• Journal of Plant Biotechnology
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• v.41 no.2
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• pp.81-88
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• 2014

Salt cress (Thellungiella halophila or Thellungiella parvula), species closely related to Arabidopsis thaliana, represents an extremophile adapted to harsh saline environments. To isolate salt-tolerance genes from this species, we constructed a cDNA library from roots and leaves of salt cress plants treated with 200 mM NaCl. This cDNA library was subsequently shuttled into the destination binary vector [driven by the cauliflower mosaic virus (CaMV) 35S promoter] designed for plant transformation and expression via recombination- assisted cloning. In total, 305,400 pools of transgenic BASTA-resistant lines were generated in Arabidopsis using either T. halophila or T. parvula cDNA libraries. These were used for functional screening of genes involved in salt tolerance. Among these pools, 168,500 pools were used for primary screening to date from which 7,157 lines showed apparent salt tolerant-phenotypes in the initial screen. A secondary screen has now identified 165 salt tolerant transgenic lines using 1,551 (10.6%) lines that emerged in the first screen. The prevalent phenotype in these lines includes accelerated seed germination often accompanied by faster root growth compared to WT Arabidopsis under salt stress condition. In addition, other lines showed non-typical development of stems and flowers compared to WT Arabidopsis. Based on the close relationship of the tolerant species to the target species we suggest this approach as an appropriate method for the large-scale identification of salt tolerance genes from salt cress.

• Journal of the Korean Society for information Management
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• v.38 no.3
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• pp.141-174
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• 2021

In this study, by examining the actual usage data of the university library website before and after COVID-19 outbreak, the usage behavior of users was analyzed, and the data before and after the virus outbreak was compared, so that university libraries can provide more efficient information services in a pandemic situation. We would like to suggest ways to improve it. In this study, the user traffic made on the website of University C was 'using Google Analytics', from January 2018 to December 2018 before the oneself of the COVID-19 virus and from January 2020 to 2020 after the outbreak of the virus. A comparative analysis was conducted until December. Web traffic variables were analyzed by classifying them into three characteristics: 'User information', 'Path', and 'Site behavior' based on metrics such as session, user, number of pageviews, number of pages per session time, and bounce rate. To summarize the study results, first, when compared with data from January 1 to January 20 before the oneself of COVID-19, users, new visitors, and sessions all increased compared to the previous year, and the number of sessions per user, number of pageviews, and number of pages per session, which showed an upward trend before the virus outbreak in 2020, increased significantly. Second, as social distancing was upgraded to the second stage, there was also a change in the use of university library websites. In 2020 and 2018, when the number os students was the lowest, the number of page views increased by 100,000 more in 2020 compared to 2018, and the number of pages per session also recorded10.46, which was about 2 more pages compared to 2018. The bounce rate also recorded 14.38 in 2018 and 2019, but decreased by 1 percentage point to 13.05 in 2020, which led to more active use of the website at a time when social distancing was raised.

• Journal of Intelligence and Information Systems
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• v.23 no.2
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• pp.1-17
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• 2017

The deep learning framework is software designed to help develop deep learning models. Some of its important functions include "automatic differentiation" and "utilization of GPU". The list of popular deep learning framework includes Caffe (BVLC) and Theano (University of Montreal). And recently, Microsoft's deep learning framework, Microsoft Cognitive Toolkit, was released as open-source license, following Google's Tensorflow a year earlier. The early deep learning frameworks have been developed mainly for research at universities. Beginning with the inception of Tensorflow, however, it seems that companies such as Microsoft and Facebook have started to join the competition of framework development. Given the trend, Google and other companies are expected to continue investing in the deep learning framework to bring forward the initiative in the artificial intelligence business. From this point of view, we think it is a good time to compare some of deep learning frameworks. So we compare three deep learning frameworks which can be used as a Python library. Those are Google's Tensorflow, Microsoft's CNTK, and Theano which is sort of a predecessor of the preceding two. The most common and important function of deep learning frameworks is the ability to perform automatic differentiation. Basically all the mathematical expressions of deep learning models can be represented as computational graphs, which consist of nodes and edges. Partial derivatives on each edge of a computational graph can then be obtained. With the partial derivatives, we can let software compute differentiation of any node with respect to any variable by utilizing chain rule of Calculus. First of all, the convenience of coding is in the order of CNTK, Tensorflow, and Theano. The criterion is simply based on the lengths of the codes and the learning curve and the ease of coding are not the main concern. According to the criteria, Theano was the most difficult to implement with, and CNTK and Tensorflow were somewhat easier. With Tensorflow, we need to define weight variables and biases explicitly. The reason that CNTK and Tensorflow are easier to implement with is that those frameworks provide us with more abstraction than Theano. We, however, need to mention that low-level coding is not always bad. It gives us flexibility of coding. With the low-level coding such as in Theano, we can implement and test any new deep learning models or any new search methods that we can think of. The assessment of the execution speed of each framework is that there is not meaningful difference. According to the experiment, execution speeds of Theano and Tensorflow are very similar, although the experiment was limited to a CNN model. In the case of CNTK, the experimental environment was not maintained as the same. The code written in CNTK has to be run in PC environment without GPU where codes execute as much as 50 times slower than with GPU. But we concluded that the difference of execution speed was within the range of variation caused by the different hardware setup. In this study, we compared three types of deep learning framework: Theano, Tensorflow, and CNTK. According to Wikipedia, there are 12 available deep learning frameworks. And 15 different attributes differentiate each framework. Some of the important attributes would include interface language (Python, C ++, Java, etc.) and the availability of libraries on various deep learning models such as CNN, RNN, DBN, and etc. And if a user implements a large scale deep learning model, it will also be important to support multiple GPU or multiple servers. Also, if you are learning the deep learning model, it would also be important if there are enough examples and references.

• Horticultural Science & Technology
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• v.28 no.6
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• pp.1025-1038
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• 2010

Carrot ($Daucus$ $carota$ L. var. $sativa$) is one of the most widely used crops in the world. Moreover it is an important crop because of its high content of ${\beta}$-carotene, well-known as the precursor of vitamin A carotenoid. However, seed-hair which is generated in epidermal cell of seeds inhibits absorption and germination. For that reason, carrot seeds are commercialized after mechanical hair removal process. To overcome such cumbersome weaknesses, new breeding program for developing hairless-seed carrot cultivar has been needed. Therefore, in this study, cDNA libraries from seeds of short-hair seed phenotype CT-ATR615 OP 666-13line and hairy seed CT-ATR615 OP-CK1-9 line were constructed and expression patterns related to generation of seed-hair were analyzed by comparison of EST sequences. Differential EST sequence results between two lines were classified into FunCat functional categories based on the results of BlastX search. Higher expression quantities belonging to metabolic category were shown on short-hair seed line than hairy-seed one. Differential expression quantities between those two lines in the protein folding and stabilization, subcellular localization categories were supposed to contribute variously on the generation of seed-hair. We confirmed 50 and 59 SSR sites, and 2 SNP sites by analyzing EST sequences in two lines; thereafter, we designed SNP and SSR primer sets from these EST sequence information as a molecular marker. These markers are thought to be used in research of molecular markers for classification of carrot family and related to various traits, as well as seed-hair characteristic.

• Journal of the Korean Institute of Landscape Architecture
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• v.46 no.3
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• pp.14-26
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• 2018

The Biotope Area Ratio (BAR) is a quantitative pre-planning index for sustainable development and an integrated indicator for the balanced development of buildings and outdoor spaces. However, it has been pointed out that there are problems in operations management: errors in area calculation, insufficiency in the underground soil condition and depth, reduction in biotope area after construction, and functional failure as a pre-planning index. To address these problems, this study proposes implementing LIM. Since the weights of the BAR are mainly decided by the underground soil condition and depth with land cover types, the study focused on the terrain and pavements. The model should conform to BIM guidelines and standards provided by government agencies and professional organizations. Thus, the scope and Level Of Detail (LOD) of the model were defined, and the method to build a model with BIM software was developed. An apartment complex on sloping ground was selected as a case study, a 3D terrain modeled, paving libraries created with property information on the BAR, and a LIM model completed for the site. Then the BAR was calculated and construction documents were created with the BAR table and pavement details. As results of the study, it was found that the application of the criteria on the BAR and calculation became accurate, and the efficiency of design tasks was improved by LIM. It also enabled the performance of evidence-based design on the terrain and underground structures. To adopt LIM, it is necessary to create and distribute LIM library manuals or templates, and build library content that comply with KBIMS standards. The government policy must also have practitioners submit BIM models in the certification system. Since it is expected that the criteria on planting types in the BAR will be expanded, further research is needed to build and utilize the information model for planting materials.

• Korean Journal of Environmental Biology
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• v.34 no.4
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• pp.304-313
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• 2016

One of the issues currently facing nuclear power plants is how to store spent nuclear waste materials which are contaminated with radionuclides such as $^{134}Cs$, $^{135}Cs$, and $^{137}Cs$. Bioremediation processes may offer a potent method of cleaning up radioactive cesium. However, there have only been limited reports on $Cs^+$ tolerant bacteria. In this study, we report the isolation and identification of $Cs^+$ tolerant bacteria in environmental soil and sediment. The resistant $Cs^+$ isolates were screened from enrichment cultures in R2A medium supplemented with 100 mM CsCl for 72 h, followed by microbial community analysis based on sequencing analysis from 16S rRNA gene clone libraries(NCBI's BlastN). The dominant Bacillus anthracis Roh-1 and B. cereus Roh-2 were successfully isolated from the cesium enrichment culture. Importantly, B. cereus Roh-2 is resistant to 30% more $Cs^+$ than is B. anthracis Roh-1 when treated with 50 mM CsCl. Growth experiments clearly demonstrated that the isolate had a higher tolerance to $Cs^+$. In addition, we investigated the adsorption of $0.2mg\;L^{-1}$ $Cs^+$ using B. anthracis Roh-1. The maximum $Cs^+$ biosorption capacity of B. anthracis Roh-1 was $2.01mg\;g^{-1}$ at pH 10. Thus, we show that $Cs^+$ tolerant bacterial isolates could be used for bioremediation of contaminated environments.

• Horticultural Science & Technology
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• v.31 no.6
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• pp.782-789
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• 2013

Carrot (Daucus carota L. var. sativa) is one of the most widely used crops in the world and is nutritionally important crop. However, seed-hair which is generated in epidermal cell of seeds causes the difficulty of the seedling process, because of the seed germination and absorption inhibitions. For these reasons, carrot seeds are commercialized after mechanical hair removal process. However, in this process, various damage and seed loss occur and breeding of hairless-seed carrot cultivar is needed to overcome these various weaknesses and additional seed production costs. In this study, cDNA libraries using 2 combinations, which were composed of short-hair seed CT-ATR 615 OP 666-13 & long-hair seed CT-ATR 615 OP 671-9, and short-hair seed CT-SMR 616 OP 659-1 & long-hair seed CT-SMR 616 OP 677-14, were constructed and EST sequences of each individuals were analyzed to reveal carrot seed-hair characteristics. Firstly, analyzed EST sequences were classified into FunCat functional categories. As a result, significant differences have been identified in metabolism category, protein folding and stabilization, protein binding, C-compound binding category from both of two combinations. Secondly, several candidate EST sequences related to seed trichome differentiation and cellulose biosynthetic process were selected based on GO data of EST sequences. These differences based on FunCat categories and candidate EST obtained by GO data analysis are thought to be involved in the formation of carrot seed hair. Finally, 741 SSR sites and 33 SNP sites were identified from analyzed EST sequences of two combinations. Then we designed SNP and SSR primer sets to develop molecular markers. These molecular markers will be used for classification of carrot cultivars and study seed-hair characteristic.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.5 no.1
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• pp.65-75
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• 2005

Purpose: To understand genetic differences and similarities between mucolipidosis and control. Methods: Using the fibroblast of the mucolipidosis II and control, forward and reverse subtracted libraries were constructed. Among these clones, we investigated mutations in the GNPTA (MGC4170) gene, which codes for the ${\alpha}/{\beta}$ subunits of phosphotransferase, and in the GNPTAG gene, which codes for the ${\gamma}$ subunits in 5 Korean patients with mucolipidosis type II or IIIA. Result: Several differentially expressed cDNAs were cloned and their sequences were determined. Mutation analysis of the interested gene, GNPTA was performed and we identified 7 mutations in the GNPTA gene, but none in the GNPTAG gene. The mutations in type II patients included p.Q104X(c.310C>T), p.R1189X(c.3565C>T), p.S1058X(c.3173C>G), p.W894X(c.2681G>A) and p.H1158fsX15(c.3474_3475delTA), all of which are non-sense or frame shift mutations. However, a splicing site mutation, IVS13+1G>A (c.2715+1G>A) was detected along with a non-sense or a frame shift mutation (p.R1189X or p.E858fsX3(c.2574_2575delGA)) in two mucolipidosis type IIIA patients. Conclusion: This report shows that mutations in the GNPTA gene coding for the ${\alpha}{\beta}$subunits of phosphotransferase, and not mutations in the GNPTAG gene, account for most of mutations found in Korean patients with mucolipidosis type II or IIIA.

• Horticultural Science & Technology
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• v.31 no.1
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• pp.80-88
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• 2013

Carrot (Daucus carota L. var. sativa) is one of the most extensively used vegetable crops in the world and a significant source of nutrient because of its high content of ${\beta}$-carotene, well known as the precursor of vitamin A carotenoid. However, seed-hairs generated and elongated from the epidermal cell of seeds inhibit absorption and germination by various factors such as carotol and so on. Accordingly, mechanical hair removal process is essential before commercialization of carrot seeds. Because of this process, producers will have additional losses such as time consuming, manpower, capital and so on. Furthermore, physical damage of seeds causes irregular germination rate. To overcome such cumbersome weaknesses, new breeding program for developing hairless-seed carrot cultivar has been needed and studies for molecular markers related to seed-hair characteristic is needed for a new breeding program. Therefore, in this study, cDNA libraries from seeds of short-hair seed phenotype CT-SMR 616 OP 659-1 line, hairy-seed phenotype CT-SMR 616 OP 677-14 line and short-hair seed phenotype CT-ATR 615 OP 666-13 line, hairy-seed phenotype CT-ATR 615 OP 671-9 were constructed, respectively. Furthermore, 1,248 ESTs in each line, total 4,992 ESTs were sequenced. As a result, 19 SNP sites and 14 SNP sites in each of 2 combinations were confirmed by analyzing these EST sequences from short-hair and hairy-seed lines. Then we designed SNP primer sets from EST sequences of SNP sites for high resolution melting (HRM) analysis. Designed HRM primers were analyzed using hairy seed phenotype CT-SMR 616 OP 1040 line and short-hair seed phenotype CT-SMR 616 OP 1024, 1025, 1026 lines. One set of HRM primers showed specific difference between the melting curves of hairy and short-hair seed phenotype lines. Based on this result, allele-specific (AS) PCR primers were designed for easier selection between hairy-seed carrot and hairless seed carrot. These results of HRM and AS-PCR are expected to be useful in breeding of hairless seed carrot cultivar as a molecular marker.

• Horticultural Science & Technology
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• v.29 no.6
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• pp.633-640
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• 2011

Brassica rapa is an A genome model species for Brassica crop genetics, genomics, and breeding. With the completion of sequencing the B. rapa genome, functional analysis of the genome is forthcoming issue. The expressed sequence tags are fundamental resources supporting annotation and functional analysis of the genome including identification of tissue-specific genes and promoters. As of July 2011, 147,217 ESTs from 39 cDNA libraries of B. rapa are reported in the public database. However, little information can be retrieved from the sequences due to lack of organized databases. To leverage the sequence information and to maximize the use of publicly-available EST collections, the Brassica rapa tissue-specific EST database (BrTED) is developed. BrTED includes sequence information of 23,962 unigenes assembled by StackPack program. The unigene set is used as a query unit for various analyses such as BLAST against TAIR gene model, functional annotation using MIPS and UniProt, gene ontology analysis, and prediction of tissue-specific unigene sets based on statistics test. The database is composed of two main units, EST sequence processing and information retrieving unit and tissue-specific expression profile analysis unit. Information and data in both units are tightly inter-connected to each other using a web based browsing system. RT-PCR evaluation of 29 selected unigene sets successfully amplified amplicons from the target tissues of B. rapa. BrTED provided here allows the user to identify and analyze the expression of genes of interest and aid efforts to interpret the B. rapa genome through functional genomics. In addition, it can be used as a public resource in providing reference information to study the genus Brassica and other closely related crop crucifer plants.