• Communications for Statistical Applications and Methods
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• 제27권6호
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• pp.701-714
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• 2020

Quantitative high throughput screening (qHTS) assays are used to assess toxicity for many chemicals in a short period by collectively analyzing them at several concentrations. Data are routinely analyzed using nonlinear regression models; however, we propose a new method to analyze qHTS data using a nonlinear mixed effects model. qHTS data are generated by repeating the same experiment several times for each chemical; therefor, they can be viewed as if they are repeated measures data and hence analyzed using a nonlinear mixed effects model which accounts for both intra- and inter-individual variabilities. Furthermore, we apply a one-step approach incorporating robust estimation methods to estimate fixed effect parameters and the variance-covariance structure since outliers or influential observations are not uncommon in qHTS data. The toxicity of chemicals from a qHTS assay is classified based on the significance of a parameter related to the efficacy of the chemicals using the proposed method. We evaluate the performance of the proposed method in terms of power and false discovery rate using simulation studies comparing with one existing method. The proposed method is illustrated using a dataset obtained from the National Toxicology Program.

• Molecules and Cells
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• 제44권7호
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• pp.500-516
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• 2021

Cardiac hypertrophic signaling cascades resulting in heart failure diseases are mediated by protein phosphorylation. Recent developments in mass spectrometry-based phosphoproteomics have led to the identification of thousands of differentially phosphorylated proteins and their phosphorylation sites. However, functional studies of these differentially phosphorylated proteins have not been conducted in a large-scale or high-throughput manner due to a lack of methods capable of revealing the functional relevance of each phosphorylation site. In this study, an integrated approach combining quantitative phosphoproteomics and cell-based functional screening using phosphorylation competition peptides was developed. A pathological cardiac hypertrophy model, junctate-1 transgenic mice and control mice, were analyzed using label-free quantitative phosphoproteomics to identify differentially phosphorylated proteins and sites. A cell-based functional assay system measuring hypertrophic cell growth of neonatal rat ventricle cardiomyocytes (NRVMs) following phenylephrine treatment was applied, and changes in phosphorylation of individual differentially phosphorylated sites were induced by incorporation of phosphorylation competition peptides conjugated with cell-penetrating peptides. Cell-based functional screening against 18 selected phosphorylation sites identified three phosphorylation sites (Ser-98, Ser-179 of Ldb3, and Ser-1146 of palladin) displaying near-complete inhibition of cardiac hypertrophic growth of NRVMs. Changes in phosphorylation levels of Ser-98 and Ser-179 in Ldb3 were further confirmed in NRVMs and other pathological/physiological hypertrophy models, including transverse aortic constriction and swimming models, using site-specific phospho-antibodies. Our integrated approach can be used to identify functionally important phosphorylation sites among differentially phosphorylated sites, and unlike conventional approaches, it is easily applicable for large-scale and/or high-throughput analyses.

• 농약과학회지
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• 제7권1호
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• pp.1-11
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• 2003

새로운 농약을 탐색하고 개발하는데 있어서 고효율 유기함성 (HTOS) 기술과 고효율 검색 (HTS) 기술 등의 발전과 더불어 컴퓨터 화학을 이용한 분자설계 (CAMD) 방법으로 보편화되고 있는 비교 분자장 분석(CoMFA)과 비교 분자 유사성 지수분석(CoMSIA) 등, 3D QSAR 기법들을 위시하여 분자 홀로그램 구조 - 활성관계 (HQSAR) 분석방법 등, QSAR 기법들을 요약하고 그 활용 사례들을 간략하게 소개하였다.

• Mass Spectrometry Letters
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• 제2권3호
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• pp.69-72
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• 2011

Defective synthesis of the steroid hormones by the adrenal cortex has profound effects on human development and homeostasis. Due to the time-consuming chromatography procedure combined with mass spectrometry, the matrix-assisted laser desorption ionization method coupled to the linear ion-trap tandem mass spectrometry (MALDI-LTQ-MS/MS) was developed for quantitative analysis of 10 adrenal steroids in human serum. Although MALDI-MS can be introduced for its applicability as a high-throughput screening method, it has a limitation on reproducibility within and between samples, which renders poor reproducibility for quantification. For quantitative MALDI-MS/MS analysis, the stable-isotope labeled internal standards were used and the conditions of crystallization were tested. The precision and accuracy were 3.1~35.5% and 83.8~138.5%, respectively, when a mixture of 10 mg/mL ${\alpha}$-cyano-4-hydroxycinnamic acid in 0.2% TFA of 70% acetonitrile was used as the MALDI matrix. The limit of quantification ranged from 5 to 340 ng/mL, and the linearity as a correlation coefficient was higher than 0.988 for all analytes in the calibration range. Clinical applications include quantitative analyses of patients with congenital adrenal hyperplasia. The devised MALDI-MS/MS technique could be successfully applied to diagnosis of clinical samples.

• 응용통계연구
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• 제31권1호
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• pp.123-137
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• 2018

비선형 혼합효과 모형은 다양한 분야에서 반복 측정 자료를 분석할 때 주로 사용된다. 비선형 혼합효과 모형은 개체 내 변동(intra-individual variation)에 대해 고려하는 제 1단계 개별수준모델(individual-level model)과 개체간 변동(inter-individual variation)에 대해 고려하는 제 2단계 개체군모델(population model)의 두 단계로 구성되어 있다. 비선형 혼합효과 모형의 첫 번째 단계인 개별수준모델은 비선형 회귀모형의 모수를 추정하는 것으로 일반적인 비선형 회귀모형과 같고, 주로 보통최소제곱추정 방법을 사용하여 모수를 추정한다. 그러나 최소제곱추정방법은 가정된 비선형 함수가 자료에 의해 명시적으로 드러나지 않는 경우 모수의 추정값과 그 표준오차가 극단적으로 커지는 문제가 발생할 수 있다. 본 논문에서는 최근에 비선형 회귀모형에서 제안된 능형회귀(ridge regression) 방법을 비선형 혼합효과 모형의 제 1단계 개별수준모델에 도입함으로써 이러한 문제를 해결할 수 있는 새로운 추정방법을 제안하였다. 제안된 추정량은 모의실험 연구를 통하여 기존의 표준적인 추정량과 그 성능을 비교하였다. 또한 미국의 National Toxicology Program으로부터 얻어진 정량적 대량고속 스크리닝(quantitative high throughput screening) 실제 자료를 사용하여 추정 방법들을 비교하였다.

• Genomics & Informatics
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• 제11권4호
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• pp.200-210
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• 2013

Studying biological networks, such as protein-protein interactions, is key to understanding complex biological activities. Various types of large-scale biological datasets have been collected and analyzed with high-throughput technologies, including DNA microarray, next-generation sequencing, and the two-hybrid screening system, for this purpose. In this review, we focus on network-based approaches that help in understanding biological systems and identifying biological functions. Accordingly, this paper covers two major topics in network biology: reconstruction of gene regulatory networks and network-based applications, including protein function prediction, disease gene prioritization, and network-based genome-wide association study.

• Asian-Australasian Journal of Animal Sciences
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• 제31권7호
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• pp.1062-1071
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• 2018

The misuse of anabolic hormones or illegal drugs is a ubiquitous problem in animal husbandry and in food safety. The ban on growth promotants in food producing animals in the European Union is well controlled. However, application regimens that are difficult to detect persist, including newly designed anabolic drugs and complex hormone cocktails. Therefore identification of molecular endogenous biomarkers which are based on the physiological response after the illicit treatment has become a focus of detection methods. The analysis of the 'transcriptome' has been shown to have promise to discover the misuse of anabolic drugs, by indirect detection of their pharmacological action in organs or selected tissues. Various studies have measured gene expression changes after illegal drug or hormone application. So-called transcriptomic biomarkers were quantified at the mRNA and/or microRNA level by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) technology or by more modern 'omics' and high throughput technologies including RNA-sequencing (RNA-Seq). With the addition of advanced bioinformatical approaches such as hierarchical clustering analysis or dynamic principal components analysis, a valid 'biomarker signature' can be established to discriminate between treated and untreated individuals. It has been shown in numerous animal and cell culture studies, that identification of treated animals is possible via our transcriptional biomarker approach. The high throughput sequencing approach is also capable of discovering new biomarker candidates and, in combination with quantitative RT-qPCR, validation and confirmation of biomarkers has been possible. These results from animal production and food safety studies demonstrate that analysis of the transcriptome has high potential as a new screening method using transcriptional 'biomarker signatures' based on the physiological response triggered by illegal substances.

• Journal of Plant Biotechnology
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• 제34권3호
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• pp.207-212
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• 2007

식물현탁배양세포의 whole cell extract의 $^1H$ NMR 스펙트럼 데이터로부터 통계분석기법을 활용하여 GABA의 간단하고 신속한 정량분석방법을 확립하였다. 이 기술을 활용하여 고등식물 8종의 9개 세포주를 MS 배지에 1 mg/L의 2,4-D를 첨가한 배지에 유지하였을 때 고수 (Coriandrum sativum L.)가 가장 많은 양의 GABA를 생산하였다. 고수 현탁배양세포로부터 2,4-D농도 및 배양기간에 따른 GABA의 생산성 변화를 조사한 결과 현탁배양세포를 0.5 mg/L 2,4-D가 첨가된 배지에서 3주간 배양된 현탁배양세포를 이용할 경우 GABA 함량이 건중량 1 g 당 16.9 mg으로 가장 높게 생산되었다. 본 연구에서 확립된 간단하고 신속한 분석법으로 다양한 식물자원으로부터 GABA의 생산성을 초고속탐색(high-throughput screenig)할 수 있을 것이며 고수 현탁세포배양법으로 GABA의 상업적 대량생산이 가능할 것으로 전망된다.

• Interdisciplinary Bio Central
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• 제4권3호
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• pp.6.1-6.12
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• 2012

Parkinson's disease (PD) is a complicated neurodegenerative disorder although it is oftentimes defined by clinical motor symptoms originated from age dependent and progressive loss of dopaminergic neurons in the midbrain. The pathogenesis of PD involves dopaminergic and nondopaminergic neurons in many brain regions and the molecular mechanisms underlying the death of different cell types still remain to be elucidated. There are indications that PD causing disease processes occur in a global scale ranging from DNA to RNA, and proteins. Several PD-associated genes have been reported to play diverse roles in controlling cellular functions in different levels, such as chromatin structure, transcription, processing of mRNA, translational modulation, and posttranslational modification of proteins. The advent of quantitative high throughput screening (HTS) tools makes it possible to monitor systemic changes in DNA, RNA and proteins in PD models. Combined with dopamine neuron isolation or derivation of dopamine neurons from PD patient specific induced pluripotent stem cells (PD iPSCs), HTS techonologies will provide opportunities to draw PD causing sequences of molecular events in pathologically relevant PD samples. Here I discuss previous studies that identified molecular functions in which PD genes are involved, especially those signaling pathways that can be efficiently studied using HTS methodologies. Brief descriptions of quantitative and systemic tools looking at DNA, RNA and proteins will be followed. Finally, I will emphasize the use and potential benefits of PD iPSCs-derived dopaminergic neurons to screen signaling pathways that are initiated by PD linked gene mutations and thus causative for dopaminergic neurodegneration in PD.

• Parasites, Hosts and Diseases
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• 제53권1호
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• pp.85-93
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• 2015

Proteomic tools allow large-scale, high-throughput analyses for the detection, identification, and functional investigation of proteome. For detection of antigens from Haemaphysalis longicornis, 1-dimensional electrophoresis (1-DE) quantitative immunoblotting technique combined with 2-dimensional electrophoresis (2-DE) immunoblotting was used for whole body proteins from unfed and partially fed female ticks. Reactivity bands and 2-DE immunoblotting were performed following 2-DE electrophoresis to identify protein spots. The proteome of the partially fed female had a larger number of lower molecular weight proteins than that of the unfed female tick. The total number of detected spots was 818 for unfed and 670 for partially fed female ticks. The 2-DE immunoblotting identified 10 antigenic spots from unfed females and 8 antigenic spots from partially fed females. Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF) of relevant spots identified calreticulin, putative secreted WC salivary protein, and a conserved hypothetical protein from the National Center for Biotechnology Information and Swiss Prot protein sequence databases. These findings indicate that most of the whole body components of these ticks are non-immunogenic. The data reported here will provide guidance in the identification of antigenic proteins to prevent infestation and diseases transmitted by H. longicornis.