• Korean Chemical Engineering Research
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• 제62권3호
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• pp.274-280
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• 2024

기계학습법의 신경망 기술을 이용한 자료분석은 질병 유전자 탐색 및 진단, 신약 개발, 약인성 간 손상 예측 등과 같은 다양한 분야에서 활용되고 있다. 질병 특징 발견을 위한 자료분석은 DNA 정보를 기반으로 이루어질 수 있다. 본 연구에서는 DNA의 분자 정보 중 DNA의 길이와 용액 내 DNA의 길이별 종 개수를 예측하는 신경망을 개발하였다. 겔 전기영동을 통한 기존 방법론의 시간 소요 한계점을 해결하고자, 미세유체역학적 농축 장치의 동역학 자료를 분석 대상으로 하여 실험 분석 과정 중의 시간 소요 문제점을 해결하였다. 동역학 자료를 공간시간 지도로 재구성하여 학습 및 예측에 필요한 계산용량을 낮추었으며, 공간시간 지도에 대한 분석 정확도를 높이기 위해 합성곱 신경망을 활용하였다. 그 결과, 단일 변수 회귀로써의 단일 DNA 길이 예측과 복합 변수 회귀로써의 다종 DNA 길이의 동시 예측 및 이진 분류로써의 DNA 혼합 종 개수 예측을 성공적으로 수행하였다. 추가적으로, 예측 과정 중 발생할 수 있는 예측 편향을 학습 자료 구성 방식을 통한 해결책을 제시하였다. 본 연구를 활용한다면, 광학 측정 자료를 이용하는 액체생검 기반의 세포유리 DNA 분석 및 암 진단 등의 의학 자료 분석을 효과적으로 수행할 수 있을 것이다.

• KSBB Journal
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• 제20권4호
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• pp.305-310
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• 2005

동결건조 양막과 자체 제작한 양막 지지체를 이용한 동적 배양법을 통하여 토끼 각막 상피층의 재구성 효과를 검토하였다. 각막 상피세포는 토끼 각막 윤부로부터 분리 배양 후 동결보존하여 사용하였고, 세포증식은 10계대까지 가능하였다. 동적배양을 한 경우가 정치배양보다 기저층이 잘 형성되었고, 세포 증식과 분화를 촉진하여 치밀한 상피층을 형성하였다. 이렇게 재구성된 각막 상피층은 심한 각막 손상을 입은 환자의 조직 이식에 좋은 생체외 모델이 될 것으로 기대된다.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2016년도 제50회 동계 정기학술대회 초록집
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• pp.190.1-190.1
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• 2016

One of the most serious problems faced by billions of people today is the availability of fresh water. According to statistics, 15% of the world's total output of dye products is discharged into the environment as dye wastewater, which seriously pollutes groundwater resources. For the treatment of chemically and biologically contaminated water the advanced oxidation processes (AOPs) shows the promising action. The main advantage with AOPs is the ability to degrade the organic pollutants to $CO_2$ and $H_2O$. For this degradation process the AOPs generation of powerful and non-selective radicals that may oxidize majority of the organic pollutants present in the water body. To generate the various reactive chemical species such as radicals (${\bullet}OH$, ${\bullet}H$, ${\bullet}O$, ${\bullet}HO_2$) and molecular species ($H_2O_2$, $H_2$, $O_2$) in large amount in water, we have used the atmospheric pressure plasma. Among the reactive and non-reactive species, the hydroxyl radical (${\bullet}OH$) plays important role due to its higher oxidation potential (E0: 2.8 V). Therefore, in this work we have checked the degradation of various dyes such as methyl orange, methylene blue and congo red using different type of atmospheric pressure plasma sources (Indirect jet and direct jet). To check the degradation we have used the UV-visible spectroscopy, HPLC and LC-MS spectroscopy. Further, to estimate role of ${\bullet}OH$ on the degradation of dyes we have studied the molecular dynamic simulation.

• 한국자기공명학회논문지
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• 제11권1호
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• pp.30-41
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• 2007

The backbone molecular dynamics of the C-terminal part of the mouse Cdt1 protein (tCdt1, residues 420-557) was studied by high field NMR spectroscopy. The Secondary structure of this protein was suggested by analyzing of chemical shift of backbone atoms with programs TALOS and PECAN, together with NOE connectivities from 3D $^{15}N-HSQC-NOESY$ data. Measurement of dynamic parameters $T_1,\;T_2$ and NOE and limited proteolysis experiment provided information for domain organization of tCdt1(420-557). Analysis of the experimental data showed that the C-terminal part of the tCdt1 has well folded domain for residues 455-553. The residues 420-453 including ${\alpha}-helix$ (432-441) are flexible and probably belong to other functional domain in intact full length Cdt1 protein.

• 한국진공학회지
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• 제21권2호
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• pp.86-92
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• 2012

기울어진 각도 증착(GLAD)에서 입사원자의 속력이 표면 지형에 미치는 영향 Molecular Dynamics와 결합한 Kinetic Monte Carlo 시뮬레이션을 통하여 증착원자의 속력이 증가함에 따라 거칠기가 줄어드는 완만한 표면이 형성되는 것을 확인하였다. GLAD 계산에서 증착원자 속력이 ${\upsilon}_0$에서 $10{\upsilon}_0$로 증가함에 따라 표면 지형을 대변하는 성장 지수 ${\beta}$값은 0.97에서 0.67로 감소하였다. 화학증기증착(CVD) 방법과 같은 증착 방법에 대해서도 증착원자의 속력 의존성을 고찰하였다. GLAD에 비해 지수 ${\beta}$값의 속력에 따른 차이는 적지만 CVD의 경우에도 증착원자의 속력이 표면 지형에 일정정도의 영향을 주는 것을 확인하였다.

• 한국토양비료학회지
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• 제49권2호
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• pp.144-156
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• 2016

Soil is a dynamic biological system, in which it is difficult to determine the composition of microbial communities. Knowledge of microbial diversity and function in soils are limited because of the taxonomic and methodological limitations associated with studying the organisms. In this review, approaches to measure microbial diversity in soil were discussed. Research on soil microbes can be categorized as structural diversity, functional diversity and genetic diversity studies, and these include cultivation based and cultivation independent methods. Cultivation independent technique to evaluate soil structural diversity include different techniques such as Phospholipid Fatty Acids (PLFA) and Fatty Acid Methyl Ester (FAME) analysis. Carbon source utilization pattern of soil microorganisms by Community Level Physiological Profiling (CLPP), catabolic responses by Substrate Induced Respiration technique (SIR) and soil microbial enzyme activities are discussed. Genetic diversity of soil microorganisms using molecular techniques such as 16S rDNA analysis Denaturing Gradient Gel Electrophoresis (DGGE) / Temperature Gradient Gel Electrophoresis (TGGE), Terminal Restriction Fragment Length Polymorphism (T-RFLP), Single Strand Conformation Polymorphism (SSCP), Restriction Fragment Length Polymorphism (RFLP) / Amplified Ribosomal DNA Restriction Analysis (ARDRA) and Ribosomal Intergenic Spacer Analysis (RISA) are also discussed. The chapter ends with a final conclusion on the advantages and disadvantages of different techniques and advances in molecular techniques to study the soil microbial diversity.

• Bulletin of the Korean Chemical Society
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• 제35권8호
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• pp.2494-2504
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• 2014

P38 mitogen activated protein (MAP) kinase is an important anti-inflammatory drug target, which can be activated by responding to various stimuli such as stress and immune response. Based on the conformation of the conserved DFG loop (in or out), binding inhibitors are termed as type-I and II. Type-I inhibitors are ATP competitive, whereas type-II inhibitors bind in DFG-out conformation of allosteric pocket. It remains unclear that how these allosteric inhibitors stabilize the DFG-out conformation and interact. Organosilicon compounds provide unusual opportunity to enhance potency and diversity of drug molecules due to their low toxicity. However, very few examples have been reported to utilize this property. In this regard, we performed docking of an inhibitor (BIRB) and its silicon analog (Si-BIRB) in an allosteric binding pocket of p38. Further, molecular dynamics (MD) simulations were performed to study the dynamic behavior of the simulated complexes. The difference in the biological activity and mechanism of action of the simulated inhibitors could be explained based on the molecular mechanics/generalized Born surface area (MM/GBSA) binding free energy per residue decomposition. MM/GBSA showed that biological activities were related with calculated binding free energy of inhibitors. Analyses of the per-residue decomposed energy indicated that van der Waals and non-polar interactions were predominant in the ligand-protein interactions. Further, crucial residues identified for hydrogen bond, salt bridge and hydrophobic interactions were Tyr35, Lys53, Glu71, Leu74, Leu75, Ile84, Met109, Leu167, Asp168 and Phe169. Our results indicate that stronger hydrophobic interaction of Si-BIRB with the binding site residues could be responsible for its greater binding affinity compared with BIRB.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.112-112
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• 2017

Rice blast caused by Magnaporthe oryzae is one of the most serious diseases that affect the quantity and quality of rice production. The use of resistant rice varieties would be the most effective way to control the rice blast. However R gene incorporation into the rice variety takes time and pathogen could overcome the R gene effects after for a while. For monitoring the rice blast resistance gene distribution in Korean varieties, the four major blast resistance genes against M. oryzae were screened in a number of Korean rice varieties using molecular markers. Of the 120 rice varieties tested, 40 were found to contain the Pi-5 gene, 25 for the Pi-9 gene, 79 for Pi-b and 40 for the Pi-ta gene. None of these rice varieties includes tested 4 R genes. 3 R genes combination, Pi-5/Pi-9/Pi-b, Pi-5, Pi-9.Pi-ta, or Pi-9/Pi-b/Pi-ta were found in 12 varieties, the rice blast disease severity were showed as resistant in the rice verities containing Pi-9/Pi-b/Pi-ta R genes combination, respectively. Also pathogenic diversity of M. oryzae isolates collected in the rice field from 2004 to 2015 in rice field in Korea were analyzed using rice blast monogenic lines, each harboring a single blast resistance gene. Compatibility of blast isolates against rice blast monogenic lines carrying the resistance genes Pi5, Pi9, Pib, and Piz showed dynamic changes by year. It indicates that pathogen has high evolutionary potential adapted host resistances to increase fitness and would lead to rice blast resistance bred into the cultivar becoming ineffective eventually.

• 생명과학회지
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• 제24권12호
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• pp.1378-1382
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• 2014

Phospholipase D (PLD)는 세포막을 구성하는 주요지질인 인지질을 분해하여, 이차신호전달물질인 phosphatidic acid (PA)를 생성함으로써 세포의 성장 및 증식, 생존신호전달등 세포내 다양한 생리현상을 조절하는 중요한 신호전달 핵심단백질로 대두되고 있다. PLD의 비정상적인 발현과 활성은 다양한 암을 비롯한 여러 질환에서 나타난다. PLD에 의해 생성된 PA는 세포사멸 유전자의 발현을 감소시켜서 세포사멸에 대한 내성을 나타내고 있다.최근에, 세포사멸과정에서 PLD 단백질의 turnover dynamics에 관한 분자수준에서의 연구가 규명되었다. PLD는, 세포사멸시 활성화되는 단백질 분해효소인 caspases의 새로운 기질로 작용하여 세포사멸을 차별적으로 조절을 한다. Caspase에 의한 PLD동위효소의 차별적인 분해양상이 PLD의 효소활성과 세포사멸억제 기능을 조절한다. 그래서 PLD는 암치료의 표적분자로서의 가능성이 제시된다. 본 리뷰논문에서, 세포사멸조절 PLD의 기능적 역할에 대해 서술하고자 한다.

• Mass Spectrometry Letters
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• 제5권1호
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• pp.16-23
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• 2014

Liquid chromatography based mass spectrometry (LC-MS) is a key technology for analyzing highly complex and dynamic proteome samples. With highly accurate and sensitive LC-MS analysis of complex proteome samples, efficient data processing is another critical issue to obtain more information from LC-MS data. A typical proteomic data processing starts with protein database search engine which assigns peptide sequences to MS/MS spectra and finds proteins. Although several search engines, such as SEQUEST and MASCOT, have been widely used, there is no unique standard way to interpret MS/MS spectra of peptides. Each search engine has pros and cons depending on types of mass spectrometers and physicochemical properties of peptides. In this study, we describe a novel data process pipeline which identifies more peptides and proteins by correcting precursor ion mass numbers and unifying multi search engines results. The pipeline utilizes two open-source software, iPE-MMR for mass number correction, and iProphet to combine several search results. The integrated pipeline identified 25% more proteins in mouse epididymal adipose tissue compared with the conventional method. Also the pipeline was validated using control and colitis induced colon tissue. The results of the present study shows that the integrated pipeline can efficiently identify increased number of proteins compared to the conventional method which can be a breakthrough in identification of a potential biomarker candidate.