Publications

Homer CM, Voorhies M, Walcott K, Ochoa E, Sil A (2024) Transcriptomic atlas of the morphologic development of the fungal pathogen Coccidioides reveals key phase-enriched transcripts. biorxiv2024.10.13.618122v1 doi: https://doi.org/10.1101/2024.10.13.618122

Voorhies M, Joehnk B, Uehling J, Walcott K, Dubin C, Mead HL, Homer CM, Galgiani JN, Barker BM, Brem RB, Sil A (2024) Inferring the composition of a mixed culture of natural microbial isolates by deep sequencing. biorxiv2024.08.05.606565v1 doi: https://doi.org/10.1101/2024.08.05.606565 PMID:39149389

Assa D, Voorhies M, Sil A (2023) Chemical stimuli override a temperature-dependent morphological program by reprogramming the transcriptome of a fungal pathogen. biorxiv2023.04.21.537729v1 doi: https://doi.org/10.1101/2023.04.21.537729 PMID:37131633

Herrera N, Odermatt PD, Voorhies M, Nakagawa R, Sil A, Chang F, Rosenberg OS (2021) The ESX-1 secretion system senses bacterial contact and prepares mycobacteria for environmental adaptation. bioRxiv 2021.10.17.464699v1 doi: https://doi.org/10.1101/2021.10.17.464699 GSE185010

Homer CM, Ochoa E, Voorhies M, Sil A (2024) Optimizing in vitro spherulation cues in the fungal pathogen Coccidioides. mSphere e0067924 PMID:39688406 GSE269000

Magnen M, You R, Rao AA, Davis RT, Rodriguez L, Bernard O, Simoneau CR, Hysenaj L, Hu KH, Maishan M, Conrad C, Gbenedio OM, Samad B, Consortium TUC, Love C, Woodruff PG, Erle DJ, Hendrickson CM, Calfee CS, Matthay MA, Roose JP, Sil A, Ott M, Langelier CR, Krummel MF, Looney MR (2024) Immediate myeloid depot for SARS-CoV-2 in the human lung. Science advances 10:(31):eadm8836 PMID:39083602

Simoneau CR, Chen PY, Xing GK, Hayashi JM, Chen IP, Khalid MM, Meyers NL, Taha TY, Leon KE, Suryawanshi RK, McCavitt-Malvido M, Ashuach T, Fontaine KA, Rodriguez L, Joehnk B, Walcott K, Vasudevan S, Fang X, Maishan M, Schultz S, Roose JP, Matthay MA, Sil A, Arjomandi M, Yosef N, Ott M (2024) NF-κB inhibitor alpha controls SARS-CoV-2 infection in ACE2-overexpressing human airway organoids. Scientific reports 14:(1):15351 PMID:38961189

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 (2023) A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response. Nature cell biology PMID:37857833 GSE205648 8JHU EMD-36294 PXD034240

Joehnk B,Ali N,Voorhies M,Walcott K,Sil A (2023) Recyclable CRISPR/Cas9-mediated gene disruption and deletions in Histoplasma. mSphere PMID:37819140 PRJNA971667

Hysenaj L, Little S, Kulhanek K, Magnen M, Bahl K, Gbenedio M, Prinz M, Rodriguez L, Andersen C, Rao AA, Shen A, Lone JC, Bonser LR, Serwas NK, Mick E, Khalid MM, Taha TY, Kumar R, Li JZ, Ding VW, Matsumoto S, Mazharul M, Sreekumar B, Simoneau C, Nazarenko I, Tomlinson M, Khan K, Sigal A, Looney MR, Fragiadakis GK, Jablons DM, Langeliers CR, Mathay M, Krummel M, Erle DJ, Combes AJ, Sil A, Ott M, Kratz JR, Roose JP (2023) SARS-CoV-2 infection of Airway Organoids Reveals Conserved Use of Tetraspanin-8 by Ancestral-, Delta-, and Omicron- Variants Stem cell reports PMID:36827975

Dubin CA, Voorhies M, Sil A, Teixeira MM, Barker BM, Brem RB (2022) Genome Organization and Copy-Number Variation Reveal Clues to Virulence Evolution in Coccidioides posadasii Journal of Fungi 8:(12):1235 PMID:36547568 source code

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, Kronstad JW, Lorch JM, McGovern V, Mitchell AP, Segre JA, Shapiro RS, Sheppard DC, Sil A, Stajich JE, Stukenbrock EE, Taylor JW, Thompson D, Wright GD, Heitman J, Cowen LE (2022) The future of fungi: threats and opportunities. G3 (Bethesda, Md.) 12:(11):jkac224 PMID:36179219

Cohen A, Jeng EE, Voorhies M, Symington J, Ali N, Rodriguez RA, Bassik MC, Sil A (2022) Genome-scale CRISPR screening reveals that C3aR signaling is critical for rapid capture of fungi by macrophages. PLoS Pathogens 18:(9):e1010237 PMID:36174103

Azimova D, Herrera N, Duvenage L, Voorhies M, Rodriguez RA, English BC, Hoving JC, Rosenberg O, Sil A (2022) Cbp1, a rapidly evolving fungal virulence factor, forms an effector complex that drives macrophage lysis. PLoS Pathogens 18:(6):e1010417 PMID:35731824 7R6U 7R79

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 (2022) COVID-19-Associated Lung Microvascular Endotheliopathy: A "From the Bench" Perspective. American journal of respiratory and critical care medicine PMID:35649173

Mandel AM, Beyhan S, Voorhies M, Shubitz LF, Galgiani JN, Orbach MJ, Sil A (2022) 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 18:(4):e1009832 PMID:35385558 GSE178277

Voorhies M, Cohen S, Shea TP, Petrus S, Muñoz JF, Poplawski S, Goldman WE, Michael TP, Cuomo CA, Sil A, Beyhan S (2022) Chromosome-Level Genome Assembly of a Human Fungal Pathogen Reveals Synteny among Geographically Distinct Species. mBio 13:e02574-21 PMID:35089059 PRJNA682643, PRJNA682644, PRJNA682645, PRJNA682647, PRJNA682647.

Li W, Crotty K, Garrido Ruiz D, Voorhies M, Rivera C, Sil A, Mullins RD, Jacobson MP, Peschek J, Walter P (2021) Protomer alignment modulates specificity of RNA substrate recognition by Ire1. eLife 10:e67425 PMID:33904404

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, Krogan NJ, Ott M, Puschnik AS (2020) Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses. Cell 184:(1):106-119 PMID:33333024

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, Meyer-Franke A, Joehnk B, Walcott K, Sil A, Langelier C, Pollard KS, Crawford ED, Puschnik AS, Phelps M, Kistler A, DeRisi JL, Doudna JA, Fletcher DA, Ott M (2020) Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy. Cell 184:(2):323-333 PMID:33306959

Mead ME, Borowsky AT, Joehnk B, Steenwyk JL, Shen XX, Sil A, and Rokas A (2020) 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 12:71119-1130 PMID:32442273

Sil A (2019) Molecular regulation of Histoplasma dimorphism. Current opinion in microbiology 52:151-157 PMID:31739263

Rodriguez L, Voorhies M, Gilmore SA, Beyhan S, Myint A, and Sil A (2019) Opposing signaling pathways regulate morphology in response to temperature in the fungal pathogen Histoplasma capsulatum. PLoS Biology 17:(9):e3000168 PMID:31568523 GEO:GSE124292 PRJNA514096

Retracted (PMID:36944162)

After this article was published, we conducted further genotypic and phenotypic analyses that revealed that the morphological phenotype studied in the article was not due to an Msb2 mutation but rather to an unlinked chromosome alteration. The nature of the chromosomal alteration is still under investigation. Given this new information, our statements attributing outcomes to Msb2 or an msb2 mutation are not supported, nor are the article’s main conclusions about Msb2 functions and temperature-dependent antagonism between the Ryp and Msb2 pathways.

In addition, we have been unable to reproduce the finding that STU1 gene is partially required for hyphae formation at room temperature. We hypothesize that the phenotype may have been due to the variable nature of the filamentation assay.

In light of these issues, we retract this article.

All authors agreed with the retraction. We apologize that these issues were not identified before the article was published.

We are currently characterizing the chromosomal alteration with the intent of submitting a corrected version of this article.

Beyhan S and Sil A (2019) Sensing the heat and the host: Virulence determinants of Histoplasma capsulatum. Virulence 10:(1):793 PMID:31560240

English BC, Van Prooyen N, Örd T, Örd T, Sil A (2017) 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 13:(9):e1006589 PMID:28953979

Van Prooyen N, Henderson CA, Hocking Murray D, Sil A (2016) CD103+ Conventional Dendritic Cells Are Critical for TLR7/9-Dependent Host Defense against Histoplasma capsulatum, an Endemic Fungal Pathogen of Humans. PLoS Pathogens 12:(7):e1005749 PMID:27459510 GEO:GSE70505

Gilmore SA, Voorhies M, Gebhart D, Sil A (2015) Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma. PLoS genetics 11:(7):e1005395 PMID:26177267 GEO:GSE68707

Coady A, Sil A (2015) MyD88-dependent signaling drives host survival and early cytokine production during Histoplasma capsulatum infection. Infection and immunity 83:(4):1265-75 PMID:25583527

Isaac DT, Berkes CA, English BC, Murray DH, Lee YN, Coady A, Sil A (2015) Macrophage cell death and transcriptional response are actively triggered by the fungal virulence factor Cbp1 during H. capsulatum infection. Molecular microbiology 98:(5):910-929 PMID:26288377 GEO:GSE23378

Sil A, Andrianopoulos A (2014) Thermally Dimorphic Human Fungal Pathogens--Polyphyletic Pathogens with a Convergent Pathogenicity Trait. Cold Spring Harbor perspectives in medicine 5:(8):a019794 PMID:25384771

Gilmore SA, Naseem S, Konopka JB, Sil A (2013) N-acetylglucosamine (GlcNAc) triggers a rapid, temperature-responsive morphogenetic program in thermally dimorphic fungi. PLoS genetics 9:(9):e1003799 PMID:24068964 GEO:GSE48044

Beyhan S, Gutierrez M, Voorhies M, Sil A (2013) A temperature-responsive network links cell shape and virulence traits in a primary fungal pathogen. PLoS biology 11:(7):e1001614 PMID:23935449 GEO:GSE47832

Inglis DO, Voorhies M, Hocking Murray DR, Sil A (2013) 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 12:(6):828-52 PMID:23563482 GEO:GSE45432

Isaac DT, Coady A, Van Prooyen N, Sil A (2013) The 3-hydroxy-methylglutaryl coenzyme A lyase HCL1 is required for macrophage colonization by human fungal pathogen Histoplasma capsulatum. Infection and immunity 81:(2):411-20 PMID:23184522

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. (2012) 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 3(3):329-38 PMID:22546902

Cain CW, Lohse MB, Homann OR, Sil A, Johnson AD (2012) A conserved transcriptional regulator governs fungal morphology in widely diverged species. Genetics 190:(2):511-21 PMID:22095082 GEO:GSE32558

Hwang LH, Seth E, Gilmore SA, Sil A (2012) SRE1 regulates iron-dependent and -independent pathways in the fungal pathogen Histoplasma capsulatum. Eukaryotic cell 11:(1):16-25 PMID:22117028 GEO:GSE33792

Voorhies M, Foo CK, Sil A (2011) Experimental annotation of the human pathogen Histoplasma capsulatum transcribed regions using high-resolution tiling arrays. BMC microbiology 11:216 PMID:21958208 GEO:GSE31155

Inglis DO, Berkes CA, Hocking Murray DR, Sil A (2010) 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 78:(9):3871-82 PMID:20605974 GEO:GSE20022

Webster RH, Sil A (2008) 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 105:(38):14573-8 PMID:18791067

Hwang LH, Mayfield JA, Rine J, Sil A (2008) Histoplasma requires SID1, a member of an iron-regulated siderophore gene cluster, for host colonization. PLoS Pathogens 4:(4):e1000044 PMID:18404210

Nguyen VQ, Sil A (2008) 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 105:(12):4880-5 PMID:18339808

Fraser JA, Stajich JE, Tarcha EJ, Cole GT, Inglis DO, Sil A, Heitman J (2007) Evolution of the mating-type locus: insights gained from the dimorphic primary fungal pathogens Histoplasma capsulatum, Coccidioides immitis and Coccidioides posadasii. Eukaryotic Cell 6(4):622-9 PMID:17337636

Sil A (2006) Using Genomics to Study the Life Cycle of Histoplasma capsulatum. In "The Mycota, Vol. XII. Editor: Alistair Brown. Publisher: Springer Verlag.

Hwang L, Sil A (2006) The future of functional genomics in Histoplasma capsulatum. In "Molecular Principles of Fungal Pathogenesis." Editors: Joseph Heitman, Scott Filler, John Edwards, Aaron Mitchell. Publisher: ASM Press.

Gebhart D, Bahrami AK, Sil A (2006) Identification of a copper-inducible promoter for use in ectopic expression in the fungal pathogen Histoplasma capsulatum. Eukaryotic cell 5:(6):935-44 PMID:16757741

Nittler MP, Hocking-Murray D, Foo CK, Sil A (2005) Identification of Histoplasma capsulatum transcripts induced in response to reactive nitrogen species. Molecular biology of the cell 16:(10):4792-813 PMID:16030248 (Histobase annotations)

Hwang L, Hocking-Murray D, Bahrami A, Andersson M, Rine J, Sil A (2003) Identifying Phase-Specific Genes in the Fungal Pathogen Histoplasma capsulatum Using a Genomic Shotgun Microarray. Molecular Biology of the Cell 14(6):2314-2326 PMID:12808032 (Histobase annotations)

McBride HJ*, Sil A*, Measday V, Yu Y, Moffat J, Maxon ME, Herskowitz I, Andrews B, Stillman DJ (2001) The protein kinase Pho85 is required for asymmetric accumulation of the Ash1 Protein in Saccharomyces cerevisiae. Mol. Microbiol. 42(2):345-53 *These two authors contributed equally to this work.11703659

Takizawa PA, Sil A, Swedlow JR, Herskowitz I, Vale RD (1997) Actin-dependent localization of an RNA encoding a cell-fate determinant in yeast. Nature 389:(6646):90-3 PMID:9288973

Sil A, Herskowitz I (1996) Identification of asymmetrically localized determinant, Ash1p, required for lineage-specific transcription of the yeast HO gene. Cell 84:(5):711-22 PMID:8625409

Kruger W, Peterson CL, Sil A, Coburn C, Arents G, Moudrianakis EN, Herskowitz I (1995) 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 9:(22):2770-9 PMID:7590252

Herskowitz I, Andrews B, Kruger W, Ogas J, Sil A, Coburn C, Peterson C (1992) Integration of Multiple Regulatory Inputs in the Control of HO Expression in Yeast. In "Transcriptional Regulation," S.L. McKnight and K.R. Yamamoto, eds., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp. 949-974.

Pryciak PM, Sil A, Varmus HE (1992) Retroviral integration into minichromosomes in vitro. The EMBO journal 11:(1):291-303 PMID:1310932