Die Autoren bedanken sich prof. Chiara Campanella und AMRA Center of Competence der Universität Neapel Federico II in Neapel, Italien, für die Bereitstellung von ihnen mit dem Einsatz des Lasers Microdissector, und Herr Vincenzo Vicidomini für die großzügige Hilfe bei der 3D-Animation.

Teil 1. Vorbereitung von Drosophila Imaginal Flügel Discs unterzogen Spezifische und lokalisierte RNAi. Als biologisches Material verwendeten wir Drosophila imaginalen Flügel Scheiben aus transgenen Larven unterzogen, um die lokale und spezifische Gen-Silencing durch die GAL4/UAS System 1 erhalten. Diese Larven Nachkommen entstammt das aus einer genetischen Kreuzung mit zwei elterlichen Linien: eine Durchführung der GAL4-Treiber, der zweite die UAS-Responder. Neben GAL4 in einem bestimmten zeitlichen und / oder räumliche Muster auszudrücken, trägt der Fahrer Linie ein UAS-GFP-Reporter, dass die GAL4 Ausdruck Domain visualisieren können. Die UAS-Responder Linie drückt, unter der Kontrolle des UAS-Sequenz, eine Haarnadel-Silencing RNA (hpRNA) in der Lage, gezielt ausgewählten Gen von Interesse (nennen wir es Gen X) 2. Einmal in der Zelle exprimiert wird, ist die hpRNA X gespalten small interfering RNA (siRNA) in der Lage, gezielt Stille des ausgewählten Gens zu erzeugen. In den Larven Nachkommen führt, dass beide Fahrer und Responder Transgene, die UAS-Silencing-Konstrukt nur in jenen Zellen, die das GAL4-Protein transkribiert wird, und ist somit in der Lage, eine räumlich beschränkte Schweigen des ausgewählten Gens X. induzieren Unter der Vielzahl der möglichen Anwendungen, wandten wir diesen Ansatz zu einem ausgewählten Gen unseres Interesses (Gen X) unter der Kontrolle des engrailed-GAL4 (en)-Treiber, welche spezifischen Silencing in der hinteren Kammer des Flügels Scheibe 3 auslösen kann Stille , wurde dessen Gebiet durch die Expression der UAS-GFP-Transgen markiert. Das Schweigen imaginalen Flügel Scheiben wurden von Hand zerlegt, wobei darauf zu achten Umgebung kontaminieren Geweben, insbesondere die Einhaltung Luftröhre zu beseitigen. Jeder isolierte Flügel Scheibe wurde dann schnell und schonend zu einem bereits behandelten, RNase frei Dissektion Rahmen für die sofortige Lasermikrodissektion ausgewählter Bereiche übertragen. Part 2. Laser Mikrodissektion ausgewählte Bereiche aus dem Schweigen (posterior) und unsilenced (anterior) Fächer des Flügels Scheibe. Sobald die Flügel Scheibe wurde auf der Membran-, Laser-Mikrodissektion von bestimmten Bereichen aus Schweigen (posterior; GFP-markierten) und unsilenced (anterior, GFP-unbeschriftet) Fächer wurde erreicht. Dies wurde durch Zeichnung einer Fläche, die leicht in beide passen könnte durchgeführt, die GFP-positiven und GFP-negativen Seiten der Scheibe. Unter dem Microdissector wir zunächst fokussiert den Laserstrahl auf die GFP-positiven Gewebe, so dass ein Schnitt entlang der gewählten Umfang. Die Microdissector Erlöse mit Schneiden in der gewählten Geschwindigkeit und Kraft, aber es ist möglich, das Schneiden von Hand zu suchen, bis der ausgewählte Bereich des Tissue fällt in die Röhre darunter. Diese Röhre enthält eine kleine Menge des TRI-Reagenz, so dass die GFP-positiven Gewebe bereit für die anschließende RNA-Extraktion ist. Wir Anschließend wechselte der Schnittfläche auf die gegenüberliegende, GFP-negative Seite des Flügels Disc, um ein gleichwertiges Gebiet von der unsilenced, GFP-negativen Gewebe zu sezieren. Wieder einmal, nach der Abschaltautomatik, begaben wir uns zur Verfeinerung der Schnitt manuell. Sobald der Schnitt gemacht wurde, auch die GFP-negativen Gewebe wurde in der TRI Reagent erholt, bereit für die RNA-Extraktion. Teil 3. RNA-Extraktion und Transkription Profiling von mikrodissezierten Tissue Areas. Wir gesponnen die Rohre, um die Flüssigkeit aus der Kappe lösen und fügte TRI-Reagenz bis zu 1 ml, dann erfolgt die RNA-Extraktion nach dem Standard TRI Reagenz-Protokoll. Um genügend Material zu sammeln, wiederholten wir den Schneidvorgang auf 100 imaginalen Flügel-Discs. Ausgehend von 100 Gebieten von etwa 5000 um je 2, war unsere Ausbeute von 1,5 pg RNA. Genauigkeit der manuellen Dissektion wurde dann, indem die GFP-Expression in den zum Schweigen gebracht und unsilenced Proben durch RT-PCR kontrolliert, mit Super-Script III (Invitrogen) zu synthetisieren cDNA mit Random Hexameren. Nachfolgende quantitative Analysen konzentrieren, um die Expression des Gens Schweigen X bestimmen, zusammen mit denen von vermeintlichen Ziele ihres Regulationsweg, wurden durch Real Time RT-PCR unter Verwendung von Master Mix (Invitrogen) durchgeführt.

<ol>
	<li>Elliott, D. A., Brand, A. H., Dahmann, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+GAL4+System+A+Versatile+System+for+the+Expression+of+Gene.">The GAL4 System A Versatile System for the Expression of Gene.</a> , (2008).</li><li>Klein, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Wing+disc+development+in+the+fly:+the+early+stages.+.">Wing disc development in the fly: the early stages. .</a> Current Opinion in Genetics &#38; Development. 11, 470-475 (2001).</li><li>Dietzl, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+genome-wide+transgenic+RNAi+library+for+conditional+gene+inactivation+in+Drosophila.">A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila.</a> Nature. 448, 151-U1-151-U1 (2007).</li><li>Martin, F. A., Morata, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Compartments+and+the+control+of+growth+in+the+Drosophila+wing+imaginal+disc.">Compartments and the control of growth in the Drosophila wing imaginal disc.</a> Development. 133, 4421-4426 (2006).</li><li>Tabata, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genetics+of+morphogen+gradients.">Genetics of morphogen gradients.</a> Nature Reviews Genetics. 2, 620-630 (2001).</li><li>Moreno, E. &. a. m. p. ;. a. m. p., Basler, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=dMyc+transforms+cells+into+super-competitors.">dMyc transforms cells into super-competitors.</a> Cell. 117, 117-129 (2004).</li></ol>

Mit Bezug auf ihre basale Expression in der vorderen / hinteren Abteile unsilenced Flügel Scheiben erreicht, wurde die Aktivität des ausgewählten Gens X gefunden reduziert auf 40% bei Schweigen. Im Gegensatz dazu war eine seiner vermeintlichen Ziele (Gene Y) deutlich hochreguliert (7-facher Anstieg) gefunden, was uns zu der Hypothese bestätigen, dass es negativ wurde von Gen X. geregelt Wir schließen daraus, dass die oben beschriebenen experimentellen Ansatz erfolgreich auf die Validier...

Fly-Stämme Drosophila UAS-silencing Linien können von VDRC RNAi-Sammlung 2 erhalten werden. Eine Sammlung von GAL4-Fahrer Linien ist an der Bloomington Drosophila Stock Center (Indiana, USA) zur Verfügung. Ausstattung Erforderliche Ausrüstung umfasst Laser Microdissector (Leica LMD6000), Coulter Microfuge 22R (Beckman), PCR (BIO-RAD Mein Cycler), Real Time PCR (BIO-RAD iQ5). Werkzeuge Benötigte Werkzeuge sind: Glas Brunnen, Pinsel, Pinzette Mikrodissektion, hängenden Tropfen gleitet, Insekten-Pins auf Injektionsnadeln, Metallrahmen mit PET-Membran-, Kunststoff-Rohre (50 ml, 05 ml, 0,25 ml) montiert.

laser microdissection applied to gene expression profiling of subset of cells from the drosophila wing disc

Heterogene Natur des Gewebes hat sich ein limitierender Faktor bei der Menge an Informationen, die aus biologischen Proben erzeugt werden können, Kompromisse Downstream-Analysen. Angesichts der komplexen und dynamischen zellulären Verbänden bestehende in vielen Geweben, um die in vivo Interaktionen gründliche molekulare Analyse rekapitulieren muss man in der Lage sein bestimmte Zellpopulationen in ihrer Muttersprache Kontext zu analysieren. Laser-vermittelte Mikrodissektion kann dieses Ziel zu erreichen, so dass eine eindeutige Identifizierung und erfolgreichen Ernte der Zellen von Interesse unter der direkten mikroskopischen Visualisierung unter Beibehaltung molekulare Integrität. Wir haben diese Technologie angewendet, um die Genexpression in definierten Gebieten der Entwicklungsländer Drosophila Flügel Disc, die ein vorteilhaftes Modellsystem, um Wachstum zu kontrollieren, der Zelldifferenzierung und Organentwicklung Studie stellt analysieren. Larven Imaginalscheiben sind frühzeitig in die vorderen und hinteren, dorsalen und ventralen Kammern durch Abstammung Einschränkung Grenzen unterteilt. Die Nutzung der induzierbaren GAL4-UAS binärer Ausdruck System, jedes dieser Fächer können gezielt in transgenen Fliegen Ausdruck einer UAS-GFP-Transgen unter der Kontrolle der entsprechenden GAL4-Treiber bauen gekennzeichnet werden. In den transgenen Discs können Genexpressionsanalysen von diskreten Untergruppen von Zellen genau nach Laser-vermittelte Mikrodissektion bestimmt werden, mit dem fluoreszierenden GFP-Signal an lasergeschnittenen führen. Unter der Vielzahl der nachgelagerten Anwendungen, konzentrierten wir uns auf RNA-Transkript Profilierung nach lokalisierten RNA-Interferenz (RNAi). Mit dem Aufkommen der RNAi-Technologie können GFP-Markierung mit lokalisierten Knockdown von einem bestimmten Gen gekoppelt werden, so dass der Transkriptions-Reaktion eines diskreten Zellpopulation, die Gen-Silencing bestimmten. Zur Validierung dieses Ansatzes haben wir entsprechende Bereiche der Scheibe aus dem hinteren (gekennzeichnet durch die GFP-Expression) zerlegt, und die anterior (unbeschriftet) Fach auf regionaler Silencing in der P-Fach eines ansonsten ubiquitär exprimierten Gen. RNA wurde aus mikrodissezierten zum Schweigen gebracht und unsilenced Bereichen und vergleichende Genexpressionsanalysen mittels quantitativer real-time RT-PCR bestimmt extrahiert. Wir zeigen, dass diese Methode effektiv für eine genaue Transkriptomik von Teilmengen von Zellen innerhalb des Drosophila Imaginalscheiben angewendet werden. In der Tat, während der massive Scheibe Zubereitung als Quelle der RNA in der Regel davon ausgegangen Zelle Homogenität, ist es bekannt, dass transkriptionelle Expression kann stark variieren innerhalb dieser Strukturen in Folge der Positionsinformationen. Mit lokalisierten fluoreszierenden GFP-Signal an lasergeschnittenen Führer, können genauere transkriptionelle Analysen durchgeführt werden und profitabel zu verschiedenen Anwendungen, einschließlich Abschrift Profilierung der verschiedenen Zelllinien in ihrer Muttersprache Kontext angewendet.

Watch this Scientific Journal Video about Laser Microdissection Applied to Gene Expression Profiling of Subset of Cells from the Drosophila Wing Disc at JoVE.com

Laser Microdissection Applied to Gene Expression Profiling of Subset of Cells from the Drosophila Wing Disc

Laser Mikrodissektion wurde angewandt, um Gene Expression Profiling in bestimmten Kompartimenten des Drosophila Flügel Scheibe analysieren unterzogen, um lokalisierte RNAi<em&gt; In vivo</em&gt;. RNA aus entsprechenden Bereichen zum Schweigen gebracht und unsilenced Fächer extrahiert wurde durch quantitative RT-PCR analysiert, um vergleichende Genexpressionsanalysen im Rahmen der nativen Gewebe Mikroökologie bestimmen.

Laser Mikrodissektion Angewandt auf Gene Expression Profiling von Untergruppe von Zellen aus dem Drosophila Wing Disc

Heterogeneous nature of tissues has proven to be a limiting factor in the amount of information that can be generated from biological samples, ...

laser-microdissection-applied-to-gene-expression-profiling-subset

Research

JoVE Journal

Biology

Laser Microdissection Applied to Gene Expression Profiling of Subset of Cells from the Drosophila Wing Disc

11.1K Aufrufe.  University of Naples. Laser Mikrodissektion wurde angewandt, um Gene Expression Profiling in bestimmten Kompartimenten des Drosophila Flügel Scheibe analysieren unterzogen, um lokalisierte RNAi In vivo. RNA aus entsprechenden Bereichen zum Schweigen gebracht und unsilenced Fächer extrahiert wurde durch quantitative RT-PCR analysiert, um vergleichende Genexpressionsanalysen im Rahmen der nativen Gewebe Mikroökologie bestimmen.

Serie: Laser Microdissection Applied to Gene Expression Profiling of Subset of Cells from the Drosophila Wing Disc

Laser Capture Microdissection of Mammalian Tissue

Laser capture microscopy, also known as laser microdissection (LMD), enables the user to isolate small numbers of cells or tissues from frozen or formalin-fixed, paraffin-embedded tissue sections. LMD techniques rely on a thermo labile membrane placed either on top of, or underneath, the tissue section. In one method, focused laser energy is used to melt the membrane onto the underlying cells, which can then be lifted out of the tissue section. In the other, the laser energy vaporizes the foil along a path "drawn" on the tissue, allowing the selected cells to fall into a collection device. Each technique allows the selection of cells with a minimum resolution of several microns. DNA, RNA, protein, and lipid samples may be isolated and analyzed from micro-dissected samples. In this video, we demonstrate the use of the Leica AS-LMD laser microdissection instrument in seven segments, including an introduction to the principles of LMD, initializing the instrument for use, general considerations for sample preparation, mounting the specimen and setting up capture tubes, aligning the microscope, adjusting the capture controls, and capturing tissue specimens. Laser-capture micro-dissection enables the investigator to isolate samples of pure cell populations as small as a few cell-equivalents. This allows the analysis of cells of interest that are free of neighboring contaminants, which may confound experimental results.

Laser Capture Mikrodissektion von Säugetiergewebe

Laser capture microscopy, also known as laser microdissection (LMD), enables the user to isolate small numbers of cells or tissues from frozen or ...

Forschung

Biologie

The Preparation of Primary Hematopoietic Cell Cultures From Murine Bone Marrow for Electroporation

It is becoming increasingly apparent that electroporation is the most effective way to introduce plasmid DNA or siRNA into primary cells. The Gene Pulser MXcell  electroporation system and Gene Pulser  electroporation buffer were specifically developed to transfect nucleic acids into mammalian cells and difficult-to-transfect cells, such as primary and stem cells.This video demonstrates how to establish primary hematopoietic cell cultures from murine bone marrow, and then prepare them for electroporation in the MXcell system. We begin by isolating femur and tibia. Bone marrow from both femur and tibia are then harvested and cultures are established. Cultured bone marrow cells are then transfected and analyzed.

This procedure describes how to establish primary hematopoietic cell cultures from murine bone marrow and is followed by transfection using the Gene Pulser MXCell electroporation system.

Die Herstellung von primären hämatopoetischen Zellkulturen aus Knochenmark der Maus für die Elektroporation

It is becoming increasingly apparent that electroporation is the most effective way to introduce plasmid DNA or siRNA into primary cells. The Gene Pulser ...

Using the Gene Pulser MXcell Electroporation System to Transfect Primary Cells with High Efficiency

It is becoming increasingly apparent that electroporation is the most effective way to introduce plasmid DNA or siRNA into primary cells. The Gene Pulser MXcell electroporation system and Gene Pulser electroporation buffer (Bio-Rad) were specifically developed to easily transfect nucleic acids into mammalian cells and difficult-to-transfect cells, such as primary and stem cells. We will demonstrate how to perform a simple experiment to quickly identify the best electroporation conditions. We will demonstrate how to run several samples through a range of electroporation conditions so that an experiment can be conducted at the same time as optimization is performed. We will also show how optimal conditions identified using 96-well electroporation plates can be used with standard electroporation cuvettes, facilitating the switch from electroporation plates to electroporation cuvettes while maintaining the same electroporation efficiency. In the video, we will also discuss some of the key factors that can lead to the success or failure of electroporation experiments.

This procedure shows how to use the Gene Pulser MXcell electroporation system to rapidly and easily identify the best electroporation conditions for mouse embryonic fibroblasts (MEFs) or other primary cells. Considerations for troubleshooting are also discussed in the associated video.

Mit dem Gene Pulser MXcell Elektroporation System zur Primary Cells mit hohem Wirkungsgrad zu transfizieren

Using an Automated Cell Counter to Simplify Gene Expression Studies: siRNA Knockdown of IL-4 Dependent Gene Expression in Namalwa Cells

The use of siRNA mediated gene knockdown is continuing to be an important tool in studies of gene expression.  siRNA studies are being conducted not only to study the effects of downregulating single genes, but also to interrogate signaling pathways and other complex interaction networks.  These pathway analyses require both the use of relevant cellular models and methods that cause less perturbation to the cellular physiology.  Electroporation is increasingly being used as an effective way to introduce siRNA and other nucleic acids into difficult to transfect cell lines and primary cells without altering the signaling pathway under investigation. There are multiple critical steps to a successful siRNA experiment, and there are ways to simplify the work while improving the data quality at several experimental stages.  To help you get started with your siRNA mediated gene knockdown project, we will demonstrate how to perform a pathway study complete from collecting and counting the cells prior to electroporation through post transfection real-time PCR gene expression analysis.  The following study investigates the role of the transcriptional activator STAT6 in IL-4 dependent gene expression of CCL17 in a Burkitt lymphoma cell line (Namalwa).  The techniques demonstrated are useful for a wide range of siRNA-based experiments on both adherent and suspension cells.  We will also show how to streamline cell counting with the TC10 automated cell counter, how to electroporate multiple samples simultaneously using the MXcell electroporation system, and how to simultaneously assess RNA quality and quantity with the Experion automated electrophoresis system.

This procedure describes a quick and easy workflow to introduce siRNA into difficult to transfect cell lines and follow gene expression by real-time PCR. Use of an automated cell counter, multi-well electroporation plate, and automated electrophoresis station provide quick and reliable results without the need for expensive robotic handling.

Verwendung eines automatisierten Cell Counter zu Genexpressionsstudien Simplify: siRNA Knockdown von IL-4 abhängige Genexpression in Namalwalzellen

The use of siRNA mediated gene knockdown is continuing to be an important tool in studies of gene expression.  siRNA studies are being conducted not only ...

Paraffin-Embedded and Frozen Sections of Drosophila Adult Muscles

The molecular characterization of muscular dystrophies and myopathies in humans has revealed the complexity of muscle disease and genetic analysis of muscle specification, formation and function in model systems has provided valuable insight into muscle physiology. Therefore, identifying and characterizing molecular mechanisms that underlie muscle damage is critical. The structure of adult Drosophila multi-fiber muscles resemble vertebrate striated muscles 1 and the genetic tractability of Drosophila has made it a great system to analyze dystrophic muscle morphology and characterize the processes affecting muscular function in ageing adult flies 2. Here we present the histological technique for preparing paraffin-embedded and frozen sections of Drosophila thoracic muscles. These preparations allow for the tissue to be stained with classical histological stains and labeled with protein detecting dyes, and specifically cryosections are ideal for immunohistochemical detection of proteins in intact muscles. This allows for analysis of muscle tissue structure, identification of morphological defects, and detection of the expression pattern for muscle/neuron-specific proteins in Drosophila adult muscles. These techniques can also be slightly modified for sectioning of other body parts.

Paraffin-Embedded and Frozen Sections of Drosophila Adult Muscles

Identification of mechanisms underlying muscle damage is crucial. Here we present the histological technique for preparing paraffin-embedded and frozen sections of Drosophila thoracic muscles. This allows analysis of muscle morphology and localization of protein and other muscle cell components.

Paraffin-Embedded-und Gefrierschnitte von Drosophila Adult Muskeln

The molecular characterization of muscular dystrophies and myopathies in humans has revealed the complexity of muscle disease and genetic analysis of ...

In vitro Reconstitution of the Active T. castaneum Telomerase

Efforts to isolate the catalytic subunit of telomerase, TERT, in sufficient quantities for structural studies, have been met with limited success for more than a decade. Here, we present methods for the isolation of the recombinant Tribolium castaneum TERT (TcTERT) and the reconstitution of the active T. castaneum telomerase ribonucleoprotein (RNP) complex in vitro.
Telomerase is a specialized reverse transcriptase1 that adds short DNA repeats, called telomeres, to the 3' end of linear chromosomes2 that serve to protect them from end-to-end fusion and degradation. Following DNA replication, a short segment is lost at the end of the chromosome3 and without telomerase, cells continue dividing until eventually reaching their Hayflick Limit4. Additionally, telomerase is dormant in most somatic cells5 in adults, but is active in cancer cells6 where it promotes cell immortality7.
The minimal telomerase enzyme consists of two core components: the protein subunit (TERT), which comprises the catalytic subunit of the enzyme and an integral RNA component (TER), which contains the template TERT uses to synthesize telomeres8,9. Prior to 2008, only structures for individual telomerase domains had been solved10,11. A major breakthrough in this field came from the determination of the crystal structure of the active12, catalytic subunit of T. castaneum telomerase, TcTERT1.
Here, we present methods for producing large quantities of the active, soluble TcTERT for structural and biochemical studies, and the reconstitution of the telomerase RNP complex in vitro for telomerase activity assays. An overview of the experimental methods used is shown in Figure 1.

In vitro Reconstitution of the Active T. castaneum Telomerase

Efforts to isolate the catalytic subunit of telomerase, TERT, in sufficient quantities for structural studies, have been met with limited success for more than a decade. Here, we present methods for the isolation of the recombinant Tribolium castaneum TERT (TcTERT) and the reconstitution of the active T. castaneum telomerase ribonucleoprotein (RNP) complex in vitro.

In vitro Rekonstitution der Active T. castaneum Telomerase

Efforts to isolate the catalytic subunit of telomerase, TERT, in sufficient quantities for structural studies, have been met with limited success for more ...

Affinity-based Isolation of Tagged Nuclei from Drosophila Tissues for Gene Expression Analysis

Drosophila melanogaster embryonic and larval tissues often contain a highly heterogeneous mixture of cell types, which can complicate the analysis of gene expression in these tissues. Thus, to analyze cell-specific gene expression profiles from Drosophila tissues, it may be necessary to isolate specific cell types with high purity and at sufficient yields for downstream applications such as transcriptional profiling and chromatin immunoprecipitation. However, the irregular cellular morphology in tissues such as the central nervous system, coupled with the rare population of specific cell types in these tissues, can pose challenges for traditional methods of cell isolation such as laser microdissection and fluorescence-activated cell sorting (FACS). Here, an alternative approach to characterizing cell-specific gene expression profiles using affinity-based isolation of tagged nuclei, rather than whole cells, is described. Nuclei in the specific cell type of interest are genetically labeled with a nuclear envelope-localized EGFP tag using the Gal4/UAS binary expression system. These EGFP-tagged nuclei can be isolated using antibodies against GFP that are coupled to magnetic beads. The approach described in this protocol enables consistent isolation of nuclei from specific cell types in the Drosophila larval central nervous system at high purity and at sufficient levels for expression analysis, even when these cell types comprise less than 2% of the total cell population in the tissue. This approach can be used to isolate nuclei from a wide variety of Drosophila embryonic and larval cell types using specific Gal4 drivers, and may be useful for isolating nuclei from cell types that are not suitable for FACS or laser microdissection.

Affinity-based Isolation of Tagged Nuclei from Drosophila Tissues for Gene Expression Analysis

Drosophila tissues often contain a heterogeneous mixture of cell types.&#160;To examine gene expression in specific cell types from a particular tissue, nuclei can be genetically tagged and subsequently isolated using an affinity-based approach. Isolated nuclei can be used for downstream applications such as gene expression analysis and chromatin immunoprecipitation.

Affinity-basierte Isolierung von Tagged Kerne aus<em&gt; Drosophila</em&gt; Tücher für Genexpressionsanalyse

Drosophila melanogaster embryonic and larval tissues often contain a highly heterogeneous mixture of cell types, which can complicate the analysis of gene ...

Analysis of Global RNA Synthesis at the Single Cell Level following Hypoxia

Hypoxia or lowering of the oxygen availability is involved in many physiological and pathological processes. At the molecular level, cells initiate a particular transcriptional program in order to mount an appropriate and coordinated cellular response. The cell possesses several oxygen sensor enzymes that require molecular oxygen as cofactor for their activity. These range from prolyl-hydroxylases to histone demethylases. The majority of studies analyzing cellular responses to hypoxia are based on cellular populations and average studies, and as such single cell analysis of hypoxic cells are seldom performed. Here we describe a method of analysis of global RNA synthesis at the single cell level in hypoxia by using Click-iT RNA imaging kits in an oxygen controlled workstation, followed by microscopy analysis and quantification.&nbsp; Using cancer cells exposed to hypoxia for different lengths of time, RNA is labeled and measured in each cell. This analysis allows the visualization of temporal and cell-to-cell changes in global RNA synthesis following hypoxic stress.

We describe a technique for analysis of global RNA synthesis in hypoxia using imaging. Click-chemistry labeling of RNA has not previously been performed under hypoxia and allows visualization of global RNA changes at the single cell level. This approach complements the existing averaged RNA techniques, allowing direct visualization of cell-to-cell changes in global RNA synthesis.

Analyse der globalen RNA-Synthese auf der Einzelzellebene folgende Hypoxie

Hypoxia or lowering of the oxygen availability is involved in many physiological and pathological processes. At the molecular level, cells initiate a ...

siRNA Screening to Identify Ubiquitin and Ubiquitin-like System Regulators of Biological Pathways in Cultured Mammalian Cells

Post-translational modification of proteins with ubiquitin and ubiquitin-like molecules (UBLs) is emerging as a dynamic cellular signaling network that regulates diverse biological pathways including the hypoxia response, proteostasis, the DNA damage response and transcription.&#160; To better understand how UBLs regulate pathways relevant to human disease, we have compiled a human siRNA &#8220;ubiquitome&#8221; library consisting of 1,186 siRNA duplex pools targeting all known and predicted components of UBL system pathways. This library can be screened against a range of cell lines expressing reporters of diverse biological pathways to determine which UBL components act as positive or negative regulators of the pathway in question.&#160; Here, we describe a protocol utilizing this library to identify ubiquitome-regulators of the HIF1A-mediated cellular response to hypoxia using a transcription-based luciferase reporter.&#160; An initial assay development stage is performed to establish suitable screening parameters of the cell line before performing the screen in three stages: primary, secondary and tertiary/deconvolution screening. &#160;The use of targeted over whole genome siRNA libraries is becoming increasingly popular as it offers the advantage of reporting only on members of the pathway with which the investigators are most interested.&#160; Despite inherent limitations of siRNA screening, in particular false-positives caused by siRNA off-target effects, the identification of genuine novel regulators of the pathways in question outweigh these shortcomings, which can be overcome by performing a series of carefully undertaken control experiments.

Here, we describe a methodology to perform a targeted siRNA &#8220;ubiquitome&#8221; screen to identify novel ubiquitin and ubiquitin-like regulators of the HIF1A-mediated cellular response to hypoxia.&#160; This can be adapted to any biological pathway where a robust read out of reporter activity is available.

siRNA Screening zu Ubiquitin und Ubiquitin-ähnlichen System Regler der biologischen Stoffwechselwege in kultivierten Säugerzellen identifizieren

Post-translational modification of proteins with ubiquitin and ubiquitin-like molecules (UBLs) is emerging as a dynamic cellular signaling network that ...

Measurement of Metabolic Rate in Drosophila using Respirometry

Metabolic disorders are a frequent problem affecting human health. Therefore, understanding the mechanisms that regulate metabolism is a crucial scientific task. Many disease causing genes in humans have a fly homologue, making Drosophila a good model to study signaling pathways involved in the development of different disorders. Additionally, the tractability of Drosophila simplifies genetic screens to aid in identifying novel therapeutic targets that may regulate metabolism. In order to perform such a screen a simple and fast method to identify changes in the metabolic state of flies is necessary. In general, carbon dioxide production is a good indicator of substrate oxidation and energy expenditure providing information about metabolic state. In this protocol we introduce a simple method to measure CO2 output from flies. This technique can potentially aid in the identification of genetic perturbations affecting metabolic rate.

Measurement of Metabolic Rate in Drosophila using Respirometry

Metabolic disorders are among one of the most common diseases in humans. The genetically tractable model organism D. melanogaster can be used to identify novel genes that regulate metabolism. This paper describes a relatively simple method which allows studying the metabolic rate in flies by measuring their CO2 production.