Elde Lab

Publications

Distinct pathways of adaptive evolution in Cryptococcus neoformans reveal a mutation in adenylyl cyclase with trade-offs for pathogenicity

Hilbert ZA, Bednarek JM, Schwiesow MJW, Chung KY, Moreau CT, Brown JCS, Elde NC.Curr Biol. 2023 Sep 8:S0960-9822(23)01134-X. doi: 10.1016/j.cub.2023.08.054. Online ahead of print.

Microbe transmission from pet shop to lab-reared zebrafish reveals a pathogenic birnavirus

Rice MC, Elde NC, Gagnon JA, Balla KM.bioRxiv. 2023 Aug 28:2023.08.28.555169. Preprint.PMID: 37693489

Structural homology screens reveal host-derived poxvirus protein families impacting inflammasome activity

Boys IN, Johnson AG, Quinlan MR, Kranzusch PJ, Elde NC.Cell Rep. 2023 Aug 29;42(8):112878. Epub 2023 Jul 25.PMID: 37494187

Rapid Evolution of Glycan Recognition Receptors Reveals an Axis of Host-Microbe Arms Races beyond Canonical Protein-Protein Interface s

Hilbert ZA, Haffener PE, Young HJ, Schwiesow MJW, Leffler EM, Elde NC.Genome Biol Evol. 2023 Jul 3;15(7):evad119. PMID: 37390614

Structural homology screens reveal poxvirus-encoded proteins impacting inflammasome-mediated defenses

Boys IN, Johnson AG, Quinlan M, Kranzusch PJ, Elde NC.bioRxiv. 2023 Apr 3:2023.02.26.529821. Preprint.PMID: 36909515

Virology under the Microscope-a Call for Rational Discourse

Goodrum F, Lowen AC, Lakdawala S, Alwine J, Casadevall A, Imperiale MJ, Atwood W, Avgousti D, Baines J, Banfield B, Banks L, Bhaduri-McIntosh S, Bhattacharya D, Blanco-Melo D, Bloom D, Boon A, Boulant S, Brandt C, Broadbent A, Brooke C, Cameron C, Campos S, Caposio P, Chan G, Cliffe A, Coffin J, Collins K, Damania B, Daugherty M, Debbink K, DeCaprio J, Dermody T, Dikeakos J, DiMaio D, Dinglasan R, Duprex WP, Dutch R, Elde N, Emerman M, Enquist L, Fane B, Fernandez-Sesma A, Flenniken M, Frappier L, Frieman M, Frueh K, Gack M, Gaglia M, Gallagher T, Galloway D, García-Sastre A, Geballe A, Glaunsinger B, Goff S, Greninger A, Hancock M, Harris E, Heaton N, Heise M, Heldwein E, Hogue B, Horner S, Hutchinson E, Hyser J, Jackson W, Kalejta R, Kamil J, Karst S, Kirchhoff F, Knipe D, Kowalik T, Lagunoff M, Laimins L, Langlois R, Lauring A, Lee B, Leib D, Liu SL, Longnecker R, Lopez C, Luftig M, Lund J, Manicassamy B, McFadden G, McIntosh M, Mehle A, Miller WA, Mohr I, Moody C, Moorman N, Moscona A, Mounce B, Munger J, Münger K, Murphy E, Naghavi M, Nelson J, Neufeldt C, Nikolich J, O'Connor C, Ono A, Orenstein W, Ornelles D, Ou JH, Parker J, Parrish C, Pekosz A, Pellett P, Pfeiffer …See abstract for full author list ➔

mBio. 2023 Feb 28;14(1):e0018823. Epub 2023 Jan 26.PMID: 36700642

J Virol. 2023 Feb 28;97(2):e0008923. Epub 2023 Jan 26.PMID: 36700640

mSphere. 2023 Jan 26:e0003423. PMID: 36700653

Extensive Recombination-driven Coronavirus Diversification Expands the Pool of Potential Pandemic Pathogens

Goldstein SA, Brown J, Pedersen BS, Quinlan AR, Elde NC.

Genome Biol Evol. 2022 Dec 8;14(12):evac161. PMID: 36477201

Adaptive duplication and genetic diversification of protein kinase R contribute to the specificity of bat-virus interactions

Jacquet S, Culbertson M, Zhang C, El Filali A, De La Myre Mory C, Pons JB, Filippi-Codaccioni O, Lauterbur ME, Ngoubangoye B, Duhayer J, Verez C, Park C, Dahoui C, Carey CM, Brennan G, Enard D, Cimarelli A, Rothenburg S, Elde NC, Pontier D, Etienne L.

Sci Adv. 2022 Nov 25;8(47):eadd7540. Epub 2022 Nov 23.PMID: 36417524

When viruses do not go gentle into that good night

Boys IN, Elde NC.

Cell Host Microbe. 2022 Nov 9;30(11):1499-1500. PMID: 36356562

Poxviruses capture host genes by LINE-1 retrotransposition

Fixsen SM, Cone KR, Goldstein SA, Sasani TA, Quinlan AR, Rothenburg S, Elde NC.

Elife. 2022 Sep 7;11:e63332. PMID: 36069526

Recurrent evolution of an inhibitor of ESCRT-dependent virus budding and LINE-1 retrotransposition in primates

Rheinemann L, Downhour DM, Davenport KA, McKeown AN, Sundquist WI, Elde NC.

Curr Biol. 2022 Apr 11;32(7):1511-1522.e6. PMID: 35245459

Natural rodent model of viral transmission reveals biological features of virus population dynamics

Fay EJ, Balla KM, Roach SN, Shepherd FK, Putri DS, Wiggen TD, Goldstein SA, Pierson MJ, Ferris MT, Thefaine CE, Tucker A, Salnikov M, Cortez V, Compton SR, Kotenko SV, Hunter RC, Masopust D, Elde NC, Langlois RA.

J Exp Med. 2022 Feb 7;219(2):e20211220. PMID: 34958350 Free PMC article.

Nels Elde

Elde N.

Curr Biol. 2021 Nov 8;31(21):R1410-R1412. PMID: 34752761

RetroCHMP3 blocks budding of enveloped viruses without blocking cytokinesis

Rheinemann L, Downhour DM, Bredbenner K, Mercenne G, Davenport KA, Schmitt PT, Necessary CR, McCullough J, Schmitt AP, Simon SM, Sundquist WI, Elde NC.

Cell. 2021 Oct 14;184(21):5419-5431.e16. PMID: 34597582

Diarrheal pathogens trigger rapid evolution of the guanylate cyclase-C signaling axis in bats

Carey CM, Apple SE, Hilbert ZA, Kay MS, Elde NC

Cell Host Microbe. 2021 Sep 8;29(9):1342-1350.e5. PMID: 34358433

Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens

Goldstein SA, Brown J, Pedersen BS, Quinlan AR, Elde NC

bioRxiv. 2021 Jun 28:2021.02.03.429646. PMID: 33564759

Signatures of host-pathogen evolutionary conflict reveal MISTR-A conserved MItochondrial STress Response network

Sorouri M, Chang T, Jesudhasan P, Pinkham C, Elde NC, Hancks DC

PLoS Biol. 2020 Dec 28;18(12):e3001045. PMID: 33370271

Linking Virus Discovery to Immune Responses Visualized during Zebrafish Infections

Balla KM, Rice MC, Gagnon JA, Elde NC

Curr Biol. 2020 Jun 8;30(11):2092-2103.e5. PMID: 32413307

Coevolution of Genome Architecture and Social Behavior

Rubenstein DR, Ågren JA, Carbone L, Elde NC, Hoekstra HE, Kapheim KM, Keller L, Moreau CS, Toth AL, Yeaman S, Hofmann HA

Trends Ecol Evol. 2019 Sep;34(9):844-855.

PMID: 31130318 Review

Recurrent Loss-of-Function Mutations Reveal Costs to OAS1 Antiviral Activity in Primates

Carey CM, Govande AA, Cooper JM, Hartley MK, Kranzusch PJ, Elde NC

Cell Host Microbe. 2019 Feb 13;25(2):336-343.e4. PMID: 30713099

Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays

Sasani TA, Cone KR, Quinlan AR, Elde NC

Elife. 2018 Aug 29;7:e35453. PMID: 30156554

Rapid Evolution of Primate Type 2 Immune Response Factors Linked to Asthma Susceptibility

Barber MF, Lee EM, Griffin H, Elde NC

Genome Biol Evol. 2017 Jun 1;9(6):1757-1765. PMID: 28854632

Emergence of a Viral RNA Polymerase Variant during Gene Copy Number Amplification Promotes Rapid Evolution of Vaccinia Virus

Cone KR, Kronenberg ZN, Yandell M, Elde NC

J Virol. 2017 Jan 31;91(4):e01428-16. PMID: 27928012

Regulatory activities of transposable elements: from conflicts to benefits

Chuong EB, Elde NC, Feschotte C.

Nat Rev Genet. 2017 Feb;18(2):71-86. PMID: 27867194

Disruption of promoter memory by synthesis of a long noncoding RNA

Yu Y, Yarrington RM, Chuong EB, Elde NC, Stillman DJ

Proc Natl Acad Sci U S A. 2016 Aug 23;113(34):9575-80. PMID: 27506791

Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans

Barber MF, Kronenberg Z, Yandell M, Elde NC.

PLoS Genet. 2016 May 20;12(5):e1006063. PMID: 27203426

Regulatory evolution of innate immunity through co-option of endogenous retroviruses.

Chuong EB, Elde NC, Feschotte C.

Science. 2016 Mar 4;351(6277):1083-7. PMID: 26941318

Wham: Identifying Structural Variants of Biological Consequence

Kronenberg ZN, Osborne EJ, Cone KR, Kennedy BJ, Domyan ET, Shapiro MD, Elde NC, Yandell M.

PLoS Comput Biol. 2015 Dec 1;11(12):e1004572. PMID: 26625158

Buried Treasure: Evolutionary Perspectives on Microbial Iron Piracy

Barber MF, Elde NC

Trends Genet. 2015 Nov;31(11):627-636. PMID: 26431675

Baculovirus protein PK2 subverts eIF2α kinase function by mimicry of its kinase domain C-lobe

Li JJ, Cao C, Fixsen SM, Young JM, Ono C, Bando H, Elde NC, Katsuma S, Dever TE, Sicheri F

Proc Natl Acad Sci U S A. 2015 Aug 11;112(32):E4364-73. PMID: 26216977

Overlapping Patterns of Rapid Evolution in the Nucleic Acid Sensors cGAS and OAS1 Suggest a Common Mechanism of Pathogen Antagonism and Escape

Hancks DC, Hartley MK, Hagan C, Clark NL, Elde NC

PLoS Genet. 2015 May 5;11(5):e1005203. PMID: 25942676

cGAS-mediated stabilization of IFI16 promotes innate signaling during herpes simplex virus infection

Orzalli MH, Broekema NM, Diner BA, Hancks DC, Elde NC, Cristea IM, Knipe DM

Proc Natl Acad Sci U S A. 2015 Apr 7;112(14):E1773-81. PMID: 25831530 Free PMC article.

Determinants for degradation of SAMHD1, Mus81 and induction of G2 arrest in HIV-1 Vpr and SIVagm Vpr

DePaula-Silva AB, Cassiday PA, Chumley J, Bosque A, Monteiro-Filho CMR, Mahon CS, Cone KR, Krogan N, Elde NC, Planelles V

Virology. 2015 Mar;477:10-17. PMID: 25618414

DisAp-dependent striated fiber elongation is required to organize ciliary arrays

Galati DF, Bonney S, Kronenberg Z, Clarissa C, Yandell M, Elde NC, Jerka-Dziadosz M, Giddings TH, Frankel J, Pearson CG

J Cell Biol. 2014 Dec 22;207(6):705-15. PMID: 25533842

Escape from bacterial iron piracy through rapid evolution of transferrin

Barber MF, Elde NC

Science. 2014 Dec 12;346(6215):1362-6. PMID: 25504720

Evolutionary biology: Mimicry all the way down

Barber MF, Elde NC

Nature. 2013 Sep 5;501(7465):38-9. PMID: 24005409

Poliovirus evolution: the strong, silent type

Elde NC

Cell Host Microbe. 2012 Nov 15;12(5):605-6. PMID: 23159048

Poxviruses deploy genomic accordions to adapt rapidly against host antiviral defenses

Elde NC, Child SJ, Eickbush MT, Kitzman JO, Rogers KS, Shendure J, Geballe AP, Malik HS

Cell. 2012 Aug 17;150(4):831-41. PMID: 22901812

A cross-species view on viruses

Sawyer SL, Elde NC

Curr Opin Virol. 2012 Oct;2(5):561-8. PMID: 22835485

Absence of positive selection on centromeric histones in Tetrahymena suggests unsuppressed centromere: drive in lineages lacking male meiosis

Elde NC, Roach KC, Yao MC, Malik HS

J Mol Evol. 2011 Jun;72(5-6):510-20. PMID: 21643829

The evolutionary conundrum of pathogen mimicry

Elde NC, Malik HS

Nat Rev Microbiol. 2009 Nov;7(11):787-97. PMID: 19806153

Protein kinase R reveals an evolutionary model for defeating viral mimicry

Elde NC, Child SJ, Geballe AP, Malik HS

Nature. 2009 Jan 22;457(7228):485-9. PMID: 19043403

A dynamin-related protein required for nuclear remodeling in Tetrahymena

Rahaman A, Elde NC, Turkewitz AP

Curr Biol. 2008 Aug 26;18(16):1227-33. PMID: 18701286

A role for convergent evolution in the secretory life of cells

Elde NC, Long M, Turkewitz AP

Trends Cell Biol. 2007 Apr;17(4):157-64. PMID: 17329106

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote

Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK Jr, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E

PLoS Biol. 2006 Sep;4(9):e286. PMID: 16933976

Publications

Nels Elde Lab