Fluorescent Protein-Based Sensors for Detecting Essential Metal Ions across the Tree of Life.

Genetically encoded fluorescent metal ion sensors are powerful tools for elucidating metal dynamics in living systems. Over the last 25 years since the first examples of genetically encoded fluorescent protein-based calcium indicators, this toolbox of probes has expanded to include other essential and non-essential metal ions. Collectively, these tools have illuminated fundamental aspects of metal homeostasis and trafficking that are crucial to fields ranging from neurobiology to human nutrition. Despite these advances, much of the application of metal ion sensors remains limited to mammalian cells and tissues and a limited number of essential metals. Applications beyond mammalian systems and in vivo applications in living organisms have primarily used genetically encoded calcium ion sensors. The aim of this Perspective is to provide, with the support of historical and recent literature, an updated and critical view of the design and use of fluorescent protein-based sensors for detecting essential metal ions in various organisms. We highlight the historical progress and achievements with calcium sensors and discuss more recent advances and opportunities for the detection of other essential metal ions. We also discuss outstanding challenges in the field and directions for future studies, including detecting a wider variety of metal ions, developing and implementing a broader spectral range of sensors for multiplexing experiments, and applying sensors to a wider range of single- and multi-species biological systems.

Zinc-Induced Fluorescence Turn-On in Native and Mutant Phycoerythrobilin-Binding Orange Fluorescent Proteins.

Cyanobacteriochrome (CBCR)-derived fluorescent proteins are a class of reporters that can bind bilin cofactors and fluoresce across the ultraviolet to the near-infrared spectrum. Derived from phytochrome-related photoreceptor proteins in cyanobacteria, many of these proteins use a single small GAF domain to autocatalytically bind a bilin and fluoresce. The second GAF domain of All1280 (All1280g2) from Nostoc sp. PCC7120 is a DXCF motif-containing protein that exhibits blue-light-responsive photochemistry when bound to its native cofactor, phycocyanobilin. All1280g2 can also bind non-photoswitching phycoerythrobilin (PEB), resulting in a highly fluorescent protein. Given the small size, high quantum yield, and that unlike green fluorescent proteins, bilin-binding proteins can be used in anaerobic organisms, the orange fluorescent All1280g2-PEB protein is a promising platform for designing new genetically encoded metal ion sensors. Here, we show that All1280g2-PEB undergoes a ∼5-fold reversible zinc-induced fluorescence enhancement with a blue-shifted emission maximum (572 to 517 nm), which is not observed for a related PEB-bound GAF from Synechocystis sp. PCC6803 (Slr1393g3). Zn2+ significantly enhances All1280g2-PEB fluorescence across a biologically relevant pH range from 6.0 to 9.0, with pH-dependent dissociation constants from 1 µM to ∼20-80 nM. Site-directed mutants aiming to sterically decrease and increase access to PEB show a decreased and similar amount of zinc-induced fluorescence enhancement. Mutation of the cysteine residue within the DXCF motif to alanine abolishes the zinc-induced fluorescence enhancement. Collectively, these results support the presence of a unique fluorescence-enhancing Zn2+ binding site in All1280g2-PEB likely involving coordination to the bilin cofactor and requiring a nearby cysteine residue.

Zinc-Induced Fluorescence Turn-on in Native and Mutant Phycoerythrobilin-Binding Orange Fluorescent Proteins.

Cyanobacteriochrome (CBCR)-derived fluorescent proteins are a class of reporters that can bind bilin cofactors and fluoresce across the ultraviolet to near-infrared spectrum. Derived from phytochrome-related photoreceptor proteins in cyanobacteria, many of these proteins use a single small GAF domain to autocatalytically bind a bilin and fluoresce. The second GAF domain of All1280 from Nostoc sp. PCC7120 is a DXCF motif-containing protein that exhibits blue light-responsive photochemistry when bound to its native cofactor, phycocyanobilin. GAF2 can also bind non-photoswitching phycoerythrobilin (PEB), resulting in a highly fluorescent protein. Given the small size, high quantum yield, and that, unlike green fluorescent proteins, bilin-binding proteins can be used in anaerobic organisms, the orange fluorescent GAF2-PEB protein is a promising platform for designing new genetically encoded metal ion sensors. Here we show that GAF2-PEB undergoes a ∼5-fold reversible zinc-induced fluorescence enhancement with blue-shifted emission maximum (572 to 517 nm), which is not observed for a related PEB-bound GAF from Synechocystis sp. PCC6803 (Slr1393g3). Zn 2+ significantly enhances GAF2-PEB fluorescence across a biologically relevant pH range from 6.0-9.0 and with pH-dependent µM to nM dissociation constants. Site-directed mutants aiming to sterically decrease and increase access to PEB show a decreased and similar amount of zinc-induced fluorescence enhancement, respectively. Mutation of the cysteine residue within the DXCF motif to alanine abolishes zinc-induced fluorescence enhancement. Collectively, these results support the presence of a fluorescence enhancing Zn 2+ binding site in GAF2-PEB likely involving coordination to the bilin cofactor and requiring a nearby cysteine residue.

Enhancement of Inducible Nitric Oxide Synthase Activity by Low Molecular Weight Peptides Derived from Protamine: A Potential Therapy for Chronic Rhinosinusitis.

Nitric oxide (NO) is a key immune defense agent that is produced from l-arginine in the airways by leukocytes and airway epithelial cells, primarily via inducible nitric oxide synthase (iNOS). Deficiencies in nasal NO levels have been associated with diseases such as primary ciliary dyskinesia and chronic rhinosinusitis. Herein, we demonstrate a proof-of-concept regarding a potential new therapeutic approach for such disorders. We show that arginine-rich low molecular weight peptides (LMWPs) derived from the FDA-approved protamine (obtained from salmon sperm) are effective at significantly raising NO production in both RAW 264.7 mouse macrophage and LA4 mouse epithelial cell lines. LMWP is produced using a stable, easily produced immobilized thermolysin gel column followed by size-exclusion purification. Monomeric l-arginine induces concentration-dependent increases in NO production in stimulated RAW 264.7 and LA4 cells, as measured by stable nitrite in the cell media. In stimulated RAW 264.7 cells, LMWP significantly increases iNOS expression and total NO production 12-24 h post-treatment compared to cells given equivalent levels of monomeric l-arginine. For stimulated LA4 cells, LMWPs are effective in significantly increasing NO production compared to equivalent l-arginine monomer concentrations over 24 h but do not substantially enhance iNOS expression. The use of the arginase inhibitor S-boronoethyl-l-cysteine in combination with LMWPs results in even higher NO production by stimulated RAW 264.7 cells and LA4 cells. Increases in NO due to LMWPs, compared to l-arginine, occur only after 4 h, which may be due to iNOS elevation rather than increased substrate availability.

Evaluation of commercial glucometer test strips for potential measurement of glucose in tears.

Tear glucose measurements have been suggested as a potential alternative to blood glucose monitoring for diabetic patients. While previous work has reported that there is a correlation between blood and tear glucose levels in humans, this link has not been thoroughly established and additional clinical studies are needed. Herein, we evaluate the potential of using commercial blood glucose test strips to measure glucose in tears. Of several blood glucose strips evaluated, only one brand exhibits the low detection limit required for quantitating glucose in tears. Calibration of these strips in the range of 0-100 µM glucose with an applied potential of 150 mV to the working electrode yields a sensitivity of 0.127 nA/µM and a limit of quantitation (LOQ) of 9 µM. The strips also exhibit ≤13% error (n = 3) for 25, 50, and 75 µM glucose in the presence of 10 µM acetaminophen, 100 µM ascorbic acid, and 100 µM uric acid. Measurements of glucose in tears from nine normal (nondiabetic) fasting human subjects using strips yielded glucose values within the range of 5-148 µM (mean = 47 µM, median = 43 µM), similar to those for human tears reported by others with more complex LC-MS methods. The glucometer strip method could facilitate more clinical studies to determine whether tear glucose and blood glucose levels sufficiently correlate for application to routine measurements in tears to supplement blood glucose testing. This would be especially helpful for children, adolescents, other Type 1 diabetics, and also for Type 2 diabetics who require treatment with insulin and cannot tolerate multiple finger sticks per day.

Amperometric nitric oxide sensors with enhanced selectivity over carbon monoxide via platinum oxide formation under alkaline conditions.

An improved planar amperometric nitric oxide (NO) sensor with enhanced selectivity over carbon monoxide (CO), which represents a volatile interfering species for NO sensors that has been largely overlooked until recently, is described. Formation of an oxide film on the inner platinum working electrode via anodic polarization using an inner alkaline electrolyte solution provides the basis for improved selectivity. Cyclic voltammetry reveals that formation of an oxidized Pt film inhibits adsorption of CO to the electrode surface, which is a necessary initial step in the electrocatalytic oxidation of CO on Pt. Previous NO gas sensors that employ internal electrolyte solutions have been assembled using acidic internal solutions that inhibit the formation of a dense platinum oxide film on the working electrode surface. It is demonstrated herein that increasing the internal electrolyte pH promotes oxidized platinum film formation, resulting in improved selectivity over CO. Selectivity coefficients (log KNO,j) for sensors assembled with internal solutions at various pH values range from -0.08 at pH 2.0 to -2.06 at pH 11.7, with average NO sensitivities of 1.24 nA/µM and a limit of detection (LOD) of <1 nM.

Inkjet-printed gold nanoparticle electrochemical arrays on plastic. Application to immunodetection of a cancer biomarker protein.

Electrochemical detection combined with nanostructured sensor surfaces offers potentially low-cost, high-throughput solutions for detection of clinically significant proteins. Inkjet printing offers an inexpensive non-contact fabrication method for microelectronics that is easily adapted for incorporating into protein immunosensor devices. Herein we report the first direct fabrication of inkjet-printed gold nanoparticle arrays, and apply them to electrochemical detection of the cancer biomarker interleukin-6 (IL-6) in serum. The gold nanoparticle ink was printed on a flexible, heat resistant polyimide Kapton substrate and subsequently sintered to create eight-electrode arrays costing <0.2 euro per array. The inkjet-printed working electrodes had reproducible surface areas with RSD <3%. Capture antibodies for IL-6 were linked onto the eight-electrode array, and used in sandwich immunoassays. A biotinylated secondary antibody with 16-18 horseradish peroxidase labels was used, and detection was achieved by hydroquinone-mediated amperometry. The arrays provided a clinically relevant detection limit of 20 pg mL(-1) in calf serum, sensitivity of 11.4 nA pg(-1) cm(-2), and a linear dynamic range of 20-400 pg mL(-1).

Gold nanoparticles with externally controlled, reversible shifts of local surface plasmon resonance bands.

We have achieved reversible tunability of local surface plasmon resonance in conjugated polymer functionalized gold nanoparticles. This property was facilitated by the preparation of 3,4-ethylenedioxythiophene (EDOT) containing polynorbornene brushes on gold nanoparticles via surface-initiated ring-opening metathesis polymerization. Reversible tuning of the surface plasmon band was achieved by electrochemically switching the EDOT polymer between its reduced and oxidized states.

Characterization of multienzyme-antibody-carbon nanotube bioconjugates for immunosensors.

Characterization studies of a multi-enzyme-antibody-carbon nanotube bioconjugate designed for the amplification of electrochemical immunosensing are described. Secondary antibodies for prostate specific antigen (PSA) were covalently linked to highly carboxylated multi-walled carbon nanotube (CNT) along with multiple horseradish peroxidase (HRP) enzyme labels. These bioconjugates provide ultra-sensitive amperometric detection of PSA on a single-wall carbon nanotube forest sandwich immunosensor platform. A single layer of HRP on the surface of the CNT was suggested by images from atomic force microscopy (AFM) and transmission electron microscopy (TEM). HRP on the bioconjugate surface was visualized by confocal microscopy using in-situ HRP-catalyzed polymerization yielding a fluorescent product, and HRP activity was estimated in a conventional assay. Binding of quantum-dot labeled PSA to antibodies on the bioconjugate was used for visualization by TEM. Combining TEM and enzyme activity results gave estimates of approximately 82 HRPs and 30 +/- 15 secondary antibodies per 100 nm of antibody-HRP-CNT bioconjugate.

The emergence of dynamic form through phase relations in dynamical systems.

Theories of visual form have been plagued with the problem of the correspondence between aspects of the form across time and across spatial location. Following Bateson's idea that knowledge emerges from the relations among multiple flows of difference, our computational model illustrates how visual form can emerge from the phase relations between two such flows in a way that eliminates the correspondence problem. Computationally, the first flow of process in a Boolean network falls into one among many different attractor cycles each of which cycles at a given fundamental frequency. A second cyclic systemic flow, with its own frequency, is computationally necessary before a person can experience the patterns (transients, attractors) of the first flow on a computer monitor; and the frequency of this second flow is a control variable. Dynamic visual form, in this computational logic, emerges from the phase relations between the frequencies of the two flows. These dynamic forms exhibit, simultaneously, many kinds of apparent motion suggesting that the processes generating apparent motion are not merely illusions but are in the service of dynamic form perception. This model of perceptual organization and moving form is discussed in relation to other approaches.

Folding control and unfolding free energy of yeast iso-1-cytochrome c bound to layered zirconium phosphate materials monitored by surface plasmon resonance.

The free energy change (Delta G degrees ) for the unfolding of immobilized yeast iso-1-cytochrome c (Cyt c) at nanoassemblies was measured by surface plasmon resonance (SPR) spectroscopy. Data show that SPR is sensitive to protein conformational changes, and protein solid interface exerts a major influence on bound protein stability. First, Cyt c was self-assembled on the Au film via the single thiol of Cys-102. Then, crystalline sheets of layered alpha-Zr(O(3)POH)(2).H(2)O (alpha-ZrP) or Zr(O(3)PCH(2)CH(2)COOH)(2).xH(2)O (alpha-ZrCEP) were adsorbed to construct alpha-ZrP/Cyt c/Au or alpha-ZrCEP/Cyt c/Au nanoassemblies. The construction of each layer was monitored by SPR, in real time, and the assemblies were further characterized by atomic force microscopy and electrochemical studies. Thermodynamic stability of the protein nanoassembly was assessed by urea-induced unfolding. Surprisingly, unfolding is reversible in all cases studied here. Stability of Cyt c in alpha-ZrP/Cyt c/Au increased by approximately 4.3 kJ/mol when compared to the unfolding free energy of Cyt c/Au assembly. In contrast, the protein stability decreased by approximately 1.5 kJ/mol for alpha-ZrCEP/Cyt c/Au layer. Thus, OH-decorated surfaces stabilized the protein whereas COOH-decorated surfaces destabilized it. These data quantitate the role of specific functional groups of the inorganic layers in controlling bound protein stability.

Dynamic constancy as a basis for perceptual hierarchies.

Bateson's difference-based epistemology can be simulated by a Boolean network model. Bateson proposed that taking differences in differences would produce emergent hierarchies of knowledge. This study simulated Bateson's proposal by taking differences in differences in a Boolean model. The crucial result is that constancies in the dynamics of the flow of differences in the model (a) define perceptually comprehensible categories of visual forms and (b) that higher-order constancies arrange these categories into a perceptually comprehensible hierarchy. We propose Dynamic Constancy as a new Gestalt-like organizational principle in perception.

Enzyme-DNA biocolloids for DNA adduct and reactive metabolite detection by chromatography-mass spectrometry.

Silica microbead bioreactors (0.5 microm diameter) coated with DNA and enzymes were fabricated to measure reactive metabolite and DNA-adduct formation rates relevant to genotoxicity screening. Cytochrome (cyt) P450 2E1, cyt P450(cam), and myoglobin (Mb) were incorporated into thin films with DNA using the electrostatic layer-by-layer (LbL) method. The utility of these biocolloids was demonstrated by oxidation of guaiacol, styrene, and (4-methylnitrosoamino)-1-(3-pyridyl)-1-butanone (NNK). Enzyme turnover rates for formation of reactive metabolites were monitored using gas chromatography/mass spectrometry (GC/MS) and liquid chromatography-mass spectrometry (LC-MS). Capillary LC-MS/MS was employed to determine DNA nucleobase adducts after catalyzing the reactive metabolite formation with DNA-enzyme biocolloids and then using neutral thermal hydrolysis on the biocolloids. Dramatic improvements in surface area to volume ratio over similar films on macroscopic surfaces opens new avenues for genotoxicity screening and enabled the first use of pure cyt P450 enzymes in enzyme-DNA films to produce DNA adducts. The method makes possible identification and formation rate measurements of major and minor DNA adducts as well as the metabolites themselves in <5 min of reaction time using relevant human liver enzymes.

Mapping knowledge to boolean dynamic systems in Bateson's epistemology.

Gregory Bateson (1972, 1979) established an epistemology that integrates mind and nature as a necessary unity, a unity in which learning and evolution share fundamental principles and in which criteria for mental process are explicitly specified. E42 is a suite of freely available Java applets that constitute an online research lab for creating and interacting with simulations of the Boolean systems developed by Kauffman (1993) in his study of evolution where he proposed that self-organization and natural selection are co-principles "weaving the tapestry of life." This paper maps Boolean systems, developed in the study of evolution, onto Bateson's epistemology in general and onto his criteria of mental process in particular.

Open courseware and shared knowledge in higher education.

Most college and university campuses in the United States and much of the developed world today maintain one, two, or several learning management systems (LMSs), which are courseware products that provide students and faculty with Web-based tools to manage course-related applications. Since the mid-1990s, two predominant models of Web courseware management systems have emerged: commercial and noncommercial. Some of the commercial products available today were created in academia as noncommercial but have since become commercially encumbered. Other products remain noncommercial but are struggling to survive in a world of fierce commercial competition. This article argues for an ethics of pedagogy in higher education that would be based on the guiding assumptions of the non-proprietary, peer-to-peer, open-source software movement.