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Engineering Microorganisms for Biomedical and Energy Applications

Engineering Microorganisms for Biomedical and Energy Applica...

第八届全国微全分析系统学术会议、第三届全国微纳尺度生物分离分析学术会议暨第五届国际微化学与微系统学术会议

作者： I-Ming Hsing Danhui Cheng Department of Chemical and Biomolecular Engineering the Hong Kong University of Science and TechnologyHong Kong SARChina Division of Biomedical Engineering and Bioengineering Graduate Programthe Hong Kong University of Science and Technology Division of Biomedical Engineering and Bioengineering Graduate Program the Hong Kong University of Science and Technology

The availability of technologies to rapidly synthesize and decode genetic sequences has provided new applications for recombinant DNA technology and genetic engineering developed in early *** new genetic engineering approach,also coined as synthetic biology by many scientists,often involves engineering of microorganism through expression of heterologous gene segments in the microbial *** ability to engineer microorganisms empowered with tailor-made characteristics has provided exciting opportunities in different areas of *** instance,drug synthesis and novel drug delivery methods based on engineered bacteria strains have been extensively studied in biomedical ***,various synthetic biology approaches have been proposed to construct novel metabolic pathways in order to achieve higher yield in bioenergy & biofuel production,such as in ethanol fermentation,hydrogen production and bioelectricity generation through a microbial fuel *** this plenary presentation,we will start with an overview of this very exciting technology (*** biology),followed by a detailed discussion of two related projects in my *** the first part,we utilized yeast display technology for developing a new cell-based immunoassay *** the second one,we engineered photosynthetic bacteria to rewire its indigenous electron transfer pathway in pursuit of converting solar energy to ***,for the interests of our microfluidic community,some thoughts and opportunities of studying and utilizing engineered microorganisms in a microfluidic platform will be discussed.

关键词： Synthetic Biology Genetic Engineering Yeast Surface Display Photosynthetic Bacteria

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2-D thresholding of the connectivity map following the multiple sequence alignments of diverse datasets

2-D thresholding of the connectivity map following the multi...

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10th IASTED International Conference on Biomedical Engineering, BioMed 2013

作者： Doǧan, Tunca Karaçali, Bilge Biotechnology and Bioengineering Graduate Program Izmir Institute of Technology Dokuz Eylül University Izmir Turkey Electrical and Electronics Engineering Department Izmir Institute of Technology Dokuz Eylül University Izmir Turkey Institute of Health Sciences Dokuz Eylül University Izmir Turkey

ISBN: (纸本)9780889869530

Multiple sequence alignment (MSA) is a widely used method to uncover the relationships between the biomolecular sequences. One essential prerequisite to apply this procedure is to have a considerable amount of similarity between the test sequences. It's usually not possible to obtain reliable results from the multiple alignments of large and diverse datasets. Here we propose a method to obtain sequence clusters of significant intragroup similarities and make sense out of the multiple alignments containing remote sequences. This is achieved by thresholding the pairwise connectivity map over 2 parameters. The first one is the inferred pairwise evolutionary distances and the second parameter is the number of gapless positions on the pairwise comparisons of the alignment. Threshold curves are generated regarding the statistical parameter values obtained from a shuffled dataset and probability distribution techniques are employed to select an optimum threshold curve that eliminate as much of the unreliable connectivities while keeping the reliable ones. We applied the method on a large and diverse dataset composed of nearly 18000 human proteins and measured the biological relevance of the recovered connectivities. Our precision measure (0.981) was nearly 20% higher than the one for the connectivities left after a classical thresholding procedure displaying a significant improvement. Finally we employed the method for the functional clustering of protein sequences in a gold standard dataset. We have also measured the performance, obtaining a higher F-measure (0.882) compared to a conventional clustering operation (0.827).

关键词： Probability distributions

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Single cell western blotting

Single cell western blotting

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17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013

作者： Hughes, Alex J. Spelke, Dawn P. Xu, Zhuchen Schaffer, David V. Herr, Amy E. Department of Bioengineering University of California UC Berkeley Berkeley CA United States UC Berkeley-UCSF Graduate Program in Bioengineering UC Berkeley Berkeley CA United States Department of Chemical Engineering UC Berkeley Berkeley CA United States Helen Wills Neuroscience Institute UC Berkeley Berkeley CA United States California Institute for Quantitative Biosciences UC Berkeley Berkeley CA United States

Understanding protein-mediated cell signaling and differentiation processes requires capturing response heterogeneity for single cells in large populations. We report single-cell western blots on standard microscope s... 详细信息

ISBN: (纸本)9781632666246

关键词： Proteins

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26th Annual Computational Neuroscience Meeting (CNS*2017) of the Organization for Computational Neuroscience Antwerp, Belgium, July 15-20, 2017

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BMC NEUROSCIENCE 2017年第SUPPL 1期18卷 59-59页

作者： [Anonymous] Indiana University Purdue University Indianapolis Indianapolis IN 46032 USA Stark Neurosciences Research Institute Indiana University School of Medicine Indianapolis IN 46032 USA Department of Mathematics East Carolina University Greenville NC 27858 USA Jülich Supercomputing Centre Forschungszentrum Jülich 52425 Jülich Germany Future Systems Swiss National Supercomputing Centre 8092 Zurich Switzerland User Engagement and Support Swiss National Supercomputing Centre 6900 Lugano Switzerland Institut de Neurosciences des Systèmes Aix Marseille Univ 13005 Marseille France Simulation Lab Neuroscience Forschungszentrum Jülich Jülich Germany Department of Experimental Psychology Ghent University 9000 Ghent Belgium Donders Center for Cognitive Neuroimaging Radboud University 6525HR Nijmegen The Netherlands Department of Electrical Computer and Energy Engineering University of Colorado Boulder CO 80309 USA Department of Neurosurgery Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Neurology Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Otolaryngology Johns Hopkins School of Medicine Baltimore MD 21287 USA INSERM U968 Paris France Sorbonne Universités UPMC University Paris 06 UMR_S 968 Institut de la Vision Paris France CNRS UMR_7210 Paris France Department of Computer Architecture and Technology University of Granada (CITIC) Granada Spain Sorbonne Universités UPMC Univ Paris 06 INSERM CNRS Institut de la Vision Paris France Department of Adaptive Machine Systems Osaka University Osaka Japan Department of Computer Science University of Cergy-Pontoise Cergy-Pontoise France Department of Physics and Astronomy College of Charleston Charleston SC 29424 USA School of Physics Faculty of Science University of Sydney Sydney NSW 2006 Australia Center of Excellence for Integrative Brain Function Australian Research Council Sydney Australia Max Planck Institute for Human Cognitive and Brain Sciences Saxony Lei

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Center of Pressure Velocity Autocorrelation as a New Measure of Postural Control During Quiet Stance

Center of Pressure Velocity Autocorrelation as a New Measure...

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International IEEE/EMBS Conference on Neural Engineering

作者： Manuel E. Hernandez Cory Stevenson Joseph Snider Howard Poizner Institute for Neural Computation University of California Institute for Neural Computation and Department of Bioengineering University of California Institute for Neural Computation and Graduate Program in Neurosciences University of California

ISBN: (纸本)9781467319676

Falls are a significant cause of mortality and serious injury in older adults and particularly in people with neurological disorders. The ability to maintain balance and postural control is commonly evaluated using center of pressure (COP) data collected with a force platform. Recent methods such as the Stabilogram Diffusion Analysis (SDA) have examined the stochastic characteristics of the COP but require numerous, long duration trials for reliable measures. To further our understanding of the underlying dynamical processes in postural control, we propose a new conceptual framework for studying human postural control using the COP velocity autocorrelation function (COP-VAF), and compare its results to SDA. Five healthy young participants were studied under quiet standing conditions with either eyes open or closed. COP trajectories were analyzed using both traditional postur-ographic measures, SDA, and the COP-VAF. It is shown that the COP-VAF leads to repeatable, physiologically meaningful measures that can distinguish postural control differences with and without vision in healthy individuals. More specifically, visual feedback was found to significantly decrease the peak COP velocity autocorrelation value and magnitude of the first minimum, while increasing the diffusion coefficient. This result is interpreted as an indication that visual input serves to rapidly eliminate any oscillatory motion in quiet stance and utilizes a smaller potential field to maintain balance. In contrast to SDA, COP-VAF measures provide a more concise and reliable measure of postural control (intraclass coefficient correlation (ICC) = 0.23-0.87 vs. 0.05-0.91 in COP-VAF vs. SDA measures, respectively). This work suggests that we can further extend our understanding of the underlying mechanisms behind postural control in quiet stance using the COP-VAF and may apply this analysis in quantifying future neurorehabilitative interventions aimed at improving balance.

关键词： CARD16 gene Center of pressure oscillating movements Standing Orders Serious Injury potential field Autocorrelation conceptual framework

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10 Minute western blotting with 54-plex throughput for clinical confirmatory hiv diagnosis in human serum

10 Minute western blotting with 54-plex throughput for clini...

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16th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2012

作者： Hughes, Alex J. Herr, Amy E. UC Berkeley UCSF Graduate Program in Bioengineering United States UC Berkeley Bioengineering United States

ISBN: (纸本)9780979806452

We translate western blotting to a microchip workflow that cuts conventional assay times from 3-18 hours to 10-60 min with up to 5-plex analyte detection and 54-plex channel throughput. An engineered photoactive protein capture matrix with tunable porosity (PACTgel) constitutes 1) a spatially addressable denaturing polyacrylamide gel electrophoresis (SDS-PAGE) separation matrix compatible with mask-based visible light photopatterning and 2) a UV light-toggled protein capture matrix with unprecedented capture efficiency (>75%). We report the first 10 minute western blot consisting of protein sizing and immunoaffinity detection in a single microchannel, and validate a rapid confirmatory HIV diagnostic using human serum. Our capability for rapid confirmatory HIV diagnosis at the point of care has the potential to circumvent the western blotting bottleneck in the current diagnostic pipeline.

关键词： Proteins

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Engineering Rhodobacter Sphaeroides for direct electron transfer by heterogenous expression of redoxactive components from electrogenic species

Engineering Rhodobacter Sphaeroides for direct electron tran...

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Food, Pharmaceutical and bioengineering Division 2013 - Core programming Area at the 2013 AIChE Annual Meeting: Global Challenges for Engineering a Sustainable Future

作者： Cheng, Danhui Wang, Wanyang Chow, King L. Hsing, I.-Ming Bioengineering Graduate Program Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong Division of Biomedical Engineering Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong Department of Chemical and Biomolecular Engineering Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong Division of Life Science Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong

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DXA-based Model for Advanced Analysis of Body Shape Variation

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Journal of Clinical Densitometry 2013年第3期16卷 262-262页

作者： Wilson, Joseph Shepherd, John Berkeley-UCSF Graduate Program in Bioengineering and University of California San Francisco San Francisco CA

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glpK和rpoC基因突变对大肠杆菌生长的调节机制

glpK和rpoC基因突变对大肠杆菌生长的调节机制

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第十八届全国波谱学学术年会

作者： Kian-Kai Cheng Baek-Seok Lee Takeshi Masuda Takuro Ito Kazutaka Ikeda Akiyoshi Hirayama Lingli Deng Jiyang Dong Kazuyuki Shimizu Tomoyoshi Soga Masaru Tomita Bernhard O.Palsson Martin Robert Institute for Advanced Biosciences Keio UniversityTsuruokaYamagata 997-0017Japan Systems Biology Program Graduate School of Media and GovernanceKeio UniversityKanagawa 252-8520Japan Institute of Bioproduct Development & Department of Bioprocess Engineering Universiti Teknologi Malaysia81310 JohorMalaysia PRESTO Japan Science and Technology AgencyKawaguchiSaitama 332-0012Japan Department of Electronic Science Xiamen University Kyushu Institute of Technology IizukaFukuoka820-8502Japan Department of Bioengineering University of CaliforniaSan DiegoLa JollaCA 92093-0412USA

自2006年开始,基因组的重新测序有效地鉴定了细菌适于新环境时所引起的基因突变[1]。然而,相关的促生长机制还没有得到很好的诠释。本文联合利用代谢组学、蛋白质组学和脂类组学的方法对适于甘油的进化菌株中的glpK和rpoC两个基因突变[2... 详细信息

自2006年开始,基因组的重新测序有效地鉴定了细菌适于新环境时所引起的基因突变[1]。然而,相关的促生长机制还没有得到很好的诠释。本文联合利用代谢组学、蛋白质组学和脂类组学的方法对适于甘油的进化菌株中的glpK和rpoC两个基因突变[2,3]的促生长机制进行深入研究,结果表明:进化大肠杆菌细胞株是通过两种不同的代谢方式来实现在甘油培基内更快的增长。首先,rpoC基因27bp的缺失提高了

关键词：基因突变大肠杆菌细胞大肠杆菌

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Metabolomics and network biology for sensitive monitoring of how growth environment changes affect the physiology of industrial-scale perfusion cultures

Metabolomics and network biology for sensitive monitoring of...

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12th IFAC Symposium on Computer Applications in Biotechnology, CAB 2013

作者： Vernardis, S.I. Goudar, C.T. Klapa, M.I. Metabolic Engineering and Systems Biology Laboratory Institute of Chemical Engineering Foundation for Research and Technology-Hellas Patras GR-265 04 Greece Cell Culture Development Global Biological Development Bayer HealthCare 800 Dwight Way Berkeley CA 94710 United States Interdepartmental Graduate Program in Informatics in Life Sciences Medical School University of Patras Greece Cell Science and Technology AMGEN Inc. Thousand Oaks CA 91320 United States Depts. of Chemical and Biomolecular Eng. and Bioengineering University of Maryland College Park MD 20742 United States

ISBN: (纸本)9783902823588

Metabolomic analysis can indeed enhance the prime variable dataset for the monitoring of perfusion cultures by providing a higher resolution view of the metabolic state. Metabolic profiles can capture physiological state shifts over the course of the perfusion cultures and indicate a metabolic "signature" of the phase transitions, which is not observable from prime variable data. Notably, metabolomics provides orthogonal (to prime variables) evidence that all cultures follow this same metabolic state shift with cell age, independently of bioreactor scale. Additionally, this analysis can increase the information content of process development experiments by helping better understand the impact of changes in bioreactor operating conditions on cell physiology. In this context, metabolic profiling could be integrated into the monitoring of cell physiology in perfusion cultures. © IFAC.

关键词： Bioreactors

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