• Molecules and Cells
• /
• v.23 no.3
• /
• pp.280-286
• /
• 2007

L-asparaginase (EC 3.5.1.1) catalyzes the hydrolysis of the amide group of L-asparagine, releasing aspartate and $NH_4{^+}$. We isolated a low temperature-inducible cDNA sequence encoding L-asparaginase from soybean leaves. The full-length L-asparaginase cDNA, designated GmASP1, contains an open reading frame of 1,258 bp coding for a protein of 326 amino acids. Genomic DNA blotting and fluorescence in situ hybridization showed that the soybean genome has two copies of GmASP1. GmASP1 mRNA was induced by low temperature, ABA and NaCl, but not by heat shock or drought stress. E. coli cells expressing recombinant GmASP1 had 3-fold increased L-asparaginase activity. A possible function of L-asparaginase in the early response to low temperature stress is discussed.

• Molecules and Cells
• /
• v.28 no.5
• /
• pp.463-472
• /
• 2009

Although the possible cellular roles of several ubiquitin-specific proteases (UBPs) were identified in Arabidopsis, almost nothing is known about UBP homologs in rice, a monocot model plant. In this report, we searched the rice genome database (http://signal.salk.edu/cgi-bin/RiceGE) and identified 21 putative UBP family members (OsUBPs) in the rice genome. These OsUBP genes each contain a ubiquitin carboxyl-terminal hydrolase (UCH) domain with highly conserved Cys and His boxes and were subdivided into 9 groups based on their sequence identities and domain structures. RT-PCR analysis indicated that rice OsUBP genes are expressed at varying degrees in different rice tissues. We isolated a full-length cDNA clone for OsUBP6, which possesses not only a UCH domain, but also an N-terminal ubiquitin motif. Bacterially expressed OsUBP6 was capable of dismantling K48-linked tetra-ubiquitin chains in vitro. Quantitative real-time RT-PCR indicated that OsUBP6 is constitutively expressed in different tissues of rice plants. An in vivo targeting experiment showed that OsUBP6 is predominantly localized to the nucleus in onion epidermal cells. We also examined how knock-out of OsUBP6 affects developmental growth of rice plants. Although homozygous T3 osubp6 T-DNA insertion mutant seedlings displayed slower growth relative to wild type seedlings, mature mutant plants appeared to be normal. These results raise the possibility that loss of OsUBP6 is functionally compensated for by an as-yet unknown OsUBP homolog during later stages of development in rice plants.

• Journal of the Korea Academia-Industrial cooperation Society
• /
• v.13 no.8
• /
• pp.3532-3536
• /
• 2012

Understanding of the maternal transcriptome increased to elucidate the underlying molecular mechanism of normal oocyte maturation, which depends on a precise sequence of changes in maternal genes expression. Previous reports that the translational potential of a maternal mRNA is generally determined by the length of the poly(A) tail, and deadenylation is usually the first sign of mRNA degradation. However, in vitro cultured system has the underlying molecular mechanisms remain unclear. We determined whether the role of molecular basis, four important maternal genes, C-mos, cyclin-B1 (regulatory subunit of MPF), BMP15 and GDF9, were selected for detection of their precise mRNA expression patterns by real-time PCR and for determination of their polyadenylation status by poly(A) tail PCR during oocyte maturation. In the present study. the abnormal expression of maternal mRNAs prior to zygotic genome activation, which results in suppression of the corresponding protein level, may be responsible for, at least in part, a profound defect in further embryonic development. Reasonable expression of maternal gene is crucial for proper oocyte maturation and further embryonic development.

• Korean Journal of Breeding Science
• /
• v.40 no.3
• /
• pp.223-227
• /
• 2008

In rice, tillering is an important trait determining yield. To study tillering at the agricultural and molecular aspects, we have examined a spontaneous rice mutant that showed reduction in the number of culms. The mutant was derived from a $F^6$ line of the cross of Junambyeo*4 / IR72. It could produce, on average, 4 tillers per hill in the paddy field while wild-type plants usually have 15. Except the reduced culm numbers, they also show pale green phenotypes. The phenotypes of this mutant were co-segregated as the monogenic Mendelian ratio (${\chi}^b=0.002$, p=0.969). In order to locate a gene responsible for the rcn phenotype, the mutant with the japonica genetic background was crossed with Milyang21 of the indica background. Bulked segregant analysis was used for rapid determination of chromosomal location. Three SSR markers (RM551, RM8213, and RM16467) on chromosome 4 were genetically associated with the mutant phenotype. Each of the 217 $F_2$ plants was genotyped with simple sequence length polymorphisms. The data showed that RM16572 on chromosome 4 was the closest marker that showed perfect co-segregation among the $F_2$ population. We suggest the new rcn gene studied here name as $rcn10^t$ because there was no report which exhibit a rcn phenotype with a pleiotropic effect of pale green (chlorophyll deficiency), and mapped at same position on chromosome 4.

• Proceedings of the Korea Water Resources Association Conference
• /
• 2018.05a
• /
• pp.445-445
• /
• 2018

기후변화에 따른 환경오염은 21세기 인류에게 가장 심각한 문제 중의 하나로 대두되고 있다. 환경적인 측면에서 하천오염은 경제적으로 많은 문제를 발생시키고 있다. 이러한 하천오염 문제를 해결하기 위해서는 오염물질의 농도 측적 및 데이터 축적이 필수적이라 할 수 있다. 그러나 일반적으로 오염물질 부하량에 대한 직접적인 측정은 비용 측면에서 쉽지 않은 것이 사실이다. 또한 실시간으로 BOD, COD, TN, TP 등의 자료를 이용하여 예측하는 것에는 자료의 부족성으로 인해 한계가 있다. 본 연구에서는 구글의 딥러닝 오픈소스 라이브러리인 텐서플로우를 활용하여 기계학습을 통한 하천오염 예측을 목적으로 하고 있다. 기계학습을 위하여 텐서플로우를 활용하여 RNN, LSTM 인공신경망 모형을 구축하였다. 하천오염의 학습과 예측을 위해 결과치 분석을 위한 자료로는 금강 유역에 위치한 옥천 관측소 충청북도 옥천군 이원면 이원대교에 위치한 $36^{\circ}14'31.0''N$ $127^{\circ}40'02.6''E$의 관측소에서 BOD, COD, DO, 부유물질의 자료를 사용하였다. 모형의 학습을 위해서 입력자료는 수위, 유량, 평균기온, 평균풍속 자료를 2004년 ~ 2017년까지의 14년간의 자료를 사용하였다. 연구를 위해 BOD, COD, DO 부유물질 자료는 물환경정보시스템(http://water.nier.go.kr/)의 자료를 활용하고 수위, 유량등의 자료는 국가수자원관리종합정보시스템 (http://www.wamis.go.kr/)의 자료를 사용하였다. 그러나 수온, 수위, 풍속등의 자료는 일 자료가 있는가 반면 BOD, COD, TN, TP등의 자료는 일 자료가 있지 않아 이를 원활히 활용할 수 있도록 예측을 위한 결과치의 선형보간법을 통해 일 자료를 획득한 후 연구를 하였다. RNN, LSTM의 분석 시 학습속도, 반복시행횟수 sequence length의 길이 등의 값을 조절 하면서 결과치를 분석하였다.

• Proceedings of the Korea Water Resources Association Conference
• /
• 2019.05a
• /
• pp.39-39
• /
• 2019

인구의 도시 집중화로 인하여 다량의 생활용수의 사용에 따라 하천의 자정능력을 초과하여 오염을 유발시키고 있다. 이에 도시하천들의 오염은 점점 심해져 경제적으로 많은 문제를 유발하고 있다. 이러한 하천오염 문제를 과학적으로 대응하기 위해서는 오염물질의 농도 측정 및 데이터 축척을 통한 오염예측이 필수적이라 할 수 있으며, 부산광역시 보건환경정보 공개시스템에서는 하천수질 자동측정망을 설치하여 시간 단위로 오염물질을 측정하고 있다. 그러나 온천천의 하천수질 데이터는 계속 쌓여가고 있는데 이 데이터를 활용해서 하천수질 인자 예측이 거의 이뤄지지 않고 있다. 본 연구에서는 순환신경망 알고리즘을 활용하여 일 단위의 하천수질 인자 예측을 시도하였다. 순환신경망은 인공신경망의 발전된 형태인 시계열 학습에 강한 RNN, LSTM 알고리즘을 활용한 일단위 하천수질 인자 예측을 하고자 하였다. 연구에 앞서 시간 단위로 쌓여있는 데이터를 평균 내어 일 단위로 변경하였고 이 데이터를 가지고 일 단위 하천수질 인자 예측을 진행하였다. 연구에는 Google에서 개발한 딥러닝 오픈소스 라이브러리인 텐서플로우를 활용하여 DO, 탁도 등 항목을 예측하였다. 하천오염의 학습과 예측을 위해 대상지로는 부산지역 온천천의 부곡교, 세병교, 이섭교 관측소를 선택하였다. 연구를 위해 DO, 탁도 등 자료 수집은 부산광역시 보건환경정보 공개시스템의 자료를 활용하였다. 모형의 학습을 위해 입력자료로는 하천수질 인자 자료를 이용하였고, 자료의 학습에는 2014년~2017년 4년간의 자료를 학습자료로 사용하였고, 2018년 1년간의 자료는 모형의 검증을 위해 사용하였다. RNN, LSTM 알고리즘을 활용하여 분석 시 은닉층의 개수, 반복시행횟수, sequence length 등의 값을 조절하여 하천수질 인자 예측을 하였다. 모형의 검증을 위해 $R^2$(r square)와 RMSE(root mean square error)을 이용하여 통계분석을 실시하였다.

• Journal of the Korea Institute of Information and Communication Engineering
• /
• v.25 no.7
• /
• pp.903-909
• /
• 2021

Caenorhabditis elegans whose DNA sequence was completely identified is a representative species used in various research fields such as gene functional analysis and animal behavioral research. In the mean time, many researches on the bio-monitoring system to determine whether water is contaminated or not by using the swimming activities of nematodes. In this paper, we show the possibility of using the swimming activities of C. elegans in the development of a machine learning based bio-monitoring system which identifies chemicals that cause water pollution. To characterize swimming activities of nematode, BLS entropy is computed for the nematode in a frame. And, BLS entropy profile, an assembly of entropies, are classified into several patterns using clustering algorithms. Finally these patterns are used to construct data sets. We recorded images of swimming behavior of nematodes in the arenas in which formaldehyde, benzene and toluene were added at a concentration of 0.1 ppm, respectively, and evaluate the performance of the developed HMM.

• Korean Journal of Agricultural Science
• /
• v.46 no.1
• /
• pp.67-78
• /
• 2019

The purpose of this study was to predict the water quality using the RNN (recurrent neutral network) and LSTM (long short-term memory). These are advanced forms of machine learning algorithms that are better suited for time series learning compared to artificial neural networks; however, they have not been investigated before for water quality prediction. Three water quality indexes, the BOD (biochemical oxygen demand), COD (chemical oxygen demand), and SS (suspended solids) are predicted by the RNN and LSTM. TensorFlow, an open source library developed by Google, was used to implement the machine learning algorithm. The Okcheon observation point in the Geum River basin in the Republic of Korea was selected as the target point for the prediction of the water quality. Ten years of daily observed meteorological (daily temperature and daily wind speed) and hydrological (water level and flow discharge) data were used as the inputs, and irregularly observed water quality (BOD, COD, and SS) data were used as the learning materials. The irregularly observed water quality data were converted into daily data with the linear interpolation method. The water quality after one day was predicted by the machine learning algorithm, and it was found that a water quality prediction is possible with high accuracy compared to existing physical modeling results in the prediction of the BOD, COD, and SS, which are very non-linear. The sequence length and iteration were changed to compare the performances of the algorithms.

• Korean Journal of Agricultural Science
• /
• v.45 no.4
• /
• pp.583-590
• /
• 2018

Genus Typha L. (Typhaceae; Cattail in common) is one of the hydrophytic plants found in semi-aquatic regions. About nine to 18 species of the genus exist all over the world. In Korea, the most commonly found cattail species are T. laxmanni and T. angustifolia. The aim of this study was to prepare a cDNA library and sequences and analyze expressed sequence tags (ESTs) from these species, T. laxmanni and T. angustifolia. In the case of T. laxmanni, we observed that 715 out of 742 ESTs had high quality sequences, whereas the remaining 27 ESTs were low quality sequences. In this study, we identified 77 contigs, 393 unassembled clones and 65.7% singletons. Furthermore, in the case of T. angustifolia, we recorded 992 high quality EST sequences, and by excluding 28 low quality sequences from among them, we retrieved 120 contigs, 348 unassembled clones and 48.9% singletons. The basic local alignment search tool (BLAST) and Kyoto encyclopedia of genes and genomes (KEGG) database results enabled us to identify the functional categories, i.e., molecular function (16.5%), biological process (22.2%) and cellular components (61.3%). In addition, between these two species, the no hits and anonymous genes were 4.2% and 11.7% and 6.2% and 11.2% in T. laxmanni and T. angustifolia, respectively, based on the BLAST results. The study concluded that they have certain species-specific genes. Hence, the results of this study on these two species could be a valuable resource for further studies.

• Entomological Research
• /
• v.48 no.5
• /
• pp.416-428
• /
• 2018

To gain an insight into the function of heat shock proteins (HSPs) in insects during thermal stress, three HSP cDNAs were identified in the transcriptome of adult Heortia vitessoides, one of the most destructive defoliating pests in Aquilaria sinensis (Loureiro) Sprenger forests. The open reading frames of HvHsp60, HvHsp70, and HvHsp90 were 1,719, 2,070, and 2,151 bp in length, respectively, and encoded proteins with molecular weights of 61.05, 75.02, and 82.23 kDa, respectively. Sequence analysis revealed that all three HSPs were highly conserved in structure. Regarding the stage-specific expression profiles, HvHsp60, HvHsp70, and HvHsp90 mRNAs were detected in all developmental stages. Regarding the tissue-specific expression profiles, the expression levels of the three HSP genes were different in various larval and adult tissues. Moreover, the expression patterns of heat-stressed larvae, pupae, and adults indicated that HvHsp60, HvHsp70, and HvHsp90 were heat-inducible. In particular, HvHsp60 transcripts increased dramatically in larvae and pupae that were heat-stressed at $40^{\circ}C$ and were upregulated in adults that were heat-stressed at $35^{\circ}C$ and $40^{\circ}C$. The expression of HvHsp70 significantly increased in all of the three different developmental stages at $35^{\circ}C$, $40^{\circ}C$, and $45^{\circ}C$. The expression of HvHsp90 obviously increased at $30^{\circ}C$, $35^{\circ}C$, and $40^{\circ}C$ in larvae and could be induced at $35^{\circ}C$ in pupae and adults. The results suggest that HSP60, HSP70, and HSP90 play a major role in protecting H. vitessoides against high-temperature stress.