Os autores reconhecem a assistência de Ander Lopez e Miren Telletxea para gravação e edição de vídeo. ACR é financiado por uma bolsa de Ikerbasque e um projeto de pesquisa do Asociación de Celiacos de Madrid (ACM). Orc é financiado pelo projeto ISCIII-PI16/00258 e co-financiado pela União Europeia FEDER/FSE "Uma maneira de tornar a Europa". É é financiado por uma concessão do projeto de pesquisa 2015111068 do departamento de saúde Basco. IRG e AJM são suportados pelo companheirismo predoctoral subvenções provenientes da UPV/EHU e o departamento de educação de Basco, respectivamente.

Este estudo foi aprovado pelo Conselho de ética Cruces University Hospital e as análises foram realizadas após consentimento informado foi obtido de todas as disciplinas ou seus pais.
1. biópsia coleção
Nota: Amostras de biópsia do duodeno distal de pacientes são obtidas durante endoscopia de rotina de diagnóstico, gerenciamento de biópsias que variam entre 2 e 10 mg de peso. Uma biópsia tecido é um tecido complexo composto por diferentes tipos de células incluindo células epiteliais, imunes e endoteliais. Gastroenterologistas clínicas realizar a endoscopia elaboradas diretrizes clínicas.
<ol><li>Coloque a biópsia em um papel de filtro estéril só depois da endoscopia.</li>
	<li>Use fórceps para transferir as biópsias em tubos de 1,5 mL, embeba-os com PBS e colocá-lo em um criotubo.</li>
	<li>Manter os tubos em gelo até a chegada no laboratório.<ol>
<li>Inicie o processamento de biópsias frescas imediatamente.</li>
	</ol>
</li>
	<li>Para biópsias congeladas, flash congelar a biópsia contendo tubos e armazenar em nitrogênio líquido até o uso. Nota: É importante manter a amostra congelada até que o buffer complementado frio 1 é adicionado.</li>
</ol>2. tampão preparação
Nota: Antes de começar, complementar os buffers como segue.
<ol><li>Adicionar 1 mM DTT (concentração final) e protease e fosfatase inibidor cocktail (1 x concentração final) para o buffer hipotônica hipertônico e 1 tampão 2 (tabela 1).<ol>
<li>Prepare-se 1,5 mL de tampão 1 e 150 µ l de tampão de 2 por amostra. DTT impede a oxidação das amostras.</li>
	</ol>
</li>
	<li>Prepare núcleos de tampão de lavagem, acrescentando 1% de detergente (nonilo phenoxypolyethoxylethanol) a uma concentração final de 0,1% para a reserva já completada 1. Prepare-se 1 mL de tampão de lavagem núcleos por amostra.</li>
</ol>3. biópsia homogeneização
<ol><li>
Biópsias de frescas
	<ol>
<li>Coloque o pilão descartável no misturador motorizado. Certifique-se de que o pilão atinge o fundo do tubo.</li>
		<li>Tirar a biópsia do criotubo e colocá-lo em um tubo de 1,5 mL com uma ponta da pipeta.</li>
		<li>Adicione 200 µ l de tampão completado 1 para o tubo de 1,5 mL.</li>
		<li>Homogeneizar a biópsia com o pilão, até que o tecido é completamente interrompido e mantê-lo no gelo.</li>
		<li>Uma vez que todas as biópsias são homogeneizadas proceda com o passo 4. Nota: Macacos descartáveis devem ser alterados entre biópsias.</li>
	</ol>
</li>
	<li>
Biópsias congeladas Atenção: Cuidado com nitrogênio líquido; contato de nitrogênio líquido com a pele ou olhos pode causar lesões graves de congelação. Protege as mãos e os olhos sempre quando se trabalha com nitrogênio líquido.<ol>
<li>Leve o nitrogênio líquido em uma caixa para armazenar o cryotubes obtido o tanque de nitrogênio.</li>
		<li>Encontrar a biópsia no tanque de nitrogênio e coloque o criotubo na caixa com o nitrogênio líquido. Repita este passo para todas as biópsias.</li>
		<li>Transfira a biópsia do criotubo para um tubo de 1,5 mL. Nota: Biópsias serão anexadas ao tubo congelado. Empurre a biópsia com uma ponta de pipeta estéril para que ele irá desanexar do tubo.</li>
		<li>Adicione 200 µ l de tampão completado 1.</li>
		<li>Homogeneizar o tecido usando o pilão e almofariz, até que o tecido é completamente interrompido, manter a temperatura a 4 ° C ao longo de todo o procedimento. Nota: Não deixe biópsias descongelar antes de adicionar o buffer.</li>
	</ol>
</li>
</ol>4. o citoplasma isolamento
<ol><li>Incube a biópsia homogeneizada no gelo por 10 min.</li>
	<li>Adicione 10 µ l de 1% de detergente (nonilo phenoxypolyethoxylethanol) para cada amostra a uma concentração final de 0,05%. Nota: Células vão inchar e explodir por lise osmótica como o detergente vai interromper a membrana celular.</li>
	<li>Incube no gelo por 5 minutos.</li>
	<li>Vórtice brevemente e centrifugar 400 x g a 4 ˚ c por 2 min.</li>
	<li>Após a utilização do vortex, remover o sobrenadante e transferir para um novo tubo limpo 1,5 mL; Esta será a fração citoplasmática. Não jogue fora a pelota.</li>
</ol>5. nuclear isolamento
<ol><li>Resuspenda o pellet da etapa anterior com 200 µ l de tampão de lavagem de núcleos.</li>
	<li>Centrifugar o tubo por 2 min em 400 x g e 4 ° C.</li>
	<li>Desprezar o sobrenadante e repita o procedimento de lavagem mais duas vezes. Nota: As lavagens irão remover a contaminação citoplasmática na fração nuclear.</li>
	<li>Após a terceira lavagem, resuspenda o pellet em 100 µ l de tampão de 2.</li>
	<li>Agitar vigorosamente a amostra no 4 ˚ c por 30 min. como alternativa, incubar a amostra em gelo e vórtice cada 5 min.</li>
	<li>Após agitação, centrifugar a amostra durante 10 minutos na velocidade máxima (> 12.000 x g) e 4 ° C.</li>
	<li>Após a utilização do vortex, transferi o sobrenadante para um novo 1.5 limpo. tubo mL. Esta será a fração nuclear.</li>
</ol>6. quantificação da proteína
Nota: Quantificar as proteínas com um kit de ensaio de proteína do ácido (BCA) do bicinchoninic. A concentração de proteínas em frações irá variar entre 0,5 e 5 µ g / µ l, sendo menor na fração nuclear (ver tabela 2 para as concentrações de proteína resultantes de biópsias de 2mg).
<ol><li>Preparar uma curva padrão com o seguinte de montantes (µ g) de albumina de soro bovino (BSA)12: 0-0.5-1-2-3-4-5-6.</li>
	<li>Prepare os reagentes necessários para a utilização de 100 µ l de mistura final do BCA por amostra.</li>
	<li>Pipetar 2 µ l de cada fração de proteína em uma placa de 96 bem, adicione a mistura do BCA e siga as instruções do fabricante para a leitura.</li>
</ol>

<ol>
	<li>Cox, B., Emili, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tissue+subcellular+fractionation+and+protein+extraction+for+use+in+mass-spectrometry-based+proteomics.">Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomics.</a> Nature Protocols. 1 (4), 1872-1878 (2006).</li><li>Itzhak, D. N., Tyanova, S., Cox, J., Borner, G. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Global,+quantitative+and+dynamic+mapping+of+protein+subcellular+localization.">Global, quantitative and dynamic mapping of protein subcellular localization.</a> eLife. 5, (2016).</li><li>Preedy, V. R., Watson, R. R., Ronald, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Methods in disease investigating the gastrointestinal tract. , (1998).</li><li>Alex, P., Gucek, M., Li, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Applications+of+proteomics+in+the+study+of+inflammatory+bowel+diseases:+Current+status+and+future+directions+with+available+technologies.">Applications of proteomics in the study of inflammatory bowel diseases: Current status and future directions with available technologies.</a> Inflammatory bowel diseases. 15 (4), 616-629 (2009).</li><li>Ericsson, C., Franz&#233;n, B., Nist&#233;r, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Frozen+tissue+biobanks.+Tissue+handling,+cryopreservation,+extraction,+and+use+for+proteomic+analysis.">Frozen tissue biobanks. Tissue handling, cryopreservation, extraction, and use for proteomic analysis.</a> Acta oncologica (Stockholm, Sweden). 45 (6), 643-661 (2006).</li><li>Hoffmann, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=New+application+of+a+subcellular+fractionation+method+to+kidney+and+testis+for+the+determination+of+conjugated+linoleic+acid+in+selected+cell+organelles+of+healthy+and+cancerous+human+tissues.">New application of a subcellular fractionation method to kidney and testis for the determination of conjugated linoleic acid in selected cell organelles of healthy and cancerous human tissues.</a> Analytical and Bioanalytical Chemistry. 381 (6), 1138-1144 (2005).</li><li>Foster, L. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Mammalian+Organelle+Map+by+Protein+Correlation+Profiling.">A Mammalian Organelle Map by Protein Correlation Profiling.</a> Cell. 125 (1), 187-199 (2006).</li><li>Baghirova, S., Hughes, B. G., Hendzel, M. J., Schulz, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sequential+fractionation+and+isolation+of+subcellular+proteins+from+tissue+or+cultured+cells.">Sequential fractionation and isolation of subcellular proteins from tissue or cultured cells.</a> MethodsX. 2, e440-e445 (2015).</li><li>B&#246;rner, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Subcellular+protein+extraction+from+human+pancreatic+cancer+tissues.">Subcellular protein extraction from human pancreatic cancer tissues.</a> BioTechniques. 46 (4), 297-304 (2009).</li><li>Antalis, T. M., Shea-Donohue, T., Vogel, S. N., Sears, C., Fasano, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanisms+of+disease:+protease+functions+in+intestinal+mucosal+pathobiology.">Mechanisms of disease: protease functions in intestinal mucosal pathobiology.</a> Nature clinical practice. Gastroenterology. 4 (7), 393-402 (2007).</li><li>Cutler, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Protein purification protocols. , (2004).</li><li>Walker, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Bicinchoninic+Acid+(BCA)+Assay+for+Protein+Quantitation.">The Bicinchoninic Acid (BCA) Assay for Protein Quantitation.</a> The Protein Protocols Handbook. , 11-14 (1996).</li><li>McLane, L. 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Os autores não têm nada para divulgar.

O protocolo descrito aqui é usado para o fraccionamento nuclear e citoplasmático de biópsias intestinais. As proteínas purificadas não são desnaturadas e pode ser usadas não apenas na análise ocidental do borrão como mostrado na Figura 2 e 3 , mas também em ensaios que exigem nativo-dobrado proteínas tais como imunoprecipitação, ensaio de turno de mobilidade electrophoretic (EMSA) ou eletroforese em gel de poliacrilamida nativo (página).
<p class="jove_cont...

As proteínas participam de quase todas as funções biológicas, dentro de uma célula e qualquer variação em sua estrutura, quantidade ou localização pode levar a um cenário de patogenicidade. Métodos de fracionamento de amostras de tecido são uma abordagem útil para reduzir a complexidade da doença relacionadas com análises de proteína. Alguns estudos usam informações de localização de proteínas ou enriquecem uma proteína de um compartimento celular específico, por um protocolo para reprodutível fraccionamento das proteínas intactas, é útil para responder a certas perguntas biológicas. Determinar a Localização subcellular das proteínas e monitorando sua redistribuição compartimental ou interações no basal e condições de doença ajudará a identificar a doença relacionadas com diferenças funcionais1,2. Assim, este método visa reproducibly fractionate biópsias do tecido intestinal, frescas e congeladas, em compartimentos subcellular citoplasmáticos e nucleares.
Amostras de biópsia intestinal são rotineiramente obtidas durante os procedimentos de endoscopia3 (Figura 1) e podem ser efetivamente usadas para quantificação de proteína ou estudos de imunoprecipitação. Desde que as amostras de tecido da intestinal epiteliais conterá proteínas que podem estar diretamente envolvidas na patogênese doença4, amostras de biópsia intestinal são uma fonte muito valiosa para a identificação de sucesso de específica da doença intestinal proteínas. Amostras de tecido congelado, paciente armazenado juntamente com as informações clínicas são recursos úteis para análise de proteínas, e uma preparação de amostras simples e reprodutível é uma questão-chave para fornecer informações compartimental célula usando quantidades limitantes de congelados tecido de5.
Existem vários kits disponíveis comercialmente para a separação de frações celulares, mas estes são mais caros e geralmente mais demorado do que o protocolo aqui apresentado. Protocolos com base em várias etapas centrifugação gradiente e gradientes contínuas também têm sido usados anteriormente para o fraccionamento de diversos compartimentos celulares em diferentes tecidos6,7. No entanto, manter a consistência dos gradientes contínuos é muitas vezes uma tarefa difícil. Protocolos semelhantes baseados o lysis sequencial das membranas têm sido descritos anteriormente mas geralmente precisam de mais de dois buffers e nas mãos na hora é mais8 .
Quando as amostras de tecido de fraccionamento, tenha em mente que o tecido amostras presentes célula-célula e célula-matriz interações que são não presentes em culturas de células e importante quando proceder à extração de proteínas. A repartição adequada entre células e matriz extracelular, sem afetar a qualidade da proteína será um fator crítico do tecido intestinal da proteína isolamento9. Neste protocolo, célula-célula e célula-matriz de contatos primeiro são quebrados, liberando as células e permitindo que o buffer alcançar as células individuais. Para evitar a proteína-compartimento de mistura antes de fracionamento, a repartição dos contatos deve ocorrer sem alterar a integridade das células ou as membranas nucleares.
Devido o enriquecimento de várias proteases na mucosa intestinal10, é importante controlar a degradação proteica durante a extração. Para minimizar a potencial degradação proteica, inibidor de protease múltipla deve ser incluído nos buffers de extração de proteínas. Além disso, se extratos vão ser utilizados para os ensaios funcionais, é essencial para evitar a desnaturação das proteínas ou proteólise, pois isto causará uma perda de proteína atividade11. Para este efeito, o protocolo é realizado a 4 ° C e fluoreto de phenylmethylsulfonyl fresco (PMSF) é adicionado aos buffers em uma concentração final de 0,1 mM apenas antes da utilização para inibir ainda mais a proteólise.
O primeiro passo no fracionamento celular é rompimento de tecido e lise celular. Como mencionado anteriormente, o objetivo é desagregar as células e quebra-los abrir com o mínimo de dano. Amostras de tecido intestinal devem ser homogeneizadas, e as células lysed para alcançar a máxima quebra da membrana celular. Neste protocolo, utilizamos um misturador motorizado pilão para quebrar o tecido intestinal que é homogeneizado em poucos segundos por meio de ação de alta velocidade num Vortex. Após a homogeneização, células do tecido são incubadas em um buffer hipotônica que vai estourar a membrana da célula, mas irá manter os núcleos intactos, seguido pela adição de um detergente não-desnaturação (nonilo phenoxypolyethoxylethanol) e um vórtice curto para separar os núcleos da fração citoplasmática. Após a remoção do citoplasma, a membrana do núcleo celular é de ruptura em um buffer hipertônico com agitação.
O método apresentado aqui é um método adequado para o fraccionamento subcelular de frescos e congelados de biópsias intestinais que foram obtidos durante os procedimentos endoscópicos e intervalo entre 2 e 10 mg de peso. O protocolo é fácil e pode ser reproduzido e pode ser realizado utilizando equipamentos básicos de laboratório e reagentes em menos de uma hora.

<table border="0" cellpadding="0" cellspacing="0" style="width:657px;" width="658">
	<tbody>
		<tr height="22">
			<td height="22" style="height:23px;width:244px;">HEPES</td>
			<td style="width:128px;">Sigma Aldrich</td>
			<td style="width:119px;">H4034-1kg</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:23px;width:244px;">KCl</td>
			<td style="width:128px;">Sigma Aldrich</td>
			<td style="width:119px;">P9333-1kg</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:23px;width:244px;">EDTA</td>
			<td style="width:128px;">Sigma Aldrich</td>
			<td style="width:119px;">E9884-100G</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:23px;width:244px;">NaCl</td>
			<td style="width:128px;">Sigma Aldrich</td>
			<td style="width:119px;">5588886-1kg</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:23px;width:244px;">DTT</td>
			<td style="width:128px;">Sigma Aldrich</td>
			<td style="width:119px;">10197777001</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:23px;width:244px;">PMSF</td>
			<td style="width:128px;">Thermo Scientific</td>
			<td style="width:119px;">36978</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:23px;width:244px;">Proteinase and phosphatase inhibitors</td>
			<td style="width:128px;">Thermo Scientific</td>
			<td style="width:119px;">A32959</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:23px;width:244px;">NP-40&#160;</td>
			<td style="width:128px;">Sigma Aldrich</td>
			<td style="width:119px;">CA-630</td>
			<td>Detergent</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:23px;width:244px;">BCA assay</td>
			<td style="width:128px;">Thermo Scientific</td>
			<td style="width:119px;">23227</td>
			<td>Protein quantification kit</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:23px;width:244px;">Disposable plastic pestles</td>
			<td style="width:128px;">Sigma Aldrich</td>
			<td style="width:119px;">Z359947-100EA</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:23px;width:244px;">Dounce homogeneizer</td>
			<td style="width:128px;">VWR</td>
			<td style="width:119px;">431-0100</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:23px;width:244px;">Microcentrifuge</td>
			<td style="width:128px;">Eppendorf</td>
			<td style="width:119px;">5415-R</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:23px;width:244px;">Shacker</td>
			<td style="width:128px;">IKA</td>
			<td style="width:119px;">MS3 basic</td>
			<td></td>
		</tr>
	</tbody>
</table>

subcellular fractionation from fresh and frozen gastrointestinal specimens

O propósito do presente protocolo é para fracionar o tecido intestinal humano obtido por endoscopia em compartimentos nucleares e citoplasmáticos para a análise de localização de proteínas específicas ou complexos de proteínas em Estados diferentes de tecido (ou seja, saudável versus doença). Este método é útil para o fraccionamento de ambas as amostras de tecido intestinal frescos e congelados; é facilmente acessível para todos os laboratórios e não demorado.

A Figura 1 mostra uma coloração de eosina hematoxilina de uma seção de biópsia intestinal com vilosidades intactas e estruturas de cripta.
Resultados representativos de fracionamento nuclear e citoplasmático, usando este protocolo são mostrados nas figuras 2 e 3. No experimento mostrado na Figura 2, um fresco (Fh) e um congelado ...

Watch this Scientific Journal Video about Subcellular Fractionation from Fresh and Frozen Gastrointestinal Specimens at JoVE.com

Subcellular Fractionation from Fresh and Frozen Gastrointestinal Specimens

Aqui, apresentamos um protocolo para executar um fracionamento celular simples para a separação subcelular de proteínas citoplasmáticas e nucleares em humanas frescas e congeladas de biópsias intestinais.

Fraccionamento subcelular de espécimes Gastrointestinal frescos e congelados

The purpose of this protocol is to fractionate human intestinal tissue obtained by endoscopy into nuclear and cytoplasmic compartments for the ...

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An Overview of the Gastrointestinal System: Anatomy, Physiology, and Assessment

SCIENTISTS IN ACTION

9.7K visualizações.  University of the Basque Country (UPV-EHU), Biocruces Health Research Institute. Aqui, apresentamos um protocolo para executar um fracionamento celular simples para a separação subcelular de proteínas citoplasmáticas e nucleares em humanas frescas e congeladas de biópsias intestinais.

Vídeo: Subcellular Fractionation from Fresh and Frozen Gastrointestinal Specimens

Combination of Adhesive-tape-based Sampling and Fluorescence in situ Hybridization for Rapid Detection of Salmonella on Fresh Produce

This protocol describes a simple approach for adhesive-tape-based sampling of tomato and other fresh produce surfaces, followed by on-tape fluorescence in situ hybridization (FISH) for rapid culture-independent detection of Salmonella spp. Cell-charged tapes can also be placed face-down on selective agar for solid-phase enrichment prior to detection. Alternatively, low-volume liquid enrichments (liquid surface miniculture) can be performed on the surface of the tape in non-selective broth, followed by FISH and analysis via flow cytometry. To begin, sterile adhesive tape is brought into contact with fresh produce, gentle pressure is applied, and the tape is removed, physically extracting microbes present on these surfaces. Tapes are mounted sticky-side up onto glass microscope slides and the sampled cells are fixed with 10% formalin (30 min) and dehydrated using a graded ethanol series (50, 80, and 95%; 3 min each concentration). Next, cell-charged tapes are spotted with buffer containing a Salmonella-targeted DNA probe cocktail and hybridized for 15 - 30 min at 55&deg;C, followed by a brief rinse in a washing buffer to remove unbound probe. Adherent, FISH-labeled cells are then counterstained with the DNA dye 4',6-diamidino-2-phenylindole (DAPI) and results are viewed using fluorescence microscopy. For solid-phase enrichment, cell-charged tapes are placed face-down on a suitable selective agar surface and incubated to allow in situ growth of Salmonella microcolonies, followed by FISH and microscopy as described above. For liquid surface miniculture, cell-charged tapes are placed sticky side up and a silicone perfusion chamber is applied so that the tape and microscope slide form the bottom of a water-tight chamber into which a small volume (&le; 500 &mu;L) of Trypticase Soy Broth (TSB) is introduced. The inlet ports are sealed and the chambers are incubated at 35 - 37&deg;C, allowing growth-based amplification of tape-extracted microbes. Following incubation, inlet ports are unsealed, cells are detached and mixed with vigorous back and forth pipetting, harvested via centrifugation and fixed in 10% neutral buffered formalin. Finally, samples are hybridized and examined via flow cytometry to reveal the presence of Salmonella spp. As described here, our "tape-FISH" approach can provide simple and rapid sampling and detection of Salmonella on tomato surfaces. We have also used this approach for sampling other types of fresh produce, including spinach and jalape&ntilde;o peppers.

Combination of Adhesive-tape-based Sampling and Fluorescence in situ Hybridization for Rapid Detection of Salmonella on Fresh Produce

This protocol describes a simple adhesive-tape-based approach for sampling of tomato and other fresh produce surfaces, followed by rapid whole cell detection of Salmonella using fluorescence in situ hybridization (FISH).

Combinação de adesivos de fita baseada em amostragem e de fluorescência In situ Hibridação para detecção rápida de Salmonella On Fresh Produce

This protocol describes a simple approach for adhesive-tape-based sampling of tomato and other fresh produce surfaces, followed by on-tape fluorescence in ...

Imunologia e Infecção

Competitive Homing Assays to Study Gut-tropic T Cell Migration

In order to exert their function lymphocytes need to leave the blood and migrate into different tissues in the body. Lymphocyte adhesion to endothelial cells and tissue extravasation is a multistep process controlled by different adhesion molecules (homing receptors) expressed on lymphocytes and their respective ligands (addressins) displayed on endothelial cells 1 2. Even though the function of these adhesion receptors can be partially studied ex vivo, the ultimate test for their physiological relevance is to assess their role during in vivo lymphocyte adhesion and migration. Two complementary strategies have been used for this purpose: intravital microscopy (IVM) and homing experiments. Although IVM has been essential to define the precise contribution of specific adhesion receptors during the adhesion cascade in real time and in different tissues, IVM is time consuming and labor intensive, it often requires the development of sophisticated surgical techniques, it needs prior isolation of homogeneous cell populations and it permits the analysis of only one tissue/organ at any given time. By contrast, competitive homing experiments allow the direct and simultaneous comparison in the migration of two (or even more) cell subsets in the same mouse and they also permit the analysis of many tissues and of a high number of cells in the same experiment.
Here we describe the classical competitive homing protocol used to determine the advantage/disadvantage of a given cell type to home to specific tissues as compared to a control cell population. We chose to illustrate the migratory properties of gut-tropic versus non gut-tropic T cells, because the intestinal mucosa is the largest body surface in contact with the external environment and it is also the extra-lymphoid tissue with the best-defined migratory requirements. Moreover, recent work has determined that the vitamin A metabolite all-trans retinoic acid (RA) is the main molecular mechanism responsible for inducing gut-specific adhesion receptors (integrin a4b7and chemokine receptor CCR9) on lymphocytes. Thus, we can readily generate large numbers of gut-tropic and non gut-tropic lymphocytes ex vivoby activating T cells in the presence or absence of RA, respectively, which can be finally used in the competitive homing experiments described here.

Competitive homing experiments allow to directly assessing the migratory properties of two different cell populations in a single mouse. Here we illustrate this procedure by comparing the migration of ex vivo-generated gut-tropic versus non-gut tropic T cells.

Competitiva Ensaios Homing para Estudar Gut trópico-Migração de Células T

In order to exert their function lymphocytes need to leave the blood and migrate into different tissues in the body. Lymphocyte adhesion to endothelial ...

RNA Isolation of Pseudomonas aeruginosa Colonizing the Murine Gastrointestinal Tract

Pseudomonas aeruginosa (PA) infections result in significant morbidity and mortality in hosts with compromised immune systems, such as patients with leukemia, severe burn wounds, or organ transplants1. In patients at high-risk for developing PA bloodstream infections, the gastrointestinal (GI) tract is the main reservoir for colonization2, but the mechanisms by which PA transitions from an asymptomatic colonizing microbe to an invasive, and often deadly, pathogen are unclear. Previously, we performed in vivo transcription profiling experiments by recovering PA mRNA from bacterial cells residing in the cecums of colonized mice 3 in order to identify changes in bacterial gene expression during alterations to the host&#x2019;s immune status.
As with any transcription profiling experiment, the rate-limiting step is in the isolation of sufficient amounts of high quality mRNA. Given the abundance of enzymes, debris, food residues, and particulate matter in the GI tract, the challenge of RNA isolation is daunting. Here, we present a method for reliable and reproducible isolation of bacterial RNA recovered from the murine GI tract. This method utilizes a well-established murine model of PA GI colonization and neutropenia-induced dissemination4. Once GI colonization with PA is confirmed, mice are euthanized and cecal contents are recovered and flash frozen. RNA is then extracted using a combination of mechanical disruption, boiling, phenol/chloroform extractions, DNase treatment, and affinity chromatography. Quantity and purity are confirmed by spectrophotometry (Nanodrop Technologies) and bioanalyzer (Agilent Technologies) (Fig 1). This method of GI microbial RNA isolation can easily be adapted to other bacteria and fungi as well.

RNA Isolation of Pseudomonas aeruginosa Colonizing the Murine Gastrointestinal Tract

A reliable method for the RNA isolation of Pseudomonas aeruginosa recovered from murine cecums is described. The RNA recovered is of sufficient quantity and quality for subsequent qPCR, transcription profiling, and RNA Seq experiments. This technique can be adapted for RNA isolation of other intestinal microbes.

Isolamento de RNA Pseudomonas aeruginosa Colonizar o trato gastrointestinal Murino

Pseudomonas aeruginosa (PA) infections result in significant morbidity and mortality in hosts with compromised immune systems, such as patients with ...

Optimized Protocols for Mycobacterium leprae Strain Management: Frozen Stock Preservation and Maintenance in Athymic Nude Mice

Leprosy, caused by Mycobacterium leprae, is an important infectious disease that is still endemic in many countries around the world, including Brazil. There are currently no known methods for growing M. leprae in vitro, presenting a major obstacle in the study of this pathogen in the laboratory. Therefore, the maintenance and growth of M. leprae strains are preferably performed in athymic nude mice (NU-Foxn1nu). The laboratory conditions for using mice are readily available, easy to perform, and allow standardization and development of protocols for achieving reproducible results. In the present report, we describe a simple protocol for purification of bacilli from nude mouse footpads using trypsin, which yields a suspension with minimum cell debris and with high bacterial viability index, as determined by fluorescent microscopy. A modification to the standard method for bacillary counting by Ziehl-Neelsen staining and light microscopy is also demonstrated. Additionally, we describe a protocol for freezing and thawing bacillary stocks as an alternative protocol for maintenance and storage of M. leprae strains.

Optimized Protocols for Mycobacterium leprae Strain Management: Frozen Stock Preservation and Maintenance in Athymic Nude Mice

Mycobacterium leprae, the causative agent of leprosy, does not grow in vitro. We describe an easy to follow protocol to prepare a bacillary suspension to ensure the maintenance of large quantities of M. leprae for a variety of applications. Protocols for propagation by mouse footpad inoculation, evaluation of viability, freezing and thawing bacillary stock are described in detail.

Protocolos otimizados para<em&gt; Mycobacterium leprae</em&gt; Gestão de Strain: congelada Stock Preservação e Manutenção em atímicos Nudez Ratos

Leprosy, caused by Mycobacterium leprae, is an important infectious disease that is still endemic in many countries around the world, including Brazil. ...

A Simple and Rapid Protocol to Non-enzymatically Dissociate Fresh Human Tissues for the Analysis of Infiltrating Lymphocytes

The ability of malignant cells to evade the immune system, characterized by tumor escape from both innate and adaptive immune responses, is now accepted as an important hallmark of cancer. Our research on breast cancer focuses on the active role that tumor infiltrating lymphocytes play in tumor progression and patient outcome. Toward this goal, we developed a methodology for the rapid isolation of intact lymphoid cells from normal and abnormal tissues in an effort to evaluate them proximate to their native state. Homogenates prepared using a mechanical dissociator show both increased viability and cell recovery while preserving surface receptor expression compared to enzyme-digested tissues. Furthermore, enzymatic digestion of the remaining insoluble material did not recover additional CD45+ cells indicating that quantitative and qualitative measurements in the primary homogenate likely genuinely reflect infiltrating subpopulations in the tissue fragment. The lymphoid cells in these homogenates can be easily characterized using immunological (phenotype, proliferation, etc.) or molecular (DNA, RNA and/or protein) approaches. CD45+ cells can also be used for subpopulation purification, in vitro expansion or cryopreservation. An additional benefit of this approach is that the primary tissue supernatant from the homogenates can be used to characterize and compare cytokines, chemokines, immunoglobulins and antigens present in normal and malignant tissues. This protocol functions extremely well for human breast tissues and should be applicable to a wide variety of normal and abnormal tissues.

This protocol describes the rapid non-enzymatic dissociation of fresh human tissue fragments for qualitative and quantitative assessment of CD45+ cells (lymphocytes/leukocytes) present in various normal and malignant human tissues. Additionally, the supernatant obtained from the primary tissue homogenate can be collected and stored for further analysis or experimentation.

Um protocolo simples e rápido para não enzimática Separar frescos Tecidos Humanos para a Análise de infiltrar Linfócitos

The ability of malignant cells to evade the immune system, characterized by tumor escape from both innate and adaptive immune responses, is now accepted ...

Induction of Murine Intestinal Inflammation by Adoptive Transfer of Effector CD4+CD45RBhigh T Cells into Immunodeficient Mice

There are many different animal models available for studying the pathogenesis of human inflammatory bowel diseases (IBD), each with its own advantages and disadvantages. We describe here an experimental colitis model that is initiated by adoptive transfer of syngeneic splenic CD4+CD45RBhigh T cells into T and B cell deficient recipient mice. The CD4+CD45RBhigh T cell population that largely consists of na&#239;ve effector cells is capable of inducing chronic intestinal inflammation, closely resembling key aspects of human IBD. This method can be manipulated to study aspects of disease onset and progression. Additionally it can be used to study the function of innate, adaptive, and regulatory immune cell populations, and the role of environmental exposures, i.e., the microbiota, in intestinal inflammation. In this article we illustrate the methodology for inducing colitis with a step-by-step protocol. This includes a video demonstration of key technical aspects required to successfully develop this murine model of experimental colitis for research purposes.

Induction of Murine Intestinal Inflammation by Adoptive Transfer of Effector CD4+CD45RBhigh T Cells into Immunodeficient Mice

Here, we present a protocol to induce colonic inflammation in mice by adoptive transfer of syngeneic CD4+CD45RBhigh T cells into T and B cell deficient recipients. Clinical and histopathological features mimic human inflammatory bowel diseases. This method allows the study of the initiation of colonic inflammation and progression of disease.

Indução de Murino inflamação intestinal por transferência adotiva de Effector CD4<sup&gt; +</sup&gt; CD45RB<sup&gt; Alta</sup&gt; Células T em imunodeficientes Mice

There are many different animal models available for studying the pathogenesis of human inflammatory bowel diseases (IBD), each with its own advantages ...

Transformation of Probiotic Yeast and Their Recovery from Gastrointestinal Immune Tissues Following Oral Gavage in Mice

Development of recombinant oral therapy would allow for more direct targeting of the mucosal immune system and improve the ability to combat gastrointestinal disorders. Adapting probiotic yeast in particular for this approach carries several advantages. These strains have not only the potential to synthesize a wide variety of complex heterologous proteins but are also capable of surviving and protecting those proteins during transit through the intestine. Critically, however, this approach requires expertise in many diverse laboratory techniques not typically used in tandem. Furthermore, although individual protocols for yeast transformation are well characterized for commonly used laboratory strains, emphasis is placed here on alternative approaches and the importance of optimizing transformation for less well characterized probiotic strains. Detailing these methods will help facilitate discussion as to the best approaches for testing probiotic yeast as oral drug delivery vehicles and indeed serve to advance the development of this novel strategy for gastrointestinal therapy.

Presented here is a unified description of techniques that can be used to develop, transform, administer, and test heterologous protein expression of the probiotic yeast Saccharomyces boulardii.

Transformação de levedura probiótica e sua recuperação a partir gastrointestinais imunitário tecidos após a sonda oral em camundongos

Development of recombinant oral therapy would allow for more direct targeting of the mucosal immune system and improve the ability to combat ...

High-throughput Detection of Respiratory Pathogens in Animal Specimens by Nanoscale PCR

Nanoliter scale real-time PCR uses spatial multiplexing to allow multiple assays to be run in parallel on a single plate without the typical drawbacks of combining reactions together. We designed and evaluated a panel based on this principle to rapidly identify the presence of common disease agents in dogs and horses with acute respiratory illness. This manuscript describes a nanoscale diagnostic PCR workflow for sample preparation, amplification, and analysis of target pathogen sequences, focusing on procedures that are different from microliter scale reactions. In the respiratory panel presented, 18 assays were each set up in triplicate, accommodating up to 48 samples per plate. A universal extraction and pre-amplification workflow was optimized for high-throughput sample preparation to accommodate multiple matrices and DNA and RNA based pathogens. Representative data are presented for one RNA target (influenza A matrix) and one DNA target (equine herpesvirus 1). The ability to quickly and accurately test for a comprehensive, syndrome-based group of pathogens is a valuable tool for improving efficiency and ergonomics of diagnostic testing and for acute respiratory disease diagnosis and management.

High-throughput testing of DNA and RNA based pathogens by nanoscale PCR is described using a syndromic canine and equine respiratory PCR panel.

Detecção de alto rendimento de patógenos respiratórios em espécimes animais por Nanoscale PCR

Nanoliter scale real-time PCR uses spatial multiplexing to allow multiple assays to be run in parallel on a single plate without the typical drawbacks of ...

Live-Cell Fluorescence Microscopy to Investigate Subcellular Protein Localization and Cell Morphology Changes in Bacteria

Investigations of factors influencing cell division and cell shape in bacteria are commonly performed in conjunction with high-resolution fluorescence microscopy as observations made at a population level may not truly reflect what occurs at a single cell level. Live-cell timelapse microscopy allows investigators to monitor the changes in cell division or cell morphology which provide valuable insights regarding subcellular localization of proteins and timing of gene expression, as it happens, to potentially aid in answering important biological questions. Here, we describe our protocol to monitor phenotypic changes in Bacillus subtilis and Staphylococcus aureus using a high-resolution deconvolution microscope. The objective of this report is to provide a simple and clear protocol that can be adopted by other investigators interested in conducting fluorescence microscopy experiments to study different biological processes in bacteria as well as other organisms.

This article provides a step-by-step guide to investigate protein subcellular localization dynamics and to monitor morphological changes using high-resolution fluorescence microscopy in Bacillus subtilis and Staphylococcus aureus.

Microscopia de Fluorescência de células vivas para investigar a localização de proteínas subcelulares e alterações da morfologia celular nas bactérias

Investigations of factors influencing cell division and cell shape in bacteria are commonly performed in conjunction with high-resolution fluorescence ...

Isolation of Macrophage Subsets and Stromal Cells from Human and Mouse Myocardial Specimens

Macrophages represent the most heterogeneous and abundant immune cell populations in the heart and are central in driving inflammation and reparative responses after cardiac injury. How various subsets of macrophages orchestrate the immune responses after cardiac injury is an active area of research. Presented here is a simple protocol that our lab performs routinely, for the extraction of macrophages from mouse and human myocardium specimens obtained from healthy and diseased individuals. Briefly, this protocol involves enzymatic digestion of cardiac tissue to generate a single cell suspension, followed by antibody staining, and flow cytometry. This technique is suitable for functional assays performed on sorted cells as well as bulk and single cell RNA sequencing. A major advantage of this protocol is its simplicity, minimal day to day variation and wide applicability allowing investigation of macrophage heterogeneity across various mouse models and human disease entities.

Presented here is a protocol to isolate various subsets of macrophages and other non-immune cells from human and mouse myocardium by preparing a single cell suspension through enzymatic digestion. Gating schemes for flow cytometry based identification and characterization of isolated macrophages are also presented.

Isolamento de subconjuntos de macrófagos e células estromais de espécimes miocárdios humanos e de camundongos

Macrophages represent the most heterogeneous and abundant immune cell populations in the heart and are central in driving inflammation and reparative ...

Fraccionamento subcelular de espécimes Gastrointestinal frescos e congelados

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