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Measuring the activity of BioBrick promoters using an in vivo reference standard

Journal of Biological Engineering 2009年第1期3卷 1-13页

作者： Kelly, Jason R. Rubin, Adam J. Davis, Joseph H. Ajo-Franklin, Caroline M. Cumbers, John Czar, Michael J. de Mora, Kim Glieberman, Aaron L. Monie, Dileep D. Endy, Drew Department of Biological Engineering Massachusetts Institute of Technology Cambridge MA 02139 77 Massachusetts Avenue United States Department of Biology Massachusetts Institute of Technology Cambridge MA 02139 77 Massachusetts Avenue United States Molecular Foundry Lawrence Berkeley National Laboratory Berkeley CA 94720 United States Department of Molecular Biology Cell Biology and Biochemistry Brown University Providence RI 02912 United States Virginia Bioinformatics Institute Virginia Polytechnic and State University Blacksburg VA 24061 Washington Street United States Institute for Materials and Processes The University of Edinburgh Edinburgh EH9 3JL Mayfield Road United Kingdom Biomedical Engineering Division of Engineering Brown University Providence RI 02912 United States Department of Ophthalmology Johns Hopkins University School of Medicine Baltimore MD 21287 600 N Wolfe St United States Profectus Biosciences Inc. Baltimore MD 21224 6411 Beckley St. United States Department of Bioengineering Stanford University Stanford CA 94305 United States

Background: The engineering of many-component, synthetic biological systems is being made easier by the development of collections of reusable, standard biological parts. However, the complexity of biology makes it difficult to predict the extent to which such efforts will succeed. As a first practical example, the Registry of Standard Biological Parts started at MIT now maintains and distributes thousands of BioBrick™ standard biological parts. However, BioBrick parts are only standardized in terms of how individual parts are physically assembled into multi-component systems, and most parts remain uncharacterized. Standardized tools, techniques, and units of measurement are needed to facilitate the characterization and reuse of parts by independent researchers across many laboratories. Results: We found that the absolute activity of BioBrick promoters varies across experimental conditions and measurement instruments. We choose one promoter (BBa_J23101) to serve as an in vivo reference standard for promoter activity. We demonstrated that, by measuring the activity of promoters relative to BBa_J23101, we could reduce variation in reported promoter activity due to differences in test conditions and measurement instruments by ∼50%. We defined a Relative Promoter Unit (RPU) in order to report promoter characterization data in compatible units and developed a measurement kit so that researchers might more easily adopt RPU as a standard unit for reporting promoter activity. We distributed a set of test promoters to multiple labs and found good agreement in the reported relative activities of promoters so measured. We also characterized the relative activities of a reference collection of BioBrick promoters in order to further support adoption of RPU-based measurement standards. Conclusion: Relative activity measurements based on an in vivoreference standard enables improved measurement of promoter activity given variation in measurement conditions and instruments. These i

关键词： Green Fluorescent Protein Promoter Activity Plasmid Copy Number Absolute Activity Cell Green Fluorescent Protein

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A genome-wide survey of alternative translational initiation events in Homo sapiens

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Science China(Life Sciences) 2007年第3期50卷 423-428页

作者： ZHANG Jing1, CAI Jun2 & LI YanDa1 1 bioinformatics division, TNLIST and Department of Automation, Tsinghua University, Beijing 100084, China 2 Department of bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801,USA 1. Bioinformatics Division TNLIST and Department of Automation Tsinghua University Beijing 100084 China 2. Department of Bioengineering University of Illinois at Urbana-Champaign Urbana IL 61801 USA

Alternative translational initiation is an important mechanism to increase the diversity of gene products. Although some of alternative translational initiation events have been reported, such information remains anecdotal and does not allow for any generalizations. The number of the known alternative translational initiation genes is so few that we know little about its mechanism. There is a great demand to discover more alternative translational initiation genes. However, it is arduously time-consuming to discover novel alternative translational initiation genes by the experimental method. Therefore we systematically analyzed protein sequences available in public database and predicted 1237 protein clusters as potential alternative translational initiation events. We concluded that about 8%—10% of human genes have alternative translational initiation sites. The results significantly increased the number of alternative translation initiation events and indicated that alternative translation initiation is an important and general regulation mechanism in the cellular process.

关键词： ATI A genome-wide survey of alternative translational initiation events in Homo sapiens

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A novel collagen sponge for cartilage tissue engineering

A novel collagen sponge for cartilage tissue engineering

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作者： Chen, Guoping Akahane, Daisuke Kawazoe, Naoki Shirasaki, Yoshio Tanaka, Junzo Yamamoto, Katsuyuki Tateishi, Tateishi Biomaterials Center National Institute for Materials Science 1-1 Namiki Tsukuba Japan Division of Bioengineering and Bioinformatics Graduate School of Information Science and Technology Hokkaido University Japan Institute for Human and Science Biomedical Engineering Advanced Industrial Science and Technology Japan Department of Metallurgy and Ceramics Science Graduate School of Science and Engineering Tokyo Institute of Technology Japan

A novel collagen sponge that can protect cell leakage during cell seeding was developed by wrapping all the surfaces except the upside of a collagen sponge with membrane that has pores smaller than cell. The collagen sponge was used for three-dimensional culture of human bone marrow-derived mesenchymal stem cells (MSCs). The cells adhered to the collagen, and proliferated to fill the spaces in the sponge. The cell seeding efficiency was higher than 95%. The MSCs cultured in the collagen sponge in the chondrogenic induction medium supplemented with TGF-3 and BMP6 expressed genes encoding type II collagen, SOX9 and aggrecan. HE staining indicated the round morphology of differentiated cells and the extracelluler matrices were positively stained by safranin O and toluidine blue. Type II collagen and cartilage proteoglycan were detected by immunostaining with anti-type II collagen and anti-cartilage proteoglycan. These results suggest the chondrogenic differentiation of MSCs. The collagen sponge facilitated cell seeding and chondrogenic differentiation of MSCs, and will be useful for cartilage tissue engineering.

关键词： Collagen

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Culture of mesenchymal stem cells in a collagen sponge to reduce the cell leak

Culture of mesenchymal stem cells in a collagen sponge to re...

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55th Society of Polymer Science Japan Symposium on Macromolecules

作者： Kawazoe, Naoki Akahane, Daisuke Chen, Guoping Shirasaki, Yoshio Yamamoto, Katsuyuki Tateishi, Tetsuya Biomaterials Center National Institute for Materials Science Namiki 1-1 Tyukuba Ibaraki 305-0044 Division of Bioengineering and Bioinformatics Graduate School of Information Science and Technology Institute for Human and Science Biomedical Engineering Advanced Indusrial Science and Technology

Collagen sponges have been used in tissue engineering to provide three dimensional scaffolds. However, it was difficult to distribute cells uniformly throughout the scaffolds because the seeded cells leak from the scaffolds. Here we prepared a collagen scaffold surrounded by a 10 micrometer mesh to prevent cell leakage from the scaffold and seeded human mesenchymal stem cells onto the scaffold. From the results of the high seed efficiency, the collagen/mesh scaffold in this study was useful for a culture of mesenchymal stem cells.

关键词： Cell culture

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Characteristics of the Muscle Activities of the Elderly wearing the Lower limb Orthosis during Gait on the Treadmill

Characteristics of the Muscle Activities of the Elderly wear...

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SICE Annual Conference

作者： Kyong Kim Kyung-ju Hong Mun-ho Ryu Tae-kyu Kwon Chul-un Hong Nam-gyun Kim Department of Biomedical Engineering Chonbuk National University of Korea Jeonju South Korea Bioengineering research center for the aged Chonbuk National University of Korea Jeonju South Korea Division of Bionics and Bioinformatics Chonbuk National University of Korea Jeonju South Korea

We have developed a lower limb orthosis with a pneumatic rubber actuator, which is intended for the assistance and the enhancement of lower limb muscular activities of the elderly. For this purpose, we investigated the characteristics of the muscular activities with and without the orthosis in gait motion on treadmill. To find out the characteristics of the muscle activities, we analyzed the gait motion of the subject and flexing and extending motion of the knees and measured muscular power in the lower limb. The subjects wearing the lower limb orthosis were instructed to perform gait on the treadmill and flexing and extending motion of the knees in sitting position for monitoring of electromyogram and muscular activities. We used the C8051F Target Board (SILICON LABORATORIES, Inc., USA) for the orthosis control. The air pressure of the pneumatic actuator was varied from one kgf/cm 2 to four kgf/cm 2 to find the most suitable air pressure. Through this study, we expect to find the effect of the lower limb orthosis in the gait motion and muscular activities along with the most suitable air pressure in the pneumatic actuator of the orthosis for the enhancement of muscular power for the elderly

关键词： Muscles Senior citizens Pneumatic actuators Motion analysis Knee Rubber Power measurement Motion measurement Monitoring Silicon

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A New Training System Using a Tilting Bed for an Early Rehabilitation

A New Training System Using a Tilting Bed for an Early Rehab...

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SICE Annual Conference

作者： Chang-ho Yu Kyung Kim Yong-yook Kim Tae-kyu Kwon Mun-ho Ryu Nam-gyun Kim Department of Biomedical Engineering Chonbuk National University of Korea Jeonju South Korea Center of Healthcare Technology Development Jeonju South Korea Division of Bionics and Bioinformatics Chonbuk National University of Korea Jeonju South Korea Bioengineering Research Center for the aged Chonbuk National University of Korea Jeonju South Korea

We propose a new training system using a tilting bed, a visual display and a force plate for an early rehabilitation. Conventional rehabilitation systems for postural control have not been applicable to the patients who have to be lying in bed all the time. The rehabilitation training using those systems is only possible when the patient can stand up by himself or herself. Moreover, there did not exist any device that could provide the sense of balance or the sensation of walking to the patients in bed. The software for the system consists of the training part and the analysis part. The training part has been developed to provide various training scheme that help improve postural control ability of the subjects via repeated training of moving COP. The training consists of the COP maintaining training and the COP movement training in mediolateral, anterior-lateral, and posterior-lateral directions. The analysis part performs the assessments on the COP moving time, COP maintaining time, and mean absolute deviation before and after the training for different tilt angles of the bed. Through the experiments on number of subjects with the system, we tried to find the effectiveness of the advanced early rehabilitation training system. The results showed that this system is an effective system for early rehabilitation training and that our system can be used as clinical equipment.

关键词： Force feedback Control systems Muscles Aging Legged locomotion Road accidents Biomedical engineering Medical services bioinformatics Displays

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Biophysical approaches for studying the integrity and function of tight junctions

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MCB Molecular and Cellular Biomechanics 2005年第3期2卷 105-123页

作者： Vedula, S.R.K. Lim, T.S. Kausalya, P.J. Hunziker, W. Rajagopal, G. Lim, C.T. Division of Bioengineering Department of Mechanical Engineering National University of Singapore Singapore Singapore Bioinformatics Institute Singapore Singapore Institute of Molecular and Cell Biology Singapore 138673 Singapore

Cell-cell adhesion is an extremely important phenomenon as it influences several biologically important processes such as inflammation, cell migration, proliferation, differentiation and even cancer metastasis. Furthermore, proteins involved in cell-cell adhesion are also important from the perspective of facilitating better drug delivery across epithelia. The adhesion forces imparted by proteins involved in cell-cell adhesion have been the focus of research for sometime. However, with the advent of nanotechnological techniques such as the atomic force microscopy (AFM), we can now quantitatively probe these adhesion forces not only at the cellular but also molecular level. Here, we review the structure and function of tight junction proteins, highlighting some mechanistic studies performed to quantify the adhesion occurring between these proteins and where possible their association with human diseases. In particular, we will highlight two important experimental techniques, namely the micropipette step pressure technique and the AFM that allow us to quantify these adhesion forces at both the cellular and molecular levels, respectively. Copyright © 2005 Tech Science Press.

关键词： Biomedical engineering

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Optimization of power compression and stability of relativistic and ponderomotive self-channeling of 248nm laser pulses in underdense plasmas

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Physical Review E 2004年第6期70卷 066406-066406页

作者： J. Davis A. B. Borisov C. K. Rhodes Plasma Physics Division Naval Research Laboratory 4555 Overlook Avenue SW Washington D.C. 20375 USA Laboratory for X-Ray Microimaging and Bioinformatics Department of Physics M∕C 273 University of Illinois at Chicago 845 West Taylor Street Chicago Illinois 60607-7059 USA Department of Bioengineering M∕C 063 University of Illinois at Chicago 851 South Morgan Street Chicago Illinois 60607-7052 USA Department of Computer Science M∕C 102 University of Illinois at Chicago 851 South Morgan Street Chicago Illinois 60607-7042 USA Department of Electrical and Computer Engineering M∕C 154 University of Illinois at Chicago 851 South Morgan Street Chicago Illinois 60607-7053 USA

The controlled formation in an underdense plasma of stable multi-PW relativistic micrometer-scale channels, which conduct a confined power at 248nm exceeding 104 critical powers and establish a peak channel intensity of ∼1023W∕cm2, can be achieved with the use of an appropriate gradient in the electron density in the initial launching phase of the confined propagation. This mode of channel formation optimizes both the power compression and the stability by smoothing the transition from the incident spatial profile to that associated with the lowest channel eigenmode, the dynamically robust structure that governs the confined propagation. A chief outcome is the ability to stably conduct coherent energy at fluences greater than 109J∕cm2.

关键词： Laser pulses

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