Identification of Microorganisms that Bind Specifically to Target Materials of Interest Using a Magnetophoretic Microfluidic Platform.

Discovery of microorganisms and their relevant surface peptides that specifically bind to target materials of interest can be achieved through iterative biopanning-based screening of cellular libraries having high diversity. Recently, microfluidics-based biopanning methods have been developed and exploited to overcome the limitations of conventional methods where controlling the shear stress applied to remove cells that do not bind or only weakly bind to target surfaces is difficult and the overall experimental procedure is labor-intensive. Despite the advantages of such microfluidic methods and successful demonstration of their utility, these methods still require several rounds of iterative biopanning. In this work, a magnetophoretic microfluidic biopanning platform was developed to isolate microorganisms that bind to target materials of interest, which is gold in this case. To achieve this, gold-coated magnetic nanobeads, which only attached to microorganisms that exhibit high affinity to gold, were used. The platform was first utilized to screen a bacterial peptide display library, where only the cells with surface peptides that specifically bind to gold could be isolated by the high-gradient magnetic field generated within the microchannel, resulting in enrichment and isolation of many isolates with high affinity and high specificity toward gold even after only a single round of separation. The amino acid profile of the resulting isolates was analyzed to provide a better understanding of the distinctive attributes of peptides that contribute to their specific material-binding capabilities. Next, the microfluidic system was utilized to screen soil microbes, a rich source of extremely diverse microorganisms, successfully isolating many naturally occurring microorganisms that show strong and specific binding to gold. The results show that the developed microfluidic platform is a powerful screening tool for identifying microorganisms that specifically bind to a target material surface of interest, which can greatly accelerate the development of new peptide-driven biological materials and hybrid organic-inorganic materials.

Aspergillus oryzae-Saccharomyces cerevisiae Consortium Allows Bio-Hybrid Fuel Cell to Run on Complex Carbohydrates.

Consortia of Aspergillus oryzae and Saccharomyces cerevisiae are examined for their abilities to turn complex carbohydrates into ethanol. To understand the interactions between microorganisms in consortia, Fourier-transform infrared spectroscopy is used to follow the concentrations of various metabolites such as sugars (e.g., glucose, maltose), longer chain carbohydrates, and ethanol to optimize consortia conditions for the production of ethanol. It is shown that with proper design A. oryzae can digest food waste simulants into soluble sugars that S. cerevisiae can ferment into ethanol. Depending on the substrate and conditions used, concentrations of 13% ethanol were achieved in 10 days. It is further shown that a direct alcohol fuel cell (FC) can be coupled with these A. oryzae-enabled S. cerevisiae fermentations using a reverse osmosis membrane. This "bio-hybrid FC" continually extracted ethanol from an ongoing consortium, enhancing ethanol production and allowing the bio-hybrid FC to run for at least one week. Obtained bio-hybrid FC currents were comparable to those from pure ethanol-water mixtures, using the same FC. The A. oryzae-S. cerevisiae consortium, coupled to a bio-hybrid FC, converted food waste simulants into electricity without any pre- or post-processing.

Simple, fast, and accurate methodology for quantitative analysis using Fourier transform infrared spectroscopy, with bio-hybrid fuel cell examples.

The standard methodologies for quantitative analysis (QA) of mixtures using Fourier transform infrared (FTIR) instruments have evolved until they are now more complicated than necessary for many users' purposes. We present a simpler methodology, suitable for widespread adoption of FTIR QA as a standard laboratory technique across disciplines by occasional users.•Algorithm is straightforward and intuitive, yet it is also fast, accurate, and robust.•Relies on component spectra, minimization of errors, and local adaptive mesh refinement.•Tested successfully on real mixtures of up to nine components. We show that our methodology is robust to challenging experimental conditions such as similar substances, component percentages differing by three orders of magnitude, and imperfect (noisy) spectra. As examples, we analyze biological, chemical, and physical aspects of bio-hybrid fuel cells.

Conjugated gold nanoparticles as a tool for probing the bacterial cell envelope: The case of Shewanella oneidensis MR-1.

The bacterial cell envelope forms the interface between the interior of the cell and the outer world and is, thus, the means of communication with the environment. In particular, the outer cell surface mediates the adhesion of bacteria to the surface, the first step in biofilm formation. While a number of ligand-based interactions are known for the attachment process in commensal organisms and, as a result, opportunistic pathogens, the process of nonspecific attachment is thought to be mediated by colloidal, physiochemical, interactions. It is becoming clear, however, that colloidal models ignore the heterogeneity of the bacterial surface, and that the so-called nonspecific attachment may be mediated by specific regions of the cell surface, whether or not the relevant interaction is ligand-mediate. The authors introduce surface functionalized gold nanoparticles to probe the surface chemistry of Shewanella oneidensis MR-1 as it relates to surface attachment to ω-substituted alkanethiolates self-assembled monolayers (SAMs). A linear relationship between the attachment of S. oneidensis to SAM modified planar substrates and the number of similarly modified nanoparticles attached to the bacterial surfaces was demonstrated. In addition, the authors demonstrate that carboxylic acid-terminated nanoparticles attach preferentially to the subpolar region of the S. oneidensis and obliteration of that binding preference corresponds in loss of attachment to carboxylic acid terminated SAMs. Moreover, this region corresponds to suspected functional regions of the S. oneidensis surface. Because this method can be employed over large numbers of cells, this method is expected to be generally applicable for understanding cell surface organization across populations.

Effect of Modified Phospholipid Bilayers on the Electrochemical Activity of a Membrane-Spanning Conjugated Oligoelectrolyte.

The incorporation and electrochemical activity of a conjugated oligoelectrolyte (COE) in model phospholipid bilayers have been characterized using cyclic voltammetry and UV-vis absorption measurements. Several other modifiers were also incorporated into the phospholipid membranes to alter properties such as charge and alkyl chain disorder. Using potassium ferricyanide to measure charge transport, it was observed that bilayers that contained cholic acid, a negatively charged additive that also promotes alkyl chain disorder, had higher COE uptake and charge permeability than unmodified bilayers. In contrast, when the positively charged choline was incorporated, charge permeability decreased and COE uptake was similar to that of unmodified bilayers. The incorporation of cholesterol at low concentrations within the phospholipid membranes was shown to enhance the COE's effectiveness at increasing membrane charge permeability without increasing the COE concentration in the bilayer. Higher concentrations of cholesterol reduce membrane fluidity and membrane charge permeability. Collectively, these results demonstrate that changes in phospholipid membrane charge permeability upon COE incorporation depend not only on the concentration in the membrane but also on interactions with the phospholipid bilayer and other additives present in the membranes. This approach of manipulating the properties of phospholipid membranes to understand COE interactions is applicable to understanding the behavior of a wide range of molecules that impart useful properties to phospholipid membranes.

Photoelectrochemistry of photosystem I bound in nafion.

Developing a solid state Photosystem I (PSI) modified electrode is attractive for photoelectrochemical applications because of the quantum yield of PSI, which approaches unity in the visible spectrum. Electrodes are constructed using a Nafion film to encapsulate PSI as well as the hole-scavenging redox mediator Os(bpy)2Cl2. The photoactive electrodes generate photocurrents of 4 µA/cm(2) when illuminated with 1.4 mW/cm(2) of 676 nm band-pass filtered light. Methyl viologen (MV(2+)) is present in the electrolyte to scavenge photoelectrons from PSI in the Nafion film and transport charges to the counter electrode. Because MV(2+) is positively charged in both reduced and oxidized states, it is able to diffuse through the cation permeable channels of Nafion. Photocurrent is produced when the working electrode is set to voltages negative of the Os(3+)/Os(2+) redox potential. Charge transfer through the Nafion film and photohole scavenging at the PSI luminal surface by Os(bpy)2Cl2 depends on the reduction of Os redox centers to Os(2+) via hole scavenging from PSI. The optimal film densities of Nafion (10 µg/cm(2) Nafion) and PSI (100 µg/cm(2) PSI) are determined to provide the highest photocurrents. These optimal film densities force films to be thin to allow the majority of PSI to have productive electrical contact with the backing electrode.

The conjugated oligoelectrolyte DSSN+ enables exceptional coulombic efficiency via direct electron transfer for anode-respiring Shewanella oneidensis MR-1-a mechanistic study.

Shewanella oneidensis MR-1 was cultivated on lactate with poised graphite electrode acceptors (E = +0.2 V vs. Ag/AgCl) in order to explore the basis for sustained increases in anodic current output following the addition of the lipid-intercalating conjugated oligoelectrolyte (COE), 4,4'-bis(4'-(N,N-bis(6''-(N,N,N-trimethylammonium)hexyl)amino)-styryl)stilbene tetraiodide (DSSN+). Microbial cultures, which were spiked with DSSN+, exhibit a ∼2.2-fold increase in charge collected, a ∼3.1-fold increase in electrode colonization by S. oneidensis, and a ∼1.7-fold increase in coulombic efficiency from 51 ± 10% to an exceptional 84 ± 7% without obvious toxicity effects. Direct microbial biofilm voltammetry reveals that DSSN+ rapidly and sustainably increases cytochrome-based direct electron transfer and subsequently increases flavin-based mediated electron transfer. Control experiments indicate that DSSN+ does not contribute to the current in the absence of bacteria.

Comparative photoactivity and stability of isolated cyanobacterial monomeric and trimeric Photosystem I.

Photoactivity of native trimeric, and non-native monomeric Photosystem I (PSI) extracted from Thermosynechococcus elongatus is compared in a photoelectrochemical system. The PSI monomer is isolated by disassembling a purified PSI trimer using a freeze-thaw technique in presence of the short-chain surfactant, octylthioglucoside. Photoactive electrodes are constructed with PSI, functioning as both light absorber and charge-separator, embedded within a conductive polymer film. Despite structural differences between PSI trimers and monomers, electrodes cast with equal chlorophyll-a concentration generate similar photoactivities. Photoaction spectra show that all photocurrent derived from electrodes of PSI and conductive polymer originates solely from PSI with no photocurrent caused by redox mediators in the conductive polymer film. Longevity studies show that the two forms of PSI photodegrade at the same rate while exposed to equal intensities of 676 nm light. Direct photo-oxidation measurements indicate that PSI's monomeric form has fewer light harvesting antennae than trimer, and also shows energy sharing between monomeric subunits in the trimer. The structure of PSI is also found to impact cell performance when applying light at incident powers above 1.5 mW/cm(2) due to the reduced optical cross-section in the monomer, causing saturation at lower light intensities than the trimer.

Photocurrent generation from surface assembled photosystem I on alkanethiol modified electrodes.

Photosystem I (PSI) is a key component of oxygenic photosynthetic electron transport because of its light-induced electron transfer to the soluble electron acceptor ferredoxin. This work demonstrates the incorporation of surface assembled cyanobacterial trimeric PSI complexes into a biohybrid system for light-driven current generation. Specifically, this work demonstrates the improved assembly of PSI via electrophoretic deposition, with controllable surface assembled PSI density, on different self-assembled alkanethiol monolayers. Using artificial electron donors and acceptors (Os(bpy)(2)Cl(2) and methyl viologen) we demonstrate photocurrent generation from a single PSI layer, which remains photoactive for at least three hours of intermittent illumination. Photoelectrochemical comparison of the biohybrid systems assembled from different alkanethiols (hexanethiol, aminohexanethiol, mercaptohexanol, and mercaptohexanoic acid) reveals that the PSI generated photocurrent is enhanced by almost 5 times on negatively charged SAM surfaces as compared to positively charged surfaces. These results are discussed in light of how PSI is oriented upon electrodeposition on a SAM.

Electrochemical characterization of riboflavin-enhanced reduction of trinitrotoluene.

There is great interest in understanding trinitrotoluene (TNT) and dinitrotoluene (DNT) contamination, detection and remediation in the environment due to TNT's negative health effects and security implications. Numerous publications have focused on detecting TNT in groundwater using multiple techniques, including electrochemistry. The main degradation pathway of nitrotoluenes in the environment is reduction, frequently with biological and/or photolytic assistance. Riboflavin has also been noted to aid in TNT remediation in soils and groundwater when exposed to light. This report indicates that adding riboflavin to a TNT or DNT solution enhances redox currents in electrochemical experiments. Here AC voltammetry was performed and peak currents compared with and without riboflavin present. Results indicated that TNT, DNT and riboflavin could be detected using AC voltammetry on modified gold electrodes and the addition of riboflavin affected redox peaks of TNT and DNT. Poised potential experiments indicated that it is possible to enhance reduction of TNT in the presence of riboflavin and light. These results were dramatic enough to explain long term enhancement of bioremediation in environments containing high levels of riboflavin and enhance the limit of detection in electrochemically-based nitrotoluene sensing.

Metabolite analysis of Clostridium acetobutylicum: fermentation in a microbial fuel cell.

Microbial fuel cells (MFCs) were used to monitor metabolism changes in Clostridium acetobutylicum fermentations. When MFCs were inoculated with C. acetobutylicum, they generated a unique voltage output pattern where two distinct voltage peaks occurred over a weeklong period. This result was markedly different to previously studied organisms which usually generate one sustained voltage peak. Analysis of the fermentation products indicated that the dual voltage peaks correlated with glucose metabolism. The first voltage peak correlated with acidogenic metabolism (acetate and butyrate production) and the second peak with solventogenic metabolism (acetone and butanol production). This demonstrates that MFCs can be applied as a novel tool to monitor the shift from acid production to solvent production in C. acetobutylicum.

Modification of the optoelectronic properties of membranes via insertion of amphiphilic phenylenevinylene oligoelectrolytes.

We report on the modification of membranes by incorporation of phenylenevinylene oligoelectrolytes with the goal of tailoring their optical and electronic properties and their applications. A water-soluble distyrylstilbene oligoelectrolyte (DSSN+), capped at each end with nitrogen bound, terminally charged pendant groups, was synthesized. The photophysical and solvatochromatic properties of DSSN+ and the shorter distyrylbenzene analogue DSBN+ were probed and found to be useful for characterizing insertion into membranes based on phospholipid vesicle systems. A combination of UV/visible absorbance and photoluminescence spectroscopies, together with confocal microscopy, were employed to confirm membrane incorporation. Examination of the emission intensity profile in stationary multilamellar vesicles obtained with a polarized excitation source provides insight into the orientation of these chromophores within lipid bilayers and indicates that these molecules are highly ordered, such that the hydrophobic electronically delocalized region positions within the inner membrane with the long molecular axis perpendicular to the bilayer plane. Cyclic voltammetry experiments provide evidence that DSSN+ and DSBN+ facilitate transmembrane electron transport across lipid bilayers supported on glassy carbon electrodes. Additionally, the interaction with living microorganisms was probed. Fluorescence imaging indicates that DSSN+ and DSBN+ preferentially accumulate within cell membranes. Furthermore, notable increases in yeast microbial fuel cell performance were observed when employing DSSN+ as the electron transport mediator.

Mitigation of the effect of catholyte contamination in microbial fuel cells using a wicking air cathode.

Cathode design greatly affects microbial fuel cell (MFC) performance. Cathode contamination is inevitable in a single-chamber MFC yet it is impossible to study the magnitude of this effect in the single-chambered format. Therefore to study the effect of contamination at the cathode two-chamber MFCs must be used. The advantages of the two-chamber MFC design used in this study include: the assembled and filled fuel cell is autoclavable and the cathode can easily be moved from the submerged to air exposed position while maintaining sterility. This study was performed with the cathode in two positions: completely submerged in the catholyte and raised to a point where wicking action was used to coat the cathode with catholyte. When the cathode was submerged and the catholyte was inoculated with Bacillus megaterium, Shewanella oneidensis or Escherichia coli current generation was greatly decreased as compared to sterile. When the cathodes were raised, allowing contact with the catholyte by wicking, the current rose to levels comparable with sterile cathode MFCs. The reduced performance of submerged cathodes is most likely due to the microbial culture in the cathode greatly reducing the available oxygen for completion of the cathode reaction. This shows simple designs with low-cost materials can be used to mitigate effects of cathode contamination.

Effect of electron mediators on current generation and fermentation in a microbial fuel cell.

Effects of select electron mediators [9,10-anthraquinone-2,6-disulfonic acid disodium salt (AQDS), safranine O, resazurin, methylene blue, and humic acids] on metabolic end-products and current production from cellulose digestion by Clostridium cellulolyticum in microbial fuel cells (MFCs) were studied using capillary electrophoresis and traditional electrochemical techniques. Addition of the mediator resazurin greatly enhanced current production but did not appear to alter the examined fermentation end-products compared to MFCs with no mediator. Assays for lactate, acetate, and ethanol indicate that the presence of safranine O, methylene blue, and humic acids alters metabolite production in the MFC: safranine O decreased the examined metabolites, methylene blue increased lactate formation, and humic acids increased the examined metabolites. Mediator standard redox potentials (E (0)) reported in the literature do not coincide with redox potentials in MFCs due presumably to the electrolytic complexity of media that supports bacterial survival and growth. Current production in MFCs: (1) can be effected by the mediator redox potential while in the media, which may be significantly shifted from E (0), and (2) depended on the ability of the mediator to access the bacterial electron source, which may be cytoplasmic. In addition, some electron mediators had significant effects on metabolic end-products and therefore the metabolism of the organism itself.

Effect of molecular crowding on the response of an electrochemical DNA sensor.

E-DNA sensors, the electrochemical equivalent of molecular beacons, appear to be a promising means of detecting oligonucleotides. E-DNA sensors are comprised of a redox-modified (here, methylene blue or ferrocene) DNA stem-loop covalently attached to an interrogating electrode. Because E-DNA signaling arises due to binding-induced changes in the conformation of the stem-loop probe, it is likely sensitive to the nature of the molecular packing on the electrode surface. Here we detail the effects of probe density, target length, and other aspects of molecular crowding on the signaling properties, specificity, and response time of a model E-DNA sensor. We find that the highest signal suppression is obtained at the highest probe densities investigated, and that greater suppression is observed with longer and bulkier targets. In contrast, sensor equilibration time slows monotonically with increasing probe density, and the specificity of hybridization is not significantly affected. In addition to providing insight into the optimization of electrochemical DNA sensors, these results suggest that E-DNA signaling arises due to hybridization-linked changes in the rate, and thus efficiency, with which the redox moiety collides with the electrode and transfers electrons.

Mediating electron transfer from bacteria to a gold electrode via a self-assembled monolayer.

Numerous bacterial genera are known to respire anaerobically using macroscopic electrodes as electron acceptors. Typically, inexpensive graphite electrodes, which are readily colonized, are used to monitor electrogenic bacterial metabolism for microbial fuel cell and bioelectronics studies. We compare current production by electrogenic bacteria on gold electrodes coated with various alkanethiol self-assembled monolayers to current production on glassy carbon electrodes. Current production is correlated to chain length and headgroup of the monolayer molecules as expected. Relative to graphite, the coated gold electrodes achieve more reproducible experimental conditions and certain headgroups enhance electronic coupling to the bacteria.

Chitosan scaffolds for biomolecular assembly: coupling nucleic acid probes for detecting hybridization.

Chitosan, a naturally occurring biopolymer, was used as a scaffold for the covalent binding of single-stranded DNA oligonucleotide probes in a fluorescence-based nucleic acid hybridization assay. Chitosan's pH dependent chemical and electrostatic properties enable its deposition on electrodes and metal surfaces, as well as on the bottom of microtiter plates. A combinatorial 96-well microtiter plate format was used to optimize chemistries and reaction conditions leading to hybridization experiments. We found the coupling of oligonucleotides using relatively common glutaraldehyde chemistry was quite robust. Our hybridization results for complementary ssDNA oligonucleotides (E. coli dnaK sequences) demonstrated linear fluorescence intensity with concentration of E. coli dnaK-specific oligonucleotide from 0.73 microM to 6.6 microM. Moreover, hybridization assays were specific as there was minimal fluorescence associated with noncomplementary groEL oligonucleotide. Finally, these results demonstrate the portability of a DNA hybridization assay based on covalent coupling to chitosan, which, in turn, can be deposited onto various surfaces. More arduous surface preparation techniques involving silanizing agents and hazardous washing reagents are eliminated using this technique.