FTIR, Raman and AFM characterization of the clinically valid biochemical parameters of the thrombi in acute ischemic stroke

Human erythrocytes under stress. Spectroscopic fingerprints of known oxidative mechanisms and beyond

In this work, we investigated the oxidative stress-related biochemical alterations in red blood cells (RBCs) and their membranes with the use of spectroscopic techniques. We aimed to show their great advantage for the in situ detection of lipid classes and secondary structures of proteins without the need for their extraction in the cellular environment. The exposition of the cells to peroxides, t-butyl hydroperoxide (tBOOH) or hydrogen peroxide (H2O2) led to different degradation processes encompassing the changes in the composition of membranes and structural modifications of hemoglobin (Hb). Our results indicated that tBOOH is generally a stronger oxidizing agent than H2O2 and this observation was congruent with the activity of superoxide and glutathione peroxidase. ATR-FTIR and Raman spectroscopies of membranes revealed that tBOOH caused primarily the partial loss and peroxidation of the lipids resulting in loss of the integrity of membranes. In turn, both peroxides induced several kinds of damage in the protein layer, including the partial decrease of their content and irreversible aggregation of spectrin, ankyrin, and membrane-bound globin. These changes were especially pronounced on the membrane surface where stress conditions induced the formation of β-sheets and intramolecular aggregates, particularly for tBOOH. Interestingly, nano-FTIR spectroscopy revealed the lipid peroxidative damage on the membrane surface in both cases. As far as hemoglobin was concerned, tBOOH and H2O2 caused the increase of the oxyhemoglobin species and conformational alterations of its polypeptide chain into β-sheets. Our findings confirm that applied spectroscopies effectively track the oxidative changes occurring in the structural components of red blood cells and the simplicity of conducting measurements and sample preparation can be readily applied to pharmacological and clinical studies.

A review of concepts and methods for FTIR imaging of biomarker changes in the post-stroke brain

Stroke represents a core area of study in neurosciences and public health due to its global contribution toward mortality and disability. The intricate pathophysiology of stroke, including ischemic and hemorrhagic events, involves the interruption in oxygen and nutrient delivery to the brain. Disruption of these crucial processes in the central nervous system leads to metabolic dysregulation and cell death. Fourier transform infrared (FTIR) spectroscopy can simultaneously measure total protein and lipid content along with a number of key biomarkers within brain tissue that cannot be observed using conventional techniques. FTIR imaging provides the opportunity to visualize this information in tissue which has not been chemically treated prior to analysis, thus retaining the spatial distribution and in situ chemical information. Here we present a review of FTIR imaging methods for investigating the biomarker responses in the post-stroke brain.

Fast screening using attenuated total reflectance- fourier transform infrared (ATR-FTIR) spectroscopy of patients based on D-dimer threshold value

Attenuated Total Reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy is an emerging technology in the medical field. Blood D-dimer was initially studied as a marker of the activation of coagulation and fibrinolysis. It is mainly used as a potential diagnosis screening test for pulmonary embolism or deep vein thrombosis but was recently associated with COVID-19 severity. This study aimed to evaluate the use of ATR-FTIR spectroscopy with machine learning to classify plasma D-dimer concentrations. The plasma ATR-FTIR spectra from 100 patients were studied through principal component analysis (PCA) and two supervised approaches: genetic algorithm with linear discriminant analysis (GA-LDA) and partial least squares with linear discriminant (PLS-DA). The spectra were truncated to the fingerprint region (1800-1000 cm-1). The GA-LDA method effectively classified patients according to D-dimer cutoff (≤0.5 μg/mL and >0.5 μg/mL) with 87.5 % specificity and 100 % sensitivity on the training set, and 85.7 % specificity, and 95.6 % sensitivity on the test set. Thus, we demonstrate that ATR-FTIR spectroscopy might be an important additional tool for classifying patients according to D-dimer values. ATR-FTIR spectral analyses associated with clinical evidence can contribute to a faster and more accurate medical diagnosis, reduce patient morbidity, and save resources and demand for professionals.

Exploration of macromolecular phenotype of human skeletal muscle in diabetes using infrared spectroscopy

Introduction

The global burden of diabetes mellitus is escalating, and more efficient investigative strategies are needed for a deeper understanding of underlying pathophysiological mechanisms. The crucial role of skeletal muscle in carbohydrate and lipid metabolism makes it one of the most susceptible tissues to diabetes-related metabolic disorders. In tissue studies, conventional histochemical methods have several technical limitations and have been shown to inadequately characterise the biomolecular phenotype of skeletal muscle to provide a holistic view of the pathologically altered proportions of macromolecular constituents.

Materials and methods

In this pilot study, we examined the composition of five different human skeletal muscles from male donors diagnosed with type 2 diabetes and non-diabetic controls. We analysed the lipid, glycogen, and collagen content in the muscles in a traditional manner with histochemical assays using different staining techniques. This served as a reference for comparison with the unconventional analysis of tissue composition using Fourier-transform infrared spectroscopy as an alternative methodological approach.

Results

A thorough chemometric post-processing of the infrared spectra using a multi-stage spectral decomposition allowed the simultaneous identification of various compositional details from a vibrational spectrum measured in a single experiment. We obtained multifaceted information about the proportions of the different macromolecular constituents of skeletal muscle, which even allowed us to distinguish protein constituents with different structural properties. The most important methodological steps for a comprehensive insight into muscle composition have thus been set and parameters identified that can be used for the comparison between healthy and diabetic muscles.

Conclusion

We have established a methodological framework based on vibrational spectroscopy for the detailed macromolecular analysis of human skeletal muscle that can effectively complement or may even serve as an alternative to histochemical assays. As this is a pilot study with relatively small sample sets, we remain cautious at this stage in drawing definitive conclusions about diabetes-related changes in skeletal muscle composition. However, the main focus and contribution of our work has been to provide an alternative, simple and efficient approach for this purpose. We are confident that we have achieved this goal and have brought our methodology to a level from which it can be successfully transferred to a large-scale study that allows the effects of diabetes on skeletal muscle composition and the interrelationships between the macromolecular tissue alterations due to diabetes to be investigated.

Direct intracellular detection of biomolecule specific bound-water with Raman spectroscopy

Lipids, proteins, and nucleic acids have closely associated water molecules (Bound water), which exhibit considerably different physical properties compared to bulk water. Here we investigate the possibility of resolving Raman spectra of the specific hydration shell of these biomolecules in intracellular regions using Raman imaging. Lipids and proteins + nucleic acids Raman spectral components resolved in the analysis showed associated water spectral features, which are uniquely different from that of bulk water. These spectral profiles agree with water spectral profile observed in the case of corresponding hydrated pure biomolecules. The results show the prospects of Raman imaging in examining intracellular hydration in biomolecules and its functional relation.

Characterising acute ischaemic stroke thrombi: insights from histology, imaging and emerging impedance-based technologies

Treatment of acute ischaemic stroke (AIS) focuses on rapid recanalisation of the occluded artery. In recent years, advent of mechanical thrombectomy devices and new procedures have accelerated the analysis of thrombi retrieved during the endovascular thrombectomy procedure. Despite ongoing developments and progress in AIS imaging techniques, it is not yet possible to conclude definitively regarding thrombus characteristics that could advise on the probable efficacy of thrombolysis or thrombectomy in advance of treatment. Intraprocedural devices with dignostic capabilities or new clinical imaging approaches are needed for better treatment of AIS patients. In this review, what is known about the composition of the thrombi that cause strokes and the evidence that thrombus composition has an impact on success of acute stroke treatment has been examined. This review also discusses the evidence that AIS thrombus composition varies with aetiology, questioning if suspected aetiology could be a useful indicator to stroke physicians to help decide the best acute course of treatment. Furthermore, this review discusses the evidence that current widely used radiological imaging tools can predict thrombus composition. Further use of new emerging technologies based on bioimpedance, as imaging modalities for diagnosing AIS and new medical device tools for detecting thrombus composition in situ has been introduced. Whether bioimpedance would be beneficial for gaining new insights into in situ thrombus composition that could guide choice of optimum treatment approach is also reviewed.

Nanomechanics of Blood Clot and Thrombus Formation

Mechanical properties have been extensively studied in pure elastic or viscous materials; however, most biomaterials possess both physical properties in a viscoelastic component. How the biomechanics of a fibrin clot is related to its composition and the microenvironment where it is formed is not yet fully understood. This review gives an outline of the building mechanisms for blood clot mechanical properties and how they relate to clot function. The formation of a blood clot in health conditions or the formation of a dangerous thrombus go beyond the mere polymerization of fibrinogen into a fibrin network. The complex composition and localization of in vivo fibrin clots demonstrate the interplay between fibrin and/or fibrinogen and blood cells. Studying these protein–cell interactions and clot mechanical properties may represent new methods for the evaluation of cardiovascular diseases (the leading cause of death worldwide), creating new possibilities for clinical diagnosis, prognosis, and therapy.

Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Tracking of the biochemical changes upon pleomorphic adenoma progression using vibrational microspectroscopy

Head and neck tumors can be very challenging to treat because of the risk of problems or complications after surgery. Therefore, prompt and accurate diagnosis is extremely important to drive appropriate treatment decisions, which may reduce the chance of recurrence. This paper presents the original research exploring the feasibility of Fourier transform infrared (FT-IR) and Raman spectroscopy (RS) methods to investigate biochemical alterations upon the development of the pleomorphic adenoma. Principal component analysis (PCA) was used for a detailed assessment of the observed changes and to determine the spectroscopic basis for salivary gland neoplastic pathogenesis. It is implied that within the healthy margin, as opposed to the tumoral tissue, there are parts that differ significantly in lipid content. This observation shed new light on the crucial role of lipids in tissue physiology and tumorigenesis. Thus, a novel approach that eliminates the influence of lipids on the elucidation of biochemical changes is proposed. The performed analysis suggests that the highly heterogeneous healthy margin contains more unsaturated triacylglycerols, while the tumoral section is rich in proteins. The difference in protein content was also observed for these two tissue types, i.e. the healthy tissue possesses more proteins in the anti-parallel β-sheet conformation, whereas the tumoral tissue is dominated by proteins rich in unordered random coils. Furthermore, the pathogenic tissue shows a higher content of carbohydrates and reveals noticeable differences in nucleic acid content. Finally, FT-IR and Raman spectroscopy methods were proposed as very promising methods in the discrimination of tumoral and healthy tissues of the salivary gland.

A Single-Center (Sibiu, Romania), Retrospective Study (March-November 2020) of COVID-19 Clinical and Epidemiological Features in Children

The aim of this study was to describe and analyze epidemiological and clinical features of children screened for COVID-19 at Sibiu Pediatric Clinical Hospital during the first 9 months (March–November) of coronavirus disease pandemic in Romania. A total of 203 pediatric patients with a confirmed diagnosis of COVID-19 were included in the study. The median age of the patients was 121 (IQR 18–181) months and 52.22% had mild clinical type with pneumonia, 35.47% were moderate cases, 3.94% severe cases, 0.99% critically ill cases and 7.39% were asymptomatic. The most common symptoms were fever (n = 130, 64.03%), nasal congestion (n = 138, 67.98%), cough (n = 128, 63.05%) followed by sore throat (n = 64, 31.52%), rhinorrhea (n = 63, 31.03%), fatigue (n = 57, 28.07%), headache (n = 47, 23.15%), diarrhea (n = 39, 19.21%), vomiting (n = 32, 15.76%), myalgia (n = 24, 11.82%), abdominal pain (n = 22, 10.83%). A higher proportion of infants with severe or critical disease was encountered with lymphopenia (n = 9, 90%), neutrophilia (n = 5, 50%), leukocytosis (n = 5, 50%) compared with asymptomatic infants (n = 10, 66.67%, n = 1, 6.67%, n = 3, 20%) or mild (n = 53, 50%, n = 19, 17.92%, n = 15, 14.15%) and moderate (n = 37, 51.39%, n = 9, 12.50%, n = 6, 8.33%) cases (p = 0.095, p = 0.042, p = 0.034). Pediatric patients generally had mild or moderate type of COVID-19, and the critically ill cases were rare. In our study, frequent symptoms were observed in both the systemic and respiratory systems, ear, nose and throat system, and less from gastrointestinal system, central nervous system or ocular system. Additionally, there is an increase in liver and myocardial enzyme levels with an increase in disease severity. Understanding the clinical and laboratory characteristics of pediatric patients is important for diagnosis, management and effective control of the disease.

Isotope-Edited Amide II Mode: A New Label for Site-Specific Vibrational Spectroscopy

Vibrational spectroscopy is a powerful tool used to analyze biological and chemical samples. However, in proteins, the most predominant peaks that arise from the backbone amide groups overlap one another, hampering site-specific analyses. Isotope editing has provided a robust, noninvasive approach to overcome this hurdle. In particular, the 1-¹³C═¹⁶O and 1-¹³C═¹⁸O labels that shift the amide I vibrational mode have enabled 1D- and 2D-IR spectroscopy to characterize proteins with excellent site-specific resolution. Herein, we expand the vibrational spectroscopy toolkit appreciably by introducing the 1-¹³C[Formula: see text]¹⁵N probe at specific locations along the protein backbone. A new, isotopically edited amide II peak is observed clearly in the spectra despite the presence of unlabeled modes arising from the rest of the protein. The experimentally determined shift of -30 cm^-1 is reproduced by DFT calculations providing further credence to the mode assignment. Since the amide II mode arises from different elements than the amide I mode, it affords molecular insights that are both distinct and complementary. Moreover, multiple labeling schemes may be used simultaneously, enhancing vibrational spectroscopy's ability to provide detailed molecular insights.

Metabolomics and metabolites in ischemic stroke

Stroke is a major reason for disability and the second highest cause of death in the world. When a patient is admitted to a hospital, it is necessary to identify the type of stroke, and the likelihood for development of a recurrent stroke, vascular dementia, and depression. These factors could be determined using different biomarkers. Metabolomics is a very promising strategy for identification of biomarkers. The advantage of metabolomics, in contrast to other analytical techniques, resides in providing low molecular weight metabolite profiles, rather than individual molecule profiles. Technically, this approach is based on mass spectrometry and nuclear magnetic resonance. Furthermore, variations in metabolite concentrations during brain ischemia could alter the principal neuronal functions. Different markers associated with ischemic stroke in the brain have been identified including those contributing to risk, acute onset, and severity of this pathology. In the brain, experimental studies using the ischemia/reperfusion model (IRI) have shown an impaired energy and amino acid metabolism and confirmed their principal roles. Literature data provide a good basis for identifying markers of ischemic stroke and hemorrhagic stroke and understanding metabolic mechanisms of these diseases. This opens an avenue for the successful use of identified markers along with metabolomics technologies to develop fast and reliable diagnostic tools for ischemic and hemorrhagic stroke.

Molecular profiling of the intestinal mucosa and immune cells of the colon by multi-parametric histological techniques

The impact of the post-mortem interval (PMI) on the optical molecular characteristics of the colonic mucosa and the gut-associated lymphoid tissue (GALT) were examined by multi-parametric measurements techniques. Inflammatory cells were identified by immunohistochemical staining. Molecular parameters were estimated using the Raman spectroscopy (RS) and Fourier Transform Infrared (FTIR) spectroscopic imaging. The 3D refractive index (3D-RI) distributions of samples were determined using the digital holographic tomography. The distribution of immune cells between post-mortem (PM) and normal controls did show significant differences for CD4 (P = 0.0016) or CD8 (P < 0.0001), whose expression level was decreased in PM cases. No association was found between individual PMI values and inflammatory cell distribution. However, there was a tendency for a negative correlation between CD4⁺ cells and PMI (r = - 0.542, P = 0.032). The alterations ongoing in post-mortem tissue may suggest that PMI has a suppressive effect on the effector properties of the cell-mediated immunity. Moreover, it was confirmed that spectroscopic and digital holotomographic histology are also a useful technique for characterization of the differences in inflammation of varying intensity and in GALT imaging in a solid tissue. Anatomical location of immune cells and methods of tissue fixation determine the molecular and optical parameters of the examined cases.

Tauroursodeoxycholic Acid (TUDCA)-Lipid Interactions and Antioxidant Properties of TUDCA Studied in Model of Photoreceptor Membranes

Tauroursodeoxycholic acid (TUDCA), a hydrophilic bile acid containing taurine conjugated with the ursodeoxycholic acid (UDCA), has been known and used from ancient times as a therapeutic compound in traditional Chinese medicine. TUDCA has recently been gaining significant interest as a neuroprotective agent, also exploited in the visual disorders. Among several mechanisms of TUDCA's protective action, its antioxidant activity and stabilizing effect on mitochondrial and plasma membranes are considered. In this work we investigated antioxidant activity of TUDCA and its impact on structural properties of model membranes of different composition using electron paramagnetic resonance spectroscopy and the spin labeling technique. Localization of TUDCA molecules in a pure POPC bilayer has been studied using a molecular dynamics simulation (MD). The obtained results indicate that TUDCA is not an efficient singlet oxygen (1O2 (1Δg)) quencher, and the determined rate constant of its interaction with 1O2 (1Δg) is only 1.9 × 105 M-1s-1. However, in lipid oxidation process induced by a Fenton reaction, TUDCA reveals substantial antioxidant activity significantly decreasing the rate of oxygen consumption in the system studied. In addition, TUDCA induces slight, but noticeable changes in the polarity and fluidity of the investigated model membranes. The results of performed MD simulation correspond very well with the experimental results.

In search of the correlation between nanomechanical and biomolecular properties of prostate cancer cells with different metastatic potential

Nanomechanical properties of living cells, as measured with atomic force microscopy (AFM), are increasingly recognized as criteria that differentiate normal and pathologically altered cells. Locally measured cell elastic properties, described by the parameter known as Young's modulus, are currently proposed as a new diagnostic parameter that can be used at the early stage of cancer detection. In this study, local mechanical properties of normal human prostate (RWPE-1) cells and a range of malignant (22Rv1) and metastatic prostate cells (LNCaP, Du145 and PC3) were investigated. It was found that non-malignant prostate cells are stiffer than cancer cells while the metastatic cells are much softer than malignant cells from the primary tumor site. Next, the biochemical properties of the cells were measured using confocal Raman (RS) and Fourier-transform infrared (FT-IR) spectroscopies to reveal these cells' biochemical composition as malignant transformation proceeds. Nanomechanical and biochemical profiles of five different prostate cell lines were subsequently analyzed using partial least squares regression (PLSR) in order to identify which spectral features of the RS and FT-IR spectra correlate with the cell's elastic properties. The PLSR-based model could predict Young's modulus values based on both RS and FT-IR spectral information. These outcomes show not only that AFM, RS and FT-IR techniques can be used for discrimination between normal and cancer cells, but also that a linear correlation between mechanical response and biomolecular composition of the cells that undergo malignant transformation can be found. This knowledge broadens our understanding of how prostate cancer cells evolve thorough the multistep process of tumor pathogenesis.

Exosomes isolated from two different cell lines using three different isolation techniques show variation in physical and molecular characteristics

Exosomes are the nanoscopic lipid bi-layered extracellular vesicles with the potential to be utilized as targeted therapeutics. In our investigation, we compared three major exosome isolation techniques that were Total Exosome Isolation reagent (TEI), Protein organic solvent precipitation (PROSPR) and differential ultracentrifugation (UC) based on the biophysical and physicochemical characteristics of exosomes isolated from COLO 205 and MCF-7 cancer cell's conditioned media with an aim to select a suitable method for translational studies. 3D image analysis and particle size distribution of exosomes from their HRTEM images depicted the morphological differences. Molecular and analytical characterization of exosomes using western blotting, Raman and ATR-FTIR spectroscopy and the multivariate analysis on the spectral data obtained, assessed for better molecular specifications and purity of particle. TEI method isolated exosomes with higher exosomal yield, purity, and recovery directly translatable into drug delivery and targeted therapeutics whereas ultracentrifuge had good recovery of particle morphology but showed particle aggregation and yielded exosomes with smaller mean size. PROSPR technique isolated a mixture of EVs, showed lower protein recovery in PAGE and western blotting but higher spectroscopic protein to lipid ratio and distinguishable EV population in multivariate analysis compared to exosomes isolated by TEI and UC. This comparative study should help in choosing a specific exosome isolation technique required for the objective of downstream applications.

Comparison between high definition FT-IR, Raman and AFM-IR for subcellular chemical imaging of cholesteryl esters in prostate cancer cells

The family of vibrational spectroscopic imaging techniques grows every few years and there is a need to compare and contrast new modalities with the better understood ones, especially in the case of demanding biological samples. Three vibrational spectroscopy techniques (high definition Fourier-transform infrared [FT-IR], Raman and atomic force microscopy infrared [AFM-IR]) were applied for subcellular chemical imaging of cholesteryl esters in PC-3 prostate cancer cells. The techniques were compared and contrasted in terms of image quality, spectral pattern and chemical information. All tested techniques were found to be useful in chemical imaging of cholesterol derivatives in cancer cells. The results obtained from FT-IR and Raman imaging showed to be comparable, whereas those achieved from AFM-IR study exhibited higher spectral heterogeneity. It confirms AFM-IR method as a powerful tool in local chemical imaging of cells at the nanoscale level. Furthermore, due to polarization effect, p-polarized AFM-IR spectra showed strong enhancement of lipid bands when compared to FT-IR.

Lipid Droplet Composition Varies Based on Medaka Fish Eggs Development as Revealed by NIR-, MIR-, and Raman Imaging

In fertilized fish eggs, lipids are an energy reservoir for the embryo development and substrate for organogenesis. They occur in the cytoplasmic area and form lipid droplets (LDs), but also the yolk egg is composed of lipids and proteins. Insight on the LD formation and distribution and their interactions with other cellular organelles could provide information about the role based on the egg development. For non-destructive, macro-scale visualization of biochemical components of fish eggs, such as lipids proteins and water, near-infrared (NIR) imaging is the method of choice. Mid-infrared (MIR) and Raman spectroscopy imaging were used to provide details on chemical composition of LDs and other egg organelles. NIR imaging illustrated main compartments of the egg including membrane, LDs, yolk, relative protein, and lipid content in well-localized egg structures and their interactions with water molecules. In the yolk, a co-existence of lipids and proteins with carotenoids and carbohydrates was detected by Raman spectroscopy. Results showed a prominent decrease of unsaturated fatty acids, phospholipids, and triglycerides/cholesteryl esters content in the eggs due to the embryo development. An opposite trend of changes was observed by MIR spectroscopy for the glycogen, suggesting that consumption of lipids occurred with production of this carbohydrate. The comprehensive vibrational spectroscopic analysis based on NIR, MIR, and Raman imaging is a unique tool in studying in situ dynamic biological processes.