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Results for “Fluorescent Dyes”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Role of Cell Wall Polysaccharides in Water Distribution During Seed Imbibition of Hymenaea courbaril L.

Seed water imbibition is critical to seedling establishment in tropical forests. The seeds of the neotropical tree Hymenaea courbaril have no oil reserves and have been used as a model to study storage cell wall polysaccharide (xyloglucan - XyG) mobilization.We studied pathways of water imbibition in Hymenaea seeds. To understand seed features, we performed carbohydrate analysis and scanning electron microscopy. We found that the seed coat comprises a palisade of lignified cells, below which are several cell layers with cell walls rich in pectin. The cotyledons are composed mainly of storage XyG. From a single point of scarification on the seed surface, we followed water imbibition pathways in the entire seed using fluorescent dye and NMRi spectroscopy. We constructed composites of cellulose with Hymenaea pectin or XyG. In vitro experiments demonstrated cell wall polymer capacity to imbibe water, with XyG imbibition much slower than the pectin-rich layer of the seed coat.We found that water rapidly crosses the lignified layer and reaches the pectin-rich palisade layer so that water rapidly surrounds the whole seed. Water travels very slowly in cotyledons (most of the seed mass) because it is imbibed in the XyG-rich storage walls. However, there are channels among the cotyledon cells through which water travels rapidly, so the primary cell walls containing pectins will retain water around each storage cell.The different seed tissue dynamic interactions between water and wall polysaccharides (pectins and XyG) are essential to determining water distribution and preparing the seed for germination.

arabinoxylan↗
DOE OSTI2022

Total Internal Reflection of Two Lasers in a Single Planar Optical Waveguide

Multiplex biomarker quantitation is ideal for tracking the progression of a disease, but sensitive, specific, and quantitative multiplex biosensing remains challenging. We achieved total internal reflection with two lasers in a single planar optical waveguide by coupling 532 nm laser light into the diffraction grating of a waveguide and 635 nm laser light directly into the thin film of the same waveguide. We confirmed that the evanescent fields generated in the waveguide can excite two fluorescent dyes (Alexa Fluor 532 and Alexa Fluor 647) held to the surface of the waveguide through biotin-streptavidin chemistry. This sensing concept holds significant potential as a platform for multiplex biomarker detection.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Laser-induced fluorescence thermometry of supercritical CO 2 flows inside a micro-channel

This work demonstrates a thermometric technique using laser-induced fluorescence (LIF) in supercritical carbon dioxide flows in a micro-channel. Rhodamine 6G was used as a temperature-sensitive fluorescent dye. The flow conditions were at a pressure of 7.9 MPa and temperature in the range of 23°–90°C. 2D spatial distributions and time-resolved temperature profiles were obtained at this high pressure. Measured LIF signals showed close relations to the temperatures obtained from resistance temperature detectors.

Park, Suhyeon↗
DOE OSTI2023

Metabolic multireactor: Practical considerations for using simple oxygen sensing optodes for high-throughput batch reactor metabolism experiments

We present a system for carrying out small batch reactor oxygen consumption experiments on water and sediment samples for environmental questions. In general, it provides several advantages that can help researchers achieve impactful experiments at relatively low costs and high data quality. In particular, it allows for multiple reactors to be operated and their oxygen concentrations to be measured simultaneously, providing high throughput and high time-resolution data, which can be advantageous. Most existing literature on similar small batch-reactor metabolic studies is limited to either only a few samples, or only a few time points per sample, which can restrict the ability for researchers to learn from their experiments. The oxygen sensing system is based very directly on the work of Larsen, et al. [2011], and similar oxygen sensing technology is widely used in the literature. As such we do not delve deeply into the specifics of the fluorescent dye sensing mechanism. Instead, we focus on practical considerations. We describe the construction and operation of the calibration and experimental systems, and answer many of the questions likely to come up when other researchers choose to build and operate a similar system themselves (questions we ourselves had when we first built the system). In this way, we hope to provide an approachable and easy to use research article that can help other researchers construct and operate a similar system that can be tailored to ask their own research questions, with a minimum of confusion and missteps along the way.

3D printing↗
DOE OSTI2024

Exposed Phosphatidylserine as a Biomarker for Clear Identification of Breast Cancer Brain Metastases in Mouse Models

Brain metastasis is the most common intracranial malignancy in adults. The prognosis is extremely poor, partly because most patients have more than one brain lesion, and the currently available therapies are nonspecific or inaccessible to those occult metastases due to an impermeable blood–tumor barrier (BTB). Phosphatidylserine (PS) is externalized on the surface of viable endothelial cells (ECs) in tumor blood vessels. In this study, we have applied a PS-targeting antibody to assess brain metastases in mouse models. Fluorescence microscopic imaging revealed that extensive PS exposure was found exclusively on vascular ECs of brain metastases. The highly sensitive and specific binding of the PS antibody enables individual metastases, even micrometastases containing an intact BTB, to be clearly delineated. Furthermore, the conjugation of the PS antibody with a fluorescence dye, IRDye 800CW, or a radioisotope, 125I, allowed the clear visualization of individual brain metastases by optical imaging and autoradiography, respectively. In conclusion, we demonstrated a novel strategy for targeting brain metastases based on our finding that abundant PS exposure occurs on blood vessels of brain metastases but not on normal brain, which may be useful for the development of imaging and targeted therapeutics for brain metastases.

Oncology↗
DOE OSTI2022

Crystal Structure of CYP3A4 Complexed with Fluorol Identifies the Substrate Access Channel as a High-Affinity Ligand Binding Site

Cytochrome P450 3A4 (CYP3A4) is a major human drug-metabolizing enzyme, notoriously known for its extreme substrate promiscuity, allosteric behavior, and implications in drug–drug interactions. Despite extensive investigations, the mechanism of ligand binding to CYP3A4 is not fully understood. We determined the crystal structure of CYP3A4 complexed with fluorol, a small fluorescent dye that can undergo hydroxylation. In the structure, fluorol associates to the substrate channel, well suited for the binding of planar polyaromatic molecules bearing polar groups, through which stabilizing H-bonds with the polar channel residues, such as Thr224 and Arg372, can be established. Mutagenesis, spectral, kinetic, and functional data confirmed the involvement but not strict requirement of Thr224 for the association of fluorol. Collectively, our data identify the substrate channel as a high-affinity ligand binding site and support the notion that hydrophobic ligands first dock to the nearby peripheral surface, before migrating to the channel and, subsequently, into the active site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Rhodol fluorophores for near-infrared imaging

The present disclosure encompasses embodiments of a novel near-infrared-emitting molecular fluorophore and probes incorporating said fluorophore advantageous for in vitro and in vivo research studies. The fluorophore is robust, photostable, and possesses functionalities for easy bioorthogonal conjugation (e.g., click chemistry, hydrazone formation, Diels Alder, Staudinger ligation, etc.). It is biocompatible and emits at 711 nm in aqueous conditions. These fluorophores may be used to fluorescently tag biological molecules or structures of interest, or used as optical reporters (i.e., activatable molecular probes, fluorescent dyes) for specific biomarkers/analytes as they can be switched from “off” to “on.” This fluorophore is useful for cellular assays and preclinical small animal imaging as the near-infrared emission is highly penetrating, and the photophysical properties are outstanding. As such, the properties of this class of fluorophores could easily be translated for use in clinical applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

BERYLLIUM DETECTION BY FLUORESCENT SPECTROSCOPY

Facilities that machine and process materials involving beryllium oxide are hazardous to workers safety and require monitoring of contamination. A primary goal in industrial worker safety in beryllium containing facilities is avoiding inhalation, which may cause chronic beryllium disease (CBD). Decontamination is labor intensive due to the miniscule size of beryllium dust and the difficulty of detecting its presence on surfaces. Current methods of beryllium detection, while successful, involve numerous intermediate steps such as obtaining wipe samples, applying buffers, centrifuging with ammonium bifluoride, additives to reduce influence of other competing metal ions, and require potentially long wait times of around 24 hours for a single surface sample. In some cases, these samples must be sent to testing facilities across the country and results may not be available for days. Therefore, for the purposes of this study, it has been deemed important to test new fluorescent dyes that can rapidly produce a beryllium presence confirmation via application spray.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2023

Defect-resistant plastic scintillators with aliphatic additives

A plastic scintillator includes a polymer matrix, an aliphatic additive present in the polymer matrix in an effective amount to impart fog resistance to the plastic scintillator, and at least one fluorescent dye in the polymer matrix, the dye being effective to provide scintillation upon exposure to radiation. The effective amount of the aliphatic additive is in a range of greater than 0 weight percent up to 5 weight percent relative to the total weight of the plastic scintillator. Moreover, the aliphatic additive has a structure comprising up to 300 repeat units.

Mabe, Andrew Neil↗
DOE OSTI2024

Methods for ultraviolet excitation microscopy of biological surfaces

Microscopy with Ultraviolet Surface Excitation (MUSE) for use in the classroom to enhance life sciences education and curricula, or for other applications, including without limtiation the operating room, other medical environments, research environments, and low resource environments. MUSE's suitability is based on multiple key factors including its simplicity of use, the incorporation of inexpensive hardware including LED illumination, and very basic tissue preparation. The ultraviolet excitation acts as passive optical sectioning confining the generated fluorescence signal to only a few micrometers below the tissue surface thus eliminating the out of focus signals. This facilitates image capture of tissue microstructure and organization from specimens at the intact or sliced surface arising from varying fluorophore concentration within the different cellular compartments. Although just the tissue auto fluorescence maybe used, image quality is enhanced with brief application of nontoxic fluorescent dyes to selectively highlight cellular compartments. Sample preparation is safe, efficient and familiar to students with basic chemistry or biology lab experience. Mixed-dye powders may be used to simplify translation of this method for educational, medical, research, low resource, and other settings.

Demos, Stavros G.↗
DOE OSTI2025

Cyanine-Incorporated Amorphous Polymeric Carbon Dots for Optical Reactive Oxygen Species Sensing

Reactive oxygen species (ROS) are common cellular oxidants that when overproduced by cellular stressors cause harm to cells. Detection of ROS is of utmost importance to understanding a wide variety of cellular function and toxicity mechanisms. Conventional ROS fluorescence assays involve using a single dye to visualize the ROS quantity. Herein, we describe ROS-sensitive, fluorescent-dye-incorporated carbon dots with dual fluorescence capabilities and good biocompatibility. Carbon dots (CDs) made of citric acid and urea were synthesized with incorporated cyanine-3-amine (Cy3), a bright red fluorescent dye, to create Cy3-CDs. Additionally, to get Cy3 into the ROS-sensitive form, this work demonstrated that Cy3 alone and Cy3 within carbon dots can be electrochemically reduced to their colorless ROS-sensitive form. Cy3, CDs, and Cy3-CDs are all responsive to additions of superoxide, leading to an increase in the fluorescence. Overall, this work examines how O 2 •– and additional oxidizers interact with CDs, Cy3, and Cy3-CDs, and molecular-level hypotheses are explored that will inform the design of future carbon dot-based ROS sensors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Species-specific ribosomal RNA-FISH identifies interspecies cellular-material exchange, active-cell population dynamics and cellular localization of translation machinery in clostridial cultures and co-cultures

ABSTRACT The development of synthetic microbial consortia in recent years has revealed that complex interspecies interactions, notably the exchange of cytoplasmic material, exist even among organisms that originate from different ecological niches. Although morphogenetic characteristics, viable RNA and protein dyes, and fluorescent reporter proteins have played an essential role in exploring such interactions, we hypothesized that ribosomal RNA-fluorescence in situ hybridization (rRNA-FISH) could be adapted and applied to further investigate interactions in synthetic or semisynthetic consortia. Despite its maturity, several challenges exist in using rRNA-FISH as a tool to quantify individual species population dynamics and interspecies interactions using high-throughput instrumentation such as flow cytometry. In this work, we resolve such challenges and apply rRNA-FISH to double and triple co-cultures of Clostridium acetobutylicum, Clostridium ljungdahlii, and Clostridium kluyveri . In pursuing our goal to capture each organism’s population dynamics, we demonstrate dynamic rRNA, and thus ribosome, exchange between the three species leading to the formation of hybrid cells. We also characterize the localization patterns of the translation machinery in the three species, identifying distinct, dynamic localization patterns among them. Our data also support the use of rRNA-FISH to assess the culture’s health and expansion potential, and, here again, our data find surprising differences among the three species examined. Taken together, our study argues for rRNA-FISH as a valuable and accessible tool for quantitative exploration of interspecies interactions, especially in organisms which cannot be genetically engineered or in consortia where selective pressures to maintain recombinant species cannot be used. IMPORTANCE Though dyes and fluorescent reporter proteins have played an essential role in identifying microbial species in co-cultures, we hypothesized that ribosomal RNA-fluorescence in situ hybridization (rRNA-FISH) could be adapted and applied to quantitatively probe complex interactions between organisms in synthetic consortia. Despite its maturity, several challenges existed before rRNA-FISH could be used to study Clostridium co-cultures of interest. First, species-specific probes for Clostridium acetobutylicum and Clostridium ljungdahlii had not been developed. Second, “state-of-the-art” labeling protocols were tedious and often resulted in sample loss. Third, it was unclear if FISH was compatible with existing fluorescent reporter proteins. We resolved these key challenges and applied the technique to co-cultures of C. acetobutylicum , C. ljungdahlii , and Clostridium kluyveri . We demonstrate that rRNA-FISH is capable of identifying rRNA/ribosome exchange between the three organisms and characterized rRNA localization patterns in each. In combination with flow cytometry, rRNA-FISH can capture sub-population dynamics in co-cultures.

Hill, John D.↗
DOE OSTI2021

Pulse Radiolysis Investigation of Radicals Derived from Water-Soluble Cyanine Dyes: Implications for Super-resolution Microscopy

Light-induced blinking, an inherent feature of many forms of super-resolution microscopy, has been linked to transient reduction of the fluorescent cyanine dye used as an imaging agent. There is, however, only scant literature information related to one-electron reduced cyanine dyes, especially in an aqueous environment. Here, we examine a small series of cyanine dyes, possessing disparate π-conjugation lengths, under selective reducing or oxidizing conditions. The experiment allows recording of both differential absorption spectra and decay kinetics of the resultant one-electron reduced or oxidized transient species in water. Relative to the ground state, absorption transitions for the various radicals are weak and somewhat broadened but do allow correlation with the π-conjugation length. In all cases, absorption maxima lie to the blue of the main ground-state transition. Under anaerobic conditions, the transient species decay on the microsecond to millisecond time scale, with the mean lifetime depending on molecular structure, radiation dose, and dye concentration. The experimental absorption spectra recorded for the one-electron reduced radicals and the presumed dimer cation radical compare well to spectra obtained from time-dependent density functional theory calculations. Furthermore, the results allow conclusions to be drawn regarding the plausibility of the reduced species being responsible for light-induced blinking in direct stochastic optical reconstruction microscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Performance of chatbots in queries concerning fundamental concepts in photochemistry

Abstract The advent of chatbots raises the possibility of a paradigm shift across society including the most technical of fields with regard to access to information, generation of knowledge, and dissemination of education and training. Photochemistry is a scientific endeavor with roots in chemistry and physics and branches that encompass diverse disciplines ranging from astronomy to zoology. Here, five chatbots have each been challenged with 13 photochemically relevant queries. The chatbots included ChatGPT 3.5, ChatGPT 4.0, Copilot, Gemini Advanced, and Meta AI. The queries encompassed fundamental concepts (e.g., “Why is the fluorescence spectrum typically the mirror image of the absorption spectrum?”), practical matters (e.g., “What is the inner filter effect and how to avoid it?”), philosophical matters (“Please create the most important photochemistry questions.”), and specific molecular features (e.g., “Why are azo dyes non‐fluorescent?”). The chatbots were moderately effective in answering queries concerning fundamental concepts in photochemistry but were glaringly deficient in specialized queries for dyes and fluorophores. In some instances, a correct response was embedded in verbose scientific nonsense whereas in others the entire response, while grammatically correct, was utterly meaningless. The unreliable accuracy makes present chatbots poorly suited for unaided educational purposes and highlights the importance of domain experts.

Taniguchi, Masahiko↗
DOE OSTI2022

Fluorescence strobo-stereoscopy for specular reflection-suppressed full field of view imaging

This report introduces fluorescence strobo-stereoscopy (FSS) to suppress strong specular reflection and enable the full field of view (FFOV) 3D surface imaging while the part is rotating. Specular reflection off the target surface significantly degrades the image quality and becomes critical for highly reflective surface measurements. In FSS, the fluorescent dye-doped fluid applied on the machined surface is excited upon incident ultra-violet light and becomes a new light source by Stokes' Law. Thus, specular reflection off of smooth surface can be suppressed by separating the fluorescent light from the excitation light. The developed FSS comprises a pair of imaging cameras, spatial filters, and an excitation light source. As a result, FSS effectively rejected the specular reflection and improved the FFOV 3D surface image quality of the machined part by enhancing contrast in the rotating target surface. Such enhancements in 3D imaging allowed to identify manufacturing tolerance of the part and to detect the surface features. The axial and lateral accuracy errors of FSS were 2.3% and 1.4% with the target size of 4.07 mm and 0.215 mm, respectively. A whole view reconstruction of the cylindrical target sample was performed, and the corresponding cylindricity and diameter deviation were assessed. The fluid media effect and the target surface quality effect were discussed.

3D surface imaging↗
DOE OSTI2026

Probing the External Surface Chemistry of Imine-Based Covalent Organic Frameworks Using Reactive Organic Dyes

The external surfaces of covalent organic frameworks (COFs) are presumably composed of free terminal functional groups from their constituent monomers. These terminal groups have been utilized to immobilize molecules onto COF surfaces for a variety of studies and potential applications. Despite the utility of these latent functional groups for COF functionalization and composite formation, the surface chemistry of the COFs has not been quantitatively investigated and is not well understood. In this work, fluorescent organic dyes bearing reactive amine and aldehyde functional groups are used to probe the surface chemistry of representative two-dimensional (2D) imine-based COFs. Furthermore, systematic dye binding and displacement experiments provide new insights into the characteristics of COF surfaces and the reactivity of different molecules with the surface groups on the COF crystallites.

COFs↗
DOE OSTI2023

NIR fluorescence lifetime macroscopic imaging with a novel time-gated SPAD camera

SwissSPAD3 is the latest of a family of widefield time-gated SPAD imagers developed for fluorescence lifetime imaging (FLI) applications. Its distinctive features are (i) the ability to define shorter gates than its predecessors (width W < 1 ns), (ii) support for laser repetition rates up to at least 80 MHz and (iii) a dual-gate architecture providing an effective duty cycle of 100%. We present widefield macroscopic FLI measurements of short lifetime NIR dyes, analyzed using the phasor approach. Furthermore, the results are compared with those previously obtained with SwissSPAD2 and to theoretical predictions.

47 OTHER INSTRUMENTATION↗