• Journal of Life Science
• /
• v.30 no.10
• /
• pp.919-929
• /
• 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
• /
• v.34 no.3 s.95
• /
• pp.192-198
• /
• 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
• /
• v.3 no.3
• /
• pp.170-174
• /
• 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
• /
• v.1 no.3
• /
• pp.9.1-9.6
• /
• 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
• /
• v.3 no.1
• /
• pp.57-65
• /
• 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
• /
• v.32 no.2
• /
• pp.112-122
• /
• 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
• /
• v.53 no.1
• /
• pp.1-10
• /
• 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.

• Journal of the Korean Society of Environmental Restoration Technology
• /
• v.15 no.2
• /
• pp.19-29
• /
• 2012

Numerous studies suggested that fish assemblage structure reflects the status of stream ecosystems. The status of streams integrity, including various trophic levels, water quality and habitat degradation, can be assessed by fish assemblages. In this study, we investigated the relationships between fish assemblages and streamline geometry of streams. Previous studies suggested that geomorphologic parameter can be a critical factor of permeability between adjacent two systems. From a landscape ecological perspective, edges may partially control the flow rate of energy between two adjacent systems. Thus, the Streamline geometry can be a geomorphologic parameter that exhibits the integrity of stream. We selected the Nakdong river for study areas, which is one of major rivers and the longest (525 km) River in South Korea. We used the revised IBI representing overall ecological characteristics of Korean fish assemblages and eight sub-assessment criteria of IBI, collected from 82 sampling sites in the Nakdong River. For calculating the Streamline geometry, we measured fractal dimension index that generally used in biology, ecology and landscape ecology. We used the digital land-use/land-cover map and generated a 1-km buffer for each sampling site and refined the shape of the Streamlines. Pearson correlation analyses were performed between Streamline geometry and IBI and sub-assessment criteria of IBI. The results show that IBI and eight sub-assessments of fish are significantly correlated with geometry of Streamline. The fractal dimension of Streamline geometry were related with IBI (r = 0.48) and six sub-assessments of IBI, including total number of native fish and native species, the number of riffle benthic species, sensitive species, tolerant species and native insectivore. Especially, the number of tolerant species(r = -0.52) and native insectivore(r = 0.52) show strong correlation with geometry of Streamline. These results indicate that lower Streamline geometry can result in poor fish assemblages, while higher geometry of Streamline can enhance fish assemblages by potentially supplying insects and better habitat conditions. We expect the results of our study to be useful for stream restoration and management. However, we see the necessity of study investigating the mechanisms how Streamline geometry affect fish assemblages.

• Journal of Food Hygiene and Safety
• /
• v.22 no.1
• /
• pp.1-14
• /
• 2007

The term, "food safety", has traditionally been viewed as a practical science aimed at assuring the prevention acute illnesses caused by biological microorganisms, and only to a minor extent, chronic diseases cause by chronic low level exposures to natural and synthetic chemicals or pollutants. "food safety" meant to prevent microbiological agents/toxins in/on foods, due to contamination any where from "farm to Fork", from causing acute health effects, especially to the young, immune-compromised, genetically-predisposed and elderly. However, today a broader view must also include the fact that diet, perse (nutrients, vitamins/minerals, calories), as well as low level toxins and pollutant or supplemented synthetic chemicals, can alter gene expressions of stem/progenitor/terminally-differentiated cells, leading to chronic inflammation and other mal-functions that could lead to diseases such as cancer, diabetes, atherogenesis and possibly reproductive and neurological disorders. Understanding of the mechanisms by which natural or synthetic chemical toxins/toxicants, in/on food, interact with the pathogenesis of acute and chronic diseases, should lead to a "systems" approach to "food safety". Clearly, the interactions of diet/food with the genetic background, gender, and developmental state of the individual, together with (a) interactions of other endogenous/exogenous chemicals/drugs; (b) the specific biology of the cells being affected; (c) the mechanisms by which the presence or absence of toxins/toxicants and nutrients work to cause toxicities; and (d) how those mechanisms affect the pathogenesis of acute and/or chronic diseases, must be integrated into a "system" approach. Mechanisms of how toxins/toxicants cause cellular toxicities, such as mutagenesis; cytotoxicity and altered gene expression, must take into account (a) irreversible or reversal changes caused by these toxins or toxicants; (b)concepts of thresholds or no-thresholds of action; and (c) concepts of differential effects on stem cells, progenitor cells and terminally differentiated cells in different organs. This brief Commentary tries to illustrate this complex interaction between what is on/in foods with one disease, namely cancer. Since the understanding of cancer, while still incomplete, can shed light on the multiple ways that toxins/toxicants, as well as dietary modulation of nutrients/vitamins/metals/ calories, can either enhance or reduce the risk to cancer. In particular, diets that alter the embryo-fetal micro-environment might dramatically alter disease formation later in life. In effect "food safety" can not be assessed without understanding how food could be 'toxic', or how that mechanism of toxicity interacts with the pathogenesis of any disease.

• Journal of Life Science
• /
• v.25 no.7
• /
• pp.839-848
• /
• 2015

A molecular marker is a molecule contained within a sample taken from an organism or other matter. The development of molecular techniques for genetic analysis has led to a great contribution to our knowledge of plant genetics and our understanding of the structure and behavior of various genomes in plants. Recently, functional molecular markers have been developed to detect the presence of major genes from the analysis of pedigreed data in absence of molecular information. DNA markers have developed into many systems based on different polymorphism-detecting techniques or methods such as RFLP, AFLP, RAPD, SSR, SNP, etc. A new class of very useful DNA markers called genic molecular markers utilizing the ever-increasing archives of gene sequence information being accumulated under the EST sequencing projects on a large number of plant species. Functional markers are derived from polymorphic sequences, and are more likely to be involved in phenotypic trait variation. Based on this conceptual framework, the marker systems discussed below are all (gene)-targeted markers, which have the potential to become functional. These markers being part of the cDNA/EST-sequences, are expected to represent the functional component of the genome i.e., gene(s), in contrast to all other random DNA based markers that are developed/generated from the anonymous genomic DNA sequences/domains irrespective of their genic content/information. Especially I sited Poczai et al’ reviews, advances in plant gene-targeted and functional markers. Their reviews may be some useful information to study molecular markers in plants.