A FTIR microspectroscopy study of the structural and biochemical perturbations induced by natively folded and aggregated transthyretin in HL-1 cardiomyocytes

Vibrational spectroscopy coupled with machine learning sheds light on the cellular effects induced by rationally designed TLR4 agonists

In this work, we present the potential of Fourier transform infrared (FTIR) microspectroscopy to compare on whole cells, in an unbiased and untargeted way, the capacity of bacterial lipopolysaccharide (LPS) and two rationally designed molecules (FP20 and FP20Rha) to activate molecular circuits of innate immunity. These compounds are important drug hits in the development of vaccine adjuvants and tumor immunotherapeutics. The biological assays indicated that FP20Rha was more potent than FP20 in inducing cytokine production in cells and in stimulating IgG antibody production post-vaccination in mice. Accordingly, the overall significant IR spectral changes induced by the treatment with LPS and FP20Rha were similar, lipids and glycans signals being the most diagnostic, while the effect of the less potent molecule FP20 on cells resulted to be closer to control untreated cells. We propose here the use of FTIR spectroscopy supported by artificial intelligence (AI) to achieve a more holistic understanding of the cell response to new drug candidates while screening them in cells.

Exposure to environmental pharmaceuticals affects the macromolecular composition of mussels digestive glands

Human pharmaceuticals represent a major challenge in natural environment. A better knowledge on their mechanisms of action and adverse effects on cellular pathways is fundamental to predict long-term consequences for marine wildlife. The FTIRI Imaging (FTIRI) spectroscopy represents a vibrational technique allowing to map specific areas of non-homogeneous biological samples, providing a unique biochemical and ultrastructural fingerprint of the tissue. In this study, FTIRI technique has been applied, for the first time, to characterize (i) the chemical building blocks of digestive glands of Mytilus galloprovincialis, (ii) alterations and (iii) resilience of macromolecular composition, after a 14-days exposure to 0.5 µg/L of carbamazepine (CBZ), valsartan (VAL) and their mixture, followed by a 14-days recovery period. Spectral features of mussels digestive glands provided insights on composition and topographical distribution of main groups of biological macromolecules, such as proteins, lipids, and glycosylated compounds. Pharmaceuticals caused an increase in the total amount of protein and a significant decrease of lipids levels. Changes in macromolecular features reflected the modulation of specific molecular and biochemical pathways thus supporting our knowledge on mechanisms of action of such emerging pollutants. Overall, the applied approach could represent an added value within integrated strategies for the effects-based evaluation of environmental contaminants.

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.

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

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

Does Ketogenic Diet Used in Pregnancy Affect the Nervous System Development in Offspring?─FTIR Microspectroscopy Study

Anti-seizure medications used during pregnancy may have transient or long-lasting impact on the nervous system of the offspring. Therefore, there is a great need to search for alternative therapies for pregnant women suffering from seizures. One of the solutions may be the use of the ketogenic diet (KD), which has been successfully applied as a treatment of drug-resistant epilepsy in children and adults. However, the risks associated with the use of this dietary therapy during pregnancy are unknown and more investigation in this area is needed. To shed some light on this problem, we attempted to determine the potential abnormalities in brain biomolecular composition that may occur in the offspring after the prenatal exposure to KD. To achieve this, the female Wistar rats were, during pregnancy, fed with either ketogenic or standard laboratory diet, and for further studies, their male offspring at 2, 6, or 14 days of age were used. Fourier transform infrared microspectroscopy was applied for topographic and quantitative analysis of main biological macromolecules (proteins, lipids, compounds containing phosphate and carbonyl groups, and cholesterol) in brain samples. Performed chemical mapping and further semi-quantitative and statistical analysis showed that the use of the KD during pregnancy, in general, does not lead to the brain biochemical anomalies in 2 and 6 days old rats. The exception from this rule was increased relative (comparing to proteins) content of compounds containing phosphate groups in white matter and cortex of 2 days old rats exposed prenatally to KD. Greater number of abnormalities was found in brains of the 14 days old offspring of KD-fed mothers. They included the increase of the relative level of compounds containing carbonyl groups (in cortex as well as multiform and molecular cells of the hippocampal formation) as well as the decrease of the relative content of lipids and their structural changes (in white matter). What is more, the surface of the internal capsule (structure of the white matter) determined for this age group was smaller in animals subjected to prenatal KD exposure. The observed changes seem to arise from the elevated exposition to ketone bodies during a fetus life and the disturbance of lipid metabolism after prenatal exposure to the KD. These changes may be also associated with the processes of compensation of mother organism, which slowly began to make up for the deficiencies in carbohydrates postpartum.

Selenite reduced uptake/translocation of cadmium via regulation of assembles and interactions of pectins, hemicelluloses, lignins, callose and Casparian strips in rice roots

Selenium (Se) can reduce cadmium (Cd) uptake/translocation via regulating pectins, hemicelluloses and lignins of plant root cell walls, but the detailed molecular mechanisms are not clear. In this study, six hydroponic experiments were set up to explore the relationships of uptake/translocation inhibition of Cd by selenite (Se(IV)) with cell wall component (CWC) synthesis and/or interactions. Cd and Se was supplied (alone or combinedly) at 1.0 mg L^-1 and 0.5 mg L^-1, respectively, with the treatment without Cd and Se as the control. When compared to the Cd1 treatment, the Se0.5Cd1 treatment 1) significantly increased total sugar concentrations in pectins, hemicelluloses and callose, suggesting an enhanced capacity of binding Cd or blocking Cd translocation; 2) stimulated the deposition of Casparian strips (CS) in root endodermis and exodermis to block Cd translocation; 3) stimulated the release of C-O-C (-OH^- or -O^-) and CO (carboxyl, carbonyl, or amide) to combine Cd; 4) regulated differential expression genes (DEGs) and metabolites (DMs) correlated with synthesis and/or interactions of CWSs to affect cell wall net structure to affect root cell division, subsequent root morphology and finally elemental uptake; and 5) stimulated de-methylesterification of pectins via reducing expression abundances of many DMs and DEGs in the Yang Cycle to reduce supply of methyls to homogalacturonan, and regulated gene expressions of pectin methylesterase to release carboxyls to combine Cd; and 6) down-regulated gene expressions associated with Cd uptake/translocation.

Impaired Extracellular Proteostasis in Patients with Heart Failure

BACKGROUND

Proteostasis impairment and the consequent increase of amyloid burden in the myocardium have been associated with heart failure (HF) development and poor prognosis. A better knowledge of the protein aggregation process in biofluids could assist the development and monitoring of tailored interventions.

AIM

To compare the proteostasis status and protein's secondary structures in plasma samples of patients with HF with preserved ejection fraction (HFpEF), patients with HF with reduced ejection fraction (HFrEF), and age-matched individuals.

METHODS

A total of 42 participants were enrolled in 3 groups: 14 patients with HFpEF, 14 patients with HFrEF, and 14 age-matched individuals. Proteostasis-related markers were analyzed by immunoblotting techniques. Fourier Transform Infrared (FTIR) Spectroscopy in Attenuated Total Reflectance (ATR) was applied to assess changes in the protein's conformational profile.

RESULTS

Patients with HFrEF showed an elevated concentration of oligomeric proteic species and reduced clusterin levels. ATR-FTIR spectroscopy coupled with multivariate analysis allowed the discrimination of HF patients from age-matched individuals in the protein amide I absorption region (1700-1600 cm^-1), reflecting changes in protein conformation, with a sensitivity of 73 and a specificity of 81%. Further analysis of FTIR spectra showed significantly reduced random coils levels in both HF phenotypes. Also, compared to the age-matched group, the levels of structures related to fibril formation were significantly increased in patients with HFrEF, whereas the β-turns were significantly increased in patients with HFpEF.

CONCLUSION

Both HF phenotypes showed a compromised extracellular proteostasis and different protein conformational changes, suggesting a less efficient protein quality control system.

A guide to studying protein aggregation

Disrupted protein folding or decreased protein stability can lead to the accumulation of (partially) un- or misfolded proteins, which ultimately cause the formation of protein aggregates. Much of the interest in protein aggregation is associated with its involvement in a wide range of human diseases and the challenges it poses for large-scale biopharmaceutical manufacturing and formulation of therapeutic proteins and peptides. On the other hand, protein aggregates can also be functional, as observed in nature, which triggered its use in the development of biomaterials or therapeutics as well as for the improvement of food characteristics. Thus, unmasking the various steps involved in protein aggregation is critical to obtain a better understanding of the underlying mechanism of amyloid formation. This knowledge will allow a more tailored development of diagnostic methods and treatments for amyloid-associated diseases, as well as applications in the fields of new (bio)materials, food technology and therapeutics. However, the complex and dynamic nature of the aggregation process makes the study of protein aggregation challenging. To provide guidance on how to analyse protein aggregation, in this review we summarize the most commonly investigated aspects of protein aggregation with some popular corresponding methods.

Application of FTIR Spectroscopy to Detect Changes in Skeletal Muscle Composition Due to Obesity with Insulin Resistance and STZ-Induced Diabetes

Age, obesity, and diabetes mellitus are pathophysiologically interconnected factors that significantly contribute to the global burden of non-communicable diseases. These metabolic conditions are associated with impaired insulin function, which disrupts the metabolism of carbohydrates, lipids, and proteins and can lead to structural and functional changes in skeletal muscle. Therefore, the alterations in the macromolecular composition of skeletal muscle may provide an indication of the underlying mechanisms of insulin-related disorders. The aim of this study was to investigate the potential of Fourier transform infrared (FTIR) spectroscopy to reveal the changes in macromolecular composition in weight-bearing and non-weight-bearing muscles of old, obese, insulin-resistant, and young streptozotocin (STZ)-induced diabetic mice. The efficiency of FTIR spectroscopy was evaluated by comparison with the results of gold-standard histochemical techniques. The differences in biomolecular phenotypes and the alterations in muscle composition in relation to their functional properties observed from FTIR spectra suggest that FTIR spectroscopy can detect most of the changes observed in muscle tissue by histochemical analyses and more. Therefore, it could be used as an effective alternative because it allows for the complete characterization of macromolecular composition in a single, relatively simple experiment, avoiding some obvious drawbacks of histochemical methods.

Methodological advances and strategies for high resolution structure determination of cellular protein aggregates

Aggregation of proteins is at the nexus of molecular processes crucial to aging, disease, and employing proteins for biotechnology and medical applications. There has been much recent progress in determining the structural features of protein aggregates that form in cells; yet, owing to prevalent heterogeneity in aggregation, many aspects remain obscure and often experimentally intractable to define. Here we review recent results of structural studies for cell-derived aggregates of normally globular proteins, with a focus on high resolution methods for their analysis and prediction. Complementary results obtained by solid-state NMR spectroscopy, Fourier transform infrared (FTIR) spectroscopy and microspectroscopy, cryo-electron microscopy, and amide hydrogen/deuterium exchange measured by NMR and mass spectrometry (MS), applied to bacterial inclusion bodies and disease inclusions, are uncovering novel information on in-cell aggregation patterns as well as great diversity in the structural features of useful and aberrant protein aggregates. Using these advances as a guide, this review aims to advise the reader on which combination of approaches may be the most appropriate to apply to their unique system.

Hydroxycinnamic acid derivatives effect on hypercholesterolemia, comparison with ezetimibe: Permeability assays and FTIR spectroscopy on Caco-2 cell line

High blood cholesterol levels may increase the risk of developing atherosclerosis. Since intestinal cholesterol absorption plays a major role in maintaining total body cholesterol homeostasis, the aim of the present study was to compare the effect of ezetimibe and three hydroxycinnamic acid derivatives (rosmarinic acid, chlorogenic acid and m-coumaric acid) that are present in several medicinal plants on cholesterol absorption in the intestinal Caco-2 ​cells. In addition to the permeability assays, studies on alteration of the biochemical properties of Caco-2 ​cells under the effect of ezetimibe and hydroxycinnamic acid derivatives was evaluated using FTIR accompanied with multivariate analysis by PCA. The cholesterol permeability assays showed that these compounds could decrease cholesterol permeability with a percentage ranging from 76.98 to 96.6% with the highest inhibition for ezetimibe. whereas the FTIR studies didn't show similar changes between ezetimibe and the three hydroxycinnamic acid derivatives in protein and nucleic acids region, suggesting that these compounds have hypocholesterolemic effect. Nevertheless, each compound originated a different change on Caco-2 treated cells suggesting a different mode of action.

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Hydroxycinnamic acid derivatives and ezetimibe permeated the intestinal barrier.

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Hydroxycinnamic acid derivatives decreased cholesterol permeability.

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Hydroxycinnamic acid derivatives could affect the cell components.

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PCA of FTIR spectra showed differences on protein and nucleic acid regions.

Contribution of Infrared Spectroscopy to the Understanding of Amyloid Protein Aggregation in Complex Systems

Infrared (IR) spectroscopy is a label-free and non-invasive technique that probes the vibrational modes of molecules, thus providing a structure-specific spectrum. The development of infrared spectroscopic approaches that enable the collection of the IR spectrum from a selected sample area, from micro- to nano-scale lateral resolutions, allowed to extend their application to more complex biological systems, such as intact cells and tissues, thus exerting an enormous attraction in biology and medicine. Here, we will present recent works that illustrate in particular the applications of IR spectroscopy to the in situ characterization of the conformational properties of protein aggregates and to the investigation of the other biomolecules surrounding the amyloids. Moreover, we will discuss the potential of IR spectroscopy to the monitoring of cell perturbations induced by protein aggregates. The essential support of multivariate analyses to objectively pull out the significant and non-redundant information from the spectra of highly complex systems will be also outlined.

Challenges in Experimental Methods

Experimental studies of amyloids encounter many challenges. There are many methods available for studying proteins, which can be applied to amyloids: from basic staining techniques, allowing visualization of fibers, to complex methods, e.g., AFM-IR used to their detailed biochemical and structural characterization in nanoscale. Which method is appropriate depends on the goal of an experiment: verification of aggregational properties of a peptide, distinguishing oligomers from mature fibers, or kinetic studies. Insolubility, rapid aggregation, and the need of using a high-purity peptide may be a limiting factor in studies involving amyloids. Moreover, the results obtained by various experimental methods often differ significantly, which may lead to misclassification of amyloid peptides. Due to ambiguity of experimental results, laborious and time-consuming analysis, bioinformatical methods become more widely used for amyloids.

Molecular-level changes induced by hydroxycinnamic acid derivatives in HepG2 cell line: Comparison with pravastatin

Hydroxycinnamic acid derivatives are an important class of polyphenols found in fruits, vegetables, and medicinal plants and widely consumed in human diet. In the present work, alterations of HepG2 cells biochemical profile under the effect of four hydroxycinnamic acid derivatives (caffeic acid, m-coumaric acid, chlorogenic acid and rosmarinic acid) relatively to the effect of pravastatin, a drug often prescribed to inhibit HMG-CoA reductase enzyme, the regulator enzyme in the cholesterol biosynthesis pathway, were reported. The application of FTIR spectroscopy in combination with multivariate analysis by PCA showed a similarity between pravastatin and the four hydroxycinnamic acid derivatives in metabolite profile modification expressed by various changes in proteins region, the phosphate region which mainly corresponds to nucleic acids as well as in lipids regions. FTIR structural analysis in the amide I region, using resolution enhancement methods, such as second derivative and amide I deconvolution method, revealed significant decrease in α-helix/random coil and intermolecular β-sheet decreased while intramolecular β-sheet in treated cells showed an increase. It was also noticed that the intracellular cholesterol as well as esterified ingredients such as cholesterol esters in the cell membrane decreased. Moreover, principal component analysis (PCA) of the spectral data showed that the compounds and pravastatin were well separated from untreated cells showing a different mode of action on HepG2 treated cells for each compound.

Transthyretin: From Structural Stability to Osteoarticular and Cardiovascular Diseases

Transthyretin (TTR) is a tetrameric protein transporting hormones in the plasma and brain, which has many other activities that have not been fully acknowledged. TTR is a positive indicator of nutrition status and is negatively correlated with inflammation. TTR is a neuroprotective and oxidative-stress-suppressing factor. The TTR structure is destabilized by mutations, oxidative modifications, aging, proteolysis, and metal cations, including Ca2+. Destabilized TTR molecules form amyloid deposits, resulting in senile and familial amyloidopathies. This review links structural stability of TTR with the environmental factors, particularly oxidative stress and Ca2+, and the processes involved in the pathogenesis of TTR-related diseases. The roles of TTR in biomineralization, calcification, and osteoarticular and cardiovascular diseases are broadly discussed. The association of TTR-related diseases and vascular and ligament tissue calcification with TTR levels and TTR structure is presented. It is indicated that unaggregated TTR and TTR amyloid are bound by vicious cycles, and that TTR may have an as yet undetermined role(s) at the crossroads of calcification, blood coagulation, and immune response.

AFM Study of Nanoscale Membrane Perturbation Induced by Antimicrobial Lipopeptide C14 KYR

Lipopeptides have been extensively studied as potential antimicrobial agents. In this study, we focused on the C₁₄-KYR lipopeptide, a modified version of the KYR tripeptide with myristic acid at the N-terminus. Here, membrane perturbation of live E. coli treated with the parent KYR and C₁₄-KYR peptides was compared at the nanoscale level using AFM imaging. AFM analyses, including average cellular roughness and force spectroscopy, revealed the severe surface disruption mechanism of C₁₄-KYR. A loss of surface roughness and changes in topographic features included membrane shrinkage, periplasmic membrane separation from the cell wall, and cytosolic leakage. Additional evidence from synchrotron radiation FTIR microspectroscopy (SR-FTIR) revealed a marked structural change in the membrane component after lipopeptide attack. The average roughness of the E. coli cell before and after treatment with C₁₄-KYR was 129.2 ± 51.4 and 223.5 ± 14.1 nm, respectively. The average rupture force of the cell treated with C₁₄-KYR was 0.16 nN, four times higher than that of the untreated cell. Our study demonstrates that the mechanistic effect of the lipopeptide against bacterial cells can be quantified through surface imaging and adhesion force using AFM.

Transthyretin amyloid fibrils alter primary fibroblast structure, function, and inflammatory gene expression

Age-related wild-type transthyretin amyloidosis (wtATTR) is characterized by systemic deposition of amyloidogenic fibrils of misfolded transthyretin (TTR) in the connective tissue of many organs. In the heart, this leads to cardiac dysfunction, which is a significant cause of age-related heart failure. The hypothesis tested is that TTR affects cardiac fibroblasts in ways that may contribute to fibrosis. When primary cardiac fibroblasts were cultured on TTR-deposited substrates, the F-actin cytoskeleton was disorganized, focal adhesion formation was decreased, and nuclear shape was flattened. Fibroblasts had faster collective and single-cell migration velocities on TTR-deposited substrates. In addition, fibroblasts cultured on microposts with TTR deposition had reduced attachment and increased proliferation above untreated. Transcriptomic and proteomic analyses of fibroblasts grown on glass covered with TTR showed significant upregulation of inflammatory genes after 48 h, indicative of progression in TTR-based diseases. Together, results suggest that TTR deposited in tissue extracellular matrix may affect the structure, function, and gene expression of cardiac fibroblasts. As therapies for wtATTR are cost-prohibitive and only slow disease progression, better understanding of cellular maladaptation may elucidate novel therapeutic targets.NEW & NOTEWORTHY Transthyretin (TTR) cardiac amyloidosis involves deposition of fibrils of misfolded TTR in the aging human heart, leading to cardiac dysfunction and heart failure. Our novel in vitro studies show that TTR fibrils alter primary cardiac fibroblast cytoskeletal and nuclear structure and focal adhesion formation. Furthermore, both fibrillar and tetrameric TTR significantly increased cellular migration velocity and caused upregulation of inflammatory genes determined by transcriptomic RNA and protein analysis. These findings may suggest new therapeutic approaches.

Systematic changes of bone hydroxyapatite along a charring temperature gradient: An integrative study with dissolution behavior

The applicability of bone char as a long-term phosphorus nutrient source was assessed by integrating their mineral transformation and physicochemical properties with their dissolution behavior. We have explored synchrotron-based spectroscopic and imaging techniques (FTIR, XRD, and TXM) to investigate the physicochemical changes of bone and bone char along a charring temperature gradient (300-1200 °C) and used a lab incubation experiment to study their dissolution behaviors in solutions of different pH (4, 6, and 6.9). The thermal decomposition of inorganic carbonate (CO₃^2-) and the loss of organic components rendered a crystallographic rearrangement (blueshift of the PO₄^3- peak) and mineral transformation with increasing temperatures. The mineral transformation from B-type to AB- and A-type carbonate substitution occurred mainly at <700 °C, while the transformation from carbonated hydroxyapatite (CHAp) to more mineralogically and chemically stable HAp occurred at >800 °C. The loss of inorganic carbonate and the increase of structural OH^- with increasing temperatures explained the change of pH buffering capacity and increase of pH and their dissolution behaviors. The higher peak area ratios of phosphate to carbonate and phosphate to amide I band with increasing temperatures corroborated the higher stability and resistivity to acidic dissolution by bone chars made at higher temperatures. Our findings suggest that bone char made at low to intermediate temperatures can be a substantial source of phosphorus for soil fertility via waste management and recycling. The bone char made at 500 °C exhibited a high pH buffering capacity in acidic and near-neutral solutions. The 700 °C bone char was proposed as a suitable liming agent for raising the soil pH and abating soil acidity. Our study has underpinned the systematic changes of bone char and interlinked the charring effect with their dissolution behavior, providing a scientific base for understanding the applicability of different bone chars as suitable P-fertilizers.

Spectroscopic assessment of oxidative damage in biomolecules and tissues

Oxidative damage is one of the main causes of cryopreservation injury compromising the use of cryopreserved biospecimens. The aim of this study was to evaluate the use of Fourier transform infrared spectroscopy (FTIR) as a non-invasive method to assess changes in biomolecular composition and structure, associated with oxidative stress in isolated biomolecules, acellular heart valve tissues, and ovarian cortex tissues. FTIR spectra of these specimens subjected to various treatments (H₂O₂- and Fenton-treatment or elevated temperatures) were vector normalized and selected spectral regions were analyzed by principal component analysis (PCA). Control and damaged biomolecules can easily be separated using PCA score plots. Acellular heart valve tissues that were subjected to different levels of oxidative damage formed separate cluster in PCA score plots. In hydrated ovarian tissue, large variation of the principal components was observed. Drying the ovarian tissues samples resulted in improved cluster separation of treatment groups. However, early signs of oxidative damage under mild stress conditions could not be detected by PCA of FTIR spectra. For the ovarian tissue samples, the standardly used nitro blue tetrazolium chloride (NBT) assay was used to monitor the amount of formazan production, reflecting reactive oxygen species (ROS) production at various temperatures. At 37 °C, formazan staining rapidly increased during the first 30 min, and then slowly reached a saturation level, but also at lower temperatures (i.e. 4 °C) formazan production was observed. In summary, we conclude that ATR-FTIR combined with PCA can be used to study oxidative damage in biomolecules as well as in tissues. In tissues, however, sample heterogeneity makes it difficult to detect early signs of oxidative damage.

ATR-FTIR spectroscopy and spectroscopic imaging for the analysis of biopharmaceuticals

Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR) spectroscopy is a label-free, non-destructive technique that can be applied to a vast range of biological applications, from imaging cancer tissues and live cells, to determining protein content and protein secondary structure composition. This review summarises the recent advances in applications of ATR-FTIR spectroscopy to biopharmaceuticals, the application of this technique to biosimilars, and the current uses of FTIR spectroscopy in biopharmaceutical production. We discuss the use of ATR-FTIR spectroscopic imaging to investigate biopharmaceuticals, and finally, give an outlook on the possible future developments and applications of ATR-FTIR spectroscopy and spectroscopic imaging to this field. Throughout the review comparisons will be made between FTIR spectroscopy and alternative analytical techniques, and areas will be identified where FTIR spectroscopy could perhaps offer a better alternative in future studies. This review focuses on the most recent advances in the field of using ATR-FTIR spectroscopy and spectroscopic imaging to characterise and evaluate biopharmaceuticals, both in industrial and academic research based environments.

A convenient protein library for spectroscopic calibrations

While several Raman, CD or FTIR spectral libraries are available for well-characterized proteins of known structure, proteins themselves are usually very difficult to acquire, preventing a convenient calibration of new instruments and new recording methods. The problem is particularly critical in the field of FTIR spectroscopy where numerous new methods are becoming available on the market.

The present papers reports the construction of a protein library (cSP92) including commercially available products, that are well characterized experimentally for their purity and solubility in conditions compatible with the recording of FTIR spectra and whose high-resolution structure is available.

Overall, 92 proteins were selected. These proteins cover well the CATH space at the level of classes and architectures. In terms of secondary structure content, an analysis of their high-resolution structure by DSSP shows that the mean content in the different secondary structures present in cSP92 is very similar to the mean content found in the PDB.

The 92-protein set is analyzed in details for the distribution of helix length, number of strands in β- sheets, length of β-strands and amino acid content, all features that may be important for the interpretation of FTIR spectra.

Alterations of bone material properties in adult patients with X-linked hypophosphatemia (XLH)

X-linked hypophosphatemia (XLH) caused by PHEX mutations results in elevated serum FGF23 levels, renal phosphate wasting and low 1,25-dihydroxyvitamin D. The glycophosphoprotein osteopontin, a potent inhibitor of mineralization normally degraded by PHEX, accumulates within the bone matrix. Conventional therapy consisting of supplementation with phosphate and vitamin D analogs is burdensome and the effects on bone material poorly characterized. We analyzed transiliac bone biopsies from four adult patients, two of them severely affected due to no diagnosis and no treatment until adulthood. We used light microscopy, qBEI and FTIRI to study histology, histomorphometry, bone mineralization density distribution, properties of the organic matrix and size of hypomineralized periosteocytic lesions. Non-treatment resulted in severe osteomalacia, twice the amount of mineralized trabecular volume, multiple osteon-like perforations, continuity of lamellae from mineralized to unmineralized areas and distinctive patches of woven bone. Periosteocytic lesions were larger than in treated patients. The latter had nearly normal osteoid thicknesses, although surface was still elevated. The median calcium content of the matrix was always within normal range, although the percentage of lowly mineralized bone areas was highly increased in non-treated patients, resulting in a marked heterogeneity in mineralization. Divalent collagen cross-links were evident independently of the mineral content of the matrix. Broad osteoid seams lacked measurable pyridinoline, a mature trivalent cross-link and exhibited considerable acidic lipid content, typically found in matrix vesicles. Based on our results, we propose a model that possibly integrates the relationship between the observed mineralization disturbances, FGF23 secretion and the known osteopontin accumulation in XLH.

Pathophysiology and pathological remodelling associated with dilated cardiomyopathy in broiler chickens predisposed to heart pump failure

Broiler chickens selected for rapid growth are highly susceptible to dilated cardiomyopathy (DCM). In order to elucidate the pathophysiology of DCM, the present study examines the fundamental features of pathological remodelling associated with DCM in broiler chickens using light microscopy, transmission electron microscopy (TEM), and synchrotron Fourier Transform Infrared (FTIR) micro-spectroscopy. The morphological features and FTIR spectra of the left ventricular myocardium were compared among broiler chickens affected by DCM with clinical signs of heart pump failure, apparently normal fast-growing broiler chickens showing signs of subclinical DCM (high risk of heart failure), slow-growing broiler chickens (low risk of heart failure) and Leghorn chickens (resistant to heart failure, used here as physiological reference). The findings indicate that DCM and heart pump failure in fast-growing broiler chickens are a result of a complex metabolic syndrome involving multiple catabolic pathways. Our data indicate that a good deal of DCM pathophysiology in chickens selected for rapid growth is associated with conformational changes of cardiac proteins, and pathological changes indicative of accumulation of misfolded and aggregated proteins in the affected cardiomyocytes. From TEM image analysis it is evident that the affected cardiomyocytes demonstrate significant difficulty in the disposal of damaged proteins and maintenance of proteostasis, which leads to pathological remodelling of the heart and contractile dysfunction. It appears that the underlying causes of accumulation of damaged proteins are associated with dysregulated auto phagosome and proteasome systems, which, in susceptible individuals, create a milieu conducive for the development of DCM and heart failure. RESEARCH HIGHLIGHTS The light and electron microscopy image analyses revealed degenerative changes and protein aggregates in the cardiomyocytes of chickens affected by DCM. The analyses of FTIR spectra of the myocardium revealed that DCM and heart pump failure in broiler chickens are associated with conformational changes of myocardial proteins. The morphological changes in cardiomyocytes and conformational changes in myocardial proteins architecture are integral constituents of pathophysiology of DCM in fast-growing broiler chickens.

Biomolecular and bioanalytical applications of infrared spectroscopy - A review

Infrared (IR; or mid-infrared, MIR; 4000-400 cm^-1; 2500-25,000 nm) spectroscopy has become one of the most powerful and versatile tools at the disposal of modern bioscience. Because of its high molecular specificity, applicability to wide variety of samples, rapid measurement and non-invasivity, IR spectroscopy forms a potent approach to elucidate qualitative and quantitative information from various kinds of biological material. For these reasons, it became an established bioanalytical technique with diverse applications. This work aims to be a comprehensive and critical review of the recent accomplishments in the field of biomolecular and bioanalytical IR spectroscopy. That progress is presented on a wider background, with fundamental characteristics, the basic principles of the technique outlined, and its scientific capability directly compared with other methods being used in similar fields (e.g. near-infrared, Raman, fluorescence). The article aims to present a complete examination of the topic, as it touches the background phenomena, instrumentation, spectra processing and data analytical methods, spectra interpretation and related information. To suit this goal, the article includes a tutorial information essential to obtain a thorough perspective of bio-related applications of the reviewed methodologies. The importance of the fundamental factors to the final performance and applicability of IR spectroscopy in various areas of bioscience is explained. This information is interpreted in critical way, with aim to gain deep understanding why IR spectroscopy finds extraordinarily intensive use in this remarkably diverse and dynamic field of research and utility. The major focus is placed on the diversity of the applications in which IR biospectroscopy has been established so far and those onto which it is expanding nowadays. This includes qualitative and quantitative analytical spectroscopy, spectral imaging, medical diagnosis, monitoring of biophysical processes, and studies of physicochemical properties and dynamics of biomolecules. The application potential of IR spectroscopy in light of the current accomplishments and the future prospects is critically evaluated and its significance in the progress of bioscience is comprehensively presented.

ATR-FTIR Spectroscopy Supported by Multivariate Analysis for the Characterization of Adipose Tissue Aspirates from Patients Affected by Systemic Amyloidosis

Deposition of misfolded proteins as extracellular amyloid aggregates is the pathological hallmark of systemic amyloidoses. Subcutaneous fat acquired by fine needle aspiration is the preferred screening tissue in suspected patients. In this study we employed Fourier transform infrared (FTIR) spectroscopy in attenuated total reflection (ATR) to investigate human abdominal fat aspirates with the aim of detecting disease-related changes in the molecular structure and composition of the tissue and exploiting the potentiality of the method to discriminate between amyloid-positive and -negative samples. The absorption and second-derivative spectra of Congo Red (CR) positive and CR-negative specimens were analyzed by three multivariate methods in four spectral regions. The proposed ATR-FTIR method is label-free, rapid, and relatively inexpensive and requires minimal sample preparation. We found that the ATR-FTIR approach can differentiate fat aspirates containing amyloid deposits from control specimens with high sensitivity and specificity, both at 100 [89-100]%. It is worth noting that the wavenumbers most important for discrimination indicate that changes both in the protein conformation and in resident lipids are intrinsic features of affected subcutaneous fat in comparison with the CR-negative controls. In this proof of concept study, we show that this approach could be useful for assessing tissue amyloid aggregates and for acquiring novel knowledge of the molecular bases of the disease.