model's accuracy, percentage errors between biomass and biosurfactant yields were determined by experimental work and calculated using model equations. The average error of biomass yield was 2.68%, and the average error percentage of biosurfactant yield was 3.39%.

• Korean Journal of Plant Resources
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• v.36 no.6
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• pp.588-596
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• 2023

Long-term culture of cell lines is an important issue in in vitro culture and in plant science. In this study, the regeneration ability and ex vitro acclimatization of regenerants were evaluated. The ploidy level of regenerants derived from long-term cultured cell lines was measured in Imperata cylindrica 'Rubra', Poaceae. Adventitious buds (shoots) were successfully induced from five-year-cultured calli on MS medium containing 0.1 mg/L BA or 2.0 mg/L TDZ, combined with 0.01 mg/L auxins (IAA, IBA, NAA and 2,4-D), respectively. Adventitious roots were also induced on MS medium containing 0.01 mg/L auxins (IBA, NAA and 2,4-D), respectively. Interestingly, regenerants with both red and green leaf were successfully obtained when regenerants were cultured on MS medium with 9% sucrose. Regenerants derived from long-term cultured calli were transferred to pots using an optimal acclimatization process and successfully adapted to both pot and soil conditions. Moreover, the ploidy level was measured using calli and regenerants that had been kept on MS medium containing various kinds of plant growth regulators (PGRs).

• Journal of Ecology and Environment
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• v.48 no.2
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• pp.152-162
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• 2024

Background: Plant species of the alpine treeline ecotone are highly sensitive to climate change and may adjust their population dynamics, and functional traits in response to changing climate. This study examined regeneration patterns and leaf traits variations in an important treeline ecotone element Rhododendron campanulatum along the elevation gradient in western Nepal to assess its potential adaptive responses to climate change. The distribution range of R. campanulatum (3,400-3,800 m above sea level [a.s.l.]) was divided into five horizontal bands, each with a 100 m elevational range. Eight plots (10 m × 10 m) were sampled in each band, resulting into a total of 40 plots. In each plot, all R. campanulatum individuals and co-occurring tree species were counted. From each elevation, R. campanulatum leaf samples were collected to determine leaf dimensions, leaf density, specific leaf area (SLA), and stomatal density (SD). Results: The density-diameter curve indicated that R. campanulatum was regenerating well, with enhanced regeneration at higher elevation (3,800 m a.s.l.) than at lower. Tree canopy cover appeared to be the major determinant of R. campanulatum regeneration, as indicated by a higher number of seedlings in treeless stands. With increasing elevation, the leaf length, width, SLA, and stomata length decreased but leaf thickness and SD increased. Conclusions: Overall, a higher regeneration and lower SLA with the high SD in the leaves at the upper limit of the species distribution suggested that R. campanulatum is well adapted at its upper distribution range with the possibility of upslope range shift as temperature increases.

• Korean Journal of Weed Science
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• v.17 no.3
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• pp.269-280
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• 1997

Collated data from the 1995-1996 field surveys of weed seeds buried in the plough layer of peat soil in Selangor district were analysed to assess species-dominance and spatial pattern of distribution of weed seeds based on selected quantitative indices and index of dispersion. Forty five species within 14 families were recorded of which 24 were broadleaves, 12 grasses and 9 sedges. They comprised ca. 53.2, 31.2 and 15.6%, respectively based on total population counts. Total seed population was ca. $8.14{\times}10^7$ seeds/ha within the fast 25cm soil depth. Wide variabilities in population counts were registered among species ranging from < $7.0{\times}10^4$ seeds/ha for Amaranthus gracilis to ca. $5.64{\times}10^6$ seeds/ha for Heteropogon contortus. Seeds of Cleome rutidesperma was the most abundant(ca. $2.347{\times}10^7$ seeds/ha). Difference in seed population counts may be attributed to inherent variation in fecundity, population fluxes, their spatial distribution patterns and the agronomic practices prevailing in the areas of survey. The profile distribution of soil seed banks was skewed within the first 0 - 10cm depth, comprising ca. 69% of the total seed counts. Seed counts in the 10 - 15, 15 - 20 and 20 - 25cm soil profiles were in the order of 17.9, 8.6 and 4.0% of the total populations, respectively. Weed seeds of all species displayed different degree of aggregated pattern of distribution with variance-to-mean ratios of > 1 and Lloyd's mean crowding($m^*$) values from 1.244 for Cyperus iria, Phyllanthus debilis, Phyllanthus urinaria, Scirpus grosses and urinaria lagopodiodes to 9607.7 for Cleome rutidosperma. Lloyd's patch indices(Ip) ranging from 5.1 for Aeschynomene indica to 188.5 for Bracharia reptans were registered. Differences in the VMR, $m^*$ and Ip values among species suggested inter-alia inherent variabilities in their disposal capacity from seed source and different agronomic practices prevailing in the areas surveyed.

• Journal of The Korean Association For Science Education
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• v.18 no.1
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• pp.93-108
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• 1998

This study investigated science textbooks used from 1906 to 1915 in Korea, which is often neglected in previous researches. By doing so, more practical and specific understanding of the science education during that period can be made. It was based on the historical achieves "School Textbook List"(Vol. $4{\sim}9$) which was published by the Ministry of Education and the Government General of Chosen and other sources. The results and conclusions of the research are as follow; (1) The science textbooks which have been used from 1906 to 1915 in Korea can be categorized into three different tapes of books, either written in Chinese, or in Japanese, or in Korean. The names of science textbooks were Nature Study, Physics, Chemistry, Natural History, Hygienics, Physiology, Zoology, Botany, Astronomy, Physiography, Mineralogy, Geology. These names were much broader than those in curriculum settled by the government and rather correspond to the names of science textbooks in curriculum which settled by private schools. Therefore those science textbooks had been mainly used in private schools. Moreover almost all of the science textbooks published in Korea have started to appear after 1906. Since then many schools were newly opened and the number of students increased. It is possible to say that substantial science education in Korea established after 1906. (2) Science textbooks from 1906 to 1915 printed in Korea were controlled in their use by the Ministry of Education and the Government General of Chosen. They were the main means of government regulations, supported by Private School Ordinance, Regulations for Official Examination of textbooks in 1908 and Law of Publication in 1909. According to the result of official examination, as the time went by under the Japanese ruling of Korea, the increasing number of science textbooks were getting banned. While the science textbooks had enjoyed more freedom than the other textbooks from the control by inspection of the Government General of Chosen, the situation has been significantly changed as Japan started to intensity the control of all kinds of textbooks in Korea. Although there were a lot of copied science textbooks, 62 science textbooks printed in Korea, 72 Japanese science textbooks were used in Korea, and 40 Korean were to be engaged in science education compiling and copying science textbooks. There developments in science textbooks alone suggest that there were enormous amount of potentials in Korean science education at that time. However, all of these effects and progresses were destroyed when the sovereign authority of Korea was lost to Japan in 1910.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.3
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• pp.1281-1287
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• 2015

Background: Early detection of hepatocellular carcinoma using serological markers with better sensitivity and specificity than alpha fetoprotein (AFP) is needed. Aims: The aim of this study was to evaluate the diagnostic value of serum sICAM-1, ${\beta}$-catenin, IL-8, proteasome and sTNFR-II in early detection of HCC. Materials and Methods: Serum levels of IL-8, sICAM-1, sTNFR-II, proteasome and ${\beta}$-catenin were measured by ELISA assay in 479 serum samples from 192 patients with HCC, 96 patients with liver cirrhosis (LC), 96 patients with chronic hepatitis C (CHC) and 95 healthy controls. Results: Serum levels of proteasome, sICAM-1, ${\beta}$-catenin and ${\alpha}FP$ were significantly elevated in HCC group compared to other groups (P-value<0.001), where serum level of IL-8 was significantly elevated in the LC and HCC groups compared to CHC and control groups (P-value <0.001), while no significant difference was noticed in patients with HCC and LC (P-value=0.09). Serum level of sTNFR-II was significantly elevated in patients with LC compared to HCC, CHC and control groups (P-value <0.001); also it was significantly higher in HCC compared to CHC and control groups (P-value <0.001). ROC curve analysis of the studied markers between HCC and other groups revealed that the serum level of proteasome had sensitivity of 75.9% and specificity of 73.4% at a cut-off value of $0.32{\mu}g/ml$ with AUC 0.803 sICAM-1 at cut off value of 778ng/ml, the sensitivity was 75.8% and the specificity was 71.8% with AUC 0.776. ${\beta}$-catenin had sensitivity and specificity of 70% and 68.6% respectively at a cut off value of 8.75ng/ml with an AUC of 0.729. sTNFR-II showed sensitivity of 86.3% and specificity of 51.8% at a cut off value of 6239.5pg/ml with an AUC of 0.722. IL-8 had sensitivity of 70.4% and specificity of 52.3% at a cut off value of 51.5pg/ml with AUC 0.631. Conclusions: Our data supported the role of proteasome, sICAM-1, sTNFR-II and ${\beta}$-catenin in early detection of HCC. Also, using this panel of serological markers in combination with ${\alpha}FP$ may offer improved diagnostic performance over ${\alpha}FP$ alone in the early detection of HCC.

• Korean Journal of Environmental Biology
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• v.35 no.2
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• pp.207-214
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• 2017

There is little information about the seed longevity of wild plants, although seed bank storage is an important tool for biodiversity conservation. This study was conducted to predict the seed viability equation of Agastache rugosa. The A. rugosa seeds were stored at moisture contents ranging from 2.7 to 12.5%, and temperatures between 10 and $50^{\circ}C$. Viability data were fitted to the seed viability equation in a one step and two step approach. The A. rugosa seeds showed orthodox seed storage behaviour. The viability constants were $K_E=6.9297$, $C_W=4.2551$ $C_H=0.0329$, and $C_Q=0.00048$. The P85 of A. rugosa seeds was predicted to 152 years under standard seed bank conditions. The P85 predicted by seed viability equation can be used as basic information for optimization of seed storage processes.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.51 no.3
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• pp.259-268
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• 2006

Miniature inverted transposable elements (MITEs) are abundant genomic components in plant including rice. MITE-transposon display (MITE-TD) is an Amplified Fragment Length Polymorphism (AFLP)-related technique based on MITE sequence. In this study, we used the MITE-AFLP for the analysis of diversity and relation-ship of the 114 japonica accessions. Of the several MITEs, the mPing family was applied to detect polymorphisms based on PCR amplification. The BfaI adaptor primer and the specific primer derived from mPing terminal inverted repeat (TIR) region were used to PCR amplification of 114 accessions. Nine primer pairs produced a total of 160 polymorphic bands. PIC values of the polymorphic bands generated by nine primer pairs ranged from 0.269 (BfaI + ACT) to 0.426 (BfaI + T). Each accession revealed a distinct fingerprint with two primer combinations, BfaI + G and BfaI + C. Cluster analysis using marker-based genetic similarity classified 114 accessions into five groups. MITE-AFLP markers were genetically mapped using a population of 80 BILs (BC1F7) derived from a cross between the rice accessions, Milyang 23 and Hapcheonaengmi 3. Eight of the markers produced with the primer pair BfaI + 0 were mapped on chromosomes 1, 2, 4, 5, 7, and 9. Considering that one MITE-AFLP marker on chromosome 7 was tightly linked to the Rc gene, the MITE-AFLP markers will be useful for gene tagging and molecular cloning.

• Korean Journal of Plant Taxonomy
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• v.42 no.4
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• pp.247-252
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• 2012

Seed morphology in the subtribe Agrimoniinae (Rosaceae) was examined using scanning electron microscopy to identify distinct characters and evaluate their evolution in a phylogenetic framework for five genera in the subtribe: Agrimonia L., Aremonia Neck. ex Nestl., Hagenia J.F. Gmel., Leucosidea Eckl. & Zeyh., and Spenceria Trimen. All genera have one or two mature achenes in a fruiting hypanthium. In the seed coats, the cell shape, size, wall features, and sculpturing vary across genera. Of most significance is the presence of papillae structures in both Agrimonia and Aremonia. Through the mapping of papillae features onto phylogenetic trees, either one or two changes in seed coats are hypothesized. The phylogenetic tree inferred from four nuclear and six chloroplast regions of sequence data suggests that at least two steps of papillae sculpturing on seed coats are required. On the other hand, in the phylogenetic tree of a low-copy nuclear gene, one independent evolutionary step is postulated to explain the current character states. In the latter hypothesis, the seed coat sculpturing also supports a monophyletic relationship for cosmopolitan Agrimonia and European endemic Aremonia. The seed coat sculpturing provides valuable information for inferring phylogenetic relationships at the generic level in the subtribe Agrimoniinae.