Questo lavoro è stato supportato dal programma di ricerca del genoma di pianta dalla National Science Foundation (NSF-PGRP-IOS-1339388).

1. la crescita delle piante
<ol><li>Seminare i semi di soia 5-10 (Williams 82) in un vaso di 13 cm in serra in condizioni di giorno lungo (16 h luce alle 1.500 µmol m-2 s-1) a 25 ° C sul mix di terreno personalizzato per la soia (1:1:1 rapporto di sabbia del suolo, la perlite e la torpedine).</li>
</ol>2. preparazione del DNA del plasmide
<ol><li>Utilizzando una pipetta sterile o uno stuzzicadenti, scegli una singola Colonia o glicerolo congelati stock di e. coli che trasportano il plasmide contenente il gene di interesse e inoculare esso in 20 mL di terreno liquido di Luria-Bertani (LB) con gli antibiotici adatti in un pallone da 50 mL.</li>
	<li>Incubare la beuta a 37 ° C durante la notte su un agitatore. Raccogliere i batteri da centrifugazione la sospensione a 12.000 x g a temperatura ambiente per 5 minuti e scartare il surnatante. Estrarre e purificare il plasmide seguendo la procedura del produttore di un kit di preparazione del plasmide.</li>
</ol>3. isolamento di protoplasti
<ol><li>Tagliare foglie unifoliate recentemente ampliate da piantine di soia 10 - giorno di vita (Figura 1). Nota: Selezione di foglie in una fase inerente allo sviluppo appropriata è la chiave per il successo per la preparazione di protoplasti di soia. Utilizzare solo foglie appena ampliati alle prime fasi dello sviluppo. Come lascia maturo, pareti cellulari diventano più difficile da digerire.</li>
	<li>Con una lama di rasoio fresca, togliere la foglia unifoliata e quindi tagliare i resti in 0,5-1 mm strisce la nervatura centrale. Nota: Due foglie unifoliate digeriti in 10 mL di soluzione di enzima darà protoplasti sufficienti per più di 10 trasformazioni.</li>
	<li>Usando un paio di pinze, trasferimento la foglia strisce immediatamente e delicatamente in 10 mL di soluzione enzimatica preparata al momento (tabella 1) in una provetta da 15 mL. Vuoto si infiltra in foglia strisce per 15 min a temperatura ambiente.</li>
	<li>Incubare le strisce di foglia nella soluzione enzimatica con agitazione delicata (40 giri) sotto luce bassa per 4-6 h a temperatura ambiente. Assicurarsi che la soluzione di enzima diventa giallo-verde come protoplasti vengono rilasciati. Verificare la soluzione di enzima/protoplasti al microscopio (X10). Nota: I protoplasti rilasciati sono sferici a forma, mentre le cellule non digerite hanno forma ovale o irregolare.</li>
	<li>Trasferire i 10 mL di soluzione di enzima/protoplasti in una provetta da 50 mL versando delicatamente e aggiungere 10 mL di soluzione di W5 (tabella 1) a temperatura ambiente per interrompere la digestione. Capovolgere delicatamente la provetta un paio di volte. Versare delicatamente la soluzione enzima/protoplasti su una maglia di nylon pulito 75 µm posizionata sopra un tubo da 50 mL per rimuovere i tessuti della foglia non digerito.</li>
	<li>Centrifugare la soluzione di flusso continuo enzima/protoplasti a 100 x g nel tubo 50 mL per 1-2 min a temperatura ambiente. Rimuovere delicatamente il supernatante utilizzando una pipetta sierologica 10ml senza disturbare il pellet di protoplasti.</li>
	<li>Risospendere i protoplasti e contando il numero di protoplasti su un emocitometro sotto il microscopio (x10), diluire ad una concentrazione di 2 x 105 mL-1 in soluzione di W5 refrigerati a 4 ° C. Mantenere i protoplasti su ghiaccio per 30 min.</li>
	<li>Centrifugare la sospensione a 100 x g per 1-2 min a temperatura ambiente e rimuovere delicatamente la soluzione W5 utilizzando una pipetta da 1 mL senza disturbare il pellet di protoplasti. Risospendere i protoplasti nella soluzione MMG (tabella 1) ad una concentrazione di 2 x 105 mL-1 a temperatura ambiente.</li>
</ol>4. trasformazione di protoplasti
<ol><li>Fai aliquote di 100 µ l dei protoplasti (2 x 104 protoplasti a 2 x 105 mL-1) in 1,5 mL bassa adesione per microcentrifuga utilizzando puntali per pipette uncut 200 µ l. Mettere un'aliquota da parte per servire come controllo negativo. Aggiungere 10 µ l di plasmide (10-20 µ g) in ciascuna dell'aliquota resto dei protoplasti.</li>
	<li>Aggiungere lentamente 110 µ l di soluzione preparata di PEG (tabella 1) sulla parete interna del tubo per microcentrifuga da 1,5 mL e quindi capovolgere delicatamente e ruotare il tubo fino a quando la soluzione diventa omogenea.</li>
	<li>Incubare la miscela di trasformazione a temperatura ambiente per 15 min.</li>
	<li>Per fermare la trasformazione, lentamente aggiungere 400 µ l di soluzione di W5 per la provetta da 1,5 mL a temperatura ambiente e capovolgere delicatamente la provetta fino a quando la soluzione diventa omogenea. Centrifugare la provetta a 100 g per 1-2 min a temperatura ambiente e scartare il surnatante con una pipetta.</li>
	<li>Aggiungere 1 mL di soluzione WI (tabella 1) al tubo e risospendere pipettando delicatamente 1 - 2 volte. Aggiungere 1 mL di siero di vitello sterile (vol/vol) 5% in ogni pozzetto di una piastra di coltura del tessuto 6 pozzetti per rivestire la superficie ed evitare i protoplasti di attaccarsi alla piastra.</li>
	<li>Dopo pochi secondi, scartare il siero di vitello utilizzando una pipetta. Trasferire i protoplasti sedimento in un pozzetto della piastra di coltura. Coprire la piastra con un coperchio.</li>
</ol>5. protoplasti incubazione e raccolta
<ol><li>Incubare i protoplasti a temperatura ambiente per 1-2 giorni al buio. Nota: Abbiamo trovato che due-giorni di incubazione produce più forte segnale di proteina fluorescente in generale rispetto ad un giorno incubazione, e che il segnale di proteina fluorescente può durare fino a 3-4 giorni.</li>
	<li>Trasferire la soluzione di protoplasti di un tubo del microcentrifuge bassa adesione di 1,5 mL. Centrifugare la provetta a 100 x g per 1-2 min a temperatura ambiente per raccogliere protoplasti. Rimuovere il surnatante con una pipetta e trasferire 10 protoplasti µ l su una lastra di vetro.</li>
	<li>Osservare il segnale fluorescente sotto fluorescenza o microscopia confocale. Utilizzare non trasformate protoplasti come controllo negativo (non dovrebbe essere osservato nessun segnale).</li>
</ol>

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Gli autori dichiarano di non avere nessun concorrenti interessi finanziari.

Questo protocollo per l'isolamento di protoplasti di soia e l'applicazione di studi di espressione transitoria è stato accuratamente testato e funziona molto bene nel nostro laboratorio. Le procedure sono semplici e facili e richiedono apparecchiature ordinarie e minimo costo. Il nostro protocollo produce grandi quantità di protoplasti di uniforme, di alta qualità rispetto ai metodi precedentemente segnalati34,35,36,</su...

Protoplasti sono cellule vegetali che hanno rimosse le pareti cellulari. Come mantengono la maggior parte delle caratteristiche e attività di cellule vegetali, protoplasti sono un sistema di buon modello di osservare e valutare diversi eventi cellulari e sono strumenti preziosi per studiare ibridazione somatica1 e impianto di rigenerazione2. Protoplasti sono stati anche ampiamente utilizzati per impianto trasformazione3,4,5, poiché le pareti cellulari altrimenti bloccherebbe il passaggio del DNA nella cellula. Protoplasti possiedono alcune delle risposte fisiologiche e processi cellulari di piante intatte, offrendo quindi un valore fondamentale nella ricerca di base per lo studio di proteine sottocellulari localizzazione6,7,8, interazioni proteina-proteina9,10e promotore attività11,12,13 in cellule vive.
L'isolamento di protoplasti di pianta in primo luogo è stato segnalato nel 196014 e i protocolli per l'isolamento e la trasformazione dei protoplasti sono stati sviluppati e ottimizzati. Una procedura standard di isolamento del protoplasto comporta il taglio delle foglie e la digestione enzimatica delle pareti cellulari, seguita dalla separazione dei protoplasti rilasciati da detriti del tessuto non digerito. Strategie di trasformazione include elettroporazione15,16, microinjection17,18e base di polietilenglicole (PEG)4,5,19 metodi. Una vasta gamma di specie sono stati segnalati successo per l'isolamento di protoplasti, compresi agrumi20, Brassica21, Solanaceae22 e altre piante ornamentali famiglie23,24. Mentre i tipi di tessuti diversi sono utilizzati in varie specie, un sistema di espressione transiente in protoplasti di Arabidopsis mesofillo (TEAMP) isolato dalle foglie della pianta modello Arabidopsis thaliana è stato affermata25 e ampiamente adottato per diverse applicazioni.
Soia (Glycine max (L.) Merr.) è una delle proteine più importanti e olio colture26. A differenza di Arabidopsis e riso, ottenimento di piante di soia transgenica è noto per essere piuttosto difficile e basso rendimento. Agrobacterium tumefaciens-mediata infiltrazione è stato popolarmente utilizzato per studi di espressione transiente in cellule epidermiche in tabacco27 e piantine in Arabidopsis28,29, considerando che Agrobacterium rhizogenes è stato utilizzato per la trasformazione delle radici pelosi in soia30. Approcci di silenziamento genica indotta da virus sono stati utilizzati per downregulation di destinazione geni31,32 e transitori espressione33 in maniera sistematica. Protoplasti forniscono una preziosa e versatile alternativa a questi approcci. Protoplasti possono essere ottenuti da materiali aboveground di soia e consentono l'espressione del transgene rapido e sincronizzato. Tuttavia, poiché l'isolamento iniziale successo dei protoplasti di soia nel 198334, ci sono stati rapporti limitati sull'applicazione dei protoplasti in soia35,36,37, 38, principalmente a causa della relativamente basse rese dei protoplasti di soia.
Qui, descriviamo un protocollo semplice ed efficiente per l'isolamento di protoplasti di soia e la sua applicazione per studi di espressione genica transitoria. Utilizzando foglie giovani unifoliate da piantine di soia, siamo stati in grado di ottenere grandi quantità di protoplasti vitali entro poche ore. Inoltre, abbiamo ottimizzato un metodo di trasformazione di PEG-calcio-mediata che è semplice e a basso costo per trasportare DNA in protoplasti di soia con alta efficienza.

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			<td>Sigma Aldrich&#160;</td>
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			<td height="24" style="height:25px;width:256px;">Zeiss 710 Confocal Microscope</td>
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			<td height="21" style="height:21px;width:256px;">15 mL Centrifuge Tubes</td>
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			<td height="21" style="height:21px;width:256px;">50 mL Centrifuge Tubes</td>
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			<td style="width:119px;">BP1427-500</td>
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a simple method for isolation of soybean protoplasts and application to transient gene expression analyses

Soia (Glycine max (L.) Merr.) è una specie di coltura importante ed è diventato un modello di legumi per gli studi delle vie genetiche e biochimiche. Pertanto, è importante stabilire un sistema di espressione genica transitoria efficiente in soia. Qui, segnaliamo un semplice protocollo per la preparazione dei protoplasti di soia e la sua applicazione per l'analisi funzionale transitorie. Abbiamo trovato che le foglie giovani unifoliate da piantine di soia ha provocato grandi quantità di protoplasti di alta qualità. Grazie all'ottimizzazione di un metodo di trasformazione PEG-calcio-mediata, abbiamo raggiunto l'efficienza di trasformazione alta utilizzando protoplasti unifoliate soia. Questo sistema fornisce un modello efficiente e versatile per l'esame dei complessi meccanismi di regolamentazione e di segnalazione in cellule di soia dal vivo e può aiutare per meglio comprendere diversi processi cellulari, inerente allo sviluppo e fisiologici dei legumi.

Diversi organi di soia 10 - giorno-vecchio sono stati testati per la preparazione del protoplasto (Figura 1) e i rendimenti sono stati osservati al microscopio (Figura 2). Pareti cellulari da ipocotile ed epicotyl erano appena digeriti, e alcune cellule siamo stati attaccati alla vicenda (Figura 2B, 2C). Nel cotiledone (Figura 2D) e radice (<strong class...

Watch this Scientific Journal Video about A Simple Method for Isolation of Soybean Protoplasts and Application to Transient Gene Expression Analyses at JoVE.com

A Simple Method for Isolation of Soybean Protoplasts and Application to Transient Gene Expression Analyses

Abbiamo sviluppato un protocollo semplice ed efficiente per la preparazione di grandi quantità di protoplasti di soia studiare i complessi meccanismi di regolamentazione e di segnalazione in cellule vive.

Un metodo semplice per l'isolamento di protoplasti di soia e l'applicazione di analisi di espressione genica transitoria

Soybean (Glycine max (L.) Merr.) is an important crop species and has become a legume model for the studies of genetic and biochemical pathways. ...

a-simple-method-for-isolation-soybean-protoplasts-application-to

Research

JoVE Journal

Biology

24.4K Views.  California State University, Northridge. Abbiamo sviluppato un protocollo semplice ed efficiente per la preparazione di grandi quantità di protoplasti di soia studiare i complessi meccanismi di regolamentazione e di segnalazione in cellule vive.

Video: A Simple Method for Isolation of Soybean Protoplasts and Application to Transient Gene Expression Analyses

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.

La preparazione di colture primarie di cellule emopoietiche dal midollo osseo murino per elettroporazione

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

Ricerca

Biologia

RNA Isolation from Embryonic Zebrafish and cDNA Synthesis for Gene Expression Analysis

Many important and complex laboratory procedures require an input of high quality, intact RNA.  A degraded sample or the presence of impurities can lead to disastrous results in downstream experimental applications.  It is therefore, of utmost importance to use solid techniques with numerous safeguards and quality control checks to ensure a superior sample.  Herein, we detail a protocol to isolate total RNA from whole zebrafish embryos using a commercially available chemical denaturant and subsequent cleanup to remove traces of DNA and impurities using a commercial RNA isolation kit. As RNA is relatively unstable and easily prone to cleavage by RNAses, most protocols assay gene expression using a cDNA product that is directly synthesized from an RNA template. We detail a procedure to convert RNA into the more stable cDNA product using a commercially available kit. Throughout these procedures there are numerous quality control checks to ensure that the sample is not degraded or contaminated.  The end product of these protocols is cDNA that is suitable for microarray analysis, RT-PCR or long-term storage.    

The isolation of high quality, intact RNA is an essential step in many laboratory protocols. Here, we demonstrate RNA extraction from whole zebrafish embryos and cDNA synthesis for subsequent application in various experimental procedures including gene expression microarray analysis.

Isolamento RNA da embrionali Sintesi Zebrafish e cDNA per l&#39;analisi di espressione genica

Many important and complex laboratory procedures require an input of high quality, intact RNA.  A degraded sample or the presence of impurities can lead ...

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.

Utilizzando il sistema di elettroporazione Gene Pulser MXcell per trasfettare cellule primarie con alta efficienza

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 metodo per studiare l&#39;architettura tridimensionale dei genomi.

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

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.

L&#39;utilizzo di un contatore automatico cella per semplificare gli studi sull&#39;espressione genica: Knockdown siRNA di IL-4 genica dipendente nelle celle Namalwa

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.

Sezioni incluse in paraffina e surgelati di Drosophila Adulti Muscoli

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.

Ricostituzione in vitro di Active T. castaneum telomerasi

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

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA

The rate of translational elongation is non-uniform. mRNA secondary structure, codon usage and mRNA associated proteins may alter ribosome movement on the messagefor review see 1. However, it's now widely accepted that synonymous codon usage is the primary cause of non-uniform translational elongation rates1. Synonymous codons are not used with identical frequency. A bias exists in the use of synonymous codons with some codons used more frequently than others2. Codon bias is organism as well as tissue specific2,3. Moreover, frequency of codon usage is directly proportional to the concentrations of cognate tRNAs4. Thus, a frequently used codon will have higher multitude of corresponding tRNAs, which further implies that a frequent codon will be translated faster than an infrequent one. Thus, regions on mRNA enriched in rare codons (potential pause sites) will as a rule slow down ribosome movement on the message and cause accumulation of nascent peptides of the respective sizes5-8. These pause sites can have functional impact on the protein expression, mRNA stability and protein foldingfor review see 9. Indeed, it was shown that alleviation of such pause sites can alter ribosome movement on mRNA and subsequently may affect the efficiency of co-translational (in vivo) protein folding1,7,10,11. To understand the process of protein folding in vivo, in the cell, that is ultimately coupled to the process of protein synthesis it is essential to gain comprehensive insights into the impact of codon usage/tRNA content on the movement of ribosomes along mRNA during translational elongation.
Here we describe a simple technique that can be used to locate major translation pause sites for a given mRNA translated in various cell-free systems6-8. This procedure is based on isolation of nascent polypeptides accumulating on ribosomes during in vitro translation of a target mRNA. The rationale is that at low-frequency codons, the increase in the residence time of the ribosomes results in increased amounts of nascent peptides of the corresponding sizes. In vitro transcribed mRNA is used for in vitro translational reactions in the presence of radioactively labeled amino acids to allow the detection of the nascent chains. In order to isolate ribosome bound nascent polypeptide complexes the translation reaction is layered on top of 30% glycerol solution followed by centrifugation. Nascent polypeptides in polysomal pellet are further treated with ribonuclease A and resolved by SDS PAGE. This technique can be potentially used for any protein and allows analysis of ribosome movement along mRNA and the detection of the major pause sites. Additionally, this protocol can be adapted to study factors and conditions that can alter ribosome movement and thus potentially can also alter the function/conformation of the protein.

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA

A technique to identify translational pause sites on mRNA is described. This procedure is based on isolation of nascent polypeptides accumulating on ribosomes during in vitro translation of a target mRNA, followed by the size analysis of the nascent chains using a denaturing gel electrophoresis.

Isolamento dei ribosomi Polipeptidi Bound nascenti<em&gt; In vitro</em&gt; Per identificare i siti di pausa traslazione lungo mRNA

The rate of translational elongation is non-uniform. mRNA secondary structure, codon usage and mRNA associated proteins may alter ribosome movement on the ...

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.

Analisi globale di RNA Sintesi a livello di singola cellula seguente ipossia

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

Transient Expression of Proteins by Hydrodynamic Gene Delivery in Mice

Efficient expression of transgenes in vivo is of critical importance in studying gene function and developing treatments for diseases. Over the past years, hydrodynamic gene delivery (HGD) has emerged as a simple, fast, safe and effective method for delivering transgenes into rodents. This technique relies on the force generated by the rapid injection of a large volume of physiological solution to increase the permeability of cell membranes of perfused organs and thus deliver DNA into cells. One of the main advantages of HGD is the ability to introduce transgenes into mammalian cells using naked plasmid DNA (pDNA). Introducing an exogenous gene using a plasmid is minimally laborious, highly efficient and, contrary to viral carriers, remarkably safe. HGD was initially used to deliver genes into mice, it is now used to deliver a wide range of substances, including oligonucleotides, artificial chromosomes, RNA, proteins and small molecules into mice, rats and, to a limited degree, other animals. This protocol describes HGD in mice and focuses on three key aspects of the method that are critical to performing the procedure successfully: correct insertion of the needle into the vein, the volume of injection and the speed of delivery. Examples are given to show the application of this method to the transient expression of two genes that encode secreted, primate-specific proteins, apolipoprotein L-I (APOL-I) and haptoglobin-related protein (HPR).

In vivo transfection of naked DNA by hydrodynamic gene delivery introduces genes into the tissue of an animal with minimal inflammatory response. Sufficient amounts of gene product are generated such that gene function and regulation as well as protein structure and function can be analyzed.

Espressione transiente di proteine ​​da parte idrodinamica Gene Consegna in topi

Efficient expression of transgenes in vivo is of critical importance in studying gene function and developing treatments for diseases. Over the past ...