• Journal of Microbiology and Biotechnology
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• 제22권6호
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• pp.788-792
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• 2012

We report the computational structural simulation of the Cry1Ab19 toxin molecule from B. thuringiensis BtX-2 based on the structure of Cry1Aa1 deduced by x-ray diffraction. Validation results showed that 93.5% of modeled residues are folded in a favorable orientation with a total energy Z-score of -8.32, and the constructed model has an RMSD of only $1.13{\AA}$. The major differences in the presented model are longer loop lengths and shortened sheet components. The overall result supports the hierarchical three-domain structural hypothesis of Cry toxins and will help in better understanding the structural variation within the Cry toxin family along with facilitating the design of domain-swapping experiments aimed at improving the toxicity of native toxins.

• Genomics & Informatics
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• 제13권3호
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• pp.90-92
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• 2015

Biological diversity, also known as biodiversity, is an important criterion for measuring the value of an ecosystem. As biodiversity is closely related to human welfare and quality of life, many efforts to restore and maintain the biodiversity of species have been made by government agencies and non-governmental organizations, thereby drawing a substantial amount of international attention. In the fields of biological research, biodiversity is widely measured using traditional statistical indices such as the Shannon-Wiener index, species richness, evenness, and relative dominance of species. However, some biologists and ecologists have difficulty using these indices because they require advanced mathematical knowledge and computational techniques. Therefore, we developed VBioindex, a user-friendly program that is capable of measuring the Shannon-Wiener index, species richness, evenness, and relative dominance. VBioindex serves as an easy to use interface and visually represents the results in the form of a simple chart and in addition, VBioindex offers functions for long-term investigations of datasets using time-series analyses.

• Genomics & Informatics
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• 제21권2호
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• pp.25.1-25.12
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• 2023

Adaptation of infections and hosts has resulted in several metabolic mechanisms adopted by intracellular pathogens to combat the defense responses and the lack of fuel during infection. Human tuberculosis caused by Mycobacterium tuberculosis (MTB) is the world's first cause of mortality tied to a single disease. This study aims to characterize and anticipate potential antigen characteristics for promising vaccine candidates for the hypothetical protein of MTB through computational strategies. The protein is associated with the catalyzation of dithiol oxidation and/or disulfide reduction because of the protein's anticipated disulfide oxidoreductase properties. This investigation analyzed the protein's physicochemical characteristics, protein-protein interactions, subcellular locations, anticipated active sites, secondary and tertiary structures, allergenicity, antigenicity, and toxicity properties. The protein has significant active amino acid residues with no allergenicity, elevated antigenicity, and no toxicity.

• Smart Structures and Systems
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• 제15권3호
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• pp.897-911
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• 2015

This study presents a novel approach based on advancements in Evolutionary Computation for data-driven modeling of complex multi-dimensional memory-dependent systems. The investigated example is a benchmark coupled three-dimensional system that incorporates 6 Bouc-Wen elements, and is subjected to external excitations at three points. The proposed technique of this research adapts Genetic Programming for discovering the optimum structure of the differential equation of an auxiliary variable associated with every specific degree-of-freedom of this system that integrates the imposed effect of vibrations at all other degrees-of-freedom. After the termination of the first phase of the optimization process, a system of differential equations is formed that represent the multi-dimensional hysteretic system. Then, the parameters of this system of differential equations are optimized in the second phase using Genetic Algorithms to yield accurate response estimates globally, because the separately obtained differential equations are coupled essentially, and their true performance can be assessed only when the entire system of coupled differential equations is solved. The resultant model after the second phase of optimization is a low-order low-complexity surrogate computational model that represents the investigated three-dimensional memory-dependent system. Hence, this research presents a promising data-driven modeling technique for obtaining optimized representative models for multi-dimensional hysteretic systems that yield reasonably accurate results, and can be generalized to many problems, in various fields, ranging from engineering to economics as well as biology.

• BMB Reports
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• 제55권3호
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• pp.113-124
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• 2022

Single-cell RNA sequencing (scRNA-seq) has greatly advanced our understanding of cellular heterogeneity by profiling individual cell transcriptomes. However, cell dissociation from the tissue structure causes a loss of spatial information, which hinders the identification of intercellular communication networks and global transcriptional patterns present in the tissue architecture. To overcome this limitation, novel transcriptomic platforms that preserve spatial information have been actively developed. Significant achievements in imaging technologies have enabled in situ targeted transcriptomic profiling in single cells at single-molecule resolution. In addition, technologies based on mRNA capture followed by sequencing have made possible profiling of the genome-wide transcriptome at the 55-100 ㎛ resolution. Unfortunately, neither imaging-based technology nor capture-based method elucidates a complete picture of the spatial transcriptome in a tissue. Therefore, addressing specific biological questions requires balancing experimental throughput and spatial resolution, mandating the efforts to develop computational algorithms that are pivotal to circumvent technology-specific limitations. In this review, we focus on the current state-of-the-art spatially resolved transcriptomic technologies, describe their applications in a variety of biological domains, and explore recent discoveries demonstrating their enormous potential in biomedical research. We further highlight novel integrative computational methodologies with other data modalities that provide a framework to derive biological insight into heterogeneous and complex tissue organization.

• 한국산학기술학회논문지
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• 제12권4호
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• pp.1703-1710
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• 2011

목적 : 성인병관리 및 개인건강관리를 위해 개인건강기록(PHR)은 매우 중요하다. 현재 노인 또는 장년층과 미래 노인, 장년층과의 차이를 비교해 보기 위해 젊은층(대학생)과 성인을 대상으로 조사하였다. 방법: 두 연령집단의 면대면 설문조사를 성인(131명)과 대학생(398명)을 2009년 5월 11일부터 22일까지 실시하였다. 설문지는 18개 문항으로 구성되었다. 결과 및 결론: 젊은층보다는 성인층에서 PHR을 사용하겠다는 의지(대학생그룹3.3, 성인그룹3.7)와 지인들에게 PHR을 추천하겠다는 의지(대학생그룹3.1, 성인그룹3.8)가 비교적 높게 나타났다. 반면, 성인그룹은 종이형 PHR(63.2%)을 선호하였으며 대학생그룹은 ePHR(71.1%)을 더 선호하였고, PHR에 담겨져 있는 정보유출에 대한 우려가 성인그룹(3.7)보다 대학생그룹(4.5)이 높은 것으로 나타났다. PHR에 대한 교육 시기는 고등학교와 대학교로 응답하였다. 따라서 젊은층의 PHR활성화를 위해서는 ePHR에 대한 조기교육과 사용이 편리한 PHR개발이 이루어져야 할 것으로 사료된다.

• Animal cells and systems
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• 제6권3호
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• pp.187-193
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• 2002

It has long been recognized that exposure to low levels of toxic chemicals could have beneficial effects, such as increased resistance to related chemicals or stimulation of growth or development. The notion of radiation hormesis, that exposure to low levels of ionizing radiation could produce beneficial effects, developed seriously in the late 1950’s, and was, to most radiation scientists, incredible. This was due in pan to the then prevailing ideas of radiobiological mechanisms, in part to the sweeping generalizations made by the leading proponents of the radiation hormesis concept, and in pan to the many failures to confirm reports of beneficial effects. More recent understanding of the mechanisms of radiation damage and repair, and discoveries of induction of gene expression by radiation and other genotoxic agents [the adaptive response] make it seem inevitable that under suitable conditions, irradiation will produce beneficial effects.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.221-227
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• 2005

THEMATICS is a simple computational method for predicting functional sites in proteins. The method computes the theoretical titration curves of the ionizable residues of a protein using its 3D structure, determines the residues with perturbed, non-Henderson-Hasselbalch titration behavior, and identifies clusters of these perturbed residues in physical proximity. We have shown previously that this method is highly successful in predicting catalytic sites in enzymes. In the present study, we apply the method to non-catalytic ligand-binding proteins. It is shown that THEMATICS can predict non-catalytic binding sites. The success rate is better than 80 % for a set of 30 non-catalytic, ligand-binding proteins. The application of the method to Glutamine-binding protein from E. coli is discussed in detail.

• BMB Reports
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• 제42권6호
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• pp.356-360
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• 2009

In the present study we have examined human-mouse homologous intronless disease and non-disease genes alongside their extent of sequence conservation, tissue expression, domain and gene ontology composition to get an idea regarding evolutionary and functional attributes. We show that selection has significantly discriminated between the two groups and the disease associated genes in particular exhibit lower $K_{a}$ and $K_{a}/K_{s}$ while $K_{s}$ although smaller is not significantly different. Our analyses suggest that majority of disease related intronless human genes have homology limited to eukaryotic genomes and their expression is localized. Also we observed that different classes of intronless disease related genes have experienced diverse selective pressures and are enriched for higher level functionality that is essentially needed for developmental processes in complex organisms. It is expected that these insights will enhance our understanding of the nature of these genes and also improve our ability to identify disease related intronless genes.

• Journal of applied mathematics & informatics
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• 제5권3호
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• pp.597-606
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• 1998

In the present study we consider a mathematical model of a non-interactive type autotroph-herbivore system in which the amount of autotroph biomass consumed by the herbivore is assumed to follow a Holling type II functional response. We have also incorpo-rated discrete time delays in the numerical response term to represent a delay due to gestation and in the recycling term which represent a delay due to gestation and in the recycling term which represents the time required for bacterial decomposition. We have derived con-dition for global asymptotic stability of the model in the absence of delays. Conditions for delay-induced asymptotic stability of the steady state are also derived. The length of the delay preserving stability has been estimated and interpreted ecologically.