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1. Discharge and Temperature Controls of Dissolved Organic Matter (DOM) in a Forested Coastal Plain Stream

   https://doi.org/10.3390/w13202919  

   Lu, Yuehan ; Shang, Peng ; Chen, Shuo ; Du, Yingxun ; Bonizzoni, Marco ; Ward, Amelia K. ( October 2021 , Water)

   Streams in the southeastern United States Coastal Plains serve as an essential source of energy and nutrients for important estuarine ecosystems, and dissolved organic matter (DOM) exported from these streams can have profound impacts on the biogeochemical and ecological functions of fluvial networks. Here, we examined hydrological and temperature controls of DOM during low-flow periods from a forested stream located within the Coastal Plain physiographic region of Alabama, USA. We analyzed DOM via combining dissolved organic carbon (DOC) analysis, fluorescence excitation–emission matrix combined with parallel factor analysis (EEM-PARAFAC), and microbial degradation experiments. Four fluorescence components were identified: terrestrial humic-like DOM, microbial humic-like DOM, tyrosine-like DOM, and tryptophan-like DOM. Humic-like DOM accounted for ~70% of total fluorescence, and biodegradation experiments showed that it was less bioreactive than protein-like DOM that accounted for ~30% of total fluorescence. This observation indicates fluorescent DOM (FDOM) was controlled primarily by soil inputs and not substantially influenced by instream production and processing, suggesting that the bulk of FDOM in these streams is transported to downstream environments with limited in situ modification. Linear regression and redundancy analysis models identified that the seasonal variations in DOM were dictated primarily by hydrology and temperature. Overall, high discharge and shallowmore »flow paths led to the enrichment of less-degraded DOM with higher percentages of microbial humic-like and tyrosine-like compounds, whereas high temperatures favored the accumulation of high-aromaticity, high-molecular-weight, terrestrial, humic-like compounds in stream water. The flux of DOC and four fluorescence components was driven primarily by water discharge. Thus, the instantaneous exports of both refractory humic-like DOM and reactive protein-like DOM were higher in wetter seasons (winter and spring). As high temperatures and severe precipitation are projected to become more prominent in the southeastern U.S. due to climate change, our findings have important implications for future changes in the amount, source, and composition of DOM in Coastal Plain streams and the associated impacts on downstream carbon and nutrient supplies and water quality.« less
2. Synthesis and characterization of high affinity fluorogenic α-synuclein probes

   https://doi.org/10.1039/c9cc09849f  

   Lengyel-Zhand, Zsofia ; Ferrie, John J. ; Janssen, Bieneke ; Hsieh, Chia-Ju ; Graham, Thomas ; Xu, Kui-ying ; Haney, Conor M. ; Lee, Virginia M.-Y. ; Trojanowski, John Q. ; Petersson, E. James ; et al ( March 2020 , Chemical Communications)

   Fluorescent small molecules are powerful tools for imaging α-synuclein pathology in vitro and in vivo . In this work, we explore benzofuranone as a potential scaffold for the design of fluorescent α-synuclein probes. These compounds have high affinity for α-synuclein, show fluorescent turn-on upon binding to fibrils, and display different binding to Lewy bodies, Lewy neurites and glial cytoplasmic inclusion pathologies in post-mortem brain tissue. These studies not only reveal the potential of benzofuranone compounds as α-synuclein specific fluorescent probes, but also have implications for the ways in which α-synucleinopathies are conformationally different and display distinct small molecule binding sites.
3. Dithioamide substitutions in proteins: effects on thermostability, peptide binding, and fluorescence quenching in calmodulin

   https://doi.org/10.1039/C8CC00104A  

   Walters, Christopher R. ; Ferrie, John J. ; Petersson, E. James ( January 2018 , Chemical Communications)

   Thioamide substitutions in the backbones of proteins can modulate their structure and thermostability, or serve as spectroscopic probes in fluorescence quenching experiments. Using native chemical ligation, we have produced the first examples of a protein (calmodulin) containing two thioamides. Dithioamide variants were made to explore the effects of combining stabilizing, neutral, and destabilizing single thioamide substitutions. One of the dithioamide calmodulin variants exhibited stabilization greater than any monothioamide variant, although the effect could not easily be anticipated from the results of single substitutions. Each of the calmodulin variants retained the ability to bind a target peptide, and the dithioamide proteins exhibited an increase in fluorescence quenching of tryptophan relative to their single thioamide counterparts. These results show that multiply thioamidated proteins can be synthesized, and that properly placed thioamides can be used to increase protein thermostability or enhance fluorecsence quenching in peptide binding experiments.
4. Synthesis and Characterization of Dye-Doped Au@SiO ₂ Core-Shell Nanoparticles for Super-Resolution Fluorescence Microscopy

   https://doi.org/10.1177/00037028221121357  

   Thompson, Shelby ; Jorns, Mychele ; Pappas, Dimitri ( October 2022 , Applied Spectroscopy)

   Dye-doped nanoparticles have been investigated as bright, fluorescent probes for localization-based super-resolution microscopy. Nanoparticle size is important in super-resolution microscopy to get an accurate size of the object of interest from image analysis. Due to their self-blinking behavior and metal-enhanced fluorescence (MEF), Ag@SiO₂and Au@Ag@SiO₂nanoparticles have shown promise as probes for localization-based super-resolution microscopy. Here, several noble metal-based dye-doped core-shell nanoparticles have been investigated as self-blinking nanomaterial probes. It was observed that both the gold- and silver-plated nanoparticle cores exhibit weak luminescence under certain conditions due to the surface plasmon resonance bands produced by each metal, and the gold cores exhibit blinking behavior which enhances the blinking and fluorescence of the dye-doped nanoparticle. However, the silver-plated nanoparticle cores, while weakly luminescent, did not exhibit any blinking; the dye-doped nanoparticle exhibited the same behavior as the core fluorescent, but did not blink. Because of the blinking behavior, stochastic optical reconstruction microscopy (STORM) super-resolution analysis was able to be performed with performed on the gold core nanoparticles. A preliminary study on the use of these nanoparticles for localization-based super-resolution showed that these nanoparticles are suitable for use in STORM super resolution. Resolution enhancement was two times better than the diffraction limited images, withmore »core sizes reduced to 15 nm using the hybrid Au–Ag cores.

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5. Rational design of small molecule fluorescent probes for biological applications

   https://doi.org/10.1039/D0OB01131B  

   Jun, Joomyung V. ; Chenoweth, David M. ; Petersson, E. James ( August 2020 , Organic & Biomolecular Chemistry)

   Fluorescent small molecules are powerful tools for visualizing biological events, embodying an essential facet of chemical biology. Since the discovery of the first organic fluorophore, quinine, in 1845, both synthetic and theoretical efforts have endeavored to “modulate” fluorescent compounds. An advantage of synthetic dyes is the ability to employ modern organic chemistry strategies to tailor chemical structures and thereby rationally tune photophysical properties and functionality of the fluorophore. This review explores general factors affecting fluorophore excitation and emission spectra, molar absorption, Stokes shift, and quantum efficiency; and provides guidelines for chemist to create novel probes. Structure–property relationships concerning the substituents are discussed in detail with examples for several dye families. We also present a survey of functional probes based on PeT, FRET, and environmental or photo-sensitivity, focusing on representative recent work in each category. We believe that a full understanding of dyes with diverse chemical moieties enables the rational design of probes for the precise interrogation of biochemical and biological phenomena.