• Natural Product Sciences
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• 제27권2호
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• pp.99-114
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• 2021

Type 2 diabetes mellitus (T2DM) and its complications are important noncommunicable diseases with high mortality rates. Protein tyrosine phosphatase 1B (PTP1B) and aldose reductase inhibitors are recently approached and advanced for T2DM and its complications therapy. Matricaria chamomilla L. is acknowledged as a worldwide medicinal herb that has many beneficial health effects as well as antidiabetic effects. Our research was designed to determine the most potential antidiabetic phytochemicals from M. chamomilla employing in silico study. 142 phytochemicals were obtained from the databases. The first screening employed iGEMdock and Swiss ADME, involving 93 phytochemicals. Finally, 30 best phytochemicals were docked. Molecular docking and visualization analysis were performed using Avogadro, AutoDock 4.2., and Biovia Discovery Studio 2016. Molecular docking results demonstrate that ligand-protein interaction's binding affinities were -5.16 to -7.54 kcal/mol and -5.30 to -12.10 kcal/mol for PTP1B and aldose reductase protein targets respectively. In silico results demonstrate that M. chamomilla has potential antidiabetic phytochemical compounds for T2DM and its complications. We recommended anthecotulide, quercetin, chlorogenic acid, luteolin, and catechin as antidiabetic agents due to their binding affinities against both PTP1B and aldose reductase protein. Those phytochemicals' significant efficacy and potential as antidiabetic must be investigated in further advanced research.

• Biotechnology and Bioprocess Engineering:BBE
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• 제10권5호
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• pp.425-431
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• 2005

The systems-level analysis of microbes with myriad of heterologous data generated by omics technologies has been applied to improve our understanding of cellular function and physiology and consequently to enhance production of various bioproducts. At the heart of this revolution resides in silico genome-scale metabolic model, In order to fully exploit the power of genome-scale model, a systematic approach employing user-friendly software is required. Metabolic flux analysis of genome-scale metabolic network is becoming widely employed to quantify the flux distribution and validate model-driven hypotheses. Here we describe the development of an upgraded MetaFluxNet which allows (1) construction of metabolic models connected to metabolic databases, (2) calculation of fluxes by metabolic flux analysis, (3) comparative flux analysis with flux-profile visualization, (4) the use of metabolic flux analysis markup language to enable models to be exchanged efficiently, and (5) the exporting of data from constraints-based flux analysis into various formats. MetaFluxNet also allows cellular physiology to be predicted and strategies for strain improvement to be developed from genome-based information on flux distributions. This integrated software environment promises to enhance our understanding on metabolic network at a whole organism level and to establish novel strategies for improving the properties of organisms for various biotechnological applications.

• 미생물학회지
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• 제55권1호
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• pp.1-8
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• 2019

Due to the major role played by several species of Streptococcus in the etiology of periodontitis, it is important to assess the pattern of Streptococcus pathogenic pathways within the infected subgingival pockets using a bacterial specific 16S rRNA fragment. From the total of 50 patients with periodontitis included in the study, only 23 Streptococcal isolates were considered for further analyses, in which their 16S rRNA fragments were amplified and sequenced. Then, a comprehensive phylogenetic tree was constructed and in silico prediction was performed for the observed Streptococcal species. The phylogenetic analysis of the subgingival Streptococcal species revealed a high discrimination power of the 16S rRNA fragment to accurately identify three groups of Streptococcus on the species level, including S. salivarius (14 isolates), S. anginosus (5 isolates), and S. gordonii (4 isolates). The employment of state-of-art in silico tools indicated that each Streptococcal species group was characterized with particular transcription factors that bound exclusively with a different 16S rRNA-based secondary structure. In conclusion, the observed data of the present study provided in-depth insights into the mechanism of each Streptococcal species in its pathogenesis, which differ in each observed group, according to the differences in the 16S rRNA secondary structure it takes, and the consequent binding with its corresponding transcription factors. This study paves the way for further interventions of the in silico prediction, with the main conventional in vitro microbiota identification to present an interesting insight in terms of the gene expression pattern and the signaling pathway that each pathogenic species follows in the infected subgingival site.

• 한국발생생물학회지:발생과생식
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• 제18권1호
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• pp.1-11
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• 2014

Early growth response 1 (Egr1) is a zinc-finger transcription factor to direct second-wave gene expression leading to cell growth, differentiation and/or apoptosis. While it is well-known that Egr1 controls transcription of an array of targets in various cell types, downstream target gene(s) whose transcription is regulated by Egr1 in the uterus has not been identified yet. Thus, we have tried to identify a list of potential target genes of Egr1 in the uterus by performing multi-step in silico promoter analyses. Analyses of mRNA microarray data provided a cohort of genes (102 genes) which were differentially expressed (DEGs) in the uterus between Egr1(+/+) and Egr1(-/-) mice. In mice, the frequency of putative EGR1 binding sites (EBS) in the promoter of DEGs is significantly higher than that of randomly selected non-DEGs, although it is not correlated with expression levels of DEGs. Furthermore, EBS are considerably enriched within -500 bp of DEG's promoters. Comparative analyses for EBS of DEGs with the promoters of other species provided power to distinguish DEGs with higher probability as EGR1 direct target genes. Eleven EBS in the promoters of 9 genes among analyzed DEGs are conserved between various species including human. In conclusion, this study provides evidence that analyses of mRNA expression profiles followed by two-step in silico analyses could provide a list of putative Egr1 direct target genes in the uterus where any known direct target genes are yet reported for further functional studies.

• Clinical and Experimental Vaccine Research
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• 제13권2호
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• pp.146-154
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• 2024

Purpose: Infection by the intracellular apicomplexan parasite Toxoplasma gondii has serious clinical consequences in humans and veterinarians around the world. Although about a third of the world's population is infected with T. gondii, there is still no effective vaccine against this disease. The aim of this study was to develop and evaluate a multimeric vaccine against T. gondii using the proteins calcium-dependent protein kinase (CDPK)1, CDPK2, CDPK3, and CDPK5. Materials and Methods: Top-ranked major histocompatibility complex (MHC)-I and MHC-II binding as well as shared, immunodominant linear B-cell epitopes were predicted and linked using appropriate linkers. Moreover, the 50S ribosomal protein L7/L12 (adjuvant) was mixed with the construct's N-terminal to increase the immunogenicity. Then, the vaccine's physicochemical characteristics, antigenicity, allergenicity, secondary and tertiary structure were predicted. Results: The finally-engineered chimeric vaccine had a length of 680 amino acids with a molecular weight of 74.66 kDa. Analyses of immunogenicity, allergenicity, and multiple physiochemical parameters indicated that the constructed vaccine candidate was soluble, non-allergenic, and immunogenic, making it compatible with humans and hence, a potentially viable and safe vaccine candidate against T. gondii parasite. Conclusion: In silico, the vaccine construct was able to trigger primary immune responses. However, further laboratory studies are needed to confirm its effectiveness and safety.

• Journal of Microbiology and Biotechnology
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• 제25권5호
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• pp.732-737
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• 2015

We present here an in silico search of fungal sterol-esterase/lipase and bacterial depolymerase sequences from environmental metagenomes. Both enzyme types contain the α/β-hydrolase protein fold. Analysis of DNA conserved motifs, protein homology search, phylogenetic analysis, and protein 3D modeling have been used, and the efficiency of these screening strategies is discussed. The presence of bacterial genes in the metagenomes was higher than those from fungi, and the sequencing depth of the metagenomes seemed to be crucial to allow finding enough diversity of enzyme sequences. As a result, a novel putative PHA-depolymerase is described.

• 생명과학회지
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• 제28권2호
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• pp.195-200
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• 2018

베타아사론은 널리 알려진 석창포의 주요 효능 성분이다. 본 연구에서는 모기의 oviposition 페로몬 성분인 MOP와 석창포 효능성분 베타아사론의 열대집모기 후각 단백질 CquiOBP1 활성 부위에 대한 친화도 분석 실험을 컴퓨터 분자결합 분석 방법을 통해 비교하였다. CquiOBP1 후각 단백질의 3차원 구조 정보는 PDB database (PDB ID: 3OGN)를 활용하였다. In silico 결합 분석을 수행하기 위해 PyRx, Autodock Vina, Discovery Studio Version 4.5, and NX-QuickPharm 프로그램을 각 분석 조건에 따라 활용하였다. CquiOBP1 후각단백질 활성 부위에 대한 베타아사론의 결합친화도는 -6.40 kcal/mol으로 나왔으며 이는 -6.00 kcal/mol으로 나온 MOP의 결합친화도 보다 훨씬 더 높고 효율적인 것으로 분석되었다. 리간드와 상호작용 하는 CquiOBP1단백질 활성 부위의 아미노산들 가운데 TRP114가 공히 MOP와 베타아사론과 결합 하였다. CquiOBP1 단백질 활성부위의 아미노산들을 전혀 다른 전기적 성질을 지닌 아미노산으로 치환 시킨 후 분자결합 분석을 해 본 결과 리간드들의 X,Y,Z Grid 값에 현격한 변화가 유도되었으며 결합 친화도 또한 감소되었다. 이러한 결과를 통하여 베타아사론은 CquiOBP1 단백질 활성을 조절하는 리간드로서 효과적으로 작용할 것으로 보인다. 결론적으로 석창포 추출물 또는 베타아사론은 곤충기피제 신물질 연구 개발 분야에 효율적으로 활용할 수 있을 것으로 사료된다.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2005년도 생물공학의 동향(XVII)
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• pp.793-794
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• 2005

• 생명과학회지
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• 제12권5호
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• pp.610-621
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• 2002

미생물 유전체(genome)들 사이의 보존된 유전자 (con-served gene)를 밝히는 것은 생명의 본질을 이해하는데 있어 다양한 의미를 갖는다고 할 수 있을 것이다. 본 연구에서는 보존적 유전자를 찾아내고, distance value를 이용하여 구한 보존성의 정도 C(conservation score)를 이용하여 종간의 유전자 변이의 정도를 단백질 관점에서 분석하였다. 분석에 사용된 자료는 COGs 데이티베이스의 총 43종의 미생물 유전체들이며, 이들은 총 n,009개의 유전자들을 포함하는 3,852 개의 ortholog들로 구성되어있었다. 분석 결과 43종의 미생물 유전체에 대하여 총 $\ulcorner$2개의 유전자들이 보존적인 것으로 나타났으며, 이들 중 72.2%인 52종의 유전자가 단백질 합성에 관련되는 것으로 나타났다. 이들 보존적 유전자들에 대하여 보존성의 정도 C를 계산하여 보존성의 순위를 얻었으며, 가장 잘 보존된 유전자는 CTPase-trans-lation elogation factor (COG0050)로 나타났다. 그리고 72개의 보존적 유전자가 나타내는 CU 모두를 이용한 분석결과 고세균(archaea)과 진정세균(bacteria)이 각각 독자적인 그룹을 형성하는 것을 관찰하였다. 본 연구의 결과에서 도출한 72개의 보존적 유전자는 생명체의 본질적 기능에 중요한 역할을 담당하는 것으로 사료되었고, 생명체의 진화 과정에서 이 유전자들이 보존된 이유와 기능적 연계에 대한 생물학적 연구에 기초 자료를 제공할 것으로 판단되어 진다.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.231-231
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• 2022

The GASA protein (Gibberellic acid-stimulated Arabidopsis) are family of small cysteine-rich peptides found in plants. These GASA gene family mainly involved in biotic/abiotic stress responses and plant development. Despite being present in a wide plant species, their action and functions still remain unclear. In this study, using the in-silico analysis method we identified 41 GASA genes in peanuts (Arachis hypogaea L.). Based on the phylogenetic analysis 41 GASA genes are classified in the four major clusters and subclades. Mainly, clusters IV and III comprise the majority of GASA genes 15 and 11 genes respectively, followed by cluster I and cluster II with 9 and 6 genes respectively. Additionally, based on in-silico analysis we predicted the post-transcriptional and post-translational changes of GASA proteins under abiotic stresses such as drought and salt stress would aid our understanding of the regulatory mechanisms. Hence, a further study is planned to evaluate the expression of these GASA genes under stress in different plant tissues to elucidate the possible functional role of GASA genes in peanut plants. These findings might offer insightful data for peanut advancement.