We thank Ueli Grossniklaus (University of Z&#252;rich) for technical and financial support. We are thankful to Valeria Gagliardini, Christof Eichenberger, Arturo Bolanos and Peter Kopf for general lab support. This research was funded by the University of Z&#252;rich, grants from the Swiss National Foundation to CB (31003A_130722) and Ueli Grossniklaus (31003A_141245 and 31003AB-126006), and the Agence Nationale de la Recherche to DG (Programme ANR-BLANC-2012).

El procedimiento se describe en el flujo de trabajo en la Figura 1, y la configuración para la disección y la incrustación de tejidos se presentan en la Figura 2. 1. Fijación del tejido <ol><li> Recoger 20-30 carpelos en un tubo de microcentrífuga que contiene recién hecho tampón fijador BVO en hielo. </li><li> Fijar el tejido 30 min con agitación suave a temperatura ambiente. </li><li> Haga girar los tubos que contienen los carpelos en fijador en una microcentrífuga de sobremesa 1 min a 400 x g. </li><li> Retire con cuidado el tampón fijador y agregar 1 ml de PBT, coloque los tubos en hielo. </li></ol> 2. Disección e incrustación <ol><li> Preparar cinco tubos Eppendorf con cada 200 l de una recién hecha, 5% de mezcla de acrilamida. </li><li> Preparar cinco portaobjetos Superfrost pre-limpiados con etanol al 70% y se marcaron con un lápiz. </li><li> Descongelar una alícuota de 20% y 20% de APS NaPS cada uno, en el hielo. </li><li> Tome 4-5 carpelos con una punta de corte final, el lugarsobre una lámina limpia, eliminar el exceso de líquido. </li><li> Haga cortes longitudinales con una aguja fina y separar las paredes carpelo para liberar filas de óvulos como se muestra la Figura 2, evitar el secado, cubriendo con PBS (no más de 10 l). </li><li> Añadir rápidamente y mezclar 12 NaPS mu l, 12 APS mu l con una alícuota de 200 l de mezcla de acrilamida. </li><li> Añadir 30 l de la acrilamida activado en los óvulos disecados. </li><li> Tapar con un cubreobjetos mm 20 x 20, por no polimeriza a temperatura ambiente, 45 a 60 min. </li><li> Retire el cubreobjetos usando una cuchilla de afeitar. En esta etapa, las muestras se pueden mantener durante la noche a 4 ° C en un vaso de Coplin que contenía PBS. </li></ol> 3. Procesamiento de tejido NOTA: Todos los pasos, excepto 3.2.1, 3.2.3, 3.3.2 y 3.4.3 se llevan a cabo en frascos de Coplin con 80 ml de solución bajo el capó química a temperatura ambiente. Las diapositivas se transfieren con una pinza de punta plana. <ol><li> Clarificación de tejidos yfijación: <ol><li> Incubar 5 min en metanol. </li><li> Incubar 5 min en etanol. </li><li> Incubar 30 min en etanol: xileno (1:1). </li><li> Incubar 5 min en etanol. </li><li> Incubar 5 min en metanol. </li><li> Incubar 15 min en metanol y PBT (01:01), complementado con 2,5% de formaldehído. </li><li> Enjuague 2 x 10 min en PBT. En esta etapa, las diapositivas se pueden mantener durante la noche a 4 ° C. </li></ol></li><li> La digestión de la pared celular: <ol><li> Descongelar una alícuota de la mezcla de la digestión de la pared celular en hielo. </li><li> Tome un portaobjetos del frasco de Coplin, drenar el exceso de líquido, colocándolo en posición vertical sobre una toalla de papel. </li><li> Añadir 100 l de mezcla de digestión de la pared celular sobre la almohadilla de acrilamida y cubrir con un cubreobjetos 23 mm x 46. Repita el procedimiento para las otras diapositivas. Incubar durante 2 horas a 37 ° C en una cámara húmeda (se describe en Materiales). </li><li> Lavar el portaobjetos 2 x 5 min en PBT. </li></ol></li><li> RNasa A de tratamiento: <ol><li> Tome un portaobjetos del frasco de Coplin, drene ªe exceso de líquido como antes. </li><li> Incubar cada portaobjetos con 100 l de ARNasa A a 100 g / ml en PBS con 1% de Tween-20 durante 1 hora a 37 ° C en una cámara húmeda. </li><li> Lavar los portaobjetos durante 2 x 5 min en PBT. </li></ol></li><li> Posteriores a la fijación y permeabilización: <ol><li> Post-fijar durante 20 minutos en recién hecha PBT-F. </li><li> Enjuagar los portaobjetos durante 10 minutos en PBT. </li><li> Permeabilizar durante 2 horas en PBS con 2% de Tween-20 a 4 ° C. </li><li> Enjuagar los portaobjetos durante 2 x 5 min en PBT. </li></ol></li></ol> 4. Inmunotinción NOTA: Para este paso, la concentración óptima del anticuerpo primario tiene que ser probado mediante el uso de diferentes diluciones (1:200, 1:500, 1:1000) de los anticuerpos. <ol><li> Incubar cada portaobjetos con 100 l de anticuerpo primario diluido en PBS con 0,2% de Tween-20 durante 12-24 horas a 4 ° C. </li><li> Lavar los portaobjetos en PBT durante 2-4 horas a temperatura ambiente bajo agitación suave. </li><li> Aplicar la1:200 de anticuerpo secundario en PBS + 0,2% de Tween-20 durante 24 horas a 4 ° C. </li><li> Lavar los portaobjetos en PBT durante 1 hora a temperatura ambiente bajo agitación suave. </li><li> Contratinción con 10 g / ml de yoduro de propidio en PBS durante 15 min, luego enjuague 15 min en PBS bajo agitación suave, a temperatura ambiente. </li><li> Monte en anti-fading medio de montaje líquido suplementado con 10 mg / ml de yoduro de propidio. Deje que el medio de montaje se endurezca durante 1 hora antes de la adquisición de imágenes por CLSM. </li></ol> 5. Imagen Cuantitativa <ol><li> La adquisición de imágenes: <ol><li> Adquirir imágenes de alta resolución utilizando CLSM, idealmente utilizando un modo de escaneo de resonancia, lo que permite una mejor conservación de las señales fluorescentes más prolongado de formación de imágenes 23, y una lente de inmersión 63X glicerol. </li><li> Compruebe los parámetros de adquisición, tales como la intensidad del láser, la ganancia, pinhole, tamaño de voxel y el factor de zoom al inicio del experimento para definir un procedimiento de adquisición estándar a seguir estrictamente lo largotodas las diapositivas para las mediciones cuantitativas consistentes. </li><li> Verificar la ausencia de interferencia entre fluorocromos. Si está presente, establecer una exploración secuencial. Adquirir imágenes de transmisión por separado y no simultáneamente. </li><li> Lleve a cabo la adquisición de imágenes en serie, en tres dimensiones con la resolución más alta posible en las dimensiones X e Y, y con sobremuestreo 2x en la dimensión z (la regla de Nyquist). </li></ol></li><li> Tratamiento de la imagen: <ol><li> Reconstruir imágenes en serie en tres dimensiones utilizando software comercial o de código abierto. </li><li> Definir las superficies de contorno alrededor de cada núcleo (o célula) de interés en 3D. </li><li> Cuantificar la fluorescencia en cada canal como la suma de intensidades de los píxeles en cada objeto. </li><li> Exportar los datos a Excel para su análisis estadístico. Normalizar las señales de anticuerpos contra las señales de tinción por ejemplo ADN. </li></ol></li></ol>

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The authors declare that they have no competing financial interests.

En las plantas con flores, el linaje reproductivo femenino está rodeado por varias capas de células incluyendo la nucela y los tegumentos de óvulos, haciendo así la tinción citológica en todo el montaje técnicamente difícil. Aquí presentamos un protocolo eficiente que permite la preparación y elaboración de un gran número de óvulos adecuados para la tinción citológica como inmunotinción, la tinción de ADN y la hibridación fluorescente in situ en todo el montaje. Se utilizó con éxito...

En las plantas con flores, el establecimiento de linajes reproductiva comienza con la diferenciación de las SMC, MMC hembra y de células madre de microsporas masculino. El MMC se desarrolla a partir de una célula nucellar sub-epidérmica en el extremo distal del primordio óvulo y la célula madre de microsporas se desarrolla a partir de tejido esporógena en la antera lóculo, que se encuentran en el interior de los órganos florales 1. CML sufren meiosis para producir esporas haploides, que luego dan lugar a los gametofitos sobre la mitosis. El gametofito femenino o saco embrionario, se compone de un óvulo, una célula central, dos y tres sinérgidas antípodas. El gametofito masculino, o el polen, se compone de una célula vegetal y dos espermatozoides. Mientras que el gametofito masculino sigue siendo un objeto de estudio-de-relativamente accesible, el gametofito femenino está incrustado dentro del óvulo, en sí encerrado en el carpelo flor, y por lo tanto plantea retos específicos para los análisis moleculares y citológicos. Recientemente, sin embargo, con ayuda de lásermicrodisección ofrece una solución elegante que permite transcriptómica analiza en el MMC y células gametofítico femeninos 2-4. Además de la expresión del gen candidato análisis, usando, por ejemplo ARN hibridación in situ o ensayos de gen reportero, análisis citológicos permite la investigación de la dinámica de los componentes celulares endógenos utilizando tinción celular directo específico o inmunotinción indirecta. En particular, la tinción citogenético mediante FISH y la tinción de ADN, junto con la inmunotinción de modificaciones de la cromatina o componentes de la cromatina son los enfoques centrales para dilucidar la dinámica de la cromatina y la organización nuclear de Arabidopsis 5. Habitualmente, la meiosis implica dinámica de los cromosomas específicos que ha sido bien investigados en planta macho meiocytes 6,7; además de gran escala, la reorganización de la cromatina de células específicos, reflejando probablemente la reprogramación epigenética dinámica ha sido descrita durante el desarrollo del polen 8-10. Por el contrario, debidoa la relativa inaccesibilidad de la meiocyte hembra y gametofito, estas investigaciones siguen siendo técnicamente difíciles de aplicar, y a menudo requieren la disección de seccionamiento o manual y la digestión enzimática (ver más abajo). Además, la frecuente falta de claridad óptica en todo el montaje es un obstáculo para imágenes de alta resolución de las células reproductoras en óvulos intactos. Un método clásico para el análisis citológico de organización de los cromosomas en óvulos de todo el montaje utiliza la tinción de Feulgen 11-13. Se trata de la hidrólisis ácida (usando ácido hipocloroso) del ADN que resulta en desnaturalización de la proteína y por lo tanto causa la destrucción de la estructura de la cromatina. Alternativamente, organización de los cromosomas en meiocytes femeninas y células gametofítico se puede observar mediante DAPI y la inmunotinción de las secciones semi-delgadas o sacos embrionarios disecados y MMC (por ejemplo, ver 14-18). Claramente, sin embargo, la disección manual y de corte pueden ser mano de obra intensiva yimpide en el análisis cualitativo y cuantitativo de un gran número de epítopos de la cromatina. Aquí les ofrecemos un protocolo eficiente para preparar un gran número de óvulos Arabidopsis adecuados para una variedad de tinción citológica aguas abajo en todo el montaje. En breve, los brotes de flor se incuban en una solución de fijación, las filas de óvulos se disecan de la carpelo y embebidos en acrilamida en la diapositiva como se hizo para meiocitos polen 19,20. Los óvulos incrustados se borrarán y se fijaron en metanol, etanol, y xileno antes de la digestión de la pared celular y permeabilización. Se discuten las posibles variaciones de estos pasos. Las muestras luego se pueden utilizar para la tinción de ADN, inmunotinción, y FISH. El modo de preparación es eficiente y permite paralelo experimental (hasta 16 diapositivas se pueden preparar en un día diferente para el análisis de aguas abajo). Los tratamientos descritos permiten señales homogéneas en todo el montaje e histológico, celular bien conservados,y la organización nuclear en las células reproductoras y las células circundantes que se benefician nucelar comparaciones cualitativas y cuantitativas entre los tipos de células. Calibrado, imágenes basadas en CLSM de alta resolución seguida de reconstrucción en 3 dimensiones permite mediciones cuantitativas significativas de señales fluorescentes. Hemos utilizado con éxito este procedimiento para analizar la dinámica de la cromatina en el MMC diferenciador 21 y desarrollando gametofito femenino 22; Presentamos aquí los resultados representativos de análisis heterocromatina, inmunotinción cromatina, la inmunotinción GFP y FISH en todo el montaje óvulos. Además, creemos que nuestro protocolo será adecuado para otros tejidos y especies de plantas.

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an efficient method for quantitative, single-cell analysis of chromatin modification and nuclear architecture in whole-mount ovules in arabidopsis

En las plantas con flores, la transición destino de la célula somática-a-reproductiva está marcada por la especificación de las células madre de esporas (CML) en los órganos florales de la planta adulta. El SMC macho (célula madre megaspore, MMC) diferencia en el primordio óvulo y sufre meiosis. El megáspora haploide seleccionado a continuación, se somete a la mitosis para formar el gametofito multicelular hembra, lo que dará lugar a los gametos, la célula del huevo y célula central, junto con las células accesorias. La accesibilidad limitada de la MMC, meiocyte y gametofito femenino dentro del óvulo es técnicamente difícil para citológico y citogenético analiza a nivel de células individuales. En particular, la inmunodetección directa o indirecta de los epítopos celulares o nucleares se deteriora por la falta de penetración de los reactivos dentro de la imagen de células de plantas y de una sola célula es arrendada por la falta de claridad óptica en todo el montaje en los tejidos. Por lo tanto, hemos desarrollado un método eficiente para analizar los nuclorganización del oído y la modificación de la cromatina en alta resolución de una de las células de todo el montaje óvulos Arabidopsis embebidos. Se basa en la disección y la incrustación de óvulos fijos en una capa delgada de gel de acrilamida en un portaobjetos de microscopio. Los óvulos incrustados son sometidos a los tratamientos químicos y enzimáticos destinados a mejorar la claridad del tejido y la permeabilidad a los reactivos de inmunotinción. Esos tratamientos preservar la organización, de ADN y de proteínas epítopos celulares y la cromatina. Las muestras se pueden utilizar para diferentes análisis citológicos aguas abajo, incluyendo la inmunotinción de la cromatina, hibridación in situ fluorescente (FISH), y la tinción de ADN para el análisis de la heterocromatina. Microscopía láser confocal (CLSM) de imágenes con alta resolución, seguida de reconstrucción 3D permite mediciones cuantitativas en la resolución de una sola célula.

Proporcionamos un protocolo robusto para la preparación a gran escala y el procesamiento de óvulos Arabidopsis adecuados para la tinción citológica en todo el montaje. Gracias a la incrustación, los óvulos conservan una estructura de 3 dimensiones (Figura 3). Además, el procesamiento de tejido incluyendo la clarificación óptica permite estructuras subcelulares de formación de imágenes en alta resolución. Figura 4 muestra la tinción de ADN en primordios óvulo todo ...

Watch this Scientific Journal Video about An Efficient Method for Quantitative, Single-cell Analysis of Chromatin Modification and Nuclear Architecture in Whole-mount Ovules in Arabidopsis at JoVE.com

An Efficient Method for Quantitative, Single-cell Analysis of Chromatin Modification and Nuclear Architecture in Whole-mount Ovules in Arabidopsis

Ofrecemos aquí un protocolo eficiente y confiable para la inmunotinción, hibridación in situ fluorescente, la tinción de ADN seguido por cuantitativos, imágenes de alta resolución en óvulos de Arabidopsis thaliana todo el montaje. Este método fue utilizado con éxito para analizar modificaciones de la cromatina nuclear y de la arquitectura.

Un método eficaz para Cuantitativo, Análisis de celda única de la cromatina modificación y Arquitectura Nuclear en Todo el montaje en Óvulos<em&gt; Arabidopsis</em

In flowering plants, the somatic-to-reproductive cell fate transition is marked by the specification of spore mother cells (SMCs) in floral organs of the ...

an-efficient-method-for-quantitative-single-cell-analysis-chromatin

Research

JoVE Journal

Biology

An Efficient Method for Quantitative, Single-cell Analysis of Chromatin Modification and Nuclear Architecture in Whole-mount Ovules in Arabidopsis

13.1K vistas.  University of Zürich.  Ofrecemos aquí un protocolo eficiente y confiable para la inmunotinción, hibridación in situ fluorescente, la tinción de ADN seguido por cuantitativos, imágenes de alta resolución en óvulos de Arabidopsis thaliana todo el montaje. Este método fue utilizado con éxito para analizar modificaciones de la cromatina nuclear y de la arquitectura. 

Video: An Efficient Method for Quantitative, Single-cell Analysis of Chromatin Modification and Nuclear Architecture in Whole-mount Ovules in Arabidopsis

Double Whole Mount in situ Hybridization of Early Chick Embryos

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ideal tool for studying  gene expression in brain, neural tube, somite and heart primordia formation. This video demonstrates the different steps in 2-color whole mount in situ hybridization; First, the embryo is dissected from the egg and fixed in paraformaldehyde. Second, the embryo is processed for prehybridization. The embryo is then hybridized with two different probes, one coupled to DIG, and one coupled to FITC.  Following overnight hybridization, the embryo is incubated with DIG coupled antibody. Color reaction for DIG substrate is performed, and the region of interest appears blue. The embryo is then incubated with FITC coupled antibody. The embryo is processed for color reaction with FITC, and the region of interest appears red. Finally, the embryo is fixed and processed for phtograph and sectioning. A troubleshooting guide is also presented.

This video demonstrates 2-color whole mount in situ hybridization, a method by which the spatial and temporal expression pattern of 2 different genes can be visualized in young chick embryos. This method was originally introduced by David Wilkinson, Domingos Henrique, Phil Ingham and David Ish -Horowicz.

Monte doble entero hibridación in situ de embriones de pollo temprano

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ...

Investigación

Biología

Method for Whole Mount Antibody Staining in Chick

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ideal tool for studying antibody expression in developing brain, neural tube and somite. This video demonstrates the different steps in whole-mount antibody staining using HRP conjugated secondary antibodies; First, the embryo is dissected from the egg and fixed in paraformaldehyde. Second, endogenous peroxidase is inactivated; The embryo is then exposed to primary antibody. After several washes, the embryo is incubated with secondary antibody conjugated to HRP. Peroxidase activity is revealed using reaction with diaminobenzidine substrate. Finally, the embryo is fixed and processed for photography and sectioning. The advantage of this method over the use of fluorescent antibodies is that embryos can be processed for wax sectioning, thus enabling the study of antigen sites in cross section. This method was originally introduced by Jane Dodd and Tom Jessell 1.

This video demonstrates whole mount immunohistochemistry, a method by which the spatial and temporal expression pattern of an antigen can be visualized in young chick embryos. This method was originally introduced by Jane Dodd and Tom Jessell.

Método para la tinción de anticuerpos enteros en el monte del polluelo

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

The three-dimensional folding of chromosomes compartmentalizes the genome and and can bring distant functional elements, such as promoters and enhancers, into close spatial proximity 2-6. Deciphering the relationship between chromosome organization and genome activity will aid in understanding genomic processes, like transcription and replication. However, little is known about how chromosomes fold. Microscopy is unable to distinguish large numbers of loci simultaneously or at high resolution. To date, the detection of chromosomal interactions using chromosome conformation capture (3C) and its subsequent adaptations required the choice of a set of target loci, making genome-wide studies impossible 7-10.
We developed Hi-C, an extension of 3C that is capable of identifying long range interactions in an unbiased, genome-wide fashion. In Hi-C, cells are fixed with formaldehyde, causing interacting loci to be bound to one another by means of covalent DNA-protein cross-links. When the DNA is subsequently fragmented with a restriction enzyme, these loci remain linked. A biotinylated residue is incorporated as the 5' overhangs are filled in. Next, blunt-end ligation is performed under dilute conditions that favor ligation events between cross-linked DNA fragments. This results in a genome-wide library of ligation products, corresponding to pairs of fragments that were originally in close proximity to each other in the nucleus. Each ligation product is marked with biotin at the site of the junction. The library is sheared, and the junctions are pulled-down with streptavidin beads. The purified junctions can subsequently be analyzed using a high-throughput sequencer, resulting in a catalog of interacting fragments.
Direct analysis of the resulting contact matrix reveals numerous features of genomic organization, such as the presence of chromosome territories and the preferential association of small gene-rich chromosomes. Correlation analysis can be applied to the contact matrix, demonstrating that the human genome is segregated into two compartments: a less densely packed compartment containing open, accessible, and active chromatin and a more dense compartment containing closed, inaccessible, and inactive chromatin regions. Finally, ensemble analysis of the contact matrix, coupled with theoretical derivations and computational simulations, revealed that at the megabase scale Hi-C reveals features consistent with a fractal globule conformation.

The Hi-C method allows unbiased, genome-wide identification of chromatin interactions (1). Hi-C couples proximity ligation and massively parallel sequencing. The resulting data can be used to study genomic architecture at multiple scales: initial results identified features such as chromosome territories, segregation of open and closed chromatin, and chromatin structure at the megabase scale.

Hi-C: Un método para estudiar la arquitectura tridimensional de los genomas.

The three-dimensional folding of chromosomes compartmentalizes the genome and and can bring distant functional elements, such as promoters and enhancers, ...

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for using FISH to quantify the number of mRNAs in single yeast cells. Cells can be grown in any condition of interest and then fixed and made permeable. Subsequently, multiple single-stranded deoxyoligonucleotides conjugated to fluorescent dyes are used to label and visualize mRNAs. Diffraction-limited fluorescence from single mRNA molecules is quantified using a spot-detection algorithm to identify and count the number of mRNAs per cell. While the more standard quantification methods of northern blots, RT-PCR and gene expression microarrays provide information on average mRNAs in the bulk population, FISH facilitates both the counting and localization of these mRNAs in single cells at single-molecule resolution.

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

This protocol describes an experimental procedure for performing Fluorescence in situ Hybridization (FISH) for counting mRNAs in single cells at single-molecule resolution.

Visualización y Análisis de las moléculas de ARNm mediante fluorescencia<em&gt; In Situ</em&gt; La hibridación en<em&gt; Saccharomyces cerevisiae</em

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for ...

Slide Preparation Method to Preserve Three-dimensional Chromatin Architecture of Testicular Germ Cells

During testicular germ cell differentiation, the structure of nuclear chromatin dynamically changes. The following describes a method designed to preserve the three-dimensional chromatin arrangement of testicular germ cells found in mice; this method has been termed as the three-dimensional (3D) slide method. In this method, testicular tubules are directly treated with a permeabilization step that removes cytoplasmic material, followed by a fixation step that fixes nuclear materials. Tubules are then dissociated, the cell suspension is cytospun, and cells adhere to slides. This method improves sensitivity towards detection of subnuclear structures and is applicable for immunofluorescence, DNA, and RNA fluorescence in situ hybridization (FISH) and the combination of these detection methods. As an example of a possible application of the 3D slide method, a Cot-1 RNA FISH is shown to detect nascent RNAs. The 3D slide method will facilitate the detailed examination of spatial relationships between chromatin structure, DNA, and RNA during testicular germ cell differentiation.

The material here describes a method developed to preserve the three-dimensional chromatin structure of testicular germ cells. This has been termed the three-dimensional (3D) slide method. This method improves sensitivity for detection of subnuclear structures and is applicable for immunofluorescence, DNA, and RNA fluorescence in situ hybridization (FISH).

Método de preparación de diapositivas para preservar la arquitectura tridimensional de la cromatina de las células germinales testiculares

During testicular germ cell differentiation, the structure of nuclear chromatin dynamically changes. The following describes a method designed to preserve ...

Measuring Spatial and Temporal Ca2+ Signals in Arabidopsis Plants

Developmental and environmental cues induce Ca2+ fluctuations in plant cells. Stimulus-specific spatial-temporal Ca2+ patterns are sensed by cellular Ca2+ binding proteins that initiate Ca2+ signaling cascades. However, we still know little about how stimulus specific Ca2+ signals are generated. The specificity of a Ca2+ signal may be attributed to the sophisticated regulation of the activities of Ca2+ channels and/or transporters in response to a given stimulus. To identify these cellular components and understand their functions, it is crucial to use systems that allow a sensitive and robust recording of Ca2+ signals at both the tissue and cellular levels. Genetically encoded Ca2+ indicators that are targeted to different cellular compartments have provided a platform for live cell confocal imaging of cellular Ca2+ signals. Here we describe instructions for the use of two Ca2+ detection systems: aequorin based FAS (film adhesive seedlings) luminescence Ca2+ imaging and case12 based live cell confocal fluorescence Ca2+ imaging. Luminescence imaging using the FAS system provides a simple, robust and sensitive detection of spatial and temporal Ca2+ signals at the tissue level, while live cell confocal imaging using Case12 provides simultaneous detection of cytosolic and nuclear Ca2+ signals at a high resolution.

Measuring Spatial and Temporal Ca2+ Signals in Arabidopsis Plants

Ca2+ signaling regulates diverse biological processes in plants. Here we present approaches for monitoring abiotic stress induced spatial and temporal Ca2+ signals in Arabidopsis cells and tissues using the genetically encoded Ca2+ indicators Aequorin or Case12.

Medición Espacial y Temporal Ca<sup&gt; 2 +</sup&gt; Las señales en plantas de Arabidopsis

Developmental and environmental cues induce Ca2+ fluctuations in plant cells. Stimulus-specific spatial-temporal Ca2+ patterns are sensed by cellular Ca2+ ...

A Whole Mount In Situ Hybridization Method for the Gastropod Mollusc Lymnaea stagnalis

Whole mount in situ hybridization (WMISH) is a technique that allows for the spatial resolution of nucleic acid molecules (often mRNAs) within a &#39;whole mount&#39; tissue preparation, or developmental stage (such as an embryo or larva) of interest. WMISH is extremely powerful because it can significantly contribute to the functional characterization of complex metazoan genomes, a challenge that is becoming more of a bottleneck with the deluge of next generation sequence data. Despite the conceptual simplicity of the technique much time is often needed to optimize the various parameters inherent to WMISH experiments for novel model systems; subtle differences in the cellular and biochemical properties between tissue types and developmental stages mean that a single WMISH method may not be appropriate for all situations. We have developed a set of WMISH methods for the re-emerging gastropod model Lymnaea stagnalis that generate consistent and clear WMISH signals for a range of genes, and across all developmental stages. These methods include the assignment of larvae of unknown chronological age to an ontogenetic window, the efficient removal of embryos and larvae from their egg capsules, the application of an appropriate Proteinase-K treatment for each ontogenetic window, and hybridization, post-hybridization and immunodetection steps. These methods provide a foundation from which the resulting signal for a given RNA transcript can be further refined with probe specific adjustments (primarily probe concentration and hybridization temperature).

A Whole Mount In Situ Hybridization Method for the Gastropod Mollusc Lymnaea stagnalis

The goal of this protocol is to provide users with a set of methods for the high-throughput decapsulation of Lymnaea stagnalis embryos and larvae in preparation for whole mount in situ hybridization, and for subsequent pre- and post-hybridization treatments.

A todo el montaje<em&gt; In Situ</em&gt; Método de hibridación para el molusco gasterópodo<em&gt; Lymnaea stagnalis</em

Whole mount in situ hybridization (WMISH) is a technique that allows for the spatial resolution of nucleic acid molecules (often mRNAs) within a ...

CUBIC Protocol Visualizes Protein Expression at Single Cell Resolution in Whole Mount Skin Preparations

The skin is essential for our survival. The outer epidermal layer consists of the interfollicular epidermis, which is a stratified squamous epithelium covering most of our body, and epidermal appendages such as the hair follicles and sweat glands. The epidermis undergoes regeneration throughout life and in response to injury. This is enabled by K14-expressing basal epidermal stem/progenitor cell populations that are tightly regulated by multiple regulatory mechanisms active within the epidermis and between epidermis and dermis. This article describes a simple method to clarify full thickness mouse skin biopsies, and visualize K14 protein expression patterns, Ki67 labeled proliferating cells, Nile Red labeled sebocytes, and DAPI nuclear labeling at single cell resolution in 3D. This method enables accurate assessment and quantification of skin anatomy and pathology, and of abnormal epidermal phenotypes in genetically modified mouse lines. The CUBIC protocol is the best method available to date to investigate molecular and cellular interactions in full thickness skin biopsies at single cell resolution.

This report describes a CUBIC protocol to clarify full thickness mouse skin biopsies, and visualize protein expression patterns, proliferating cells, and sebocytes at the single cell resolution in 3D. This method enables accurate assessment of skin anatomy and pathology, and of abnormal epidermal phenotypes in genetically modified mouse lines.

Protocolo CÚBICO Visualiza la expresión de la proteína en la resolución de la celda individual en su totalidad para la piel Mount

The skin is essential for our survival. The outer epidermal layer consists of the interfollicular epidermis, which is a stratified squamous epithelium ...

Visualization of 3D White Adipose Tissue Structure Using Whole-mount Staining

Adipose tissue is an important metabolic organ with high plasticity and is responsive to environmental stimuli and nutrient status. As such, various techniques have been developed to study the morphology and biology of adipose tissue. However, conventional visualization methods are limited to studying the tissue in 2D sections, failing to capture the 3D architecture of the whole organ. Here we present whole-mount staining, an immunohistochemistry method that preserves intact adipose tissue morphology with minimal processing steps. Hence, the structures of adipocytes and other cellular components are maintained without distortion, achieving the most representative 3D visualization of the tissue. In addition, whole-mount staining can be combined with lineage tracing methods to determine cell fate decisions. However, this technique has some limitations to providing accurate information regarding deeper parts of adipose tissue. To overcome this limitation, whole-mount staining can be further combined with tissue clearing techniques to remove the opaqueness of tissue and allow for complete visualization of entire adipose tissue anatomy using light-sheet fluorescent microscopy. Therefore, a higher resolution and more accurate representation of adipose tissue structures can be captured with the combination of these techniques.

The focus of the present study is to demonstrate the whole-mount immunostaining and visualization technique as an ideal method for 3D imaging of adipose tissue architecture and cellular component.

Visualización de estructura del tejido adiposo blanco 3D utilizando tinción de Whole-mount

Adipose tissue is an important metabolic organ with high plasticity and is responsive to environmental stimuli and nutrient status. As such, various ...

An Easy and Flexible Inoculation Method for Accurately Assessing Powdery Mildew-Infection Phenotypes of Arabidopsis and Other Plants

Reducing crop losses due to fungal diseases requires improved understanding of the mechanisms governing plant immunity and fungal pathogenesis, which in turn requires accurate determination of disease phenotypes of plants upon infection with a particular fungal pathogen. However, accurate disease phenotyping with unculturable biotrophic fungal pathogens such as powdery mildew is not easy to achieve and can be a rate-limiting step of a research project. Here, we have developed a safe, efficient, and easy-to-operate disease phenotyping system using the Arabidopsis-powdery mildew interaction as an example. This system mainly consists of three components: (i) a wooden inoculation box fitted with a removable lid mounted with a stainless steel or nylon mesh of ~50 &#181;m pores for inoculating a flat of plants with fungal spores, (ii) a transparent plastic chamber with a small front opening for minimizing spore escape while conducting inoculation inside, and (iii) a spore-dislodging and distribution method for even and effective inoculation. The protocols described here include the steps and parameters for making the inoculation box and the plastic chamber at a low cost, and a video demonstration of how to use the system to enable even inoculation with powdery mildew spores, thereby improving accuracy and reproducibility of disease phenotyping.

We present a protocol for constructing a simple spore-distribution system consisting of an inoculation box with a ~50 &#181;m mesh and a transparent plastic chamber. This can be used to evenly inoculate plants with powdery mildew spores, thereby enabling accurate and reproducible assessment of disease phenotypes of plants under study.

Un método de inoculación fácil y flexible para evaluar con precisión los fenotipos de infección por mildiú polvoriento de Arabidopsis y otras plantas

Reducing crop losses due to fungal diseases requires improved understanding of the mechanisms governing plant immunity and fungal pathogenesis, which in ...