M.D.Y, S.M.G-S., and L.M.T. acknowledge the Office of Naval Research (Award #N0001415WX01038 and N0001415WX00195), the Naval Research Laboratory, and the Naval Research Laboratory Nanosciences Institute; M.Y.E.-N. is supported by the U.S. Department of Energy Grant DE-FG02-13ER16415.

1. Interdigitated microelectrode array (IDA) preparation
<ol>
	<li>Obtain commercially available IDA electrodes patterned on a nonconductive substrate or synthesize them using standard lithographic methods.28 
	NOTE: IDA dimensions and/or materials can be varied based on desired conditions for different experiments. IDAs used here were obtained commercially and consisted of two interdigitated gold microelectrodes patterned on a glass substrate connected to large electrode pads at opposite e...

<ol>
	<li>Boyd, D. A., 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=.">.</a> Biofilms in Bioelectrochemical Systems. , 177-210 (2015).</li><li>Natan, M. J., Wrighton, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chemically+modified+microelectrode+arrays.">Chemically modified microelectrode arrays.</a> Prog Inorg Chem. 7, 391-494 (1990).</li><li>Paul, E. W., Ricco, A. J., Wrighton, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Resistance+of+polyaniline+films+as+a+function+of+electrochemical+potential+and+the+fabrication+of+polyaniline-based+microelectronic+devices.">Resistance of polyaniline films as a function of electrochemical potential and the fabrication of polyaniline-based microelectronic devices.</a> J Phys Chem-US. 89, 1441-1447 (1985).</li><li>Dalton, E. 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=Charge+transport+in+electroactive+polymers+consisting+of+fixed+molecular+redox+sites.">Charge transport in electroactive polymers consisting of fixed molecular redox sites.</a> Chem Phys. 141, 143-157 (1990).</li><li>Chidsey, C. E. D., Murray, R. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electroactive+Polymers+and+Macromolecular+Electronics.">Electroactive Polymers and Macromolecular Electronics.</a> Science. 231, 25-31 (1986).</li><li>Chidsey, C. E. D., Murray, R. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Redox+capacity+and+direct+current+electron+conductivity+in+electroactive+materials.">Redox capacity and direct current electron conductivity in electroactive materials.</a> J Phys Chem-US. 90, 1479-1484 (1986).</li><li>Gregoire, K. P., Glaven, S. M., Hervey, J., Lin, B., Tender, L. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enrichment+of+a+High-Current+Density+Denitrifying+Microbial+Biocathode.">Enrichment of a High-Current Density Denitrifying Microbial Biocathode.</a> J Electrochem Soc. 161, H3049-H3057 (2014).</li><li>Siegert, M., Yates, M. D., Spormann, A. M., Logan, B. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Methanobacterium+dominates+biocathodic+Archaeal+communities+in+methanogenic+microbial+electrolysis+cells.">Methanobacterium dominates biocathodic Archaeal communities in methanogenic microbial electrolysis cells.</a> ACS Sus Chem Eng. 3, 1668-1676 (2015).</li><li>Wang, Z., 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=A+previously+uncharacterized,+nonphotosynthetic+member+of+the+Chromatiaceae+is+the+primary+CO2-fixing+constituent+in+a+self-regenerating+biocathode.">A previously uncharacterized, nonphotosynthetic member of the Chromatiaceae is the primary CO2-fixing constituent in a self-regenerating biocathode.</a> Appl Environ Microbiol. 81, 699-712 (2015).</li><li>Marshall, C. W., Ross, D. E., Fichot, E. B., Norman, R. S., May, H. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Long-term+Operation+of+Microbial+Electrosynthesis+Systems+Improves+Acetate+Production+by+Autotrophic+Microbiomes.">Long-term Operation of Microbial Electrosynthesis Systems Improves Acetate Production by Autotrophic Microbiomes.</a> Environ Sci Technol. 47, 6023-6029 (2013).</li><li>Strik, D. P. B. T. B., Picot, M., Buisman, C. J. N., Barri&#232;re, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=pH+and+Temperature+Determine+Performance+of+Oxygen+Reducing+Biocathodes.">pH and Temperature Determine Performance of Oxygen Reducing Biocathodes.</a> Electroanalysis. 25, 652-655 (2013).</li><li>Strycharz, S. M., 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=Reductive+dechlorination+of+2-chlorophenol+by+Anaeromyxobacter+dehalogenans+with+an+electrode+serving+as+the+electron+donor.">Reductive dechlorination of 2-chlorophenol by Anaeromyxobacter dehalogenans with an electrode serving as the electron donor.</a> Environ Microbiol Report. 2, 289-294 (2010).</li><li>Yates, M. D., 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=Microbial+Electrochemical+Energy+Storage+and+Recovery+in+a+Combined+Electrotrophic+and+Electrogenic+Biofilm.">Microbial Electrochemical Energy Storage and Recovery in a Combined Electrotrophic and Electrogenic Biofilm.</a> Environ Sci Technol Lett. 4, 374-379 (2017).</li><li>Tender, L. M., 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=Harnessing+microbially+generated+power+on+the+seafloor.">Harnessing microbially generated power on the seafloor.</a> Nature Biotechnology. 20, 821-825 (2002).</li><li>Yates, M. D., Siegert, M., Logan, B. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hydrogen+evolution+catalyzed+by+viable+and+non-viable+cells+on+biocathodes.">Hydrogen evolution catalyzed by viable and non-viable cells on biocathodes.</a> Int J Hydrogen Energ. 39, 16841-16851 (2014).</li><li>Fokina, O., Eipper, J., Winandy, L., Kerzenmacher, S., Fischer, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Improving+the+performance+of+a+biofuel+cell+cathode+with+laccase-containing+culture+supernatant+from+Pycnoporus+sanguineus.">Improving the performance of a biofuel cell cathode with laccase-containing culture supernatant from Pycnoporus sanguineus.</a> Bioresource Technol. 175, 445-453 (2015).</li><li>Yates, M. D., 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=Thermally+activated+long+range+electron+transport+in+living+biofilms.">Thermally activated long range electron transport in living biofilms.</a> Phys Chem Chem Phys. 17, 32564-32570 (2015).</li><li>Yates, M. D., 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+conductivity+of+living+Geobacter+sulfurreducens+biofilms.">Measuring conductivity of living Geobacter sulfurreducens biofilms.</a> Nat Nano. 11, 910-913 (2016).</li><li>Snider, R. M., Strycharz-Glaven, S. M., Tsoi, S. D., Erickson, J. S., Tender, L. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Long-range+electron+transport+in+Geobacter+sulfurreducens+biofilms+is+redox+gradient-driven.">Long-range electron transport in Geobacter sulfurreducens biofilms is redox gradient-driven.</a> Proc Natl Acad Sci USA. 109, 15467-15472 (2012).</li><li>Strycharz-Glaven, S. M., Snider, R. M., Guiseppi-Elie, A., Tender, L. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+the+electrical+conductivity+of+microbial+nanowires+and+biofilms.">On the electrical conductivity of microbial nanowires and biofilms.</a> Energ Environ Sci. 4, 4366-4379 (2011).</li><li>Malvankar, N. S., Tuominen, M. T., Lovley, D. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comment+on+"On+electrical+conductivity+of+microbial+nanowires+and+biofilms"+by+S.+M.+Strycharz-Glaven,+R.+M.+Snider,+A.+Guiseppi-Elie+and+L.+M.+Tender,+Energy+Environ.+Sci.,+2011,+4,+4366.">Comment on "On electrical conductivity of microbial nanowires and biofilms" by S. M. Strycharz-Glaven, R. M. Snider, A. Guiseppi-Elie and L. M. Tender, Energy Environ. Sci., 2011, 4, 4366.</a> Energy Environ. Sci. 5, 6247-6249 (2012).</li><li>Malvankar, N. S., 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=Tunable+metallic-like+conductivity+in+microbial+nanowire+networks.">Tunable metallic-like conductivity in microbial nanowire networks.</a> Nat Nanotechnol. 6, 573-579 (2011).</li><li>Strycharz-Glaven, S. M., Tender, L. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reply+to+the+'Comment+on+"On+electrical+conductivity+of+microbial+nanowires+and+biofilms"'+by+N.+S.+Malvankar,+M.+T.+Tuominen+and+D.+R.+Lovley,+Energy+Environ.+Sci.,+2012,+5.">Reply to the 'Comment on "On electrical conductivity of microbial nanowires and biofilms"' by N. S. Malvankar, M. T. Tuominen and D. R. Lovley, Energy Environ. Sci., 2012, 5.</a> Energy Environ. Sci. 5, 6250-6255 (2012).</li><li>Strycharz-Glaven, S. M., 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=Electron+Transport+through+Early+Exponential-Phase+Anode-Grown+Geobacter+sulfurreducens+Biofilms.">Electron Transport through Early Exponential-Phase Anode-Grown Geobacter sulfurreducens Biofilms.</a> Chem Electro Chem. 1, 1957-1965 (2014).</li><li>Chidsey, C. E., Feldman, B. J., Lundgren, C., Murray, R. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Micrometer-spaced+platinum+interdigitated+array+electrode:+fabrication,+theory,+and+initial+use.">Micrometer-spaced platinum interdigitated array electrode: fabrication, theory, and initial use.</a> Anal Chem. 58, 601-607 (1986).</li><li>Li, C., Lesnik, K. L., Fan, Y., Liu, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Redox+Conductivity+of+Current-Producing+Mixed+Species+Biofilms.">Redox Conductivity of Current-Producing Mixed Species Biofilms.</a> PLOS ONE. 11, e0155247 (2016).</li><li>Malvankar, N. S., 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=Tunable+metallic-like+conductivity+in+microbial+nanowire+networks.">Tunable metallic-like conductivity in microbial nanowire networks.</a> Nat Nano. 6, 573-579 (2011).</li><li>Ing, N. L., Nusca, T. D., Hochbaum, A. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Geobacter+sulfurreducens+pili+support+ohmic+electronic+conduction+in+aqueous+solution.">Geobacter sulfurreducens pili support ohmic electronic conduction in aqueous solution.</a> Phys Chem Chem Phys. 19, 21791-21799 (2017).</li><li>Fricke, K., Harnisch, F., Schr&#246;der, U. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+the+use+of+cyclic+voltammetry+for+the+study+of+anodic+electron+transfer+in+microbial+fuel+cells.">On the use of cyclic voltammetry for the study of anodic electron transfer in microbial fuel cells.</a> Energ Environ Sci. 1, 144-147 (2008).</li><li>Marsili, E., Rollefson, J. B., Baron, D. B., Hozalski, R. M., Bond, D. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microbial+biofilm+voltammetry:+direct+electrochemical+characterization+of+catalytic+electrode-attached+biofilms.">Microbial biofilm voltammetry: direct electrochemical characterization of catalytic electrode-attached biofilms.</a> Appl Environ Microbiol. 74, 7329-7337 (2008).</li><li>Kankare, J., Kupila, E. -. L. <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+conductance+measurement+during+electropolymerization.">In-situ conductance measurement during electropolymerization.</a> J Electroanal Chem. 322, 167-181 (1992).</li><li>Byun, H. S., Pirbadian, S., Nakano, A., Shi, L., El-Naggar, M. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Kinetic+Monte+Carlo+Simulations+and+Molecular+Conductance+Measurements+of+the+Bacterial+Decaheme+Cytochrome+MtrF.">Kinetic Monte Carlo Simulations and Molecular Conductance Measurements of the Bacterial Decaheme Cytochrome MtrF.</a> Chem Electro Chem. 1, 1932-1939 (2014).</li><li>El Kasmi, A., Wallace, J. M., Bowden, E. F., Binet, S. M., Linderman, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Controlling+interfacial+electron-transfer+kinetics+of+cytochrome+c+with+mixed+self-assembled+monolayers.">Controlling interfacial electron-transfer kinetics of cytochrome c with mixed self-assembled monolayers.</a> J Am Chem Soc. 120, 225-226 (1998).</li><li>Bortolotti, C. A., 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=The+Reorganization+Energy+in+Cytochrome+c+is+Controlled+by+the+Accessibility+of+the+Heme+to+the+Solvent.">The Reorganization Energy in Cytochrome c is Controlled by the Accessibility of the Heme to the Solvent.</a> J Phys Chem Lett. 2, 1761-1765 (2011).</li><li>Gallaway, J. W., Calabrese Barton, S. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Kinetics+of+Redox+Polymer-Mediated+Enzyme+Electrodes.">Kinetics of Redox Polymer-Mediated Enzyme Electrodes.</a> J Am Chem Soc. 130, 8527-8536 (2008).</li><li>Thackeray, J. W., White, H. S., Wrighton, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Poly(3-methylthiophene)-coated+electrodes:+optical+and+electrical+properties+as+a+function+of+redox+potential+and+amplification+of+electrical+and+chemical+signals+using+poly(3-methylthiophene)-based+microelectrochemical+transistors.">Poly(3-methylthiophene)-coated electrodes: optical and electrical properties as a function of redox potential and amplification of electrical and chemical signals using poly(3-methylthiophene)-based microelectrochemical transistors.</a> J Phys Chem-US. 89, 5133-5140 (1985).</li><li>Jugnet, Y., Tourillon, G., Duc, T. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evidence+of+Intrinsic+Extended+&#960;-Bonding+Band+and+Metalliclike+Behavior+in+Undoped+and+Doped+Electropolymerized+Poly+(3-methylthiophene)+Films.">Evidence of Intrinsic Extended &#960;-Bonding Band and Metalliclike Behavior in Undoped and Doped Electropolymerized Poly (3-methylthiophene) Films.</a> Phys Rev Lett. 56, 1862-1865 (1986).</li></ol>

During the setup of the IDA, it is critical to test that the source and the drain are not shorted together prior to electrochemical gating measurements, as this will alter the ISD vs. EG curve and could lead to erroneous results and interpretations. It is also critical to select VSD and v such that the current is linearly dependent on VSD and independent of v. If this is not the case, then the equations described above cannot be utilized to calculate conductivity.
<p class=...

Extracellular electron transport (EET) is a process that enables certain microorganisms to transport electrons between intracellular metabolic processes and insoluble electron acceptors or donors that reside outside the cell, ranging from natural minerals to electrodes. In some cases, EET enables microorganisms to form electrically conductive multi-cell thick biofilms on electrode surfaces, in which cells not in direct contact with the electrode can still utilize it as a metabolic electron acceptor or donor. There is considerable interest in such biofilms as electrode catalysts for various applications, such as microbial electrosynthesis, contaminant sensing/removal, and remote energy generation and storage,7,8,9,10,11,12,13,14 due to the diversity of metabolic processes performed by microorganisms and the durability of microbial biofilms compared to enzyme-based bioelectrodes.15,16 In addition, EET pathways may potentially be utilized to electrically control or signal changes in naturally occurring or genetically engineered microbial metabolic processes involved, for example, in production of a desired product or detection of a target analyte or stimulus. The electrical conductivity of electrocatalytic biofilms, which sets them apart from other biological materials, is a central aspect of their electrocatalytic properties, yet little is understood about the underlying EET process in the electrode environment, and that which is known is highly contested.17,18,19,20,21,22,23,24
Described here is a 2-electrode method to measure conductivity through living, electrode-grown biofilms using interdigitated electrode arrays (IDAs). IDAs consist of parallel rectangular electrodes patterned on flat glass surface such that every other band is connected at opposite sides of the array resulting in 2 electrodes (the source and drain). Careful examination of an IDA (see for example, Figure 6.12b of ref #1) reveals that that the gaps separating adjacent bands are also connected in such a way as to form a single gap that weaves back and forth across the array separating the two electrodes. The result is a long and narrow gap separating the source and drain electrodes, yielding very high source-drain currents when a conductive material is formed, cast, polymerized, or grown (in the case of the type of biofilms considered here) over the array. In addition, the small size of the electrodes results in small background current due to capacitance charging and to change in oxidation state of the conductive material with change in gate potential, since the amount of material needed to make conductivity measurements using IDAs is so small. The technique of IDA-based electrochemical gating described here, developed to characterize thin film conductive polymers,2,3,4,25 has only recently been applied to living systems.18 Another technique used to measure conductivity of living biofilms utilized a large format split source and drain electrodes and source meters to set the gate potential.26,27 However, concerns over these methods have been detailed previously.18
The protocol below encapsulates our experience with making conductivity measurements of living Geobacter sulfurreducens and biocathode MCL biofilms. G. sulfurreducens is a model electrode reducing organism able to use insoluble materials, including electrodes, as the sole metabolic electron acceptor. Additionally, it forms thick biofilms that are able to transport electrons over multiple cell lengths, making it an ideal model organism to study anodic long-distance extracellular electron transfer. We also include details for the study of biocathode MCL, an aerobic, autotrophic mixed community biofilm isolated from the cathode of a benthic microbial fuel cell. Biocathode MCL (named for the three primary constituents &#8211; Marinobacter, Chromatiaceaea and Labrenzia) is capable of oxidizing an electrode as its sole electron donor and transporting electrons over multiple cell lengths, making it an interesting cathodic system to study. Additionally, biocathode MCL has the highest reported conductivity for a living system to date using these methods. The inclusion of these diverse electroactive biofilms in this protocol is meant to highlight that this technique is applicable to measure the transport of electrons through any living biofilm able to electrically interact with electrodes.

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		<tr height="21">
			<td height="21" style="height:21px;width:259px;">IDAs</td>
			<td style="width:192px;">CH Instruments</td>
			<td style="width:219px;">012125</td>
			<td style="width:337px;">Manufactured by ALS-Japan; sold by CH Instruments</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">Wire</td>
			<td style="width:192px;">Digikey</td>
			<td style="width:219px;">W7-ND</td>
			<td></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:259px;">Conductive silver epoxy</td>
			<td style="width:192px;">Electron microscopy sciences</td>
			<td style="width:219px;">12670-EE</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">Insulating material</td>
			<td style="width:192px;">3M</td>
			<td style="width:219px;">2131-B</td>
			<td>Scotchast flame retardant compound</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">15 mL conical centrifuge tube</td>
			<td style="width:192px;">VWR</td>
			<td style="width:219px;">89004-368</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">21g needle</td>
			<td style="width:192px;">VWR</td>
			<td style="width:219px;">BD-305165</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">5 mL pipette tips</td>
			<td style="width:192px;">VWR</td>
			<td style="width:219px;">82018-842</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">5 mL pipettor</td>
			<td style="width:192px;">VWR</td>
			<td>89079-976</td>
			<td></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:259px;">Freshwater medium components</td>
			<td style="width:192px;">Sigma Aldrich</td>
			<td style="width:219px;">All standard laboratory chemicals</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">&#160;&#160;&#160; Ammonium chloride</td>
			<td style="width:192px;"></td>
			<td style="width:219px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">&#160;&#160;&#160; Sodium phosphate monobasic</td>
			<td style="width:192px;"></td>
			<td style="width:219px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">&#160;&#160;&#160; Sodium bicarbonate</td>
			<td style="width:192px;"></td>
			<td style="width:219px;"></td>
			<td></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:259px;">Artificial seawater medium components</td>
			<td style="width:192px;">Sigma Aldrich</td>
			<td style="width:219px;">All standard laboratory chemicals</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">&#160;&#160;&#160; Sodium chloride</td>
			<td style="width:192px;"></td>
			<td style="width:219px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">&#160;&#160;&#160; Magnesium chloride hexahydrate</td>
			<td style="width:192px;"></td>
			<td style="width:219px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">&#160;&#160;&#160; Magnesium sulfate heptahydrate</td>
			<td style="width:192px;"></td>
			<td style="width:219px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">&#160;&#160;&#160; Potassium chloride</td>
			<td style="width:192px;"></td>
			<td style="width:219px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">&#160;&#160;&#160; Sodium bicarbonate</td>
			<td style="width:192px;"></td>
			<td style="width:219px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">&#160;&#160;&#160; Calcium chloride dihydrate</td>
			<td style="width:192px;"></td>
			<td style="width:219px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">&#160;&#160;&#160; Ammonium chloride</td>
			<td style="width:192px;"></td>
			<td style="width:219px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">&#160;&#160;&#160; Potassium phosphate dibasic</td>
			<td style="width:192px;"></td>
			<td style="width:219px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">Ag/AgCl reference electrode</td>
			<td style="width:192px;">Basi</td>
			<td style="width:219px;">MF-2079</td>
			<td></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:259px;">Graphite rod counter electrode</td>
			<td style="width:192px;">Electron microscopy sciences</td>
			<td>70230</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">Recirculating water bath</td>
			<td style="width:192px;">Thermo Scientific</td>
			<td>152-5256</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">Bipotentiostat</td>
			<td style="width:192px;">Pine Instruments</td>
			<td style="width:219px;">WD-20</td>
			<td>http://www.voltammetry.net/pine/aftermath/user</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">Stir bars</td>
			<td style="width:192px;">VWR</td>
			<td>58947-114</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">G. sulfurreducens culture</td>
			<td style="width:192px;">ATCC</td>
			<td style="width:219px;">51573</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:259px;">Jacketed reactor</td>
			<td style="width:192px;">Pine Instruments</td>
			<td>RRPG085</td>
			<td></td>
		</tr>
	</tbody>
</table>

characterizing electron transport through living biofilms

Here we demonstrate the method of electrochemical gating used to characterize electrical conductivity of electrode-grown microbial biofilms under physiologically relevant conditions.1 These measurements are performed on living biofilms in aqueous medium using source and drain electrodes patterned on a glass surface in a specialized configuration referred to as an interdigitated electrode (IDA) array. A biofilm is grown that extends across the gap connecting the source and drain. Potentials are applied to the electrodes (ES and ED) generating a source-drain current (ISD) through the biofilm between the electrodes. The dependency of electrical conductivity on gate potential (the average of the source and drain potentials, EG = [ED + ES]/2) is determined by systematically changing the gate potential and measuring the resulting source-drain current. The dependency of conductivity on gate potential provides mechanistic information about the extracellular electron transport process underlying the electrical conductivity of the specific biofilm under investigation. The electrochemical gating measurement method described here is based directly on that used by M. S. Wrighton2,3 and colleagues and R. W. Murray4,5,6 and colleagues in the 1980&#39;s to investigate thin film conductive polymers.

IDAs were wired, insulated and tested to ensure that the two electrodes were electrically isolated from each other (Figure 1). Reactors were assembled, inoculated with G. sulfurreducens, and incubated until a biofilm bridged the gap between the electrodes. The G. sulfurreducens biofilm can be visually seen to be covering the array. Other biofilms may require the researcher to do an electrochemical gating measurements to see if the two electr...

Watch this Scientific Journal Video about Characterizing Electron Transport through Living Biofilms at JoVE.com

Characterizing Electron Transport through Living Biofilms

A protocol for measuring electrical conductivity of living microbial biofilms under physiologically relevant conditions is presented.

Here we demonstrate the method of electrochemical gating used to characterize electrical conductivity of electrode-grown microbial biofilms under ...

The overall goal of this experimental procedure is to determine the amount of current that can be conducted through a living material in situ as well as the mechanism employed by the living material to transport the current. This method could help answer key questions in the field of microbial electrochemistry such as, How can certain biofilms move electrons over hundreds of microns to support cellular metabolism? The main advantage of this technique is that the interdigitated electrodes give a very high signal-to-noise ratio and can be scaled to fit into many different reactor configurations.Those method can provide insight into multi-cell length extracellular electron transport in biofilms. It can also be applied to other systems, such as electrically conductive polymer films. Researchers new to this method will struggle because it requires a bipotentiostat to set the potentials of both electrodes separately and measure current at each electrode separately.To begin, obtain commercially available IDA electrodes patterned on a non-conductive substrate or synthesize them using standard lithographic methods. Prepare conductive silver epoxy according to the manufacturer's instructions with a mixing rod or pipette tip. Then, place a wire on each gold pad and secure them in place using lab tape.Cover the wire and pad with silver epoxy using a mixing rod or pipette tip. Carefully move the apparatus to an 80 degree Celsius oven for one hour to cure. After the epoxy cures, use a multimeter to ensure electrical conductivity between the end of the wire and the pads.The resistance between the wire and the pads should be less than five ohms. Also, use the multimeter to verify that no conductive epoxy is connecting multiple electrode pads, as this can short the array. If conductive epoxy is connecting multiple leads, use the scribe to isolate the leads.Next, remove the tip of a 15 milliliter conical centrifuge tube to use as a mold for the insulating material. Use a 21 gauge needle to make two small holes in the bottom of the mold for the wires to protrude through. Insert the IDA into the mold and insert the wires through the holes in the bottom of the mold.Next, prepare a thermal electrical and waterproof insulating material. Flame retardant polyurethane resins are often suitable. Pipette the insulator into the mold so that the silver epoxy is completely covered and allow the insulator to dry according to manufacturer's specifications.To set up the electrochemical cell, insert the IDA, counter electrode, and reference electrode into the electrochemical cell. Fill the electrochemical cell with sterile medium suitable for biofilm growth. For Geobacter sulfurreducens, use freshwater medium excluding fumarate.Next, connect the electrodes to a bipotentiostat. Connect one IDA electrode to the working lead one, the other IDA electrode to the working lead two, the reference electrode to the reference lead, and the counter electrode to the counter lead. Perform a control experiment by performing cyclic voltammetry on electrode one and holding electrode two at open circuit to ensure that the electrodes are not connected.To grow the relevant electroactive biofilm, inoculate the electrochemical reactor from a stock culture or enrichment of the desired electrochemically active microorganisms using standard aseptic microbiological techniques. For standard tests, inoculate in a 1 to 20 ratio of inoculum-to-reactor volume. Set the stirring in the reactor to the desired level and set the incubator or water bath to the desired temperature based on the growth conditions of the biofilm of interest.Incubate the system based on specific requirements of the microorganism of interest until the biofilm bridges the gap separating the two electrodes. For stationary Geobacter sulfurreducens biofilm, incubate for seven to ten days at 30 degrees Celsius. Begin setup of the experimental parameters that will be used to determine the current potential dependence for the gating measurements as described in the text protocol.Set up the bipotentiostat software to perform the gating measurements over the selected range at the selected source drain voltage and at the desired scan rate. Additionally, perform a baseline measurement as described in the text protocol. Perform gating measurements using the same conditions under turnover with soluble electron donor or acceptor present in non-turnover without soluble electron donor or acceptor conditions.Obtain a control reactor to ensure that the set point and actual temperature of the medium is the same. Place a thermometer or a thermocouple in a control reactor where the IDA would be. Then, make source strain current measurements over the range of temperatures selected under turnover and non-turnover conditions using the bipotentiostat.To do so, set and hold the IDA at the gate potential that yields maximum conducted current using the bipotentiostat. Record the maximum conducted current using the bipotentiostat while the temperature is cycled between the range of temperatures selected using the onboard controls of the water bath or incubator. Cycle the temperature from one set point to the other and back against using the onboard controls of the incubator or the water bath.This determines the reversibility of the reaction to ensure that the temperature cycling does not harm the biofilm. Finally, reset the temperature back to the normal growth temperature and allow the system to stabilize. Shown here are representative results of an IDA that is functioning properly in freshwater medium.Versus one where the electrodes have been shorted. Representative electrochemical gating measurements performed on a Geobacter sulfurreducens biofilm under non-turnover conditions with a source strain voltage of 10 millivolts exhibit the peak shaped conducted current versus gate potential curve characteristic of redox conductivity. Here, representative raw data shows the dependence of the conducted current on the temperature of the reactor medium.The decrease in conducted current with decreasing temperature is another characteristic of redox conductors. Once mastered, this technique can be done in approximately two days if it is performed properly. While attempting this procedure it is important to remember to make sure that the IDA bands are not shorted prior to inoculating the reactor.The implications of this technique extend towards therapy when applied to study how to disrupt cellular metabolism of biofilm forming pathogens. This procedure can be applied to any living material able to transport electrons in order to address additional questions, such as the correlation between biofilm refology and conductivity.

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8.3K ビュー.  Naval Research Laboratory. The overall goal of this experimental procedure is to determine the amount of current that can be conducted through a living material in situ as well as the mechanism employed by the living material to transport the current. This method could help answer key questions in the field of microbial electrochemistry such as, How can certain biofilms move electrons over hundreds of microns to support cellular metabolism? The main advantage of this technique is that the interdigitated electrodes give...

ビデオ: Characterizing Electron Transport through Living Biofilms

A protocol for measuring electrical conductivity of living microbial biofilms under physiologically relevant conditions is...

methodologies for studying b. subtilis biofilms as a model for characterizing small molecule biofilm inhibitors

Methodologies for Studying B. subtilis Biofilms as a Model for Characterizing Small Molecule Biofilm Inhibitors

This study presents the development of reproducible methodologies to study biofilm inhibitors and their effects on Bacillus subtilis...

Methodologies for Studying B. subtilis Biofilms as a Model for Characterizing Small Molecule Biofilm Inhibitors

characterizing mammalian zinc transporters using an in vitro zinc transport assay

Author Spotlight: Exploring Cellular Zinc Regulation Through ZnT1 Functionality 

Zinc transport has proven challenging to measure due to the weak causal links to protein function and the low temporal resolution. This protocol describes a method for monitoring, with high temporal resolution, Zn2+ extrusion from living cells by utilizing a Zn2+ sensitive fluorescent dye, thus providing a direct measure of Zn2+...

Characterizing Mammalian Zinc Transporters Using an In Vitro Zinc Transport Assay

a new method for qualitative multi-scale analysis of bacterial biofilms on filamentous fungal colonies using confocal and electron microscopy

A New Method for Qualitative Multi-scale Analysis of Bacterial Biofilms on Filamentous Fungal Colonies Using Confocal and Electron Microscopy

This protocol describes a new method to grow and qualitatively analyze bacterial biofilms on fungal hyphae by confocal and electron...

measuring trans-plasma membrane electron transport by c2c12 myotubes

Measuring Trans-Plasma Membrane Electron Transport by C2C12 Myotubes

The goal of this protocol is to spectrophotometrically monitor trans-plasma membrane electron transport utilizing extracellular electron acceptors and to analyze enzymatic interactions that may occur with these extracellular electron...

electrochemical detection of deuterium kinetic isotope effect on extracellular electron transport in shewanella oneidensis mr-1

Electrochemical Detection of Deuterium Kinetic Isotope Effect on Extracellular Electron Transport in Shewanella oneidensis MR-1

Here we present a protocol of whole-cell electrochemical experiments to study the contribution of proton transport to the rate of extracellular electron transport via the outer-membrane cytochromes complex in Shewanella oneidensis...

Electrochemical Detection of Deuterium Kinetic Isotope Effect on Extracellular Electron Transport in Shewanella oneidensis MR-1

transport of surface-modified carbon nanotubes through a soil column

Transport of Surface-modified Carbon Nanotubes through a Soil Column

Surface properties of a nanoparticle are important for their interaction with the surrounding medium. Therefore the surface modification of carbon nanotubes can be critical for their transport and retention through porous media. Here, lab scale column experiments are used to understand the possible transport and retention of these nanoparticles.

analysis of protein folding, transport, and degradation in living cells by radioactive pulse chase

Analysis of Protein Folding, Transport, and Degradation in Living Cells by Radioactive Pulse Chase

Here we describe a protocol for a general pulse-chase method that allows the kinetic analysis of folding, transport, and degradation of proteins to be followed in live...

characterizing mediated extracellular electron transfer in lactic acid bacteria with a three-electrode, two-chamber bioelectrochemical system

Author Spotlight: Exploring Extracellular Electron Transfer in Lactiplantibacillus plantarum for Food Fermentation and Biosensing Applications

Here we present a protocol for characterizing mediated extracellular electron transfer (EET) in lactic acid bacteria using a three-electrode, two-chamber bioelectrochemical system. We illustrate this method with Lactiplantibacillus plantarum and the redox mediator 1,4-dihydroxy-2-naphthoic acid and provide a thorough description of the electrochemical techniques used to evaluate mediated...

Characterizing Mediated Extracellular Electron Transfer in Lactic Acid Bacteria with a Three-Electrode, Two-Chamber Bioelectrochemical System

picometer-precision atomic position tracking through electron microscopy

Picometer-Precision Atomic Position Tracking through Electron Microscopy

This work presents a workflow for atomic position tracking in atomic resolution transmission electron microscopy imaging. This workflow is performed using an open-source Matlab app (EASY-STEM).

characterizing mechanical properties of primary cell wall in living plant organs using atomic force microscopy

Characterizing Mechanical Properties of Primary Cell Wall in Living Plant Organs Using Atomic Force Microscopy

Studies of cell wall biomechanics are essential for understanding plant growth and morphogenesis. The following protocol is proposed to investigate thin primary cell walls in the internal tissues of young plant organs using atomic force...

optimizing visualization of axonal transport of endogenous cargo by fluorescence microscopy in living caenorhabditis elegans

Author Spotlight: Advanced Techniques for Visualizing Endogenous Axonal Transport Dynamics

The paper describes the optimization of fluorescence microscopy acquisition parameters to visualize the axonal transport of endogenous labeled cargos at single-neuron resolution in a living...

Optimizing Visualization of Axonal Transport of Endogenous Cargo by Fluorescence Microscopy in Living Caenorhabditis elegans

characterization of aquatic biofilms with flow cytometry

Characterization of Aquatic Biofilms with Flow Cytometry

Flow cytometry in combination with visual clustering offers an easy-to-use and fast method for studying aquatic biofilms. It can be used for biofilm characterization, detection of changes in biofilm community structure, and detection of abiotic particles embedded in the...

clarifying and imaging candida albicans biofilms

Clarifying and Imaging Candida albicans Biofilms

To view and quantify the internal features of Candida albicans biofilms, we prepare fixed intact specimens that are clarified by refractive index matching. Then, optical sectioning microscopy can be used to obtain three-dimensional image data though the full thickness of the...

Clarifying and Imaging Candida albicans Biofilms

quantifying elastic properties of environmental biofilms using optical coherence elastography

Author Spotlight: Characterizing Environmental Biofilm Mechanics Using Optical Coherence Elastography and its Applications in Wastewater Treatment

This paper highlights the optical coherence elastography (OCE) technique's efficacy in rapidly and non-destructively characterizing biofilm elastic properties. We elucidate critical OCE implementation procedures for accurate measurements and present Young's modulus values for two granular...

Rapid and Non-Destructive Characterization of Biofilm Elastic Properties

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growth of mycobacterium tuberculosis biofilms

Growth of Mycobacterium tuberculosis Biofilms

Mycobacterium tuberculosis forms drug tolerant biofilms when cultured in certain conditions. Here we describe methods for culturing M. tuberculosis biofilms and determining the frequency of drug tolerant persisters. These protocols will be useful for further studies into the mechanisms of drug tolerance in M.

Growth of Mycobacterium tuberculosis Biofilms

analyzing supercomplexes of the mitochondrial electron transport chain with native electrophoresis, in-gel assays, and electroelution

Analyzing Supercomplexes of the Mitochondrial Electron Transport Chain with Native Electrophoresis, In-gel Assays, and Electroelution

This protocol describes the separation of functional mitochondrial electron transport chain complexes (Cx) I-V and supercomplexes thereof using native electrophoresis to reveal information about their assembly and structure. The native gel can be subjected to immunoblotting, in-gel assays, and purification by electroelution to further characterize individual complexes.

ratiometric imaging of extracellular ph in dental biofilms

Ratiometric Imaging of Extracellular pH in Dental Biofilms

A pH-sensitive ratiometric dye is used in combination with confocal laser scanning microscopy and digital image analysis to monitor extracellular pH in dental biofilms in...

waste water derived electroactive microbial biofilms: growth, maintenance, and basic characterization

Waste Water Derived Electroactive Microbial Biofilms: Growth, Maintenance, and Basic Characterization

Chronoamperometric growth of anodic electroactive microbial biofilms in a fed-batch reactor using a three-electrode setup, controlled by a potentiostat, is demonstrated. The extracellular electron transfer is characterized using cyclic voltammetry in the presence of the electron donor and in the absence of the electron donor. Fundamental data analysis is...

Quantifying Elastic Properties of Environmental Biofilms using Optical Coherence Elastography

Carbon nanotubes (CNTs) are widely manufactured nanoparticles, which are being utilized in a number of consumer products, such as sporting goods, electronics and biomedical applications. Due to their accelerating production and use, CNTs constitute a potential environmental risk if they are released to soil and groundwater systems. It is therefore essential to improve the current understanding of environmental fate and transport of CNTs. The transport and retention of CNTs in both natural and artificial media have been reported in literature, but the findings widely vary and are thus not conclusive. There are a number of physical and chemical parameters responsible for variation in retention and transport. In this study, a complete procedure of selected multiwalled carbon nanotubes (MWCNTs) is presented starting from their surface modification to a complete set of laboratory column experiments at critical physical and chemical scenarios. Results indicate that the stability of the commercially available MWCNTs are critical with their attached surface functional group which can also influence the transport and retention of MWCNT through the surrounding medium.

Surface properties of a nanoparticle are important for their interaction with the surrounding medium. Therefore the surface modification of carbon nanotubes can be critical for their transport and retention through porous media. Here, lab scale column experiments are used to understand the possible transport and retention of these nanoparticles.

Carbon nanotubes (CNTs) are widely manufactured nanoparticles, which are being utilized in a number of consumer products, such as sporting goods, ...

Synthesis of Non-uniformly Pr-doped SrTiO3 Ceramics and Their Thermoelectric Properties

We demonstrate a novel synthesis strategy for the preparation of Pr-doped SrTiO3 ceramics via a combination of solid state reaction and spark plasma sintering techniques. Polycrystalline ceramics possessing a unique morphology can be achieved by optimizing the process parameters, particularly spark plasma sintering heating rate. The phase and morphology of the synthesized ceramics were investigated in detail using X-ray diffraction, scanning electron microcopy and energy-dispersive X-ray spectroscopy. It was observed that the grains of these bulk Pr-doped SrTiO3 ceramics were enhanced with Pr-rich grain boundaries. Electronic and thermal transport properties were also investigated as a function of temperature and doping concentration. Such a microstructure was found to give rise to improved thermoelectric properties. Specifically, it resulted in a significant improvement in carrier mobility and the thermoelectric power factor. Simultaneously, it also led to a marked reduction in the thermal conductivity. As a result, a significant improvement (> 30%) in the thermoelectric figure of merit was achieved for the whole temperature range over all previously reported maximum values for SrTiO3-based ceramics. This synthesis demonstrates the steps for the preparation of bulk polycrystalline ceramics of non-uniformly Pr-doped SrTiO3.

Synthesis of Non-uniformly Pr-doped SrTiO3 Ceramics and Their Thermoelectric Properties

A protocol for the synthesis and processing of polycrystalline SrTiO3 ceramics doped non-uniformly with Pr is presented along with the investigation of their thermoelectric properties.

We demonstrate a novel synthesis strategy for the preparation of Pr-doped SrTiO3 ceramics via a combination of solid state reaction and spark plasma ...

Original Experimental Approach for Assessing Transport Fuel Stability

The study of fuel oxidation stability is an important issue for the development of future fuels. Diesel and kerosene fuel systems have undergone several technological changes to fulfill environmental and economic requirements. These developments have resulted in increasingly severe operating conditions whose suitability for conventional and alternative fuels needs to be addressed. For example, fatty acid methyl esters (FAMEs) introduced as biodiesel are more prone to oxidation and may lead to deposit formation. Although several methods exist to evaluate fuel stability (induction period, peroxides, acids, and insolubles), no technique allows one to monitor the real-time oxidation mechanism and to measure the formation of oxidation intermediates that may lead to deposit formation. In this article, we developed an advanced oxidation procedure (AOP) based on two existing reactors. This procedure allows the simulation of different oxidation conditions and the monitoring of the oxidation progress by the means of macroscopic parameters, such as total acid number (TAN) and advanced analytical methods like gas chromatography coupled to mass spectrometry (GC-MS) and Fourier Transform Infrared - Attenuated Total Reflection (FTIR-ATR). We successfully applied AOP to gain an in-depth understanding of the oxidation kinetics of a model molecule (methyl oleate) and commercial diesel and biodiesel fuels. These developments represent a key strategy for fuel quality monitoring during logistics and on-board utilization.

Oxidation stability of transport fuels has become a concern for future fuel development. This work presents an original methodology developed by IFP Energies Nouvelles for assessing fuel stability using two different reactors. This methodology was successfully applied to gain an in-depth understanding of the oxidation kinetics and pathways of model molecules and commercial fuels.

The study of fuel oxidation stability is an important issue for the development of future fuels. Diesel and kerosene fuel systems have undergone several ...

1,3,5-Triphenylbenzene and Corannulene as Electron Receptors for Lithium Solvated Electron Solutions

The authors report on conductivity studies carried out on lithium solvated electron solutions (LiSES) prepared using two types of polyaromatic hydrocarbons (PAH), namely 1,3,5-triphenylbenzene and corannulene, as electron receptors. The solid PAHs were first dissolved in tetrahydrofuran (THF) to form a solution. Metallic lithium was then dissolved into these PAH/THF solutions to yield either blue or greenish blue solutions, colors which are indicative of the presence of solvated electrons. Conductivity measurements at ambient temperature carried out on 1,3,5-triphenylbenzene-based LiSES, denoted by LixTPB(THF)24.7 (x = 1, 2, 3, 4), showed an increase of conductivity with increase of Li:PAH ratio from x = 1 to 2. However, the conductivity gradually decreased upon further increasing the ratio. Indeed the conductivity of LixTPB(THF)24.7 for x = 4 is even lower than for x = 1. Such behavior is similar to that of the previously reported LiSES prepared from biphenyl and naphthalene. Conductivity versus temperature measurements on corannulene-based LiSES, denoted by LixCor(THF)247 (x = 1, 2, 3, 4, 5), showed linear relationships with negative slopes, indicating a metallic behavior similar to biphenyl and naphthalene-based LiSES.

The authors report on conductivity studies carried out on lithium solvated electron solutions (LiSES) prepared using 1,3,5-triphenylbenzene (TPB) and corannulene as electron receptors.

The authors report on conductivity studies carried out on lithium solvated electron solutions (LiSES) prepared using two types of polyaromatic ...

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

Bacterial biofilms are surface-associated communities that are vastly studied to understand their self-produced extracellular polymeric substances (EPS) and their roles in environmental microbiology. This study outlines a method to cultivate biofilm attachment to the System for Analysis at the Liquid Vacuum Interface (SALVI) and achieve in situ chemical mapping of a living biofilm by time-of-flight secondary ion mass spectrometry (ToF-SIMS). This is done through the culturing of bacteria both outside and within the SALVI channel with our specialized setup, as well as through optical imaging techniques to detect the biofilm presence and thickness before ToF-SIMS analysis. Our results show the characteristic peaks of the Shewanella biofilm in its natural hydrated state, highlighting upon its localized water cluster environment, as well as EPS fragments, which are drastically different from the same biofilm's dehydrated state. These results demonstrate the breakthrough capability of SALVI that allows for in situ biofilm imaging with a vacuum-based chemical imaging instrument.

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

This article presents a method for growing a biofilm for in situ time-of-flight secondary ion mass spectrometry for chemical mapping in its hydrated state, enabled by a microfluidic reactor, System for Analysis at the liquid Vacuum Interface. The Shewanella oneidensis MR-1 with green fluorescence protein was used as a model.

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

Quantifying X-Ray Fluorescence Data Using MAPS

The quantification of X-ray fluorescence (XRF) microscopy maps by fitting the raw spectra to a known standard is crucial for evaluating chemical composition and elemental distribution within a material. Synchrotron-based XRF has become an integral characterization technique for a variety of research topics, particularly due to its non-destructive nature and its high sensitivity. Today, synchrotrons can acquire fluorescence data at spatial resolutions well below a micron, allowing for the evaluation of compositional variations at the nanoscale. Through proper quantification, it is then possible to obtain an in-depth, high-resolution understanding of elemental segregation, stoichiometric relationships, and clustering behavior.
This article explains how to use the MAPS fitting software developed by Argonne National Laboratory for the quantification of full 2-D XRF maps. We use as an example results from a Cu(In,Ga)Se2 solar cell, taken at the Advanced Photon Source beamline 2-ID-D at Argonne National Laboratory. We show the standard procedure for fitting raw data, demonstrate how to evaluate the quality of a fit and present the typical outputs generated by the program. In addition, we discuss in this manuscript certain software limitations and offer suggestions for how to further correct the data to be numerically accurate and representative of spatially resolved, elemental concentrations.

Here, we demonstrate the use of the X-ray fluorescence fitting software, MAPS, created by Argonne National Laboratory for the quantification of fluorescence microscopy data. The quantified data that results is useful for understanding the elemental distribution and stoichiometric ratios within a sample of interest.

The quantification of X-ray fluorescence (XRF) microscopy maps by fitting the raw spectra to a known standard is crucial for evaluating chemical ...

The Effect of Charging and Discharging Lithium Iron Phosphate-graphite Cells at Different Temperatures on Degradation

The effect of charging and discharging lithium iron phosphate-graphite cells at different temperatures on their degradation is evaluated systematically. The degradation of the cells is assessed by using 10 charging and discharging temperature permutations ranging from -20 &#176;C to 30 &#176;C. This allows an analysis of the effect of charge and discharge temperatures on aging, and their associations. A total of 100 charge/discharge cycles were carried out. Every 25 cycles a reference cycle was performed to assess the reversible and irreversible capacity degradation. A multi-factor analysis of variance was used, and the experimental results were fitted showing: i) a quadratic relationship between the rate of degradation and the temperature of charge, ii) a linear relationship with the temperature of discharge, and iii) a correlation between the temperature of charge and discharge. It was found that the temperature combination for charging at +30 &#176;C and discharging at -5 &#176;C led to the highest rate of degradation. On the other hand, the cycling in a temperature range from -20 &#176;C to 15 &#176;C (with various combinations of temperatures of charge and discharge), led to a much lower degradation. Additionally, when the temperature of charge is 15 &#176;C, it was found that the degradation rate is nondependent on the temperature of discharge.

This article describes the effect of dissimilar charging/discharging temperatures on the degradation of lithium iron phosphate-graphite pouch cells, aiming at simulating close to real case scenarios. In total, 10 temperature combinations are investigated in the range -20 to 30 &#176;C in order to analyze the impact of temperature on degradation.

The effect of charging and discharging lithium iron phosphate-graphite cells at different temperatures on their degradation is evaluated systematically. ...

A Rhodopsin Transport Assay by High-Content Imaging Analysis

Rhodopsin misfolding mutations lead to rod photoreceptor death that is manifested as autosomal dominant retinitis pigmentosa (RP), a progressive blinding disease that lacks effective treatment. We hypothesize that the cytotoxicity of the misfolded rhodopsin mutant can be alleviated by pharmacologically stabilizing the mutant rhodopsin protein. The P23H mutation, among the other Class II rhodopsin mutations, encodes a structurally unstable rhodopsin mutant protein that is accumulated in the endoplasmic reticulum (ER), whereas the wild type rhodopsin is transported to the plasma membrane in mammalian cells. We previously performed a luminescence-based high-throughput screen (HTS) and identified a group of pharmacological chaperones that rescued the transport of the P23H rhodopsin from ER to the plasma membrane. Here, using an immunostaining method followed by a high-content imaging analysis, we quantified the mutant rhodopsin protein amount in the whole cell and on the plasma membrane. This method is informative and effective to identify true hits from false positives following HTS. Additionally, the high-content image analysis enabled us to quantify multiple parameters from a single experiment to evaluate the pharmacological properties of each compound. Using this assay, we analyzed the effect of 11 different compounds towards six RP associated rhodopsin mutants, obtaining a 2-D pharmacological profile for a quantitative and qualitative understanding about the structural stability of these rhodopsin mutants and efficacy of different compounds towards these mutants.

Here, we described a high-content imaging method to quantify the transport of rhodopsin mutants associated with retinitis pigmentosa. A multiple-wavelength scoring analysis was used to quantify rhodopsin protein on the cell surface or in the whole cell.

Rhodopsin misfolding mutations lead to rod photoreceptor death that is manifested as autosomal dominant retinitis pigmentosa (RP), a progressive blinding ...

Preparation of Graphene-Supported Microwell Liquid Cells for In Situ Transmission Electron Microscopy

The fabrication and preparation of graphene-supported microwell liquid cells (GSMLCs) for in situ electron microscopy is presented in a stepwise protocol. The versatility of the GSMLCs is demonstrated in the context of a study about etching and growth dynamics of gold nanostructures from a HAuCl4 precursor solution. GSMLCs combine the advantages of conventional silicon- and graphene-based liquid cells by offering reproducible well depths together with facile cell manufacturing and handling of the specimen under investigation. The GSMLCs are fabricated on a single silicon substrate which drastically reduces the complexity of the manufacturing process compared to two-wafer-based liquid cell designs. Here, no bonding or alignment process steps are required. Furthermore, the enclosed liquid volume can be tailored to the respective experimental requirements by simply adjusting the thickness of a silicon nitride layer. This enables a significant reduction of window bulging in the electron microscope vacuum. Finally, a state-of-the-art quantitative evaluation of single particle tracking and dendrite formation in liquid cell experiments using only open source software is presented.

Preparation of Graphene-Supported Microwell Liquid Cells for In Situ Transmission Electron Microscopy

A protocol for preparation of graphene-supported microwell liquid cells for in situ electron microscopy of gold nanocrystals from HAuCl4 precursor solution is presented. Furthermore, an analysis routine is presented to quantify observed etching and growth dynamics.

The fabrication and preparation of graphene-supported microwell liquid cells (GSMLCs) for in situ electron microscopy is presented in a stepwise protocol. ...

Photodeposition of Pd onto Colloidal Au Nanorods by Surface Plasmon Excitation

A protocol is described to photocatalytically guide Pd deposition onto Au nanorods (AuNR) using surface plasmon resonance (SPR). Excited plasmonic hot electrons upon SPR irradiation drive reductive deposition of Pd on colloidal AuNR in the presence of [PdCl4]2-. Plasmon-driven reduction of secondary metals potentiates covalent, sub-wavelength deposition at targeted locations coinciding with electric field &#8220;hot-spots&#8221; of the plasmonic substrate using an external field (e.g., laser). The process described herein details a solution-phase deposition of a catalytically-active noble metal (Pd) from a transition metal halide salt (H2PdCl4) onto aqueously-suspended, anisotropic plasmonic structures (AuNR). The solution-phase process is amenable to making other bimetallic architectures. Transmission UV-vis monitoring of the photochemical reaction, coupled with ex situ XPS and statistical TEM analysis, provide immediate experimental feedback to evaluate properties of the bimetallic structures as they evolve during the photocatalytic reaction. Resonant plasmon irradiation of AuNR in the presence of [PdCl4]2- creates a thin, covalently-bound Pd0 shell without any significant dampening effect on its plasmonic behavior in this representative experiment/batch. Overall, plasmonic photodeposition offers an alternative route for high-volume, economical synthesis of optoelectronic materials with sub-5 nm features (e.g., heterometallic photocatalysts or optoelectronic interconnects).

A protocol for anisotropic photodeposition of Pd onto aqueously-suspended Au nanorods via localized surface plasmon excitation is presented.

A protocol is described to photocatalytically guide Pd deposition onto Au nanorods (AuNR) using surface plasmon resonance (SPR). Excited plasmonic hot ...