• Parasites, Hosts and Diseases
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• 제49권4호
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• pp.341-347
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• 2011

Acanthamoeba infection is difficult to treat because of the resistance property of Acanthamoeba cyst against the host immune system, diverse antibiotics, and therapeutic agents. To identify encystation mediating factors of Acanthamoeba, we compared the transcription profile between cysts and trophozoites using microarray analysis. The DNA chip was composed of 12,544 genes based on expressed sequence tag (EST) from an Acanthamoeba ESTs database (DB) constructed in our laboratory, genetic information of Acanthamoeba from TBest DB, and all of Acanthamoeba related genes registered in the NCBI. Microarray analysis indicated that 701 genes showed higher expression than 2 folds in cysts than in trophozoites, and 859 genes were less expressed in cysts than in trophozoites. The results of real-time PCR analysis of randomly selected 9 genes of which expression was increased during cyst formation were coincided well with the microarray results. Eukaryotic orthologous groups (KOG) analysis showed an increment in T article (signal transduction mechanisms) and O article (posttranslational modification, protein turnover, and chaperones) whereas significant decrement of C article (energy production and conversion) during cyst formation. Especially, cystein proteinases showed high expression changes (282 folds) with significant increases in real-time PCR, suggesting a pivotal role of this proteinase in the cyst formation of Acanthamoeba. The present study provides important clues for the identification and characterization of encystation mediating factors of Acanthamoeba.

• Horticulture, Environment, and Biotechnology : HEB
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• 제59권6호
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• pp.875-888
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• 2018

Tulip (Tulipa L.) is one of the most important ornamental geophytes in the world. Analysis of molecular variability of tulips is of great importance in conservation and parental lines selection in breeding programs. Of the 70 genic microsatellites, 15 highly polymorphic and reproducible markers were used to assess the genetic diversity, structure, and relationships among 280 individuals of 36 wild and cultivated tulip accessions from two countries: Iran and the Netherlands. The mean values of gene diversity and polymorphism information content were 0.69 and 0.66, respectively, which indicated the high discriminatory power of markers. The calculated genetic diversity parameters were found to be the highest in wild T. systola Stapf (Derak region). Bayesian model-based STRU CTU RE analysis detected five gene pools for 36 germplasms which corresponded with morphological observations and traditional classifications. Based on analysis of molecular variance, to conserve wild genetic resources in some geographical locations, sampling should be performed from distant locations to achieve high diversity. The unweighted pair group method with arithmetic mean dendrogram and principal component analysis plot indicated that among wild tulips, T. systola and T. micheliana Hoog exhibited the closest relationships with cultivated tulips. Thus, it can be assumed that wild tulips from Iran and perhaps other Middle East countries played a role in the origin of T. gesneriana, which is likely a tulip species hybrid of unclear origin. In conclusion, due to the high genetic variability of wild tulips, they can be used in tulip breeding programs as a source of useful alleles related to resistance against stresses.

• Asian-Australasian Journal of Animal Sciences
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• 제33권6호
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• pp.949-956
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• 2020

Objective: This study was conducted to confirm the effects of new inoculants producing-antifungal or esterase substances on rye silage and its rumen fermentation indices by comparing wild with mutated types. Methods: Rye harvested at dough stage was ensiled into 3 L mini bucket silo (1 kg) for 90 d in triplicate following: distilled water at 20 μL/g (CON); Lactobacillus brevis 100D8 (AT) and its inactivation of antifungal genes (AT-m) at 1.2×10⁵ cfu/g, respectively; and Leuconostoc holzapfelii 5H4 (FD) and its inactivation of esterase genes (FD-est) at 1.0×10⁵ cfu/g, respectively. After silo opened, silage was sub-sampled for the analysis of ensiling quality and its rumen fermentation indices. Results: Among the wild type inoculants (CON vs AT vs FD), FD inoculant had higher (p<0.05) in vitro digestibilities of dry matter and neutral detergent fiber, the total degradable fraction, and total volatile fatty acid in rumen, while AT inoculant had higher (p<0.05) lactate, acetate, and lactic acid bacteria in silage. Silage pH and the potentially degradable fraction in rumen increased (p<0.05) by inactivation of antifungal activity (AT vs AT-m), but lactate, acetate, and lactic acid bacteria of silage decreased (p<0.05). In silage, acetate increased (p<0.05) by inactivation of esterase activity (FD vs FD-est) with decreases (p<0.05) of pH, ammonia-N, lactate, and yeast. Moreover, inactivation of esterase activity clearly decreased (p<0.05) in vitro digestibilities of dry matter and neutral detergent fiber, the total degradable fraction, and total volatile fatty acid in the rumen. Conclusion: This study concluded that FD inoculant confirmed esterase activity on rye silage harvested at dough stage, while AT inoculant could not be confirmed with antifungal activity due to the absence of mold in all silages.

• 한국해안·해양공학회논문집
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• 제30권3호
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• pp.103-113
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• 2018

경험모의기법을 통해 국내 서남해안의 조석과 해일특성을 고찰하였다. 그 결과 인천, 군산, 목포, 완도 등은 조석지배해역이고 여수, 통영, 부산 등은 해일지배해역으로 구분되었다. 조석지배해역에서는 태풍해일이 발생하지 않아도 50년 이하의 빈도를 갖는 극치해면고가 형성될 수 있는 반면 해일지배해역에서는 10년 빈도에서만 태풍해일 없이 극치해면고가 형성될 수 있는 양상을 보이고 있다. 각 해역에서 빈도별로 평균적인 상황으로 어느 정도의 조위에 어느 정도의 해일이 겹쳐 극치해면고가 형성되는지 고찰한 결과 이 역시 해역별로 구분되는 특성을 보이고 있다. 이와 함께 설계조위 산정을 위한 세 가지 방법을 비교고찰한 결과 약최고고조위방법은 과다설계의 우려가 매우 큰 비현실적인 결과를 보이고 있으며, 확률분포함수방법은 대형태풍이 소조기나 저조시 발생할 경우 해당자료가 결과에 반영되지 않거나 매우 축소된 결과가 도출될 우려가 있다는 단점이 있다. 이러한 단점들을 해결함과 동시에 서해안과 같이 조석이 지배적인 해역에 적합한 방법으로 경험모의기법의 적용성을 확인하였다.

• Genomics & Informatics
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• 제8권4호
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• pp.165-169
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• 2010

The Korean Bioinformation Center (KOBIC) is a national bioinformatics research center in Korea. We developed many bioinformatics algorithms and applications to facilitate the biological interpretation of OMICS data. Here we present an introduction to major bioinformatics resources of databases and tools developed at KOBIC. These resources are classified into three main fields: genome, proteome, and literature. In the genomic resources, we constructed several pipelines for next generation sequencing (NGS) data processing and developed analysis algorithms and web-based database servers including miRGator, ESTpass, and CleanEST. We also built integrated databases and servers for microarray expression data such as MDCDP. As for the proteome data, VnD database, WDAC, Localizome, and CHARMM_HM web servers are available for various purposes. We constructed IntoPub server and Patome database in the literature field. We continue constructing and maintaining the bioinformatics infrastructure and developing algorithms.

• International Journal of Aeronautical and Space Sciences
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• 제13권2호
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• pp.127-153
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• 2012

This paper presents an advanced computational method for the prediction of the responses in the frequency domain of general linear dissipative structural-acoustic and fluid-structure systems, in the low-and medium-frequency domains and this includes uncertainty quantification. The system under consideration is constituted of a deformable dissipative structure that is coupled with an internal dissipative acoustic fluid. This includes wall acoustic impedances and it is surrounded by an infinite acoustic fluid. The system is submitted to given internal and external acoustic sources and to the prescribed mechanical forces. An efficient reduced-order computational model is constructed by using a finite element discretization for the structure and an internal acoustic fluid. The external acoustic fluid is treated by using an appropriate boundary element method in the frequency domain. All the required modeling aspects for the analysis of the medium-frequency domain have been introduced namely, a viscoelastic behavior for the structure, an appropriate dissipative model for the internal acoustic fluid that includes wall acoustic impedance and a model of uncertainty in particular for the modeling errors. This advanced computational formulation, corresponding to new extensions and complements with respect to the state-of-the-art are well adapted for the development of a new generation of software, in particular for parallel computers.

• The Plant Pathology Journal
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• 제30권4호
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• pp.425-431
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• 2014

Leaf scald caused by the infection of Rhynchosporium secalis, is a worldwide crop disease resulting in significant loss of barley yield. In this study, a systematic sequencing of expressed sequence tags (ESTs) was chosen to obtain a global picture of the assembly of genes involved in pathogenesis. To identify a large number of plant ESTs, which are induced at different time points, an amplified fragment length polymorphism (AFLP) display of complementary DNA (cDNA) was utilized. Transcriptional changes of 140 ESTs were observed, of which 19 have no previously described function. Functional annotation of the transcripts revealed a variety of infection-induced host genes encoding classical pathogenesis-related (PR) or genes that play a role in the signal transduction pathway. The expression analyses by a semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) revealed that Rar1 and Rpg4 are defense inducible genes, and were consistent with the cDNA-AFLP data in their expression patterns. Hence, the here presented transcriptomic approach provides novel global catalogue of genes not currently represented in the EST databases.

• Reproductive and Developmental Biology
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• 제33권1호
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• pp.19-24
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• 2009

This study was conducted to investigate the specific expression genes in the cloned bovine tissues. Donor cells, cloned tissues were analysed by RAPD-RFLP method. The results were detected three genes (CH-U7B, CH-U7M and CH-U7P) in the cloned fetus. It was found a single copy genes by southern hybridization. Sequence analysis of CH-U7M gene was shown 99% homology to a previously reported EST from a cloned bovine fetus. The putative ORF was encode a protein of hydrophobicity index 0.03. Semi-quantitative RT-PCR by using the CH-LS001 specific primer was remarkably detected in the lung tissue of cloned fetus. Further investigation of these genes may provide one of the key information to explain the early death, abnormal fetus, large off-spring and the low pregnancy rate in the production of cloned bovine.

• ALGAE
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• 제21권1호
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• pp.1-10
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• 2006

Genomic data is accumulating in public database at an unprecedented rate. Although presently dominated by the sequences of metazoan, plant, parasitic, and picoeukaryotic taxa, both expressed sequence tag (EST) and complete genomes of free-living algae are also slowly appearing. This wealth of information offers the opportunity to clarify many long-standing issues in algal and plant evolution such as the contribution of the plastid endosymbiont to nuclear genome evolution using the tools of comparative genomics and multi-gene phylogenetics. A particularly powerful approach for the automated analysis of genome data from multiple taxa is termed phylogenomics. Phylogenomics is the convergence of genomics science (the study of the function and structure of genes and genomes) and molecular phylogenetics (the study of the hierarchical evolutionary relationships among organisms, their genes and genomes). The use of phylogenetics to drive comparative genome analyses has facilitated the reconstruction of the evolutionary history of genes, gene families, and organisms. Here we survey the available genome data, introduce phylogenomic pipelines, and review some initial results of phylogenomic analyses of algal genome data.

• The Journal of Korean Physical Therapy
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• 제21권1호
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• pp.49-55
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• 2009

Purpose: The purpose of this study was to evaluate influence of contract-relax exercise on functional leg length inequality (FLLI) and muscle activity. Methods: The subjects were consisted of 40 healthy adults who had FLLI of which degree was at least 10mm. All subjects were randomly assigned to two groups : Contract-Relax Exercise (CRE) group (n=20), control group (n=20). The experimental group underwent CRE for 3 times a week for 4 weeks. Myosystem 1200 was used to measure the activity of rectus femoris and hamstring muscle. The tape measure method was used to measure FLLI. Statistical analysis was used repeated ANOVA know comparison of period, independent T-est know comparison of experiment group and control group. Results: All measurements for each subject took the following test : pre-test, post-test in 2 weeks, post-test in 4 weeks. The FLLI of the experimental group was significantly reduced according to within intervention period (p<0.05). Rectus femoris and hamstring muscle activity of the experimental group was significantly increased (p<0.05). Conclusion: The CRE can reduce FLLI and increase rectus femoris and hamstring muscle activity. Various contract-relax exercise for reduced of FLLI and the methods should be customized for the patients.