• Clinical and Experimental Pediatrics
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• 제65권5호
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• pp.239-249
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• 2022

Cells survive and proliferate through complex interactions among diverse molecules across multiomics layers. Conventional experimental approaches for identifying these interactions have built a firm foundation for molecular biology, but their scalability is gradually becoming inadequate compared to the rapid accumulation of multiomics data measured by high-throughput technologies. Therefore, the need for data-driven computational modeling of interactions within cells has been highlighted in recent years. The complexity of multiomics interactions is primarily due to their nonlinearity. That is, their accurate modeling requires intricate conditional dependencies, synergies, or antagonisms between considered genes or proteins, which retard experimental validations. Artificial intelligence (AI) technologies, including deep learning models, are optimal choices for handling complex nonlinear relationships between features that are scalable and produce large amounts of data. Thus, they have great potential for modeling multiomics interactions. Although there exist many AI-driven models for computational biology applications, relatively few explicitly incorporate the prior knowledge within model architectures or training procedures. Such guidance of models by domain knowledge will greatly reduce the amount of data needed to train models and constrain their vast expressive powers to focus on the biologically relevant space. Therefore, it can enhance a model's interpretability, reduce spurious interactions, and prove its validity and utility. Thus, to facilitate further development of knowledge-guided AI technologies for the modeling of multiomics interactions, here we review representative bioinformatics applications of deep learning models for multiomics interactions developed to date by categorizing them by guidance mode.

• Journal of Microbiology and Biotechnology
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• 제10권3호
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• pp.333-337
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• 2000

An oil-degrading yeast, Yarrowia lipolytica 180, exhibits interesting cell surface characteristics under the growth on hydrocarbons. An electron microscopic study revealed that the cells grown on crude oil showed protrusions on the cell surface, and thicker periplasmic space and cell wall than the cell surface, and thicker periplasmic space and cell wall than the cells grown on glucose. Y. lipolytica cells lost its cell hydrophobicity after pronase(0.1 mg/ml) treatment. The strain produced two types of emulsifying materials during the growth on hydrocarbons; one was water-soluble extracellular materials and the other was cell wall-associated materials. Both emulsifying materials at lower concentration (0.12%) enhanced the oil-degrading activity of Moraxella sp. K12-7, which had medium emulsifying activity and negative cell hydrophobicity; however, it inhibited the oil-degrading activity of Pseudomunas sp. K12-5, which had medium emulsifying activity and cell hydrophobicity. These results suggest that the oil-degrading activity of Y. lipolytica 180 is closely associated with cell surface structure, and that a finely controlled application of Y.lipolytica 180 in combination with other oil-degrading microorganisms showed a possible enhancing efficiency of oil degradation.

• 한국환경복원기술학회지
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• 제15권2호
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• pp.41-56
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• 2012

Landscape space can and should play as a multi-functional agent : healing contaminated soil, reducing natural hazards, supporting living things, making comfortable environment for human, and appealing to human aesthetics, etc. This article aims to show the possibility and role of landscape space as such agent. In landscape design for National Marine Biology Resource Institute, distributed rain water treatment system and rain gardens are introduced to replace a mono-functioning large detention pond which was suggested by disaster impact assesment. Phytoremediation and vegetation filtering system with muti-cell wetlands are also adapted to heal the contaminated soil. This kind of landscape as a 'living machine' which can play as an operational control utility of multi-environment and thus can be combined effectively into green infrastructure is important for post-industrial city, especially in an era of climate change.

• Advances in environmental research
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• 제9권4호
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• pp.251-273
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• 2020

Soil degradation has become a major worldwide environmental problem, particularly in arid and semi-arid climate zones due to irregular rainfall and the intensity of storms that frequently generate heavy flooding. The main objective of this study is the use of geographic information system and remote sensing techniques to quantify and to map the soil losses in the Wadi Saida watershed (624 ㎢) through the revised universal soil loss equation model and a proposed model based on the surface erosive runoff. The results Analysis revealed that the Wadi Saida watershed showed moderate to moderately high soil loss, between 0 and 1000 t/㎢/year. In the northern part of the basin in the region of Sidi Boubkeur and the mountains of Daia; which are characterized by steep slopes, values can reach up to 3000 t/㎢/year. The two models in comparison showed a good correlation with R = 0.95 and RMSE = 0.43; the use of the erosive surface runoff parameter is effective to estimate the rate of soil loss in the watersheds. The problem of soil erosion requires serious interventions, particularly in basins with disturbances and aggressive climatic parameters. Good agricultural practices and forest preservation areas play an important role in soil conservation.

• Journal of Plant Biology
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• 제26권1호
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• pp.41-51
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• 1983

This study was carried out to investigate ontogeny of stomata and aerenchyma tissue in Trapa natans L. var. bispinosa Makino, an aquatic plant. Ontogeny of stomata in this plant was an aperigenous type surrounding with 5 to 8 epidermal cells without subsidiary cells. Stomata were distributed abundantly on the upper surface of leaf, however, no stoma was found on the lower surface of leaf, and on the epidermis of reproductive organ, petiole and stem. Ontogency of aerenchyma tissue was progressed with five steps; 1) formation of angular cells by division of cortex cells, 2) development of small and large globular cells in accompany with schizogenous intercellular space, 3) enlargement of globular cells and more expansion of intercellular space, 4) cell induction of long elliptic and triarmed shape, 5) completion of the largest intercellular space from endodermis toepidermis. During the growth period two types of leaf were appeared at each node of stems; one type was a submerged and early-fallen leaf, the other was a floating leaf on water surface.

• Genomics & Informatics
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• 제10권4호
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• pp.249-255
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• 2012

In this study, fosmid cloning strategies were used to assess the microbial populations in water from the International Space Station (ISS) drinking water system (henceforth referred to as Prebiocide and Tank A water samples). The goals of this study were: to compare the sensitivity of the fosmid cloning strategy with that of traditional culture-based and 16S rRNA-based approaches and to detect the widest possible spectrum of microbial populations during the water purification process. Initially, microbes could not be cultivated, and conventional PCR failed to amplify 16S rDNA fragments from these low biomass samples. Therefore, randomly primed rolling-circle amplification was used to amplify any DNA that might be present in the samples, followed by size selection by using pulsed-field gel electrophoresis. The amplified high-molecular- weight DNA from both samples was cloned into fosmid vectors. Several hundred clones were randomly selected for sequencing, followed by Blastn/Blastx searches. Sequences encoding specific genes from Burkholderia, a species abundant in the soil and groundwater, were found in both samples. Bradyrhizobium and Mesorhizobium, which belong to rhizobia, a large community of nitrogen fixers often found in association with plant roots, were present in the Prebiocide samples. Ralstonia, which is prevalent in soils with a high heavy metal content, was detected in the Tank A samples. The detection of many unidentified sequences suggests the presence of potentially novel microbial fingerprints. The bacterial diversity detected in this pilot study using a fosmid vector approach was higher than that detected by conventional 16S rRNA gene sequencing.

• International Journal of Oral Biology
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• 제38권3호
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• pp.87-92
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• 2013

Periodontal inflammation increases the risk of tooth loss, particularly in cases where there is an associated loss of alveolar bone and periodontal ligament (PDL). Histological and morphometric evaluation of periodontal inflammation is difficult. Especially, the lengths of the periodontal ligament and interdental alveolar bone space have not been quantified. A quantitative imaging procedure applicable to an animal model would be an important clinical study. The purpose of this study was to quantify the loss of alveolar bone and periodontal ligament by evaluation with micro-computed tomography (micro-CT). Another purpose was to investigate differences in infections with systemic E. coli LPS and TNF-${\alpha}$ on E. coli lipopolysaccharide (LPS) in loss of alveolar bone and periodontal ligament model on mice. This study showed that linear measurements of alveolar bone loss were represented with an increasing trend of the periodontal ligament length and interdental alveolar process space. The effects of systemic E. coli LPS and TNF-${\alpha}$ on an E. coli LPS-induced periodontitis mice model were investigated in this research. Loss of periodontal ligament and alveolar bone were evaluated by micro-computed tomography (micro-CT) and calculated by the two- and three dimensional microstructure morphometric parameters. Also, there was a significantly increasing trend of the interdental alveolar process space in E. coli LPS and TNF-${\alpha}$ on E. coli LPS compared to PBS. And E. coli LPS and TNF-${\alpha}$ on E. coli LPS had a slightly increasing trend of the periodontal ligament length. The increasing trend of TNF-${\alpha}$ on the LPS-induced mice model in this experiment supports the previous studies on the contribution of periodontal diseases in the pathogenesis of systemic diseases. Also, our findings offer a unique model for the study of the role of LPS-induced TNF-${\alpha}$ in systemic and chronic local inflammatory processes and inflammatory diseases. In this study, we performed rapidly quantification of the periodontal inflammatory processes and periodontal bone loss using micro-computed tomography (micro-CT) in mice.

• BMB Reports
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• 제49권1호
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• pp.37-44
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• 2016

Spectraplakins are crucially important communicators, linking cytoskeletal components to each other and cellular junctions. Microtubule actin crosslinking factor 1 (MACF1), also known as actin crosslinking family 7 (ACF7), is a member of the spectraplakin family. It is expressed in numerous tissues and cells as one extensively studied spectraplakin. MACF1 has several isoforms with unique structures and well-known function to be able to crosslink F-actin and microtubules. MACF1 is one versatile spectraplakin with various functions in cell processes, embryo development, tissue-specific functions, and human diseases. The importance of MACF1 has become more apparent in recent years. Here, we summarize the current knowledge on the presence and function of MACF1 and provide perspectives on future research of MACF1 based on our studies and others. [BMB Reports 2016; 49(1): 37-44]

• 한국응용곤충학회지
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• 제55권3호
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• pp.235-243
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• 2016

꽈리허리노린재는 가지과 및 메꽃과 기주에 피해를 주는 해충이다. 꽈리허리노린재는 실내의 $25^{\circ}C$ 조건에서 1세대는 평균 76일정도 소요되며, 성충으로 월동하기 때문에 수명이 길고, 일정한 주기 없이 알을 덩어리로 산란한다. 주로 잎 뒷면에 산란하며, 암컷 한 마리당 평균 195개, 최대 468개까지 산란하는 것으로 나타났다. 또한, 온도가 높아질수록 부화율은 높아지며, 발육기간은 짧아졌지만, $25^{\circ}C$를 제외한 다른 온도에서는 탈피율이 30%이하를 나타냈다. 위 결과를 토대로 선형모델로 추정한 결과 발육영점온도는 $13.9^{\circ}C$, 유효적산온도는 526.3DD를 나타냈다. 고추재배지에서 월동 성충이 6월 말 평균기온 $25.7^{\circ}C$에서 나타나기 시작하여, 9월초에 가장 높은 밀도를 나타내었다. 부화한 개체들은 성충이 될 때까지 이동성이 적었으며 밀집하여 분포하였다. 집단을 형성하는 요인을 알아보고자 Net cage와 Y-tube olfactometer를 이용한 행동실험 결과, 암컷은 수컷과 암컷이 모두 있는 곳을 선택하였지만, 수컷은 암컷과 수컷이 모두 없는 곳을 선택하였다. 수컷이 새로운 기주를 찾아 정착하면, 암컷은 기주를 독점한 동종이 많이 있는 기주를 찾아가는 교미와 관련된 행동을 나타냈으며, 통신화합물의 영향은 알 수 없었다. 집단이 미치는 영향을 알아본 결과 꽈리허리노린재는 좁은 공간에서 집단으로 사육시 약충의 발육기간이 길고 우화율이 높아지는 반면, 개체 사육시 발육기간이 짧고, 우화율이 낮게 나타났다. 반면에 넓은 공간에서는 집단으로 사육 시 약충의 발육기간은 짧고 우화율은 낮게 나타났다.

• 한국과학교육학회지
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• 제22권4호
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• pp.779-795
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• 2002

인터넷의 사용으로 사람들은 거리나 시간에 관계없이 정보를 서로 공유할 수 있게 되어 인터넷을 정보의 바다라 부르게 되었다. 그러나 이러한 인터넷의 장점에도 불구하고, 우리나라의 생물 교육 현장에서는 그 활용이 극히 미비한 실정이다. 따라서 본 연구에서는 이러한 인터넷상의 생물 학습사이트 이용에 대한 한계를 인식하고, 고등학교 학생들의 인터넷 활용 환경과 학생들이 자주 이용하며 비교적 내용과 구성이 잘 된 생물 홈페이지를 조사, 분석하여 이를 토대로 고등학교 생물 영역에서 인터넷을 보다 쉽고 유용하게 활용할 수 있는 방안을 모색하는 데에 그 목적이 있다. 본 연구에서는 인터넷 검색 엔진을 통하여 고등학교 공통과학 생물 학습사이트를 검색한 후 4개의 사이트를 선정하여 학습 내용과 구성을 분석하고, 선정 된 사이트의 이용자를 대상으로 설문조사를 실시하였다. 그 결과는 생물 학습 홈페이지들이 생물학습에 많은 도움이 되는 것으로 나타났으며, 자세하고 심도있는 내용뿐만 아니라 그림과 영상 등의 다양한 멀티미디어를 적극 활용하는 것이 좋은 홈페이지라는 견해를 보였다. 그리고 기존의 학습 사이트 분석과 설문 조사 결과에 근거하여 학생들에게 도움이 되는 고등학교 생물 학습용 홈페이지 제작의 구성요소를 제시하고자 하였다. 홈페이지 구성에서 가장 중요한 요소는 학습자와 홈페이지간의 상호작용성을 높이기 위해 효과적인 피이드백 방법과 학습자 스스로 자신의 수준에 맞는 학습을 할 수 있도록 구성하는 것이다. 이와 같이 학습자와 홈페이지간의 피드백을 통한 학습은 학습자의 지적 욕구를 만족시킬 수 있을 뿐만 아니라 내적 동기를 유발하는 촉진적인 역할을 할 것으로 기대된다. 이상의 연구를 통해 교수-학습에 활용할 수 있는 체계적인 교육용 홈페이지가 개발되어야 할 필요가 있으며 여기에는 교사뿐 아니라 학생, 교육연구가와 전문가, 엔지니어 등 교육과 관련된 다양한 인력이 참여해야 한다는 것이다. 또한 학습에 도움이 되는 좋은 홈페이지를 교사가 학생에게 안내해서 효과적으로 이용할 수 있도록 해야 할 것이다.