Nanoscale Structural Characterization of Individual Viral Particles Using Atomic Force Microscopy Infrared Spectroscopy (AFM-IR) and Tip-Enhanced Raman Spectroscopy (TERS)

Enhancement of waterborne pathogen removal by functionalized biochar with ε-polylysine ″dynamic arms″: Potential application in ultrafiltration system

Widespread outbreaks of threatening infections caused by unknown pathogens and water transmission have spawned the development of adsorption methods for pathogen elimination. We proposed a biochar functionalization strategy involving ε-polylysine (PLL), a bio-macromolecular poly(amino acid)s with variable folding conformations, as a "pathogen gripper" on biochar. PLL was successfully bridged onto biochar via polydopamine (PDA) crosslinking. The extension of electropositive side chains within PLL enables the capture of both nanoscale viruses and micrometer-scale bacteria in water, achieving excellent removal performances. This functionalized biochar was tentatively incorporated into ultrafiltration (UF) system, to achieve effective and controllable adsorption and retention of pathogens, and to realize the transfer of pathogens from membrane surface/pore to biochar surface as well as flushing water. The biochar-amended UF systems presents complete retention (∼7 LRV) and hydraulic elution of pathogens into membrane flushing water. Improvements in removal of organics and anti-fouling capability were observed, indicating the broken trade-off in UF pathogen removal dependent on irreversible fouling. Chemical characterizations revealed adsorption mechanisms encompassing electrostatic/hydrophobic interactions, pore filling, electron transfer, chemical bonding and secondary structure transitions. Microscopic and mechanical analyses validated the mechanisms for rapid adsorption and pathogen lysis. Low-concentration alkaline solution for used biochar regeneration, facilitated the deprotonation and transformation of PLL side chain to folded structures (α-helix/β-sheet). Biochar regeneration process also promoted the effective detachment/inactivation of pathogens and protection of functional groups on biochar, corroborated by physicochemical inspection and molecular dynamics simulation. The foldability of poly(amino acid)s acting like dynamic arms, significantly contributed to pathogen capture/desorption/inactivation and biochar regeneration. This study also inspires future investigation for performances of UF systems amended by poly(amino acid)s-functionalized biochar under diverse pressure, temperature, reactive oxygen species of feeds and chemical cleaning solutions, with far-reaching implications for public health, environmental applications of biochar, and UF process improvement.

Advanced Vibrational Spectroscopy and Bacteriophages Team Up: Dynamic Synergy for Medical and Environmental Applications

Bacteriophages are emerging as a promising alternative in combating antibiotic-resistant bacteria amidst the escalating global antimicrobial resistance crisis. Recently, there has been a notable resurgence of interest in phages, prompting extensive research into their therapeutic potential. Beyond conventional microbiology and virology techniques, such as genomics and proteomics, novel phenotypic and chemical characterization methods are being explored. Among these, there is a growing interest in vibrational spectroscopy, especially in advanced modalities such as surface-enhanced Raman spectroscopy (SERS), tip-enhanced Raman spectroscopy (TERS), and atomic force microscopy-infrared spectroscopy (AFM-IR), which offer improved sensitivity and spatial resolution. This review explores the spectrum of uses of vibrational spectroscopy for bacteriophages, including its role in diagnostics, biosensing, phage detection, assistance in phage-based therapy, and advancing basic research.

Light-Induced Transformation of Virus-Like Particles on TiO2

Titanium dioxide (TiO2) shows significant potential as a self-cleaning material to inactivate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and prevent virus transmission. This study provides insights into the impact of UV-A light on the photocatalytic inactivation of adsorbed SARS-CoV-2 virus-like particles (VLPs) on a TiO2 surface at the molecular and atomic levels. X-ray photoelectron spectroscopy, combined with density functional theory calculations, reveals that spike proteins can adsorb on TiO2 predominantly via their amine and amide functional groups in their amino acids blocks. We employ atomic force microscopy and grazing-incidence small-angle X-ray scattering (GISAXS) to investigate the molecular-scale morphological changes during the inactivation of VLPs on TiO2 under light irradiation. Notably, in situ measurements reveal photoinduced morphological changes of VLPs, resulting in increased particle diameters. These results suggest that the denaturation of structural proteins induced by UV irradiation and oxidation of the virus structure through photocatalytic reactions can take place on the TiO2 surface. The in situ GISAXS measurements under an N2 atmosphere reveal that the virus morphology remains intact under UV light. This provides evidence that the presence of both oxygen and UV light is necessary to initiate photocatalytic reactions on the surface and subsequently inactivate the adsorbed viruses. The chemical insights into the virus inactivation process obtained in this study contribute significantly to the development of solid materials for the inactivation of enveloped viruses.

Fast Nano-IR Hyperspectral Imaging Empowered by Large-Dataset-Free Miniaturized Spatial-Spectral Network

The emerging field of nanoscale infrared (nano-IR) offers label-free molecular contrast, yet its imaging speed is limited by point-by-point traverse acquisition of a three-dimensional (3D) data cube. Here, we develop a spatial-spectral network (SS-Net), a miniaturized deep-learning model, together with compressive sampling to accelerate the nano-IR imaging. The compressive sampling is performed in both the spatial and spectral domains to accelerate the imaging process. The SS-Net is trained to learn the mapping from small nano-IR image patches to the corresponding spectra. With this elaborated mapping strategy, the training can be finished quickly within several minutes using the subsampled data, eliminating the need for a large-labeled dataset of common deep learning methods. We also designed an efficient loss function, which incorporates the image and spectral similarity to enhance the training. We first validate the SS-Net on an open stimulated Raman-scattering dataset; the results exhibit the potential of 10-fold imaging speed improvement with state-of-the-art performance. We then demonstrate the versatility of this approach on atomic force microscopy infrared (AFM-IR) microscopy with 7-fold imaging speed improvement, even on nanoscale Fourier transform infrared (nano-FTIR) microscopy with up to 261.6 folds faster imaging speed. We further showcase the generalization of this method on AFM-force volume-based multiparametric nanoimaging. This method establishes a paradigm for rapid nano-IR imaging, opening new possibilities for cutting-edge research in materials, photonics, and beyond.

AFM-IR investigation of thin PECVD SiO x films on a polypropylene substrate in the surface-sensitive mode

Thin silicon oxide films deposited on a polypropylene substrate by plasma-enhanced chemical vapor deposition were investigated using atomic force microscopy-based infrared (AFM-IR) nanospectroscopy in contact and surface-sensitive mode. The focus of this work is the comparison of the different measurement methods (i.e., contact mode and surface-sensitive mode) with respect to the chemical surface sensitivity. The use of the surface-sensitive mode in AFM-IR shows an enormous improvement for the analysis of thin films on the IR-active substrate. As a result, in this mode, the signal of the substrate material could be significantly reduced. Even layers that are so thin that they could hardly be measured in the contact mode can be analyzed with the surface-sensitive mode.

The influence of zwitterionic and anionic phospholipids on protein aggregation

The progressive aggregation of misfolded proteins is the underlying molecular cause of numerous pathologies including Parkinson's disease and injection and transthyretin amyloidosis. A growing body of evidence indicates that protein deposits detected in organs and tissues of patients diagnosed with such pathologies contain fragments of lipid membranes. In vitro experiments also showed that lipid membranes could strongly change the aggregation rate of amyloidogenic proteins, as well as alter the secondary structure and toxicity of oligomers and fibrils formed in their presence. In this review, the effect of large unilamellar vesicles (LUVs) composed of zwitterionic and anionic phospholipids on the aggregation rate of insulin, lysozyme, transthyretin (TTR) and α- synuclein (α-syn) will be discussed. The manuscript will also critically review the most recent findings on the lipid-induced changes in the secondary structure of protein oligomers and fibrils, as well as reveal the extent to which lipids could alter the toxicity of protein aggregates formed in their presence.

Phospholipids and Cholesterol Determine Molecular Mechanisms of Cytotoxicity of α-Synuclein Oligomers and Fibrils

Progressive loss of dopaminergic (DA) neurons in the substantia nigra pars compacta, hypothalamus, and thalamus is a hallmark of Parkinson's disease. Neuronal death is linked to the abrupt aggregation of α-synuclein (α-Syn), a small membrane protein that regulates cell vesicle trafficking. α-Syn aggregation rate, as well as the secondary structure and toxicity of α-Syn fibrils, could be uniquely altered by lipids. However, molecular mechanisms that determine such a remarkable difference in the toxicity of α-Syn fibrils formed in the presence of lipids remain unclear. In this study, we used a set of molecular assays to determine the molecular mechanism by which α-Syn fibrils formed in the presence of phosphatidylcholine (PC), cardiolipin (CL), and cholesterol (Cho) exert cell toxicity. We found that rat dopaminergic cells exposed to α-Syn fibrils formed in the presence of different lipids exert drastically different magnitudes and dynamics of unfolded protein response (UPR) in the endoplasmic reticulum (ER) and mitochondria (MT). Specifically, α-Syn:CL were found to cause the strongest, whereas α-Syn fibrils formed in the absence of lipids had the lowest magnitude of the UPR cell response. We also found the opposite dynamics of the ER- and MT-UPR responses in rat dopaminergic cells exposed to protein aggregates. These results could suggest that facing severe ER stress, dopaminergic cells suppress MT-UPR response, enabling the maximal ATP production to restore their normal physiological function. These findings help to better understand complex mechanisms of cell toxicity of amyloid aggregates and ultimately find neuroprotective drug candidates that will be able to suppress the spread of Parkinson's disease.

Isotopic effects on in-plane hyperbolic phonon polaritons in MoO3

Hyperbolic phonon polaritons (HPhPs), hybrids of light and lattice vibrations in polar dielectric crystals, empower nanophotonic applications by enabling the confinement and manipulation of light at the nanoscale. Molybdenum trioxide (α-MoO3) is a naturally hyperbolic material, meaning that its dielectric function deterministically controls the directional propagation of in-plane HPhPs within its reststrahlen bands. Strategies such as substrate engineering, nano- and heterostructuring, and isotopic enrichment are being developed to alter the intrinsic die ectric functions of natural hyperbolic materials and to control the confinement and propagation of HPhPs. Since isotopic disorder can limit phonon-based processes such as HPhPs, here we synthesize isotopically enriched 92MoO3 (92Mo: 99.93 %) and 100MoO3 (100Mo: 99.01 %) crystals to tune the properties and dispersion of HPhPs with respect to natural α-MoO3, which is composed of seven stable Mo isotopes. Real-space, near-field maps measured with the photothermal induced resonance (PTIR) technique enable comparisons of inplane HPhPs in α-MoO3 and isotopically enriched analogues within a reststrahlen band (≈820 cm-1 to ≈ 972 cm-1). Results show that isotopic enrichment (e.g., 92MoO3 and 100MoO3) alters the dielectric function, shifting the HPhP dispersion (HPhP angular wavenumber × thickness vs IR frequency) by ≈-7% and ≈ +9 %, respectively, and changes the HPhP group velocities by ≈ ±12 %, while the lifetimes (≈ 3 ps) in 92MoO3 were found to be slightly improved (≈ 20 %). The latter improvement is attributed to a decrease in isotopic disorder. Altogether, isotopic enrichment was found to offer fine control over the properties that determine the anisotropic in-plane propagation of HPhPs in α-MoO3, which is essential to its implementation in nanophotonic applications.

Time-resolved vibrational dynamics: Novel opportunities for sensing and imaging

The evolution of time-resolved spectroscopies has resulted in significant advancements across numerous scientific disciplines, particularly those concerned with molecular electronic states. However, the intricacy of molecular vibrational spectroscopies, which provide comprehensive molecular-level information within complex structures, has presented considerable challenges due to the ultrashort dephasing time. Over recent decades, an increasing focus has been placed on exploring the temporal progression of bond vibrations, thereby facilitating an improved understanding of energy redistribution within and between molecules. This review article focuses on an array of time-resolved detection methodologies, each distinguished by unique technological attributes that offer exclusive capabilities for investigating the physical phenomena propelled by molecular vibrational dynamics. In summary, time-resolved vibrational spectroscopy emerges as a potent instrument for deciphering the dynamic behavior of molecules. Its potential for driving future progress across fields as diverse as biology and materials science is substantial, marking a promising future for this innovative tool.

Secondary structure and toxicity of transthyretin fibrils can be altered by unsaturated fatty acids

Transthyretin amyloidosis is a severe pathology characterized by the progressive accumulation of transthyretin (TTR) in various organs and tissues. This highly conserved through vertebrate evolution protein transports thyroid hormone thyroxine. In our bodies, TTR can interact with a large number of molecules, including ω-3 and ω-6 polyunsaturated fatty acids (PUFAs) that are broadly used as food supplies. In this study, we investigated the effect of ω-3 and ω-6 PUFAs, as well as their fully saturated analog, on TTR aggregation. Our results showed that both ω-3 and ω-6 PUFAs strongly decreased the rate of TTR aggregation. We also found that in the presence of PUFAs, TTR formed morphologically different fibrils compared to the lipid-free environment. Nano-Infrared imaging revealed that these fibrils had drastically different secondary structures compared to the secondary structure of TTR aggregates formed in the PUFAs-free environment. Furthermore, TTR fibrils formed in the presence of ω-3 and ω-6 PUFAs exerted significantly lower cell toxicity compared to the fibrils formed in the absence of fatty acids.

Cholesterol and Sphingomyelin Uniquely Alter the Rate of Transthyretin Aggregation and Decrease the Toxicity of Amyloid Fibrils

Transthyretin (TTR) is a small tetrameric protein that aggregates, forming highly toxic oligomers and fibrils. In the blood and cerebrospinal fluid, TTR can interact with various biomolecules, phospho- and sphingolipids, and cholesterol on the red blood cell plasma membrane. However, the role of these molecules in TTR aggregation remains unclear. In this study, we investigated the extent to which phosphatidylcholine (PC), sphingomyelin (SM), and cholesterol (Cho), important components of plasma membranes, could alter the rate of TTR aggregation. We found that PC and SM inhibited TTR aggregation whereas Cho strongly accelerated it. The presence of these lipids during the stage of protein aggregation uniquely altered the morphology and secondary structure of the TTR fibrils, which changed the toxicity of these protein aggregates. These results suggest that interactions of TTR with red blood cells, whose membranes are rich with these lipids, can trigger irreversible aggregation of TTR and cause transthyretin amyloidosis.

Simulating biological surface dynamics in high-speed atomic force microscopy experiments

High-speed atomic force microscopy (HSAFM) is an important tool for studying the dynamic behavior of large biomolecular assemblies at surfaces. However, unlike light microscopy techniques, which visualize each point in the field of view at the same time, in HSAFM, the surface is literally imaged pixel-by-pixel with a variable extent of time separation existing between recordings made at one pixel and all others within the surface image. Such "temporal asynchronicity" in the recording of the spatial information can introduce distortions into the image when the surface components move at a rate comparable to that at which the surface is imaged. This Letter describes recently released software developments that are able to predict the likely form of these distortions and estimate confidence levels when assigning the identity of observed structures. These described approaches may facilitate both the design and optimization of future HSAFM experimental protocols. Further to this, they may assist in the interpretation of results from already published HSAFM studies.

Nanoscale structural characterization of transthyretin aggregates formed at different time points of protein aggregation using atomic force microscopy-infrared spectroscopy

Transthyretin (TTR) amyloidosis is a progressive disease characterized by an abrupt aggregation of misfolded protein in multiple organs and tissues TTR is a tetrameric protein expressed in the liver and choroid plexus. Protein misfolding triggers monomerization of TTR tetramers. Next, monomers assemble forming oligomers and fibrils. Although the secondary structure of TTR fibrils is well understood, there is very little if anything is known about the structural organization of TTR oligomers. To end this, we used nano-infrared spectroscopy, also known as atomic force microscopy infrared (AFM-IR) spectroscopy. This emerging technique can be used to determine the secondary structure of individual amyloid oligomers and fibrils. Using AFM-IR, we examined the secondary structure of TTR oligomers formed at the early (3-6 h), middle (9-12 h), and late (28 h) of protein aggregation. We found that aggregating, TTR formed oligomers (Type 1) that were dominated by α-helix (40%) and β-sheet (~30%) together with unordered protein (30%). Our results showed that fibril formation was triggered by another type of TTR oligomers (Type 2) that appeared at 9 h. These new oligomers were primarily composed of parallel β-sheet (55%), with a small amount of antiparallel β-sheet, α-helix, and unordered protein. We also found that Type 1 oligomers were not toxic to cells, whereas TTR fibrils formed at the late stages of protein aggregation were highly cytotoxic. These results show the complexity of protein aggregation and highlight the drastic difference in the protein oligomers that can be formed during such processes.

Elucidating the Role of Lipids in the Aggregation of Amyloidogenic Proteins

The abrupt aggregation of misfolded proteins is linked to the onset and spread of amyloidogenic diseases, including diabetes type 2, systemic amyloidosis, and Alzheimer's (AD) and Parkinson's diseases (PD). Although the exact cause of these pathological processes is unknown, a growing body of evidence suggests that amyloid diseases are triggered by misfolded or unfolded proteins, forming highly toxic oligomers. These transient species exhibit high structural and morphological heterogeneity. Protein oligomers can also propagate into β-sheet-rich filaments that braid and coil with other filaments to form amyloid fibrils and supramolecular structures with both flat and twisted morphologies. Microscopic examination of protein deposits formed in the brains of both AD and PD patients revealed the presence of fragments of lipid membranes. Furthermore, nanoscale infrared analysis of ex vivo extracted fibrils revealed the presence of lipids in their structure (Zhaliazka, K.; Kurouski, D. Protein Sci. 2023, 32, e4598). These findings demonstrated that lipid bilayers could play an important role in the aggregation of misfolded proteins.Experimental findings summarized in this Account show that (i) lipids uniquely change the aggregation rate of amyloidogenic proteins. In this case, the observed changes in the rates directly depend on the net charge of the lipid and the length and saturation of lipid fatty acids (FAs). For instance, zwitterionic phosphatidylcholine (PC) with 14:0 FAs inhibited the aggregation of insulin, lysozyme, and α-synuclein (α-Syn), whereas anionic phosphatidylserine with the same FAs dramatically accelerated the aggregation rate of these proteins (Dou, T., et al. J. Phys. Chem. Lett. 2021, 12, 4407. Matveyenka, M., et al. FASEB J. 2022, 36, e22543. Rizevsky, S., et al. J. Phys. Chem. Lett. 2022, 13, 2467). Furthermore, (ii) lipids uniquely alter the secondary structure and morphology of protein oligomers and fibrils formed in their presence. Utilization of nano-infrared spectroscopy revealed that such aggregates, as well as ex vivo extracted fibrils, possessed lipids in their structure. These findings are significant because (iii) lipids uniquely alter the toxicity of amyloid oligomers and fibrils formed in their presence. Specifically, PC lowered the toxicity of insulin and lysozyme oligomers, whereas α-Syn oligomers formed in the presence of this phospholipid were found to be significantly more toxic to rat dopaminergic cells compared to α-Syn oligomers grown in the lipid-free environment. Thus, the toxicity of protein oligomers and fibrils is directly determined by the chemical structure of the lipid and the secondary structure of amyloidogenic proteins (Dou, T., et al. J. Phys. Chem. Lett. 2021, 12, 4407. Matveyenka, M., et al. FASEB J. 2022, 36, e22543. Rizevsky, S., et al. J. Phys. Chem. Lett. 2022, 13, 2467). Experimental results discussed in this Account also suggest that amyloidogenic diseases could be caused by pathological changes in the lipid composition of both plasma and organelle membranes, which, in turn, may trigger protein aggregation that results in the formation of highly toxic oligomers and fibrils. Finally, the Account discusses the effects of polyunsaturated FAs on the aggregation properties of amyloidogenic proteins. Experimental findings reported by the author's laboratory revealed that polyunsaturated FAs drastically accelerated the aggregation rate of both insulin and α-Syn as well as strongly changed the secondary structure of amyloid fibrils formed in their presence.

Stability of bacteriophages in organic solvents for formulations

Bacteriophages or phages used as an alternative therapy for treating multi-drug resistant infections require formulation consideration. Current strategies to produce phage formulations involving organic solvents are based on empirical practices without a good understanding of phage stability during formulation development. In this study, we investigated the effect of common formulation organic solvents (ethanol, isopropyl alcohol, tetrahydrofuran (THF) and dimethyl sulfoxide (DMSO)) on the stability of Pseudomonas aeruginosa-specific myovirus (PEV1, PEV20) and podovirus (PEV31) phages using biological assay, transmission electron microscopy (TEM) and scattering near field optical microscopy (SNOM). The three phages were mixed with the solvents at different concentrations (25%, 50%, and 75% (v/v)) for 20 min. All phages were fully viable in the organic solvents at 25% (v/v) showing negligible titre changes. At the higher solvent concentration of 50% (v/v), the myoviruses PEV1 and PEV20 remained relatively stable (titre loss 0.4-1.3 log10), whereas the podovirus PEV31 became less stable (titre loss 0.25-3.8 log10), depending on the solvent used. Increasing the solvent level to 75% (v/v) caused increased morphological changes in TEM and decreased viability as indicated by the titre loss (0.32-7.4 log10), with DMSO being the most phage-destabilising solvent. SNOM spectra showed differences in the signal intensity and peak positions in the amide I and amide II regions, revealing altered phage proteins by the solvents. In conclusion, the choice of the solvents for phage formulation depends on both the phages and solvent types. Our results showed (1) the phages are more stable in the alcohols than DMSO and THF, and (2) the myoviruses tend to be more stable than the podovirus in the solvents. Overall, a low to moderate (25-50 % v/v) level of organic solvents (except 50% THF) can be used in formulation of the phages without a substantial titre loss.

Saturation of fatty acids in phosphatidic acid uniquely alters transthyretin stability changing morphology and toxicity of amyloid fibrils

Transthyretin (TTR) is a small, β-sheet-rich tetrameric protein that transports thyroid hormone thyroxine and retinol. Phospholipids, including phosphatidic acid (PA), can uniquely alter the stability of amyloidogenic proteins. However, the role of PA in TTR aggregation remains unclear. In this study, we investigated the effect of saturation of fatty acids (FAs) in PA on the rate of TTR aggregation. We also reveal the extent to which PAs with different length and saturation of FAs altered the morphology and secondary structure of TTR aggregates. Our results showed that TTR aggregation in the equimolar presence of PAs with different length and saturation of FAs yielded structurally and morphologically different fibrils compared to those formed in the lipid-free environment. We also found that PAs drastically lowered the toxicity of TTR aggregates formed in the presence of this phospholipid. These results shed light on the role of PA in the stability of TTR and transthyretin amyloidosis.

Single virus fingerprinting by widefield interferometric defocus-enhanced mid-infrared photothermal microscopy

Clinical identification and fundamental study of viruses rely on the detection of viral proteins or viral nucleic acids. Yet, amplification-based and antigen-based methods are not able to provide precise compositional information of individual virions due to small particle size and low-abundance chemical contents (e.g., ~ 5000 proteins in a vesicular stomatitis virus). Here, we report a widefield interferometric defocus-enhanced mid-infrared photothermal (WIDE-MIP) microscope for high-throughput fingerprinting of single viruses. With the identification of feature absorption peaks, WIDE-MIP reveals the contents of viral proteins and nucleic acids in single DNA vaccinia viruses and RNA vesicular stomatitis viruses. Different nucleic acid signatures of thymine and uracil residue vibrations are obtained to differentiate DNA and RNA viruses. WIDE-MIP imaging further reveals an enriched β sheet components in DNA varicella-zoster virus proteins. Together, these advances open a new avenue for compositional analysis of viral vectors and elucidating protein function in an assembled virion.

AFM-IR for Nanoscale Chemical Characterization in Life Sciences: Recent Developments and Future Directions

Despite the ubiquitous absorption of mid-infrared (IR) radiation by virtually all molecules that belong to the major biomolecules groups (proteins, lipids, carbohydrates, nucleic acids), the application of conventional IR microscopy to the life sciences remained somewhat limited, due to the restrictions on spatial resolution imposed by the diffraction limit (in the order of several micrometers). This issue is addressed by AFM-IR, a scanning probe-based technique that allows for chemical analysis at the nanoscale with resolutions down to 10 nm and thus has the potential to contribute to the investigation of nano and microscale biological processes. In this perspective, in addition to a concise description of the working principles and operating modes of AFM-IR, we present and evaluate the latest key applications of AFM-IR to the life sciences, summarizing what the technique has to offer to this field. Furthermore, we discuss the most relevant current limitations and point out potential future developments and areas for further application for fruitful interdisciplinary collaboration.

Elucidation of Secondary Structure and Toxicity of α-Synuclein Oligomers and Fibrils Grown in the Presence of Phosphatidylcholine and Phosphatidylserine

Abrupt aggregation of α-synuclein (α-Syn) in the midbrain hypothalamus and thalamus is a hallmark of Parkinson's disease (PD), the fastest growing neurodegenerative pathology, projected to strike 12 million people by 2040 worldwide. In this study, we examine the effect of two phospholipids that are present in neuronal membranes, phosphatidylcholine (PC) and phosphatidylserine (PS), on the rate of α-Syn aggregation. We found that PS accelerated α-Syn aggregation, whereas PC strongly inhibited α-Syn aggregation. We also utilized the nano-infrared imaging technique, also known as atomic force microscopy infrared (AFM-IR) spectroscopy, to investigate whether PC and PS only change the rates or also modify the secondary structure of α-Syn aggregates. We found that both phospholipids uniquely altered the secondary structure of α-Syn aggregates present at the lag and growth phase, as well as the late stage of protein aggregation. In addition, compared to the α-Syn aggregates formed in the lipid-free environment, α-Syn:PC and α-Syn:PS aggregates demonstrated higher cellular toxicity to N27 rat neurons. Interestingly, both α-Syn:PC and α-Syn:PS aggregates showed similar levels of oxidative stress, but α-Syn:PC aggregates exhibited a greater degree of mitochondrial dysfunction compared to α-Syn:PS aggregates.

Unsaturated fatty acids uniquely alter aggregation rate of α-synuclein and insulin and change the secondary structure and toxicity of amyloid aggregates formed in their presence

Docosahexaenoic (DHA) and arachidonic acids (ARA) are omega-3 and omega-6 long-chain polyunsaturated fatty acids (LCPUFAs). These molecules constitute a substantial portion of phospholipids in plasma membranes. Therefore, both DHA and ARA are essential diet components. Once consumed, DHA and ARA can interact with a large variety of biomolecules, including proteins such as insulin and α-synuclein (α-Syn). Under pathological conditions known as injection amyloidosis and Parkinson's disease, these proteins aggregate forming amyloid oligomers and fibrils, toxic species that exert high cell toxicity. In this study, we investigate the role of DHA and ARA in the aggregation properties of α-Syn and insulin. We found that the presence of both DHA and ARA at the equimolar concentrations strongly accelerated aggregation rates of α-Syn and insulin. Furthermore, LCPUFAs substantially altered the secondary structure of protein aggregates, whereas no noticeable changes in the fibril morphology were observed. Nanoscale Infrared analysis of α-Syn and insulin fibrils grown in the presence of both DHA and ARA revealed the presence of LCPUFAs in these aggregates. We also found that such LCPUFAs-rich α-Syn and insulin fibrils exerted significantly greater toxicities compared to the aggregates grown in the LCPUFAs-free environment. These findings show that interactions between amyloid-associated proteins and LCPUFAs can be the underlying molecular cause of neurodegenerative diseases.

Advancements of Nanotechnology and Nanomaterials in Environmental and Human Protection for Combatting the COVID-19 During and Post-pandemic Era: A Comprehensive Scientific Review

In December 2019, an outbreak of unknown pneumonia emerged in Wuhan City, Hubei Province, China. It was later identified as the SARS-CoV-2 virus and has since infected over 9 million people in more than 213 countries worldwide. Massive papers on the topic of SARS-CoV-2 that have already been published are necessary to be analyzed and discussed. This paper used the combination of systematic literature network analysis and content analysis to develop a comprehensive discussion related to the use of nanotechnology and materials in environmental and human protection. Its is shown that various efforts have been made to control the transmission of this pandemic. Nanotechnology plays a crucial role in modern vaccine design, as nanomaterials are essential tools for antigen delivery, adjuvants, and mimics of viral structures. In addition, nanomaterials and nanotechnology also reported a crucial role in environmental protection for defence and treating the pandemic. To eradicate pandemics now and in the future, successful treatments must enable rapid discovery, scalable manufacturing, and global distribution. In this review, we discuss the current approaches to COVID-19 development and highlight the critical role of nanotechnology and nanomaterials in combating the virus in the human body and the environment.

Elucidation of the Effect of Phospholipid Charge on the Rate of Insulin Aggregation and Structure and Toxicity of Amyloid Fibrils

The plasma membrane is a dynamic structure that separates the cell interior from the extracellular space. The fluidity and plasticity of the membrane determines a large number of physiologically important processes ranging from cell division to signal transduction. In turn, membrane fluidity is determined by phospholipids that possess different charges, lengths, and saturation states of fatty acids. A growing body of evidence suggests that phospholipids may play an important role in the aggregation of misfolded proteins, which causes pathological conditions that lead to severe neurodegenerative diseases. In this study, we investigate the role of the charge of the most abundant phospholipids in the plasma membrane: phosphatidylcholine and phosphatidylethanolamine, zwitterions: phosphatidylserine and phosphatidylglycerol, lipids that possess a negative charge, and cardiolipin that has double negative charge on its polar head. Our results show that both zwitterions strongly inhibit insulin aggregation, whereas negatively charged lipids accelerate fibril formation. We also found that in the equimolar presence of zwitterions insulin yields oligomers that exert significantly lower cell toxicity compared to fibrils that were grown in the lipid-free environment. Such aggregates were not formed in the presence of negatively charged lipids. Instead, long insulin fibrils that had strong cell toxicity were grown in the presence of such negatively charged lipids. However, our results showed no correlation between the charge of the lipid and secondary structure and toxicity of the aggregates formed in its presence. These findings show that the secondary structure and toxicity are determined by the chemical structure of the lipid rather than by the charge of the phospholipid polar head.

Nanoscale imaging of individual amyloid aggregates extracted from brains of Alzheimer and Parkinson patients reveals presence of lipids in α-synuclein but not in amyloid β1-42 fibrils

Abrupt aggregation of misfolded proteins is the underlying molecular cause of Alzheimer disease (AD) and Parkinson disease (PD). Both AD and PD are severe pathologies that affect millions of people around the world. A small 42 amino acid long peptide, known as amyloid β (Aβ), aggregates in the frontal cortex of AD patients forming oligomers and fibrils, highly toxic protein aggregates that cause progressive neuron death. Similar aggregates of α-synuclein (α-Syn), a small protein that facilitates neurotransmitter release, are observed in the midbrain, hypothalamus, and thalamus of people with PD. In this study, we utilized the innovative nano-Infrared imaging technique to investigate the structural organization of individual Aβ and α-syn fibrils postmortem extracted from brains of AD and PD patients, respectively. We observed two morphologically different Aβ and α-Syn fibril polymorphs in each patient's brain. One had twisted topology, whereas another exhibited flat tape-like morphology. We found that both polymorphs shared the same parallel β-sheet-dominated secondary structure. These findings suggested that both fibril polymorphs were built from structurally similar if not identical filaments that coiled forming twisted fibrils or associated side-by-side in the case of straight Aβ and α-Syn fibrils. Nano-Infrared analysis of individual protein aggregates also revealed the presence of lipids in the structure of both twisted and tape-like α-Syn fibrils that were not observed in any of the Aβ fibril polymorphs. These findings demonstrate that lipid membranes can play a critically important role in the onset and progression of PD.

Raman spectroscopy for viral diagnostics

Raman spectroscopy offers the potential for fingerprinting biological molecules at ultra-low concentration and therefore has potential for the detection of viruses. Here we review various Raman techniques employed for the investigation of viruses. Different Raman techniques are discussed including conventional Raman spectroscopy, surface-enhanced Raman spectroscopy, Raman tweezer, tip-enhanced Raman Spectroscopy, and coherent anti-Stokes Raman scattering. Surface-enhanced Raman scattering can play an essential role in viral detection by multiplexing nanotechnology, microfluidics, and machine learning for ensuring spectral reproducibility and efficient workflow in sample processing and detection. The application of these techniques to diagnose the SARS-CoV-2 virus is also reviewed.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s12551-023-01059-4.

Lipids uniquely alter rates of insulin aggregation and lower toxicity of amyloid aggregates

Amyloid formation is a hallmark of many medical diseases including diabetes type 2, Alzheimer's and Parkinson diseases. Under these pathological conditions, misfolded proteins self-assemble forming oligomers and fibrils, structurally heterogeneous aggregates that exhibit a large variety of shapes and forms. A growing body of evidence points to drastic changes in the lipid profile in organs affected by amyloidogenic diseases. In this study, we investigated the extent to which individual phospho- and sphingolipids, as well as their mixtures can impact insulin aggregation. Our results show that lipids and their mixtures uniquely alter rates of insulin aggregation simultaneously changing the secondary structure of protein aggregates that are grown in their presence. These structurally different protein-lipid aggregates impact cell viability to different extent while using distinct mechanisms of toxicity. These findings suggest that irreversible changes in lipid profiles of organs may trigger formation of toxic protein species that in turn are responsible for the onset and progression of amyloidogenic diseases.

Nanomechanical and Vibrational Signature of Chikungunya Viral Particles

Chikungunya virus (CHIKV) belongs to the genus Alphaviridae, with a single-stranded positive-sense RNA genome of 11.8 kbp encoding a polyprotein that generates both non-structural proteins and structural proteins. The virus is transmitted by the Aedes aegypti and A. albopictus mosquitoes, depending on the location. CHIKV infection leads to dengue-like musculoskeletal symptoms and has been responsible for several outbreaks worldwide since its discovery in 1952. Patients often experience fever, headache, muscle pain, joint swelling, and skin rashes. However, the ultrastructural and mechanical properties of CHIKV have not been fully characterized. Thus, this study aims to apply a physical approach to investigate CHIKV's ultrastructural morphology and mechanical properties, using atomic force microscopy and Raman spectroscopy as the main tools. Using nanomechanical assays of AFM and a gold nanoparticles substrate for Raman signal enhancement, we explored the conformational plasticity, morphology, vibrational signature, and nanomechanical properties of the chikungunya virus, providing new information on its ultrastructure at the nanoscale and offering a novel understanding of the virus' behavior upon mechanical disruptions besides its molecular composition.

Visible to Mid-IR Spectromicroscopy with Top-Down Illumination and Nanoscale (≈10 nm) Resolution

Photothermal induced resonance (PTIR), an atomic force microscopy (AFM) analogue of IR spectroscopy also known as AFM-IR, is capable of nanoscale lateral resolution and finds broad applications in biology and materials science. Here, the spectral range of a top-illumination PTIR setup operating in contact-mode is expanded for the first time to the visible and near-IR spectral ranges. The result is a tool that yields absorption spectra and maps of electronic and vibrational features with spatial resolution down to ≈10 nm. In addition to the improved resolution, the setup enables light-polarization-dependent PTIR experiments in the visible and near-IR ranges for the first time. While previous PTIR implementations in the visible used total internal reflection illumination requiring challenging sample preparations on an optically transparent prism, the top illumination used here greatly simplifies sample preparation and will foster a broad application of this method.

Amyloid aggregates exert cell toxicity causing irreversible damages in the endoplasmic reticulum

Amyloid oligomers and fibrils are protein aggregates that cause an onset and progression of many neurodegenerative diseases, diabetes type 2 and systemic amyloidosis. Although a growing body of evidence shows that oligomers and fibrils trigger mitochondrial dysfunction simultaneously enhancing production of reactive oxygen species, exact mechanisms by which these protein aggregates exert their toxicities remain unclear. In this study, we used advanced microscopic and spectroscopic methods to examine topography and structure of insulin aggregates grown in the lipid-free environment, as well as in the presence of major classes of phospho- and sphingolipids. We also employed a set of molecular markers to determine the extent to which insulin aggregates induce a damage of cell endoplasmic reticulum (ER), an important cell organelle used for calcium storage, protein synthesis and folding. Our results show that insulin aggregates activate the expression of Activating Transcription Factor 6 (ATF6), a transmembrane protein that is involved in unfolded protein response (UPR) of the stressed ER. At the same time, two other ER transmembrane proteins, Inositol Requiring 1 (IRE1α) and eLF2a, the product of PKR-like ER kinase (PERK), exhibited very low expression levels. Furthermore, amyloid aggregates trigger an expression of the 78-kDa glucose-regulated protein GRP78, which is also involved in the UPR. We also observed UPR-induced expression of a proapoptotic transcription factor CHOP, which, in turn, regulates expression of caspase 3 kinase and BCL2 protein family members, including the ER localized Bax. These findings show that insulin oligomers and fibrils induce UPR-associated ER stress and ultimately fatal changes in cell homeostasis.

Lipids uniquely alter secondary structure and toxicity of lysozyme aggregates

Abrupt aggregation of misfolded proteins is a hallmark of the large group of amyloid pathologies that include diabetes type 2, Alzheimer and Parkinson's diseases. Protein aggregation yields oligomers and fibrils, β-sheet-rich structures that exert cell toxicity. Microscopic examination of amyloid deposits reveals the presence of lipids membranes, which suggests that lipids can be involved in the process of pathogenic protein assembly. In this study, we show that lipids can uniquely alter the aggregation rates of lysozyme, a protein that is associated with systemic amyloidosis. Specifically, cardiolipin (CL), ceramide (CER), and sphingomyelin (SM) accelerate, phosphatidylcholine (PC) strongly inhibits, whereas phosphatidylserine (PS) has no effect on the rate of protein aggregation. Furthermore, lipids uniquely alter the secondary structure of lysozyme aggregates. Furthermore, we found that lysozyme aggregates grown in the presence of CL, CER, SM, PS, and CL:PC mixtures exert significantly lower production of reactive oxygen species and mitochondrial dysfunction compared to lysozyme:PC aggregates and lysozyme fibrils grown in the lipid-free environment. These findings suggest that a change in the lipid composition of cell membranes, which is taken place upon neurodegeneration, may trigger the formation of toxic protein species that otherwise would not be formed.

Charge of Phospholipids Determines the Rate of Lysozyme Aggregation but Not the Structure and Toxicity of Amyloid Aggregates

Biophysical properties of plasma membranes are determined by a chemical structure of phospholipids, including saturation of fatty acids and charge of polar heads of these molecules. Phospholipids not only determine fluidity and plasticity of membranes but also play an important role in abrupt aggregation of misfolded proteins. In this study, we investigate the role of the charge of the most abundant phospholipids in the plasma membrane on the aggregation properties of the lysozyme. We found that the charge of phospholipids determines the aggregation rate of lysozyme and the morphology of the protein aggregates. However, the secondary structure and toxicity of these protein specimens are determined by the chemical nature rather than the charge of phospholipids. These findings show that the charge of phospholipids can be a key factor that determines the stability and aggregation mechanism of amyloidogenic proteins.

Understanding Cantilever Transduction Efficiency and Spatial Resolution in Nanoscale Infrared Microscopy

Photothermal induced resonance (PTIR), also known as AFM-IR, enables nanoscale infrared (IR) imaging and spectroscopy by using the tip of an atomic force microscope to transduce the local photothermal expansion and contraction of a sample. The signal transduction efficiency and spatial resolution of PTIR depend on a multitude of sample, cantilever, and illumination source parameters in ways that are not yet well understood. Here, we elucidate and separate the effects of laser pulse length, pulse shape, sample thermalization time (τ), interfacial thermal conductance, and cantilever detection frequency by devising analytical and numerical models that link a sample's photothermal excitations to the cantilever dynamics over a broad bandwidth (10 MHz). The models indicate that shorter laser pulses excite probe oscillations over broader bandwidths and should be preferred for measuring samples with shorter thermalization times. Furthermore, we show that the spatial resolution critically depends on the interfacial thermal conductance between dissimilar materials and improves monotonically, but not linearly, with increasing cantilever detection frequencies. The resolution can be enhanced for samples that do not fully thermalize between pulses (i.e., laser repetition rates ≳ 1/3τ) as the probed depth becomes smaller than the film thickness. We believe that the insights presented here will accelerate the adoption and impact of PTIR analyses across a wide range of applications by informing experimental designs and measurement strategies as well as by guiding future technical advances.

Length and Unsaturation of Fatty Acids of Phosphatidic Acid Determines the Aggregation Rate of Insulin and Modifies the Structure and Toxicity of Insulin Aggregates

Phosphatidic acid (PA) is a unique plasma membrane lipid that contains fatty acids (FAs) with different lengths and degrees of unsaturation. Under physiological conditions, PA acts as a second messenger regulating a wide variety of cellular processes. At the same time, the role of PA under pathological conditions, which are caused by an abrupt aggregation of amyloid proteins, remains unclear. In this study, we investigated the effect of PA with different lengths and unsaturation of FAs on insulin aggregation. We found that PA with C16:0 FAs strongly inhibited insulin aggregation, whereas PA with C18:0 FAs accelerated it. Furthermore, PA with unsaturated (C18:1) FAs made the insulin form extremely long and thick fibrils that were not observed for PAs with saturated FAs. We also found that the presence of PA with C16:0 FAs resulted in the formation of aggregates that exerted significantly lower cell toxicity compared to the aggregates formed in the presence of PAs with C18:0 and C18:1 FAs. These results suggest that PA may play a key role in neurodegeneration.

Phosphatidylcholine and Phosphatidylserine Uniquely Modify the Secondary Structure of α-Synuclein Oligomers Formed in Their Presence at the Early Stages of Protein Aggregation

Abrupt aggregation of α-synuclein (α-Syn) leads to a formation of highly toxic protein oligomers. These aggregates are the underlying molecular cause of an onset of the irreversible degeneration of dopaminergic neurons in midbrain, hypothalamus, and thalamus, a pathology known as Parkinson's disease. The transient nature of oligomers, as well as their structural and morphological heterogeneity, limits the use of cryo-electron microscopy and solid-state NMR, classical tools of structural biology, for elucidation of their secondary structure. Despite this limitation, numerous pieces of experimental evidence suggest that phospholipids can uniquely alter the structure and toxicity of oligomers. In this study, we utilize an innovative nano-infrared imaging technique, also known as atomic force microscopy infrared (AFM-IR) spectroscopy, to examine the structure of individual α-Syn oligomers grown in the presence of phosphatidylcholine (α-Syn:PC) and phosphatidylserine (α-Syn:PS). We determined the amount of the parallel and the antiparallel β-sheets, as well as the amount the α-helix and the unordered protein, in the secondary structure of α-Syn:PC and α-Syn:PS formed at day 2 (D2), 8 (D8), and 15 (D15) after initiation of protein aggregation. We found a gradual decrease in the amount of the parallel β-sheet in both α-Syn:PC and α-Syn:PS from D2 to D15 together with an increase in the α-helix and the unordered protein secondary structure. We infer that this is due to the presence of lipids in the structure of oligomers that prevent an expansion of the parallel β-sheet upon interaction of the oligomers with monomeric α-Syn.

Diagnosing COVID-19 in human serum using Raman spectroscopy

This study proposed the diagnosis of COVID-19 by means of Raman spectroscopy. Samples of blood serum from 10 patients positive and 10 patients negative for COVID-19 by RT-PCR RNA and ELISA tests were analyzed. Raman spectra were obtained with a dispersive Raman spectrometer (830 nm, 350 mW) in triplicate, being submitted to exploratory analysis with principal component analysis (PCA) to identify the spectral differences and discriminant analysis with PCA (PCA-DA) and partial least squares (PLS-DA) for classification of the blood serum spectra into Control and COVID-19. The spectra of both groups positive and negative for COVID-19 showed peaks referred to the basal constitution of the serum (mainly albumin). The difference spectra showed decrease in the peaks referred to proteins and amino acids for the group positive. PCA variables showed more detailed spectral differences related to the biochemical alterations due to the COVID-19 such as increase in lipids, nitrogen compounds (urea and amines/amides) and nucleic acids, and decrease of proteins and amino acids (tryptophan) in the COVID-19 group. The discriminant analysis applied to the principal component loadings (PC2, PC4, PC5, and PC6) could classify spectra with 87% sensitivity and 100% specificity compared to 95% sensitivity and 100% specificity indicated in the RT-PCR kit leaflet, demonstrating the possibilities of a rapid, label-free, and costless technique for diagnosing COVID-19 infection.

Unsaturation in the Fatty Acids of Phospholipids Drastically Alters the Structure and Toxicity of Insulin Aggregates Grown in Their Presence

Lipid bilayers play an important role in the pathological assembly of amyloidogenic proteins and peptides. This assembly yields oligomers and fibrils, which are highly toxic protein aggregates. In this study, we investigated the role of saturation in fatty acids of two phospholipids that are present in cell membranes. We found that unsaturated cardiolipin (CL) drastically shortened the lag phase of insulin aggregation. Furthermore, structurally and morphologically different aggregates were formed in the presence of unsaturated CL vs saturated CL. These aggregates exerted drastically different cell toxicity. Both saturated and unsaturated phosphatidylcholine (PC) were able to inhibit insulin aggregation equally efficiently. Similar to CL, structurally different aggregates were formed in the presence of saturated and unsaturated PC. These aggregates exerted different cell toxicities. These results show that unsaturated phospholipids catalyze the formation of more toxic amyloid aggregates comparing to those formed in the presence of saturated lipids.

Current Status and Challenges of Analytical Methods for Evaluation of Size and Surface Modification of Nanoparticle-Based Drug Formulations

The present review discusses the current status and difficulties of the analytical methods used to evaluate size and surface modifications of nanoparticle-based pharmaceutical products (NPs) such as liposomal drugs and new SARS-CoV-2 vaccines. We identified the challenges in the development of methods for (1) measurement of a wide range of solid-state NPs, (2) evaluation of the sizes of polydisperse NPs, and (3) measurement of non-spherical NPs. Although a few methods have been established to analyze surface modifications of NPs, the feasibility of their application to NPs is unknown. The present review also examined the trends in standardization required to validate the size and surface measurements of NPs. It was determined that there is a lack of available reference materials and it is difficult to select appropriate ones for modified NP surface characterization. Research and development are in progress on innovative surface-modified NP-based cancer and gene therapies targeting cells, tissues, and organs. Next-generation nanomedicine should compile studies on the practice and standardization of the measurement methods for NPs to design surface modifications and ensure the quality of NPs.

The Degree of Unsaturation of Fatty Acids in Phosphatidylserine Alters the Rate of Insulin Aggregation and the Structure and Toxicity of Amyloid Aggregates

Phosphatidylserine (PS) in the plasma membrane plays an important role in cell signaling and apoptosis. Cell degeneration is also linked to numerous amyloid diseases, pathologies that are associated with aggregation of misfolded proteins. In this work, we examine the effect of both saturated PS (DMPS) and unsaturated PS (DOPS and POPS) on the aggregation properties of insulin, as well as the structure and toxicity of insulin aggregates formed in the presence of these phospholipids. We found that the degree of unsaturation of fatty acids in PS alters the rate of insulin aggregation. We also found that toxicity of insulin-DMPS aggregates is significantly lower than the toxicity of DOPS- and POPS-insulin fibrils, whereas all these lipid-containing aggregates exert lower cell toxicity than insulin fibrils grown in a lipid-free environment.

Progress of tip-enhanced Raman scattering for the last two decades and its challenges in very recent years

Tip-enhanced Raman scattering (TERS) has recently attracted remarkable attention as a novel nano-spectroscopy technique. TERS, which provides site-specific information, can be performed on any material surface regardless of morphology. Moreover, it can be applied in various environments, such as ambient air, ultrahigh vacuum (UHV), solutions, and electrochemical environments. This review reports on one hand progress of TERS for the last two decades, and on the other hand, its challenges in very recent years. Part of the progress of TERS starts with the prehistory and history of TERS, and then, the characteristics and advantages of TERS are described. Significant emphasis is put on the development of TERS instrumentation and equipment such as ultrahigh vacuum TERS, liquid TERS, electrochemical-TERS, and tip-preparations. Applications of TERS, particularly those with nanocarbons, biological materials, and surface and interface analysis, are mentioned in some detail. In the part on challenges, we focus on the very recent advances in TERS; progress in spatial resolution to the angstrom scale is the hottest topic. Recent TERS studies performed under UHV, for example chemical imaging at the angstrom scale and Raman detection of bond breaking and making of a chemisorbed up-standing single molecules at single-bond level, are reviewed. Of course, there is no clear border between the two parts. In the last part the perspective of TERS is discussed.

Photothermal Atomic Force Microscopy Coupled with Infrared Spectroscopy (AFM-IR) Analysis of High Extinction Coefficient Materials: A Case Study with Silica and Silicate Glasses

Photothermal atomic force microscopy coupled with infrared spectroscopy (AFM-IR) brings significant value as a spatially resolved surface analysis technique for disordered oxide materials such as glasses, but additional development and fundamental understanding of governing principles is needed to interpret AFM-IR spectra, since the existing theory described for organic materials does not work for materials with high extinction coefficients for infrared (IR) absorption. This paper describes theoretical calculation of a transient temperature profile inside the IR-absorbing material considering IR refraction at the interface as well as IR adsorption and heat transfer inside the sample. This calculation explains the differences in peak positions and amplitudes of AFM-IR spectra from those of specular reflectance and extinction coefficient spectra. It also addresses the information depth of the AFM-IR characterization of bulk materials. AFM-IR applied to silica and silicate glass surfaces has demonstrated novel capability of characterizing subsurface structural changes and surface heterogeneity due to mechanical stresses from physical contacts, as well as chemical alterations manifested in surface layers through aqueous corrosion.

Characterization of Substrates and Surface-Enhancement in Atomic Force Microscopy Infrared Analysis of Amyloid Aggregates

Atomic force microscopy infrared (AFM-IR) spectroscopy is an emerging analytical technique that can be used to probe the structural organization of specimens with nanometer spatial resolution. A growing body of evidence suggests that nanoscale structural analysis of very small (<10 nm) biological objects, such as viruses and amyloid aggregates, requires substrates that must fit strict criteria of low surface roughness and low IR background, simultaneously. In this study, we examine the suitability of a broad range of substrates commonly used in AFM and IR fields, and we determined that silicon, zinc sulfide, and calcium fluoride are the most ideal substrates for nanoscale imaging of amyloid oligomers, protein aggregates that are directly linked to the onset and progression of neurodegenerative diseases. Our data show that these substrates provide the lowest roughness and the lowest background in the 800-1800 cm^-1 spectral window from all examined AFM and IR substrates. We also investigate a contribution of surface enhancement in AFM-IR by the direct comparison of signal intensities from oligomers located on silicon and gold-coated silicon surfaces. We found that metallization of such substrates provides a factor of ~7 enhancements to the IR signal and induces an equivalent enhancement of the sample background in the 950-1250 cm^-1 spectral region.

Diagnosing COVID-19 in human serum using Raman spectroscopy

This study proposed the diagnosis of COVID-19 by means of Raman spectroscopy. Samples of blood serum from 10 patients positive and 10 patients negative for COVID-19 by RT-PCR RNA and ELISA tests were analyzed. Raman spectra were obtained with a dispersive Raman spectrometer (830 nm, 350 mW) in triplicate, being submitted to exploratory analysis with principal component analysis (PCA) to identify the spectral differences and discriminant analysis with PCA (PCA-DA) and partial least squares (PLS-DA) for classification of the blood serum spectra into Control and COVID-19. The spectra of both groups positive and negative for COVID-19 showed peaks referred to the basal constitution of the serum (mainly albumin). The difference spectra showed decrease in the peaks referred to proteins and amino acids for the group positive. PCA variables showed more detailed spectral differences related to the biochemical alterations due to the COVID-19 such as increase in lipids, nitrogen compounds (urea and amines/amides) and nucleic acids, and decrease of proteins and amino acids (tryptophan) in the COVID-19 group. The discriminant analysis applied to the principal component loadings (PC2, PC4, PC5, and PC6) could classify spectra with 87% sensitivity and 100% specificity compared to 95% sensitivity and 100% specificity indicated in the RT-PCR kit leaflet, demonstrating the possibilities of a rapid, label-free, and costless technique for diagnosing COVID-19 infection.

Identification of Chemical Bonds and Microstructure of Hydrated Tricalcium Silicate (C3S) by a Coupled Micro-Raman/BSE-EDS Evaluation

Identifying the phase evolution and revealing the chemical bonds of hydrated cements accurately is crucial to regulate the performance of cementitious materials. In this paper, a coupled Raman/BSE-EDS analysis was proposed to determine the chemical bonds of tricalcium silicate hydrates and the interface transition zone (ITZ) between inner C-S-H and anhydrates. The results show that the Raman/BSE-EDS method can accurately identify the chemical bonds of inner C-S-H and inner ITZ regions, which confirms the mixed structure of inner C-S-H and nano calcium hydroxide (CH). The inner ITZ shows a lattice change region with a thickness of 700–1000 nm, which can be attributed to the pre-disassembly process of C₃S crystal. The successful application of coupled Raman/BSE-EDS provides new insight into the hydration process and multi-structure features of traditional cementitious materials.

Development of Marine-Derived Compounds for Cancer Therapy

Cancer has always been a threat to human health with its high morbidity and mortality rates. Traditional therapy, including surgery, chemotherapy and radiotherapy, plays a key role in cancer treatment. However, it is not able to prevent tumor recurrence, drug resistance and treatment side effects, which makes it a very attractive challenge to search for new effective and specific anticancer drugs. Nature is a valuable source of multiple pharmaceuticals, and most of the anticancer drugs are natural products or derived from them. Marine-derived compounds, such as nucleotides, proteins, peptides and amides, have also shed light on cancer therapy, and they are receiving a fast-growing interest due to their bioactive properties. Their mechanisms contain anti-angiogenic, anti-proliferative and anti-metastasis activities; cell cycle arrest; and induction of apoptosis. This review provides an overview on the development of marine-derived compounds with anticancer properties, both their applications and mechanisms, and discovered technologies.

Low-Background Tip-Enhanced Raman Spectroscopy Enabled by a Plasmon Thin-Film Waveguide Probe

Tip-enhanced Raman spectroscopy (TERS) is a nano-optical approach to extract spatially resolved chemical information with nanometer precision. However, in the case of direct-illumination TERS, which is often employed in commercial TERS instruments, strong fluorescence or far-field Raman signals from the illuminated areas may be excited as a background. They may overwhelm the near-field TERS signal and dramatically decrease the near-field to far-field signal contrast of TERS spectra. It is still challenging for TERS to study the surface of fluorescent materials or a bulk sample that cannot be placed on an Au/Ag substrate. In this study, we developed an indirect-illumination TERS probe that allows a laser to be focused on a flat interface of a thin-film waveguide located far away from the region generating the TERS signal. Surface plasmon polaritons are generated stably on the waveguide and eventually accumulated at the tip apex, thereby producing a spatially and energetically confined hotspot to ensure stable and high-resolution TERS measurements with a low background. With this thin-film waveguide probe, TERS spectra with obvious contrast from a diamond plate can be acquired. Furthermore, the TERS technique based on this probe exhibits excellent TERS signal stability, a long lifetime, and good spatial resolution. This technique is expected to have commercial potential and enable further popularization and development of TERS technology as a powerful analytical method.

Towards a Quantitative Single Particle Characterization by Super Resolution Microscopy: From Virus Structures to Antivirals Design

In the last year the COVID19 pandemic clearly illustrated the potential threat that viruses pose to our society. The characterization of viral structures and the identification of key proteins involved in each step of the cycle of infection are crucial to develop treatments. However, the small size of viruses, invisible under conventional fluorescence microscopy, make it difficult to study the organization of protein clusters within the viral particle. The applications of super-resolution microscopy have skyrocketed in the last years, converting this group into one of the leading techniques to characterize viruses and study the viral infection in cells, breaking the diffraction limit by achieving resolutions up to 10 nm using conventional probes such as fluorescent dyes and proteins. There are several super-resolution methods available and the selection of the right one it is crucial to study in detail all the steps involved in the viral infection, quantifying and creating models of infection for relevant viruses such as HIV-1, Influenza, herpesvirus or SARS-CoV-1. Here we review the use of super-resolution microscopy (SRM) to study all steps involved in the viral infection and antiviral design. In light of the threat of new viruses, these studies could inspire future assays to unveil the viral mechanism of emerging viruses and further develop successful antivirals against them.