Spectroscopy Journal

12 pages, 1414 KiB

Open AccessArticle

Optimizing Automated Detection for Cytoplasmic TDP25 Aggregates in Fluorescence Imaging

by Sumire Sogawa, Kotetsu Sasaki and Akira Kitamura

Spectrosc. J. 2025, 3(2), 18; https://doi.org/10.3390/spectroscj3020018 - 19 May 2025

Protein aggregates are known to disrupt normal cellular functions and homeostasis, serving as key hallmarks of various neurodegenerative disorders, including Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis (ALS). Automated detection of cytoplasmic, disease-associated aggregates in fluorescence images is crucial for characterizing these [...] Read more.

Protein aggregates are known to disrupt normal cellular functions and homeostasis, serving as key hallmarks of various neurodegenerative disorders, including Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis (ALS). Automated detection of cytoplasmic, disease-associated aggregates in fluorescence images is crucial for characterizing these aggregates and exploring potential strategies for their prevention. In this study, we demonstrate that removing background fluorescence and improving the brightness of aggregates using an automated aggregate detection algorithm significantly enhances the detection efficiency of cytoplasmic aggregates formed by the 25 kDa C-terminal fragment of ALS-associated TDP-43 (TDP25). A high signal-to-noise ratio can improve detection efficiency. Our findings contribute to the development of more effective detection methods for disease-associated aggregates of heterogeneous sizes and fluorescence intensities, which are typically challenging to identify automatically. Full article

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10 pages, 1772 KiB

Open AccessArticle

Determination of the Activation Energy of the Thermal Isomerization of Oleic Acid with Raman Spectroscopy and Partial Least Squares Regression

by Akihiro Watanabe and Yasushi Numata

Spectrosc. J. 2025, 3(2), 17; https://doi.org/10.3390/spectroscj3020017 - 8 May 2025

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Abstract

Unsaturated fatty acids have cis and trans isomers. The naturally stable isomer is the cis isomer, which is changed to the trans isomer by a thermal reaction. The reaction order, reaction constant, and activation energy are required to confirm the reaction mechanism. Therefore, [...] Read more.

Unsaturated fatty acids have cis and trans isomers. The naturally stable isomer is the cis isomer, which is changed to the trans isomer by a thermal reaction. The reaction order, reaction constant, and activation energy are required to confirm the reaction mechanism. Therefore, the concentrations of the cis and trans isomers must be determined simultaneously. In the present study, oleic acid (cis isomer) and elaidic acid (trans isomer) were measured using Raman spectroscopy and partial least squares regression. The thermal reaction of oleic acid was performed at several temperatures. The reaction was determined as a first-order reaction. The reaction rate constants at several temperatures were determined as 1.3 × 10⁻³ to 5.2 × 10⁻³/h at 100 °C to 160 °C by plotting the logarithm of the oleic acid concentration against reaction time. The activation energy obtained by the Arrhenius plot was 31 kJ/mol. Full article

(This article belongs to the Special Issue Feature Papers in Spectroscopy Journal)

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26 pages, 3631 KiB

Open AccessArticle

Exploring Time-Resolved Fluorescence Data: A Software Solution for Model Generation and Analysis

by Thomas-Otavio Peulen

Spectrosc. J. 2025, 3(2), 16; https://doi.org/10.3390/spectroscj3020016 - 1 May 2025

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Abstract

Time-resolved fluorescence techniques, such as fluorescence lifetime imaging microscopy (FLIM), fluorescence correlation spectroscopy (FCS), and time-resolved fluorescence spectroscopy, are ideally suited for investigating molecular dynamics and interactions in biological and chemical systems. However, the analysis and interpretation of these datasets require advanced computational [...] Read more.

Time-resolved fluorescence techniques, such as fluorescence lifetime imaging microscopy (FLIM), fluorescence correlation spectroscopy (FCS), and time-resolved fluorescence spectroscopy, are ideally suited for investigating molecular dynamics and interactions in biological and chemical systems. However, the analysis and interpretation of these datasets require advanced computational tools capable of handling diverse models and datasets. This paper presents a comprehensive software solution designed for model generation and analysis of time-resolved fluorescence data with a strong focus on fluorescence for quantitative structural analysis and biophysics. The software supports the integration of multiple fluorescence techniques and provides users with robust tools for performing complex model analysis across diverse experimental data. By enabling global analysis, model generation, data visualization, and sampling over model parameters, the software enhances the interpretability of intricate fluorescence phenomena. By providing flexible modeling capabilities, this solution offers a versatile platform for researchers to extract meaningful insights from time-resolved fluorescence data, aiding in the understanding of dynamic biomolecular processes. Full article

(This article belongs to the Special Issue Feature Papers in Spectroscopy Journal)

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19 pages, 6192 KiB

Open AccessArticle

Dynamic FTIR Spectroscopy for Assessing the Changing Biomolecular Composition of Bacterial Cells During Growth

by Gary Hastings, Michael Nelson, Caroline Taylor, Alex Marchesani, Wilbur Hudson, Yi Jiang and Eric Gilbert

Spectrosc. J. 2025, 3(2), 15; https://doi.org/10.3390/spectroscj3020015 - 14 Apr 2025

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Abstract

Fourier-transform infrared (FTIR) spectroscopy can detect biomolecular changes in bacterial cells in response to drugs or other stimuli. Fully developing this area requires an understanding of IR spectral changes associated with the growth of unperturbed cells. Such an understanding is still lacking, however. [...] Read more.

Fourier-transform infrared (FTIR) spectroscopy can detect biomolecular changes in bacterial cells in response to drugs or other stimuli. Fully developing this area requires an understanding of IR spectral changes associated with the growth of unperturbed cells. Such an understanding is still lacking, however. To address this issue, attenuated total reflectance (ATR) FTIR spectroscopy has been used to probe changes in the composition of Staphylococcus aureus ATCC 6538 cells during exponential growth, with a 30 min time resolution. We find prominent spectral changes in proteins, nucleic acids, and carbohydrates evolving from the early (30–120 min) to the late (240–360 min) log phase of growth. Principal component analysis (PCA) shows that spectra obtained for cells during the early and late log phases of growth can be discriminated against with 100% accuracy. Protein-related spectral features are most significant in spectra collected at 30- and 90-min post-inoculation and provide a robust basis for temporal differentiation. Spectral changes that occur during the first 30 min after inoculation are shown to reverse over the next 30–120 min, indicating dynamic adaptations during cellular growth. Overall, we demonstrate a band assignment strategy based on time resolution, underscoring the utility of FTIR spectroscopy in dynamic studies of bacterial cells. Full article

(This article belongs to the Special Issue Feature Papers in Spectroscopy Journal)

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18 pages, 3200 KiB

Open AccessArticle

Influence of Tissue Curvature on the Absolute Quantification in Frequency-Domain Diffuse Optical Spectroscopy

by Giovani G. Martins, Rodrigo M. Forti and Rickson C. Mesquita

Spectrosc. J. 2025, 3(2), 14; https://doi.org/10.3390/spectroscj3020014 - 13 Apr 2025

Viewed by 196

Abstract

Accurate estimation of optical properties and hemodynamic parameters is critical for advancing frequency-domain diffuse optical spectroscopy (FD-DOS) techniques in clinical neuroscience. However, conventional FD-DOS models often assume planar air–tissue interfaces, introducing errors in anatomically curved regions such as the forehead or infant heads. [...] Read more.

Accurate estimation of optical properties and hemodynamic parameters is critical for advancing frequency-domain diffuse optical spectroscopy (FD-DOS) techniques in clinical neuroscience. However, conventional FD-DOS models often assume planar air–tissue interfaces, introducing errors in anatomically curved regions such as the forehead or infant heads. This study evaluates the impact of incorporating tissue curvature into forward models for FD-DOS analysis. Using simulations and optical phantoms, we demonstrate that curved models reduce errors in absorption coefficient estimation from 20% to less than 10% in high-curvature scenarios. Within the curvatures tested, even minor curvature mismatches resulted in errors significantly lower than those observed from planar approximations (p < 0.001). In low-curvature regions, curved models yielded errors comparable to planar models (<5% in both cases). When applied to human data, our proposed curved model increased absorption and hemoglobin concentration estimates by 10–15% compared to standard semi-infinite models, closer to physiological expectations. Overall, these results quantitatively demonstrate that accounting for tissue curvature in FD-DOS forward models significantly improves the accuracy of optical property estimation. We propose a numerical framework that achieves this in a fast and reliable manner, advancing FD-DOS as a robust tool for clinical and research applications in anatomically complex regions. Full article

(This article belongs to the Special Issue Feature Papers in Spectroscopy Journal)

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16 pages, 5391 KiB

Open AccessArticle

Mid-Infrared Spectrometer for Black Plastics Sorting Using a Broadband Uncooled Micro-Bolometer Array

by Gabriel Jobert and Xavier Brenière

Spectrosc. J. 2025, 3(2), 13; https://doi.org/10.3390/spectroscj3020013 - 3 Apr 2025

Viewed by 432

Abstract

We report the design, implementation and test of a Mid-Infrared spectrometer proof-of-concept that utilizes an uncooled micro-bolometer array, sensitive in the 3–14 µm spectral range, integrated in a conventional optical dispersive spectrometry setup. Such a spectrometer enables instantaneous measurements across this broad spectral [...] Read more.

We report the design, implementation and test of a Mid-Infrared spectrometer proof-of-concept that utilizes an uncooled micro-bolometer array, sensitive in the 3–14 µm spectral range, integrated in a conventional optical dispersive spectrometry setup. Such a spectrometer enables instantaneous measurements across this broad spectral range, comparable to that of a FTIR but with a more compact design and without moving parts. This makes it ideal for integration into portable, battery-powered devices such as handheld scanners. The Mid-IR range offers significant advantages over NIR-SWIR spectrometers, especially for organic compound analysis. A notable application for this instrument: plastic waste sorting—including black plastics—was tested with significant accuracy and effectiveness of plastic classification (on PP, PET and PE samples) with a very simple machine learning algorithm. Full article

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24 pages, 1224 KiB

Open AccessReview

Spectroscopic Advances in Real Time Monitoring of Pharmaceutical Bioprocesses: A Review of Vibrational and Fluorescence Techniques

by Abhishek Mishra, Mohammad Aghaee, Ibrahim M. Tamer and Hector Budman

Spectrosc. J. 2025, 3(2), 12; https://doi.org/10.3390/spectroscj3020012 - 1 Apr 2025

Viewed by 672

Abstract

The pharmaceutical industry has witnessed exponential growth in production volumes, driven by factors such as an aging global population and the COVID-19 pandemic. To meet the demand for high product quality alongside increased productivity, there is a growing emphasis on developing innovative Fermentation [...] Read more.

The pharmaceutical industry has witnessed exponential growth in production volumes, driven by factors such as an aging global population and the COVID-19 pandemic. To meet the demand for high product quality alongside increased productivity, there is a growing emphasis on developing innovative Fermentation Analytical Technology (FAT) and Process Analytical Technology (PAT) tools for real-time performance monitoring, modeling, measurement, and control. Building on our earlier work involving in-line monitoring of Bordetella pertussis fermentations using fluorescence spectroscopy, this review explores and compares the applications of vibrational and fluorescence spectroscopy for real-time bioprocess monitoring. We examine recent technological advancements and ongoing challenges in the field. Various spectroscopic techniques are evaluated in terms of cost-effectiveness and practical applicability, with a particular focus on in-line spectroscopy as a promising, low-cost solution for effective bioprocess monitoring. Full article

(This article belongs to the Special Issue Feature Papers in Spectroscopy Journal)

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18 pages, 5740 KiB

Open AccessArticle

The Presence of Excitons in Short Single-Stranded DNA Revealed by Absorption and Circular Dichroism Spectroscopy

by Alessandra Picchiotti, Amy L. Stevens, Valentyn I. Prokhorenko and R. J. Dwayne Miller

Spectrosc. J. 2025, 3(2), 11; https://doi.org/10.3390/spectroscj3020011 - 28 Mar 2025

Viewed by 336

Abstract

This paper presents a systematic absorption and circular dichroism spectroscopy study of short single strands of DNA, from 2 to 20 bases. They are composed of a sequence-specific nucleobase composition, either adenine (A), thymine (T), or AT repeats. The absorption spectra hypochromism and [...] Read more.

This paper presents a systematic absorption and circular dichroism spectroscopy study of short single strands of DNA, from 2 to 20 bases. They are composed of a sequence-specific nucleobase composition, either adenine (A), thymine (T), or AT repeats. The absorption spectra hypochromism and the circular dichroism one show butterfly-shaped spectra. Data analysis conducted on the spectra of these oligomers provides evidence for the formation of excitons and their delocalization length along the strand of DNA in relation to how many bases are involved in the excitonic coupling. In particular, the extent of this coupling is limited to adjacent nucleobases in the case of pure adenine strands but spans multiple nucleobases in the case of pure thymine strands. Predictably, AT repeats show a mixed behavior between the two. Full article

(This article belongs to the Special Issue Feature Papers in Spectroscopy Journal)

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Spectrosc. J., Volume 3, Issue 2 (June 2025) – 8 articles

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