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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5821195/pdf/jciinsight-3-96914.pdf

Shair KHY, A Reddy, VS Cooper. (2018). New Insights from elucidating the role of LMP1 in nasopharyngeal carcinoma. Cancers. 10(4):86. https://www.mdpi.com/2072-6694/10/4/86

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. https://msphere.asm.org/content/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) https://onlinelibrary.wiley.com/doi/full/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) https://jb.asm.org/content/200/17/e00216-18

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. https://mbio.asm.org/content/9/4/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. https://doi.org/10.1371/journal.pgen.1007615

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) https://academic.oup.com/jac/article/73/11/2952/5074234

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. https://doi.org/10.1093/jac/dky420

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. https://www.amjcaserep.com/download/index/idArt/912055

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  https://msystems.asm.org/content/3/6/e00275-18

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. https://doi.org/10.1371/journal.pgen.1007615

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 https://www.cambridge.org/core/journals/international-journal-of-astrobiology/article/thermodynamic-limit-constrains-complexity-and-primitive-social-function/EBA991749DF1E2B72A356246505B5591

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). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6124120/pdf/rsos180912.pdf

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. https://doi.org/10.1155/2018/9376183

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. https://doi.org/10.1089/ast.2017.1738

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 https://doi.org/10.21428/5e41a54a


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. https://www.pnas.org/content/115/2/E226  Discussed in Science Daily https://www.sciencedaily.com/releases/2018/01/180106103424.htm

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. https://doi.org/10.1073/pnas.1803245115

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. https://mbio.asm.org/content/9/6/e02104-18.long


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 https://doi.org/10.1093/gbe/evy099

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//doi.org/10.1007/s00248-018-1267-0  https://link.springer.com/article/10.1007%2Fs00248-018-1267-0


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. https://www.nature.com/articles/s41598-017-18687-y
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. https://www.nature.com/articles/s41567-017-0002-y
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). https://journals.aps.org/pre/abstract/10.1103/PhysRevE.97.050401

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) http://www.jbmethods.org/jbm/article/view/218

Boyd, M, F Rosenzweig, M Herron. (2018). Motility in multicellular Chlamydomonas reinhardtii (Chlamydomonadales, Chlorophyceae) PLoS One 13(1): e0192184. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5790280/pdf/pone.0192184.pdf

Herron, MD, WC Ratcliff, J Boswell, F Rosenzweig. (2018). Genetics of a de novo origin of undifferentiated multicellularity. Royal Society Open Science 5:180912. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6124120/pdf/rsos180912.pdf

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. https://www.biorxiv.org/content/10.1101/247361v2 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. https://academic.oup.com/nar/article/46/7/e42/4817401

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) https://www.nature.com/articles/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. https://doi.org/10.1016/j.cub.2018.01.009

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 https://www.nature.com/articles/s41559-018-0758-1
(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. https://www.biorxiv.org/content/early/2018/11/02/460113


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. https://academic.oup.com/jole/article/3/2/94/5035080


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. https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007324

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. https://doi.org/10.1073/pnas.1715996115.

Raynes, Y, PD Sniegowski, DM Weinreich. (201_). Migration promotes mutator alleles in subdivided populations. Evolution, accepted pending minor revision. https://doi.org/10.1111/evo.13681