1
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Abbaali I, Truong D, Wetzel DM, Morrissette NS. Toxoplasma replication is inhibited by MMV676477 without development of resistance. Cytoskeleton (Hoboken) 2024. [PMID: 38757481 DOI: 10.1002/cm.21876] [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: 01/05/2024] [Revised: 03/20/2024] [Accepted: 04/24/2024] [Indexed: 05/18/2024]
Abstract
Protozoan parasites cause life-threatening infections in both humans and animals, including agriculturally significant livestock. Available treatments are typically narrow spectrum and are complicated by drug toxicity and the development of resistant parasites. Protozoan tubulin is an attractive target for the development of broad-spectrum antimitotic agents. The Medicines for Malaria Pathogen Box compound MMV676477 was previously shown to inhibit replication of kinetoplastid parasites, such as Leishmania amazonensis and Trypanosoma brucei, and the apicomplexan parasite Plasmodium falciparum by selectively stabilizing protozoan microtubules. In this report, we show that MMV676477 inhibits intracellular growth of the human apicomplexan pathogen Toxoplasma gondii with an EC50 value of ~50 nM. MMV676477 does not stabilize vertebrate microtubules or cause other toxic effects in human fibroblasts. The availability of tools for genetic studies makes Toxoplasma a useful model for studies of the cytoskeleton. We conducted a forward genetics screen for MMV676477 resistance, anticipating that missense mutations would delineate the binding site on protozoan tubulin. Unfortunately, we were unable to use genetics to dissect target interactions because no resistant parasites emerged. This outcome suggests that future drugs based on the MMV676477 scaffold would be less likely to be undermined by the emergence of drug resistance.
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Affiliation(s)
- Izra Abbaali
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Danny Truong
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Dawn M Wetzel
- Department of Pediatrics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Naomi S Morrissette
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
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2
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Ellers O, Ellers KI, Johnson AS, Po T, Heydari S, Kanso E, McHenry MJ. Soft skeletons transmit force with variable gearing. J Exp Biol 2024; 227:jeb246901. [PMID: 38738313 DOI: 10.1242/jeb.246901] [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: 10/25/2023] [Accepted: 04/12/2024] [Indexed: 05/14/2024]
Abstract
A hydrostatic skeleton allows a soft body to transmit muscular force via internal pressure. A human's tongue, an octopus' arm and a nematode's body illustrate the pervasive presence of hydrostatic skeletons among animals, which has inspired the design of soft engineered actuators. However, there is a need for a theoretical basis for understanding how hydrostatic skeletons apply mechanical work. We therefore modeled the shape change and mechanics of natural and engineered hydrostatic skeletons to determine their mechanical advantage (MA) and displacement advantage (DA). These models apply to a variety of biological structures, but we explicitly consider the tube feet of a sea star and the body segments of an earthworm, and contrast them with a hydraulic press and a McKibben actuator. A helical winding of stiff, elastic fibers around these soft actuators plays a critical role in their mechanics by maintaining a cylindrical shape, distributing forces throughout the structure and storing elastic energy. In contrast to a single-joint lever system, soft hydrostats exhibit variable gearing with changes in MA generated by deformation in the skeleton. We found that this gearing is affected by the transmission efficiency of mechanical work (MA×DA) or, equivalently, the ratio of output to input work. The transmission efficiency changes with the capacity to store elastic energy within helically wrapped fibers or associated musculature. This modeling offers a conceptual basis for understanding the relationship between the morphology of hydrostatic skeletons and their mechanical performance.
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Affiliation(s)
- Olaf Ellers
- Biology Department, Bowdoin College, Brunswick, ME 04011, USA
| | - Kai-Isaak Ellers
- Physics Department, University of California, Berkeley, Berkeley, CA 94720-7300, USA
| | - Amy S Johnson
- Biology Department, Bowdoin College, Brunswick, ME 04011, USA
| | - Theodora Po
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697-2525, USA
| | - Sina Heydari
- Department of Aerospace and Mechanical Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Mechanical Engineering, Santa Clara University, Santa Clara, CA 95053, USA
| | - Eva Kanso
- Department of Aerospace and Mechanical Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Matthew J McHenry
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697-2525, USA
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3
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Ede SR, Yu H, Sung CH, Kisailus D. Bio-Inspired Functional Materials for Environmental Applications. Small Methods 2024; 8:e2301227. [PMID: 38133492 DOI: 10.1002/smtd.202301227] [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: 09/12/2023] [Indexed: 12/23/2023]
Abstract
With the global population expected to reach 9.7 billion by 2050, there is an urgent need for advanced materials that can address existing and developing environmental issues. Many current synthesis processes are environmentally unfriendly and often lack control over size, shape, and phase of resulting materials. Based on knowledge from biological synthesis and assembly processes, as well as their resulting functions (e.g., photosynthesis, self-healing, anti-fouling, etc.), researchers are now beginning to leverage these biological blueprints to advance bio-inspired pathways for functional materials for water treatment, air purification and sensing. The result has been the development of novel materials that demonstrate enhanced performance and address sustainability. Here, an overview of the progress and potential of bio-inspired methods toward functional materials for environmental applications is provided. The challenges and opportunities for this rapidly expanding field and aim to provide a valuable resource for researchers and engineers interested in developing sustainable and efficient processes and technologies is discussed.
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Affiliation(s)
- Sivasankara Rao Ede
- Department of Materials Science and Engineering, University of California, Irvine, California, 92697, USA
| | - Haitao Yu
- Department of Materials Science and Engineering, University of California, Irvine, California, 92697, USA
| | - Chao Hsuan Sung
- Department of Materials Science and Engineering, University of California, Irvine, California, 92697, USA
| | - David Kisailus
- Department of Materials Science and Engineering, University of California, Irvine, California, 92697, USA
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4
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Lee JL, Biswas S, Ziller JW, Bominaar EL, Hendrich MP, Borovik AS. Accessing a synthetic Fe IIIMn IV core to model biological heterobimetallic active sites. Chem Sci 2024; 15:2817-2826. [PMID: 38404374 PMCID: PMC10882444 DOI: 10.1039/d3sc04900k] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/22/2023] [Indexed: 02/27/2024] Open
Abstract
Metalloproteins with dinuclear cores are known to bind and activate dioxygen, with a subclass of these proteins having active sites containing FeMn cofactors and activities ranging from long-range proton-coupled electron transfer (PCET) to post-translational peptide modification. While mechanistic studies propose that these metallocofactors access FeIIIMnIV intermediates, there is a dearth of related synthetic analogs. Herein, the first well-characterized synthetic FeIII-(μ-O)-MnIV complex is reported; this complex shows similar spectroscopic features as the catalytically competent FeIIIMnIV intermediate X found in Class Ic ribonucleotide reductase and demonstrates PCET function towards phenolic substrates. This complex is prepared from the oxidation of the isolable FeIII-(μ-O)-MnIII species, whose stepwise assembly is facilitated by a tripodal ligand containing phosphinic amido groups. Structural and spectroscopic studies found proton movement involving the FeIIIMnIII core, whereby the initial bridging hydroxido ligand is converted to an oxido ligand with concomitant protonation of one phosphinic amido group. This series of FeMn complexes allowed us to address factors that may dictate the preference of an active site for a heterobimetallic cofactor over one that is homobimetallic: comparisons of the redox properties of our FeMn complexes with those of the di-Fe analogs suggested that the relative thermodynamic ease of accessing an FeIIIMnIV core can play an important role in determining the metal ion composition when the key catalytic steps do not require an overly potent oxidant. Moreover, these complexes allowed us to demonstrate the effect of the hyperfine interaction from non-Fe nuclei on 57Fe Mössbauer spectra which is relevant to MnFe intermediates in proteins.
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Affiliation(s)
- Justin L Lee
- Department of Chemistry, University of California-Irvine Irvine CA 92697 USA
| | - Saborni Biswas
- Department of Chemistry, Carnegie Mellon University Pittsburgh PA 15213 USA
| | - Joseph W Ziller
- Department of Chemistry, University of California-Irvine Irvine CA 92697 USA
| | - Emile L Bominaar
- Department of Chemistry, Carnegie Mellon University Pittsburgh PA 15213 USA
| | - Michael P Hendrich
- Department of Chemistry, Carnegie Mellon University Pittsburgh PA 15213 USA
| | - A S Borovik
- Department of Chemistry, University of California-Irvine Irvine CA 92697 USA
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5
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Samdin TD, Jones CR, Guaglianone G, Kreutzer AG, Freites JA, Wierzbicki M, Nowick JS. A β-barrel-like tetramer formed by a β-hairpin derived from Aβ. Chem Sci 2023; 15:285-297. [PMID: 38131075 PMCID: PMC10732006 DOI: 10.1039/d3sc05185d] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
β-Hairpins formed by the β-amyloid peptide Aβ are building blocks of Aβ oligomers. Three different alignments of β-hairpins have been observed in the structures of Aβ oligomers or fibrils. Differences in β-hairpin alignment likely contribute to the heterogeneity of Aβ oligomers and thus impede their study at high-resolution. Here, we designed, synthesized, and studied a series of β-hairpin peptides derived from Aβ12-40 in one of these three alignments and investigated their solution-phase assembly and folding. These assays reveal the formation of tetramers and octamers that are stabilized by intermolecular hydrogen bonding interactions between Aβ residues 12-14 and 38-40 as part of an extended β-hairpin conformation. X-ray crystallographic studies of one peptide from this series reveal the formation of β-barrel-like tetramers and octamers that are stabilized by edge-to-edge hydrogen bonding and hydrophobic packing. Dye-leakage and caspase 3/7 activation assays using tetramer and octamer forming peptides from this series reveal membrane-damaging and apoptotic properties. A molecular dynamics simulation of the β-barrel-like tetramer embedded in a lipid bilayer shows membrane disruption and water permeation. The tetramers and octamers described herein provide additional models of how Aβ may assemble into oligomers and supports the hypothesis that β-hairpin alignment and topology may contribute directly to oligomer heterogeneity.
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Affiliation(s)
- Tuan D Samdin
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - Chelsea R Jones
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - Gretchen Guaglianone
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - Adam G Kreutzer
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - J Alfredo Freites
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - Michał Wierzbicki
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - James S Nowick
- Department of Chemistry, University of California Irvine California 92697-2025 USA
- Department of Pharmaceutical Sciences, University of California, Irvine Irvine California 92697-2025 USA
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6
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Le N, Heras J, Herrera MJ, German DP, Crummett LT. The genome of Anoplarchus purpurescens (Stichaeidae) reflects its carnivorous diet. Mol Genet Genomics 2023; 298:1419-1434. [PMID: 37690047 PMCID: PMC10657299 DOI: 10.1007/s00438-023-02067-5] [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: 03/29/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]
Abstract
Digestion is driven by digestive enzymes and digestive enzyme gene copy number can provide insights on the genomic underpinnings of dietary specialization. The "Adaptive Modulation Hypothesis" (AMH) proposes that digestive enzyme activity, which increases with increased gene copy number, should correlate with substrate quantity in the diet. To test the AMH and reveal some of the genetics of herbivory vs carnivory, we sequenced, assembled, and annotated the genome of Anoplarchus purpurescens, a carnivorous prickleback fish in the family Stichaeidae, and compared the gene copy number for key digestive enzymes to that of Cebidichthys violaceus, a herbivorous fish from the same family. A highly contiguous genome assembly of high quality (N50 = 10.6 Mb) was produced for A. purpurescens, using combined long-read and short-read technology, with an estimated 33,842 protein-coding genes. The digestive enzymes that we examined include pancreatic α-amylase, carboxyl ester lipase, alanyl aminopeptidase, trypsin, and chymotrypsin. Anoplarchus purpurescens had fewer copies of pancreatic α-amylase (carbohydrate digestion) than C. violaceus (1 vs. 3 copies). Moreover, A. purpurescens had one fewer copy of carboxyl ester lipase (plant lipid digestion) than C. violaceus (4 vs. 5). We observed an expansion in copy number for several protein digestion genes in A. purpurescens compared to C. violaceus, including trypsin (5 vs. 3) and total aminopeptidases (6 vs. 5). Collectively, these genomic differences coincide with measured digestive enzyme activities (phenotypes) in the two species and they support the AMH. Moreover, this genomic resource is now available to better understand fish biology and dietary specialization.
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Affiliation(s)
- Ninh Le
- Life Sciences Concentration, Soka University of America, Aliso Viejo, CA, 92656, USA
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Joseph Heras
- Department of Biology, California State University, San Bernardino, CA, 92407, USA
| | - Michelle J Herrera
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Donovan P German
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.
| | - Lisa T Crummett
- Life Sciences Concentration, Soka University of America, Aliso Viejo, CA, 92656, USA.
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7
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Mendoza E, Martinez M, Olberding JP, Azizi E. The effects of temperature on elastic energy storage and release in a system with a dynamic mechanical advantage latch. J Exp Biol 2023; 226:jeb245805. [PMID: 37727106 PMCID: PMC10617612 DOI: 10.1242/jeb.245805] [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: 03/10/2023] [Accepted: 09/01/2023] [Indexed: 09/21/2023]
Abstract
Changes in temperature alter muscle kinetics and in turn affect whole-organism performance. Some organisms use the elastic recoil of biological springs, structures which are far less temperature sensitive, to power thermally robust movements. For jumping frogs, the use of elastic energy in tendons is facilitated through a geometric latching mechanism that operates through dynamic changes in the mechanical advantage (MA) of the hindlimb. Despite the well-documented use of elastic energy storage, frog jumping is a locomotor behavior that is significantly affected by changes in temperature. Here, we used an in vitro muscle preparation interacting in real time with an in silico model of a legged jumper to understand how changes in temperature affect the flow of energy in a system using a MA latch. We used the plantaris longus muscle-tendon unit (MTU) to power a virtual limb with changing MA and a mass being accelerated through a real-time feedback controller. We quantified the amount of energy stored in and recovered from elastic structures and the additional contribution of direct muscle work after unlatching. We found that temperature altered the duration of the energy loading and recovery phase of the in vitro/in silico experiments. We found that the early phase of loading was insensitive to changes in temperature. However, an increase in temperature did increase the rate of force development, which in turn allowed for increased energy storage in the second phase of loading. We also found that the contribution of direct muscle work after unlatching was substantial and increased significantly with temperature. Our results show that the thermal robustness achieved by an elastic mechanism depends strongly on the nature of the latch that mediates energy flow, and that the relative contribution of elastic and direct muscle energy likely shapes the thermal sensitivity of locomotor systems.
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Affiliation(s)
- Elizabeth Mendoza
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Maya Martinez
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
- Biomedical Engineering Department, California State University, Long Beach, CA 90840, USA
| | - Jeffrey P. Olberding
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biological Science, California State University, Fullerton, CA 92831, USA
| | - Emanuel Azizi
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
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8
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Zhao R, Lukacsovich T, Gaut R, Emerson JJ. FREQ-Seq2: a method for precise high-throughput combinatorial quantification of allele frequencies. G3 (Bethesda) 2023; 13:jkad162. [PMID: 37494033 PMCID: PMC10542570 DOI: 10.1093/g3journal/jkad162] [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] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 01/26/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023]
Abstract
The accurate determination of allele frequencies is crucially important across a wide range of problems in genetics, such as developing population genetic models, making inferences from genome-wide association studies, determining genetic risk for diseases, as well as other scientific and medical applications. Furthermore, understanding how allele frequencies change over time in populations is central to ascertaining their evolutionary dynamics. We present a precise, efficient, and economical method (FREQ-Seq2) for quantifying the relative frequencies of different alleles at loci of interest in mixed population samples. Through the creative use of paired barcode sequences, we exponentially increased the throughput of the original FREQ-Seq method from 48 to 2,304 samples. FREQ-Seq2 can be targeted to specific genomic regions of interest, which are amplified using universal barcoded adapters to generate Illumina sequencing libraries. Our enhanced method, available as a kit along with open-source software for analyzing sequenced libraries, enables the detection and removal of errors that are undetectable in the original FREQ-Seq method as well as other conventional methods for allele frequency quantification. Finally, we validated the performance of our sequencing-based approach with a highly multiplexed set of control samples as well as a competitive evolution experiment in Escherichia coli and compare the latter to estimates derived from manual colony counting. Our analyses demonstrate that FREQ-Seq2 is flexible, inexpensive, and produces large amounts of data with low error, low noise, and desirable statistical properties. In summary, FREQ-Seq2 is a powerful method for quantifying allele frequency that provides a versatile approach for profiling mixed populations.
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Affiliation(s)
- Roy Zhao
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
| | - Tamas Lukacsovich
- Brain Research Institute, University of Zürich, 8057 Zürich, Switzerland
| | - Rebecca Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - J J Emerson
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
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9
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Lim S, Cordova DLM, Robang AS, Kuang Y, Ogura KS, Paravastu AK, Arguilla MQ, Ardoña HAM. Thermochromic Behavior of Polydiacetylene Nanomaterials Driven by Charged Peptide Amphiphiles. Biomacromolecules 2023; 24:4051-4063. [PMID: 37552220 PMCID: PMC10498447 DOI: 10.1021/acs.biomac.3c00422] [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: 04/25/2023] [Revised: 07/18/2023] [Indexed: 08/09/2023]
Abstract
The tunability of chromatic phases adapted by chromogenic polymers such as polydiacetylene (PDA) is key to their utility for robust sensing applications. Here, we investigated the influence of charged peptide interactions on the structure-dependent thermochromicity of amphiphilic PDAs. Solid-state NMR and circular dichroism analyses show that our oppositely charged peptide-PDA samples have distinct degrees of structural order, with the coassembled sample being in between the β-sheet-like positive peptide-PDA and the relatively disordered negative peptide-PDA. All solutions exhibit thermochromicity between 20 and 80 °C, whereby the hysteresis of the blue, planar phase is much larger than that of the red, twisted phase. Resonance Raman spectroscopy of films demonstrates that only coassemblies with electrostatic complementarity stabilize coexisting blue and red PDA phases. This work reveals the nature of the structural changes responsible for the thermally responsive chromatic transitions of biomolecule-functionalized polymeric materials and how this process can be directed by sequence-dictated electrostatic interactions.
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Affiliation(s)
- Sujeung Lim
- Department
of Chemical and Biomolecular Engineering, Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Dmitri Leo M. Cordova
- Department
of Chemistry, School of Physical Sciences, University of California, Irvine, California 92697, United States
| | - Alicia S. Robang
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yuyao Kuang
- Department
of Chemical and Biomolecular Engineering, Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Kaleolani S. Ogura
- Department
of Chemistry, School of Physical Sciences, University of California, Irvine, California 92697, United States
| | - Anant K. Paravastu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Maxx Q. Arguilla
- Department
of Chemistry, School of Physical Sciences, University of California, Irvine, California 92697, United States
| | - Herdeline Ann M. Ardoña
- Department
of Chemical and Biomolecular Engineering, Samueli School of Engineering, University of California, Irvine, California 92697, United States
- Department
of Chemistry, School of Physical Sciences, University of California, Irvine, California 92697, United States
- Department
of Biomedical Engineering, Samueli School of Engineering, University of California, Irvine, California 92697, United States
- Sue
& Bill Gross Stem Cell Research Center, University of California, Irvine, California 92697, United States
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10
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Kuang Y, Yao ZF, Lim S, Ngo C, Rocha MA, Fishman DA, Ardoña HAM. Biomimetic Sequence-Templating Approach toward a Multiscale Modulation of Chromogenic Polymer Properties. Macromolecules 2023; 56:4526-4540. [PMID: 37397164 PMCID: PMC10311629 DOI: 10.1021/acs.macromol.3c00403] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/28/2023] [Indexed: 07/04/2023]
Abstract
Precision control via molecular structure over adaptive conjugated polymer properties in aqueous environments is critical for realizing their biomedical applications. Here, we unravel the dependence of amphiphilic peptide-polydiacetylene (PDA) conjugate properties on the characteristic steric and hydrophobic contributions within peptide segments that serve as a biomimetic template for diacetylene polymerization in water. We investigated the functional impacts of molecular volume and polarity changes brought by dipeptide substitution domains on the following peptide-PDA material properties at multiple length scales: supramolecular assembly behavior, chain conformation-dependent photophysical properties, cell-material interfacing, and for the first time, bulk electrical properties of their films processed in water. A library of peptide-PDAs with systematically varied sequences show that the contributions of steric effects predominantly influence the electronic structure and resulting trends in photophysical properties, while the interplay between size and hydrophobicity of individual residues becomes more significant for higher-order assemblies affecting bulk properties. This work demonstrates sequence-tunable molecular volume and polarity as synthetic handles to rationally modulate PDA material properties across length scales, providing insights into the programmability of biomimetic conjugated polymers with adaptive functionalities.
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Affiliation(s)
- Yuyao Kuang
- Department
of Chemical and Biomolecular Engineering, Samueli School of Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Ze-Fan Yao
- Department
of Chemical and Biomolecular Engineering, Samueli School of Engineering, University of California, Irvine, Irvine, California 92697, United States
- Department
of Biomedical Engineering, Samueli School of Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Sujeung Lim
- Department
of Chemical and Biomolecular Engineering, Samueli School of Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Catherine Ngo
- Department
of Chemical and Biomolecular Engineering, Samueli School of Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Megan Alma Rocha
- Department
of Chemistry, School of Physical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Dmitry A. Fishman
- Department
of Chemistry, School of Physical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Herdeline Ann M. Ardoña
- Department
of Chemical and Biomolecular Engineering, Samueli School of Engineering, University of California, Irvine, Irvine, California 92697, United States
- Department
of Biomedical Engineering, Samueli School of Engineering, University of California, Irvine, Irvine, California 92697, United States
- Department
of Chemistry, School of Physical Sciences, University of California, Irvine, Irvine, California 92697, United States
- Sue
& Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California 92697, United States
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11
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Smith N, Crescenzo GV, Bertram AK, Nizkorodov SA, Faiola CL. Insect Infestation Increases Viscosity of Biogenic Secondary Organic Aerosol. ACS Earth Space Chem 2023; 7:1060-1071. [PMID: 37223424 PMCID: PMC10201571 DOI: 10.1021/acsearthspacechem.3c00007] [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] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/20/2023] [Accepted: 04/13/2023] [Indexed: 05/25/2023]
Abstract
Plant stress alters emissions of volatile organic compounds. However, little is known about how this could influence climate-relevant properties of secondary organic aerosol (SOA), particularly from complex mixtures such as real plant emissions. In this study, the chemical composition and viscosity were examined for SOA generated from real healthy and aphid-stressed Canary Island pine (Pinus canariensis) trees, which are commonly used for landscaping in Southern California. Healthy Canary Island pine (HCIP) and stressed Canary Island pine (SCIP) aerosols were generated in a 5 m3 environmental chamber at 35-84% relative humidity and room temperature via OH-initiated oxidation. Viscosities of the collected particles were measured using an offline poke-flow method, after conditioning the particles in a humidified air flow. SCIP particles were consistently more viscous than HCIP particles. The largest differences in particle viscosity were observed in particles conditioned at 50% relative humidity where the viscosity of SCIP particles was an order of magnitude larger than that of HCIP particles. The increased viscosity for the aphid-stressed pine tree SOA was attributed to the increased fraction of sesquiterpenes in the emission profile. The real pine SOA particles, both healthy and aphid-stressed, were more viscous than α-pinene SOA particles, demonstrating the limitation of using a single monoterpene as a model compound to predict the physicochemical properties of real biogenic SOA. However, synthetic mixtures composed of only a few major compounds present in emissions (<10 compounds) can reproduce the viscosities of SOA observed from the more complex real plant emissions.
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Affiliation(s)
- Natalie
R. Smith
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| | - Giuseppe V. Crescenzo
- Department
of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Allan K. Bertram
- Department
of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Sergey A. Nizkorodov
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| | - Celia L. Faiola
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
- Department
of Ecology and Evolutionary Biology, University
of California, Irvine, Irvine, California 92697, United States
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12
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Allen BD, Alaghband Y, Kramár EA, Ru N, Petit B, Grilj V, Petronek MS, Pulliam CF, Kim RY, Doan NL, Baulch JE, Wood MA, Bailat C, Spitz DR, Vozenin MC, Limoli CL. Elucidating the neurological mechanism of the FLASH effect in juvenile mice exposed to hypofractionated radiotherapy. Neuro Oncol 2023; 25:927-939. [PMID: 36334265 PMCID: PMC10158064 DOI: 10.1093/neuonc/noac248] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 08/02/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Ultrahigh dose-rate radiotherapy (FLASH-RT) affords improvements in the therapeutic index by minimizing normal tissue toxicities without compromising antitumor efficacy compared to conventional dose-rate radiotherapy (CONV-RT). To investigate the translational potential of FLASH-RT to a human pediatric medulloblastoma brain tumor, we used a radiosensitive juvenile mouse model to assess adverse long-term neurological outcomes. METHODS Cohorts of 3-week-old male and female C57Bl/6 mice exposed to hypofractionated (2 × 10 Gy, FLASH-RT or CONV-RT) whole brain irradiation and unirradiated controls underwent behavioral testing to ascertain cognitive status four months posttreatment. Animals were sacrificed 6 months post-irradiation and tissues were analyzed for neurological and cerebrovascular decrements. RESULTS The neurological impact of FLASH-RT was analyzed over a 6-month follow-up. FLASH-RT ameliorated neurocognitive decrements induced by CONV-RT and preserved synaptic plasticity and integrity at the electrophysiological (long-term potentiation), molecular (synaptophysin), and structural (Bassoon/Homer-1 bouton) levels in multiple brain regions. The benefits of FLASH-RT were also linked to reduced neuroinflammation (activated microglia) and the preservation of the cerebrovascular structure, by maintaining aquaporin-4 levels and minimizing microglia colocalized to vessels. CONCLUSIONS Hypofractionated FLASH-RT affords significant and long-term normal tissue protection in the radiosensitive juvenile mouse brain when compared to CONV-RT. The capability of FLASH-RT to preserve critical cognitive outcomes and electrophysiological properties over 6-months is noteworthy and highlights its potential for resolving long-standing complications faced by pediatric brain tumor survivors. While care must be exercised before clinical translation is realized, present findings document the marked benefits of FLASH-RT that extend from synapse to cognition and the microvasculature.
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Affiliation(s)
- Barrett D Allen
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Yasaman Alaghband
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Eniko A Kramár
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
| | - Ning Ru
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Benoit Petit
- Laboratory of Radiation Oncology, Department of Radiation Oncology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Veljko Grilj
- Laboratory of Radiation Oncology, Department of Radiation Oncology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Michael S Petronek
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242, USA
| | - Casey F Pulliam
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242, USA
| | - Rachel Y Kim
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Ngoc-Lien Doan
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Janet E Baulch
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
| | - Claude Bailat
- Institute of Radiation Physics/CHUV, Lausanne University Hospital, Lausanne, Switzerland
| | - Douglas R Spitz
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242, USA
| | - Marie-Catherine Vozenin
- Laboratory of Radiation Oncology, Department of Radiation Oncology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Charles L Limoli
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
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13
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Luong J, Wang X, Tsung A, Humphrey N, Guo H, Lam BX, Mallikarjun Sharada S, Bowman WJ. Nanoscale Iron Redistribution during Thermochemical Decomposition of CaTi 1-x Fe x O 3-δ Alters the Electrical Transport Pathway: Implications for Oxygen-Transport Membranes, Electrocatalysis, and Photocatalysis. ACS Appl Nano Mater 2023; 6:1620-1630. [PMID: 36818540 PMCID: PMC9926871 DOI: 10.1021/acsanm.2c04537] [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] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
Potential applications of the earth-abundant, low-cost, and non-critical perovskite CaTi1-x Fe x O3-δ in electrocatalysis, photocatalysis, and oxygen-transport membranes have motivated research to tune its chemical composition and morphology. However, investigations on the decomposition mechanism(s) of CaTi1-x Fe x O3-δ under thermochemically reducing conditions are limited, and direct evidence of the nano- and atomic-level decomposition process is not available in the literature. In this work, the phase evolution of CaTi1-x Fe x O3-δ (x = 0-0.4) was investigated in a H2-containing atmosphere after heat treatments up to 600 °C. The results show that CaTi1-x Fe x O3-δ maintained a stable perovskite phase at low Fe contents while exhibiting a phase decomposition to Fe/Fe oxide nanoparticles as the Fe content increases. In CaTi0.7Fe0.3O3-δ and CaTi0.6Fe0.4O3-δ, the phase evolution to Fe/Fe oxide was greatly influenced by the temperature: Only temperatures of 300 °C and greater facilitated phase evolution. Fully coherent Fe-rich and Fe-depleted perovskite nanodomains were observed directly by atomic-resolution scanning transmission electron microscopy. Prior evidence for such nanodomain formation was not found, and it is thought to result from a near-surface Kirkendall-like phenomenon caused by Fe migration in the absence of Ca and Ti co-migration. Density functional theory simulations of Fe-doped bulk models reveal that Fe in an octahedral interstitial site is energetically more favorable than in a tetrahedral site. In addition to coherent nanodomains, agglomerated Fe/Fe oxide nanoparticles formed on the ceramic surface during decomposition, which altered the electrical transport mechanism. From temperature-dependent electrical conductivity measurements, it was found that heat treatment and phase decomposition change the transport mechanism from thermally activated p-type electronic conductivity through the perovskite to electronic conduction through the iron oxide formed by thermochemical decomposition. This understanding will be useful to those who are developing or employing this and similar earth-abundant functional perovskites for use under reducing conditions, at elevated temperatures, and when designing materials syntheses and processes.
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Affiliation(s)
- Jason Luong
- Department
of Materials Science and Engineering, University
of California, Irvine, Irvine, California92697, United States
| | - Xin Wang
- Department
of Materials Science and Engineering, University
of California, Irvine, Irvine, California92697, United States
| | - Alicia Tsung
- Mork
Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California90089, United States
| | - Nicholas Humphrey
- Mork
Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California90089, United States
| | - Huiming Guo
- Department
of Materials Science and Engineering, University
of California, Irvine, Irvine, California92697, United States
| | - Benjamin X. Lam
- Department
of Materials Science and Engineering, University
of California, Irvine, Irvine, California92697, United States
| | - Shaama Mallikarjun Sharada
- Mork
Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California90089, United States
- Department
of Chemistry, University of Southern California, Los Angeles, California90089, United States
| | - William J. Bowman
- Department
of Materials Science and Engineering, University
of California, Irvine, Irvine, California92697, United States
- Irvine
Materials Research Institute, University
of California, Irvine, Irvine, California92697, United States
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14
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Lim J, Wang PT, Shaw SJ, Gong H, Armacost M, Liu CY, Do AH, Heydari P, Nenadic Z. Artifact propagation in subdural cortical electrostimulation: Characterization and modeling. Front Neurosci 2022; 16:1021097. [PMID: 36312030 PMCID: PMC9596776 DOI: 10.3389/fnins.2022.1021097] [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: 08/17/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Cortical stimulation via electrocorticography (ECoG) may be an effective method for inducing artificial sensation in bi-directional brain-computer interfaces (BD-BCIs). However, strong electrical artifacts caused by electrostimulation may significantly degrade or obscure neural information. A detailed understanding of stimulation artifact propagation through relevant tissues may improve existing artifact suppression techniques or inspire the development of novel artifact mitigation strategies. Our work thus seeks to comprehensively characterize and model the propagation of artifacts in subdural ECoG stimulation. To this end, we collected and analyzed data from eloquent cortex mapping procedures of four subjects with epilepsy who were implanted with subdural ECoG electrodes. From this data, we observed that artifacts exhibited phase-locking and ratcheting characteristics in the time domain across all subjects. In the frequency domain, stimulation caused broadband power increases, as well as power bursts at the fundamental stimulation frequency and its super-harmonics. The spatial distribution of artifacts followed the potential distribution of an electric dipole with a median goodness-of-fit of R2 = 0.80 across all subjects and stimulation channels. Artifacts as large as ±1,100 μV appeared anywhere from 4.43 to 38.34 mm from the stimulation channel. These temporal, spectral and spatial characteristics can be utilized to improve existing artifact suppression techniques, inspire new strategies for artifact mitigation, and aid in the development of novel cortical stimulation protocols. Taken together, these findings deepen our understanding of cortical electrostimulation and provide critical design specifications for future BD-BCI systems.
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Affiliation(s)
- Jeffrey Lim
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- *Correspondence: Jeffrey Lim
| | - Po T. Wang
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Susan J. Shaw
- Rancho Los Amigos National Rehabilitation Center, Downey, CA, United States
| | - Hui Gong
- Rancho Los Amigos National Rehabilitation Center, Downey, CA, United States
| | - Michelle Armacost
- Rancho Los Amigos National Rehabilitation Center, Downey, CA, United States
| | - Charles Y. Liu
- Rancho Los Amigos National Rehabilitation Center, Downey, CA, United States
| | - An H. Do
- Department of Neurology, University of California, Irvine, Irvine, CA, United States
| | - Payam Heydari
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Electrical Engineering and Computer Science, University of California, Irvine, Irvine, CA, United States
| | - Zoran Nenadic
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Electrical Engineering and Computer Science, University of California, Irvine, Irvine, CA, United States
- Zoran Nenadic
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15
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Gonzàlez-Rosell A, Guha R, Cerretani C, Rück V, Liisberg MB, Katz BB, Vosch T, Copp SM. DNA Stabilizes Eight-Electron Superatom Silver Nanoclusters with Broadband Downconversion and Microsecond-Lived Luminescence. J Phys Chem Lett 2022; 13:8305-8311. [PMID: 36037464 PMCID: PMC9465679 DOI: 10.1021/acs.jpclett.2c02207] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 07/14/2022] [Accepted: 08/26/2022] [Indexed: 05/25/2023]
Abstract
DNA oligomers are known to serve as stabilizing ligands for silver nanoclusters (AgN-DNAs) with rod-like nanocluster geometries and nanosecond-lived fluorescence. Here, we report two AgN-DNAs that possess distinctly different structural properties and are the first to exhibit only microsecond-lived luminescence. These emitters are characterized by significant broadband downconversion from the ultraviolet/visible to the near-infrared region. Circular dichroism spectroscopy shows that the structures of these two AgN-DNAs differ significantly from previously reported AgN-DNAs. We find that these nanoclusters contain eight valence electrons, making them the first reported DNA-stabilized luminescent quasi-spherical superatoms. This work demonstrates the important role that nanocluster composition and geometry play in dictating luminescence properties of AgN-DNAs and significantly expands the space of structure-property relations that can be achieved for AgN-DNAs.
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Affiliation(s)
- Anna Gonzàlez-Rosell
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
| | - Rweetuparna Guha
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
| | - Cecilia Cerretani
- Nanoscience
Center and Department of Chemistry, University
of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Vanessa Rück
- Nanoscience
Center and Department of Chemistry, University
of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Mikkel B. Liisberg
- Nanoscience
Center and Department of Chemistry, University
of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Benjamin B. Katz
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Tom Vosch
- Nanoscience
Center and Department of Chemistry, University
of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Stacy M. Copp
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
- Department
of Physics and Astronomy, University of
California, Irvine, California 92697, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
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16
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Han L, Ou P, Liu W, Wang X, Wang HT, Zhang R, Pao CW, Liu X, Pong WF, Song J, Zhuang Z, Mirkin MV, Luo J, Xin HL. Design of Ru-Ni diatomic sites for efficient alkaline hydrogen oxidation. Sci Adv 2022; 8:eabm3779. [PMID: 35648856 PMCID: PMC9159574 DOI: 10.1126/sciadv.abm3779] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Anion exchange membrane fuel cells are limited by the slow kinetics of alkaline hydrogen oxidation reaction (HOR). Here, we establish HOR catalytic activities of single-atom and diatomic sites as a function of *H and *OH binding energies to screen the optimal active sites for the HOR. As a result, the Ru-Ni diatomic one is identified as the best active center. Guided by the theoretical finding, we subsequently synthesize a catalyst with Ru-Ni diatomic sites supported on N-doped porous carbon, which exhibits excellent catalytic activity, CO tolerance, and stability for alkaline HOR and is also superior to single-site counterparts. In situ scanning electrochemical microscopy study validates the HOR activity resulting from the Ru-Ni diatomic sites. Furthermore, in situ x-ray absorption spectroscopy and computational studies unveil a synergistic interaction between Ru and Ni to promote the molecular H2 dissociation and strengthen OH adsorption at the diatomic sites, and thus enhance the kinetics of HOR.
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Affiliation(s)
- Lili Han
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697, USA
| | - Pengfei Ou
- Department of Mining and Materials Engineering, McGill University, Montreal H3A 0C5, Canada
| | - Wei Liu
- Institute for New Energy Materials and Low-Carbon Technologies and Tianjin Key Laboratory of Photoelectric Materials and Devices, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Xiang Wang
- Department of Chemistry and Biochemistry, Queens College–CUNY, Flushing, Queens, NY 11367, USA
| | - Hsiao-Tsu Wang
- Department of Physics, Tamkang University, New Taipei City 25137, Taiwan
| | - Rui Zhang
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697, USA
| | - Chih-Wen Pao
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Xijun Liu
- MOE Key Laboratory of New Processing Technology for Non-Ferrous Metals and Materials, and Guangxi Key Laboratory of Processing for Non-Ferrous Metals and Featured Materials, School of Resource, Environments and Materials, Guangxi University, Nanning 530004, China
- Corresponding author. (X.L.); (H.L.X.)
| | - Way-Faung Pong
- Department of Physics, Tamkang University, New Taipei City 25137, Taiwan
| | - Jun Song
- Department of Mining and Materials Engineering, McGill University, Montreal H3A 0C5, Canada
| | - Zhongbin Zhuang
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, China
| | - Michael V. Mirkin
- Department of Chemistry and Biochemistry, Queens College–CUNY, Flushing, Queens, NY 11367, USA
| | - Jun Luo
- Institute for New Energy Materials and Low-Carbon Technologies and Tianjin Key Laboratory of Photoelectric Materials and Devices, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Huolin L. Xin
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697, USA
- Corresponding author. (X.L.); (H.L.X.)
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17
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Simakov O, Bredeson J, Berkoff K, Marletaz F, Mitros T, Schultz DT, O’Connell BL, Dear P, Martinez DE, Steele RE, Green RE, David CN, Rokhsar DS. Deeply conserved synteny and the evolution of metazoan chromosomes. Sci Adv 2022; 8:eabi5884. [PMID: 35108053 PMCID: PMC8809688 DOI: 10.1126/sciadv.abi5884] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [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: 03/21/2021] [Accepted: 12/10/2021] [Indexed: 05/04/2023]
Abstract
Animal genomes show networks of deeply conserved gene linkages whose phylogenetic scope and chromosomal context remain unclear. Here, we report chromosome-scale conservation of synteny among bilaterians, cnidarians, and sponges and use comparative analysis to reconstruct ancestral chromosomes across major animal groups. Comparisons among diverse metazoans reveal the processes of chromosome evolution that produced contemporary karyotypes from their Precambrian progenitors. On the basis of these findings, we introduce a simple algebraic representation of chromosomal change and use it to establish a unified systematic framework for metazoan chromosome evolution. We find that fusion-with-mixing, a previously unappreciated mode of chromosome change, has played a central role. We find that relicts of several metazoan chromosomal units are preserved in unicellular eukaryotes. These conserved pre-metazoan linkages include the chromosomal unit that encodes the most diverse set of metazoan homeobox genes, suggesting a candidate genomic context for the early diversification of this key gene family.
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Affiliation(s)
- Oleg Simakov
- Department for Neurosciences and Developmental
Biology, University of Vienna, Vienna 1010, Austria
| | - Jessen Bredeson
- Department of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Kodiak Berkoff
- Department of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Ferdinand Marletaz
- Molecular Genetics Unit, Okinawa Institute of Science
and Technology Graduate University, 1919-1, Tancha, Onna, Okinawa 904-0495,
Japan
- Division of Biosciences, University College London,
Gower St., London WC1E 6BT, UK
| | - Therese Mitros
- Department of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Darrin T. Schultz
- Department of Biomolecular Engineering, University of
California, Santa Cruz, Santa Cruz, CA 95064, USA
- Monterey Bay Aquarium Research Institute, Moss
Landing, CA 95039, USA
| | - Brendan L. O’Connell
- Department of Biomolecular Engineering, University of
California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Paul Dear
- Mote Research Ltd, Babraham Hall, Babraham, Cambridge
CB2 4AT, UK
| | | | - Robert E. Steele
- Department of Biological Chemistry, University of
California, Irvine, Irvine, CA 92697-1700, USA
| | - Richard E. Green
- Department of Biomolecular Engineering, University of
California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Charles N. David
- Faculty of Biology, Ludwig Maximilian University of
Munich, Munich 80539, Germany
| | - Daniel S. Rokhsar
- Department of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, CA 94720, USA
- Molecular Genetics Unit, Okinawa Institute of Science
and Technology Graduate University, 1919-1, Tancha, Onna, Okinawa 904-0495,
Japan
- Chan Zuckerberg Biohub, 499 Illinois St., San
Francisco, CA 94158, USA
- U.S. Department of Energy Joint Genome Institute,
Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720,
USA
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18
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Abstract
Elastic recoil drives some of the fastest and most powerful biological movements. For effective use of elastic recoil, the tuning of muscle and spring force capacity is essential. Although studies of invertebrate organisms that use elastic recoil show evidence of increased force capacity in their energy loading muscle, changes in the fundamental properties of such muscles have yet to be documented in vertebrates. Here, we used three species of frogs (Cuban tree frogs, bullfrogs and cane toads) that differ in jumping power to investigate functional shifts in muscle-spring tuning in systems using latch-mediated spring actuation (LaMSA). We hypothesized that variation in jumping performance would result from increased force capacity in muscles and relatively stiffer elastic structures, resulting in greater energy storage. To test this, we characterized the force-length property of the plantaris longus muscle-tendon unit (MTU), and quantified the maximal amount of energy stored in elastic structures for each species. We found that the plantaris longus MTU of Cuban tree frogs produced higher mass-specific energy and mass-specific forces than the other two species. Moreover, we found that the plantaris longus MTU of Cuban tree frogs had higher pennation angles than the other species, suggesting that muscle architecture was modified to increase force capacity through packing of more muscle fibers. Finally, we found that the elastic structures were relatively stiffer in Cuban tree frogs. These results provide a mechanistic link between the tuned properties of LaMSA components, energy storage capacity and whole-system performance.
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Affiliation(s)
- Elizabeth Mendoza
- Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall, University of California Irvine, Irvine, CA 92617, USA
| | - Emanuel Azizi
- Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall, University of California Irvine, Irvine, CA 92617, USA
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19
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Frey SE, Stapleton JT, Ballas ZK, Rasmussen WL, Kaufman TM, Blevins TP, Jensen TL, Davies DH, Tary-Lehmann M, Chaplin P, Hill H, Goll JB. Human Antibody Responses Following Vaccinia Immunization Using Protein Microarrays and Correlation With Cell-Mediated Immunity and Antibody-Dependent Cellular Cytotoxicity Responses. J Infect Dis 2021; 224:1372-1382. [PMID: 33675226 PMCID: PMC8861366 DOI: 10.1093/infdis/jiab111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 10/14/2020] [Accepted: 03/05/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND There are limited data regarding immunological correlates of protection for the modified vaccinia Ankara (MVA) smallpox vaccine. METHODS A total of 523 vaccinia-naive subjects were randomized to receive 2 vaccine doses, as lyophilized MVA given subcutaneously, liquid MVA given subcutaneously (liquid-SC group), or liquid MVA given intradermally (liquid-ID group) 28 days apart. For a subset of subjects, antibody-dependent cellular cytotoxicity (ADCC), interferon-γ release enzyme-linked immunospot (ELISPOT), and protein microarray antibody-binding assays were conducted. Protein microarray responses were assessed for correlations with plaque reduction neutralization titer (PRNT), enzyme-linked immunosorbent assay, ADCC, and ELISPOT results. RESULTS MVA elicited significant microarray antibody responses to 15 of 224 antigens, mostly virion membrane proteins, at day 28 or 42, particularly WR113/D8L and WR101H3L. In the liquid-SC group, responses to 9 antigens, including WR113/D8L and WR101/H3L, correlated with PRNT results. Three were correlated in the liquid-ID group. No significant correlations were observed with ELISPOT responses. In the liquid-ID group, WR052/F13L, a membrane glycoprotein, correlated with ADCC responses. CONCLUSIONS MVA elicited antibodies to 15 vaccinia strain antigens representing virion membrane. Antibody responses to 2 proteins strongly increased and significantly correlated with increases in PRNT. Responses to these proteins are potential correlates of protection and may serve as immunogens for future vaccine development. CLINICAL TRIALS REGISTRATION NCT00914732.
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Affiliation(s)
- Sharon E Frey
- Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, Missouri, USA
| | - Jack T Stapleton
- Department of Internal Medicine, University of Iowa and Iowa City VA Medical Center, Iowa City, Iowa, USA
| | - Zuhair K Ballas
- Department of Internal Medicine, University of Iowa and Iowa City VA Medical Center, Iowa City, Iowa, USA
| | - Wendy L Rasmussen
- Department of Internal Medicine, University of Iowa and Iowa City VA Medical Center, Iowa City, Iowa, USA
| | - Thomas M Kaufman
- Department of Internal Medicine, University of Iowa and Iowa City VA Medical Center, Iowa City, Iowa, USA
| | - Tammy P Blevins
- Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, Missouri, USA
| | | | - D Huw Davies
- Vaccine Research & Development Center, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, California, USA
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20
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Thomas BB, Lin B, Martinez-Camarillo JC, Zhu D, McLelland BT, Nistor G, Keirstead HS, Humayun MS, Seiler MJ. Co-grafts of Human Embryonic Stem Cell Derived Retina Organoids and Retinal Pigment Epithelium for Retinal Reconstruction in Immunodeficient Retinal Degenerate Royal College of Surgeons Rats. Front Neurosci 2021; 15:752958. [PMID: 34764853 PMCID: PMC8576198 DOI: 10.3389/fnins.2021.752958] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 08/04/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
End-stage age-related macular degeneration (AMD) and retinitis pigmentosa (RP) are two major retinal degenerative (RD) conditions that result in irreversible vision loss. Permanent eye damage can also occur in battlefields or due to accidents. This suggests there is an unmet need for developing effective strategies for treating permanent retinal damages. In previous studies, co-grafted sheets of fetal retina with its retinal pigment epithelium (RPE) have demonstrated vision improvement in rat retinal disease models and in patients, but this has not yet been attempted with stem-cell derived tissue. Here we demonstrate a cellular therapy for irreversible retinal eye injuries using a "total retina patch" consisting of retinal photoreceptor progenitor sheets and healthy RPE cells on an artificial Bruch's membrane (BM). For this, retina organoids (ROs) (cultured in suspension) and polarized RPE sheets (cultured on an ultrathin parylene substrate) were made into a co-graft using bio-adhesives [gelatin, growth factor-reduced matrigel, and medium viscosity (MVG) alginate]. In vivo transplantation experiments were conducted in immunodeficient Royal College of Surgeons (RCS) rats at advanced stages of retinal degeneration. Structural reconstruction of the severely damaged retina was observed based on histological assessments and optical coherence tomography (OCT) imaging. Visual functional assessments were conducted by optokinetic behavioral testing and superior colliculus electrophysiology. Long-term survival of the co-graft in the rat subretinal space and improvement in visual function were observed. Immunohistochemistry showed that co-grafts grew, generated new photoreceptors and developed neuronal processes that were integrated into the host retina. This novel approach can be considered as a new therapy for complete replacement of a degenerated retina.
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Affiliation(s)
- Biju B. Thomas
- Department of Ophthalmology, USC Roski Eye Institute, University of Southern California, Los Angeles, CA, United States
- USC Ginsburg Institute for Biomedical Therapeutics, University of Southern California, Los Angeles, CA, United States
| | - Bin Lin
- Department of Physical Medicine and Rehabilitation, University of California, Irvine, Irvine, CA, United States
- Stem Cell Research Center, University of California, Irvine, Irvine, CA, United States
| | - Juan Carlos Martinez-Camarillo
- Department of Ophthalmology, USC Roski Eye Institute, University of Southern California, Los Angeles, CA, United States
- USC Ginsburg Institute for Biomedical Therapeutics, University of Southern California, Los Angeles, CA, United States
| | - Danhong Zhu
- Department of Ophthalmology, USC Roski Eye Institute, University of Southern California, Los Angeles, CA, United States
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Bryce T. McLelland
- Department of Physical Medicine and Rehabilitation, University of California, Irvine, Irvine, CA, United States
- Stem Cell Research Center, University of California, Irvine, Irvine, CA, United States
| | | | | | - Mark S. Humayun
- Department of Ophthalmology, USC Roski Eye Institute, University of Southern California, Los Angeles, CA, United States
- USC Ginsburg Institute for Biomedical Therapeutics, University of Southern California, Los Angeles, CA, United States
| | - Magdalene J. Seiler
- Department of Physical Medicine and Rehabilitation, University of California, Irvine, Irvine, CA, United States
- Stem Cell Research Center, University of California, Irvine, Irvine, CA, United States
- Department of Ophthalmology, University of California, Irvine, Irvine, CA, United States
- Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA, United States
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21
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Tian X, Yan X, Varnavides G, Yuan Y, Kim DS, Ciccarino CJ, Anikeeva P, Li MY, Li LJ, Narang P, Pan X, Miao J. Capturing 3D atomic defects and phonon localization at the 2D heterostructure interface. Sci Adv 2021; 7:eabi6699. [PMID: 34524846 PMCID: PMC8443181 DOI: 10.1126/sciadv.abi6699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/23/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
The three-dimensional (3D) local atomic structures and crystal defects at the interfaces of heterostructures control their electronic, magnetic, optical, catalytic, and topological quantum properties but have thus far eluded any direct experimental determination. Here, we use atomic electron tomography to determine the 3D local atomic positions at the interface of a MoS2-WSe2 heterojunction with picometer precision and correlate 3D atomic defects with localized vibrational properties at the epitaxial interface. We observe point defects, bond distortion, and atomic-scale ripples and measure the full 3D strain tensor at the heterointerface. By using the experimental 3D atomic coordinates as direct input to first-principles calculations, we reveal new phonon modes localized at the interface, which are corroborated by spatially resolved electron energy-loss spectroscopy. We expect that this work will pave the way for correlating structure-property relationships of a wide range of heterostructure interfaces at the single-atom level.
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Affiliation(s)
- Xuezeng Tian
- Department of Physics and Astronomy and California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Xingxu Yan
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, CA 92697, USA
- Irvine Materials Research Institute, University of California, Irvine, Irvine, CA 92697, USA
| | - Georgios Varnavides
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yakun Yuan
- Department of Physics and Astronomy and California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dennis S. Kim
- Department of Physics and Astronomy and California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christopher J. Ciccarino
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Polina Anikeeva
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ming-Yang Li
- Physical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Lain-Jong Li
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Prineha Narang
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Xiaoqing Pan
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, CA 92697, USA
- Irvine Materials Research Institute, University of California, Irvine, Irvine, CA 92697, USA
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697, USA
| | - Jianwei Miao
- Department of Physics and Astronomy and California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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22
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Wu SL, Bennett JB, Sánchez C. HM, Dolgert AJ, León TM, Marshall JM. MGDrivE 2: A simulation framework for gene drive systems incorporating seasonality and epidemiological dynamics. PLoS Comput Biol 2021; 17:e1009030. [PMID: 34019537 PMCID: PMC8186770 DOI: 10.1371/journal.pcbi.1009030] [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] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 06/08/2021] [Accepted: 05/02/2021] [Indexed: 12/30/2022] Open
Abstract
Interest in gene drive technology has continued to grow as promising new drive systems have been developed in the lab and discussions are moving towards implementing field trials. The prospect of field trials requires models that incorporate a significant degree of ecological detail, including parameters that change over time in response to environmental data such as temperature and rainfall, leading to seasonal patterns in mosquito population density. Epidemiological outcomes are also of growing importance, as: i) the suitability of a gene drive construct for release will depend on its expected impact on disease transmission, and ii) initial field trials are expected to have a measured entomological outcome and a modeled epidemiological outcome. We present MGDrivE 2 (Mosquito Gene Drive Explorer 2): a significant development from the MGDrivE 1 simulation framework that investigates the population dynamics of a variety of gene drive architectures and their spread through spatially-explicit mosquito populations. Key strengths and fundamental improvements of the MGDrivE 2 framework are: i) the ability of parameters to vary with time and induce seasonal population dynamics, ii) an epidemiological module accommodating reciprocal pathogen transmission between humans and mosquitoes, and iii) an implementation framework based on stochastic Petri nets that enables efficient model formulation and flexible implementation. Example MGDrivE 2 simulations are presented to demonstrate the application of the framework to a CRISPR-based split gene drive system intended to drive a disease-refractory gene into a population in a confinable and reversible manner, incorporating time-varying temperature and rainfall data. The simulations also evaluate impact on human disease incidence and prevalence. Further documentation and use examples are provided in vignettes at the project’s CRAN repository. MGDrivE 2 is freely available as an open-source R package on CRAN (https://CRAN.R-project.org/package=MGDrivE2). We intend the package to provide a flexible tool capable of modeling gene drive constructs as they move closer to field application and to infer their expected impact on disease transmission. Malaria, dengue and other mosquito-borne diseases continue to pose a major global health burden through much of the world. Currently available tools, such as insecticides and antimalarial drugs, are not expected to be sufficient to eliminate these diseases from highly-endemic areas, hence there is interest in novel strategies including genetics-based approaches. In recent years, the advent of CRISPR-based gene-editing has greatly expanded the range of genetic control tools available, and MGDrivE 1 (Mosquito Gene Drive Explorer 1) was proposed to simulate the dynamics of these systems through spatially-structured mosquito populations. As the technology has advanced and potential field trials are being discussed, models are now needed that incorporate additional details, such as life history parameters that respond to daily and seasonal environmental fluctuations, and transmission of pathogens between mosquito and vertebrate hosts. Here, we present MGDrivE 2, a gene drive simulation framework that significantly improves upon MGDrivE 1 by addressing these modeling needs. MGDrivE 2 has also been reformulated as a stochastic Petri net, enabling model specification to be decoupled from simulation, making it easier to adapt the model for application to other insect and mammalian species.
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Affiliation(s)
- Sean L. Wu
- Divisions of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, California, United States of America
- * E-mail: (SLW); (JMM)
| | - Jared B. Bennett
- Biophysics Graduate Group, Division of Biological Sciences, College of Letters and Science, University of California, Berkeley, California, United States of America
| | - Héctor M. Sánchez C.
- Divisions of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, California, United States of America
| | - Andrew J. Dolgert
- Institute for Health Metrics and Evaluation, Seattle, Washington, United States of America
| | - Tomás M. León
- Divisions of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, California, United States of America
| | - John M. Marshall
- Divisions of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
- * E-mail: (SLW); (JMM)
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23
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Abstract
We define a new family of similarity and distance measures on graphs, and explore their theoretical properties in comparison to conventional distance metrics. These measures are defined by the solution(s) to an optimization problem which attempts find a map minimizing the discrepancy between two graph Laplacian exponential matrices, under norm-preserving and sparsity constraints. Variants of the distance metric are introduced to consider such optimized maps under sparsity constraints as well as fixed time-scaling between the two Laplacians. The objective function of this optimization is multimodal and has discontinuous slope, and is hence difficult for univariate optimizers to solve. We demonstrate a novel procedure for efficiently calculating these optima for two of our distance measure variants. We present numerical experiments demonstrating that (a) upper bounds of our distance metrics can be used to distinguish between lineages of related graphs; (b) our procedure is faster at finding the required optima, by as much as a factor of 103; and (c) the upper bounds satisfy the triangle inequality exactly under some assumptions and approximately under others. We also derive an upper bound for the distance between two graph products, in terms of the distance between the two pairs of factors. Additionally, we present several possible applications, including the construction of infinite "graph limits" by means of Cauchy sequences of graphs related to one another by our distance measure.
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Affiliation(s)
- C. B. Scott
- Department of Computer Science, University of California, Irvine, CA, United States of America
- * E-mail:
| | - Eric Mjolsness
- Department of Computer Science, University of California, Irvine, CA, United States of America
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24
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Chow DS, Glavis-Bloom J, Soun JE, Weinberg B, Loveless TB, Xie X, Mutasa S, Monuki E, Park JI, Bota D, Wu J, Thompson L, Boden-Albala B, Khan S, Amin AN, Chang PD. Development and external validation of a prognostic tool for COVID-19 critical disease. PLoS One 2020; 15:e0242953. [PMID: 33296357 PMCID: PMC7725393 DOI: 10.1371/journal.pone.0242953] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 05/15/2020] [Accepted: 10/10/2020] [Indexed: 01/06/2023] Open
Abstract
Background The rapid spread of coronavirus disease 2019 (COVID-19) revealed significant constraints in critical care capacity. In anticipation of subsequent waves, reliable prediction of disease severity is essential for critical care capacity management and may enable earlier targeted interventions to improve patient outcomes. The purpose of this study is to develop and externally validate a prognostic model/clinical tool for predicting COVID-19 critical disease at presentation to medical care. Methods This is a retrospective study of a prognostic model for the prediction of COVID-19 critical disease where critical disease was defined as ICU admission, ventilation, and/or death. The derivation cohort was used to develop a multivariable logistic regression model. Covariates included patient comorbidities, presenting vital signs, and laboratory values. Model performance was assessed on the validation cohort by concordance statistics. The model was developed with consecutive patients with COVID-19 who presented to University of California Irvine Medical Center in Orange County, California. External validation was performed with a random sample of patients with COVID-19 at Emory Healthcare in Atlanta, Georgia. Results Of a total 3208 patients tested in the derivation cohort, 9% (299/3028) were positive for COVID-19. Clinical data including past medical history and presenting laboratory values were available for 29% (87/299) of patients (median age, 48 years [range, 21–88 years]; 64% [36/55] male). The most common comorbidities included obesity (37%, 31/87), hypertension (37%, 32/87), and diabetes (24%, 24/87). Critical disease was present in 24% (21/87). After backward stepwise selection, the following factors were associated with greatest increased risk of critical disease: number of comorbidities, body mass index, respiratory rate, white blood cell count, % lymphocytes, serum creatinine, lactate dehydrogenase, high sensitivity troponin I, ferritin, procalcitonin, and C-reactive protein. Of a total of 40 patients in the validation cohort (median age, 60 years [range, 27–88 years]; 55% [22/40] male), critical disease was present in 65% (26/40). Model discrimination in the validation cohort was high (concordance statistic: 0.94, 95% confidence interval 0.87–1.01). A web-based tool was developed to enable clinicians to input patient data and view likelihood of critical disease. Conclusions and relevance We present a model which accurately predicted COVID-19 critical disease risk using comorbidities and presenting vital signs and laboratory values, on derivation and validation cohorts from two different institutions. If further validated on additional cohorts of patients, this model/clinical tool may provide useful prognostication of critical care needs.
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Affiliation(s)
- Daniel S. Chow
- Department of Radiological Sciences, University of California, Irvine, California, United States of America
- * E-mail:
| | - Justin Glavis-Bloom
- Department of Radiological Sciences, University of California, Irvine, California, United States of America
| | - Jennifer E. Soun
- Department of Radiological Sciences, University of California, Irvine, California, United States of America
| | - Brent Weinberg
- Department of Radiological Sciences, Emory University, Atlanta, Georgia, United States of America
| | - Theresa Berens Loveless
- Department of Biomedical Engineering, University of California, Irvine, California, United States of America
| | - Xiaohui Xie
- Department of Computer Science, University of California, Irvine, California, United States of America
| | - Simukayi Mutasa
- Department of Radiological Sciences, Columbia University Medical Center, New York, New York, United States of America
| | - Edwin Monuki
- Department of Pathology and Laboratory Medicine, University of California, Irvine, California, United States of America
| | - Jung In Park
- Sue and Bill Gross School of Nursing, University of California, Irvine, California, United States of America
| | - Daniela Bota
- UCI Center for Clinical Research, University of California, Irvine, California, United States of America
| | - Jie Wu
- School of Biological Sciences, University of California, Irvine, California, United States of America
| | - Leslie Thompson
- School of Biological Sciences, University of California, Irvine, California, United States of America
| | - Bernadette Boden-Albala
- Department of Population Health and Disease Prevention and Department of Epidemiology, University of California, Irvine, California, United States of America
| | - Saahir Khan
- Division of Infectious Diseases, University of California, Irvine, California, United States of America
- Department of Medicine, University of California, Irvine, California, United States of America
| | - Alpesh N. Amin
- Department of Medicine, University of California, Irvine, California, United States of America
| | - Peter D. Chang
- Department of Radiological Sciences, University of California, Irvine, California, United States of America
- Department of Computer Science, University of California, Irvine, California, United States of America
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25
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Hedde PN, Abram TJ, Jain A, Nakajima R, Ramiro de Assis R, Pearce T, Jasinskas A, Toosky MN, Khan S, Felgner PL, Gratton E, Zhao W. A modular microarray imaging system for highly specific COVID-19 antibody testing. Lab Chip 2020; 20:3302-3309. [PMID: 32743622 PMCID: PMC8462184 DOI: 10.1039/d0lc00547a] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/11/2020] [Indexed: 05/12/2023]
Abstract
To detect the presence of antibodies in blood against SARS-CoV-2 in a highly sensitive and specific manner, here we describe a robust, inexpensive ($200), 3D-printable portable imaging platform (TinyArray imager) that can be deployed immediately in areas with minimal infrastructure to read coronavirus antigen microarrays (CoVAMs) that contain a panel of antigens from SARS-CoV-2, SARS-1, MERS, and other respiratory viruses. Application includes basic laboratories and makeshift field clinics where a few drops of blood from a finger prick could be rapidly tested in parallel for the presence of antibodies to SARS-CoV-2 with a test turnaround time of only 2-4 h. To evaluate our imaging device, we probed and imaged coronavirus microarrays with COVID-19-positive and negative sera and achieved a performance on par with a commercial microarray reader 100× more expensive than our imaging device. This work will enable large scale serosurveillance, which can play an important role in the months and years to come to implement efficient containment and mitigation measures, as well as help develop therapeutics and vaccines to treat and prevent the spread of COVID-19.
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Affiliation(s)
- Per Niklas Hedde
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA.
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, CA, USA
| | | | - Aarti Jain
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Rie Nakajima
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Rafael Ramiro de Assis
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Trevor Pearce
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Algis Jasinskas
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | | | - Saahir Khan
- Division of Infectious Diseases, Department of Medicine, University of California Irvine Health, Orange, CA, USA
| | - Philip L Felgner
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, CA, USA
| | - Weian Zhao
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA.
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
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26
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Maini Rekdal V, Nol Bernadino P, Luescher MU, Kiamehr S, Le C, Bisanz JE, Turnbaugh PJ, Bess EN, Balskus EP. A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols. eLife 2020; 9:e50845. [PMID: 32067637 PMCID: PMC7028382 DOI: 10.7554/elife.50845] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 08/05/2019] [Accepted: 01/03/2020] [Indexed: 12/23/2022] Open
Abstract
Catechol dehydroxylation is a central chemical transformation in the gut microbial metabolism of plant- and host-derived small molecules. However, the molecular basis for this transformation and its distribution among gut microorganisms are poorly understood. Here, we characterize a molybdenum-dependent enzyme from the human gut bacterium Eggerthella lenta that dehydroxylates catecholamine neurotransmitters. Our findings suggest that this activity enables E. lenta to use dopamine as an electron acceptor. We also identify candidate dehydroxylases that metabolize additional host- and plant-derived catechols. These dehydroxylases belong to a distinct group of largely uncharacterized molybdenum-dependent enzymes that likely mediate primary and secondary metabolism in multiple environments. Finally, we observe catechol dehydroxylation in the gut microbiotas of diverse mammals, confirming the presence of this chemistry in habitats beyond the human gut. These results suggest that the chemical strategies that mediate metabolism and interactions in the human gut are relevant to a broad range of species and habitats.
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Affiliation(s)
- Vayu Maini Rekdal
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Paola Nol Bernadino
- Department of Chemistry and Molecular BiologyUniversity of California, IrvineIrvineUnited States
- Department of Chemistry and Molecular BiochemistryUniversity of California, IrvineIrvineUnited States
| | - Michael U Luescher
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Sina Kiamehr
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Chip Le
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Jordan E Bisanz
- Department of Microbiology and ImmunologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Peter J Turnbaugh
- Department of Microbiology and ImmunologyUniversity of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Elizabeth N Bess
- Department of Chemistry and Molecular BiologyUniversity of California, IrvineIrvineUnited States
- Department of Chemistry and Molecular BiochemistryUniversity of California, IrvineIrvineUnited States
| | - Emily P Balskus
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
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27
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Rotstan KA, Abdelsayed MM, Passalacqua LFM, Chizzolini F, Sudarshan K, Chamberlin AR, Míšek J, Luptak A. Regulation of mRNA translation by a photoriboswitch. eLife 2020; 9:e51737. [PMID: 32053109 PMCID: PMC7051177 DOI: 10.7554/elife.51737] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 09/09/2019] [Accepted: 02/12/2020] [Indexed: 12/15/2022] Open
Abstract
Optogenetic tools have revolutionized the study of receptor-mediated processes, but such tools are lacking for RNA-controlled systems. In particular, light-activated regulatory RNAs are needed for spatiotemporal control of gene expression. To fill this gap, we used in vitro selection to isolate a novel riboswitch that selectively binds the trans isoform of a stiff-stilbene (amino-tSS)-a rapidly and reversibly photoisomerizing small molecule. Structural probing revealed that the RNA binds amino-tSS about 100-times stronger than the cis photoisoform (amino-cSS). In vitro and in vivo functional analysis showed that the riboswitch, termed Werewolf-1 (Were-1), inhibits translation of a downstream open reading frame when bound to amino-tSS. Photoisomerization of the ligand with a sub-millisecond pulse of light induced the protein expression. In contrast, amino-cSS supported protein expression, which was inhibited upon photoisomerization to amino-tSS. Reversible photoregulation of gene expression using a genetically encoded RNA will likely facilitate high-resolution spatiotemporal analysis of complex RNA processes.
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Affiliation(s)
- Kelly A Rotstan
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
| | - Michael M Abdelsayed
- Department of Molecular Biology and Biochemistry, University of CaliforniaIrvineUnited States
| | - Luiz FM Passalacqua
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
| | - Fabio Chizzolini
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
| | | | - A Richard Chamberlin
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
- Department of Chemistry, University of CaliforniaIrvineUnited States
| | - Jiří Míšek
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
- Department of Organic Chemistry, Charles UniversityPragueCzech Republic
| | - Andrej Luptak
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
- Department of Molecular Biology and Biochemistry, University of CaliforniaIrvineUnited States
- Department of Chemistry, University of CaliforniaIrvineUnited States
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28
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Abstract
BACKGROUND The assembly of animal microbiomes is influenced by multiple environmental factors and host genetics, although the relative importance of these factors remains unclear. Bifidobacteria (genus Bifidobacterium, phylum Actinobacteria) are common first colonizers of gut microbiomes in humans and inhabit other mammals, social insects, food, and sewages. In humans, the presence of bifidobacteria in the gut has been correlated with health-promoting benefits. Here, we compared the genome sequences of a subset of the over 400 Bifidobacterium strains publicly available to investigate the adaptation of bifidobacteria diversity. We tested 1) whether bifidobacteria show a phylogenetic signal with their isolation sources (hosts and environments) and 2) whether key traits encoded by the bifidobacteria genomes depend on the host or environment from which they were isolated. We analyzed Bifidobacterium genomes available in the PATRIC and NCBI repositories and identified the hosts and/or environment from which they were isolated. A multilocus phylogenetic analysis was conducted to compare the genetic relatedness the strains harbored by different hosts and environments. Furthermore, we examined differences in genomic traits and genes related to amino acid biosynthesis and degradation of carbohydrates. RESULTS We found that bifidobacteria diversity appears to have evolved with their hosts as strains isolated from the same host were non-randomly associated with their phylogenetic relatedness. Moreover, bifidobacteria isolated from different sources displayed differences in genomic traits such as genome size and accessory gene composition and on particular traits related to amino acid production and degradation of carbohydrates. In contrast, when analyzing diversity within human-derived bifidobacteria, we observed no phylogenetic signal or differences on specific traits (amino acid biosynthesis genes and CAZymes). CONCLUSIONS Overall, our study shows that bifidobacteria diversity is strongly adapted to specific hosts and environments and that several genomic traits were associated with their isolation sources. However, this signal is not observed in human-derived strains alone. Looking into the genomic signatures of bifidobacteria strains in different environments can give insights into how this bacterial group adapts to their environment and what types of traits are important for these adaptations.
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Affiliation(s)
- Cynthia I Rodriguez
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
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Lu KD, Bar-Yoseph R, Radom-Aizik S, Cooper DM. A new approach to estimate aerobic fitness using the NHANES dataset. Scand J Med Sci Sports 2019; 29:1392-1401. [PMID: 31063607 PMCID: PMC6860366 DOI: 10.1111/sms.13461] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 04/18/2019] [Accepted: 04/30/2019] [Indexed: 02/01/2023]
Abstract
INTRODUCTION Physical activity and fitness are essential for healthy growth in children. The National Health and Nutrition Examination Survey (NHANES) evaluated fitness by estimating V̇O2 max from submaximal measurements of heart rate (HR) during graded treadmill exercise. Our aims were (a) to examine how well NHANES methodology used to estimate V̇O2 max correlated with actual VO2 max and (b) to evaluate a novel fitness metric using actual data collected during exercise and its relationship to physical activity and sedentary time, lipid profiles, and body composition. METHODS Fifty-three adolescents completed NHANES submaximal exercise protocol and maximal graded cardiopulmonary exercise testing. We used a novel approach to quantifying fitness (Δvelocity × incline × body mass (VIM)/ΔHR slopes) and evaluated its relationship to physical activity and sedentary time using NHANES data (n = 4498). In a subset (n = 740), we compared ΔVIM/ΔHR slopes to NHANES estimated V̇O2 max and examined their relationship to cardiovascular risk factors (BMI percentiles and lipid levels). RESULTS Measured V̇O2 peak was moderately correlated with NHANES estimated V̇O2 max (r = 0.53, P < 0.01). Significantly higher ΔVIM/ΔHR slopes were associated with increased physical activity and decreased sedentary time. ΔVIM/ΔHR slopes were negatively associated with LDL, triglycerides, and BMI percentiles (P < 0.01). In general, the two fitness models were similar; however, ΔVIM/ΔHR was more discriminating than NHANES in quantifying the relationship between fitness and LDL levels. CONCLUSION We found that the NHANES estimated V̇O2 max accounted for approximately 28% of the variability in the measured V̇O2 peak. Our approach to estimating fitness (ΔVIM/ΔHR slopes) using actual data provided similar relationships to lipid levels. We suggest that fitness measurements based on actually measured data may produce more accurate assessments of fitness and, ultimately, better approaches linking exercise to health in children.
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Affiliation(s)
- Kim D Lu
- Department of Pediatrics, Pediatric Exercise and Genomics Research Center (PERC), University of California, Irvine School of Medicine, Irvine, California
| | - Ronen Bar-Yoseph
- Department of Pediatrics, Pediatric Exercise and Genomics Research Center (PERC), University of California, Irvine School of Medicine, Irvine, California
| | - Shlomit Radom-Aizik
- Department of Pediatrics, Pediatric Exercise and Genomics Research Center (PERC), University of California, Irvine School of Medicine, Irvine, California
| | - Dan M Cooper
- Department of Pediatrics, Pediatric Exercise and Genomics Research Center (PERC), University of California, Irvine School of Medicine, Irvine, California
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Kim J, Chen B, Bru JL, Huynh E, Momen M, Aswad DW. New findings on SNP variants of human protein L-isoaspartyl methyltransferase that affect catalytic activity, thermal stability, and aggregation. PLoS One 2018; 13:e0198266. [PMID: 29856810 PMCID: PMC5983485 DOI: 10.1371/journal.pone.0198266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 01/26/2018] [Accepted: 05/16/2018] [Indexed: 12/12/2022] Open
Abstract
Protein L-isoaspartyl methyltransferase (PIMT/PCMT1), a product of the pcmt1 gene, catalyzes repair of abnormal L-isoaspartyl linkages in age-damaged proteins. Pcmt1 knockout mice exhibit a profound neuropathology and die 30–60 days postnatal from an epileptic seizure. Here we characterize four new SNP variants of human PIMT with respect to enzymatic activity, thermal stability, and propensity to aggregation. Under standard assay conditions, L191S, A150V, P174H and A65V showed activity losses of 72%, 64%, 61%, and 11% respectively. By differential scanning fluorimetry, melting temperature deviations were -5.2, -4.5, +0.5, and -3.4°C. SDS-PAGE of purified protein reveal significant aggregation of L191S, A150V, and P174H, but not A65V. We also report new data on three unusual PIMT variants among the 13 recently characterized by our laboratory. A7P and I58V were previously found to have 1.8–2.0 times the activity of WT PIMT in the standard assay; however, upon kinetic analysis, we find both variants exhibit reduced catalytic efficiency (Vmax/Km) due to weak isoaspartyl substrate binding. The near complete loss of activity (<1%) seen in R36C was investigated by comparing activity of two artificial variants. R36K shows 4.6X the activity of R36C, while R36A shows no improvement, suggesting the guanidino nitrogens of the R36 play a key role in binding the methyl donor S-adenosyl-L-methionine (AdoMet). The new findings reported here extend the list of human PIMT variants that may contribute to neurological diseases in the young and the decline of CNS function in the aged.
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Affiliation(s)
- Jeungjin Kim
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Baihe Chen
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Jean-Louis Bru
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Eric Huynh
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Mahsa Momen
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Dana W. Aswad
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, United States of America
- * E-mail:
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Quas JA, Dickerson KL, Matthew R, Harron C, Quas CM. Adversity, emotion recognition, and empathic concern in high-risk youth. PLoS One 2017; 12:e0181606. [PMID: 28738074 PMCID: PMC5524326 DOI: 10.1371/journal.pone.0181606] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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: 02/13/2017] [Accepted: 07/04/2017] [Indexed: 01/09/2023] Open
Abstract
Little is known about how emotion recognition and empathy jointly operate in youth growing up in contexts defined by persistent adversity. We investigated whether adversity exposure in two groups of youth was associated with reduced empathy and whether deficits in emotion recognition mediated this association. Foster, rural poor, and comparison youth from Swaziland, Africa identified emotional expressions and rated their empathic concern for characters depicted in images showing positive, ambiguous, and negative scenes. Rural and foster youth perceived greater anger and happiness in the main characters in ambiguous and negative images than did comparison youth. Rural children also perceived less sadness. Youth’s perceptions of sadness in the negative and ambiguous expressions mediated the relation between adversity and empathic concern, but only for the rural youth, who perceived less sadness, which then predicted less empathy. Findings provide new insight into processes that underlie empathic tendencies in adversity-exposed youth and highlight potential directions for interventions to increase empathy.
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Affiliation(s)
- Jodi A. Quas
- Department of Psychology and Social Behavior, University of California Irvine, Irvine, California, United States of America
| | - Kelli L. Dickerson
- Department of Psychology and Social Behavior, University of California Irvine, Irvine, California, United States of America
- * E-mail:
| | - Richard Matthew
- Department of Planning, Policy, and Design, University of California Irvine, Irvine, California, United States of America
| | - Connor Harron
- Department of Social Ecology, University of California Irvine, Irvine, California, United States of America
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