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2018 Publications

NAI CAN-7 Reliving the Past               
42: 4 of which were co-authored by two or more RLP members

Cooper, Vaughn (co-I, University of Pittsburgh) [

Qu Y, T Olonisakin, W Bain, J Zupetic, R Brown, M Hulver, Z Xiong, J Tejero, RMQ Shanks, JM Bomberger , VS Cooper, ME Zegans, H Ryu, J Han, J Pilewski, A Ray, Z Cheng, P Ray, JS Lee. (2018). Thrombospondin-1 protects against pathogen-induced lung injury by limiting extracellular matrix proteolysis. JCI Insight 3. 10.1172/jci.insight.96914.

Shair KHY, A Reddy, VS Cooper. (2018). New Insights from elucidating the role of LMP1 in nasopharyngeal carcinoma. Cancers. 10(4):86.

Grosser MR, E Paluscio, LR Thurlow, MM Dillon, VS Cooper, TH Kawula, et al. (2018). Genetic requirements for Staphylococcus aureus nitric oxide resistance and virulence. PLoS Pathog. 14(3):e1006907.

Cooper VS. (2018). Experimental evolution as a high-throughput screen for genetic adaptations. mSphere. 3(3):e00121-18.

Turner CB*, CW Marshall, VS Cooper. (2018). Parallel genetic adaptation across environments differing in mode of growth or resource availability. Evolution Letters 2(4):355-367. [*NPP fellow] (doi: 10.1002/evl3.75)

Silva IN, FD Pessoa FD, MJ Ramires, MR Santos, JD Becker, VS Cooper, LM Moreira. (2018). OmpR regulator of Burkholderia multivorans controls mucoid-to-nonmucoid transition and other cell envelope properties associated with persistence in the cystic fibrosis lung. J Bacteriol.  200(17): pii: e00216-18 (doi: 10.1128/JB.00216-18)

Dillon MM, W Sung, M Lynch, VS Cooper. (2018). Periodic variation of mutation rates in bacterial genomes associated with replication timing. mBio 9:e01371-18.

Kristofich, J-C, AB Morgenthaler, WR Kinney, CC Ebmeier, DJ Snyder, WM Old, VS Cooper, SD Copley. (2018). Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme. PLoS Genetics, 14, e1007615.

Mustapha MM, B Li, MP Pacey, RT Mettus, CL McElheny, CW Marshall, RK Ernst, VS Cooper, Y Doi. (2018). Phylogenomics of colistin-susceptible and resistant XDR Acinetobacter baumannii. J Antimicrob Chemother. 73(11):2952-2959. (doi: 10.1093/jac/dky290)

Marsh, J, MP Pacey, C Ezeonwuka, SL Ohm, D Snyder, VS Cooper, LH Harrison, Y Doi, MM Mustapha. (2018) Clostridium difficile: a potential source of NpmA in the clinical environment. J Antimicrob Chemother. 74(2):521-523.

Dunlap DG, CW Marshall, A Fitch, SF Rapport, VS Cooper, BJ McVerry, A Morris, GD Kitsios. (2018). Improved detection of culprit pathogens by bacterial DNA sequencing affects antibiotic management decisions in severe pneumonia. Am J Case Rep 19:1405–1409.

Copley, Shelley (co-I, University of Colorado)

Flood, JJ, SD Copley. (2018). Genome-wide analysis of transcriptional changes and genes that contribute to fitness during degradation of the anthropogenic pollutant pentachlorophenol by S. chlorophenolicum. mSystems, 3, e00275-18. doi: 10.1128/mSystems.00275-18

Kristofich, J-C, AB Morgenthaler, WR Kinney, CC Ebmeier, DJ Snyder, WM Old, VS Cooper, SD Copley. (2018). Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme. PLoS Genetics, 14, e1007615.

Gerrrish, Phil (co-I, Georgia Tech)

Gerrish PJ, Ferreira C. (2018). A thermodynamic limit constrains complexity and primitive social function. Intl J Astrobiology. 1-7. doi:10.1017/S1473550418000149

Herron, Matthew (co-I, Georgia Tech)

Boyd M, F Rosenzweig, MD Herron. (2018) Analysis of motility in multicellular Chlamydomonas reinhardtii evolved under predation. PLoS One 13, e0192184. (doi:10.1371/journal.pone.0192184)

Herron MD, WC Ratcliff, J Boswell, F Rosenzweig. (2018). Genetics of a de novo origin of undifferentiated multicellularity. R. Soc. Open Sci. 5, 180912. (doi:10.1098/rsos.180912).

Hanschen ER, MD Herron, JJ Wiens, H Nozaki, RE Michod. (2018). Multicellularity drives the evolution of sexual traits. Am. Nat. 192, E93–E105. (doi:10.1086/698301)

Herron M, S Zamani-Dahaj, WC Ratcliff. (2018). Trait heritability in major transitions. BMC Biol. 16:145 (https//doi:10.1186/s12915-018-0612-6)

Kacar, Betul (co-I, University of Arizona)
Adam ZR, AC Fahrenbach,  B Kacar, M Aono. (2018). Prebiotic geochemical automata at the intersection of radiolytic chemistry, physical and systems biology. Complexity. Article ID 9376183.

Walker, SI, W Bains, L Cronin, S DasSarma, S Danielache, S Domagal-Goldman, B Kacar, NY Kiang, A Lenardic, CT Reinhard, W Moore, EW Schieterman, EL Shkolnik, HB Smith. (2018). Exoplanet biosignatures: Future directions Astrobiology 18(6) 779-824.

Adam ZR, B Kacar, S Som, K Lynch, M Antonio, K Williford (2018) The origin of animals as microbial host volumes in nutrient-limited seas Peer J 6: e27173v1

B Kacar, Y Womack (2018) Future shaped by pasts that could have been. Journal of Design and Science

McCutcheon, John (co-I, University of Montana)

Łukasik P, K Nazario, JT Van Leuven, MA Campbell, M Meyer, A Michalik, P Pessacq, C Simon, C Veloso, JP McCutcheon. (2018). Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas. Proc Natl Acad Sci USA 115:E226-E235.  Discussed in Science Daily

Matsuura Y, Moriyama M, Łukasik P, Vanderpool D, Tanahashi M, Meng X-Y, McCutcheon JP, Fukatsu T. (2018). Recurrent symbiont recruitment from fungal parasites in cicadas. Proc Natl Acad Sci USA 115:E5970-E5979.

Campbell MA, Łukasik P, Meyer MM, Buckner M, Simon C, Veloso C, Michalik A, McCutcheon JP. (2018). Changes in endosymbiont complexity drive host-level compensatory adaptations in cicadas. mBio 9:e02104-18.

Miller, Scott (co-I, University of Montana)

Gallagher, AL, SR Miller. (2018). Expression of novel gene content drives adaptation to low iron in the cyanobacterium Acaryopchloris. Genome Biol Evol 10:1484-1492

Sano, EB, CA Wall, PR Hutchins, SR Miller. (2018). Ancient balancing selection on heterocyst function in a cosmopolitan cyanobacterium. Nature Ecol Evol https://doi:10.1038/s41559-017-0435-9

Miller, SR, D Carvey. (2018). Ecological divergence with gene flow in a thermophilic cyanobacterium. Microbial Ecology, https//

Ratcliff, Will (co-I, Georgia Tech)
Libby E, WW Driscoll, WC Ratcliff. (2018). Programmed cell death can increase the efficacy of microbial bet hedging. Scientific Reports 8(1):1120.
Jacobeen, S, JT Pentz, E Graba, CG Brandys, WC Ratcliff, PJ Yunker. (2018). Cellular packing, mechanical stress and the evolution of multicellularity. Nature Physics 14:286-290.
Jacobeen S, EC Graba, CG Brandys, TC Day, WC Ratcliff, PJ Yunker. (2018). Geometry, packing, and evolutionary paths to increased multicellular size. Physical Review E. 97: 050401(R).

Mai T, M Mihail, I Panageas, V Vazirani, WC Ratcliff, PJ Yunker. Cycles in zero-sum differential games and biological diversity. The 19th ACM conference on Economics and Computation (ACM EC’18). DOI: 10.1145/3219166.3219227

Rosenzweig, Frank (PI, Georgia Tech)

Hicks, L, L van der Graaf, J Childress, E Cook, K Schmidt, F Rosenzweig, E Kroll.. (2018). Streamlined preparation of genomic DNA in agarose plugs for pulsed-field gel electrophoresis. J Biological Methods 5(1):886. (doi:10.14440/jbm.2018.218)

Boyd, M, F Rosenzweig, M Herron. (2018). Motility in multicellular Chlamydomonas reinhardtii (Chlamydomonadales, Chlorophyceae) PLoS One 13(1): e0192184.

Herron, MD, WC Ratcliff, J Boswell, F Rosenzweig. (2018). Genetics of a de novo origin of undifferentiated multicellularity. Royal Society Open Science 5:180912.

Lynch, KL, WA Jackson, K Rey, JR Spear, F Rosenzweig, JM Marr. (201_). Evidence for biotic perchlorate reduction in naturally perchlorate-rich sediments of Pilot Valley Basin, Utah. Astrobiology. In Press.

Herron, MD, JM Borin, JC Boswell, J Walker, I-CK Chen, CA Knox, M Boyd, F Rosenzweig, W Ratcliff. (201_). De novo origins of multicellularity in response to predation. Scientific Reports. In Press.

Sherlock, Gavin (co-I, Stanford University)

Aggeli D, VO Karas , NA Sinnott-Armstrong, V Varghese, RW Shafer, WJ Greenleaf, G Sherlock. (2018). Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery. Nucleic Acids Res. 46(7):e42.

Ropars J, C Maufrais, D Diogo, M Marcet-Houben, A Perin, N Sertour, K Mosca, E Permal, G Laval, C Bouchier, L Ma, K Schwartz, K Voelz, RC May, J Poulain, C Battail, P Wincker, AM Borman, A Chowdhary, S Fan, SH Kim, P Le Pape, O Romeo, JH Shin , T Gabaldon T, G Sherlock, ME Bougnoux, C d'Enfert. (2018). Gene flow contributes to diversification of the major fungal pathogen Candida albicans. Nat Commun. 9(1):2253. (doi: 10.1038/s41467-018-04787-4)

Li, Y, S Venkataram, A Agarwala, B Dunn, DA Petrov, G Sherlock, DS Fisher. (2018) Hidden complexity of yeast adaptation under simple evolutionary conditions. Current Biol. 28(4):515-525.e6.

Blundell JR, Schwartz K, Francois D, Fisher DS, Sherlock G and Levy SF. The dynamics of genetic diversity during the early stages of clonal evolution. Nature Ecology Evolution
(doi: 10.1038/s41559-018-0758-1) Epub 2018 Dec 31

Tamburini, FB, GS Sherlock, AS Bhatt. Transmission and persistence of crAssphage, a ubiquitous human-associated bacteriophage. Nature Communications, under review.

Smith, Eric (co-I, Georgia Tech)

Bhattacharya, T, N Retzlaff, DE Blasi, W Croft, M Cysouw, D Hruschka, I Maddieson, L Muller, E Smith, P F Stadler, G Starostin, H Youn.  Studying language evolution in the age of big data.  J. Lang. Evol. 3(2), 94—129.

Sniegowski, Paul (co-I, University of Pennsylvania)

Sprouffske, K, J Aguilar-Rodríguez, P Sniegowski, A Wagner. (2018). High mutation rates limit evolutionary adaptation in Escherichia coli. PLoS Genetics 14(4), e1007324-31.

Raynes, Y, CS Wylie, PD Sniegowski, DM Weinreich. (2018). Sign of selection on mutation rate modifiers depends on population size. Proc Natl Acad Sci USA  66: 201715996-6.

Raynes, Y, PD Sniegowski, DM Weinreich. (201_). Migration promotes mutator alleles in subdivided populations. Evolution, accepted pending minor revision.