Machine learning method for the classification of the state of living organisms' oscillations.

The World Health Organization highlights the urgent need to address the global threat posed by antibiotic-resistant bacteria. Efficient and rapid detection of bacterial response to antibiotics and their virulence state is crucial for the effective treatment of bacterial infections. However, current methods for investigating bacterial antibiotic response and metabolic state are time-consuming and lack accuracy. To address these limitations, we propose a novel method for classifying bacterial virulence based on statistical analysis of nanomotion recordings. We demonstrated the method by classifying living Bordetella pertussis bacteria in the virulent or avirulence phase, and dead bacteria, based on their cellular nanomotion signal. Our method offers significant advantages over current approaches, as it is faster and more accurate. Additionally, its versatility allows for the analysis of cellular nanomotion in various applications beyond bacterial virulence classification.

Nanomotion Spectroscopy as a New Approach to Characterize Bacterial Virulence.

Atomic force microscopy (AFM)-based nanomotion detection is a label-free technique that has been used to monitor the response of microorganisms to antibiotics in a time frame of minutes. The method consists of attaching living organisms onto an AFM cantilever and in monitoring its nanometric scale oscillations as a function of different physical-chemical stimuli. Up to now, we only used the cantilever oscillations variance signal to assess the viability of the attached organisms. In this contribution, we demonstrate that a more precise analysis of the motion pattern of the cantilever can unveil relevant medical information about bacterial phenotype. We used B. pertussis as the model organism, it is a slowly growing Gram-negative bacteria which is the agent of whooping cough. It was previously demonstrated that B. pertussis can expresses different phenotypes as a function of the physical-chemical properties of the environment. In this contribution, we highlight that B. pertussis generates a cantilever movement pattern that depends on its phenotype. More precisely, we noticed that nanometric scale oscillations of B. pertussis can be correlated with the virulence state of the bacteria. The results indicate a correlation between metabolic/virulent bacterial states and bacterial nanomotion pattern and paves the way to novel rapid and label-free pathogenic microorganism detection assays.

Pectin-Coated Plasmonic Nanoparticles for Photodynamic Therapy: Inspecting the Role of Serum Proteins.

Plasmonic metal nanoparticles (NPs) can be used as enhancers of the efficiency of standard photosensitizers (PSs) in photodynamic therapy (PDT). Protein corona, the adsorption layer that forms spontaneously around NPs once in contact with biological fluids, determines to a great extent the efficiency of PDT. In this work, we explore the possibility that pectin-coated Au NPs (Au@Pec NPs) could act as adjuvants in riboflavin (Rf)-based PDT by comparing the photodamage in HeLa cells cultured in the presence and in the absence of the NPs. Moreover, we investigate the impact that the preincubation of Rf and Au@Pec NPs (or Ag@Pec NPs) at two very different serum concentrations could have on cell's photodamage. Because reactive oxygen species (ROS) precursors are the excited states of the PS, the effect of proteins on the photophysics of Rf and Rf/plasmonic NPs was studied by transient absorption experiments. The beneficial effect of Au@Pec NPs in Rf-based PDT on HeLa cells cultured under standard serum conditions was demonstrated for the first time. However, the preincubation of Rf and Au@Pec NPs (or Ag@Pec NPs) with serum has undesirable results regarding the enhancement of Rf-based PDT. In this sense, we also verified that more concentrated protein conditions result in lower amounts of the triplet excited state of Rf and thus an expected lower production of ROS, which are the key elements for PDT's efficacy. These findings point out the relevance of serum concentration in the design of in vitro cell culture experiments carried out to determine the best way to combine and use potential sensitizers with plasmonic NPs to develop more effective PDTs.

Binary Medical Nanofluids by Combination of Polymeric Eudragit Nanoparticles for Vehiculization of Tobramycin and Resveratrol: Antimicrobial, Hemotoxicity and Protein Corona Studies.

The development of smart nanoparticles (NPs) became a trend to enhance the delivery of drugs. In the present work, Tobramycin (TB), an aminoglycoside antibiotic that displays several undesirable side effects, has been encapsulated into cationic Eudragit®E100 (E100) NPs for the treatment of infections caused by Pseudomonas aeruginosa. Combination with neutral Eudragit®NE30D (NE30D) NPs containing resveratrol (RSV), a strong natural antioxidant, increased the antimicrobial activity of TB (75% higher than free TB). NPs were stabilized with 1.0% (w/v) poloxamer 188 (P188) or poloxamer 407 (P407) as surfactants. E100 NPs showed 83.3 ± 8.5%, and 70.1 ± 2.7 encapsulation efficiency (EE) of TB with P188 and P407 coatings, respectively. The presence of NPs was confirmed by DLS and TEM studies. TB was controlled released from NPs for 6 h. Hemotoxicity tests of NPs in the range of MIC values on human blood gave negative results. Analysis of Surface Plasmon Resonance verified that NE30D/P407/RSV does not interact with plasma proteins BSA, IgG or fibrinogen, besides E100/P188/TB interact with BSA, findings that are compatible with a negligible in vivo clearance of the nanovehicles. The obtained results show a potential binary fluid composed of two NPs to highly improve the effectiveness of conventional antibiotics.

A perspective view on the nanomotion detection of living organisms and its features.

The insurgence of newly arising, rapidly developing health threats, such as drug-resistant bacteria and cancers, is one of the most urgent public-health issues of modern times. This menace calls for the development of sensitive and reliable diagnostic tools to monitor the response of single cells to chemical or pharmaceutical stimuli. Recently, it has been demonstrated that all living organisms oscillate at a nanometric scale and that these oscillations stop as soon as the organisms die. These nanometric scale oscillations can be detected by depositing living cells onto a micro-fabricated cantilever and by monitoring its displacements with an atomic force microscope-based electronics. Such devices, named nanomotion sensors, have been employed to determine the resistance profiles of life-threatening bacteria within minutes, to evaluate, among others, the effect of chemicals on yeast, neurons, and cancer cells. The data obtained so far demonstrate the advantages of nanomotion sensing devices in rapidly characterizing microorganism susceptibility to pharmaceutical agents. Here, we review the key aspects of this technique, presenting its major applications. and detailing its working protocols.

Impact of sphingomyelin acyl chain (16:0 vs 24:1) on the interfacial properties of Langmuir monolayers: A PM-IRRAS study.

Membrane structure is a key factor for the cell`s physiology, pathology, and therapy. Evaluating the importance of lipid species such as N-nervonoyl sphingomyelin (24:1-SM) -able to prevent phase separation- to membrane structuring remains a formidable challenge. This is the first report in which polarization-modulated infrared reflection-absorption spectroscopy (PM-IRRAS) is applied to investigate the lipid-lipid interactions in 16:0 vs 24:1-SM monolayers and their mixtures with 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC) and cholesterol (Chol) (DOPC/SM/Chol 2:1:1). From the results we inferred that the cis double bond (Δ15) in 24:1-SM molecule diminishes intermolecular H-bonding and chain packing density compared to that of 16:0-SM. In ternary mixtures containing 16:0-SM, the relative intensity of the two components of the Amide I band reflected changes in the H-bonding network due to SM-Chol interactions. In contrast, the contribution of the main components of the Amide I band in DOPC/24:1-SM/Chol remained as in 24:1-SM monolayers, with a larger contribution of the non-H-bonded component. The most interesting feature in these ternary films is that the CO stretching mode of DOPC appeared with an intensity similar to that of SM Amide I band in DOPC/16:0-SM/Chol monolayers (a two-phase [Lo/Le] system), whereas an extremely low intensity of the CO band was detected in DOPC/24:1-SM/Chol monolayers (single Le phase). This is evidence that the unsaturation in 24:1-SM affected not only the conformational properties of acyl chains but also the orientation of the chemical groups at the air/water interface. The physical properties and overall H-bonding ability conferred by 24:1-SM may have implications in cell signaling and binding of biomolecules.

Phase-segregated Membrane Model assessed by a combined SPR-AFM Approach.

Model biomembranes can provide valuable insights into the properties of complex biological membranes. Among several techniques, Surface Plasmon Resonance (SPR) provides a label-free analysis of the interactions of bioactive molecules with biomembranes with an experimental setup that allows mimicking biological environments. Nevertheless, protocols that enable the preparation of stable supported membrane systems with reproducible structural and functional properties on the biosensor chip are still needed. In this work, we present a simple protocol to modify SPR substrates that allows the formation of a phase-segregated supported lipid bilayer (SLB). SLBs are formed by fusion of lipid vesicles of pure phospholipids (DMPC, DPPC and DOPC) and of a ternary mixture (DOPC/16:0 SM/Cho in 2:1:1 molar ratio) on a SPR gold sensor chip covered with a dithiothreitol monolayer. The formation of a SLB on the SPR sensing surface in a reproducible way was assessed by the combined use of the SPR technique with AFM. The interaction of a cholesterol-extracting drug with SLBs was studied as a model of membrane-lipophilic biomolecule interaction. The proposed strategy allowed us to obtain a membrane model where phase coexistence is present and where Cho depletion from ternary mixtures was comparable to the extraction results reported for human erythrocytes.

Interaction of acylated and unacylated forms of E. coli alpha-hemolysin with lipid monolayers: a PM-IRRAS study.

Uropathogenic strains of Escherichia coli produce virulence factors, such as the protein toxin alpha-hemolysin (HlyA), that enable the bacteria to colonize the host and establish an infection. HlyA is synthetized as a protoxin (ProHlyA) that is transformed into the active form in the bacterial cytosol by the covalent linkage of two fatty-acyl moieties to the polypeptide chain before the secretion of HlyA into the extracellular medium. The aim of this work was to investigate the effect of the fatty acylation of HlyA on protein conformation and protein-membrane interactions. Polarization-modulated infrared reflection-absorption spectroscopy (PM-IRRAS) experiments were performed at the air-water interface, and lipid monolayers mimicking the outer leaflet of red-blood-cell membranes were used as model systems for the study of protein-membrane interaction. According to surface-pressure measurements, incorporation of the acylated protein into the lipid films was faster than that of the nonacylated form. PM-IRRAS measurements revealed that the adsorption of the proteins to the lipid monolayers induced disorder in the lipid acyl chains and also changed the elastic properties of the films independently of protein acylation. No significant difference was observed between HlyA and ProHlyA in the interaction with the model lipid monolayers; but when these proteins became adsorbed on a bare air-water interface, they adopted different secondary structures. The assumption of the correct protein conformation at a hydrophobic-hydrophilic interface could constitute a critical condition for biologic activity.

Boundary region between coexisting lipid phases as initial binding sites for Escherichia coli alpha-hemolysin: a real-time study.

α-Hemolysin (HlyA) is a protein toxin, a member of the pore-forming Repeat in Toxin (RTX) family, secreted by some pathogenic strands of Escherichia coli. The mechanism of action of this toxin seems to involve three stages that ultimately lead to cell lysis: binding, insertion, and oligomerization of the toxin within the membrane. Since the influence of phase segregation on HlyA binding and insertion in lipid membranes is not clearly understood, we explored at the meso- and nanoscale-both in situ and in real-time-the interaction of HlyA with lipid monolayers and bilayers. Our results demonstrate that HlyA could insert into monolayers of dioleoylphosphatidylcholine/sphingomyelin/cholesterol (DOPC/16:0SM/Cho) and DOPC/24:1SM/Cho. The time course for HlyA insertion was similar in both lipidic mixtures. HlyA insertion into DOPC/16:0SM/Cho monolayers, visualized by Brewster-angle microscopy (BAM), suggest an integration of the toxin into both the liquid-ordered and liquid-expanded phases. Atomic-force-microscopy imaging reported that phase boundaries favor the initial binding of the toxin, whereas after a longer time period the HlyA becomes localized into the liquid-disordered (Ld) phases of supported planar bilayers composed of DOPC/16:0SM/Cho. Our AFM images, however, showed that the HlyA interaction does not appear to match the general strategy described for other invasive proteins. We discuss these results in terms of the mechanism of action of HlyA.

Strong correlation between molecular configurations and charge-transfer processes probed at the single-molecule level by surface-enhanced Raman scattering.

Single-molecule (SM) electrochemistry studied by surface-enhanced Raman scattering (SERS) with high spectral resolution reveals a picture in which the frequency of Raman modes is correlated with the electrochemical process through the interaction with the surface. Previously unexplored phenomena can be revealed by the synergy of electrochemistry and SM-SERS, which explores in this case subtler spectroscopic aspects (like the frequency of a vibration within the inhomogeneous broadening of a many-molecules Raman peak) to gain the information. We demonstrate, among other things, that the interaction with the surface is correlated both with the molecule vibrational frequencies and with the ability of single molecules to be reduced/oxidized at different potentials along the electrochemical cycle. Qualitative models of the interaction of molecules with surfaces are also touched upon.

Human apolipoprotein A-I natural variants: molecular mechanisms underlying amyloidogenic propensity.

Human apolipoprotein A-I (apoA-I)-derived amyloidosis can present with either wild-type (Wt) protein deposits in atherosclerotic plaques or as a hereditary form in which apoA-I variants deposit causing multiple organ failure. More than 15 single amino acid replacement amyloidogenic apoA-I variants have been described, but the molecular mechanisms involved in amyloid-associated pathology remain largely unknown. Here, we have investigated by fluorescence and biochemical approaches the stabilities and propensities to aggregate of two disease-associated apoA-I variants, apoA-IGly26Arg, associated with polyneuropathy and kidney dysfunction, and apoA-ILys107-0, implicated in amyloidosis in severe atherosclerosis. Results showed that both variants share common structural properties including decreased stability compared to Wt apoA-I and a more flexible structure that gives rise to formation of partially folded states. Interestingly, however, distinct features appear to determine their pathogenic mechanisms. ApoA-ILys107-0 has an increased propensity to aggregate at physiological pH and in a pro-inflammatory microenvironment than Wt apoA-I, whereas apoA-IGly26Arg elicited macrophage activation, thus stimulating local chronic inflammation. Our results strongly suggest that some natural mutations in apoA-I variants elicit protein tendency to aggregate, but in addition the specific interaction of different variants with macrophages may contribute to cellular stress and toxicity in hereditary amyloidosis.

Sulfidization of Au(111) from thioacetic acid: an experimental and theoretical study.

We have studied the adsorption of thioacetic acid (TAAH) on Au(111) from solution deposition. The close proximity of the SH groups to CO groups makes this molecule very attractive for exploring the effect of the functional group on the stability of the S-C and S-Au bonds. Although thioacetic acid was supposed to decompose slowly in water by hydrolysis supplying hydrogen sulfide, this behavior is not expected in nonpolar solvents such as toluene or hexane. Therefore, we have used these solvents for TAAH self-assembly on the Au(111) surface. The characterization of the adsorbates has been done by electrochemical techniques, X-ray photoelectron spectroscopy (XPS), and scanning tunneling microscopy (STM). We have found that even in nonpolar solvents thioacetic acid decomposes to S. The results have been discussed on the basis that the adsorbed species suffer a cleavage on the Au surface, leaving the S attached to it. The dissociation is a spontaneous process that reaches the final state very fast once it is energetically favorable, as can be interpreted from DFT calculations. The thioacetic acid adsorption reveals the strong effect that produces a functional group and the key role of the S-H bond cleavage in the self-assembly process.

Human apolipoprotein A-I-derived amyloid: its association with atherosclerosis.

Amyloidoses constitute a group of diseases in which soluble proteins aggregate and deposit extracellularly in tissues. Nonhereditary apolipoprotein A-I (apoA-I) amyloid is characterized by deposits of nonvariant protein in atherosclerotic arteries. Despite being common, little is known about the pathogenesis and significance of apoA-I deposition. In this work we investigated by fluorescence and biochemical approaches the impact of a cellular microenvironment associated with chronic inflammation on the folding and pro-amyloidogenic processing of apoA-I. Results showed that mildly acidic pH promotes misfolding, aggregation, and increased binding of apoA-I to extracellular matrix elements, thus favoring protein deposition as amyloid like-complexes. In addition, activated neutrophils and oxidative/proteolytic cleavage of the protein give rise to pro amyloidogenic products. We conclude that, even though apoA-I is not inherently amyloidogenic, it may produce non hereditary amyloidosis as a consequence of the pro-inflammatory microenvironment associated to atherogenesis.

From single to multiple Ag-layer modification of Au nanocavity substrates: a tunable probe of the chemical surface-enhanced Raman scattering mechanism.

We present experimental and computational results that enlighten the mechanisms underlying the chemical contribution to surface-enhanced Raman scattering (SERS). Gold void metallic arrays electrochemically covered either by a Ag monolayer or 10-100 Ag layers were modified with a self-assembled monolayer of 4-mercaptopyridine as a molecular Raman probe displaying a rich and unexpected Raman response. A resonant increase of the Raman intensity in the red part of the spectrum is observed that cannot be related to plasmon excitations of the cavity-array. Notably, we find an additional 10-20 time increase of the SERS amplification upon deposition of a single Ag layer on the Au substrate, which is, however, almost quenched upon deposition of 10 atomic layers. Further deposition of 100 atomic Ag layers results in a new increase of the SERS signal, consistent with the improved plasmonic efficiency of Ag bulk-like structures. The SERS response as a function of the Ag layer thickness is analyzed in terms of ab initio calculations and a microscopic model for the SERS chemical mechanism based on a resonant charge transfer process between the molecular HOMO state and the Fermi level in the metal surface. We find that a rearrangement of the electronic charge density related to the presence of the Ag monolayer in the Au/Ag/molecule complex causes an increase in the distance between the HOMO center of charge and the metallic image plane that is responsible for the variation of Raman enhancement between the studied substrates. Our results provide a general platform for studying the chemical contribution to SERS, and for enhancing the Raman efficiency of tailored Au-SERS templates through electrochemical modification with Ag films.

Monitoring the electrochemistry of single molecules by surface-enhanced Raman spectroscopy.

Coherent control of chemical species in complex systems is always subject to intrinsic inhomogeneities from the environment. For example, slight chemical modifications can decisively affect transport properties of molecules on surfaces. Hence, single-molecule (SM) studies are the best solution to avoid these problems and to study diverse phenomena in biology, physics, and chemistry. Along these lines, monitoring SM redox processes has always been a "holy grail" in electrochemistry. To date, claims of SM electrochemistry by spectroscopy have come only from fluorescence quenching of polymers and redox-fluorescent molecules. In unconnected developments, the potential of the bianalyte surface-enhanced Raman scattering (SERS) method as a technique with SM sensitivity has been demonstrated. Raman spectroscopy has the potential to explore SM detection of any molecule, independent of its chemical nature. We provide definitive proof of SM events following redox cycles using SERS. The superior sensitivity and spectral richness of SERS makes it general enough to study, in principle, SM electron transfer of any (label-free) molecule.

Electrochemical modulation for signal discrimination in surface enhanced Raman scattering (SERS).

Electrochemical modulation to induce controlled fluctuations in SERS signals is introduced as a method to discriminate and isolate different contributions to the spectra. The modulation--which can be changed in potential range, amplitude, and frequency--acts as a controllable "switch" to turn on, off, or change specific Raman signals which can then be correlated within the spectra by different fluctuation analysis techniques. Principal component analysis (PCA), either by itself or assisted by fast fourier transform (FFT) prefiltering, are shown to provide viable tools to isolate the different components of the spectra. Electrochemical modulation provides, therefore, a technique to study complex cases of coadsorption, and resolve problems of spectral congestion in SERS signals.

From monomers to geometry-constrained molecules: one step further toward cyanide bridged wires.

We report on the synthesis and properties of a family of linear cyanide bridged mixed-valence heptanuclear complexes with the formula: trans-[L(4)Ru(II){(mu-NC)Fe(III)(NC)(4)(mu-CN)Ru(II)L'(4)(mu-NC)Fe(III)(CN)(5)}(2)](6-) (with L and L' a para substituted pyridine). We also report on the properties of a related pentanuclear complex. These oligomers were purified by size exclusion chromatography, characterized by electrospray ionization (ESI) mass spectrometry and elemental analysis, and their linear shape was confirmed by scanning tunneling microscopy (STM). These complexes present a rich electrochemistry associated with the seven redox active centers. The redox potential split of identical fragments indicates that there is considerable communication along the cyanide bridged backbone of the compounds, even for centers more than 3 nm apart. This small attenuation of the interaction at long distances make these cyanide bridged compounds good candidates for molecular wires. Interestingly, the extent of the communication depends on the relative energy of the fragments, as evaluated by their redox potentials, providing a guide for improvement of this interesting property.

Ag-modified Au nanocavity SERS substrates.

The engineering of cavity void metallic arrays allows to vary the plasmon-polariton mode energies from the near infrared to the ultraviolet through the tuning of the void height and diameter, and the selection of the appropriate material. Typically Au nanocavity substrates can be grown with better reproducibility, homogeneity, and stability, while Ag structures display significantly larger SERS enhancements. To exploit these two apparently excluding aspects, quality and enhancement, we report a detailed study of 500 nm Au-nanocavity templates modified by the controlled electrochemical deposition of 100 Ag layers, a thickness similar to the visible light skin-depth of bulk Ag. The SERS amplification of the ordered cavity-arrays is determined using 4-mercaptopyridine as a non-electronic resonant molecular probe. The ultrathin Ag layer modification of the Au substrates results in a strong amplification of the SERS signal both in the red and the green part of the spectrum, and in a spectral shift of the Raman resonance scans. These observations are assigned to Ag-induced changes in the plasmon-polariton response of the nanostructure. The reported results provide a general platform for the preparation of renewable SERS-active substrates that combine the durability and higher quality of Au nanotemplates, with the enhanced SERS amplification factors of Ag.

Phospholipid bilayers supported on thiolate-covered nanostructured gold: in situ Raman spectroscopy and electrochemistry of redox species.

Thiol-covered nanostructured gold has been tested as a platform for the preparation of high-area phospholipid bilayer systems suitable for optical and electrochemical sensing. In situ and ex situ Raman spectroscopy and electrochemical measurements are made to study methylene blue (MB) and flavin-adenine dinucleotide (FAD) incorporation into dimyristoylphosphatidylcholine (DMPC) bilayers prepared by vesicle fusion on dithiothreitol (DTT)-covered nanostructured gold. Results show that lipophilic positively charged MB molecules are incorporated in the bilayer reaching the DTT-gold interface. On the other hand, the negatively charged FAD molecules are immobilized at the outer part of the phospholipid bilayer and cannot be electrochemically detected. Our results demonstrate that DTT-covered nanostructured gold provides a suitable high-area platform for phospholipid membranes that are able to separate and sense different kinds of molecules and biomolecules.

Self-assembled dithiothreitol on Au surfaces for biological applications: phospholipid bilayer formation.

Self-assembly of dithiothreitol (DTT) on Au(111) from solution deposition has been studied by X-ray photoelectron spectroscopy and electrochemical data. DTT molecules self-assemble on Au(111) in a lying-down configuration irrespective of the concentration and temperature. XPS and electrochemical data indicate a DTT surface coverage of theta approximately 0.16 with two S-head-Au covalent bonds per DTT molecule. The DTT monolayer turns the Au surface hydrophilic enough to allow the formation of fluid dimyristoylphosphatidylcholine (DMPC) bilayer domains by vesicle fusion as revealed by in situ atomic force imaging. Methylene blue (MB) and flavin adenine dinucleotide (FAD) have been used as probes to study molecule transport across the bilayer.