• 한국축산식품학회지
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• 제43권3호
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• pp.540-551
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• 2023

Milk protein concentrate (MPC) is widely used to enhance the stability and texture of fermented dairy products. However, most research has focused on yogurt products, and the effects of MPC on sour cream characteristics remain unknown. Therefore, we investigated the effects of different MPC levels (0%, 1%, 2%, and 3% w/w) on the rheological, physicochemical, microbiological, and aroma characteristics of sour creams in this study. We found that MPC supplementation stimulated the growth of lactic acid bacteria (LAB) in sour creams, resulting in higher acidity than that in the control sample due to the lactic acid produced by LAB. Three aroma compounds, acetaldehyde, diacetyl, and acetoin, were detected in all sour cream samples. All sour creams showed shear-thinning behavior (n=0.41-0.50), and the addition of MPC led to an increase in the rheological parameters (η_a,50, K, G', and G"). In particular, sour cream with 3% MPC showed the best elastic property owing to the interaction between denatured whey protein and caseins. In addition, these protein interactions resulted in the formation of a gel network, which enhanced the water-holding capacity and improved the whey separation. These findings revealed that MPC can be used as a supplementary protein to improve the rheological and physicochemical characteristics of sour cream.

• Biotechnology and Bioprocess Engineering:BBE
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• 제6권5호
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• pp.326-331
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• 2001

With the aim of developing of pH-sensitive controlled drug release system, a poly(Llysine) (PLL) based cationic semi-interpenetrating polymer network (semi-IPN) has been synthesized. This cationic hydrogel was designed to swell at lower pH and de-swell at higher pH and therefore be applicable for achieving regulated drug release at a specific pH range. In addition to the pH sensitivity, this hydrogel was anticipated to interact with an ionic drug, providing another means to regulate the release rate of ionic drugs. This semi-IPN hydrogel was prepared using a free-radical polymerization method and by crosslinking of the polyethylene glycol (PEG)-methacrylate polymer through the PLL network. The two polymers were penetrated with each other via interpolymer complexation to yield the semi-IPN structures. The PLL hydrogel thus prepared showed dynamic swelling/de-swelling behavior in response to pH change, and such a behavior was influenced by both the concentrations of PLL and PEG-methacrylate. Drug release from this semi-IPN hydrogel was also investigated using a model protein drug, streptokinase. Streptokinase release was found to be dependent on its ionic interaction with the PLL backbones as well as on the swelling of the semi-IPN hydrogel. These results suggest that a PLL semi-IPN hydrogel could potentially be used as a drug delivery platform to modulate drug release by pH-sensitivity and ionic interaction.

• Genomics & Informatics
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• 제19권4호
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• pp.42.1-42.17
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• 2021

Salivary gland carcinoma (SGC) is rare cancer, constituting 6% of neoplasms in the head and neck area. The most responsible genes and pathways involved in the pathology of this disorder have not been fully understood. We aimed to identify differentially expressed genes (DEGs), the most critical hub genes, transcription factors, signaling pathways, and biological processes (BPs) associated with the pathogenesis of primary SGC. The mRNA dataset GSE153283 in the Gene Expression Omnibus database was re-analyzed for determining DEGs in cancer tissue of patients with primary SGC compared to the adjacent normal tissue (adjusted p-value < 0.001; |Log2 fold change| > 1). A protein interaction map (PIM) was built, and the main modules within the network were identified and focused on the different pathways and BP analyses. The hub genes of PIM were discovered, and their associated gene regulatory network was built to determine the master regulators involved in the pathogenesis of primary SGC. A total of 137 genes were found to be differentially expressed in primary SGC. The most significant pathways and BPs that were deregulated in the primary disease condition were associated with the cell cycle and fibroblast proliferation procedures. TP53, EGF, FN1, NOTCH1, EZH2, COL1A1, SPP1, CDKN2A, WNT5A, PDGFRB, CCNB1, and H2AFX were demonstrated to be the most critical genes linked with the primary SGC. SPIB, FOXM1, and POLR2A significantly regulate all the hub genes. This study illustrated several hub genes and their master regulators that might be appropriate targets for the therapeutic aims of primary SGC.

• 정보처리학회논문지D
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• 제18D권2호
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• pp.89-100
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• 2011

인간 유전체에 존재하는 유전적 구조 변이(genetic structural variation) 중 하나인 유전체 단위반복변이(Copy Number Variation, CNV)은 유전자의 기능 발현과 밀접한 관련이 있다. 특히 특정 유전 질병이 있는 사람들을 대상으로 CNV와 유전자발현의 관계를 밝히는 연구가 계속 진행되고 있지만, 정상인 유전체에 대한 CNV의 기능적 분석은 아직 활발히 이루어지고 있지 않다. 본 논문에서는 다수의 정상인 샘플에서 찾아낸 공통된 CNV에 대하여 유전자들과의 기능적 관계를 유전자의 분자적 위치와 상관없이 밝힐 수 있는 분석 방법을 제시한다. 이를 위해 서로 다른 이질적인 생물학데이터를 통합하는 방법을 제시하고 공통된 CNV와 유전자와의 연관성을 분자적 위치와 상관없이 계산할 수 있는 새로운 방법을 제시한다. 제안된 방법의 유의성을 보이기 위해서 유전자 온톨로지 (Gene Ontology) 데이터베이스를 이용한 다양한 검증 실험들을 수행하였다. 실험결과 새롭게 제안된 연관성 측정방법은 유의성이 있으며 공통된 CNV와 강한 연관성을 갖는 유전적 기능의 후보들을 시스템적으로 제시할 수 있는 것으로 나타났다.

• 한국정보과학회논문지:시스템및이론
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• 제34권10호
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• pp.474-492
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• 2007

단백질 상호작용 네트워크는 생체 내에서 특정 역할을 담당하는 패스웨이나 복합체와 같은 중요한 의미의 많은 기능 모듈들을 포함하고 있다. 본 논문에서는 이 기능 모듈들과 정합될 수 있는 개념 모듈을 정의하고 이를 기반으로 원하는 기능 모듈들을 개념적으로 표현하고 효율적으로 탐색할 수 있는 새로운 방법을 제안한다. 개념 모듈은 트리플들과 이들 사이의 연산자로 이루어진 표현 규칙에 의해 정의 되며 탐색하고자 하는 기능 모듈들의 구조를 개념적으로 표현한다. 이 표현 규칙에서의 트리플은 한 기능 모듈을 구성하는 단백질들 사이의 구체적인 상호작용 관계를, 연산자는 트리플들 사이의 구조적인 연관 관계를 각각 개념적으로 정의한다. 또한, 사용자는 사전에 표현 규칙에 의해 잘 정의된 개념들을 조합하여 새로운 의미의 복합 개념 모듈을 정의할 수도 있다. 복합 개념 모듈은 복잡한 기능 모듈들의 개념적 구조를 보다 정교하게 표현할 수 있기 때문에, 사용자 탐색 질의의 의미적 표현력을 획기적으로 높일 수 있다. 정의된 규칙들은 XML로 관리될 수 있어 다른 종류의 단백질 상호작용 네트워크에서 사용자가 유사한 모듈들을 탐색하기 위해 쉽게 적용 가능하다. 본 논문에서는 또한, 구조적으로 복잡한 규칙들을 직관적으로 표현하고 효율적으로 탐색하기 위한 시각화된 질의 환경도 구현하였다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.263-266
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• 2005

We made a stepping stone for asthma study by analyzing an asthma-specific protein-protein interaction network. It follows the power-law degree distribution and its hub nodes and skeleton frame of the network agreed with the prior knowledge about asthma pathway. This study is providing a systematic approach to analyze the complex effect of genes or to represent the frame of their relations associated with specific disease.

• Bulletin of the Korean Chemical Society
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• 제29권5호
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• pp.1013-1017
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• 2008

Syndecan-3 is a cell-surface heparan sulfate proteoglycan, which performs a variety of functions during cell adhension process. It is also a coreceptor for growth factor, mediating cell-cell and cell-matrix interaction. Syndecan-3 contains a cytoplasmic domain potentially associated with the cytoskeleton. Syndecan-3 is specifically expressed in neuron cell and has related to neuron cell differentiation and development of actin filament in cell migration. Syndecans each have a unique, central, and variable (V) region in their cytoplasmic domains. And that region of syndecan-3 may modulate the interactions of the conserved C1 regions of the cytoplasmic domains by tyrosine phosphorylation. Cytoplasmic domain of syndecan-3 has been synthesized for NMR structural studies. The solution structure of syndecan-3 cytoplasmic domain has been determined by two-dimensional NMR spectroscopy and simulated-annealing calculation. The cytoplasmic domain of the syndecan proteins has a tendency to form a dimmer conformation with a central cavity, however, that of syndecan-3 demonstrated a monomer conformation with a flexible region near C-terminus. The structural information might add knowledge about the structure-function relationships among syndecan proteins.

• 한국비블리아학회지
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• 제26권1호
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• pp.217-231
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• 2015

본 연구에서는 췌장암의 유전자-단백질 상호작용 네트워크를 구성하고, 관련 연구에서 주요하게 언급되는 유전자-단백질의 유발관계 사슬을 파악함으로써, 췌장암의 원인을 규명하는 실증적인 연구로 이어질 수 있는 미발견 공공 지식을 제공하려 하였다. 이를 위하여 텍스트마이닝과 주경로 분석을 Swanson의 ABC 모델에 적용해 중간 개념인 B를 방향성을 가진 다단계 모델로 확장하고 가장 의미 있는 경로를 도출하였다. 본 연구의 주제가 된 췌장암의 사례처럼 시작점과 끝점조차 한정할 수 없는 미발견 공공 지식 추론에서 주경로 분석은 유용한 도구가 될 수 있을 것이다.

• Genomics & Informatics
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• 제19권2호
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• pp.14.1-14.6
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• 2021

Coronavirus disease 2019 (COVID-19) is an on-going pandemic disease infecting millions of people across the globe. Recent reports of reduction in antibody levels and the re-emergence of the disease in recovered patients necessitated the understanding of the pandemic at the core level. The cases of multiple organ failures emphasized the consideration of different organ systems while managing the disease. The present study employed RNA sequencing data to determine the disease associated differentially regulated genes and their related protein interactions in several organ systems. It signified the importance of early diagnosis and treatment of the disease. A map of protein interactions of multiple organ systems was built and uncovered CAV1 and CTNNB1 as the top degree nodes. A core interactions sub-network was analyzed to identify different modules of functional significance. AR, CTNNB1, CAV1, and PIK3R1 proteins were unfolded as bridging nodes interconnecting different modules for the information flow across several pathways. The present study also highlighted some of the druggable targets to analyze in drug re-purposing strategies against the COVID-19 pandemic. Therefore, the protein interactions map and the modular interactions of the differentially regulated genes in the multiple organ systems would incline the scientists and researchers to investigate in novel therapeutics for the COVID-19 pandemic expeditiously.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2006년도 한국컴퓨터종합학술대회 논문집 Vol.33 No.1 (A)
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• pp.7-9
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• 2006

단백질 상호작용 관계들은 고 성능 실험 기법을 이용한 생물학적 실험에 의해서 대규모로 추출되고, 동시에 이들을 구성하는 단백질 데이터 역시 공공 데이터베이스에 빈번하게 갱신되고 있다. 이 갱신으로 인하여 인터넷을 통해 공개되는 공공 데이터베이스와 PPI(Protein-Protein interaction) 네트워크에 포함된 단백질 데이터가 서로 일치하지 않게 된다. 본 논문에서는 PPI 네트워크에 존재하는 단백질을 래퍼(Wrapper)를 이용하여 빈번하게 갱신되는 공공 데이터베이스의 단백질로 식별하고, 이 식별을 통해 PPI 네트워크에 존재하는 데이터들을 항상 최신 데이터로 동기화함으로써 데이터의 실시간성을 제공하고 데이터에 대한 신뢰도를 보장할 수 있도록 하였다.