International Journal of Molecular Sciences

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2 pages, 192 KiB

Open AccessEditorial

Special Issue on “Raman Spectroscopy for Chemical and Structural Characterization in Biology”

by Sébastien Bonhommeau

Int. J. Mol. Sci. 2022, 23(19), 11795; https://doi.org/10.3390/ijms231911795 - 4 Oct 2022

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Abstract

Raman spectroscopy is a popular non-invasive spectroscopic technique for molecular characterization and imaging with a high spatial resolution [...] Full article

(This article belongs to the Special Issue Raman Spectroscopy for Chemical and Structural Characterization in Biology)

Research

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21 pages, 1688 KiB

Open AccessArticle

Raman Spectra and Ancient Life: Vibrational ID Profiles of Fossilized (Bone) Tissues

by Zuzana Jurašeková, Gabriela Fabriciová, Luis F. Silveira, Yuong-Nam Lee, Jaroslav M. Gutak, Majid Mirzaie Ataabadi and Martin Kundrát

Int. J. Mol. Sci. 2022, 23(18), 10689; https://doi.org/10.3390/ijms231810689 - 14 Sep 2022

Cited by 5 | Viewed by 2263

Abstract

Raman micro-spectroscopy is a non-destructive and non-contact analytical technique that combines microscopy and spectroscopy, thus providing a potential for non-invasive and in situ molecular identification, even over heterogeneous and rare samples such as fossilized tissues. Recently, chemical imaging techniques have become an increasingly [...] Read more.

Raman micro-spectroscopy is a non-destructive and non-contact analytical technique that combines microscopy and spectroscopy, thus providing a potential for non-invasive and in situ molecular identification, even over heterogeneous and rare samples such as fossilized tissues. Recently, chemical imaging techniques have become an increasingly popular tool for characterizing trace elements, isotopic information, and organic markers in fossils. Raman spectroscopy also shows a growing potential in understanding bone microstructure, chemical composition, and mineral assemblance affected by diagenetic processes. In our lab, we have investigated a wide range of different fossil tissues, mainly of Mesozoic vertebrates (from Jurassic through Cretaceous). Besides standard spectra of sedimentary rocks, including pigment contamination, our Raman spectra also exhibit interesting spectral features in the 1200–1800 cm⁻¹ spectral range, where Raman bands of proteins, nucleic acids, and other organic molecules can be identified. In the present study, we discuss both a possible origin of the observed bands of ancient organic residues and difficulties with definition of the specific spectral markers in fossilized soft and hard tissues. Full article

(This article belongs to the Special Issue Raman Spectroscopy for Chemical and Structural Characterization in Biology)

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13 pages, 1444 KiB

Open AccessArticle

Revealing the Chemical Composition of Birch Pollen Grains by Raman Spectroscopic Imaging

by Clara Stiebing, Nele Post, Claudia Schindler, Bianca Göhrig, Harald Lux, Jürgen Popp, Astrid Heutelbeck and Iwan W. Schie

Int. J. Mol. Sci. 2022, 23(9), 5112; https://doi.org/10.3390/ijms23095112 - 4 May 2022

Cited by 5 | Viewed by 1892

Abstract

The investigation of the biochemical composition of pollen grains is of the utmost interest for several environmental aspects, such as their allergenic potential and their changes in growth conditions due to climatic factors. In order to fully understand the composition of pollen grains, [...] Read more.

The investigation of the biochemical composition of pollen grains is of the utmost interest for several environmental aspects, such as their allergenic potential and their changes in growth conditions due to climatic factors. In order to fully understand the composition of pollen grains, not only is an in-depth analysis of their molecular components necessary but also spatial information of, e.g., the thickness of the outer shell, should be recorded. However, there is a lack of studies using molecular imaging methods for a spatially resolved biochemical composition on a single-grain level. In this study, Raman spectroscopy was implemented as an analytical tool to investigate birch pollen by imaging single pollen grains and analyzing their spectral profiles. The imaging modality allowed us to reveal the layered structure of pollen grains based on the biochemical information of the recorded Raman spectra. Seven different birch pollen species collected at two different locations in Germany were investigated and compared. Using chemometric algorithms such as hierarchical cluster analysis and multiple-curve resolution, several components of the grain wall, such as sporopollenin, as well as the inner core presenting high starch concentrations, were identified and quantified. Differences in the concentrations of, e.g., sporopollenin, lipids and proteins in the pollen species at the two different collection sites were found, and are discussed in connection with germination and other growth processes. Full article

(This article belongs to the Special Issue Raman Spectroscopy for Chemical and Structural Characterization in Biology)

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25 pages, 5968 KiB

Open AccessArticle

A Single-Cell Raman Spectroscopy Analysis of Bone Marrow Mesenchymal Stem/Stromal Cells to Identify Inter-Individual Diversity

by Tamara Kukolj, Jasmina Lazarević, Ana Borojević, Uroš Ralević, Dragana Vujić, Aleksandra Jauković, Nenad Lazarević and Diana Bugarski

Int. J. Mol. Sci. 2022, 23(9), 4915; https://doi.org/10.3390/ijms23094915 - 28 Apr 2022

Cited by 7 | Viewed by 2815

Abstract

The heterogeneity of stem cells represents the main challenge in regenerative medicine development. This issue is particularly pronounced when it comes to the use of primary mesenchymal stem/stromal cells (MSCs) due to a lack of identification markers. Considering the need for additional approaches [...] Read more.

The heterogeneity of stem cells represents the main challenge in regenerative medicine development. This issue is particularly pronounced when it comes to the use of primary mesenchymal stem/stromal cells (MSCs) due to a lack of identification markers. Considering the need for additional approaches in MSCs characterization, we applied Raman spectroscopy to investigate inter-individual differences between bone marrow MSCs (BM-MSCs). Based on standard biological tests, BM-MSCs of analyzed donors fulfill all conditions for their characterization, while no donor-related specifics were observed in terms of BM-MSCs morphology, phenotype, multilineage differentiation potential, colony-forming capacity, expression of pluripotency-associated markers or proliferative capacity. However, examination of BM-MSCs at a single-cell level by Raman spectroscopy revealed that despite similar biochemical background, fine differences in the Raman spectra of BM-MSCs of each donor can be detected. After extensive principal component analysis (PCA) of Raman spectra, our study revealed the possibility of this method to diversify BM-MSCs populations, whereby the grouping of cell populations was most prominent when cell populations were analyzed in pairs. These results indicate that Raman spectroscopy, as a label-free assay, could have a huge potential in understanding stem cell heterogeneity and sorting cell populations with a similar biochemical background that can be significant for the development of personalized therapy approaches. Full article

(This article belongs to the Special Issue Raman Spectroscopy for Chemical and Structural Characterization in Biology)

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21 pages, 5890 KiB

Open AccessArticle

Raman Research on Bleomycin-Induced DNA Strand Breaks and Repair Processes in Living Cells

by Michał Czaja, Katarzyna Skirlińska-Nosek, Olga Adamczyk, Kamila Sofińska, Natalia Wilkosz, Zenon Rajfur, Marek Szymoński and Ewelina Lipiec

Int. J. Mol. Sci. 2022, 23(7), 3524; https://doi.org/10.3390/ijms23073524 - 24 Mar 2022

Cited by 9 | Viewed by 2428

Abstract

Even several thousands of DNA lesions are induced in one cell within one day. DNA damage may lead to mutations, formation of chromosomal aberrations, or cellular death. A particularly cytotoxic type of DNA damage is single- and double-strand breaks (SSBs and DSBs, respectively). [...] Read more.

Even several thousands of DNA lesions are induced in one cell within one day. DNA damage may lead to mutations, formation of chromosomal aberrations, or cellular death. A particularly cytotoxic type of DNA damage is single- and double-strand breaks (SSBs and DSBs, respectively). In this work, we followed DNA conformational transitions induced by the disruption of DNA backbone. Conformational changes of chromatin in living cells were induced by a bleomycin (BLM), an anticancer drug, which generates SSBs and DSBs. Raman micro-spectroscopy enabled to observe chemical changes at the level of single cell and to collect hyperspectral images of molecular structure and composition with sub-micrometer resolution. We applied multivariate data analysis methods to extract key information from registered data, particularly to probe DNA conformational changes. Applied methodology enabled to track conformational transition from B-DNA to A-DNA upon cellular response to BLM treatment. Additionally, increased expression of proteins within the cell nucleus resulting from the activation of repair processes was demonstrated. The ongoing DNA repair process under the BLM action was also confirmed with confocal laser scanning fluorescent microscopy. Full article

(This article belongs to the Special Issue Raman Spectroscopy for Chemical and Structural Characterization in Biology)

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11 pages, 1853 KiB

Open AccessArticle

Strategies and Perspectives for UV Resonance Raman Applicability in Clinical Analyses of Human Sperm RNA

by Maria Pachetti, Francesco D’Amico, Luisa Zupin, Stefania Luppi, Monica Martinelli, Sergio Crovella, Giuseppe Ricci and Lorella Pascolo

Int. J. Mol. Sci. 2021, 22(23), 13134; https://doi.org/10.3390/ijms222313134 - 4 Dec 2021

Cited by 2 | Viewed by 1893

Abstract

Developing a deeper knowledge about the impact of DNA and RNA epigenetic mutations on sperm production and fertilization performance is essential for selecting best quality samples in Assisted Reproductive Technologies (ART). Indeed, sperm RNAs adenine and guanine are likely to be methylated in [...] Read more.

Developing a deeper knowledge about the impact of DNA and RNA epigenetic mutations on sperm production and fertilization performance is essential for selecting best quality samples in Assisted Reproductive Technologies (ART). Indeed, sperm RNAs adenine and guanine are likely to be methylated in low quality RNA sperm samples and their study requires the employment of techniques able to isolate high quality nucleic acids. UV resonance Raman spectroscopy represents a valuable tool that is able to monitor peculiar molecular modifications occurring predominantly in nucleic acids, being less sensitive to the presence of other biological compounds. In this work, we used an UV Resonance Raman (UVRR) setup coupled to a synchrotron radiation source tuned at 250 nm, in order to enhance sperm RNAs adenine and guanine vibrational signals, reducing also the impact of a fluorescence background typically occurring at lower energies. Despite that our protocol should be further optimized and further analyses are requested, our results support the concept that UVRR can be applied for setting inexpensive tools to be employed for semen quality assessment in ART. Full article

(This article belongs to the Special Issue Raman Spectroscopy for Chemical and Structural Characterization in Biology)

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23 pages, 4381 KiB

Open AccessArticle

Assessment of Biotechnologically Important Filamentous Fungal Biomass by Fourier Transform Raman Spectroscopy

by Simona Dzurendová, Volha Shapaval, Valeria Tafintseva, Achim Kohler, Dana Byrtusová, Martin Szotkowski, Ivana Márová and Boris Zimmermann

Int. J. Mol. Sci. 2021, 22(13), 6710; https://doi.org/10.3390/ijms22136710 - 23 Jun 2021

Cited by 13 | Viewed by 3580

Abstract

Oleaginous filamentous fungi can accumulate large amount of cellular lipids and biopolymers and pigments and potentially serve as a major source of biochemicals for food, feed, chemical, pharmaceutical, and transport industries. We assessed suitability of Fourier transform (FT) Raman spectroscopy for screening and [...] Read more.

Oleaginous filamentous fungi can accumulate large amount of cellular lipids and biopolymers and pigments and potentially serve as a major source of biochemicals for food, feed, chemical, pharmaceutical, and transport industries. We assessed suitability of Fourier transform (FT) Raman spectroscopy for screening and process monitoring of filamentous fungi in biotechnology. Six Mucoromycota strains were cultivated in microbioreactors under six growth conditions (three phosphate concentrations in the presence and absence of calcium). FT-Raman and FT-infrared (FTIR) spectroscopic data was assessed in respect to reference analyses of lipids, phosphorus, and carotenoids by using principal component analysis (PCA), multiblock or consensus PCA, partial least square regression (PLSR), and analysis of spectral variation due to different design factors by an ANOVA model. All main chemical biomass constituents were detected by FT-Raman spectroscopy, including lipids, proteins, cell wall carbohydrates, and polyphosphates, and carotenoids. FT-Raman spectra clearly show the effect of growth conditions on fungal biomass. PLSR models with high coefficients of determination (0.83–0.94) and low error (approximately 8%) for quantitative determination of total lipids, phosphates, and carotenoids were established. FT-Raman spectroscopy showed great potential for chemical analysis of biomass of oleaginous filamentous fungi. The study demonstrates that FT-Raman and FTIR spectroscopies provide complementary information on main fungal biomass constituents. Full article

(This article belongs to the Special Issue Raman Spectroscopy for Chemical and Structural Characterization in Biology)

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21 pages, 326 KiB

Open AccessReview

Current and Future Advancements of Raman Spectroscopy Techniques in Cancer Nanomedicine

by Elisabetta Canetta

Int. J. Mol. Sci. 2021, 22(23), 13141; https://doi.org/10.3390/ijms222313141 - 5 Dec 2021

Cited by 16 | Viewed by 3564

Abstract

Raman scattering is one of the most used spectroscopy and imaging techniques in cancer nanomedicine due to its high spatial resolution, high chemical specificity, and multiplexity modalities. The flexibility of Raman techniques has led, in the past few years, to the rapid development [...] Read more.

Raman scattering is one of the most used spectroscopy and imaging techniques in cancer nanomedicine due to its high spatial resolution, high chemical specificity, and multiplexity modalities. The flexibility of Raman techniques has led, in the past few years, to the rapid development of Raman spectroscopy and imaging for nanodiagnostics, nanotherapy, and nanotheranostics. This review focuses on the applications of spontaneous Raman spectroscopy and bioimaging to cancer nanotheranostics and their coupling to a variety of diagnostic/therapy methods to create nanoparticle-free theranostic systems for cancer diagnostics and therapy. Recent implementations of confocal Raman spectroscopy that led to the development of platforms for monitoring the therapeutic effects of anticancer drugs in vitro and in vivo are also reviewed. Another Raman technique that is largely employed in cancer nanomedicine, due to its ability to enhance the Raman signal, is surface-enhanced Raman spectroscopy (SERS). This review also explores the applications of the different types of SERS, such as SERRS and SORS, to cancer diagnosis through SERS nanoprobes and the detection of small-size biomarkers, such as exosomes. SERS cancer immunotherapy and immuno-SERS (iSERS) microscopy are reviewed. Full article

(This article belongs to the Special Issue Raman Spectroscopy for Chemical and Structural Characterization in Biology)

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