• Parasites, Hosts and Diseases
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• v.41 no.4
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• pp.209-219
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• 2003

The evolutionary course of the CsRn1 long-terminal-repeat (LTR) retrotransposon was predicted by conducting a phylogenetic analysis with its paralog LTR sequences. Based on the clustering patterns in the phylogenetic tree, multiple CsRn1 copies could be grouped into four subsets, which were shown to have different integration times. Their differential sequence divergences and heterogeneous integration patterns strongly suggested that these subsets appeared sequentially in the genome of C. sinensis. Members of recently expanding subset showed the lowest level of divergence in their L TR and reverse transcriptase gene sequences. They were also shown to be highly polymorphic among individual genomes of the trematode. The CsRn1 element exhibited a preference for repetitive, agenic chromosomal regions in terms of selecting integration targets. Our results suggested that CsRn1 might induce a considerable degree of intergenomic variation and, thereby, have influenced the evolution of the C. sinensis genome.

• Journal of Microbiology and Biotechnology
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• v.27 no.4
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• pp.838-843
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• 2017

Sepsis is a major health problem worldwide, with an extremely high rate of morbidity and mortality, partly due to delayed diagnosis during early disease. Currently, sepsis diagnosis requires bacterial culturing of blood samples over several days, whereas PCR-based molecular diagnosis methods are faster but lack sensitivity. The use of biosensors containing nucleic acid aptamers that bind targets with high affinity and specificity could accelerate sepsis diagnosis. Previously, we used the systematic evolution of ligands by exponential enrichment technique to develop the aptamers Antibac1 and Antibac2, targeting the ubiquitous bacterial peptidoglycan. Here, we show that these aptamers bind to four gram-positive and seven gram-negative bacterial sepsis agents with high binding efficiency. Thus, these aptamers could be used in combination as biological recognition elements in the development of biosensors that are an alternative to rapid bacteria detection, since they could provide culture and amplification-free tests for rapid clinical sepsis diagnosis.

• Journal of Veterinary Science
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• v.19 no.6
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• pp.771-781
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• 2018

Staphylococcus aureus is one of the major pathogens causing bovine mastitis and foodborne diseases associated with dairy products. To determine the genetic relationships between human and bovine or bovine isolates of S. aureus, various molecular methods have been used. Previously we developed an rpoB sequence typing (RSTing) method for molecular differentiation of S. aureus isolates and identification of RpoB-related antibiotic resistance. In this study, we performed spa typing and RSTing with 84 isolates from mastitic cows (22 farms, 72 cows, and 84 udders) and developed a molecular prophage typing (mPPTing) method for molecular epidemiological analysis of bovine mastitis. To compare the results, human isolates from patients (n = 14) and GenBank (n = 166) were used for real and in silico RSTing and mPPTing, respectively. Based on the results, RST10-2 and RST4-1 were the most common rpoB sequence types (RSTs) in cows and humans, respectively, and most isolates from cows and humans clearly differed. Antibiotic resistance-related RSTs were not detected in the cow isolates. A single dominant prophage type and gradual evolution through prophage acquisition were apparent in most of the tested farms. Thus, RSTing and mPPTing are informative, simple, and economic methods for molecular epidemiological analysis of S. aureus infections.

• Korean Journal of Microbiology
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• v.46 no.4
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• pp.383-388
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• 2010

Alkaline protease-overproducing strains of Vibrio metschnikovii were developed by using the molecular evolution from the classical mutants V. metschnikovii L12-23, N4-8, and KS1. Each vapK (Vibrio alkaline protease K) was obtained from the genomic DNAs of mutants by PCR to carry out the DNA shuffling. The modified vapK-1 obtained by DNA shuffling was used again as a template for the error-prone PCR to make the vapK-2. Both genes were cloned in the plasmid pKF3 to construct the recombinant plasmids which have one or two copies of the modified genes. The recombinant plasmids were back-transformed to V. metschnikovii KS1 to construct recombinant V. metschnikovii that expresses the alkaline protease. About 3.9-fold more protease activity was measured in the strain which has the plasmid containing two copies of vapK-2 when compared to strain KS1. When compared to wild type V. metschnikovii RH530, 43-fold more activity was achieved. Comparison of amino acids among vapK, vapK-1, and vapK-2 revealed that the active sites was highly conserved and not changed. However, many amino acids except the active sites were changed. These results suggested that the changes in amino acids might play an important role in the increase of protease activity by allowing the easy access of substrate to active sites of the protease. The fermentation of alkaline protease from the V. metschnikovii KS1 harboring the plasmid that contains two copies of vapK-1 showed the possibility of this strain to be used as industrial producer.

• Korean Journal of Agricultural Science
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• v.37 no.2
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• pp.209-216
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• 2010

In order to understand the effects of a single or combined treatments of 1-MCP($1{\mu}L/L$) and $CO_2$(100%) on the firmness of melting type peach fruit(cv. Chunjungdo), fruit were harvested at commercial maturity and examined physiological changes including flesh firmness during 10 days of shelf-life. Firmness loss of fruit was delayed by both single and combined treatments of 1-MCP and $CO_2$. The treatment of 1-MCP was more effective than $CO_2$ treatment but no additive effective on firmness retention was found in the combined treatment. The upsurge of ethylene evolution occurred 5 days of shelf-life in air treated control but ethylene evolution gradually increased in fruit treated by 1-MCP and 1-MCP+$CO_2$. The suppression of ethylene evolution seemed stronger in $CO_2$ treatment. The respiration of fruit significantly inhibited up to 10 days except control where climacteric increase of respiration was found at 10 days of shelf-life. A molecular shift of pectic polymers(an increase of chelator soluble pectins and decrease of water soluble pectins) was induced by both 1-MCP and $CO_2$ treatments. An increase of water soluble pectins was coincident with firmness loss. The delay of firmness loss seemed to be associated with the migration of calcium to wall matrix, especially pectins, resulting in the increase of wall bound calcium. The polygalacturonase activity was significantly reduced by 1-MCP alone 1 day after treatment and increased to similar level of activity 5 days after treatment compared to other treatment except air treated control whereas pectin methylesterase activity seemed not to be affected by both 1-MCP and $CO_2$ treatments. Thus, the molecular shift of pectic polymers appeared not to be related with pectin methylesterase. Further study is required to clarify the softening mechanism associated with molecular shift of pectic polymers and the inter- or intra-cellular movement of calcium ions induced by postharvest treatments of 1-MCP and $CO_2$.

• The Bulletin of The Korean Astronomical Society
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• v.46 no.1
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• pp.50.2-51
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• 2021

Stars form exclusively in cold and dense molecular clouds. To fully understand star formation processes, it is hence a key to investigate how molecular clouds form out of the surrounding diffuse atomic gas. With an aim of shedding light in the process of the atomic-to-molecular transition in the interstellar medium, we analyze Arecibo HI emission and absorption spectral pairs along with TRAO/PMO 12CO(1-0) emission spectra toward 58 lines of sight probing in and around molecular clouds in the solar neighborhood, i.e., Perseus, Taurus, and California. 12CO(1-0) is detected from 19 out of 58 lines of sight, and we report the physical properties of HI (e.g., central velocity, spin temperature, and column density) in the vicinity of CO. Our preliminary results show that the velocity difference between the cold HI (Cold Neutral Medium or CNM) and CO (median ~ 0.7 km/s) is on average more than a factor of two smaller than the velocity difference between the warm HI (Warm Neutral Medium or WNM) and CO (median ~ 1.7 km/s). In addition, we find that the CNM tends to become colder (median spin temperature ~ 43 K) and abundant (median CNM fraction ~ 0.55) as it gets closer to CO. These results hints at the evolution of the CNM in the vicinity of CO, implying a close association between the CNM and molecular gas. Finally, in order to examine the role of HI in the formation of molecular gas, we compare the observed CNM properties to the theoretical model by Bialy & Sternberg (2016), where the HI column density for the HI-to-H2 transition point is predicted as a function of density, metallicity, and UV radiation field. Our comparison shows that while the model reproduces the observations reasonably well on average, the observed CNM components with high column densities are much denser than the model prediction. Several sources of this discrepancy, e.g., missing physical and chemical ingredients in the model such as the multi-phase ISM, non-equilibrium chemistry, and turbulence, will be discussed.

• The Korean Journal of Mycology
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• v.27 no.4 s.91
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• pp.274-279
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• 1999

The internal transcribed spacer regions(ITS) of the ribosomal DNA gene repeat from Coprinus and Psathyrella spp. were amplified using polymerase chain reaction (PCR) and sequenced. Sequences from 11 species including Coprinus comatus, C. atramentarius, C. micaceus, C. cinereus, C. rhizophorus, C. radians, C. echinosporus, C. disseminatus, Psathyrella candolleana, P. spadiceogrisea and Stropharia rugosoannulata were compared. The spacer region I and II were $258{\sim}301\;bp\;and\;253{\sim}275\;bp$ in length respectively and partially contained 17S, 5.8S and 25S. The reciprocal homologies of ITS sequences among these strains were in the range of $43.9{\sim}96.0%$. According to the analysis of ITS sequences, Coprinus and Psathyrella spp. were classified into three clusters. Cluster I consisted of Coprinus lagopus, C. cinereus, C. echinosporus, C. rhizophorus, and C. atramentarius. Cluster II comprised C. micaceus, C. radians, C. disseminatus, Psathyrella candolleana, and P. spadiceogrisea. On the other hand C. comatus is in Cluster III with Stropharia rugosoannulata even though this species is belonging to the section Coprinus in morphological aspect. These results suggest that taxonomic position of Psathyrella would better be inculded in genus Coprinus. Coprinus comatus, the type species of Coprinus, gives a doubt on monophyletic evolution and is assumed to be paraphyletic or polyphyletic.

• Molecules and Cells
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• v.43 no.4
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• pp.331-339
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• 2020

Genetic modifications in noncoding regulatory regions are likely critical to human evolution. Human-accelerated noncoding elements are highly conserved noncoding regions among vertebrates but have large differences across humans, which implies human-specific regulatory potential. In this study, we found that human-accelerated noncoding elements were frequently coupled with DNase I hypersensitive sites (DHSs), together with monomethylated and trimethylated histone H3 lysine 4, which are active regulatory markers. This coupling was particularly pronounced in fetal brains relative to adult brains, non-brain fetal tissues, and embryonic stem cells. However, fetal brain DHSs were also specifically enriched in deeply conserved sequences, implying coexistence of universal maintenance and human-specific fitness in human brain development. We assessed whether this coexisting pattern was a general one by quantitatively measuring evolutionary rates of DHSs. As a result, fetal brain DHSs showed a mixed but distinct signature of regional conservation and outlier point acceleration as compared to other DHSs. This finding suggests that brain developmental sequences are selectively constrained in general, whereas specific nucleotides are under positive selection or constraint relaxation simultaneously. Hence, we hypothesize that human- or primate-specific changes to universally conserved regulatory codes of brain development may drive the accelerated, and most likely adaptive, evolution of the regulatory network of the human brain.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.02a
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• pp.358-358
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• 2010

Ion beam bombardment at low energy forms nanosize patterns such as ripples, dots or wrinkles on the surface of polymers in ambient temperature and pressure. It has been known that the ion beam can alter the polymer surface that induces skins stiffer or the density higher by higher compressive stress or strain energies associated with chain scissions and crosslinks of the polymer. Atomic scale structure evolution in polymers is essential to understand a stress generation mechanism during the ion beam bombardment, which governs the nanoscale surface structure evolution. In this work, Molecular Dynamics (MD) simulations are employed to characterize the phenomenon occurred in bombardment between the ion beam and polymers that forms nanosize patterns. We investigate the structure evolution of Low Density Polyethylene (LDPE) at 300 K as the polymer is bombarded with Argon ions having various kinetic energies ranging from 100 eV to 1 KeV with 50 eV intervals having the fluence of $1.45\;{\times}\;1014 #/cm2$. These simulations use the Reactive Force Field (ReaxFF), which can mimic chemical covalent bonds and includes van der Waals potentials for describing the intermolecular interactions. The results show the details of the structural evolution of LDPE by the low energy Ar ion bombardment. Analyses through kinetic and potential energy, number of crosslinks and chain scissions, level of local densification and motions of atoms support that the residual strain energies on the surface is strongly associated with the number of crosslinks or scissored chains. Also, we could find an optimal Ar ion beam energy to make crosslinks well.

• Journal of The Korean Astronomical Society
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• v.38 no.2
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• pp.271-278
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• 2005

Athough planetary nebulae (PNe) have been discovered for over 200 years, it was not until 30 years ago that we arrived at a basic understanding of their origin and evolution. Even today, with observations covering the entire electromagnetic spectrum from radio to X-ray, there are still many unanswered questions on their structure and morphology. In this review, we summarize recent theoretical and observational advances in PNe research, and discuss the roles of PNe in the chemical (atomic, molecular, and solid-state) enrichment of the galaxy and as tracers of the large scale structure of the Universe.