Anita Sil, MD, PhD
Professor
Microbiology and Immunology
School of Medicine

Education & Training

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• M.D. Medicine University of California, San Francisco 1998
• Ph.D. Graduate Division (Biochemistry) University of California, San Francisco 1996

Websites

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• Profile at histo.ucsf.edu (histo.ucsf.edu)

Grants and Projects

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• Gene circuits that control morphology in Histoplasma, NIH, 2005-2025
• Evolutionary multispecies transcriptomics to reveal genes that govern fungal spore germination and pathogenesis, NIH, 2019-2024
• Elucidating the mechanism of macrophage death during infection with the AIDS-associated opportunistic pathogen Histoplasma capsulatum, NIH, 2018-2022
• Intracellular pathogens and innate immunity, NIH, 2004-2021
• Using Genetics and Genomics to Dissect Coccidioides Spherulation, NIH, 2019-2021
• Gene circuits that control morphology in Histoplasma, NIH, 2005-2020
• Proteomics Analysis of Host-Pathogen Interactions in Histoplasma, NIH, 2015-2017
• Molecular dissection of Histoplasma-induced host-cell death, NIH, 2012-2016
• Pacific Southwest RCE for Biodefense & Emerging Infectious Diseases Research, NIH, 2005-2015
• Natural products from a human-asssociated fungal pathogen, NIH, 2012-2014

Publications (54)

Top publication keywords:
Genes, FungalVirulence FactorsCalcium-Binding ProteinsFungal ProteinsMycosesHistoplasmaSpores, FungalCoccidioidesHistoplasmosisVirulenceGene Expression Regulation, FungalHost-Pathogen InteractionsMacrophagesHyphaeTemperature

• Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora.
  PLoS genetics 2023 Wang Z, Wang YW, Kasuga T, Lopez-Giraldez F, Zhang Y, Zhang Z, Wang Y, Dong C, Sil A, Trail F, Yarden O, Townsend JP
• A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response.
  Nature cell biology 2023 Subramanian A, Wang L, Moss T, Voorhies M, Sangwan S, Stevenson E, Pulido EH, Kwok S, Chalkley RJ, Li KH, Krogan NJ, Swaney DL, Burlingame AL, Floor SN, Sil A, Walter P, Mukherjee S
• Recyclable CRISPR/Cas9-mediated gene disruption and deletions in Histoplasma.
  mSphere 2023 Joehnk B, Ali N, Voorhies M, Walcott K, Sil A
• Recyclable CRISPR/Cas9 mediated gene disruption and deletions in Histoplasma.
  bioRxiv : the preprint server for biology 2023 Joehnk B, Ali N, Voorhies M, Walcott K, Sil A
• Chemical stimuli override a temperature-dependent morphological program by reprogramming the transcriptome of a fungal pathogen.
  bioRxiv : the preprint server for biology 2023 Assa D, Voorhies M, Sil A

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• Retraction: Opposing signaling pathways regulate morphology in response to temperature in the fungal pathogen Histoplasma capsulatum.
  PLoS biology 2023 Rodriguez L, Voorhies M, Gilmore S, Beyhan S, Myint A, Sil A
• SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants.
  Stem cell reports 2023 Hysenaj L, Little S, Kulhanek K, Magnen M, Bahl K, Gbenedio OM, Prinz M, Rodriguez L, Andersen C, Rao AA, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Mick E, Khalid MM, Taha TY, Kumar R, …
• Genome Organization and Copy-Number Variation Reveal Clues to Virulence Evolution in Coccidioides posadasii.
  Journal of fungi (Basel, Switzerland) 2022 Dubin CA, Voorhies M, Sil A, Teixeira MM, Barker BM, Brem RB
• The future of fungi: threats and opportunities.
  G3 (Bethesda, Md.) 2022 Case NT, Berman J, Blehert DS, Cramer RA, Cuomo C, Currie CR, Ene IV, Fisher MC, Fritz-Laylin LK, Gerstein AC, Glass NL, Gow NAR, Gurr SJ, Hittinger CT, Hohl TM, Iliev ID, James TY, Jin H, Klein BS, …
• COVID-19-associated Lung Microvascular Endotheliopathy: A "From the Bench" Perspective.
  American journal of respiratory and critical care medicine 2022 Joffre J, Rodriguez L, Matthay ZA, Lloyd E, Fields AT, Bainton RJ, Kurien P, Sil A, Calfee CS, Woodruff PG, Erle DJ, Hendrickson C, Krummel MF, Langelier CR, Matthay MA, Kornblith LZ, Hellman J, COVID…
• Genome-scale CRISPR screening reveals that C3aR signaling is critical for rapid capture of fungi by macrophages.
  PLoS pathogens 2022 Cohen A, Jeng EE, Voorhies M, Symington J, Ali N, Rodriguez RA, Bassik MC, Sil A
• NF-κB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids.
  bioRxiv : the preprint server for biology 2022 Simoneau CR, Chen PY, Xing GK, Khalid MM, Meyers NL, Hayashi JM, Taha TY, Leon KE, Ashuach T, Fontaine KA, Rodriguez L, Joehnk B, Walcott K, Vasudevan S, Fang X, Maishan M, Schultz S, Roose J, Matthay…
• Cbp1, a fungal virulence factor under positive selection, forms an effector complex that drives macrophage lysis.
  PLoS pathogens 2022 Azimova D, Herrera N, Duvenage L, Voorhies M, Rodriguez RA, English BC, Hoving JC, Rosenberg O, Sil A
• Immediate myeloid depot for SARS-CoV-2 in the human lung.
  Research square 2022 Magnen M, You R, Rao AA, Davis RT, Rodriguez L, Simoneau CR, Hysenaj L, Hu KH, UCSF COMET Consortium, Love C, Woodruff PG, Erle DJ, Hendrickson CM, Calfee CS, Matthay MA, Roose JP, Sil A, Ott M, …
• Immediate myeloid depot for SARS-CoV-2 in the human lung.
  bioRxiv : the preprint server for biology 2022 Magnen M, You R, Rao AA, Davis RT, Rodriguez L, Simoneau CR, Hysenaj L, Hu KH, UCSF COMET Consortium, Love C, Woodruff PG, Erle DJ, Hendrickson CM, Calfee CS, Matthay MA, Roose JP, Sil A, Ott M, …
• The WOPR family protein Ryp1 is a key regulator of gene expression, development, and virulence in the thermally dimorphic fungal pathogen Coccidioides posadasii.
  PLoS pathogens 2022 Mandel MA, Beyhan S, Voorhies M, Shubitz LF, Galgiani JN, Orbach MJ, Sil A
• Chromosome-Level Genome Assembly of a Human Fungal Pathogen Reveals Synteny among Geographically Distinct Species.
  mBio 2022 Voorhies M, Cohen S, Shea TP, Petrus S, Muñoz JF, Poplawski S, Goldman WE, Michael TP, Cuomo CA, Sil A, Beyhan S
• SARS-CoV-2 infection studies in lung organoids identify TSPAN8 as novel mediator.
  bioRxiv : the preprint server for biology 2021 Hysenaj L, Little S, Kulhanek K, Gbenedio OM, Rodriguez L, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Bahl K, Mick E, Li JZ, Ding VW, Matsumoto S, Maishan M, Simoneau C, Fragiadakis G, …
• Protomer alignment modulates specificity of RNA substrate recognition by Ire1.
  eLife 2021 Li W, Crotty K, Garrido Ruiz D, Voorhies M, Rivera C, Sil A, Mullins RD, Jacobson MP, Peschek J, Walter P
• Correction: Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma.
  PLoS genetics 2021 Gilmore SA, Voorhies M, Gebhart D, Sil A
• Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses.
  Cell 2020 Wang R, Simoneau CR, Kulsuptrakul J, Bouhaddou M, Travisano KA, Hayashi JM, Carlson-Stevermer J, Zengel JR, Richards CM, Fozouni P, Oki J, Rodriguez L, Joehnk B, Walcott K, Holden K, Sil A, Carette JE…
• Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy.
  Cell 2020 Fozouni P, Son S, Díaz de León Derby M, Knott GJ, Gray CN, D'Ambrosio MV, Zhao C, Switz NA, Kumar GR, Stephens SI, Boehm D, Tsou CL, Shu J, Bhuiya A, Armstrong M, Harris AR, Chen PY, Osterloh JM, …
• Recurrent Loss of abaA, a Master Regulator of Asexual Development in Filamentous Fungi, Correlates with Changes in Genomic and Morphological Traits.
  Genome biology and evolution 2020 Mead ME, Borowsky AT, Joehnk B, Steenwyk JL, Shen XX, Sil A, Rokas A
• Sensing the heat and the host: Virulence determinants of Histoplasma capsulatum.
  Virulence 2019 Beyhan S, Sil A
• Molecular regulation of Histoplasma dimorphism.
  Current opinion in microbiology 2019 Sil A
• Opposing signaling pathways regulate morphology in response to temperature in the fungal pathogen Histoplasma capsulatum.
  PLoS biology 2019 Rodriguez L, Voorhies M, Gilmore S, Beyhan S, Myint A, Sil A
• The transcription factor CHOP, an effector of the integrated stress response, is required for host sensitivity to the fungal intracellular pathogen Histoplasma capsulatum.
  PLoS pathogens 2017 English BC, Van Prooyen N, Örd T, Örd T, Sil A
• CD103+ Conventional Dendritic Cells Are Critical for TLR7/9-Dependent Host Defense against Histoplasma capsulatum, an Endemic Fungal Pathogen of Humans.
  PLoS pathogens 2016 Van Prooyen N, Henderson CA, Hocking Murray D, Sil A
• Macrophage cell death and transcriptional response are actively triggered by the fungal virulence factor Cbp1 during H. capsulatum infection.
  Molecular microbiology 2015 Isaac DT, Berkes CA, English BC, Murray DH, Lee YN, Coady A, Sil A
• Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma.
  PLoS genetics 2015 Gilmore SA, Voorhies M, Gebhart D, Sil A
• MyD88-dependent signaling drives host survival and early cytokine production during Histoplasma capsulatum infection.
  Infection and immunity 2015 Coady A, Sil A
• Thermally Dimorphic Human Fungal Pathogens--Polyphyletic Pathogens with a Convergent Pathogenicity Trait.
  Cold Spring Harbor perspectives in medicine 2014 Sil A, Andrianopoulos A
• N-acetylglucosamine (GlcNAc) triggers a rapid, temperature-responsive morphogenetic program in thermally dimorphic fungi.
  PLoS genetics 2013 Gilmore SA, Naseem S, Konopka JB, Sil A
• A temperature-responsive network links cell shape and virulence traits in a primary fungal pathogen.
  PLoS biology 2013 Beyhan S, Gutierrez M, Voorhies M, Sil A
• Comparative transcriptomics of infectious spores from the fungal pathogen Histoplasma capsulatum reveals a core set of transcripts that specify infectious and pathogenic states.
  Eukaryotic cell 2013 Inglis DO, Voorhies M, Hocking Murray DR, Sil A
• The 3-hydroxy-methylglutaryl coenzyme A lyase HCL1 is required for macrophage colonization by human fungal pathogen Histoplasma capsulatum.
  Infection and immunity 2012 Isaac DT, Coady A, Van Prooyen N, Sil A
• Mouse models for the study of fungal pneumonia: a collection of detailed experimental protocols for the study of Coccidioides, Cryptococcus, Fusarium, Histoplasma and combined infection due to Aspergillus-Rhizopus.
  Virulence 2012 Muhammed M, Feldmesser M, Shubitz LF, Lionakis MS, Sil A, Wang Y, Glavis-Bloom J, Lewis RE, Galgiani JN, Casadevall A, Kontoyiannis DP, Mylonakis E
• SRE1 regulates iron-dependent and -independent pathways in the fungal pathogen Histoplasma capsulatum.
  Eukaryotic cell 2011 Hwang LH, Seth E, Gilmore SA, Sil A
• A conserved transcriptional regulator governs fungal morphology in widely diverged species.
  Genetics 2011 Cain CW, Lohse MB, Homann OR, Sil A, Johnson AD
• Experimental annotation of the human pathogen Histoplasma capsulatum transcribed regions using high-resolution tiling arrays.
  BMC microbiology 2011 Voorhies M, Foo CK, Sil A
• Conidia but not yeast cells of the fungal pathogen Histoplasma capsulatum trigger a type I interferon innate immune response in murine macrophages.
  Infection and immunity 2010 Inglis DO, Berkes CA, Hocking Murray DR, Sil A
• Conserved factors Ryp2 and Ryp3 control cell morphology and infectious spore formation in the fungal pathogen Histoplasma capsulatum.
  Proceedings of the National Academy of Sciences of the United States of America 2008 Webster RH, Sil A
• Histoplasma requires SID1, a member of an iron-regulated siderophore gene cluster, for host colonization.
  PLoS pathogens 2008 Hwang LH, Mayfield JA, Rine J, Sil A
• Temperature-induced switch to the pathogenic yeast form of Histoplasma capsulatum requires Ryp1, a conserved transcriptional regulator.
  Proceedings of the National Academy of Sciences of the United States of America 2008 Nguyen VQ, Sil A
• Evolution of the mating type locus: insights gained from the dimorphic primary fungal pathogens Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii.
  Eukaryotic cell 2007 Fraser JA, Stajich JE, Tarcha EJ, Cole GT, Inglis DO, Sil A, Heitman J
• Identification of a copper-inducible promoter for use in ectopic expression in the fungal pathogen Histoplasma capsulatum.
  Eukaryotic cell 2006 Gebhart D, Bahrami AK, Sil A
• Identification of Histoplasma capsulatum transcripts induced in response to reactive nitrogen species.
  Molecular biology of the cell 2005 Nittler MP, Hocking-Murray D, Foo CK, Sil A
• Identifying phase-specific genes in the fungal pathogen Histoplasma capsulatum using a genomic shotgun microarray.
  Molecular biology of the cell 2003 Hwang L, Hocking-Murray D, Bahrami AK, Andersson M, Rine J, Sil A
• Vectors allowing amplified expression of the Saccharomyces cerevisiae Gal3p-Gal80p-Gal4p transcription switch: applications to galactose-regulated high-level production of proteins.
  Protein expression and purification 2000 Sil AK, Xin P, Hopper JE
• The Gal3p-Gal80p-Gal4p transcription switch of yeast: Gal3p destabilizes the Gal80p-Gal4p complex in response to galactose and ATP.
  Molecular and cellular biology 1999 Sil AK, Alam S, Xin P, Ma L, Morgan M, Lebo CM, Woods MP, Hopper JE
• Actin-dependent localization of an RNA encoding a cell-fate determinant in yeast.
  Nature 1997 Takizawa PA, Sil A, Swedlow JR, Herskowitz I, Vale RD
• Identification of asymmetrically localized determinant, Ash1p, required for lineage-specific transcription of the yeast HO gene.
  Cell 1996 Sil A, Herskowitz I
• Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription.
  Genes & development 1995 Kruger W, Peterson CL, Sil A, Coburn C, Arents G, Moudrianakis EN, Herskowitz I
• Retroviral integration into minichromosomes in vitro.
  The EMBO journal 1992 Pryciak PM, Sil A, Varmus HE