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Iracane E, Arias-Sardá C, Maufrais C, Ene IV, d’Enfert C, Buscaino A. Identification of an active RNAi pathway in Candida albicans. Proc Natl Acad Sci U S A 2024; 121:e2315926121. [PMID: 38625945 PMCID: PMC11047096 DOI: 10.1073/pnas.2315926121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/08/2024] [Indexed: 04/18/2024] Open
Abstract
RNA interference (RNAi) is a fundamental regulatory pathway with a wide range of functions, including regulation of gene expression and maintenance of genome stability. Although RNAi is widespread in the fungal kingdom, well-known species, such as the model yeast Saccharomyces cerevisiae, have lost the RNAi pathway. Until now evidence has been lacking for a fully functional RNAi pathway in Candida albicans, a human fungal pathogen considered critically important by the World Health Organization. Here, we demonstrated that the widely used C. albicans reference strain (SC5314) contains an inactivating missense mutation in the gene encoding for the central RNAi component Argonaute. In contrast, most other C. albicans isolates contain a canonical Argonaute protein predicted to be functional and RNAi-active. Indeed, using high-throughput small and long RNA sequencing combined with seamless CRISPR/Cas9-based gene editing, we demonstrate that an active C. albicans RNAi machinery represses expression of subtelomeric gene families. Thus, an intact and functional RNAi pathway exists in C. albicans, highlighting the importance of using multiple reference strains when studying this dangerous pathogen.
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Affiliation(s)
- Elise Iracane
- Kent Fungal Group, School of Biosciences, Division of Natural Sciences, University of Kent, CanterburyCT2 7NZ, United Kingdom
| | - Cristina Arias-Sardá
- Kent Fungal Group, School of Biosciences, Division of Natural Sciences, University of Kent, CanterburyCT2 7NZ, United Kingdom
| | - Corinne Maufrais
- Institut Pasteur, Université Paris Cité, Bioinformatic Hub, ParisF-75015, France
| | - Iuliana V. Ene
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Group, ParisF-75015, France
| | - Christophe d’Enfert
- Institut Pasteur, Université Paris Cité, Institut national de recherche pour l’agriculture, l’alimentation et l’environnement USC2019, Fungal Biology and Pathogenicity Unit, ParisF-75015, France
| | - Alessia Buscaino
- Kent Fungal Group, School of Biosciences, Division of Natural Sciences, University of Kent, CanterburyCT2 7NZ, United Kingdom
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Lim SJ, Muhd Noor ND, Sabri S, Mohamad Ali MS, Salleh AB, Oslan SN. Bibliometric analysis and thematic review of Candida pathogenesis: Fundamental omics to applications as potential antifungal drugs and vaccines. Med Mycol 2024; 62:myad126. [PMID: 38061839 DOI: 10.1093/mmy/myad126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/21/2023] [Accepted: 12/06/2023] [Indexed: 01/11/2024] Open
Abstract
Invasive candidiasis caused by the pathogenic Candida yeast species has resulted in elevating global mortality. The pathogenicity of Candida spp. is not only originated from its primary invasive yeast-to-hyphal transition; virulence factors (transcription factors, adhesins, invasins, and enzymes), biofilm, antifungal drug resistance, stress tolerance, and metabolic adaptation have also contributed to a greater clinical burden. However, the current research theme in fungal pathogenicity could hardly be delineated with the increasing research output. Therefore, our study analysed the research trends in Candida pathogenesis over the past 37 years via a bibliometric approach against the Scopus and Web of Science databases. Based on the 3993 unique documents retrieved, significant international collaborations among researchers were observed, especially between Germany (Bernhard Hube) and the UK (Julian Naglik), whose focuses are on Candida proteinases, adhesins, and candidalysin. The prominent researchers (Neils Gow, Alistair Brown, and Frank Odds) at the University of Exeter and the University of Aberdeen (second top performing affiliation) UK contribute significantly to the mechanisms of Candida adaptation, tolerance, and stress response. However, the science mapping of co-citation analysis performed herein could not identify a hub representative of subsequent work since the clusters were semi-redundant. The co-word analysis that was otherwise adopted, revealed three research clusters; the cluster-based thematic analyses indicated the severeness of Candida biofilm and antifungal resistance as well as the elevating trend on molecular mechanism elucidation for drug screening and repurposing. Importantly, the in vivo pathogen adaptation and interactions with hosts are crucial for potential vaccine development.
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Affiliation(s)
- Si Jie Lim
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Suriana Sabri
- Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Glazier VE, Kramara J, Ollinger T, Solis NV, Zarnowski R, Wakade RS, Kim MJ, Weigel GJ, Liang SH, Bennett RJ, Wellington M, Andes DR, Stamnes MA, Filler SG, Krysan DJ. The Candida albicans reference strain SC5314 contains a rare, dominant allele of the transcription factor Rob1 that modulates filamentation, biofilm formation, and oral commensalism. mBio 2023; 14:e0152123. [PMID: 37737633 PMCID: PMC10653842 DOI: 10.1128/mbio.01521-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/27/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE Candida albicans is a commensal fungus that colonizes the human oral cavity and gastrointestinal tract but also causes mucosal as well as invasive disease. The expression of virulence traits in C. albicans clinical isolates is heterogeneous and the genetic basis of this heterogeneity is of high interest. The C. albicans reference strain SC5314 is highly invasive and expresses robust filamentation and biofilm formation relative to many other clinical isolates. Here, we show that SC5314 derivatives are heterozygous for the transcription factor Rob1 and contain an allele with a rare gain-of-function SNP that drives filamentation, biofilm formation, and virulence in a model of oropharyngeal candidiasis. These findings explain, in part, the outlier phenotype of the reference strain and highlight the role heterozygosity plays in the strain-to-strain variation of diploid fungal pathogens.
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Affiliation(s)
| | - Juraj Kramara
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Tomye Ollinger
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Norma V. Solis
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute and Harbor-UCLA Medical Center, Torrance, California, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Robert Zarnowski
- Department of Medicine, Section of Infectious Disease, University of Wisconsin, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, USA
| | - Rohan S. Wakade
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Min-Ju Kim
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Gabriel J. Weigel
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Shen-Huan Liang
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Richard J. Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Melanie Wellington
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - David R. Andes
- Department of Medicine, Section of Infectious Disease, University of Wisconsin, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, USA
| | - Mark A. Stamnes
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Scott G. Filler
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute and Harbor-UCLA Medical Center, Torrance, California, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Damian J. Krysan
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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Brandquist ND, Lampman C, Smith EJ, Basilio L, Almansob A, Iwen PC, Blankenship JR. Significant variation of filamentation phenotypes in clinical Candida albicans strains. Front Cell Infect Microbiol 2023; 13:1207083. [PMID: 37928181 PMCID: PMC10623444 DOI: 10.3389/fcimb.2023.1207083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction Candida albicans is an opportunistic human pathogen that typically resides as part of the microbiome in the gastrointestinal and genitourinary tracts of a large portion of the human population. This fungus lacks a true sexual cycle and evolves in a largely clonal pattern. The ability to cause disease is consistent across the species as strains causing systemic infections appear across the known C. albicans intra-species clades. Methods In this work, strains collected from patients with systemic C. albicans infections isolated at the Nebraska Medicine clinical laboratory were typed by MLST analysis. Since the ability to form filaments has been linked to pathogenesis in C. albicans, these clinical strains, as well as a previously genotyped set of clinical strains, were tested for their ability to filament across a variety of inducing conditions. Results Genotyping of the clinical strains demonstrated that the strains isolated at one of the major medical centers in our region were as diverse as strains collected across the United States. We demonstrated that clinical strains exhibit a variety of filamentation patterns across differing inducing conditions. The only consistent pattern observed in the entire set of clinical strains tested was an almost universal inability to filament in standard solid inducing conditions used throughout the C. albicans field. A different solid filamentation assay that produces more robust filamentation profiles from clinical strains is proposed in this study, although not all strains expected to filament in vivo were filamentous in this assay. Discussion Our data supports growing evidence that broad phenotypic diversity exists between the C. albicans type strain and clinical strains, suggesting that the type strain poorly represents filamentation patterns observed in most clinical isolates. These data further highlight the need to use diverse clinical strains in pathogenesis assays.
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Affiliation(s)
| | - Cierra Lampman
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, United States
| | - Elias J. Smith
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, United States
| | - Lizeth Basilio
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, United States
| | - Akram Almansob
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, United States
| | - Peter C. Iwen
- Nebraska Public Health Laboratory, University of Nebraska Medical Center, Omaha, NE, United States
| | - Jill R. Blankenship
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, United States
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Sharma A, Mitchell AP. Strain variation in gene expression impact of hyphal cyclin Hgc1 in Candida albicans. G3 (BETHESDA, MD.) 2023; 13:jkad151. [PMID: 37405402 PMCID: PMC10468301 DOI: 10.1093/g3journal/jkad151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 07/06/2023]
Abstract
Formation of hyphae is a key virulence trait of the fungal pathogen Candida albicans. Hypha morphogenesis depends upon the cyclin Hgc1, which acts together with cyclin-dependent protein kinase Cdc28 to phosphorylate effectors that drive polarized growth. Hgc1 has also been implicated in gene regulation through its effects on 2 transcription factors, Efg1 and Ume6. Here, we report RNA-sequencing (RNA-seq) analysis of 2 pairs of hgc1Δ/Δ mutants and their respective wild-type strains, which lie in 2 different genetic backgrounds. We find that hgc1Δ/Δ mutations alter expression of 271 genes in both genetic backgrounds and 266 of those genes respond consistently with regard to up- or down-regulation. Consistency is similar to what has been observed with efg1Δ/Δ mutations and greater than observed with nrg1Δ/Δ mutations in these 2 backgrounds. The gene expression response includes genes under Efg1 control, as expected from prior studies. Hgc1-responsive genes also include ergosterol biosynthetic genes and bud neck-related genes, which may reflect interactions between Hgc1 and additional transcription factors as well as effects of Hgc1 on cellular length-to-width ratios.
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Affiliation(s)
- Anupam Sharma
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Aaron P Mitchell
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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Kumar D, Kumar A. Molecular Determinants Involved in Candida albicans Biofilm Formation and Regulation. Mol Biotechnol 2023:10.1007/s12033-023-00796-x. [PMID: 37410258 DOI: 10.1007/s12033-023-00796-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023]
Abstract
Candida albicans is known for its pathogenicity, although it lives within the human body as a commensal member. The commensal nature of C. albicans is well controlled and regulated by the host's immune system as they live in the harmonized microenvironment. However, the development of certain unusual microhabitat conditions (change in pH, co-inhabiting microorganisms' population ratio, debilitated host-immune system) pokes this commensal fungus to transform into a pathogen in such a way that it starts to propagate very rapidly and tries to breach the epithelial barrier to enter the host's systemic circulations. In addition, Candida is infamous as a major nosocomial (hospital-acquired infection) agent because it enters the human body through venous catheters or medical prostheses. The hysterical mode of C. albicans growth builds its microcolony or biofilm, which is pathogenic for the host. Biofilms propose additional resistance mechanisms from host immunity or extracellular chemicals to aid their survival. Differential gene expressions and regulations within the biofilms cause altered morphology and metabolism. The genes associated with adhesiveness, hyphal/pseudo-hyphal growth, persister cell transformation, and biofilm formation by C. albicans are controlled by myriads of cell-signaling regulators. These genes' transcription is controlled by different molecular determinants like transcription factors and regulators. Therefore, this review has focused discussion on host-immune-sensing molecular determinants of Candida during biofilm formation, regulatory descriptors (secondary messengers, regulatory RNAs, transcription factors) of Candida involved in biofilm formation that could enable small-molecule drug discovery against these molecular determinants, and lead to disrupt the well-structured Candida biofilms effectively.
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Affiliation(s)
- Dushyant Kumar
- Department of Biotechnology, National Institute of Technology, Raipur, Chhattisgarh, 492010, India
| | - Awanish Kumar
- Department of Biotechnology, National Institute of Technology, Raipur, Chhattisgarh, 492010, India.
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Glazier VE, Kramara J, Ollinger T, Solis NV, Zarnowski R, Wakade RS, Kim MJ, Weigel GJ, Liang SH, Bennett RJ, Wellington M, Andes DR, Stamnes MA, Filler SG, Krysan DJ. The Candida albicans reference strain SC5314 contains a rare, dominant allele of the transcription factor Rob1 that modulates biofilm formation and oral commensalism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.17.545405. [PMID: 37398495 PMCID: PMC10312810 DOI: 10.1101/2023.06.17.545405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Candida albicans is a diploid human fungal pathogen that displays significant genomic and phenotypic heterogeneity over a range of virulence traits and in the context of a variety of environmental niches. Here, we show that the effects of Rob1 on biofilm and filamentation virulence traits is dependent on both the specific environmental condition and the clinical strain of C. albicans . The C. albicans reference strain SC5314 is a ROB1 heterozygote with two alleles that differ by a single nucleotide polymorphism at position 946 resulting in a serine or proline containing isoform. An analysis of 224 sequenced C. albicans genomes indicates that SC5314 is the only ROB1 heterozygote documented to date and that the dominant allele contains a proline at position 946. Remarkably, the ROB1 alleles are functionally distinct and the rare ROB1 946S allele supports increased filamentation in vitro and increased biofilm formation in vitro and in vivo, suggesting it is a phenotypic gain-of-function allele. SC5314 is amongst the most highly filamentous and invasive strains characterized to date. Introduction of the ROB1 946S allele into a poorly filamenting clinical isolate increases filamentation and conversion of an SC5314 laboratory strain to a ROB1 946S homozygote increases in vitro filamentation and biofilm formation. In a mouse model of oropharyngeal infection, the predominant ROB1 946P allele establishes a commensal state while the ROB1 946S phenocopies the parent strain and invades into the mucosae. These observations provide an explanation for the distinct phenotypes of SC5314 and highlight the role of heterozygosity as a driver of C. albicans phenotypic heterogeneity. Importance Candida albicans is a commensal fungus that colonizes human oral cavity and gastrointestinal tracts but also causes mucosal as well as invasive disease. The expression of virulence traits in C. albicans clinical isolates is heterogenous and the genetic basis of this heterogeneity is of high interest. The C. albicans reference strain SC5314 is highly invasive and expresses robust filamentation and biofilm formation relative to many other clinical isolates. Here, we show that SC5314 derivatives are heterozygous for the transcription factor Rob1 and contain an allele with a rare gain-of-function SNP that drives filamentation, biofilm formation, and virulence in a model of oropharyngeal candidiasis. These finding explain, in part, the outlier phenotype of the reference strain and highlight the role of heterozygosity plays in the strain-to-strain variation of diploid fungal pathogens.
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Affiliation(s)
| | - Juraj Kramara
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City IA
| | - Tomye Ollinger
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City IA
| | - Norma V. Solis
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute and Harbor-UCLA Medical Center, Torrance, CA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Robert Zarnowski
- Department of Medicine, Section of Infectious Disease, University of Wisconsin, Madison WI
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison WI
| | - Rohan S. Wakade
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City IA
| | - Min-Ju Kim
- Department of Microbiology, University of Georgia, Athens, GA
| | - Gabriel J. Weigel
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City IA
| | - Shen-Huan Liang
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI
| | - Richard J. Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI
| | - Melanie Wellington
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City IA
| | - David R. Andes
- Department of Medicine, Section of Infectious Disease, University of Wisconsin, Madison WI
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison WI
| | - Mark A. Stamnes
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Scott G. Filler
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute and Harbor-UCLA Medical Center, Torrance, CA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Damian J. Krysan
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City IA
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City IA
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