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At least 649 records · Page 36

Fluorescence Assay for Tolyporphins Amidst Abundant Chlorophyll in Crude Cyanobacterial Extracts

Abstract Tolyporphins are distinctive tetrapyrrole natural products found singularly in a filamentous cyanobacterial‐microbial holobiont (termed HT‐58‐2) from Micronesia. The absorption and fluorescence features of tolyporphins resemble those of chlorophyll a , complicating direct analysis of culture samples. Treatment of the crude (unfractionated) organic extract (CH 2 Cl 2 /2‐propanol, 1:1) of HT‐58‐2 cultures with NaBH 4 in methanol causes reduction of the peripheral ketone auxochromes, whereupon tolyporphins (predominantly 7,17‐dioxobacteriochlorins) exhibit a bathochromic shift ( λ abs ˜ 676 → ˜ 700 nm) and chlorophyll a (a 13 1 ‐oxochlorin) exhibits a hypsochromic shift ( λ abs 665 → 634 nm). Fluorescence excitation spectroscopy (at 368 and 491 nm with λ em 710 nm) enabled detection of reduced tolyporphins amidst abundant reduced chlorophyll a (1:19 ratio), a detection sensitivity >5 times that without reduction. The resulting assay combines simple sample preparation from non‐axenic cultures at microscale quantities (2 mL, 2 μ m ), absence of any fractionation procedures, and fluorescence detection. Tolyporphins were readily detected in cultures of HT‐58‐2 at reasonable growth periods in the absence of environmental stressors, which was not possible previously.

Nguyen, Kathy‐Uyen↗

Substituent effect on napthodithiophene-fused porphyrins: Understanding the unusual trend of fluorescence quantum yield quenching

A series of π-extended porphyrins containing thiophene units was prepared to investigate an unusual trend observed in the fluorescence quantum yield of naphtho[2,1-b:3,4-b']dithiophene-fused porphyrins. Monobenzoporphyrins carrying 2-thiophenyl (vinyl thiophene porphyrin) groups (2VTP, 2VTBr and Br2VTP) (numbering 2 and 3 refers to the position of sulfur on the thiophene ring) were synthesized through a Heck-based cascade reaction followed by a newly developed bromination method. These were converted to naphtho[2,1-b:3,4-b']dithiophene-fused porphyrin derivatives (FBr2VTP and F2VTBr) via ring closure with an intramolecular Scholl reaction. Increasingly larger Stokes shifts with a higher number of bromo groups were observed in the unfused π-extended molecular systems, reflecting the heavy atom effect. Fluorescence spectroscopy further confirmed the unusual trend seen in the previous work: structural rigidification in naphtho[2,1-b:3,4-b']dithiophene-fused porphyrins leads to longer fluorescence lifetimes but unexpectedly lowers the quantum yield. Adding one bromo group to the naphtho[2,1-b:3,4-b']dithiophene unit does not change this trend. Furthermore, the presence of two bromo groups prevents the quantum yield from dropping. DFT, TDDFT, and NICS analyses suggest a drastic change in aromaticity in the pyrrole ring where the naphtho[2,1-b:3,4-b']dithiophene is fused in FBr2VTP, which might contribute to the quantum yield reductions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fluorescent Amplification of Next Generation Sequencing Libraries Tools (FA-NGS tools) v1

This is a software utility for calculating pooling volumes and graphing quality control data of next generation sequencing libraries amplified with fluorescent intercalating agents and monitored by real-time quantitative PCR (qPCR). The tool is used to calculate pooling volumes of individual next generation sequencing libraries based on experimentally determined fluorescence values. To do this, fluorescent values are used as a proxy for relative concentration to determine the ratio of transfer volumes. The output is a "transfer file" that specifies the transfer volume and destination well of a given library. The tool can also be used to assess the quality of individual next generation sequencing libraries by melting curve analysis. The output are small-multiples graphs of the melting curves of individual sequencing libraries according to the specified plate layout.

Garber, Megan↗

Computational microscopy for fast widefield deep-tissue fluorescence imaging using a commercial dual-cannula probe

A solid-glass cannula serves as a micro-endoscope that can deliver excitation light deep inside tissue while also collecting emitted fluorescence. Then, we utilize deep neural networks to reconstruct images from the collected intensity distributions. By using a commercially available dual-cannula probe, and training a separate deep neural network for each cannula, we effectively double the field of view compared to prior work. We demonstrated ex vivo imaging of fluorescent beads and brain slices and in vivo imaging from whole brains. We clearly resolved 4 µm beads, with FOV from each cannula of 0.2 mm (diameter), and produced images from a depth of ∼1.2 mm in the whole brain, currently limited primarily by the labeling. Since no scanning is required, fast widefield fluorescence imaging limited primarily by the brightness of the fluorophores, collection efficiency of our system, and the frame rate of the camera becomes possible.

42 ENGINEERING↗

mMaple: A Photoconvertible Fluorescent Protein for Use in Multiple Imaging Modalities

Recent advances in fluorescence microscopy have extended the spatial resolution to the nanometer scale. Here, we report an engineered photoconvertible fluorescent protein (pcFP) variant, designated as mMaple, that is suited for use in multiple conventional and super-resolution imaging modalities, specifically, widefield and confocal microscopy, structured illumination microscopy (SIM), and single-molecule localization microscopy. We demonstrate the versatility of mMaple by obtaining super-resolution images of protein organization in Escherichia coli and conventional fluorescence images of mammalian cells. Beneficial features of mMaple include high photostability of the green state when expressed in mammalian cells and high steady state intracellular protein concentration of functional protein when expressed in E. coli. mMaple thus enables both fast live-cell ensemble imaging and high precision single molecule localization for a single pcFPcontaining construct.

59 BASIC BIOLOGICAL SCIENCES↗

X-ray crystal structure and properties of Phanta, a weakly fluorescent photochromic GFP-like protein

Phanta is a reversibly photoswitching chromoprotein (Φ F , 0.003), useful for pcFRET, that was isolated from a mutagenesis screen of the bright green fluorescent eCGP123 (Φ F , 0.8). We have investigated the contribution of substitutions at positions His193, Thr69 and Gln62, individually and in combination, to the optical properties of Phanta. Single amino acid substitutions at position 193 resulted in proteins with very low Φ F , indicating the importance of this position in controlling the fluorescence efficiency of the variant proteins. The substitution Thr69Val in Phanta was important for supressing the formation of a protonated chromophore species observed in some His193 substituted variants, whereas the substitution Gln62Met did not significantly contribute to the useful optical properties of Phanta. X-ray crystal structures for Phanta (2.3 Å), eCGP123 T69V (2.0 Å) and eCGP123 H193Q (2.2 Å) in their non-photoswitched state were determined, revealing the presence of a cis-coplanar chromophore. We conclude that changes in the hydrogen-bonding network supporting the cis-chromophore, and its contacts with the surrounding protein matrix, are responsible for the low fluorescence emission of eCGP123 variants containing a His193 substitution.

59 BASIC BIOLOGICAL SCIENCES↗

FLIMJ: An open-source ImageJ toolkit for fluorescence lifetime image data analysis

In the field of fluorescence microscopy, there is continued demand for dynamic technologies that can exploit the complete information from every pixel of an image. One imaging technique with proven ability for yielding additional information from fluorescence imaging is Fluorescence Lifetime Imaging Microscopy (FLIM). FLIM allows for the measurement of how long a fluorophore stays in an excited energy state, and this measurement is affected by changes in its chemical microenvironment, such as proximity to other fluorophores, pH, and hydrophobic regions. This ability to provide information about the microenvironment has made FLIM a powerful tool for cellular imaging studies ranging from metabolic measurement to measuring distances between proteins. The increased use of FLIM has necessitated the development of computational tools for integrating FLIM analysis with image and data processing. To address this need, we have created FLIMJ, an ImageJ plugin and toolkit that allows for easy use and development of extensible image analysis workflows with FLIM data. Built on the FLIMLib decay curve fitting library and the ImageJ Ops framework, FLIMJ offers FLIM fitting routines with seamless integration with many other ImageJ components, and the ability to be extended to create complex FLIM analysis workflows. Building on ImageJ Ops also enables FLIMJ’s routines to be used with Jupyter notebooks and integrate naturally with science-friendly programming in, e.g., Python and Groovy. We show the extensibility of FLIMJ in two analysis scenarios: lifetime-based image segmentation and image colocalization. We also validate the fitting routines by comparing them against industry FLIM analysis standards.

47 OTHER INSTRUMENTATION↗

The Next Generation of Split-Fluorescent Proteins and What They Can Do for You

A symmetrically split fluorescent protein (split-FP) systems provide unique advantages over conventional fluorophores as well as whole fluorescent proteins for cellular imaging and biochemical assays. In this presentation I will discuss some of these advantages, as well as new optimizations and applications for existing LANL split-FP tools in the emerging field of intrinsically disordered protein (IDP) biology, host-pathogen interactions and materials science. I will also briefly present additions to the LANL split-FP toolbox, such as a new split red fluorescent protein (a vast improvement over the current state of the art) and a new technique to develop multimerization-resistant proteins. Lastly, I will discuss some use-cases for these new materials.

59 BASIC BIOLOGICAL SCIENCES↗

Expanding the utility and range of quantum and polymer dots for multiplexed super resolution fluorescence imaging in plants (Final Progress Report)

The emission spectra of plant pigments currently limit the number of fluorescent colors that can be imaged simultaneously and, therefore, the number of cellular components that can be imaged within a single experiment. Hence, developing fluorescent tags and a microscope system that can image beyond the visible range (NIR) would greatly enhance plant imaging capabilities. Extending imaging into the NIR would support the interrogation of multiple proteins/molecules simultaneously, but would inevitably decrease spatial resolution due to the increase of the diffraction limit of light. To address this need, we propose to develop a super resolution fluorescence imaging (SRFI) platform that would allow imaging of NIR-emitting molecules, as well as quantum dots (QDs) and polymer dots (Pdots).

59 BASIC BIOLOGICAL SCIENCES↗

Development of High Energy Resolution Fluorescence Detection Methods for Advanced Microscale X-ray Absorption Fine Structure Analysis of Critical Elements (Final Report)

This project is developing High-Energy Resolution Fluorescence Detection (HERFD) X-ray Absorption Fine-Structure Spectroscopy (XAFS) at the hard X-ray microprobe beamline at GSECARS beamline 13-ID-E, at the Advanced Photon Source at Argonne National Laboratory. This enhancement will improve sensitivity and spectral interpretation limitations of conventional XAFS which uses energy dispersive solid-state detectors (SSD) to measure the total fluorescence yield (TFY-XAFS). By using high-quality Si and Ge crystal analyzers to select X-ray fluorescence (XRF) from specific emission lines, background signals from other elements or X-ray scattering that can paralyze SSDs can be nearly eliminated, improving the sensitivity to the oxidation and chemical state of dilute species even though the solid angle of the analyzers is relatively small. Furthermore, by using analyzers of low-strain Si or Ge, the energy selection can be smaller than the natural widths of the core electron level. We are particularly interested in applying these enhanced sensitivities to Lanthanide series of rare-earth elements, which are typically at concentrations at or below 10 ppm, and where spectral overlaps with the 3rd row transition metals degrade sensitivity.

47 OTHER INSTRUMENTATION↗

Upgrading Linear Fluorescent Fixtures to LED in Schools

Lighting is a key component to creating a functional and high-quality learning environment for students and staff. Light-emitting diode or LED lighting fixtures have gained traction in common commercial building applications and quality replacement options for common fixture types are widely available. Compared to most fluorescent lighting systems, using LEDs can reduce energy consumption and therefore decrease carbon dioxide emissions, reduce maintenance and operation cost, and improve the visual appearance and lighting quality of the classroom and school environments. When additional controls are considered, more energy can be saved and some controls, like dimming, can offer amenities to occupants. As LEDs become an even more prominent lighting technology, fluorescent equipment may become challenging or expensive to replace. Additionally, school buildings are typically in use for many decades; maintaining a long-term view can be important when deciding which upgrade path to take. This fact sheet provides guidance on the various factors to consider when deciding on an LED upgrade for fluorescent lighting systems.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Inactivation of Fluorescent Lipid Bilayers by Irradiation With 300 keV Electrons Using Liquid Cell Transmission Electron Microscopy

Liquid cell transmission electron microscopy allows for imaging of samples in a fully hydrated state at high resolution and has the potential for visualizing static or dynamic biological structures. However, the ionizing nature of the electron beam makes it difficult to discern real physiological dynamics from radiation induced artifacts within liquid cell samples. Electron flux thresholds for achieving high resolution structures from biological samples frozen in ice have been described extensively by the cryo-electron microscopy field, while electron flux thresholds which do not result in a functional change for biological samples within the hydrated environment of a transmission electron microscope liquid cell is less clear. Establishing these functional thresholds for biologically relevant samples is important for accurate interpretation of results from liquid cell experiments. Here we demonstrate the electron damage threshold of fluorescently tagged lipid bilayers by quantifying the change in fluorescence before and after electron exposure. We observe the reduction of fluorescent signal in bilayers by 25% after only 0.0005 e − /Å 2 and a reduction of over 90% after 0.01 e − /Å 2 . These results indicate that the loss of function occurs at irradiation thresholds far below a typical single high resolution (scanning) transmission electron microscopy image and orders of magnitude below fluxes used for preserving structural features with cryo-electron microscopy.

Moser, Trevor↗

X-ray Free Electron Laser Determination of Crystal Structures of Dark and Light States of a Reversibly Photoswitching Fluorescent Protein at Room Temperature

The photochromic fluorescent protein Skylan-NS (Nonlinear Structured illumination variant mEos3.1H62L) is a reversibly photoswitchable fluorescent protein which has an unilluminated/ground state with an anionic and cis chromophore conformation and high fluorescence quantum yield. Photo-conversion with illumination at 515 nm generates a meta-stable intermediate with neutral trans-chromophore structure that has a 4 h lifetime. We present X-ray crystal structures of the cis (on) state at 1.9 Angstrom resolution and the trans (off) state at a limiting resolution of 1.55 Angstrom from serial femtosecond crystallography experiments conducted at SPring-8 Angstrom Compact Free Electron Laser (SACLA) at 7.0 keV and 10.5 keV, and at Linac Coherent Light Source (LCLS) at 9.5 keV. We present a comparison of the data reduction and structure determination statistics for the two facilities which differ in flux, beam characteristics and detector technologies. Furthermore, a comparison of droplet on demand, grease injection and Gas Dynamic Virtual Nozzle (GDVN) injection shows no significant differences in limiting resolution. The photoconversion of the on- to the off-state includes both internal and surface exposed protein structural changes, occurring in regions that lack crystal contacts in the orthorhombic crystal form.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Workflow Using a Cryogenic Coincident Fluorescence, Electron, and Ion Beam Microscope for Targeted Milling of Cells

This workflow enables lamella production targeting fluorescently labeled biological structures that are small (<1 μm in axial extent) and rare (1 copy per cell) using a cryogenic tri-coincident imaging platform. In conclusion, this platform integrates fluorescence microscopy, focused ion beam milling, and scanning electron microscopy at a single focal position and enables simultaneous fluorescence microscopy while milling.

Wang, Jue [California Institute of Technology (Cal↗

Fluorescence of the gamma, epsilon, and delta systems of nitric oxide - Polarization and use of calculated intensities for spectrometer calibration.

Results of a study in which fluorescence of the gamma system of nitric oxide was obtained by excitation from both the 2144 A line of ionized cadmium and a continuum source. Individual rotational lines of the 2144 A excited fluorescence spectrum were found to be partially polarized and to have polarizations of differ ing sign. Measured relative vibrational band intensities from line and continuum excitation were compared to calculated Franck-Condon factors. Those Franck-Condon factors based on a single potential for the two spin states of the X super pi state agreed better with measured values than those based on separate potentials for the two spin states. Calculated intensities of the v prime = 3 progression were used to calibrate the instrument response in the wavelength region from 2000 to 2500 A and were checked with measured intensities of the v prime = 0.1, and 2 progressions. Fluorescence of the epsilon and delta bands obtained with continuum lamp excitation also were compared to calculated intensities.

Poland, H. M.↗

Laser induced fluorescence in algae: A new technique for remote detection

Measurements of the absorption and fluorescence spectra were obtained for four various types of marine and fresh water algae using a pulsed N2/Ne dye laser as the source of excitation. The absorption maxima for the algae ranged from 420 to 675 nm, while their fluorescent spectra ranged from 580 to 685 nm. It appears feasible that various algal species can be identified by detection of their fluorescent signatures using a tunable laser as the excitation source. However, if one is concerned only with detection of chlorophyll a, the optimum excitation is approximately 600 + 50 nm while detection is at 685 nm. An analysis of both calculations and laboratory results indicates that it should be feasible to measure chlorophyll a in concentrations as low as 1.0 mg/m3 using a 100 kW peak pulsed laser from an altitude of 500 meters.

Friedman, E. J.↗

Multiplet effects on the L(2,3) fluorescence yield of multiply ionized Ar

The 2p fluorescence yield of argon in the presence of 0 to 6 3p holes was calculated by statistically averaging the fluorescence yields of initial state that consist of individual multiplet configurations. These configurations were formed by coupling the 2p vacancy to the partially filled 3p shell. Results agree reasonably well with experimental fluorescence yields deduced from ion-atom collision measurements.

Chen, M. H.↗

Molecular fluorescence as a monitor of minor stratospheric constituents

The potential of molecular fluorescence was assessed as a stratospheric monitor of the concentrations of various minor species. Seventeen molecules were considered and all spectral regions from the vacuum ultraviolet through to the infrared are included. The exercise has produced few surprises; however, further confirmation has emerged as to the feasibility of this sensitive technique for monitoring stratospheric OH, NO2, and SO2, sufficient to warrant its development as analytical flight hardware for these species. All the other molecules have been eliminated with the exception of C10 which appears to have promise but requires additional information before its detection limit can be calculated; its fluorescence spectrum is as yet uninvestigated. A handbook for molecular fluorescence is presented, and a compilation of all reported studies for simple molecules using line source excitation is included.

Schofield, K.↗