Direct and Fast Assessment of Antimicrobial Surface Activity Using Molecular Dynamics Simulation and Time-Lapse Imaging.

With the alarming rise of antimicrobial resistance, studies on bacteria-surface interactions are both relevant and timely. Scanning electron microscopy and colony forming unit counting are commonly used techniques but require sophisticated sample preparation and long incubation time. Here, we present a direct method based on molecular dynamics simulation of nanostructured surfaces providing in silico predictions, complemented with time-lapse fluorescence imaging to study live interactions of bacteria at the membrane-substrate level. We evaluate its effectiveness in predicting and statistically analyzing the temporal evolution and spatial distribution of prototypical bacteria with costained nucleoids and membranes (E. coli) on surfaces with nanopillars. We observed cell reorientation, clustering, membrane damage, growth inhibition, and in the extreme case of hydrocarbon-coated nanopillars, this was followed by cell disappearance, validating the obtained simulation results. Contrary to commonly used experimental methods, microscopy data are fast processed, in less than 1 h. In particular, the bactericidal effects can be straightforwardly detected and correlated with surface morphology and/or wettability.

Effects of fullerene on lipid bilayers displaying different liquid ordering: a coarse-grained molecular dynamics study.

BACKGROUND: The toxic effects and environmental impact of nanomaterials, and in particular of Fullerene particles, are matters of serious concern. It has been reported that fullerene molecules enter the cell membrane and occupy its hydrophobic region. Understanding the effects of carbon-based nanoparticles on biological membranes is therefore of critical importance to determine their exposure risks. METHODS: We report on a systematic coarse-grained molecular dynamics study of the interaction of fullerene molecules with simple model cell membranes. We have analyzed bilayers consisting of lipid species with different degrees of unsaturation and a variety of cholesterol fractions. Addition of fullerene particles to phase-segregated ternary membranes is also investigated in the context of the lipid raft model for the organization of the cell membrane. RESULTS: Fullerene addition to lipid membranes modifies their structural properties like thickness, area and internal ordering of the lipid species, as well as dynamical aspects such as molecular diffusion and cholesterol flip-flop. Interestingly, we show that phase-segregating ternary lipid membranes accumulate fullerene molecules preferentially in the liquid-disordered domains promoting phase-segregation and domain alignment across the membrane. CONCLUSIONS: Lipid membrane internal ordering determines the behavior and distribution of fullerene particle, and this, in turn, determines the influence of fullerene on the membrane. Lipid membranes are good solvents of fullerene molecules, and in particular those with low internal ordering. GENERAL SIGNIFICANCE: Preference of fullerene molecules to be dissolved in the more disordered hydrophobic regions of a lipid bilayer and the consequent alteration of its phase behavior may have important consequences on the activity of biological cell membranes and on the bioconcentration of fullerene in living organisms.

Lipid Vesicle Interaction with Hydrophobic Surfaces: A Coarse-Grained Molecular Dynamics Study.

Active surfaces are presently tailored to cause specific effects on living cells, which can be useful in many fields. Their development requires the understanding of the molecular mechanisms of interaction between lipid-enveloped entities and solid surfaces. Here, using coarse-grained molecular dynamics simulations, we have analyzed the different interaction modes of coated substrates with lipid vesicles that mimic biological envelopes. For neutral and hydrophobically functionalized substrates, three action modes on contacting vesicles have been obtained including intact, partially broken, and completely destroyed vesicles. The molecular mechanisms for each interaction pathway and the corresponding energy balances have been analyzed in detail. Interestingly, we have shown that any specific action mode can be obtained by appropriately tailoring the wetting characteristics of the surface coating. In particular, we have shown that surfaces that are simultaneously hydrophobic and oleophilic are optimal to fully disrupt the contacting vesicle lipid bilayer.

Ultrasensitive interferometric on-chip microscopy of transparent objects.

Light microscopes can detect objects through several physical processes, such as scattering, absorption, and reflection. In transparent objects, these mechanisms are often too weak, and interference effects are more suitable to observe the tiny refractive index variations that produce phase shifts. We propose an on-chip microscope design that exploits birefringence in an unconventional geometry. It makes use of two sheared and quasi-overlapped illuminating beams experiencing relative phase shifts when going through the object, and a complementary metal-oxide-semiconductor image sensor array to record the resulting interference pattern. Unlike conventional microscopes, the beams are unfocused, leading to a very large field of view (20 mm(2)) and detection volume (more than 0.5 cm(3)), at the expense of lateral resolution. The high axial sensitivity (<1 nm) achieved using a novel phase-shifting interferometric operation makes the proposed device ideal for examining transparent substrates and reading microarrays of biomarkers. This is demonstrated by detecting nanometer-thick surface modulations on glass and single and double protein layers.

Functionalized Surfaces with Tailored Wettability Determine Influenza A Infectivity.

Surfaces contaminated with pathogenic microorganisms contribute to their transmission and spreading. The development of "active surfaces" that can reduce or eliminate this contamination necessitates a detailed understanding of the molecular mechanisms of interactions between the surfaces and the microorganisms. Few studies have shown that, among the different surface characteristics, the wetting properties play an important role in reducing virus infectivity. Here, we systematically tailored the wetting characteristics of flat and nanostructured glass surfaces by functionalizing them with alkyl- and fluoro-silanes. We studied the effects of these functionalized surfaces on the infectivity of Influenza A viruses using a number of experimental and computational methods including real-time fluorescence microscopy and molecular dynamics simulations. Overall, we show that surfaces that are simultaneously hydrophobic and oleophilic are more efficient in deactivating enveloped viruses. Our results suggest that the deactivation mechanism likely involves disruption of the viral membrane upon its contact with the alkyl chains. Moreover, enhancing these specific wetting characteristics by surface nanostructuring led to an increased deactivation of viruses. These combined features make these substrates highly promising for applications in hospitals and similar infrastructures where antiviral surfaces can be crucial.

Microcontact printing and microspotting as methods for direct protein patterning on plasma deposited polyethylene oxide: application to stem cell patterning.

Two methods for protein patterning on antifouling surfaces have been applied to analyze the density and bioactivity of the proteins after deposition. Microcontact printing has been used as a technique to transfer fibronectin through conformal contact, while piezoelectric deposition has been employed as a non-contact technique for producing arrays of fibronectin (FN). Plasma deposited polyethylene oxide-like (PEO-like) films have been used as non-fouling background to achieve the bioadhesive/biorepellent surface contrast. Both patterning methods allow the direct fabrication of protein arrays on a non-fouling substrate, and the subsequent formation of a pattern of stem cells by cell attachment on the arrayed substrates. Microcontact printing produced fully packed homogeneous fibronectin patterns, much denser than microspotted patterns. Both printing and spotting technologies generated functional protein arrays, their bioactivity being primarily modulated by the density of the deposited protein layer. Optimization of the FN parameters used for deposition has lead to the achievement of high-quality microarrays with large population of neural stem cells immobilized in the patterns in serum-free conditions, where cells exhibit a more homogeneous starting population and factors influencing fate decisions can be more easily tracked. The immunorecognition of fibronectin targeted antibodies, as well as the cell density, increase with the protein density up to a saturation point. Over 100 ng/cm² of fibronectin on the surface leads to a decrease in the number of attached cells and a raise of cell spreading.

Recent advances in analytical and bioanalysis applications of noble metal nanorods.

In the last decade the use of anisotropic nanoparticles in analytical and bioanalytical applications has increased substantially. In particular, noble metal nanorods have unique optical properties that have attracted the interest of many research groups. The localized surface plasmon resonance (LSPR) generated by interaction of light at a specific wavelength with noble metal nanoparticles was found to depend on particle size and shape and on the constituting material and the surrounding dielectric solution. Because of their anisotropic shape, nanorods are characterized by two LSPR peaks: the transverse, fixed at approximately 530 nm, and the longitudinal, which is in the visible-near infra-red region of the spectrum and varies with nanorod aspect ratio. The intense surface plasmon band enables nanorods to absorb and scatter light in the visible and near infra-red regions, and fluorescence and two-photon induced luminescence are also observed. These optical properties, with the reactivity towards binding events that induce changes in the refractive index of the surrounding solution, make nanorods a useful tool for tracking binding events in different applications, for example assembly, biosensing, in-vivo targeting and imaging, and single-molecule detection by surface-enhanced Raman spectroscopy. This review presents the promising strategies proposed for functionalizing gold nanorods and their successful use in a variety of analytical and biomedical applications.

pH-dependent immobilization of proteins on surfaces functionalized by plasma-enhanced chemical vapor deposition of poly(acrylic acid)- and poly(ethylene oxide)-like films.

The interaction of the proteins bovine serum albumin (BSA), lysozyme (Lys), lactoferrin (Lf), and fibronectin (Fn) with surfaces of protein-resistant poly(ethylene oxide) (PEO) and protein-adsorbing poly(acrylic acid) (PAA) fabricated by plasma-enhanced chemical vapor deposition has been studied with quartz crystal microbalance with dissipation monitoring (QCM-D). We focus on several parameters which are crucial for protein adsorption, i.e., the isoelectric point (pI) of the proteins, the pH of the solution, and the charge density of the sorbent surfaces, with the zeta-potential as a measure for the latter. The measurements reveal adsorption stages characterized by different segments in the plots of the dissipation vs frequency change. PEO remains protein-repellent for BSA, Lys, and Lf at pH 4-8.5, while weak adsorption of Fn was observed. On PAA, different stages of protein adsorption processes could be distinguished under most experimental conditions. BSA, Lys, Lf, and Fn generally exhibit a rapid initial adsorption phase on PAA, often followed by slower processes. The evaluation of the adsorption kinetics also reveals different adsorption stages, whereas the number of these stages does not always correspond to the structurally different phases as revealed by the D- f plots. The results presented here, together with information obtained in previous studies by other groups on the properties of these proteins and their interaction with surfaces, allow us to develop an adsorption scenario for each of these proteins, which takes into account electrostatic protein-surface and protein-protein interaction, but also the pH-dependent properties of the proteins, such as shape and exposure of specific domains.

DNA immobilisation procedures for surface plasmon resonance imaging (SPRI) based microarray systems.

Two different surface chemistries have been studied for the development of surface plasmon resonance imaging (SPRI) based DNA microarray affinity sensors: (1) 11-mercaptoundecanoic acid-poly(ethylenimine) (MUA-PEI) and (2) dextran procedures. The MUA-PEI method consists of assembling a multilayer on the basis of electrostatic interactions formed with: 11-mercaptoundecanoic acid (MUA), poly(ethylenimine) (PEI) and extravidin layers. The dextran procedure involves assembling a multilayer formed with 11-mercaptoundecanol, dextran and streptavidin layers, which are linked by covalent bonds. The oligonucleotide probes are immobilised onto the sensor surface as spots forming a matrix 14x14, which is spotted by a robot, while the target sequences are free in solution. The system allows the interaction (hybridisation) monitoring, in real-time and in parallel, of unlabeled oligonucleotide solution targets to oligonucleotide probes immobilised on a 196 spots matrix. Using oligonucleotides as probes and targets, both functionalised surfaces have been evaluated in view of their application to the diagnosis of gene mutations involved in human diseases. In particular, we demonstrate the ability to detect, in parallel, several mutations causing human cystic fibrosis (CF), which lie within exon 10 of the human cystic fibrosis transmembrane conductance regulator (CFTR) gene. The immobilised probes were complementary to sequences corresponding the mutant or wild type alleles. Two deletions of three bases (DeltaF508 and DeltaI507) and four single nucleotide polymorphisms (M470V, Q493X, V520F and 1716 G>A) were investigated. In both functionalised surfaces, the system showed the capacity to discriminate normal and mutant sequences differing by a single base.

Surface plasmon resonance imaging as a multidimensional surface characterization instrument--application to biochip genotyping.

Surface plasmon resonance imaging (SPRI) sensors allow the characterization of a metal/dielectric interface. Providing proper biochemical functionalization and spatial structuration of the functionalized surface, an optical biochip system--label free and real time--can be achieved. We study the impact of the different physical parameters on the quality of the measurements. Such a SPRI system has a great sensitivity to small variations of the physical parameters (layer optical index, thickness, etc.) occurring at the sensor surface. Precision and reliability of the measurements are provided by a multidimensional approach (4D i.e. spatial coordinates x-y, time t, angle of incidence theta) allowing multiple self-calibration procedures. Such apparatus has already been successfully applied in genomics and proteomics, studying DNA:DNA and oligosaccharide:protein interactions. In this article, we illustrate the advantages of the SPRI setup applied to the detection of gene mutations, using as a model the genetic disease Cystic Fibrosis. The results demonstrate that the system is able to monitor and analyse the interaction under investigation, allowing the diagnosis of genetic single nucleotide polymorphisms by exploiting only a part of the multidimensional potential (x, y, t, theta).

Direct immobilisation of DNA probes for the development of affinity biosensors.

An immobilisation procedure based on the direct coupling of thiolated probes (Probe-C6-SH) to bare gold sensor surfaces has been compared with a reference immobilisation method, based on the coupling of biotinylated probes onto a streptavidin-coated dextran-modified surface. The instrumentations used were a quartz crystal microbalance (QCM) and the optical instruments Biacore X and Spreeta based on surface plasmon resonance (SPR). The performances of the DNA-based sensors resulting from direct coupling of thiolated DNA probes onto electrodes of quartz crystals or gold SPR-chips have been studied in terms of the main analytical parameters, i.e. selectivity, sensitivity, reproducibility, etc. In particular, the two immobilisation approaches have been applied to the analysis of oligonucleotides, DNA amplified by polymerase chain reaction (PCR) and genomic DNA enzymatically digested.

Quartz crystal microbalance (QCM) affinity biosensor for genetically modified organisms (GMOs) detection.

A DNA piezoelectric sensor has been developed for the detection of genetically modified organisms (GMOs). Single stranded DNA (ssDNA) probes were immobilised on the sensor surface of a quartz crystal microbalance (QCM) device and the hybridisation between the immobilised probe and the target complementary sequence in solution was monitored. The probe sequences were internal to the sequence of the 35S promoter (P) and Nos terminator (T), which are inserted sequences in the genome of GMOs regulating the transgene expression. Two different probe immobilisation procedures were applied: (a) a thiol-dextran procedure and (b) a thiol-derivatised probe and blocking thiol procedure. The system has been optimised using synthetic oligonucleotides, which were then applied to samples of plasmidic and genomic DNA isolated from the pBI121 plasmid, certified reference materials (CRM), and real samples amplified by the polymerase chain reaction (PCR). The analytical parameters of the sensor have been investigated (sensitivity, reproducibility, lifetime etc.). The results obtained showed that both immobilisation procedures enabled sensitive and specific detection of GMOs, providing a useful tool for screening analysis in food samples.