1。解决方案和材料的制备这些步骤应该进行提前几天。 <ol><li>盖玻片。盖玻片清洗浸泡10分钟到一个解决方案Linbro 7X清洁剂：水混合1：3的比例和加热，搅拌，直到明确。盖玻片被广泛冲洗去离子水，然后在450℃烘烤6小时。装入陶瓷染色架盖玻片（见试剂）简化了这个过程。 </li><li>蛋白质溶液冲压。重组纤维连接蛋白的1 mg / ml浓度的原液制造商的说明。 </li></ol> 2。从拓扑主演员邮票这些步骤可以进行提前几天。商店邮票图案在有盖菜，如组织培养皿。 <ol><li>使用压缩，过滤空气或惰性气体流，删除主浮尘。 </li><li>广场主图案的一面，在一个塑料盘仅比主底部。 60 - 100毫米组织培养皿非常适合用于这一目的。 </li><li>聚苯乙烯50 mL离心管，在固化剂的比例结合Sylgard组件：1：10的橡胶基地重量。调匀使用塑料的设备，如一次性吸管。准备好至少0.2毫升弹性体每平方厘米的菜面积。 </li><li> 300 G 50毫升管离心5分钟，以去除气泡。 </li><li>倒在主的弹性，然后放置在干燥器中，在真空条件下，30分钟。 </li><li>烘箱中固化在65℃至少2个小时的弹性。固化在更高的温度和更长的时间，结果更严厉的弹性。让冷却到室温。 </li><li>从主分离的邮票纸。 </li></ol> 3。微接触印刷到玻璃纤维连接蛋白<ol><li>切出单枚邮票。邮票测量4毫米x 4毫米至1厘米× 1厘米，面积1 - 2毫米厚的最简单的开始。广场图案的一面，在玻片上或小塑料盘。 </li><li>放置在等离子体清洁和过程的邮票，在真空条件下，30秒。一个科学Harrick等离子清洗器（设备），其最高输出设置渲染的PDMS表面的亲水性。更长的时间，在弹性体开裂。 </li><li>用去离子水稀释到一个冲压浓度为50微克/毫升的纤维连接蛋白的解决方案。 </li><li>将一小滴（10 - 50μL）冲压邮票上的解决方案。将分散在亲水表面。只添加足够的解决方案，下降涵盖了邮票，但不超过边缘运行。让蛋白质吸附邮票5分钟。 </li><li>使用Kimwipe ®或其他清洁纸巾，灯芯从邮票大部分蛋白质溶​​液，而不触及图案的区域。 </li><li>下一个清洁，干燥，惰性气体，如氮，流干从邮票的解决方案。 </li><li>使用镊子，取出载玻片邮票，反转，并在清洗玻璃盖玻片（表面图案）接触的地方。放置在顶部的重量，以促进良好的接触。具体的重量，提供了最好的图案是邮票大小和图案的依赖;开始用5克重，和调整之间的冲压件。离开邮票与表面1分钟接触。 </li><li>仔细拆解堆栈，并从盖玻片单独的邮票。 </li><li>大力漂洗，去离子水，在PBS图案盖玻片删除不被吸附到表面的蛋白质，是。干盖玻片下氮气流。 </li></ol>代表性的成果微接触印刷是表面上的图案分子的强大的过程。这个过程有能力创造，从几十微米到几百纳米的尺寸不等的功能;图。 1A，在左边的标志是每200微米的高度，而绿色的点如图所示。 1B是直径在1微米，间距4微米的间隔，测量中心到中心。图1B也说明了微接触印刷的强大属性，即它是和添加剂的过程。微接触印刷的多轮可用于创建一个表面多组分体系 3 。 <img src="/files/ftp_upload/old/1065_2008_11_24_3/Figure_a.jpg" alt="图A" /><img src="/files/ftp_upload/old/1065_2008_11_24_4/FIGURE_B.jpg" alt="图B" />

<ol>
	<li>Chen, C. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Geometric+control+of+cell+life+and+death.">Geometric control of cell life and death.</a> Science. 276, 1425-1425 (1997).</li><li>Kumar, A., Whitesides, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Features+of+Gold+Having+Micrometer+to+Centimeter+Dimensions+can+be+Formed+Through+a+Combination+of+Stamping+with+an+Elastomeric+Stamp+and+an+Alkanethiol+"Ink"+Followed+by+Chemical+Etching.">Features of Gold Having Micrometer to Centimeter Dimensions can be Formed Through a Combination of Stamping with an Elastomeric Stamp and an Alkanethiol "Ink" Followed by Chemical Etching.</a> Applied Physics Letters. 63, 4-4 (1993).</li><li>St. John, P. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Preferential+Glial+Cell+Attachment+to+Microcontact-printed+Surfaces.">Preferential Glial Cell Attachment to Microcontact-printed Surfaces.</a> Journal of Neuroscience Methods. 75, 171-171 (1997).</li><li>Kam, L., Boxer, S. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell+adhesion+to+protein-micropatterned-supported+lipid+bilayer+membranes.">Cell adhesion to protein-micropatterned-supported lipid bilayer membranes.</a> Journal of Biomedical Materials Research. 55, 487-487 (2001).</li><li>Kung, L. A., Kam, L., Hovis, J. S., Boxer, S. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Patterning+Hybrid+Surfaces+of+Proteins+and+Supported+Lipid+Bilayers.">Patterning Hybrid Surfaces of Proteins and Supported Lipid Bilayers.</a> Langmuir. 16, 6773-6773 (2000).</li><li>Shen, K., Thomas, V. K., Dustin, M. L., Kam, L. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Micropatterning+of+costimulatory+ligands+enhances+CD4++T+cell+function.">Micropatterning of costimulatory ligands enhances CD4+ T cell function.</a> Proceedings of the National Academy of Sciences. 105, 7791-7791 (2008).</li><li>Shi, P., Shen, K., Kam, L. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Local+presentation+of+L1+and+N-cadherin+in+multicomponent,+microscale+patterns+differentially+direct+neuron+function+in+vitro.">Local presentation of L1 and N-cadherin in multicomponent, microscale patterns differentially direct neuron function in vitro.</a> Developmental Neurobiology. 67, 1765-1765 (2007).</li></ol>

The authors have nothing to disclose.

微接触印刷过程的概念很简单，非常强大的，已被应用于各种基材上的广泛的分子图案。然而，这个过程仍然是一门艺术的东西。创建，该模式的具体几何图案的蛋白质，适用于重量，和涂料/冲压条件都影响冲压件的质量。例如，过小，重量轻，适用于大的特点，往往在模式中的正确的标志在图上可以看到差距的结果。 1A。相反，过多的重量会导致下垂和邮票的崩溃，造成意想不到的沉积蛋白质在图案之间的地...

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<td>Plasma Cleaner</td>
<td>&nbsp;</td>
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<td>Desiccator</td>
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<td>Nalgene</td>
<td>5315-0150</td>
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<td>Invitrogen</td>
<td>10010-072</td>
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<td>Reagent</td>
<td>Invitrogen</td>
<td>A30006</td>
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<td>Diffraction Grating</td>
<td>Reagent</td>
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microcontact printing of proteins for cell biology

模式到基板的蛋白质和其他生物大分子的能力是非常重要的捕捉外环境的空间复杂性。微接触印刷的发展怀特赛德斯组（<a href="http://gmwgroup.harvard.edu/"&gt; http://gmwgroup.harvard.edu/</a&gt;）在20世纪90年代中期revolutionalized这​​一领域，微电子/微细加工技术，生命科学重点​​实验室访问。这种方法的初步实现，用于聚二甲基硅氧烷（PDMS）邮票上创建材料表面的功能化化学品模式<sup&gt; 1</sup&gt;。从那时起，已经开发了一系列创新的方法模式的其他分子，包括蛋白质<sup&gt; 2</sup&gt;。这个视频演示的创造的PDMS邮票的基本过程和使用模式的蛋白质，这些步骤是很难准确地用言语表达。我们专注于盖玻片作为一个具体的例子，图案到细胞外基质蛋白纤维连接蛋白图案。微接触印刷过程中的一个重要组成部分，是拓扑的主，从投邮票;主的升高和降低的地区，都反映到邮票，并确定最终的模式。通常情况下，主涂层与光致抗蚀剂，然后通过光刻图案硅片组成，都是在这里完成。包含一个特定的模式创建的主人，需要专门的设备，最好是在与一个制造中心或设施咨询走近。然而，几乎任何与拓扑结构的基板可以被用来作为一个高手，如塑料光栅（见一个例子试剂），和这样的偶然的主人提供现成的，简单的模式。该协议开始掌握在手的点。

Watch this Scientific Journal Video about Microcontact Printing of Proteins for Cell Biology at JoVE.com

Microcontact Printing of Proteins for Cell Biology

微接触印刷被广泛使用模式的蛋白质和其他分子在材料表面。我们展示这一过程的基本步骤，冲压到玻璃纤维连接蛋白的模式。

微接触印刷的蛋白细胞生物学

The ability to pattern proteins and other biomolecules onto substrates is important for capturing the spatial complexity of the extracellular environment. ...

microcontact-printing-of-proteins-for-cell-biology

Research

JoVE Journal

Biology

19.9K 次观看.  Columbia University. 微接触印刷被广泛使用模式的蛋白质和其他分子在材料表面。我们展示这一过程的基本步骤，冲压到玻璃纤维连接蛋白的模式。

视频: Microcontact Printing of Proteins for Cell Biology

A Gradient-generating Microfluidic Device for Cell Biology

 The fabrication and operation of a gradient-generating microfluidic device for studying cellular behavior is described.  A microfluidic platform is an enabling experimental tool, because it can precisely manipulate fluid flows, enable high-throughput experiments, and generate stable soluble concentration gradients.  Compared to conventional gradient generators, poly(dimethylsiloxane) (PDMS)-based  microfluidic devices can generate stable concentration gradients of growth factors with well-defined profiles.  Here, we developed simple gradient-generating microfluidic devices with three separate inlets.  Three microchannels combined into one microchannel to generate concentration gradients.  The stability and shape of growth factor gradients were confirmed by fluorescein isothyiocyanate (FITC)-dextran with a molecular weight similar to epidermal growth factor (EGF).  Using this microfluidic device, we demonstrated that fibroblasts exposed to concentration gradients of EGF migrated toward higher concentrations.  The directional orientation of cell migration and motility of migrating cells were quantitatively assessed by cell tracking analysis.  Thus, this gradient-generating microfluidic device might be useful for studying and analyzing the behavior of migrating cells.

We describe a protocol for the microfabrication of the gradient-generating microfluidic device that can generate spatial and temporal gradients in well-defined microenvironment. In this approach, the gradient-generating microfluidic device can be used to study directed cell migration, embryogenesis, wound healing, and cancer metastasis.

一个渐变产生的微流体装置，细胞生物学

 The fabrication and operation of a gradient-generating microfluidic device for studying cellular behavior is described.  A microfluidic platform is an ...

科研

生物学

Micro-scale Engineering for Cell Biology

细胞生物学的微观尺度工程

Assessing Two-dimensional Crystallization Trials of Small Membrane Proteins for Structural Biology Studies by Electron Crystallography

Electron crystallography has evolved as a method that can be used either alternatively or in combination with three-dimensional crystallization and X-ray crystallography to study structure-function questions of membrane proteins, as well as soluble proteins. Screening for two-dimensional (2D) crystals by transmission electron microscopy (EM) is the critical step in finding, optimizing, and selecting samples for high-resolution data collection by cryo-EM. Here we describe the fundamental steps in identifying both large and ordered, as well as small 2D arrays, that can potentially supply critical information for optimization of crystallization conditions.
By working with different magnifications at the EM, data on a range of critical parameters is obtained. Lower magnification supplies valuable data on the morphology and membrane size. At higher magnifications, possible order and 2D crystal dimensions are determined. In this context, it is described how CCD cameras and online-Fourier Transforms are used at higher magnifications to assess proteoliposomes for order and size.
While 2D crystals of membrane proteins are most commonly grown by reconstitution by dialysis, the screening technique is equally applicable for crystals produced with the help of monolayers, native 2D crystals, and ordered arrays of soluble proteins. In addition, the methods described here are applicable to the screening for 2D crystals of even smaller as well as larger membrane proteins, where smaller proteins require the same amount of care in identification as our examples and the lattice of larger proteins might be more easily identifiable at earlier stages of the screening.

Evaluating two-dimensional (2D) crystallization trials for the formation of ordered membrane protein arrays is a highly critical and difficult task in electron crystallography. Here we describe our approach in screening for and identifying 2D crystals of predominantly small membrane proteins in the range of 15 &#x2013; 90kDa.

评估电子晶体结构生物学研究的小膜蛋白的二维结晶试验

Electron crystallography has evolved as a method that can be used either alternatively or in combination with three-dimensional crystallization and X-ray ...

Fluorescent Labeling of COS-7 Expressing SNAP-tag Fusion Proteins for Live Cell Imaging

SNAP-tag and CLIP-tag protein labeling systems enable the specific, covalent attachment of molecules, including fluorescent dyes, to a protein of interest in live cells. These systems offer a broad selection of fluorescent substrates optimized for a range of imaging instrumentation. Once cloned and expressed, the tagged protein can be used with a variety of substrates for numerous downstream applications without having to clone again. There are two steps to using this system: cloning and expression of the protein of interest as a SNAP-tag fusion, and labeling of the fusion with the SNAP-tag substrate of choice. The SNAP-tag is a small protein based on human O6-alkylguanine-DNA-alkyltransferase (hAGT), a DNA repair protein. SNAP-tag labels are dyes conjugated to guanine or chloropyrimidine leaving groups via a benzyl linker. In the labeling reaction, the substituted benzyl group of the substrate is covalently attached to the SNAP-tag. CLIP-tag is a modified version of SNAP-tag, engineered to react with benzylcytosine rather than benzylguanine derivatives. When used in conjunction with SNAP-tag, CLIP-tag enables the orthogonal and complementary labeling of two proteins simultaneously in the same cells.

SNAP-tag and CLIP-tag protein labeling systems enable the specific, covalent attachment of molecules, including fluorescent dyes, to a protein of interest in live cells. Once cloned and expressed, the tagged protein can be used with a variety of substrates for numerous downstream applications without having to clone again.

对活细胞成像的SNAP - Tag融合蛋白的荧光标记的COS - 7

SNAP-tag and CLIP-tag protein labeling systems enable the specific, covalent attachment of molecules, including fluorescent dyes, to a protein of interest ...

Protein Membrane Overlay Assay: A Protocol to Test Interaction Between Soluble and Insoluble Proteins in vitro

Validating interactions between different proteins is vital for investigation of their biological functions on the molecular level. There are several methods, both in vitro and in vivo, to evaluate protein binding, and at least two methods that complement the shortcomings of each other should be conducted to obtain reliable insights. 
For an in vivo assay, the bimolecular fluorescence complementation (BiFC) assay represents the most popular and least invasive approach that enables to detect protein-protein interaction within living cells, as well as identify the intracellular localization of the interacting proteins 1,2. In this assay, non-fluorescent N- and C-terminal halves of GFP or its variants are fused to tested proteins, and when the two fusion proteins are brought together due to the tested proteins&#x2019; interactions, the fluorescent signal is reconstituted3-6. Because its signal is readily detectable by epifluorescence or confocal microscopy, BiFC has emerged as a powerful tool of choice among cell biologists for studying about protein-protein interactions in living cells 3. This assay, however, can sometimes produce false positive results. For example, the fluorescent signal can be reconstituted by two GFP fragments arranged as far as 7 nm from each other due to close packing in a small subcellular compartment, rather that due to specific interactions7.
Due to these limitations, the results obtained from live cell imaging technologies should be confirmed by an independent approach based on a different principle for detecting protein interactions. Co-immunoprecipitation (Co-IP) or glutathione transferase (GST) pull-down assays represent such alternative methods that are commonly used to analyze protein-protein interactions in vitro. However, iIn these assays, however, the tested proteins must be readily soluble in the buffer that supportsused for the binding reaction. Therefore, specific interactions involving an insoluble protein cannot be assessed by these techniques.
 Here, we illustrate the protocol for the protein membrane overlay binding assay, which circumvents this difficulty. In this technique, interaction between soluble and insoluble proteins can be reliably tested because one of the proteins is immobilized on a membrane matrix. This method, in combination with in vivo experiments, such as BiFC, provides a reliable approach to investigate and characterize interactions faithfully between soluble and insoluble proteins. In this article, binding between Tobacco mosaic virus (TMV) movement protein (MP), which exerts multiple functions during viral cell-to-cell transport8-14, and a recently identified plant cellular interactor, tobacco ankyrin repeat-containing protein (ANK) 15, is demonstrated using this technique.

Protein Membrane Overlay Assay: A Protocol to Test Interaction Between Soluble and Insoluble Proteins in vitro

Testing protein-protein interaction is indispensable for dissection of protein functionality. Here, we introduce an in vitro protein-protein binding assay to probe a membrane-immobilized protein with a soluble protein. This assay provides a reliable method to test interaction between an insoluble protein and a protein in solution.

蛋白膜覆盖含量：一个协议测试可溶性和不溶性蛋白质之间的相互作用在体外</em

Validating interactions between different proteins is vital for investigation of their biological functions on the molecular level.  There are several ...

Pull-down of Calmodulin-binding Proteins

Calcium (Ca2+) is an ion vital in regulating cellular function through a variety of mechanisms. Much of Ca2+ signaling is mediated through the calcium-binding protein known as calmodulin (CaM)1,2. CaM is involved at multiple levels in almost all cellular processes, including apoptosis, metabolism, smooth muscle contraction, synaptic plasticity, nerve growth, inflammation and the immune response. A number of proteins help regulate these pathways through their interaction with CaM. Many of these interactions depend on the conformation of CaM, which is distinctly different when bound to Ca2+ (Ca2+-CaM) as opposed to its Ca2+-free state (ApoCaM)3.
While most target proteins bind Ca2+-CaM, certain proteins only bind to ApoCaM. Some bind CaM through their IQ-domain, including neuromodulin4, neurogranin (Ng)5, and certain myosins6. These proteins have been shown to play important roles in presynaptic function7, postsynaptic function8, and muscle contraction9, respectively. Their ability to bind and release CaM in the absence or presence of Ca2+ is pivotal in their function. In contrast, many proteins only bind Ca2+-CaM and require this binding for their activation. Examples include myosin light chain kinase10, Ca2+/CaM-dependent kinases (CaMKs)11 and phosphatases (e.g. calcineurin)12, and spectrin kinase13, which have a variety of direct and downstream effects14.
The effects of these proteins on cellular function are often dependent on their ability to bind to CaM in a Ca2+-dependent manner. For example, we tested the relevance of Ng-CaM binding in synaptic function and how different mutations affect this binding. We generated a GFP-tagged Ng construct with specific mutations in the IQ-domain that would change the ability of Ng to bind CaM in a Ca2+-dependent manner. The study of these different mutations gave us great insight into important processes involved in synaptic function8,15. However, in such studies, it is essential to demonstrate that the mutated proteins have the expected altered binding to CaM.
Here, we present a method for testing the ability of proteins to bind to CaM in the presence or absence of Ca2+, using CaMKII and Ng as examples. This method is a form of affinity chromatography referred to as a CaM pull-down assay. It uses CaM-Sepharose beads to test proteins that bind to CaM and the influence of Ca2+ on this binding. It is considerably more time efficient and requires less protein relative to column chromatography and other assays. Altogether, this provides a valuable tool to explore Ca2+/CaM signaling and proteins that interact with CaM.

Calmodulin (CaM) pull-down assay is an effective way to investigate the interaction of CaM with various proteins. This method uses CaM-sepharose beads for efficient and specific analysis of CaM-binding proteins. This provides an important tool to explore CaM signaling in cellular function.

钙调蛋白结合蛋白的下拉

Calcium (Ca2+) is an ion vital in regulating cellular function through a variety of mechanisms. Much of Ca2+ signaling is mediated through the ...

Modified Yeast-Two-Hybrid System to Identify Proteins Interacting with the Growth Factor Progranulin

Progranulin (PGRN), also known as granulin epithelin precursor (GEP), is a 593-amino-acid autocrine growth factor. PGRN is known to play a critical role in a variety of physiologic and disease processes, including early embryogenesis, wound healing 1, inflammation 2, 3, and host defense 4. PGRN also functions as a neurotrophic factor 5, and mutations in the PGRN gene resulting in partial loss of the PGRN protein cause frontotemporal dementia 6, 7. Our recent studies have led to the isolation of PGRN as an important regulator of cartilage development and degradation 8-11. Although PGRN, discovered nearly two decades ago, plays crucial roles in multiple physiological and pathological conditions, efforts to exploit the actions of PGRN and understand the mechanisms involved have been significantly hampered by our inability to identify its binding receptor(s). To address this issue, we developed a modified yeast two-hybrid (MY2H) approach based on the most commonly used GAL4 based 2-hybrid system. Compared with the conventional yeast two-hybrid screen, MY2H dramatically shortens the screen process and reduces the number of false positive clones. In addition, this approach is reproducible and reliable, and we have successfully employed this system in isolating the binding proteins of various baits, including ion channel 12, extracellular matrix protein 10, 13, and growth factor14. In this paper, we describe this MY2H experimental procedure in detail using PGRN as an example that led to the identification of TNFR2 as the first known PGRN-associated receptor 14, 15.

We have modified the conventional yeast two-hybrid screening, an effective genetic tool in identifying protein interaction. This modification markedly shortens the process, reduces the workload, and most importantly, reduces the number of false positives. In addition, this approach is reproducible and reliable.

改良酵母双杂交系统，以确定蛋白与生长因子Progranulin的相互作用

Progranulin (PGRN), also known as granulin epithelin precursor (GEP), is a 593-amino-acid autocrine growth factor. PGRN is known to play a critical role ...

Cell Tracking Using Photoconvertible Proteins During Zebrafish Development

Embryogenesis is a dynamic process that is best studied by using techniques that allow the documentation of developmental changes in vivo. The use of genetically-encoded fluorescent proteins has proven a valuable strategy for elucidating dynamic morphogenetic processes as they occur in the intact organism. During the past decade, the development of photoactivatable and photoconvertible fluorescent proteins has opened the possibility to investigate the fate of discrete subpopulations of tagged proteins1. Unlike photoactivatable proteins, photoconvertible fluorescent proteins (PCFPs) are readily tracked and imaged in their native emission state prior to photoconversion, making it easier to identify and select regions by optical inspection. PCFPs, such as Kaede2, KikGR3, Dendra4 and EosFP5, can be shifted from green to red upon exposure to UV or blue light due to a His-Tyr-Gly tripeptide sequence which forms a green chromophore that can be photoconverted to a red one by a light-catalyzed &beta;-elimination and subsequent extension of a &pi;-conjugated system3. PCFPs and their monomeric variants are useful tools for tracking cells6-10 and studying protein dynamics11-14, respectively. During recent years, PCFPs have been expressed in different animal model, such as zebrafish6, chicken7,8 and mouse9,10 for cell fate tracking. Here we report a protocol for cell-specific photoconversion of PCFPs in the living zebrafish embryo and further tracking of photoconverted proteins at later developmental stages. This methodology allows studying, in a tissue-specific manner, cell biological events underlying morphogenesis in the zebrafish animal model.

Here, we present a method for the photoactivated switch of photoconvertible fluorescent proteins (PCFPs) in the living zebrafish embryo and further tracking of photoconverted protein at specific time points during development. This methodology allows monitoring of cell biological events underlying different developmental processes in a live vertebrate organism.

在斑马鱼发育的细胞追踪使用Photoconvertible蛋白

Embryogenesis is a dynamic process that is best studied by using techniques that allow the documentation of developmental changes in vivo. The use of ...

The Use of Chemostats in Microbial Systems Biology

Cells regulate their rate of growth in response to signals from the external world. As the cell grows, diverse cellular processes must be coordinated including macromolecular synthesis, metabolism and ultimately, commitment to the cell division cycle. The chemostat, a method of experimentally controlling cell growth rate, provides a powerful means of systematically studying how growth rate impacts cellular processes - including gene expression and metabolism - and the regulatory networks that control the rate of cell growth. When maintained for hundreds of generations chemostats can be used to study adaptive evolution of microbes in environmental conditions that limit cell growth. We describe the principle of chemostat cultures, demonstrate their operation and provide examples of their various applications. Following a period of disuse after their introduction in the middle of the twentieth century, the convergence of genome-scale methodologies with a renewed interest in the regulation of cell growth and the molecular basis of adaptive evolution is stimulating a renaissance in the use of chemostats in biological research.

Cell growth rate is a regulated process and a primary determinant of cell physiology. Continuous culturing using chemostats enables extrinsic control of cell growth rate by nutrient limitation facilitating the study of molecular networks that control cell growth and how those networks evolve to optimize cell growth.

恒化器中微生物系统生物学中的应用

Cells regulate their rate of growth in response to signals from the external world. As the cell grows, diverse cellular processes must be coordinated ...

Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology

Ideal cell-free expression systems can theoretically emulate an in vivo cellular environment in a controlled in vitro platform.1 This is useful for expressing proteins and genetic circuits in a controlled manner as well as for providing a prototyping environment for synthetic biology.2,3 To achieve the latter goal, cell-free expression systems that preserve endogenous Escherichia coli transcription-translation mechanisms are able to more accurately reflect in vivo cellular dynamics than those based on T7 RNA polymerase transcription. We describe the preparation and execution of an efficient endogenous E. coli based transcription-translation (TX-TL) cell-free expression system that can produce equivalent amounts of protein as T7-based systems at a 98% cost reduction to similar commercial systems.4,5 The preparation of buffers and crude cell extract are described, as well as the execution of a three tube TX-TL reaction. The entire protocol takes five days to prepare and yields enough material for up to 3000 single reactions in one preparation. Once prepared, each reaction takes under 8 hr from setup to data collection and analysis. Mechanisms of regulation and transcription exogenous to E. coli, such as lac/tet repressors and T7 RNA polymerase, can be supplemented.6 Endogenous properties, such as mRNA and DNA degradation rates, can also be adjusted.7 The TX-TL cell-free expression system has been demonstrated for large-scale circuit assembly, exploring biological phenomena, and expression of proteins under both T7- and endogenous promoters.6,8 Accompanying mathematical models are available.9,10 The resulting system has unique applications in synthetic biology as a prototyping environment, or "TX-TL biomolecular breadboard."

Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology

This five-day protocol outlines all steps, equipment, and supplemental software necessary for creating and running an efficient endogenous Escherichia coli based TX-TL cell-free expression system from scratch. With reagents, the protocol takes 8 hours or less to setup a reaction, collect, and process data.

协议用于实现<em&gt;大肠杆菌</em&gt;基于TX-TL无细胞表达系统合成生物学

Ideal cell-free expression systems can theoretically emulate an in vivo cellular environment in a controlled in vitro platform.1 This is useful for ...