Multivariate image analysis of a set of FTIR microspectroscopy images of aged bovine muscle tissue combining image and design information

Applying synchrotron radiation-based attenuated total reflection-fourier transform infrared to chemically characterise organic functional groups in terrestrial soils of King George Island, Antarctica

Anthropogenic activities, especially associated with fossil fuel combustion, are raising concerns worldwide, but remote areas with extreme climate conditions, such as Antarctica, are isolated from the adverse influence of human civilisation. Antarctica is considered as the most untouched place on Earth. Such pristine areas, which have extremely low chemical pollutant concentrations owing to restricted anthropogenic impacts, exemplify plausible model environments to test the reliability and sensitivity of advanced analytical techniques employed to chemically characterise and evaluate the spatial distribution of chemical pollutants. Here, synchrotron radiation-based attenuated total reflection-Fourier transform infrared (SR-ATR-FTIR) spectroscopy was employed to evaluate the variations in the organic functional groups (OFGs) of terrestrial soils of King George Island, Antarctica. Second-derivative SR-ATR-FTIR spectroscopy coupled with several multivariate statistical techniques highlighted the influence of anthropogenic activities on the alterations of OFGs in terrestrial soils collected near airports. Moreover, the daily activities of penguins could also have caused fluctuations in some OFGs of the samples the close to the Tombolo area and Ardley Island. The findings proved the effectiveness of SR-ATR-FTIR in evaluating the potential sources of variations in the chemical constituents, especially OFGs, in Antarctic terrestrial soils.

Wet Blue Enzymatic Treatment and Its Effect on Leather Properties and Post-Tanning Processes

Due to their variety, specific activity, and mild reaction conditions, enzymes have a wide application in beam house processes such as soaking, dehairing, bating, and de-greasing. Recently, due to improvements in biotechnology, re-bating after chroming has received increased attention. The aim of this work was to investigate the application of enzyme preparation in the re-bating process and its effect on the semifinished and finished product, as well as its influence on post-tanning operations. The enzymatic treatment of chromed semifinished leather (wet blue) led to a higher shrinkage temperature (1-6 °C), greater water vapour absorption (0.3-5.5%), better chromium compounds exhaustion during re-chroming (4-21%), and better dye penetration. Moreover, collagen was affected during the enzymatic process; the results showed a greater concentration influence in the operation compared to the process time. On the other hand, no effect on the physical and mechanical properties and fat-liquoring process was observed. Overall, these results indicate that some properties and processes are improved; however, before use for re-bating, every enzyme should be carefully investigated.

Roles of Bothrops jararacussu toxins I and II: Antiviral findings against Zika virus

Zika virus is the etiologic agent of Zika fever, and has been previously associated with cases of microcephaly, drawing the attention of the health authorities worldwide. However, no vaccine or antiviral are currently available. Phospholipases A₂ (PLA₂) isolated from snake venoms have demonstrated antiviral activity against several viruses. Here we demonstrated the anti-ZIKV activity of bothropstoxins-I and II (BthTX-I and II) isolated from Bothrops jararacussu venom. Vero E6 cells were infected with ZIKVPE243 in the presence of compounds for 72 h, when virus titers were evaluated. BthTX-I and II presented strong dose-dependent inhibition of ZIKV, with a SI of 149.1 and 1.44 × 10⁵, respectively. These toxins mainly inhibited the early stages of the replicative cycle, such as during the entry of ZIKV into host cells, as shown by the potent virucidal effect, suggesting the action of these toxins on the virus particles. Moreover, BthTX-I and II presented significant activity towards post-entry stages of the ZIKV replicative cycle. Molecular docking analyses showed that BthTX-I and II potentially interact with DII and DIII domains from ZIKV Envelope protein. Our findings show that these PLA₂s could be used as useful templates for the development of future antiviral candidate drugs against Zika fever.

Imidazonaphthyridine effects on Chikungunya virus replication: Antiviral activity by dependent and independent of interferon type 1 pathways

The Chikungunya virus (CHIKV) causes Chikungunya fever, a disease characterized by symptoms such as arthralgia/polyarthralgia. Currently, there are no antivirals approved against CHIKV, emphasizing the need to develop novel therapies. The imidazonaphthyridine compound (RO8191), an interferon-α (IFN-α) agonist, was reported as a potent inhibitor of HCV. Here RO8191 was investigated for its potential to inhibit CHIKV replication in vitro. RO8191 inhibited CHIKV infection in BHK-21 and Vero-E6 cells with a selectivity index (SI) of 12.3 and 37.3, respectively. Additionally, RO8191 was capable to protect cells against CHIKV infection, inhibit entry by virucidal activity, and strongly impair post-entry steps of viral replication. An effect of RO8191 on CHIKV replication was demonstrated in BHK-21 through type-1 IFN production mechanism and in Vero-E6 cells which has a defective type-1 IFN production, also suggesting a type-1 IFN independent mode of action. Molecular docking calculations demonstrated interactions of RO8191 with the CHIKV E proteins, corroborated by the ATR-FTIR assay, and with non-structural proteins, supported by the CHIKV-subgenomic replicon cells assay.

Repurposing potential of rimantadine hydrochloride and development of a promising platinum(II)-rimantadine metallodrug for the treatment of Chikungunya virus infection

Most of the patients infected with Chikungunya virus (CHIKV) develop chronic manifestations characterized by pain and deformity in joints, impacting their quality of life. The aminoadamantanes, in their turn, have been exploited due to their biological activities, with amantadine and memantine recently described with anti-CHIKV activities. Here we evaluated the antiviral activity of rimantadine hydrochloride (rtdH), a well-known antiviral agent against influenza A, its platinum complex (Pt-rtd), and the precursor cis-[PtCl₂(dmso)₂], against CHIKV infection in vitro. The rtdH demonstrated significant antiviral activity in all stages of CHIKV replication (29% in pre-treatment; 57% in early stages of infection; 60% in post-entry stages). The Pt-rtd complex protected the cells against infection in 92%, inhibited 100% of viral entry, mainly by a virucidal effect, and impaired 60% of post-entry stages. Alternatively, cis-[PtCl₂(dmso)₂] impaired viral entry in 100% and post-entry steps in 60%, but had no effect in protecting cells when administered prior to CHIKV infection. Collectively, the obtained data demonstrated that rtdH and Pt-rtd significantly interfered in the early stages of CHIKV life cycle, with the strongest effect observed to Pt-rtd complex, which reduced up to 100% of CHIKV infection. Moreover, molecular docking analysis and infrared spectroscopy data (ATR-FTIR) suggest an interaction of Pt-rtd with CHIKV glycoproteins, potentially related to the mechanism of inhibition of viral entry by Pt-rtd. Through a migration retardation assay, it was also shown that Pt-rtd and cis-[PtCl₂(dmso)₂] interacted with the dsRNA in 87% and 100%, respectively. The obtained results highlight the repurposing potential of rtdH as an anti-CHIKV drug, as well as the synthesis of promising platinum(II) metallodrugs with potential application for the treatment of CHIKV infections. Importance Chikungunya fever is a disease that can result in persistent symptoms due to the chronic infection process. Infected patients can develop physical disability, resulting and high costs to the health system and significant impacts on the quality of life of affected individuals. Additionally, there are no licensed vaccines or antivirals against the Chikungunya virus (CHIKV) and the virus is easily transmitted due to the abundance of viable vectors in epidemic regions. In this context, our study highlights the repurposing potential of the commercial drug rimantadine hydrochloride (rtdH) as an antiviral agent for the treatment of CHIKV infections. Moreover, our data demonstrated that a platinum(II)-rimantadine metallodrug (Pt-rtd) poses as a potent anti-CHIKV molecule with potential application for the treatment of Chikungunya fever. Altogether, rtdH and Pt-rtd significantly interfered in the early stages of CHIKV life cycle, reducing up to 100% of CHIKV infection in vitro.

Arecanut-induced fibrosis display dual phases of reorganising glycans and amides in skin extracellular matrix

The habit of chewing arecanut leads to fibrosis in the oral tissues, which can lead to cancer. Despite high mortality, fibrosis has limited clinical success owing to organ-specific variations, genetic predispositions, and slow progression. Fibrosis is a progressive condition that is unresponsive to medications in the severe phase. To understand underlying macromolecular changes we studied the extracellular matrix's (ECM) key molecular modifications in the early and late phase of arecanut-induced fibrosis in skin. To study the fibrosis, we topically applied arecanut extract on the mice skin. We observed that the matrix changes observe early and late phases based on ECM characteristics including the matrix proteins and the glycans. A spike in the levels of proteoglycans and β-sheet structures are noted in the early phase. A significant drop in the proteoglycans and strengthening of amide covalent interactions is observed in the late phase. Although, almost no physical changes are noticeable only in the early phase; the late phase observes thick collagen bundling and a 4-fold stiffening of the skin tissue. The study indicates that the temporal interplay of proteins and glycans determine the matrix's severity state while opening avenues to research directed towards the phase-specific clinical discovery.

Discriminant Analysis of the Geographical Origin of Asian Red Pepper Powders Using Second-Derivative FT-IR Spectroscopy

This study aimed to discriminate between the geographical origins of Asian red pepper powders distributed in Korea using Fourier-transform infrared (FT-IR) spectroscopy coupled with multivariate statistical analyses. Second-derivative spectral data were obtained from a total of 105 red pepper powder samples, 86 of which were used for statistical analysis, and the remaining 19 were used for blind testing. A one-way analysis of variance (ANOVA) test confirmed that eight peak variables exhibited significant origin-dependent differences, and the canonical discriminant functions derived from these variables were used to correctly classify all the red pepper powder samples based on their origins. The applicability of the canonical discriminant functions was examined by performing a blind test wherein the origins of 19 new red pepper powder samples were correctly classified. For simplicity, the four most significant variables were selected as discriminant indicator variables, and the applicable range for each indicator variable was set for each geographical origin. By applying the indicator variable ranges, the origins of the red pepper powders of all the statistical and blind samples were correctly identified. The study findings indicate the feasibility of using FT-IR spectroscopy in combination with multivariate analysis for identifying the geographical origins of red pepper powders.

Visualizing Different Crystalline States during the Infrared Imaging of Calcium Phosphates

Methods utilizing relatively simple mathematical operations during physical analyses to enable the visualization of otherwise invisible correlations and effects are of particular appeal to researchers and students in pedagogical settings. At the same time, discerning the amorphous phase from its crystalline counterpart in materials is challenging with the use of vibrational spectroscopy and is nowhere as straightforward as in phase composition analytical methods such as X-ray diffraction. A method is demonstrated for the use of first- and second-order differentiation of Fourier transform infrared spectra of calcium phosphates to distinguish their amorphous states from the crystalline ones based on the exact line positioning rather than on comparatively vaguer band broadening and splitting effects. The study utilizes a kinetic approach, focusing on the comparison of spectral features of amorphous precursors annealed in air at different temperatures and aged for different periods of time in an aqueous solution until transforming to one or a mixture of crystalline phases, including hydroxyapatite and α- and β-tricalcium phosphate. One of the findings challenges the concept of the nucleation lag time preceding the crystallization from amorphous precursors as a "dead" period and derives a finite degree of constructive changes occurring at the atomic scale in its course. The differential method for highlighting spectral differences depending on the sample crystallinity allows for monitoring in situ the process of conversion of the amorphous calcium phosphate phase to its crystalline analogue(s). One such method can be of practical significance for synthetic solid state chemists testing for the chemical stability and/or concentration of the reactive amorphous phase in these materials, but also for biologists measuring the maturity of bone and medical researchers evaluating its phase composition and, thus, the state of metabolic and mechanical stability.

Extended multiplicative signal correction for FTIR spectral quality test and pre-processing of infrared imaging data

Spectral quality control is an important step in the analysis of infrared spectral data, however, often neglected in scientific literature. A frequently used quality test that was originally developed for infrared spectra of bacteria is provided by OPUS software from Bruker Optik GmbH. In this study, the OPUS quality test is applied to a large number of spectra of bacteria, yeasts and moulds and hyperspectral images of microorganisms. It is shown that the use of strict thresholds for parameters of the OPUS quality test leads to discarding too many spectra. A strategy for optimizing parameters thresholds of the OPUS quality test is provided and a novel approach for spectral quality testing based on extended multiplicative signal correction (EMSC) is suggested. For all the data sets considered in our study, the EMSC quality test is shown to be the best among different alternatives of OPUS quality test provided.

The use of Fourier-transform infrared spectroscopy to characterize connective tissue components in skeletal muscle of Atlantic cod (Gadus morhua L.)

In the present study, Fourier-transform infrared spectroscopy (FTIR) is investigated as a method to measure connective tissue components that are important for the quality of Atlantic cod filets (Gadus morhua L.). The Atlantic cod used in this study originated from a feeding trial, which found that fish fed a high starch diet contained relative more collagen type I, while fish fed a low starch (LS) diet contained relative more glycosaminoglycans (GAGs) in the connective tissue. FTIR spectra of pure commercial collagen type I and GAGs were acquired to identify spectral markers and compare them with FTIR spectra and images from connective tissue. Using principal component analysis, high and LS diets were separated due to collagen type I in the spectral region 1800 to 800 cm-1 . The spatial distribution of collagen type I and GAGs were further investigated by FTIR imaging in combination with immunohistochemistry. Pixel-wise correlation images were calculated between preprocessed connective tissue images and preprocessed pure components spectra of collagen type I and GAGs, respectively. For collagen, the FTIR images reveal a collagen distribution that closely resembles the collagen distribution as imaged by immunohistochemistry. For GAGs, the concentration is very low. Still, the FTIR images detect the most GAGs rich regions.

Classification and identification of Rhodobryum roseum Limpr. and its adulterants based on fourier-transform infrared spectroscopy (FTIR) and chemometrics

Fourier-transform infrared spectroscopy (FTIR) with the attenuated total reflectance technique was used to identify Rhodobryum roseum from its four adulterants. The FTIR spectra of six samples in the range from 4000 cm-1 to 600 cm-1 were obtained. The second-derivative transformation test was used to identify the small and nearby absorption peaks. A cluster analysis was performed to classify the spectra in a dendrogram based on the spectral similarity. Principal component analysis (PCA) was used to classify the species of six moss samples. A cluster analysis with PCA was used to identify different genera. However, some species of the same genus exhibited highly similar chemical components and FTIR spectra. Fourier self-deconvolution and discrete wavelet transform (DWT) were used to enhance the differences among the species with similar chemical components and FTIR spectra. Three scales were selected as the feature-extracting space in the DWT domain. The results show that FTIR spectroscopy with chemometrics is suitable for identifying Rhodobryum roseum and its adulterants.

Imaging of Osteoarthritic Human Articular Cartilage using Fourier Transform Infrared Microspectroscopy Combined with Multivariate and Univariate Analysis

The changes in chemical composition of human articular cartilage (AC) caused by osteoarthritis (OA) were investigated using Fourier transform infrared microspectroscopy (FTIR-MS). We demonstrate the sensitivity of FTIR-MS for monitoring compositional changes that occur with OA progression. Twenty-eight AC samples from tibial plateaus were imaged with FTIR-MS. Hyperspectral images of all samples were combined for K-means clustering. Partial least squares regression (PLSR) analysis was used to compare the spectra with the OARSI grade (histopathological grading of OA). Furthermore, the amide I and the carbohydrate regions were used to estimate collagen and proteoglycan contents, respectively. Spectral peak at 1338 cm(-1) was used to estimate the integrity of the collagen network. The layered structure of AC was revealed using the carbohydrate region for clustering. Statistically significant correlation was observed between the OARSI grade and the collagen integrity in the superficial (r = -0.55) and the deep (r = -0.41) zones. Furthermore, PLSR models predicted the OARSI grade from the superficial (r = 0.94) and the deep (r = 0.77) regions of the AC with high accuracy. Obtained results suggest that quantitative and qualitative changes occur in the AC composition during OA progression, and these can be monitored by the use of FTIR-MS.

A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis

The accumulation of bacteria in surface-attached biofilms can be detrimental to human health, dental hygiene, and many industrial processes. Natural biofilms are soft and often transparent, and they have heterogeneous biological composition and structure over micro- and macroscales. As a result, it is challenging to quantify the spatial distribution and overall intensity of biofilms. In this work, a new method was developed to enhance the visibility and quantification of bacterial biofilms. First, broad-spectrum biomolecular staining was used to enhance the visibility of the cells, nucleic acids, and proteins that make up biofilms. Then, an image analysis algorithm was developed to objectively and quantitatively measure biofilm accumulation from digital photographs and results were compared to independent measurements of cell density. This new method was used to quantify the growth intensity of Pseudomonas putida biofilms as they grew over time. This method is simple and fast, and can quantify biofilm growth over a large area with approximately the same precision as the more laborious cell counting method. Stained and processed images facilitate assessment of spatial heterogeneity of a biofilm across a surface. This new approach to biofilm analysis could be applied in studies of natural, industrial, and environmental biofilms.

Graphical abstract

Understanding the cryotolerance of lactic acid bacteria using combined synchrotron infrared and fluorescence microscopies

Freezing is widely used for preserving different types of cells. Frozen concentrates of lactic acid bacteria (LAB) are extensively used for manufacturing food, probiotic products and for green chemistry and medical applications. However, the freezing and thawing processes cause cell injuries that result in significant cell death. Producing homogeneous bacterial populations with high cryotolerance remains a real challenge. Our objective was to investigate the biochemical and physiological changes in a LAB model at the cell scale following fermentation and freezing in order to identify cellular biomarkers of cryotolerance. Infrared spectra of individual bacteria produced by applying different fermentation and freezing conditions were acquired using synchrotron radiation-based Fourier-transform infrared (SR-FTIR) microspectroscopy to achieve sub-cellular spatial resolution. Fluorescent microscopy was concomitantly assessed, thus making possible to simultaneously analyse the biochemistry and physiological state of a single cell for the first time. Principal component analysis was used to evaluate changes in cell composition, with particular focus on lipids, proteins and polysaccharides. SR-FTIR results indicated that before freezing, freeze-resistant cells grown in a rich medium presented a high content of CH3 groups from lipid chains, of cell proteins in an α-helix secondary structure and of charged polymers such as teichoic and lipoteichoic acids that constitute the Gram-positive bacterial wall. Moreover, SR-FTIR microspectroscopy made it possible to reveal cell heterogeneity within the cluster of resistant cells, which was ascribed to the diversity of potential substrates in the growth medium. Freezing and thawing processes induced losses of membrane integrity and cell viability in more than 90% of the freeze-sensitive bacterial population. These damages leading to cell death were ascribed to biochemical modification of cell membrane phospholipids, in particular a rigidification of the cytoplasmic membrane following freezing. Furthermore the freeze-resistant cells remained viable after freezing and thawing but a modification of protein secondary structure was detected by SR-FTIR analysis. These results highlighted the potential application of bimodal analysis by SR-FTIR and fluorescence microscopy to increase our knowledge about mechanisms related to cell damage.

An evaluation of Fourier transforms infrared spectroscopy method for the classification and discrimination of bovine, porcine and fish gelatins

The objective of this research was to develop a rapid spectroscopic technique as an alternative method for the differentiation and authentication of gelatin sources in food products by using attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectra combined with chemometrics. Clear discrimination and classification of all the studied gelatin sources (bovine, porcine, and fish) were achieved by hierarchical cluster and principle component analysis (PCA). Amide-I (1700-1600 cm(-1)) and Amide-II (1565-1520 cm(-1)) spectral bands were used in a chemometric method. Moreover, ATR-FTIR spectral data successfully discriminated pure bovine gelatin from mixture of bovine and porcine gelatins, which is very important for the food industry. The method that we adopted could be beneficial for rapid, simple and economic determination of both gelatin presence and its origin from food products such as yogurt, ice cream, milk dessert or other gelatin containing products such as pharmaceuticals and cosmetics.

Vibrational spectroscopic imaging for the evaluation of matrix and mineral chemistry

Metabolic bone diseases manifesting fragility fractures (such as osteoporosis) are routinely diagnosed based on bone mineral density (BMD) measurements, and the effect of various therapies also evaluated based on the same outcome. Although useful, it is well recognized that this metric does not fully account for either fracture incidence or the effect of various therapies on fracture incidence, thus, the emergence of bone quality as a contributing factor in the determination of bone strength. Infrared and Raman vibrational spectroscopic techniques are particularly well-suited for the determination of bone quality as they provide quantitative and qualitative information of the mineral and organic matrix bone components, simultaneously. Through the use of microspectroscopic techniques, this information is available in a spatially resolved manner, thus, the outcomes may be easily correlated with outcomes from techniques such as histology, histomorphometry, and nanoindentation, linking metabolic status with material properties.

Infrared metrics for fixation-free liver tumor detection

Infrared (IR) spectroscopic imaging of human liver tissue slices has been used to identify and characterize liver tumors. Liver tissue, containing a liver metastasis of breast origin (mucinous carcinoma), was surgically removed from a consenting patient and frozen without formalin fixation or dehydration procedures, so that lipids and water remained in the tissues. A set of IR metrics (ratios of various IR peaks) was determined for tumors in fixation-free liver tissues. K-means cluster analysis was used to tell tumor from nontumor. In this case, there was a large reduction in lipid content upon going from nontumor to tumor tissue, and a well-resolved IR spectrum of nontumor liver lipid was obtained and analyzed. These IR metrics may someday guide work on IR spectroscopic diagnostics on patients in the operating room. This work also suggests utility for these methods beyond the identification of liver tumors, perhaps in the study of liver lipids.

FTIR imaging for structural analysis of frankfurter sausages subjected to salt reduction and salt substitution

In this study, the effects of NaCl, KCl, and MgSO4 in various concentrations on structural and sensory properties of frankfurter sausages were investigated. FTIR was used to analyze the overall homogeneousness of the sausages by simultaneously following the distribution of main sausage ingredients, i.e., proteins, fats, and starch. A more homogeneous distribution of the main ingredients was observed with higher concentration of added salts, while it was most pronounced for the MgSO4 recipe. Furthermore, FTIR imaging was used in order to follow the distribution of protein secondary structure motifs throughout the sausage matrix. It was confirmed that KCl inhibited the partial denaturation of proteins, unlike that observed for MgSO4 recipes, where an additional increase in protein hydration was detected. These findings were unequivocally supported by WHC measurements. However, the sensory analysis clearly distinguished the sausages prepared with MgSO4 due to undesired sensory attributes, which underlines the necessity for using taste masking agents.

Prediction of compressive stiffness of articular cartilage using Fourier transform infrared spectroscopy

Unique biomechanical behavior of articular cartilage is a result of its structure and composition. Interrelationships of tissue constituents (collagen, proteoglycans (PGs) and water) and tissue biomechanical parameters have been studied, but it is evident that no constituent alone explains the tissue mechanics. Fourier transform infrared (FT-IR) spectra can provide detailed information about the biochemical composition of articular cartilage. In this study, a chemometric approach to predict the biomechanical behavior of articular cartilage directly from the FT-IR spectra, i.e., without converting the data into collagen and PG information, was investigated. Partial least squares regression (PLSR) was used to predict equilibrium modulus (n=32) and dynamic modulus (n=24) of bovine cartilage samples from their average FT-IR spectra. The linear correlation coefficients between the reference and predicted values of Young's modulus and dynamic modulus were r=0.866 (p<0.001) and r=0.898 (p<0.001), respectively. When the compressive biomechanical behavior of AC is predicted, the present study indicates that similar or improved results can be obtained with FT-IR spectroscopy as compared to those of traditional biochemical methods.

Cluster analysis of infrared spectra can differentiate intact and repaired articular cartilage

OBJECTIVE

Successful repair of articular cartilage (AC) defects would be a major advantage due to the low ability of AC to heal spontaneously. Sensitive methods to determine changes in AC composition and structure are required to monitor the success of repair. This study evaluates the ability of unsupervised cluster analysis applied to Fourier transform infrared (FTIR) microspectroscopy to discriminate between healthy and repaired AC.

METHODS

Osteochondral lesions (3 mm in depth) were surgically created in patellar grooves of rabbit femurs and were either left to heal spontaneously (n = 6) or surgically repaired with autologous chondrocytes in type II collagen gel (n = 6). After 6 months, tissues were harvested, FTIR microspectroscopy was conducted and Fuzzy c-means (FCM) cluster analysis applied to spectra of pairs of intact and repaired AC samples from each rabbit. Two spectral regions [amide I and carbohydrate (CHO)] were analyzed and the results from the two types of repair were compared.

RESULTS

Two separate regions of repair were detected with FCM. The estimated proteoglycan content (from CHO region) in the repaired AC was significantly lower than that in intact AC. The spontaneously repaired AC was better distinguished from the intact AC than the collagen II gel repaired AC. The most distinct clustering was observed for spontaneously repaired samples using CHO region.

CONCLUSIONS

This study revealed that unsupervised cluster analysis applied to FTIR microspectroscopy can detect subtle differences in infrared spectra between normal and repaired AC. The method may help in evaluation and optimization of future AC repair strategies.

Clustering of infrared spectra reveals histological zones in intact articular cartilage

OBJECTIVE

Articular cartilage (AC) exhibits specific zonal structure that follows the organization of collagen network and concentration of tissue constituents. The aim of this study was to investigate the potential of unsupervised clustering analysis applied to Fourier transform infrared (FTIR) microspectroscopy to detect depth-dependent structural and compositional differences in intact AC.

METHOD

Seven rabbit and eight bovine intact patellae AC samples were imaged using FTIR microspectroscopy and normalized raw spectra were clustered using the fuzzy C-means algorithm. Differences in mean spectra of clusters were investigated by quantitative estimation of collagen and proteoglycan (PG) contents, as well as by careful visual investigation of locations of spectral changes.

RESULTS

Clustering revealed the typical layered structure of AC in both species. However, more distinct clusters were found for rabbit samples, whereas bovine AC showed more complex layered structure. In both species, clustering structure corresponded with that in polarized light microscopic (PLM) images; however, some differences were also observed. Spectral differences between clusters were identified at the same spectral locations for both species. Estimated PG/collagen ratio decreased significantly from superficial to middle or deep zones, which might explain the difference in clustering results compared to PLM.

CONCLUSION

FTIR microspectroscopy in combination with cluster analysis allows detailed examination of spatial changes in AC. As far as we know, no previous single technique could reveal a layered structure of AC without any a priori information.

Application of second derivative spectroscopy for increasing molecular specificity of Fourier transform infrared spectroscopic imaging of articular cartilage

OBJECTIVE

Fourier transform infrared (FT-IR) spectroscopic imaging is a promising method that enables the analysis of spatial distribution of biochemical components within histological sections. However, analysis of FT-IR spectroscopic data is complicated since absorption peaks often overlap with each other. Second derivative spectroscopy is a technique which enhances the separation of overlapping peaks. The objective of this study was to evaluate the specificity of the second derivative peaks for the main tissue components of articular cartilage (AC), i.e., collagen and proteoglycans (PGs).

MATERIALS AND METHODS

Histological bovine AC sections were measured before and after enzymatic removal of PGs. Both formalin-fixed sections (n = 10) and cryosections (n = 6) were investigated. Relative changes in the second derivative peak heights caused by the removal of PGs were calculated for both sample groups.

RESULTS

The results showed that numerous peaks, e.g., peaks located at 1202 cm(-1) and 1336 cm(-1), altered less than 5% in the experiment. These peaks were assumed to be specific for collagen. In contrast, two peaks located at 1064 cm(-1) and 1376 cm(-1) were seen to alter notably, approximately 50% or more. These peaks were regarded to be specific for PGs. The changes were greater in cryosections than formalin-fixed sections.

CONCLUSIONS

The results of this study suggest that the second derivative spectroscopy offers a practical and more specific method than routinely used absorption spectrum analysis methods to obtain compositional information on AC with FT-IR spectroscopic imaging.

Fourier transform infrared spectroscopic imaging and multivariate regression for prediction of proteoglycan content of articular cartilage

Fourier Transform Infrared (FT-IR) spectroscopic imaging has been earlier applied for the spatial estimation of the collagen and the proteoglycan (PG) contents of articular cartilage (AC). However, earlier studies have been limited to the use of univariate analysis techniques. Current analysis methods lack the needed specificity for collagen and PGs. The aim of the present study was to evaluate the suitability of partial least squares regression (PLSR) and principal component regression (PCR) methods for the analysis of the PG content of AC. Multivariate regression models were compared with earlier used univariate methods and tested with a sample material consisting of healthy and enzymatically degraded steer AC. Chondroitinase ABC enzyme was used to increase the variation in PG content levels as compared to intact AC. Digital densitometric measurements of Safranin O –stained sections provided the reference for PG content. The results showed that multivariate regression models predict PG content of AC significantly better than earlier used absorbance spectrum (i.e. the area of carbohydrate region with or without amide I normalization) or second derivative spectrum univariate parameters. Increased molecular specificity favours the use of multivariate regression models, but they require more knowledge of chemometric analysis and extended laboratory resources for gathering reference data for establishing the models. When true molecular specificity is required, the multivariate models should be used.

Vibrational spectroscopy: a tool being developed for the noninvasive monitoring of wound healing

Wound care and management accounted for over 1.8 million hospital discharges in 2009. The complex nature of wound physiology involves hundreds of overlapping processes that we have only begun to understand over the past three decades. The management of wounds remains a significant challenge for inexperienced clinicians. The ensuing inflammatory response ultimately dictates the pace of wound healing and tissue regeneration. Consequently, the eventual timing of wound closure or definitive coverage is often subjective. Some wounds fail to close, or dehisce, despite the use and application of novel wound-specific treatment modalities. An understanding of the molecular environment of acute and chronic wounds throughout the wound-healing process can provide valuable insight into the mechanisms associated with the patient's outcome. Pathologic alterations of wounds are accompanied by fundamental changes in the molecular environment that can be analyzed by vibrational spectroscopy. Vibrational spectroscopy, specifically Raman and Fourier transform infrared spectroscopy, offers the capability to accurately detect and identify the various molecules that compose the extracellular matrix during wound healing in their native state. The identified changes might provide the objective markers of wound healing, which can then be integrated with clinical characteristics to guide the management of wounds.

Quantitative analysis of spatial proteoglycan content in articular cartilage with Fourier transform infrared imaging spectroscopy: Critical evaluation of analysis methods and specificity of the parameters

OBJECTIVE

To evaluate the specificity of the current Fourier transform infrared imaging spectroscopy (FT-IRIS) methods for the determination of depthwise proteoglycan (PG) content in articular cartilage (AC). In addition, curve fitting was applied to study whether the specificity of FT-IRIS parameters for PG determination could be improved.

METHODS

Two sample groups from the steer AC were prepared for the study (n = 8 samples/group). In the first group, chondroitinase ABC enzyme was used to degrade the PGs from the superficial cartilage, while the samples in the second group served as the controls. Samples were examined with FT-IRIS and analyzed using previously reported direct absorption spectrum techniques and multivariate methods and, in comparison, by curve fitting. Safranin O-stained sections were measured with digital densitometry to obtain a reference for depthwise PG distribution.

RESULTS

Carbohydrate region-based absorption spectrum methods showed a statistically weaker correlation with the PG reference distributions than the results of the curve fitting (subpeak located approximately at 1,060 cm(-1)). Furthermore, the shape of the depthwise profiles obtained using the curve fitting was more similar to the reference profiles than with the direct absorption spectrum analysis.

CONCLUSIONS

Results suggest that the current FT-IRIS methods for PG analysis lack the specificity for quantitative measurement of PGs in AC. The curve fitting approach demonstrated that it is possible to improve the specificity of the PG analysis. However, the findings of the present study suggest that further development of the FT-IRIS analysis techniques is still needed.

Infrared spectroscopy indicates altered bone turnover and remodeling activity in renal osteodystrophy

Renal osteodystrophy alters metabolic activity and remodeling rate of bone and also may lead to different bone composition. The objective of this study was to characterize the composition of bone in high-turnover renal osteodystrophy patients by means of Fourier transform infrared spectroscopic imaging (FTIRI). Iliac crest biopsies from healthy bone (n = 11) and patients with renal osteodystrophy (ROD, n = 11) were used in this study. The ROD samples were from patients with hyperparathyroid disease. By using FTIRI, phosphate-to-amide I ratio (mineral-to-matrix ratio), carbonate-to-phosphate ratio, and carbonate-to-amide I ratio (turnover rate/remodeling activity), as well as the collagen cross-link ratio (collagen maturity), were quantified. Histomorphometric analyses were conducted for comparison. The ROD samples showed significantly lower carbonate-to-phosphate (p < .01) and carbonate-to-amide I (p < .001) ratios. The spatial variation across the trabeculae highlighted a significantly lower degree of mineralization (p < .05) at the edges of the trabeculae in the ROD samples than in normal bone. Statistically significant linear correlations were found between histomorphometric parameters related to bone-remodeling activity and number of bone cells and FTIRI-calculated parameters based on carbonate-to-phosphate and carbonate-to-amide I ratios. Hence the results suggested that FTIRI parameters related to carbonate may be indicative of turnover and remodeling rate of bone.

Depth-wise progression of osteoarthritis in human articular cartilage: investigation of composition, structure and biomechanics

OBJECTIVE

Osteoarthritis (OA) is characterized by the changes in structure and composition of articular cartilage. However, it is not fully known, what is the depth-wise change in two major components of the cartilage solid matrix, i.e., collagen and proteoglycans (PGs), during OA progression. Further, it is unknown how the depth-wise changes affect local tissue strains during compression. Our aim was to address these issues.

METHODS

Data from the previous microscopic and biochemical measurements of the collagen content, distribution and orientation, PG content and distribution, water content and histological grade of normal and degenerated human patellar articular cartilage (n=73) were reanalyzed in a depth-wise manner. Using this information, a composition-based finite element (FE) model was used to estimate tissue function solely based on its composition and structure.

RESULTS

The orientation angle of collagen fibrils in the superficial zone of cartilage was significantly less parallel to the surface (P<0.05) in samples with early degeneration than in healthy samples. Similarly, PG content was reduced in the superficial zone in early OA (P<0.05). However, collagen content decreased significantly only at the advanced stage of OA (P<0.05). The composition-based FE model showed that under a constant stress, local tissue strains increased as OA progressed.

CONCLUSION

For the first time, depth-wise point-by-point statistical comparisons of structure and composition of human articular cartilage were conducted. The present results indicated that early OA is primarily characterized by the changes in collagen orientation and PG content in the superficial zone, while collagen content does not change until OA has progressed to its late stage. Our simulation results suggest that impact loads in OA joint could create a risk for tissue failure and cell death.

Orthogonal projections to latent structures discriminant analysis modeling on in situ FT-IR spectral imaging of liver tissue for identifying sources of variability

In this study, the orthogonal projections to latent structures discriminant analysis (OPLS-DA) method was used to assess the in situ chemical composition of two different cell types in mouse liver samples, hepatocytes and erythrocytes. High spatial resolution FT-IR microspectroscopy equipped with a focal plan array (FPA) detector is capable of simultaneously recording over 4000 spectra from 64 x 64 pixels with a maximum spatial resolution of about 5 microm x 5 microm, which allows for the differentiation of individual cells. The main benefit with OPLS-DA lies in the ability to separate predictive variation (between cell type) from variation that is uncorrelated to cell type in order to facilitate understanding of different sources of variation. OPLS-DA was able to differentiate between chemical properties and physical properties (e.g., edge effects). OPLS-DA model interpretation of the chemical features that separated the two cell types clearly highlighted proteins and lipids/bile acids. The modeled variation that was uncorrelated to cell type made up a larger portion of the total variation and displayed strong variability in the amide I region. This could be traced back to a gradient in the high intensity (high-density) areas vs the low intensity areas (close to empty areas) that as a result of normalization had an adverse effect on FT-IR spectral profiles. This highlights that OPLS-DA provides an effective solution to identify different sources of variability, both predictive and uncorrelated, and also facilitates understanding of any sampling, experimental, or preprocessing issues.

How to measure image quality in tissue-based diagnosis (diagnostic surgical pathology)

Background

Automated image analysis, measurements of virtual slides, and open access electronic measurement user systems require standardized image quality assessment in tissue-based diagnosis.

Aims

To describe the theoretical background and the practical experiences in automated image quality estimation of colour images acquired from histological slides.

Theory, material and measurements

Digital images acquired from histological slides should present with textures and objects that permit automated image information analysis. The quality of digitized images can be estimated by spatial independent and local filter operations that investigate in homogenous brightness, low peak to noise ratio (full range of available grey values), maximum gradients, equalized grey value distribution, and existence of grey value thresholds. Transformation of the red-green-blue (RGB) space into the hue-saturation-intensity (HSI) space permits the detection of colour and intensity maxima/minima. The feature distance of the original image to its standardized counterpart is an appropriate measure to quantify the actual image quality. These measures have been applied to a series of H&E stained, fluorescent (DAPI, Texas Red, FITC), and immunohistochemically stained (PAP, DAB) slides. More than 5,000 slides have been measured and partly analyzed in a time series.

Results

Analysis of H&E stained slides revealed low shading corrections (10%) and moderate grey value standardization (10 – 20%) in the majority of cases. Immunohistochemically stained slides displayed greater shading and grey value correction. Fluorescent stained slides are often revealed to high brightness. Images requiring only low standardization corrections possess at least 5 different statistically significant thresholds, which are useful for object segmentation. Fluorescent images of good quality only posses one singular intensity maximum in contrast to good images obtained from H&E stained slides that present with 2 – 3 intensity maxima.

Conclusion

Evaluation of image quality and creation of formally standardized images should be performed prior to automatic analysis of digital images acquired from histological slides. Spatial dependent and local filter operations as well as analysis of the RGB and HSI spaces are appropriate methods to reproduce evaluated formal image quality.

Meat quality assessment using biophysical methods related to meat structure

This paper overviews the biophysical methods developed to gain access to meat structure information. The meat industry needs reliable meat quality information throughout the production process in order to guarantee high-quality meat products for consumers. Fast and non-invasive sensors will shortly be deployed, based on the development of biophysical methods for assessing meat structure. Reliable meat quality information (tenderness, flavour, juiciness, colour) can be provided by a number of different meat structure assessment either by means of mechanical (i.e., Warner-Bratzler shear force), optical (colour measurements, fluorescence) electrical probing or using ultrasonic measurements, electromagnetic waves, NMR, NIR, and so on. These measurements are often used to construct meat structure images that are fusioned and then processed via multi-image analysis, which needs appropriate processing methods. Quality traits related to mechanical properties are often better assessed by methods that take into account the natural anisotropy of meat due to its relatively linear myofibrillar structure. Biophysical methods of assessment can either measure meat component properties directly, or calculate them indirectly by using obvious correlations between one or several biophysical measurements and meat component properties. Taking these calculations and modelling the main relevant biophysical properties involved can help to improve our understanding of meat properties and thus of eating quality.