The authors thank Dara Frank and Carrie Harwood for their generous contribution of strains. University of Wisconsin Milwaukee Research Foundation holds patent no. 8,354,451; with claims broadly directed to treating or inhibiting the progression of infection of a microorganism in a patient by administering a 4-hydroxyphenylpyruvate dioxygenase-inhibiting compound such as 2-[2-nitro-4-(trifluoromethyl)benzoyl]-1,3-cyclohexanedione (NTBC). Inventors are Graham Moran and Pang He. This research was supported by the National Institutes of Health (R00-GM083147). The University of Washington P. aeruginosa transposon mutant library is supported by NIH P30 DK089507.

1. Preparación de medios de cultivo, antibióticos, y 2- [2-nitro-4- (trifluorometil) benzoil] -1,3-ciclohexanodiona (NTBC) <ol><li> Hacer caldo LB (1% triptona, extracto de levadura 0,5%, 0,25% de NaCl en H 2 O) y alícuota en volúmenes apropiados. Esterilizar en autoclave. Almacenar a temperatura ambiente. </li><li> Hacer 100 ml de LB agar (1% triptona, extracto de levadura 0,5%, 0,25% de NaCl, 1,5% de agar en H 2 O) en matraces de 250 ml. Esterilizar en autoclave y almacenar a temperatura ambiente. Asegúrese de que el agar se derrita antes de verter en placas. NOTA: Los frascos que contienen 100 ml de agar LB producirá 4 platos. La cantidad de agar LB puede ser alterado para que se corresponda con el número de placas necesarias para el ensayo. </li><li> Hacer PBS (NaCl 137 mM, 2,7 mM KCl, 10 mM Na 2 HPO 4, 2 mM KH 2 PO 4) 16. Esterilizar en autoclave o filtración y se almacena a temperatura ambiente. </li><li> Preparar las soluciones madre de antibióticos para la gentamicina, kanamicina, und tobramicina. <ol><li> Preparar las concentraciones de valores antibióticos apropiados para P. aeruginosa cepas que contienen 100 mg / ml de gentamicina, 30 mg / ml de kanamicina, y 10 mg / ml de tobramicina. Disolver los antibióticos en el agua, esterilizar filtro (0,2 micras), y se almacena a 4 ° C. Alterar los antibióticos y concentraciones dependiendo de la bacteria estudiada. </li></ol></li><li> Preparar las soluciones madre NTBC. Disolver 10 mg de NTBC en 400 l de DMSO. Esto produce una concentración de 75,9 mM NTBC. Tienda soluciones NTBC acciones a -20 ° C. Soluciones Descongelar a temperatura ambiente, según sea necesario. NOTA: Diferentes fuentes de NTBC tienen diferencias en la solubilidad. Determinar el vehículo apropiado en el que se disuelva el NTBC basado en las recomendaciones del fabricante y ajuste Paso 1.5 en consecuencia. </li></ol> 2. NTBC titulaciones de Cepas bacterianas <ol><li> Establecer cultivos de una noche de las cepas a ensayar. Añadir 2 ml de LB tubo de ensayo de caldo de 16 x 150 mms (uno por cepa) y inoculan con 1 aislada colonia de cada cepa. Incubar durante la noche a 37 ° C con aireación en un rotador de cultivo de tejidos en una incubadora de aire. </li><li> El día siguiente, se preparan titulaciones de NTBC en caldo LB. Utilice un rango inicial de 0 a 900 mM NTBC desde diferentes cepas tienen diferencias en la sensibilidad a la NTBC. <ol><li> Añadir 1 ml de caldo LB a 4 a 5 tubos de ensayo (16 x 150 mm) por cepa. </li><li> Añadir la solución madre NTBC (75,9 mM) a los tubos de ensayo (16 x 150 mm) en un intervalo de concentraciones. Ver Tabla 1 para las concentraciones NTBC y volúmenes de valores correspondientes a añadir a 1 ml de caldo LB. </li></ol></li><li> Mida la OD 600 de los cultivos de una noche. Lávese las culturas antes de tomar OD 600 lecturas para eliminar pyomelanin presente en los medios de comunicación. <ol><li> Lávese las culturas mediante la centrifugación de 1 ml de la cultura en una microcentrífuga a 16.000 xg durante 2 min. Eliminar el sobrenadante y las células sedimentadas vagamente conuna micropipeta y resuspender el sedimento celular sólida en 1 ml de LB. </li></ol></li><li> Inocular los tubos de titulación a una DO 600 0,05. Calcular la cantidad de cultivo se lavó necesaria para inocular los tubos. NOTA: Utilice las culturas lavadas para inoculaciones desde pyomelanin no debe estar presente. </li><li> Incubar los tubos de titulación durante aproximadamente 24 horas a 37 ° C con aireación usando un cultivo de tejido de los rotadores en una incubadora de aire. </li><li> Fotografiar los tubos de valoración y comparación de la producción de pigmento dentro y entre las cepas para determinar la cantidad de NTBC utilizar para los ensayos de MIC y el estrés oxidativo. Utilice OD 600 lecturas para determinar la cantidad de pyomelanin en la celda sobrenadante del cultivo libre y para determinar la densidad celular. NOTA: La relación de OD 600 de pyomelanin en el sobrenadante del cultivo de células se puede calcular para cuantificar las diferencias en la producción pyomelanin después del tratamiento con NTBC. </li></ol> 3. antibióticos inhibi mínimoConcentración (MIC) Ensayo tory en placas de 96 pocillos <ol><li> Establecer cultivos de una noche de las cepas a ensayar en LB con y sin NTBC. NOTA: Este protocolo se describe utilizando el nivel representativo de 300 M NTBC. El nivel apropiado de NTBC para ser utilizado se determina en el paso 2.6. <ol><li> Añadir 300 mM NTBC a 2 ml LB. Añadir un volumen equivalente de vehículo (DMSO) a 2 ml de LB para la condición no NTBC. </li><li> El uso de palillos de dientes estériles, inocular tubos con una colonia aislada de bacterias. Habrá una cultura con NTBC y una cultura sin NTBC para cada cepa. Incubar durante la noche a 37 ° C con aireación usando un cultivo de tejido de los rotadores en una incubadora de aire. </li></ol></li><li> Al día siguiente, hacer que las soluciones magistrales LB + DMSO LB + NTBC y para configurar el ensayo MIC. Añadir NTBC a una concentración de 600 mM como este se diluirá doble cuando se añade inóculo, produciendo una concentración final de 300 mM. <ol><li> Para probar un solo antibiótica de una cepa, añadir 600 M NTBC a 2 ml de LB y mezclar para que la solución principal NTBC. Añadir un volumen equivalente de vehículo (DMSO) a 2 ml de LB y se mezcla para hacer la solución ningún maestro NTBC. Utilice estas soluciones para crear soluciones madre de antibióticos, así como para la creación de la serie de dilución en placas de 96 pocillos. NOTA: Las formulaciones de solución maestros darán solución adicional para tener en cuenta los errores de pipeteo. Las soluciones magistrales se pueden escalar hacia arriba o hacia abajo según sea necesario en función de la cantidad de antibióticos y cepas probadas. </li></ol></li><li> Preparar las soluciones de antibióticos en las soluciones magistrales LB + NTBC o LB + DMSO. NOTA: La concentración de antibiótico en estas soluciones debería ser el doble de la concentración final deseada. Suficiente solución se debe hacer para transferir 100 l de cuatro pozos en una placa de 96 pocillos. <ol><li> Preparar gentamicina +/- NTBC solución madre a los 64 mg / ml. Para hacer esta solución, añadir 0,288 l de Stock gentamicina (100 mg / ml) para 450l LB + NTBC o solución maestro LB + DMSO. NOTA: La concentración máxima de gentamicina para P. aeruginosa PAO1 es 32 mg / ml. </li><li> Haga la kanamicina +/- NTBC solución madre a 256 g / ml. Para que esta solución, añadir 3,84 l de kanamicina social (30 mg / ml) a 450 mu l LB + NTBC o LB + DMSO soluciones magistrales. NOTA: La concentración máxima de kanamicina para P. aeruginosa PAO1 es 128 g / ml. </li><li> Preparar tobramicina +/- NTBC solución madre a 8 mg / ml. Para que esta solución, añadir 0,36 l de tobramicina social (10 mg / ml) a 450 mu l LB + NTBC o LB + DMSO soluciones magistrales. NOTA: Para P. aeruginosa PAO1, la concentración máxima de tobramicina es 4 mg / ml. NOTA: Los antibióticos y concentraciones se pueden ajustar para las bacterias a ensayar. </li></ol></li><li> Añadir 100 l de cada solución de antibiótico 2x para cuatro pozos en una placa de 96 pocillos. Coloque estas soluciones en la fila A. Para example, gentamicina debe ser colocado en A1 a A4, kanamicina debe ser colocado en A5 a A8, y tobramicina debe ser colocado en A9 a través de A12. Ver Figura 1A para un diagrama de una placa de 96 pocillos de configurar. NOTA: Múltiples antibióticos pueden ser probados en un plato, pero sólo una cepa debe ser probado por placa para eliminar el potencial de contaminación cruzada de otras cepas. </li><li> Añadir 50 l de la solución maestro LB + NTBC o LB + DMSO a las filas B a H de la placa de 96 pocillos. Asegúrese de que un plato es LB + NTBC y una placa es LB + DMSO. Ver Figura 1A. <ol><li> Utilice LB + NTBC para los antibióticos en LB + NTBC. Utilice LB + DMSO para los antibióticos en LB + DMSO. </li></ol></li><li> Usando una micropipeta realizar dos diluciones seriadas dobles de los antibióticos mediante la transferencia de 50 l de la solución de la fila A a la fila B. Mezcle la solución, cambiar las puntas de pipeta y transferir 50 l de la solución de la línea B de la fila C. Repita el procedimiento para el remainifilas NG. Después de diluir la fila G, retirar 50 l de la solución de esa fila y descarte. Utilice la fila H como un control de antibióticos para el crecimiento bacteriano. Ver Figura 1B. NOTA: Cada Un pozo en filas a G ahora contiene 50 l de antibióticos en LB + NTBC o LB + DMSO a 2X la concentración final deseada. Fila H contiene LB + NTBC o LB + DMSO sin antibióticos. </li><li> Mida la OD 600 de los cultivos de una noche. Lave todas las culturas antes de tomar OD 600 lecturas para eliminar pyomelanin presente en los medios de comunicación. <ol><li> Lávese las culturas mediante la centrifugación de 1 ml de la cultura en una microcentrífuga a 16.000 xg durante 2 min. Eliminar el sobrenadante con una micropipeta y resuspender el botón celular en 1 ml de LB. </li></ol></li><li> Diluir los cultivos de una noche de 2.75x10 5 UFC / ml en LB. NOTA: Supongamos que un OD 600 unidad es el equivalente de 1x10 9 UFC / ml para P. aeruginosa. OD / a conversiones ml CFU puede ser different en otras bacterias. </li><li> Añadir 50 l de cultivo bacteriano diluido al pocillo apropiado. NOTA: Los cultivos cultivados en NTBC deben añadirse a los pocillos que contienen NTBC y culturas crecido en DMSO deben añadirse a los pocillos que contienen DMSO. Ver Figura 1B. <ol><li> Añadir bacterias para tres pozos para cada cepa y la concentración de antibiótico. Añadir 50 l de LB a la cuarta bien para actuar como un control para la contaminación bacteriana. Ver Figura 1B. </li><li> Utilice una micropipeta multicanal para inocular los pozos. Asegúrese de que la pipeta consejos son cerca de la parte inferior de los pozos cuando se añade inóculo para evitar la contaminación de los pozos vecinos. NOTA: La adición de cultivo bacteriano a los pozos diluirá las concentraciones de antibióticos y NTBC doble. </li></ol></li><li> Cubrir las placas de 96 pocillos con parafilm y se incuba aproximadamente 24 horas a 37 ° C. Incubar las placas de 96 pocillos de forma estática, en una incubadora de aire. </li><li> Examinarlas placas para el crecimiento bacteriano en los pocillos. El MIC es la concentración más baja de antibiótico en el que no se observa crecimiento bacteriano para las tres repeticiones de cada cepa. <ol><li> Examine visualmente la placa para el crecimiento o leer mediante un conjunto lector de placas a OD 600. </li></ol></li></ol> Ensayo Placa 4. Punto de Estrés Oxidativo Respuesta <ol><li> Establecer cultivos de una noche de las cepas a ensayar en LB con y sin NTBC como se describe en el paso 3.1. </li><li> Al día siguiente, se preparan placas de agar LB que contenían H 2 O 2 como un factor de estrés oxidativo. Una gama de H 2 O 2 concentraciones de 0 a 1 mm es un buen punto de partida. <ol><li> Derretir los frascos de agar LB. Frescos medios a aproximadamente 50 ° C a la temperatura ambiente. </li><li> Añadir H 2 O 2 directamente a los medios de comunicación enfriados a las concentraciones deseadas. Frascos del remolino para mezclar. Ver Tabla 2 para las concentraciones de H 2 O 2y los volúmenes de H 2 O 2 concentrada para agregar. Estos valores se basan en 100 ml de LB agar. </li><li> Vierta platos inmediatamente después de la adición de H 2 O 2 y la llama de la superficie para eliminar las burbujas. El rendimiento es de 4 placas por cada 100 ml de agar LB. Marque las placas con la concentración de H 2 O 2. </li><li> Colocar las placas descubiertos en una campana de flujo biológica con el ventilador funcionando durante 30 min para eliminar el exceso de humedad de las placas. NOTA: Utilice las placas el mismo día que se preparan. El no hacerlo puede resultar en datos inconsistentes. NOTA: los factores de estrés oxidativo como el paraquat pueden ser sustituidos por H 2 O 2 en este ensayo. Las concentraciones utilizadas para otros factores de estrés oxidativo puede ser diferente de los utilizados para H 2 O 2. </li></ol></li><li> Lavar y medir el OD 600 de los cultivos de una noche como se describe en el paso 3.7. </li><li> Normalizar el OD 600 de todo el cu nocheltures al valor más bajo para el conjunto de cepas están probando. P. aeruginosa en general, tiene un OD 600 de aproximadamente 2,5 cuando se desarrolló durante la noche en LB + NTBC o LB + DMSO. <ol><li> Determinar el volumen de cultivo necesario para diluir la cultura al más bajo OD 600 en un volumen total de 1 ml. Por ejemplo, si una cultura tiene una DO 600 de 3 y el más bajo OD 600 para el conjunto de las cepas es 2.5, realice el siguiente cálculo: (2,5) (1 ml) = (3) (x). x = 0,833 ml. Se colocarán 0,833 ml de cultivo en un tubo de microcentrífuga. </li><li> Calcular la cantidad de LB + NTBC (300 mM) o LB + DMSO necesario para llevar el volumen a 1 ml de cultivo. Para el ejemplo en el paso 4.4.1, la cantidad de LB + NTBC o LB + DMSO añade al cultivo sería 0,167 ml (1 ml de volumen total de 0.833 ml - Cultura). Hacer que las soluciones stock de LB + NTBC y LB + DMSO a utilizar para estas diluciones basado en el volumen necesario para diluir todas las cepas. </li><li> Mezclar la cultura y LB + NTBC o LB + DMSO mediante agitación con vórtex. </li></ol></li><li> Para mantener los cultivos en una concentración constante de NTBC o DMSO, realizar diluciones en serie de diez veces de los cultivos de una noche normalizados en PBS + NTBC o PBS + DMSO. <ol><li> Haga soluciones madre de PBS + NTBC y PBS + DMSO. Para un conjunto de diluciones de una cepa, mezclar 300 mM NTBC o un volumen equivalente de DMSO con PBS para dar un volumen total de 720 l. Escala estas poblaciones hacia arriba o abajo dependiendo del número de cepas se ponen a prueba. </li><li> Tubos de microcentrífuga Etiqueta para 10 -1 a través de diluciones 10 -7 serie. Añadir 90 l de PBS + NTBC o PBS + DMSO a los tubos apropiados. Utilice PBS + NTBC para las cepas cultivadas en LB + NTBC y utilizar PBS + DMSO para las cepas cultivadas en LB + DMSO. </li><li> Añadir 10 l de la cultura al tubo de dilución 10 -1 apropiado. Mezclar mediante agitación y la transferencia de 10 l de la dilución 10 -1 al tubo de dilución 10 -2. Repita hasta que todas las diluciones han sido performó. Cambie puntas de pipeta entre las diluciones. </li></ol></li><li> Spot 5 l de la 10 -3 a través de 10 -7 diluciones en LB + H 2 O 2 placas por duplicado para cada cepa. Utilice una punta de pipeta si se colocan puntos de la mayoría diluir al menos diluido (10 -7 a 10 -3). No incline o inclinar la placa hasta que el líquido se haya secado en la placa. </li><li> Incubar las placas durante 24-48 horas a 37 ° C (incubadora de aire), dependiendo de la cepa. NOTA: P. aeruginosa PAO1 tendrá buenas colonias de tamaño en LB después de 24 h de incubación. Incubar las cepas hasta que tienen colonias de aproximadamente el mismo tamaño que PAO1. </li><li> Fotografiar las placas utilizando una cámara CCD por encima de un transiluminador. Opcionalmente, editar las fotos para el contraste y la cosecha al mismo tamaño. Contar el número de colonias en cada punto para determinar cambios en la sensibilidad al estrés oxidativo. </li></ol>

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D., Dankai, W., Vanittanakom, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Melanogenesis+in+dermatophyte+species+in+vitro++during+infection.">Melanogenesis in dermatophyte species in vitro during infection.</a> Microbiology. 157, 2348-2356 (2011).</li><li>Khajo, 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=Protection+of+Melanized+Cryptococcus+neoformans+Lethal+Dose+Gamma+Irradiation+Involves+Changes+in+Melanin's+Chemical+Structure+and+Paramagnetism.">Protection of Melanized Cryptococcus neoformans Lethal Dose Gamma Irradiation Involves Changes in Melanin's Chemical Structure and Paramagnetism.</a> PLoS ONE. 6, e25092 (2011).</li><li>Hancock, R. E. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Hancock Laboratory Methods. , (2015).</li></ol>

The authors declare that they have no competing financial interests.

The NTBC titration method described in this protocol will allow the user to determine if NTBC can reduce or eliminate pyomelanin production in bacteria, and determine the concentration of NTBC required. The most critical step in the NTBC titration assay is determining the range of NTBC concentrations to use in the assay. Different strains of P. aeruginosa have different sensitivities to NTBC, and laboratory strains may be more sensitive to NTBC than clinical isolates12 (Figure 2). The...

Pseudomonas aeruginosa is a Gram negative bacterium that produces a variety of pigments including pyomelanin, a red-brown pigment that helps provide protection from oxidative stress1-4 and binds a variety of compounds, including aminoglycoside antibiotics5-7. Pyomelanin production is caused by a defect in the tyrosine catabolism pathway4,8, either through deletions or mutations of the gene encoding homogentisate 1,2-dioxygenase (HmgA)1,9 or through imbalances in the various enzymes in the pathway10. Homogentisate accumulates due to inactivation of HmgA, and is secreted and oxidized to form pyomelanin11. Production of pyomelanin can be abolished or reduced in a dose dependent manner through treatment with the herbicide 2-[2-nitro-4-(trifluoromethyl)benzoyl]-1,3-cyclohexanedione (NTBC)12, which inhibits 4-hydroxyphenylpyruvate dioxygenase (Hpd) in the tyrosine catabolism pathway13. Hpd is required for the formation of homogentisate, and therefore pyomelanin11. 
We describe in detail three techniques that were important in our studies of NTBC treatment of pyomelanin producing strains of P. aeruginosa. These techniques include titration of NTBC to determine the concentrations that will abolish or reduce pyomelanin production in laboratory and clinical pyomelanin producing strains, determination of the minimum inhibitory concentration (MIC) of antibiotics when bacteria are treated with NTBC, and the resulting sensitivity to oxidative stress with NTBC treatment.
The titration assay we developed serves two purposes. First, the assay will allow the user to determine if NTBC can abolish or reduce pyomelanin production in the bacterium being studied and at which concentrations. This will allow the user to determine sensitivity to NTBC, since different strains of bacteria may have different sensitivities to this compound, as observed in P. aeruginosa12. Second, the NTBC titration assay will allow the user to determine the appropriate concentration of NTBC to use in subsequent assays, such as antibiotic MIC and oxidative stress response assays, if the goal is to abolish or reduce pyomelanin production and determine the effects of pigment reduction. 
The titration assay works because a visible difference in pyomelanin production can be seen in strains treated with NTBC and the differences in pyomelanin production are dose dependent12. Additionally, this technique can be applied to the study of other compounds that may eliminate or enhance pigment production in bacteria.
Antibiotic MICs are used to determine the sensitivity of bacteria to antibiotics. There are several methods to determine MICs, including agar dilution plates and broth dilutions14. Broth dilutions can be performed in small test tubes or in a 96-well microtiter plate. The microtiter plate method of MIC determination described herein will allow the user to test a wide range of antibiotics using a minimum of resources. The assay provides reproducibility as well as flexibility in the number of antibiotics and strains tested by this method. Additionally, with the incorporation of NTBC in the assay, the user can determine if elimination or reduction of pyomelanin production alters antibiotic sensitivity in bacteria that produce pyomelanin.
Bacterial response to oxidative stress can be tested in several ways. The most common methods described are either viable counts of bacteria subjected to oxidative stress for a period of time1, or oxidative stress disc diffusion assays15. These methods tend to use high concentrations of oxidative stressors to examine the effects of oxidative stress in bacteria and results can be quite variable between biological replicates. The viable count assay also tends to use more agar plates than the other methods. The spot plate assay we describe uses low concentrations of H2O2 and allows the user to test the oxidative stress response of multiple strains using a minimum of plates. The assay is also consistently reproducible between technical and biological replicates. As pyomelanin is involved in resistance to oxidative stress, the incorporation of NTBC in the assay allows the user to determine the effects of elimination of pyomelanin production on oxidative stress resistance.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>2-[2-nitro-4-(trifluoromethyl)benzoyl]-1,3-cyclohexanedione (NTBC)</td>
			<td>Sigma-Aldrich</td>
			<td>SML0269-50mg</td>
			<td>Also called nitisinone.&#160; Soluble in DMSO.</td>
		</tr>
		<tr>
			<td>H2O2</td>
			<td>Sigma-Aldrich</td>
			<td>216763-100ML</td>
			<td>30 wt. % in H2O.&#160; Stabilized.</td>
		</tr>
		<tr>
			<td>Gentamycin</td>
			<td>Gold Bio</td>
			<td>G-400-100</td>
			<td>Soluble in H2O.&#160; Filter sterilize.</td>
		</tr>
		<tr>
			<td>Kanamycin</td>
			<td>Fisher Scientific</td>
			<td>BP906-5</td>
			<td>Soluble in H2O.&#160; Filter sterilize.</td>
		</tr>
		<tr>
			<td>Tobramycin</td>
			<td>Sigma-Aldrich</td>
			<td>T4014-100MG</td>
			<td>Soluble in H2O.&#160; Filter sterilize.</td>
		</tr>
	</tbody>
</table>

methods to inhibit bacterial pyomelanin production and determine the corresponding increase in sensitivity to oxidative stress

Pyomelanin is an extracellular red-brown pigment produced by several bacterial and fungal species. This pigment is derived from the tyrosine catabolism pathway and contributes to increased oxidative stress resistance. Pyomelanin production in Pseudomonas aeruginosa is reduced in a dose dependent manner through treatment with 2-[2-nitro-4-(trifluoromethyl)benzoyl]-1,3-cyclohexanedione (NTBC). We describe a titration method using multiple concentrations of NTBC to determine the concentration of drug that will reduce or abolish pyomelanin production in bacteria. The titration method has an easily quantifiable outcome, a visible reduction in pigment production with increasing drug concentrations. We also describe a microtiter plate method to assay antibiotic minimum inhibitory concentration (MIC) in bacteria. This method uses a minimum of resources and can easily be scaled up to test multiple antibiotics in one microtiter plate for one strain of bacteria. The MIC assay can be adapted to test the affects of non-antibiotic compounds on bacterial growth at specific concentrations. Finally, we describe a method for testing bacterial sensitivity to oxidative stress by incorporating H2O2 into agar plates and spotting multiple dilutions of bacteria onto the plates. Sensitivity to oxidative stress is indicated by reductions in colony number and size for the different dilutions on plates containing H2O2 compared to a no H2O2 control. The oxidative stress spot plate assay uses a minimum of resources and low concentrations of H2O2. Importantly, it also has good reproducibility. This spot plate assay could be adapted to test bacterial sensitivity to various compounds by incorporating the compounds in agar plates and characterizing the resulting bacterial growth.

Titulaciones NTBC Las titulaciones NTBC se utilizaron para determinar si NTBC fue capaz de reducir la producción de pyomelanin en P. aeruginosa, y también identificar la concentración de NTBC que elimina o reduce la producción pyomelanin para uso en ensayos adicionales. Es posible que haya variaciones en los niveles de pyomelanin producido en diferentes repeticiones, pero las tendencias generales permanecer constante. El ensayo de valoración NTBC también podría ser m...

Watch this Scientific Journal Video about Methods to Inhibit Bacterial Pyomelanin Production and Determine the Corresponding Increase in Sensitivity to Oxidative Stress at JoVE.com

Methods to Inhibit Bacterial Pyomelanin Production and Determine the Corresponding Increase in Sensitivity to Oxidative Stress

Bacterial pyomelanin production results in increased resistance to oxidative stress and virulence. We report on techniques that can be used to determine inhibition of pyomelanin production and assay the resulting increase in sensitivity to oxidative stress in bacteria, as well as determine antibiotic minimum inhibitory concentration (MIC).

Métodos para inhibir bacteriana Pyomelanin Producción y determinar el correspondiente aumento en la sensibilidad al estrés oxidativo

Pyomelanin is an extracellular red-brown pigment produced by several bacterial and fungal species. This pigment is derived from the tyrosine catabolism ...

methods-to-inhibit-bacterial-pyomelanin-production-determine

Research

JoVE Journal

Immunology and Infection

8.1K vistas.  University of Wisconsin Milwaukee. Bacterial pyomelanin production results in increased resistance to oxidative stress and virulence. We report on techniques that can be used to determine inhibition of pyomelanin production and assay the resulting increase in sensitivity to oxidative stress in bacteria, as well as determine antibiotic minimum inhibitory concentration (MIC).

Video: Methods to Inhibit Bacterial Pyomelanin Production and Determine the Corresponding Increase in Sensitivity to Oxidative Stress

Introducing Shear Stress in the Study of Bacterial Adhesion

During bacterial infections a sequence of interactions occur between the pathogen and its host. Bacterial adhesion to the host cell surface is often the initial and determining step of the pathogenesis. Although experimentally adhesion is mostly studied in static conditions adhesion actually takes place in the presence of flowing liquid. First encounters between bacteria and their host often occur at the mucosal level, mouth, lung, gut, eye, etc. where mucus flows along the surface of epithelial cells. Later in infection, pathogens occasionally access the blood circulation causing life-threatening illnesses such as septicemia, sepsis and meningitis. A defining feature of these infections is the ability of these pathogens to interact with endothelial cells in presence of circulating blood. The presence of flowing liquid, mucus or blood for instance, determines adhesion because it generates a mechanical force on the pathogen. To characterize the effect of flowing liquid one usually refers to the notion of shear stress, which is the tangential force exerted per unit area by a fluid moving near a stationary wall, expressed in dynes/cm2. Intensities of shear stress vary widely according to the different vessels type, size, organ, location etc. (0-100 dynes/cm2). Circulation in capillaries can reach very low shear stress values and even temporarily stop during periods ranging between a few seconds to several minutes 1. On the other end of the spectrum shear stress in arterioles can reach 100 dynes/cm2 2. The impact of shear stress on different biological processes has been clearly demonstrated as for instance during the interaction of leukocytes with the endothelium 3. To take into account this mechanical parameter in the process of bacterial adhesion we took advantage of an experimental procedure based on the use of a disposable flow chamber 4. Host cells are grown in the flow chamber and fluorescent bacteria are introduced in the flow controlled by a syringe pump. We initially focused our investigations on the bacterial pathogen Neisseria meningitidis, a Gram-negative bacterium responsible for septicemia and meningitis. The procedure described here allowed us to study the impact of shear stress on the ability of the bacteria to: adhere to cells 1, to proliferate on the cell surface 5and to detach to colonize new sites 6 (Figure 1). Complementary technical information can be found in reference 7. Shear stress values presented here were chosen based on our previous experience1 and to represent values found in the literature. The protocol should be applicable to a wide range of pathogens with specific adjustments depending on the objectives of the study.

During the infection process, a key step is the adhesion of pathogens with host cells. In most instances this adhesion step occurs in the presence of mechanical stress generated by flowing liquid. We describe a technique that introduces shear stress as an important parameter in the study of bacterial adhesion.

La introducción de la tensión de cizallamiento en el Estudio de la adhesión bacteriana

During bacterial infections a sequence of interactions occur between the pathogen and its host. Bacterial adhesion to the host cell surface is often the ...

Investigación

Inmunología e Infección

Using the Overlay Assay to Qualitatively Measure Bacterial Production of and Sensitivity to Pneumococcal Bacteriocins

Streptococcus pneumoniae colonizes the highly diverse polymicrobial community of the nasopharynx where it must compete with resident organisms. We have shown that bacterially produced antimicrobial peptides (bacteriocins) dictate the outcome of these competitive interactions. All fully-sequenced pneumococcal strains harbor a bacteriocin-like peptide (blp) locus. The blp locus encodes for a range of diverse bacteriocins and all of the highly conserved components needed for their regulation, processing, and secretion. The diversity of the bacteriocins found in the bacteriocin immunity region (BIR) of the locus is a major contributor of pneumococcal competition. Along with the bacteriocins, immunity genes are found in the BIR and are needed to protect the producer cell from the effects of its own bacteriocin. The overlay assay is a quick method for examining a large number of strains for competitive interactions mediated by bacteriocins. The overlay assay also allows for the characterization of bacteriocin-specific immunity, and detection of secreted quorum sensing peptides. The assay is performed by pre-inoculating an agar plate with a strain to be tested for bacteriocin production followed by application of a soft agar overlay containing a strain to be tested for bacteriocin sensitivity. A zone of clearance surrounding the stab indicates that the overlay strain is sensitive to the bacteriocins produced by the pre-inoculated strain. If no zone of clearance is observed, either the overlay strain is immune to the bacteriocins being produced or the pre-inoculated strain does not produce bacteriocins. To determine if the blp locus is functional in a given strain, the overlay assay can be adapted to evaluate for peptide pheromone secretion by the pre-inoculated strain. In this case, a series of four lacZ-reporter strains with different pheromone specificity are used in the overlay.

Competition in Streptococcus pneumoniae is mediated by bacteriocins, small antimicrobial peptides with inhibitory activity towards pneumococcus and other related species.&#160; Here we describe an optimized bacterial overlay assay that allows for the characterization of bacteriocin activity and inhibitory spectrum, bacteriocin-specific immunity, and detection of secreted quorum sensing peptides.

Uso de la superposición de ensayo para medir cualitativamente la producción bacteriana y sensibilidad hacia neumocócica bacteriocinas

Streptococcus pneumoniae colonizes the highly diverse polymicrobial community of the nasopharynx where it must compete with resident organisms.  We have ...

Methods to Increase the Sensitivity of High Resolution Melting Single Nucleotide Polymorphism Genotyping in Malaria

Despite decades of eradication efforts, malaria remains a global burden. Recent renewed interest in regional elimination and global eradication has been accompanied by increased genomic information about Plasmodium parasite species responsible for malaria, including characteristics of geographical populations as well as variations associated with reduced susceptibility to anti-malarial drugs.
One common genetic variation, single-nucleotide polymorphisms (SNPs), offers attractive targets for parasite genotyping. These markers are useful not only for tracking drug resistance markers but also for tracking parasite populations using markers not under drug or other selective pressures.
SNP genotyping methods offer the ability to track drug resistance as well as to fingerprint individual parasites for population surveillance, particularly in response to malaria control efforts in regions nearing elimination status.
While informative SNPs have been identified that are agnostic to specific genotyping technologies, high-resolution melting (HRM) analysis is particularly suited to field-based studies. Compared to standard fluorescent-probe based methods that require individual SNPs in a single labeled probe and offer at best 10% sensitivity to detect SNPs in samples that contain multiple genomes (polygenomic), HRM offers 2-5% sensitivity. Modifications to HRM, such as blocked probes and asymmetric primer concentrations as well as optimization of amplification annealing temperatures to bias PCR towards amplification of the minor allele, further increase the sensitivity of HRM. While the sensitivity improvement depends on the specific assay, we have increased detection sensitivities to less than 1% of the minor allele.
In regions approaching malaria eradication, early detection of emerging or imported drug resistance is essential for prompt response. Similarly, the ability to detect polygenomic infections and differentiate imported parasite types from cryptic local reservoirs can inform control programs.
This manuscript describes modifications to high resolution melting technology that further increase its sensitivity to identify polygenomic infections in patient samples.

While high resolution melting analysis offers the ability to differentiate between single nucleotide polymorphisms in a heterogeneous population, mutant allele amplification bias can increase its ability to detect alleles present at relatively low percentages within a sample. This protocol describes improvements that improve the sensitivity of high resolution melting analysis.

Los métodos para aumentar la sensibilidad de alta resolución de fusión polimorfismo de nucleótido único Genotipado de la Malaria

Despite decades of eradication efforts, malaria remains a global burden. Recent renewed interest in regional elimination and global eradication has been ...

In Vitro and In Vivo Model to Study Bacterial Adhesion to the Vessel Wall Under Flow Conditions

In order to cause endovascular infections and infective endocarditis, bacteria need to be able to adhere to the vessel wall while being exposed to the shear stress of flowing blood.
To identify the bacterial and host factors that contribute to vascular adhesion of microorganisms, appropriate models that study these interactions under physiological shear conditions are needed. Here, we describe an in vitro flow chamber model that allows to investigate bacterial adhesion to different components of the extracellular matrix or to endothelial cells, and an intravital microscopy model that was developed to directly visualize the initial adhesion of bacteria to the splanchnic circulation in vivo. These methods can be used to identify the bacterial and host factors required for the adhesion of bacteria under flow. We illustrate the relevance of shear stress and the role of von Willebrand factor for the adhesion of Staphylococcus aureus using both the in vitro and in vivo model.

In Vitro and In Vivo Model to Study Bacterial Adhesion to the Vessel Wall Under Flow Conditions

To study the interaction of bacteria with the blood vessels under shear stress, a flow chamber and an in vivo mesenteric intravital microscopy model are described that allow to dissect the bacterial and host factors contributing to vascular adhesion.

In vitro e in vivo modelo para estudiar la adhesión bacteriana a la pared del recipiente en condiciones de flujo

In order to cause endovascular infections and infective endocarditis, bacteria need to be able to adhere to the vessel wall while being exposed to the ...

Neutrophil Isolation and Analysis to Determine their Role in Lymphoma Cell Sensitivity to Therapeutic Agents

Neutrophils are the most abundant (40% to 75%) type of white blood cells and among the first inflammatory cells to migrate towards the site of inflammation. They are key players in the innate immune system and play major roles in cancer biology. Neutrophils have been proposed as key mediators of malignant transformation, tumor progression, angiogenesis and in the modulation of the antitumor immunity; through their release of soluble factors or their interaction with tumor cells. To characterize the specific functions of neutrophils, a fast and reliable method is coveted for in vitro isolation of neutrophils from human blood. Here, a density gradient separation method is demonstrated to isolate neutrophils as well as mononuclear cells from the blood. The procedure consists of layering the density gradient solution such as Ficoll carefully above the diluted blood obtained from patients diagnosed with chronic lymphocytic leukemia (CLL), followed by centrifugation, isolation of mononuclear layer, separation of neutrophils from RBCsby dextran then lysis of residual erythrocytes. This method has been shown to isolate neutrophils &#8805; 90 % pure. To mimic the tumor microenvironment, 3-dimensional (3D) experiments were performed using basement membrane matrix such as Matrigel. Given the short half-life of neutrophils in vitro, 3D experiments with fresh human neutrophils cannot be performed. For this reason promyelocytic HL60 cells are differentiated along the granulocytic pathway using the differentiation inducers dimethyl sulfoxide (DMSO) and retinoic acid (RA). The aim of our experiments is to study the role of neutrophils on the sensitivity of lymphoma cells to anti-lymphoma agents. However these methods can be generalized to study the interactions of neutrophils or neutrophil-like cells with a large range of cell types in different situations.

Neutrophils are the most abundant type of white blood cells. The isolation of neutrophils from human blood by density gradient separation method and the differentiation of human promyelocytic (HL60) cells along the granulocytic pathway are described here; to test their role on sensitivity of lymphoma cells to anti-lymphoma agents.

Aislamiento de neutrófilos y análisis para determinar su papel en el linfoma de células sensibles a los agentes terapéuticos

Neutrophils are the most abundant (40% to 75%) type of white blood cells and among the first inflammatory cells to migrate towards the site of ...

A RAPID Method for Blood Processing to Increase the Yield of Plasma Peptide Levels in Human Blood

Research in the field of food intake regulation is gaining importance. This often includes the measurement of peptides regulating food intake. For the correct determination of a peptide&#39;s concentration, it should be stable during blood processing. However, this is not the case for several peptides which are quickly degraded by endogenous peptidases. Recently, we developed a blood processing method employing Reduced temperatures, Acidification, Protease inhibition, Isotopic exogenous controls and Dilution (RAPID) for the use in rats. Here, we have established this technique for the use in humans and investigated recovery, molecular form and circulating concentration of food intake regulatory hormones. The RAPID method significantly improved the recovery for 125I-labeled somatostatin-28 (+39%), glucagon-like peptide-1 (+35%), acyl ghrelin and glucagon (+32%), insulin and kisspeptin (+29%), nesfatin-1 (+28%), leptin (+21%) and peptide YY3-36 (+19%) compared to standard processing (EDTA blood on ice, p&#160;&#60;0.001). High performance liquid chromatography showed the elution of endogenous acyl ghrelin at the expected position after RAPID processing, while after standard processing 62% of acyl ghrelin were degraded resulting in an earlier peak likely representing desacyl ghrelin. After RAPID processing the acyl/desacyl ghrelin ratio in blood of normal weight subjects was 1:3 compared to 1:23 following standard processing (p&#160;= 0.03). Also endogenous kisspeptin levels were higher after RAPID compared to standard processing (+99%, p&#160;= 0.02). The RAPID blood processing method can be used in humans, yields higher peptide levels and allows for assessment of the correct molecular form.

The RAPID blood processing method can be used in humans and yields higher peptide levels as well as allows for assessment of the correct molecular form. Therefore, this method will be a valuable tool in peptide research.

Un método rápido para el procesamiento de sangre para aumentar el rendimiento de los niveles plasmáticos de péptido en la sangre humana

Research in the field of food intake regulation is gaining importance. This often includes the measurement of peptides regulating food intake. For the ...

Overexpression and Purification of Human Cis-prenyltransferase in Escherichia coli

Prenyltransferases (PT) are a group of enzymes that catalyze chain elongation of allylic diphosphate using isopentenyl diphosphate (IPP) via multiple condensation reactions. DHDDS (dehydrodolichyl diphosphate synthase) is a eukaryotic long-chain cis-PT (forming cis double bonds from the condensation reaction) that catalyzes chain elongation of farnesyl diphosphate (FPP, an allylic diphosphate) via multiple condensations with isopentenyl diphosphate (IPP). DHDDS is of biomedical importance, as a non-conservative mutation (K42E) in the enzyme results in retinitis pigmentosa, ultimately leading to blindness. Therefore, the present protocol was developed in order to acquire large quantities of purified DHDDS, suitable for mechanistic studies. Here, the usage of protein fusion, optimized culture conditions and codon-optimization were used to allow the overexpression and purification of functionally active human DHDDS in E. coli. The described protocol is simple, cost-effective and time sparing. The homology of cis-PT among different species suggests that this protocol may be applied for other eukaryotic cis-PT as well, such as those involved in natural rubber synthesis.

Overexpression and Purification of Human Cis-prenyltransferase in Escherichia coli

A simple protocol for overexpression and purification of codon-optimized, human cis-prenyltransferase, under non-denaturing conditions, from Escherichia coli, is described, along with an enzymatic activity assay. This protocol can be generalized for production of other cis- prenyltransferase proteins in quantity and quality suitable for mechanistic studies.

Sobreexpresión y Purificación de Humanos<em&gt; Cis</em&gt; -preniltransferasa en<em&gt; Escherichia coli</em

Prenyltransferases (PT) are a group of enzymes that catalyze chain elongation of allylic diphosphate using isopentenyl diphosphate (IPP) via multiple ...

Isolation of Salmonella typhimurium-containing Phagosomes from Macrophages

Salmonella typhimurium is a facultative intracellular bacterium that causes gastroenteritis in humans. After invasion of the lamina propria, S. typhimurium bacteria are quickly detected and phagocytized by macrophages, and contained in vesicles known as phagosomes in order to be degraded. Isolation of S. typhimurium-containing phagosomes have been widely used to study how S. typhimurium infection alters the process of phagosome maturation to prevent bacterial degradation. Classically, the isolation of bacteria-containing phagosomes has been performed by sucrose gradient centrifugation. However, this process is time-consuming, and requires specialized equipment and a certain degree of dexterity. Described here is a simple and quick method for the isolation of S. typhimurium-containing phagosomes from macrophages by coating the bacteria with biotin-streptavidin-conjugated magnetic beads. Phagosomes obtained by this method can be suspended in any buffer of choice, allowing the utilization of isolated phagosomes for a broad range of assays, such as protein, metabolite, and lipid analysis. In summary, this method for the isolation of S. typhimurium-containing phagosomes is specific, efficient, rapid, requires minimum equipment, and is more versatile than the classical method of isolation by sucrose gradient-ultracentrifugation.

Isolation of Salmonella typhimurium-containing Phagosomes from Macrophages

We describe here a simple and quick method for the isolation of Salmonella typhimurium-containing phagosomes from macrophages by coating the bacteria with biotin and streptavidin.

Aislamiento de Salmonella typhimurium-que contienen fagosomas de los macrófagos

Salmonella typhimurium is a facultative intracellular bacterium that causes gastroenteritis in humans. After invasion of the lamina propria, S. ...

A Novel Feeder-free System for Mass Production of Murine Natural Killer Cells In Vitro

Natural killer (NK) cells belong to the innate immune system and are a first-line anti-cancer immune defense; however, they are suppressed in the tumor microenvironment and the underlying mechanism is still largely unknown. The lack of a consistent and reliable source of NK cells limits the research progress of NK cell immunity. Here, we report an in vitro system that can provide high quality and quantity of bone marrow-derived murine NK cells under a feeder-free condition. More importantly, we also demonstrate that siRNA-mediated gene silencing successfully inhibits the E4bp4-dependent NK cell maturation by using this system. Thus, this novel in vitro NK cell differentiating system is a biomaterial solution for immunity research.

A Novel Feeder-free System for Mass Production of Murine Natural Killer Cells In Vitro

Here, we present a protocol to mass-produce gene-silencing murine NK cells by using a feeder-free differentiation system for mechanistic study in vitro and in vivo.

Un novedoso sistema de alimentador-libre para la producción masiva de células de asesino naturales murinos In Vitro

Natural killer (NK) cells belong to the innate immune system and are a first-line anti-cancer immune defense; however, they are suppressed in the tumor ...

Metabolic Mapping: Quantitative Enzyme Cytochemistry and Histochemistry to Determine the Activity of Dehydrogenases in Cells and Tissues

Altered cellular metabolism is a hallmark of many diseases, including cancer, cardiovascular diseases and infection. The metabolic motor units of cells are enzymes and their activity is heavily regulated at many levels, including the transcriptional, mRNA stability, translational, post-translational and functional level. This complex regulation means that conventional quantitative or imaging assays, such as quantitative mRNA experiments, Western Blots and immunohistochemistry, yield incomplete information regarding the ultimate activity of enzymes, their function and/or their subcellular localization. Quantitative enzyme cytochemistry and histochemistry (i.e., metabolic mapping) show in-depth information on in situ enzymatic activity and its kinetics, function and subcellular localization in an almost true-to-nature situation.
We describe a protocol to detect the activity of dehydrogenases, which are enzymes that perform redox reactions to reduce cofactors such as NAD(P)+ and FAD. Cells and tissue sections are incubated in a medium that is specific for the enzymatic activity of one dehydrogenase. Subsequently, the dehydrogenase that is the subject of investigation performs its enzymatic activity in its subcellular site. In a chemical reaction with the reaction medium, this ultimately generates blue-colored formazan at the site of the dehydrogenase&#39;s activity. The formazan&#39;s absorbance is therefore a direct measure of the dehydrogenase&#39;s activity and can be quantified using monochromatic light microscopy and image analysis. The quantitative aspect of this protocol enables researchers to draw statistical conclusions from these assays.
Besides observational studies, this technique can be used for inhibition studies of specific enzymes. In this context, studies benefit from the true-to-nature advantages of metabolic mapping, giving in situ results that may be physiologically more relevant than in vitro enzyme inhibition studies. In all, metabolic mapping is an indispensable technique to study metabolism at the cellular or tissue level. The technique is easy to adopt, provides in-depth, comprehensive and integrated metabolic information and enables rapid quantitative analysis.

Here, we present a protocol that can be used to microscopically visualize and quantify activity of dehydrogenases in cells and tissues and its kinetics, function and subcellular localization.

Mapeo metabólico: Citoquímica enzimática cuantitativa y la histoquímica para determinar la actividad de Deshidrogenasas en células y tejidos

Altered cellular metabolism is a hallmark of many diseases, including cancer, cardiovascular diseases and infection. The metabolic motor units of cells ...