Label-free SERS detection of proteins based on machine learning classification of chemo-structural determinants.

Establishing standardized methods for a consistent analysis of spectral data remains a largely underexplored aspect in surface-enhanced Raman spectroscopy (SERS), particularly applied to biological and biomedical research. Here we propose an effective machine learning classification of protein species with closely resembled spectral profiles by a mixed data processing based on principal component analysis (PCA) applied to multipeak fitting on SERS spectra. This strategy simultaneously assures a successful discrimination of proteins and a thorough characterization of the chemostructural differences among them, ultimately opening up new routes for SERS evolution toward sensing applications and diagnostics of interest in life sciences.

Ion-exchanged glass microrods as hybrid SERS/fluorescence substrates for molecular beacon-based DNA detection.

Ion-exchange in molten nitrate salts containing metal ions (i.e. silver, copper, etc.) represents a well-established technique able to modify the chemical-physical properties of glass materials. It is widely used not only in the field of integrated optics (IO) but also, more recently, in plasmonics due to the possibility to induce the formation of metal nanoparticles in the glass matrix by an ad hoc thermal post-process. In this work, the application of this technology for the realisation of low-cost and stable surface-enhanced Raman scattering (SERS) active substrates, based on soda-lime glass microrods, is reported. The microrods, with a radius of a few tens of microns, were obtained by cutting the end of an ion-exchanged soda-lime fibre for a length less than 1 cm. As ion source, silver nitrate was selected due to the outstanding SERS properties of silver. The ion-exchange and thermal annealing post-process parameters were tuned to expose the embedded silver nanoparticles on the surface of the glass microrods, avoiding the use of any further chemical etching step. In order to test the combined SERS/fluorescence response of these substrates, labelled molecular beacons (MBs) were immobilised on their surface for deoxyribonucleic acid (DNA) detection. Our experiments confirm that target DNA is attached on the silver nanoparticles and its presence is revealed by both SERS and fluorescence measurements. These results pave the way towards the development of low-cost and stable hybrid fibres, in which SERS and fluorescence interrogation techniques are combined in the same optical device.

Seeding variability of different alpha synuclein strains in synucleinopathies.

OBJECTIVES: Currently, the exact reasons why different α-synucleinopathies exhibit variable pathologies and phenotypes are still unknown. A potential explanation may be the existence of distinctive α-synuclein conformers or strains. Here, we intend to analyze the seeding activity of dementia with Lewy bodies (DLB) and Parkinson's disease (PD) brain-derived α-synuclein seeds by real-time quaking-induced conversion (RT-QuIC) and to investigate the structure and morphology of the α-synuclein aggregates generated by RT-QuIC. METHODS: A misfolded α-synuclein-enriched brain fraction from frontal cortex and substantia nigra pars compacta tissue, isolated by several filtration and centrifugation steps, was subjected to α-synuclein/RT-QuIC analysis. Our study included neuropathologically well-characterized cases with DLB, PD, and controls (Ctrl). Biochemical and morphological analyses of RT-QuIC products were conducted by western blot, dot blot analysis, Raman spectroscopy, atomic force microscopy, and transmission electron microscopy. RESULTS: Independently from the brain region, we observed different seeding kinetics of α-synuclein in the RT-QuIC in patients with DLB compared to PD and Ctrl. Biochemical characterization of the RT-QuIC product indicated the generation of a proteinase K-resistant and fibrillary α-synuclein species in DLB-seeded reactions, whereas PD and control seeds failed in the conversion of wild-type α-synuclein substrate. INTERPRETATION: Structural variances of α-synuclein seeding kinetics and products in DLB and PD indicated, for the first time, the existence of different α-synuclein strains in these groups. Therefore, our study contributes to a better understanding of the clinical heterogeneity among α-synucleinopathies, offers an opportunity for a specific diagnosis, and opens new avenues for the future development of strain-specific therapies. Ann Neurol 2019;85:691-703.

Biosensor surface functionalization by a simple photochemical immobilization of antibodies: experimental characterization by mass spectrometry and surface enhanced Raman spectroscopy.

Surface functionalization is a key step in biosensing since it is the basis of an effective analyte recognition. Among all the bioreceptors, antibodies (Abs) play a key role thanks to their superior specificity, although the available immobilization strategies suffer from several drawbacks. When gold is the interacting surface, the recently introduced Photochemical Immobilization Technique (PIT) has been shown to be a quick, easy-to-use and very effective method to tether Abs oriented upright by means of thiols produced via tryptophan mediated disulphide bridge reduction. Although the molecular mechanism of this process is quite well identified, the detailed morphology of the immobilized antibodies is still elusive due to inherent difficulties related to the microscopy imaging of Abs. The combination of Mass Spectrometry, Surface-Enhanced Raman Spectroscopy and Ellman's assay demonstrates that Abs irradiated under the conditions in which PIT is realized show only two effective disulphide bridges available for binding. They are located in the constant region of the immunoglobulin light chain so that the most likely position Ab assumes is side-on, i.e. with one Fab (i.e. the antigen binding portion of the antibody) exposed to the solution. This is not a limitation of the recognition efficiency in view of the intrinsic flexibility of the Ab structure, which makes the free Fab able to sway in the solution, a feature of great importance in many biosensing applications.

Nanoscale Discrimination between Toxic and Nontoxic Protein Misfolded Oligomers with Tip-Enhanced Raman Spectroscopy.

Highly toxic protein misfolded oligomers associated with neurological disorders such as Alzheimer's and Parkinson's diseases are nowadays considered primarily responsible for promoting synaptic failure and neuronal death. Unraveling the relationship between structure and neurotoxicity of protein oligomers appears pivotal in understanding the causes of the pathological process, as well as in designing novel diagnostic and therapeutic strategies tuned toward the earliest and presymptomatic stages of the disease. Here, it is benefited from tip-enhanced Raman spectroscopy (TERS) as a surface-sensitive tool with spatial resolution on the nanoscale, to inspect the spatial organization and surface character of individual protein oligomers from two samples formed by the same polypeptide sequence and different toxicity levels. TERS provides direct assignment of specific amino acid residues that are exposed to a large extent on the surface of toxic species and buried in nontoxic oligomers. These residues, thanks to their outward disposition, might represent structural factors driving the pathogenic behavior exhibited by protein misfolded oligomers, including affecting cell membrane integrity and specific signaling pathways in neurodegenerative conditions.

Exploring the Aß1-42 fibrillogenesis timeline by atomic force microscopy and surface enhanced Raman spectroscopy.

Introduction: Alzheimer's disease (AD) is a progressive debilitating neurological disorder representing the most common neurodegenerative disease worldwide. Although the exact pathogenic mechanisms of AD remain unresolved, the presence of extracellular amyloid-ß peptide 1-42 (Aß1-42) plaques in the parenchymal and cortical brain is considered one of the hallmarks of the disease. Methods: In this work, we investigated the Aß1-42 fibrillogenesis timeline up to 48 h of incubation, providing morphological and chemo-structural characterization of the main assemblies formed during the aggregation process of Aß1-42, by atomic force microscopy (AFM) and surface enhanced Raman spectroscopy (SERS), respectively. Results: AFM topography evidenced the presence of characteristic protofibrils at early-stages of aggregation, which form peculiar macromolecular networks over time. SERS allowed to track the progressive variation in the secondary structure of the aggregation species involved in the fibrillogenesis and to determine when the ß-sheet starts to prevail over the random coil conformation in the aggregation process. Discussion: Our research highlights the significance of investigating the early phases of fibrillogenesis to better understand the molecular pathophysiology of AD and identify potential therapeutic targets that may prevent or slow down the aggregation process.

Development of stretchable microneedle arrays via single-step digital light-processing printing for delivery of rhodamine B into skin tissue.

This paper introduces a novel approach for loading and releasing Rhodamine B (RhB) into the skin using minimally-invasive microneedle technology developed through digital light-processing (DLP) printing. Notably, this process involves the direct 3D fabrication of rigid microneedle arrays affixed to a flexible patch, marking a pioneering application of DLP printing in this context. The stretchable and durable design of the microneedle substrate enables it to adapt to dynamic movements associated with human activities. Moreover, the microneedle features a pore on each side of the pyramid needle, effectively optimizing its drug-loading capabilities. Results indicate that the microneedle patch can withstand up to 50 % strain without failure and successfully penetrates rat skin. In vitro drug release profiles, conducted through artificial and rat skin, were observed over a 70 h period. This study establishes the potential of a simple manufacturing process for the creation of pore-designed microneedle arrays with a stretchable substrate, showcasing their viability in transdermal drug delivery applications.

In vivo laser assisted microvascular repair and end-to-end anastomosis by means of indocyanine green-infused chitosan patches: a pilot study.

BACKGROUND AND OBJECTIVES: Laser-based repairing techniques offer several advantages respect to standard suturing in microsurgery. In this work we evaluate the applicability and feasibility of two innovative laser-based approaches for microvascular repair and anastomoses: (1) laser-assisted vascular repair (LAVR); (2) laser-assisted end-to-end vascular anastomosis (LAVA). All these procedures have been executed by the use of diode laser irradiation and chitosan-patches infused with Indocyanine Green (ICG). STUDY DESIGN/MATERIALS AND METHODS: Experiments were performed on 30 rabbits. Twenty animals underwent LAVR and 10 end-to-end LAVA procedures. In the LAVR group, a 5-mm longitudinal cut was performed on the common carotid artery (CCA), then an ICG-infused chitosan patch was topically applied and laser-soldered over the arterial lesion. In the LAVA group the end-to-end anastomosis was executed on CCA by means of application of the three interrupted sutures and subsequent laser soldering of the ICG-infused patch. Animals underwent different follow-up periods (2, 7, 30, and 90 days). At the end of every follow-up, the animals were re-anesthetized and a microdoppler analysis was performed in order to check patency of the treated vessels. Then soldered segments were excised and subjected to histological and ultrastructural evaluations. RESULTS: At the end of surgery no bleeding from the treated segment was observed; all the treated vessels were patent. At the end of follow-up periods, no signs of perivascular haemorrhage were found. An intraoperative microdoppler evaluation assessed the patency of all the treated vessels. Histology showed a good reorganization of the vascular wall structures and an early endothelial regeneration was observed by SEM. CONCLUSIONS: Our study demonstrated the efficacy of laser tissue soldering by means of ICG-infused chitosan patches for the in vivo repairing of microvascular lesions and end-to-end anastomoses. This approach offers several advantages over conventional suturing methods and is technically easy to perform, minimizing the surgical trauma to vessels.

Photothermally activated hybrid films for quantitative confined release of chemical species.

Illuminating films of a porous chitosan matrix containing gold nanorods and thermosensitive micelles loaded with a chemical stimulates local photothermal conversion of the gold nanorods. The heat produced activates the ejection of the chemical from the micelles (see scheme), and causes the transient permeabilization of adjacent cell membranes, resulting in a selective cellular uptake of the released chemical with control over spatiotemporal parameters and dosage.

Molecular beacon decorated silver nanowires for quantitative miRNA detection by a SERS approach.

Advantages of biosensors based on surface enhanced Raman scattering (SERS) rely on improved sensitivity and specificity, and suited reproducibility in detecting a target molecule that is localized in close proximity to a SERS-active surface. Herein, a comprehensive study on the realization of a SERS biosensor designed for detecting miRNA-183, a miRNA biomarker that is specific for chronic obstructive pulmonary disease (COPD), is presented. The used strategy exploits a signal-off mechanism by means of a labelled molecular beacon (MB) as the oligonucleotide biorecognition element immobilized on a 2D SERS substrate, based on spot-on silver nanowires (AgNWs) and a multi-well low volume cell. The MB was properly designed by following a dedicated protocol to recognize the chosen miRNA. A limit of detection down to femtomolar concentration (3 × 10-16 M) was achieved and the specificity of the biosensor was proved. Furthermore, the possibility to regenerate the sensing system through a simple procedure is shown: with regeneration by using HCl 1 mM, two detection cycles were performed with a good recovery of the initial MB signal (83%) and a reproducible signal after hybridization.

Impact of seed amplification assay and surface-enhanced Raman spectroscopy combined approach on the clinical diagnosis of Alzheimer's disease.

BACKGROUND: The current diagnosis of Alzheimer's disease (AD) is based on a series of analyses which involve clinical, instrumental and laboratory findings. However, signs, symptoms and biomarker alterations observed in AD might overlap with other dementias, resulting in misdiagnosis. METHODS: Here we describe a new diagnostic approach for AD which takes advantage of the boosted sensitivity in biomolecular detection, as allowed by seed amplification assay (SAA), combined with the unique specificity in biomolecular recognition, as provided by surface-enhanced Raman spectroscopy (SERS). RESULTS: The SAA-SERS approach supported by machine learning data analysis allowed efficient identification of pathological Aß oligomers in the cerebrospinal fluid of patients with a clinical diagnosis of AD or mild cognitive impairment due to AD. CONCLUSIONS: Such analytical approach can be used to recognize disease features, thus allowing early stratification and selection of patients, which is fundamental in clinical treatments and pharmacological trials.

An in situ and in vitro investigation of cytoplasmic TDP-43 inclusions reveals the absence of a clear amyloid signature.

Introduction: Several neurodegenerative conditions are associated with a common histopathology within neurons of the central nervous system, consisting of the deposition of cytoplasmic inclusions of TAR DNA-binding protein 43 (TDP-43). Such inclusions have variably been described as morphologically and molecularly ordered aggregates having amyloid properties, as filaments without the cross-ß-structure and dye binding specific for amyloid, or as amorphous aggregates with no defined structure and fibrillar morphology.Aims and Methods: Here we have expressed human full-length TDP-43 in neuroblastoma x spinal cord 34 (NSC-34) cells to investigate the morphological, structural, and tinctorial properties of TDP-43 inclusions in situ. We have used last-generation amyloid diagnostic probes able to cross the cell membrane and detect amyloid in the cytoplasm and have adopted Raman and Fourier transform infrared microspectroscopies to study in situ the secondary structure of the TDP-43 protein in the inclusions. We have then used transmission electron microscopy to study the morphology of the TDP-43 inclusions.Results: The results show the absence of amyloid dye binding, the lack of an enrichment of cross-ß structure in the inclusions, and of a fibrillar texture in the round inclusions. The aggregates formed in vitro from the purified protein under conditions in which it is initially native also lack all these characteristics, ruling out a clear amyloid-like signature.Conclusions: These findings indicate a low propensity of TDP-43 to form amyloid fibrils and even non-amyloid filaments, under conditions in which the protein is initially native and undergoes its typical nucleus-to-cell mislocalization. It cannot be excluded that filaments emerge on the long time scale from such inclusions, but the high propensity of the protein to form initially other types of inclusions appear to be an essential characteristic of TDP-43 proteinopathies.KEY MESSAGESCytoplasmic inclusions of TDP-43 formed in NSC-34 cells do not stain with amyloid-diagnostic dyes, are not enriched with cross-ß structure, and do not show a fibrillar morphology.TDP-43 assemblies formed in vitro from pure TDP-43 do not have any hallmarks of amyloid.

Thermal transitions of fibrillar collagen unveiled by second-harmonic generation microscopy of corneal stroma.

The thermal transitions of fibrillar collagen are investigated with second-harmonic generation polarization anisotropy microscopy. Second-harmonic generation images and polarization anisotropy profiles of corneal stroma heated in the 35-80°C range are analyzed by means of a theoretical model that is suitable to probe principal intramolecular and interfibrillar parameters of immediate physiological interest. Our results depict the tissue modification with temperature as the interplay of three destructuration stages at different hierarchical levels of collagen assembly including its tertiary structure and interfibrillar alignment, thus supporting and extending previous findings. This method holds the promise of a quantitative inspection of fundamental biophysical and biochemical processes and may find future applications in real-time and postsurgical functional imaging of collagen-rich tissues subjected to thermal treatments.

Mini Review of Reliable Fabrication of Electrode under Stretching for Supercapacitor Application.

Currently, there is an increasing demand for portable and wearable electronics. This has necessitated the development of stretchable energy storage devices, while simultaneously maintaining performance. Hence, the electrodes and electrolyte materials used in stretchable supercapacitors should be robust under severe mechanical deformation. Polymers are widely used in the fabrication of stretchable supercapacitors. It is not only crucial to choose good polymer candidates with inherent advantages, but it is also important to design suitable polymer materials for both electrodes and electrolytes. This mini-review explains the concept of stretchable supercapacitors, the theoretical background of polymer-based electrodes for supercapacitors, and the fabrication strategies of stretchable electrodes for supercapacitors. Finally, we present the drawbacks and areas that still need to be developed.

Effect of the Blade-Coating Conditions on the Electrical and Optical Properties of Transparent Ag Nanowire Electrodes.

Optimizing the coating conditions for a doctor blading system is important when seeking to improve the performance of Ag nanowire electrodes. In this study, the effect of the blading height and speed on the optical and electrical properties of Ag nanowire electrodes was investigated. Ag nanowires were first spread on a PET substrate using a doctor blade with differing heights at a fixed blading speed. An increase in the blading height resulted in the degradation of the optical transmittance and stronger haze due to the higher probability of Ag nanowire agglomeration arising from the greater wet thickness. When the blading speed was varied, the optical transmittance and haze were unaffected up until 20 mm/s, followed by minor degradation of the optical properties at blading speeds over 25 mm/s. The higher speeds hindered the spread of the Ag nanowire solution, which also increased the probability of Ag nanowire agglomeration. However, this degradation was less serious compared to that observed with a change in the blading height. Therefore, optimizing the blading height was confirmed to be the priority for the production of high-performance transparent Ag nanowire electrodes. Our study thus provides practical guidance for the fabrication of Ag nanowire electrodes using doctor blading systems.

Raman Spectroscopy Techniques for the Investigation and Diagnosis of Alzheimer's Disease.

Alzheimer's disease (AD) is the most common neurodegenerative disorder, resulting in memory loss, cognitive decline, bodily function impairment, and finally death. The growing number of people suffering from AD increasingly urges the development of effective early diagnosis and monitoring techniques. Here, we review the most recent developments in the field of Raman-based techniques, which have shown a significant potential in identifying AD by detecting specific biomarkers in biological fluids, as well as in providing fundamental insights into key molecules involved in the disease progression or in the analysis of histological specimens of patients with AD. These techniques comprise spontaneous and resonant Raman spectroscopies, exploit plasmon- or fiber- enhanced effects, such as surface-, tip- or fiber- enhanced Raman spectroscopies, or involve non-linear techniques like coherent Raman scattering. The scientific efforts employed up to now as well as the rapid technological advancements in optical detection instruments (spectrometers, lasers, substrates for analysis, etc.) and the diffusion of advanced data processing methods suggest a leading role of Raman techniques in the perspective of a preclinical or clinical detection of AD.

Cyanine-Doped Nanofiber Mats for Laser Tissue Bonding.

In spite of an extensive body of academic initiatives and innovative products, the toolkit of wound dressing has always revolved around a few common concepts such as adhesive patches and stitches and their variants. Our work aims at an alternative solution for an immediate restitutio ad integrum of the mechanical functionality in cutaneous repairs. We describe the fabrication and the application of electrospun mats of bioactive nanofibers all made of biocompatible components such as a natural polysaccharide and a cyanine dye for use as laser-activatable plasters, resembling the ultrastructure of human dermis. In particular, we investigate their morphological features and mechanical moduli under conditions of physiological relevance, and we test their use to bind a frequent benchmark of connective tissue as rabbit tendon and a significant case of clinical relevance as human dermis. Altogether, our results point to the feasibility of a new material for wound dressing combining translational potential, strength close to human dermis, extensibility exceeding 15% and state-of-art adhesive properties.

Application of ultrafast gold luminescence to measuring the instrument response function for multispectral multiphoton fluorescence lifetime imaging.

When performing multiphoton fluorescence lifetime imaging in multiple spectral emission channels, an instrument response function must be acquired in each channel if accurate measurements of complex fluorescence decays are to be performed. Although this can be achieved using the reference reconvolution technique, it is difficult to identify suitable fluorophores with a mono-exponential fluorescence decay across a broad emission spectrum. We present a solution to this problem by measuring the IRF using the ultrafast luminescence from gold nanorods. We show that ultrafast gold nanorod luminescence allows the IRF to be directly obtained in multiple spectral channels simultaneously across a wide spectral range. We validate this approach by presenting an analysis of multispectral autofluorescence FLIM data obtained from human skin ex vivo.

Cost Effective Silver Nanowire-Decorated Graphene Paper for Drop-On SERS Biodetection.

The use of SERS for real-world bioanalytical applications represents a concrete opportunity, which, however, is being largely delayed by the inadequacy of existing substrates used to collect SERS spectra. In particular, the main bottleneck is their poor usability, as in the case of unsupported noble metal colloidal nanoparticles or because of the need for complex or highly specialized fabrication procedures, especially in view of a large-scale commercial diffusion. In this work, we introduce a graphene paper-supported plasmonic substrate for biodetection as obtained by a simple and rapid aerosol deposition patterning of silver nanowires. This substrate is compatible with the analysis of small (2 µL) analyte drops, providing stable SERS signals at sub-millimolar concentration and a detection limit down to the nanogram level in the case of hemoglobin. The presence of a graphene underlayer assures an even surface distribution of SERS hotspots with improved stability of the SERS signal, the collection of well-resolved and intense SERS spectra, and an ultra-flat and photostable SERS background in comparison with other popular disposable supports.

Probing the Structure of Toxic Amyloid-ß Oligomers with Electron Spin Resonance and Molecular Modeling.

Structural models of the toxic species involved in the development of Alzheimer's disease are of utmost importance to understand the molecular mechanism and to describe early biomarkers of the disease. Among toxic species, soluble oligomers of amyloid-ß (Aß) peptides are particularly important, because they are responsible for spreading cell damages over brain regions, thus rapidly impairing brain functions. In this work we obtain structural information on a carefully prepared Aß(1-42) sample, representing a toxic state for cell cultures, by combining electron spin resonance spectroscopy and computational models. We exploited the binding of Cu2+ to Aß(1-42) and used copper as a probe for estimating Cu-Cu distances in the oligomers by applying double electron-electron resonance (DEER) pulse sequence. The DEER trace of this sample displays a unique feature that fits well with structural models of oligomers formed by Cu-cross-linked peptide dimers. Because Cu is bound to the Aß(1-42) N-terminus, for the first time structural constraints that are missing in reported studies are provided at physiological conditions for the Aß N-termini. These constraints suggest the Aß(1-42) dimer as the building block of soluble oligomers, thus changing the scenario for any kinetic model of Aß(1-42) aggregation.