• Reproductive and Developmental Biology
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• v.29 no.3
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• pp.181-186
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• 2005

This experiment was conducted to investigate effects of the two different in vitro production systems, serumcontaining system (IVM, IVF and IVC; TCM199, TALP and CR1aa) and serum-free system (IVM, IVF and IVC; IVMD101, IVMD100 and IVMD101), on the development of in vitro fertilized or DNA-microiniected embryos. We also examined the effect of DNA dosage and its expression pattern in embryos. The DNA used for microinjection was a green fluorescence protein gene. The development rates to $\geq$ 2cell, 8cell and blastocyst stage were significantly higher in vitro fertilized embryos than those in DNA-microinjected embryos. The development rate to the 8-cell stage was significantly higher in serum-free system than in serum-containing system (p<0.05; $3.3\%\;vs.\;15.5\%\;and\;21.4\%$, respectively). The development rates to the blastocyst stage of in vitro fertilzed or DNA-microinjected embryos between two different culture system ($2.7\%\;vs.\;2.3\%\;and\;23.0\%\;vs.\;23.6\%$, respectively) were not different. The development rates of embryos injected 2 ng/uL DNA was higher. than those of embryos injected 4 or 8 ng/uL DNA. The GFP expression rate of 1-cell embryos was significantly higher than that of 2-cell and 4-cell embryos, whereas the rates were not different between 4-cell and blastocyst-stage embryos.

• Molecules and Cells
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• v.40 no.9
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• pp.655-666
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• 2017

We constructed a large $na{\ddot{i}}ve$ human Fab library ($3{\times}10^{10}$ colonies) from the lymphocytes of 809 human donors, assessed available diversities of the heavy-chain variable (VH) and ${\kappa}$ light-chain variable (VK) domain repertoires, and validated the library by selecting Fabs against 10 therapeutically relevant antigens by phage display. We obtained a database of unique 7,373 VH and 41,804 VK sequences by 454 pyrosequencing, and analyzed the repertoires. The distribution of VH and VK subfamilies and germline genes in our antibody repertoires slightly differed from those in earlier published natural antibody libraries. The frequency of somatic hypermutations (SHMs) in heavy-chain complementarity determining region (HCDR)1 and HCDR2 are higher compared with the natural IgM repertoire. Analysis of position-specific SHMs in CDRs indicates that asparagine, threonine, arginine, aspartate and phenylalanine are the most frequent non-germline residues on the antibody-antigen interface and are converted mostly from the germline residues, which are highly represented in germline SHM hotspots. The amino acid composition and length-dependent changes in amino acid frequencies of HCDR3 are similar to those in previous reports, except that frequencies of aspartate and phenylalanine are a little higher in our repertoire. Taken together, the results show that this antibody library shares common features of natural antibody repertoires and also has unique features. The antibody library will be useful in the generation of human antibodies against diverse antigens, and the information about the diversity of natural antibody repertoires will be valuable in the future design of synthetic human antibody libraries with high functional diversity.

• ALGAE
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• v.30 no.2
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• pp.121-137
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• 2015

Studies on carbon flux in the oceans have been highlighted in recent years due to increasing awareness about climate change, but the coastal ecosystem remains one of the unexplored fields in this regard. In this study, the dynamics of carbon flux in a vegetative coastal ecosystem were examined by an evaluation of net and gross ecosystem production (NEP and GEP) and $CO_2$ exchange rates (net ecosystem exchange, NEE). To estimate NEP and GEP, community production and respiration were measured along different habitat types (eelgrass and macroalgal beds, shallow and deep sedimentary, and deep rocky shore) at Gwangyang Bay, Korea from 20 June to 20 July 2007. Vegetative areas showed significantly higher ecosystem production than the other habitat types. Specifically, eelgrass beds had the highest daily GEP ($6.97{\pm}0.02g\;C\;m^{-2}\;d^{-1}$), with a large amount of biomass and high productivity of eelgrass, whereas the outer macroalgal vegetation had the lowest GEP ($0.97{\pm}0.04g\;C\;m^{-2}\;d^{-1}$). In addition, macroalgal vegetation showed the highest daily NEP ($3.31{\pm}0.45g\;C\;m^{-2}\;d^{-1}$) due to its highest P : R ratio (2.33). Furthermore, the eelgrass beds acted as a $CO_2$ sink through the air-seawater interface according to NEE data, with a carbon sink rate of $0.63mg\;C\;m^{-2}\;d^{-1}$. Overall, ecosystem production was found to be extremely high in the vegetated systems (eelgrass and macroalgal beds), which occupy a relatively small area compared to the unvegetated systems according to our conceptual diagram of a carbon-flux box model. These results indicate that the vegetative ecosystems showed significantly high capturing efficiency of inorganic carbon through coastal primary production.

• Journal of Life Science
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• v.30 no.10
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• pp.919-929
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• 2020

Aromatic compounds are widely used in the chemical, food, polymer, cosmetic, and pharmaceutical industries and are produced by mainly chemical synthesis using benzene, toluene, and xylene or by plant extraction methods. Due to many rising threats, including the depletion of fossil fuels, global warming, the strengthening of international environmental regulations, and the excessive harvesting of plant resources, the microbial production of aromatic compounds using renewable biomass is regarded as a promising alternative. By integrating metabolic engineering with synthetic and systems biology, artificial biosynthetic pathways have been reconstituted from L-tryptophan biosynthetic pathway in relevant microorganisms, such as Escherichia coli and Corynebacterium glutamicum, enabling the production of a variety of value-added aromatic compounds, such as 5-hydroxytryptophan, serotonin, melatonin, 7-chloro-L-tryptophan, 7-bromo-L-tryptophan, indigo, indirubin, indole-3-acetic acid, violacein, and dexoyviolacein. In this review, we summarize the characteristics, usage, and biosynthetic pathways of these aromatic compounds and highlight the latest metabolic engineering strategies for the microbial production of aromatic compounds and suitable solution strategies to overcome problems in increasing production titers. It is expected that strain development based on systems metabolic engineering and the optimization of media and bioprocesses using renewable biomass will enable the development of commercially viable technologies for the microbial production of many aromatic compounds.

• Korean Journal of Ecology and Environment
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• v.34 no.3 s.95
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• pp.192-198
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• 2001

The Kyongan Stream and the inlet part of Paltang Reservoir are under significant influence of the effluent of sewage wastewater treatment plant (SWTP) and untreated domestic wastewater (DOW). The fertility of wastewater was evaluated through bioassay using natural phytoplankton population diluted in five levels. The concentrations of $NH_4$, SRP and SRSi were positively correlated with the biomass of phytoplankton. P concentration showed stronger correlation (r = 0.959, p<0.001)than other nutrients. Compared with the initial concentrations, $NH_4$ concentrations in samples from SWTP and DOW decreased 96% and 7%, respectively during the cultivation, and those of SRSi decreased 97% and 60%. However, $NO_3$ concentrations in samples neither showed any particular change nor any increase. Chl-a concentration ranged between $20\;{\mu}g/l$ and $125\;{\mu}g/l$, which maximum value increased up to 83 times. Estimated from the relationship between chl-a and SRP, the P concentration that can maintain the biomass of algae under mesotrophic state (<25\;{mu}g$\;chl-a/l$) was $83\;{mu}g\; P/l$. The volume of flow to maintain this level solely by natural dilution was about $16{\sim}25$ times of in flowing volume in the stream. However, it is not feasible to tap water of such quantity. Therefore, it is imperative to build an advanced sewage wastewater treatment facility that can reduce $NH_4$ and SRP concentrations that promote the growth of phytoplankton in discharged water.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.3 no.3
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• pp.170-174
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• 1998

The water quality of offshore waters around the Korean coast was evaluated by bioassay using gametes, embryoss and early development systems of a sea urchin species Hemicentrotus pulcherrimus. The results show that despite the inflows of several river systems, the west coast maintain the grade II water. This is thought to be due to the decrease in pollutant input resulting from the purification of inflow rivers (e.g., the control of waste water discharge and the construction of sewage treatment facilities), and the dilution of pollutants by a strong tidal mixing with a large difference between the ebb and flood tides. However, Asan, Hampyong and Chonsu bays, where circulations of water are relatively poor, and the Kunsan and Mokpo harbors which are influenced by pollutants from neighboring cities have shown the grade III water. The south coast has maintain the grade II or III because developments of sea urchins were moderately or strongly inhibited. Also, Kangjin, Duekryang, Kwangyang, Masan, and Jinhae bays where water circulations are relatively poor, show the grade III water, with strong inhibitions of the early development of sea urchins. The east coast has maintained the grade I and II due to monotonous coastlines and smooth circulation of sea water. However, Chongcho Lake shows the worst water quality due to the breakwater which is constructed to maintain port functions.

• Interdisciplinary Bio Central
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• v.1 no.3
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• pp.9.1-9.6
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• 2009

Introduction: In the mass spectrometry-based proteomics, biological samples are analyzed to identify proteins by mass spectrometer and database search. Database search is the process to select the best matches to the experimental mass spectra among the amino acid sequence database and we identify the protein as the matched sequence. The match score is defined to find the matches from the database and declare the highest scored hit as the most probable protein. According to the score definition, search result varies. In this study, the difference among search results of different search engines or different databases was investigated, in order to suggest a better way to identify more proteins with higher reliability. Materials and Methods: The protein extract of human mesenchymal stem cell was separated by several bands by one-dimensional electrophorysis. One-dimensional gel was excised one by one, digested by trypsin and analyzed by a mass spectrometer, FT LTQ. The tandem mass (MS/MS) spectra of peptide ions were applied to the database search of X!Tandem, Mascot and Sequest search engines with IPI human database and SwissProt database. The search result was filtered by several threshold probability values of the Trans-Proteomic Pipeline (TPP) of the Institute for Systems Biology. The analysis of the output which was generated from TPP was performed. Results and Discussion: For each MS/MS spectrum, the peptide sequences which were identified from different conditions such as search engines, threshold probability, and sequence database were compared. The main difference of peptide identification at high threshold probability was caused by not the difference of sequence database but the difference of the score. As the threshold probability decreases, the missed peptides appeared. Conversely, in the extremely high threshold level, we missed many true assignments. Conclusion and Prospects: The different identification result of the search engines was mainly caused by the different scoring algorithms. Usually in proteomics high-scored peptides are selected and low-scored peptides are discarded. Many of them are true negatives. By integrating the search results from different parameter and different search engines, the protein identification process can be improved.

• The Korean Journal of Pesticide Science
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• v.3 no.1
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• pp.57-65
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• 1999

The midge Chironomus riparius is a member of widespread dipteran insect which has been used for sediment toxicity test. The 2nd-3rd larvae Chironomus riparius were exposed to $^{14}C$-lambda-cyhalothrin in laboratory water only system(A) and sediment-water system(B) at $20{\pm}2^{\circ}C$. The concentration was nominally in the range of 0.16 to $20{\mu}g/{\ell}$ and 62.5 to 8000 ${\mu}g/kg$, respectively. System(A) was prepared by applying the chemical to 250 ml water and introducing Chironomus riparius larvae into the system(day 0). System(B) was prepared by applying the chemical to the 25 g of soil and 250 ml water and shaking and rolling them for two hours. After allowing the system to settle for two days, Chironomus riparius larvae were introduced into the system. After 72 hours, the two systems were terminated and dead larvae were observed. The measurement of residue in water was conducted at the start(day 0) and the end of the study(day 3). The residue of $^{14}C$-lambda-cyhalothrin in water was accounted for approximately 65% of nominal concentration in system(A) and $0.2{\sim}0.4%$ in system) on 3 days. $LC_{50}$ was less than $0.156{\mu}g/{\ell}$ in system(A) and 889 ${\mu}g/kg$ in system(B), based on the nominally applied concentration.

• The Plant Pathology Journal
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• v.32 no.2
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• pp.112-122
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• 2016

Virus-induced gene silencing (VIGS) is an effective tool for the study of soybean gene function. Successful VIGS depends on the interaction between virus spread and plant growth, which can be influenced by environmental conditions. Recently, we developed a new VIGS system derived from the Soybean yellow common mosaic virus (SYCMV). Here, we investigated several environmental and developmental factors to improve the efficiency of a SYCMV-based VIGS system to optimize the functional analysis of the soybean. Following SYCMV: Glycine max-phytoene desaturase (GmPDS) infiltration, we investigated the effect of photoperiod, inoculation time, concentration of Agrobacterium inoculm, and growth temperature on VIGS efficiency. In addition, the relative expression of GmPDS between non-silenced and silenced plants was measured by qRT-PCR. We found that gene silencing efficiency was highest at a photoperiod of 16/8 h (light/dark) at a growth temperature of approximately $27^{\circ}C$ following syringe infiltration to unrolled unifoliolate leaves in cotyledon stage with a final SYCMV:GmPDS optimal density $(OD)_{600}$ of 2.0. Using this optimized protocol, we achieved high efficiency of GmPDS-silencing in various soybean germplasms including cultivated and wild soybeans. We also confirmed that VIGS occurred in the entire plant, including the root, stem, leaves, and flowers, and could transmit GmPDS to other soybean germplasms via mechanical inoculation. This optimized protocol using a SYCMV-based VIGS system in the soybean should provide a fast and effective method to elucidate gene functions and for use in large-scale screening experiments.

• Korean Journal of Ecology and Environment
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• v.53 no.1
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• pp.1-10
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• 2020

The Stream/River Ecosystem Survey and Health Assessment has been carried out regarding the ecological health of the streams by the Ministry of Environment (MOE), South Korea. However, the sources of impairment of the stream ecosystem and the interactions between the sources, stressors, and the responses of impaired streams have not been taken into consideration. The purpose of this study is to propose the establishment of diagnosis systems for the impaired stream ecosystem because of the need to incorporate the same in the making of the policy to enable the recovery and improvement of the health of the impaired streams or river ecosystem. First, we define the concept of a diagnosis of the impaired stream or river ecosystem through a literature review. Second, through case studies [e.g., US CADDIS (Causal Analysis/Diagnosis Decision Information System), AUS. Eco Evidence, EU WFD (Water Framework Directive)], we try to develop the diagnosis system for the making of policy. In this study, the diagnosis system that is proposed consists of eight steps including the basic data collection, detecting or suspecting impairment, defining the impaired stream reach, identifying the biological impaired cases and listing the candidate causes, illustrating the interactive conceptual diagrams between stressors and responses, investigating the stressors-responses in the field, verifying causes and identifying the probable causes of the impaired cases, and summarizing and proposing the restoration of the streams. The results of this study will support and enable efficient decision-making for sustainable stream restoration and management based on the diagnosis of the probable causes for the impaired complex and the diverse stream ecosystem.