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2017 Publications

Copley, SD. Shining a light on enzyme promiscuity. Current Opinion in Structural Biology. 2017 47, 167-175.

Honsa ES*, Cooper VS*, Mhaissen MH, Frank M, Shakera J, Iverson I, Rubnitz J, Hayden RT, Lee RE, Rock CO, Tuomanen EI, Wolf J, Rosch JW. RelA mutant Enterococcus faecium with multi-antibiotic tolerance arising in an immunocompromised host. MBio. 2017 Jan 3;8(1). pii: e02124-16. doi: 10.1128/mBio.02124-16 *equal contributions.

Haidar G, Philips NJ, Shields RK, Snyder D, Cheng S, Potoski BA, Doi Y, Hao B, Press EG, Cooper VS, Clancy CJ, Nguyen MH. Ceftolozane-tazobactam for the treatment of multidrug-resistant Pseudomonas aeruginosa infections: Clinical effectiveness and evolution of resistance. Clin Infect Dis. 2017 cix182. 2017. doi: 10.1093/cid/cix182

Peeters C, Cooper VS, Hatcher PJ, Verheyde B, Carlier A, Vandamme P. Comparative genomics of Burkholderia multivorans, a ubiquitous pathogen with a highly conserved genomic structure. PLoS ONE. 2017. doi: 10.1371/pone/017619

Pankey MA, Foxall RL, Ster IM, Perry LA, Schuster BM, Donner RA, Coyle M, Cooper VS, Whistler CA. Host-selected mutations converging on a global regulator drive an adaptive leap by bacteria to symbiosis. eLife 2017 Apr 27;6. pii: e24414. doi: 10.7554/eLife.24414

Hassan AA, Maldonado RF, dos Santos SC, Di Lorenzo F, Silipo A, Coutinho CP, Cooper VS, Molinaro A, Valvano MA, Sá-Correia I. Structure of O-Antigen and Hybrid Biosynthetic Locus in Burkholderia cenocepacia clonal variants recovered from a Cystic Fibrosis patient. Frontiers in Microbiology. 2017 8(1027). doi: 10.3389/fmicb.2017.01027

Lee N, Le Sage V, Nanni AV, Snyder DJ, Cooper VS, Lakdawala SS. Genome-wide analysis of influenza viral RNA and nucleoprotein association. Nucleic Acids Res. 2017 gkx584. doi: 10.1093/nar/gkx584

Xu F, Gonzalez-Escalona N, Drees KP, Sebra RP, Cooper VS, Jones SH, Whistler CA. Parallel evolution of two clades of a major Atlantic endemic Vibrio parahaemolyticus pathogen lineage by independent acquisition of related pathogenicity islands. Appl Environ Microbiol. 2017. PMID: 28687650

Guo Y, Tomich AD, McElheny CL, Cooper VS, Tait-Kamradt A, Wang M, Hu F, Rice LB, Sluis-Cremer N, Yohei Doi. High-level fosfomycin resistance in vancomycin-resistant Enterococcus 14 faecium. Emerg Infect Dis. 2017 Nov.

Leung LM, Cooper VS, Rasko DA, Guo Q, Pacey MP, McElheny CL, Mettus RT, Yoon SH, Goodlett DR, Ernst RK, Doi Y. Structural modification of LPS in colistin-resistant, KPC-producing Klebsiella pneumoniae. J Antimicrob Chemother. 2017. PubMed PMID: 28961916

Lucas, A., Ito R, Mustapha MM, McElheny CL, Mettus R, Bowler SL, Kantz SF, Pacey MP, Pasculle AW, Cooper VS, and Doi Y. 2017. Frequency and mechanisms of spontaneous fosfomycin non-susceptibility observed upon disk diffusion testing of Escherichia coli. J Clin Microbiol. Dec 26;56(1). pii: e01368-17. doi: 10.1128/JCM.01368-17. PMID: 29093108

Gerrish PJ, Hengartner N. Inferring the distribution of fitness effects of newly-arising mutations using samples taken from evolving populations in real time. In C Martin-Vide (Ed.) Algorithms for Computational Biology. (pp. 103-114), 2017 Heidelberg: Springer.

Gerrish PJ, Hengartner N. A Fourier framework for solving the inverse problem of characterizing the mutational input to evolution. J Comp Biology. 2017 (invited).

Gerrish PJ, Ferreira CP. A thermodynamic limit constrains complexity and primitive social

function. International Journal of Astrobiology (submitted).

Nozaki H, Mahakham W, Athibaf S, Yamamoto K, Takusagawa M, Misumi O, Herron MD, Rosenzweig F, Kawachi M. Rediscovery of the “ancestral Volvox” species: Morphology and phylogenetic position of Pleodorina sphaerica (Volvocales, Chlorophyceae) from Thailand. Phycologia. 2017 56:469–475. doi: 10.2216/17-3.1

Herron MD. Cells, colonies, and clones: individuality in the volvocine algae. in S. Lidgard & L. Nyhart (eds.) Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives. (pp. 63-83). 2017 Chicago, University of Chicago Press.

Hanschen, ER, MD Herron, J. J. Wiens, P. J. Ferris, H. Nozaki, & R. E. Michod. 2017. Repeated evolution and reversibility of self-fertilization in the volvocine green algae. Evolution, (in press). doi: 10.1111/evo.13394.

Kacar B, Ge X, Sanya S, Gaucher EA. Experimental Evolution of Escherichia coli harboring an ancient translation protein. J Mol Evol. 2017. doi: 10.1007/s00239-017-9781-0

Kacar B, Guy L, Smith E, Baross J. Paleophenotype reconstruction of carbon fixation proteins as a window into historic biological states. Phil Trans A. 2017. doi: org/10.1101/16403

Kacar B, Garmendia E, Tuncbag N, Andersson DI, Hughes D. Functional constraints on replacing an essential gene with its ancient and modern homologs. mBio. 2017. doi: 10.1128/mBio.01276-17

Kacar B, Hanson-Smith V, Adam ZR, Boekelheide N. Reconstruction and dynamic modeling of ancestral rubisco proteins. Geobiology. 2017 1-13. doi: 10.1111/gbi.12243

Walker SI, Bains W, Cronin L, DasSarma S, Danielache S, Goldman S, Kacar B, Kiang NY, Lenardic A, Reinhard CT and others. Exoplanet biosignatures: Future directions. Astrobiology. 2017. arXiv:1705.08071v3

Keeling PJ and McCutcheon JP. Endosymbiosis: the feeling is not mutual. J Theor Biol. 2017. 434:75-79.

Łukasik P, Nazario K, Van Leuven JT, Campbell MA, Meyer M, Michalik A, Pessacq P, Simon C, Veloso C, McCutcheon JP. Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas. Proc Natl Acad Sci USA. 2017. 115: E226-E235.

Husnik F, McCutcheon JP. Functional horizontal gene transfer from bacteria to eukaryotes. Nat Rev Microbiol. 2017. 16:67–79.

Campbell MA, Lukasik P, Simon C, McCutcheon JP. Idiosyncratic genome degradation in a bacterial endosymbiont of periodical cicadas. Curr Biol. 2017. 27:3568–3575.

Vanderpool D, Bracewell R, McCutcheon JP. Know your farmer: ancient origins and multiple independent domestications of ambrosia beetle fungal cultivars. Mol Ecol. doi:10.1111/mec.14394

Miller SR. An appraisal of the enzyme stability-activity trade-off. Evolution. 2017. doi: 10.1111/evo.13275

Sano EB, Wall CA, Hutchins PR, Miller SR. Ancient balancing selection on heterocyst function in a cosmopolitan cyanobacterium. Nature Ecol Evol (accepted).

de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram Ö, Benocci T, Braus- Stromeyer SA, Caldana C, Cánovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, Dos Santos RA, Damásio AR, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hildén KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kraševec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, MacCabe A, Mäkelä MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnár ÁP, Mulé G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AF, Ramón A, Rauscher S, Record E, Riaño-Pachón DM, Robert V, Röhrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schütze T, Sepčić K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JV, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pócsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol. 2017. 18(1):28.

E. Libby, Driscoll WW. and Ratcliff WC*. Programmed cell death can increase the efficacy of microbial bet-hedging. Scientific Reports (in press).

Sherlock G, Petrov DA. Seeking Goldilocks during evolution of drug resistance. PLoS Biology. 2017. 15(2): e2001872.

Zhu YO, Sherlock G, Petrov DA. Extremely rare polymorphisms in Saccharomyces cerevisiae allow inference of the mutational spectrum. PLoS Genetics. 2017.13(1): e1006455.

Jaffe M, Sherlock G, Levy SF. iSeq: A New double-barcode method for detecting dynamic genetic interactions in yeast. G3. 2017 7(1):143-153.

Aggeli, D., Karas, V.O., Sinnott-Armstrong, N., Varghese, V., Shafer, R.W., Greenleaf, W.J.*, and Sherlock, G.* (2018). A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery. Nucleic Acids Research (in press).

Li, Y., Venkataram, S., Agarwala, A., Dunn, B., Petrov, D.A.*, Sherlock, G.*, and Fisher, D.S.* (2018). Hidden complexity of yeast adaptation under simple evolutionary conditions. Current Biology (in press).

Krishnamurthy S, Smith E. Solving moment hierarchies for Chemical Reaction Networks. Journal of Physics A: Mathematical and Theoretical. 2017. arXiv:1702.01364

Singh T, Hyun M, Sniegowski PD. Evolution of mutation rates in hypermutable populations of Escherichia coli propagated at very small effective population size. Biology Letters. 2017. doi: 10.1098/rsbl.2016.0849

Pénisson S, Singh T, Sniegowski P, Gerrish P. Dynamics and fate of beneficial mutations under lineage contamination by linked deleterious mutations. Genetics 2017 doi: 10.1534/genetics.116.194597/-/DC1

Hicks L, van der Graaf L, Childress J, Cook E, Schmidt K, Rosenzweig F, Kroll E. Streamlined preparation of genomic DNA in agarose plugs for pulsed-field gel electrophoresis. Journal of Biological Methods (accepted).

Smith E. and Krishnamurthy, S. Flows, scaling, and the control of moment hierarchies for stochastic chemical reaction networks. Physical Review E (accepted).

Yang, DD, G Billebeck, JJ Zhang, F Rosenzweig, J-M Francois .Deciphering the origin, evolution and physiological function of the subtelomeric aryl-alcohol dehydrogenase gene family in the yeast Saccharomyces cerevisiae. Applied Env Microbiol. 2017. Dec 15; (84(1). Pii: e01553-17. doi: 10.1128/AEM.01553-17