UMBC Chemistry & Biochemistry Department

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RNA-Puzzles Round V: blind predictions of 23 RNA structures
(Springer Nature, 2024-12-02) Bu, Fan; Adam, Yagoub; Adamiak, Ryszard W.; Antczak, Maciej; de Aquino, Belisa Rebeca H.; Badepally, Nagendar Goud; Batey, Robert T.; Baulin, Eugene F.; Boinski, Pawel; Boniecki, Michal J.; Bujnicki, Janusz M.; Carpenter, Kristy A.; Chacon, Jose; Chen, Shi-Jie; Chiu, Wah; Cordero, Pablo; Das, Naba Krishna; Das, Rhiju; Dawson, Wayne K.; DiMaio, Frank; Ding, Feng; Dock-Bregeon, Anne-Catherine; Dokholyan, Nikolay V.; Dror, Ron O.; Dunin-Horkawicz, Stanisław ; Eismann, Stephan; Ennifar, Eric; Esmaeeli, Reza; Farsani, Masoud Amiri; Ferré-D’Amaré, Adrian R.; Geniesse, Caleb; Ghanim, George E.; Guzman, Horacio V.; Hood, Iris V.; Huang, Lin; Jain, Dharm Skandh; Jaryani, Farhang; Jin, Lei; Joshi, Astha; Karelina, Masha; Kieft, Jeffrey S.; Kladwang, Wipapat; Kmiecik, Sebastian; Koirala, Deepak; Kollmann, Markus; Kretsch, Rachael C.; Kurciński, Mateusz; Li, Jun; Li, Shuang; Magnus, Marcin; Masquida, BenoÎt; Moafinejad, S. Naeim; Mondal, Arup; Mukherjee, Sunandan; Nguyen, Thi Hoang Duong; Nikolaev, Grigory; Nithin, Chandran; Nye, Grace; Pandaranadar Jeyeram, Iswarya P. N.; Perez, Alberto; Pham, Phillip; Piccirilli, Joseph A.; Pilla, Smita Priyadarshini; Pluta, Radosław ; Poblete, Simón; Ponce-Salvatierra, Almudena; Popenda, Mariusz; Popenda, Lukasz; Pucci, Fabrizio; Rangan, Ramya; Ray, Angana; Ren, Aiming; Sarzynska, Joanna; Sha, Congzhou Mike; Stefaniak, Filip; Su, Zhaoming; Suddala, Krishna C.; Szachniuk, Marta; Townshend, Raphael; Trachman, Robert J.; Wang, Jian; Wang, Wenkai; Watkins, Andrew; Wirecki, Tomasz K.; Xiao, Yi; Xiong, Peng; Xiong, Yiduo; Yang, Jianyi; Yesselman, Joseph David; Zhang, Jinwei; Zhang, Yi; Zhang, Zhenzhen; Zhou, Yuanzhe; Zok, Tomasz; Zhang, Dong; Zhang, Sicheng; Żyła, Adriana; Westhof, Eric; Miao, Zhichao
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication of the experimental structures. We report a large-scale set of predictions by 18 groups for 23 RNA-Puzzles: 4 RNA elements, 2 Aptamers, 4 Viral elements, 5 Ribozymes and 8 Riboswitches. We describe automatic assessment protocols for comparisons between prediction and experiment. Our analyses reveal some critical steps to be overcome to achieve good accuracy in modeling RNA structures: identification of helix-forming pairs and of non-Watson–Crick modules, correct coaxial stacking between helices and avoidance of entanglements. Three of the top four modeling groups in this round also ranked among the top four in the CASP15 contest.
Assessing the K₂BO₃ family of materials as multiferroics
(APS, 2024-11-26) Casale, Anthony; Bennett, Joseph
We evaluate the potential of an overlooked family of materials to support both the magnetization and polarization required to be classified as multiferroics. This family of materials has a stoichiometry of A₂BX₃ and was uncovered in the Inorganic Crystal Structure Database (ICSD) while searching for structural platforms that could support low energy polarization switching. The examples here have the general chemical formula of K₂BO₃, where B is a magnetically active cation located within edge-sharing square pyramids that form a 1D chain. Density functional theory with Hubbard U corrections (DFT + U) are used to determine the potential energy landscape of K₂BO₃, which include investigating multiple magnetic and polarization orderings. We analyze the ground state and electronic structures and report on how the choice of Hubbard U will affect both, which is important when predicting functional properties of low-dimensional and potentially exfoliable systems. This family contains a ferromagnetic insulator, K₂VO₃, as well as antiferromagnetic (K₂NbO₃) and nonmagnetic (K₂MoO₃) insulators with antipolar ground state symmetries, and accessible polar metastable states, that we predict to be antiferroelectric. This preliminary assessment of the K₂BO₃ members of the A₂BX₃ family reveals a new class of materials, that with further optimization via compositional tuning, could be multiferroic.
Mononuclear Aluminum–Fluoride Ions, AlFx(⁺/⁻)—Study of Plausible Frameworks of Complexes with Biomolecules and Their In Vitro Toxicity
(MDPI, 2025-1) Pavlovič, Anja; Janžič, Larisa; Sršen, Lucija; Kopitar, Andreja Nataša; Edwards, Kathleen F.; Liebman, Joel F.; Ponikvar-Svet, Maja
The importance of fluorine and aluminum in all aspects of daily life has led to an enormous increase in human exposure to these elements in their various forms. It is therefore important to understand the routes of exposure and to investigate and understand the potential toxicity. Of particular concern are aluminum–fluoride complexes (AlFx), which are able to mimic the natural isostructural phosphate group and influence the activity of numerous essential phosphoryl transferases. Our review of salts of ionic AlFx species, which plausibly form the framework of complexes with biomolecules, revealed that the octahedral configuration of aluminum in the active site of the enzyme is preferred over the trigonal-bipyramidal structure. The effects of varying concentrations of fluoride, aluminum and AlFx—from micromolar to millimolar levels—on the viability and apoptosis rate of THP-1 monocytes were investigated using phosphate buffer solution as a culture media to simulate physiological conditions. Our results suggest that aluminum can reduce the direct toxicity of fluoride through the formation of AlFx. In view of the results found, further in vitro studies are required to clarify the toxicity mechanisms of these species.
Quantitation of Per- and Polyfluoroalkyl Substances (PFAS) in Aquaculture Systems
(2024-01-01) Belunis, Amanda; LaCourse, William R; Chemistry & Biochemistry; Chemistry
Per- and polyfluoroalkyl substances (PFAS) are a group of synthetic chemicals that have been used since the 1940s in a wide variety of applications including water-repellant clothing, stain-resistant sprays, food packaging, and aqueous film forming foam (AFFF). Due to their prevalent use in consumer products, and their persistence in the environment, PFAS have leached into the air, soil, and water, leaving almost no ecosystem untouched. PFAS are known to be bioaccumulative and studies have shown potential links between exposure and several negative human health effects. A large focus has been placed on understanding and regulating PFAS exposure. Contaminated food and water are believed to be the main routes of exposure for the general population. It has been hypothesized that fish and seafood are one of the main dietary sources of exposure, as associations between consumption and PFAS serum concentrations have been observed globally. With efforts to improve environmental conservation and sustainability while keeping up with increasing demands for fish and seafood, aquaculture has grown rapidly since the 1980s. While numerous studies have shown the presence of PFAS in various environments, data regarding the compounds in aquaculture environments is scarce. In recent years, a large focus has been to reduce the potential for environmental interactions with coastal aquaculture facilities, leading to the increase in land-based marine and freshwater systems. There is currently a lack of understanding with regards to the presence of PFAS in aquaculture environments. As farmed fish continues to account for a large portion of fish for consumption, it is important to understand the fate and transport of PFAS in these environments, requiring proper analytical techniques to be developed. A liquid chromatography tandem mass spectrometry (LC-MS/MS) method was developed for the separation and detection of 40 target PFAS. Various solid phase extraction (SPE) cartridges were selected and tested to determine the best extraction technique for the target analytes. Automated and manual SPE setups were compared, and the automated setup shows a statistically significant increase in average recovery and reproducibility. Instrument and method figures of merit show the sensitivity, reproducibility, and robustness of the developed method. The method was applied to a proof-of-concept study testing various types of aquaculture tanks across two facilities and PFAS were found in each of the samples tested.
Hybrid Gold Nanostructures with Unique Architectures: From Potential Applications in Drug Delivery to Photonic Devices
(2024-01-01) Baradaran Kayyal, Tohid; Daniel, Marie-Christine; Chemistry & Biochemistry; Chemistry
The domain of nanotechnology has experienced remarkable progress through the engineering of hybrid nanostructures. These structures integrate diverse materials to create synergistic properties that are unachievable or less efficient when using individual components alone. Central to this progress are gold-based hybrid nanostructures, favored for their inherent advantages ranging from structural diversity and biocompatibility to remarkable optical properties. The present study focuses on the creation of gold-based hybrid systems with special nanostructures (rattle and bipyramid shapes), which have potential for medical and optical applications. The first project focuses on the design of a porous gold nanoarchitecture, termed nanorattles. These structures consist of a porous gold cage surrounding a core, offering two accessible surfaces within a single system. This design can enhance the surface area available for cargo loading, which is advantageous for drug delivery applications. Incorporated within these nanorattles are dendrons—highly branched nanopolymers—that play a crucial role in forming a hybrid structure. Dendrons not only act as catalysts, facilitating the formation of the porous cage and the overall nanorattle structure, but also serve as a nanosystem capable of covalently carrying cargo. Cisplatin, a widely used anticancer drug, is employed as a model cargo to demonstrate the potential of gold nanorattles in targeted drug delivery applications. The other project explores the directed assemblies of gold nanoparticles and quantum dots (QDs) to form a novel hybrid nanostructure yielding unique optical characteristics through plasmon-exciton coupling. The gold used in this assembly is in the form of bipyramids, chosen for their distinctive asymmetrical shape and sharp end tips. The sharp end tips of the gold nano bipyramids (AuBPs) are the designated locations for placing the QDs. Upon light irradiation, the excitons from the QDs couple with the plasmons resonating from the ends of the AuBPs, facilitating efficient plasmon-exciton coupling. The resulting coupling occurs through a selective copper-free click reaction between surface modified QDs and AuBPs. The significance of this plasmon-exciton coupling extends particularly to photonic devices, where it can greatly enhance device performance and efficiency in light manipulation, driving next-generation photonic technologies. The PhD dissertation comprehensively explains the foundational concepts, intrinsic properties, and importance of hybrid nanomaterials as outlined in the literature review. It details the experimental procedures for synthesizing the aforementioned gold nanostructures, presents characterizations and analyses to validate their structure, size, and properties, and discusses the results, interprets data, and explores potential applications.
eIF4E-Dependent Capture of the Monomeric HIV-1 RNA Genome
(2024-01-01) Singh, Karndeep; Summers, Michael F; Chemistry & Biochemistry; Biochemistry
The human immunodeficiency virus type-1 (HIV-1) RNA genome’s 5'- untranslated region (5'-Leader, 5'-L) serves as a master regulator for numerous viral replication processes within a cell such as genome dimerization, splicing, packaging, and translation initiation. This 5'-Leader adopts two conformations dependent on the transcriptional start site usage: 5'-capped RNAs beginning with one guanosine (Cap1G) adopt the dimeric conformation whereas 5'-capped RNAs beginning with two or three guanosines (Cap2G and Cap3G, respectively) adopt a monomeric conformation. Published work from our laboratory revealed that Cap1G leader RNAs sequester the 5'-cap through a coaxial stacking of two 5'-hairpins – the TAR and polyA hairpin. This prevents binding to the human eukaryotic translation initiation factor 4E (eIF4E) cap binding protein – the initial recognition step in cap/eIF4E dependent translation of HIV-1 mRNAs. For the monomeric RNA transcripts, the 5'-cap is exposed and accessible for the recruitment and binding of eIF4E. Therefore, the exposure and sequestration of the 5'-cap (a 7- methylguanosine triphosphate) within the HIV-1 5'-Leader dictates the capture of the RNAtranscripts by cap-dependent translation machinery for translation of viral proteins or genome packaging by the Gag polyprotein, respectively. While it is well-established that cap-dependent translation serves as the primary mechanism of HIV-1 genome translation in eukaryotes, the molecular nature of interactions between Cap3G RNAs and eIF4E remain unknown. Electrophoretic mobility shift assays (EMSAs) and isothermal titration calorimetry (ITC) experiments reveal that the human eIF4E binds to the HIV-1MAL Cap3G RNAs at least 2.5-fold tighter than the 5'-cap, suggesting that RNA elements influence binding of the human eIF4E. Using nuclear magnetic resonance (NMR) spectroscopy with a variety of selectively labeled 1H-, 15N-, and 13C-labeling schemes, we worked to characterize the first three-dimensional structure of a structured 5'-capped RNA – a HIV- 1MAL Cap3G RNA oligo (~13 kDa) – bound to the human eIF4E (~22 kDa). The 5'-cap forms a pi-pi stacking interaction with two tryptophan residues (W56 and W102) while residues of the TAR hairpin forming electrostatic interactions with eIF4E’s exposed charged residues to orient the RNA oligo out of the 5'-cap binding pocket. Surprisingly, the unstructured residues of the polyA region at the 3'-end interact with lysine residues of eIF4E. Our findings reveal that HIV-1 5'-Leader’s structural elements influence the recruitment and binding of eIF4E, suggesting an additional quality control mechanism that HIV-1 uses to ensure the translation of its Cap3G mRNA transcripts into viral proteins.
STRUCTURAL & BIOPHYSICAL CHARACTERIZATIONS OF MEMBRANE-BOUND AND MEMBRANE-ASSOCIATED COMPONENTS OF THE FERROUS IRON TRANSPORT (FEO) SYSTEM
(2024-01-01) Lee, Mark; Smith, Aaron T.; Chemistry & Biochemistry; Chemistry
Iron (Fe) is a vital transition metal for virtually all living organisms. In its ionic form, this element functions as a powerful cofactor within a multitude of enzymes responsible for a wide range of complex chemical reactions including, but not limited to, de novo DNA biosynthesis, central carbon metabolism, vitamin biogenesis, and even N2 fixation. Due to its critical necessity in these essential metabolic processes, organisms such as bacteria have a high demand for the uptake of iron. However, the mode of iron acquisition is linked to the oxidation state of the iron ion, which is a product of the prevailing environmental conditions. In acidic and reducing conditions commonly encountered by pathogenic bacteria within the human gut or locations within biofilms, ferrous iron (Fe2+) dominates the environment, but the precise mechanism by prokaryotes acquire Fe2+ remains unclear. In this dissertation, the structural and biophysical characteristics of the membrane-bound and membrane-associated components of the ferrous iron transport (Feo) system, the most widely distributed and the primary Fe2+ transport system utilized by bacteria, are investigated. First, structures of the N-terminal domain of FeoB (NFeoB) from Vibrio cholerae (VcNFeoB), the causative agent of the disease cholera, are presented for the first time and give critical insight into the surprising nucleotide promiscuity of FeoB. Next, in an attempt to provide homogeneous, near-native samples of full-length, intact FeoB for future structural characterization, V. cholerae FeoB (VcFeoB) was extracted directly from bacterial membranes in near native-like lipid environments through the use of styrene-maleic acid (SMA)-copolymers. SMA-extracted VcFeoB showed high purity, good monodispersity, and displayed differences in NTP-dependent activity in the presence of lipids compared to detergent-solubilized VcFeoB. Finally, a newly discovered single-pass transmembrane protein of the Feo system termed FeoD (formally FeoI) from Streptococcus thermophilus (StFeoD) was first modeled using AlphaFold3 before being cloned, expressed, purified, and partially characterized. Contrary to previous reports, we show that the Cys-rich StFeoD co-purifies with a partially bound [Fe-S] cluster, similarly to FeoC, and optimization and further characterization is currently underway. When taken all together, this dissertation deepens our understanding of the membrane-bound and membrane-associated components of the Feo system and paves the way for future structural work to understand the precise mechanism of prokaryotic Fe2+ transport.
Broad spectrum antiviral nucleosides—Our best hope for the future
(Elsevier, 2021) Seley-Radtke, Katherine L.; Thames, Joy E.; Waters, Charles D.
The current focus for many researchers has turned to the development of therapeutics that have the potential for serving as broad-spectrum inhibitors that can target numerous viruses, both within a particular family, as well as to span across multiple viral families. This will allow us to build an arsenal of therapeutics that could be used for the next outbreak. In that regard, nucleosides have served as the cornerstone for antiviral therapy for many decades. As detailed herein, many nucleosides have been shown to inhibit multiple viruses due to the conserved nature of many viral enzyme binding sites. Thus, it is somewhat surprising that up until very recently, many researchers focused more on “one bug one drug,” rather than trying to target multiple viruses given those similarities. This attitude is now changing due to the realization that we need to be proactive rather than reactive when it comes to combating emerging and reemerging infectious diseases. A brief summary of prominent nucleoside analogues that previously exhibited broad-spectrum activity and are now under renewed interest, as well as new analogues, that are currently under investigation against SARS-CoV-2 and other viruses is discussed herein.
Synthetic anti-RNA antibody derivatives for RNA visualization in mammalian cells
(Oxford, 2024-12-31) Banna, Hasan Al; Berg, Kimberley; Sadat, Tasnia; Das, Naba Krishna; Paudel, Roshan; D'Souza, Victoria; Koirala, Deepak
Although antibody derivatives, such as Fabs and scFvs, have revolutionized the cellular imaging, quantification and tracking of proteins, analogous tools and strategies are unavailable for cellular RNA visualization. Here, we developed four synthetic anti-RNA scFv (sarabody) probes and their green fluorescent protein (GFP) fusions and demonstrated their potential to visualize RNA in live mammalian cells. We expressed these sarabodies and sarabody–GFP modules, purified them as soluble proteins, characterized their binding interactions with their corresponding epitopes and finally employed two of the four modules, sara1-GFP and sara1c-GFP, to visualize a target messenger RNA in live U2OS cells. Our current RNA imaging strategy is analogous to the existing MCP-MS₂ system for RNA visualization, but additionally, our approach provides robust flexibility for developing target RNA-specific imaging modules, as epitope-specific probes can be selected from a library generated by diversifying the sarabody complementarity determining regions. While we continue to optimize these probes, develop new probes for various target RNAs and incorporate other fluorescence proteins like mCherry and HaloTag, our groundwork results demonstrated that these first-of-a-kind immunofluorescent probes will have tremendous potential for tracking mature RNAs and may aid in visualizing and quantifying many cellular processes as well as examining the spatiotemporal dynamics of various RNAs.
Relaxation optimized heteronuclear experiments for extending the size limit of RNA nuclear magnetic resonance
(2024-12-11) Shah, Aarsh; Patel, Heer; Kanjarpane, Arjun; Summers, Michael; Marchant, Jan
The application of NMR to large RNAs has been limited by the inability to perform heteronuclear correlation experiments essential for resolving overlapping 1H NMR signals, determining inter-proton distance restraints and inter-helical orientations for structure calculations, and evaluating conformational dynamics. Approaches exploiting 1H-13C correlations that are routinely applied to proteins and small RNAs of ~50 nucleotides or fewer are impractical for larger RNAs due to rapid dipolar relaxation of protons by their attached carbons. Here we report a 2H-enhanced, 1H-15N correlation approach that enables atom-specific NMR characterization of much larger RNAs. Purine H8 transverse relaxation rates are reduced ~20-fold with ribose perdeuteration, enabling efficient magnetization transfer via two-bond 1H-15N couplings. We focus on H8-N9 correlation spectra which benefit from favorable N9 chemical shift anisotropy. Chemical shift assignment is enabled by retention of protons at the C1′ position, which allow measurement of H8-H1′ NOEs and two-bond H1′-N9 correlation strategies with only a minor effect on H8 relaxation. The approach is demonstrated for the 232 nucleotide HIV-1 Rev response element, where chemical shift assignments, 15N-edited nuclear Overhauser effects, and 1H-15N residual dipolar couplings are readily obtained from sensitive, high-resolution spectra. Heteronuclear correlated NMR methods that have been essential for the study of proteins can now be extended to RNAs of at least 78 kDa.
Multiphase sulfur chemistry facilitates particle growth in a cold and dark urban environment
(Royal Society of Chemistry, 2024-11-15) Mao, Jingqiu; Bali, Kunal; Campbell, James Raemond; Robinson, Ellis Shipley; DeCarlo, Peter F.; Ijaz, Amna; Temime-Roussel, Brice; Barbara, D'Anna; Ketcherside, Damien; Yokelson, Robert J.; Hu, Lu; Cesler-Maloney, Meeta; Simpson, William; Guo, Fangzhou; Flynn, James; St. Clair, Jason; Nenes, Athanasios; Weber, Rodney
Sulfate comprises an average of 20% of the ambient PM2.5 mass during the winter months in Fairbanks, based on 24-hour filter measurements. During the ALPACA 2022 field campaign (Jan 15th-Feb 28th of 2022), we deployed two aerosol mass spectrometers (AMS) and one aerosol chemical speciation monitor (ACSM) at three urban sites, combined with Scanning Mobility Particle Sizers (SMPS), to examine the evolution of aerosol composition and size distribution at a sub-hourly time scale. During an intense pollution episode with ambient temperature between -25 and -35°C, all three instruments (two AMS and one ACSM) recorded a sharp increase in sulfate mass, ranging from 5 to 40 μg/m³ within a few hours. This increase contributed up to half of the observed rise in ambient PM2.5 mass concentration and coincided with a substantial shift in the number distribution from particle sizes less than 100 nm diameter (Dp < 100 nm) to larger particles (Dp > 100 nm) with little increase in number concentration. The corresponding increase in the volume concentration and distribution shift to larger particle size suggests the secondary formation of sulfate and organic aerosol onto pre-existing aerosols. Comparing AMS-sulfate (all sulfur species) to inorganic sulfate measured by online particle-into-liquid sampler−ion chromatography (PILS-IC), we find roughly 80% of sulfate increase was due to organic sulfur, consistent with the observation of mass spectral signatures in the AMS of organosulfur compounds. The rapid formation of sulfate appears to coincide with spikes in ambient aldehyde concentrations (formaldehyde and acetaldehyde) and an increase in S(IV) in ambient PM2.5. This likely results from multiphase chemistry, where hydroxymethanesulfonate (HMS) and other aldehyde-S(IV) adducts are formed through reactions between aldehydes and SO2 in deliquesced aerosols. We estimate that all S(IV) species, including HMS, contribute an average of 30% to aerosol sulfur, with a dominant fraction occurring during rapid sulfate increase events. Our work highlights the crucial role of controlling aldehydes to mitigate severe air pollution events in Fairbanks and may apply to other urban areas. It also emphasizes the significance of multiphase chemistry in driving particle growth from Aitken mode to accumulation mode, a key step for aerosol-cloud interactions.
Morphology and Luminescence Properties of Transition Metal Doped Zinc Selenide Crystals
(Springer Nature, 2024-11-11) Bowman, Eric; Scheurer, Leslie; Arnold, Bradley; Su, Ching Hua; Choa, Fow-Sen; Cullum, Brian; Singh, Narsingh
Zinc selenide is an excellent matrix material to dope with rare-earth and transition metal to achieve mid-infrared luminescence to develop high power lasers. The luminescence, morphology and refractive index is significantly affected by the doping and defects generated due to size and valency of dopants, concentration, growth process and convection during the growth. The aim of the study is to investigate effect of point and line defects generated due to low doping of iron and chromium on the emission and morphology of the zinc selenide. Luminescence and morphological properties of large iron and chromium doped zinc selenide single crystals were studied to evaluate the effect of extremely low residual impurities and defects associated with the doping process. The emission properties following both short wavelength (i.e., ultraviolet; 350–370 nm) excitation and longer wavelength (i.e., near infrared; 850–870 nm) excitation were characterized. Luminescence emission bands were identified in both doped crystals. In addition to the primary emission bands, satellite peaks and intra-center transitions were also observed. Due to local population defects associated with the residual impurities (ppm to ppb) in the Fe-ZnSe and Cr-ZnSe crystals, peak emission wavelengths were observed to shift. The emission bands were found to decrease in intensity due to recombination of residual impurity co-dopants and complex defects generated during growth and fabrication. Cryogenic temperature analyses revealed a very clean emission band due to freezing of some of the point and line defects. An emission band observed at 980 nm for both crystals at room temperature as well as cryogenic temperatures indicates a vibronic peak in ZnSe. The scanning electron microscopy (SEM) images of the local morphology support the conclusion that small crystallites in doped crystals are also present.
Evolution of Reactive Organic Compounds and Their Potential Health Risk in Wildfire Smoke
(ACS, 2024-10-22) Pye, Havala O. T.; Xu, Lu; Henderson, Barron H.; Pagonis, Demetrios; Campuzano-Jost, Pedro; Guo, Hongyu; Jimenez, Jose L.; Allen, Christine; Skipper, T. Nash; Halliday, Hannah S.; Murphy, Benjamin N.; D’Ambro, Emma L.; Wennberg, Paul O.; Place, Bryan K.; Wiser, Forwood C.; McNeill, V. Faye; Apel, Eric C.; Blake, Donald R.; Coggon, Matthew M.; Crounse, John D.; Gilman, Jessica B.; Gkatzelis, Georgios I.; Hanisco, Thomas F.; Huey, L. Gregory; Katich, Joseph M.; Lamplugh, Aaron; Lindaas, Jakob; Peischl, Jeff; St Clair, Jason; Warneke, Carsten; Wolfe, Glenn; Womack, Caroline
Wildfires are an increasing source of emissions into the air, with health effects modulated by the abundance and toxicity of individual species. In this work, we estimate reactive organic compounds (ROC) in western U.S. wildland forest fire smoke using a combination of observations from the 2019 Fire Influence on Regional to Global Environments and Air Quality (FIREX-AQ) field campaign and predictions from the Community Multiscale Air Quality (CMAQ) model. Standard emission inventory methods capture 40–45% of the estimated ROC mass emitted, with estimates of primary organic aerosol particularly low (5–8×). Downwind, gas-phase species abundances in molar units reflect the production of fragmentation products such as formaldehyde and methanol. Mass-based units emphasize larger compounds, which tend to be unidentified at an individual species level, are less volatile, and are typically not measured in the gas phase. Fire emissions are estimated to total 1250 ± 60 g·C of ROC per kg·C of CO, implying as much carbon is emitted as ROC as is emitted as CO. Particulate ROC has the potential to dominate the cancer and noncancer risk of long-term exposure to inhaled smoke, and better constraining these estimates will require information on the toxicity of particulate ROC from forest fires.
Fixed-angle observation of surface plasmon coupled chemiluminescence from palladium thin films
(AIP, 2009-09-25) Aslan, Kadir; Weisenberg, Micah; Hortle, Elinor; Geddes, Chris
In this letter, the fixed-angle observation of surface plasmon coupled chemiluminescence (SPCC) from palladium thin films is reported. Fresnel calculations predict that light 492–549 nm spectral range can efficiently induce surface plasmon modes in 15 nm palladium thin films. Free-space emission from blue, green, and chartreuse chemiluminescent solutions on palladium thin films was isotropic, while the SPCC emission was highly directional and predominantly p-polarized in accordance with the predictions of the Fresnel calculations. In addition, the decay rates of the SPCC and free-space emission were similar, which suggests that palladium thin films have no catalytic effect on chemiluminescence emission.
Indium nanodeposits: A substrate for metal-enhanced fluorescence in the ultraviolet spectral region
(AIP, 2010-11-03) Dragan, Anatoliy; Geddes, Chris
We have studied a metallic substrate, composed of indium nanodeposits, for metal-enhanced fluorescence (MEF) in the ultraviolet (UV) spectral region. Indium coated slides were prepared using the thermal vapor deposition technique. Theoretical finite difference time domain simulations and experimental studies show that plasmon enhanced absorption and coupled radiation through the scattering component of the extinction spectra of indium nanoparticles, lie in UV region, and are sensitive to the size and density of the nanoparticles, the thickness of the indium film, and polarity of the medium. The MEF effect, measured for intrinsic protein tryptophan and tyrosine residues, loaded onto indium films of different thickness, changes in a wavelike fashion, reflecting changes in the metal film landscape and, consequently, the chromophores coupling with surface plasmons. Indium films also significantly enhance intrinsic fluorescence of proteins themselves [bovine serum albumin]. In this case the wavelength dependence of MEF shows different emission enhancements of protein Tyr and Trp residues. Subsequently, indium-enhanced intrinsic protein fluorescence in the UV spectral region can be of great potential importance for quantitation assays as well as for the labeless detection of biomolecules in the biosciences.
Metal-enhanced fluorescence from tin nanostructured surfaces
(AIP, 2010-01-20) Zhang, Yongxia; Dragan, Anatoliy; Geddes, Chris
The recent surge in interest in the metal-enhanced fluorescence (MEF) phenomenon and its numerous applications in the biosciences has fueled research into identifying alternative metals to silver which have desirable properties, such as enhanced emission and fluorophore photostability. In this paper, we subsequently study and reveal that tin nanodeposits are a suitable metal for MEF with an electric field wavelength dependence somewhat different than silver. An enhanced fluorescence emission coupled with a reduced fluorophore lifetime suggests both an electric field and plasmon-coupling component are the underlying mechanisms for tin-based MEF. In addition, an enhanced fluorophore photostability is observed near-to tin nanodeposits.
Metal-enhanced chemiluminescence from chromium, copper, nickel, and zinc nanodeposits: Evidence for a second enhancement mechanism in metal-enhanced fluorescence
(AIP, 2010-09-28) Weisenberg, Micah; Zhang, Yongxia; Geddes, Chris
Over the past decade metal-fluorophore interactions, metal-enhanced fluorescence, have attracted significant research attention, with the technology now becoming common place in life science applications. In this paper, we address the underlying mechanisms of metal-enhanced fluorescence (MEF) and experimentally show using chemiluminescence solutions that MEF is indeed underpinned by two complimentary mechanisms, consistent with the recent reports by Geddes and co-workers [Zhang et al., J. Phys. Chem. C 113, 12095 (2009)] and their enhanced fluorescence hypothesis.
Development of a Microwave—Accelerated Metal-Enhanced Fluorescence 40 Second, <100 cfu/mL Point of Care Assay for the Detection of Chlamydia Trachomatis
(IEEE, 2011-03) Zhang, Yongxia; Agreda, Patricia; Kelley, Shannon; Gaydos, Charlotte; Geddes, Chris
An inexpensive technology to both lyse Chlamydia trachomatis (CT) and detect DNA released from CT within 40 s is demonstrated. In a microwave cavity, energy is highly focused using 100-nm gold films with “bow-tie” structures to lyse CT within 10 s. The ultrafast detection of the released DNA from less than 100 cfu/mL CT is accomplished in an additional 30 s by employing the microwave-accelerated metal-enhanced fluorescence technique. This new “ release and detect” platform technology is a highly attractive alternative method for the lysing of bacteria, DNA extraction, and the fast quantification of bacteria and potentially other pathogenic species and cells as well. Our approach is a significant step forward for the development of a point of care test for CT.
Ultra-Fast and Sensitive Detection of Non-Typhoidal Salmonella Using Microwave-Accelerated Metal-Enhanced Fluorescence (“MAMEF”)
(PLOS, 2011-04-08) Tennant, Sharon M.; Zhang, Yongxia; Galen, James E.; Geddes, Chris; Levine, Myron M.
Certain serovars of Salmonella enterica subsp. enterica cause invasive disease (e.g., enteric fever, bacteremia, septicemia, meningitis, etc.) in humans and constitute a global public health problem. A rapid, sensitive diagnostic test is needed to allow prompt initiation of therapy in individual patients and for measuring disease burden at the population level. An innovative and promising new rapid diagnostic technique is microwave-accelerated metal-enhanced fluorescence (MAMEF). We have adapted this assay platform to detect the chromosomal oriC locus common to all Salmonella enterica subsp. enterica serovars. We have shown efficient lysis of biologically relevant concentrations of Salmonella spp. suspended in bacteriological media using microwave-induced lysis. Following lysis and DNA release, as little as 1 CFU of Salmonella in 1 ml of medium can be detected in <30 seconds. Furthermore the assay is sensitive and specific: it can detect oriC from Salmonella serovars Typhi, Paratyphi A, Paratyphi B, Paratyphi C, Typhimurium, Enteritidis and Choleraesuis but does not detect Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae or Acinetobacter baumanii. We have also performed preliminary experiments using a synthetic Salmonella oriC oligonucleotide suspended in whole human blood and observed rapid detection when the sample was diluted 1:1 with PBS. These pre-clinical data encourage progress to the next step to detect Salmonella in blood (and other ordinarily sterile, clinically relevant body fluids).
Sialyl Residues Modulate LPS-Mediated Signaling through the Toll-Like Receptor 4 Complex
(PLOS, 2012-04-09) Feng, Chiguang; Stamatos, Nicholas M.; Dragan, Anatoliy; Medvedev, Andrei; Whitford, Melissa; Zhang, Lei; Song, Chang; Rallabhandi, Prasad; Cole, Leah; Nhu, Quan M.; Vogel, Stefanie N.; Geddes, Chris; Cross, Alan S.
We previously reported that neuraminidase (NA) pretreatment of human PBMCs markedly increased their cytokine response to lipopolysaccharide (LPS). To study the mechanisms by which this occurs, we transfected HEK293T cells with plasmids encoding TLR4, CD14, and MD2 (three components of the LPS receptor complex), as well as a NFₖB luciferase reporting system. Both TLR4 and MD2 encoded by the plasmids are α-2,6 sialylated. HEK293T cells transfected with TLR4/MD2/CD14 responded robustly to the addition of LPS; however, omission of the MD2 plasmid abrogated this response. Addition of culture supernatants from MD2 (sMD2)-transfected HEK293T cells, but not recombinant, non-glycosylated MD2 reconstituted this response. NA treatment of sMD2 enhanced the LPS response as did NA treatment of the TLR4/CD14-transfected cell supplemented with untreated sMD2, but optimal LPS-initiated responses were observed with NA-treated TLR4/CD14-transfected cells supplemented with NA-treated sMD2. We hypothesized that removal of negatively charged sialyl residues from glycans on the TLR4 complex would hasten the dimerization of TLR4 monomers required for signaling. Co-transfection of HEK293T cells with separate plasmids encoding either YFP- or FLAG-tagged TLR4, followed by treatment with NA and stimulation with LPS, led to an earlier and more robust time-dependent dimerization of TLR4 monomers on co-immunoprecipitation, compared to untreated cells. These findings were confirmed by fluorescence resonance energy transfer (FRET) analysis. Overexpression of human Neu1 increased LPS-initiated TLR4-mediated NFₖB activation and a NA inhibitor suppressed its activation. We conclude that (1) sialyl residues on TLR4 modulate LPS responsiveness, perhaps by facilitating clustering of the homodimers, and that (2) sialic acid, and perhaps other glycosyl species, regulate MD2 activity required for LPS-mediated signaling. We speculate that endogenous sialidase activity mobilized during cell activation may play a role in this regulation.

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