Authors thank Mr. Kotaro Okubo for the kind assistance with SEM imaging. This work was supported by the Japan Society for the Promotion of Science Grant-in-Aid for Basic Research (B) (20310069), Grant-in-Aid for Research Activity Start-up (25880021), and by research grants from the Kurata Memorial Hitachi Science and Technology Foundation and the Nippon Sheet Glass Foundation for Materials Science and Engineering.

1. Preparação de TiO 2 -Revestido vidro Lamela <ol><li> Número as lamelas usando um riscador de diamante. Isso ajuda não só para manter o controle de cada lamelas, mas também para garantir que o lado correto da amostra está virada para cima. Limpar as lamelas, pela primeira vez sob a executar ddH2O, seguida por imersão em solução de piranha (H 2 SO 4: H 2 O 2 = 4: 1). Após 10 minutos, enxaguar as lamelas completamente, 8 vezes em ddH 2 O. Secam-se as lamelas em fluxo de N2. </li><li> Definir TiO2 alvo no sistema de pulverização de rádio-frequência (RF). Anexar as lamelas em um suporte de amostra do dispositivo de pulverização utilizando uma fita de poliimida. Coloque o suporte de amostras na câmara de pulverização. Evacuar a câmara até a pressão atingir 2,0 x 10 -4 Pa. </li><li> Introduzir Ar gasoso para dentro da câmara e ajustar a pressão de deposição a 4,0 mTorr. Enquanto mantém o obturador fechado, aumentar gradualmentea energia RF a 70 W. </li><li> Abrir o obturador e por pulverização catódica durante 15 minutos para se obter uma película com uma espessura de 120-150 nm (Figura 1: Passo A). A velocidade de crescimento do filme necessita de ser derivada para cada máquina. </li></ol> 2. Revestimento de Superfícies com Cell-repelente Film <ol><li> Hidrofilizar a superfície de TiO 2, tratando a amostra do plasma com O 2, seguindo as instruções fornecidas pelo fabricante do reactor de plasma. Nós tratar a amostra durante 5 minutos a 200 W com O2 fluxo de 100 sccm. Mergulhe a amostra em DDH 2 O e confirmar que a superfície é superhydrophilic. Secar completamente a superfície sob fluxo de N2. </li><li> Preparar a solução 1 mM octadecyltrichlorosilane (OTS) por adição de 39,6 ul de OTS 100 ml de tolueno. Imergir a amostra na solução durante 1 h à TA. Realizar este passo dentro de um saco de luvas -filled 2 N (Figura 1: Etapa B). </li><li> Para remover moléculas physisorbed, sonicate a amostra em tolueno, acetona, etanol, e ddH2O durante 5 min cada, por essa ordem. Lavar a amostra quatro vezes em fresco ddH2O e secar a superfície sob um fluxo de N2. A superfície deve ser hidrofóbico com um ângulo de contacto de 100-110 °. </li></ol> 3. Ex-Situ Superfície Patterning <ol><li> Trabalhando em fluxo laminar capô, desenhe várias marcas de arranhões com um riscador de diamantes na superfície. As marcas de ajudar a manter o controle das regiões processados ​​e também trazendo microscópios em foco. Esteriliza-se o TiO 2 OTS-revestidos por imersão da amostra em etanol a 70% durante 5 min. Em seguida, enxaguar a amostra duas vezes em esterilizado DDH 2 O. </li><li> Colocar a amostra em um prato de 35 mm, e adicionar 2 ml de meio de crescimento PC12 (ver Passo 4.2). Incubar durante mais 3 horas num incubador de CO2 (37 ° C). Este procedimento destina-se a deixar albuminas do soro absorvem na superfície. Albuminas adsorvido inibir a adsorção posterior de outros proteins e células (Figura 1: o passo c). </li><li> Enquanto espera, configurar o microscópio de fluorescência invertido. <ol><li> Ligue a lâmpada de arco, insira o cubo filtro UV, e definir a lente objetiva de 20X. </li><li> Medir a intensidade da luz I (W cm-2) utilizando um medidor de intensidade de UV, e calcular o tempo de irradiação t (em segundos) para uma dose de d (em J cm-2) como: t = d / I. Por exemplo, para irradiar a uma dose de 200 J cm-2 utilizando uma fonte de luz de 600 mW cm de -2, é necessária a irradiação de 333 seg. </li><li> Usar um micrómetro de plataforma e fechar o diafragma de campo para definir o tamanho da região a ser irradiada, por exemplo, 200 um. </li></ol></li><li> Após a incubação de 3 horas, completar o meio com 200 mL de 3,0 mg ml -1 de colágeno tipo IV (Col-IV; finais concentração de 300 ug ml -1). </li><li> Transferir a 35 mm de prato de platina do microscópio. Encontre o zero marca, focar o microscópio sobre a superfície da amostra, e irradiar luz UV, numa dose de 200 J cm-2 (Figura 1: Passo D). A área de irradiação UV pode ser alterado quer através do ajuste da abertura do diafragma de campo ou por substituição do diafragma de campo com uma máscara metálica de geometria de arbitragem. </li><li> Substituir o meio com um meio de crescimento fresco (sem Col-IV), e colocar a amostra de volta na incubadora. </li></ol> 4. Cultura celular <ol><li> Cultura de rotina de células PC12 é levada a cabo em um prato de plástico revestidas com colagénio. <ol><li> Para revestimento de 60 mm de cultura de tecidos prato com Col-IV, primeiro molhar a superfície com DDH 2 O e aspirar tudo DDH 2 O. </li><li> Preparar 300 ng mL -1 Col-IV por diluição da solução original (3 mg ml-1) 10x com ddH 2 O. </li><li> Adicionar 200 ul de 300 ng mL -1 Col-IV por 60 mm de prato. Deixe a solução se espalhar através da superfície. </li><li> Seco tele prato em uma câmara de fluxo laminar durante aproximadamente 1 h. </li><li> Lavar a superfície duas vezes com 4 ml de solução salina tamponada com fosfato de Dulbecco (D-PBS). Quando não utilizar a placa revestida imediatamente, lavar o prato uma vez com 4 ml de DDH 2 O. Após aspiração DDH 2 O, armazenar o prato na incubadora. Tente não para mantê-lo guardado por mais de duas semanas. </li></ol></li><li> As células PC12 são cultivadas num meio de crescimento, que consiste em: meio (baixo teor de glucose) de Eagle modificado por Dulbecco solução de penicilina-estreptomicina + 1% de soro + 10% de soro fetal de bovino a 5% + cavalo. Incubar as células em uma incubadora de CO 2 (37 ° C, 5% de CO 2), e substituir metade do meio todos os outros dias. Células de passagem antes que eles atinjam confluência. <ol><li> Aspirar o meio de crescimento, e adicionar 2 ml de PBS + (D-PBS + 10 mg mL -1 de albumina de soro bovino (BSA) + EDTA a 10 mM) pré-aquecido a 37 ° C. Incubar durante 5 min a 37 ° C. Bata levemente o prato para retirar todo cells. </li><li> Recolher as células num tubo cónico de 15 ml. Lavar a placa com 3 ml de D-PBS fresco, pré-aquecido a 37 ° C. </li><li> Centrifuga-se o tubo a 150 × g durante 4 min. </li><li> Aspirar o sobrenadante e adicionar 1 ml de meio de crescimento. </li><li> Para cultura de rotina, dividir as células 1: 3 a 1: 5. </li></ol></li><li> Ao prato células na OTS / TiO 2 amostra modificada-UV, contar densidade de células e adicionar 3,0 × 10 5 células em um prato de 35 mm (Figura 1: Passo E). Incubar a placa na incubadora humidificada (37 ° C, 5% CO2) durante 1-2 dias. Tanto o factor de crescimento ingénuos e do nervo (NGF), as células PC12 -differentiated pode ser usado para as experiências de modelação. Para a diferenciação de NGF, 100 ng ml -1 de 7S-NGF é adicionado ao meio o crescimento de vários dias antes do plaqueamento das células na amostra. NGF-diferenciação parece aumentar a adhesibility das células PC12 e torna o manuseamento mais fácil, especialmente no in situ e padronizaçãoxperiments. </li></ol> 5. In Situ superfície de modelação <ol><li> Após 1-2 dias de cultura na superfície do ex-situ modificado, confirmar que as células estão a crescer e anexar apenas na região do irradiadas com UV. Defina-se o microscópio, conforme descrito no Passo 3.4. </li><li> Transferir a amostra para um novo 35-mm de placa de cultura de tecidos contendo o meio de crescimento, 100 ng ml -1 de NGF (no caso da utilização de células diferenciadas por NGF), e 100? G ml -1 Col-IV. </li><li> Coloque o prato no palco microscópio. Localizar a posição adequada e irradiar luz UV, numa dose de 200 J cm-2 (Figura 1: Passo F, G). A região permissiva recém-criado é indicado com um asterisco na Figura 1: Passo G. </li><li> Tente completar o processamento de uma única amostra no prazo de 30 min. Após a irradiação, transferir a amostra de volta para o meio sem Col-IV. </li><li> Tenha muito cuidado ao transportar o prato com cucélulas ltured e transferir a amostra do prato de prato para evitar desanexação das células estampados. </li></ol><img alt="figura 1" src="/files/ftp_upload/53045/53045fig1highres.jpg" width="700" /> Figura 1. Ilustração esquemática do processo global. Veja o texto para maiores detalhes. <a href="https://www.jove.com/files/ftp_upload/53045/53045fig1large.jpg" target="_blank">Por favor clique aqui para ver uma versão maior desta figura.</a>

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The authors have nothing to disclose.

Em nosso protocolo atual, TiO 2 filme foi formado por RF-pulverização catódica. Somos a favor deste método de deposição, uma vez que nos permite preparar de forma reprodutível um fotocatalítico TiO 2 filme com uma rugosidade sub-nm. Embora os processos de deposição por pulverização catódica são familiares aos cientistas de materiais e engenheiros eletrônicos, não pode ser bastante acessível para os biólogos. Nesse caso, o TiO 2 película revestida por rotação seria um...

Processos de litografia de semicondutores e seus derivados, tais como 1,2 - fotolitografia, litografia por feixe de electrões 3-6, e microcontact impressão 7-10 - tornaram-se agora uma ferramenta estabelecida na biologia das células para crescer as células vivas numa posição definida e geometria. O método baseia-se na modelação da utilização de substratos microfabricados, que consiste em micro-ilha de revestimento celular permissiva em um fundo não permissiva. Tal substrato serve como um modelo padrão para as células. Essas tecnologias nos forneceu os novos métodos para manipular células e sua função em um nível simples e multi-celular, para extrair as propriedades intrínsecas das células, e para aumentar a taxa de transferência com base em células de triagem de drogas 11. O grau de liberdade na modelação de células aumentariam grandemente, se a geometria do modelo padrão pode ser alterada in situ, ou seja, enquanto que as células são cultivadas sobre o Sseu rosto. Os métodos convencionais para a formação de padrão não pode ser directamente aplicados aqui, uma vez que eles processam amostras em atmosfera ou em vácuo. Por isso têm sido propostos várias novas técnicas de modificação de superfície, que se baseiam, por exemplo, em compostos fotorreactivos 12,13 ou ablação a laser 5,14, apenas para citar alguns. Os métodos propostos foram bem avaliada pelo Robertus et al. 15, e mais recentemente por Choi et al. 16 e 17 por Nakanishi. Aqui neste artigo, descreve-se um novo protocolo de modificação in situ superfície, o que tira proveito da decomposição fotocatalítica de moléculas orgânicas num dióxido de titânio (TiO2) de superfície 18,19. Neste método, é inserida uma película de TiO2 entre o substrato de vidro e o filme orgânico que faz interface das células, e o filme orgânico é decomposto in situ por localmente irradiação ultravioleta (UV)luz de uma região de interesse (λ &lt;388 nm). Mostra-se que o novo protocolo pode ser utilizado para criar micropadrões de proteínas da matriz extracelular e células vivas tanto ex situ e in situ. TiO 2 é biocompatível, quimicamente estável e opticamente transparentes, recursos de que o torna amigável para introduzir em experimentos de cultura celular. Este protocolo fornece uma alternativa ciência dos materiais à base de andaimes para a modificação de cultura celular no ambiente de cultura de células.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Glass coverslip</td>
			<td>Warner Instruments</td>
			<td>CS-15R15</td>
			<td>15 mm, #1.5 thickness</td>
		</tr>
		<tr>
			<td>Diamond scriber</td>
			<td>Ogura Jewel Industry</td>
			<td>D-Point Pen</td>
			<td></td>
		</tr>
		<tr>
			<td>RF sputtering system</td>
			<td>ANELVA</td>
			<td>SPC350</td>
			<td></td>
		</tr>
		<tr>
			<td>TiO2 sputtering target</td>
			<td>Kojundo Chemical Lab</td>
			<td>Titanium (IV) oxide, target</td>
			<td>Purity, 99.9%</td>
		</tr>
		<tr>
			<td>Plasma reactor</td>
			<td>Yamato</td>
			<td>PR301</td>
			<td></td>
		</tr>
		<tr>
			<td>n-octadecyltrichlorosilane 
			(OTS)</td>
			<td>Aldrich</td>
			<td>104817</td>
			<td></td>
		</tr>
		<tr>
			<td>Toluene</td>
			<td>Wako</td>
			<td>204-01866</td>
			<td></td>
		</tr>
		<tr>
			<td>Tissue-culture dish (35 mm)</td>
			<td>Greiner</td>
			<td>627160</td>
			<td></td>
		</tr>
		<tr>
			<td>Tissue-culture dish (60 mm)</td>
			<td>BD Falcon</td>
			<td>353002</td>
			<td></td>
		</tr>
		<tr>
			<td>Type-IV collagen</td>
			<td>Nitta Gelatin</td>
			<td>Cellmatrix Type IV</td>
			<td></td>
		</tr>
		<tr>
			<td>D-PBS</td>
			<td>Gibco</td>
			<td>14190-144</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s modified Eagle&#39;s medium (DMEM)</td>
			<td>Gibco</td>
			<td>11885-084</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal bovine serum</td>
			<td>Gibco</td>
			<td>12483-020</td>
			<td>Heat-inactivate and pass through a 0.22 mm filter before use</td>
		</tr>
		<tr>
			<td>Horse serum</td>
			<td>Gibco</td>
			<td>26050-088</td>
			<td>Pass through a 0.22 mm filter before use</td>
		</tr>
		<tr>
			<td>Penicillin-streptomycin (100x)</td>
			<td>Nacalai tesque</td>
			<td>26253-84</td>
			<td></td>
		</tr>
		<tr>
			<td>7S nerve growth factor (NGF)</td>
			<td>Alomone Labs</td>
			<td>N-130</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine serum albumin (BSA)</td>
			<td>Sigma</td>
			<td>A2153</td>
			<td></td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>Dojindo</td>
			<td>N001</td>
			<td>Stock solution in 0.5 M</td>
		</tr>
		<tr>
			<td>TiO2 nanoparticle</td>
			<td>Tayca</td>
			<td>TKD-701</td>
			<td></td>
		</tr>
	</tbody>
</table>

photopatterning proteins and cells in aqueous environment using tio2 photocatalysis

Os contaminantes orgânicos adsorvidos sobre a superfície de dióxido de titânio (TiO 2) pode ser decomposto por fotocatálise sob luz ultravioleta (UV). Descrevemos aqui um novo protocolo empregando o TiO 2 fotocatálise para alterar localmente afinidade de células da superfície do substrato. Para esta experiência, uma fina película de TiO2 era de uma lamela de vidro revestido por borrifamento, e a superfície de TiO2 foi posteriormente modificado com um derivado de organo-silano monocamada octadecyltrichlorosilane (OTS), que inibe a adesão celular. A amostra foi imersa em um meio de cultura celular, e focada luz UV foi irradiada para uma região octogonal. Quando uma linha celular de células PC12 neuronais foram plaqueadas sobre a amostra, as células aderiram apenas na área de irradiação com UV. Mostramos ainda que esta modificação da superfície pode também ser realizada in situ, ou seja, mesmo quando as células estão em crescimento sobre o substrato. Modificação adequada da superfície necessária uma matriz extracelular protein colagénio de estar presente no meio no momento da irradiação UV. A técnica aqui apresentada pode, potencialmente, ser empregues em vários tipos de células para a construção de sistemas de padronização ou co-cultura para manipular células arbitrariamente sob cultura.

A Figura 2A apresenta uma imagem de microscopia electrónica de varrimento do corte transversal (SEM) do TiO 2 filme depositado por borrifamento. A partir da observação, da espessura do filme foi estimada como sendo de aproximadamente 150 nm. Perceptível aqui é a planura do filme depositado de TiO 2. Uma análise mais aprofundada por microscopia de força atômica (AFM) revelou que a rugosidade root mean square (RMS) da superfície foi de 0,2 nm (Figura 2B). </...

Watch this Scientific Journal Video about Photopatterning Proteins and Cells in Aqueous Environment Using TiO2 Photocatalysis at JoVE.com

Photopatterning Proteins and Cells in Aqueous Environment Using TiO2 Photocatalysis

We describe a protocol for modifying cell affinity of a scaffold surface in aqueous environment. The method takes advantage of titanium dioxide photocatalysis to decompose organic film in the photo-irradiated region. We show that it can be used to create microdomains of scaffolding proteins, both ex situ and in situ.

Photopatterning proteínas e células em Aqueous Ambiente Usando TiO<sub&gt; 2</sub&gt; Photocatalysis

Organic contaminants adsorbed on the surface of titanium dioxide (TiO2) can be decomposed by photocatalysis under ultraviolet (UV) light. Here we describe ...

photopatterning-proteins-cells-aqueous-environment-using-tio2

Research

JoVE Journal

Bioengineering

Photopatterning Proteins and Cells in Aqueous Environment Using TiO2 Photocatalysis

7.8K visualizações.  Tohoku University. We describe a protocol for modifying cell affinity of a scaffold surface in aqueous environment. The method takes advantage of titanium dioxide photocatalysis to decompose organic film in the photo-irradiated region. We show that it can be used to create microdomains of scaffolding proteins, both ex situ and in situ.

Vídeo: Photopatterning Proteins and Cells in Aqueous Environment Using TiO2 Photocatalysis

Fabrication of Electrochemical-DNA Biosensors for the Reagentless Detection of Nucleic Acids, Proteins and Small Molecules

As medicine is currently practiced, doctors send specimens to a central laboratory for testing and thus must wait hours or days to 
receive the results. Many patients would be better served by rapid, bedside tests. To this end our laboratory and others have developed a versatile, reagentless 
biosensor platform that supports the quantitative, reagentless, electrochemical detection of nucleic acids (DNA, RNA), proteins (including antibodies) and small 
molecules analytes directly in unprocessed clinical and environmental samples. In this video, we demonstrate the preparation and use of several biosensors in this 
"E-DNA" class. In particular, we fabricate and demonstrate sensors for the detection of a target DNA sequence in a polymerase chain reaction mixture, an HIV-specific antibody and the drug cocaine. The preparation procedure requires only three hours of hands-on effort followed by an overnight incubation, and their use requires only minutes.

"E-DNA" sensors, reagentless, electrochemical biosensors that perform well even when challenged directly in blood and other complex matrices, have been adapted to the detection of a wide range of nucleic acid, protein and small molecule analytes. Here we present a general procedure for the fabrication and use of such sensors.

Fabricação de Eletroquímica-DNA Biossensores para Detecção Reagentless de ácidos nucléicos, proteínas e pequenas moléculas

As medicine is currently practiced, doctors send specimens to a central laboratory for testing and thus must wait hours or days to 
receive the results. ...

Bioengenharia

Visualizing Proteins and Macromolecular Complexes by Negative Stain EM: from Grid Preparation to Image Acquisition

Single particle electron microscopy (EM), of both negative stained or frozen hydrated biological samples, has become a versatile tool in structural biology 1. In recent years, this method has achieved great success in studying structures of proteins and macromolecular complexes 2, 3. Compared with electron cryomicroscopy (cryoEM), in which frozen hydrated protein samples are embedded in a thin layer of vitreous ice 4, negative staining is a simpler sample preparation method in which protein samples are embedded in a thin layer of dried heavy metal salt to increase specimen contrast 5. The enhanced contrast of negative stain EM allows examination of relatively small biological samples. In addition to determining three-dimensional (3D) structure of purified proteins or protein complexes 6, this method can be used for much broader purposes. For example, negative stain EM can be easily used to visualize purified protein samples, obtaining information such as homogeneity/heterogeneity of the sample, formation of protein complexes or large assemblies, or simply to evaluate the quality of a protein preparation.
In this video article, we present a complete protocol for using an EM to observe negatively stained protein sample, from preparing carbon coated grids for negative stain EM to acquiring images of negatively stained sample in an electron microscope operated at 120kV accelerating voltage. These protocols have been used in our laboratory routinely and can be easily followed by novice users.

Visualizing protein samples by negative stain electron microscopy (EM) has become a popular structural analysis method. It is useful for quantitative structural analysis, such as calculating a 3D reconstruction of the molecules being studied, and also for qualitative examination of the quality of protein preparations. In this article we present detailed protocols for preparing the EM grids, staining the sample and visualizing the sample in an electron microscope. Novice users can follow these protocols easily and to utilize negative stain EM as a routine assay, in addition to other biochemical assays, for evaluating their protein samples.

Visualizando Proteínas e Complexos Macromoleculares por Negative EM Stain: Preparação de Grid para Aquisição de Imagem

Single particle electron microscopy (EM), of both negative stained or frozen hydrated biological samples, has become a versatile tool in structural ...

Live-cell Imaging of Migrating Cells Expressing Fluorescently-tagged Proteins in a Three-dimensional Matrix

Traditionally, cell migration has been studied on two-dimensional, stiff plastic surfaces. However, during important biological processes such as wound healing, tissue regeneration, and cancer metastasis, cells must navigate through complex, three-dimensional extracellular tissue. To better understand the mechanisms behind these biological processes, it is important to examine the roles of the proteins responsible for driving cell migration. Here, we outline a protocol to study the mechanisms of cell migration using the epithelial cell line (MDCK), and a three-dimensional, fibrous, self-polymerizing matrix as a model system. This optically clear extracellular matrix is easily amenable to live-cell imaging studies and better mimics the physiological, soft tissue environment. This report demonstrates a technique for directly visualizing protein localization and dynamics, and deformation of the surrounding three-dimensional matrix. 
Examination of protein localization and dynamics during cellular processes provides key insight into protein functions. Genetically encoded fluorescent tags provide a unique method for observing protein localization and dynamics. Using this technique, we can analyze the subcellular accumulation of key, force-generating cytoskeletal components in real-time as the cell maneuvers through the matrix. In addition, using multiple fluorescent tags with different wavelengths, we can examine the localization of multiple proteins simultaneously, thus allowing us to test, for example, whether different proteins have similar or divergent roles. Furthermore, the dynamics of fluorescently tagged proteins can be quantified using Fluorescent Recovery After Photobleaching (FRAP) analysis. This measurement assays the protein mobility and how stably bound the proteins are to the cytoskeletal network.
By combining live-cell imaging with the treatment of protein function inhibitors, we can examine in real-time the changes in the distribution of proteins and morphology of migrating cells. Furthermore, we also combine live-cell imaging with the use of fluorescent tracer particles embedded within the matrix to visualize the matrix deformation during cell migration. Thus, we can visualize how a migrating cell distributes force-generating proteins, and where the traction forces are exerted to the surrounding matrix. Through these techniques, we can gain valuable insight into the roles of specific proteins and their contributions to the mechanisms of cell migration.

Cellular processes such as cell migration have traditionally been studied on two-dimensional, stiff plastic surfaces. This report describes a technique for directly visualizing protein localization and analyzing protein dynamics in cells migrating in a more physiologically relevant, three-dimensional matrix.

Em células vivas, imagens de células que expressam proteínas fluorescentes Migrando-marcado em uma matriz tridimensional

Traditionally, cell migration has been studied on two-dimensional, stiff plastic surfaces. However, during important biological processes such as wound ...

A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments

This work puts forward a toolkit that enables the conversion of alkanes by Escherichia coli and presents a proof of principle of its applicability. The toolkit consists of multiple standard interchangeable parts (BioBricks)9 addressing the conversion of alkanes, regulation of gene expression and survival in toxic hydrocarbon-rich environments.
A three-step pathway for alkane degradation was implemented in E. coli to enable the conversion of medium- and long-chain alkanes to their respective alkanols, alkanals and ultimately alkanoic-acids. The latter were metabolized via the native &beta;-oxidation pathway. To facilitate the oxidation of medium-chain alkanes (C5-C13) and cycloalkanes (C5-C8), four genes (alkB2, rubA3, rubA4and rubB) of the alkane hydroxylase system from Gordonia sp. TF68,21 were transformed into E. coli. For the conversion of long-chain alkanes (C15-C36), theladA gene from Geobacillus thermodenitrificans was implemented. For the required further steps of the degradation process, ADH and ALDH (originating from G. thermodenitrificans) were introduced10,11. The activity was measured by resting cell assays. For each oxidative step, enzyme activity was observed.
To optimize the process efficiency, the expression was only induced under low glucose conditions: a substrate-regulated promoter, pCaiF, was used. pCaiF is present in E. coli K12 and regulates the expression of the genes involved in the degradation of non-glucose carbon sources.
The last part of the toolkit - targeting survival - was implemented using solvent tolerance genes, PhPFD&alpha; and &beta;, both from Pyrococcus horikoshii OT3. Organic solvents can induce cell stress and decreased survivability by negatively affecting protein folding. As chaperones, PhPFD&alpha; and &beta; improve the protein folding process e.g. under the presence of alkanes. The expression of these genes led to an improved hydrocarbon tolerance shown by an increased growth rate (up to 50%) in the presences of 10% n-hexane in the culture medium were observed.
Summarizing, the results indicate that the toolkit enables E. coli to convert and tolerate hydrocarbons in aqueous environments. As such, it represents an initial step towards a sustainable solution for oil-remediation using a synthetic biology approach.

A sustainable auto regulating bacterial system for the remediation of oil pollutions was designed using standard interchangeable DNA parts (BioBricks). An engineered E. coli strain was used to degrade alkanes via &beta;-oxidation in toxic aqueous environments. The respective enzymes from different species showed alkane degradation activity. Additionally, an increased tolerance to n-hexane was achieved by introducing genes from alkane-tolerant bacteria.

Um kit de ferramentas para permitir a conversão de hidrocarbonetos em ambientes aquosos

This work puts forward a toolkit that enables the conversion of alkanes by Escherichia coli and presents a proof of principle of its applicability. The ...

Time-lapse Fluorescence Imaging of Arabidopsis Root Growth with Rapid Manipulation of The Root Environment Using The RootChip

The root functions as the physical anchor of the plant and is the organ responsible for uptake of water and mineral nutrients such as nitrogen, phosphorus, sulfate and trace elements that plants acquire from the soil. If we want to develop sustainable approaches to producing high crop yield, we need to better understand how the root develops, takes up a wide spectrum of nutrients, and interacts with symbiotic and pathogenic organisms. To accomplish these goals, we need to be able to explore roots in microscopic detail over time periods ranging from minutes to days.
We developed the RootChip, a polydimethylsiloxane (PDMS)- based microfluidic device, which allows us to grow and image roots from Arabidopsis seedlings while avoiding any physical stress to roots during preparation for imaging1 (Figure 1). The device contains a bifurcated channel structure featuring micromechanical valves to guide the fluid flow from solution inlets to each of the eight observation chambers2. This perfusion system allows the root microenvironment to be controlled and modified with precision and speed. The volume of the chambers is approximately 400 nl, thus requiring only minimal amounts of test solution.
Here we provide a detailed protocol for studying root biology on the RootChip using imaging-based approaches with real time resolution. Roots can be analyzed over several days using time lapse microscopy. Roots can be perfused with nutrient solutions or inhibitors, and up to eight seedlings can be analyzed in parallel. This system has the potential for a wide range of applications, including analysis of root growth in the presence or absence of chemicals, fluorescence-based analysis of gene expression, and the analysis of biosensors, e.g. FRET nanosensors3.

This article provides a protocol for cultivation of Arabidopsis seedlings in the RootChip, a microfluidic imaging platform that combines automated control of growth conditions with microscopic root monitoring and FRET-based measurement of intracellular metabolite levels.

Time-lapse imagens de fluorescência de crescimento de raiz Arabidopsis com Manipulação acelerada do meio root usando o RootChip

The root functions as the physical anchor of the plant and is the organ responsible for uptake of water and mineral nutrients such as nitrogen, ...

Cell Co-culture Patterning Using Aqueous Two-phase Systems

Cell patterning technologies that are fast, easy to use and affordable will be required for the future development of high throughput cell assays, platforms for studying cell-cell interactions and tissue engineered systems. This detailed protocol describes a method for generating co-cultures of cells using biocompatible solutions of dextran (DEX) and polyethylene glycol (PEG) that phase-separate when combined above threshold concentrations. Cells can be patterned in a variety of configurations using this method. Cell exclusion patterning can be performed by printing droplets of DEX on a substrate and covering them with a solution of PEG containing cells. The interfacial tension formed between the two polymer solutions causes cells to fall around the outside of the DEX droplet and form a circular clearing that can be used for migration assays. Cell islands can be patterned by dispensing a cell-rich DEX phase into a PEG solution or by covering the DEX droplet with a solution of PEG. Co-cultures can be formed directly by combining cell exclusion with DEX island patterning. These methods are compatible with a variety of liquid handling approaches, including manual micropipetting, and can be used with virtually any adherent cell type.

Aqueous two-phase systems were used to simultaneously pattern multiple populations of cells. This fast and easy method for cell patterning takes advantage of the phase separation of aqueous solutions of dextran and polyethylene glycol and the interfacial tension that exists between the two polymer solutions.

Padronização de células co-cultura Usando duas fases aquosas Sistemas

Cell patterning  technologies that are fast, easy to use and affordable will be required for the  future development of high throughput cell assays, ...

Transplantation of Induced Pluripotent Stem Cell-derived Mesoangioblast-like Myogenic Progenitors in Mouse Models of Muscle Regeneration

Patient-derived iPSCs could be an invaluable source of cells for future autologous cell therapy protocols. iPSC-derived myogenic stem/progenitor cells similar to pericyte-derived mesoangioblasts (iPSC-derived mesoangioblast-like stem/progenitor cells: IDEMs) can be established from iPSCs generated from patients affected by different forms of muscular dystrophy. Patient-specific IDEMs can be genetically corrected with different strategies (e.g. lentiviral vectors, human artificial chromosomes) and enhanced in their myogenic differentiation potential upon overexpression of the myogenesis regulator MyoD. This myogenic potential is then assessed in vitro with specific differentiation assays and analyzed by immunofluorescence. The regenerative potential of IDEMs is further evaluated in vivo, upon intramuscular and intra-arterial transplantation in two representative mouse models displaying acute and chronic muscle regeneration. The contribution of IDEMs to the host skeletal muscle is then confirmed by different functional tests in transplanted mice. In particular, the amelioration of the motor capacity of the animals is studied with treadmill tests. Cell engraftment and differentiation are then assessed by a number of histological and immunofluorescence assays on transplanted muscles. Overall, this paper describes the assays and tools currently utilized to evaluate the differentiation capacity of IDEMs, focusing on the transplantation methods and subsequent outcome measures to analyze the efficacy of cell transplantation.

Induced pluripotent stem cell (iPSC)-derived myogenic progenitors are promising candidates for cell therapy strategies to treat muscular dystrophies. This protocol describes transplantation and functional measurements required to evaluate the engraftment and differentiation of iPSC-derived mesoangioblasts (a type of muscle progenitors) in mouse models of acute and chronic muscle regeneration.

Transplante de Progenitores Miogênicos derivados de células-tronco pluripotentes induzidos em modelos de regeneração muscular

Patient-derived iPSCs could be an invaluable source of cells for future autologous cell therapy protocols. iPSC-derived myogenic stem/progenitor cells ...

Luminescence Resonance Energy Transfer to Study Conformational Changes in Membrane Proteins Expressed in Mammalian Cells

Luminescence Resonance Energy Transfer, or LRET, is a powerful technique used to measure distances between two sites in proteins within the distance range of 10-100 &#197;. By measuring the distances under various ligated conditions, conformational changes of the protein can be easily assessed. With LRET, a lanthanide, most often chelated terbium, is used as the donor fluorophore, affording advantages such as a longer donor-only emission lifetime, the flexibility to use multiple acceptor fluorophores, and the opportunity to detect sensitized acceptor emission as an easy way to measure energy transfer without the risk of also detecting donor-only signal. Here, we describe a method to use LRET on membrane proteins expressed and assayed on the surface of intact mammalian cells. We introduce a protease cleavage site between the LRET fluorophore pair. After obtaining the original LRET signal, cleavage at that site removes the specific LRET signal from the protein of interest allowing us to quantitatively subtract the background signal that remains after cleavage. This method allows for more physiologically relevant measurements to be made without the need for purification of protein.

We describe here an improved Luminescence Resonance Energy Transfer (LRET) method where we introduce a protease cleavage site between the donor and acceptor fluorophore sites. This modification allows us to obtain specific LRET signals arising from membrane proteins of interest, allowing for the study of membrane proteins without protein purification.

Luminescência Ressonância transferência de energia para estudar mudanças conformacionais na membrana proteínas expressas em células de mamíferos

Luminescence Resonance Energy Transfer, or LRET, is a powerful technique used to measure distances between two sites in proteins within the distance range ...

Aqueous Droplets Used as Enzymatic Microreactors and Their Electromagnetic Actuation

For the successful implementation of microfluidic reaction systems, such as PCR and electrophoresis, the movement of small liquid volumes is essential. In conventional lab-on-a-chip-platforms, solvents and samples are passed through defined microfluidic channels with complex flow control installations. The droplet actuation platform presented here is a promising alternative. With it, it is possible to move a liquid drop (microreactor) on a planar surface of a reaction platform (lab-in-a-drop). The actuation of microreactors on the hydrophobic surface of the platform is based on the use of magnetic forces acting on the outer shell of the liquid drops which is made of a thin layer of superhydrophobic magnetite particles. The hydrophobic surface of the platform is needed to avoid any contact between the liquid core and the surface to allow a smooth movement of the microreactor. On the platform, one or more microreactors with volumes of 10 &#181;L can be positioned and moved simultaneously. The platform itself consists of a 3 x 3 matrix of electrical double coils which accommodate either neodymium or iron cores. The magnetic field gradients are automatically controlled. By variation of the magnetic field gradients, the microreactors' magnetic hydrophobic shell can be manipulated automatically to move the microreactor or open the shell reversibly. Reactions of substrates and corresponding enzymes can be initiated by merging the microreactors or bringing them into contact with surface immobilized catalysts.

Lab-in-a-drop reaction systems allow the versatile implementation of complex reactions in a microfluidic scale. An automated actuation platform consisting of a 3 x 3 matrix of electromagnetic coils was developed and successfully used to merge two 10 &#181;L microreactors and thereby initiate an enzymatic reaction in the resulting liquid marbles.

Aquosas gotículas usadas como Microreactors enzimática e sua atuação eletromagnética

For the successful implementation of microfluidic reaction systems, such as PCR and electrophoresis, the movement of small liquid volumes is essential. In ...

A Versatile Method of Patterning Proteins and Cells

Substrate and cell patterning techniques are widely used in cell biology to study cell-to-cell and cell-to-substrate interactions. Conventional patterning techniques work well only with simple shapes, small areas and selected bio-materials. This article describes a method to distribute cell suspensions as well as substrate solutions into complex, long, closed (dead-end) polydimethylsiloxane (PDMS) microchannels using negative pressure. This method enables researchers to pattern multiple substrates including fibronectin, collagen, antibodies (Sal-1), poly-D-lysine (PDL), and laminin. Patterning of substrates allows one to indirectly pattern a variety of cells. We have tested C2C12 myoblasts, the PC12 neuronal cell line, embryonic rat cortical neurons, and amphibian retinal neurons. In addition, we demonstrate that this technique can directly pattern fibroblasts in microfluidic channels via brief application of a low vacuum on cell suspensions. The low vacuum does not significantly decrease cell viability as shown by cell viability assays. Modifications are discussed for application of the method to different cell and substrate types. This technique allows researchers to pattern cells and proteins in specific patterns without the need for exotic materials or equipment and can be done in any laboratory with a vacuum.

This report describes a simple, easy to perform technique, using low pressure vacuum, to fill microfluidic channels with cells and substrates for biological research.

Um método versátil de padronização proteínas e células

Substrate and cell patterning techniques are widely used in cell biology to study cell-to-cell and cell-to-substrate interactions. Conventional patterning ...