Questo lavoro è stato supportato anche da finanziamenti della Fondazione canadese per l&#39;innovazione (CFI), il Canadian Institute of Health Research (CIHR), e le scienze naturali e ingegneria Research Council del Canada (NSERC).

Parte 1: L&#39;interruzione della Influenza A Virion <ol><li> Aggiungere 750 ml di tampone MNT (20 mM MES, 150 mM NaCl, 30 mM Tris, pH 7,5) in una centrifuga Beckman tubo di policarbonato (11 mm x 34 mm) progettato per adattarsi in un TLA-120,2 rotore per l&#39;uso in Optima Beckman Max-E ultracentrifuga. </li><li> Aggiungere 500 ml di virus influenzale A (H3N2 X-31 A/AICHI/68 ceppo; 2 mg / ml) in quel tubo. Mescolare il virus con il tampone MNT pipettando su e giù parecchie volte. </li><li> Centrifugare per 10 minuti a 109.000 xg, 4 ° C, in una Optima Max Beckman-E centrifuga con un TLA-120,2 rotore. </li><li> Rimuovere il surnatante e risospendere il pellet in 500 microlitri di buffer interruzione (100 mM KCl, 5 mM MgCl 2, 5% (w / v) glicerolo, 50 octylglucoside mM, 10 mg / ml lisolecitina, 1,5 mM ditiotreitolo, 100 mM MES, pH 5,5). </li><li> Energicamente, e poi agitare a 31 ° C per 20 minuti in un Thermomixer eppendorf. </li></ol> Parte 2: gradiente Glicerolo centrifugazione sedimenti Velocity <ol><li> Preparazione di un gradiente di glicerolo inserendo i seguenti importi di glicerolo in una provetta per centrifuga Beckman UltraClear (13 mm x 51 mm): 1 ml 70% (v / v) glicerolo, 0,75 ml di glicerolo 50%, 0,375 ml di glicerolo al 40%, e 1,8 ml di glicerolo al 33%. Soluzioni di glicerolo sono fatto mescolando glicerina pura con tampone NM (150 mM NaCl, 50 mM MES, pH 5,5). Anche preparare un tubo di equilibrio che contiene sia glicerolo e buffer. </li><li> Il vortice perturbato campione virale di nuovo, e caricarlo sul gradiente di glicerolo. </li><li> Centrifugare il gradiente di 3,75 ore a 217.000 xg, 4 ° C, in un MLS-50 Beckman-rotore oscillante. </li><li> Dopo la centrifugazione è completo, manualmente raccogliere 250 ml di aliquote del gradiente partendo dalla parte superiore del tubo. Tenere frazioni su ghiaccio o a 4 ° C. </li></ol> Parte 3: Analisi delle frazioni del gradiente di glicerolo mediante elettroforesi su gel poliacrilammide SDS <ol><li> Togliere 20 l di ogni frazione in una nuova provetta. </li><li> Aggiungere 5 ml di 5x SDS-PAGE tampone del campione. </li><li> Di calore a 95 ° C per 5 minuti. </li><li> Spin down dei campioni brevemente e caricarli su un gel di poliacrilammide al 10%, e comprendono i marcatori di peso molecolare in uno dei pozzi. </li><li> Eseguire gli esempi sul gel fino a quando il colorante blu bromofenolo di carico raggiunge vicino al fondo del gel. </li><li> Macchia il gel con Coomassie blu. </li></ol> Parte 4: Concentrazione delle frazioni vRNP <ol><li> Scegliere il glicerolo frazioni contenenti principalmente NP, li uniscono e li distribuiscono in due provette da centrifuga Beckman in policarbonato (11 mm x 34 mm). </li><li> Riempire ogni tubo con dietil pirocarbonato (DEPC) trattati con acqua ultrapura, e seminare su e giù parecchie volte per mescolare. </li><li> Centrifuga per 4,5 ore a 157.000 xg, 4 ° C, in un TLA-120,2 Beckman rotore. </li><li> Rimuovere il surnatante e risospendere il pellet in 50 ml di DEPC trattati con acqua. </li><li> Se lo si desidera, la A 280 del vRNPs concentrato può essere misurata. Come NP è il principale componente presente nelle frazioni in pool, una stima della molarità di NP può essere calcolata utilizzando il suo coefficiente di estinzione di 55.350 M -1 cm -1 (come determinato tramite ProtParam 3). </li><li> Aliquota del vRNPs purificata, e conservarli congelati a -80 ° C per un uso successivo. </li></ol> Parte 5: colorazione negativa di vRNPs <ol><li> Diluire 1 ml di purificata vRNP in 9 ml di appena fatti due volte e filtrata-tampone MNT (20 mM MES, 150 mM NaCl, 30 mM Tris, pH 7,5). Altri buffer sono OK per diluire il vRNPs e lavare la griglia del campione (punto 5.5), ma non usare PBS se acetato di uranile viene utilizzato per la colorazione negativa. </li><li> Glow-scarica un esemplare (TEM rame) griglia precedentemente rivestito con una pellicola di carbonio parlodion e per 30 secondi. </li><li> Tenere la luce appena dimessi griglia-campione con una pinzetta, e applicare un 5-microlitri goccia di vRNP diluito sulla griglia campione. </li><li> Lascia la goccia di campione sulla griglia per 8 minuti. </li><li> In attesa, inserire una piccola striscia di Parafilm in panchina, ed erogare 2 gocce ciascuno contenente 10 microlitri di tampone MNT (per lavare la griglia) e un 80-microlitri goccia della soluzione di colorazione appena fatto (1 molibdato di ammonio% o 1 % acetato di uranile) sul Parafilm. </li><li> Dopo l&#39;8-minuti di adsorbimento, stoppino spento una parte della soluzione del campione dalla griglia campione con un pezzo di carta da filtro (tagliata in triangoli). Non lasciate che la griglia campione ad asciugare. </li><li> Lavare griglia campione in 2 gocce contenenti 10 microlitri di tampone MNT ciascuno per un tempo totale di 1 minuto. Questo viene fatto con attenzione abbassando la griglia campione sulla goccia, e poi wicking una parte della soluzione del campione dalla griglia campione con un pezzo di carta da filtro (senza lasciare che la griglia di campione secco). </li><li> Immediatamente dopo wicking fuori l&#39;ultima goccia di tampone dalla rete campione, completoLy immergere la griglia del campione all&#39;interno della goccia macchia e attendere 1 minuto. </li><li> Stoppino completamente fuori la soluzione macchia dalla griglia campione con un pezzo di carta da filtro. </li><li> Lasciare che la griglia di campione asciugare all&#39;aria per qualche minuto prima osservazione al microscopio elettronico a trasmissione. </li></ol> Parte 6: Risultati Rappresentante: <img src="/files/ftp_upload/old/1105_2009_1_22_1/1105_Figure2.png" alt="Figura 2" width="600" height="215" /> Figura 1 Come l&#39;influenza A NP (~ 56 kDa) è la principale proteina trovato in complessi ribonucleoproteina virale, la band NP è generalmente il più forte gruppo nelle frazioni contenenti la vRNPs (Figura 1). Oltre a NP, ogni vRNP influenza contiene anche una copia di un RNA polimerasi trimeriche (peso molecolare di kDa 82, 86 e 86,5) complesse. Questi possono essere o non essere visibili dalla colorazione Coomassie blu perché la loro abbondanza è bassa rispetto a quella di NP. La polimerasi, invece, può essere rilevato se, invece di un azzurro Commassie macchia, una macchia d&#39;argento del gel viene eseguita. L&#39;influenza matrice proteica M1 (~ 28 kDa) dovrebbe essere minimamente presenti nelle frazioni in cui le frazioni proteiche picco NP sono presenti. <img src="/files/ftp_upload/old/1105_2009_1_22_2/1105_3.png" alt="Figura 3" width="600" height="360" /> Figura 2 VRNPs negativamente macchiato come visualizzato sotto un microscopio elettronico a trasmissione dovrebbe produrre vRNPs che assomigliano a forma di bastoncello particelle con lunghezza variabile che sono circa 30 nm a 120 nm di lunghezza (Figura 2a). La NP oligomerici è organizzato come una catena di molecole NP che è ulteriormente piegato in una struttura a doppia elica ripetere, loop così su entrambi le estremità di queste particelle a forma di bastoncello a volte può essere visto (Figura 2b).

<ol>
	<li>Kemler, I., Whittaker, G., Helenius, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nuclear+import+of+microinjected+influenza+virus+ribonucleoproteins.">Nuclear import of microinjected influenza virus ribonucleoproteins.</a> Virology. 202, 1028-1033 (1994).</li><li>Wu, W. W. H., Weaver, L. L., Pant&#233;, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ultrastructural+analysis+of+the+nuclear+localization+sequences+on+influenza+a+ribonucleoprotein+complexes.">Ultrastructural analysis of the nuclear localization sequences on influenza a ribonucleoprotein complexes.</a> J Mol Biol. 374, 910-916 (2007).</li><li>Gasteiger, E., Walker, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> The Proteomics Protocols Handbook. , 571-607 (2005).</li><li>Wu, W. W. H., Sun, Y. H. B., Pant&#233;, . <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nuclear+import+of+influenza+A+viral+ribonucleoprotein+complexes+is+mediated+by+two+nuclear+localization+sequences+on+viral+nucleoprotein.">Nuclear import of influenza A viral ribonucleoprotein complexes is mediated by two nuclear localization sequences on viral nucleoprotein.</a> Virol J. 4, 49-49 (2007).</li><li>Babcock, H. P., Chen, C., Zhuang, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Using+single-particle+tracking+to+study+nuclear+trafficking+of+viral+genes.">Using single-particle tracking to study nuclear trafficking of viral genes.</a> Biophys J. 87, 2749-2758 (2004).</li></ol>

La purificazione di vRNPs si basa sulla procedura descritta da Kemler et al. (1994) 1. Noi e gli altri hanno usato anche questo protocollo per isolare vRNPs di studiare la loro importazione nucleare. 2,4,5 Si consiglia l&#39;uso di RNasi-free suggerimenti e tubi durante la manipolazione vRNPs perché il genoma virale è costituito da RNA, e quindi facilmente degrada in presenza di RNA. Inoltre, tutti i buffer dovrebbe essere effettuato in acqua che è RNasi lib...

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		<div>
		<table border="1">
		<thead>
		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>H3N2 X-31 A/AICHI/68 influenza A</td>
<td>&nbsp;</td>
<td>Charles River Laboratories</td>
<td>490715</td>
<td>&nbsp;</td>
<tr>
<td>Tris</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>T1503</td>
<td>&nbsp;</td>
<tr>
<td>MES</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>M-8250</td>
<td>&nbsp;</td>
<tr>
<td>Glycerol</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>G33-1</td>
<td>&nbsp;</td>
<tr>
<td>Octylglucoside</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>O-8001</td>
<td>&nbsp;</td>
<tr>
<td>Lysolecithin</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>L-4129</td>
<td>&nbsp;</td>
<tr>
<td>Dithiothreitol</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>D-9779</td>
<td>&nbsp;</td>
<tr>
<td>Coomassie brilliant blue G-250</td>
<td>&nbsp;</td>
<td>Kodak</td>
<td>1367796</td>
<td>&nbsp;</td>
<tr>
<td>diethyl pyrocarbonate (DEPC)-treated water</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>750024</td>
<td>&nbsp;</td>
<tr>
<td>Uranyl Acetate</td>
<td>&nbsp;</td>
<td>Ted Pella</td>
<td>19481</td>
<td>&nbsp;</td>
<tr>
<td>Ammonium Molybdate</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>A-674</td>
<td>&nbsp;</td>
<tr>
<td>Optima MAX-E Ultracentrifuge</td>
<td>&nbsp;</td>
<td>Beckman Coulter</td>
<td>434491</td>
<td>&nbsp;</td>
<tr>
<td>MLS-50 Rotor Package, Swinging Bucket</td>
<td>&nbsp;</td>
<td>Beckman Coulter</td>
<td>367280</td>
<td>&nbsp;</td>
<tr>
<td>TLA-120.2 Rotor Assembly, Fixed-Angle, Titanium</td>
<td>&nbsp;</td>
<td>Beckman Coulter</td>
<td>362046</td>
<td>&nbsp;</td>
<tr>
<td>Eppendorf Thermomixer</td>
<td>&nbsp;</td>
<td>Brinkman</td>
<td>022670000</td>
<td>&nbsp;</td>		</tbody>
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purification and visualization of influenza a viral ribonucleoprotein complexes

L&#39;influenza A genoma virale è costituito da otto-senso negativo, singole molecole di RNA, confezionati singolarmente con più copie del influenza A nucleoproteina (NP) in particelle ribonulceoprotein virale (vRNPs). Il vRNPs dell&#39;influenza sono racchiusi all&#39;interno della busta virale. Durante l&#39;immissione delle cellule, tuttavia, questi complessi vRNP vengono rilasciati nel citoplasma, dove l&#39;accesso al macchinario di trasporto nucleare host. Per studiare l&#39;importazione nucleare di vRNPs influenza e la replicazione del genoma dell&#39;influenza, è utile per lavorare con vRNPs isolato in modo che gli altri componenti del virus non interferiscono con questi processi. Qui, descriviamo una procedura per purificare queste vRNPs dal virus. La procedura inizia con la rottura del virione influenza A con detergenti al fine di rilasciare i complessi vRNP dal virione avvolto. Il vRNPs vengono separati dagli altri componenti del virione influenza A su una pendenza 33-70% glicerolo discontinuo per sedimentazione velocità. Le frazioni ottenuto dal gradiente di glicerolo vengono poi analizzati attraverso SDS-PAGE dopo colorazione con Coomassie blu. Le frazioni di punta contenenti NP sono poi sommati insieme e concentrato per centrifugazione. Dopo la concentrazione, l&#39;integrità del vRNPs è verificata da visualizzazione del vRNPs tramite microscopia elettronica a trasmissione dopo colorazione negativa. La purificazione gradiente di glicerolo è una modifica di quella di Kemler<em&gt; Et al.</em&gt; (1994)<sup&gt; 1</sup&gt;, E la colorazione negativa è stata eseguita da Wu<em&gt; Et al.</em&gt; (2007).<sup&gt; 2</sup

Watch this Scientific Journal Video about Purification and Visualization of Influenza A Viral Ribonucleoprotein Complexes at JoVE.com

Purification and Visualization of Influenza A Viral Ribonucleoprotein Complexes

Il genoma del virus influenzale A si compone di otto complessi separati di RNA e proteine, chiamate complessi ribonucleoproteina virale (vRNPs). Questo documento descrive la purificazione gradiente glicerolo e microscopia elettronica visualizzazione trasmissione di influenza A vRNPs.

Purificazione e visualizzazione di influenza A Complessi Ribonucleoproteina virale

The influenza A viral genome consists of eight negative-sense, single stranded RNA molecules, individually packed with multiple copies of the influenza A ...

purification-visualization-influenza-viral-ribonucleoprotein

Research

JoVE Journal

Biology

12.9K Views.  University of British Columbia - UBC. Il genoma del virus influenzale A si compone di otto complessi separati di RNA e proteine, chiamate complessi ribonucleoproteina virale (vRNPs). Questo documento descrive la purificazione gradiente glicerolo e microscopia elettronica visualizzazione trasmissione di influenza A vRNPs.

Video: Purification and Visualization of Influenza A Viral Ribonucleoprotein Complexes

Staining of Proteins in Gels with Coomassie G-250 without Organic Solvent and Acetic Acid

In classical protein staining protocols using Coomassie Brilliant Blue (CBB), solutions with high contents of toxic and flammable organic solvents (Methanol, Ethanol or 2-Propanol) and acetic acid are used for fixation, staining and destaining of proteins in a gel after SDS-PAGE. To speed up the procedure, heating the staining solution in the microwave oven for a short time is frequently used. This usually results in evaporation of toxic or hazardous Methanol, Ethanol or 2-Propanol and a strong smell of acetic acid in the lab which should be avoided due to safety considerations. In a protocol originally published in two patent applications by E.M. Wondrak (US2001046709 (A1), US6319720 (B1)), an alternative composition of the staining solution is described in which no organic solvent or acid is used. The CBB is dissolved in bidistilled water (60-80mg of CBB G-250 per liter) and 35 mM HCl is added as the only other compound in the staining solution. The CBB staning of the gel is done after SDS-PAGE and thorough washing of the gel in bidistilled water. By heating the gel during the washing and staining steps, the process can be finished faster and no toxic or hazardous compunds are evaporating. The staining of proteins occurs already within 1 minute after heating the gel in staining solution and is fully developed after 15-30 min with a slightly blue background that is destained completely by prolonged washing of the stained gel in bidistilled water, without affecting the stained protein bands.

A short protocol for protein staining with Coomassie Brilliant Blue (CBB) G-250 in polyacrylamide gels is described without using organic solvents or acetic acid as in the classical staining procedures with CBB.

La colorazione delle proteine ​​in gel con Coomassie G-250, senza solventi organici acido acetico e

In classical protein staining protocols using Coomassie Brilliant Blue (CBB), solutions with high contents of toxic and flammable organic solvents ...

Ricerca

Biologia

Preparation, Purification, and Characterization of Lanthanide Complexes for Use as Contrast Agents for Magnetic Resonance Imaging

Polyaminopolycarboxylate-based ligands are commonly used to chelate lanthanide ions, and the resulting complexes are 
useful as contrast agents for magnetic resonance imaging (MRI). Many commercially available ligands are especially useful because they contain 
functional groups that allow for fast, high-purity, and high-yielding conjugation to macromolecules and biomolecules via amine-reactive 
activated esters and isothiocyanate groups or thiol-reactive maleimides. While metalation of these ligands is considered common 
knowledge in the field of bioconjugation chemistry, subtle differences in metalation procedures must be taken into account when 
selecting metal starting materials. Furthermore, multiple options for purification and characterization exist, and selection of the most 
effective procedure partially depends on the selection of starting materials. These subtle differences are often neglected in published 
protocols. Here, our goal is to demonstrate common methods for metalation, purification, and characterization of lanthanide complexes 
that can be used as contrast agents for MRI (Figure 1). We expect that this publication will enable biomedical scientists to incorporate 
lanthanide complexation reactions into their repertoire of commonly used reactions by easing the selection of starting materials and 
purification methods.

We demonstrate the metalation, purification, and characterization of lanthanide complexes. The complexes described here can be conjugated to macromolecules to enable tracking of these molecules using magnetic resonance imaging.

Preparazione, purificazione e caratterizzazione di complessi lantanidi per l&#39;uso di agenti di contrasto per Risonanza Magnetica

Polyaminopolycarboxylate-based ligands are commonly used to chelate lanthanide ions, and the resulting complexes are 
useful as contrast agents for ...

Purification of Hsp104, a Protein Disaggregase

Hsp104 is a hexameric AAA+ protein1 from yeast, which couples ATP hydrolysis to protein disaggregation2-10 (Fig. 1). This activity imparts two key selective advantages. First, renaturation of disordered aggregates by Hsp104 empowers yeast survival after various protein-misfolding stresses, including heat shock3,5,11,12. Second, remodeling of cross-beta amyloid fibrils by Hsp104 enables yeast to exploit myriad prions (infectious amyloids) as a reservoir of beneficial and heritable phenotypic variation13-22. Remarkably, Hsp104 directly remodels preamyloid oligomers and amyloid fibrils, including those comprised of the yeast prion proteins Sup35 and Ure223-30. This amyloid-remodeling functionality is a specialized facet of yeast Hsp104. The E. coli orthologue, ClpB, fails to remodel preamyloid oligomers or amyloid fibrils26,31,32.
Hsp104 orthologues are found in all kingdoms of life except, perplexingly, animals. Indeed, whether animal cells possess any enzymatic system that couples protein disaggregation to renaturation (rather than degradation) remains unknown33-35. Thus, we and others have proposed that Hsp104 might be developed as a therapeutic agent for various neurodegenerative diseases connected with the misfolding of specific proteins into toxic preamyloid oligomers and amyloid fibrils4,7,23,36-38. There are no treatments that directly target the aggregated species associated with these diseases. Yet, Hsp104 dissolves toxic oligomers and amyloid fibrils composed of alpha-synuclein, which are connected with Parkinson's Disease23 as well as amyloid forms of PrP39. Importantly, Hsp104 reduces protein aggregation and ameliorates neurodegeneration in rodent models of Parkinson's Disease23 and Huntington's disease38. Ideally, to optimize therapy and minimize side effects, Hsp104 would be engineered and potentiated to selectively remodel specific aggregates central to the disease in question4,7. However, the limited structural and mechanistic understanding of how Hsp104 disaggregates such a diverse repertoire of aggregated structures and unrelated proteins frustrates these endeavors30,40-42.
To understand the structure and mechanism of Hsp104, it is essential to study the pure protein and reconstitute its disaggregase activity with minimal components. Hsp104 is a 102kDa protein with a pI of ~5.3, which hexamerizes in the presence of ADP or ATP, or at high protein concentrations in the absence of nucleotide43-46. Here, we describe an optimized protocol for the purification of highly active, stable Hsp104 from E. coli. The use of E. coli allows simplified large-scale production and our method can be performed quickly and reliably for numerous Hsp104 variants. Our protocol increases Hsp104 purity and simplifies His6-tag removal compared to a previous purification method from E. coli47. Moreover, our protocol is more facile and convenient than two more recent protocols26,48.

Here, we describe a protocol for the purification of highly active Hsp104, a hexameric AAA+ protein from yeast, which couples ATP hydrolysis to protein disaggregation. This scheme exploits a His6-tagged construct for affinity purification from E. coli followed by anion-exchange chromatography, His6-tag removal with TEV protease, and size-exclusion chromatography.

Purificazione di Hsp104, una proteina Disaggregase

Hsp104 is a hexameric AAA+ protein1 from yeast, which couples ATP hydrolysis to protein disaggregation2-10 (Fig. 1). This activity imparts two key ...

Chromatographic Purification of Highly Active Yeast Ribosomes

Eukaryotic ribosomes are much more labile as compared to their eubacterial and archael counterparts, thus posing a significant challenge to researchers. Particularly troublesome is the fact that lysis of cells releases a large number of proteases and nucleases which can degrade ribosomes. Thus, it is important to separate ribosomes from these enzymes as quickly as possible. Unfortunately, conventional differential ultracentrifugation methods leaves ribosomes exposed to these enzymes for unacceptably long periods of time, impacting their structural integrity and functionality. To address this problem, we utilize a chromatographic method using a cysteine charged Sulfolink resin. This simple and rapid application significantly reduces co-purifying proteolytic and nucleolytic activities, producing high yields of intact, highly biochemically active yeast ribosomes. We suggest that this method should also be applicable to mammalian ribosomes. The simplicity of the method, and the enhanced purity and activity of chromatographically purified ribosome represents a significant technical advancement for the study of eukaryotic ribosomes.

Contamination of preparations of eukaryotic ribosomes purified by traditional methods by co-purifying nucleases and proteases negatively impacts on downstream biochemical and structural analyses. A rapid and simple chromatographic purification method is used to solve this problem using yeast ribosomes as a model system.

Purificazione cromatografica dei ribosomi di lievito Highly Active

Eukaryotic ribosomes are much more labile as compared to their eubacterial and archael counterparts, thus posing a significant challenge to researchers.  ...

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip

As a result of the development of high-throughput sequencing and efficient microarray analysis, global gene expression analysis has become an easy and readily available form of data collection. In many research and disease models however, steady state levels of target gene mRNA does not always directly correlate with steady state protein levels. Post-transcriptional gene regulation is a likely explanation of the divergence between the two. Driven by the binding of RNA Binding Proteins (RBP), post-transcriptional regulation affects mRNA localization, stability and translation by forming a Ribonucleoprotein (RNP) complex with target mRNAs. Identifying these unknown de novo mRNA targets from cellular extracts in the RNP complex is pivotal to understanding mechanisms and functions of the RBP and their resulting effect on protein output. This protocol outlines a method termed RNP immunoprecipitation-microarray (RIP-Chip), which allows for the identification of specific mRNAs associated in the ribonucleoprotein complex, under changing experimental conditions, along with options to further optimize an experiment for the individual researcher. With this important experimental tool, researchers can explore the intricate mechanisms associated with post-transcriptional gene regulation as well as other ribonucleoprotein interactions.

A step by step protocol to isolating and identifying RNA associated complexes through RIP-Chip.

Metodo per l&#39;isolamento e l&#39;identificazione di mRNA, microRNA e componenti proteiche dei complessi Ribonucleoproteina da estratti cellulari con RIP-Chip

As a result of the development of high-throughput sequencing and efficient microarray analysis, global gene expression analysis has become an easy and ...

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Since most cellular processes are mediated by macromolecular assemblies, the systematic identification of protein-protein interactions (PPI) and the identification of the subunit composition of multi-protein complexes can provide insight into gene function and enhance understanding of biological systems1, 2. Physical interactions can be mapped with high confidence vialarge-scale isolation and characterization of endogenous protein complexes under near-physiological conditions based on affinity purification of chromosomally-tagged proteins in combination with mass spectrometry (APMS). This approach has been successfully applied in evolutionarily diverse organisms, including yeast, flies, worms, mammalian cells, and bacteria1-6. In particular, we have generated a carboxy-terminal Sequential Peptide Affinity (SPA) dual tagging system for affinity-purifying native protein complexes from cultured gram-negative Escherichia coli, using genetically-tractable host laboratory strains that are well-suited for genome-wide investigations of the fundamental biology and conserved processes of prokaryotes1, 2, 7. Our SPA-tagging system is analogous to the tandem affinity purification method developed originally for yeast8, 9, and consists of a calmodulin binding peptide (CBP) followed by the cleavage site for the highly specific tobacco etch virus (TEV) protease and three copies of the FLAG epitope (3X FLAG), allowing for two consecutive rounds of affinity enrichment. After cassette amplification, sequence-specific linear PCR products encoding the SPA-tag and a selectable marker are integrated and expressed in frame as carboxy-terminal fusions in a DY330 background that is induced to transiently express a highly efficient heterologous bacteriophage lambda recombination system10. Subsequent dual-step purification using calmodulin and anti-FLAG affinity beads enables the highly selective and efficient recovery of even low abundance protein complexes from large-scale cultures. Tandem mass spectrometry is then used to identify the stably co-purifying proteins with high sensitivity (low nanogram detection limits).
Here, we describe detailed step-by-step procedures we commonly use for systematic protein tagging, purification and mass spectrometry-based analysis of soluble protein complexes from E. coli, which can be scaled up and potentially tailored to other bacterial species, including certain opportunistic pathogens that are amenable to recombineering. The resulting physical interactions can often reveal interesting unexpected components and connections suggesting novel mechanistic links. Integration of the PPI data with alternate molecular association data such as genetic (gene-gene) interactions and genomic-context (GC) predictions can facilitate elucidation of the global molecular organization of multi-protein complexes within biological pathways. The networks generated for E. coli can be used to gain insight into the functional architecture of orthologous gene products in other microbes for which functional annotations are currently lacking.

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Affinity purification of tagged proteins in combination with mass spectrometry (APMS) is a powerful method for the systematic mapping of protein interaction networks and for investigating the mechanistic basis of biological processes. Here, we describe an optimized sequential peptide affinity (SPA) APMS procedure developed for the bacterium Escherichia coli that can be used to isolate and characterize stable multi-protein complexes to near homogeneity even starting from low copy numbers per cell.

Identificazione di complessi proteici in<em&gt; Escherichia coli</em&gt; Con sequenziale purificazione per affinità Peptide in combinazione con Tandem Mass Spectrometry

Since most cellular processes are mediated by macromolecular assemblies, the systematic identification of protein-protein interactions (PPI) and the ...

Visualization of Endoplasmic Reticulum Localized mRNAs in Mammalian Cells

In eukaryotes, most of the messenger RNAs (mRNAs) that encode secreted and membrane proteins are localized to the surface of the endoplasmic reticulum (ER). However, the visualization of these mRNAs can be challenging. This is especially true when only a fraction of the mRNA is ER-associated and their distribution to this organelle is obstructed by non-targeted (i.e. "free") transcripts. In order to monitor ER-associated mRNAs, we have developed a method in which cells are treated with a short exposure to a digitonin extraction solution that selectively permeabilizes the plasma membrane, and thus removes the cytoplasmic contents, while simultaneously maintaining the integrity of the ER. When this method is coupled with fluorescent in situ hybridization (FISH), one can clearly visualize ER-bound mRNAs by fluorescent microscopy. Using this protocol the degree of ER-association for either bulk poly(A) transcripts or specific mRNAs can be assessed and even quantified. In the process, one can use this assay to investigate the nature of mRNA-ER interactions.

Here we describe a method to visualize endoplasmic reticulum-associated mRNAs in mammalian tissue culture cells. This technique involves the selective permeabilization of the plasma membrane with digitonin to remove cytoplasmic contents followed by fluorescent in situ hybridization to detect either bulk poly(A) mRNA or specific transcripts.

Visualizzazione di mRNA reticolo endoplasmatico localizzate in cellule di mammifero

In eukaryotes, most of the messenger RNAs (mRNAs) that encode secreted and membrane proteins are localized to the surface of the endoplasmic reticulum ...

Purification of Transcripts and Metabolites from Drosophila Heads

For the last decade, we have tried to understand the molecular and cellular mechanisms of neuronal degeneration using Drosophila as a model organism. Although fruit flies provide obvious experimental advantages, research on neurodegenerative diseases has mostly relied on traditional techniques, including genetic interaction, histology, immunofluorescence, and protein biochemistry. These techniques are effective for mechanistic, hypothesis-driven studies, which lead to a detailed understanding of the role of single genes in well-defined biological problems. However, neurodegenerative diseases are highly complex and affect multiple cellular organelles and processes over time. The advent of new technologies and the omics age provides a unique opportunity to understand the global cellular perturbations underlying complex diseases. Flexible model organisms such as Drosophila are ideal for adapting these new technologies because of their strong annotation and high tractability. One challenge with these small animals, though, is the purification of enough informational molecules (DNA, mRNA, protein, metabolites) from highly relevant tissues such as fly brains. Other challenges consist of collecting large numbers of flies for experimental replicates (critical for statistical robustness) and developing consistent procedures for the purification of high-quality biological material. Here, we describe the procedures for collecting thousands of fly heads and the extraction of transcripts and metabolites to understand how global changes in gene expression and metabolism contribute to neurodegenerative diseases. These procedures are easily scalable and can be applied to the study of proteomic and epigenomic contributions to disease.

Purification of Transcripts and Metabolites from Drosophila Heads

We describe here the procedures for the extraction and purification of mRNA and metabolites from Drosophila heads. We are applying these techniques to better understand the cellular perturbations underlying neuronal degeneration. These methodologies can be easily scaled and adapted for other "omic" projects.

Purificazione di Trascrizioni e metaboliti<em&gt; Drosophila</em&gt; Teste

For the last decade, we have tried to understand the molecular and cellular mechanisms of neuronal degeneration using Drosophila as a model organism. ...

AFM-based Mapping of the Elastic Properties of Cell Walls: at Tissue, Cellular, and Subcellular Resolutions

We describe a recently developed method to measure mechanical properties of the surfaces of plant tissues using atomic force microscopy (AFM) micro/nano-indentations, for a JPK&#160;AFM. Specifically, in this protocol we measure the apparent Young&#8217;s modulus of cell walls at subcellular resolutions across regions of up to 100 &#181;m&#160;x 100 &#181;m in floral meristems, hypocotyls, and roots. This requires careful preparation of the sample, the correct selection of micro-indenters and indentation depths. To account for cell wall properties only, measurements are performed in highly concentrated solutions of mannitol in order to plasmolyze the cells and thus remove the contribution of cell turgor pressure.
In contrast to other extant techniques, by using different indenters and indentation depths, this method allows simultaneous multiscale measurements, i.e. at subcellular resolutions and across hundreds of cells comprising a tissue. This means that it is now possible&#160;to spatially-temporally characterize the changes that take place in the mechanical properties of cell walls during development, enabling these changes to be correlated with growth and differentiation. This represents a key step to understand how coordinated microscopic cellular changes bring about macroscopic morphogenetic events.
However, several limitations remain: the method can only be used on fairly small samples (around 100 &#181;m in diameter) and only on external tissues; the method is sensitive to tissue topography; it measures only certain aspects of the tissue&#8217;s complex mechanical properties. The technique is being developed rapidly and it is likely that most of these limitations will be resolved in the near future.

We describe a method to map mechanical properties of plant tissues using an atomic force microscope (AFM). We focus on how to record mechanical changes that take place in cell walls during plant development at wide-field mesoscale, enabling these changes to be correlated with growth and morphogenesis.

Mapping basato AFM delle proprietà elastiche delle pareti cellulari: al Tissue, cellulare, e le risoluzioni subcellulari

We describe a recently developed method to measure mechanical properties of the surfaces of plant tissues using atomic force microscopy (AFM) ...

Rapid Isolation And Purification Of Mitochondria For Transplantation By Tissue Dissociation And Differential Filtration

Previously described mitochondrial isolation methods using differential centrifugation and/or Ficoll gradient centrifugation require 60 to 100 min to complete. We describe a method for the rapid isolation of mitochondria from mammalian biopsies using a commercial tissue dissociator and differential filtration. In this protocol, manual homogenization is replaced with the tissue dissociator&#8217;s standardized homogenization cycle. This allows for uniform and consistent homogenization of tissue that is not easily achieved with manual homogenization. Following tissue dissociation, the homogenate is filtered through nylon mesh filters, which eliminate repetitive centrifugation steps. As a result, mitochondrial isolation can be performed in less than 30 min. This isolation protocol yields approximately 2 x 1010 viable and respiration competent mitochondria from 0.18 &#177; 0.04 g (wet weight) tissue sample.

A method for rapid isolation of mitochondria from mammalian tissue biopsies is described. Rat liver or skeletal muscle preparations were homogenized with a commercial tissue dissociator and mitochondria were isolated by differential filtration through nylon mesh filters. Mitochondrial isolation time is &#60;30 min compared to 60 - 100 min using alternative methods.

Isolamento rapida e purificazione di mitocondri per il trapianto da tessuto Dissociazione e Filtrazione Differenziale

Previously described mitochondrial isolation methods using differential centrifugation and/or Ficoll gradient centrifugation require 60 to 100 min to ...