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Article ; Online: Perspectives for infrared beamlines in fourth-generation synchrotron facilities.

Borondics, Ferenc

2024 Volume 31, Issue Pt 3, Page(s) 430–431

Abstract: With several fourth-generation, or diffraction-limited, storage rings and multiple beamlines in operation, the missing range of the spectrum was infrared…until recently. ...

Abstract	With several fourth-generation, or diffraction-limited, storage rings and multiple beamlines in operation, the missing range of the spectrum was infrared…until recently.
Language	English
Publishing date	2024-04-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2021413-3
ISSN	1600-5775 ; 0909-0495
ISSN (online)	1600-5775
ISSN	0909-0495
DOI	10.1107/S1600577524003813
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Article ; Online: Super-resolution infrared microspectroscopy reveals heterogeneous distribution of photosensitive lipids in human hair medulla.

Sandt, Christophe / Borondics, Ferenc

Talanta

2022 Volume 254, Page(s) 124152

Abstract: Human hair medulla chemical composition appears mostly homogenous when mapped by FTIR microspectroscopy even when using a synchrotron radiation source (SR-μFTIR) but it is expected to be heterogeneous. We performed sub-micron chemical mapping of hair ... ...

Abstract	Human hair medulla chemical composition appears mostly homogenous when mapped by FTIR microspectroscopy even when using a synchrotron radiation source (SR-μFTIR) but it is expected to be heterogeneous. We performed sub-micron chemical mapping of hair cortex and medullas using Optical Photothermal Infrared microspectroscopy (OPTIR) and a mid-infrared Quantum Cascade Laser (QCL) source covering the fingerprint and the CH stretching region. Photodamages were observed in the hair cortex at mild laser power and occurred in the hair medulla even at the lowest power settings of the IR QCL pulsed at 100 kHz rate (4 μW/μm
Language	English
Publishing date	2022-12-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1500969-5
ISSN	1873-3573 ; 0039-9140
ISSN (online)	1873-3573
ISSN	0039-9140
DOI	10.1016/j.talanta.2022.124152
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Article ; Online: A new typology of human hair medullas based on lipid composition analysis by synchrotron FTIR microspectroscopy.

Sandt, Christophe / Borondics, Ferenc

The Analyst

2021 Volume 146, Issue 12, Page(s) 3942–3954

Abstract: Human hair is an organ that connects fundamental and applied research with everyday life through the cosmetic industry. Yet, the accurate compositional description of the human hair medulla is lacking due to their small size and difficulty with ... ...

Abstract	Human hair is an organ that connects fundamental and applied research with everyday life through the cosmetic industry. Yet, the accurate compositional description of the human hair medulla is lacking due to their small size and difficulty with microextraction. Medullas are thus generally classified based on morphology. We investigated the chemical composition of the human hair medulla using synchrotron based infrared microspectroscopy. We confirmed that lipid signatures dominate the medulla infrared spectrum having 3-20 times higher lipid concentration compared to their surrounding cortex. Human hair medullas contain a mixture of non-esterified and esterified lipids, and carboxylate soaps in various proportions. We reveal the first direct spectroscopic evidence that medulla carboxylates are coordinated to calcium since they exhibit the specific calcium carboxylate signature. Using a representative sample, we observed a strong compositional variability between medullas that was unreported before. We detected calcium carboxylates in 76% of the medullas with one order of magnitude concentration variability between samples. All medullas contained esters with esterification varying by a factor of 30. Moreover, we detected the presence of crystalline calcium stearate in 9% of the medullas. We described a series of spectral markers to characterize medullas based on their lipid composition and propose to classify medullas in four to five groups. Our analysis provides a more detailed understanding of the chemical composition of human hair medullas that may impact cosmetics and biology. The origin and biological meaning of these variations must still be investigated.
Language	English
Publishing date	2021-05-12
Publishing country	England
Document type	Journal Article
ZDB-ID	210747-8
ISSN	1364-5528 ; 0003-2654
ISSN (online)	1364-5528
ISSN	0003-2654
DOI	10.1039/d1an00695a
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Article ; Online: Does dinocyst wall composition really reflect trophic affinity? New evidence from ATR micro‐FTIR spectroscopy measurements

Meyvisch, Pjotr / Mertens, Kenneth Neil / Gurdebeke, Pieter Roger / Sandt, Christophe / Pospelova, Vera / Vrielinck, Henk / Borondics, Ferenc / Louwye, Stephen

Journal of Phycology. 2023 Oct., v. 59, no. 5 p.1064-1084

2023

Abstract: Attenuated total reflection (ATR) microscope Fourier transform infrared (micro‐FTIR) spectroscopy was used to investigate the dinosporin composition in the walls of modern, organic‐walled dinoflagellate resting cysts (dinocysts). Variable cyst wall ... ...

Abstract	Attenuated total reflection (ATR) microscope Fourier transform infrared (micro‐FTIR) spectroscopy was used to investigate the dinosporin composition in the walls of modern, organic‐walled dinoflagellate resting cysts (dinocysts). Variable cyst wall compositions were observed, which led to the erection of four spectrochemical groups, some with striking similarities to other resistant biomacromolecules such as sporopollenin and algaenan. Furthermore, possible proxies derivable from the spectrochemical composition of modern and fossil dinocysts were discussed. The color of the dinocyst walls was reflected in the spectral data. When comparing that color with a standard and the results of a series of bleaching experiments with oxidative agents, eumelanin was assigned as a likely pigment contributing to the observed color. Following this assignment, the role of eumelanin as an ultraviolet sunscreen in colored dinocysts was hypothesized, and its implications on the autofluorescence and morphological preservation of dinocysts were further discussed. Unlike what had previously been assumed, it was shown that micro‐FTIR data from dinocysts cannot be used to unambiguously infer trophic affinities of their associated cells. Finally, using methods with high spatial resolutions (synchrotron transmission micro‐FTIR and optical photothermal infrared spectroscopy), it was shown that dinocyst wall layers are chemically homogenous at the probed scales. This study fills a large knowledge gap in our understanding of the chemical nature of dinocyst walls and has nuanced certain assumptions and interpretations made in the past.
Keywords	Fourier transform infrared spectroscopy ; Miozoa ; algology ; color ; eumelanin ; fossils ; spectral analysis ; sporopollenin ; sunscreens
Language	English
Dates of publication	2023-10
Size	p. 1064-1084.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	281226-5
ISSN	1529-8817 ; 0022-3646
ISSN (online)	1529-8817
ISSN	0022-3646
DOI	10.1111/jpy.13382
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Article: Super-Resolved 3D Mapping of Molecular Orientation Using Vibrational Techniques

Koziol, Paulina / Kosowska, Karolina / Liberda, Danuta / Borondics, Ferenc / Wrobel, Tomasz P.

Journal of the American Chemical Society. 2022 July 26, v. 144, no. 31

2022

Abstract: When a sample has an anisotropic structure, it is possible to obtain additional information controlling the polarization of incident light. With their straightforward instrumentation approaches, infrared (IR) and Raman spectroscopies are widely popular ... ...

Abstract	When a sample has an anisotropic structure, it is possible to obtain additional information controlling the polarization of incident light. With their straightforward instrumentation approaches, infrared (IR) and Raman spectroscopies are widely popular in this area. Single-band-based determination of molecular in-plane orientation, typically used in materials science, is here extended by the concurrent use of two vibration bands, revealing the orientational ordering in three dimension. The concurrent analysis was applied to IR spectromicroscopic data to obtain orientation angles of a model polycaprolactone spherulite sample. The applicability of this method spans from high-resolution, diffraction-limited Fourier transform infrared (FT-IR) and Raman imaging to super-resolved optical photothermal infrared (O-PTIR) imaging. Due to the nontomographic experimental approach, no image distortion is visible and nanometer scale orientation domains can be observed. Three-dimensional (3D) bond orientation maps enable in-depth characterization and consequently precise control of the sample’s physicochemical properties and functions.
Keywords	Fourier transform infrared spectroscopy ; anisotropy ; instrumentation ; vibration
Language	English
Dates of publication	2022-0726
Size	p. 14278-14287.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.2c05306
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Article ; Online: Quasar: Easy Machine Learning for Biospectroscopy.

Toplak, Marko / Read, Stuart T / Sandt, Christophe / Borondics, Ferenc

Cells

2021 Volume 10, Issue 9

Abstract: Data volumes collected in many scientific fields have long exceeded the capacity of human comprehension. This is especially true in biomedical research where multiple replicates and techniques are required to conduct reliable studies. Ever-increasing ... ...

Abstract	Data volumes collected in many scientific fields have long exceeded the capacity of human comprehension. This is especially true in biomedical research where multiple replicates and techniques are required to conduct reliable studies. Ever-increasing data rates from new instruments compound our dependence on statistics to make sense of the numbers. The currently available data analysis tools lack user-friendliness, various capabilities or ease of access. Problem-specific software or scripts freely available in supplementary materials or research lab websites are often highly specialized, no longer functional, or simply too hard to use. Commercial software limits access and reproducibility, and is often unable to follow quickly changing, cutting-edge research demands. Finally, as machine learning techniques penetrate data analysis pipelines of the natural sciences, we see the growing demand for user-friendly and flexible tools to fuse machine learning with spectroscopy datasets. In our opinion, open-source software with strong community engagement is the way forward. To counter these problems, we develop Quasar, an open-source and user-friendly software, as a solution to these challenges. Here, we present case studies to highlight some Quasar features analyzing infrared spectroscopy data using various machine learning techniques.
MeSH term(s)	Humans ; Machine Learning ; Reproducibility of Results ; Software ; Spectrum Analysis/methods
Language	English
Publishing date	2021-09-03
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells10092300
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Article ; Online: Super-Resolved 3D Mapping of Molecular Orientation Using Vibrational Techniques.

Koziol, Paulina / Kosowska, Karolina / Liberda, Danuta / Borondics, Ferenc / Wrobel, Tomasz P

Journal of the American Chemical Society

2022 Volume 144, Issue 31, Page(s) 14278–14287

Abstract	When a sample has an anisotropic structure, it is possible to obtain additional information controlling the polarization of incident light. With their straightforward instrumentation approaches, infrared (IR) and Raman spectroscopies are widely popular in this area. Single-band-based determination of molecular in-plane orientation, typically used in materials science, is here extended by the concurrent use of two vibration bands, revealing the orientational ordering in three dimension. The concurrent analysis was applied to IR spectromicroscopic data to obtain orientation angles of a model polycaprolactone spherulite sample. The applicability of this method spans from high-resolution, diffraction-limited Fourier transform infrared (FT-IR) and Raman imaging to super-resolved optical photothermal infrared (O-PTIR) imaging. Due to the nontomographic experimental approach, no image distortion is visible and nanometer scale orientation domains can be observed. Three-dimensional (3D) bond orientation maps enable in-depth characterization and consequently precise control of the sample's physicochemical properties and functions.
MeSH term(s)	Molecular Conformation ; Spectroscopy, Fourier Transform Infrared ; Spectrum Analysis, Raman ; Vibration
Language	English
Publishing date	2022-07-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.2c05306
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Article ; Online: Direct Visualization of Ultrastrong Coupling between Luttinger-Liquid Plasmons and Phonon Polaritons.

Németh, Gergely / Otsuka, Keigo / Datz, Dániel / Pekker, Áron / Maruyama, Shigeo / Borondics, Ferenc / Kamarás, Katalin

Nano letters

2022 Volume 22, Issue 8, Page(s) 3495–3502

Abstract: Ultrastrong coupling of light and matter creates new opportunities to modify chemical reactions or develop novel nanoscale devices. One-dimensional Luttinger-liquid plasmons in metallic carbon nanotubes are long-lived excitations with extreme ... ...

Abstract	Ultrastrong coupling of light and matter creates new opportunities to modify chemical reactions or develop novel nanoscale devices. One-dimensional Luttinger-liquid plasmons in metallic carbon nanotubes are long-lived excitations with extreme electromagnetic field confinement. They are promising candidates to realize strong or even ultrastrong coupling at infrared frequencies. We applied near-field polariton interferometry to examine the interaction between propagating Luttinger-liquid plasmons in individual carbon nanotubes and surface phonon polaritons of silica and hexagonal boron nitride. We extracted the dispersion relation of the hybrid Luttinger-liquid plasmon-phonon polaritons (LPPhPs) and explained the observed phenomena by the coupled harmonic oscillator model. The dispersion shows pronounced mode splitting, and the obtained value for the normalized coupling strength shows we reached the ultrastrong coupling regime with both native silica and hBN phonons. Our findings predict future applications to exploit the extraordinary properties of carbon nanotube plasmons, ranging from nanoscale plasmonic circuits to ultrasensitive molecular sensing.
Language	English
Publishing date	2022-03-22
Publishing country	United States
Document type	Journal Article
ISSN	1530-6992
ISSN (online)	1530-6992
DOI	10.1021/acs.nanolett.1c04807
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Article ; Online: Diffraction-limited mid-infrared microspectroscopy to reveal a micron-thick interfacial water layer signature.

Mozhdehei, Armin / Slodczyk, Aneta / Almklov Magnussen, Eirik / Kohler, Achim / Sandt, Christophe / Borondics, Ferenc / Mercury, Lionel

The Analyst

2023 Volume 148, Issue 13, Page(s) 2941–2955

Abstract: Mid-infrared microspectroscopy is a non-invasive tool for identifying the molecular structure and chemical composition at the scale of the probe, ...

Abstract	Mid-infrared microspectroscopy is a non-invasive tool for identifying the molecular structure and chemical composition at the scale of the probe,
Language	English
Publishing date	2023-06-26
Publishing country	England
Document type	Journal Article
ZDB-ID	210747-8
ISSN	1364-5528 ; 0003-2654
ISSN (online)	1364-5528
ISSN	0003-2654
DOI	10.1039/d3an00138e
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Article ; Online: Fluorescently Guided Optical Photothermal Infrared Microspectroscopy for Protein-Specific Bioimaging at Subcellular Level.

Prater, Craig / Bai, Yeran / Konings, Sabine C / Martinsson, Isak / Swaminathan, Vinay S / Nordenfelt, Pontus / Gouras, Gunnar / Borondics, Ferenc / Klementieva, Oxana

Journal of medicinal chemistry

2023 Volume 66, Issue 4, Page(s) 2542–2549

Abstract: Infrared spectroscopic imaging is widely used for the visualization of biomolecule structures, and techniques such as optical photothermal infrared (OPTIR) microspectroscopy can achieve <500 nm spatial resolution. However, these approaches lack ... ...

Abstract	Infrared spectroscopic imaging is widely used for the visualization of biomolecule structures, and techniques such as optical photothermal infrared (OPTIR) microspectroscopy can achieve <500 nm spatial resolution. However, these approaches lack specificity for particular cell types and cell components and thus cannot be used as a stand-alone technique to assess their properties. Here, we have developed a novel tool, fluorescently guided optical photothermal infrared microspectroscopy, that simultaneously exploits epifluorescence imaging and OPTIR to perform fluorescently guided IR spectroscopic analysis. This novel approach exceeds the diffraction limit of infrared microscopy and allows structural analysis of specific proteins directly in tissue and single cells. Experiments described herein used epifluorescence to rapidly locate amyloid proteins in tissues or neuronal cultures, thus guiding OPTIR measurements to assess amyloid structures at the subcellular level. We believe that this new approach will be a valuable addition to infrared spectroscopy providing cellular specificity of measurements in complex systems for studies of structurally altered protein aggregates.
MeSH term(s)	Spectrophotometry, Infrared/methods ; Amyloidogenic Proteins ; Spectroscopy, Fourier Transform Infrared/methods
Chemical Substances	Amyloidogenic Proteins
Language	English
Publishing date	2023-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/acs.jmedchem.2c01359
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