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From Static to Dynamic Proteomics - Visualizing the 4th dimension in Biological Systems

Auditorium A134, Agricultural Technology Building
2011/01/10 09:00~10:00 AM
Dr. Wen-Ping Chen (Department of Horticultural Science, Microbial and Plant Genomics Institute, University of Minnesota)
Host: Ming-Che Shih

Mechanism of herbal combinations explored with text mining and network-based analysis

Auditorium A134, Agricultural Technology Building
2011/01/11 10:00 AM
Dr. Aiping Lu (Director, Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences)
Host: Ning-Sun Yang
In recent years, the available data of Traditional Chinese Medicine therapy used to treat rheumatoid arthritis continue to accumulate rapidly. Text mining can retrieve knowledge hidden in text and present the distilled knowledge such as the possible therapeutic mechanisms. The therapeutic mechanism of drug is in fact a biological network comprising hundreds to thousands of gene expression changed in various affected tissues and effector cells. Systems biology approaches predict biological network, can lead to a deeper understanding of system as a whole. Here, we combine text mining with methods of systems biology for the first time, to predict functional networks for therapeutic mechanisms of Traditional Chinese Medicine on rheumatoid arthritis and coronary heart disease.
The text mining results indicated rheumatoid arthritis may be highly associated with Tripterygium wilfordii, and eleven genes associated with both. Protein-protein interaction information for these genes from databases and Literature data was searched and visualized using cytoscape. The results showed that therapeutic mechanisms of Tripterygium wilfordii on rheumatoid arthritis should be involved in suppressing viral protein synthesis of infected cells and antiviral immune responses.
Salvia miltiorrhiza (SM) and Panax notoginseng (PN) in combination have been widely used primarily in Traditional Chinese Medicine for the treatment of coronary heart disease. We combine text mining with methods of systems biology to predict functional networks for Salvia miltiorrhiza and Panax notoginseng in combination (SMPN). 53 genes related with SMPN were found with text mining. Protein-protein interaction information for these genes from databases and Literature data was searched and visualized using cytoscape. The results suggested that the therapeutic mechanisms of SMPN were likely to associate with proliferation and apoptosis of endothelial cell, apoptosis of arterial smooth muscle cell, apoptosis and regulation of immune system process within macrophages during foam cell formation, cardiocyte apoptosis. Analysis of the subnetwork composition indicated that there were some nodes came from intersection between SM network and PN network in each subnetworks, and in the most subnetworks were dominant, the nodes came from SM network more than from PN network.


Auditorium A134, Agricultural Technology Building
2011/01/17 16:00~18:00 PM
Dr. Liang-Tsung Huang (Assistant Professor, Department of Biotechnology, Mingdao University)
Host: Ming-Che Shih

The LOV domain: An ancient photoreceptor chromopeptide that has found its way from the most primitive bacteria to higher plants

Auditorium A134, Agricultural Technology Building
2011/02/14 16:00~18:00 PM
Dr. Winslow Briggs (Professor, Department of Plant Biology, Carnegie Institution for Science, Stanford, USA & Member, the National Academy of Sciences and the American Academy of Arts and Sciences, USA)
Host: Ming-Che Shih
There are a large number of responses of higher plants to blue light: induction of stomatal opening, positioning of chloroplasts, positioning of leaves, rapid growth inhibition, and phototropism. The photoreceptor for all of these responses is one or both phototropins—peripheral membrane proteins with two ca. 110 amino-acid domains called LOV domains, both binding a flavins moiety and both upstream from a classic serine-threonine kinase. These domains undergo a unique photochemistry: blue light-induced formation of a covalent sulfur-carbon bond between a cysteine and the C(4a) carbon of the flavin. This reaction causes a conformational change in the protein leading to activation of the kinase and extensive autophosphorylation. As more and more genomic sequences are obtained, putative LOV domains are being found in proteins in ferns, mosses, algae, all major groups of fungi, and innumerable bacterial proteins. Most of these proteins resemble a phototropin only in possessing a LOV domain. Some are light-activated enzymes such as histidine kinases, some are light-activated transcription factors, and some have completely unknown function. A phototropin will be used to describe the properties of LOV domains and the role of a LOV-domain protein in a pathogenic bacterium will be described.

Galectins: on regulation of inflammation, cancer progression, and adiposity

Auditorium A134, Agricultural Technology Building
2011/03/21 16:00~18:00 PM
Dr. Fu-Tong Liu, MD (Distinguished Research Fellow and Director, Institute of Biomedical Sciences, Academia Sinica)
Host: Shu-Mei Liang

Pathogen and Host Interplay: the Glyco- and Redox-scenarios

Auditorium A134, Agricultural Technology Building
2011/04/11 16:00~18:00 PM
Dr. Chun-Hung Lin (Research Fellow, Institute of Biological Chemistry, Academia Sinica)
Host: Shu-Mei Liang

Cell-cell signaling and transcriptional control during Arabidopsis anther development

Auditorium A134, Agricultural Technology Building
2011/04/18 16:00~18:00 PM
Dr. Hong Ma (Professor and Dean, School of Life Sciences, Fudan University)
Host: Yee-Yung Charng
Anther development is essential for plant male fertility and is important for normal reproductive yield and breeding of crop plants. Early anther development involves cell division and differentiationm, resulting in the formation of sporogenous cells and several somatic cells, such as the tapetal cells. Our laboratory has used molecular genetic analysis in the model plant Arabidopsis thaliana to dissect the molecular basis of anther cell division and differentiation, with additional approaches including cell biology, genomics and bioinformatics. We found that some of the early steps in anther development requires the function of several receptor-like protein kinases, strongly suggesting that cell-cell communication is important. In addition, we have identified key transcriptional regulators that are essential for normal tapetum function, and have obtain strong evidence supporting a transcriptional network operating in the anther. Several of the genes identified in Arabidopsis have homologs in rice that show similar functions, suggesting that key regulatory genes are highly conserved.

A non-model system for study plant-virus interaction: Orchids and Cymbidium mosaic virus

Auditorium A134, Agricultural Technology Building
2011/04/25 16:00~18:00 PM
Dr. Hsin-Hung Yeh (Associate Professor, Department of Plant Pathology and Microbiology, National Taiwan University)
Host: Tzyy-Jen Chiou

Cross-disciplinary Learning and Networking: how to change the world with your research

Conference Room A133, Agricultural Technology Building
2011/05/09 16:00~18:00 PM
Dr. Joseph Limoli Deyama, M.D.

Host: Ning-Sun Yang

Assessment of low levels of toxins by Electric Cell-substrate Impedance Sensing

Conference Room A133, Agricultural Technology Building
2011/05/16 16:00~18:00 PM
Dr. Chun-Min Lo (Visiting Associate Professor, Department of Biomedical Engineering, National Yang-Ming University)
Host: Wen-Chin Yang
Over the past decades, cell-based biosensors have been developed for a variety of applications such as pharmaceutical screening, environmental monitoring, and toxin detection. Among various cell-based assays, electrochemical impedance spectroscopy (EIS) using microelectrode arrays has emerged as a promising label-free method for detecting cellular responses to toxins of chemical or biological origin. Despite the documented success in the EIS measurement of the impedance time series and the derivation of the half-inhibition concentration, the application of EIS for cytotoxicity assessment can go considerably beyond this. Here, we applied electric cell-substrate impedance sensing (ECIS) to evaluate dose-dependent responses of human umbilical vein endothelial cells exposed to cytochalasin B or other toxins. In this method, cell layers are cultured on small gold film electrodes, and the electrical impedance of the cell-covered electrode is measured as a function of frequency or time. To detect subtle changes in cell morphology, the frequency-dependent impedance data of the cell monolayer were measured and analyzed with a theoretical cell-electrode model. To detect the alternation of cell micromotion in response to cytotoxic challenge, time-series impedance fluctuations of cell-covered electrodes were monitored and the values of power spectrum, variance, and variance of the increment were calculated to verify the difference. While a dose-dependent relationship was generally observed from the overall resistance of the cell monolayer, the analysis of frequency-dependent impedance and impedance fluctuations distinguished cytochalasin B levels as low as 0.1μM. In this talk, in addition to the general characteristics of ECIS, I will emphasize the in vitro assessment of cytotoxicity, as well as the detection of trans-endothelial invasion of human ovarian carcinoma cells in culture. The analytical methods used in this study can serve as a model approach for ECIS and other electrochemical impedance biosensors to investigate various aspects of cellular responses to toxins in general.

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