Scholarly Work - Chemistry & Biochemistry

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    Synthesis and characterization of aluminum-doped graphitic carbon
    (Springer Nature, 2024-02) Gordon, Isabelle P.; Suenram, Grace; McGlamery, Devin; Stadie, Nicholas P.
    Heteroatom doping of graphitic carbon is of high interest for tuning its physicochemical properties. Aluminum is commonly reported as a high-interest dopant, but few synthetic strategies have been reported owing to the low equilibrium solubility of Al within graphite. Herein we report several strategies to achieve metastable aluminum-substituted turbostratic graphitic carbon materials with aluminum contents up to ~ 0.5 at%, via co-pyrolysis of two molecular precursors between 800 and 1100°C. The resulting materials exhibit turbostratic graphitic structure and a previously unreported aluminum environment detectable by X-ray absorption spectroscopy (XAS), a likely signature of trigonal planar or puckered AlC3-type sites.
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    Metabolomic profiles of cartilage and bone reflect tissue type, radiography-confirmed osteoarthritis, and spatial location within the joint
    (Elsevier BV, 2024-02) Welhaven, Hope D.; Viles, Ethan; Starke, Jenna; Wallace, Cameron; Bothner, Brian; June, Ronald K.; Hahn, Alyssa K.
    Osteoarthritis is the most common chronic joint disease, characterized by the abnormal remodeling of joint tissues including articular cartilage and subchondral bone. However, there are currently no therapeutic drug targets to slow the progression of disease because disease pathogenesis is largely unknown. Thus, the goals of this study were to identify metabolic differences between articular cartilage and subchondral bone, compare the metabolic shifts in osteoarthritic grade III and IV tissues, and spatially map metabolic shifts across regions of osteoarthritic hip joints. Articular cartilage and subchondral bone from 9 human femoral heads were obtained after total joint arthroplasty, homogenized and metabolites were extracted for liquid chromatography-mass spectrometry analysis. Metabolomic profiling revealed that distinct metabolic endotypes exist between osteoarthritic tissues, late-stage grades, and regions of the diseased joint. The pathways that contributed the most to these differences between tissues were associated with lipid and amino acid metabolism. Differences between grades were associated with nucleotide, lipid, and sugar metabolism. Specific metabolic pathways such as glycosaminoglycan degradation and amino acid metabolism, were spatially constrained to more superior regions of the femoral head. These results suggest that radiography-confirmed grades III and IV osteoarthritis are associated with distinct global metabolic and that metabolic shifts are not uniform across the joint. The results of this study enhance our understanding of osteoarthritis pathogenesis and may lead to potential drug targets to slow, halt, or reverse tissue damage in late stages of osteoarthritis.
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    GaMF1.39’s antibiotic efficacy and its enhanced antitubercular activity in combination with clofazimine, Telacebec, ND-011992, or TBAJ-876
    (2023-11) Ragunathan, Priya; Shuyi Ng, Pearly; Singh, Samsher; Poh, Wee Han; Litty, Dennis; Kalia, Nitin Pal; Larsson, Simon; Harikishore, Amaravadhi; Rice, Scott A.; Ingham, Philip W.; Müller, Volker; Moraski, Garrett; Miller, Marvin J.; Dick, Thomas; Pethe, Kevin; Grüber, Gerhard
    The Mycobacterium tuberculosis (Mtb) F-ATP synthase generates most of the biological energy currency ATP. Previously, we identified the mycobacterium-specific loop of the F-ATP synthase subunit γ as a new anti-tuberculosis target and discovered the novel diaminopyrimidine GaMF1, whose potency was improved by structure-activity relationship studies leading to the analog GaMF1.39. Here, we report that GaMF1.39 depletes cellular ATP formation by targeting the mycobacterial F-ATP synthase without affecting proton coupling or oxygen consumption. The antimycobacterial compound is bactericidal and potent against Mtb in macrophages without inducing phenotypic changes in biofilm formation, planktonic bacteria, or being toxic to zebrafish larvae. Combining GaMF1.39 with the NADH dehydrogenase inhibitor clofazimine, the cyt-bcc:aa3 inhibitor Telacebec, or the F-ATP synthase inhibitor TBAJ-876 showed enhanced whole ATP synthesis inhibition and anti-tuberculosis activity. These results suggest that GaMF1.39 may add value to a compound combination targeting oxidative phosphorylation for tuberculosis treatment.
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    Primary Human M2 Macrophage Subtypes Are Distinguishable by Aqueous Metabolite Profiles
    (MDPI, 2024-02) Fuchs, Amanda L.; Costello, Stephanann M.; Schiller, Sage M.; Tripet, Brian P.; Copié, Valérie
    The complexity of macrophage (MΦ) plasticity and polarization states, which include classically activated pro-inflammatory (M1) and alternatively activated anti-inflammatory (M2) MΦ phenotypes, is becoming increasingly appreciated. Within the M2 MΦ polarization state, M2a, M2b, M2c, and M2d MΦ subcategories have been defined based on their expression of specific cell surface receptors, secreted cytokines, and specialized immune effector functions. The importance of immunometabolic networks in mediating the function and regulation of MΦ immune responses is also being increasingly recognized, although the exact mechanisms and extent of metabolic modulation of MΦ subtype phenotypes and functions remain incompletely understood. In this study, proton (1H) nuclear magnetic resonance (NMR) metabolomics was employed to determine the polar metabolomes of M2 MΦ subtypes and to investigate the relationship between aqueous metabolite profiles and M2 MΦ functional phenotypes. Results from this study demonstrate that M2a MΦs are most distinct from M2b, M2c, and M2d MΦ subtypes, and that M2b MΦs display several metabolic traits associated with an M1-like MΦ phenotype. The significance of metabolome differences for metabolites implicated in glycolysis, the tricarboxylic acid (TCA) cycle, phospholipid metabolism, and creatine–phosphocreatine cycling is discussed. Altogether, this study provides biochemical insights into the role of metabolism in mediating the specialized effector functions of distinct M2 MΦ subtypes and supports the concept of a continuum of macrophage activation states rather than two well-separated and functionally distinct M1/M2 MΦ classes, as originally proposed within a classical M1/M2 MΦ framework.
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    Quantitative measurements of reactive oxygen species partitioning in electron transfer flavoenzyme magnetic field sensing
    (Frontiers Media SA, 2024-02) Austvold, Chase K.; Keable, Stephen M.; Procopio, Maria; Usselman, Robert J.
    Biological magnetic field sensing that gives rise to physiological responses is of considerable importance in quantum biology. The radical pair mechanism (RPM) is a fundamental quantum process that can explain some of the observed biological magnetic effects. In magnetically sensitive radical pair (RP) reactions, coherent spin dynamics between singlet and triplet pairs are modulated by weak magnetic fields. The resulting singlet and triplet reaction products lead to distinct biological signaling channels and cellular outcomes. A prevalent RP in biology is between flavin semiquinone and superoxide (O2•−) in the biological activation of molecular oxygen. This RP can result in a partitioning of reactive oxygen species (ROS) products to form either O2•− or hydrogen peroxide (H2O2). Here, we examine magnetic sensing of recombinant human electron transfer flavoenzyme (ETF) reoxidation by selectively measuring O2•− and H2O2 product distributions. ROS partitioning was observed between two static magnetic fields at 20 nT and 50 μT, with a 13% decrease in H2O2 singlet products and a 10% increase in O2•− triplet products relative to 50 µT. RPM product yields were calculated for a realistic flavin/superoxide RP across the range of static magnetic fields, in agreement with experimental results. For a triplet born RP, the RPM also predicts about three times more O2•− than H2O2, with experimental results exhibiting about four time more O2•− produced by ETF. The method presented here illustrates the potential of a novel magnetic flavoprotein biological sensor that is directly linked to mitochondria bioenergetics and can be used as a target to study cell physiology.
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    Hydrogen Adsorption in Ultramicroporous Metal–Organic Frameworks Featuring Silent Open Metal Sites
    (American Chemical Society, 2023-11) Chiu, Nan Chieh; Compton, Dalton; Gładysiak, Andrzej; Simrod, Scott; Khivantsev, Konstantin; Woo, Tom K.; Stadie, Nicholas P.; Stylianou, Kyriakos C.
    In this study, we utilized an ultramicroporous metal–organic framework (MOF) named [Ni3(pzdc)2(ade)2(H2O)4]·2.18H2O (where H3pzdc represents pyrazole-3,5-dicarboxylic acid and ade represents adenine) for hydrogen (H2) adsorption. Upon activation, [Ni3(pzdc)2(ade)2] was obtained, and in situ carbon monoxide loading by transmission infrared spectroscopy revealed the generation of open Ni(II) sites. The MOF displayed a Brunauer–Emmett–Teller (BET) surface area of 160 m2/g and a pore size of 0.67 nm. Hydrogen adsorption measurements conducted on this MOF at 77 K showed a steep increase in uptake (up to 1.93 mmol/g at 0.04 bar) at low pressure, reaching a H2 uptake saturation at 2.11 mmol/g at ∼0.15 bar. The affinity of this MOF for H2 was determined to be 9.7 ± 1.0 kJ/mol. In situ H2 loading experiments supported by molecular simulations confirmed that H2 does not bind to the open Ni(II) sites of [Ni3(pzdc)2(ade)2], and the high affinity of the MOF for H2 is attributed to the interplay of pore size, shape, and functionality.
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    Prominent Structural Dependence of Quantum Capacitance Unraveled by Nitrogen‐Doped Graphene Mesosponge
    (Wiley, 2023-12) Tang, Rui; Aziz, Alex; Yu, Wei; Pan, Zheng‐Ze; Nishikawa, Ginga; Yoshii, Takeharu; Nomura, Keita; Taylor, Erin E.; Stadie, Nicholas P.; Inoue, Kazutoshi; Kotani, Motoko; Kyotani, Takashi; Nishihara, Hirotomo
    Porous carbons are important electrode materials for supercapacitors. One of the challenges associated with supercapacitors is improving their energy density without relying on pseudocapacitance, which is based on fast redox reactions that often shorten device lifetimes. A possible solution involves achieving high total capacitance (Ctot), which comprises Helmholtz capacitance (CH) and possibly quantum capacitance (CQ), in high-surface carbon materials comprising minimally stacked graphene walls. In this work, a templating method is used to synthesize 3D mesoporous graphenes with largely identical pore structures (≈2100 m2 g−1 with an average pore size of ≈7 nm) but different concentrations of oxygen-containing functional groups (0.3–6.7 wt.%) and nitrogen dopants (0.1–4.5 wt.%). Thus, the impact of the heteroatom functionalities on Ctot is systematically investigated in an organic electrolyte excluding the effect of pore structures. It is found that heteroatom functionalities determine Ctot, resulting in the cyclic voltammetry curves being rectangular or butterfly-shaped. The nitrogen functionalities are found to significantly enhance Ctot owing to increased CQ.
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    Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea
    (Public Library of Science, 2023-09) Murali, Ranjani; Yu, Hang; Speth, Daan R.; Wu, Fabai; Metcalfe, Kyle S.; Crémière, Antoine; Laso-Pèrez, Rafael; Malmstrom, Rex R.; Goudeau, Danielle; Woyke, Tanja; Hatzenpichler, Roland; Chadwick, Grayson L.; Connon, Stephanie A.; Orphan, Victoria J.
    Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.
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    Fe protein docking transduces conformational changes to MoFe nitrogenase active site in a nucleotide-dependent manner
    (Springer Science and Business Media LLC, 2023-11) Tokmina-Lukaszewska, Monika; Huang, Qi; Berry, Luke; Kallas, Hayden; Peters, John W.; Seefeldt, Lance C.; Raugei, Simone; Bothner, Brian
    The reduction of dinitrogen to ammonia catalyzed by nitrogenase involves a complex series of events, including ATP hydrolysis, electron transfer, and activation of metal clusters for N2 reduction. Early evidence shows that an essential part of the mechanism involves transducing information between the nitrogenase component proteins through conformational dynamics. Here, millisecond time-resolved hydrogen-deuterium exchange mass spectrometry was used to unravel peptide-level protein motion on the time scale of catalysis of Mo-dependent nitrogenase from Azotobacter vinelandii. Normal mode analysis calculations complemented this data, providing insights into the specific signal transduction pathways that relay information across protein interfaces at distances spanning 100 Å. Together, these results show that conformational changes induced by protein docking are rapidly transduced to the active site, suggesting a specific mechanism for activating the metal cofactor in the enzyme active site.
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    Soluble CD4 and low molecular weight CD4-mimetic compounds sensitize cells to be killed by anti-HIV cytotoxic immunoconjugates
    (American Society for Microbiology, 2023-09) Pincus, Seth H.; Stackhouse, Megan; Watt, Connie; Ober, Kelli; Cole, Frances M.; Chen, Hung-Ching; Smith III, Amos B.; Peters, Tami
    The reservoir of HIV-infected cells that persist in the face of effective anti-retroviral therapy (ART) is the barrier to curing HIV infection. These long-lived CD4+ cells carry a functional provirus that can become activated upon immune stimulation. When ART is stopped, this leads to a rapid rebound in viremia. A variety of approaches are proposed to eliminate these cells, many dependent upon the expression of virus proteins. We are examining the use of cytotoxic immunoconjugates targeting the HIV envelope protein (Env) as a method to eradicate cells producing virus and have demonstrated that soluble CD4 enhances the cytotoxic effect of gp41-targeted immunoconjugates. Mechanisms include increased antigen exposure and greater internalization of the immunoconjugate. Here we have tested different protein forms of CD4 and the small molecule CD4-mimetic BNM-III-170 for their effects on cells expressing cell-surface Env. Effects studied include sensitization to immunoconjugate killing, cell surface antigen expression, viability, and virus secretion. The CD4 proteins and BNM-III-170 produced comparable effects in these Env-expressing cell lines, each sensitizing cells to cytotoxicity by anti-gp41 immunoconjugates. The results provide further evidence that low molecular weight CD4 mimetics produce biologic effects similar to those caused by soluble CD4 itself and suggest additional therapeutic uses for these molecules.
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    Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment
    (Frontiers Media SA, 2023-09) Frates, Erin S.; Spietz, Rachel L.; Silverstein, Michael R.; Girguis, Peter; Hatzenpichler, Roland; Marlow, Jeffrey J.
    Salt marshes are dynamic, highly productive ecosystems positioned at the interface between terrestrial and marine systems. They are exposed to large quantities of both natural and anthropogenic carbon input, and their diverse sediment-hosted microbial communities play key roles in carbon cycling and remineralization. To better understand the effects of natural and anthropogenic carbon on sediment microbial ecology, several sediment cores were collected from Little Sippewissett Salt Marsh (LSSM) on Cape Cod, MA, USA and incubated with either Spartina alterniflora cordgrass or diesel fuel. Resulting shifts in microbial diversity and activity were assessed via bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Both Spartina and diesel amendments resulted in initial decreases of microbial diversity as well as clear, community-wide shifts in metabolic activity. Multi-stage degradative frameworks shaped by fermentation were inferred based on anabolically active lineages. In particular, the metabolically versatile Marinifilaceae were prominent under both treatments, as were the sulfate-reducing Desulfovibrionaceae, which may be attributable to their ability to utilize diverse forms of carbon under nutrient limited conditions. By identifying lineages most directly involved in the early stages of carbon processing, we offer potential targets for indicator species to assess ecosystem health and highlight key players for selective promotion of bioremediation or carbon sequestration pathways.
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    Yeast Rad52 is a homodecamer and possesses BRCA2-like bipartite Rad51 binding modes
    (Springer Science and Business Media LLC, 2023-10) Deveryshetty, Jaigeeth; Chadda, Rahul; Mattice, Jenna R.; Karunakaran, Simrithaa; Rau, Michael J.; Basore, Katherine; Pokhrel, Nilisha; Englander, Noah; Fitzpatrick, James A. J.; Bothner, Brian; Antony, Edwin
    Homologous recombination (HR) is an essential double-stranded DNA break repair pathway. In HR, Rad52 facilitates the formation of Rad51 nucleoprotein filaments on RPA-coated ssDNA. Here, we decipher how Rad52 functions using single-particle cryo-electron microscopy and biophysical approaches. We report that Rad52 is a homodecameric ring and each subunit possesses an ordered N-terminal and disordered C-terminal half. An intrinsic structural asymmetry is observed where a few of the C-terminal halves interact with the ordered ring. We describe two conserved charged patches in the C-terminal half that harbor Rad51 and RPA interacting motifs. Interactions between these patches regulate ssDNA binding. Surprisingly, Rad51 interacts with Rad52 at two different bindings sites: one within the positive patch in the disordered C-terminus and the other in the ordered ring. We propose that these features drive Rad51 nucleation onto a single position on the DNA to promote formation of uniform pre-synaptic Rad51 filaments in HR.
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    Viruses of the Turriviridae: an emerging model system for studying archaeal virus-host interactions
    (Frontiers Media SA, 2023-09) Overton, Michael S.; Manuel, Robert D.; Lawrence, C. Martin; Snyder, Jamie C.
    Viruses have played a central role in the evolution and ecology of cellular life since it first arose. Investigations into viral molecular biology and ecological dynamics have propelled abundant progress in our understanding of living systems, including genetic inheritance, cellular signaling and trafficking, and organismal development. As well, the discovery of viral lineages that infect members of all three domains suggest that these lineages originated at the earliest stages of biological evolution. Research into these viruses is helping to elucidate the conditions under which life arose, and the dynamics that directed its early development. Archaeal viruses have only recently become a subject of intense study, but investigations have already produced intriguing and exciting results. STIV was originally discovered in Yellowstone National Park and has been the focus of concentrated research. Through this research, a viral genetic system was created, a novel lysis mechanism was discovered, and the interaction of the virus with cellular ESCRT machinery was revealed. This review will summarize the discoveries within this group of viruses and will also discuss future work.
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    Metabolic Phenotypes Reflect Patient Sex and Injury Status: A Cross-Sectional Analysis of Human Synovial Fluid
    (Elsevier BV, 2023-09) Welhaven, Hope D.; Welfley, Avery H.; Pershad, Prayag; Satalich, James; O'Connell, Robert; Bothner, Brian; Vap, Alexander R.; June, Ronald K.
    Objective. Osteoarthritis is a heterogeneous disease. The objective was to compare differences in underlying cellular mechanisms and endogenous repair pathways between synovial fluid (SF) from male and female participants with different injuries to improve the current understanding of the pathophysiology of downstream post-traumatic osteoarthritis (PTOA). Design. SF from n = 33 knee arthroscopy patients between 18 and 70 years with no prior knee injuries was obtained pre-procedure and injury pathology assigned post-procedure. SF was extracted and analyzed via liquid chromatography-mass spectrometry metabolomic profiling to examine differences in metabolism between injury pathologies (ligament, meniscal, and combined ligament and meniscal) and patient sex. Samples were pooled and underwent secondary fragmentation to identify metabolites. Results. Different knee injuries uniquely altered SF metabolites and downstream pathways including amino acid, lipid, and inflammatory-associated metabolic pathways. Notably, sexual dimorphic metabolic phenotypes were examined between males and females and within injury pathology. Cervonyl carnitine and other identified metabolites differed in concentrations between sexes. Conclusions. These results suggest that different injuries and patient sex are associated with distinct metabolic phenotypes. Considering these phenotypic associations, a greater understanding of metabolic mechanisms associated with specific injuries, sex, and PTOA development may yield data regarding how endogenous repair pathways differ between male and female injury types. Ongoing metabolomic analysis of SF in injured male and female patients can be performed to monitor PTOA development and progression.
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    Anomalous Temperature and Polarization Dependences of Photoluminescence of Metal‐Organic Chemical Vapor Deposition‐Grown GeSe2
    (Wiley, 2023-08) Lee, Eunji; Dhakal, Krishna Prasad; Song, Hwayoung; Choi, Heenang; Chung, Taek‐Mo; Oh, Saeyoung; Young Jeong, Hu; Marmolejo‐Tejada, Juan M.; Mosquera, Martín A.; Loc Duong, Dinh; Kang, Kibum; Kim, Jeongyong
    Germanium diselenide (GeSe2) is a 2D semiconductor with air stability, a wide bandgap, and anisotropic optical properties. The absorption and photoluminescence (PL) of single-crystalline 2D GeSe2 grown by metal-organic chemical vapor deposition and their dependence on temperature and polarization are studied. The PL spectra exhibit peaks at 2.5 eV (peak A) and 1.8 eV (peak B); peak A displays a strongly polarized emission along the short axis of the crystal, and peak B displays a weak polarization perpendicular to that of peak A. With increasing temperature, peak B shows anomalous behaviors, i.e., an increasing PL energy and intensity. The excitation energy-dependent PL, time-resolved PL, and density functional theory calculations suggest that peak A corresponds to the band-edge transition, whereas peak B originates from the inter-band mid-gap states caused by selenium vacancies passivated by oxygen atoms. The comprehensive study on the PL of single-crystalline GeSe2 sheds light on the origins of light emission in terms of the band structure of anisotropic GeSe2, making it beneficial for the corresponding optoelectronic applications.
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    Structural insights into redox signal transduction mechanisms in the control of nitrogen fixation by the NifLA system
    (Proceedings of the National Academy of Sciences, 2023-07) Boyer, Nathaniel R.; Tokmina-Lukaszewska, Monika; Bueno Batista, Marcelo; Mus, Florence; Dixon, Ray; Bothner, Brian; Peters, John W.
    NifL is a conformationally dynamic flavoprotein responsible for regulating the activity of the σ54-dependent activator NifA to control the transcription of nitrogen fixation (nif) genes in response to intracellular oxygen, cellular energy, or nitrogen availability. The NifL-NifA two-component system is the master regulatory system for nitrogen fixation. NifL serves as a sensory protein, undergoing signal-dependent conformational changes that modulate its interaction with NifA, forming the NifL–NifA complex, which inhibits NifA activity in conditions unsuitable for nitrogen fixation. While NifL-NifA regulation is well understood, these conformationally flexible proteins have eluded previous attempts at structure determination. In work described here, we advance a structural model of the NifL dimer supported by a combination of scattering techniques and mass spectrometry (MS)-coupled structural analyses that report on the average structure in solution. Using a combination of small angle X-ray scattering-derived electron density maps and MS-coupled surface labeling, we investigate the conformational dynamics responsible for NifL oxygen and energy responses. Our results reveal conformational differences in the structure of NifL under reduced and oxidized conditions that provide the basis for a model for modulating NifLA complex formation in the regulation of nitrogen fixation in response to oxygen in the model diazotroph, Azotobacter vinelandii.
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    Base-Catalyzed Phenol-Mannich Condensation of Preformed Cesium Iminodiacetate. The Direct Synthesis of Calcein Blue AM and Related Acyloxymethyl Esters
    (American Chemical Society, 2023-08) Mikesell, Logan D.; Livinghouse, Tom
    A rapid and highly practical one-flask procedure for the positionally selective preparation of (acyloxy)methyl N-(2-hydroxybenzyl)iminodiacetate and related diesters from iminodiacetic acid and phenols is described. The key to this multicomponent phenol-Mannich condensation resides in the use of cesium iminodiacetate as the reaction partner. This protocol has been applied in an unusually direct synthesis of the intracellular fluorescent dye Calcein blue AM, for which scant experimental and spectroscopic data are presently available.
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    Hydrogen-Type Binding Sites in Carbonaceous Electrodes for Rapid Lithium Insertion
    (American Chemical Society, 2023-08) McGlamery, Devin; McDaniel, Charles; Xu, Wei; Stadie, Nicholas P.
    Direct pyrolysis of coronene at 800 °C produces low-surface-area, nanocrystalline graphitic carbon containing a uniquely high content of a class of lithium binding sites referred to herein as “hydrogen-type” sites. Correspondingly, this material exhibits a distinct redox couple under electrochemical lithiation that is characterized as intermediate-strength, capacitive lithium binding, centered at ∼0.5 V vs Li/Li+. Lithiation of hydrogen-type sites is reversible and electrochemically distinct from capacitive lithium adsorption and from intercalation-type binding between graphitic layers. Hydrogen-type site lithiation can be fully retained even up to ultrafast current rates (e.g., 15 A g–1, ∼40 C) where intercalation is severely hampered by ion desolvation kinetics; at the same time, the bulk nature of these sites does not require a large surface area, and only minimal electrolyte decomposition occurs during the first charge/discharge cycle, making coronene-derived carbon an exceptional candidate for high-energy-density battery applications.
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    Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea
    (Public Library of Science, 2022-01) Chadwick, Grayson L.; Skennerton, Connor T.; Laso-Pérez, Rafael; Leu, Andy O.; Speth, Daan R.; Yu, Hang; Morgan-Lang, Connor; Hatzenpichler, Roland; Goudeau, Danielle; Malmstrom, Rex; Brazelton, William J.; Woyke, Tanja; Hallam, Steven J.; Tyson, Gene W.; Wegener, Gunter; Boetius, Antje; Orphan, Victoria J.
    The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.
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    An Aurora B-RPA signaling axis secures chromosome segregation fidelity
    (Springer Science and Business Media LLC, 2023-05) Roshan, Poonam; Kuppa, Sahiti; Mattice, Jenna R.; Kaushik, Vikas; Chadda, Rahul; Pokhrel, Nilisha; Tumala, Brunda R.; Biswas, Aparna; Bothner, Brian; Antony, Edwin; Origanti, Sofia
    Errors in chromosome segregation underlie genomic instability associated with cancers. Resolution of replication and recombination intermediates and protection of vulnerable single-stranded DNA (ssDNA) intermediates during mitotic progression requires the ssDNA binding protein Replication Protein A (RPA). However, the mechanisms that regulate RPA specifically during unperturbed mitotic progression are poorly resolved. RPA is a heterotrimer composed of RPA70, RPA32 and RPA14 subunits and is predominantly regulated through hyperphosphorylation of RPA32 in response to DNA damage. Here, we have uncovered a mitosis-specific regulation of RPA by Aurora B kinase. Aurora B phosphorylates Ser-384 in the DNA binding domain B of the large RPA70 subunit and highlights a mode of regulation distinct from RPA32. Disruption of Ser-384 phosphorylation in RPA70 leads to defects in chromosome segregation with loss of viability and a feedback modulation of Aurora B activity. Phosphorylation at Ser-384 remodels the protein interaction domains of RPA. Furthermore, phosphorylation impairs RPA binding to DSS1 that likely suppresses homologous recombination during mitosis by preventing recruitment of DSS1-BRCA2 to exposed ssDNA. We showcase a critical Aurora B-RPA signaling axis in mitosis that is essential for maintaining genomic integrity.
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