Este trabalho foi financiado pelo NIH concede R01-GM-098977 e R21-AI-098122 a CBK e KEG. RSS foi apoiado em parte por uma Luce Foundation Fellowship e, em parte, por um Fellowship Thayer Programa de Inovação da Escola de Engenharia Thayer.

Quatro principais atividades compreendem o ensaio de ligação peptídeo-MHC II: 1-Encadernação: peptídeos de teste competir com peptídeos de controle marcados para a ligação fase de solução de proteínas MHC II solúveis. A ligação é medida ao longo de uma vasta gama de concentrações de péptidos de teste. 2-Captura: Após a reacção de ligação se aproxima do equilíbrio, complexos de péptido-MHC II são capturadas e separadas a partir do péptido não ligado e proteína de reconhecimento dependente da conformação com um anticorpo imobilizado. 3-Detecção: capturado péptido de controlo é quantitativamente detectados utilizando a fluorescência resolvida no tempo. 4-Análise: Os dados espectroscópicos são processados, traçados e analisados ​​para determinar as propriedades de ligação dependente da dose de péptido de teste e proteínas do MHC II. Em vários passos no procedimento abaixo, a utilização de um robô de manipulação líquido é recomendada quando se está disponível. Particularmente em um formato de 384 poços, de distribuição automatizada e diluição de líquidos minimiza erros de utilizador, os resultados em maisconsistentes bem aos poços volumes, e produz mais estreitos intervalos de confiança de 95% para os valores de IC50 em comparação com ensaios manuais de 96 poços (dados não mostrados). Se um robô de manipulação de líquidos não estiver disponível, os passos anotados com &quot;(líquido manipulação robô)&quot; pode ser feito à mão. Do mesmo modo, se possível, um lavador automático de placas, que é compatível com o formato de 384 poços é recomendado. Isso efetivamente padroniza o processo de lavagem da placa. Se uma anilha de chapa não está disponível, as etapas anotados com &quot;(placa de lavagem)&quot; pode ser feito à mão. 1. Cubra a placa ELISA (Dia 1) <ol><li> Dilui-se anticorpo L243 estoque (0,5 mg / ml) em tampão borato a uma concentração de trabalho de 10 ug / ml. <ol><li> Para revestir uma única placa de 384 poços, adicione 200 mL de anticorpo estoque para 9,8 ml de tampão borato. (Veja calculadora planilha complementar para o dimensionamento alternativa). </li></ol></li><li> Adicionar 25 ul da solução do anticorpo L243 a cada poço de um 384-well alta de ligação placa ELISA branco. (Manipulação de líquidos robô) </li><li> Selar a placa com uma película de poliéster e incubar durante a noite a 4 ° C. Nota: Cada placa de ELISA de 384 poços podem acomodar até 15 péptidos de teste em oito diluições para um alelo de MHC II, bem como os controlos positivos e negativos. Isto vai dar finalmente medições em triplicado. </li></ol> 2. Adicione o teste de peptídeo diluições (Dia 1) <ol><li> Começando com um estoque de 10 mM de cada péptido de teste em DMSO, fazer a seguinte diluição em série em tampão de citrato-fosfato, utilizando placas de polipropileno de 384 cavidades (Tabela 1). (Manipulação de líquidos robô) Nota: Um prato cheio de polipropileno de 384 cavidades requer três placas de ELISA separados. Um terço de uma placa de polipropileno, exigirão apenas uma placa de ELISA (Figura 1). </li></ol><table border="0" cellpadding="0" cellspacing="0"><tbody align="center"><tr><td rowspan="2"> Número de diluição </td><td> Volume to tirar de diluição / estoque antes </td><td> Volume de tampão citrato para adicionar </td><td> Conc. de diluição </td><td> Conc. na reação de ligação </td><td> Conc. em Neutralized ELISA </td></tr><tr><td> (Ul) </td><td> (Ul) </td><td> (UM) </td><td> (UM) </td><td> (UM) </td></tr><tr><td> 1 </td><td> 0,7 </td><td> 35.1 </td><td> 195,531 </td><td> 97,765 </td><td> 48,883 </td></tr><tr><td> 2 </td><td> 14,3 </td><td> 14,3 </td><td> 97,765 </td><td> 48,883 </td><td> 24,441 </td></tr><tr><td> 3 </td><td> 7.1 </td><td> 28,7 </td><td> 19,389 </td><td> 9,695 </td><td> 4,847 </td></tr><tr><td> 4 </td><td> 14,3 </td><td> 14,3 </td><td> 9,695 </td><td> 4,847 </td><td> 2.424 </td></tr><tr><td> 5 </td><td> 7.1 </td><td> 28,7 </td><td> 1.923 </td><td> 0,961 </td><td> 0,481 </td></tr><tr><td> 6 </td><td> 14,3 </td><td> 14,3 </td><td> 0,961 </td><td> 0,481 </td><td> 0,24 </td></tr><tr><td> 7 </td><td> 7.1 </td><td> 28,7 </td><td> 0,191 </td><td> 0,095 </td><td> 0,048 </td></tr><tr><td> 8 </td><td> 14,3 </td><td> 14,3 </td><td> 0,095 </td><td> 0,048 </td><td> 0,024 </td></tr><tr><td colspan="6"> Remova e descarte 7.1 ml de solução de peptídeo a partir do número de diluição 8. </td></tr></tbody></table> Tabela 1. Preparação do péptido teste da série de diluição. <img alt="Figura 1" fo:content-width="5in" fo:src="/files/ftp_upload/51308/51308fig1highres.jpg" src="/files/ftp_upload/51308/51308fig1.jpg" /> Figura 1. Placa Mapa do péptido Ensaio de Ligação. (A) Mapa das diluições de peptídeos em placas de polipropileno de 384 cavidades. Cada placa de polipropileno pode acomodar três grupos de 15 peptídeos nas reações de ligação da competição contra a cantar<html> le alelo MHC II. (B) Depois de a reacção de ligação se aproxima do equilíbrio, cada grupo de péptidos são transferidos, em triplicado, numa placa de 384 poços de ELISA separado que foi pré-revestido com um anticorpo anti-MHC de classe II. 3. Prepare o MHC II Master Mix (Dia 1) <ol><li> Faça o Tampão de reacção <ol><li> Adicionar 80 ul de 1 mM PEFA bloco e 60 mg de octil-β-D-glucopyranaside a 3920 ul de tampão fosfato citrato. (Veja calculadora planilha complementar para o dimensionamento alternativa). </li></ol></li><li> Diluir as soluções de selecionados MHC II a 101 nm de Tampão de Reacção usando um tubo de 15 ml (Tabela 2). Nota: concentração de MHC II será finalmente de 50 nM na reacção de ligação e 25 nM no ensaio ELISA neutralizado. As concentrações de amostra de MHC II irá variar de acordo com o número do lote do fabricante. (Veja calculadora planilha suplementar). </li></ol>&quot;&gt; <tbody><tr><td> MHC da classe II de alelos DRB1 *: </td><td> 1501 </td></tr><tr><td> II do MHC da Concentração (mg / ml) </td><td> 1.3 </td></tr><tr><td> II do MHC da Concentração (mM) </td><td> 20 </td></tr><tr><td> Vol. II MHC Para adicionar (ml) </td><td> 14.65 </td></tr><tr><td> Vol. Tampão de reacção para adicionar (ml): </td><td> 2.885,35 </td></tr><tr><td> MHC II Mistura Concentração (nM) </td><td> 101 </td></tr></tbody></table> Tabela 2. Preparação de mistura principal MHC II. 4. Prepare os controles negativo e positivo (dia 1) <ol><li> Adicionar 21.5 ul de tampão fosfato citrato para o &quot;controlo negativo&quot; poço da placa de polipropileno de 384 cavidades a partir do passo 2.1 (Figura 1A). </li><li> Adicionar 21.5 ul de tampão fosfato citrato para o &quot;controlo positivo&quot; poço da placa de polipropileno de 384 cavidades. Nota: a &quot;posiçãocontrole tiva &quot;será concluída na seção 5, a seguir. </li><li> Remover 49,5 mL da MHC II Master Mix a partir do passo 3.2 e pipeta para um tubo de 1,5 ml Eppendorf. </li><li> Adicionar 0,5 mL de tampão citrato para os 49,5 mL do MHC II Master Mix a partir do passo 4.3. </li><li> Adicionar 21.5 ul de concentração ajustada MHC II Mistura do passo 4.4 para o &quot;controlo negativo&quot; poço da placa de polipropileno de 384 cavidades (Figura 1A). Nota: esta amostra representa o controle negativo do sinal de zero que contém proteína MHC II, NO peptídeo controle, e NÃO peptídeo teste. </li></ol> 5. Adicionar a um controlo adequado Peptide ao MHC II Master Mix (Dia 1) <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td> MHC da classe II de alelos DRB1 * </td><td> Biotinylated Controle Peptide </td><td> (Resíduos) </td><td> Seqüência </td></tr><tr><td> 0101 </td><td> Flu-HA-B </td><td> (306-318) </td><td> Biotina-(Ahx) (Ahx) PRYVKQNTLKLAT-amida </td></tr><tr><td> 0301 </td><td> A mioglobina </td><td> (137-148) </td><td> Biotina-(Ahx) - (Ahx)-OH-LFRKDIAAKYKE </td></tr><tr><td> 0401 </td><td> YAR-B </td><td> (1-14) </td><td> Biotina-(Ahx) (Ahx)-OH YARFQSQTTLKQKT </td></tr><tr><td> 0701 </td><td> TetTox-B </td><td> (830-843) </td><td> Biotina-(Ahx) (Ahx)-OH QYIKANSKFIGITE </td></tr><tr><td> 1101 </td><td> Flu-HA-B </td><td> (306-318) </td><td> Biotina-(Ahx) (Ahx)-amida PRYVKQNTLKLAT </td></tr><tr><td> 1501 </td><td> MBP-B </td><td> (84-102) </td><td> Biotina-(Ahx) (Ahx)-OH NPVVHFFKNIVTPRTPPPS </td></tr></tbody></table> * Recomendamos 10 mg escala encomendar para a economia. Tabela 3. Peptídeos de controle para diversas MHC II alelos. * <ol><li> Dilui-se o péptido de controlo (armazenada a 400 uM em DMSO) a 1:20 em DMSO fresco para produzir um estoque diluído a 20 uM. <ol><li> Adicionar 25 uL de 400 uM de péptido de controle475 ul de DMSO. Nota: este é um grande excesso, mas permite uma manipulação precisa de soluções em DMSO viscosos. </li></ol></li><li> Além disso diluir o Peptídeo de Controle do passo 5.1 (20 mM) de 1:100 para o MHC II Master Mix a partir do passo 3.2. <ol><li> Adicionar 28.8 ul de Controlo Peptide diluídas no passo 5.2 para os restantes 2,850.5 ul de MHC II Master Mix. </li></ol></li><li> Adicionar 21.5 ul de MHC II Master Mix com o péptido de controlo (passo 5.2) para o poço de controlo positivo da placa de polipropileno de 384 cavidades (passo 4.2) (Figura 1A). Nota: esta amostra representa o controle positivo de alto sinal contendo proteína MHC II, peptídeo controle, e NÃO peptídeo teste. </li></ol> 6. Faça a reação de ligação (Dia 1) <ol><li> Adicionar a mistura padrão de MHC II contendo Controlo Péptido (passo 5.2), para cada uma das diluições de teste peptídicos (passo 2.1) em uma proporção de 1:1 para criar a reacção de ligação. <ol><li> Adicionar 21,5 mL de MHC II Master Mix contendo Control peptídeo do passo 5,2-21,5 ul de cada diluição de teste com peptídeo do passo 2.1. (Manipulação de líquidos robô) </li></ol></li><li> Selar a reacção de ligação com um filme de poliéster e incubar 12-24 horas em um não-CO 2 incubador controlado a 37 ° C sem agitação. </li></ol> 7. Neutralizar e transferir a reação de ligação (dia 2) <ol><li> Remova a placa de polipropileno de 384 cavidades contendo a reacção de ligação (passo 6.2) da incubadora a 37 ° C. </li><li> Diluir a 1:01 reação de ligação com Neutralização Buffer. (Manipulação de líquidos robô) <ol><li> Adicionar 43 mL do tampão de neutralização para cada reacção de ligação bem. </li></ol></li><li> Remova a placa de ELISA (passo 1.3) a partir de 4 ° C e lavar 3x com 60 mL / poço de PBS-Tween 20 0,05%. (Lavadora) </li><li> Transferir 25 uL de cada reacção de ligação neutralizada do passo 7.2 em poços em triplicado de a placa revestida de anticorpo de 384 poços de ELISA a partir do passo 7.3. (Figura 1 </strong&gt;) (líquido manuseio robô) </li><li> Cobrir a placa de ELISA com uma película de poliéster e, em lugar de uma incubadora a 37 ° C durante 2,5 horas ou num frigorífico a 4 ° C durante a noite. </li></ol> 8. Desenvolvimento de ELISA (Dia 2 ou 3) <ol><li> Remova a placa de ELISA a partir do passo 7.5, lava-se 3 vezes com 60 ul / poço de PBS-Tween a 0,05%. (Lavadora) </li><li> Diluir solução Estreptavidina-európio estoque (0,1 mg / ml de estreptavidina, 7 Eu 3 + / estreptavidina) 1000 vezes no tampão de ensaio de DELFIA. <ol><li> Para uma placa de 384 poços, diluem-se 10 ul de estreptavidina-európio, em 10 ml de Tampão de Ensaio. </li></ol></li><li> Adicionar 25 ul da diluído Estreptavidina-európio a cada poço da placa de 384 poços de ELISA a partir do passo 8.1. (Manipulação de líquidos robô) </li><li> Cobrir a placa com uma película de poliéster e lugar no escuro e à temperatura ambiente durante 1 hora. Nota: Durante a incubação de 1 hora, retire a solução Aperfeiçoamento da geladeira e reserve 10 ml / placa no escuro a rotemperatura om. </li><li> A seguir à incubação de 1 h, lavar a placa de 384 poços de ELISA a partir do passo 8.3 3x com 60 ul / poço de PBS-Tween a 0,05%. (Lavadora) </li><li> Adicionar 25 ul de solução de melhoria para cada poço da placa de 384 poços de ELISA a partir do passo 8.5. (Manipulação de líquidos robô) </li><li> Cobrir a placa ELISA de 384 poços com um filme de poliéster e permitir que a placa de sentar-se no escuro à temperatura ambiente por 10-15 min. </li><li> Após a incubação de 10-15 min, ler a fluorescência da placa de 384 poços de ELISA a partir do passo 8.7 utilizando um leitor fluorescente resolvida no tempo com as configurações de placa de európio (por exemplo, Start Int.: 200, Pare Int.:. 1,000, Ex 340, Em . 615, Cutoff: Nenhum, PMT: Auto, Lê / Bem: 50). </li></ol> 9. Análise de Dados <ol><li> Insira os dados em formato de gráfico XY com 3 valores replicar em colunas lado a lado (X = teste de concentração peptídeo; Y = medição de fluorescência). </li><li> Entrar transformar os valores de X para todos os dados: X = log (X) </li><li> Coloque os tra lognsformed dados com o modelo de ligação competitiva de um local para extrair o valor de IC 50. </li><li> Restringir o valor inferior ao valor médio de controlo negativo. </li><li> Globalmente ajustar o valor superior e assegurar que o parâmetro global ajuste é inferior ou igual ao do controlo positivo. </li></ol>

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E., Bailey-Kellogg, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure-guided+deimmunization+of+therapeutic+proteins.">Structure-guided deimmunization of therapeutic proteins.</a> J. Comput. Biol. 20, 152-165 (2013).</li><li>Parker, A. S., Griswold, K. E., Bailey-Kellogg, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optimization+of+therapeutic+proteins+to+delete+T-cell+epitopes+while+maintaining+beneficial+residue+interactions.">Optimization of therapeutic proteins to delete T-cell epitopes while maintaining beneficial residue interactions.</a> J. Bioinform. Comput. Biol. 9, 207-229 (2011).</li><li>Parker, A. S., Zheng, W., Griswold, K. E., Bailey-Kellogg, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optimization+algorithms+for+functional+deimmunization+of+therapeutic+proteins.">Optimization algorithms for functional deimmunization of therapeutic proteins.</a> BMC Bioinformatics. 11, 180 (2010).</li><li>De Groot, A. S., Martin, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reducing+risk,+improving+outcomes:+Bioengineering+less+immunogenic+protein+therapeutics.">Reducing risk, improving outcomes: Bioengineering less immunogenic protein therapeutics.</a> Clin. Immunol. 131, 189-201 (2009).</li><li>Wang, P., 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+systematic+assessment+of+MHC+class+II+peptide+binding+predictions+and+evaluation+of+a+consensus+approach.">A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach.</a> PLoS Comput. Biol. 4, e1000048 (2008).</li><li>Sette, A., Rappuoli, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reverse+vaccinology:+developing+vaccines+in+the+era+of+genomics.">Reverse vaccinology: developing vaccines in the era of genomics.</a> Immunity. 33, 530-541 (2010).</li><li>Moise, L., Cousens, L., Fueyo, J., De Groot, A. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Harnessing+the+power+of+genomics+and+immunoinformatics+to+produce+improved+vaccines.">Harnessing the power of genomics and immunoinformatics to produce improved vaccines.</a> Expert Opin. Drug Discov. 6, 9-15 (2011).</li><li>Sturniolo, T., 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=Generation+of+tissue-specific+and+promiscuous+HLA+ligand+databases+using+DNA+microarrays+and+virtual+HLA+class+II+matrices.">Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices.</a> Nat. Biotechnol. 17, 555-561 (1999).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biologic+drugs+set+to+top+2012+sales.">Biologic drugs set to top 2012 sales.</a> Nat. Med. 18, 636 (2012).</li><li>Seib, K. L., Zhao, X., Rappuoli, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Developing+vaccines+in+the+era+of+genomics:+a+decade+of+reverse+vaccinology.">Developing vaccines in the era of genomics: a decade of reverse vaccinology.</a> Clin. Microbiol. Infect. 18, 109-116 (2012).</li><li>Jiang, W., Boder, E. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+engineering+and+analysis+of+peptide+binding+to+class+II+MHC.">High-throughput engineering and analysis of peptide binding to class II MHC.</a> Proc. Natl. Acad. Sci. U.S.A. 107, 13258-13263 (2010).</li><li>Justesen, S., Harndahl, M., Lamberth, K., Nielsen, L. -. L. B., Buus, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Functional+recombinant+MHC+class+II+molecules+and+high-throughput+peptide-binding+assays.">Functional recombinant MHC class II molecules and high-throughput peptide-binding assays.</a> Immun. 5, 1-20 (2009).</li></ol>

Leonard Moise é empregado por e possui opções de ações em EpiVax, Inc., uma empresa de biotecnologia de propriedade privada localizada em Providence, RI. O trabalho contidas neste relatório de pesquisa é livre de qualquer preconceito que possa ser associada com as metas comerciais da empresa.

Biotherapeutics se estabeleceram como um dos pilares da medicina moderna, o que representa quatro dos cinco melhores vendendo drogas em 2012 32. O setor biopharmaceutics tem mostrado um crescimento sustentado por vários anos 6, eo desenvolvimento contínuo de novos agentes, bem como o surgimento de biossimilares ampliou pipelines biofarmacêutica. Olhando para o futuro, avaliar e mitigar a imunogenicidade de proteínas terapêuticas vai se tornar parte integrante da fase inicial de desenvolvimento...

An erratum was issued for: <a href="https://www.jove.com/video/51308/a-high-throughput-mhc-ii-binding-assay-for-quantitative-analysis">A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes</a>.&#160; There were typos in the Protocol section and Table 2.
Step 3.1.1 in the Protocol was updated from:
Add 80 &#181;l of 1 mM Pefa Bloc and 60 mg of octyl-&#946;-D-glucopyranaside to 3,920 &#181;l of Citrate Phosphate Buffer. (See supplemental spreadsheet calculator for alternative scaling).
to:
Add 80 &#181;l of 1 mM Pefa Bloc and 60 &#181;g of octyl-&#946;-D-glucopyranaside to 3,920 &#181;l of Citrate Phosphate Buffer. (See supplemental spreadsheet calculator for alternative scaling).
Step 5.2&#160;in the Protocol was updated from:
Further dilute the Control Peptide from step 5.1 (20 mM) 1:100 into the MHC II Master Mix from step 3.2.
to:
Further dilute the Control Peptide from step 5.1 (20 &#181;M) 1:100 into the MHC II Master Mix from step 3.2.
Table 2 was updated from:
<table border="0" cellpadding="0" cellspacing="0" width="376">
	<tbody>
		<tr>
			<td>MHC II Allele DRB1*:</td>
			<td>1501</td>
		</tr>
		<tr>
			<td>MHC II Stock Concentration (mg/ml)</td>
			<td>1.3</td>
		</tr>
		<tr>
			<td>MHC II Stock Concentration (mM)</td>
			<td>20</td>
		</tr>
		<tr>
			<td>Vol. MHC II Stock to Add (ml)</td>
			<td>14.65</td>
		</tr>
		<tr>
			<td>Vol. Reaction Buffer to Add (ml):</td>
			<td>2885.35</td>
		</tr>
		<tr>
			<td>MHC II Master Mix Concentration (nM)</td>
			<td>101</td>
		</tr>
	</tbody>
</table>
to:
<table border="0" cellpadding="0" cellspacing="0" width="376">
	<tbody>
		<tr>
			<td>MHC II Allele DRB1*:</td>
			<td>1501</td>
		</tr>
		<tr>
			<td>MHC II Stock Concentration (mg/ml)</td>
			<td>1.3</td>
		</tr>
		<tr>
			<td>MHC II Stock Concentration (&#956;M)</td>
			<td>20</td>
		</tr>
		<tr>
			<td>Vol. MHC II Stock to Add (&#956;l)</td>
			<td>14.65</td>
		</tr>
		<tr>
			<td>Vol. Reaction Buffer to Add (&#956;l):</td>
			<td>2885.35</td>
		</tr>
		<tr>
			<td>MHC II Master Mix Concentration (nM)</td>
			<td>101</td>
		</tr>
	</tbody>
</table>

An erratum was issued for: <a href="https://www.jove.com/video/51308/a-high-throughput-mhc-ii-binding-assay-for-quantitative-analysis">A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes</a>.&#160; There were typos in the Protocol section and Table 2.

Erratum: A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

As proteínas são a classe que mais cresce de agentes terapêuticos 6, e da rápida expansão de dutos bioterapêuticos tem se concentrado cada vez mais atenção sobre os desafios associados com o desenvolvimento e uso de drogas de proteína. Uma consideração única deriva do facto de que, em um sistema imunitário saudável e funcionamento, todas as proteínas extracelulares são recolhidos por células apresentadoras de antígenos (APCs). Uma vez internalizado por APCs, uma proteína é clivada em fragmentos de péptidos pequenos, e segmentos imunogénicas putativos são carregados para dentro da ranhura de classe II principais proteínas do complexo de histocompatibilidade (MHC II). Os complexos de péptido-MHC II são, então, exibidos na superfície da APC, e os verdadeiros péptidos imunogénicos, denominados epitopos de células T, receptores de células formar complexos ternários II do MHC-peptídeo T-CD4 com receptores da superfície celular cognato 7. Este evento crítico reconhecimento molecular inicia uma cascata de sinalização complexo, que resulta na activação de células T, a libertação de citocinas, a maturação de células B mediada por células T CD4 e, finalmente, a produção de anticorpos IgG circulantes que se ligam e limpar a proteína exógena ofensivo. Assim, as proteínas imunogénicas pode ser deimmunized por identificar epitopos de células T constituintes e mutando resíduos chave responsáveis ​​pela formação de complexos MHC II. Vale a pena notar, no entanto, que os epitopos de células T podem ser numerosas e amplamente distribuídos em todo proteínas imunogénicas, e a maioria das mutações-exclusão de epitopo são susceptíveis de provocar uma perda inadvertida da função da proteína ou estabilidade. Portanto, engenharia deimmunized bioterapias pode ser um objetivo complexo e tecnicamente difícil, mas existem vários exemplos de sucesso T epitopos de células projetos de eliminação 3,5,8-12. Ao contrário à base de enxerto de &quot;humanização&quot;, o qual é restrita a terapêutica do anticorpo, epitopo deleção pode ser aplicado a essencialmente qualquer proteína alvo, independentemente da sequência, estrutura, função ou disponibilidade de homólogonos andaimes humanos. O primeiro passo para implementar tal abordagem é a identificação de epítopos peptídicos principais incorporados dentro da sequência da proteína alvo. Alto rendimento ensaios bioquímicos, utilizando peptídeos sintéticos e moléculas recombinantes humanos MHC II pode proporcionar rápidas idéias preliminares para identificação e mitigação epítopo 1,3-5. Estes ensaios do tipo ELISA pode ser um poderoso complemento de outros design e desenvolvimento de ferramentas de proteína / vacinas. Por exemplo, uma bem estabelecida abordagem experimental para mapeamento de epítopos depende de tempo, trabalho e recursos intensivos ex vivo ensaios de proliferação celular 15. Resumidamente, a sequência primária de uma proteína-alvo é primeiramente dividido em um painel de péptidos que se sobrepõem, muitas vezes de 15-meros com 12 resíduos de sobreposição entre os péptidos adjacentes. O painel de péptidos quimicamente sintetizados e a imunogenicidade de cada peptídeo é testado em um de vários imunoensaios diferentes que empregam bloo periféricaAs células mononucleares de d (PBMC) isoladas a partir de dadores humanos 13,14. Para proporcionar uma maior confiança nos resultados, os peptídeos são normalmente testadas em replicar com PBMC de 50 ou mais doadores diferentes. Nos casos em que deimmunization é o objetivo final, o trabalho é agravado ainda mais pela necessidade de produzir painéis adicionais de peptídeos mutantes e testar os novos painéis de peptídeos em ensaios de PBMC antes de introduzir quaisquer mutações deimmunizing na proteína de comprimento total para a análise funcional posterior 10. Embora estes ensaios celulares continuam a ser o padrão-ouro para avaliar o potencial imunogênico em pacientes humanos, a eficiência de uma abordagem exaustiva pode ser melhorada através de pré-filtragem epítopos imunogênicos putativos usando uma rápida e alta taxa de transferência ensaio de ligação MHC II-peptídeo. Da mesma forma, os ensaios de ligação bioquímicas péptido-MHC II pode ser combinado com métodos de previsão em silico para acelerar o processo de identificação radicalmente epitopo.Existem uma variedade de ferramentas computacionais para a predição epitopo de célula T; exemplos incluem ProPred 16, MHCPred 17, SVRMHC 18, ARB 19, SMM-alinhar 20, NetMHCIIpan 21, bem como ferramentas proprietárias, como EpiMatrix por EpiVax 22. Da mesma forma, os preditores de epítopos foram recentemente combinada com outras ferramentas de bioinformática e modelagem molecular para produzir algoritmos deimmunization proteína integrados projetados para reduzir o risco de que as mutações deimmunizing pode afectar a estrutura e função da proteína 23-26. Enquanto vários preditores epitopos têm provado ser razoavelmente precisa 27,28, resultados computacionais invariavelmente necessitam de validação experimental. Rápido, alto rendimento, e de baixo custo métodos experimentais são mais adequados como um filtro preliminar no previsões epítopos silico. Na mesma linha, os preditores de epítopos pode dirigir seleção antígeno para vaccinolo reversagy 29,30. Por exemplo, os avanços em bioinformática produziram telas genoma inteiro que identifica rapidamente os candidatos de vacina sob a forma de proteínas inteiras ou epitopos peptídicos extraídos do proteoma dos agentes patogénicos. Embora esta tecnologia capacitadora está reformulando a descoberta e desenvolvimento de vacinas protetoras, introduz um novo desafio na forma de intratável grandes listas de candidatos a vacinas imunogênicas. Ensaios de ligação alta capacidade peptídeo-MHC II podem orientar a seleção epítopo quantificando afinidade de ligação de peptídeos e promiscuidade de ligação entre alelos múltiplos MHC II. Tal como acontece com deimmunization proteína, tais métodos experimentais são em última instância é necessária para validar previsão computacional de ligações vacina promissora. Aqui, um ensaio de ligação ao péptido de MHC-II em escala para o formato de 384 poços é descrito. O protocolo é altamente paralelizado e reduz o custo dos reagentes por 75% em relação ao anteriormente descrito 96 cavidades formatos de placa 1,3-5. Usando um único liquid manuseamento robô, este método permite que um investigador para analisar facilmente aproximadamente noventa péptidos de teste, em triplicado, durante um intervalo de oito concentrações e quatro tipos de alelos do MHC II, em menos de 48 horas. Este artigo descreve a configuração de uma placa de 384 poços de ELISA para análise de sete péptidos experimentais contra um alelo de MHC II, mas calculadoras folha distribuídos são fornecidos como material suplementar, de modo a dimensionar facilmente o experimento de qualquer número de péptidos e / ou MHC desejadas moléculas II.

<table border="0" cellpadding="0" cellspacing="0">
	<colgroup>
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="35">
			<td height="35" style="height:35px;width:587px;">Sodium Tetraborate Decahydrate</td>
			<td style="width:357px;">Sigma</td>
			<td style="width:217px;">221732</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">Citric Acid</td>
			<td>Sigma</td>
			<td>C1901</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">Dibasic Sodium Phosphate</td>
			<td>Sigma</td>
			<td>S7907</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">Trizma HCl</td>
			<td>OmniPur</td>
			<td>9310</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">Tween-20</td>
			<td>Sigma</td>
			<td>P7949</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">100% DMSO</td>
			<td>Sigma</td>
			<td>D8418</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">Octyl-&#946;-D-Glucopyranaside</td>
			<td>Fischer</td>
			<td>29836-26-8</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">Pefa Bloc SCF</td>
			<td>Roche</td>
			<td>1158591600</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">Dulbecco&#8217;s 10X Phosphate Buffered Saline</td>
			<td>Invitrogen</td>
			<td>14200-166</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">DELFIA Assay Buffer</td>
			<td>Perkin Elmer</td>
			<td>4002-0010</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">DELFIA Enhancement Buffer</td>
			<td>Perkin Elmer</td>
			<td>4001-0010</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">Europium Labelled Streptavidin</td>
			<td>Perkin Elmer</td>
			<td>1244-360</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">L243 anti-HLA-DR antibody</td>
			<td>Biolegend</td>
			<td>307602</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">Biotinylated tracer peptides</td>
			<td>21st Century Biochemicals</td>
			<td>Custom Order</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">Test peptides (1-4mg, 85% purity)</td>
			<td>Genscript</td>
			<td>Custom Order</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">Purified HLA-DRB1 monomers (non-biotinylated)</td>
			<td>Benaroya Research Institute*</td>
			<td>Custom Order</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">384-well white EIA/RIA plate</td>
			<td>Thermo</td>
			<td>460372</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">Polypropylene 384-well plate</td>
			<td>Costar</td>
			<td>3656</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">Film, AxySeal, 80 &#181;m, ELISA Applicator&#160;</td>
			<td>Axygen Asicentific</td>
			<td>PCR-SP</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">MilliQ Water</td>
			<td>N/A</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">Epimotion Liquid Handler (or similar)</td>
			<td>Eppendorf</td>
			<td>5075</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">Select TS Plate Washer (or similar)</td>
			<td>BioTek</td>
			<td>405</td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;">SpectraMax Gemini Microplate Reader (or similar)</td>
			<td>Molecular Devices</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td colspan="4" height="98" style="height:99px;width:1161px;">*Recombinant human MHC II molecules can be obtained from the Benaroya Tetramer Core Laboratory. See: https://www.benaroyaresearch.org/our-research/core-resources/tetramer-core-laboratory</td>
		</tr>
	</tbody>
</table>

a high throughput mhc ii binding assay for quantitative analysis of peptide epitopes

Ensaios bioquímicos com moléculas recombinantes humanos MHC II pode proporcionar rápidos, insights quantitativos em identificação epítopo imunogênico, exclusão ou desenho 1,2. Aqui, um ensaio de ligação ao péptido de MHC-II é dimensionado para o formato de 384 poços. O protocolo reduzida reduz o custo dos reagentes de 75% e é mais elevado do que o rendimento descrito anteriormente protocolos de 96 poços 1,3-5. Especificamente, o delineamento experimental permite uma análise robusta e reprodutível de até 15 péptidos contra um alelo de MHC II por 384 poços de placas de ELISA. Utilizando uma única manipulação robô líquido, este método permite que um investigador para analisar aproximadamente noventa péptidos de teste, em triplicado, durante um intervalo de oito concentrações e quatro tipos de alelos do MHC II, em menos de 48 horas. Outros que trabalham nas áreas de deimmunization proteína ou projeto e desenvolvimento de vacinas pode achar o protocolo a ser útil para facilitar o seu próprio trabalho. Em particular, as instruções passo-a-passo eo formato visualde Jove deve permitir que outros usuários para estabelecer de forma rápida e facilmente esta metodologia em seus próprios laboratórios.

A sequência do péptido maduro de Enterobacter cloacae P99 beta-lactamase (BLA) (GenBank ID # X07274.1) foi analisada com ProPred 16 por ligantes peptídicos putativos para MHC II alelo DRB1 * 1501 (Tabela 4). ProPred identificado 117 peptídeos nonâmero com um resíduo P1 âncora obrigatória (isto é, uma M, L, I, V, F, Y ou W na posição 1, que é necessária para MHC II 31 de ligação). Em um limiar de 5%, apenas peptídeos com pontuação maior ou igual a...

Watch this Scientific Journal Video about A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes at JoVE.com

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

Ensaios bioquímicos com moléculas recombinantes humanos MHC II pode proporcionar rápidos, insights quantitativos em identificação epítopo imunogênico, exclusão ou design. Aqui, um ensaio de ligação ao péptido de MHC-II dimensionado para placas de 384 poços é descrito. Este formato de baixo custo deve ser útil nos campos da deimmunization proteína e design e desenvolvimento de vacinas.

Um Ensaio de Ligação de Alto Rendimento II do MHC para análise quantitativa de Peptide Epitopes

Biochemical assays with recombinant human MHC II molecules can provide rapid, quantitative insights into immunogenic epitope identification, deletion, or ...

a-high-throughput-mhc-ii-binding-assay-for-quantitative-analysis

Research

JoVE Journal

Biology

14.8K visualizações.  Dartmouth College.  Ensaios bioquímicos com moléculas recombinantes humanos MHC II pode proporcionar rápidos, insights quantitativos em identificação epítopo imunogênico, exclusão ou design. Aqui, um ensaio de ligação ao péptido de MHC-II dimensionado para placas de 384 poços é descrito. Este formato de baixo custo deve ser útil nos campos da deimmunization proteína e design e desenvolvimento de vacinas. 

Vídeo: A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

Visualizing Antigen Specific CD4+ T Cells using MHC Class II Tetramers

Major histocompatibility complex (MHC) class II tetramers allow the direct visualization of antigen specific CD4+ T cells by flow cytometry.  This method relies on the highly specific interaction between peptide loaded MHC and the corresponding T-cell receptor.  While the affinity of a single MHC/peptide molecule is low, cross-linking MHC/peptide complexes with streptavidin increases the avidity of the interaction, enabling their use as staining reagents.  Because of the relatively low frequencies of CD4+ T cells (~1 in 300,000 for a single specificity) this assay utilizes an in vitro amplification step to increase its threshold of detection.  Mononuclear cells are purified from peripheral blood by Ficoll underlay.  CD4+ cells are then separated by negative selection using biotinylated antibody cocktail and anti-biotin labeled magnetic beads.  Using adherent cells from the CD4- cell fraction as antigen presenting cells, CD4+ T cells are expanded in media by adding an antigenic peptide and IL-2.  The expanded cells are stained with the corresponding class II tetramer by incubating at 37 C for one hour and subsequently stained using surface antibodies such as anti-CD4, anti-CD3, and anti-CD25.  After labeling, the cells can be directly analyzed by flow cytometry.  The tetramer positive cells typically form a distinct population among the expanded CD4+ cells.  Tetramer positive cells are usually CD25+ and often CD4 high.  Because the level of background tetramer staining can vary, positive staining results should always be compared to the staining of the same cells with an irrelevant tetramer.  Multiple variations of this basic assay are possible.  Tetramer positive cells may be sorted for further phenotypic analysis, inclusion in ELISPOT or proliferation assays, or other secondary assays.  Several groups have also demonstrated co-staining using tetramers and either anti-cytokine or anti-FoxP3 antibodies.  

This procedure demonstrates the purification and in vitro expansion of antigen specific CD4+ T cells from whole peripheral blood and their visualization using MHC class II tetramers. Tetramers permit the direct visualization of T cells with a single antigen specificity and defined MHC class II restriction.

Visualizando CD4 + antígeno específico Células T usando MHC Classe II tetrâmeros

Major histocompatibility complex (MHC) class II tetramers allow the direct visualization of antigen specific CD4+ T cells by flow cytometry.  This method ...

Biologia

A Neuronal and Astrocyte Co-Culture Assay for High Content Analysis of Neurotoxicity

High Content Analysis (HCA) assays combine cells and detection reagents with automated imaging and powerful image analysis algorithms, allowing measurement of multiple cellular phenotypes within a single assay. In this study, we utilized HCA to develop a novel assay for neurotoxicity. Neurotoxicity assessment represents an important part of drug safety evaluation, as well as being a significant focus of environmental protection efforts. Additionally, neurotoxicity is also a well-accepted in vitro marker of the development of neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Recently, the application of HCA to neuronal screening has been reported. By labeling neuronal cells with &beta;III-tubulin, HCA assays can provide high-throughput, non-subjective, quantitative measurements of parameters such as neuronal number, neurite count and neurite length, all of which can indicate neurotoxic effects. However, the role of astrocytes remains unexplored in these models. Astrocytes have an integral role in the maintenance of central nervous system (CNS) homeostasis, and are associated with both neuroprotection and neurodegradation when they are activated in response to toxic substances or disease states. GFAP is an intermediate filament protein expressed predominantly in the astrocytes of the CNS. Astrocytic activation (gliosis) leads to the upregulation of GFAP, commonly accompanied by astrocyte proliferation and hypertrophy. This process of reactive gliosis has been proposed as an early marker of damage to the nervous system. The traditional method for GFAP quantitation is by immunoassay. This approach is limited by an inability to provide information on cellular localization, morphology and cell number. We determined that HCA could be used to overcome these limitations and to simultaneously measure multiple features associated with gliosis - changes in GFAP expression, astrocyte hypertrophy, and astrocyte proliferation - within a single assay. In co-culture studies, astrocytes have been shown to protect neurons against several types of toxic insult and to critically influence neuronal survival. Recent studies have suggested that the use of astrocytes in an in vitro neurotoxicity test system may prove more relevant to human CNS structure and function than neuronal cells alone. Accordingly, we have developed an HCA assay for co-culture of neurons and astrocytes, comprised of protocols and validated, target-specific detection reagents for profiling &beta;III-tubulin and glial fibrillary acidic protein (GFAP). This assay enables simultaneous analysis of neurotoxicity, neurite outgrowth, gliosis, neuronal and astrocytic morphology and neuronal and astrocytic development in a wide variety of cellular models, representing a novel, non-subjective, high-throughput assay for neurotoxicity assessment. The assay holds great potential for enhanced detection of neurotoxicity and improved productivity in neuroscience research and drug discovery.

This article describes a novel protocol and reagent set designed for sensitive measurement of neurotoxic effects of compounds and treatments on co-cultures of neurons and astrocytes using high content analysis. Results demonstrate that high content analysis represents an exciting novel technology for neurotoxicity assessment.

A Neuronal e astrocitária Ensaio Co-Cultura de Análise de Conteúdo de Alta de neurotoxicidade

High Content Analysis (HCA) assays combine cells and detection reagents with automated imaging and powerful image analysis algorithms, allowing ...

Mutagenesis and Functional Analysis of Ion Channels Heterologously Expressed in Mammalian Cells

We will demonstrate how to study the functional effects of introducing a point mutation in an ion channel. We study G protein-gated inwardly rectifying potassium (referred to as GIRK) channels, which are important for regulating the excitability of neurons. There are four different mammalian GIRK channel subunits (GIRK1-GIRK4) - we focus on GIRK2 because it forms a homotetramer. Stimulation of different types of G protein-coupled receptors (GPCRs), such as the muscarinic receptor (M2R), leads to activation of GIRK channels. Alcohol also directly activates GIRK channels. We will show how to mutate one amino acid by specifically changing one or more nucleotides in the cDNA for the GIRK channel. This mutated cDNA sequence will be amplified in bacteria, purified, and the presence of the point mutation will be confirmed by DNA sequencing. The cDNAs for the mutated and wild-type GIRK channels will be transfected into human embryonic kidney HEK293T cells cultured in vitro. Lastly, whole-cell patch-clamp electrophysiology will be used to study the macroscopic potassium currents through the ectopically expressed wild-type or mutated GIRK channels. In this experiment, we will examine the effect of a L257W mutation in GIRK2 channels on M2R-dependent and alcohol-dependent activation.

We will demonstrate how to study the effect of a single point mutation on the function of an ion channel.

Mutagênese e Análise Funcional de canais iônicos Heterologously Expresso em células de mamíferos

We will demonstrate how to study the functional effects of introducing a point mutation in an ion channel. We study G protein-gated inwardly rectifying ...

High-throughput Saccharification Assay for Lignocellulosic Materials

Polysaccharides that make up plant lignocellulosic biomass can be broken down to produce a range of sugars that subsequently can be 
used in establishing a biorefinery. These raw materials would constitute a new industrial platform, which is both sustainable and carbon neutral, to replace 
the current dependency on fossil fuel. The recalcitrance to deconstruction observed in lignocellulosic materials is produced by several intrinsic properties 
of plant cell walls. Crystalline cellulose is embedded in matrix polysaccharides such as xylans and arabinoxylans, and the whole structure is encased by the 
phenolic polymer lignin, that is also difficult to digest 1. In order to improve the digestibility of plant materials we need to discover the main bottlenecks 
for the saccharification of cell walls and also screen mutant and breeding populations to evaluate the variability in saccharification 2. These tasks require 
a high throughput approach and here we present an analytical platform that can perform saccharification analysis in a 96-well plate format. This platform has 
been developed to allow the screening of lignocellulose digestibility of large populations from varied plant species. We have scaled down the reaction volumes 
for gentle pretreatment, partial enzymatic hydrolysis and sugar determination, to allow large numbers to be assessed rapidly in an automated system.
This automated platform works with milligram amounts of biomass, performing ball milling under controlled conditions to reduce the plant 
materials to a standardised particle size in a reproducible manner. Once the samples are ground, the automated formatting robot dispenses specified and recorded 
amounts of material into the corresponding wells of 96 deep well plate (Figure 1). Normally, we dispense the same material into 4 wells to have 4 replicates for 
analysis. Once the plates are filled with the plant material in the desired layout, they are manually moved to a liquid handling station (Figure 2). In this 
station the samples are subjected to a mild pretreatment with either dilute acid or alkaline and incubated at temperatures of up to 90&deg;C. The pretreatment solution 
is subsequently removed and the samples are rinsed with buffer to return them to a suitable pH for hydrolysis. The samples are then incubated with an enzyme
mixture for a variable length of time at 50&deg;C. An aliquot is taken from the hydrolyzate and the reducing sugars are automatically determined by the MBTH 
colorimetric method.

A simple, rapid method for determining the saccharification potential of large numbers of plant biomass samples is described. The automated platform for this analysis involves the preparation of the plant biomass for analysis in 96 well plates and the subsequent performance of pretreatment, hydrolysis and quantification of the sugars released.

Alto rendimento Assay Sacarificação para materiais lignocelulósicos

Polysaccharides that make up plant lignocellulosic biomass can be broken down to produce a range of sugars that subsequently can be 
used in establishing ...

A Quantitative Fitness Analysis Workflow

Quantitative Fitness Analysis (QFA) is an experimental and computational workflow for comparing fitnesses of microbial cultures grown in parallel1,2,3,4. QFA can be applied to focused observations of single cultures but is most useful for genome-wide genetic interaction or drug screens investigating up to thousands of independent cultures. The central experimental method is the inoculation of independent, dilute liquid microbial cultures onto solid agar plates which are incubated and regularly photographed. Photographs from each time-point are analyzed, producing quantitative cell density estimates, which are used to construct growth curves, allowing quantitative fitness measures to be derived. Culture fitnesses can be compared to quantify and rank genetic interaction strengths or drug sensitivities. The effect on culture fitness of any treatments added into substrate agar (e.g. small molecules, antibiotics or nutrients) or applied to plates externally (e.g. UV irradiation, temperature) can be quantified by QFA.
The QFA workflow produces growth rate estimates analogous to those obtained by spectrophotometric measurement of parallel liquid cultures in 96-well or 200-well plate readers. Importantly, QFA has significantly higher throughput compared with such methods. QFA cultures grow on a solid agar surface and are therefore well aerated during growth without the need for stirring or shaking.
QFA throughput is not as high as that of some Synthetic Genetic Array (SGA) screening methods5,6. However, since QFA cultures are heavily diluted before being inoculated onto agar, QFA can capture more complete growth curves, including exponential and saturation phases3. For example, growth curve observations allow culture doubling times to be estimated directly with high precision, as discussed previously1.
Here we present a specific QFA protocol applied to thousands of S. cerevisiae cultures which are automatically handled by robots during inoculation, incubation and imaging. Any of these automated steps can be replaced by an equivalent, manual procedure, with an associated reduction in throughput, and we also present a lower throughput manual protocol. The same QFA software tools can be applied to images captured in either workflow.
We have extensive experience applying QFA to cultures of the budding yeast S. cerevisiae but we expect that QFA will prove equally useful for examining cultures of the fission yeast S. pombe and bacterial cultures.

Quantitative Fitness Analysis (QFA) is a complementary series of experimental and computational methods for estimating microbial culture fitnesses. QFA estimates the effect of genetic mutations, drugs or other applied treatments on microbe growth. Experiments scaling from focussed analysis of single cultures to thousands of parallel cultures can be designed.

Um fluxo de trabalho Análise Quantitativa de Fitness

Quantitative Fitness Analysis (QFA) is an experimental and computational workflow for comparing fitnesses of microbial cultures grown in parallel1,2,3,4. ...

High-throughput Functional Screening using a Homemade Dual-glow Luciferase Assay

We present a rapid and inexpensive high-throughput screening protocol to identify transcriptional regulators of alpha-synuclein, a gene associated with Parkinson&#39;s disease. 293T cells are transiently transfected with plasmids from an arrayed ORF expression library, together with luciferase reporter plasmids, in a one-gene-per-well microplate format. Firefly luciferase activity is assayed after 48 hr to determine the effects of each library gene upon alpha-synuclein transcription, normalized to expression from an internal control construct (a hCMV promoter directing Renilla luciferase). This protocol is facilitated by a bench-top robot enclosed in a biosafety cabinet, which performs aseptic liquid handling in 96-well format. Our automated transfection protocol is readily adaptable to high-throughput lentiviral library production or other functional screening protocols requiring triple-transfections of large numbers of unique library plasmids in conjunction with a common set of helper plasmids. We also present an inexpensive and validated alternative to commercially-available, dual luciferase reagents which employs PTC124, EDTA, and pyrophosphate to suppress firefly luciferase activity prior to measurement of Renilla luciferase. Using these methods, we screened 7,670 human genes and identified 68 regulators of alpha-synuclein. This protocol is easily modifiable to target other genes of interest.

We present a rapid and inexpensive screening method for identifying transcriptional regulators using high-throughput robotic transfections and a homemade dual-glow luciferase assay. This protocol rapidly generates direct side-by-side functional data for thousands of genes and is easily modifiable to target any gene of interest.

De alta capacidade de Triagem funcional usando um caseiro Dual-brilho ensaio de luciferase

We present a rapid and inexpensive high-throughput screening protocol to identify transcriptional regulators of alpha-synuclein, a gene associated with ...

Flow Cytometric Analysis of Bimolecular Fluorescence Complementation: A High Throughput Quantitative Method to Study Protein-protein Interaction

Among methods to study protein-protein interaction inside cells, Bimolecular Fluorescence Complementation (BiFC) is relatively simple and sensitive. BiFC is based on the production of fluorescence using two non-fluorescent fragments of a fluorescent protein (Venus, a Yellow Fluorescent Protein variant, is used here). Non-fluorescent Venus fragments (VN and VC) are fused to two interacting proteins (in this case, AKAP-Lbc and PDE4D3), yielding fluorescence due to VN-AKAP-Lbc-VC-PDE4D3 interaction and the formation of a functional fluorescent protein inside cells.
BiFC provides information on the subcellular localization of protein complexes and the strength of protein interactions based on fluorescence intensity. However, BiFC analysis using microscopy to quantify the strength of protein-protein interaction is time-consuming and somewhat subjective due to heterogeneity in protein expression and interaction. By coupling flow cytometric analysis with BiFC methodology, the fluorescent BiFC protein-protein interaction signal can be accurately measured for a large quantity of cells in a short time. Here, we demonstrate an application of this methodology to map regions in PDE4D3 that are required for the interaction with AKAP-Lbc. This high throughput methodology can be applied to screening factors that regulate protein-protein interaction.

Flow cytometric analysis of Bimolecular Fluorescence Complementation provides a high throughput quantitative method to study protein-protein interaction. This methodology can be applied to mapping protein binding sites and for screening factors that regulate protein-protein interaction.

Citometria de fluxo e de Complementação de fluorescência Bimolecular: A alta taxa de transferência método quantitativo para estudo de interação proteína-proteína

Among methods to study protein-protein interaction inside cells, Bimolecular Fluorescence Complementation (BiFC) is relatively simple and sensitive. BiFC ...

High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes

Both transcriptional and post-transcriptional regulation have a profound impact on genes expression. However, commonly adopted cell-based screening assays focus on transcriptional regulation, being essentially aimed at the identification of promoter-targeting molecules. As a result, post-transcriptional mechanisms are largely uncovered by gene expression targeted drug development. Here we describe a cell-based assay aimed at investigating the role of the 3&#39; untranslated region (3&#8217; UTR) in the modulation of the fate of its mRNA, and at identifying compounds able to modify it. The assay is based on the use of a luciferase reporter construct containing the 3&#8217; UTR of a gene of interest stably integrated into a disease-relevant cell line. The protocol is divided into two parts, with the initial focus on the primary screening aimed at the identification of molecules affecting luciferase activity after 24 hr of treatment. The second part of the protocol describes the counter-screening necessary to discriminate compounds modulating luciferase activity specifically through the 3&#8217; UTR. In addition to the detailed protocol and representative results, we provide important considerations about the assay development and the validation of the hit(s) on the endogenous target. The described cell-based reporter gene assay will allow scientists to identify molecules modulating protein levels via post-transcriptional mechanisms dependent on a 3&#8217; UTR.

Here we describe a cell-based reporter gene assay as a valuable tool to screen chemical libraries for compounds modulating post-transcriptional control mechanisms exerted through 3&#8217; UTR.

Rastreio de alto rendimento para moduladores químicos de Genes Post-transcriptionally Regulamentados

Both transcriptional and post-transcriptional regulation have a profound impact on genes expression. However, commonly adopted cell-based screening assays ...

qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping

The Synthetic Yeast Genome Project (Sc2.0) aims to build 16 designer yeast chromosomes and combine them into a single yeast cell. To date one synthetic chromosome, synIII1, and one synthetic chromosome arm, synIXR2, have been constructed and their in vivo function validated in the absence of the corresponding wild type chromosomes. An important design feature of Sc2.0 chromosomes is the introduction of PCRTags, which are short, re-coded sequences within open reading frames (ORFs) that enable differentiation of synthetic chromosomes from their wild type counterparts. PCRTag primers anneal selectively to either synthetic or wild type chromosomes and the presence/absence of each type of DNA can be tested using a simple PCR assay. The standard readout of the PCRTag assay is to assess presence/absence of amplicons by agarose gel electrophoresis. However, with an average PCRTag amplicon density of one per 1.5 kb and a genome size of ~12 Mb, the completed Sc2.0 genome will encode roughly 8,000 PCRTags. To improve throughput, we have developed a real time PCR-based detection assay for PCRTag genotyping that we call qPCRTag analysis. The workflow specifies 500 nl reactions in a 1,536 multiwell plate, allowing us to test up to 768 PCRTags with both synthetic and wild type primer pairs in a single experiment.

Designer chromosomes of the Synthetic Yeast Genome project, Sc2.0, can be distinguished from their native counterparts using a PCR-based genotyping assay called PCRTagging, which has a presence/absence endpoint. Here we describe a high-throughput real time PCR detection method for PCRTag genotyping.

Análise qPCRTag - A High Throughput, PCR em Tempo Real Ensaio para Sc2.0 Genotipagem

The Synthetic Yeast Genome Project (Sc2.0) aims to build 16 designer yeast chromosomes and combine them into a single yeast cell. To date one synthetic ...

High Throughput Danio Rerio Energy Expenditure Assay

Zebrafish are an important model organism with inherent advantages that have the potential to make zebrafish a widely applied model for the study of energy homeostasis and obesity. The small size of zebrafish allows for assays on embryos to be conducted in a 96- or 384-well plate format, Morpholino and CRISPR based technologies promote ease of genetic manipulation, and drug treatment by bath application is viable. Moreover, zebrafish are ideal for forward genetic screens allowing for novel gene discovery. Given the relative novelty of zebrafish as a model for obesity, it is necessary to develop tools that fully exploit these benefits. Herein, we describe a method to measure energy expenditure in thousands of embryonic zebrafish simultaneously. We have developed a whole animal microplate platform in which we use 96-well plates to isolate individual fish and we assess cumulative NADH2 production using the commercially available cell culture viability reagent alamarBlue. In poikilotherms the relationship between NADH2 production and energy expenditure is tightly linked. This energy expenditure assay creates the potential to rapidly screen pharmacological or genetic manipulations that directly alter energy expenditure or alter the response to an applied drug (e.g. insulin sensitizers).

High Throughput Danio Rerio Energy Expenditure Assay

Zebrafish are an important model organism for the study of energy homeostasis. By utilizing a NADH2 sensitive redox indicator, alamar Blue, we have developed an assay that measures the metabolic rate of zebrafish larvae in a 96 well plate format and can be applied to drug or gene discovery.

High Throughput<em&gt; Danio rerio</em&gt; Energia Despesas Assay

Zebrafish are an important model organism with inherent advantages that have the potential to make zebrafish a widely applied model for the study of ...