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Open access publications by faculty, postdocs, and graduate students in the Department of Chemistry and Biochemistry.
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Item A histochemical approach to activity-based copper sensing reveals cuproplasia-dependent vulnerabilities in cancer(Proceedings of the National Academy of Sciences, 2025-01-15) Messina, Marco S.; Torrente, Laura; Pezacki, Aidan T.; Humpel, Hanna I.; Li, Erin L.; Miller, Sophia G.; Verdejo-Torres, Odette; Padilla-Benavides, Teresita; Brady, Donita C.; Killilea, David W.; Killilea, Alison N.; Ralle, Martina; Ward, Nathan P.; Ohata, Jun; DeNicola, Gina M.; Chang, Christopher J.Significance Copper is an essential element for life, where it mediates copper-dependent cell growth and proliferation (cuproplasia) and cell death (cuproptosis) processes that underpin health and disease. We present a histochemical activity-based sensing strategy that enables systematic profiling of bioavailable copper levels, termed the labile copper pool, across many cell lines in parallel to assess their copper dependencies. We identified that cancer cells with heightened activation of the antioxidant response transcription factor NRF2 have reciprocally lower levels of labile Cu(I). In turn, these cells are more susceptible to cell death induced by copper chelation. By revealing a cuproplasia-dependent vulnerability in cancer, this work showcases the utility of chemical copper detection methods for studying metals in biology and medicine. Abstract Copper is an essential nutrient for sustaining vital cellular processes spanning respiration, metabolism, and proliferation. However, loss of copper homeostasis, particularly misregulation of loosely bound copper ions which are defined as the labile copper pool, occurs in major diseases such as cancer, where tumor growth and metastasis have a heightened requirement for this metal. To help decipher the role of copper in the etiology of cancer, we report a histochemical activity-based sensing approach that enables systematic, high-throughput profiling of labile copper status across many cell lines in parallel. Coppermycin-1 reacts selectively with Cu(I) to release puromycin, which is then incorporated into nascent peptides during protein translation, thus leaving a permanent and dose-dependent marker for labile copper that can be visualized with standard immunofluorescence assays. We showcase the utility of this platform for screening labile Cu(I) pools across the National Cancer Institute’s 60 (NCI-60) human tumor cell line panel, identifying cell types with elevated basal levels of labile copper. Moreover, we use Coppermycin-1 to show that lung cancer cells with heightened activation of nuclear factor-erythroid 2-related factor 2 (NRF2) possess lower resting labile Cu(I) levels and, as a result, have reduced viability when treated with a copper chelator. This work establishes that methods for labile copper detection can be used to assess cuproplasia, an emerging form of copper-dependent cell growth and proliferation, providing a starting point for broader investigations into the roles of transition metal signaling in biology and medicine.Item Post-synthetic modification of amine-functionalized permanently porous coordination cages(Chemical Communications, 2024-12-04) Hoq, Jahidul; Dworzak, Michael R.; Dissanayake, Duleeka; Skalla, Rebecca X.; Yamamoto, Nobuyuki; Yap, Glenn P. A.; Bloch, Eric D.This manuscript explores the post-synthetic modification (PSM) of amine-functionalized porous coordination cages, specifically focusing on the formation of imine bonds through reactions with aldehydes. Targeting various cage topologies, including zirconium-, magnesium-, and molybdenum-based structures, we demonstrate the tunability of cage solubility and porosity through selective functionalization where the proximity of amine groups on the parent cage impacts the extent of modification. The work highlights the reversible nature of imine formation, offering potential applications in solubility switching and mixed-metal solid synthesis.Item Phonons reveal coupled cholesterol-lipid dynamics in ternary membranes(Biophysical Journal, 2024-12-03) Fitzgerald, James E.; Soloviov, Dmytro; Cai, Yong Q.; Heberle, Frederick A.; Ishikawa, Daisuke; Baron, Alfred Q.R.; Bolmatov, Dima; Zhernenkov, Mikhail; Lyman, Edward R.Experimental studies of collective dynamics in lipid bilayers have been challenging due to the energy resolution required to observe these low-energy phonon-like modes. However, inelastic x-ray scattering (IXS) measurements—a technique for probing vibrations in soft and biological materials—are now possible with sub-meV resolution, permitting direct observation of low-energy, phonon-like modes in lipid membranes. Here, IXS measurements with sub-meV energy resolution reveal a low-energy optic-like phonon mode at roughly 3 meV in the liquid-ordered ðLoÞ and liquid-disordered phases of a ternary lipid mixture. This mode is only observed experimentally at momentum transfers greater than 5 nm 1 in the Lo system. A similar gapped mode is also observed in all-atom molecular dynamics (MD) simulations of the same mixture, indicating that the simulations accurately represent the fast, collective dynamics in the L o phase. Its optical nature and the Q range of the gap together suggest that the observed mode is due to the coupled motion of cholesterol-lipid pairs, separated by several hydrocarbon chains within the membrane plane. Analysis of the simulations provides molecular insight into the origin of the mode in transient, nanoscale substructures of hexagonally packed hydrocarbon chains. This nanoscale hexagonal packing was previously reported based on MD simulations and, later, by NMR measurements. Here, however, the integration of IXS and MD simulations identifies a new signature of the Lo substructure in the collective lipid dynamics, thanks to the recent confluence of IXS sensitivity and MD simulation capabilities.Item Composition Quantification of SiGeSn Alloys Through Time-of-Flight Secondary Ion Mass Spectrometry: Calibration Methodologies and Validation With Atom Probe Tomography(IEEE Journal of Selected Topics in Quantum Electronics, 2024-09-09) Zhao, Haochen; Liu, Shang; Park, Suho; Feng, Xu; Zeng, Zhaoquan; Kolodzey, JamesTime-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) is a powerful technique for elemental compositional analysis and depth profiling of materials. However, it encounters the problem of matrix effects that hinder its application. In this work, we introduce a pioneering ToF-SIMS calibration method tailored for SixGeySnz ternary alloys. SixGe1-x and Ge1-zSnz binary alloys with known compositions are used as calibration reference samples. Through a systematic SIMS quantification study of SiGe and GeSn binary alloys, we unveil a linear correlation between secondary ion intensity ratio and composition ratio for both SiGe and GeSn binary alloys, effectively mitigating the matrix effects. Extracted relative sensitivity factor (RSF) value from SixGe1-x (0.07 < x < 0.83) and Ge1-zSnz (0.066 < z < 0.183) binary alloys are subsequently applied to those of SixGeySnz (0.011 < x < 0.113, 0.863 < y < 0.935 and 0.023 < z < 0.103) ternary alloys for elemental compositions quantification. These values are cross-checked by Atom Probe Tomography (APT) analysis, an indication of the great accuracy and reliability of as-developed ToF-SIMS calibration process. The proposed method and its reference sample selection strategy in this work provide a low-cost as well as simple-to-follow calibration route for SiGeSn composition analysis, thus driving the development of next-generation multifunctional SiGeSn-related semiconductor devices.Item Flexible Cation Exchange Environment via Ligand-Free Metal Chalcogenide Thin Films(ACS Nanoscience Au, 2024-11-07) Lacey, Hannah R.; Dobson, Kevin D.; Hernández- Pagán, Emil A.Cation exchange (CE) has emerged as a premier postsynthetic method to carefully tune the chemical composition and properties of nanocrystals with excellent morphology retention. However, reaction conditions are typically dictated by the ubiquitous ligands bound to their surface, limiting their solubility and influencing the thermodynamics/kinetics of the reaction. To bypass these challenges, we report on CE reactions with Cu+, Ag+, Cu2+, Cd2+, Zn2+, and Mn2+ utilizing ligand-free CdS and CuxSey thin films as host templates. The exchange reactions could be performed sequentially or simultaneously (i.e., two guest cations) to access compositionally diverse products. The incorporation of cations on the host films was confirmed using SEM-EDS, XPS, and ICP-MS analyses, as well as tracking wavelength shifts in the UV–vis absorption spectra. The flexibility of this approach was demonstrated as reactions were carried out using an array of different guest precursor salts and solvents with a range of polarities. Moreover, the reactions were generalizable among selenide and sulfide films and proceeded under milder conditions in comparison with reported nanocrystal reactions. A ligand-free environment with flexible reaction conditions, as the work herein, could aid in deconvoluting the different factors involved in CE reactions and further expand its use for fundamental research and applications like photovoltaics, optoelectronics, and catalysis.Item Self-assembled thin films as alternative surface textures in assistive aids with users who are blind(Journal of Materials Chemistry B, 2024-09-05) Swain, Zachary; Derkaloustian, Maryanne; Hepler, Kayla A.; Nolin, Abigail; Damani, Vidhika S.; Bhattacharyya, Pushpita; Shrestha, Tulaja; Medina, Jared; Kayser, Laure V.; Dhong, Charles B.Current tactile graphics primarily render tactile information for blind users through physical features, such as raised bumps or lines. However, the variety of distinctive physical features that can be created is effectively saturated, and alternatives to these physical features are not currently available for static tactile aids. Here, we explored the use of chemical modification through self-assembled thin films to generate distinctive textures in tactile aids. We used two silane precursors, n-butylaminopropyltrimethoxysilane and n-pentyltrichlorosilane, to coat playing card surfaces and investigated their efficacy as a tactile coating. We verified the surface coating process and examined their durability to repeated use by traditional materials characterization and custom mesoscale friction testing. Finally, we asked participants who were both congenitally blind and braille-literate to sort the cards based on touch. We found that participants were able to identify the correct coated card with 82% accuracy, which was significantly above chance, and two participants achieved 100% accuracy. This success with study participants demonstrates that surface coatings and surface modifications might augment or complement physical textures in next-generation tactile aids.Item Mechanistic differences between linear vs. spirocyclic dialkyldiazirine probes for photoaffinity labeling(Chemical Science, 2024-08-13) O'Brien, Jessica G. K.; Conway, Louis P.; Ramaraj, Paramesh K.; Jadhav, Appaso M.; Jin, Jun; Dutra, Jason K.; Evers, Parrish; Masoud, Shadi S.; Schupp, Manuel; Saridakis, Iakovos; Chen, Yong; Maulide, Nuno; Pezacki, John P.; Ende, Christopher W. am; Parker, Christopher G.; Fox, Joseph M.Dialkyldiazirines have emerged as a photo-reactive group of choice for interactome mapping in live cell experiments. Upon irradiation, ‘linear’ dialkyldiazirines produce dialkylcarbenes which are susceptible to both intramolecular reactions and unimolecular elimination processes, as well as diazoalkanes, which also participate in intermolecular labeling. Cyclobutylidene has a nonclassical bonding structure and is stable enough to be captured in bimolecular reactions. Cyclobutanediazirines have more recently been studied as photoaffinity probes based on cyclobutylidene, but the mechanism, especially with respect to the role of putative diazo intermediates, was not fully understood. Here, we show that photolysis (365 nm) of cyclobutanediazirines can produce cyclobutylidene intermediates as evidenced by formation of their expected bimolecular and unimolecular products, including methylenecyclopropane derivatives. Unlike linear diazirines, cyclobutanediazirine photolysis in the presence of tetramethylethylene produces a [2 + 1] cycloaddition adduct. By contrast, linear diazirines produce diazo compounds upon low temperature photolysis in THF, whereas diazo compounds are not detected in similar photolyses of cyclobutanediazirines. Diazocyclobutane, prepared by independent synthesis, is labile, reactive toward water and capable of protein alkylation. The rate of diazocyclobutane decomposition is not affected by 365 nm light, suggesting that the photochemical conversion of diazocyclobutane to cyclobutylidene is not an important pathway. Finally, chemical proteomic studies revealed that a likely consequence of this primary conversion to a highly reactive carbene is a marked decrease in labeling by cyclobutanediazirine-based probes relative to linear diazirine counterparts both at the individual protein and proteome-wide levels. Collectively, these observations are consistent with a mechanistic picture for cyclobutanediazirine photolysis that involves carbene chemistry with minimal formation of diazo intermediates, and contrasts with the photolyses of linear diazirines where alkylation by diazo intermediates plays a more significant role.Item Chemomechanical damage prediction from phase-field simulation video sequences using a deep-learning-based methodology(iScience, 2024-09-12) Zeng, Quan; Rezaei, Shahed; Carrillo, Luis; Davidson, Rachel; Xu, Bai-Xiang; Banerjee, Sarbajit; Ding, YuHighlights • Deep-learning-based method to predict chemo-mechanical processes in electrode materials • Prognostication of crack development and propagation based on machine learning • Potential to integrate in battery management systems of large-format batteries Summary Understanding the failure mechanisms of lithium-ion batteries is essential for their greater adoption in diverse formats. Operando X-ray and electron microscopy enable the evaluation of concentration, phase, and stress heterogeneities in electrode architectures. Phase-field models are commonly used to capture multi-physics coupling including the interplay between electrochemistry and mechanics. However, very little has been explored regarding developing predictive models that would forecast imminent failure. This study explores the application of convolutional long short-term memory networks for damage prediction in cathode materials using video sequence from phase-field simulations as a proxy for video microscopy. Two models are examined making use of, respectively, the damage video only and the damage and hydrostatic stress videos combined. We use customized quantitative metrics to compare the performance of the models. Our work demonstrates the outstanding capability of deep learning models using limited data to predict fracture behavior of battery materials, including crack propagation angle and length. Graphical abstract available at: https://doi.org/10.1016/j.isci.2024.110822Item Glycolysis Can Be Fun: Rediscovering Glycolysis as a Problem-Solving Introduction to Metabolism(CourseSource, 2024-08-19) Genova, Lauren A.; Procko, Kristen; Grimes, Catherine L.; Williams, Caroline; Cornely, Kathleen; Shor, Audrey; Greene, Amy Styer; Bibel, Brianna; Kumar, Sanjana V.; White, Harold B.A thorough understanding of glycolysis forms a foundation for students to analyze subsequent topics in metabolism, a core competency recognized by multiple national societies for biology and biochemistry. However, when confronted with the names of over ten chemicals and enzymes, along with various energy inputs and outputs, students can regard glycolysis as a daunting memorization task. Here we describe a card sorting activity in which small groups of students work out the steps of the glycolysis pathway before any lectures on the topic. They examine the chemical structures of glycolytic intermediates and deduce their logical order. Subsequent analysis of the reactions and the role of cofactors and substrates is reinforced with a POGIL®-inspired worksheet. In the process, the students engage in productive discussions of topics often introduced didactically in lecture. The activity was implemented at six different institutions in small (~12 students) and large classrooms (100+ students), and can be adapted to hybrid/online formats. This highly engaging exercise has been well-received by students and instructors in various undergraduate course contexts.Item Thermoelectric Zintl phases with ultralow thermal conductivity: synthesis, structural characterization, and transport properties of Ca10AlSb9 and Ca10CdSb9(Journal of Materials Chemistry A, 2024-09-02) Ghosh, Kowsik; Borgsmiller, Leah; Baranets, Sviatoslav; Snyder, G. Jeffrey; Bobev, SvilenTwo new Zintl antimonides, Ca10MSb9 (M = Al and Cd), have been synthesized and characterized for the first time and their thermoelectric performance has been evaluated without additional optimization. The two phases can be readily synthesized either by Sn-flux or direct solid-state reactions. The compounds are isotypic and crystallize in a tetragonal crystal system with the space group P42/mnm (no. 136). The crystal structure is highly complex with significant structural disorder—both occupational and positional. For its careful elucidation, both single-crystal X-ray diffraction methods and Rietveld refinements of powder X-ray diffraction data for polycrystalline bulk samples were required. Despite the significant disorder, the structures retain their charge balance and these new Zintl phases are shown to be intrinsic semiconductors with a bandgap of about 0.5 eV. High-temperature transport measurements reveal remarkably low thermal conductivity (0.6–0.7 W m−1 K−1) in the temperature range 323 K to 573 K, which is even lower than that of the well-known thermoelectric Zintl material Yb14MnSb11. Additionally, Seebeck coefficient measurements showed a very high value for Ca10AlSb9, approaching 350 μV K−1 at 573 K. Therefore, we speculate that with proper systematic work and further optimization, these and potentially other Zintl compounds from this extended family can show excellent thermoelectric performance.Item Helicobacter pylori and Campylobacter jejuni bacterial holocytochrome c synthase structure-function analysis reveals conservation of heme binding(Communications Biology, 2024-08-13) Yeasmin, Tania; Carroll, Susan C.; Hawtof, David J.; Sutherland, Molly C.Heme trafficking is essential for cellular function, yet mechanisms of transport and/or heme interaction are not well defined. The System I and System II bacterial cytochrome c biogenesis pathways are developing into model systems for heme trafficking due to their functions in heme transport, heme stereospecific positioning, and mediation of heme attachment to apocytochrome c. Here we focus on the System II pathway, CcsBA, that is proposed to be a bi-functional heme transporter and holocytochrome c synthase. An extensive structure-function analysis of recombinantly expressed Helicobacter pylori and Campylobacter jejuni CcsBAs revealed key residues required for heme interaction and holocytochrome c synthase activity. Homologous residues were previously identified to be required for heme interaction in Helicobacter hepaticus CcsBA. This study provides direct, biochemical evidence that mechanisms of heme interaction are conserved, leading to the proposal that the CcsBA WWD heme-handling domain represents a novel target for therapeutics.Item The emergence of a robust lithium gallium oxide surface layer on gallium-doped LiNiO2 cathodes enables extended cycling stability(Materials Advances, 2024-08-01) Mishra, Mritunjay; Yao, Koffi P. C.LiNiO2 is a promising cobalt-free cathode for lithium-ion batteries due to its high theoretical capacity and low cost. Although intensely studied, the occurrence of several phase transformations and particle pulverization causing capacity fading in cobalt-free LiNiO2 have yet to be effectively resolved. Herein, a sol–gel synthesis process is utilized for gallium (Ga) doping of LiNiO2 at 2% (solution-doping) and 5% (excess-doping) molar ratios. Transmission electron microscopy and X-ray diffraction Rietveld refinement reveal the opportune formation of an α-LiGaO2 shell at 5% doping beyond the solubility limit of 2%. Alongside solution-doping at the Ni and Li crystallographic sites, the emergence of this α-LiGaO2, isostructural and lattice-matched to the R[3 with combining macron]m LiNiO2, is shown to improve capacity retention by a factor of 2.45 after 100 cycles at C/3. Particles with the LiGaO2 shell experience significantly less pulverization during extended cycling. In contrast, the solution-doped LiNiO2 with 2% Ga experiences extensive particle fracturing similar to the baseline undoped LiNiO2. In turn, no significant electrochemical performance difference is found between the solution-doped and baseline LiNiO2. The evidence garnered suggests that a surface gallium oxide phase achievable with excess Ga is key to enabling extended cycling using Ga doping.Item Plant extract mediated synthesis of gold nanoparticles and its application to treatment of cancer(World Journal of Advanced Engineering Technology and Sciences, 2024-07-28) Onivefu, Asishana Paul; Adekunle, Adewale Philip; Okebugwu, Joseph Chibuike; Benibo, Paul Gberiye; Aibor, Lucky Ehimen; Raji-Ayoola, Jumoke Ayodele; Latinwo, Opeyemi Olaoluwa; Onyedum, Nwamaka Nneka; Amoo, Ayosunkanmi Damilola; Ukem, David EffiongPlant extract-mediated synthesis of gold nanoparticles is a promising research area with potential applications in various fields including medicine-cancer research, catalysis, and nanoelectronics. Gold nanoparticles have gained serious attention in recent years as a potential cancer treatment due to their unique optical and physical properties. Plant-mediated synthesis of gold nanoparticles is a promising method to produce biocompatible and non-toxic gold nanoparticles (Au-NPs). This study focuses on the current research on the plant-mediated synthesis of gold nanoparticles and their potential treatment for cancer. It also discussed the latest advancement in nanobot technology. The study will also describe the type of plants used for the synthesis of gold nanoparticles, the mechanisms involved in the synthesis, the advantages of using plant-mediated synthesis, and the disadvantages. Additionally, this study will discuss the efficacy of gold nanoparticles as cancer therapeutics and the instrumentation involved in characterizing the gold nanoparticles (Au-NPs), the opportunities for the use of gold nanoparticles (Au-NPs) in cancer treatment and future possible research in the use of nanotechnology in the fight against cancer. Overall, plant-mediated synthesis of gold nanoparticles holds promise as a safe and effective method for cancer treatment.Item Imidazolium-Based Sulfonating Agent to Control the Degree of Sulfonation of Aromatic Polymers and Enable Plastics-to-Electronics Upgrading(JACS Au, 2024-07-03) Lo, Chun-Yuan; Koutsoukos, Kelsey P.; Nguyen, Dan My; Wu, Yuhang; Angel Trujillo, David Alejandro; Miller, Tabitha; Shrestha, Tulaja; Mackey, Ethan; Damani, Vidhika S.; Kanbur, Uddhav; Opila, Robert; Martin, David C.; Kaphan, David; Kayser, Laure V.The accumulation of plastic waste in the environment is a growing environmental, economic, and societal challenge. Plastic upgrading, the conversion of low-value polymers to high-value materials, could address this challenge. Among upgrading strategies, the sulfonation of aromatic polymers is a powerful approach to access high-value materials for a range of applications, such as ion-exchange resins and membranes, electronic materials, and pharmaceuticals. While many sulfonation methods have been reported, achieving high degrees of sulfonation while minimizing side reactions that lead to defects in the polymer chains remains challenging. Additionally, sulfonating agents are most often used in large excess, which prevents precise control over the degree of sulfonation of aromatic polymers and their functionality. Herein, we address these challenges using 1,3-disulfonic acid imidazolium chloride ([Dsim]Cl), a sulfonic acid-based ionic liquid, to sulfonate aromatic polymers and upgrade plastic waste to electronic materials. We show that stoichiometric [Dsim]Cl can effectively sulfonate model polystyrene up to 92% in high yields, with minimal defects and high regioselectivity for the para position. Owing to its high reactivity, the use of substoichiometric [Dsim]Cl uniquely allows for precise control over the degree of sulfonation of polystyrene. This approach is also applicable to a wide range of aromatic polymers, including waste plastic. To prove the utility of our approach, samples of poly(styrene sulfonate) (PSS), obtained from either partially sulfonated polystyrene or expanded polystyrene waste, are used as scaffolds for poly(3,4-ethylenedioxythiophene) (PEDOT) to form the ubiquitous conductive material PEDOT:PSS. PEDOT:PSS from plastic waste is subsequently integrated into organic electrochemical transistors (OECTs) or as a hole transport layer (HTL) in a hybrid solar cell and shows the same performance as commercial PEDOT:PSS. This imidazolium-mediated approach to precisely sulfonating aromatic polymers provides a pathway toward upgrading postconsumer plastic waste to high-value electronic materials.Item Applicability of the Zintl Concept to Understanding the Crystal Chemistry of Lithium-Rich Germanides and Stannides(Inorganic Chemistry, 2024-05-29) Ghosh, Kowsik; Rahman, Salina; Ovchinnikov, Alexander; Bobev, SvilenWith this contribution, we take a new, critical look at the structures of the binary phases Li5Ge2 and Li5Sn2. Both are isostructural (centrosymmetric space group R3̅m, no. 166), and in their structures, all germanium (tin) atoms are dimerized. Application of the valence rules will require the allocation of six additional valence electrons per [Ge2] or [Sn2] unit considering single covalent bonds, akin to those in the dihalogen molecules. Alternatively, four additional valence electrons per [Ge2] or [Sn2] anion will be needed if homoatomic double bonds exist, in an analogy with dioxygen. Therefore, five lithium atoms in one formula unit cannot provide the exact number of electrons, leaving open questions as to what is the nature of the chemical bonding within these moieties. Additionally, by means of single-crystal X-ray diffraction, synchrotron powder X-ray diffraction, and neutron powder diffraction, we established that the Li and Sn atoms in Li5Sn2 are partially disordered, i.e., the actual chemical formula of this compound is Li5–xSn2+x (0 < x < 0.1). The convoluted atomic bonding in the case where tin atoms partially displace lithium atoms results in the formation of larger covalently bonded fragments. Our first-principle calculations suggest that such disorder leads to electron doping. Contrary to that, both experimental and computational findings indicate that in the Li5Ge2 structure, the [Ge2] dimers are slightly oxidized, i.e., hole-doped, as a result of approximately 30% vacancies on a Li site, i.e., the actual chemical formula of this compound is Li5–xGe2 (x ≈ 0.3).Item Development of an efficient, effective, and economical technology for proteome analysis(Cell Reports: Methods, 2024-06-11) Martin, Katherine R.; Le, Ha T.; Abdelgawad, Ahmed; Yang, Canyuan; Lu, Guotao; Keffer, Jessica L.; Zhang, Xiaohui; Zhuang, Zhihao; Asare-Okai, Papa Nii; Chan, Clara S.; Batish, Mona; Yu, YanbaoHighlights • Rapid, robust, and cost-effective alternative to proteomics sample preparation • Versatile filter devices can meet a wide range of proteomics analysis needs • On-filter in-cell digestion facilitates low-input proteomics • Ready-to-go E3 and E4 filter devices are available Motivation Conventional proteomics sample processing methods often have high technical barriers to broad biomedical scientists, leading to difficulties for quick adoption and standardization. Existing protocols are also typically associated with costly reagents and accessories, making them less feasible for resource-limited settings as well as for clinical proteomics and/or core facilities where large numbers of samples are usually processed. Thus, there is a strong unmet need for an easy-to-use, reliable, and low-cost approach for general proteomics sample preparation. Summary We present an efficient, effective, and economical approach, named E3technology, for proteomics sample preparation. By immobilizing silica microparticles into the polytetrafluoroethylene matrix, we develop a robust membrane medium, which could serve as a reliable platform to generate proteomics-friendly samples in a rapid and low-cost fashion. We benchmark its performance using different formats and demonstrate them with a variety of sample types of varied complexity, quantity, and volume. Our data suggest that E3technology provides proteome-wide identification and quantitation performance equivalent or superior to many existing methods. We further propose an enhanced single-vessel approach, named E4technology, which performs on-filter in-cell digestion with minimal sample loss and high sensitivity, enabling low-input and low-cell proteomics. Lastly, we utilized the above technologies to investigate RNA-binding proteins and profile the intact bacterial cell proteome. Graphical abstract available at: https://doi.org/10.1016/j.crmeth.2024.100796Item Fibroblast expression of transmembrane protein smoothened governs microenvironment characteristics after acute kidney injury(The Journal of Clinical Investigation, 2024-07-01) Gui, Yuan; Fu, Haiyan; Palanza, Zachary; Tao, Jianling; Lin, Yi-Han; Min, Wenjian; Qiao, Yi; Bonin, Christopher; Hargis, Geneva; Wang, Yuanyuan; Yang, Peng; Kreutzer, Donald L.; Wang, Yanlin; Liu, Yansheng; Yu, Yanbao; Liu, Youhua; Zhou, DongThe smoothened (Smo) receptor facilitates hedgehog signaling between kidney fibroblasts and tubules during acute kidney injury (AKI). Tubule-derived hedgehog is protective in AKI, but the role of fibroblast-selective Smo is unclear. Here, we report that Smo-specific ablation in fibroblasts reduced tubular cell apoptosis and inflammation, enhanced perivascular mesenchymal cell activities, and preserved kidney function after AKI. Global proteomics of these kidneys identified extracellular matrix proteins, and nidogen-1 glycoprotein in particular, as key response markers to AKI. Intriguingly, Smo was bound to nidogen-1 in cells, suggesting that loss of Smo could affect nidogen-1 accessibility. Phosphoproteomics revealed that the ‘AKI protector’ Wnt signaling pathway was activated in these kidneys. Mechanistically, nidogen-1 interacted with integrin β1 to induce Wnt in tubules to mitigate AKI. Altogether, our results support that fibroblast-selective Smo dictates AKI fate through cell-matrix interactions, including nidogen-1, and offers a robust resource and path to further dissect AKI pathogenesis. Graphical Abstract available at: https://doi.org/10.1172/JCI165836Item Total and Class-Specific Determination of Fluorinated Compounds in Consumer and Food Packaging Samples Using Fluorine-19 Solid-State Nuclear Magnetic Resonance Spectroscopy(Analytical Chemistry, 2024-05-28) Thijs, Mike; Laletas, Ernest; Quinn, Caitlin M.; Raguraman, Subbu V.; Carr, Bryan; Bierganns, PatricHamburger wrapping paper, coated with water-based barrier coatings, used in the food packaging industry was studied by using the total organic fluorine (TOF) method based on combustion ion chromatography and fluorine-19 solid-state nuclear magnetic resonance (19F ss-NMR) spectroscopy. Although the TOF method is a fast and affordable method used to screen for per- and polyfluoroalkyl substances (PFAS), the amount of fluorine it measures is heavily dependent on the extraction step and, therefore could lead to inaccurate results. Fluorine-19 ss-NMR spectroscopy can differentiate between organic and inorganic fluorinated sources, eliminating the need for sample clean up. To illustrate this, the 19F ss-NMR spectra of clean coated paper samples that contained naturally occurring F- ions from the talc raw material and spiked samples containing perfluorooctanoic acid were compared. A range of experimental conditions was explored to improve sensitivity for low PFAS concentrations (in the order of 10–20 mg/kg). Despite the disadvantages of ss-NMR spectroscopy, such as the low limit of detection and resolution, the results demonstrate it can be a viable tool to directly detect PFAS moieties in consumer and food packaging. Therefore, 19F solid-state NMR spectroscopy challenges and complements current methods, which only provide indirect evidence of the presence of PFAS.Item Unraveling the molecular and growth mechanism of colloidal black In2O3−x(Nanoscale, 2024-04-19) Armstrong, Cameron; Otero, Kayla; Hernandez-Pagan, Emil A.Black metal oxides with varying concentrations of O-vacancies display enhanced optical and catalytic properties. However, direct solution syntheses of this class of materials have been limited despite being highly advantageous given the different synthetic handles that can be leveraged towards control of the targeted material. Herein, we present an alternate colloidal synthesis of black In2O3−x nanoparticles from the simple reaction between In(acac)3 and oleyl alcohol. Growth studies by PXRD, TEM, and STEM-EDS coupled to mechanistic insights from 1H, 13C NMR revealed the particles form via two paths, one of which involves In0. We also show that variations in the synthesis atmosphere, ligand environment, and indium precursor can inhibit formation of the black In2O3−x. The optical spectrum for the black nanoparticles displayed a significant redshift when compared to pristine In2O3, consistent with the presence of O-vacancies. Raman spectra and surface analysis also supported the presence of surface oxygen vacancies in the as-synthesized black In2O3−x.Item Interfacial electron transfer of perylenes: Influence of the anchor binding mode(The Journal of Chemical Physics, 2024-01-21) Yan, Han; Harmer, Ryan; Zafar, Binish; Galoppini, Elena; Gundlach, LarsInterfacial electron transfer (IET) through saturated single-linker and dual-linker groups from a perylene chromophore into nanostructured TiO2 films was studied by ultrafast spectroscopy. Perylene chromophores with one and two propanoic acid linker groups in the peri and ortho positions were investigated. In comparison to previously studied perylenes bound via unsaturated acrylic acid linkers, the chromophores with saturated linkers showed bi-exponential IET dynamics. Two distinct transfer times were observed that indicate the presence of two concurrent binding modes. A comparison between ortho- and peri-substituted sensitizers resulted in slower IET dynamics and weaker electronic coupling for ortho substitution. Finally, IET from sensitizers with saturated linker groups is neither promoted nor hindered by a second linker group. This indicates that only one of the two linkers binds covalently to the surface. This study reveals the importance of the anchor-binding mode and design considerations of the linker for regulating IET.