The authors thank Bryan T. Vinyard of the USDA, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, Biometrical Consulting Service, Beltsville, MD for statistical analyses. This work was supported in part by a grant to J.C.D. from the Deployed War Fighter Protection (DWFP) Research Program funded by the Department of Defense through the Armed Forces Pest Management Board (AFPMB).

1. Crianza Ae. adultos aegypti <ol><li> Los huevos eclosionan en aproximadamente ¾ de pulgada de agua en la bandeja poco profunda. El hacinamiento reducirá el tamaño de los adultos. </li><li> Larvas posterior a 25 ° C (12 hL: 12-HD) y alimentarlos con comida para peces suelo. NOTA: La sobrealimentación puede reducir las tasas de supervivencia. </li><li> Retire pupas individualmente por pipeta Pasteur diario y transferir a los platos de plástico (9 cm x 5,5 cm) dentro de pequeños cubos de contención con tapas de malla fina, estableciendo así 24 grupos de edad hr. </li><li> Alimentación mosquitos adultos 10% de solución de sacarosa por bola de algodón colocado en las paredes de pantalla de una carcasa de la jaula de los mosquitos en una cámara ambiental a 27 ° C y humedad relativa del 70% bajo el mismo fotoperiodo como larvas. </li><li> Para electrofisiología, utilice 5-10 días los animales viejos. En general, los animales más grandes producirán mejores resultados. Para el aislamiento de ARN, utilizar animales que están dentro de un mismo grupo de edad de 24 horas en el rango de edad 5-10 días. </li></ol><ol><li> Determinar una concentración adecuada de electrolito (por ejemplo, 1-10 mM) que provoca una mínima actividad de las neuronas sensoriales seleccionados. NaCl 10 mM o 1 mM KCl son electrolitos razonables para poner a prueba la actividad basal al comenzar un experimento. </li><li> Disolver cada producto químico experimental en un disolvente apropiado (si no el agua, utilizar etanol o DMSO) que tiene poco o ningún efecto sobre la actividad de pico en comparación con electrolito solo. Las concentraciones finales de etanol al 10% o 1% de DMSO son concentraciones de partida razonables. </li><li> Seleccionar apropiado (por ejemplo la quinina por amargo o sacarosa para dulces) productos químicos de control que están bien descritos disuasorias de la alimentación o estimulantes en los insectos. </li></ol> 3. Electrofisiología (grabación punta 8. La figura 1) <ol><li> Electrodos de vidrio Forma tirando mecánicamente capilares de vidrio. Optimizar calor y tire ajustes para tirar de vidrio para formar recordi forma apropiadaelectrodos NG. Romper con cuidado extremo del electrodo de vidrio usando pinzas bajo un microscopio de disección para crear electrodo de punta abertura que es lo suficientemente amplia como para envolver sensillum objetivo, pero lo suficientemente pequeño para evitar el contacto con las estructuras vecinas. </li><li> Bajo el microscopio, identificar visualmente por la morfología y la posición del objetivo sensilla / sensillum para asegurar la repetibilidad de grabación punta. Animales de preparación para permitir el libre acceso a sensilla de ángulo de entrada del electrodo. </li><li> Insectos anestesiar adultos fríos en el congelador a -20 ° C. Evitar daños a las neuronas periféricas por la sobreexposición a las bajas temperaturas. Cortar tiras angostas de cinta de celofán con hoja de afeitar en portaobjetos de vidrio. Inmovilizar todo insecto en un portaobjetos de vidrio utilizando tiras estrechas. </li><li> Insertar un alambre de tungsteno afilado químicamente en el tórax dorsal o el ojo para servir como el electrodo (tierra) indiferente. </li><li> Rellene electrodo de vidrio realizada en el paso 3.1 con una solución estimulante de interés. Usando una jeringa insertada, la tapa de llenadoIllary desde finales tirado al extremo romo. Flick a cabo todas las burbujas de aire, la celebración de fin derribado. Inserte un alambre de plata (cloruración opcional) en el electrodo de vidrio realizada en el paso 3.1 para servir como registro y electrodo de estimulación. </li><li> Conectar los electrodos a un preamplificador que está diseñado para grabaciones de contacto quimiorreceptora sensilla en los insectos. Este preamplificador (300 Hz-3 filtro de banda kHz) reducirá el tiempo de establecimiento para capturar la actividad neuronal tan cerca a los estímulos introducción posible. Recoger, almacenar y analizar las señales eléctricas utilizando un microordenador equipado con software de grabación de espiga. NOTA: Conexión a tierra del sistema de grabación correctamente puede mejorar drásticamente la relación señal-ruido. </li><li> Estimular sensilla con una solución de control (sólo electrolito) para asegurar la funcionalidad. Cuente picos a partir de 200 ms siguientes el artefacto de estímulo para todas las preparaciones. </li><li> Selección aleatoria de la orden de sustancias químicas de prueba para todos los experimentos, excepto los estudios de dosis-respuesta,para eliminar los prejuicios. Para los estudios de dosis-respuesta, exponer sensilla a concentraciones crecientes de la sustancia química experimental. Permita un mínimo de 3 minutos entre estímulos para asegurar una adecuada recuperación. NOTA: Este requisito puede variar dependiendo de los insectos y sensilla. Umbral se define como la concentración para la cual el error estándar no se superponga con el error estándar para la concentración más baja ensayada. </li></ol> 4. Aislamiento de ARN y secuenciación (Figura 2) <ol><li> Preparar las majas RNasa libre herméticamente cerradas al enfriarlos en hielo seco antes de tejido disruption.Prepare acompañan majas sin RNasa para aerosol que se ajusten a los tubos de tapa a presión con fuerza. Mantenga los tubos de recogida cerrados a menos que la disección de forma activa para evitar el exceso de condensación. </li><li> Utilizando aspirador filtrada, colocar 30 a 40 mosquitos en frío anestesiados (15 seg en congelador a -20ºC) en el escenario frío y ordenar por sexo. Coloque los animales dorsal lado de abajo, agarrando las alas para no dañar apéndices gustativas.</li><li> El uso de dos pares de pinzas finas, diseccionar labella emparejado o tarsos de los machos o hembras con un microscopio de disección y limitar la inclusión de los tejidos adyacentes. NOTA: 500 labella emparejado rinde aproximadamente 800-1,000 nanogramos de mRNA total. 400 tarsos individual (5 segmentos cada uno) producen 1,200-1,800 nanogramos de mRNA total. </li><li> Con un par de fórceps-jadeantes, ligeramente captar proboscis de mosquitos justo proximal a labella exponer estiletes interiores. Uso de otro par de collection-forceps, quitar y agregar labella tejido a lado del tubo de recogida de frío. </li><li> Con un par de fórceps, ligeramente captar la pierna mosquito en la salida de la tibia y el primer segmento tarsal. Uso de otro par de pinzas, retire tarsos y añadir tejido a lado del tubo de recogida de frío. NOTA: Tener en cuenta los tipos de células en la superficie del tejido deseado y no deseado. Si bien es importante para limitar la inclusión de los tejidos vecinos, es igualmente importante no omitir porciones de tejido deseado. El fimuestra final debe representar con precisión todo el órgano de interés. Crear un límite preciso con las pinzas de agarre de tal manera que el fórceps de recogida pueden liberar precisamente por raspado o agarrar sólo el tejido deseado. </li><li> Periódicamente, de girar el tubo de recogida brevemente en 0 ° C centrifugar a 9000 xg para mantener el tejido en la parte inferior del tubo. Si la humedad se acumula en tubos de recogida durante la disección, añadir 50uL de reactivo Trizol fría para cubrir el tejido recogido. </li><li> El uso de marcadores de laboratorio anti-manchas, identificándolas claramente uno-RNasa libre de 1,5 ml encajen tubo con tapa para cada tipo de tejido para su recogida. El uso de 1,5 ml Gradilla para tubos y nitrógeno líquido, por congelación luego moler tejido en polvo fino (finas piezas si en Trizol). Repetir una vez. Aumentar el volumen total de Trizol a 1 ml y resuspender tejido fundamental por agitación. </li><li> Añadir 200 ul de cloroformo y mezclar bien. Después de 5 min a temperatura ambiente, de girar en centrífuga a 4 ° C y 11.000 xg durante 15 min. Cuidadosamenteañadir capa acuosa directamente a una columna de filtro de ADN genómico. Centrifugar a 11.000 x g durante 5 min. Añadir un volumen igual de RNasa libre de 70% de etanol a fluir a través y mezclar pipeta. Traslado líquido a una columna colección ARN y continuar la extracción de RNA según las instrucciones proporcionadas. </li><li> Cuantificar y evaluar la pureza del ARN total en un espectrofotómetro precisión y proceder con cualquier método de secuenciación de ARN estándar. </li></ol> 5. RT-PCR cuantitativa Validación de RNA Sequencing (Figura 3) <ol><li> Seleccione tantos genes como posible comparar relativos niveles de expresión génica en un rango dinámico, tanto en abundancia predicho secuencia y función de los genes quimiosensorial presunta. </li><li> Pares de cebadores de diseño para cada gen diana para amplificar un 100 a 180 pares de bases producto de PCR específico. Excluir amplificación gDNA no específica asegurando al menos un cebador por juego abarca un límite de intrón. También puede utilizar el tratamiento DNasa para reducir la contaminación genómica. </li><li> Recogertejido de insectos como se describe en la sección anterior. Calcular la cantidad de tejido que se requiere para proporcionar suficiente ARN para completar todas las reacciones QRT-PCR. NOTA: triplicado Biológica y reacciones por triplicado técnicos proporcionarán máxima confianza en los resultados. </li><li> Calcula la cuantificación relativa de genes como objetivo X - (Ct [target] -Ct [referencia]) para cada gen diana y medio para cada replicar, tanto biológica como técnico. Utilice gen (s) de limpieza para normalizar los valores de Ct entre las réplicas biológicas y erradicar la escala del eje Y en las comparaciones de expresión relativa. </li><li> Evaluar la similitud de RNA-seq y conjuntos de datos qRT-PCR utilizando el, procedimiento de equivalencia de arranque basado en la regresión 9, iterativa aplicado, a los datos de cada tejido. NOTA: Este procedimiento identifica la &quot;región de similitud&quot; más pequeño que puede ser construido en torno a los datos de RNA-seq y QRT-PCR observado, y permitir la expresión génica relativa medido por QRT-PCR para ser considerado estadísticamente equivalente a la medición de la expresión génica relativa por RNA-seq. </li></ol>

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The authors have nothing to disclose.

El aspecto más difícil de potenciales de acción de grabación de sensilla gustativa es decidir qué respuestas son &quot;normales&quot;. Cuando se emplea un solo punta sensillum gustativa grabar la primera vez que una especie de insectos dado, el número total y sensibilidades de las neuronas receptoras gustativas (GRNs) son probablemente desconocido. Muchas grabaciones preliminares primera obligados a decidir el alcance y las concentraciones de los productos químicos para probar. En este caso, empezamos con la obse...

Compuestos como DEET, Picaridin, citronelal y IR3535 se ha demostrado eficaz para repeler mosquitos, incluyendo las importantes vectores de enfermedades Aedes aegypti 1,2. Registramos los potenciales de acción de las neuronas sensoriales asociadas con sensilla gustativo específico para determinar las células involucradas con la repelencia de mosquitos. Junto con la secuenciación de aguas abajo de los genes expresados ​​en estos tejidos, podemos identificar los genes más probable que median las respuestas de estas células con el fin de cribar nuevos compuestos para la mejora de las capacidades de repelencia. RNA-seq es una herramienta poderosa, convirtiéndose rápidamente en estándar para el seguimiento de los cambios temporales y espaciales en la expresión génica. Análisis de RNA-seq de apéndices quimiosensoriales de insectos y los órganos se han utilizado para descubrir receptores moleculares en varias especies de insectos 3-5, mejorando en gran medida de gen convencional búsquedas basado en la PCR-6 por el gen. Los insectos representan la clase de animales más diverso, presenta muchas oportunidades para estudiar la relación entre los genes y fenotipos únicos. Tecnología de RNA-seq se puede emplear en cualquier tejido de insectos que viven. Asimismo, el registro electrofisiológico de las células sensoriales dentro de sensilla gustativa uniporous se puede lograr en muchas especies de insectos diferentes. El emparejamiento de estas dos técnicas permite a los investigadores Para limitar los genes que participan en conjunto un fenotipo observado quimiosensorial. Las diferentes especies presentarán desafíos específicos, pero pueden informar a la conexión entre los genes de los receptores quimiosensoriales y una adaptación quimiosensorial. El tamaño y la morfología de sensilla quimiosensorial es variable y pueden requerir extensa resolución de problemas durante la grabación de los potenciales de acción para reducir el ruido e identificar señales repetibles. Las disecciones de los órganos quimiosensoriales pueden ser triviales o delicada y requiere mucho tiempo, dependiendo de la morfología y el tamaño del insecto. La recuperación de ARN de alta calidad puede requerir alguna solución de problemas, así como evitar ciertos pigmentos durantela recogida de tejidos. Al tiempo que demuestran los efectos de los compuestos repelentes a través de ensayos de comportamiento es directa e informativo, este enfoque es intensiva en tiempo y amplia con respecto a mecanismo de acción. Electrofisiología junto con RNA-seq permite análisis más específicos de lo que impulsa a comportamientos de evitación en los insectos. Una vez que el &quot;kit de herramientas&quot; de la discriminación químico ha sido identificado en una especie de insecto, los intentos más específicas para mejorar en los repelentes conocidos son posibles. Los receptores y proteínas asociadas en las células sensoriales responsables de estos comportamientos pueden ser expresados ​​de forma heteróloga para la detección química directa. Además, el modelado molecular puede predecir que los productos químicos se provocar respuestas fuertes de estos receptores 7. La instantánea de todos los genes activos en un conjunto limitado de tejidos quimiosensoriales también puede ser útil en la identificación de genes similares en otras especies. Usando homología de secuencia y si la expresiónmilarities, los investigadores pueden formar conjuntos de receptores moleculares más probable que median las respuestas a los repelentes que son ampliamente eficaces en insectos. Presentamos el siguiente protocolo para ayudar a los investigadores en la deconstrucción de las vías chemosensory insectos y persuadir más que ahondar en la neuroetología de la no-modelo y los insectos de importancia económica.

<table border="0" cellpadding="0" cellspacing="0" width="1272">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Name of Material/ Equipment</td>
			<td style="width:367px;">Company</td>
			<td style="width:189px;">Catalog Number</td>
			<td style="width:467px;">Comments/Description</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Glass capillary</td>
			<td style="width:367px;">A-M Systems</td>
			<td style="width:189px;">628000</td>
			<td>Standard, 1.5mm X 0.86mm, 4&#34;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Silver wire</td>
			<td style="width:367px;">A-M Systems</td>
			<td style="width:189px;">7875</td>
			<td>.015&#34; bare</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Tungsten wire</td>
			<td style="width:367px;">Alfa Products</td>
			<td style="width:189px;">369</td>
			<td>0.127mm diameter</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Fine forceps</td>
			<td style="width:367px;">Fine Science Tools</td>
			<td style="width:189px;">11252</td>
			<td>#5SF Inox</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Refridgerated stage</td>
			<td style="width:367px;">BioQuip Products</td>
			<td style="width:189px;">1429</td>
			<td>Chill Table</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Preamplifier</td>
			<td style="width:367px;">Syntech</td>
			<td style="width:189px;">Taste Probe</td>
			<td style="width:467px;">preamplifier</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Software for electrophysiology</td>
			<td style="width:367px;">Syntech</td>
			<td style="width:189px;">Autospike</td>
			<td style="width:467px;">software for electrophysiology</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;">TetraMin fish food</td>
			<td style="width:367px;">Tetra</td>
			<td style="width:189px;">Tropical fish food granules</td>
			<td>fish food ground to fine powder</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">TRIzol</td>
			<td>Life Technologies</td>
			<td>15596-026</td>
			<td>RNA isolation reagent</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">RNeasy Plus Mini Kit</td>
			<td>Qiagen</td>
			<td style="width:189px;">74136</td>
			<td style="width:467px;">includes gDNA eliminator and RNeasy spin columns</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Nanodrop spectrophotometer</td>
			<td>Nano Drop Products</td>
			<td style="width:189px;">ND-1000</td>
			<td>tabletop spectrometer</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:251px;">R statistics</td>
			<td style="width:367px;">freeware (created by Robert Gentleman and Ross Ihaka)</td>
			<td>www.r-project.org</td>
			<td>Use the lm function of the stats package and the equiv.boot function of the equivalence package in the R computing environment.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">1.5ml tube rack</td>
			<td style="width:367px;">Evergreen</td>
			<td style="width:189px;">240-6388-030</td>
			<td>Pour liquid nitrogen into a few empty wells to freeze and grind tissue.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">1.5mL collection tubes with pestle</td>
			<td style="width:367px;">Grainger</td>
			<td style="width:189px;">6HAX6</td>
			<td>RNase free</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:251px;">Centrifuge</td>
			<td style="width:367px;">Thermo Scientific</td>
			<td style="width:189px;">11178160</td>
			<td>Spin down frozen tissue to keep at bottom of 1.5 mL tube.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Primer-BLAST Primer Designing tool</td>
			<td style="width:367px;">NCBI</td>
			<td style="width:189px;">n/a</td>
			<td></td>
		</tr>
	</tbody>
</table>

physiological recordings and rna sequencing of the gustatory appendages of the yellow-fever mosquito aedes aegypti

Electrophysiological recording of action potentials from sensory neurons of mosquitoes provides investigators a glimpse into the chemical perception of these disease vectors. We have recently identified a bitter sensing neuron in the labellum of female Aedes aegypti that responds to DEET and other repellents, as well as bitter quinine, through direct electrophysiological investigation. These gustatory receptor neuron responses prompted our sequencing of total mRNA from both male and female labella and tarsi samples to elucidate the putative chemoreception genes expressed in these contact chemoreception tissues. Samples of tarsi were divided into pro-, meso- and metathoracic subtypes for both sexes. We then validated our dataset by conducting qRT-PCR on the same tissue samples and used statistical methods to compare results between the two methods. Studies addressing molecular function may now target specific genes to determine those involved in repellent perception by mosquitoes. These receptor pathways may be used to screen novel repellents towards disruption of host-seeking behavior to curb the spread of harmful viruses.

Los registros de Trace de potenciales de acción de Ae. aegypti sensilla gustativa (Figura 1) demuestran la eficacia de la estimulación directa con una gama de productos químicos. Esta técnica se puede utilizar para cuantificar las respuestas a la estimulación de cualquier producto químico contando los picos de una amplitud y duración dada durante un intervalo de tiempo razonable (generalmente menos de 500 ms). Grabaciones de rastreo deben ser fácilmente reproducible bajo un conjunto dad...

Watch this Scientific Journal Video about Physiological Recordings and RNA Sequencing of the Gustatory Appendages of the Yellow-fever Mosquito Aedes aegypti at JoVE.com

Physiological Recordings and RNA Sequencing of the Gustatory Appendages of the Yellow-fever Mosquito Aedes aegypti

El uso de dos métodos para estimar la expresión génica en las principales apéndices gustativas de Aedes aegypti, hemos identificado el conjunto de genes supuestamente subyacentes a las respuestas neuronales a compuestos amargos y repulsivas, como se determina por examen electrofisiológico.

Fisiológicos Grabaciones y RNA Secuenciación de los apéndices gustativas del mosquito de la fiebre amarilla<em&gt; Aedes aegypti</em

Electrophysiological recording of action potentials from sensory neurons of mosquitoes provides investigators a glimpse into the chemical perception of ...

physiological-recordings-rna-sequencing-gustatory-appendages-yellow

Research

JoVE Journal

Biology

Physiological Recordings and RNA Sequencing of the Gustatory Appendages of the Yellow-fever Mosquito Aedes aegypti

8.0K vistas.  United States Department of Agriculture.  El uso de dos métodos para estimar la expresión génica en las principales apéndices gustativas de Aedes aegypti, hemos identificado el conjunto de genes supuestamente subyacentes a las respuestas neuronales a compuestos amargos y repulsivas, como se determina por examen electrofisiológico. 

Video: Physiological Recordings and RNA Sequencing of the Gustatory Appendages of the Yellow-fever Mosquito Aedes aegypti

Building a Better Mosquito: Identifying the Genes Enabling Malaria and Dengue Fever Resistance in A. gambiae and A. aegypti Mosquitoes

In this interview, George Dimopoulos focuses on the physiological mechanisms used by mosquitoes to combat Plasmodium falciparum and dengue virus infections.   Explanation is given for how key refractory genes, those genes conferring resistance to vector pathogens, are identified in the mosquito and how this knowledge can be used to generate transgenic mosquitoes that are unable to carry the malaria parasite or dengue virus.

In this interview, George Dimopoulos focuses on the physiological mechanisms used by mosquitoes to combat Plasmodium falciparum and dengue virus infections. Explanation is given for how key refractory genes, those genes conferring resistance to vector pathogens, are identified in the mosquito and how this knowledge can be used to generate transgenic mosquitoes that are unable to carry the malaria parasite or dengue virus.

La construcción de un mosquito mejor: La identificación de los genes que permiten resistencia a la malaria y el dengue en A. gambiae y A. aegypti

In this interview, George Dimopoulos focuses on the physiological mechanisms used by mosquitoes to combat Plasmodium falciparum and dengue virus ...

Investigación

Biología

Depletion of Ribosomal RNA for Mosquito Gut Metagenomic RNA-seq

The mosquito gut accommodates dynamic microbial communities across different stages of the insect's life cycle. Characterization of the genetic capacity and functionality of the gut community will provide insight into the effects of gut microbiota on mosquito life traits. Metagenomic RNA-Seq has become an important tool to analyze transcriptomes from various microbes present in a microbial community. Messenger RNA usually comprises only 1-3% of total RNA, while rRNA constitutes approximately 90%. It is challenging to enrich messenger RNA from a metagenomic microbial RNA sample because most prokaryotic mRNA species lack stable poly(A) tails. This prevents oligo d(T) mediated mRNA isolation. Here, we describe a protocol that employs sample derived rRNA capture probes to remove rRNA from a metagenomic total RNA sample. To begin, both mosquito and microbial small and large subunit rRNA fragments are amplified from a metagenomic community DNA sample. Then, the community specific biotinylated antisense ribosomal RNA probes are synthesized in vitro using T7 RNA polymerase. The biotinylated rRNA probes are hybridized to the total RNA. The hybrids are captured by streptavidin-coated beads and removed from the total RNA. This subtraction-based protocol efficiently removes both mosquito and microbial rRNA from the total RNA sample. The mRNA enriched sample is further processed for RNA amplification and RNA-Seq.

A ribosomal RNA (rRNA) depletion protocol was developed to enrich messenger RNA (mRNA) for RNA-seq of the mosquito gut metatranscriptome. Sample specific rRNA probes, which were used to remove rRNA via subtraction, were created from the mosquito and its gut microbes. Performance of the protocol can result in the removal of approximately 90-99% of rRNA.

El agotamiento de ARN ribosomal de metagenómica intestino del mosquito RNA-seq

The mosquito gut accommodates dynamic microbial communities across different stages of the insect's life cycle. Characterization of the genetic capacity ...

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

One of the major questions in microbial ecology is &#8220;who is there?&#8221; This question can be answered using various tools, but one of the long-lasting gold standards is to sequence 16S ribosomal RNA (rRNA) gene amplicons generated by domain-level PCR reactions amplifying from genomic DNA. Traditionally, this was performed by cloning and Sanger (capillary electrophoresis) sequencing of PCR amplicons. The advent of next-generation sequencing has tremendously simplified and increased the sequencing depth for 16S rRNA gene sequencing. The introduction of benchtop sequencers now allows small labs to perform their 16S rRNA sequencing in-house in a matter of days. Here, an approach for 16S rRNA gene amplicon sequencing using a benchtop next-generation sequencer is detailed. The environmental DNA is first amplified by PCR using primers that contain sequencing adapters and barcodes. They are then coupled to spherical particles via emulsion PCR. The particles are loaded on a disposable chip and the chip is inserted in the sequencing machine after which the sequencing is performed. The sequences are retrieved in fastq format, filtered and the barcodes are used to establish the sample membership of the reads. The filtered and binned reads are then further analyzed using publically available tools. An example analysis where the reads were classified with a taxonomy-finding algorithm within the software package Mothur is given. The method outlined here is simple, inexpensive and straightforward and should help smaller labs to take advantage from the ongoing genomic revolution.

Characterizing microbial community has been a longstanding goal in environmental microbiology. Next-generation sequencing methods now allow for the characterization of microbial communities at an unprecedented depth with minimal cost and labor. We detail here our approach to sequence bacterial 16S ribosomal RNA genes using a benchtop sequencer.

La secuenciación de próxima generación de 16S ARN ribosomal genes Amplicones

One of the major questions in microbial ecology is &#8220;who is there?&#8221; This question can be answered using various tools, but one of the ...

An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

Photoperiodic diapause is an important adaptation that allows individuals to escape harsh seasonal environments via a series of physiological changes, most notably developmental arrest and reduced metabolism. Global gene expression profiling via RNA-Seq can provide important insights into the transcriptional mechanisms of photoperiodic diapause. The Asian tiger mosquito, Aedes albopictus, is an outstanding organism for studying the transcriptional bases of diapause due to its ease of rearing, easily induced diapause, and the genomic resources available. This manuscript presents a general experimental workflow for identifying diapause-induced transcriptional differences in A. albopictus. Rearing techniques, conditions necessary to induce diapause and non-diapause development, methods to estimate percent diapause in a population, and RNA extraction and integrity assessment for mosquitoes are documented. A workflow to process RNA-Seq data from Illumina sequencers culminates in a list of differentially expressed genes. The representative results demonstrate that this protocol can be used to effectively identify genes differentially regulated at the transcriptional level in A. albopictus due to photoperiodic differences. With modest adjustments, this workflow can be readily adapted to study the transcriptional bases of diapause or other important life history traits in other mosquitoes.

An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

RNA-Seq analyses are becoming increasingly important for identifying the molecular underpinnings of adaptive traits in non-model organisms. Here, a protocol to identify differentially expressed genes between diapause and non-diapause Aedes albopictus mosquitoes is described, from mosquito rearing, to RNA sequencing and bioinformatics analyses of RNA-Seq data.

Un Experimental y Protocolo Bioinformática para análisis de ARN-ss de fotoperiódica diapausa en el Mosquito Tigre Asiático,<em&gt; Aedes albopictus</em

Photoperiodic diapause is an important adaptation that allows individuals to escape harsh seasonal environments via a series of physiological changes, ...

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

Hematopoietic stem cells (HSCs) are used clinically for transplantation treatment to rebuild a patient&#39;s hematopoietic system in many diseases such as leukemia and lymphoma. Elucidating the mechanisms controlling HSCs self-renewal and differentiation is important for application of HSCs for research and clinical uses. However, it is not possible to obtain large quantity of HSCs due to their inability to proliferate in vitro. To overcome this hurdle, we used a mouse bone marrow derived cell line, the EML (Erythroid, Myeloid, and Lymphocytic) cell line, as a model system for this study.
RNA-sequencing (RNA-Seq) has been increasingly used to replace microarray for gene expression studies. We report here a detailed method of using RNA-Seq technology to investigate the potential key factors in regulation of EML cell self-renewal and differentiation. The protocol provided in this paper is divided into three parts. The first part explains how to culture EML cells and separate Lin-CD34+ and Lin-CD34- cells. The second part of the protocol offers detailed procedures for total RNA preparation and the subsequent library construction for high-throughput sequencing. The last part describes the method for RNA-Seq data analysis and explains how to use the data to identify differentially expressed transcription factors between Lin-CD34+ and Lin-CD34- cells. The most significantly differentially expressed transcription factors were identified to be the potential key regulators controlling EML cell self-renewal and differentiation. In the discussion section of this paper, we highlight the key steps for successful performance of this experiment.
In summary, this paper offers a method of using RNA-Seq technology to identify potential regulators of self-renewal and differentiation in EML cells. The key factors identified are subjected to downstream functional analysis in vitro and in vivo.

RNA-sequencing and bioinformatics analyses were used to identify significantly and differentially expressed transcription factors in Lin-CD34+ and Lin-CD34- subpopulations of mouse EMLcells. These transcription factors might play important roles in determining the switch between self-renewing Lin-CD34+ and partially differentiated Lin-CD34- cells.

Identificación de los factores clave que regula la auto-renovación y diferenciación de las células precursoras hematopoyéticas EML por análisis de secuenciación de ARN-

Hematopoietic stem cells (HSCs) are used clinically for transplantation treatment to rebuild a patient&#39;s hematopoietic system in many diseases such as ...

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

RNA sequencing (RNAseq) is a versatile method that can be utilized to detect and characterize gene expression, mutations, gene fusions, and noncoding RNAs. Standard RNAseq requires 30 - 100 million sequencing reads and can include multiple RNA products such as mRNA and noncoding RNAs. We demonstrate how targeted RNAseq (capture) permits a focused study on selected RNA products using a desktop sequencer. RNAseq capture can characterize unannotated, low, or transiently expressed transcripts that may otherwise be missed using traditional RNAseq methods. Here we describe the extraction of RNA from cell lines, ribosomal RNA depletion, cDNA synthesis, preparation of barcoded libraries, hybridization and capture of targeted transcripts and multiplex sequencing on a desktop sequencer. We also outline the computational analysis pipeline, which includes quality control assessment, alignment, fusion detection, gene expression quantification and identification of single nucleotide variants. This assay allows for targeted transcript sequencing to characterize gene expression, gene fusions, and mutations.

We describe a targeted RNA sequencing-based method that includes preparation of indexed cDNA libraries, hybridization and capture with custom probes and data analysis to interrogate selected transcripts for gene expression, mutations, and gene fusions. Targeted RNAseq permits cost-effective, rapid evaluation of selected transcripts on a desktop sequencer.

La secuenciación de ARN dirigidos Ensayo para caracterizar la expresión génica y la genómica alteraciones

RNA sequencing (RNAseq) is a versatile method that can be utilized to detect and characterize gene expression, mutations, gene fusions, and noncoding ...

Fat Body Organ Culture System in Aedes Aegypti, a Vector of Zika Virus

The insect fat body plays a central role in insect metabolism and nutrient storage, mirroring functions of the liver and fat tissue in vertebrates. Insect fat body tissue is usually distributed throughout the insect body. However, it is often concentrated in the abdomen and attached to the abdominal body wall.
The mosquito fat body is the sole source of yolk proteins, which are critical for egg production. Therefore, the in vitro culture of mosquito fat body tissues represents an important system for the study of mosquito physiology, metabolism, and, ultimately, egg production. The fat body culture process begins with the preparation of solutions and reagents, including amino acid stock solutions, Aedes physiological saline salt stock solution (APS), calcium stock solution, and fat body culture medium. The process continues with fat body dissection, followed by an experimental treatment. After treatment, a variety of different analyses can be performed, including RNA sequencing (RNA-Seq), qPCR, Western blots, proteomics, and metabolomics.
In our example experiment, we demonstrate the protocol through the excision and culture of fat bodies from the yellow fever mosquito, Aedes aegypti, a principal vector of arboviruses including dengue, chikungunya, and Zika. RNA from fat bodies cultured under a physiological condition known to upregulate yolk proteins versus the control were subject to RNA-Seq analysis to demonstrate the potential utility of this procedure for investigations of gene expression.

Fat Body Organ Culture System in Aedes Aegypti, a Vector of Zika Virus

The fat body is the central metabolic organ in insects. We present a live organ culture system that enables the user to study the responses of isolated fat body tissue to various stimuli.

Sistema de cultivo de órganos de grasa corporal en Aedes Aegypti, Vector del Virus Zika

The insect fat body plays a central role in insect metabolism and nutrient storage, mirroring functions of the liver and fat tissue in vertebrates. Insect ...

Maintaining Aedes aegypti Mosquitoes Infected with Wolbachia

Aedes aegypti mosquitoes experimentally infected with Wolbachia are being utilized in programs to control the spread of arboviruses such as dengue, chikungunya and Zika. Wolbachia-infected mosquitoes can be released into the field to either reduce population sizes through incompatible matings or to transform populations with mosquitoes that are refractory to virus transmission. For these strategies to succeed, the mosquitoes released into the field from the laboratory must be competitive with native mosquitoes. However, maintaining mosquitoes in the laboratory can result in inbreeding, genetic drift and laboratory adaptation which can reduce their fitness in the field and may confound the results of experiments. To test the suitability of different Wolbachia infections for deployment in the field, it is necessary to maintain mosquitoes in a controlled laboratory environment across multiple generations. We describe a simple protocol for maintaining Ae. aegypti mosquitoes in the laboratory, which is suitable for both Wolbachia-infected and wild-type mosquitoes. The methods minimize laboratory adaptation and implement outcrossing to increase the relevance of experiments to field mosquitoes. Additionally, colonies are maintained under optimal conditions to maximize their fitness for open field releases.

Maintaining Aedes aegypti Mosquitoes Infected with Wolbachia

Aedes aegypti mosquitoes infected with Wolbachia are being released into natural populations to suppress the transmission of arboviruses. We describe methods to rear Ae. aegypti with Wolbachia infections in the laboratory for experiments and field release, taking precautions to minimize laboratory adaptation and selection.

Mantener los mosquitos Aedes aegypti infectados con Wolbachia

Aedes aegypti mosquitoes experimentally infected with Wolbachia are being utilized in programs to control the spread of arboviruses such as dengue, ...

Studying the Activity of Neuropeptides and Other Regulators of the Excretory System in the Adult Mosquito

Studies of insect physiology, particularly in those species that are vectors of pathogens causing disease in humans and other vertebrates, provide the foundation to develop novel strategies for pest control. Here, a series of methods are described that are routinely utilized to determine the functional roles of neuropeptides and other neuronal factors (i.e., biogenic amines) on the excretory system of the mosquito, Aedes aegypti. The Malpighian tubules (MTs), responsible for primary urine formation, can continue functioning for hours when removed from the mosquito, allowing for fluid secretion measurements following hormone treatments. As such, the Ramsay assay is a useful technique to measure secretion rates from isolated MTs. Ion-selective microelectrodes (ISME) can sequentially be used to measure ion concentrations (i.e., Na+ and K+) in the secreted fluid. This assay allows for the measurement of several MTs at a given time, determining the effects of various hormones and drugs. The Scanning Ion-selective Electrode Technique uses ISME to measure voltage representative of ionic activity in the unstirred layer adjacent to the surface of ion transporting organs to determine transepithelial transport of ions in near real time. This method can be used to understand the role of hormones and other regulators on ion absorption or secretion across epithelia. Hindgut contraction assays are also a useful tool to characterize myoactive neuropeptides, that may enhance or reduce the ability of this organ to remove excess fluid and waste. Collectively, these methods provide insight into how the excretory system is regulated in adult mosquitoes. This is important because functional coordination of the excretory organs is crucial in overcoming challenges such as desiccation stress after eclosion and before finding a suitable vertebrate host to obtain a bloodmeal.

This protocol outlines methodologies behind the Ramsay assay, ion-selective microelectrodes, Scanning Ion-selective Electrode Technique (SIET) and in vitro contraction assays, applied to study the adult mosquito excretory system, comprised of the Malpighian tubules and hindgut, to collectively measure ion and fluid secretion rates, contractile activity, and transepithelial ion transport.

Estudio de la actividad de los neuropéptidos y otros reguladores del sistema excretor en el mosquito adulto

Studies of insect physiology, particularly in those species that are vectors of pathogens causing disease in humans and other vertebrates, provide the ...

A Step-by-Step Guide to Mosquito Electroantennography

Female mosquitoes are the deadliest animals on earth, claiming the lives of more than 1 million people every year due to pathogens they transmit when acquiring a blood-meal. To locate a host to feed on, mosquitoes rely on a wide range of sensory cues, including visual, mechanical, thermal, and olfactory. The study details a technique, electroantennography (EAG), that allows researchers to assess whether the mosquitoes can detect individual chemicals and blends of chemicals in a concentration-dependent manner. When coupled with gas-chromatography (GC-EAG), this technique allows to expose the antennae to a full headspace/complex mixture and determines which chemicals present in the sample of interest, the mosquito can detect. This is applicable to host body odors as well as plant floral bouquets or other ecologically relevant odors (e.g., oviposition sites odorants). Here, we described a protocol that permits long durations of preparation responsiveness time and is applicable to both female and male mosquitoes from multiple genera, including Aedes, Culex, Anopheles, and Toxorhynchites mosquitoes. As olfaction plays a major part in mosquito-host interactions and mosquito biology in general, EAGs and GC-EAG can reveal compounds of interest for the development of new disease vector control strategies (e.g., baits). Complemented with behavioral assays, the valence (e.g., attractant, repellent) of each chemical can be determined.

The present article details a step-by-step protocol for successful and low noise electroantennograms in several genera of mosquitoes, including both females and males.

Una guía paso a paso para la electroantenografía de mosquitos

Female mosquitoes are the deadliest animals on earth, claiming the lives of more than 1 million people every year due to pathogens they transmit when ...

Fisiológicos Grabaciones y RNA Secuenciación de los apéndices gustativas del mosquito de la fiebre amarilla

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