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Spectroscopic Imaging Techniques for Biological Metabolisms Investigations

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (15 January 2023) | Viewed by 10660

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Special Issue Editors

Dr. Alessandra Gianoncelli

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Guest Editor

ELETTRA Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy
Interests: X-ray microscopy; X-ray fluorescence; ptychography and related applications in life sciences; environmental science and cultural heritage
Special Issues, Collections and Topics in MDPI journals

Dr. Lorella Pascolo

E-Mail Website
Guest Editor

IRCCS Burlo Garofolo, Trieste, Italy
Interests: elementomics; iron-dyshomeostasis diseases; reproductive toxicology; endometriosis; nanomedicine; asbestos and nano-toxicology; membrane transport mechanisms; advanced imaging techniques
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over the past few decades, the advent of advanced spectroscopic imaging techniques has paved the way for new approaches in biochemical molecular investigations at different length scales.

The novel methods, which include X-ray fluorescence microscopy and tomography, X-ray microscopy, PIXE, vibrational spectroscopy such as FTIR and Raman, and other advanced spectro-microscopies, allow one to characterize biological samples through multi-level data, from the ion and molecular level, from single cells all the way to whole organs and beyond.

High-throughput elemental imaging techniques such as XRF, PIXE, and LA-ICP enable ionomics, which is the study of metal, non-metal, and metalloid compositions in both plant and animal living organisms. Chemical imaging via spectroscopic microscopy, using techniques such as FTIR, Raman, and fMRI, provides label-free mapping with micro- and submicrometric resolution and can explore intracellular metabolism by tracing small biomolecules including amino acids, nucleic acids, lipids, and carbohydrates. Image-processing capabilities sometimes allow for 3D reconstruction of image data, as well as the quantification of biological features.

We invite colleagues involved in applying such advanced analytical techniques for ionomics and/or molecular studies to contribute to this issue.

Dr. Alessandra Gianoncelli
Dr. Lorella Pascolo
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

X-ray fluorescence
FTIR microscopy
Raman
fMRI
ionomics
chemical imaging
PIXE
elemental imaging
metabolism

Published Papers (5 papers)

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Research

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11 pages, 1343 KiB

Open AccessCommunication

Upside-Down Preference in the Forskolin-Induced In Vitro Differentiation of 50B11 Sensory Neurons: A Morphological Investigation by Label-Free Non-Linear Microscopy

by Luisa Zupin, Sotiris Psilodimitrakopoulos, Fulvio Celsi, Lina Papadimitriou, Anthi Ranella, Sergio Crovella, Giuseppe Ricci, Emmanuel Stratakis and Lorella Pascolo

Int. J. Mol. Sci. 2023, 24(9), 8354; https://doi.org/10.3390/ijms24098354 - 6 May 2023

Cited by 2 | Viewed by 1603

Abstract

In this study, we revealed a peculiar morphological feature of 50B11 nociceptive sensory neurons in in vitro culture related to the forskolin-induced differentiation of these cells growing upside-down on cover glass supports. Multi-photon non-linear microscopy was applied to monitor increased neurite arborization and elongation. Under live and unstained conditions, second harmonic generation (SHG) microscopy could monitor microtubule organization inside the cells while also correlating with the detection of cellular multi-photon autofluorescence, probably derived from mitochondria metabolites. Although the differentiated cells of each compartment did not differ significantly in tubulin or multi-photon autofluorescence contents, the upturned neurons were more elongated, presenting a higher length/width cellular ratio and longer neurites, indicative of differentiated cells. SHG originating from the axons’ microtubules represented a proper tool to study neurons’ inverted culture in live conditions without exogenous staining. This work represents the first instance of examining neuronal cell lines growing and differentiated in an upside-down orientation, allowing a possible improvement of 50B11 as a model in physiology studies of sensory neurons in peripheric nervous system disease (e.g., Fabry disease, Friedreich ataxia, Charcot–Marie–Tooth, porphyria, type 1 diabetes, Guillain–Barré syndrome in children) and analgesic drug screening. Full article

(This article belongs to the Special Issue Spectroscopic Imaging Techniques for Biological Metabolisms Investigations)

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20 pages, 6564 KiB

Open AccessArticle

Multidimensional Profiling of Human Body Hairs Using Qualitative and Semi-Quantitative Approaches with SR-XRF, ATR-FTIR, DSC, and SEM-EDX

by Karen J. Cloete, Žiga Šmit and Alessandra Gianoncelli

Int. J. Mol. Sci. 2023, 24(4), 4166; https://doi.org/10.3390/ijms24044166 - 19 Feb 2023

Cited by 4 | Viewed by 2466

Abstract

This study aimed to assess the potential of a multidimensional approach to differentiate body hairs based on their physico-chemical properties and whether body hairs can replace the use of scalp hair in studies linked to forensic and systemic intoxication. This is the first case report controlling for confounding variables to explore the utility of multidimensional profiling of body hair using synchrotron synchrotron microbeam X-ray fluorescence (SR-XRF) for longitudinal and hair morphological region mapping) and benchtop methods, including attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) (complemented with chemometrics analysis), energy dispersive X-ray analysis (EDX) (complemented with heatmap analysis), differential scanning calorimetry (DSC), and scanning electron microscopy (SEM) analysis (complemented by descriptive statistics) to profile different body hairs in terms of their elemental, biochemical, thermal, and cuticle properties. This multidimensional approach provided supportive information to emphasize the intricate and rather complex interplay between the organization and levels of elements and biomolecules within the crystalline and amorphous matrix of different body hairs responsible for the differences in physico-chemical properties between body hairs that are predominantly affected by the growth rate, follicle or apocrine gland activity, and external factors such as cosmetic use and exposure to environmental xenobiotics. The data from this study may have important implications for forensic science, toxicology and systemic intoxication, or other studies involving hair as a research matrix. Full article

(This article belongs to the Special Issue Spectroscopic Imaging Techniques for Biological Metabolisms Investigations)

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Graphical abstract

28 pages, 5257 KiB

Open AccessArticle

Combination of Biochemical, Molecular, and Synchrotron-Radiation-Based Techniques to Study the Effects of Silicon in Tomato (Solanum Lycopersicum L.)

by Marta Marmiroli, Francesca Mussi, Valentina Gallo, Alessandra Gianoncelli, William Hartley and Nelson Marmiroli

Int. J. Mol. Sci. 2022, 23(24), 15837; https://doi.org/10.3390/ijms232415837 - 13 Dec 2022

Cited by 4 | Viewed by 1269

Abstract

The work focused on the analysis of two cultivars of tomato (Solanum lycopersicum L.), Aragon and Gladis, under two different treatments of silicon, Low, 2 L of 0.1 mM CaSiO_3, and High, 0.5 mM CaSiO₃, weekly, for 8 weeks, under stress-free conditions. We subsequently analyzed the morphology, chemical composition, and elemental distribution using synchrotron-based µ-XRF techniques, physiological, and molecular aspects of the response of the two cultivars. The scope of the study was to highlight any significant response of the plants to the Si treatments, in comparison with any response to Si of plants under stress. The results demonstrated that the response was mainly cultivar-dependent, also at the level of mitochondrial-dependent oxidative stress, and that it did not differ from the two conditions of treatments. With Si deposited mainly in the cell walls of the cells of fruits, leaves, and roots, the treatments did not elicit many significant changes from the point of view of the total elemental content, the physiological parameters that measured the oxidative stress, and the transcriptomic analyses focalized on genes related to the response to Si. We observed a priming effect of the treatment on the most responsive cultivar, Aragon, in respect to future stress, while in Gladis the Si treatment did not significantly change the measured parameters. Full article

(This article belongs to the Special Issue Spectroscopic Imaging Techniques for Biological Metabolisms Investigations)

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Review

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14 pages, 1201 KiB

Open AccessReview

Soft X-ray Fluorescence and Near-Edge Absorption Microscopy for Investigating Metabolic Features in Biological Systems: A Review

by Valentina Bonanni and Alessandra Gianoncelli

Int. J. Mol. Sci. 2023, 24(4), 3220; https://doi.org/10.3390/ijms24043220 - 6 Feb 2023

Cited by 5 | Viewed by 1899

Abstract

Scanning transmission X-ray microscopy (STXM) provides the imaging of biological specimens allowing the parallel collection of localized spectroscopic information by X-ray fluorescence (XRF) and/or X-ray Absorption Near Edge Spectroscopy (XANES). The complex metabolic mechanisms which can take place in biological systems can be explored by these techniques by tracing even small quantities of the chemical elements involved in the metabolic pathways. Here, we present a review of the most recent publications in the synchrotrons’ scenario where soft X-ray spectro-microscopy has been employed in life science as well as in environmental research. Full article

(This article belongs to the Special Issue Spectroscopic Imaging Techniques for Biological Metabolisms Investigations)

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18 pages, 888 KiB

Open AccessReview

Raman Spectroscopy as a Tool to Study the Pathophysiology of Brain Diseases

by Oihana Terrones, June Olazar-Intxausti, Itxaso Anso, Maier Lorizate, Jon Ander Nieto-Garai and Francesc-Xabier Contreras

Int. J. Mol. Sci. 2023, 24(3), 2384; https://doi.org/10.3390/ijms24032384 - 25 Jan 2023

Cited by 8 | Viewed by 2798

Abstract

The Raman phenomenon is based on the spontaneous inelastic scattering of light, which depends on the molecular characteristics of the dispersant. Therefore, Raman spectroscopy and imaging allow us to obtain direct information, in a label-free manner, from the chemical composition of the sample. Since it is well established that the development of many brain diseases is associated with biochemical alterations of the affected tissue, Raman spectroscopy and imaging have emerged as promising tools for the diagnosis of ailments. A combination of Raman spectroscopy and/or imaging with tagged molecules could also help in drug delivery and tracing for treatment of brain diseases. In this review, we first describe the basics of the Raman phenomenon and spectroscopy. Then, we delve into the Raman spectroscopy and imaging modes and the Raman-compatible tags. Finally, we center on the application of Raman in the study, diagnosis, and treatment of brain diseases, by focusing on traumatic brain injury and ischemia, neurodegenerative disorders, and brain cancer. Full article

(This article belongs to the Special Issue Spectroscopic Imaging Techniques for Biological Metabolisms Investigations)

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