Cooperation in bioluminescence: understanding the role of autoinducers by a stochastic random resistor model

Quorum sensing is a communication mechanism adopted by different bacterial strains for the regulation of gene transcription. It takes place through the exchange of molecules called autoinducers. Bioluminescence is an emergent threshold phenomenon shown by some bacteria strains. Its precise relationship to quorum sensing is a debated topic, particularly regarding the role of the different autoinducers used by bacteria. In this paper, assuming a direct relationship between bioluminescence and quorum sensing, we investigate the role of multiple autoinducers in the bioluminescence response of Vibrio harveyi, considered as a model bioluminescent strain, due to its quorum sensing circuitry involving an array of three different autoinducers. Experiments on mutants of this bacterium, obtained by suppression of one or more autoinducers, reveal their relative non-trivial relevance and cooperative interaction patterns. The proposed analysis is implemented on a regular lattice, whose nodes represent microbial entities equipped with charges, which represent the ability to up/down regulate the gene expression. Quorum sensing results from a Coulomb-type field, produced by the charges. In analogy with random resistor network models, the lattice is permeated by an effective current which accounts for the amount and distribution of the charges. We propose that the presence of different autoinducers correspond to a different up/down regulation of gene expression, i.e., to a different way to account for the charges. Then, by introducing a modulation of the charge dependence into the current flowing within the network, we show that it is able to describe the bioluminescence exhibited by V. harveyi mutants. Furthermore, modulation of the charge dependence allows the interactions between the different autoinducers to be taken into account, providing a prediction regarding the data obtainable under specific growth conditions.

TBA for Sensing Toxic Cations: A Critical Analysis of Structural and Electrical Properties

Food and drinks can be contaminated with pollutants such as lead and strontium, which poses a serious danger to human health. For this reason, a number of effective sensors have been developed for the rapid and highly selective detection of such contaminants. TBA, a well-known aptamer developed to selectively target and thereby inhibit the protein of clinical interest α-thrombin, is receiving increasing attention for sensing applications, particularly for the sensing of different cations. Indeed, TBA, in the presence of these cations, folds into the stable G-quadruplex structure. Furthermore, different cations produce small but significant changes in this structure that result in changes in the electrical responses that TBA can produce. In this article, we give an overview of the expected data regarding the use of TBA in the detection of lead and strontium, calculating the expected electrical response using different measurement techniques. Finally, we conclude that TBA should be able to detect strontium with a sensitivity approximately double that achievable for lead.

MEED: A novel robust contrast enhancement procedure yielding highly-convergent thresholding of biofilm images

Morphological and statistical investigation of biofilm images may be even more critical than the image acquisition itself, in particular in the presence of morphologically complex distributions, due to the unavoidable impact of the measurement technique too. Hence, digital image pre-processing is mandatory for reliable feature extraction and enhancement preliminary to segmentation. Also, pattern recognition in automated deep learning (both supervised and unsupervised) models often requires a preliminary effective contrast-enhancement. However, no universal consensus exists on the optimal contrast enhancement approach. This paper presents and discusses a new general, robust, reproducible, accurate and easy to implement contrast enhancement procedure, briefly named MEED-procedure, able to work on images with different bacterial coverages and biofilm structures, coming from different imaging instrumentations (herein stereomicroscope and transmission microscope). It exploits a proper succession of basic morphological operations (erosion and dilation) and a horizontal line structuring element, to minimize the impact on size and shape of the even finer bacterial features. It systematically enhances the objects of interest, without histogram stretching and/or undesirable artifacts yielded by common automated methods. The quality of the MEED-procedure is ascertained by segmentation tests which demonstrate its robustness regarding the determination of threshold and convergence of the thresholding algorithm. Extensive validation tests over a rich image database, comparison with the literature and comprehensive discussion of the conceptual background support the superiority of the MEED-procedure over the existing methods and demonstrate it is not a routine application of morphological operators.

Aptamers Which Target Proteins: What Proteotronics Suggests to Pharmaceutics

Aptamers represent a challenging field of research, relevant for diagnosis in macular degeneration, cancer, thrombosis and many inflammatory diseases, and promising in drug discovery and development. Their selection is currently performed by a stable in vitro technology, namely, SELEX. Furthermore, computationalstatistical tools have been developed to complement the SELEX selection; they work both in the preliminary stage of selection, by designing high affinity aptamers for the assigned target, and also in the final stage, analyzing the features of the best performers to implement the selection technique further. A massive use of the in silico approach is, at present, only restricted by the limited knowledge of the specific aptamer-target topology. Actually, only about fifty X-ray structures of aptamer-protein complexes have been experimentally resolved, highlighting how this knowledge has to be improved. The structure of biomolecules like aptamer-protein complexes can be represented by networks, from which several parameters can be extracted. This work briefly reviews the literature, discussing if and how general network parameters in the framework of Proteotronics and graph theory (such as electrical features, link number, free energy change, and assortativity), are important in characterizing the complexes, anticipating some features of the biomolecules. To better explain this topic, a case-study is proposed, constituted by a set of anti-angiopoietin (Ang2) aptamers, whose performances are known from the experiments, and for which two different types of conformers were predicted. A topological indicator is proposed, named Möbius (M), which combines local and global information, and seems able to discriminate between the two possible types of conformers, so that it can be considered as a useful complement to the in vitro screening for pharmaceutical aims.

Assessing the Quality of in Silico Produced Biomolecules: The Discovery of a New Conformer

The computational procedures for predicting the 3D structure of aptamers interacting with different biological molecules have gained increasing attention in recent years. The information acquired through these methods represents a crucial input for research, especially when relevant crystallographic data are not available. A number of software programs able to perform macromolecular docking are currently accessible, leading to the prediction of the quaternary structure of complexes formed by two or more interacting biological macromolecules. Nevertheless, the scoring protocols employed for ranking the candidate structures do not always produce satisfactory results, making difficult the identification of structures that are most likely to occur in nature. In this paper, we propose a novel procedure to improve the predictive performances of computational scoring protocols, using a maximum likelihood estimate based on topological and electrical properties of interacting biomolecules. The reliability of the new computational approach, enabling the ranking of aptamer-protein configurations produced by an open source docking program, has been assessed by its successful application to a set of antiangiopoietin aptamers, for which experimental data highlighting the sequence-dependent affinity toward the target protein are available. The procedure led to the identification of two main types of aptamer conformers involved in angiopoietin binding. Interestingly, one of these reproduces the arrangement of angiopoietin with its natural target, tyrosine kinase, while the other one is completely unexpected. The possible scenarios related to these results have been discussed. The methodology here described can be used to refine the outcomes of different computational procedures and can be applied to a wide range of biological molecules, thus representing a new tool for guiding the design of bioinspired sensors with enhanced selectivity.

Hierarchy and Assortativity as New Tools for Binding-Affinity Investigation: The Case of the TBA Aptamer-Ligand Complex

Aptamers are single stranded DNA, RNA, or peptide sequences having the ability to bind several specific targets (proteins, molecules as well as ions). Therefore, aptamer production and selection for therapeutic and diagnostic applications is very challenging. Usually, they are generated in vitro, although computational approaches have been recently developed for the in silico production. Despite these efforts, the mechanism of aptamer-ligand formation is not completely clear, and producing high-affinity aptamers is still quite difficult. This paper aims to develop a computational model able to describe aptamer-ligand affinity. Topological tools, such as the conventional degree distribution, the rank-degree distribution (hierarchy), and the node assortativity are employed. In doing so, the macromolecules tertiary-structures are mapped into appropriate graphs. These graphs reproduce the main topological features of the macromolecules, by preserving the distances between amino acids (nucleotides). Calculations are applied to the thrombin binding aptamer (TBA), and the TBA-thrombin complex produced in the presence of Na⁺ or K⁺. The topological analysis is able to detect several differences between complexes obtained in the presence of the two cations, as expected by previous investigations. These results support graph analysis as a novel computational tool for testing affinity. Otherwise, starting from the graphs, an electrical network can be obtained by using the specific electrical properties of amino acids and nucleobases. Therefore, a further analysis concerns with the electrical response, revealing that the resistance is sensitively affected by the presence of sodium or potassium, thus suggesting resistance as a useful physical parameter for testing binding affinity.

A validation strategy for in silico generated aptamers

The selection of high-affinity aptamers is of paramount interest for clinical and technological applications. A novel strategy is proposed to validate the reliability of the 3D structures of a group of anti- Angiopoietin-2 aptamers, produced in silico by using free software. In a previous literature these aptamers were processed both in vitro and in silico, by using an approach different from that here presented, and finally tested with a SPS experiment. Computational expectations and experimental outcomes did not agree. The procedure here proposed consists of three steps: a. the production of a large set of conformations for each candidate aptamer; b. the rigid docking upon the receptor; c. the topological and electrical characterization of the products. Steps a. and b. allow a global binding score of the ligand-receptor complexes based on the distribution of the "effective affinity", i.e. the sum of the conformational and the docking energies. Step c. employs a complex network approach (Proteotronics) to characterize the electrical properties of the aptamers and the ligand-receptor complexes. Finally, the results are discussed and compared with the literature on the same aptamers. The computational predictions are in good agreement with the known experimental measurements.

Modeling the microscopic electrical properties of thrombin binding aptamer (TBA) for label-free biosensors

Aptamers are chemically produced oligonucleotides, able to bind a variety of targets such as drugs, proteins and pathogens with high sensitivity and selectivity. Therefore, aptamers are largely employed for producing label-free biosensors (aptasensors), with significant applications in diagnostics and drug delivery. In particular, the anti-thrombin aptamers are biomolecules of high interest for clinical use, because of their ability to recognize and bind the thrombin enzyme. Among them, the DNA 15-mer aptamer (TBA), has been widely explored around the possibility of using it in aptasensors. This paper proposes a microscopic model of the electrical properties of TBA and of the aptamer-thrombin complex, combining information from both structure and function, following the issues addressed in an emerging branch of electronics known as proteotronics. The theoretical results are compared and validated with measurements reported in the literature. Finally, the model suggests resistance measurements as a novel tool for testing aptamer-target affinity.

Duality and reciprocity of fluctuation-dissipation relations in conductors

By analogy with linear response, we formulate the duality and reciprocity properties of current and voltage fluctuations expressed by Nyquist relations, including the intrinsic bandwidths of the respective fluctuations. For this purpose, we individuate total-number and drift-velocity fluctuations of carriers inside a conductor as the microscopic sources of noise. The spectral densities at low frequency of the current and voltage fluctuations and the respective conductance and resistance are related in a mutually exclusive way to the corresponding noise source. The macroscopic variances of current and voltage fluctuations are found to display a dual property via a plasma conductance that admits a reciprocal plasma resistance. Analogously, the microscopic noise sources are found to obey a dual property and a reciprocity relation. The formulation is carried out in the frame of the grand canonical (for current noise) and canonical (for voltage noise) ensembles, and results are derived that are valid for classical as well as degenerate statistics, including fractional exclusion statistics. The unifying theory so developed sheds new light on the microscopic interpretation of dissipation and fluctuation phenomena in conductors. In particular, it is proven that for fermions, as a consequence of the Pauli principle, nonvanishing single-carrier velocity fluctuations at zero temperature are responsible for diffusion but not for current noise, which vanishes in this limit.

Critical behavior in a stochastic model of vector mediated epidemics

The extreme vulnerability of humans to new and old pathogens is constantly highlighted by unbound outbreaks of epidemics. This vulnerability is both direct, producing illness in humans (dengue, malaria), and also indirect, affecting its supplies (bird and swine flu, Pierce disease, and olive quick decline syndrome). In most cases, the pathogens responsible for an illness spread through vectors. In general, disease evolution may be an uncontrollable propagation or a transient outbreak with limited diffusion. This depends on the physiological parameters of hosts and vectors (susceptibility to the illness, virulence, chronicity of the disease, lifetime of the vectors, etc.). In this perspective and with these motivations, we analyzed a stochastic lattice model able to capture the critical behavior of such epidemics over a limited time horizon and with a finite amount of resources. The model exhibits a critical line of transition that separates spreading and non-spreading phases. The critical line is studied with new analytical methods and direct simulations. Critical exponents are found to be the same as those of dynamical percolation.

Current-voltage characteristics of seven-helix proteins from a cubic array of amino acids

The electrical properties of a set of seven-helix transmembrane proteins, whose space arrangement [three-dimensional (3D) structure] is known, are investigated by using regular arrays of the amino acids. These structures, specifically cubes, have topological features similar to those shown by the chosen proteins. The theoretical results show a good agreement between the predicted current-voltage characteristics obtained from a cubic array and those obtained from a detailed 3D structure. The agreement is confirmed by available experiments on bacteriorhodopsin. Furthermore, all the analyzed proteins are found to share the same critical behavior of the voltage-dependent conductance and of its variance. In particular, the cubic arrangement evidences a short plateau of the excess conductance and its variance at high voltages. The results of the present investigation show the possibility to predict the I-V characteristics of a multiple-protein sample even in the absence of detailed knowledge of the proteins' 3D structure.

Mechanisms responsible for the photocurrent in bacteriorhodopsin

Recently, there has been growing interest in the electrical properties of bacteriorhodopsin (bR), a protein belonging to the transmembrane protein family. Several experiments pointed out the role of green light in enhancing the current flow in nanolayers of bR, thus confirming potential applications of this protein in the field of optoelectronics. By contrast, the mechanisms underlying the charge transfer and the associated photocurrent are still far from being understood at a microscopic level. To take into account the structure-dependent nature of the current, in a previous set of papers we suggested a mechanism of sequential tunneling among neighboring amino acids. As a matter of fact, when irradiated with green light, bR undergoes a conformational change at a molecular level. Thus, the role played by the protein tertiary-structure in modeling the charge transfer cannot be neglected. The aim of this paper is to go beyond previous models, in the framework of a new branch of electronics we call proteotronics, which exploits the ability of using proteins as reliable, well-understood materials for the development of novel bioelectronic devices. In particular, the present approach assumes that the conformational change is not the unique transformation the protein undergoes when irradiated by light. Instead, the light can also promote an increase of the protein state free energy that, in turn, should modify its internal degree of connectivity. This phenomenon is here described by the change of the value of an interaction radius associated with the physical interactions among amino acids. The implemented model enables us to achieve a better agreement between theory and experiments in the region of a low applied bias by preserving the level of agreement at high values of applied bias. Furthermore, results provide new insights on the mechanisms responsible for bR photoresponse.

Photoreceptors for a light biotransducer: a comparative study of the electrical responses of two (type-1) opsins

The increasing interest in photoactivated proteins as natural replacements for standard inorganic materials in photocells leads to the comparison analysis of bacteriorhodopsin and proteorhodopsin, two widely diffused proteins belonging to the family of type-1 opsins. These proteins share similar behaviors but exhibit relevant differences in the sequential chain of the amino acids constituting their tertiary structure. The use of an impedance network analog to model the protein main features provides a microscopic interpretation of a set of experiments on their photo-conductance properties. In particular, this model links the protein electrical responses to the tertiary structure and to the interactions between neighboring amino acids. The same model is also used to predict the small-signal response in terms of the Nyquist plot. Interestingly, these rhodopsins are found to behave like a wide-gap semiconductor with intrinsic conductivities of the order of 10⁻⁷ S cm⁻¹.

Evidence of Gumbel distributions of conductance fluctuations in bacteriorhodopsin thin films

By considering a set of experiments carried out on bacteriorhodopsin in vitro by Casuso et al (2007 Phys. Rev. E 76 041919), we extract the conductance as function of the applied voltage. The microscopic interpretation of experiments shows that charge transfer is ruled by a direct tunneling (DT) mechanism at low bias and by a Fowler–Nordheim (FN) tunneling mechanism at high bias. A nucleation region at the cross-over between the DT and FN regimes can be identified. A theoretical analysis of conductance fluctuations is performed by calculating the corresponding variance and the probability density functions (PDFs): these constitute a powerful indicator in order to understand the internal dynamics of the system. Conductance fluctuations are non-Gaussian and follow well the standard generalized Gumbel distributions G(a). In particular, at low bias, the PDFs are bimodal and can be resolved in at least a couple of G(a) functions with different values of the shape parameter a. The nucleation region is characterized by a single Gumbel distribution, G(1). At increasing bias, the G(1) distribution turns in a bimodal distribution. We discuss possible correlations between the voltage dependence of the G(a) and the microscopic mechanisms that determine the electrical response of the system.

The electrical properties of olfactory receptors in the development of biological smell sensors

We present here the results of the investigation of the electrical properties of two olfactory receptors (ORs): rat, OR I7, and human, OR 17-40, which are of interest in the creation of smell nanobiosensors. Described here is our investigation comparing the results from experiments using electrochemical impedance spectroscopy with the theoretical predictions obtained from a recently developed impedance network protein analog. The changes in the OR response following excitation correlated with the protein conformational change. The satisfactory agreement between theory and experiment points to a promising development of a new class of nanobiosensors based on the electrical properties of sensing proteins.

Charge transport in purple membrane monolayers: a sequential tunneling approach

Current-voltage (I-V) characteristics in proteins are sensitive to conformational changes induced by an external stimulus (photons, chemical, etc.). This sensitivity can be used in medical and industrial applications as well as shedding new light on the microscopic structure of biological materials. Here, we show that a sequential tunneling model of carrier transfer between neighboring amino acids in a single protein is the basic mechanism responsible for the electrical properties measured over a wide range of applied potentials. We also show that such a strict correlation between the protein structure and the electrical response can lead to a new generation of nanobiosensors that mimic the sensorial activity of living species. To demonstrate the potential usefulness of protein electrical properties, we provide a microscopic interpretation of recent I-V experiments carried out in bacteriorhodopsin at a nanoscale length.

Role of topology in electrical properties of bacterio-rhodopsin and rat olfactory receptor I7

We report on electrical properties of the two sensing proteins: bacteriorhodopsin and rat olfactory receptor OR-I7. As relevant transport parameters we consider the small-signal impedance spectrum and the static current-voltage characteristics. Calculations are compared with available experimental results and the model predictability is tested for future perspectives.

A network model to correlate conformational change and the impedance spectrum of single proteins

Integrated nanodevices based on proteins or biomolecules are attracting increasing interest in today's research. In fact, it has been shown that proteins such as azurin and bacteriorhodopsin manifest some electrical properties that are promising for the development of active components of molecular electronic devices. Here we focus on two relevant kinds of protein: bovine rhodopsin, prototype of G-protein-coupled-receptor (GPCR) proteins, and the enzyme acetylcholinesterase (AChE), whose inhibition is one of the most qualified treatments of Alzheimer's disease. Both these proteins exert their function starting with a conformational change of their native structure. Our guess is that such a change should be accompanied with a detectable variation of their electrical properties. To investigate this conjecture, we present an impedance network model of proteins, able to estimate the different impedance spectra associated with the different configurations. The distinct types of conformational change of rhodopsin and AChE agree with their dissimilar electrical responses. In particular, for rhodopsin the model predicts variations of the impedance spectra up to about 30%, while for AChE the same variations are limited to about 10%, which supports the existence of a dynamical equilibrium between its native and complexed states.

A novel detection strategy for odorant molecules based on controlled bioengineering of rat olfactory receptor I7

In this study, we report a dose-dependent detection of odorant molecules in solution by rat olfactory receptor I7 (OR I7) in its membrane fraction. The OR I7 is immobilized on a gold electrode by multilayer bioengineering based on a mixed self-assembled monolayer and biotin/avidin system, which allows for a well-controlled immobilization of the bioreceptor within its lipid environment. The odorant detection is electronically performed in a quantitative manner by electrochemical impedance spectroscopy (EIS) measurements on samples and controls.

Immobilization of rhodopsin on a self-assembled multilayer and its specific detection by electrochemical impedance spectroscopy

Rhodopsin, the G protein-coupled receptor (GPCR) which mediates the sense of vision, was prepared from calf eyes and used as receptor enriched membrane fraction. In this study it was immobilized onto gold electrode by two different techniques: Langmuir-Blodgett (LB) and a strategy based on a self-assembled multilayer. We demonstrated that Langmuir and LB films of rhodopsin are not stable. Thus, in this study a new protein multilayer was prepared on gold electrode by building up layer-by-layer a self-assembled multilayer. It is composed of a mixed self-assembled monolayer formed by MHDA and biotinyl-PE, followed by a biotin-avidin system which allows binding of biotinylated antibody specific to rhodopsin. The immobilization of rhodopsin in membrane fraction, by the specific antibody bound previously on self-assembled multilayer, was monitored with electrochemical impedance spectroscopy (EIS). In addition, the specificity and sensitivity of this self-assembled multilayer system to the presence of rhodopsin were investigated. No effect was observed when the system was in contact with olfactory receptor I7 in membrane fraction used for control measurements. All these results demonstrate that rhodopsin can be immobilized efficiently, specifically, quantitatively and stably on gold electrode through the self-assembled multilayer.

Resistance and resistance fluctuations in random resistor networks under biased percolation

We consider a two-dimensional random resistor network (RRN) in the presence of two competing biased processes consisting of the breaking and recovering of elementary resistors. These two processes are driven by the joint effects of an electrical bias and of the heat exchange with a thermal bath. The electrical bias is set up by applying a constant voltage or, alternatively, a constant current. Monte Carlo simulations are performed to analyze the network evolution in the full range of bias values. Depending on the bias strength, electrical failure or steady state are achieved. Here we investigate the steady state of the RRN focusing on the properties of the non-Ohmic regime. In constant-voltage conditions, a scaling relation is found between <R>/<R>(0) and V/V(0), where <R> is the average network resistance, <R>(0) the linear regime resistance, and V0 the threshold value for the onset of nonlinearity. A similar relation is found in constant-current conditions. The relative variance of resistance fluctuations also exhibits a strong nonlinearity whose properties are investigated. The power spectral density of resistance fluctuations presents a Lorentzian spectrum and the amplitude of fluctuations shows a significant non-Gaussian behavior in the prebreakdown region. These results compare well with electrical breakdown measurements in thin films of composites and of other conducting materials.