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Schmitz KS, Rennick LJ, Tilston-Lunel NL, Comvalius AD, Laksono BM, Geers D, van Run P, de Vries RD, de Swart RL, Duprex WP. Rational attenuation of canine distemper virus (CDV) to develop a morbillivirus animal model that mimics measles in humans. J Virol 2024; 98:e0185023. [PMID: 38415596 PMCID: PMC10949419 DOI: 10.1128/jvi.01850-23] [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: 11/27/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024] Open
Abstract
Morbilliviruses are members of the family Paramyxoviridae and are known for their ability to cause systemic disease in a variety of mammalian hosts. The prototypic morbillivirus, measles virus (MeV), infects humans and still causes morbidity and mortality in unvaccinated children and young adults. Experimental infection studies in non-human primates have contributed to the understanding of measles pathogenesis. However, ethical restrictions call for the development of new animal models. Canine distemper virus (CDV) infects a wide range of animals, including ferrets, and its pathogenesis shares many features with measles. However, wild-type CDV infection is almost always lethal, while MeV infection is usually self-limiting. Here, we made five recombinant CDVs, predicted to be attenuated, and compared their pathogenesis to the non-attenuated recombinant CDV in a ferret model. Three viruses were insufficiently attenuated based on clinical signs, fatality, and systemic infection, while one virus was too attenuated. The last candidate virus caused a self-limiting infection associated with transient viremia and viral dissemination to all lymphoid tissues, was shed transiently from the upper respiratory tract, and did not result in acute neurological signs. Additionally, an in-depth phenotyping of the infected white blood cells showed lower infection percentages in all lymphocyte subsets when compared to the non-attenuated CDV. In conclusion, infection models using this candidate virus mimic measles and can be used to study pathogenesis-related questions and to test interventions for morbilliviruses in a natural host species.IMPORTANCEMorbilliviruses are transmitted via the respiratory route but cause systemic disease. The viruses use two cellular receptors to infect myeloid, lymphoid, and epithelial cells. Measles virus (MeV) remains an important cause of morbidity and mortality in humans, requiring animal models to study pathogenesis or intervention strategies. Experimental MeV infections in non-human primates are restricted by ethical and practical constraints, and animal morbillivirus infections in natural host species have been considered as alternatives. Inoculation of ferrets with wild-type canine distemper virus (CDV) has been used for this purpose, but in most cases, the virus overwhelms the immune system and causes highly lethal disease. Introduction of an additional transcription unit and an additional attenuating point mutation in the polymerase yielded a candidate virus that caused self-limiting disease with transient viremia and virus shedding. This rationally attenuated CDV strain can be used for experimental morbillivirus infections in ferrets that reflect measles in humans.
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Affiliation(s)
| | - Linda J. Rennick
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Natasha L. Tilston-Lunel
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | | | - Daryl Geers
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Peter van Run
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Rory D. de Vries
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Rik L. de Swart
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - W. Paul Duprex
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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2
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Chan HY, Scholz C, Cosme D, Martin RE, Benitez C, Resnick A, Carreras-Tartak J, Cooper N, Paul AM, Falk EB. Neural signals predict information sharing across cultures. Proc Natl Acad Sci U S A 2023; 120:e2313175120. [PMID: 37871199 PMCID: PMC10622920 DOI: 10.1073/pnas.2313175120] [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: 08/09/2023] [Accepted: 09/25/2023] [Indexed: 10/25/2023] Open
Abstract
Information sharing influences which messages spread and shape beliefs, behavior, and culture. In a preregistered neuroimaging study conducted in the United States and the Netherlands, we demonstrate replicability, predictive validity, and generalizability of a brain-based prediction model of information sharing. Replicating findings in Scholz et al., Proc. Natl. Acad. Sci. U.S.A. 114, 2881-2886 (2017), self-, social-, and value-related neural signals in a group of individuals tracked the population sharing of US news articles. Preregistered brain-based prediction models trained on Scholz et al. (2017) data proved generalizable to the new data, explaining more variance in population sharing than self-report ratings alone. Neural signals (versus self-reports) more reliably predicted sharing cross-culturally, suggesting that they capture more universal psychological mechanisms underlying sharing behavior. These findings highlight key neurocognitive foundations of sharing, suggest potential target mechanisms for interventions to increase message effectiveness, and advance brain-as-predictor research.
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Affiliation(s)
- Hang-Yee Chan
- Department of Marketing, King’s Business School, King’s College London, LondonWC2B 4BG, United Kingdom
| | - Christin Scholz
- Amsterdam School of Communication Research, University of Amsterdam, Amsterdam1018 WV, The Netherlands
| | - Danielle Cosme
- Annenberg School for Communication, University of Pennsylvania, Philadelphia, PA19104
| | - Rebecca E. Martin
- Annenberg School for Communication, University of Pennsylvania, Philadelphia, PA19104
| | - Christian Benitez
- Annenberg School for Communication, University of Pennsylvania, Philadelphia, PA19104
| | - Anthony Resnick
- Annenberg School for Communication, University of Pennsylvania, Philadelphia, PA19104
| | - José Carreras-Tartak
- Annenberg School for Communication, University of Pennsylvania, Philadelphia, PA19104
| | - Nicole Cooper
- Annenberg School for Communication, University of Pennsylvania, Philadelphia, PA19104
| | - Alexandra M. Paul
- Annenberg School for Communication, University of Pennsylvania, Philadelphia, PA19104
| | - Emily B. Falk
- Annenberg School for Communication, University of Pennsylvania, Philadelphia, PA19104
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3
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Matthews D, Spielberg A, Rus D, Kriegman S, Bongard J. Efficient automatic design of robots. Proc Natl Acad Sci U S A 2023; 120:e2305180120. [PMID: 37788314 PMCID: PMC10576117 DOI: 10.1073/pnas.2305180120] [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: 03/29/2023] [Accepted: 07/22/2023] [Indexed: 10/05/2023] Open
Abstract
Robots are notoriously difficult to design because of complex interdependencies between their physical structure, sensory and motor layouts, and behavior. Despite this, almost every detail of every robot built to date has been manually determined by a human designer after several months or years of iterative ideation, prototyping, and testing. Inspired by evolutionary design in nature, the automated design of robots using evolutionary algorithms has been attempted for two decades, but it too remains inefficient: days of supercomputing are required to design robots in simulation that, when manufactured, exhibit desired behavior. Here we show de novo optimization of a robot's structure to exhibit a desired behavior, within seconds on a single consumer-grade computer, and the manufactured robot's retention of that behavior. Unlike other gradient-based robot design methods, this algorithm does not presuppose any particular anatomical form; starting instead from a randomly-generated apodous body plan, it consistently discovers legged locomotion, the most efficient known form of terrestrial movement. If combined with automated fabrication and scaled up to more challenging tasks, this advance promises near-instantaneous design, manufacture, and deployment of unique and useful machines for medical, environmental, vehicular, and space-based tasks.
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Affiliation(s)
- David Matthews
- Center for Robotics and Biosystems, Northwestern University, Evanston, IL60208
| | - Andrew Spielberg
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Daniela Rus
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Sam Kriegman
- Center for Robotics and Biosystems, Northwestern University, Evanston, IL60208
| | - Josh Bongard
- Department of Computer Science, University of Vermont, Burlington, VT05405
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4
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Mivalt F, Kremen V, Sladky V, Cui J, Gregg NM, Balzekas I, Marks V, St Louis EK, Croarkin P, Lundstrom BN, Nelson N, Kim J, Hermes D, Messina S, Worrell S, Richner T, Brinkmann BH, Denison T, Miller KJ, Van Gompel J, Stead M, Worrell GA. Impedance Rhythms in Human Limbic System. J Neurosci 2023; 43:6653-6666. [PMID: 37620157 PMCID: PMC10538585 DOI: 10.1523/jneurosci.0241-23.2023] [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: 02/07/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
The impedance is a fundamental electrical property of brain tissue, playing a crucial role in shaping the characteristics of local field potentials, the extent of ephaptic coupling, and the volume of tissue activated by externally applied electrical brain stimulation. We tracked brain impedance, sleep-wake behavioral state, and epileptiform activity in five people with epilepsy living in their natural environment using an investigational device. The study identified impedance oscillations that span hours to weeks in the amygdala, hippocampus, and anterior nucleus thalamus. The impedance in these limbic brain regions exhibit multiscale cycles with ultradian (∼1.5-1.7 h), circadian (∼21.6-26.4 h), and infradian (∼20-33 d) periods. The ultradian and circadian period cycles are driven by sleep-wake state transitions between wakefulness, nonrapid eye movement (NREM) sleep, and rapid eye movement (REM) sleep. Limbic brain tissue impedance reaches a minimum value in NREM sleep, intermediate values in REM sleep, and rises through the day during wakefulness, reaching a maximum in the early evening before sleep onset. Infradian (∼20-33 d) impedance cycles were not associated with a distinct behavioral correlate. Brain tissue impedance is known to strongly depend on the extracellular space (ECS) volume, and the findings reported here are consistent with sleep-wake-dependent ECS volume changes recently observed in the rodent cortex related to the brain glymphatic system. We hypothesize that human limbic brain ECS changes during sleep-wake state transitions underlie the observed multiscale impedance cycles. Impedance is a simple electrophysiological biomarker that could prove useful for tracking ECS dynamics in human health, disease, and therapy.SIGNIFICANCE STATEMENT The electrical impedance in limbic brain structures (amygdala, hippocampus, anterior nucleus thalamus) is shown to exhibit oscillations over multiple timescales. We observe that impedance oscillations with ultradian and circadian periodicities are associated with transitions between wakefulness, NREM, and REM sleep states. There are also impedance oscillations spanning multiple weeks that do not have a clear behavioral correlate and whose origin remains unclear. These multiscale impedance oscillations will have an impact on extracellular ionic currents that give rise to local field potentials, ephaptic coupling, and the tissue activated by electrical brain stimulation. The approach for measuring tissue impedance using perturbational electrical currents is an established engineering technique that may be useful for tracking ECS volume.
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Affiliation(s)
- Filip Mivalt
- Bioelectronics Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, Minnesota 55905
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, 61600 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, 60200 Brno, Czech Republic
| | - Vaclav Kremen
- Bioelectronics Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, Minnesota 55905
- Czech Institute of Informatics, Robotics, and Cybernetics, Czech Technical University, 16000 Prague, Czech Republic
| | - Vladimir Sladky
- Bioelectronics Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, Minnesota 55905
- International Clinical Research Center, St. Anne's University Hospital, 60200 Brno, Czech Republic
- Faculty of Biomedical Engineering, Czech Technical University, 16000 Prague, Czech Republic
| | - Jie Cui
- Bioelectronics Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, Minnesota 55905
| | - Nicholas M Gregg
- Bioelectronics Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, Minnesota 55905
| | - Irena Balzekas
- Bioelectronics Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, Minnesota 55905
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905
| | - Victoria Marks
- Bioelectronics Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, Minnesota 55905
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905
| | - Erik K St Louis
- Center for Sleep Medicine, Departments of Neurology and Medicine, Divisions of Sleep Neurology and Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota 55905
| | | | - Brian Nils Lundstrom
- Bioelectronics Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, Minnesota 55905
| | - Noelle Nelson
- Bioelectronics Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, Minnesota 55905
| | - Jiwon Kim
- Bioelectronics Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, Minnesota 55905
| | - Dora Hermes
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905
| | - Steven Messina
- Department of Radiology, Mayo Clinic Rochester, Minnesota 55905
| | - Samuel Worrell
- Bioelectronics Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, Minnesota 55905
| | - Thomas Richner
- Bioelectronics Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, Minnesota 55905
| | - Benjamin H Brinkmann
- Bioelectronics Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, Minnesota 55905
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905
| | - Timothy Denison
- Department of Engineering Science, Medical Research Council Brain Network Dynamics Unit, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Kai J Miller
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota 55905
| | - Jamie Van Gompel
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota 55905
| | - Matthew Stead
- Bioelectronics Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, Minnesota 55905
| | - Gregory A Worrell
- Bioelectronics Neurophysiology and Engineering Laboratory, Department of Neurology, Mayo Clinic, Rochester, Minnesota 55905
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905
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5
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Skavicus S, Heaton NS. Approaches for timeline reductions in pathogenesis studies using genetically modified mice. Microbiol Spectr 2023; 11:e0252123. [PMID: 37695101 PMCID: PMC10580824 DOI: 10.1128/spectrum.02521-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 07/22/2023] [Indexed: 09/12/2023] Open
Abstract
Although genetically modified mouse models have long been a powerful tool for microbiology research, the manipulation of the mouse genome is expensive, time consuming, and has historically remained the domain of dedicated animal facilities. The recent use of in vivo clustered regularly interspaced short palindromic repeats (CRISPR)-based editing technology has been reported to reduce the expertise, cost, and time required to generate novel mouse lines; it has remained unclear, however, if this new technology could meaningfully alter experimental timelines. Here, we report the optimization of an in oviduct murine genetic manipulation technique for use by microbiologists. We use this approach to generate a series of knockout mice and detail a protocol using an influenza A virus infection model to test the preliminary importance of a host factor in as short as 11 weeks (with a fully backcrossed knockout line in ~22 weeks) from initiation of the study. Broader use of this approach by the microbiology community will allow for more efficient, and rapid, definition of novel pathogenic mechanisms in vivo. IMPORTANCE Clustered regularly interspaced short palindromic repeats (CRISPR)-based technologies have already begun to revolutionize biomedical science. An emerging application of this technology is in the development of genetically modified model organisms to study the mechanisms underlying infectious disease. Here, we describe a protocol using an in vivo CRISPR-based approach that can be used to test the importance of a candidate host factor for microbial pathogenesis in less than 3 months and before complete establishment of a new mouse line. Adoption of this approach by the broader microbiology community will help to decrease the resources and time required to understand how pathogens cause disease which will ultimately speed up the development of new clinical interventions and therapies.
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Affiliation(s)
- Samantha Skavicus
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
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6
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Nguyen M, Elmore Z, Ihle C, Moen FS, Slater AD, Turner BN, Parrello B, Best AA, Davis JJ. Predicting variable gene content in Escherichia coli using conserved genes. mSystems 2023; 8:e0005823. [PMID: 37314210 PMCID: PMC10469788 DOI: 10.1128/msystems.00058-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/25/2023] [Indexed: 06/15/2023] Open
Abstract
Having the ability to predict the protein-encoding gene content of an incomplete genome or metagenome-assembled genome is important for a variety of bioinformatic tasks. In this study, as a proof of concept, we built machine learning classifiers for predicting variable gene content in Escherichia coli genomes using only the nucleotide k-mers from a set of 100 conserved genes as features. Protein families were used to define orthologs, and a single classifier was built for predicting the presence or absence of each protein family occurring in 10%-90% of all E. coli genomes. The resulting set of 3,259 extreme gradient boosting classifiers had a per-genome average macro F1 score of 0.944 [0.943-0.945, 95% CI]. We show that the F1 scores are stable across multi-locus sequence types and that the trend can be recapitulated by sampling a smaller number of core genes or diverse input genomes. Surprisingly, the presence or absence of poorly annotated proteins, including "hypothetical proteins" was accurately predicted (F1 = 0.902 [0.898-0.906, 95% CI]). Models for proteins with horizontal gene transfer-related functions had slightly lower F1 scores but were still accurate (F1s = 0.895, 0.872, 0.824, and 0.841 for transposon, phage, plasmid, and antimicrobial resistance-related functions, respectively). Finally, using a holdout set of 419 diverse E. coli genomes that were isolated from freshwater environmental sources, we observed an average per-genome F1 score of 0.880 [0.876-0.883, 95% CI], demonstrating the extensibility of the models. Overall, this study provides a framework for predicting variable gene content using a limited amount of input sequence data. IMPORTANCE Having the ability to predict the protein-encoding gene content of a genome is important for assessing genome quality, binning genomes from shotgun metagenomic assemblies, and assessing risk due to the presence of antimicrobial resistance and other virulence genes. In this study, we built a set of binary classifiers for predicting the presence or absence of variable genes occurring in 10%-90% of all publicly available E. coli genomes. Overall, the results show that a large portion of the E. coli variable gene content can be predicted with high accuracy, including genes with functions relating to horizontal gene transfer. This study offers a strategy for predicting gene content using limited input sequence data.
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Affiliation(s)
- Marcus Nguyen
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
| | - Zachary Elmore
- Biology Department, Hope College, Holland, Michigan, USA
| | - Clay Ihle
- Biology Department, Hope College, Holland, Michigan, USA
| | | | - Adam D. Slater
- Biology Department, Hope College, Holland, Michigan, USA
| | | | - Bruce Parrello
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Fellowship for Interpretation of Genomes, Burr Ridge, Illinois, USA
| | - Aaron A. Best
- Biology Department, Hope College, Holland, Michigan, USA
| | - James J. Davis
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
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Laksono BM, Roelofs D, Comvalius AD, Schmitz KS, Rijsbergen LC, Geers D, Nambulli S, van Run P, Duprex WP, van den Brand JMA, de Vries RD, de Swart RL. Infection of ferrets with wild type-based recombinant canine distemper virus overwhelms the immune system and causes fatal systemic disease. mSphere 2023; 8:e0008223. [PMID: 37377421 PMCID: PMC10449521 DOI: 10.1128/msphere.00082-23] [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: 02/12/2023] [Accepted: 04/12/2023] [Indexed: 06/29/2023] Open
Abstract
Canine distemper virus (CDV) causes systemic infection resulting in severe and often fatal disease in a large spectrum of animal host species. The virus is closely related to measles virus and targets myeloid, lymphoid, and epithelial cells, but CDV is more virulent and the infection spreads more rapidly within the infected host. Here, we aimed to study the pathogenesis of wild-type CDV infection by experimentally inoculating ferrets with recombinant CDV (rCDV) based on an isolate directly obtained from a naturally infected raccoon. The recombinant virus was engineered to express a fluorescent reporter protein, facilitating assessment of viral tropism and virulence. In ferrets, this wild type-based rCDV infected myeloid, lymphoid, and epithelial cells, and the infection resulted in systemic dissemination to multiple tissues and organs, especially those of the lymphatic system. High infection percentages in immune cells resulted in depletion of these cells both from circulation and from lymphoid tissues. The majority of CDV-infected ferrets reached their humane endpoints within 20 d and had to be euthanized. In that period, the virus also reached the central nervous system in several ferrets, but we did not observe the development of neurological complications during the study period of 23 d. Two out of 14 ferrets survived CDV infection and developed neutralizing antibodies. We show for the first time the pathogenesis of a non-adapted wild type-based rCDV in ferrets. IMPORTANCE Infection of ferrets with recombinant canine distemper virus (rCDV) expressing a fluorescent reporter protein has been used as proxy to understand measles pathogenesis and immune suppression in humans. CDV and measles virus use the same cellular receptors, but CDV is more virulent, and infection is often associated with neurological complications. rCDV strains in current use have complicated passage histories, which may have affected their pathogenesis. Here, we studied the pathogenesis of the first wild type-based rCDV in ferrets. We used macroscopic fluorescence to identify infected cells and tissues; multicolor flow cytometry to determine viral tropism in immune cells; and histopathology and immunohistochemistry to characterize infected cells and lesions in tissues. We conclude that CDV often overwhelmed the immune system, resulting in viral dissemination to multiple tissues in the absence of a detectable neutralizing antibody response. This virus is a promising tool to study the pathogenesis of morbillivirus infections.
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Affiliation(s)
| | - Dagmar Roelofs
- Department of Biomolecular Health Sciences, Division of Pathology, Universiteit Utrecht, Utrecht, the Netherlands
| | | | | | | | - Daryl Geers
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Sham Nambulli
- Centre for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Peter van Run
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - W. Paul Duprex
- Centre for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Judith M. A. van den Brand
- Department of Biomolecular Health Sciences, Division of Pathology, Universiteit Utrecht, Utrecht, the Netherlands
| | - Rory D. de Vries
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Rik L. de Swart
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, the Netherlands
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8
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Wang G, Li C, Tang H, Li B, Madonini F, Alsallom FF, Calvin Sun WK, Peng P, Villa F, Li J, Cappellaro P. Manipulating solid-state spin concentration through charge transport. Proc Natl Acad Sci U S A 2023; 120:e2305621120. [PMID: 37527342 PMCID: PMC10410760 DOI: 10.1073/pnas.2305621120] [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: 04/06/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023] Open
Abstract
Solid-state defects are attractive platforms for quantum sensing and simulation, e.g., in exploring many-body physics and quantum hydrodynamics. However, many interesting properties can be revealed only upon changes in the density of defects, which instead is usually fixed in material systems. Increasing the interaction strength by creating denser defect ensembles also brings more decoherence. Ideally one would like to control the spin concentration at will while keeping fixed decoherence effects. Here, we show that by exploiting charge transport, we can take some steps in this direction, while at the same time characterizing charge transport and its capture by defects. By exploiting the cycling process of ionization and recombination of NV centers in diamond, we pump electrons from the valence band to the conduction band. These charges are then transported to modulate the spin concentration by changing the charge state of material defects. By developing a wide-field imaging setup integrated with a fast single photon detector array, we achieve a direct and efficient characterization of the charge redistribution process by measuring the complete spectrum of the spin bath with micrometer-scale spatial resolution. We demonstrate a two-fold concentration increase of the dominant spin defects while keeping the T2 of the NV center relatively unchanged, which also provides a potential experimental demonstration of the suppression of spin flip-flops via hyperfine interactions. Our work paves the way to studying many-body dynamics with temporally and spatially tunable interaction strengths in hybrid charge-spin systems.
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Affiliation(s)
- Guoqing Wang
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Changhao Li
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Hao Tang
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Boning Li
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Francesca Madonini
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA02139
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano20133, Italy
| | - Faisal F. Alsallom
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Won Kyu Calvin Sun
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Pai Peng
- Department of Electrical Engineering, Princeton University, Princeton, NJ08544
| | - Federica Villa
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano20133, Italy
| | - Ju Li
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Paola Cappellaro
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
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9
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Aguilar Rangel M, Dolan PT, Taguwa S, Xiao Y, Andino R, Frydman J. High-resolution mapping reveals the mechanism and contribution of genome insertions and deletions to RNA virus evolution. Proc Natl Acad Sci U S A 2023; 120:e2304667120. [PMID: 37487061 PMCID: PMC10400975 DOI: 10.1073/pnas.2304667120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 03/21/2023] [Accepted: 06/07/2023] [Indexed: 07/26/2023] Open
Abstract
RNA viruses rapidly adapt to selective conditions due to the high intrinsic mutation rates of their RNA-dependent RNA polymerases (RdRps). Insertions and deletions (indels) in viral genomes are major contributors to both deleterious mutational load and evolutionary novelty, but remain understudied. To characterize the mechanistic details of their formation and evolutionary dynamics during infection, we developed a hybrid experimental-bioinformatic approach. This approach, called MultiMatch, extracts insertions and deletions from ultradeep sequencing experiments, including those occurring at extremely low frequencies, allowing us to map their genomic distribution and quantify the rates at which they occur. Mapping indel mutations in adapting poliovirus and dengue virus populations, we determine the rates of indel generation and identify mechanistic and functional constraints shaping indel diversity. Using poliovirus RdRp variants of distinct fidelity and genome recombination rates, we demonstrate tradeoffs between fidelity and Indel generation. Additionally, we show that maintaining translation frame and viral RNA structures constrain the Indel landscape and that, due to these significant fitness effects, Indels exert a significant deleterious load on adapting viral populations. Conversely, we uncover positively selected Indels that modulate RNA structure, generate protein variants, and produce defective interfering genomes in viral populations. Together, our analyses establish the kinetic and mechanistic tradeoffs between misincorporation, recombination, and Indel rates and reveal functional principles defining the central role of Indels in virus evolution, emergence, and the regulation of viral infection.
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Affiliation(s)
| | - Patrick T. Dolan
- Department of Biology, Stanford University, Stanford, CA94305
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA94143
| | - Shuhei Taguwa
- Department of Biology, Stanford University, Stanford, CA94305
- Research Institute for Microbial Diseases, Osaka University, Yamadaoka, Suita, Osaka565-0871, Japan
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA94143
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA94143
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA94305
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10
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Byrne E, Schum S, Schaerer L, Techtmann SM. Impacts of Nutrients on Alkene Biodegradation Rates and Microbial Community Composition in Enriched Consortia from Natural Inocula. Microbiol Spectr 2023; 11:e0031622. [PMID: 37017561 PMCID: PMC10269803 DOI: 10.1128/spectrum.00316-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 01/25/2023] [Indexed: 04/06/2023] Open
Abstract
There is a growing need for biological and chemical methods for upcycling plastic waste streams. Pyrolysis processes can accelerate plastic depolymerization by breaking polyethylene into smaller alkene components which may be more biodegradable than the initial polymer. While the biodegradation of alkanes has been extensively studied, the role microorganisms play in alkene breakdown is not well understood. Alkene biodegradation holds the potential to contribute to the coupling of chemical and biological processing of polyethylene plastics. In addition, nutrient levels are known to impact rates of hydrocarbon degradation. Model alkenes were used (C6, C10, C16, and C20) to follow the breakdown capability of microbial communities from three environmental inocula in three nutrient levels over the course of 5 days. Higher-nutrient cultures were anticipated to exhibit enhanced biodegradation capabilities. Alkene mineralization was assessed by measuring CO2 production in the culture headspace using GC-FID (gas chromatography-flame ionization detection), and alkene breakdown was directly quantified by measuring extracted residual hydrocarbons using gas chromatography-mass spectrometry (GC/MS). Here, the efficacy of enriched consortia derived from the microbial communities of three inoculum sources (farm compost, Caspian Sea sediment, and an iron-rich sediment) at alkene breakdown was investigated over the course of 5 days across three nutrient treatments. No significant differences in CO2 production across nutrient levels or inoculum types were found. A high extent of biodegradation was observed in all sample types, with most samples achieving 60% to 95% biodegradation of all quantified compounds. Here, our findings indicate that alkene biodegradation is a common metabolic process in diverse environments and that nutrient levels common to culture media can support the growth of alkene-biodegrading consortia, primarily from the families Xanthamonadaceae, Nocardiaceae, and Beijerinkiaceae. IMPORTANCE Excess plastic waste poses a major environmental problem. Microorganisms can metabolize many of the breakdown products (alkenes) of plastics. While microbial degradation of plastics is typically slow, coupling chemical and biological processing of plastics has the potential to lead to novel methods for the upcycling of plastic wastes. Here, we explored how microbial consortia derived from diverse environments metabolize alkenes, which are produced by the pyrolysis of polyolefin plastics such as HDPE, and PP. We found that microbial consortia from diverse environments can rapidly metabolize alkenes of different chain lengths. We also explored how nutrients affect the rates of alkene breakdown and the microbial diversity of the consortia. Here, the findings indicate that alkene biodegradation is a common metabolism in diverse environments (farm compost, Caspian sediment, and iron-rich sediment) and that nutrient levels common to culture medium can support growth of alkene-biodegrading consortia, primarily from families Xanthamonadaceae, Nocardiaceae, and Beijerinkiaceae.
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Affiliation(s)
- Emily Byrne
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, USA
| | - Simeon Schum
- Great Lakes Research Center, Houghton, Michigan, USA
| | - Laura Schaerer
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, USA
| | - Stephen M. Techtmann
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, USA
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11
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Motta FC, McGoff K, Moseley RC, Cho CY, Kelliher CM, Smith LM, Ortiz MS, Leman AR, Campione SA, Devos N, Chaorattanakawee S, Uthaimongkol N, Kuntawunginn W, Thongpiam C, Thamnurak C, Arsanok M, Wojnarski M, Vanchayangkul P, Boonyalai N, Smith PL, Spring MD, Jongsakul K, Chuang I, Harer J, Haase SB. The parasite intraerythrocytic cycle and human circadian cycle are coupled during malaria infection. Proc Natl Acad Sci U S A 2023; 120:e2216522120. [PMID: 37279274 PMCID: PMC10268210 DOI: 10.1073/pnas.2216522120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
During infections with the malaria parasites Plasmodium vivax, patients exhibit rhythmic fevers every 48 h. These fever cycles correspond with the time the parasites take to traverse the intraerythrocytic cycle (IEC). In other Plasmodium species that infect either humans or mice, the IEC is likely guided by a parasite-intrinsic clock [Rijo-Ferreiraet al., Science 368, 746-753 (2020); Smith et al., Science 368, 754-759 (2020)], suggesting that intrinsic clock mechanisms may be a fundamental feature of malaria parasites. Moreover, because Plasmodium cycle times are multiples of 24 h, the IECs may be coordinated with the host circadian clock(s). Such coordination could explain the synchronization of the parasite population in the host and enable alignment of IEC and circadian cycle phases. We utilized an ex vivo culture of whole blood from patients infected with P. vivax to examine the dynamics of the host circadian transcriptome and the parasite IEC transcriptome. Transcriptome dynamics revealed that the phases of the host circadian cycle and the parasite IEC are correlated across multiple patients, showing that the cycles are phase coupled. In mouse model systems, host-parasite cycle coupling appears to provide a selective advantage for the parasite. Thus, understanding how host and parasite cycles are coupled in humans could enable antimalarial therapies that disrupt this coupling.
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Affiliation(s)
- Francis C. Motta
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, FL33431
| | - Kevin McGoff
- Department of Mathematics and Statistics, University of North Carolina, Charlotte, NC28223
| | | | - Chun-Yi Cho
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
| | - Christina M. Kelliher
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH03755
| | | | | | | | | | | | - Suwanna Chaorattanakawee
- Department of Parasitology and Entomology, Faculty of Public Health, Mahidol University, Bangkok10400, Thailand
| | | | | | - Chadin Thongpiam
- US-Armed Forces Research Institute of Medical Sciences, Bangkok10400, Thailand
| | | | - Montri Arsanok
- US-Armed Forces Research Institute of Medical Sciences, Bangkok10400, Thailand
| | | | | | - Nonlawat Boonyalai
- US-Armed Forces Research Institute of Medical Sciences, Bangkok10400, Thailand
| | - Philip L. Smith
- U.S. Military HIV Research Program Walter Reed Army Institute of Research, Bethesda, MD20817
| | - Michele D. Spring
- US-Armed Forces Research Institute of Medical Sciences, Bangkok10400, Thailand
| | - Krisada Jongsakul
- US-Armed Forces Research Institute of Medical Sciences, Bangkok10400, Thailand
| | - Ilin Chuang
- US Naval Medical Research Center-Asia in Singapore, Assigned to Armed Forces Research Institute of Medical Sciences, Bangkok10400, Thailand
| | - John Harer
- Geometric Data Analytics, Durham, NC27701
| | - Steven B. Haase
- Department of Biology, Duke University, Durham, NC27708
- Department of Medicine Duke University, Durham, NC27710
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12
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Verhagen JV, Baker KL, Vasan G, Pieribone VA, Rolls ET. Odor encoding by signals in the olfactory bulb. J Neurophysiol 2023; 129:431-444. [PMID: 36598147 PMCID: PMC9925169 DOI: 10.1152/jn.00449.2022] [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: 11/15/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/05/2023] Open
Abstract
To understand the operation of the olfactory system, it is essential to know how information is encoded in the olfactory bulb. We applied Shannon information theoretic methods to address this, with signals from up to 57 glomeruli simultaneously optically imaged from presynaptic inputs in glomeruli in the mouse dorsal (dOB) and lateral (lOB) olfactory bulb, in response to six exemplar pure chemical odors. We discovered that, first, the tuning of these signals from glomeruli to a set of odors is remarkably broad, with a mean sparseness of 0.83 and a mean signal correlation of 0.64. Second, both of these factors contribute to the low information that is available from the responses of even populations of many tens of glomeruli, which was only 1.35 bits across 33 glomeruli on average, compared with the 2.58 bits required to perfectly encode these six odors. Third, although there is considerable interest in the possibility of temporal encoding of stimulus including odor identity, the amount of information in the temporal aspects of the presynaptic glomerular responses was low (mean 0.11 bits) and, importantly, was redundant with respect to the information available from the rates. Fourth, the information from simultaneously recorded glomeruli asymptotes very gradually and nonlinearly, showing that glomeruli do not have independent responses. Fifth, the information from a population became available quite rapidly, within 100 ms of sniff onset, and the peak of the glomerular response was at 200 ms. Sixth, the information from the lOB was not additive with that of the dOB.NEW & NOTEWORTHY We report broad tuning and low odor information available across the lateral and dorsal bulb populations of glomeruli. Even though response latencies can be significantly predictive of stimulus identity, such contained very little information and none that was not redundant with information based on rate coding alone. Last, in line with the emerging notion of the important role of earliest stages of responses ("primacy"), we report a very rapid rise in information after each inhalation.
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Affiliation(s)
- Justus V Verhagen
- The John B. Pierce Laboratory, New Haven, Connecticut
- Department of Neuroscience, Yale University, New Haven, Connecticut
| | - Keeley L Baker
- The John B. Pierce Laboratory, New Haven, Connecticut
- Department of Neuroscience, Yale University, New Haven, Connecticut
| | - Ganesh Vasan
- The John B. Pierce Laboratory, New Haven, Connecticut
- Department of Neuroscience, Yale University, New Haven, Connecticut
| | - Vincent A Pieribone
- The John B. Pierce Laboratory, New Haven, Connecticut
- Department of Neuroscience, Yale University, New Haven, Connecticut
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut
| | - Edmund T Rolls
- Oxford Centre for Computational Neuroscience, Oxford, United Kingdom
- University of Warwick, Coventry, United Kingdom
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13
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Gahbauer S, Correy GJ, Schuller M, Ferla MP, Doruk YU, Rachman M, Wu T, Diolaiti M, Wang S, Neitz RJ, Fearon D, Radchenko DS, Moroz YS, Irwin JJ, Renslo AR, Taylor JC, Gestwicki JE, von Delft F, Ashworth A, Ahel I, Shoichet BK, Fraser JS. Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proc Natl Acad Sci U S A 2023; 120:e2212931120. [PMID: 36598939 PMCID: PMC9926234 DOI: 10.1073/pnas.2212931120] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small-molecule inhibitors of Mac1 have great therapeutic potential, at the outset of the COVID-19 pandemic, there were no well-validated inhibitors for this protein nor, indeed, the macrodomain enzyme family, making this target a pharmacological orphan. Here, we report the structure-based discovery and development of several different chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high-resolution protein crystallography, and binding evaluation. Potent scaffolds were designed with in silico fragment linkage and by ultra-large library docking of over 450 million molecules. Both techniques leverage the computational exploration of tangible chemical space and are applicable to other pharmacological orphans. Overall, 160 ligands in 119 different scaffolds were discovered, and 153 Mac1-ligand complex crystal structures were determined, typically to 1 Å resolution or better. Our analyses discovered selective and cell-permeable molecules, unexpected ligand-mediated conformational changes within the active site, and key inhibitor motifs that will template future drug development against Mac1.
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Affiliation(s)
- Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA94158
| | - Galen J. Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA94158
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, UK
| | - Matteo P. Ferla
- Wellcome Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, OxfordOX4 2PG, UK
| | - Yagmur Umay Doruk
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94158
| | - Moira Rachman
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA94158
| | - Taiasean Wu
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA94158
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA94158
| | - Morgan Diolaiti
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94158
| | - Siyi Wang
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA94158
| | - R. Jeffrey Neitz
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, CA94158
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, DidcotOX11 0DE, UK
- Research Complex at Harwell Harwell Science and Innovation Campus, DidcotOX11 0FA, UK
| | - Dmytro S. Radchenko
- Enamine Ltd., Kyiv02094, Ukraine
- Taras Shevchenko National University of Kyiv, Kyiv01601, Ukraine
| | - Yurii S. Moroz
- Taras Shevchenko National University of Kyiv, Kyiv01601, Ukraine
- Chemspace, Kyiv02094, Ukraine
| | - John J. Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA94158
| | - Adam R. Renslo
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94158
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, CA94158
| | - Jenny C. Taylor
- Wellcome Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, OxfordOX4 2PG, UK
| | - Jason E. Gestwicki
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA94158
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, CA94158
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, DidcotOX11 0DE, UK
- Research Complex at Harwell Harwell Science and Innovation Campus, DidcotOX11 0FA, UK
- Centre for Medicines Discovery, University of Oxford, HeadingtonOX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, HeadingtonOX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park2006, South Africa
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94158
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, UK
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA94158
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA94158
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14
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Yin C, Imms P, Cheng M, Amgalan A, Chowdhury NF, Massett RJ, Chaudhari NN, Chen X, Thompson PM, Bogdan P, Irimia A. Anatomically interpretable deep learning of brain age captures domain-specific cognitive impairment. Proc Natl Acad Sci U S A 2023; 120:e2214634120. [PMID: 36595679 PMCID: PMC9926270 DOI: 10.1073/pnas.2214634120] [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: 08/26/2022] [Accepted: 11/10/2022] [Indexed: 01/05/2023] Open
Abstract
The gap between chronological age (CA) and biological brain age, as estimated from magnetic resonance images (MRIs), reflects how individual patterns of neuroanatomic aging deviate from their typical trajectories. MRI-derived brain age (BA) estimates are often obtained using deep learning models that may perform relatively poorly on new data or that lack neuroanatomic interpretability. This study introduces a convolutional neural network (CNN) to estimate BA after training on the MRIs of 4,681 cognitively normal (CN) participants and testing on 1,170 CN participants from an independent sample. BA estimation errors are notably lower than those of previous studies. At both individual and cohort levels, the CNN provides detailed anatomic maps of brain aging patterns that reveal sex dimorphisms and neurocognitive trajectories in adults with mild cognitive impairment (MCI, N = 351) and Alzheimer's disease (AD, N = 359). In individuals with MCI (54% of whom were diagnosed with dementia within 10.9 y from MRI acquisition), BA is significantly better than CA in capturing dementia symptom severity, functional disability, and executive function. Profiles of sex dimorphism and lateralization in brain aging also map onto patterns of neuroanatomic change that reflect cognitive decline. Significant associations between BA and neurocognitive measures suggest that the proposed framework can map, systematically, the relationship between aging-related neuroanatomy changes in CN individuals and in participants with MCI or AD. Early identification of such neuroanatomy changes can help to screen individuals according to their AD risk.
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Affiliation(s)
- Chenzhong Yin
- Ming Hsieh Department of Electrical and Computer Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA90089
| | - Phoebe Imms
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
| | - Mingxi Cheng
- Ming Hsieh Department of Electrical and Computer Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA90089
| | - Anar Amgalan
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
| | - Nahian F. Chowdhury
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
| | - Roy J. Massett
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
| | - Nikhil N. Chaudhari
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
- Corwin D. Denney Research Center, Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA90089
| | - Xinghe Chen
- Ming Hsieh Department of Electrical and Computer Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA90089
| | - Paul M. Thompson
- Corwin D. Denney Research Center, Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA90089
- Imaging Genetics Center, Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA90033
- Department of Quantitative & Computational Biology, Dana & David Dornsife College of Arts & Sciences, University of Southern California, Los Angeles, CA90089
- Department of Ophthalmology, Keck School of Medicine, University of Southern California, Los Angeles, CA90033
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA90033
- Department of Radiology, Keck School of Medicine, University of Southern California, Los Angeles, CA90033
- Department of Psychiatry, Keck School of Medicine, University of Southern California, Los Angeles, CA90033
- Department of Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA90033
| | - Paul Bogdan
- Ming Hsieh Department of Electrical and Computer Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA90089
| | - Andrei Irimia
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
- Corwin D. Denney Research Center, Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA90089
- Department of Quantitative & Computational Biology, Dana & David Dornsife College of Arts & Sciences, University of Southern California, Los Angeles, CA90089
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15
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Loveday EK, Sanchez HS, Thomas MM, Chang CB. Single-Cell Infection of Influenza A Virus Using Drop-Based Microfluidics. Microbiol Spectr 2022; 10:e0099322. [PMID: 36125315 PMCID: PMC9603537 DOI: 10.1128/spectrum.00993-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 04/13/2022] [Accepted: 08/22/2022] [Indexed: 12/30/2022] Open
Abstract
Drop-based microfluidics has revolutionized single-cell studies and can be applied toward analyzing tens of thousands to millions of single cells and their products contained within picoliter-sized drops. Drop-based microfluidics can shed insight into single-cell virology, enabling higher-resolution analysis of cellular and viral heterogeneity during viral infection. In this work, individual A549, MDCK, and siat7e cells were infected with influenza A virus (IAV) and encapsulated into 100-μm-size drops. Initial studies of uninfected cells encapsulated in drops demonstrated high cell viability and drop stability. Cell viability of uninfected cells in the drops remained above 75%, and the average drop radii changed by less than 3% following cell encapsulation and incubation over 24 h. Infection parameters were analyzed over 24 h from individually infected cells in drops. The number of IAV viral genomes and infectious viruses released from A549 and MDCK cells in drops was not significantly different from bulk infection as measured by reverse transcriptase quantitative PCR (RT-qPCR) and plaque assay. The application of drop-based microfluidics in this work expands the capacity to propagate IAV viruses and perform high-throughput analyses of individually infected cells. IMPORTANCE Drop-based microfluidics is a cutting-edge tool in single-cell research. Here, we used drop-based microfluidics to encapsulate thousands of individual cells infected with influenza A virus within picoliter-sized drops. Drop stability, cell loading, and cell viability were quantified from three different cell lines that support influenza A virus propagation. Similar levels of viral progeny as determined by RT-qPCR and plaque assay were observed from encapsulated cells in drops compared to bulk culture. This approach enables the ability to propagate influenza A virus from encapsulated cells, allowing for future high-throughput analysis of single host cell interactions in isolated microenvironments over the course of the viral life cycle.
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Affiliation(s)
- Emma Kate Loveday
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
| | - Humberto S. Sanchez
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
| | - Mallory M. Thomas
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Connie B. Chang
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
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16
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Bai H, Ingber DE. What Can an Organ-on-a-Chip Teach Us About Human Lung Pathophysiology? Physiology (Bethesda) 2022; 37:0. [PMID: 35658627 PMCID: PMC9394778 DOI: 10.1152/physiol.00012.2022] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 05/06/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 12/25/2022] Open
Abstract
The intertwined relationship between structure and function has been key to understanding human organ physiology and disease pathogenesis. An organ-on-a-chip (organ chip) is a bioengineered microfluidic cell culture device lined by living cells and tissues that recapitulates organ-level functions in vitro. This is accomplished by recreating organ-specific tissue-tissue interfaces and microenvironmental biochemical and mechanical cues while providing dynamic perfusion through endothelium-lined vascular channels. In this review, we discuss how this emerging technology has contributed to the understanding of human lung structure-function relationships at the cell, tissue, and organ levels.
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Affiliation(s)
- Haiqing Bai
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts
- Vascular Biology Program, Boston Children's Hospital and Department of Surgery, Harvard Medical School, Boston, Massachusetts
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, Massachusetts
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17
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Lai J, German J, Hong F, Tai SHS, McPhaul KM, Milton DK. Comparison of Saliva and Midturbinate Swabs for Detection of SARS-CoV-2. Microbiol Spectr 2022; 10:e0012822. [PMID: 35311575 PMCID: PMC9045394 DOI: 10.1128/spectrum.00128-22] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/17/2022] [Indexed: 01/25/2023] Open
Abstract
Saliva is an attractive sample for detecting SARS-CoV-2. However, contradictory reports exist concerning the sensitivity of saliva versus nasal swabs. We followed close contacts of COVID-19 cases for up to 14 days from the last exposure and collected self-reported symptoms, midturbinate swabs (MTS), and saliva every 2 or 3 days. Ct values, viral load, and frequency of viral detection by MTS and saliva were compared. Fifty-eight contacts provided 200 saliva-MTS pairs, and 14 contacts (13 with symptoms) had one or more positive samples. Saliva and MTS had similar rates of viral detection (P = 0.78) and substantial agreement (κ = 0.83). However, sensitivity varied significantly with time since symptom onset. Early on (days -3 to 2), saliva had 12 times (95% CI: 1.2, 130) greater likelihood of viral detection and 3.2 times (95% CI: 2.8, 3.8) higher RNA copy numbers compared to MTS. After day 2 of symptoms, there was a nonsignificant trend toward greater sensitivity using MTS. Saliva and MTS demonstrated high agreement making saliva a suitable alternative to MTS for SARS-CoV-2 detection. Saliva was more sensitive early in the infection when the transmission was most likely to occur, suggesting that it may be a superior and cost-effective screening tool for COVID-19. IMPORTANCE The findings of this manuscript are increasingly important with new variants that appear to have shorter incubation periods emerging, which may be more prone to detection in saliva before detection in nasal swabs. Therefore, there is an urgent need to provide the science to support the use of a detection method that is highly sensitive and widely acceptable to the public to improve screening rates and early detection. The manuscript presents the first evidence that saliva-based RT-PCR is more sensitive than MTS-based RT-PCR in detecting SARS-CoV-2 during the presymptomatic period - the critical period for unwitting onward transmission. Considering other advantages of saliva samples, including the lower cost, greater acceptability within the general population, and less risk to health care workers, our findings further supported the use of saliva to identify presymptomatic infection and prevent transmission of the virus.
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Affiliation(s)
- Jianyu Lai
- Department of Epidemiology and Biostatistics, University of Maryland School of Public Health, College Park, Maryland, USA
- Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Jennifer German
- Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Filbert Hong
- Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - S.-H. Sheldon Tai
- Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Kathleen M. McPhaul
- Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Donald K. Milton
- Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
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18
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Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight R. Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy. mSystems 2022; 7:e0016722. [PMID: 35369727 PMCID: PMC9040630 DOI: 10.1128/msystems.00167-22] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 02/19/2022] [Accepted: 02/25/2022] [Indexed: 02/06/2023] Open
Abstract
We introduce the operational genomic unit (OGU) method, a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference genomes as the minimum unit for assessing the diversity of microbial communities and their relevance to environmental factors. This approach is independent of taxonomic classification, granting the possibility of maximal resolution of community composition, and organizes features into an accurate hierarchy using a phylogenomic tree. The outputs are suitable for contemporary analytical protocols for community ecology, differential abundance, and supervised learning while supporting phylogenetic methods, such as UniFrac and phylofactorization, that are seldom applied to shotgun metagenomics despite being prevalent in 16S rRNA gene amplicon studies. As demonstrated in two real-world case studies, the OGU method produces biologically meaningful patterns from microbiome data sets. Such patterns further remain detectable at very low metagenomic sequencing depths. Compared with taxonomic unit-based analyses implemented in currently adopted metagenomics tools, and the analysis of 16S rRNA gene amplicon sequence variants, this method shows superiority in informing biologically relevant insights, including stronger correlation with body environment and host sex on the Human Microbiome Project data set and more accurate prediction of human age by the gut microbiomes of Finnish individuals included in the FINRISK 2002 cohort. We provide Woltka, a bioinformatics tool to implement this method, with full integration with the QIIME 2 package and the Qiita web platform, to facilitate adoption of the OGU method in future metagenomics studies. IMPORTANCE Shotgun metagenomics is a powerful, yet computationally challenging, technique compared to 16S rRNA gene amplicon sequencing for decoding the composition and structure of microbial communities. Current analyses of metagenomic data are primarily based on taxonomic classification, which is limited in feature resolution. To solve these challenges, we introduce operational genomic units (OGUs), which are the individual reference genomes derived from sequence alignment results, without further assigning them taxonomy. The OGU method advances current read-based metagenomics in two dimensions: (i) providing maximal resolution of community composition and (ii) permitting use of phylogeny-aware tools. Our analysis of real-world data sets shows that it is advantageous over currently adopted metagenomic analysis methods and the finest-grained 16S rRNA analysis methods in predicting biological traits. We thus propose the adoption of OGUs as an effective practice in metagenomic studies.
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Affiliation(s)
- Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Antonio Gonzalez
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Imran McGrath
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Niina Haiminen
- IBM T. J. Watson Research Center, Yorktown Heights, New York, USA
| | - George Armstrong
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California, USA
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Julian Yu
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona, USA
| | | | | | - Austin D. Swafford
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Promi Das
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Justin P. Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Franck Lejzerowicz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Aki S. Havulinna
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Guillaume Méric
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Teemu Niiranen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Internal Medicine, University of Turku, Turku, Finland
- Division of Medicine, Turku University Hospital, Finland
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Ho-Cheol Kim
- IBM Almaden Research Center, San Jose, California, USA
| | - Mohit Jain
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Public Health and Primary Care, Cambridge University, Cambridge, United Kingdom
| | - Jack A. Gilbert
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
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19
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Pandarinath C, Bensmaia SJ. The science and engineering behind sensitized brain-controlled bionic hands. Physiol Rev 2022; 102:551-604. [PMID: 34541898 PMCID: PMC8742729 DOI: 10.1152/physrev.00034.2020] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [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: 08/11/2020] [Revised: 09/07/2021] [Accepted: 09/13/2021] [Indexed: 12/13/2022] Open
Abstract
Advances in our understanding of brain function, along with the development of neural interfaces that allow for the monitoring and activation of neurons, have paved the way for brain-machine interfaces (BMIs), which harness neural signals to reanimate the limbs via electrical activation of the muscles or to control extracorporeal devices, thereby bypassing the muscles and senses altogether. BMIs consist of reading out motor intent from the neuronal responses monitored in motor regions of the brain and executing intended movements with bionic limbs, reanimated limbs, or exoskeletons. BMIs also allow for the restoration of the sense of touch by electrically activating neurons in somatosensory regions of the brain, thereby evoking vivid tactile sensations and conveying feedback about object interactions. In this review, we discuss the neural mechanisms of motor control and somatosensation in able-bodied individuals and describe approaches to use neuronal responses as control signals for movement restoration and to activate residual sensory pathways to restore touch. Although the focus of the review is on intracortical approaches, we also describe alternative signal sources for control and noninvasive strategies for sensory restoration.
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Affiliation(s)
- Chethan Pandarinath
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia
- Department of Neurosurgery, Emory University, Atlanta, Georgia
| | - Sliman J Bensmaia
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois
- Committee on Computational Neuroscience, University of Chicago, Chicago, Illinois
- Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, Illinois
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20
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Graczyk EL, Christie BP, He Q, Tyler DJ, Bensmaia SJ. Frequency Shapes the Quality of Tactile Percepts Evoked through Electrical Stimulation of the Nerves. J Neurosci 2022; 42:2052-2064. [PMID: 35074865 PMCID: PMC8916769 DOI: 10.1523/jneurosci.1494-21.2021] [Citation(s) in RCA: 13] [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: 07/21/2021] [Revised: 09/29/2021] [Accepted: 11/22/2021] [Indexed: 11/21/2022] Open
Abstract
Electrical stimulation of the peripheral nerves of human participants provides a unique opportunity to study the neural determinants of perceptual quality using a causal manipulation. A major challenge in the study of neural coding of touch has been to isolate the role of spike timing-at the scale of milliseconds or tens of milliseconds-in shaping the sensory experience. In the present study, we address this question by systematically varying the pulse frequency (PF) of electrical stimulation pulse trains delivered to the peripheral nerves of seven participants with upper and lower extremity limb loss via chronically implanted neural interfaces. We find that increases in PF lead to systematic increases in perceived frequency, up to ∼50 Hz, at which point further changes in PF have little to no impact on sensory quality. Above this transition frequency, ratings of perceived frequency level off, the ability to discriminate changes in PF is abolished, and verbal descriptors selected to characterize the sensation change abruptly. We conclude that sensation quality is shaped by temporal patterns of neural activation, even if these patterns are imposed on a fixed neural population, but this temporal patterning can only be resolved up to ∼50 Hz. These findings highlight the importance of spike timing in shaping the quality of a sensation and will contribute to the development of encoding strategies for conveying touch feedback through bionic hands and feet.SIGNIFICANCE STATEMENT A major challenge in the study of neural coding of touch has been to understand how temporal patterns in neuronal responses shape the sensory experience. We address this question by varying the pulse frequency (PF) of electrical pulse trains delivered through implanted nerve interfaces in seven amputees. We concomitantly vary pulse width to separate the effect of changing PF on sensory quality from its effect on perceived magnitude. We find that increases in PF lead to increases in perceived frequency, a qualitative dimension, up to ∼50 Hz, beyond which changes in PF have little impact on quality. We conclude that temporal patterning in the neuronal response can shape quality and discuss the implications for restoring touch via neural interfaces.
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Affiliation(s)
- Emily L Graczyk
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio 44106
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106
| | - Breanne P Christie
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio 44106
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Qinpu He
- Committee on Computational Neuroscience, University of Chicago, Chicago, Illinois 60637
| | - Dustin J Tyler
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio 44106
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106
| | - Sliman J Bensmaia
- Committee on Computational Neuroscience, University of Chicago, Chicago, Illinois 60637
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois 60637
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21
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Son J, Huang S, Zeng Q, Bricker TL, Case JB, Zhou J, Zang R, Liu Z, Chang X, Darling TL, Xu J, Harastani HH, Chen L, Gomez Castro MF, Zhao Y, Kohio HP, Hou G, Fan B, Niu B, Guo R, Rothlauf PW, Bailey AL, Wang X, Shi PY, Martinez ED, Brody SL, Whelan SPJ, Diamond MS, Boon ACM, Li B, Ding S. JIB-04 Has Broad-Spectrum Antiviral Activity and Inhibits SARS-CoV-2 Replication and Coronavirus Pathogenesis. mBio 2022; 13:e0337721. [PMID: 35038906 PMCID: PMC8764536 DOI: 10.1128/mbio.03377-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 11/11/2021] [Accepted: 12/09/2021] [Indexed: 01/18/2023] Open
Abstract
Pathogenic coronaviruses are a major threat to global public health. Here, using a recombinant reporter virus-based compound screening approach, we identified small-molecule inhibitors that potently block the replication of severe acute respiratory syndrome virus 2 (SARS-CoV-2). Among them, JIB-04 inhibited SARS-CoV-2 replication in Vero E6 cells with a 50% effective concentration of 695 nM, with a specificity index of greater than 1,000. JIB-04 showed in vitro antiviral activity in multiple cell types, including primary human bronchial epithelial cells, against several DNA and RNA viruses, including porcine coronavirus transmissible gastroenteritis virus. In an in vivo porcine model of coronavirus infection, administration of JIB-04 reduced virus infection and associated tissue pathology, which resulted in improved weight gain and survival. These results highlight the potential utility of JIB-04 as an antiviral agent against SARS-CoV-2 and other viral pathogens. IMPORTANCE The coronavirus disease 2019 (COVID-19), the disease caused by SARS-CoV-2 infection, is an ongoing public health disaster worldwide. Although several vaccines are available as a preventive measure and the FDA approval of an orally bioavailable drug is on the horizon, there remains a need for developing antivirals against SARS-CoV-2 that could work on the early course of infection. By using infectious reporter viruses, we screened small-molecule inhibitors for antiviral activity against SARS-CoV-2. Among the top hits was JIB-04, a compound previously studied for its anticancer activity. Here, we showed that JIB-04 inhibits the replication of SARS-CoV-2 as well as different DNA and RNA viruses. Furthermore, JIB-04 conferred protection in a porcine model of coronavirus infection, although to a lesser extent when given as therapeutic rather than prophylactic doses. Our findings indicate a limited but still promising utility of JIB-04 as an antiviral agent in the combat against COVID-19 and potentially other viral diseases.
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Affiliation(s)
- Juhee Son
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Program in Molecular Cell Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shimeng Huang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation, Base of Ministry of Science and Technology, Nanjing, China
| | - Qiru Zeng
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Traci L. Bricker
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - James Brett Case
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jinzhu Zhou
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation, Base of Ministry of Science and Technology, Nanjing, China
| | - Ruochen Zang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, China
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Xinjian Chang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation, Base of Ministry of Science and Technology, Nanjing, China
| | - Tamarand L. Darling
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jian Xu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Houda H. Harastani
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lu Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | | | - Yongxiang Zhao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation, Base of Ministry of Science and Technology, Nanjing, China
| | - Hinissan P. Kohio
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gaopeng Hou
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Baochao Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation, Base of Ministry of Science and Technology, Nanjing, China
| | - Beibei Niu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation, Base of Ministry of Science and Technology, Nanjing, China
| | - Rongli Guo
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation, Base of Ministry of Science and Technology, Nanjing, China
| | - Paul W. Rothlauf
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Program in Virology, Harvard Medical School, Boston, Massachusetts, USA
| | - Adam L. Bailey
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Xin Wang
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, China
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Steven L. Brody
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sean P. J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael S. Diamond
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Adrianus C. M. Boon
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation, Base of Ministry of Science and Technology, Nanjing, China
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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22
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Pelz L, Rüdiger D, Dogra T, Alnaji FG, Genzel Y, Brooke CB, Kupke SY, Reichl U. Semi-continuous Propagation of Influenza A Virus and Its Defective Interfering Particles: Analyzing the Dynamic Competition To Select Candidates for Antiviral Therapy. J Virol 2021; 95:e0117421. [PMID: 34550771 PMCID: PMC8610589 DOI: 10.1128/jvi.01174-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/19/2021] [Indexed: 12/26/2022] Open
Abstract
Defective interfering particles (DIPs) of influenza A virus (IAV) are naturally occurring mutants that have an internal deletion in one of their eight viral RNA (vRNA) segments, rendering them propagation-incompetent. Upon coinfection with infectious standard virus (STV), DIPs interfere with STV replication through competitive inhibition. Thus, DIPs are proposed as potent antivirals for treatment of the influenza disease. To select corresponding candidates, we studied de novo generation of DIPs and propagation competition between different defective interfering (DI) vRNAs in an STV coinfection scenario in cell culture. A small-scale two-stage cultivation system that allows long-term semi-continuous propagation of IAV and its DIPs was used. Strong periodic oscillations in virus titers were observed due to the dynamic interaction of DIPs and STVs. Using next-generation sequencing, we detected a predominant formation and accumulation of DI vRNAs on the polymerase-encoding segments. Short DI vRNAs accumulated to higher fractions than longer ones, indicating a replication advantage, yet an optimum fragment length was observed. Some DI vRNAs showed breaking points in a specific part of their bundling signal (belonging to the packaging signal), suggesting its dispensability for DI vRNA propagation. Over a total cultivation time of 21 days, several individual DI vRNAs accumulated to high fractions, while others decreased. Using reverse genetics for IAV, purely clonal DIPs derived from highly replicating DI vRNAs were generated. We confirm that these DIPs exhibit a superior in vitro interfering efficacy compared to DIPs derived from lowly accumulated DI vRNAs and suggest promising candidates for efficacious antiviral treatment. IMPORTANCE Defective interfering particles (DIPs) emerge naturally during viral infection and typically show an internal deletion in the viral genome. Thus, DIPs are propagation-incompetent. Previous research suggests DIPs as potent antiviral compounds for many different virus families due to their ability to interfere with virus replication by competitive inhibition. For instance, the administration of influenza A virus (IAV) DIPs resulted in a rescue of mice from an otherwise lethal IAV dose. Moreover, no apparent toxic effects were observed when only DIPs were administered to mice and ferrets. IAV DIPs show antiviral activity against many different IAV strains, including pandemic and highly pathogenic avian strains, and even against nonhomologous viruses, such as SARS-CoV-2, by stimulation of innate immunity. Here, we used a cultivation/infection system, which exerted selection pressure toward accumulation of highly competitive IAV DIPs. These DIPs showed a superior interfering efficacy in vitro, and we suggest them for effective antiviral therapy.
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Affiliation(s)
- Lars Pelz
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Daniel Rüdiger
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Tanya Dogra
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Fadi G. Alnaji
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, Illinois, USA
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Christopher B. Brooke
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, Illinois, USA
| | - Sascha Y. Kupke
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
- Otto-von-Guericke-University Magdeburg, Bioprocess Engineering, Magdeburg, Germany
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23
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Pascal Andreu V, Augustijn HE, van den Berg K, van der Hooft JJJ, Fischbach MA, Medema MH. BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes. mSystems 2021; 6:e0093721. [PMID: 34581602 PMCID: PMC8547482 DOI: 10.1128/msystems.00937-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 07/19/2021] [Accepted: 08/24/2021] [Indexed: 12/28/2022] Open
Abstract
Microbial gene clusters encoding the biosynthesis of primary and secondary metabolites play key roles in shaping microbial ecosystems and driving microbiome-associated phenotypes. Although effective approaches exist to evaluate the metabolic potential of such bacteria through identification of these metabolic gene clusters in their genomes, no automated pipelines exist to profile the abundance and expression levels of such gene clusters in microbiome samples to generate hypotheses about their functional roles, and to find associations with phenotypes of interest. Here, we describe BiG-MAP, a bioinformatic tool to profile abundance and expression levels of gene clusters across metagenomic and metatranscriptomic data and evaluate their differential abundance and expression under different conditions. To illustrate its usefulness, we analyzed 96 metagenomic samples from healthy and caries-associated human oral microbiome samples and identified 252 gene clusters, including unreported ones, that were significantly more abundant in either phenotype. Among them, we found the muc operon, a gene cluster known to be associated with tooth decay. Additionally, we found a putative reuterin biosynthetic gene cluster from a Streptococcus strain to be enriched but not exclusively found in healthy samples; metabolomic data from the same samples showed masses with fragmentation patterns consistent with (poly)acrolein, which is known to spontaneously form from the products of the reuterin pathway and has been previously shown to inhibit pathogenic Streptococcus mutans strains. Thus, we show how BiG-MAP can be used to generate new hypotheses on potential drivers of microbiome-associated phenotypes and prioritize the experimental characterization of relevant gene clusters that may mediate them. IMPORTANCE Microbes play an increasingly recognized role in determining host-associated phenotypes by producing small molecules that interact with other microorganisms or host cells. The production of these molecules is often encoded in syntenic genomic regions, also known as gene clusters. With the increasing numbers of (multi)omics data sets that can help in understanding complex ecosystems at a much deeper level, there is a need to create tools that can automate the process of analyzing these gene clusters across omics data sets. This report presents a new software tool called BiG-MAP, which allows assessing gene cluster abundance and expression in microbiome samples using metagenomic and metatranscriptomic data. Here, we describe the tool and its functionalities, as well as its validation using a mock community. Finally, using an oral microbiome data set, we show how it can be used to generate hypotheses regarding the functional roles of gene clusters in mediating host phenotypes.
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Affiliation(s)
| | | | - Koen van den Berg
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | | | - Michael A. Fischbach
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
- ChEM-H, Stanford University, Stanford, California, USA
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
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24
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Yeo YY, Buchholz DW, Gamble A, Jager M, Aguilar HC. Headless Henipaviral Receptor Binding Glycoproteins Reveal Fusion Modulation by the Head/Stalk Interface and Post-receptor Binding Contributions of the Head Domain. J Virol 2021; 95:e0066621. [PMID: 34288734 PMCID: PMC8475510 DOI: 10.1128/jvi.00666-21] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/13/2021] [Indexed: 11/20/2022] Open
Abstract
Cedar virus (CedV) is a nonpathogenic member of the Henipavirus (HNV) genus of emerging viruses, which includes the deadly Nipah (NiV) and Hendra (HeV) viruses. CedV forms syncytia, a hallmark of henipaviral and paramyxoviral infections and pathogenicity. However, the intrinsic fusogenic capacity of CedV relative to NiV or HeV remains unquantified. HNV entry is mediated by concerted interactions between the attachment (G) and fusion (F) glycoproteins. Upon receptor binding by the HNV G head domain, a fusion-activating G stalk region is exposed and triggers F to undergo a conformational cascade that leads to viral entry or cell-cell fusion. Here, we demonstrate quantitatively that CedV is inherently significantly less fusogenic than NiV at equivalent G and F cell surface expression levels. We then generated and tested six headless CedV G mutants of distinct C-terminal stalk lengths, surprisingly revealing highly hyperfusogenic cell-cell fusion phenotypes 3- to 4-fold greater than wild-type CedV levels. Additionally, similarly to NiV, a headless HeV G mutant yielded a less pronounced hyperfusogenic phenotype compared to wild-type HeV. Further, coimmunoprecipitation and cell-cell fusion assays revealed heterotypic NiV/CedV functional G/F bidentate interactions, as well as evidence of HNV G head domain involvement beyond receptor binding or G stalk exposure. All evidence points to the G head/stalk junction being key to modulating HNV fusogenicity, supporting the notion that head domains play several distinct and central roles in modulating stalk domain fusion promotion. Further, this study exemplifies how CedV may help elucidate important mechanistic underpinnings of HNV entry and pathogenicity. IMPORTANCE The Henipavirus genus in the Paramyxoviridae family includes the zoonotic Nipah (NiV) and Hendra (HeV) viruses. NiV and HeV infections often cause fatal encephalitis and pneumonia, but no vaccines or therapeutics are currently approved for human use. Upon viral entry, Henipavirus infections yield the formation of multinucleated cells (syncytia). Viral entry and cell-cell fusion are mediated by the attachment (G) and fusion (F) glycoproteins. Cedar virus (CedV), a nonpathogenic henipavirus, may be a useful tool to gain knowledge on henipaviral pathogenicity. Here, using homotypic and heterotypic full-length and headless CedV, NiV, and HeV G/F combinations, we discovered that CedV G/F are significantly less fusogenic than NiV or HeV G/F, and that the G head/stalk junction is key to modulating cell-cell fusion, refining the mechanism of henipaviral membrane fusion events. Our study exemplifies how CedV may be a useful tool to elucidate broader mechanistic understanding for the important henipaviruses.
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Affiliation(s)
- Yao Yu Yeo
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - David W. Buchholz
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Amandine Gamble
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Mason Jager
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Hector C. Aguilar
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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25
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Gamble A, Fischer RJ, Morris DH, Yinda CK, Munster VJ, Lloyd-Smith JO. Heat-Treated Virus Inactivation Rate Depends Strongly on Treatment Procedure: Illustration with SARS-CoV-2. Appl Environ Microbiol 2021; 87:e0031421. [PMID: 34288702 PMCID: PMC8432576 DOI: 10.1128/aem.00314-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 03/23/2021] [Accepted: 07/12/2021] [Indexed: 12/05/2022] Open
Abstract
Decontamination helps limit environmental transmission of infectious agents. It is required for the safe reuse of contaminated medical, laboratory, and personal protective equipment, and for the safe handling of biological samples. Heat treatment is a common decontamination method, notably used for viruses. We show that for liquid specimens (here, solution of SARS-CoV-2 in cell culture medium), the virus inactivation rate under heat treatment at 70°C can vary by almost two orders of magnitude depending on the treatment procedure, from a half-life of 0.86 min (95% credible interval [CI] 0.09, 1.77) in closed vials in a heat block to 37.04 min (95% CI 12.64, 869.82) in uncovered plates in a dry oven. These findings suggest a critical role of evaporation in virus inactivation via dry heat. Placing samples in open or uncovered containers may dramatically reduce the speed and efficacy of heat treatment for virus inactivation. Given these findings, we reviewed the literature on temperature-dependent coronavirus stability and found that specimen container types, along with whether they are closed, covered, or uncovered, are rarely reported in the scientific literature. Heat-treatment procedures must be fully specified when reporting experimental studies to facilitate result interpretation and reproducibility, and must be carefully considered when developing decontamination guidelines. IMPORTANCE Heat is a powerful weapon against most infectious agents. It is widely used for decontamination of medical, laboratory, and personal protective equipment, and for biological samples. There are many methods of heat treatment, and methodological details can affect speed and efficacy of decontamination. We applied four different heat-treatment procedures to liquid specimens containing SARS-CoV-2. Our results show that the container used to store specimens during decontamination can substantially affect inactivation rate; for a given initial level of contamination, decontamination time can vary from a few minutes in closed vials to several hours in uncovered plates. Reviewing the literature, we found that container choices and heat treatment methods are only rarely reported explicitly in methods sections. Our study shows that careful consideration of heat-treatment procedure-in particular the choice of specimen container and whether it is covered-can make results more consistent across studies, improve decontamination practice, and provide insight into the mechanisms of virus inactivation.
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Affiliation(s)
- Amandine Gamble
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Robert J. Fischer
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, USA
| | - Dylan H. Morris
- Department of Ecology & Evolutionary Biology, Princeton University, New Jersey, USA
| | - Claude Kwe Yinda
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, USA
| | - Vincent J. Munster
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, USA
| | - James O. Lloyd-Smith
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, California, USA
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26
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Zeller MA, Gauger PC, Arendsee ZW, Souza CK, Vincent AL, Anderson TK. Machine Learning Prediction and Experimental Validation of Antigenic Drift in H3 Influenza A Viruses in Swine. mSphere 2021; 6:e00920-20. [PMID: 33731472 PMCID: PMC8546707 DOI: 10.1128/msphere.00920-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 02/23/2021] [Indexed: 11/20/2022] Open
Abstract
The antigenic diversity of influenza A viruses (IAV) circulating in swine challenges the development of effective vaccines, increasing zoonotic threat and pandemic potential. High-throughput sequencing technologies can quantify IAV genetic diversity, but there are no accurate approaches to adequately describe antigenic phenotypes. This study evaluated an ensemble of nonlinear regression models to estimate virus phenotype from genotype. Regression models were trained with a phenotypic data set of pairwise hemagglutination inhibition (HI) assays, using genetic sequence identity and pairwise amino acid mutations as predictor features. The model identified amino acid identity, ranked the relative importance of mutations in the hemagglutinin (HA) protein, and demonstrated good prediction accuracy. Four previously untested IAV strains were selected to experimentally validate model predictions by HI assays. Errors between predicted and measured distances of uncharacterized strains were 0.35, 0.61, 1.69, and 0.13 antigenic units. These empirically trained regression models can be used to estimate antigenic distances between different strains of IAV in swine by using sequence data. By ranking the importance of mutations in the HA, we provide criteria for identifying antigenically advanced IAV strains that may not be controlled by existing vaccines and can inform strain updates to vaccines to better control this pathogen.IMPORTANCE Influenza A viruses (IAV) in swine constitute a major economic burden to an important global agricultural sector, impact food security, and are a public health threat. Despite significant improvement in surveillance for IAV in swine over the past 10 years, sequence data have not been integrated into a systematic vaccine strain selection process for predicting antigenic phenotype and identifying determinants of antigenic drift. To overcome this, we developed nonlinear regression models that predict antigenic phenotype from genetic sequence data by training the model on hemagglutination inhibition assay results. We used these models to predict antigenic phenotype for previously uncharacterized IAV, ranked the importance of genetic features for antigenic phenotype, and experimentally validated our predictions. Our model predicted virus antigenic characteristics from genetic sequence data and provides a rapid and accurate method linking genetic sequence data to antigenic characteristics. This approach also provides support for public health by identifying viruses that are antigenically advanced from strains used as pandemic preparedness candidate vaccine viruses.
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Affiliation(s)
- Michael A Zeller
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, USA
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, USA
| | - Phillip C Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, USA
| | - Zebulun W Arendsee
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
| | - Carine K Souza
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
| | - Amy L Vincent
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
| | - Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
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27
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Elston KM, Perreau J, Maeda GP, Moran NA, Barrick JE. Engineering a Culturable Serratia symbiotica Strain for Aphid Paratransgenesis. Appl Environ Microbiol 2021; 87:AEM.02245-20. [PMID: 33277267 PMCID: PMC7851701 DOI: 10.1128/aem.02245-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 09/15/2020] [Accepted: 11/22/2020] [Indexed: 02/07/2023] Open
Abstract
Aphids are global agricultural pests and important models for bacterial symbiosis. To date, none of the native symbionts of aphids have been genetically manipulated, which limits our understanding of how they interact with their hosts. Serratia symbiotica CWBI-2.3T is a culturable, gut-associated bacterium isolated from the black bean aphid. Closely related Serratia symbiotica strains are facultative aphid endosymbionts that are vertically transmitted from mother to offspring during embryogenesis. We demonstrate that CWBI-2.3T can be genetically engineered using a variety of techniques, plasmids, and gene expression parts. Then, we use fluorescent protein expression to track the dynamics with which CWBI-2.3T colonizes the guts of multiple aphid species, and we measure how this bacterium affects aphid fitness. Finally, we show that we can induce heterologous gene expression from engineered CWBI-2.3T in living aphids. These results inform the development of CWBI-2.3T for aphid paratransgenesis, which could be used to study aphid biology and enable future agricultural technologies.IMPORTANCE Insects have remarkably diverse and integral roles in global ecosystems. Many harbor symbiotic bacteria, but very few of these bacteria have been genetically engineered. Aphids are major agricultural pests and an important model system for the study of symbiosis. This work describes methods for engineering a culturable aphid symbiont, Serratia symbiotica CWBI-2.3T These approaches and genetic tools could be used in the future to implement new paradigms for the biological study and control of aphids.
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Affiliation(s)
- Katherine M Elston
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA 78712, USA
| | - Julie Perreau
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA 78712, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA 78712, USA
| | - Gerald P Maeda
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA 78712, USA
| | - Nancy A Moran
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA 78712, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA 78712, USA
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28
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Long SW, Olsen RJ, Christensen PA, Bernard DW, Davis JJ, Shukla M, Nguyen M, Saavedra MO, Yerramilli P, Pruitt L, Subedi S, Kuo HC, Hendrickson H, Eskandari G, Nguyen HAT, Long JH, Kumaraswami M, Goike J, Boutz D, Gollihar J, McLellan JS, Chou CW, Javanmardi K, Finkelstein IJ, Musser JM. Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area. mBio 2020; 11:e02707-20. [PMID: 33127862 PMCID: PMC7642679 DOI: 10.1128/mbio.02707-20] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [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: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 01/18/2023] Open
Abstract
We sequenced the genomes of 5,085 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains causing two coronavirus disease 2019 (COVID-19) disease waves in metropolitan Houston, TX, an ethnically diverse region with 7 million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston and from viruses recovered in an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. We found little evidence of a significant relationship between virus genotype and altered virulence, stressing the linkage between disease severity, underlying medical conditions, and host genetics. Some regions of the spike protein-the primary target of global vaccine efforts-are replete with amino acid replacements, perhaps indicating the action of selection. We exploited the genomic data to generate defined single amino acid replacements in the receptor binding domain of spike protein that, importantly, produced decreased recognition by the neutralizing monoclonal antibody CR3022. Our report represents the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in a major metropolitan region. The findings will help us to understand the origin, composition, and trajectory of future infection waves and the potential effect of the host immune response and therapeutic maneuvers on SARS-CoV-2 evolution.IMPORTANCE There is concern about second and subsequent waves of COVID-19 caused by the SARS-CoV-2 coronavirus occurring in communities globally that had an initial disease wave. Metropolitan Houston, TX, with a population of 7 million, is experiencing a massive second disease wave that began in late May 2020. To understand SARS-CoV-2 molecular population genomic architecture and evolution and the relationship between virus genotypes and patient features, we sequenced the genomes of 5,085 SARS-CoV-2 strains from these two waves. Our report provides the first molecular characterization of SARS-CoV-2 strains causing two distinct COVID-19 disease waves.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Antibodies, Neutralizing/immunology
- Base Sequence
- Betacoronavirus/genetics
- Betacoronavirus/immunology
- COVID-19
- COVID-19 Testing
- Clinical Laboratory Techniques
- Coronavirus Infections/diagnosis
- Coronavirus Infections/epidemiology
- Coronavirus Infections/immunology
- Coronavirus Infections/virology
- Coronavirus RNA-Dependent RNA Polymerase
- Genome, Viral
- Genotype
- Humans
- Machine Learning
- Models, Molecular
- Molecular Diagnostic Techniques
- Pandemics
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/immunology
- Pneumonia, Viral/virology
- RNA-Dependent RNA Polymerase/chemistry
- RNA-Dependent RNA Polymerase/genetics
- SARS-CoV-2
- Sequence Analysis, Protein
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Texas/epidemiology
- Viral Nonstructural Proteins/chemistry
- Viral Nonstructural Proteins/genetics
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Affiliation(s)
- S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Paul A Christensen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - David W Bernard
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - James J Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, USA
| | - Maulik Shukla
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, USA
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, USA
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Sishir Subedi
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Heather Hendrickson
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Ghazaleh Eskandari
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Hoang A T Nguyen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - J Hunter Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Jule Goike
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Daniel Boutz
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas, USA
| | - Jimmy Gollihar
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
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29
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Hobley L, Summers JK, Till R, Milner DS, Atterbury RJ, Stroud A, Capeness MJ, Gray S, Leidenroth A, Lambert C, Connerton I, Twycross J, Baker M, Tyson J, Kreft JU, Sockett RE. Dual Predation by Bacteriophage and Bdellovibrio bacteriovorus Can Eradicate Escherichia coli Prey in Situations where Single Predation Cannot. J Bacteriol 2020; 202:e00629-19. [PMID: 31907203 PMCID: PMC7043672 DOI: 10.1128/jb.00629-19] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/17/2019] [Indexed: 01/05/2023] Open
Abstract
Bacteria are preyed upon by diverse microbial predators, including bacteriophage and predatory bacteria, such as Bdellovibrio bacteriovorus While bacteriophage are used as antimicrobial therapies in Eastern Europe and are being applied for compassionate use in the United States, predatory bacteria are only just beginning to reveal their potential therapeutic uses. However, predation by either predator type can falter due to different adaptations arising in the prey bacteria. When testing poultry farm wastewater for novel Bdellovibrio isolates on Escherichia coli prey lawns, individual composite plaques were isolated containing both an RTP (rosette-tailed-phage)-like-phage and a B. bacteriovorus strain and showing central prey lysis and halos of extra lysis. Combining the purified phage with a lab strain of B. bacteriovorus HD100 recapitulated haloed plaques and increased killing of the E. coli prey in liquid culture, showing an effective side-by-side action of these predators compared to their actions alone. Using approximate Bayesian computation to select the best fitting from a variety of different mathematical models demonstrated that the experimental data could be explained only by assuming the existence of three prey phenotypes: (i) sensitive to both predators, (ii) genetically resistant to phage only, and (iii) plastic resistant to B. bacteriovorus only. Although each predator reduces prey availability for the other, high phage numbers did not abolish B. bacteriovorus predation, so both predators are competent to coexist and are causing different selective pressures on the bacterial surface while, in tandem, controlling prey bacterial numbers efficiently. This suggests that combinatorial predator therapy could overcome problems of phage resistance.IMPORTANCE With increasing levels of antibiotic resistance, the development of alternative antibacterial therapies is urgently needed. Two potential alternatives are bacteriophage and predatory bacteria. Bacteriophage therapy has been used, but prey/host specificity and the rapid acquisition of bacterial resistance to bacteriophage are practical considerations. Predatory bacteria are of interest due to their broad Gram-negative bacterial prey range and the lack of simple resistance mechanisms. Here, a bacteriophage and a strain of Bdellovibrio bacteriovorus, preyed side by side on a population of E. coli, causing a significantly greater decrease in prey numbers than either alone. Such combinatorial predator therapy may have greater potential than individual predators since prey surface changes selected for by each predator do not protect prey against the other predator.
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Affiliation(s)
- Laura Hobley
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - J Kimberley Summers
- Institute of Microbiology and Infection and Centre for Computational Biology and School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Rob Till
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - David S Milner
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Robert J Atterbury
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Amy Stroud
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Michael J Capeness
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Stephanie Gray
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Andreas Leidenroth
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Carey Lambert
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Ian Connerton
- School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Jamie Twycross
- School of Computer Science, University of Nottingham, Nottingham, United Kingdom
| | - Michelle Baker
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jess Tyson
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jan-Ulrich Kreft
- Institute of Microbiology and Infection and Centre for Computational Biology and School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - R Elizabeth Sockett
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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Naydich AD, Nangle SN, Bues JJ, Trivedi D, Nissar N, Inniss MC, Niederhuber MJ, Way JC, Silver PA, Riglar DT. Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface. mSystems 2019; 4:e00125-19. [PMID: 31186335 PMCID: PMC6561318 DOI: 10.1128/msystems.00125-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 02/21/2019] [Accepted: 05/18/2019] [Indexed: 01/22/2023] Open
Abstract
Engineering synthetic circuits into intestinal bacteria to sense, record, and respond to in vivo signals is a promising new approach for the diagnosis, treatment, and prevention of disease. However, because the design of disease-responsive circuits is limited by a relatively small pool of known biosensors, there is a need for expanding the capacity of engineered bacteria to sense and respond to the host environment. Here, we apply a robust genetic memory circuit in Escherichia coli to identify new bacterial biosensor triggers responding in the healthy and diseased mammalian gut, which may be used to construct diagnostic or therapeutic circuits. We developed a pipeline for rapid systems-level library construction and screening, using next-generation sequencing and computational analysis, which demonstrates remarkably reliable identification of responsive biosensor triggers from pooled libraries. By testing libraries of potential triggers-each consisting of a promoter and ribosome binding site (RBS)-and using RBS variation to augment the range of trigger sensitivity, we identify and validate triggers that selectively activate our synthetic memory circuit during transit through the gut. We further identify biosensor triggers with increased response in the inflamed gut through comparative screening of one of our libraries in healthy mice and those with intestinal inflammation. Our results demonstrate the power of systems-level screening for the identification of novel biosensor triggers in the gut and provide a platform for disease-specific screening that is capable of contributing to both the understanding and clinical management of intestinal illness.IMPORTANCE The gut is a largely obscure and inaccessible environment. The use of live, engineered probiotics to detect and respond to disease signals in vivo represents a new frontier in the management of gut diseases. Engineered probiotics have also shown promise as a novel mechanism for drug delivery. However, the design and construction of effective strains that respond to the in vivo environment is hindered by our limited understanding of bacterial behavior in the gut. Our work expands the pool of environmentally responsive synthetic circuits for the healthy and diseased gut, providing insight into host-microbe interactions and enabling future development of increasingly complex biosensors. This method also provides a framework for rapid prototyping of engineered systems and for application across bacterial strains and disease models, representing a practical step toward the construction of clinically useful synthetic tools.
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Affiliation(s)
- Alexander D Naydich
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Shannon N Nangle
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Johannes J Bues
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Disha Trivedi
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Nabeel Nissar
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Mara C Inniss
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Jeffrey C Way
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - David T Riglar
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
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31
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Alnaji FG, Holmes JR, Rendon G, Vera JC, Fields CJ, Martin BE, Brooke CB. Sequencing Framework for the Sensitive Detection and Precise Mapping of Defective Interfering Particle-Associated Deletions across Influenza A and B Viruses. J Virol 2019; 93:e00354-19. [PMID: 30867305 PMCID: PMC6532088 DOI: 10.1128/jvi.00354-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [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: 03/01/2019] [Accepted: 03/06/2019] [Indexed: 11/20/2022] Open
Abstract
The mechanisms and consequences of defective interfering particle (DIP) formation during influenza virus infection remain poorly understood. The development of next-generation sequencing (NGS) technologies has made it possible to identify large numbers of DIP-associated sequences, providing a powerful tool to better understand their biological relevance. However, NGS approaches pose numerous technical challenges, including the precise identification and mapping of deletion junctions in the presence of frequent mutation and base-calling errors, and the potential for numerous experimental and computational artifacts. Here, we detail an Illumina-based sequencing framework and bioinformatics pipeline capable of generating highly accurate and reproducible profiles of DIP-associated junction sequences. We use a combination of simulated and experimental control data sets to optimize pipeline performance and demonstrate the absence of significant artifacts. Finally, we use this optimized pipeline to reveal how the patterns of DIP-associated junction formation differ between different strains and subtypes of influenza A and B viruses and to demonstrate how these data can provide insight into mechanisms of DIP formation. Overall, this work provides a detailed roadmap for high-resolution profiling and analysis of DIP-associated sequences within influenza virus populations.IMPORTANCE Influenza virus defective interfering particles (DIPs) that harbor internal deletions within their genomes occur naturally during infection in humans and during cell culture. They have been hypothesized to influence the pathogenicity of the virus; however, their specific function remains elusive. The accurate detection of DIP-associated deletion junctions is crucial for understanding DIP biology but is complicated by an array of technical issues that can bias or confound results. Here, we demonstrate a combined experimental and computational framework for detecting DIP-associated deletion junctions using next-generation sequencing (NGS). We detail how to validate pipeline performance and provide the bioinformatics pipeline for groups interested in using it. Using this optimized pipeline, we detect hundreds of distinct deletion junctions generated during infection with a diverse panel of influenza viruses and use these data to test a long-standing hypothesis concerning the molecular details of DIP formation.
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Affiliation(s)
- Fadi G Alnaji
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jessica R Holmes
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Gloria Rendon
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - J Cristobal Vera
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher J Fields
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Brigitte E Martin
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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32
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Thommes M, Wang T, Zhao Q, Paschalidis IC, Segrè D. Designing Metabolic Division of Labor in Microbial Communities. mSystems 2019; 4:e00263-18. [PMID: 30984871 PMCID: PMC6456671 DOI: 10.1128/msystems.00263-18] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/15/2019] [Indexed: 12/19/2022] Open
Abstract
Microbes face a trade-off between being metabolically independent and relying on neighboring organisms for the supply of some essential metabolites. This balance of conflicting strategies affects microbial community structure and dynamics, with important implications for microbiome research and synthetic ecology. A "gedanken" (thought) experiment to investigate this trade-off would involve monitoring the rise of mutual dependence as the number of metabolic reactions allowed in an organism is increasingly constrained. The expectation is that below a certain number of reactions, no individual organism would be able to grow in isolation and cross-feeding partnerships and division of labor would emerge. We implemented this idealized experiment using in silico genome-scale models. In particular, we used mixed-integer linear programming to identify trade-off solutions in communities of Escherichia coli strains. The strategies that we found revealed a large space of opportunities in nuanced and nonintuitive metabolic division of labor, including, for example, splitting the tricarboxylic acid (TCA) cycle into two separate halves. The systematic computation of possible solutions in division of labor for 1-, 2-, and 3-strain consortia resulted in a rich and complex landscape. This landscape displayed a nonlinear boundary, indicating that the loss of an intracellular reaction was not necessarily compensated for by a single imported metabolite. Different regions in this landscape were associated with specific solutions and patterns of exchanged metabolites. Our approach also predicts the existence of regions in this landscape where independent bacteria are viable but are outcompeted by cross-feeding pairs, providing a possible incentive for the rise of division of labor. IMPORTANCE Understanding how microbes assemble into communities is a fundamental open issue in biology, relevant to human health, metabolic engineering, and environmental sustainability. A possible mechanism for interactions of microbes is through cross-feeding, i.e., the exchange of small molecules. These metabolic exchanges may allow different microbes to specialize in distinct tasks and evolve division of labor. To systematically explore the space of possible strategies for division of labor, we applied advanced optimization algorithms to computational models of cellular metabolism. Specifically, we searched for communities able to survive under constraints (such as a limited number of reactions) that would not be sustainable by individual species. We found that predicted consortia partition metabolic pathways in ways that would be difficult to identify manually, possibly providing a competitive advantage over individual organisms. In addition to helping understand diversity in natural microbial communities, our approach could assist in the design of synthetic consortia.
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Affiliation(s)
- Meghan Thommes
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Taiyao Wang
- Division of Systems Engineering, Boston University, Boston, Massachusetts, USA
| | - Qi Zhao
- Division of Systems Engineering, Boston University, Boston, Massachusetts, USA
| | - Ioannis C. Paschalidis
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, USA
- Division of Systems Engineering, Boston University, Boston, Massachusetts, USA
| | - Daniel Segrè
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biology, Boston University, Boston, Massachusetts, USA
- Department of Physics, Boston University, Boston, Massachusetts, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
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Chen HI, Jagadeesh KA, Birgmeier J, Wenger AM, Guturu H, Schelley S, Bernstein JA, Bejerano G. An MTF1 binding site disrupted by a homozygous variant in the promoter of ATP7B likely causes Wilson Disease. Eur J Hum Genet 2018; 26:1810-1818. [PMID: 30087448 PMCID: PMC6244090 DOI: 10.1038/s41431-018-0221-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/09/2018] [Accepted: 06/26/2018] [Indexed: 12/16/2022] Open
Abstract
Approximately 2% of the human genome accounts for protein-coding genes, yet most known Mendelian disease-causing variants lie in exons or splice sites. Individuals who symptomatically present with monogenic disorders but do not possess function-altering variants in the protein-coding regions of causative genes may harbor variants in the surrounding gene regulatory domains. We present such a case: a male of Afghani descent was clinically diagnosed with Wilson Disease-a disorder of systemic copper buildup-but was found to have no function-altering coding variants in ATP7B (ENST00000242839.4), the typically causative gene. Our analysis revealed the homozygous variant chr13:g.52,586,149T>C (NC_000013.10, hg19) 676 bp into the ATP7B promoter, which disrupts a metal regulatory transcription factor 1 (MTF1) binding site and diminishes expression of ATP7B in response to copper intake, likely resulting in Wilson Disease. Our approach to identify the causative variant can be generalized to systematically discover function-altering non-coding variants underlying disease and motivates evaluation of gene regulatory variants.
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Affiliation(s)
- Heidi I Chen
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Karthik A Jagadeesh
- Department of Computer Science, Stanford University School of Engineering, Stanford, CA, USA
| | - Johannes Birgmeier
- Department of Computer Science, Stanford University School of Engineering, Stanford, CA, USA
| | - Aaron M Wenger
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Harendra Guturu
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Susan Schelley
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Computer Science, Stanford University School of Engineering, Stanford, CA, USA.
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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34
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Fourati S, Talla A, Mahmoudian M, Burkhart JG, Klén R, Henao R, Yu T, Aydın Z, Yeung KY, Ahsen ME, Almugbel R, Jahandideh S, Liang X, Nordling TEM, Shiga M, Stanescu A, Vogel R, Pandey G, Chiu C, McClain MT, Woods CW, Ginsburg GS, Elo LL, Tsalik EL, Mangravite LM, Sieberts SK. A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection. Nat Commun 2018; 9:4418. [PMID: 30356117 PMCID: PMC6200745 DOI: 10.1038/s41467-018-06735-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 04/30/2018] [Accepted: 09/12/2018] [Indexed: 01/17/2023] Open
Abstract
The response to respiratory viruses varies substantially between individuals, and there are currently no known molecular predictors from the early stages of infection. Here we conduct a community-based analysis to determine whether pre- or early post-exposure molecular factors could predict physiologic responses to viral exposure. Using peripheral blood gene expression profiles collected from healthy subjects prior to exposure to one of four respiratory viruses (H1N1, H3N2, Rhinovirus, and RSV), as well as up to 24 h following exposure, we find that it is possible to construct models predictive of symptomatic response using profiles even prior to viral exposure. Analysis of predictive gene features reveal little overlap among models; however, in aggregate, these genes are enriched for common pathways. Heme metabolism, the most significantly enriched pathway, is associated with a higher risk of developing symptoms following viral exposure. This study demonstrates that pre-exposure molecular predictors can be identified and improves our understanding of the mechanisms of response to respiratory viruses.
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Affiliation(s)
- Slim Fourati
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Aarthi Talla
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Mehrad Mahmoudian
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
- Department of Future Technologies, University of Turku, FI-20014 Turku, Finland
| | - Joshua G Burkhart
- Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health & Science University, Portland, OR, 97239, USA
- Laboratory of Evolutionary Genetics, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Riku Klén
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | - Ricardo Henao
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
| | - Thomas Yu
- Sage Bionetworks, Seattle, WA, 98121, USA
| | - Zafer Aydın
- Department of Computer Engineering, Abdullah Gul University, Kayseri, 38080, Turkey
| | - Ka Yee Yeung
- School of Engineering and Technology, University of Washington Tacoma, Tacoma, WA, 98402, USA
| | - Mehmet Eren Ahsen
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Reem Almugbel
- School of Engineering and Technology, University of Washington Tacoma, Tacoma, WA, 98402, USA
| | | | - Xiao Liang
- School of Engineering and Technology, University of Washington Tacoma, Tacoma, WA, 98402, USA
| | - Torbjörn E M Nordling
- Department of Mechanical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Motoki Shiga
- Department of Electrical, Electronic and Computer Engineering, Faculty of Engineering, Gifu University, Gifu, 501-1193, Japan
| | - Ana Stanescu
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Computer Science, University of West Georgia, Carrolton, GA, 30116, USA
| | - Robert Vogel
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- IBM T.J. Watson Research Center, Yorktown Heights, NY, 10598, USA
| | - Gaurav Pandey
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Christopher Chiu
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Micah T McClain
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Medical Service, Durham VA Health Care System, Durham, NC, 27705, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Christopher W Woods
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Medical Service, Durham VA Health Care System, Durham, NC, 27705, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Geoffrey S Ginsburg
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Laura L Elo
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | - Ephraim L Tsalik
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Emergency Medicine Service, Durham VA Health Care System, Durham, NC, 27705, USA
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35
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Abstract
Health in the United States is markedly heterogeneous, with large disparities in disease incidence, treatment choices and health spending. Drug prescription is one major component of health care-reflecting the accuracy of diagnosis, the adherence to evidence-based guidelines, susceptibility to drug marketing and regulatory factors. Using medical claims data covering nearly half of the USA population, we have developed and validated a framework to compare prescription rates of 600 popular drugs in 2334 counties. Our approach uncovers geographically separated sub-Americas, where patients receive treatment for different diseases, and where physicians choose different drugs for the same disease. The geographical variation suggests influences of racial composition, state-level health care laws and wealth. Some regions consistently prefer more expensive drugs, even when they have not been proven more efficacious than cheaper alternatives. Our study underlines the benefit of aggregating massive information on medical practice into a summarized and actionable form.
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Affiliation(s)
- Rachel D Melamed
- Institute of Genomics, Genetics, and Systems Biology, Biological Sciences Division, Chicago, 60637, IL, USA
- Section of Computational Biomedicine and Data-Intensive Science, Biological Sciences Division, Chicago, 60637, IL, USA
| | - Andrey Rzhetsky
- Institute of Genomics, Genetics, and Systems Biology, Biological Sciences Division, Chicago, 60637, IL, USA.
- Section of Computational Biomedicine and Data-Intensive Science, Biological Sciences Division, Chicago, 60637, IL, USA.
- Department of Human Genetics, and Computation Institute University of Chicago, 900 E 57 St, KBCD 10160A, Chicago, IL, 60637, USA.
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36
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Covington BC, Spraggins JM, Ynigez-Gutierrez AE, Hylton ZB, Bachmann BO. Response of Secondary Metabolism of Hypogean Actinobacterial Genera to Chemical and Biological Stimuli. Appl Environ Microbiol 2018; 84:e01125-18. [PMID: 30030223 PMCID: PMC6146984 DOI: 10.1128/aem.01125-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 05/11/2018] [Accepted: 07/05/2018] [Indexed: 12/24/2022] Open
Abstract
Microorganisms within microbial communities respond to environmental challenges by producing biologically active secondary metabolites, yet the majority of these small molecules remain unidentified. We have previously demonstrated that secondary metabolite biosynthesis in actinomycetes can be activated by model environmental chemical and biological stimuli, and metabolites can be identified by comparative metabolomics analyses under different stimulus conditions. Here, we surveyed the secondary metabolite productivity of a group of 20 phylogenetically diverse actinobacteria isolated from hypogean (cave) environments by applying a battery of stimuli consisting of exposure to antibiotics, metals, and mixed microbial culture. Comparative metabolomics was used to reveal secondary metabolite responses from stimuli. These analyses revealed substantial changes in global metabolomic dynamics, with over 30% of metabolomic features increasing more than 10-fold under at least one stimulus condition. Selected features were isolated and identified via nuclear magnetic resonance (NMR), revealing several known secondary metabolite families, including the tetarimycins, aloesaponarins, hypogeamicins, actinomycins, and propeptins. One prioritized metabolite was identified to be a previously unreported aminopolyol polyketide, funisamine, produced by a cave isolate of Streptosporangium when exposed to mixed culture. The production of funisamine was most significantly increased in mixed culture with Bacillus species. The biosynthetic gene cluster responsible for the production of funisamine was identified via genomic sequencing of the producing strain, Streptosporangium sp. strain KDCAGE35, which facilitated a deduction of its biosynthesis. Together, these data demonstrate that comparative metabolomics can reveal the stimulus-induced production of natural products from diverse microbial phylogenies.IMPORTANCE Microbial secondary metabolites are an important source of biologically active and therapeutically relevant small molecules. However, much of this active molecular diversity is challenging to access due to low production levels or difficulty in discerning secondary metabolites within complex microbial extracts prior to isolation. Here, we demonstrate that ecological stimuli increase secondary metabolite production in phylogenetically diverse actinobacteria isolated from understudied hypogean environments. Additionally, we show that comparative metabolomics linking stimuli to metabolite response data can effectively reveal secondary metabolites within complex biological extracts. This approach highlighted secondary metabolites in almost all observed natural product classes, including low-abundance analogs of biologically relevant metabolites, as well as a new linear aminopolyol polyketide, funisamine. This study demonstrates the generality of activating stimuli to potentiate secondary metabolite production across diverse actinobacterial genera.
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Affiliation(s)
- Brett C Covington
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Zachary B Hylton
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
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37
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Abstract
Interfaces with the peripheral nerve provide the ability to extract motor activation and restore sensation to amputee patients. The ability to chronically extract motor activations from the peripheral nervous system remains an unsolved problem. In this study, chronic recordings with the Flat Interface Nerve Electrode (FINE) are employed to recover the activation levels of innervated muscles. The FINEs were implanted on the sciatic nerves of canines, and neural recordings were obtained as the animal walked on a treadmill. During these trials, electromyograms (EMG) from the surrounding hamstring muscles were simultaneously recorded and the neural recordings are shown to be free of interference or crosstalk from these muscles. Using a novel Bayesian algorithm, the signals from individual fascicles were recovered and then compared to the corresponding target EMG of the lower limb. High correlation coefficients (0.84 ± 0.07 and 0.61 ± 0.12) between the extracted tibial fascicle/medial gastrocnemius and peroneal fascicle/tibialis anterior muscle were obtained. Analysis calculating the information transfer rate (ITR) from the muscle to the motor predictions yielded approximately 5 and 1 bit per second (bps) for the two sources. This method can predict motor signals from neural recordings and could be used to drive a prosthesis by interfacing with residual nerves.
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Affiliation(s)
- Thomas E Eggers
- Neural Engineering Center, Biomedical Engineering, Case Western Reserve University, Cleveland, USA
| | - Yazan M Dweiri
- Department of Biomedical Engineering, Jordan University of Science and Technology, Irbid, Jordan
| | - Grant A McCallum
- Neural Engineering Center, Biomedical Engineering, Case Western Reserve University, Cleveland, USA
| | - Dominique M Durand
- Neural Engineering Center, Biomedical Engineering, Case Western Reserve University, Cleveland, USA.
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38
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Abstract
Organisms result from adaptive processes interacting across different time scales. One such interaction is that between development and evolution. Models have shown that development sweeps over several traits in a single agent, sometimes exposing promising static traits. Subsequent evolution can then canalize these rare traits. Thus, development can, under the right conditions, increase evolvability. Here, we report on a previously unknown phenomenon when embodied agents are allowed to develop and evolve: Evolution discovers body plans robust to control changes, these body plans become genetically assimilated, yet controllers for these agents are not assimilated. This allows evolution to continue climbing fitness gradients by tinkering with the developmental programs for controllers within these permissive body plans. This exposes a previously unknown detail about the Baldwin effect: instead of all useful traits becoming genetically assimilated, only traits that render the agent robust to changes in other traits become assimilated. We refer to this as differential canalization. This finding also has implications for the evolutionary design of artificial and embodied agents such as robots: robots robust to internal changes in their controllers may also be robust to external changes in their environment, such as transferal from simulation to reality or deployment in novel environments.
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Affiliation(s)
- Sam Kriegman
- University of Vermont, Department of Computer Science, Burlington, VT, USA.
| | - Nick Cheney
- University of Vermont, Department of Computer Science, Burlington, VT, USA
| | - Josh Bongard
- University of Vermont, Department of Computer Science, Burlington, VT, USA
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39
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Zhang L, Khattar N, Kemenes I, Kemenes G, Zrinyi Z, Pirger Z, Vertes A. Subcellular Peptide Localization in Single Identified Neurons by Capillary Microsampling Mass Spectrometry. Sci Rep 2018; 8:12227. [PMID: 30111831 PMCID: PMC6093924 DOI: 10.1038/s41598-018-29704-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/17/2018] [Indexed: 12/22/2022] Open
Abstract
Single cell mass spectrometry (MS) is uniquely positioned for the sequencing and identification of peptides in rare cells. Small peptides can take on different roles in subcellular compartments. Whereas some peptides serve as neurotransmitters in the cytoplasm, they can also function as transcription factors in the nucleus. Thus, there is a need to analyze the subcellular peptide compositions in identified single cells. Here, we apply capillary microsampling MS with ion mobility separation for the sequencing of peptides in single neurons of the mollusk Lymnaea stagnalis, and the analysis of peptide distributions between the cytoplasm and nucleus of identified single neurons that are known to express cardioactive Phe-Met-Arg-Phe amide-like (FMRFamide-like) neuropeptides. Nuclei and cytoplasm of Type 1 and Type 2 F group (Fgp) neurons were analyzed for neuropeptides cleaved from the protein precursors encoded by alternative splicing products of the FMRFamide gene. Relative abundances of nine neuropeptides were determined in the cytoplasm. The nuclei contained six of these peptides at different abundances. Enabled by its relative enrichment in Fgp neurons, a new 28-residue neuropeptide was sequenced by tandem MS.
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Affiliation(s)
- Linwen Zhang
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Nikkita Khattar
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Ildiko Kemenes
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Gyorgy Kemenes
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Zita Zrinyi
- Department of Experimental Zoology, Balaton Limnological Institute, MTA Center for Ecological Research, 8237, Tihany, Hungary
| | - Zsolt Pirger
- Department of Experimental Zoology, Balaton Limnological Institute, MTA Center for Ecological Research, 8237, Tihany, Hungary
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA.
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40
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Magden ES, Li N, Raval M, Poulton CV, Ruocco A, Singh N, Vermeulen D, Ippen EP, Kolodziejski LA, Watts MR. Transmissive silicon photonic dichroic filters with spectrally selective waveguides. Nat Commun 2018; 9:3009. [PMID: 30068975 PMCID: PMC6070617 DOI: 10.1038/s41467-018-05287-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [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: 11/20/2017] [Accepted: 06/16/2018] [Indexed: 11/08/2022] Open
Abstract
Many optical systems require broadband filters with sharp roll-offs for efficiently splitting or combining light across wide spectra. While free space dichroic filters can provide broadband selectivity, on-chip integration of these high-performance filters is crucial for the scalability of photonic applications in multi-octave interferometry, spectroscopy, and wideband wavelength-division multiplexing. Here we present the theory, design, and experimental characterization of integrated, transmissive, 1 × 2 port dichroic filters using spectrally selective waveguides. Mode evolution through adiabatic transitions in the demonstrated filters allows for single cutoff and flat-top responses with low insertion losses and octave-wide simulated bandwidths. Filters with cutoffs around 1550 and 2100 nm are fabricated on a silicon-on-insulator platform with standard complementary metal-oxide-semiconductor processes. A filter roll-off of 2.82 dB nm-1 is achieved while maintaining ultra-broadband operation. This new class of nanophotonic dichroic filters can lead to new paradigms in on-chip communications, sensing, imaging, optical synthesis, and display applications.
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Affiliation(s)
- Emir Salih Magden
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- Department of Electrical and Electronics Engineering, Koç University, Rumelifeneri Yolu, Sariyer, 34450, Istanbul, Turkey.
| | - Nanxi Li
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- John A. Paulson School of Engineering and Applied Science, Harvard University, 29 Oxford Street, Cambridge, MA, 02138, USA
| | - Manan Raval
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Christopher V Poulton
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Analog Photonics, One Marina Park Drive, Boston, MA, 02210, USA
| | - Alfonso Ruocco
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Cambridge Graphene Centre, University of Cambridge, 9 JJ Thomson Avenue, Cambridge, CB3 0FA, UK
| | - Neetesh Singh
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Diedrik Vermeulen
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Analog Photonics, One Marina Park Drive, Boston, MA, 02210, USA
| | - Erich P Ippen
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Leslie A Kolodziejski
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Michael R Watts
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
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41
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Kobayashi T, Sapienza A, Ferrara E. Extracting the multi-timescale activity patterns of online financial markets. Sci Rep 2018; 8:11184. [PMID: 30046150 PMCID: PMC6060124 DOI: 10.1038/s41598-018-29537-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 02/22/2018] [Accepted: 07/13/2018] [Indexed: 11/08/2022] Open
Abstract
Online financial markets can be represented as complex systems where trading dynamics can be captured and characterized at different resolutions and time scales. In this work, we develop a methodology based on non-negative tensor factorization (NTF) aimed at extracting and revealing the multi-timescale trading dynamics governing online financial systems. We demonstrate the advantage of our strategy first using synthetic data, and then on real-world data capturing all interbank transactions (over a million) occurred in an Italian online financial market (e-MID) between 2001 and 2015. Our results demonstrate how NTF can uncover hidden activity patterns that characterize groups of banks exhibiting different trading strategies (normal vs. early vs. flash trading, etc.). We further illustrate how our methodology can reveal "crisis modalities" in trading triggered by endogenous and exogenous system shocks: as an example, we reveal and characterize trading anomalies in the midst of the 2008 financial crisis.
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Affiliation(s)
- Teruyoshi Kobayashi
- Graduate School of Economics, Center for Computational Social Science, Kobe University, Kobe, Japan
| | - Anna Sapienza
- Information Sciences Institute, University of Southern California, Los Angeles, CA, USA
| | - Emilio Ferrara
- Information Sciences Institute, University of Southern California, Los Angeles, CA, USA.
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42
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Mitchell BA, Petzold LR. Control of neural systems at multiple scales using model-free, deep reinforcement learning. Sci Rep 2018; 8:10721. [PMID: 30013195 PMCID: PMC6048054 DOI: 10.1038/s41598-018-29134-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 01/09/2018] [Accepted: 07/03/2018] [Indexed: 12/27/2022] Open
Abstract
Recent improvements in hardware and data collection have lowered the barrier to practical neural control. Most of the current contributions to the field have focus on model-based control, however, models of neural systems are quite complex and difficult to design. To circumvent these issues, we adapt a model-free method from the reinforcement learning literature, Deep Deterministic Policy Gradients (DDPG). Model-free reinforcement learning presents an attractive framework because of the flexibility it offers, allowing the user to avoid modeling system dynamics. We make use of this feature by applying DDPG to models of low-level and high-level neural dynamics. We show that while model-free, DDPG is able to solve more difficult problems than can be solved by current methods. These problems include the induction of global synchrony by entrainment of weakly coupled oscillators and the control of trajectories through a latent phase space of an underactuated network of neurons. While this work has been performed on simulated systems, it suggests that advances in modern reinforcement learning may enable the solution of fundamental problems in neural control and movement towards more complex objectives in real systems.
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Affiliation(s)
- B A Mitchell
- Department of Computer Science, University of California, Santa Barbara, USA.
| | - L R Petzold
- Department of Computer Science, University of California, Santa Barbara, USA
- Department of Mechanical Engineering, University of California, Santa Barbara, USA
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43
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Bayat FM, Prezioso M, Chakrabarti B, Nili H, Kataeva I, Strukov D. Implementation of multilayer perceptron network with highly uniform passive memristive crossbar circuits. Nat Commun 2018; 9:2331. [PMID: 29899421 PMCID: PMC5998062 DOI: 10.1038/s41467-018-04482-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [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: 11/28/2017] [Accepted: 05/02/2018] [Indexed: 11/09/2022] Open
Abstract
The progress in the field of neural computation hinges on the use of hardware more efficient than the conventional microprocessors. Recent works have shown that mixed-signal integrated memristive circuits, especially their passive (0T1R) variety, may increase the neuromorphic network performance dramatically, leaving far behind their digital counterparts. The major obstacle, however, is immature memristor technology so that only limited functionality has been reported. Here we demonstrate operation of one-hidden layer perceptron classifier entirely in the mixed-signal integrated hardware, comprised of two passive 20 × 20 metal-oxide memristive crossbar arrays, board-integrated with discrete conventional components. The demonstrated network, whose hardware complexity is almost 10× higher as compared to previously reported functional classifier circuits based on passive memristive crossbars, achieves classification fidelity within 3% of that obtained in simulations, when using ex-situ training. The successful demonstration was facilitated by improvements in fabrication technology of memristors, specifically by lowering variations in their I-V characteristics.
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Affiliation(s)
- F Merrikh Bayat
- Electrical and Computer Engineering Department, University of California, Santa Barbara, CA, 93117, USA
| | - M Prezioso
- Electrical and Computer Engineering Department, University of California, Santa Barbara, CA, 93117, USA
| | - B Chakrabarti
- Electrical and Computer Engineering Department, University of California, Santa Barbara, CA, 93117, USA
| | - H Nili
- Electrical and Computer Engineering Department, University of California, Santa Barbara, CA, 93117, USA
| | - I Kataeva
- DENSO CORP, 500-1 Minamiyama, Komenoki-cho, Nisshin, 470-0111, Japan.
| | - D Strukov
- Electrical and Computer Engineering Department, University of California, Santa Barbara, CA, 93117, USA.
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44
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Baby V, Lachance JC, Gagnon J, Lucier JF, Matteau D, Knight T, Rodrigue S. Inferring the Minimal Genome of Mesoplasma florum by Comparative Genomics and Transposon Mutagenesis. mSystems 2018; 3:e00198-17. [PMID: 29657968 PMCID: PMC5893858 DOI: 10.1128/msystems.00198-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 12/05/2017] [Accepted: 03/09/2018] [Indexed: 12/14/2022] Open
Abstract
The creation and comparison of minimal genomes will help better define the most fundamental mechanisms supporting life. Mesoplasma florum is a near-minimal, fast-growing, nonpathogenic bacterium potentially amenable to genome reduction efforts. In a comparative genomic study of 13 M. florum strains, including 11 newly sequenced genomes, we have identified the core genome and open pangenome of this species. Our results show that all of the strains have approximately 80% of their gene content in common. Of the remaining 20%, 17% of the genes were found in multiple strains and 3% were unique to any given strain. On the basis of random transposon mutagenesis, we also estimated that ~290 out of 720 genes are essential for M. florum L1 in rich medium. We next evaluated different genome reduction scenarios for M. florum L1 by using gene conservation and essentiality data, as well as comparisons with the first working approximation of a minimal organism, Mycoplasma mycoides JCVI-syn3.0. Our results suggest that 409 of the 473 M. mycoides JCVI-syn3.0 genes have orthologs in M. florum L1. Conversely, 57 putatively essential M. florum L1 genes have no homolog in M. mycoides JCVI-syn3.0. This suggests differences in minimal genome compositions, even for these evolutionarily closely related bacteria. IMPORTANCE The last years have witnessed the development of whole-genome cloning and transplantation methods and the complete synthesis of entire chromosomes. Recently, the first minimal cell, Mycoplasma mycoides JCVI-syn3.0, was created. Despite these milestone achievements, several questions remain to be answered. For example, is the composition of minimal genomes virtually identical in phylogenetically related species? On the basis of comparative genomics and transposon mutagenesis, we investigated this question by using an alternative model, Mesoplasma florum, that is also amenable to genome reduction efforts. Our results suggest that the creation of additional minimal genomes could help reveal different gene compositions and strategies that can support life, even within closely related species.
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Affiliation(s)
- Vincent Baby
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Jules Gagnon
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Dominick Matteau
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Tom Knight
- Ginkgo Bioworks, Boston, Massachusetts, USA
| | - Sébastien Rodrigue
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
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45
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Zhu Y, Li Z, Hao Z, DiMarco C, Maturavongsadit P, Hao Y, Lu M, Stein A, Wang Q, Hone J, Yu N, Lin Q. Optical conductivity-based ultrasensitive mid-infrared biosensing on a hybrid metasurface. Light Sci Appl 2018; 7:67. [PMID: 30275947 PMCID: PMC6156330 DOI: 10.1038/s41377-018-0066-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 08/04/2018] [Accepted: 08/17/2018] [Indexed: 05/05/2023]
Abstract
Optical devices are highly attractive for biosensing as they can not only enable quantitative measurements of analytes but also provide information on molecular structures. Unfortunately, typical refractive index-based optical sensors do not have sufficient sensitivity to probe the binding of low-molecular-weight analytes. Non-optical devices such as field-effect transistors can be more sensitive but do not offer some of the significant features of optical devices, particularly molecular fingerprinting. We present optical conductivity-based mid-infrared (mid-IR) biosensors that allow for sensitive and quantitative measurements of low-molecular-weight analytes as well as the enhancement of spectral fingerprints. The sensors employ a hybrid metasurface consisting of monolayer graphene and metallic nano-antennas and combine individual advantages of plasmonic, electronic and spectroscopic approaches. First, the hybrid metasurface sensors can optically detect target molecule-induced carrier doping to graphene, allowing highly sensitive detection of low-molecular-weight analytes despite their small sizes. Second, the resonance shifts caused by changes in graphene optical conductivity is a well-defined function of graphene carrier density, thereby allowing for quantification of the binding of molecules. Third, the sensor performance is highly stable and consistent thanks to its insensitivity to graphene carrier mobility degradation. Finally, the sensors can also act as substrates for surface-enhanced infrared spectroscopy. We demonstrated the measurement of monolayers of sub-nanometer-sized molecules or particles and affinity binding-based quantitative detection of glucose down to 200 pM (36 pg/mL). We also demonstrated enhanced fingerprinting of minute quantities of glucose and polymer molecules.
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Affiliation(s)
- Yibo Zhu
- Department of Mechanical Engineering, Columbia University, New York, NY 10027 USA
| | - Zhaoyi Li
- Department of Applied Physics and Applied Math, Columbia University, New York, NY 10027 USA
| | - Zhuang Hao
- Department of Mechanical Engineering, Columbia University, New York, NY 10027 USA
| | - Christopher DiMarco
- Department of Mechanical Engineering, Columbia University, New York, NY 10027 USA
| | - Panita Maturavongsadit
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208 USA
| | - Yufeng Hao
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093 China
| | - Ming Lu
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973 USA
| | - Aaron Stein
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973 USA
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208 USA
| | - James Hone
- Department of Mechanical Engineering, Columbia University, New York, NY 10027 USA
| | - Nanfang Yu
- Department of Applied Physics and Applied Math, Columbia University, New York, NY 10027 USA
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY 10027 USA
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46
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Shrestha S, Overvig AC, Lu M, Stein A, Yu N. Broadband achromatic dielectric metalenses. Light Sci Appl 2018; 7:85. [PMID: 30416721 PMCID: PMC6220161 DOI: 10.1038/s41377-018-0078-x] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 05/03/2023]
Abstract
Metasurfaces offer a unique platform to precisely control optical wavefronts and enable the realization of flat lenses, or metalenses, which have the potential to substantially reduce the size and complexity of imaging systems and to realize new imaging modalities. However, it is a major challenge to create achromatic metalenses that produce a single focal length over a broad wavelength range because of the difficulty in simultaneously engineering phase profiles at distinct wavelengths on a single metasurface. For practical applications, there is a further challenge to create broadband achromatic metalenses that work in the transmission mode for incident light waves with any arbitrary polarization state. We developed a design methodology and created libraries of meta-units-building blocks of metasurfaces-with complex cross-sectional geometries to provide diverse phase dispersions (phase as a function of wavelength), which is crucial for creating broadband achromatic metalenses. We elucidated the fundamental limitations of achromatic metalens performance by deriving mathematical equations that govern the tradeoffs between phase dispersion and achievable lens parameters, including the lens diameter, numerical aperture (NA), and bandwidth of achromatic operation. We experimentally demonstrated several dielectric achromatic metalenses reaching the fundamental limitations. These metalenses work in the transmission mode with polarization-independent focusing efficiencies up to 50% and continuously provide a near-constant focal length over λ = 1200-1650 nm. These unprecedented properties represent a major advance compared to the state of the art and a major step toward practical implementations of metalenses.
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Affiliation(s)
- Sajan Shrestha
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027 USA
| | - Adam C. Overvig
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027 USA
| | - Ming Lu
- Brookhaven National Laboratory, Center for Functional Nanomaterials, Upton, NY 11973 USA
| | - Aaron Stein
- Brookhaven National Laboratory, Center for Functional Nanomaterials, Upton, NY 11973 USA
| | - Nanfang Yu
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027 USA
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