Siamo grati al Pacific Northwest National Laboratory (PNNL) terra e scienze biologiche (EBD) missione seme laboratorio diretto di ricerca e sviluppo (LDRD) fondo per il sostegno. Accesso strumentale è stata fornita attraverso una proposta di utente generale W. R. Wiley Ambientale Molecular Sciences Laboratory (EMSL). EMSL è una struttura di uso scientifico nazionale sponsorizzata dall'ufficio di biologico e ambientale ricerca (BER) a PNNL. Gli autori ringraziano il Dr. Yuanzhao Ding per prova leggere il manoscritto e fornire un feedback utile. PNNL è gestito da Battelle per il DOE sotto contratto DE-AC05-76RL01830.

<ol>
	<li>Renner, L. D., Weibel, D. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Physicochemical+regulation+of+biofilm+formation.">Physicochemical regulation of biofilm formation.</a> MRS Bull. 36 (5), 347-355 (2011).</li><li>Flemming, H. C., Wingender, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+biofilm+matrix.">The biofilm matrix.</a> Nat Rev Microbiol. 8 (9), 623-633 (2010).</li><li>Aldeek, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Patterned+hydrophobic+domains+in+the+exopolymer+matrix+of+Shewanella+oneidensis+MR-1+biofilms.">Patterned hydrophobic domains in the exopolymer matrix of Shewanella oneidensis MR-1 biofilms.</a> Appl Environ Microbiol. 79 (4), 1400-1402 (2013).</li><li>Hua, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+situ+molecular+imaging+of+a+hydrated+biofilm+in+a+microfluidic+reactor+by+ToF-SIMS.">In situ molecular imaging of a hydrated biofilm in a microfluidic reactor by ToF-SIMS.</a> Analyst. 139 (7), 1609-1613 (2014).</li><li>Yu, X. Y., Yang, L., Cowin, J. P., Iedema, M., Zhu, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Systems+and+methods+for+analyzing+liquids+under+vacuum.">Systems and methods for analyzing liquids under vacuum.</a> US Patent. , (2013).</li><li>Yu, X. Y., Liu, B., Yang, L., Zhu, Z., Marshall, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microfluidic+electrochemical+device+and+process+for+chemical+imaging+and+electrochemical+analysis+at+the+electrode-liquid+interface+in+situ.">Microfluidic electrochemical device and process for chemical imaging and electrochemical analysis at the electrode-liquid interface in situ.</a> US Patent. , (2014).</li><li>Yang, L., Yu, X. Y., Zhu, Z. H., Thevuthasan, T., Cowin, J. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Making+a+hybrid+microfluidic+platform+compatible+for+in+situ+imaging+by+vacuum-based+techniques.">Making a hybrid microfluidic platform compatible for in situ imaging by vacuum-based techniques.</a> J Vac Sci Technol A. 29 (6), (2011).</li><li>Yang, L., Yu, X. Y., Zhu, Z. H., Iedema, M. J., Cowin, J. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Probing+liquid+surfaces+under+vacuum+using+SEM+and+ToF-SIMS.">Probing liquid surfaces under vacuum using SEM and ToF-SIMS.</a> Lab Chip. 11 (15), 2481-2484 (2011).</li><li>Ding, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+Situ+Molecular+Imaging+of+the+Biofilm+and+Its+Matrix.">In Situ Molecular Imaging of the Biofilm and Its Matrix.</a> Anal Chem. , (2016).</li><li>Yang, J., Ghobadian, S., Montazami, R., Hashemi, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Proceedings of the Asme 11th Fuel Cell Science, Engineering, and Technology Conference, 2013. , (2013).</li><li>Yu, F., Wang, C. X., Ma, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Applications+of+Graphene-Modified+Electrodes+in+Microbial+Fuel+Cells.">Applications of Graphene-Modified Electrodes in Microbial Fuel Cells.</a> Materials. 9 (10), (2016).</li><li>Yu, J., Zhou, Y., Hua, X., Zhu, Z., Yu, X. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+Situ+Characterization+of+Hydrated+Proteins+in+Water+by+SALVI+and+ToF-SIMS.">In Situ Characterization of Hydrated Proteins in Water by SALVI and ToF-SIMS.</a> J Vis Exp. (108), e53708 (2016).</li><li>Hill, E. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Effects of Electron-Transport-System Impairment on Hydrogen Gas Production by the Bacterium Shewanella oneidensis MR-1. , (2007).</li><li>McCormick, A. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biophotovoltaics:+oxygenic+photosynthetic+organisms+in+the+world+of+bioelectrochemical+systems.">Biophotovoltaics: oxygenic photosynthetic organisms in the world of bioelectrochemical systems.</a> Energy Environ Sci. 8 (4), 1092-1109 (2015).</li><li>Liu, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+situ+chemical+probing+of+the+electrode-electrolyte+interface+by+ToF-SIMS.">In situ chemical probing of the electrode-electrolyte interface by ToF-SIMS.</a> Lab Chip. 14, 855-859 (2014).</li><li>Keune, K., Hoogland, F., Boon, J. J., Peggie, D., Higgitt, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+of+the+"added+value"+of+SIMS:+A+mass+spectrometric+and+spectroscopic+study+of+an+unusual+Naples+yellow+oil+paint+reconstruction.">Evaluation of the "added value" of SIMS: A mass spectrometric and spectroscopic study of an unusual Naples yellow oil paint reconstruction.</a> Int J mass Spectrom. 284 (1-3), 22-34 (2009).</li><li>Lee, 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> Mass Spectrometry Handbook. , 988 (2012).</li><li>Petrovic, M., Barcelo, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+anionic+and+nonionic+surfactants,+their+degradation+products,+and+endocrine-disrupting+compounds+in+sewage+sludge+by+liquid+chromatography/mass+spectrometry.">Determination of anionic and nonionic surfactants, their degradation products, and endocrine-disrupting compounds in sewage sludge by liquid chromatography/mass spectrometry.</a> Anal Chem. 72 (19), 4560-4567 (2000).</li><li>Vickerman, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+Imaging+and+Depth+Profiling+by+Mass+Spectrometry--Sims,+MALDI+or+DESI.">Molecular Imaging and Depth Profiling by Mass Spectrometry--Sims, MALDI or DESI.</a> Analyst. 136 (11), (2011).</li><li>Weng, L. T., Bertrand, P., Stonemasui, J. H., Stone, W. E. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tof+Sims+Study+of+the+Desorption+of+Emulsifiers+from+Polystyrene+Latexes.">Tof Sims Study of the Desorption of Emulsifiers from Polystyrene Latexes.</a> Surf Interface Anal. 21 (6-7), 387-394 (1994).</li><li>Pe&#241;uelas-Urquides, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measuring+of+Mycobacterium+tuberculosis+crowth.+A+correlation+of+the+optical+measurements+with+colony+forming+units.">Measuring of Mycobacterium tuberculosis crowth. A correlation of the optical measurements with colony forming units.</a> Braz J Microbiol. 44 (1), 287-289 (2013).</li><li>Dohnalkova, A. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+hydrated+microbial+extracellular+polymers:+comparative+analysis+by+electron+microscopy.">Imaging hydrated microbial extracellular polymers: comparative analysis by electron microscopy.</a> Appl Environ Microbiol. 77 (4), 1254-1262 (2011).</li><li>Yang, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+situ+SEM+and+ToF-SIMS+analysis+of+IgG+conjugated+gold+nanoparticles+at+aqueous+surfaces.">In situ SEM and ToF-SIMS analysis of IgG conjugated gold nanoparticles at aqueous surfaces.</a> Surf Interface Anal. 46, 224-228 (2013).</li><li>Yu, J. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Capturing+the+transient+species+at+the+electrode-electrolyte+interface+by+in+situ+dynamic+molecular+imaging.">Capturing the transient species at the electrode-electrolyte interface by in situ dynamic molecular imaging.</a> Chem Commun. 52 (73), 10952-10955 (2016).</li></ol>

Gli autori non hanno nulla a rivelare.

Dopo inoculando in ritardo-fase, è importante verificare il numero di giorni e la temperatura alla quale il biofilm dovrebbe crescere prima che sia sano e abbastanza spessa per imaging, come descritto al punto 3.1. Questa procedura riguarda in particolare la coltura di un S. oneidensis MR1 biofilm a temperatura ambiente; Tuttavia diverse temperature ambiente possono influenzare il tasso di crescita. Pertanto, è fondamentale utilizzare imaging ottico per capire se il biofilm è pronto prima di procedere all'analisi ToF-...

Biofilm batterici sono comunità di superficie-associati che si sono evolute nel tempo come una difesa per i batteri di sopravvivere variando negativi stimoli fisici e meccanici, in cui le cellule sono in grado di allegare e sopravvivere in molti ambienti possibili. 1 , 2 i biofilm sono ampiamente studiati e hanno applicazioni in molti campi quali la biomedicina, ingegneria biomedica, l'agricoltura e ricerca industriale e sviluppo. 1 , 2 comprendere la mappatura chimica di queste comunità microbiche complesse, tra cui loro autoprodotti sostanze polimeriche extracellulari (EPS) e il loro ambiente di cluster di acqua locale, è essenziale per ottenere un'accurata e dettagliata rappresentazione della loro attività biologica. 2
Biofilm esistano e crescono all'interno di uno stato altamente idratato. Questo presenta una grande sfida nell'utilizzo di tecniche di analisi delle superfici basate su vuoto come spettrometria di massa di ioni secondari di tempo di volo (ToF-SIMS) dovuto la difficoltà nello studio liquidi volatili nel vuoto. Di conseguenza, tecniche di analisi delle superfici basate su vuoto sono stati limitati quasi esclusivamente a studiare campioni di biofilm al solo allo stato secco. Tuttavia, studiando un biofilm nel suo stato essiccato inibisce l'indagine accurata del suo microambiente biologico vero. Causa spesso drastici cambiamenti alla morfologia EPS integrità e biofilm, che è stata dimostrata dopo aver confrontato i risultati spettrali di massa secca biofilm agli studi in situ di liquido. 3 , 4 questo articolo presenta una soluzione per lo studio di biofilm nel loro naturale stato idratato impiegando l'uso del nostro sistema per l'analisi a liquido vuoto interfaccia (SALVI),5,6 un reattore microfluidici che contiene liquido sotto la sua membrana di nitruro (SiN) di silicio sottile in un microchannel di polidimetilsilossano (PMD), fornendo così accesso diretto per il fascio di ioni secondari sonda pur mantenendo l'integrità strutturale della matrice liquida all'interno di un vuoto camera. 7 , 8
S. oneidensis MR-1 mutato per esprimere proteine di fluorescenza verde (GFP) è stato scelto come organismo modello per questa illustrazione di procedura di biofilm grazie alla sua versatilità metabolica e di uso comune in microbiologia applicata ed ambientale, che è stato basato pesantemente sulla sua capacità uniche per la riduzione del metallo e trasferimento di elettroni extracellulare. 9 , 10 , 11 inoltre, la presenza di GFP ammessi per facile biofilm-spessore continuo monitoraggio mediante microscopia a fluorescenza, utilizzando un filtro di fluoresceina isotiocianato (FITC). Nostri studi precedenti hanno indicato la prova di questo batterio favorendo allegato alla finestra peccato utilizzando l'imaging di fluorescenza in operando per la crescita di biofilm ad uno spessore di fino a 100 micrometri. 4 , 12 mentre questa carta discuterà solo la conferma della presenza di biofilm attraverso microscopia di fluorescenza, la SALVI è compatibile con altri metodi di imaging ottici come super-resolution imaging di fluorescenza (cioè, illuminazione strutturata microscopia (SIM)9) e laser confocale microscopia (CLSM)4di imaging). Imaging ottico può servire per misurare lo spessore del biofilm e ottenere un'immagine 3D di, la forma del biofilm come appare, confermando il suo spessore ed il suo attaccamento alla finestra di peccato. 9 mentre GFP è stato utilizzato nell'analisi SIMS, s. oneidensis senza GFP è stato usato per la curva di crescita, come questa unica misura necessaria della densità ottica e non richiede alcuna formazione immagine fluorescente. Generalmente, la differenza tra la GFP taggati e senza tag specie nella curva di crescita è insignificante. Inoltre, mentre questo protocollo utilizza S. oneidensis MR-1 GFP come organismo modello per descrivere la procedura, questa procedura è stata progettata per qualsiasi ceppo batterico che può essere necessaria per la coltivazione all'interno di SALVI. Anche se, data la conoscenza del ceppo batterico necessario, alcune condizioni di crescita come tempo, temperatura e ossigeno ambiente potrebbero essere necessario essere modificati per accogliere il ceppo di batteri per essere utilizzato. Per mezzo di crescita, questa procedura utilizza il brodo di soia medio, Trittico "nanofili" (TSB) senza destrosio e tryptic soy agar (TSA) senza destrosio per la coltura. La composizione del mezzo "nanofili" è stato appositamente formulata per la crescita e per il monitoraggio delle estensioni della membrana e Periplasma di S. oneidensis che sembrano prendere la forma di piccoli fili e la composizione media è stata stabilito nella precedente ricerca. 13 , 14
Il nostro protocollo precedente su in situ liquido ToF-SIMS ha illustrato il beneficio che SALVI ha da offrire per immobilizzazione della proteina e l'attaccamento al peccato, come pure un protocollo dettagliato sulla riduzione dei dati e analisi ToF-SIMS. 12 piuttosto che ripetere passaggi di riduzione dei dati, questa carta servirà invece focalizzare l'approccio unico di impostazione e coltivando i biofilm all'interno nostro microchannel SALVI, come pure i passaggi imaging per rilevare la presenza di biofilm e spessore preventivo per l'analisi ToF-SIMS. Mentre biofilm sono stati precedentemente limitati solo asciugato campioni all'interno della camera di vuoto-base superficie tecniche analitiche, EPS e biofilm chimica mappatura dettagliata di biofilm live possa ora essere ottenuto in situ a causa di questa nuova funzionalità.

<table><tbody><tr><td>ToF-SIMS</td><td>IONTOF</td><td>TOF.SIMS 5</td><td>Resolution:&gt;10,000 m/&amp;Delta;m for mass resolution;&gt;4,000 m/&amp;Delta;m for high spatial resolution</td></tr><tr><td>System for Analysis at the Liquid Vacuum Interface (SALVI)</td><td>Pacific Northwest National Laboratory</td><td>N/A</td><td>SALVI is a unique, self-contained, portable analytical tool that, for the first time, enables vacuum based scientific instruments such as time-of-flight secondary ion mass spectrometry (ToF-SIMS) to analyze liquid surfaces in their natural state at the molecular level.</td></tr><tr><td>-80&amp;deg;C Freezer</td><td>New Brunswick Scientific</td><td>N/A</td><td>U410 Premium Energy Efficient Ultra-Low Temperature Freezer</td></tr><tr><td>4&amp;deg;C Refrigerator</td><td>BioCold Scientific</td><td>N/A</td><td>COLDBOX1</td></tr><tr><td>Orbital Shaker</td><td>New Brunswick Scientific</td><td>N/A</td><td>Innova 4900 Multi-Tier Environmental Shaker, set at 30 degrees Celsius for serum bottle and flask culturing, set at 150rpm.</td></tr><tr><td>Syringe Pump</td><td>Cole-Parmer</td><td>EW-74905-02</td><td>Cole-Parmer Syringe Pump, Infusion Only, Touchscreen Control 74905-02, used for injecting liquid into the tubing system and SALVI at a constant flowrate.</td></tr><tr><td>Incubator</td><td>Barnstead International</td><td>LT1465X3</td><td>Lab-Line incubator, set at 30 degrees Celsius for plate culturing.</td></tr><tr><td>Autoclave</td><td>Getinge</td><td>533LS</td><td>Used to sterilize PEEK fittings, tubing systems, serum vials, and medium. Model 533LS Vacuum Steam Sterilizer</td></tr><tr><td>Spectrophotometer</td><td>Thermo Fisher Scientific</td><td>4001-000</td><td>GENESYS 20 spectrophotometer for OD600 readings of cuvettes for growth curves.</td></tr><tr><td>Biological Safety Cabinet</td><td>Thermo Fisher Scientific</td><td>1385</td><td>1300 Series AZ Biological Safety Cabinet</td></tr><tr><td>Fluorescence Microscope</td><td>Nikon</td><td>N/A</td><td>Nikon OPTIPHOT-2 fluorescence microscope with camera and super high pressure mercury lamp power supply.</td></tr><tr><td>pH Meter</td><td>Mettler Toledo</td><td>51302803</td><td>Used to test the pH of the &amp;ldquo;nanowires&amp;rdquo; medium after finished and before autoclaving.</td></tr><tr><td>PEEK Union</td><td>Valco</td><td>ZU1TPK</td><td>For connecting the inlet and outlet of SALVI, the syringe to the tubing system, and the inlet of the SALVI to the drip chamber of the tubing system.</td></tr><tr><td>5 Axes Sample Stage</td><td>IONTOF</td><td>N/A</td><td>Stage is self-made for mounting SALVI in ToF-SIMS.</td></tr><tr><td>Barnstead Nanopure Water Purification System</td><td>Thermo Fisher Scientific</td><td>D11921</td><td>ROpure LP Reverse Osmosis filtration module (D2716)</td></tr><tr><td>Pipette</td><td>Thermo Fisher Scientific</td><td>21-377-821</td><td>Range: 100 to 1,000 &amp;micro;L.</td></tr><tr><td>Pipette Tip</td><td>Neptune</td><td>2112.96.BS</td><td>1,000 &amp;micro;L pipette tips</td></tr><tr><td>Razor Blade Handle</td><td>Stanley</td><td>N/A</td><td>Stanley Bostitch Razor Blade Scraper with 5 Single-Edge Blades, used for cutting PTFE tubing</td></tr><tr><td>Syringe</td><td>BD</td><td>309659</td><td>1 mL</td></tr><tr><td>Syringe</td><td>BD</td><td>309657</td><td>3 mL</td></tr><tr><td>Syringe</td><td>BD</td><td>309646</td><td>5 mL; Used for making the drip chamber</td></tr><tr><td>Syringe</td><td>BD</td><td>309604</td><td>10 mL</td></tr><tr><td>Syringe</td><td>BD</td><td>302830</td><td>20 mL</td></tr><tr><td>Disposable Pipette</td><td>Thermo Fisher Scientific</td><td>13-678-11</td><td>25 mL Fisherbrand&amp;trade; Sterile Polystyrene Disposable Serological Pipets with Magnifier Stripe, for filling serum bottles.</td></tr><tr><td>Electric Pipette Filler</td><td>Pipet-aid</td><td>P-57260</td><td>Vacuum pressure electric serological pipette filler</td></tr><tr><td>Serum Bottle</td><td>Sigma</td><td>33109-U</td><td>Holds approximately 69 mL of liquid for culture growth, optimum for use of 20mL culture per bottle.</td></tr><tr><td>Anaerobic Culture Tube</td><td>VWR</td><td>89167-178</td><td>Anaerobic Tubes, 18 x 150 mm, Supplied with 20 mm Blue Butyl Rubber Stopper and Aluminum Seal.</td></tr><tr><td>Rubber Stopper</td><td>Sigma</td><td>27235-U</td><td>Silicone stopper, used for sealing serum bottles and for creating the tubing system/drip chamber.</td></tr><tr><td>Aluminum Crimp Seal (without septum)</td><td>Sigma</td><td>27227-U</td><td>Aluminum seal for top of serum bottle for use with serum bottle crimper.</td></tr><tr><td>Serum Bottle Aluminum Seal Crimper</td><td>Wheaton</td><td>224307</td><td>30 mm crimper with standard seal.</td></tr><tr><td>PTFE Tubing</td><td>Supelco</td><td>58697-U</td><td>1.58 mm OD x 0.5 mm ID 50 ft. PTFE Teflon tubing, used for creating the tubing system.</td></tr><tr><td>Disposable Cuvettes</td><td>GMBH</td><td>759085D</td><td>1.5 Ml for use with spectrophotometer.</td></tr><tr><td>Needle</td><td>BD</td><td>303015</td><td>22G; used for serum bottle injection.</td></tr><tr><td>Needle</td><td>BD</td><td>305120</td><td>23G; used for punching-through rubber stopper to create drip tubing system.</td></tr><tr><td>Shewanella oneidensis MR-1 with GFP</td><td>N/A</td><td>N/A</td><td>Matthysse AG, Stretton S, Dandie C, McClure NC, &amp;amp; Goodman AE (1996) Construction of GFP vectors for use in Gram-negative bacteria other than Escherichia coli. FEMS Microbiol Lett 145(1):87-94.&amp;nbsp;</td></tr><tr><td>Ethanol</td><td>Thermo Fisher Scientific</td><td>&amp;nbsp;S25310A</td><td>95% Denatured</td></tr><tr><td>TSA</td><td>BD</td><td>212305</td><td>Tryptic soy agar for culturing the model organism (S. oneidensis) used in this protocol</td></tr><tr><td>PIPES Buffer</td><td>Sigma</td><td>P-1851</td><td>Used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Sodium Hydroxide</td><td>Sigma</td><td>S-5881</td><td>Used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Ammonium Chloride</td><td>Sigma</td><td>A-5666</td><td>Used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Potassium Chloride</td><td>Sigma</td><td>P-4504</td><td>Used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Sodium Phosphate Monobasic</td><td>Sigma</td><td>S-9638</td><td>Used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Sodium Chloride</td><td>Thermo Fisher Scientific</td><td>S271-3</td><td>Used for &amp;ldquo;nanowires&amp;rdquo; medium, and used to make mineral solution used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Sodium lactate</td><td>Sigma</td><td>L-1375</td><td>60%(w/w) syrup @ 98% pure, d=1.3 g/mL, 7M, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Sodium Bicarbonate</td><td>Sigma</td><td>S-5761</td><td>Used to make ferric NTA solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Nitrilotriacetic Acid Trisodium Salt</td><td>Sigma</td><td>N-0253</td><td>Used to make ferric NTA solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Iron (III) Chloride</td><td>Sigma</td><td>451649</td><td>Used to make ferric NTA solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Magnesium Sulfate</td><td>Sigma</td><td>208094</td><td>Used to make minerals solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Manganese (II) Sulfate Monohydrate</td><td>Sigma</td><td>M-7634</td><td>Used to make minerals solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Iron(II) Sulfate Heptahydrate</td><td>Sigma</td><td>215422</td><td>Used to make minerals solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Calcium Chloride Dihydrate</td><td>Sigma</td><td>223506</td><td>Used to make minerals solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Cobalt(II) Chloride</td><td>Sigma</td><td>60818</td><td>Used to make minerals solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Zinc Chloride</td><td>Sigma</td><td>229997</td><td>Used to make minerals solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Copper(II) Sulfate Pentahydrate</td><td>Sigma</td><td>C-8027</td><td>Used to make minerals solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Aluminum Potassium Sulfate Dodecahydrate</td><td>Sigma</td><td>237086</td><td>Used to make minerals solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Boric Acid</td><td>Sigma</td><td>B-6768</td><td>Used to make minerals solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Sodium Molybdate Dihydrate</td><td>Sigma</td><td>331058</td><td>Used to make minerals solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Nickel(II) Chloride</td><td>Sigma</td><td>339350</td><td>Used to make minerals solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Sodium Tungstate Dihydrate</td><td>Sigma</td><td>14304</td><td>Used to make minerals solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>D-Biotin</td><td>Sigma</td><td>47868</td><td>Used to make vitamin solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Folic Acid</td><td>Sigma</td><td>F-7876</td><td>Used to make vitamin solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Pyridoxine Hydrochloride</td><td>Sigma</td><td>P-9755</td><td>Used to make vitamin solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Riboflavin (B2)</td><td>Sigma</td><td>47861</td><td>Used to make vitamin solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Thiamine Hydrochloride</td><td>Sigma</td><td>T-4625</td><td>Used to make vitamin solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Nicotinic Acid</td><td>Sigma</td><td>N4126</td><td>Used to make vitamin solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>D-Pantothenic Acid Hemicalcium Salt</td><td>Sigma</td><td>21210</td><td>Used to make vitamin solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Vitamin B12</td><td>Sigma</td><td>V-2876</td><td>Used to make vitamin solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>4-Aminobenzoic Acid</td><td>Sigma</td><td>A-9878</td><td>Used to make vitamin solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr><tr><td>Thioctic Acid</td><td>Sigma</td><td>T-1395</td><td>Used to make vitamin solution, used for &amp;ldquo;nanowires&amp;rdquo; medium {Hill, E.A. 2007}</td></tr></tbody></table>

in situ characterization of shewanella oneidensis mr1 biofilms by salvi and tof-sims

Biofilm batterici sono comunità di superficie-collegati che sono ampiamente studiata per capire la loro auto-prodotti sostanze polimeriche extracellulari (EPS) e i loro ruoli in microbiologia ambientale. Questo studio descrive un metodo per coltivare biofilm allegato al sistema per l'analisi all'interfaccia liquido di vuoto (SALVI) e raggiungere in situ chemical mapping di un biofilm vivente mediante spettrometria di massa di ioni secondari di tempo di volo (ToF-SIMS). Questo viene fatto attraverso la coltura di batteri sia all'esterno che all'interno del canale SALVI con la nostra installazione specializzata, nonché attraverso tecniche di imaging ottici per rilevare la presenza di biofilm e spessore prima analisi ToF-SIMS. I nostri risultati mostrano picchi caratteristici del biofilm Shewanella nel suo stato naturale idrata, evidenziando al suo ambiente cluster d'acqua localizzate, come pure di EPS frammenti, che sono drasticamente diversi di biofilm stesso disidratato stato. Questi risultati dimostrano la capacità di innovazione di SALVI che permette per l'imaging di biofilm in situ con uno strumento di imaging chimico basati su vuoto.

Questi risultati rappresentativi servono a mostrare come il profilo chimico del biofilm allegato può essere identificato e interpretato, come ottenuta attraverso ToF-SIMS. Dopo aver tracciato spettri di massa da acquisizione dati ToF-SIMS, brevemente evidenziato nella sezione procedure, identificazione del picco dovrebbe essere condotta al fine di assegnare le identità di ogni valore rispettivo m/z. Questo può essere fatto attraverso la revisione di una vasta letteratura sulla spettrom...

Watch this Scientific Journal Video about In Situ Characterization of Shewanella oneidensis MR1 Biofilms by SALVI and ToF-SIMS at JoVE.com

In Situ Characterization of Shewanella oneidensis MR1 Biofilms by SALVI and ToF-SIMS

Questo articolo presenta un metodo per la coltivazione di un biofilm per in situ spettrometria totale di ione secondaria tempo di volo per la mappatura chimica allo stato idratato, attivata da un reattore di microfluidica, sistema per analisi presso l'interfaccia liquida di vuoto. Shewanella oneidensis MR-1 con proteine di fluorescenza verde è stato usato come modello.

In Situ Caratterizzazione di Shewanella oneidensis MR1 biofilm di SALVI e ToF-SIMS

Bacterial biofilms are surface-associated communities that are vastly studied to understand their self-produced extracellular polymeric substances (EPS) ...

in-situ-characterization-shewanella-oneidensis-mr1-biofilms-salvi-tof

Research

JoVE Journal

Chemistry

In Situ Characterization of Shewanella oneidensis MR1 Biofilms by SALVI and ToF-SIMS

8.9K Views.  Pacific Northwest National Laboratory. Questo articolo presenta un metodo per la coltivazione di un biofilm per in situ spettrometria totale di ione secondaria tempo di volo per la mappatura chimica allo stato idratato, attivata da un reattore di microfluidica, sistema per analisi presso l'interfaccia liquida di vuoto. Shewanella oneidensis MR-1 con proteine di fluorescenza verde è stato usato come modello.

Video: In Situ Characterization of Shewanella oneidensis MR1 Biofilms by SALVI and ToF-SIMS

Cell-Free DNA Integrity Analysis in Urine Samples

Although the presence of circulating cell-free DNA in plasma or serum has been widely shown to be a suitable source of biomarkers for many types of cancer, few studies have focused on the potential use of urine cell-free (UCF) DNA. Starting from the hypotheses that normal apoptotic cells produce highly fragmented DNA and that cancer cells release longer DNA, the potential role of UCF DNA integrity was evaluated as an early diagnostic marker capable of distinguishing between patients with prostate or bladder cancer and healthy individuals.
A UCF DNA integrity analysis is proposed on the basis of four quantitative real-time PCRs of four sequences longer than 250 bp: c-MYC, BCAS1, HER2, and AR. Sequences that frequently have an increased DNA copy number in bladder and prostate cancers were chosen for the analysis, but the method is flexible, and these genes could be substituted with other genes of interest. The potential utility of UCF DNA as a source of biomarkers has already been demonstrated for urologic malignancies, thus paving the way for further studies on UCF DNA characterization. The UCF DNA integrity test has the advantage of being non-invasive, rapid, and easy to perform, with only a few milliliters of urine needed to carry out the analysis.

A method for analyzing DNA integrity in the cell-free supernatant fraction of urine samples is proposed. The method is suitable for early detection of urological malignancies and has proven accurate for the early diagnosis of bladder cancer.

Cell-libero DNA analisi di integrità nei campioni di urina

Although the presence of circulating cell-free DNA in plasma or serum has been widely shown to be a suitable source of biomarkers for many types of ...

Ricerca

Ricerca sul cancro

In Situ SIMS and IR Spectroscopy of Well-defined Surfaces Prepared by Soft Landing of Mass-selected Ions

Soft landing of mass-selected ions onto surfaces is a powerful approach for the highly-controlled preparation of materials that are inaccessible using conventional synthesis techniques. Coupling soft landing with in situ characterization using secondary ion mass spectrometry (SIMS) and infrared reflection absorption spectroscopy (IRRAS) enables analysis of well-defined surfaces under clean vacuum conditions. The capabilities of three soft-landing instruments constructed in our laboratory are illustrated for the representative system of surface-bound organometallics prepared by soft landing of mass-selected ruthenium tris(bipyridine) dications, [Ru(bpy)3]2+ (bpy = bipyridine), onto carboxylic acid terminated self-assembled monolayer surfaces on gold (COOH-SAMs). In situ time-of-flight (TOF)-SIMS provides insight into the reactivity of the soft-landed ions. In addition, the kinetics of charge reduction, neutralization and desorption occurring on the COOH-SAM both during and after ion soft landing are studied using in situ Fourier transform ion cyclotron resonance (FT-ICR)-SIMS measurements. In situ IRRAS experiments provide insight into how the structure of organic ligands surrounding metal centers is perturbed through immobilization of organometallic ions on COOH-SAM surfaces by soft landing. Collectively, the three instruments provide complementary information about the chemical composition, reactivity and structure of well-defined species supported on surfaces.

In Situ SIMS and IR Spectroscopy of Well-defined Surfaces Prepared by Soft Landing of Mass-selected Ions

Soft landing of mass-selected ions onto surfaces is a powerful approach for the highly-controlled preparation of novel materials. Coupled with analysis by in situ secondary ion mass spectrometry (SIMS) and infrared reflection absorption spectroscopy (IRRAS), soft landing provides unprecedented insights into the interactions of well-defined species with surfaces.

In Situ SIMS e IR Spettroscopia di superfici ben definite Preparato da atterraggio morbido di ioni Mass-selezionati

Soft landing of mass-selected ions onto surfaces is a powerful approach for the highly-controlled preparation of materials that are inaccessible using ...

Chimica

Serum and Plasma Copy Number Detection Using Real-time PCR

Serum and plasma cell free DNA (cfDNA) has been shown as an informative, non-invasive source of biomarkers for cancer diagnosis, prognosis, monitoring, and prediction of treatment resistance. Starting from the hypothesis that androgen receptor (AR) gene copy number (CN) gain is a frequent event in metastatic castration resistance prostate cancer (mCRPC), we propose to analyze this event in cfDNA as a potential predictive biomarker.
We evaluated AR CN in cfDNA using 2 different real-time PCR assays and 2 reference genes (RNaseP and AGO1). DNA amount of 60 ng was used for each assay combination. AR CN gain was confirmed using Digital PCR as a more accurate method. CN variation analysis has already been demonstrated to be informative for the prediction of treatment resistance in the setting of mCRPC, but it could be useful also for other purposes in different patient settings. CN analysis on cfDNA has several advantages: it is non-invasive, rapid and easy to perform, and it starts from a small volume of serum or plasma material.

This manuscript describes the copy number variation analysis performed in serum or plasma DNA using real-time PCR approach. This method is suitable for the prediction of drug resistance in castration resistant prostate cancer patients, but it could be informative also for other diseases.

Siero e Plasma copia numero rilevazione mediante PCR in tempo reale

Serum and plasma cell free DNA (cfDNA) has been shown as an informative, non-invasive source of biomarkers for cancer diagnosis, prognosis, monitoring, ...

Detection of a CDH1 Rare Transcript Variant in Fresh-frozen Gastric Cancer Tissues by Chip-based Digital PCR

CDH1a, a non-canonical transcript of the CDH1 gene, has been found to be expressed in some gastric cancer (GC) cell lines, whereas it is absent in normal gastric mucosa. Recently, we detected CDH1a transcript variant in fresh-frozen tumor tissues obtained from patients with GC. The expression of this variant in tissue samples was investigated by the chip-based digital PCR (dPCR) approach presented here. dPCR offers the potential for an accurate, robust, and highly sensitive measurement of nucleic acids and is increasingly utilized for many applications in different fields. dPCR is capable of detecting rare targets; in addition, dPCR offers the possibility for absolute and precise quantification of nucleic acids without the need for calibrators and standard curves. In fact, the reaction partitioning enriches the target from the background, which improves amplification efficiency and tolerance to inhibitors. Such characteristics make dPCR an optimal tool for the detection of the CDH1a rare transcript.

Detection of a CDH1 Rare Transcript Variant in Fresh-frozen Gastric Cancer Tissues by Chip-based Digital PCR

The manuscript describes a chip-based digital PCR assay to detect a rare CDH1 transcript variant (CDH1a) in fresh-frozen normal and tumor tissues obtained from patients with gastric cancer.

Rilevamento di una variante rara trascrizione CDH1 in tessuti di cancro gastrico fresco congelato mediante PCR digitale basata su Chip

CDH1a, a non-canonical transcript of the CDH1 gene, has been found to be expressed in some gastric cancer (GC) cell lines, whereas it is absent in normal ...

Assessment of Boron Doped Diamond Electrode Quality and Application to In Situ Modification of Local pH by Water Electrolysis

Boron doped diamond (BDD) electrodes have shown considerable promise as an electrode material where many of their reported properties such as extended solvent window, low background currents, corrosion resistance, etc., arise from the catalytically inert nature of the surface. However, if during the growth process, non-diamond-carbon (NDC) becomes incorporated into the electrode matrix, the electrochemical properties will change as the surface becomes more catalytically active. As such it is important that the electrochemist is aware of the quality and resulting key electrochemical properties of the BDD electrode prior to use. This paper describes a series of characterization steps, including Raman microscopy, capacitance, solvent window and redox electrochemistry, to ascertain whether the BDD electrode contains negligible NDC i.e. negligible sp2 carbon. One application is highlighted which takes advantage of the catalytically inert and corrosion resistant nature of an NDC-free surface i.e. stable and quantifiable local proton and hydroxide production due to water electrolysis at a BDD electrode. An approach to measuring the local pH change induced by water electrolysis using iridium oxide coated BDD electrodes is also described in detail.

Assessment of Boron Doped Diamond Electrode Quality and Application to In Situ Modification of Local pH by Water Electrolysis

A protocol is described for the characterization of the key electrochemical parameters of a boron doped diamond (BDD) electrode and subsequent application for in situ pH generation experiments.

Valutazione del Boro Doped Diamante elettrodi Qualità e applicazioni per<em&gt; In Situ</em&gt; Modifica del pH locale da acqua Elettrolisi

Boron doped diamond (BDD) electrodes have shown considerable promise as an electrode material where many of their reported properties such as extended ...

Radiolabeling and Quantification of Cellular Levels of Phosphoinositides by High Performance Liquid Chromatography-coupled Flow Scintillation

Phosphoinositides (PtdInsPs) are essential signaling lipids responsible for recruiting specific effectors and conferring organelles with molecular identity and function. Each of the seven PtdInsPs varies in their distribution and abundance, which are tightly regulated by specific kinases and phosphatases. The abundance of PtdInsPs can change abruptly in response to various signaling events or disturbance of the regulatory machinery. To understand how these events lead to changes in the amount of PtdInsPs and their resulting impact, it is important to quantify PtdInsP levels before and after a signaling event or between control and abnormal conditions. However, due to their low abundance and similarity, quantifying the relative amounts of each PtdInsP can be challenging. This article describes a method for quantifying PtdInsP levels by metabolically labeling cells with 3H-myo-inositol, which is incorporated into PtdInsPs. Phospholipids are then precipitated and deacylated. The resulting soluble 3H-glycero-inositides are further extracted, separated by high-performance liquid chromatography (HPLC), and detected by flow scintillation. The labeling and processing of yeast samples is described in detail, as well as the instrumental setup for the HPLC and flow scintillator. Despite losing structural information regarding acyl chain content, this method is sensitive and can be optimized to concurrently quantify all seven PtdInsPs in cells.

Phosphoinositides are signaling lipids whose relative abundance rapidly changes in response to various stimuli. This article describes a method to measure the abundance of phosphoinositides by metabolically labeling cells with 3H-myo-inositol, followed by extraction and deacylation. Extracted glycero-inositides are then separated by high-performance liquid chromatography and quantified by flow scintillation.

Radiomarcatura e quantificazione dei livelli cellulari di fosfoinositidi da alte prestazioni cromatografia liquida accoppiata flusso scintillazione

Phosphoinositides (PtdInsPs) are essential signaling lipids responsible for recruiting specific effectors and conferring organelles with molecular ...

In Situ Characterization of Hydrated Proteins in Water by SALVI and ToF-SIMS

This work demonstrates in situ characterization of protein biomolecules in the aqueous solution using the System for Analysis at the Liquid Vacuum Interface (SALVI) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). The fibronectin protein film was immobilized on the silicon nitride (SiN) membrane that forms the SALVI detection area. During ToF-SIMS analysis, three modes of analysis were conducted including high spatial resolution mass spectrometry, two-dimensional (2D) imaging, and depth profiling. Mass spectra were acquired in both positive and negative modes. Deionized water was also analyzed as a reference sample. Our results show that the fibronectin film in water has more distinct and stronger water cluster peaks compared to water alone. Characteristic peaks of amino acid fragments are also observable in the hydrated protein ToF-SIMS spectra. These results illustrate that protein molecule adsorption on a surface can be studied dynamically using SALVI and ToF-SIMS in the liquid environment for the first time.

In Situ Characterization of Hydrated Proteins in Water by SALVI and ToF-SIMS

This work presents a protocol for liquid handling and sample introduction to a microchannel for in situ time-of-flight secondary ion mass spectrometry analysis of protein biomolecules in an aqueous solution.

In Situ Caratterizzazione di idrate proteine ​​in acqua da Salvi e TOF-SIMS

This work demonstrates in situ characterization of protein biomolecules in the aqueous solution using the System for Analysis at the Liquid Vacuum ...

Synthesis and Characterization of Supramolecular Colloids

Control over colloidal assembly is of utmost importance for the development of functional colloidal materials with tailored structural and mechanical properties for applications in photonics, drug delivery and coating technology. Here we present a new family of colloidal building blocks, coined supramolecular colloids, whose self-assembly is controlled through surface-functionalization with a benzene-1,3,5-tricarboxamide (BTA) derived supramolecular moiety. Such BTAs interact via directional, strong, yet reversible hydrogen-bonds with other identical BTAs. Herein, a protocol is presented that describes how to couple these BTAs to colloids and how to quantify the number of coupling sites, which determines the multivalency of the supramolecular colloids. Light scattering measurements show that the refractive index of the colloids is almost matched with that of the solvent, which strongly reduces the van der Waals forces between the colloids. Before photo-activation, the colloids remain well dispersed, as the BTAs are equipped with a photo-labile group that blocks the formation of hydrogen-bonds. Controlled deprotection with UV-light activates the short-range hydrogen-bonds between the BTAs, which triggers the colloidal self-assembly. The evolution from the dispersed state to the clustered state is monitored by confocal microscopy. These results are further quantified by image analysis with simple routines using ImageJ and Matlab. This merger of supramolecular chemistry and colloidal science offers a direct route towards light- and thermo-responsive colloidal assembly encoded in the surface-grafted monolayer.

A protocol for the synthesis and characterization of colloids coated with supramolecular moieties is described. These supramolecular colloids undergo self-assembly upon the activation of the hydrogen-bonds between the surface-anchored molecules by UV-light.

Sintesi e caratterizzazione di supramolecolari colloidi

Control over colloidal assembly is of utmost importance for the development of functional colloidal materials with tailored structural and mechanical ...

Preparation of Chloroplast Sub-compartments from Arabidopsis for the Analysis of Protein Localization by Immunoblotting or Proteomics

Chloroplasts are major components of plant cells. Such plastids fulfill many crucial functions, such as assimilation of carbon, sulfur and nitrogen as well as synthesis of essential metabolites. These organelles consist of the following three key sub-compartments. The envelope, characterized by two membranes, surrounds the organelle and controls the communication of the plastid with other cell compartments. The stroma is the soluble phase of the chloroplast and the main site where carbon dioxide is converted into carbohydrates. The thylakoid membrane is the internal membrane network consisting of grana (flat compressed sacs) and lamellae (less dense structures), where oxygenic photosynthesis takes place. The present protocol describes step by step procedures required for the purification, using differential centrifugations and Percoll gradients, of intact chloroplasts from Arabidopsis, and their fractionation, using sucrose gradients, in three sub-compartments (i.e., envelope, stroma, and thylakoids). This protocol also provides instructions on how to assess the purity of these fractions using markers associated to the various chloroplast sub-compartments. The method described here is valuable for subplastidial localization of proteins using immunoblotting, but also for subcellular and subplastidial proteomics and other studies.

Here, we describe a method to purify intact chloroplasts from Arabidopsis leaves and their three main sub-compartments (envelope, stroma, and thylakoids), using a combination of differential centrifugations, continuous Percoll gradients, and discontinuous sucrose gradients. The method is valuable for subplastidial and subcellular localization of proteins by immunoblotting and proteomics.

Preparazione del cloroplasto Sub-compartimenti da Arabidopsis per l'analisi di localizzazione della proteina di Immunoblotting o proteomica

Chloroplasts are major components of plant cells. Such plastids fulfill many crucial functions, such as assimilation of carbon, sulfur and nitrogen as ...

Biochimica

Physiological Preparation of Hair Cells from the Sacculus of the American Bullfrog (Rana catesbeiana)

The study of hearing and balance rests upon insights drawn from biophysical studies of model systems. One such model, the sacculus of the American bullfrog, has become a mainstay of auditory and vestibular research. Studies of this organ have revealed how sensory cells hair can actively detect signals from the environment. Because of these studies, we now better understand the mechanical gating and localization of a hair cell&#39;s transduction channels, calcium&#39;s role in mechanical adaptation, and the identity of hair cell currents. This highly accessible organ continues to provide insight into the workings of hair cells. Here we describe the preparation of the bullfrog&#39;s sacculus for biophysical studies on its hair cells. We include the complete dissection procedure and provide specific protocols for the preparation of the sacculus in specific contexts. We additionally include representative results using this preparation, including the calculation of a hair bundle&#39;s instantaneous force-displacement relation and measurement of a bundle&#39;s spontaneous oscillation.

Physiological Preparation of Hair Cells from the Sacculus of the American Bullfrog Rana catesbeiana

The American bullfrog&#39;s (Rana catesbeiana) sacculus permits direct examination of hair-cell physiology. Here the dissection and preparation of the bullfrog&#39;s sacculus for biophysical studies is described. We show representative experiments from these hair cells, including the calculation of a bundle&#39;s force-displacement relation and measurement of its unforced motion.

In Situ Caratterizzazione di Shewanella oneidensis MR1 biofilm di SALVI e ToF-SIMS

Riepilogo

Esplora Altri Video

Capitoli in questo video

Cell-libero DNA analisi di integrità nei campioni di urina

In Situ SIMS e IR Spettroscopia di superfici ben definite Preparato da atterraggio morbido di ioni Mass-selezionati

Siero e Plasma copia numero rilevazione mediante PCR in tempo reale

Rilevamento di una variante rara trascrizione CDH1 in tessuti di cancro gastrico fresco congelato mediante PCR digitale basata su Chip

Valutazione del Boro Doped Diamante elettrodi Qualità e applicazioni per

Radiomarcatura e quantificazione dei livelli cellulari di fosfoinositidi da alte prestazioni cromatografia liquida accoppiata flusso scintillazione

In Situ Caratterizzazione di idrate proteine in acqua da Salvi e TOF-SIMS

Sintesi e caratterizzazione di supramolecolari colloidi

Preparazione del cloroplasto Sub-compartimenti da Arabidopsis per l'analisi di localizzazione della proteina di Immunoblotting o proteomica

Preparazione fisiologico delle cellule ciliate dalla sacculus del toro americana (

In Situ Caratterizzazione di Shewanella oneidensis MR1 biofilm di SALVI e ToF-SIMS

Riepilogo

Esplora Altri Video

Capitoli in questo video

Cell-libero DNA analisi di integrità nei campioni di urina

In Situ SIMS e IR Spettroscopia di superfici ben definite Preparato da atterraggio morbido di ioni Mass-selezionati

Siero e Plasma copia numero rilevazione mediante PCR in tempo reale

Rilevamento di una variante rara trascrizione CDH1 in tessuti di cancro gastrico fresco congelato mediante PCR digitale basata su Chip

Valutazione del Boro Doped Diamante elettrodi Qualità e applicazioni per

Radiomarcatura e quantificazione dei livelli cellulari di fosfoinositidi da alte prestazioni cromatografia liquida accoppiata flusso scintillazione

In Situ Caratterizzazione di idrate proteine ​​in acqua da Salvi e TOF-SIMS

Sintesi e caratterizzazione di supramolecolari colloidi

Preparazione del cloroplasto Sub-compartimenti da Arabidopsis per l'analisi di localizzazione della proteina di Immunoblotting o proteomica

Preparazione fisiologico delle cellule ciliate dalla sacculus del toro americana (

In Situ Caratterizzazione di idrate proteine in acqua da Salvi e TOF-SIMS