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12 pages, 2638 KiB

Open AccessArticle

AFM and FTIR Investigation of the Effect of Water Flow on Horseradish Peroxidase

by Yuri D. Ivanov, Tatyana O. Pleshakova, Ivan D. Shumov, Andrey F. Kozlov, Anastasia A. Valueva, Irina A. Ivanova, Maria O. Ershova, Dmitry I. Larionov, Victor V. Repnikov, Nina D. Ivanova, Vadim Yu. Tatur, Igor N. Stepanov and Vadim S. Ziborov

Molecules 2021, 26(2), 306; https://doi.org/10.3390/molecules26020306 - 9 Jan 2021

Cited by 14 | Viewed by 3413

Abstract

Atomic force microscopy (AFM)-based fishing is a promising method for the detection of low-abundant proteins. This method is based on the capturing of the target proteins from the analyzed solution onto a solid substrate, with subsequent counting of the captured protein molecules on [...] Read more.

Atomic force microscopy (AFM)-based fishing is a promising method for the detection of low-abundant proteins. This method is based on the capturing of the target proteins from the analyzed solution onto a solid substrate, with subsequent counting of the captured protein molecules on the substrate surface by AFM. Protein adsorption onto the substrate surface represents one of the key factors determining the capturing efficiency. Accordingly, studying the factors influencing the protein adsorbability onto the substrate surface represents an actual direction in biomedical research. Herein, the influence of water motion in a flow-based system on the protein adsorbability and on its enzymatic activity has been studied with an example of horseradish peroxidase (HRP) enzyme by AFM, attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) and conventional spectrophotometry. In the experiments, HRP solution was incubated in a setup modeling the flow section of a biosensor communication. The measuring cell with the protein solution was placed near a coiled silicone pipe, through which water was pumped. The adsorbability of the protein onto the surface of the mica substrate has been studied by AFM. It has been demonstrated that incubation of the HRP solution near the coiled silicone pipe with flowing water leads to an increase in its adsorbability onto mica. This is accompanied by a change in the enzyme’s secondary structure, as has been revealed by ATR-FTIR. At the same time, its enzymatic activity remains unchanged. The results reported herein can be useful in the development of models describing the influence of liquid flow on the properties of enzymes and other proteins. The latter is particularly important for the development of biosensors for biomedical applications—particularly for serological analysis, which is intended for the early diagnosis of various types of cancer and infectious diseases. Our results should also be taken into account in studies of the effects of protein aggregation on hemodynamics, which plays a key role in human body functioning. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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12 pages, 2239 KiB

Open AccessFeature PaperArticle

Resonance Raman Optical Activity Spectroscopy in Probing Structural Changes Invisible to Circular Dichroism Spectroscopy: A Study on Truncated Vitamin B₁₂ Derivatives

by Ewa Machalska, Grzegorz Zajac, Monika Halat, Aleksandra J. Wierzba, Dorota Gryko and Malgorzata Baranska

Molecules 2020, 25(19), 4386; https://doi.org/10.3390/molecules25194386 - 24 Sep 2020

Cited by 9 | Viewed by 4156

Abstract

This work demonstrates resonance Raman optical activity (RROA) spectra of three truncated vitamin B₁₂ derivatives modified within the nucleotide loop. Since truncated cobalamins possess sufficiently high rotational strength in the range of ROA excitation (532 nm), it was possible to record their [...] Read more.

This work demonstrates resonance Raman optical activity (RROA) spectra of three truncated vitamin B₁₂ derivatives modified within the nucleotide loop. Since truncated cobalamins possess sufficiently high rotational strength in the range of ROA excitation (532 nm), it was possible to record their spectra in the resonance condition. They showed several distinct spectral features allowing for the distinguishing of studied compounds, in contrast to other methods, i.e., UV-Vis absorption, electronic circular dichroism, and resonance Raman spectroscopy. The improved capacity of the RROA method is based here on the excitation of molecules via more than two electronic states, giving rise to the bisignate RROA spectrum, significantly distinct from a parent Raman spectrum. This observation is an important step in the dissemination of using RROA spectroscopy in studying the complex structure of corrinoids which may prove crucial for a better understanding of their biological role. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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18 pages, 3391 KiB

Open AccessArticle

Infrared Microspectroscopy and Imaging Analysis of Inflammatory and Non-Inflammatory Breast Cancer Cells and Their GAG Secretome

by Hossam Taha Mohamed, Valérie Untereiner, Gianfelice Cinque, Sherif Abdelaziz Ibrahim, Martin Götte, Nguyet Que Nguyen, Romain Rivet, Ganesh D. Sockalingum and Stéphane Brézillon

Molecules 2020, 25(18), 4300; https://doi.org/10.3390/molecules25184300 - 19 Sep 2020

Cited by 12 | Viewed by 3422

Abstract

Glycosaminoglycans (GAGs)/proteoglycans (PGs) play a pivotal role in the metastasis of inflammatory breast cancer (IBC). They represent biomarkers and targets in diagnosis and treatment of different cancers including breast cancer. Thus, GAGs/PGs could represent potential prognostic/diagnostic biomarkers for IBC. In the present study, [...] Read more.

Glycosaminoglycans (GAGs)/proteoglycans (PGs) play a pivotal role in the metastasis of inflammatory breast cancer (IBC). They represent biomarkers and targets in diagnosis and treatment of different cancers including breast cancer. Thus, GAGs/PGs could represent potential prognostic/diagnostic biomarkers for IBC. In the present study, non-IBC MDA-MB-231, MCF7, SKBR3 cells and IBC SUM149 cells, as well as their GAG secretome were analyzed. The latter was measured in toto as dried drops with high-throughput (HT) Fourier Transform InfraRed (FTIR) spectroscopy and imaging. FTIR imaging was also employed to investigate single whole breast cancer cells while synchrotron-FTIR microspectroscopy was used to specifically target their cytoplasms. Data were analyzed by hierarchical cluster analysis and principal components analysis. Results obtained from HT-FTIR analysis of GAG drops showed that the inter-group variability enabled us to delineate between cell types in the GAG absorption range 1350–800 cm⁻¹. Similar results were obtained for FTIR imaging of GAG extracts and fixed single whole cells. Synchrotron-FTIR data from cytoplasms allowed discrimination between non-IBC and IBC. Thus, by using GAG specific region, not only different breast cancer cell lines could be differentiated, but also non-IBC from IBC cells. This could be a potential diagnostic spectral marker for IBC detection useful for patient management. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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14 pages, 10391 KiB

Open AccessFeature PaperArticle

Orientation Matters: Polarization Dependent IR Spectroscopy of Collagen from Intact Tendon Down to the Single Fibril Level

by Gorkem Bakir, Benoit E. Girouard, Richard Wiens, Stefan Mastel, Eoghan Dillon, Mustafa Kansiz and Kathleen M. Gough

Molecules 2020, 25(18), 4295; https://doi.org/10.3390/molecules25184295 - 19 Sep 2020

Cited by 32 | Viewed by 6573

Abstract

Infrared (IR) spectroscopy has been used for decades to study collagen in mammalian tissues. While many changes in the spectral profiles appear under polarized IR light, the absorption bands are naturally broad because of tissue heterogeneity. A better understanding of the spectra of [...] Read more.

Infrared (IR) spectroscopy has been used for decades to study collagen in mammalian tissues. While many changes in the spectral profiles appear under polarized IR light, the absorption bands are naturally broad because of tissue heterogeneity. A better understanding of the spectra of ordered collagen will aid in the evaluation of disorder in damaged collagen and in scar tissue. To that end, collagen spectra have been acquired with polarized far-field (FF) Fourier Transform Infrared (FTIR) imaging with a Focal Plane Array detector, with the relatively new method of FF optical photothermal IR (O-PTIR), and with nano-FTIR spectroscopy based on scattering-type scanning near-field optical microscopy (s-SNOM). The FF methods were applied to sections of intact tendon with fibers aligned parallel and perpendicular to the polarized light. The O-PTIR and nano-FTIR methods were applied to individual fibrils of 100–500 nm diameter, yielding the first confirmatory and complementary results on a biopolymer. We observed that the Amide I and II bands from the fibrils were narrower than those from the intact tendon, and that both relative intensities and band shapes were altered. These spectra represent reliable profiles for normal collagen type I fibrils of this dimension, under polarized IR light, and can serve as a benchmark for the study of collagenous tissues. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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9 pages, 1854 KiB

Open AccessArticle

A New Method for In-Situ Skin Penetration Analysis by Confocal Raman Microscopy

by Richard Krombholz and Dominique Lunter

Molecules 2020, 25(18), 4222; https://doi.org/10.3390/molecules25184222 - 15 Sep 2020

Cited by 23 | Viewed by 4107

Abstract

In the development of dermal drug formulations and cosmetics, understanding the penetration properties of the active ingredients is crucial. Given that widespread methods, including tape stripping, lack in spatial resolution, while being time- and labour-intensive, Confocal Raman Microscopy is a promising alternative. In [...] Read more.

In the development of dermal drug formulations and cosmetics, understanding the penetration properties of the active ingredients is crucial. Given that widespread methods, including tape stripping, lack in spatial resolution, while being time- and labour-intensive, Confocal Raman Microscopy is a promising alternative. In optimizing topically applied formulations, or the development of generic formulations, comparative in-situ measurements have a huge potential of saving time and resources. In this work, we show our approach to in-situ skin penetration analysis by confocal Raman Microscopy. To analyse feasibility of the approach, we used caffeine solutions as model vehicles and tested the effectiveness of 1,2-pentanediol as a penetration enhancer for delivery to the skin. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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16 pages, 3728 KiB

Open AccessFeature PaperArticle

Analysis of Hepatic Fibrosis Characteristics in Cirrhotic Patients with and without Hepatocellular Carcinoma by FTIR Spectral Imaging

by Johanna Moreau, Pascaline Bouzy, Julien Guillard, Valérie Untereiner, Roselyne Garnotel, Aude Marchal, Cyril Gobinet, Christine Terryn, Ganesh D. Sockalingum and Gérard Thiéfin

Molecules 2020, 25(18), 4092; https://doi.org/10.3390/molecules25184092 - 7 Sep 2020

Cited by 10 | Viewed by 2986

Abstract

The evolution of cirrhosis is marked by quantitative and qualitative modifications of the fibrosis tissue and an increasing risk of complications such as hepatocellular carcinoma (HCC). Our purpose was to identify by FTIR imaging the spectral characteristics of hepatic fibrosis in cirrhotic patients [...] Read more.

The evolution of cirrhosis is marked by quantitative and qualitative modifications of the fibrosis tissue and an increasing risk of complications such as hepatocellular carcinoma (HCC). Our purpose was to identify by FTIR imaging the spectral characteristics of hepatic fibrosis in cirrhotic patients with and without HCC. FTIR images were collected at projected pixel sizes of 25 and 2.7 μm from paraffinized hepatic tissues of five patients with uncomplicated cirrhosis and five cirrhotic patients with HCC and analyzed by k-means clustering. When compared to the adjacent histological section, the spectral clusters corresponding to hepatic fibrosis and regeneration nodules were easily identified. The fibrosis area estimated by FTIR imaging was correlated to that evaluated by digital image analysis of histological sections and was higher in patients with HCC compared to those without complications. Qualitative differences were also observed when fibrosis areas were specifically targeted at higher resolution. The partition in two clusters of the fibrosis tissue highlighted subtle differences in the spectral characteristics of the two groups of patients. These data show that the quantitative and qualitative changes of fibrosis tissue occurring during the course of cirrhosis are detectable by FTIR imaging, suggesting the possibility of subclassifying cirrhosis into different steps of severity. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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14 pages, 3290 KiB

Open AccessArticle

FLIm and Raman Spectroscopy for Investigating Biochemical Changes of Bovine Pericardium upon Genipin Cross-Linking

by Tanveer Ahmed Shaik, Alba Alfonso-Garcia, Martin Richter, Florian Korinth, Christoph Krafft, Laura Marcu and Jürgen Popp

Molecules 2020, 25(17), 3857; https://doi.org/10.3390/molecules25173857 - 25 Aug 2020

Cited by 7 | Viewed by 4258

Abstract

Biomaterials used in tissue engineering and regenerative medicine applications benefit from longitudinal monitoring in a non-destructive manner. Label-free imaging based on fluorescence lifetime imaging (FLIm) and Raman spectroscopy were used to monitor the degree of genipin (GE) cross-linking of antigen-removed bovine pericardium (ARBP) [...] Read more.

Biomaterials used in tissue engineering and regenerative medicine applications benefit from longitudinal monitoring in a non-destructive manner. Label-free imaging based on fluorescence lifetime imaging (FLIm) and Raman spectroscopy were used to monitor the degree of genipin (GE) cross-linking of antigen-removed bovine pericardium (ARBP) at three incubation time points (0.5, 1.0, and 2.5 h). Fluorescence lifetime decreased and the emission spectrum redshifted compared to that of uncross-linked ARBP. The Raman signature of GE-ARBP was resonance-enhanced due to the GE cross-linker that generated new Raman bands at 1165, 1326, 1350, 1380, 1402, 1470, 1506, 1535, 1574, 1630, 1728, and 1741 cm⁻¹. These were validated through density functional theory calculations as cross-linker-specific bands. A multivariate multiple regression model was developed to enhance the biochemical specificity of FLIm parameters fluorescence intensity ratio (R² = 0.92) and lifetime (R² = 0.94)) with Raman spectral results. FLIm and Raman spectroscopy detected biochemical changes occurring in the collagenous tissue during the cross-linking process that were characterized by the formation of a blue pigment which affected the tissue fluorescence and scattering properties. In conclusion, FLIm parameters and Raman spectroscopy were used to monitor the degree of cross-linking non-destructively. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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22 pages, 6250 KiB

Open AccessFeature PaperArticle

Chiral Lanthanide Complexes with l- and d-Alanine: An X-ray and Vibrational Circular Dichroism Study

by Krzysztof Lyczko, Joanna E. Rode and Jan Cz. Dobrowolski

Molecules 2020, 25(12), 2729; https://doi.org/10.3390/molecules25122729 - 12 Jun 2020

Cited by 4 | Viewed by 3971

Abstract

A whole series of [Ln(H₂O)₄(Ala)₂]₂⁶⁺ dimeric cationic lanthanide complexes with both l- and d-alanine enantiomers was synthesized. The single-crystal X-ray diffraction at 100 and 292 K shows the formation of two types of [...] Read more.

A whole series of [Ln(H₂O)₄(Ala)₂]₂⁶⁺ dimeric cationic lanthanide complexes with both l- and d-alanine enantiomers was synthesized. The single-crystal X-ray diffraction at 100 and 292 K shows the formation of two types of dimers (I and II) in crystals. Between the dimer centers, the alanine molecules behave as bridging (μ₂-O,O’-) and chelating bridging (μ₂-O,O,O’-) ligands. The first type of bridge is present in dimers I, while both bridge forms can be observed in dimers II. The IR and vibrational circular dichroism (VCD) spectra of all l- and d-alanine complexes were registered in the 1750–1250 cm⁻¹ range as KBr pellets. Despite all the studied complexes are exhibiting similar crystal structures, the spectra reveal correlations or trends with the Ln–O1 distances which exemplify the lanthanide contraction effect in the IR spectra. This is especially true for the positions and intensities of some IR bands. Unexpectedly, the ν(C=O) VCD bands are quite intense and their composed shapes reveal the inequivalence of the C=O vibrators in the unit cell which vary with the lanthanide. Unlike in the IR spectra, the ν(C=O) VCD band positions are only weakly correlated with the change of Ln and the VCD intensities at most show some trends. Nevertheless, this is the first observation of the lanthanide contraction effect in the VCD spectra. Generally, for the heavier lanthanides (Ln: Dy–Lu), the VCD band maxima are very close to each other and the mirror reflection of the band of two enantiomers is usually better than that of the lighter Lns. DFT calculations show that the higher the multiplicity the higher the stability of the system. Actually, the molecular geometry in crystals (at 100 K) is well predicted based on the highest-spin structures. Also, the simulated IR and VCD spectra strongly depend on the Ln electron configuration but the best overall agreement was reached for the Lu complex, which is the only system with a fully filled f-shell. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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23 pages, 8316 KiB

Open AccessArticle

Zinc Phthalocyanine Photochemistry by Raman Imaging, Fluorescence Spectroscopy and Femtosecond Spectroscopy in Normal and Cancerous Human Colon Tissues and Single Cells

by Beata Brozek-Pluska, Arkadiusz Jarota, Rafal Kania and Halina Abramczyk

Molecules 2020, 25(11), 2688; https://doi.org/10.3390/molecules25112688 - 10 Jun 2020

Cited by 18 | Viewed by 5383

Abstract

Photodynamic therapy is a clinically approved alternative method for cancer treatment in which a combination of nontoxic drugs known as photosensitizers and oxygen is used. Despite intensive investigations and encouraging results, zinc phthalocyanines (ZnPcs) have not yet been approved as photosensitizers for clinical [...] Read more.

Photodynamic therapy is a clinically approved alternative method for cancer treatment in which a combination of nontoxic drugs known as photosensitizers and oxygen is used. Despite intensive investigations and encouraging results, zinc phthalocyanines (ZnPcs) have not yet been approved as photosensitizers for clinical use. Label-free Raman imaging of nonfixed and unstained normal and cancerous colon human tissues and normal human CCD18-Co and cancerous CaCo-2 cell lines, without and after adding ZnPcS₄ photosensitizer, was analyzed. The biochemical composition of normal and cancerous colon tissues and colon cells without and after adding ZnPcS₄ at the subcellular level was determined. Analyzing the fluorescence/Raman signals of ZnPcS₄, we found that in normal human colon tissue samples, in contrast to cancerous ones, there is a lower affinity to ZnPcS₄ phthalocyanine. Moreover, a higher concentration in cancerous tissue was concomitant with a blue shift of the maximum peak position specific for the photosensitizer from 691–695 nm to 689 nm. Simultaneously for both types of samples, the signal was observed in the monomer region, confirming the excellent properties of ZnPcS₄ for photo therapy (PDT). For colon cell experiments with a lower concentration of ZnPcS₄ photosensitizer, c = 1 × 10⁻⁶ M, the phthalocyanine was localized in mitochondria/lipid structures; for a higher concentration, c = 9 × 10⁻⁶ M, localization inside the nucleus was predominant. Based on time-resolved experiments, we found that ZnPcS₄ in the presence of biological interfaces features longer excited-state lifetime photosensitizers compared to the aqueous solution and bare ZnPcS₄ film on CaF₂ substrate, which is beneficial for application in PDT. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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23 pages, 6395 KiB

Open AccessArticle

Fatty-Acid Uptake in Prostate Cancer Cells Using Dynamic Microfluidic Raman Technology

by Nga-Tsing Tang, Richard D. Snook, Mick D. Brown, Bryan A. Haines, Andrew Ridley, Peter Gardner and Joanna L. Denbigh

Molecules 2020, 25(7), 1652; https://doi.org/10.3390/molecules25071652 - 3 Apr 2020

Cited by 11 | Viewed by 4699

Abstract

It is known that intake of dietary fatty acid (FA) is strongly correlated with prostate cancer progression but is highly dependent on the type of FAs. High levels of palmitic acid (PA) or arachidonic acid (AA) can stimulate the progression of cancer. In [...] Read more.

It is known that intake of dietary fatty acid (FA) is strongly correlated with prostate cancer progression but is highly dependent on the type of FAs. High levels of palmitic acid (PA) or arachidonic acid (AA) can stimulate the progression of cancer. In this study, a unique experimental set-up consisting of a Raman microscope, coupled with a commercial shear-flow microfluidic system is used to monitor fatty acid uptake by prostate cancer (PC-3) cells in real-time at the single cell level. Uptake of deuterated PA, deuterated AA, and the omega-3 fatty acids docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) were monitored using this new system, while complementary flow cytometry experiments using Nile red staining, were also conducted for the validation of the cellular lipid uptake. Using this novel experimental system, we show that DHA and EPA have inhibitory effects on the uptake of PA and AA by PC-3 cells. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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11 pages, 1519 KiB

Open AccessFeature PaperArticle

Influence of the Sample Preparation Method in Discriminating Candida spp. Using ATR-FTIR Spectroscopy

by Savithri Pebotuwa, Kamila Kochan, Anton Peleg, Bayden R. Wood and Philip Heraud

Molecules 2020, 25(7), 1551; https://doi.org/10.3390/molecules25071551 - 28 Mar 2020

Cited by 17 | Viewed by 3923

Abstract

Several studies have investigated the capacity of ATR-FTIR spectroscopy for fungal species discrimination. However, preparation methods vary among studies. This study aims to ascertain the effect of sample preparation on the discriminatory capacity of ATR-FTIR spectroscopy. Candida species were streaked to obtain colonies [...] Read more.

Several studies have investigated the capacity of ATR-FTIR spectroscopy for fungal species discrimination. However, preparation methods vary among studies. This study aims to ascertain the effect of sample preparation on the discriminatory capacity of ATR-FTIR spectroscopy. Candida species were streaked to obtain colonies and spectra were collected from each preparation type, which included: (a) untreated colonies being directly transferred to the ATR crystal, (b) following washing and (c) following 24-h fixation in formalin. Spectra were pre-processed and principal component analysis (PCA) and K-means cluster analysis (KMC) were performed. Results showed that there was a clear discrimination between preparation types. Groups of spectra from untreated and washed isolates clustered separately due to intense protein, DNA and polysaccharide bands, whilst fixed spectra clustered separately due to intense polysaccharide bands. This signified that sample preparation had influenced the chemical composition of samples. Nevertheless, across preparation types, significant species discrimination was observed, and the polysaccharide (1200–900 cm⁻¹) region was a common critical marker for species discrimination. However, different discriminatory marker bands were observed across preparation methods. Thus, sample preparation appears to influence the chemical composition of Candida samples; however, does not seem to significantly impact the species discrimination potential for ATR-FTIR spectroscopy. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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11 pages, 3003 KiB

Open AccessFeature PaperArticle

Flexible and Reusable Ag Coated TiO₂ Nanotube Arrays for Highly Sensitive SERS Detection of Formaldehyde

by Tong Zhu, Hang Wang, Libin Zang, Sila Jin, Shuang Guo, Eungyeong Park, Zhu Mao and Young Mee Jung

Molecules 2020, 25(5), 1199; https://doi.org/10.3390/molecules25051199 - 6 Mar 2020

Cited by 31 | Viewed by 4471

Abstract

Quantitative analysis of formaldehyde (HCHO, FA), especially at low levels, in various environmental media is of great importance for assessing related environmental and human health risks. A highly efficient and convenient FA detection method based on surface-enhanced Raman spectroscopy (SERS) technology has been [...] Read more.

Quantitative analysis of formaldehyde (HCHO, FA), especially at low levels, in various environmental media is of great importance for assessing related environmental and human health risks. A highly efficient and convenient FA detection method based on surface-enhanced Raman spectroscopy (SERS) technology has been developed. This SERS-based method employs a reusable and soft silver-coated TiO₂ nanotube array (TNA) material, such as an SERS substrate, which can be used as both a sensing platform and a degradation platform. The Ag-coated TNA exhibits superior detection sensitivity with high reproducibility and stability compared with other SERS substrates. The detection of FA is achieved using the well-known redox reaction of FA with 4-amino-3-hydrazino-5-mercapto-1,2,4-triazole (AHMT) at room temperature. The limit of detection (LOD) for FA is 1.21 × 10⁻⁷ M. In addition, the stable catalytic performance of the array allows the degradation and cleaning of the AHMT-FA products adsorbed on the array surface under ultraviolet irradiation, making this material recyclable. This SERS platform displays a real-time monitoring platform that combines the detection and degradation of FA. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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15 pages, 8062 KiB

Open AccessArticle

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

by Ewelina Bik, Mika Ishigaki, Aneta Blat, Agnieszka Jasztal, Yukihiro Ozaki, Kamilla Malek and Malgorzata Baranska

Molecules 2020, 25(4), 817; https://doi.org/10.3390/molecules25040817 - 13 Feb 2020

Cited by 16 | Viewed by 4489

Abstract

In fertilized fish eggs, lipids are an energy reservoir for the embryo development and substrate for organogenesis. They occur in the cytoplasmic area and form lipid droplets (LDs), but also the yolk egg is composed of lipids and proteins. Insight on the LD [...] Read more.

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

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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19 pages, 3546 KiB

Open AccessArticle

A New Look into the Mode of Action of Metal-Based Anticancer Drugs

by M. Paula M. Marques, Ana L. M. Batista de Carvalho, Adriana P. Mamede, Asha Dopplapudi, Svemir Rudić, Madhusudan Tyagi, Victoria Garcia Sakai and Luís A. E. Batista de Carvalho

Molecules 2020, 25(2), 246; https://doi.org/10.3390/molecules25020246 - 7 Jan 2020

Cited by 19 | Viewed by 3724

Abstract

The mode of action of Pt- and Pd-based anticancer agents (cisplatin and Pd₂Spm) was studied by characterising their impact on DNA. Changes in conformation and mobility at the molecular level in hydrated DNA were analysed by quasi-elastic and inelastic neutron scattering [...] Read more.

The mode of action of Pt- and Pd-based anticancer agents (cisplatin and Pd₂Spm) was studied by characterising their impact on DNA. Changes in conformation and mobility at the molecular level in hydrated DNA were analysed by quasi-elastic and inelastic neutron scattering techniques (QENS and INS), coupled to Fourier transform infrared (FTIR) and microRaman spectroscopies. Although INS, FTIR and Raman revealed drug-triggered changes in the phosphate groups and the double helix base pairing, QENS allowed access to the nanosecond motions of the biomolecule’s backbone and confined hydration water within the minor groove. Distinct effects were observed for cisplatin and Pd₂Spm, the former having a predominant effect on DNA’s spine of hydration, whereas the latter had a higher influence on the backbone dynamics. This is an innovative way of tackling a drug’s mode of action, mediated by the hydration waters within its pharmacological target (DNA). Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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14 pages, 2587 KiB

Open AccessFeature PaperArticle

Tracking Extracellular Matrix Remodeling in Lungs Induced by Breast Cancer Metastasis. Fourier Transform Infrared Spectroscopic Studies

by Karolina Chrabaszcz, Katarzyna Kaminska, Karolina Augustyniak, Monika Kujdowicz, Marta Smeda, Agnieszka Jasztal, Marta Stojak, Katarzyna M. Marzec and Kamilla Malek

Molecules 2020, 25(1), 236; https://doi.org/10.3390/molecules25010236 - 6 Jan 2020

Cited by 12 | Viewed by 5740

Abstract

This work focused on a detailed assessment of lung tissue affected by metastasis of breast cancer. We used large-area chemical scanning implemented in Fourier transform infrared (FTIR) spectroscopic imaging supported with classical histological and morphological characterization. For the first time, we differentiated and [...] Read more.

This work focused on a detailed assessment of lung tissue affected by metastasis of breast cancer. We used large-area chemical scanning implemented in Fourier transform infrared (FTIR) spectroscopic imaging supported with classical histological and morphological characterization. For the first time, we differentiated and defined biochemical changes due to metastasis observed in the lung parenchyma, atelectasis, fibrous, and muscle cells, as well as bronchi ciliate cells, in a qualitative and semi-quantitative manner based on spectral features. The results suggested that systematic extracellular matrix remodeling with the progress of the metastasis process evoked a decrease in the fraction of the total protein in atelectasis, fibrous, and muscle cells, as well as an increase of fibrillar proteins in the parenchyma. We also detected alterations in the secondary conformations of proteins in parenchyma and atelectasis and changes in the level of hydroxyproline residues and carbohydrate moieties in the parenchyma. The results indicate the usability of FTIR spectroscopy as a tool for the detection of extracellular matrix remodeling, thereby enabling the prediction of pre-metastatic niche formation. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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14 pages, 4342 KiB

Open AccessArticle

Characterization of Intact Eukaryotic Cells with Subcellular Spatial Resolution by Photothermal-Induced Resonance Infrared Spectroscopy and Imaging

by Luca Quaroni

Molecules 2019, 24(24), 4504; https://doi.org/10.3390/molecules24244504 - 9 Dec 2019

Cited by 6 | Viewed by 3900

Abstract

Photothermal-induced resonance (PTIR) spectroscopy and imaging with infrared light has seen increasing application in the molecular spectroscopy of biological samples. The appeal of the technique lies in its capability to provide information about IR light absorption at a spatial resolution better than that [...] Read more.

Photothermal-induced resonance (PTIR) spectroscopy and imaging with infrared light has seen increasing application in the molecular spectroscopy of biological samples. The appeal of the technique lies in its capability to provide information about IR light absorption at a spatial resolution better than that allowed by light diffraction, typically below 100 nm. In the present work, we tested the capability of the technique to perform measurements with subcellular resolution on intact eukaryotic cells, without drying or fixing. We demonstrate the possibility of obtaining PTIR images and spectra from the nucleus and multiple organelles with high resolution, better than that allowed by diffraction with infrared light. We obtain particularly strong signal from bands typically assigned to acyl lipids and proteins. We also show that while a stronger signal is obtained from some subcellular structures, other large subcellular components provide a weaker or undetectable PTIR response. The mechanism that underlies such variability in response is presently unclear. We propose and discuss different possibilities, addressing thermomechanical, geometrical, and electrical properties of the sample and the presence of cellular water, from which the difference in response may arise. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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15 pages, 3720 KiB

Open AccessArticle

SERS Studies of Adsorption on Gold Surfaces of Mononucleotides with Attached Hexanethiol Moiety: Comparison with Selected Single-Stranded Thiolated DNA Fragments

by Edyta Pyrak, Aleksandra Jaworska and Andrzej Kudelski

Molecules 2019, 24(21), 3921; https://doi.org/10.3390/molecules24213921 - 30 Oct 2019

Cited by 23 | Viewed by 4894

Abstract

The attachment of DNA strands to gold surfaces is performed in many devices, such as various DNA sensors. One of the standard methods used to immobilize DNA on gold surfaces involves two steps: the attachment of a thiol linker group (usually in the [...] Read more.

The attachment of DNA strands to gold surfaces is performed in many devices, such as various DNA sensors. One of the standard methods used to immobilize DNA on gold surfaces involves two steps: the attachment of a thiol linker group (usually in the form of alkanethiol moiety) to the DNA strand, and the chemical reaction between the thiol-terminated DNA and the gold surface. Since thiols react chemically with the surface of gold substrates, forming very stable Au–S bonds, it is often assumed that the chemisorption on the gold surface of nucleotides with an attached thiol linker group leads to the formation of an order layer with the linking moieties relatively densely packed on the gold surface. In this contribution we show that chemisorption of thiolated mononucleotides does not occur according to this model. For example, the thiolated mononucleotide containing adenine strongly interacts with the gold surface via the adenine moiety. Moreover, bonding of the mononucleotide containing adenine to the gold surface is relatively similar to the bonding of adenine, and the main difference is that the adenine interacts with the gold surface mainly through the pyrimidine ring, while for adenine mononucleotide interaction via the imidazole ring also significantly contributes to the total bonding. A similar effect was observed for the mononucleotide containing cytosine, and the main difference between the interaction with the gold surface of cytosine and cytosine mononucleotide is that mononucleotide containing cytosine interacts with the gold surface to a significantly larger extend via the carboxylic group of the base. We also show that the structure of the layer formed on the gold surface by the thiolated mononucleotides may be significantly different than the structure of the layer formed by thiolated single-stranded DNA containing even as few as two bases. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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Review

Jump to: Research

22 pages, 14274 KiB

Open AccessReview

Vibrational Spectroscopy for In Vitro Monitoring Stem Cell Differentiation

by Francesca Ravera, Esen Efeoglu and Hugh J. Byrne

Molecules 2020, 25(23), 5554; https://doi.org/10.3390/molecules25235554 - 26 Nov 2020

Cited by 12 | Viewed by 5081

Abstract

Stem cell technology has attracted considerable attention over recent decades due to its enormous potential in regenerative medicine and disease therapeutics. Studying the underlying mechanisms of stem cell differentiation and tissue generation is critical, and robust methodologies and different technologies are required. Towards [...] Read more.

Stem cell technology has attracted considerable attention over recent decades due to its enormous potential in regenerative medicine and disease therapeutics. Studying the underlying mechanisms of stem cell differentiation and tissue generation is critical, and robust methodologies and different technologies are required. Towards establishing improved understanding and optimised triggering and control of differentiation processes, analytical techniques such as flow cytometry, immunohistochemistry, reverse transcription polymerase chain reaction, RNA in situ hybridisation analysis, and fluorescence-activated cell sorting have contributed much. However, progress in the field remains limited because such techniques provide only limited information, as they are only able to address specific, selected aspects of the process, and/or cannot visualise the process at the subcellular level. Additionally, many current analytical techniques involve the disruption of the investigation process (tissue sectioning, immunostaining) and cannot monitor the cellular differentiation process in situ, in real-time. Vibrational spectroscopy, as a label-free, non-invasive and non-destructive analytical technique, appears to be a promising candidate to potentially overcome many of these limitations as it can provide detailed biochemical fingerprint information for analysis of cells, tissues, and body fluids. The technique has been widely used in disease diagnosis and increasingly in stem cell technology. In this work, the efforts regarding the use of vibrational spectroscopy to identify mechanisms of stem cell differentiation at a single cell and tissue level are summarised. Both infrared absorption and Raman spectroscopic investigations are explored, and the relative merits, and future perspectives of the techniques are discussed. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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27 pages, 1499 KiB

Open AccessReview

Vibrational Spectroscopy Saliva Profiling as Biometric Tool for Disease Diagnostics: A Systematic Literature Review

by Stéphane Derruau, Julien Robinet, Valérie Untereiner, Olivier Piot, Ganesh D. Sockalingum and Sandrine Lorimier

Molecules 2020, 25(18), 4142; https://doi.org/10.3390/molecules25184142 - 10 Sep 2020

Cited by 34 | Viewed by 4456

Abstract

Saliva is a biofluid that can be considered as a “mirror” reflecting our body’s health status. Vibrational spectroscopy, Raman and infrared, can provide a detailed salivary fingerprint that can be used for disease biomarker discovery. We propose a systematic literature review based on [...] Read more.

Saliva is a biofluid that can be considered as a “mirror” reflecting our body’s health status. Vibrational spectroscopy, Raman and infrared, can provide a detailed salivary fingerprint that can be used for disease biomarker discovery. We propose a systematic literature review based on the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines to evaluate the potential of vibrational spectroscopy to diagnose oral and general diseases using saliva as a biological specimen. Literature searches were recently conducted in May 2020 through MEDLINE-PubMed and Scopus databases, without date limitation. Finally, over a period of 10 years, 18 publications were included reporting on 10 diseases (three oral and seven general diseases), with very high diagnostic performance rates in terms of sensitivity, specificity, and accuracy. Thirteen articles were related to six different cancers of the following anatomical sites: mouth, nasopharynx, lung, esophagus, stomach, and breast. The other diseases investigated and included in this review were periodontitis, Sjögren’s syndrome, diabetes, and myocardial infarction. Moreover, most articles focused on Raman spectroscopy (n = 16/18) and more specifically surface-enhanced Raman spectroscopy (n = 12/18). Interestingly, vibrational spectroscopy appears promising as a rapid, label-free, and non-invasive diagnostic salivary biometric tool. Furthermore, it could be adapted to investigate subclinical diseases—even if developmental studies are required. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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16 pages, 2522 KiB

Open AccessReview

Optical Identification of Middle Ear Infection

by Alisha Prasad, Syed Mohammad Abid Hasan and Manas Ranjan Gartia

Molecules 2020, 25(9), 2239; https://doi.org/10.3390/molecules25092239 - 9 May 2020

Cited by 5 | Viewed by 12436

Abstract

Ear infection is one of the most commonly occurring inflammation diseases in the world, especially for children. Almost every child encounters at least one episode of ear infection before he/she reaches the age of seven. The typical treatment currently followed by physicians is [...] Read more.

Ear infection is one of the most commonly occurring inflammation diseases in the world, especially for children. Almost every child encounters at least one episode of ear infection before he/she reaches the age of seven. The typical treatment currently followed by physicians is visual inspection and antibiotic prescription. In most cases, a lack of improper treatment results in severe bacterial infection. Therefore, it is necessary to design and explore advanced practices for effective diagnosis. In this review paper, we present the various types of ear infection and the related pathogens responsible for middle ear infection. We outline the conventional techniques along with clinical trials using those techniques to detect ear infections. Further, we highlight the need for emerging techniques to reduce ear infection complications. Finally, we emphasize the utility of Raman spectroscopy as a prospective non-invasive technique for the identification of middle ear infection. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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24 pages, 2627 KiB

Open AccessReview

Molecular Spectroscopic Markers of DNA Damage

by Kamila Sofińska, Natalia Wilkosz, Marek Szymoński and Ewelina Lipiec

Molecules 2020, 25(3), 561; https://doi.org/10.3390/molecules25030561 - 28 Jan 2020

Cited by 42 | Viewed by 8103

Abstract

Every cell in a living organism is constantly exposed to physical and chemical factors which damage the molecular structure of proteins, lipids, and nucleic acids. Cellular DNA lesions are the most dangerous because the genetic information, critical for the identity and function of [...] Read more.

Every cell in a living organism is constantly exposed to physical and chemical factors which damage the molecular structure of proteins, lipids, and nucleic acids. Cellular DNA lesions are the most dangerous because the genetic information, critical for the identity and function of each eukaryotic cell, is stored in the DNA. In this review, we describe spectroscopic markers of DNA damage, which can be detected by infrared, Raman, surface-enhanced Raman, and tip-enhanced Raman spectroscopies, using data acquired from DNA solutions and mammalian cells. Various physical and chemical DNA damaging factors are taken into consideration, including ionizing and non-ionizing radiation, chemicals, and chemotherapeutic compounds. All major spectral markers of DNA damage are presented in several tables, to give the reader a possibility of fast identification of the spectral signature related to a particular type of DNA damage. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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31 pages, 4236 KiB

Open AccessReview

Surface Enhanced Raman Spectroscopy for DNA Biosensors—How Far Are We?

by Edyta Pyrak, Jan Krajczewski, Artur Kowalik, Andrzej Kudelski and Aleksandra Jaworska

Molecules 2019, 24(24), 4423; https://doi.org/10.3390/molecules24244423 - 4 Dec 2019

Cited by 77 | Viewed by 8332

Abstract

A sensitive and accurate identification of specific DNA fragments (usually containing a mutation) can influence clinical decisions. Standard methods routinely used for this type of detection are PCR (Polymerase Chain Reaction, and its modifications), and, less commonly, NGS (Next Generation Sequencing). However, these [...] Read more.

A sensitive and accurate identification of specific DNA fragments (usually containing a mutation) can influence clinical decisions. Standard methods routinely used for this type of detection are PCR (Polymerase Chain Reaction, and its modifications), and, less commonly, NGS (Next Generation Sequencing). However, these methods are quite complicated, requiring time-consuming, multi-stage sample preparation, and specially trained staff. Usually, it takes weeks for patients to obtain their results. Therefore, different DNA sensors are being intensively developed by many groups. One technique often used to obtain an analytical signal from DNA sensors is Raman spectroscopy. Its modification, surface-enhanced Raman spectroscopy (SERS), is especially useful for practical analytical applications due to its extra low limit of detection. SERS takes advantage of the strong increase in the efficiency of Raman signal generation caused by a local electric field enhancement near plasmonic (typically gold and silver) nanostructures. In this condensed review, we describe the most important types of SERS-based nanosensors for genetic studies and comment on their potential for becoming diagnostic tools. Full article

(This article belongs to the Special Issue Biomedical Raman and Infrared Spectroscopy: Recent Advancement and Applications)

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