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Archives of Biochemistry and Biophysics Mar 2011Cytochromes P450 constitute a broad class of heme monooxygenase enzymes with more than 11,500 isozymes which have been identified in organisms from all biological... (Review)
Review
Cytochromes P450 constitute a broad class of heme monooxygenase enzymes with more than 11,500 isozymes which have been identified in organisms from all biological kingdoms [1]. These enzymes are responsible for catalyzing dozens chemical oxidative transformations such as hydroxylation, epoxidation, N-demethylation, etc., with very broad range of substrates [2,3]. Historically these enzymes received their name from 'pigment 450' due to the unusual position of the Soret band in UV-vis absorption spectra of the reduced CO-saturated state [4,5]. Despite detailed biochemical characterization of many isozymes, as well as later discoveries of other 'P450-like heme enzymes' such as nitric oxide synthase and chloroperoxidase, the phenomenological term 'cytochrome P450' is still commonly used as indicating an essential spectroscopic feature of the functionally active protein which is now known to be due to the presence of a thiolate ligand to the heme iron [6]. Heme proteins with an imidazole ligand such as myoglobin and hemoglobin as well as an inactive form of P450 are characterized by Soret maxima at 420nm [7]. This historical perspective highlights the importance of spectroscopic methods for biochemical studies in general, and especially for heme enzymes, where the presence of the heme iron and porphyrin macrocycle provides rich variety of specific spectroscopic markers available for monitoring chemical transformations and transitions between active intermediates of catalytic cycle.
Topics: Animals; Circular Dichroism; Cytochrome P-450 Enzyme System; Electron Spin Resonance Spectroscopy; Heme; Humans; Nuclear Magnetic Resonance, Biomolecular; Spectrophotometry; Spectroscopy, Mossbauer; Spectrum Analysis; Spectrum Analysis, Raman; X-Ray Absorption Spectroscopy
PubMed: 21167809
DOI: 10.1016/j.abb.2010.12.008 -
Journal of Synchrotron Radiation Nov 2022Skin reactions are well described complications of tattooing, usually provoked by red inks. Chemical characterizations of these inks are usually based on limited...
Skin reactions are well described complications of tattooing, usually provoked by red inks. Chemical characterizations of these inks are usually based on limited subjects and techniques. This study aimed to determine the organic and inorganic composition of inks using X-ray fluorescence spectroscopy (XRF), X-ray absorption spectroscopy (XANES) and Raman spectroscopy, in a cohort of patients with cutaneous hypersensitivity reactions to tattoo. A retrospective multicenter study was performed, including 15 patients diagnosed with skin reactions to tattoos. Almost half of these patients developed skin reactions on black inks. XRF identified known allergenic metals - titanium, chromium, manganese, nickel and copper - in almost all cases. XANES spectroscopy distinguished zinc and iron present in ink from these elements in endogenous biomolecules. Raman spectroscopy showed the presence of both reported (azo pigments, quinacridone) and unreported (carbon black, phtalocyanine) putative organic sensitizer compounds, and also defined the phase in which Ti was engaged. To the best of the authors' knowledge, this paper reports the largest cohort of skin hypersensitivity reactions analyzed by multiple complementary techniques. With almost half the patients presenting skin reaction on black tattoo, the study suggests that black modern inks should also be considered to provoke skin reactions, probably because of the common association of carbon black with potential allergenic metals within these inks. Analysis of more skin reactions to tattoos is needed to identify the relevant chemical compounds and help render tattoo ink composition safer.
Topics: Humans; Tattooing; Ink; Soot; Spectrum Analysis, Raman; Spectrometry, X-Ray Emission
PubMed: 36345752
DOI: 10.1107/S1600577522008165 -
Optics Express May 2013We present a method to dynamically image structures at nanometer spatial resolution with far-field instruments. We propose the use of engineered nanoprobes with...
We present a method to dynamically image structures at nanometer spatial resolution with far-field instruments. We propose the use of engineered nanoprobes with distinguishable spectral responses and the measurement of coherent scattering, rather than fluorescence. Approaches such as PALM/STORM have relied on the rarity of emission events in time to distinguish signals from distinct probes. By distinguishing signals in the spectral domain, we enable the acquisition of data in a multiplex fashion and thus circumvent the fundamental problem of slow data acquisition of current techniques. The described method has the potential to image dynamic systems with a spatial resolution only limited to the size of the scattering probes.
Topics: Algorithms; Equipment Design; Equipment Failure Analysis; Molecular Probe Techniques; Spectrum Analysis
PubMed: 23736501
DOI: 10.1364/OE.21.012822 -
Journal of Biomedical Optics Sep 2022Point-of-care (POC) platforms utilizing optical biosensing strategies can achieve on-site detection of biomarkers to improve the quality of care for patients in...
SIGNIFICANCE
Point-of-care (POC) platforms utilizing optical biosensing strategies can achieve on-site detection of biomarkers to improve the quality of care for patients in low-resource settings.
AIM
We aimed to develop a portable, multi-modal spectroscopic platform capable of performing Raman and fluorescence measurements from a single sample site.
APPROACH
We designed the spectroscopic platform in OpticStudio using commercial optical components and built the system on a portable optical breadboard. Two excitation and collection arms were utilized to detect the two optical signals. The multi-modal functionality was validated using ratiometric Raman/fluorescence samples, and the potential utility was demonstrated using a model bioassay for cardiac troponin I.
RESULTS
The designed spectroscopic platform achieved a spectral resolution of 0.67 ± 0.2 nm across the Raman detection range (660 to 770 nm). The ratiometric Raman/fluorescence samples demonstrated no crosstalk between the two detector arms across a gradient of high molar concentrations. Testing of the model bioassay response showed that the integrated approach improved the linearity of the calibration curve from (R = 0.977) for the Raman only and (R = 0.972) for the fluorescence only to (R2 = 0.988) for the multi-modal approach.
CONCLUSION
These findings demonstrate the potential impact of a multi-modal POC spectroscopic platform to improve the sensitivity and robustness necessary for biomarker detection.
Topics: Biomarkers; Humans; Point-of-Care Systems; Spectrometry, Fluorescence; Spectrum Analysis, Raman; Troponin I
PubMed: 36163635
DOI: 10.1117/1.JBO.27.9.095006 -
Annual Review of Physical Chemistry 2013New free-electron laser and high-harmonic generation X-ray light sources are capable of supplying pulses short and intense enough to perform resonant nonlinear... (Review)
Review
New free-electron laser and high-harmonic generation X-ray light sources are capable of supplying pulses short and intense enough to perform resonant nonlinear time-resolved experiments in molecules. Valence-electron motions can be triggered impulsively by core excitations and monitored with high temporal and spatial resolution. We discuss possible experiments that employ attosecond X-ray pulses to probe the quantum coherence and correlations of valence electrons and holes, rather than the charge density alone, building on the analogy with existing studies of vibrational motions using femtosecond techniques in the visible regime.
Topics: Algorithms; Spectrometry, X-Ray Emission; Spectrum Analysis; Spectrum Analysis, Raman; X-Rays
PubMed: 23245522
DOI: 10.1146/annurev-physchem-040412-110021 -
Analytical Chemistry Sep 2016A cavity ring-down spectroscopy (CRDS) instrument was developed using mature, robust hardware for the measurement of carbon-14 in biological studies. The system was...
A cavity ring-down spectroscopy (CRDS) instrument was developed using mature, robust hardware for the measurement of carbon-14 in biological studies. The system was characterized using carbon-14 elevated glucose samples and returned a linear response up to 387 times contemporary carbon-14 concentrations. Carbon-14 free and contemporary carbon-14 samples with varying carbon-13 concentrations were used to assess the method detection limit of approximately one-third contemporary carbon-14 levels. Sources of inaccuracies are presented and discussed, and the capability to measure carbon-14 in biological samples is demonstrated by comparing pharmacokinetics from carbon-14 dosed guinea pigs analyzed by both CRDS and accelerator mass spectrometry. The CRDS approach presented affords easy access to powerful carbon-14 tracer techniques that can characterize complex biochemical systems.
Topics: Carbon Radioisotopes; Glucose; Spectrum Analysis
PubMed: 27458740
DOI: 10.1021/acs.analchem.6b02054 -
International Journal of Surgery... 2012Barrett's oesophagus is a metaplastic condition with an inherent risk of progression to adenocarcinoma. It is essential to identify dysplastic changes within Barrett's... (Review)
Review
Barrett's oesophagus is a metaplastic condition with an inherent risk of progression to adenocarcinoma. It is essential to identify dysplastic changes within Barrett's oesophagus in order to individualise surveillance strategies and establish which patients warrant endoscopic treatment. There is a trend towards endoscopic resection of focal high-grade dysplasia followed by whole segment ablation. However, endoscopic identification of dysplastic lesions is unreliable and subjective making targeted therapy extremely difficult. In addition, the current practice of taking random quadrantic biopsies may miss dysplastic disease and intramucosal adenocarcinoma. Several advanced endoscopic imaging techniques have been described and tested in clinical trials in an effort to improve the detection of early lesions, although none are routinely used in clinical practice. In this article we will review these techniques and discuss their potential for clinical implementation. We will also discuss the potential benefits of multimodal imaging and highlight several newer techniques which have shown early promise for in vivo diagnosis.
Topics: Barrett Esophagus; Esophagoscopy; Humans; Microscopy, Confocal; Spectrometry, Fluorescence; Spectrum Analysis, Raman; Tomography, Optical Coherence
PubMed: 22510441
DOI: 10.1016/j.ijsu.2012.04.003 -
Philosophical Transactions. Series A,... Dec 2005The chemical compositions and emission rates of volcanic gases carry important information about underground magmatic and hydrothermal conditions, with application in... (Review)
Review
The chemical compositions and emission rates of volcanic gases carry important information about underground magmatic and hydrothermal conditions, with application in eruption forecasting. Volcanic plumes are also studied because of their impacts upon the atmosphere, climate and human health. Remote sensing techniques are being increasingly used in this field because they provide real-time data and can be applied at safe distances from the target, even throughout violent eruptive episodes. However, notwithstanding the many scientific insights into volcanic behaviour already achieved with these approaches, technological limitations have placed firm restrictions upon the utility of the acquired data. For instance, volcanic SO(2) emission rate measurements are typically inaccurate (errors can be greater than 100%) and have poor time resolution (ca once per week). Volcanic gas geochemistry is currently being revolutionized by the recent implementation of a new generation of remote sensing tools, which are overcoming the above limitations and are providing degassing data of unprecedented quality. In this article, I review this field at this exciting point of transition, covering the techniques used and the insights thereby obtained, and I speculate upon the breakthroughs that are now tantalizingly close.
Topics: Environmental Monitoring; Geology; Spectrum Analysis; Volcanic Eruptions
PubMed: 16286297
DOI: 10.1098/rsta.2005.1668 -
Biosensors Nov 2017Modern instrumentation for Raman microspectroscopy and current techniques in analysis of spectral data provide new opportunities to study molecular interactions and... (Review)
Review
Modern instrumentation for Raman microspectroscopy and current techniques in analysis of spectral data provide new opportunities to study molecular interactions and dynamics at subcellular levels in biological systems. Implementation of biomolecular component analysis (BCA) to microRaman spectrometry provides basis for the emergence of Ramanomics, a new biosensing discipline with unprecedented capabilities to measure concentrations of distinct biomolecular groups in live cells and organelles. Here we review the combined use of microRaman-BCA techniques to probe absolute concentrations of proteins, DNA, RNA and lipids in single organelles of live cells. Assessing biomolecular concentration profiles of organelles at the single cell level provides a physiologically relevant set of biomarkers for cellular heterogeneity. In addition, changes to an organelle's biomolecular concentration profile during a cellular transformation, whether natural, drug induced or disease manifested, can provide molecular insight into the nature of the cellular process.
Topics: Nuclear Magnetic Resonance, Biomolecular; Spectrum Analysis, Raman
PubMed: 29140259
DOI: 10.3390/bios7040052 -
Proteomics Jul 2018In this article, current and future applications of spectral clustering are discussed in the context of mass spectrometry-based proteomics approaches. First of all, the...
In this article, current and future applications of spectral clustering are discussed in the context of mass spectrometry-based proteomics approaches. First of all, the main algorithms and tools that can currently be used to perform spectral clustering are introduced. In addition, its main applications and their use in current computational proteomics workflows are explained, including the generation of spectral libraries and spectral archives. Finally, possible future directions for spectral clustering, including its potential use to achieve a deeper coverage of the proteome and the discovery of novel post-translational modifications and single amino acid variants.
Topics: Algorithms; Cluster Analysis; Databases, Protein; Humans; Proteome; Proteomics; Spectrum Analysis
PubMed: 29882266
DOI: 10.1002/pmic.201700454