1. Çözümler ve malzemelerin hazırlanması Bu adımlar, birkaç gün önceden yapılmalıdır. <ol><li> Cam lamelleri. Temizleyene kadar karıştırarak ile, 3 oranı ve ısıtmalı su, 1 karışık: lameller Linbro 7X deterjan bir çözüm olarak 10 dakika boyunca daldırma tarafından temizlendi. Lameller yoğun deiyonize su ile durulanır ve sonra 6 saat boyunca 450 ° C&#39;de pişirilir. (Reaktifler) seramik boyama rafları lamelleri Yükleniyor bu süreci basitleştirilmiş. </li><li> Protein damgalama için çözüm. 1 mg / ml konsantrasyonu bir stok çözüm üretici talimatlarına sulandırın fibronektin. </li></ol> 2. Topolojik ustadan pulları Oyuncular Bu adımlar, birkaç gün önceden yapılabilir. Böyle bir doku kültürü yemek olarak kapalı bir çanak Mağaza pulları desen,. <ol><li> Ustadan sıkıştırılmış, filtre edilmiş hava veya inert gaz akışı kullanarak gevşek toz çıkarın. </li><li> Sadece master daha büyük bir plastik çanak alt, ana, desenli yan yerleştirin. 60 - ya da 100 mm doku kültürü yemekleri de bu amaç için uygundur. </li><li> Polistiren 50 ml santrifüj tüpüne, sertleştirici oranında Sylgard bileşenleri bir araya getirir: 1: 10 elastomer tabanı kilo. Böyle bir pipet gibi, plastik bir cihaz kullanarak iyice karıştırın. Elastomer çanak alanının santimetre kare başına en az 0.2 ml hazırlayın. </li><li> Hava kabarcıklarını çıkarmak için 5 dakika boyunca 300 G 50 ml tüp santrifüjleyin. </li><li> Elastomer master üzerine dökün, sonra 30 dakika süreyle vakum altında bir desikatöre yerde. </li><li> 65 ° C&#39;de en az 2 saat süreyle bir fırında elastomer Cure. Yüksek sıcaklıklarda ve daha sert elastomer uzun zamanlar sonuçları Kür. Oda sıcaklığına kadar soğumasını bekleyin. </li><li> Ana sayfa pullarının ayırın. </li></ol> 3. Camına fibronektin Microcontact baskı <ol><li> Tek bir damga kesin. 4 mm uzunluğunda Pullar X 4 mm X 1 cm alanda ve 1 - 2 mm kalınlığında 1 cm ile başlamak daha kolay olacaktır. Bir cam slayt veya küçük plastik tabak koyun desen yüzü yukarı. </li><li> 30 saniye boyunca, vakum altında, bir plazma temizleyici, ve süreç damga yerleştirin. En yüksek çıkış ayarı harrick Bilimsel plazma temizleyici (Ekipman), PDMS yüzeyi hidrofilik verecek. Elastomer çatlama kat daha uzun. </li><li> 50 mcg / ml deiyonize su ile bir damgalama konsantrasyonu fibronektin çözüm sulandırınız. </li><li> Çözümü damga damgalama küçük bir damla (50 ul 10) yerleştirin. Hidrofilik yüzeye yayılmış. Damla damga kapsar, ancak kenarları üzerinde çalışmaz, sadece yeterli bir çözüm ekleyin. 5 dakika damga protein adsorbe edelim. </li><li> Kimwipe ® veya diğer temiz bir kağıt mendil kullanarak, desenli bölgeye dokunmadan, damga protein solüsyonu en fitil. </li><li> Kuru, temiz, kuru, böyle bir azot gibi inert gaz, bir dere altında damga kalan çözüm. </li><li> Cımbız kullanarak, cam slayt damga kaldırmak ters ve temizlenmiş cam lamel (yüzeyi desenli) ile temas yer. Iyi temas teşvik etmek üstüne bir ağırlık koyun. Iyi desenlendirme sağlar özgül ağırlık damga boyut ve desen bağlıdır; 5 gr ağırlığı ile başlar, ve HARDWARE arasında ayarlayın. 1 dakika yüzey ile temas halinde damga bırakın. </li><li> Dikkatli bir yığın sökmeye ve lamel ayrı bir damga. </li><li> Şiddetle yüzeye adsorbe değildir protein kaldırmak için deiyonize su ile PBS içinde desenli lamel, durulayın. Kuru bir azot akışı altında lamel. </li></ol> Temsilcisi Sonuçlar Microcontact baskı yüzeylerde desenlendirme moleküller için güçlü bir süreçtir. Bu süreç, Şekil mikrometre onlarca yüzlerce nanometre arasında değişen boyutları ile özellikleri oluşturmak için yeteneğine sahiptir. Yeşil noktalar ise Şekil gösterildiği 1A, soldaki logolar, her yüksekliği 200 mm. 1B, çapı 1 mm ve merkez-merkez ölçülen 4 mikron aralıklarla aralıklı. Şekil 1B, aynı zamanda, güçlü olduğunu microcontact baskı, yani mülkiyet, ve katkı süreci göstermektedir. Microcontact baskı birden fazla mermi, çok bileşenli sistemler 3 oluşturmak için tek bir yüzeye uygulanabilir . <img src="/files/ftp_upload/old/1065_2008_11_24_3/Figure_a.jpg" alt="Şekil A" /><img src="/files/ftp_upload/old/1065_2008_11_24_4/FIGURE_B.jpg" alt="Şekil 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.

Microcontact baskı işlemi desenlendirme moleküllerin geniş bir yelpazede çeşitli yüzeylere uygulanabilir olan, kavramsal olarak basit ve çok sağlam. Ancak bu süreç, bir sanat bir şey kalır. Desen oluşturulacak özel geometri, protein desenli, uygulanan ağırlık ve kaplama / damgalama koşulları damgalama kalitesini etkileyebilir. Örneğin, sık sık büyük özellikleri, desen Şekil sağ üst logosu görülebileceği gibi boşlukları sonuçları uygulanan çok az ağırlık,. 1A. Tersine, çok fazla kilo plazma tedavisi ...

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microcontact printing of proteins for cell biology

Desen proteinleri ve diğer substratlar üzerine biyomoleküllerin yeteneği ekstrasellüler çevre mekansal karmaşıklığı yakalamak için önemlidir. Whitesides grup tarafından microcontact baskı Gelişimi (<a href="http://gmwgroup.harvard.edu/"&gt; Http://gmwgroup.harvard.edu/</a&gt;) 1990&#39;ların ortalarında mikroelektronik / yaşam bilimleri üzerine odaklanmıştır laboratuarlara imalat teknikleri yaparak bu alanda revolutionalized. Polidimetilsiloksan (PDMS) pulları malzeme yüzeyleri Fonksiyonlu kimyasalların desenleri oluşturmak için kullanılan bu yöntem ilk uygulamaları<sup&gt; 1</sup&gt;. O zamandan beri, proteinler de dahil olmak üzere bir dizi yenilikçi yaklaşımlar, desen diğer moleküllerin geliştirilmiştir var<sup&gt; 2</sup&gt;. Bu video PDMS pulları yaratmanın temel sürecini gösterir ve bu adımları doğru kelimelerle ifade etmek zor olduğundan, desen proteinler için bunları kullanır. Biz desenlendirme ekstrasellüler matriks proteini fibronektin desenlendirme belirli bir örnek olarak cam lamelleri üzerine odaklanır. Microcontact baskı sürecinin önemli bir bileşeni pulları dökme topolojik master, ana kaldırdı ve alçaltılmış bölgelerde damga yansıtılmış ve son deseni tanımlamak. Tipik olarak, bir ana, fotorezist ile kaplı ve sonra fotolitografi ile desenli bir silikon gofret oluşur, burada yapıldığı gibi. Belirli bir desen içeren ustaların oluşturulması, özel ekipman gerektirir ve en iyi bir imalat merkezi veya tesis ile istişare yaklaştı. Ancak, topoloji ile hemen hemen herhangi bir yüzeye plastik gibi kırınım ızgaralar gibi bir usta, (bir örnek için Reaktifler) olarak kullanılır ve bu tür şans eseri ustaları hazır, basit desenler sağlamak olabilir. Bu protokol, elinde bir ana noktada başlar.

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

Microcontact Printing of Proteins for Cell Biology

Microcontact baskı malzemesi yüzeylerde desen proteinleri ve diğer molekülleri yaygın bir biçimde kullanılmaktadır. Biz fibronektin cam üzerine desen damgalama, bu sürecin temel adımları göstermektedir.

Proteinlerin Hücre Biyolojisi Microcontact Baskı

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 Görüntüleme.  Columbia University. Microcontact baskı malzemesi yüzeylerde desen proteinleri ve diğer molekülleri yaygın bir biçimde kullanılmaktadır. Biz fibronektin cam üzerine desen damgalama, bu sürecin temel adımları göstermektedir.

Video: 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.

Hücre Biyolojisi Degrade üreten mikroakışkan Aygıt

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

Biyoloji

Micro-scale Engineering for Cell Biology

Hücre Biyolojisi Mikro ölçekli Mühendisliği

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.

Elektron Kristalografi Yapısal Biyoloji Araştırmaları Küçük Membran Proteinleri İki boyutlu Kristalizasyon Denemeler değerlendirilmesi

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.

Canlı Hücre Görüntüleme için SNAP-tag Fusion Proteinler ifade COS-7 Floresan Etiketleme

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.

Protein Membran Kaplama Testi: Çözünür ve çözünmez Proteinler Arasında Etkileşim Test Protokolü In vitro</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.

Kalmodulin bağlayıcı Proteinler, Pull-down

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.

Büyüme Faktörü Progranulin ile etkileşimde Proteinler tanımlamak Modifiye Maya-İki Hybrid Sistemi

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.

Zebra balığı Geliştirme Sırasında Photoconvertible Proteinler kullanma Cep Takip

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.

Mikrobiyal Systems Biyoloji Chemostats Kullanımı

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.

Bir uygulama için Protokoller<em&gt; Escherichia coli</emSentetik Biyoloji&gt; Tabanlı TX-TL Hücre-Özgür İfade Sistemi

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