<html> Aquí hablamos de los procedimientos experimentales que están involucrados en LUCAS [1-3]. Para ilustrar la prueba de concepto de LUCAS vamos a describir el proceso de imágenes para una muestra de sangre entera. A. Imagen Set-up La plataforma LUCAS imágenes muestra ventajas significativas para proporcionar una alternativa rentable y compacto a los actuales puntos de atención médica y la citometría de herramientas de diagnóstico, especialmente para entornos de recursos limitados. En lugar de detectar la imagen de las células, en lugar LUCAS capta hologramas digitales de las células que son creados por la interferencia de la luz dispersada por cada celda con la luz de fondo. El control cuidadoso de la coherencia parcial espacial de la iluminación es fundamental para activar la grabación holográfica. 1. Matriz de sensores digitales La plataforma LUCAS utiliza una serie de sensores optoelectrónicos para grabar digitalmente los hologramas de celdas individuales. Para ello, los dispositivos de carga par (CCD, Modelos de la muestra: KAI-11002, KAF-39000, de Kodak) o complementary metal-oxide-semiconductor chips (CMOS, modelo de la muestra: MT9P031, Micron) se puede utilizar. Tamaño de píxel de la Kodak cargada dispositivos pareja, KAI-11002, KAF-39000, y sensores de imagen CMOS de Micron son de 9 m, m 6,8 y 2,2 micras, con un activo campo de visión de 10 cm2, 18 cm2, mm2 y 24,4, respectivamente. [1-2]. 2. Fuente de luz A diferencia de la mayoría de otras modalidades de imágenes microscópicas, LUCAS no requiere de un láser, por lo que incluso un simple diodo emisor de luz (LED) se puede utilizar para la iluminación. A fin de que la iluminación longitud de onda sintonizable, también podemos utilizar un monocromador con una lámpara de xenón (Cornerstone T260, Newport Corp.), junto con una fibra de sílice fundido de calidad estándar, que consiste en un haz de fibras (77.564, Newport) y orificio de ~ 100 m de diámetro situado en ~ 5-10 cm por encima de la superficie del sensor. Esta configuración de longitud de onda sintonizable iluminación ofrece una plataforma flexible, donde las firmas holográficas de las células puede ser ajustado, híbridos y firmas digitales pueden ser sintetizados para mejorar la relación señal-ruido para una precisión mejor caracterización y la especificidad. [3] B. Preparación de muestras y de imagen Una prueba de concepto de LUCAS basada en el chip de imagen se demostrará mediante una solución heterogénea como se describe a continuación. Un protocolo similar se podría aplicar a diferentes tipos de células [1-3]. 1. Dilución de la sangre total y la preparación de la solución heterogénea <ol><li> Para comenzar el proceso, obtener una muestra de sangre entera y microesferas de poliestireno de distintos diámetros (m 5, 10 y 20. Duque Científica), y llevar a todos a temperatura ambiente. </li><li> Añadir 2 ml de RPMI 1640 los medios líquidos clásicos (Fisher Scientific) como diluyente en un tubo de polipropileno estériles de 5 ml. </li><li> Después de incubar la muestra de sangre entera durante 30 minutos, pipetas hasta 10 l de la muestra de eritrocitos sedimentados y la transferencia en la solución de RPMI. </li><li> Añadir un volumen total de 20 microesferas de poliestireno l en los eritrocitos de dilución RPMI, y agitar la solución de células pipeteando con suavidad o mediante el uso de un agitador magnético con una barra agitadora. </li><li> Colocar un volumen total de 15.5 l solución heterogénea en una hoja de cubierta y colocar una hoja de segundo, la cobertura idéntica a la solución mediante el uso de fórceps. La muestra debe ser colocada entre los dos cubreobjetos de manera uniforme. </li><li> Luego, utilizando un lápiz de vacío (NT57-636, Edmund Optics) carga la muestra en la región activa de la matriz de sensores de imagen. </li></ol> 2. Manchas de sangre entera <ol><li> Empezando con la preparación de una mezcla de 0,1% tamponado eosina y solución diluida de metileno nuevo mediante el uso de energía tipo puro Eosina Y (MW = 691,85, Acros Organics), libre de zinc puro Nuevo azul de metileno colorante (MW = 347,90, Acros Organics), y monohidrato de oxalato de potasio (99,0% de ACS reactivo, Acros Organics), cada solución se purifica con un tamaño de 0,45 micras de poro Syringless filtro (Whatman) para soluciones acuosas de tinción de células blancas en la sangre. </li><li> Luego, revuelva suavemente un reactivo disuelto manchas acuosas con la muestra de sangre entera en una proporción de volumen de 1:1 en un vaso de polipropileno mediante el uso de un agitador magnético durante 2 minutos y se incuba durante 10 minutos. </li><li> Transferencia de una solución manchadas de sangre de 50 L en un tubo de polipropileno de 5 ml y diluir con solución de RPMI 1640 classic líquido (Fisher Scientific) de 1,95 ml para adquirir una proporción de volumen de 1:200. Entonces, el vórtice de dilución durante 30 segundos. Una tasa de dilución diferentes también pueden ser introducidos en esta etapa. </li><li> Pipeta una solución células teñidas de 10-100 l entre cubreobjetos o dentro de un yacimiento de microfluidos. Luego, utilizando un lápiz de vacío (NT57-636, Edmund Optics), colocar la muestra en la región activa de la matriz de sensores. </li></ol> Los resultados representativos ve_content &quot;&gt; <img src="/files/ftp_upload/1650/1650Fig1tmb.jpg" alt="Figura 1" border="0" /> Figura 1: LUCAS permite un recuento preciso y la diferenciación de las células digitales y objetos de micro-basados ​​en sus firmas holográficas 2D sin necesidad de utilizar las lentes, láseres y otros componentes ópticos voluminosos. Características de las diversas firmas LUCAS micro-objetos se muestran en esta figura y se comparan con una imagen de microscopio convencional obtenida con una lente objetivo de 40X. Por favor, <a href="https://www.jove.com/files/ftp_upload/1650/1650Fig1.jpg">haga clic aquí</a> para ver una versión ampliada de la figura 1. <img src="/files/ftp_upload/1650/1650Fig2.jpg" alt="Figura 2" /> Figura 2: (izquierda) la imagen en bruto, de una mezcla heterogénea que contiene glóbulos rojos, 10um, 5 um y 3 partículas um. (Derecho) totalmente automatizado resultados de la caracterización LUCAS para el mismo campo de visión se muestran. Tenga en cuenta que el algoritmo de decisión es sólido en la caracterización de las regiones de alta densidad, así como partículas con baja señal a ruido, tales como las cuentas de 3 um. <img src="/files/ftp_upload/1650/1650Fig3tmb.jpg" alt="Figura 3" border="0" /> Figura 3: La interfaz personalizada LUCAS se ilustra. Java permite el software basado en LUCAS insumos para diversas condiciones experimentales, tales como el tamaño en píxeles del sensor o la longitud de onda de la luz. La selección de un campo específico de vista sobre la imagen también se pueden hacer y los patrones de la célula diana puede ser definido por el usuario para crear una biblioteca de células sombra estadística. La adquisición de imágenes LUCAS puede ser caracterizado sobre la base de datos de este entrenamiento (es decir, la biblioteca de la sombra de células) y el marcado (contado) la imagen se muestra al usuario. Estadísticas de los resultados del conteo también se almacenan como un archivo XML para su posterior análisis.

<ol>
	<li>Seo, S., Su, T., Tseng, D. K., Erlinger, A., Ozcan, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term="Lensfree+Holographic+Imaging+for+On-Chip+Cytometry+and+Diagnostics".">"Lensfree Holographic Imaging for On-Chip Cytometry and Diagnostics".</a> Lab Chip. , (2009).</li><li>Su, T., Seo, S., Erlinger, A., Ozcan, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term="High-throughput+Imaging+and+Characterization+of+a+Heterogeneous+Cell+Solution+on+a+Chip"+.">"High-throughput Imaging and Characterization of a Heterogeneous Cell Solution on a Chip" .</a> Biotechnology and Bioengineering. , (2008).</li><li>Su, T., Seo, S., Erlinger, A., Ozcan, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term="Multi-color+LUCAS:+Lensfree+on-chip+cytometry+using+tunable+monochromatic+illumination+and+digital+noise+reduction".">"Multi-color LUCAS: Lensfree on-chip cytometry using tunable monochromatic illumination and digital noise reduction".</a> Cellular and Molecular Bioengineering. , (2008).</li></ol>

Hemos ilustrado que la plataforma LUCAS precisión puede contar e identificar los diversos micro-objects/cells en un chip basado en su firma holográfica, y proporciona una herramienta prometedora para el diagnóstico de los puntos de atención médica y de alto rendimiento de la biología celular. Con el fin de procesar con precisión los patrones holográficos registrados, hemos implementado un software desarrollado a medida LUCAS decisión. Este algoritmo, que utiliza una base de datos de difracción de la imagen est...

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		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
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<td>Charged couple device (CCD)</td>
<td>&nbsp;</td>
<td>KODAK</td>
<td>KAI-11002</td>
<td>&nbsp;</td>
<tr>
<td>Charged couple device (CCD)</td>
<td>&nbsp;</td>
<td>KODAK</td>
<td>KAF-39000</td>
<td>&nbsp;</td>
<tr>
<td>Complementary Metal-Oxide-Semiconductor (CMOS)</td>
<td>&nbsp;</td>
<td>Micron</td>
<td>MT9P031</td>
<td>&nbsp;</td>
<tr>
<td>Xenon Lamp</td>
<td>&nbsp;</td>
<td>Newport Corp.</td>
<td>Cornerstone T260</td>
<td>&nbsp;</td>
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<td>Vacuum pen</td>
<td>&nbsp;</td>
<td>Edmund Optics</td>
<td>NT57-636</td>
<td>&nbsp;</td>
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<td>5, 10, and 20 &mu;m Microbeads</td>
<td>&nbsp;</td>
<td>Thermo Scientific</td>
<td>4000 Series</td>
<td>&nbsp;</td>
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<td>RPMI</td>
<td>&nbsp;</td>
<td>Fisher Scientific</td>
<td>1640</td>
<td>&nbsp;</td>
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<td>Pure Eosin Y</td>
<td>&nbsp;</td>
<td>Acros Organics</td>
<td>MW=691.85</td>
<td>&nbsp;</td>
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<td>New Methylene Blue(NMB) Dye</td>
<td>&nbsp;</td>
<td>Acros Organics</td>
<td>MW=347.90</td>
<td>&nbsp;</td>
<tr>
<td>Potassium Oxalate Monohydrate</td>
<td>&nbsp;</td>
<td>Acros Organics</td>
<td>99.0% Reagent ACS</td>
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lensless on-chip imaging of cells provides a new tool for high-throughput cell-biology and medical diagnostics

Los microscopios ópticos convencionales celdas de imagen mediante el uso de lentes del objetivo que trabajan en conjunto con otros objetivos y componentes ópticos. Aunque muy eficaz, este enfoque clásico tiene ciertas limitaciones de la miniaturización de la plataforma de imágenes para que sea compatible con el avanzado estado de la técnica de microfluidos. En este informe, presentamos los detalles del experimento de un concepto de imagen sin cristalino en un chip llamado LUCAS (<strong<em&gt; L</em</strong&gt; Ensless<strong<em&gt; U</em</strong&gt; ARLT en todo el campo de visión<strong<em&gt; C</em</strong&gt; Ell control<strong<em&gt; A</em</strong&gt; Rray plataforma basada en<strong<em&gt; S</em</strong&gt; Hadow imagen) que no requiere de objetivos de microscopio o de otros componentes ópticos voluminosos a la imagen de una solución de células heterogéneas sobre un campo ultra amplio de visión que puede abarcar tan grande como 18 cm ~<sup&gt; 2</sup&gt;. Además, a diferencia de los microscopios convencionales, LUCAS puede imaginar una solución de células heterogéneas de interés en una profundidad de campo de ~ 5 mm sin la necesidad de reorientar lo que corresponde a un máximo de ~ 9 ml volumen de la muestra. Esta plataforma de imágenes registros de las sombras (es decir, sin lentes hologramas digitales) de cada célula de interés dentro de su campo de visión, y el procesamiento digital automatizada de estas sombras de células puede determinar el tipo, el número y las posiciones relativas de las células dentro de la solución. Ya que no requiere ningún componente voluminoso ópticas o mecánicas etapas de exploración que ofrece una plataforma significativa en miniatura que al mismo tiempo reduce el costo, lo cual es muy importante para todo punto de atención herramientas de diagnóstico. Por otra parte, el rendimiento de imagen de esta plataforma es varios órdenes de magnitud mejor que los microscopios ópticos convencionales, lo que podría ser muy valiosa de alto rendimiento para la biología celular de experimentos.

Watch this Scientific Journal Video about Lensless On-chip Imaging of Cells Provides a New Tool for High-throughput Cell-Biology and Medical Diagnostics at JoVE.com

Lensless On-chip Imaging of Cells Provides a New Tool for High-throughput Cell-Biology and Medical Diagnostics

Lensfree en el chip de imagen y caracterización de las células se ilustra. Este enfoque de células en el chip de imagen proporciona una herramienta compacta y rentable para el diagnóstico médico y de alto rendimiento de aplicaciones de la biología celular, por lo que es especialmente adecuado para entornos de escasos recursos.

Sin cristalino en el chip de imagen de las células proporciona una nueva herramienta de alto rendimiento Biología celular y el diagnóstico médico

Conventional optical microscopes image cells by use of objective lenses that work together with other lenses and optical components. While quite ...

lensless-on-chip-imaging-cells-provides-new-tool-for-high-throughput

Research

JoVE Journal

Biology

11.9K vistas.  University of California, Los Angeles. Lensfree en el chip de imagen y caracterización de las células se ilustra. Este enfoque de células en el chip de imagen proporciona una herramienta compacta y rentable para el diagnóstico médico y de alto rendimiento de aplicaciones de la biología celular, por lo que es especialmente adecuado para entornos de escasos recursos.

Video: Lensless On-chip Imaging of Cells Provides a New Tool for High-throughput Cell-Biology and Medical Diagnostics

Tracheotomy: A Method for Transplantation of Stem Cells to the Lung

Lung disease is a leading cause of death and likely to become an epidemic given increases in pollution and smoking worldwide. Advances in stem cell therapy may alleviate many of the symptoms associated with lung disease and induce alveolar repair in adults. Concurrent with the ongoing search for stem cells applicable for human treatment, precise delivery and homing (to the site of disease) must be reassured for successful therapy. Here, I report that stem cells can safely be instilled via the trachea opening a non-stop route to the lung. This method involves a skin incision, caudal insertion of a cannula into and along the tracheal lumen, and injection of a stem cell vehicle mixture into airways of the lung. A broad range of media solutions and stabilizers can be instilled via tracheotomy, resulting in the ability to deliver a wider range of cell types. With alveolar epithelium confining these cells to the lumen, lung expansion and negative pressure during inhalation may also assist in stem cell integration. Tracheal delivery of stem cells, with a quick uptake and the ability to handle a large range of treatments, could accelerate the development of cell-based therapies, opening new avenues for treatment of lung disease.

Significant breakthroughs in stem cell identification are continuously being made. To translate these discoveries, however, novel methods for cellular delivery must be devised. Here I report that the airways provide a safe route for stem cell transplantation to the lungs.

Traqueotomía: Un método para el trasplante de células madre para el pulmón

Lung disease is a leading cause of death and likely to become an epidemic given increases in pollution and smoking worldwide. Advances in stem cell ...

Investigación

Biología

A Gradient-generating Microfluidic Device for Cell Biology

 The fabrication and operation of a gradient-generating microfluidic device for studying cellular behavior is described.  A microfluidic platform is an enabling experimental tool, because it can precisely manipulate fluid flows, enable high-throughput experiments, and generate stable soluble concentration gradients.  Compared to conventional gradient generators, poly(dimethylsiloxane) (PDMS)-based  microfluidic devices can generate stable concentration gradients of growth factors with well-defined profiles.  Here, we developed simple gradient-generating microfluidic devices with three separate inlets.  Three microchannels combined into one microchannel to generate concentration gradients.  The stability and shape of growth factor gradients were confirmed by fluorescein isothyiocyanate (FITC)-dextran with a molecular weight similar to epidermal growth factor (EGF).  Using this microfluidic device, we demonstrated that fibroblasts exposed to concentration gradients of EGF migrated toward higher concentrations.  The directional orientation of cell migration and motility of migrating cells were quantitatively assessed by cell tracking analysis.  Thus, this gradient-generating microfluidic device might be useful for studying and analyzing the behavior of migrating cells.

We describe a protocol for the microfabrication of the gradient-generating microfluidic device that can generate spatial and temporal gradients in well-defined microenvironment. In this approach, the gradient-generating microfluidic device can be used to study directed cell migration, embryogenesis, wound healing, and cancer metastasis.

Un dispositivo de microfluidos gradiente de generación de Biología Celular

 The fabrication and operation of a gradient-generating microfluidic device for studying cellular behavior is described.  A microfluidic platform is an ...

Biochemical and High Throughput Microscopic Assessment of Fat Mass in Caenorhabditis Elegans

The nematode C. elegans has emerged as an important model for the study of conserved genetic pathways regulating fat metabolism as it relates to human obesity and its associated pathologies. Several previous methodologies developed for the visualization of C. elegans triglyceride-rich fat stores have proven to be erroneous, highlighting cellular compartments other than lipid droplets. Other methods require specialized equipment, are time-consuming, or yield inconsistent results. We introduce a rapid, reproducible, fixative-based Nile red staining method for the accurate and rapid detection of neutral lipid droplets in C. elegans. A short fixation step in 40% isopropanol makes animals completely permeable to Nile red, which is then used to stain animals. Spectral properties of this lipophilic dye allow it to strongly and selectively fluoresce in the yellow-green spectrum only when in a lipid-rich environment, but not in more polar environments. Thus, lipid droplets can be visualized on a fluorescent microscope equipped with simple GFP imaging capability after only a brief Nile red staining step in isopropanol. The speed, affordability, and reproducibility of this protocol make it ideally suited for high throughput screens. We also demonstrate a paired method for the biochemical determination of triglycerides and phospholipids using gas chromatography mass-spectrometry. This more rigorous protocol should be used as confirmation of results obtained from the Nile red microscopic lipid determination. We anticipate that these techniques will become new standards in the field of C. elegans metabolic research.

Biochemical and High Throughput Microscopic Assessment of Fat Mass in Caenorhabditis Elegans

We present robust biochemical and microscopic methods for studying Caenorhabditis elegans lipid stores. A rapid, simple, fixing-staining procedure for fluorescent lipid droplet imaging leverages the spectral properties of the lipophilic dye Nile red. We then present biochemical measurement of triglycerides and phospholipids using solid phase extraction and gas chromatography-mass spectrometry.

Bioquímica y de Evaluación de Rendimiento microscópica de masa grasa en<em&gt; Caenorhabditis elegans</em

The nematode C. elegans has emerged as an important  model for the study of conserved genetic pathways regulating fat metabolism as  it relates to human ...

Anti-Nuclear Antibody Screening Using HEp-2 Cells

The American College of Rheumatology position statement on ANA testing stipulates the use of IIF as the gold standard method for ANA screening1. Although IIF is an excellent screening test in expert hands, the technical difficulties of processing and reading IIF slides &#8211; such as the labor intensive slide processing, manual reading, the need for experienced, trained technologists and the use of dark room &#8211; make the IIF method difficult to fit in the workflow of modern, automated laboratories.
The first and crucial step towards high quality ANA screening is careful slide processing. This procedure is labor intensive, and requires full understanding of the process, as well as attention to details and experience.
Slide reading is performed by fluorescent microscopy in dark rooms, and is done by trained technologists who are familiar with the various patterns, in the context of cell cycle and the morphology of interphase and dividing cells. Provided that IIF is the first line screening tool for SARD, understanding the steps to correctly perform this technique is critical.
Recently, digital imaging systems have been developed for the automated reading of IIF slides. These systems, such as the NOVA View Automated Fluorescent Microscope, are designed to streamline the routine IIF workflow. NOVA View acquires and stores high resolution digital images of the wells, thereby separating image acquisition from interpretation; images are viewed an interpreted on high resolution computer monitors. It stores images for future reference and supports the operator&#8217;s interpretation by providing fluorescent light intensity data on the images. It also preliminarily categorizes results as positive or negative, and provides pattern recognition for positive samples. In summary, it eliminates the need for darkroom, and automates and streamlines the IIF reading/interpretation workflow. Most importantly, it increases consistency between readers and readings. Moreover, with the use of barcoded slides, transcription errors are eliminated by providing sample traceability and positive patient identification. This results in increased patient data integrity and safety.
The overall goal of this video is to demonstrate the IIF procedure, including slide processing, identification of common IIF patterns, and the introduction of new advancements to simplify and harmonize this technique.

Indirect immunofluorescent (IIF) assays have traditionally been used for the detection of antinuclear antibodies (ANA) in human serum. The presence of these antibodies can aid in the diagnosis of systemic autoimmune rheumatic diseases (SARD). This protocol demonstrates how to effectively perform the IIF technique to accurately detect these autoantibodies.

Antinuclear Anticuerpo de detección sistemática mediante células Hep-2

The American College of Rheumatology position statement on ANA testing stipulates the use of IIF as the gold standard method for ANA screening1. Although ...

High-throughput Image Analysis of Tumor Spheroids: A User-friendly Software Application to Measure the Size of Spheroids Automatically and Accurately

The increasing number of applications of three-dimensional (3D) tumor spheroids as an in vitro model for drug discovery requires their adaptation to large-scale screening formats in every step of a drug screen, including large-scale image analysis. Currently there is no ready-to-use and free image analysis software to meet this large-scale format. Most existing methods involve manually drawing the length and width of the imaged 3D spheroids, which is a tedious and time-consuming process. This study presents a high-throughput image analysis software application &#8211; SpheroidSizer, which measures the major and minor axial length of the imaged 3D tumor spheroids automatically and accurately; calculates the volume of each individual 3D tumor spheroid; then outputs the results in two different forms in spreadsheets for easy manipulations in the subsequent data analysis. The main advantage of this software is its powerful image analysis application that is adapted for large numbers of images. It provides high-throughput computation and quality-control workflow. The estimated time to process 1,000 images is about 15 min&#160;on a minimally configured laptop, or around 1 min&#160;on a multi-core performance workstation. The graphical user interface (GUI) is also designed for easy quality control, and users can manually override the computer results. The key method used in this software is adapted from the active contour algorithm, also known as Snakes, which is especially suitable for images with uneven illumination and noisy background that often plagues automated imaging processing in high-throughput screens. The complimentary &#8220;Manual Initialize&#8221; and &#8220;Hand Draw&#8221; tools provide the flexibility to SpheroidSizer in dealing with various types of spheroids and diverse quality images. This high-throughput image analysis software remarkably reduces labor and speeds up the analysis process. Implementing this software is beneficial for 3D tumor spheroids to become a routine in vitro model for drug screens in industry and academia.

We present a high-throughput image analysis software application to measure the size of three-dimensional tumor spheroids imaged with bright-field microscopy. This application provides a fast and effective way to examine the effects of therapeutic drugs on spheroids, which is beneficial for researchers who wish to use spheroids in drug screens.

De alto rendimiento de imagen Análisis de esferoides tumorales: una aplicación de software fácil de usar para medir el tamaño de esferoides forma automática y precisa

The increasing number of applications of three-dimensional (3D) tumor spheroids as an in vitro model for drug discovery requires their adaptation to ...

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

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

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

Selección de alto rendimiento para moduladores químicos de genes post-transcripcionalmente regulados

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

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Metabolic models are reconstructed based on an organism&#39;s available genome annotation and provide predictive tools to study metabolic processes at a systems-level. Genome-scale metabolic models may include gaps as well as reactions that are unverified experimentally. Reconstructed models of newly isolated microalgal species will result in weaknesses due to these gaps, as there is usually sparse biochemical evidence available for the metabolism of such isolates. The phenotype microarray (PM) technology is an effective, high-throughput method that functionally determines cellular metabolic activities&#160;in response to a wide array of entry metabolites. Combining the high throughput phenotypic assays with metabolic modeling can allow existing metabolic network models to be rapidly reconstructed or optimized by providing biochemical evidence to support and expand genomic evidence. This work will show the use of PM assays for the study of microalgae by using the green microalgal model species Chlamydomonas reinhardtii as an example. Experimental evidence for over 254 reactions obtained by PM was used in this study to expand and refine a genome-scale C. reinhardtii metabolic network model, iRC1080, by approximately 25 percent. The protocol created here can be used as a basis for functionally profiling the metabolism of other microalgae, including known microalgae mutants and new isolates.

This protocol demonstrates the use of a phenotype microarray (PM) technology platform to define metabolic requirements of Chlamydomonas reinhardtii, a green microalga, and refine an existing metabolic network model.

Perfiles metabólicos de alto rendimiento para refinamientos de modelos de microalgas

Metabolic models are reconstructed based on an organism&#39;s available genome annotation and provide predictive tools to study metabolic processes at a ...

High-Throughput Live Imaging of Microcolonies to Measure Heterogeneity in Growth and Gene Expression

Precise measurements of between- and within-strain heterogeneity in microbial growth rates are essential for understanding genetic and environmental inputs into stress tolerance, pathogenicity, and other key components of fitness. This manuscript describes a microscope-based assay that tracks approximately 105&#160;Saccharomyces cerevisiae microcolonies per experiment. After automated time-lapse imaging of yeast immobilized in a multiwell plate, microcolony growth rates are easily analyzed with custom image-analysis software. For each microcolony, expression and localization of fluorescent proteins and survival of acute stress can also be monitored. This assay allows precise estimation of strains&#39; average growth rates, as well as comprehensive measurement of heterogeneity in growth, gene expression, and stress tolerance within clonal populations.

Yeast growth phenotypes are precisely measured through highly parallel time-lapse imaging of immobilized cells growing into microcolonies. Simultaneously, stress tolerance, protein expression, and protein localization can be monitored, generating integrated datasets to study how environmental and genetic differences, as well as gene-expression heterogeneity among isogenic cells, modulate growth.

Imágenes en vivo de alto rendimiento de microcolonias para medir la heterogeneidad en crecimiento y expresión génica

Precise measurements of between- and within-strain heterogeneity in microbial growth rates are essential for understanding genetic and environmental ...

A High-Throughput Comet Assay Approach for Assessing Cellular DNA Damage

Cells are continually exposed to agents arising from the internal and external environments, which may damage DNA. This damage can cause aberrant cell function, and therefore DNA damage may play a critical role in the development of, conceivably, all major human diseases, e.g., cancer, neurodegenerative and cardiovascular disease, and aging. Single-cell gel electrophoresis (i.e., the comet assay) is one of the most common and sensitive methods to study the formation and repair of a wide range of types of DNA damage (e.g., single- and double-strand breaks, alkali-labile sites, DNA-DNA crosslinks, and, in combination with certain repair enzymes, oxidized purines, and pyrimidines), in both in vitro and in vivo systems. However, the low sample throughput of the conventional assay and laborious sample workup are limiting factors to its widest possible application. With the "scoring" of comets increasingly automated, the limitation is now the ability to process significant numbers of comet slides. Here, a high-throughput (HTP) variant of the comet assay (HTP comet assay) has been developed, which significantly increases the number of samples analyzed, decreases assay run time, the number of individual slide manipulations, reagent requirements, and risk of physical damage to the gels. Furthermore, the footprint of the electrophoresis tank is significantly decreased due to the vertical orientation of the slides and integral cooling. Also reported here is a novel approach to chilling comet assay slides, which conveniently and efficiently facilitates the solidification of the comet gels. Here, the application of these devices to representative comet assay methods has been described. These simple innovations greatly support the use of the comet assay and its application to areas of study such as exposure biology, ecotoxicology, biomonitoring, toxicity screening/testing, together with understanding pathogenesis.

The comet assay is a popular means of detecting DNA damage. This study describes an approach to running slides in representative variants of the comet assay. This approach significantly increased the number of samples while decreasing assay run-time, the number of slide manipulations, and the risk of damage to gels.

Un enfoque de ensayo cometario de alto rendimiento para evaluar el daño del ADN celular

Cells are continually exposed to agents arising from the internal and external environments, which may damage DNA. This damage can cause aberrant cell ...

A High-Throughput Platform for Culture and 3D Imaging of Organoids

The characterization of a large number of three-dimensional (3D) organotypic cultures (organoids) at different resolution scales is currently limited by standard imaging approaches. This protocol describes a way to prepare microfabricated organoid culture chips, which enable multiscale, 3D live imaging on a user-friendly instrument requiring minimal manipulations and capable of up to 300 organoids/h imaging throughput. These culture chips are compatible with both air and immersion objectives (air, water, oil, and silicone) and a wide range of common microscopes (e.g., spinning disk, point scanner confocal, wide field, and brightfield). Moreover, they can be used with light-sheet modalities such as the single-objective, single-plane illumination microscopy (SPIM) technology (soSPIM). 
The protocol described here gives detailed steps for the preparation of the microfabricated culture chips and the culture and staining of organoids. Only a short length of time is required to become familiar with, and consumables and equipment can be easily found in normal biolabs. Here, the 3D imaging capabilities will be demonstrated only with commercial standard microscopes (e.g., spinning disk for 3D reconstruction and wide field microscopy for routine monitoring).

This paper presents a fabrication protocol for a new type of culture substrate with hundreds of microcontainers per mm2, in which organoids can be cultured and observed using high-resolution microscopy. The cell seeding and immunostaining protocols are also detailed.

Una plataforma de alto rendimiento para el cultivo y la obtención de imágenes 3D de organoides

The characterization of a large number of three-dimensional (3D) organotypic cultures (organoids) at different resolution scales is currently limited by ...