1
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Sánchez M, Baltrusaitis J, Vasquez-Ríos MG, Campillo-Alvarado G, MacGillivray LR, Höpfl H. Nanoscale Dodecahedral and Fullerene-Type Organoboroxine and Borazine Cages from Planar Building Units. Nano Lett 2024; 24:5824-5830. [PMID: 38712765 PMCID: PMC11100284 DOI: 10.1021/acs.nanolett.4c01024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/08/2024]
Abstract
Boroxine- and borazine-cage analogs to C20, C60, and C70 were calculated and compared in terms of structure, strain indicators, and physical properties relevant to nanoscale applications. The results show C60 and C70 type cages are less strained than the smaller congener, primarily due to minimized bending in the B-arylene-B segments. The smallest cage calculated has a diameter of 2.4 nm, which increases up to 4.9 nm by either variation of the polyhedron (C20 < C60 < C70-type cage) or organic spacer elongation between boron centers. All calculated cages are porous (apertures ranging from 0.6 to 1.9 nm). Molecular electrostatic potential and Hirshfeld population analysis revealed both nucleophilic and electrophilic sites in the interior and exterior cage surfaces. HOMO-LUMO gaps range from 3.98 to 4.89 eV and 5.10-5.18 eV for the boroxine- and borazine-cages, respectively. Our findings provide insights into the design and properties of highly porous boroxine and borazine cages for nanoscience.
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Affiliation(s)
- Mario Sánchez
- Centro
de Investigación en Materiales Avanzados, S.C., Alianza Norte
202, Parque de Investigación en Innovación
Tecnológica (PIIT), Carretera Monterrey-Aeropuerto Km 11, Apodaca 66628, Nuevo León, México
| | - Jonas Baltrusaitis
- Department
of Chemical and Biomolecular Engineering, Lehigh University, Research Drive 111, Bethlehem, Pennsylvania 18015, United States
| | | | | | | | - Herbert Höpfl
- Centro
de Investigaciones Químicas, Instituto de Investigación
en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Morelos, México
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2
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Henriques WS, Young JM, Nemudryi A, Nemudraia A, Wiedenheft B, Malik HS. The Diverse Evolutionary Histories of Domesticated Metaviral Capsid Genes in Mammals. Mol Biol Evol 2024; 41:msae061. [PMID: 38507667 PMCID: PMC11011659 DOI: 10.1093/molbev/msae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
Selfish genetic elements comprise significant fractions of mammalian genomes. In rare instances, host genomes domesticate segments of these elements for function. Using a complete human genome assembly and 25 additional vertebrate genomes, we re-analyzed the evolutionary trajectories and functional potential of capsid (CA) genes domesticated from Metaviridae, a lineage of retrovirus-like retrotransposons. Our study expands on previous analyses to unearth several new insights about the evolutionary histories of these ancient genes. We find that at least five independent domestication events occurred from diverse Metaviridae, giving rise to three universally retained single-copy genes evolving under purifying selection and two gene families unique to placental mammals, with multiple members showing evidence of rapid evolution. In the SIRH/RTL family, we find diverse amino-terminal domains, widespread loss of protein-coding capacity in RTL10 despite its retention in several mammalian lineages, and differential utilization of an ancient programmed ribosomal frameshift in RTL3 between the domesticated CA and protease domains. Our analyses also reveal that most members of the PNMA family in mammalian genomes encode a conserved putative amino-terminal RNA-binding domain (RBD) both adjoining and independent from domesticated CA domains. Our analyses lead to a significant correction of previous annotations of the essential CCDC8 gene. We show that this putative RBD is also present in several extant Metaviridae, revealing a novel protein domain configuration in retrotransposons. Collectively, our study reveals the divergent outcomes of multiple domestication events from diverse Metaviridae in the common ancestor of placental mammals.
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Affiliation(s)
- William S Henriques
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Janet M Young
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Artem Nemudryi
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Anna Nemudraia
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Harmit S Malik
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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3
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McGlamery D, McDaniel C, Ladd DM, Ha Y, Mosquera MA, Mock MT, Stadie NP. Halide-free synthesis of metastable graphitic BC 3. Chem Sci 2024; 15:4358-4363. [PMID: 38516090 PMCID: PMC10952104 DOI: 10.1039/d3sc06837d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/15/2024] [Indexed: 03/23/2024] Open
Abstract
Layered BC3, a metastable phase within the binary boron-carbon system that is composed of graphite-like sheets with hexagonally symmetric C6B6 units, has never been successfully crystallized. Instead, poorly-crystalline BC3-like materials with significant stacking disorder have been isolated, based on the co-pyrolysis of a boron trihalide precursor with benzene at around 800 °C. The halide leaving group (-X) is a significant driving force of these reactions, but the subsequent evolution of gaseous HX species at such high temperatures hampers their scaling up and also prohibits their further use in the presence of hard-casting templates such as ordered silicates. Herein, we report a novel halide-free synthesis route to turbostratic BC3 with long-range in-plane ordering, as evidenced by multi-wavelength Raman spectroscopy. Judicious pairing of the two molecular precursors is crucial to achieving B-C bond formation and preventing phase-segregation into the thermodynamically favored products. A simple computational method used herein to evaluate the compatibility of bottom-up molecular precursors can be generalized to guide the future synthesis of other metastable materials beyond the boron-carbon system.
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Affiliation(s)
- Devin McGlamery
- Department of Chemistry & Biochemistry, Montana State University Bozeman Montana 59717 USA
| | - Charles McDaniel
- Department of Chemistry & Biochemistry, Montana State University Bozeman Montana 59717 USA
| | - Dylan M Ladd
- Department of Chemistry & Biochemistry, Montana State University Bozeman Montana 59717 USA
| | - Yang Ha
- Advanced Light Source, Lawrence Berkeley National Laboratory Berkeley California 94720 USA
| | - Martín A Mosquera
- Department of Chemistry & Biochemistry, Montana State University Bozeman Montana 59717 USA
| | - Michael T Mock
- Department of Chemistry & Biochemistry, Montana State University Bozeman Montana 59717 USA
| | - Nicholas P Stadie
- Department of Chemistry & Biochemistry, Montana State University Bozeman Montana 59717 USA
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4
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Martin CD, Bender AT, Sullivan BP, Lillis L, Boyle DS, Posner JD. SARS-CoV-2 recombinase polymerase amplification assay with lateral flow readout and duplexed full process internal control. Sens Diagn 2024; 3:421-430. [PMID: 38495597 PMCID: PMC10939122 DOI: 10.1039/d3sd00246b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/08/2024] [Indexed: 03/19/2024]
Abstract
Nucleic acid amplification tests for the detection of SARS-CoV-2 have been an important testing mechanism for the COVID-19 pandemic. While these traditional nucleic acid diagnostic methods are highly sensitive and selective, they are not suited to home or clinic-based uses. Comparatively, rapid antigen tests are cost-effective and user friendly but lack in sensitivity and specificity. Here we report on the development of a one-pot, duplexed reverse transcriptase recombinase polymerase amplification SARS-CoV-2 assay with MS2 bacteriophage as a full process control. Detection is carried out with either real-time fluorescence or lateral flow readout with an analytical sensitivity of 50 copies per reaction. Unlike previously published assays, the RNA-based MS2 bacteriophage control reports on successful operation of lysis, reverse transcription, and amplification. This SARS-CoV-2 assay features highly sensitive detection, visual readout through an LFA strip, results in less than 25 minutes, minimal instrumentation, and a useful process internal control to rule out false negative test results.
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Affiliation(s)
- Coleman D Martin
- Department of Chemical Engineering, University of Washington Seattle Washington USA
| | - Andrew T Bender
- Department of Mechanical Engineering, University of Washington Seattle Washington USA
| | - Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington Seattle Washington USA
| | | | | | - Jonathan D Posner
- Department of Chemical Engineering, University of Washington Seattle Washington USA
- Department of Mechanical Engineering, University of Washington Seattle Washington USA
- Department of Family Medicine, University of Washington Seattle Washington USA
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5
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Eskew MW, Reardon P, Benight AS. DNA-based assay for calorimetric determination of protein concentrations in pure or mixed solutions. PLoS One 2024; 19:e0298969. [PMID: 38427623 PMCID: PMC10906865 DOI: 10.1371/journal.pone.0298969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/01/2024] [Indexed: 03/03/2024] Open
Abstract
It was recently reported that values of the transition heat capacities, as measured by differential scanning calorimetry, for two globular proteins and a short DNA hairpin in NaCl buffer are essentially equivalent, at equal concentrations (mg/mL). To validate the broad applicability of this phenomenon, additional evidence for this equivalence is presented that reveals it does not depend on DNA sequence, buffer salt, or transition temperature (Tm). Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions. The scheme uses direct comparisons between the thermodynamic stability of a short DNA hairpin standard of known concentration, and thermodynamic stability of protein solutions of unknown concentrations. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm values. In all cases, evaluated protein concentrations determined from the DNA standard curves agreed with the UV-Vis concentration for monomeric proteins. For multimeric proteins evaluated concentrations were greater than determined by UV-Vis suggesting the calorimetric approach can also be an indicator of molecular stoichiometry.
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Affiliation(s)
- Matthew W. Eskew
- ThermoCap Laboratories Inc, Portland, Oregon, United States of America
- Department of Chemistry, Portland State University, Portland, Oregon, United States of America
| | - Patrick Reardon
- OSU NMR Facility, Oregon State University, Corvallis, Oregon, United States of America
| | - Albert S. Benight
- ThermoCap Laboratories Inc, Portland, Oregon, United States of America
- Department of Chemistry, Portland State University, Portland, Oregon, United States of America
- Department of Physics, Portland State University, Portland, Oregon, United States of America
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6
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Long ES, Tham EJ, Ferrer RP. Succession and climatic stochasticity induce long-term decline of a forest browser. PLoS One 2024; 19:e0298231. [PMID: 38412173 PMCID: PMC10898743 DOI: 10.1371/journal.pone.0298231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
Removal of predators and creation of early seral habitat have, in many systems, caused substantial population growth of herbivores. Hyperabundant herbivores, in turn, induce cascading ecosystem effects, but few studies have investigated long-term browser density trends in relation to succession and stochastic climate events. Here, we use annual, empirical population estimates of a forest browser to relate forest succession to long-term decline of an herbivore that prefers early seral habitat. From 2007-2021, concurrent with reduced timber harvest, we used line-transect distance sampling to document annual changes in Columbian black-tailed deer (Odocoileus hemionus columbianus) density on a mid-sized (17.3km2) predator-free island. We documented successional changes associated with forest aggradation and decreased forage quality for deer: early successional shrub/scrub habitat declined 3.8%/year; timber volume increased 4.5%/year; and canopy coverage increased 2.5%. In 2007-2008, deer densities were the greatest observed (~44/km2), but then an historic snowstorm reduced deer density by 39%. From 2010-2021, as forests continued to mature, deer density decreased 4.0%/year, declining to 20 deer/km2. Using a multivariate approach to combine habitat variables (i.e., early seral coverage, timber volume, and canopy closure) into a measure of forest maturation, we found a significant negative relationship between deer density and forest aggradation. Thus, consistent with predictions for bottom-up limited browsers, we observed significant annual declines in a deer population throughout an extended period of forest regrowth. Despite declines, deer density on the island exceeds mainland densities, and overbrowsing likely continues to disrupt ecosystem processes.
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Affiliation(s)
- Eric S. Long
- Department of Biology, Seattle Pacific University, Seattle, Washington, United States of America
| | - Enoch J. Tham
- Department of Biology, Seattle Pacific University, Seattle, Washington, United States of America
| | - Ryan P. Ferrer
- Department of Biology, Seattle Pacific University, Seattle, Washington, United States of America
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7
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Shohel M, Bustos J, Roseborough A, Nyman M. Pertechnetate/perrhenate-capped Zr/Hf-Dihydroxide Dimers: Elucidating Zr-TcO 4 Co-Mobility in the Nuclear Fuel Cycle. Chemistry 2024; 30:e202303218. [PMID: 38109648 DOI: 10.1002/chem.202303218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 12/20/2023]
Abstract
Spent nuclear fuel contains heavy element fission products that must be separated for effective reprocessing for a safe and sustainable nuclear fuel cycle. 93 Zr and 99 Tc are high-yield fission products that co-transport in liquid-liquid extraction processes. Here we seek atomic-level information of this co-extraction process, as well as fundamental knowledge about ZrIV (and HfIV ) aqueous speciation in the presence of topology-directing ligands such as pertechnetate (TcO4 - ) and non-radioactive surrogate perrhenate (ReO4 - ). In this context, we show that the flat tetrameric oxyhydroxyl-cluster [MIV 4 (OH)8 (H2 O)16 ]8+ (and related polymers) is dissociated by perrhenate/pertechnetate to yield isostructural dimers, M2 (OH)2 (XO4 - )6 (H2 O)6 ⋅ 3H2 O (M=Zr/HfIV ; X=Re/TcVII ), elucidated by single-crystal X-ray diffraction. We used these model compounds to understand the pervasive 93 Zr-99 Tc coextraction with further speciation studies in water, nitric acid, and tetrabutylphosphate (TBP) -kerosene; where the latter two media are relevant to nuclear fuel reprocessing. SAXS (small angle X-ray scattering), compositional evaluation, and where experimentally feasible, ESI-MS (electrospray ionization mass spectrometry) showed that perrhenate/pertechnetate influence Zr/HfIV -speciation in water. In Zr-XO4 solvent extraction studies to simulate fuel reprocessing, we provide evidence that TcO4 - enhances extraction of ZrIV , and compositional analysis of the extracted metal-complexes (Zr-ReO4 study) is consistent with the crystallized ZrIV 2 (OH)2 (ReVII O4 - )6 (H2 O)6 ⋅dimer.
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Affiliation(s)
- Mohammad Shohel
- Department of Chemistry, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Jenna Bustos
- Department of Chemistry, Oregon State University, Corvallis, Oregon, 97331, USA
| | | | - May Nyman
- Department of Chemistry, Oregon State University, Corvallis, Oregon, 97331, USA
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8
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Mass OA, Watt DR, Patten LK, Pensack RD, Lee J, Turner DB, Yurke B, Knowlton WB. Exciton delocalization in a fully synthetic DNA-templated bacteriochlorin dimer. Phys Chem Chem Phys 2023; 25:28437-28451. [PMID: 37843877 PMCID: PMC10599410 DOI: 10.1039/d3cp01634j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/23/2023] [Indexed: 10/17/2023]
Abstract
A bacteriochlorophyll a (Bchla) dimer is a basic functional unit in the LH1 and LH2 photosynthetic pigment-protein antenna complexes of purple bacteria, where an ordered, close arrangement of Bchla pigments-secured by noncovalent bonding to a protein template-enables exciton delocalization at room temperature. Stable and tunable synthetic analogs of this key photosynthetic subunit could lead to facile engineering of exciton-based systems such as in artificial photosynthesis, organic optoelectronics, and molecular quantum computing. Here, using a combination of synthesis and theory, we demonstrate that exciton delocalization can be achieved in a dimer of a synthetic bacteriochlorin (BC) featuring stability, high structural modularity, and spectral properties advantageous for exciton-based devices. The BC dimer was covalently templated by DNA, a stable and highly programmable scaffold. To achieve exciton delocalization in the absence of pigment-protein interactions critical for the Bchla dimer, we relied on the strong transition dipole moment in BC enabled by two auxochromes along the Qy transition, and omitting the central metal and isocyclic ring. The spectral properties of the synthetic "free" BC closely resembled those of Bchla in an organic solvent. Applying spectroscopic modeling, the exciton delocalization in the DNA-templated BC dimer was evaluated by extracting the excitonic hopping parameter, J to be 214 cm-1 (26.6 meV). For comparison, the same method applied to the natural protein-templated Bchla dimer yielded J of 286 cm-1 (35.5 meV). The smaller value of J in the BC dimer likely arose from the partial bacteriochlorin intercalation and the difference in medium effect between DNA and protein.
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Affiliation(s)
- Olga A Mass
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Devan R Watt
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Lance K Patten
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Jeunghoon Lee
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
- Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, USA
| | - Daniel B Turner
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, USA
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9
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Sawyer M, Eixenberger J, Nielson O, Manzi J, Francis C, Montenegro-Brown R, Subbaraman H, Estrada D. Correlative Imaging of Three-Dimensional Cell Culture on Opaque Bioscaffolds for Tissue Engineering Applications. ACS Appl Bio Mater 2023; 6:3717-3725. [PMID: 37655758 PMCID: PMC10521016 DOI: 10.1021/acsabm.3c00408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023]
Abstract
Three-dimensional (3D) tissue engineering (TE) is a prospective treatment that can be used to restore or replace damaged musculoskeletal tissues, such as articular cartilage. However, current challenges in TE include identifying materials that are biocompatible and have properties that closely match the mechanical properties and cellular microenvironment of the target tissue. Visualization and analysis of potential 3D porous scaffolds as well as the associated cell growth and proliferation characteristics present additional problems. This is particularly challenging for opaque scaffolds using standard optical imaging techniques. Here, we use graphene foam (GF) as a 3D porous biocompatible substrate, which is scalable, reproducible, and a suitable environment for ATDC5 cell growth and chondrogenic differentiation. ATDC5 cells are cultured, maintained, and stained with a combination of fluorophores and gold nanoparticles to enable correlative microscopic characterization techniques, which elucidate the effect of GF properties on cell behavior in a 3D environment. Most importantly, the staining protocol allows for direct imaging of cell growth and proliferation on opaque scaffolds using X-ray MicroCT, including imaging growth of cells within the hollow GF branches, which is not possible with standard fluorescence and electron microscopy techniques.
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Affiliation(s)
- Mone’t Sawyer
- Biomedical
Engineering Doctoral Program, Boise State
University, Boise, Idaho 83725, United States
| | - Josh Eixenberger
- Department
of Physics, Boise State University, Boise, Idaho 83725, United States
- Center
for Advanced Energy Studies, Boise State
University, Boise, Idaho 83725, United States
| | - Olivia Nielson
- Department
of Chemical and Biological Engineering, University of Idaho, Moscow, Idaho 83844, United States
| | - Jacob Manzi
- School
of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon 97331, United States
| | - Cadré Francis
- Micron
School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Raquel Montenegro-Brown
- Center for
Atomically Thin Multifunctional Coatings, Boise State University, Boise, Idaho 83725, United States
- Micron
School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Harish Subbaraman
- School
of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon 97331, United States
| | - David Estrada
- Center
for Advanced Energy Studies, Boise State
University, Boise, Idaho 83725, United States
- Center for
Atomically Thin Multifunctional Coatings, Boise State University, Boise, Idaho 83725, United States
- Micron
School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
- Idaho
National Laboratory, Idaho Falls, Idaho 83401, United States
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10
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Yu P, Baker MC, Crump AR, Vogler M, Strawn DG, Möller G. Biochar integrated reactive filtration of wastewater for P removal and recovery, micropollutant catalytic oxidation, and negative CO 2 e: Process operation and mechanism. Water Environ Res 2023; 95:e10926. [PMID: 37696540 DOI: 10.1002/wer.10926] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/30/2023] [Accepted: 09/06/2023] [Indexed: 09/13/2023]
Abstract
Biochar (BC) use in water treatment is a promising approach that can simultaneously help address societal needs of clean water, food security, and climate change mitigation. However, novel BC water treatment technology approaches require operational testing in field pilot-scale scenarios to advance their technology readiness assessment. Therefore, the objective of this study is to evaluate the system performance of BC integrated into hydrous ferric oxide reactive filtration (Fe-BC-RF) with and without catalytic ozonation (CatOx) process in laboratory and field pilot-scale scenarios. For this investigation, Fe-BC-RF and Fe-CatOx-BC-RF pilot-scale trials were conducted on synthetic lake water variants and at three municipal water resource recovery facilities (WRRFs) at process flows of 0.05 and 0.6 L/s, respectively. Three native and two iron-modified BCs were used in these studies. The commercially available reactive filtration process (Fe-RF without BC) had 96%-98% total phosphorus (TP) removal from 0.075- and 0.22-mg/L TP, as orthophosphate process influent in these trials. With BC integration, phosphorus removal yielded 94%-98% with the same process-influent conditions. In WRRF field pilot-scale studies, the Fe-CatOx-BC-RF process removed 84%-99% of influent total phosphorus concentrations that varied from 0.12 to 8.1 mg/L. Nutrient analysis on BC showed that the recovered BC used in the pilot-scale studies had an increase in TP from its native concentration, with the Fe-amended BC showing better P recovery at 110% than its unmodified state, which was 16%. Lastly, the field WRRF Fe-CatOx-BC-RF process studies showed successful destructive removals at >90% for more than 20 detected micropollutants, thus addressing a critical human health and environmental water quality concern. The research demonstrated that integration of BC into Fe-CatOx-RF for micropollutant removal, disinfection, and nutrient recovery is an encouraging tertiary water treatment technology that can address sustainable phosphorus recycling needs and the potential for carbon-negative operation. PRACTITIONER POINTS: A pilot-scale hydrous ferric oxide reactive sand filtration process integrating biochar injection typically yields >90% total phosphorus removal to ultralow levels. Biochar, modified with iron, recovers phosphorus from wastewater, creating a P/N nutrient upcycled soil amendment. Addition of ozone to the process stream enables biochar-iron-ozone catalytic oxidation demonstrating typically excellent (>90%) micropollutant destructive removals for the compounds tested. A companion paper to this work explores life cycle assessment (LCA) and techno-economic analysis (TEA) to explore biochar water treatment integrated reactive filtration impacts, costs, and readiness. Biochar use can aid in long-term carbon sequestration by reducing the carbon footprint of advanced water treatment in a dose-dependent manner, including enabling an overall carbon-negative process.
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Affiliation(s)
- Paulo Yu
- Department of Soil and Water Systems, University of Idaho, Moscow, Idaho, USA
| | - Martin C Baker
- Department of Soil and Water Systems, University of Idaho, Moscow, Idaho, USA
| | - Alex R Crump
- Department of Soil and Water Systems, University of Idaho, Moscow, Idaho, USA
| | - Michael Vogler
- Department of Soil and Water Systems, University of Idaho, Moscow, Idaho, USA
| | - Daniel G Strawn
- Department of Soil and Water Systems, University of Idaho, Moscow, Idaho, USA
| | - Gregory Möller
- Department of Soil and Water Systems, University of Idaho, Moscow, Idaho, USA
- Department of Chemical and Biological Engineering, University of Idaho, Moscow, Idaho, USA
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11
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Guadalupe Vasquez-Ríos M, Campillo-Alvarado G, MacGillivray LR. Mechanochemical Mediated Coexistence of B←N Coordination and Hydrogen Bonding. Angew Chem Int Ed Engl 2023; 62:e202308350. [PMID: 37365138 DOI: 10.1002/anie.202308350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Mechanochemistry afforded a photoactive cocrystal via coexisting (B)O-H⋅⋅⋅N hydrogen bonds and B←N coordination. Specifically, solvent-free mechanochemical ball mill grinding and liquid-assisted grinding of a boronic acid and an alkene resulted in mixtures of hydrogen-bonded and coordinated complexes akin to mixtures of noncovalent complexes that can be obtained in solution in equilibria processes. The alkenes of the hydrogen-bonded assembly undergo an intermolecular [2+2] photodimerization in quantitative conversion, effectively reporting the outcome of the self-assembly processes. Our results suggest that interplay involving noncovalent bonds subjected to mechanochemical conditions can lead to functional solids where, in the current case, the structure composed of the weaker hydrogen bonding interactions predominates.
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12
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Zhu P, Stanisheuski S, Franklin R, Vogel A, Vesely CH, Reardon P, Sluchanko NN, Beckman JS, Karplus PA, Mehl RA, Cooley RB. Autonomous Synthesis of Functional, Permanently Phosphorylated Proteins for Defining the Interactome of Monomeric 14-3-3ζ. ACS Cent Sci 2023; 9:816-835. [PMID: 37122473 PMCID: PMC10141581 DOI: 10.1021/acscentsci.3c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Indexed: 05/03/2023]
Abstract
14-3-3 proteins are dimeric hubs that bind hundreds of phosphorylated "clients" to regulate their function. Installing stable, functional mimics of phosphorylated amino acids into proteins offers a powerful strategy to study 14-3-3 function in cellular-like environments, but a previous genetic code expansion (GCE) system to translationally install nonhydrolyzable phosphoserine (nhpSer), with the γ-oxygen replaced with CH2, site-specifically into proteins has seen limited usage. Here, we achieve a 40-fold improvement in this system by engineering into Escherichia coli a six-step biosynthetic pathway that produces nhpSer from phosphoenolpyruvate. Using this autonomous "PermaPhos" expression system, we produce three biologically relevant proteins with nhpSer and confirm that nhpSer mimics the effects of phosphoserine for activating GSK3β phosphorylation of the SARS-CoV-2 nucleocapsid protein, promoting 14-3-3/client complexation, and monomerizing 14-3-3 dimers. Then, to understand the biological function of these phosphorylated 14-3-3ζ monomers (containing nhpSer at Ser58), we isolate its interactome from HEK293T lysates and compare it with that of wild-type 14-3-3ζ. These data identify two new subsets of 14-3-3 client proteins: (i) those that selectively bind dimeric 14-3-3ζ and (ii) those that selectively bind monomeric 14-3-3ζ. We discover that monomeric-but not dimeric-14-3-3ζ interacts with cereblon, an E3 ubiquitin-ligase adaptor protein of pharmacological interest.
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Affiliation(s)
- Phillip Zhu
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Stanislau Stanisheuski
- Department
of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Rachel Franklin
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Amber Vogel
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Cat Hoang Vesely
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Patrick Reardon
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Nikolai N. Sluchanko
- A.N.
Bach Institute of Biochemistry, Federal Research Center of Biotechnology
of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Joseph S. Beckman
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- e-MSion
Inc., 2121 NE Jack London
St., Corvallis, Oregon 97330, United States
| | - P. Andrew Karplus
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Ryan A. Mehl
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Richard B. Cooley
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
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13
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Lulich A, Amiri M, Stephen D, Shohel M, Mao Z, Nyman M. Bismuth Coordination Polymers with Fluorinated Linkers: Aqueous Stability, Bivolatility, and Adsorptive Behavior. ACS Omega 2023; 8:10476-10486. [PMID: 36969471 PMCID: PMC10034978 DOI: 10.1021/acsomega.3c00114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Bismuth metal-organic frameworks and coordination polymers (CP) are challenging to synthesize, given the poor solubility of bismuth precursors and asymmetric and labile ligation of Bi3+ due to its intrinsic lone pair. Here, we synthesize and structurally characterize three Bi3+-CPs, exploiting a tetrafluoroterephtalate (F4BDC) linker to determine the effect of high acidity on these synthesis and coordination challenges. Single-crystal X-ray diffraction characterization showed that pi-pi stacking of linkers directs framework arrangement and generally deters open porosity in the three structures, respectively featuring Bi chains (Bi chain -F 4 BDC), Bi dimers (Bi 2 -F 4 BDC) linked into chains, and Bi tetramers (Bi 4 -F 4 BDC). Powder X-ray diffraction and microscopic imaging show the high purity and stability of these compounds in water. Naphthalenedisulfonate (NDS) was used as a mineralizer in the synthesis of (Bi chain -F 4 BDC) and (Bi 4 -F 4 BDC), and studies of its role in assembly pathways yielded two additional structures featuring mixed NDS and F4BDC, respectively, linking monomer and octamer Bi nodes, and confirmed that F4BDC is the preferred (less labile) linker. Methylene blue (MB) adsorption studies show differing efficacies of the three Bi-F4BDC phases, attributed to surface characteristics of the preferential growth facets, while generally most effective adsorption is attributed to the hydrophobicity of fluorinated ligands. Finally, thermogravimetric analysis of all three Bi-F4BDC phases indicates simultaneous ligand degradation and in situ formation of volatile Bi compounds, which could be exploited in the chemical vapor deposition of Bi-containing thin films.
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14
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Berg A, Swartchick CB, Forrest N, Chavarria M, Deem MC, Sillin AN, Li Y, Riscoe TM, Nilsen A, Riscoe MK, Wood WJL. 2-hydroxy-1,4-naphthoquinones with 3-alkyldiarylether groups: synthesis and Plasmodium falciparum inhibitory activity. Future Med Chem 2022; 14:1611-1620. [PMID: 36349868 PMCID: PMC9832320 DOI: 10.4155/fmc-2022-0127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/21/2022] [Indexed: 11/10/2022] Open
Abstract
Background: In 1948, the synthesis and Plasmodium lophurae activity of 2-hydroxy-1,4-naphthoquinones containing 3-alkyldiarylether side chains was reported. Method/results: The synthesis of five related compounds, designed to be more metabolically stable, was pursued. The compounds were synthesized using a radical alkylation reaction with naphthoquinones. One compound had a lower IC50 value against various strains of Plasmodium falciparum and assay data indicate that it binds to the Qo site of cytochrome bc1. With a low yield for the radical alkylation of the most active compound, a reductive alkylation method with used to improve reaction yields. Conclusion: Further synthetic knowledge was obtained, and the assay data indicate that there are sensitivity differences between avian and human malarial parasites for these molecules.
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Affiliation(s)
- Amanda Berg
- Department of Chemistry & Biochemistry, University of Portland, 5000 N. Willamette Blvd., Portland, OR 97203, USA
| | - Chelsea B Swartchick
- Department of Chemistry & Biochemistry, University of Portland, 5000 N. Willamette Blvd., Portland, OR 97203, USA
| | - Noah Forrest
- Department of Chemistry & Biochemistry, University of Portland, 5000 N. Willamette Blvd., Portland, OR 97203, USA
| | - Matthew Chavarria
- Department of Chemistry & Biochemistry, University of Portland, 5000 N. Willamette Blvd., Portland, OR 97203, USA
| | - Madeleine C Deem
- Department of Chemistry & Biochemistry, University of Portland, 5000 N. Willamette Blvd., Portland, OR 97203, USA
| | - Alyson N Sillin
- Department of Chemistry & Biochemistry, University of Portland, 5000 N. Willamette Blvd., Portland, OR 97203, USA
| | - Yuexin Li
- Portland VA Medical Center, 3710 SW US Veterans Hospital Road, Portland, OR 97239, USA
| | - Teresa M Riscoe
- Portland VA Medical Center, 3710 SW US Veterans Hospital Road, Portland, OR 97239, USA
| | - Aaron Nilsen
- Portland VA Medical Center, 3710 SW US Veterans Hospital Road, Portland, OR 97239, USA
| | - Michael K Riscoe
- Portland VA Medical Center, 3710 SW US Veterans Hospital Road, Portland, OR 97239, USA
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, 3181 Sam Jackson Boulevard, Portland, OR 97239, USA
| | - Warren JL Wood
- Department of Chemistry & Biochemistry, University of Portland, 5000 N. Willamette Blvd., Portland, OR 97203, USA
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15
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Tehan R, Blount RR, Goold RL, Mattos DR, Spatafora NR, Tabima JF, Gazis R, Wang C, Ishmael JE, Spatafora JW, McPhail KL. Tolypocladamide H and the Proposed Tolypocladamide NRPS in Tolypocladium Species. J Nat Prod 2022; 85:1363-1373. [PMID: 35500108 PMCID: PMC9150700 DOI: 10.1021/acs.jnatprod.2c00153] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The genome of entomopathogenic fungus Tolypocladium inflatum Gams encodes 43 putative biosynthetic gene clusters for specialized metabolites, although genotype-phenotype linkages have been reported only for the cyclosporins and fumonisins. T. inflatum was cultured in defined minimal media, supplemented with or without one of nine different amino acids. Acquisition of LC-MS/MS data for molecular networking and manual analysis facilitated annotation of putative known and unknown metabolites. These data led us to target a family of peptaibols and guided the isolation and purification of tolypocladamide H (1), which showed modest antibacterial activity and toxicity to mammalian cells at micromolar concentrations. HRMS/MS, NMR, and advanced Marfey's analysis were used to assign the structure of 1 as a peptaibol containing 4-[(E)-2-butenyl]-4-methyl-l-threonine (Bmt), a hallmark structural motif of the cyclosporins. LC-MS detection of homologous tolypocladamide metabolites and phylogenomic analyses of peptaibol biosynthetic genes in other cultured Tolypocladium species allowed assignment of a putative tolypocladamide nonribosomal peptide synthetase gene.
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Affiliation(s)
- Richard
M. Tehan
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Rheannon R. Blount
- Department
of Botany and Plant Pathology, College of Agricultural and Life Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - Ryan L. Goold
- Department
of Botany and Plant Pathology, College of Agricultural and Life Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - Daphne R. Mattos
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Nicolas R. Spatafora
- Department
of Botany and Plant Pathology, College of Agricultural and Life Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - Javier F. Tabima
- Department
of Botany and Plant Pathology, College of Agricultural and Life Sciences, Oregon State University, Corvallis, Oregon 97331, United States
- Department
of Biology, Clark University, Worcester, Massachusetts 01610, United States
| | - Romina Gazis
- Department
of Plant Pathology, Tropical Research and Education Center, University of Florida, Homestead, Florida 33031, United States
| | - Chengshu Wang
- Key
Laboratory of Insect Developmental and Evolutionary Biology, CAS Center
for Excellence in Molecular Plant Sciences, Shanghai Institute of
Plant Physiology and Ecology, Chinese Academy
of Sciences, Shanghai 200032, People’s Republic
of China
| | - Jane E. Ishmael
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Joseph W. Spatafora
- Department
of Botany and Plant Pathology, College of Agricultural and Life Sciences, Oregon State University, Corvallis, Oregon 97331, United States
- Tel: +1 541 737 8134. E-mail:
| | - Kerry L. McPhail
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
- Tel: +1 541 737 5808. E-mail:
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16
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Hurlburt NK, Homad LJ, Sinha I, Jennewein MF, MacCamy AJ, Wan YH, Boonyaratanakornkit J, Sholukh AM, Jackson AM, Zhou P, Burton DR, Andrabi R, Ozorowski G, Ward AB, Stamatatos L, Pancera M, McGuire AT. Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit. Commun Biol 2022; 5:342. [PMID: 35411021 PMCID: PMC9001700 DOI: 10.1038/s42003-022-03262-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/11/2022] [Indexed: 12/11/2022] Open
Abstract
Three betacoronaviruses have crossed the species barrier and established human-to-human transmission causing significant morbidity and mortality in the past 20 years. The most current and widespread of these is SARS-CoV-2. The identification of CoVs with zoonotic potential in animal reservoirs suggests that additional outbreaks could occur. Monoclonal antibodies targeting conserved neutralizing epitopes on diverse CoVs can form the basis for prophylaxis and therapeutic treatments and enable the design of vaccines aimed at providing pan-CoV protection. We previously identified a neutralizing monoclonal antibody, CV3-25 that binds to the SARS-CoV-2 spike, neutralizes the SARS-CoV-2 Beta variant comparably to the ancestral Wuhan Hu-1 strain, cross neutralizes SARS-CoV-1 and binds to recombinant proteins derived from the spike-ectodomains of HCoV-OC43 and HCoV-HKU1. Here, we show that the neutralizing activity of CV3-25 is maintained against the Alpha, Delta, Gamma and Omicron variants of concern as well as a SARS-CoV-like bat coronavirus with zoonotic potential by binding to a conserved linear peptide in the stem-helix region. Negative stain electron microscopy and a 1.74 Å crystal structure of a CV3-25/peptide complex demonstrates that CV3-25 binds to the base of the stem helix at the HR2 boundary to an epitope that is distinct from other stem-helix directed neutralizing mAbs.
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Affiliation(s)
- Nicholas K Hurlburt
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Leah J Homad
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Irika Sinha
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Madeleine F Jennewein
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Anna J MacCamy
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Yu-Hsin Wan
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Jim Boonyaratanakornkit
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Anton M Sholukh
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Abigail M Jackson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Panpan Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
| | - Marie Pancera
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA.
- Vaccine Research Center, NAID, NIH, Bethesda, MD, USA.
| | - Andrew T McGuire
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
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17
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Tasker BR, Honebein KN, Erickson AM, Misslin JE, Hurst P, Cooney S, Riley S, Griffith SA, Bancroft BA. Effects of elevated temperature, reduced hydroperiod, and invasive bullfrog larvae on pacific chorus frog larvae. PLoS One 2022; 17:e0265345. [PMID: 35290408 PMCID: PMC8923472 DOI: 10.1371/journal.pone.0265345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/28/2022] [Indexed: 11/20/2022] Open
Abstract
Climate change and invasive species threaten many ecosystems, including surface freshwater systems. Increasing temperatures and reduced hydroperiod due to climate change may promote the persistence of invasive species and facilitate new invasions due to potentially higher tolerance to environmental stress in successful invaders. Amphibians demonstrate high levels of plasticity in life history characteristics, particularly those species which inhabit both ephemeral and permanent water bodies. We tested the influence of two projected effects of climate change (increased temperature and reduced hydroperiod) on Pacific chorus frog (Pseudacris regilla) tadpoles alone and in combination with the presence of tadpoles of a wide-spread invasive amphibian, the American bullfrog (Lithobates catesbeianus). Specifically, we explored the effects of projected climate change and invasion on survival, growth, mass at stage 42, and development rate of Pacific chorus frogs. Direct and indirect interactions between the invasive tadpole and the native tadpole were controlled via a cage treatment and were included to account for differences in presence of the bullfrog compared to competition for food resources and other direct effects. Overall, bullfrogs had larger negative effects on Pacific chorus frogs than climate conditions. Under future climate conditions, Pacific chorus frogs developed faster and emerged heavier. Pacific chorus frog tadpoles developing in the presence of American bullfrogs, regardless of cage treatment, emerged lighter. When future climate conditions and presence of invasive American bullfrog tadpoles were combined, tadpoles grew less. However, no interaction was detected between climate conditions and bullfrog presence for mass, suggesting that tadpoles allocated energy towards mass rather than length under the combined stress treatment. The maintenance of overall body condition (smaller but heavier metamorphs) when future climate conditions overlap with bullfrog presence suggests that Pacific chorus frogs may be partially compensating for the negative effects of bullfrogs via increased allocation of energy towards mass. Strong plasticity, as demonstrated by Pacific chorus frog larvae in our study, may allow species to match the demands of new environments, including under future climate change.
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Affiliation(s)
- Bailey R. Tasker
- Department of Biology, Gonzaga University, Spokane, Washington, United States of America
- Department of Environmental Studies and Sciences, Gonzaga University, Spokane, Washington, United States of America
| | - Karli N. Honebein
- Department of Biology, Gonzaga University, Spokane, Washington, United States of America
- Department of Environmental Studies and Sciences, Gonzaga University, Spokane, Washington, United States of America
| | - Allie M. Erickson
- Department of Biology, Gonzaga University, Spokane, Washington, United States of America
- Department of Environmental Studies and Sciences, Gonzaga University, Spokane, Washington, United States of America
| | - Julia E. Misslin
- Department of Biology, Gonzaga University, Spokane, Washington, United States of America
| | - Paul Hurst
- Department of Biology, Gonzaga University, Spokane, Washington, United States of America
- Department of Environmental Studies and Sciences, Gonzaga University, Spokane, Washington, United States of America
| | - Sarah Cooney
- Department of Biology, Gonzaga University, Spokane, Washington, United States of America
| | - Skylar Riley
- Department of Biology, Gonzaga University, Spokane, Washington, United States of America
| | - Scott A. Griffith
- Department of Mathematics and Computer Science, Whitworth University, Spokane, Washington, United States of America
| | - Betsy A. Bancroft
- Department of Biology, Gonzaga University, Spokane, Washington, United States of America
- Department of Environmental Studies and Sciences, Gonzaga University, Spokane, Washington, United States of America
- * E-mail:
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18
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Elias EK, Rehbein SM, Neufeldt SR. Solvent coordination to palladium can invert the selectivity of oxidative addition. Chem Sci 2022; 13:1618-1628. [PMID: 35282616 PMCID: PMC8827013 DOI: 10.1039/d1sc05862b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022] Open
Abstract
Reaction solvent was previously shown to influence the selectivity of Pd/P t Bu3-catalyzed Suzuki-Miyaura cross-couplings of chloroaryl triflates. The role of solvents has been hypothesized to relate to their polarity, whereby polar solvents stabilize anionic transition states involving [Pd(P t Bu3)(X)]- (X = anionic ligand) and nonpolar solvents do not. However, here we report detailed studies that reveal a more complicated mechanistic picture. In particular, these results suggest that the selectivity change observed in certain solvents is primarily due to solvent coordination to palladium. Polar coordinating and polar noncoordinating solvents lead to dramatically different selectivity. In coordinating solvents, preferential reaction at triflate is likely catalyzed by Pd(P t Bu3)(solv), whereas noncoordinating solvents lead to reaction at chloride through monoligated Pd(P t Bu3). The role of solvent coordination is supported by stoichiometric oxidative addition experiments, density functional theory (DFT) calculations, and catalytic cross-coupling studies. Additional results suggest that anionic [Pd(P t Bu3)(X)]- is also relevant to triflate selectivity in certain scenarios, particularly when halide anions are available in high concentrations.
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Affiliation(s)
- Emily K Elias
- Department of Chemistry and Biochemistry, Montana State University Bozeman Montana 59717 USA
| | - Steven M Rehbein
- Department of Chemistry and Biochemistry, Montana State University Bozeman Montana 59717 USA
| | - Sharon R Neufeldt
- Department of Chemistry and Biochemistry, Montana State University Bozeman Montana 59717 USA
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19
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Mills MG, Bruce E, Huang ML, Crothers JW, Hyrien O, Oura CAL, Blake L, Brown Jordan A, Hester S, Wehmas L, Mari B, Barby P, Lacoux C, Fassy J, Vial P, Vial C, Martinez JRW, Oladipo OO, Inuwa B, Shittu I, Meseko CA, Chammas R, Santos CF, Dionísio TJ, Garbieri TF, Parisi VA, Mendes-Correa MC, de Paula AV, Romano CM, Góes LGB, Minoprio P, Campos AC, Cunha MP, Vilela APP, Nyirenda T, Mkakosya RS, Muula AS, Dumm RE, Harris RM, Mitchell CA, Pettit S, Botten J, Jerome KR. An international, interlaboratory ring trial confirms the feasibility of an extraction-less "direct" RT-qPCR method for reliable detection of SARS-CoV-2 RNA in clinical samples. PLoS One 2022; 17:e0261853. [PMID: 35025926 PMCID: PMC8758094 DOI: 10.1371/journal.pone.0261853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/11/2021] [Indexed: 11/29/2022] Open
Abstract
Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is used worldwide to test and trace the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). "Extraction-less" or "direct" real time-reverse transcription polymerase chain reaction (RT-PCR) is a transparent and accessible qualitative method for SARS-CoV-2 detection from nasopharyngeal or oral pharyngeal samples with the potential to generate actionable data more quickly, at a lower cost, and with fewer experimental resources than full RT-qPCR. This study engaged 10 global testing sites, including laboratories currently experiencing testing limitations due to reagent or equipment shortages, in an international interlaboratory ring trial. Participating laboratories were provided a common protocol, common reagents, aliquots of identical pooled clinical samples, and purified nucleic acids and used their existing in-house equipment. We observed 100% concordance across laboratories in the correct identification of all positive and negative samples, with highly similar cycle threshold values. The test also performed well when applied to locally collected patient nasopharyngeal samples, provided the viral transport media did not contain charcoal or guanidine, both of which appeared to potently inhibit the RT-PCR reaction. Our results suggest that direct RT-PCR assay methods can be clearly translated across sites utilizing readily available equipment and expertise and are thus a feasible option for more efficient COVID-19 coronavirus disease testing as demanded by the continuing pandemic.
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Affiliation(s)
- Margaret G. Mills
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Emily Bruce
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Meei-Li Huang
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Jessica W. Crothers
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Ollivier Hyrien
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Christopher A. L. Oura
- School of Veterinary Medicine, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Lemar Blake
- School of Veterinary Medicine, University of the West Indies, St. Augustine, Trinidad and Tobago
| | | | - Susan Hester
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
| | - Leah Wehmas
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
| | - Bernard Mari
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Pascal Barby
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Caroline Lacoux
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Julien Fassy
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Pablo Vial
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | - Cecilia Vial
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | - Jose R. W. Martinez
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | | | - Bitrus Inuwa
- Infectious and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Ismaila Shittu
- Infectious and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Clement A. Meseko
- Infectious and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Roger Chammas
- Faculdade de Medicina da Universidade de São Paulo, Departamento de Radiologia e Oncologia, Centro de Investigação Translacional em Oncologia, Instituto do Cancer do Estado de São Paulo, São Paulo, Brazil
| | - Carlos Ferreira Santos
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Thiago José Dionísio
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Thais Francini Garbieri
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Viviane Aparecida Parisi
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | | | - Anderson V. de Paula
- Department of Infectious Diseases, Institute of Tropical Medicine of São Paulo, São Paulo, Brazil
| | - Camila M. Romano
- Department of Infectious Diseases, Institute of Tropical Medicine of São Paulo, São Paulo, Brazil
| | - Luiz Gustavo Bentim Góes
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Paola Minoprio
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
| | - Angelica C. Campos
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
| | - Marielton P. Cunha
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
| | - Ana Paula P. Vilela
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
| | - Tonney Nyirenda
- Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | | | - Adamson S. Muula
- Department of Public Health, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Rebekah E. Dumm
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Rebecca M. Harris
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Constance A. Mitchell
- Health and Environmental Sciences Institute, Washington, DC, United States of America
| | - Syril Pettit
- Health and Environmental Sciences Institute, Washington, DC, United States of America
| | - Jason Botten
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Keith R. Jerome
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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Dinca SC, Greiner D, Weidenfeld K, Bond L, Barkan D, Jorcyk CL. Novel mechanism for OSM-promoted extracellular matrix remodeling in breast cancer: LOXL2 upregulation and subsequent ECM alignment. Breast Cancer Res 2021; 23:56. [PMID: 34011405 PMCID: PMC8132418 DOI: 10.1186/s13058-021-01430-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 04/20/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Invasive ductal carcinoma (IDC) is a serious problem for patients as it metastasizes, decreasing 5-year patient survival from > 95 to ~ 27%. The breast tumor microenvironment (TME) is often saturated with proinflammatory cytokines, such as oncostatin M (OSM), which promote epithelial-to-mesenchymal transitions (EMT) in IDC and increased metastasis. The extracellular matrix (ECM) also plays an important role in promoting invasive and metastatic potential of IDC. Specifically, the reorganization and alignment of collagen fibers in stromal ECM leads to directed tumor cell motility, which promotes metastasis. Lysyl oxidase like-2 (LOXL2) catalyzes ECM remodeling by crosslinking of collagen I in the ECM. We propose a novel mechanism whereby OSM induces LOXL2 expression, mediating stromal ECM remodeling of the breast TME. METHODS Bioinformatics was utilized to determine survival and gene correlation in patients. IDC cell lines were treated with OSM (also IL-6, LIF, and IL-1β) and analyzed for LOXL2 expression by qRT-PCR and immunolabelling techniques. Collagen I contraction assays, 3D invasion assays, and confocal microscopy were performed with and without LOXL2 inhibition to determine the impact of OSM-induced LOXL2 on the ECM. RESULTS Our studies demonstrate that IDC patients with high LOXL2 and OSM co-expression had worse rates of metastasis-free survival than those with high levels of either, individually, and LOXL2 expression is positively correlated to OSM/OSM receptor (OSMR) expression in IDC patients. Furthermore, human IDC cells treated with OSM resulted in a significant increase in LOXL2 mRNA, which led to upregulated protein expression of secreted, glycosylated, and enzymatically active LOXL2. The expression of LOXL2 in IDC cells did not affect OSM-promoted EMT, and LOXL2 was localized to the cytoplasm and/or secreted. OSM-induced LOXL2 promoted an increase in ECM collagen I fiber crosslinking, which led to significant fiber alignment between cells and increased IDC cell invasion. CONCLUSIONS Aligned collagen fibers in the ECM provide pathways for tumor cells to migrate more easily through the stroma to nearby vasculature and tissue. These results provide a new paradigm through which proinflammatory cytokine OSM promotes tumor progression. Understanding the nuances in IDC metastasis will lead to better potential therapeutics to combat against the possibility.
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Affiliation(s)
- Simion C. Dinca
- Biomolecular Sciences Graduate Program, Boise State University, 1910 University Drive, MS1515, Boise, ID 83725 USA
| | - Daniel Greiner
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
- Department of Biological Sciences, Boise State University, 1910 University Drive, MS1515, Boise, ID 83725 USA
| | - Keren Weidenfeld
- Department of Human Biology and Medical Sciences, University of Haifa, Haifa, Israel
| | - Laura Bond
- Biomolecular Research Center, Boise State University, 1910 University Drive, MS1515, Boise, ID 83725 USA
| | - Dalit Barkan
- Department of Human Biology and Medical Sciences, University of Haifa, Haifa, Israel
| | - Cheryl L. Jorcyk
- Biomolecular Sciences Graduate Program, Boise State University, 1910 University Drive, MS1515, Boise, ID 83725 USA
- Department of Biological Sciences, Boise State University, 1910 University Drive, MS1515, Boise, ID 83725 USA
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21
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Nizioł J, Copié V, Tripet BP, Nogueira LB, Nogueira KOPC, Ossoliński K, Arendowski A, Ruman T. Metabolomic and elemental profiling of human tissue in kidney cancer. Metabolomics 2021; 17:30. [PMID: 33661419 PMCID: PMC7932981 DOI: 10.1007/s11306-021-01779-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 02/22/2021] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Kidney cancer is one of the most frequently diagnosed and the most lethal urinary cancer. Despite advances in treatment, no specific biomarker is currently in use to guide therapeutic interventions. OBJECTIVES Major aim of this work was to perform metabolomic and elemental profiling of human kidney cancer and normal tissue and to evaluate cancer biomarkers. METHODS Metabolic and elemental profiling of tumor and adjacent normal human kidney tissue from 50 patients with kidney cancer was undertaken using three different analytical methods. RESULTS Five potential tissue biomarkers of kidney cancer were identified and quantified using with high-resolution nuclear magnetic resonance spectroscopy. The contents of selected chemical elements in tissues was analyzed using inductively coupled plasma optical emission spectrometry. Eleven mass spectral features differentiating between kidney cancer and normal tissues were detected using silver-109 nanoparticle enhanced steel target laser desorption/ionization mass spectrometry. CONCLUSIONS Our results, derived from the combination of ICP-OES, LDI MS and 1H NMR methods, suggest that tissue biomarkers identified herein appeared to have great potential for use in clinical prognosis and/or diagnosis of kidney cancer.
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Affiliation(s)
- Joanna Nizioł
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave., 35-959, Rzeszów, Poland.
| | - Valérie Copié
- The Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Brian P Tripet
- The Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Leonardo B Nogueira
- Department of Geology, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Katiane O P C Nogueira
- Department of Biological Sciences, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Krzysztof Ossoliński
- Department of Urology, John Paul II Hospital, Grunwaldzka 4 St., 36-100, Kolbuszowa, Poland
| | - Adrian Arendowski
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave., 35-959, Rzeszów, Poland
| | - Tomasz Ruman
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave., 35-959, Rzeszów, Poland
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22
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Bruce EA, Huang ML, Perchetti GA, Tighe S, Laaguiby P, Hoffman JJ, Gerrard DL, Nalla AK, Wei Y, Greninger AL, Diehl SA, Shirley DJ, Leonard DGB, Huston CD, Kirkpatrick BD, Dragon JA, Crothers JW, Jerome KR, Botten JW. Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step. PLoS Biol 2020; 18:e3000896. [PMID: 33006983 PMCID: PMC7556528 DOI: 10.1371/journal.pbio.3000896] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 10/14/2020] [Accepted: 09/10/2020] [Indexed: 11/24/2022] Open
Abstract
The ongoing COVID-19 pandemic has created an unprecedented need for rapid diagnostic testing. The World Health Organization (WHO) recommends a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 testing. The goal of this study was to determine whether SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether. The direct RT-qPCR approach correctly identified 92% of a reference set of blinded NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Importantly, the direct method had sufficient sensitivity to reliably detect those patients with viral loads that correlate with the presence of infectious virus. Thus, this strategy has the potential to ease supply choke points to substantially expand COVID-19 testing and screening capacity and should be applicable throughout the world.
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Affiliation(s)
- Emily A. Bruce
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Meei-Li Huang
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Garrett A. Perchetti
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Scott Tighe
- Vermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Pheobe Laaguiby
- Vermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Jessica J. Hoffman
- Vermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Diana L. Gerrard
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, Vermont, United States of America
| | - Arun K. Nalla
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Yulun Wei
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Alexander L. Greninger
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Sean A. Diehl
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Vaccine Testing Center, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - David J. Shirley
- Data Science Division, IXIS, Burlington, Vermont, United States of America
| | - Debra G. B. Leonard
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- University of Vermont Health Network, Burlington, Vermont, United States of America
| | - Christopher D. Huston
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Division of Infectious Disease, Department of Medicine, University of Vermont Medical Center, Burlington, Vermont, United States of America
| | - Beth D. Kirkpatrick
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Vaccine Testing Center, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Division of Infectious Disease, Department of Medicine, University of Vermont Medical Center, Burlington, Vermont, United States of America
| | - Julie A. Dragon
- Vermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Jessica W. Crothers
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- University of Vermont Health Network, Burlington, Vermont, United States of America
| | - Keith R. Jerome
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jason W. Botten
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Vaccine Testing Center, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
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Ramos Báez R, Buckley Y, Yu H, Chen Z, Gallavotti A, Nemhauser JL, Moss BL. A Synthetic Approach Allows Rapid Characterization of the Maize Nuclear Auxin Response Circuit. Plant Physiol 2020; 182:1713-1722. [PMID: 32123041 PMCID: PMC7140906 DOI: 10.1104/pp.19.01475] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/22/2020] [Indexed: 05/20/2023]
Abstract
Auxin plays a key role across all land plants in growth and developmental processes. Although auxin signaling function has diverged and expanded, differences in the molecular functions of signaling components have largely been characterized in Arabidopsis (Arabidopsis thaliana). Here, we used the nuclear Auxin Response Circuit recapitulated in yeast (Saccharomyces cerevisiae) system to functionally annotate maize (Zea mays) auxin signaling components, focusing on genes expressed during the development of ear and tassel inflorescences. All 16 maize auxin/indole-3-acetic acid repressor proteins were degraded in response to auxin with rates that depended on both receptor and repressor identities. When fused to the maize TOPLESS homolog RAMOSA1 ENHANCER LOCUS2, maize auxin/indole-3-acetic acids were able to repress AUXIN RESPONSE FACTOR transcriptional activity. A complete auxin response circuit comprising all maize components, including the ZmAFB2/3 b1 maize AUXIN SIGNALING F-BOX (AFB) receptor, was fully functional. The ZmAFB2/3 b1 auxin receptor was more sensitive to hormone than AtAFB2 and allowed for rapid circuit activation upon auxin addition. These results validate the conserved role of predicted auxin response genes in maize as well as provide evidence that a synthetic approach can facilitate broader comparative studies across the wide range of species with sequenced genomes.
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Affiliation(s)
- Román Ramos Báez
- University of Washington, Department of Biology, Seattle, Washington 98105
| | - Yuli Buckley
- Whitman College, Department of Biology, Walla Walla, Washington 99362
| | - Han Yu
- Whitman College, Department of Biology, Walla Walla, Washington 99362
| | - Zongliang Chen
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey 08901
| | | | - Britney L Moss
- Whitman College, Department of Biology, Walla Walla, Washington 99362
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Frankel-Bricker J, Song MJ, Benner MJ, Schaack S. Variation in the Microbiota Associated with Daphnia magna Across Genotypes, Populations, and Temperature. Microb Ecol 2020; 79:731-742. [PMID: 31377832 PMCID: PMC7176607 DOI: 10.1007/s00248-019-01412-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/04/2019] [Indexed: 05/09/2023]
Abstract
Studies of how the microbiome varies among individuals, populations, and abiotic conditions are critical for understanding this key component of an organism's biology and ecology. In the case of Daphnia, aquatic microcrustaceans widely used in population/community ecology and environmental science studies, understanding factors that influence microbiome shifts among individuals is useful for both basic and applied research contexts. In this study, we assess differences in the microbiome among genotypes of D. magna collected from three regions along a large latitudinal gradient (Finland, Germany, and Israel). After being reared in the lab for many years, we sought to characterize any differences in genotype- or population-specific microbial communities, and to assess whether the microbiota varied among temperatures. Our study is similar to a recent comparison of the microbial communities among D. magna genotypes raised in different temperatures published by Sullam et al. (Microb Ecol 76(2):506-517, 2017), and as such represents one of the first examples of a reproducible result in microbiome research. Like the previous study, we find evidence for a strong effect of temperature on the microbiome of D. magna, although across a much smaller temperature range representing potential near-future climates. In addition, we find evidence that the microbiomes of D. magna genotypes from different regions are distinct, even years after being brought into the laboratory. Finally, our results highlight a potentially common finding in the expanding area of microbiome research-differences among treatments are not necessarily observed in the most abundant taxonomic groups. This highlights the importance of considering sampling scheme and depth of coverage when characterizing the microbiome, as different experimental designs can significantly impact taxon-specific results, even when large-scale effects are reproduced.
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Affiliation(s)
- Jonas Frankel-Bricker
- Department of Biology, Reed College, Portland, OR, 97202, USA
- Department of Biological Sciences, Boise State University, Boise, ID, 83725, USA
| | - Michael J Song
- University and Jepson Herbaria and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Maia J Benner
- Department of Biology, Reed College, Portland, OR, 97202, USA
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR, 97202, USA.
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Schneider D, Lopez LS, Li M, Crawford JD, Kirchhoff H, Kunz HH. Fluctuating light experiments and semi-automated plant phenotyping enabled by self-built growth racks and simple upgrades to the IMAGING-PAM. Plant Methods 2019; 15:156. [PMID: 31889980 PMCID: PMC6927185 DOI: 10.1186/s13007-019-0546-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/09/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Over the last years, several plant science labs have started to employ fluctuating growth light conditions to simulate natural light regimes more closely. Many plant mutants reveal quantifiable effects under fluctuating light despite being indistinguishable from wild-type plants under standard constant light. Moreover, many subtle plant phenotypes become intensified and thus can be studied in more detail. This observation has caused a paradigm shift within the photosynthesis research community and an increasing number of scientists are interested in using fluctuating light growth conditions. However, high installation costs for commercial controllable LED setups as well as costly phenotyping equipment can make it hard for small academic groups to compete in this emerging field. RESULTS We show a simple do-it-yourself approach to enable fluctuating light growth experiments. Our results using previously published fluctuating light sensitive mutants, stn7 and pgr5, confirm that our low-cost setup yields similar results as top-prized commercial growth regimes. Moreover, we show how we increased the throughput of our Walz IMAGING-PAM, also found in many other departments around the world. We have designed a Python and R-based open source toolkit that allows for semi-automated sample segmentation and data analysis thereby reducing the processing bottleneck of large experimental datasets. We provide detailed instructions on how to build and functionally test each setup. CONCLUSIONS With material costs well below USD$1000, it is possible to setup a fluctuating light rack including a constant light control shelf for comparison. This allows more scientists to perform experiments closer to natural light conditions and contribute to an emerging research field. A small addition to the IMAGING-PAM hardware not only increases sample throughput but also enables larger-scale plant phenotyping with automated data analysis.
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Affiliation(s)
- Dominik Schneider
- Compact Plants Phenomics Center, Washington State University, PO Box 646340, Pullman, WA 99164-6340 USA
- Institute of Biological Chemistry, Washington State University, PO Box 646340, Pullman, WA 99164-6340 USA
| | - Laura S. Lopez
- Plant Physiology, School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236 USA
| | - Meng Li
- Institute of Biological Chemistry, Washington State University, PO Box 646340, Pullman, WA 99164-6340 USA
| | - Joseph D. Crawford
- Plant Physiology, School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236 USA
| | - Helmut Kirchhoff
- Institute of Biological Chemistry, Washington State University, PO Box 646340, Pullman, WA 99164-6340 USA
| | - Hans-Henning Kunz
- Plant Physiology, School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236 USA
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Hay EA, Parthasarathy R. Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets. PLoS Comput Biol 2018; 14:e1006628. [PMID: 30507940 PMCID: PMC6292638 DOI: 10.1371/journal.pcbi.1006628] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 12/13/2018] [Accepted: 11/07/2018] [Indexed: 12/23/2022] Open
Abstract
Three-dimensional microscopy is increasingly prevalent in biology due to the development of techniques such as multiphoton, spinning disk confocal, and light sheet fluorescence microscopies. These methods enable unprecedented studies of life at the microscale, but bring with them larger and more complex datasets. New image processing techniques are therefore called for to analyze the resulting images in an accurate and efficient manner. Convolutional neural networks are becoming the standard for classification of objects within images due to their accuracy and generalizability compared to traditional techniques. Their application to data derived from 3D imaging, however, is relatively new and has mostly been in areas of magnetic resonance imaging and computer tomography. It remains unclear, for images of discrete cells in variable backgrounds as are commonly encountered in fluorescence microscopy, whether convolutional neural networks provide sufficient performance to warrant their adoption, especially given the challenges of human comprehension of their classification criteria and their requirements of large training datasets. We therefore applied a 3D convolutional neural network to distinguish bacteria and non-bacterial objects in 3D light sheet fluorescence microscopy images of larval zebrafish intestines. We find that the neural network is as accurate as human experts, outperforms random forest and support vector machine classifiers, and generalizes well to a different bacterial species through the use of transfer learning. We also discuss network design considerations, and describe the dependence of accuracy on dataset size and data augmentation. We provide source code, labeled data, and descriptions of our analysis pipeline to facilitate adoption of convolutional neural network analysis for three-dimensional microscopy data.
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Affiliation(s)
- Edouard A. Hay
- Department of Physics, Institute of Molecular Biology, Materials Science Institute, University of Oregon, Eugene, Oregon, United States of America
| | - Raghuveer Parthasarathy
- Department of Physics, Institute of Molecular Biology, Materials Science Institute, University of Oregon, Eugene, Oregon, United States of America
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Fuchs AL, Weaver AJ, Tripet BP, Ammons MCB, Teintze M, Copié V. Characterization of the antibacterial activity of Bald's eyesalve against drug resistant Staphylococcus aureus and Pseudomonas aeruginosa. PLoS One 2018; 13:e0208108. [PMID: 30485362 PMCID: PMC6261618 DOI: 10.1371/journal.pone.0208108] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/12/2018] [Indexed: 11/18/2022] Open
Abstract
Bald's eyesalve is an Anglo-Saxon medicinal remedy that has been used through ancient times to treat eye sty infections and may represent a source of ancientbiotics. This study assessed the efficacy of Bald's eyesalve against several strains of Staphylococcus aureus and Pseudomonas aeruginosa, including a multi-drug resistant phenotype, and identified the principal compound conveying antibacterial activity. Bald's eyesalve formulations were produced by combining garlic, onion or leek, wine, bovine bile, and brass, with specific ingredient omissions in several formulations, followed by incubation at 4 °C for 9 days. Bald's eyesalve formulation ES-GBBr exhibited the greatest antibacterial activity against S. aureus and P. aeruginosa. Fractionation of ES-GBBr using molecular size exclusion and organic solvent partitioning isolated its antibacterial activity to the small molecule nonpolar fraction, and 1D 1H NMR revealed the identity of the antibacterial agent to be allicin. Depletion of allicin from this fraction by addition of exogenous cysteine established that all observable growth inhibition originated from allicin. Quantification of allicin demonstrated that its concentration was significantly greater in ES-GBBr compared to the ES-O formulation; however, this was not due to greater yield. The antibacterial activity of allicin against S. aureus was antagonized by other ingredients within Bald's eyesalve, whereas they were additive or synergistic against P. aeruginosa. These results suggest that neither leek nor onion is necessary for the antibacterial efficacy of Bald's eyesalve against S. aureus or P. aeruginosa, and while allicin was identified as the principal antibacterial agent present, its activity is influenced differentially in the presence of additional Bald's eyesalve ingredients when used against S. aureus compared to P. aeruginosa. Ancientbiotics may provide a source of promising antibacterials; however, identifying the source of activity and assessing distinct formulations for cooperative effects are essential to using ancient remedies, such as Bald's eyesalve, effectively against drug resistant pathogens.
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Affiliation(s)
- Amanda L. Fuchs
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - Alan J. Weaver
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - Brian P. Tripet
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - Mary Cloud B. Ammons
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - Martin Teintze
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - Valérie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
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Logan SL, Dudley C, Baker RP, Taormina MJ, Hay EA, Parthasarathy R. Automated high-throughput light-sheet fluorescence microscopy of larval zebrafish. PLoS One 2018; 13:e0198705. [PMID: 30427839 PMCID: PMC6235235 DOI: 10.1371/journal.pone.0198705] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/23/2018] [Indexed: 12/21/2022] Open
Abstract
Light sheet fluorescence microscopy enables fast, minimally phototoxic, three-dimensional imaging of live specimens, but is currently limited by low throughput and tedious sample preparation. Here, we describe an automated high-throughput light sheet fluorescence microscope in which specimens are positioned by and imaged within a fluidic system integrated with the sheet excitation and detection optics. We demonstrate the ability of the instrument to rapidly examine live specimens with minimal manual intervention by imaging fluorescent neutrophils over a nearly 0.3 mm3 volume in dozens of larval zebrafish. In addition to revealing considerable inter-individual variability in neutrophil number, known previously from labor-intensive methods, three-dimensional imaging allows assessment of the correlation between the bulk measure of total cellular fluorescence and the spatially resolved measure of actual neutrophil number per animal. We suggest that our simple experimental design should considerably expand the scope and impact of light sheet imaging in the life sciences.
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Affiliation(s)
- Savannah L. Logan
- Materials Science Institute, Institute of Molecular Biology, and Department of Physics, The University of Oregon, Eugene, OR, United States of America
| | - Christopher Dudley
- Materials Science Institute, Institute of Molecular Biology, and Department of Physics, The University of Oregon, Eugene, OR, United States of America
| | - Ryan P. Baker
- Materials Science Institute, Institute of Molecular Biology, and Department of Physics, The University of Oregon, Eugene, OR, United States of America
| | - Michael J. Taormina
- Materials Science Institute, Institute of Molecular Biology, and Department of Physics, The University of Oregon, Eugene, OR, United States of America
| | - Edouard A. Hay
- Materials Science Institute, Institute of Molecular Biology, and Department of Physics, The University of Oregon, Eugene, OR, United States of America
| | - Raghuveer Parthasarathy
- Materials Science Institute, Institute of Molecular Biology, and Department of Physics, The University of Oregon, Eugene, OR, United States of America
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Njikan S, Manning AJ, Ovechkina Y, Awasthi D, Parish T. High content, high-throughput screening for small molecule inducers of NF-κB translocation. PLoS One 2018; 13:e0199966. [PMID: 29953522 PMCID: PMC6023200 DOI: 10.1371/journal.pone.0199966] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/18/2018] [Indexed: 12/22/2022] Open
Abstract
NF-κB is an important mediator of immune activity and its activation is essential in mounting immune response to pathogens. Here, we describe the optimization and implementation of a high-throughput screening platform that utilizes high content imaging and analysis to monitor NF-κB nuclear translocation. We screened 38,991 compounds from three different small molecule libraries and identified 103 compound as hits; 31% of these were active in a dose response assay. Several of the molecules lacked cytotoxicity or had a selectivity index of more than 2-fold. Our image-based approach provides an important first step towards identifying small molecules with immunomodulatory activity.
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Affiliation(s)
- Samuel Njikan
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States of America
| | - Alyssa J. Manning
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States of America
| | - Yulia Ovechkina
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States of America
| | - Divya Awasthi
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States of America
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States of America
- * E-mail:
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Carlson NV, Pargeter HM, Templeton CN. Sparrowhawk movement, calling, and presence of dead conspecifics differentially impact blue tit ( Cyanistes caeruleus) vocal and behavioral mobbing responses. Behav Ecol Sociobiol 2017; 71:133. [PMID: 28860673 PMCID: PMC5558234 DOI: 10.1007/s00265-017-2361-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/27/2017] [Accepted: 07/31/2017] [Indexed: 11/25/2022]
Abstract
ABSTRACT Many animals alter their anti-predator behavior in accordance to the threat level of a predator. While much research has examined variation in mobbing responses to different predators, few studies have investigated how anti-predator behavior is affected by changes in a predator's own state or behavior. We examined the effect of sparrowhawk (Accipiter nisus) behavior on the mobbing response of wild blue tits (Cyanistes caeruleus) using robotic taxidermy sparrowhawks. We manipulated whether the simulated predator moved its head, produced vocalizations, or held a taxidermy blue tit in its talons. When any sparrowhawk model was present, blue tits decreased foraging and increased anti-predator behavior and vocalizations. Additionally, each manipulation of the model predator's state (moving, vocalizing, or the presence of a dead conspecific) impacted different types of blue tit anti-predator behavior and vocalizations. These results indicate that different components of mobbing vary according to the specific state of a given predator-beyond its presence or absence-and suggest that each might play a different role in the overall mobbing response. Last, our results indicate that using more life-like predator stimuli-those featuring simple head movements and audio playback of vocalizations-changes how prey respond to the predator; these 'robo-raptor' models provide a powerful tool to provide increased realism in simulated predator encounters without sacrificing experimental control. SIGNIFICANCE STATEMENT Anti-predatory behavior is often modulated by the threat level posed by a particular predator. While much research has tested how different types of predators change prey behavior, few experiments have examined how predator behavior affects anti-predatory responses of prey. By experimentally manipulating robotic predators, we show that blue tits not only respond to the presence of a sparrowhawk, by decreasing feeding and increasing anti-predator behavior and vocalizations, but that they vary specific anti-predator behaviors when encountering differently behaving predators (moving, vocalizing, or those with captured prey), suggesting that prey pay attention to their predators' state and behavior.
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Affiliation(s)
- Nora V. Carlson
- School of Biology, University of St Andrews, Harold Mitchell Building, St Andrews, Fife, Scotland KY16 9TH UK
| | - Helen M. Pargeter
- School of Biology, University of St Andrews, Harold Mitchell Building, St Andrews, Fife, Scotland KY16 9TH UK
- Present Address: Departament de Biologia Animal (Vertebrats), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Christopher N. Templeton
- School of Biology, University of St Andrews, Harold Mitchell Building, St Andrews, Fife, Scotland KY16 9TH UK
- Department of Biology, Pacific University, 2043 College Way, Forest Grove, Oregon, 97116 USA
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31
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Leiser SF, Jafari G, Primitivo M, Sutphin GL, Dong J, Leonard A, Fletcher M, Kaeberlein M. Age-associated vulval integrity is an important marker of nematode healthspan. Age (Dordr) 2016; 38:419-431. [PMID: 27566309 PMCID: PMC5266215 DOI: 10.1007/s11357-016-9936-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/13/2016] [Indexed: 06/06/2023]
Abstract
Improving healthspan, defined as the period where organisms live without frailty and/or disease, is a major goal of biomedical research. While healthspan measures in people are relatively easy to identify, developing robust markers of healthspan in model organisms has proven challenging. Studies using the nematode Caenorhabditis elegans have provided vital information on the basic mechanisms of aging; however, worm health is difficult to define, and the impact of interventions that increase lifespan on worm healthspan has been controversial. Here, we describe a marker of population healthspan in C. elegans that we term age-associated vulval integrity defects, or Avid, frequently described elsewhere as rupture or exploding. We connect the presence of this phenotype with temperature, reproduction, diet, and longevity. Our results show that Avid occurs in post-reproductive worms under common laboratory conditions at a frequency that correlates negatively with temperature; Avid is rare in worms kept at 25 °C and more frequent in worms kept at 15 °C. We describe the kinetics of Avid, link the phenotype to oocyte production, and describe how Avid involves the ejection of worm proteins and/or internal organ(s) from the vulva. Finally, we find that Avid is preventable by removing worms from food, suggesting that Avid results from the intake, digestion, and/or absorption of food. Our results show that Avid is a significant cause of death in worm populations maintained under laboratory conditions and that its prevention often correlates with worm longevity. We propose that Avid is a powerful marker of worm healthspan whose underlying molecular mechanisms may be conserved.
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Affiliation(s)
- Scott F Leiser
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA.
| | - Gholamali Jafari
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Melissa Primitivo
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - George L Sutphin
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Jingyi Dong
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Alison Leonard
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Marissa Fletcher
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA.
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