Search Google Appliance


Recent Publications

Since our new facility opened in 2010, CLEE faculty and students have published over 80 papers and counting...

Bartlett Lab 

Gründberg, S., C Reich, ME Zeller, MS Bartlett, and M Thomm (2010).  Rearrangement of the RNA polymerase unit H and the lower jaw in archaeal elongation complexes.  Nuc. Acids Res. 38:1950-63.

 

Buckley Lab 

Buckley, B.A. (in press). Rapid change in shallow water fish species composition in a  historically stable Antarctic environment. Antarctic Sci.

Kelley, A.L, deRivera, C.E. and Buckley, B.A. (in press). Cold tolerance of the invasive Carcinus maenas in the East Pacific: Molecular mechanisms and implications for range expansion in a changing climate. Bioinvasions

Sleadd, I.M. and Buckley, B.A. (2012). The CCAAT/Enhancer-binding protein δ (C/EBP-δ) transcription factor is heat-inducible in the cold-adapted Antarctic fish Trematomus bernacchii. Polar Biol.

Detrich III, H.W., B.A. Buckley, D.F. Doolittle, C.D. Jones, and Lockhart S.J. (2012).  Sub-Antarctic and high Antarctic notothenioid fishes: Ecology and adaptational biology revealed by the ICEFISH 2004 Cruise of TVIB Nathaniel B. Palmer. Oceanography 25(3):184–187.

Buckley, B.A. (2011). Acute heat stress and thermal acclimation induce CCAAT/Enhancer-Binding Protein delta (C/EBP-δ) in the goby Gillichthys mirabilis. J. Comp. Physiol. B. 181(6), 773-780.

Kelley, A.L., deRivera, C.E. and Buckley, B.A. (2011). Intraspecific variation in thermotolerance and morphology of the invasive European green crab, Carcinus maenas, on the west coast of North America. J. Exp. Mar. Biol. Ecol. 409, 70-78.

Rodriguez del Rey, Z., Granek, E.F. and Buckley, B.A. (2011). Expression of HSP70 in Mytilus californianus following exposure to caffeine. J. Ecotoxicol. 20(4), 855-861.  

 

Eppley and Rosenstiel Labs 

Rogers, S. and Eppley. S. (2012).  Testing inter-sexual competition along a phosphorus gradient in a dioecious grass. Botany, 90: 704-710.

Rosenstiel TN, Shortlidge EE, Melynchenko AN, Pankow JF, & Eppley SM.  (2012) Sex-specific volatile compounds influence microarthropod-mediated fertilization of moss.  Nature. 489: 431-433.

Shortlidge, E. Rosenstiel, TNEppley, E. (2012). Desiccation tolerance in bryophyte sperm. New Phytologist 194: 741-750.

Monson RK, Jones RT, Rosenstiel TN, Schnitzler JP. (2012) Why only some plants emitisoprenePlant Cell and Environment, (doi: 10.1111/pce.12015)

Porter W, Barsanti K, Baughman E, and Rosenstiel TN. (2012)  Considering the air quality impacts of bioenergy crop production: a case study involving Arundo donax.  Environmental Science and Technology, 46: 9777-9784.

Sivy TL, Fall R, Rosenstiel TN. (2012)  Evidence for isoprenoid precursor toxicity in Bacillus subtilisBiosciences, Biotechnology, Biochemistry. 75:2376-2383.

Pankow JF, Luo W, Melnychenko AN*, Barsanti KC, Isabelle LM, Chen C, Guenther AB, and Rosenstiel TN (2011). Volatilizable biogenic organic compounds (VBOCs) with two dimensional gas chromatography-time of flight mass spectrometry (GC × GC-TOFMS): sampling methods, VBOC complexity, and chromatographic retention data. Atmos. Meas. Techniques., 4, 3647-3684. 

Eppley, SMRosenstiel, TN, Graves, CB, Garcia, E. (2011). Limits to sexual reproduction in geothermal bryophytes.Int.l J. of Plant Sciences. 172: 870-978.

Stark, LR, McLetchie, DN, and Eppley, SM. 2010. Sex ratios and the shy male hypothesis in the moss Bryum argenteum. Bryologist 113: 788-797.

Mercer C and Eppley, SM. 2010. Intra- versus inter-sexual competition in the dioecious grass, Distichlis spicata.  Oecologia 164: 657-664

Lee L, Rosenstiel TN, and Eppley, SM. 2010. Variation of photoperiod response in moss gametangia formation. Bryologist 113: 673-678

 

Iwata-Reuyl Lab

Yu CH, Luo J, Iwata-Reuyl D, Olsthoorn RC. (2013).  Exploiting preQ(1) Riboswitches To Regulate Ribosomal Frameshifting." ACS Chem Biol. 2013 Jan 25. [Epub ahead of print]

Deutsch C, El Yacoubi B, de Crécy-Lagard V, Iwata-Reuyl D. (2012).  Biosynthesis of Threonylcarbamoyl Adenosine (t6A), a Universal tRNA Nucleoside. J. Biol. Chem. 287(17):13666-73 (PMID: 22378793, PMCID: PMC3340167)

Phillips G, Grochowski LL, Bonnett S, Xu H, Bailly M, Blabt-Haas C, El Yacoubi B, Iwata-Reuyl D, White RH, de Crécy-Lagard V. (2012).  Functional promiscuity of the COG0720 family.” ACS Chem. Biol., 7(1):197-209 (PMID: 21999246, PMCID: PMC3262898)

Chikwana VM, Stec B, Lee BW, de Crécy-Lagard V, Iwata-Reuyl D, Swairjo MA. (2012).  Structural basis of biological nitrile reduction.” J. Biol. Chem., 287(36):30560-70 (PMID: 22787148, PMCID: PMC3436371)

Phillips G, Swairjo MA, Gaston KW, Bailly M, Limbach PA, Iwata-Reuyl D, de Crécy-Lagard V. 2012.  Diversity of archaeosine synthesis in crenarchaeota.” ACS Chem. Biol., 7(2):300-5 (DOI: 10.1021/cb200361w)

El Yacoubi B, Hatin I, Deutsch C, Kahveci T, Rousset JP, Iwata-Reuyl D, Murzin AG, de Crécy-Lagard V. (2011).  A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification." EMBO J., 30(5):882-93 (PMID: 21285948, PMCID: PMC3049207)

Rakovich T., Boland C, Bernstein I., Chikwana V. M., Iwata-Reuyl D, Kelly V. P. (2011).  Queuosine deficiency in eukaryotes compromises tyrosine production through increased tetrahydrobiopterin oxidation.  J. Biol. Chem., 286(22):19354-19363

Phillips G, Chikwana VM, Maxwell A, El-Yacoubi B, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2010).  Discovery and characterization of an amidinotransferase involved in the modification of archaeal tRNA. J. Biol. Chem., 285(17):12706-13. (PMID: 20129918, PMCID: PMC2857094).
 

 

Lehman Lab 

Diaz Arenas C, Lehman, N (2013).  Partitioning the fitness components of RNA populations evolving in vitro.  PLoS ONE, 8(12): e84454.

Vaidya, N., Walker, SI, Lehman, N (2013).  Recycling of Informational Units Leads to Selection of Replicators in a Prebiotic Soup.  Chemistry & Biology, 20(2): 24-1252. doi:10.1016/j.chembiol.2013.01.007.

Larson BC, Jensen RP, Lehman N (2012). The chemical origin of behavior is rooted in abiogenesis. Life 2:313–322.

Vaidya, N, Manapat, ML, ChenIA, Xulvi-Brunet, R, Hayden, EJ & Lehman, N (2012) Spontaneous network formation amongcooperative RNA replicators.  Nature.  Online early at doi:10.1038/nature11549 .

Lehman N, Hayden EJ (2011). Template-directed RNA polymerization: the taming of the milieu. Chem. BioChem (“Highlights”) 12: 2727–2728.


Lindgren (CLEE Lab Manager) 

De Silva-Dávila, R, Hochberg, FG, Lindgren, AR, Del Carmen Franco-Gordo, M.  (2013)  Paralarval development, abundance, and distribution of Pterygioteuthis hoylei (Cephalopoda: Oegopsida: Pyroteuthidae) in the Gulf of California, Mexico.  Molluscan Res.  (2013).

Oakley, TH. Wolfe, JM, Lindgren, AR, Zaharoff, AK. (2013) Phylotranscriptomics to bring the understudied into the fold: monophyletic Ostracoda, fossil placement and pancrustacean phylogeny.  Mol. Biol. Evol. Jan; 30(1): 175-188.

Lindgren AR, Pankey, MS, Hochberg, FG & Oakley TH.  (2012)  A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment. BMC Evol. Biol. 12:129.  doi:10.1186/1471-2148-12-129. 

Albertin CB, Bonnaud L, Brown CT, Crookes-Goodson WJ, da Fonseca RR, Di Cristo C, Dilkes BP, Edsinger-Gonzales E, Freeman RM Jr, Hanlon RT, Koenig KM, Lindgren AR, Martindale MQ, Minx P, Moroz LL, Nödl MT, Nyholm SV, Ogura A, Pungor JR, Rosenthal JJ, Schwarz EM, Shigeno S, Strugnell JM, Wollesen T, Zhang G, Ragsdale CW.  (2012).  Cephalopod Genomics: A plan for strategies and organization.  Stand Genomic Sci. 2012 Oct 10;7(1):175-88. doi: 10.4056/sigs.3136559

 

Perona Lab 

Perona JJ & Hadd A.  Structural diversity and protein engineering of the aminoacyl-tRNA synthetases. (2012). Biochemistry 51, 8705-8729.

Bhaskaran H, Rodríguez-Hernández A & Perona JJ.  (2012). Kinetics of tRNA folding monitored by aminoacylation.  RNA 18, 569-580.
 
Oza JP, Sowers KR & Perona JJ.  (2012). Linking energy production and protein synthesis in hydrogenotrophic methanogens.  Biochemistry 51, 2378-2389.
 
Grant TD, Snell EH, Luft JR, Quartley E, Corretore S, Wolfley JR, Snell ME, Hadd A, Perona JJ, Phizicky EM & Grayhack EJ. (2012).  Structural conservation of an ancient tRNA sensor in eukaryotic glutaminyl-tRNA synthetase.  Nucleic Acids Res. 40, 3723-3731.
 
Cvetesic N, Perona JJ & Gruic-Sovulj I. (2012).  Kinetic partitioning between synthetic and editing pathways in class I aminoacyl-tRNA synthetases occurs at both pre-transfer and post-transfer hydrolytic steps.  J. Biol. Chem. 287, 25381-25394.

Hancock S, Hiller DA, Perona JJ & Jen-Jacobson L. (2011) The energetic,contribution of induced electrostatic asymmetry to DNA bending by a site-specific protein.  J. Mol. Biol. 406, 285-312.

Rodríguez-Hernández A & Perona JJ. (2011).  Heat maps for intramolecular communication in an RNP enzyme encoding glutamine.  Structure 19, 386-396.

Bhaskaran H & Perona JJ.  (2011).  Two-step aminoacylation of tRNA without channeling in Archaea.  J. Mol. Biol. 411, 854-869.

 Menezes S, Kirk G, Krivos KL, Apolinario EE, Reich NO, Sowers KR,Limbach P & Perona JJ.  (2011) Enzymatic synthesis of tRNA m2G6 in thermophilic methanogens by the novel tRNA methyltransferase Trm14.  Nucleic Acids Res. 39, 7641-7655.


Podrabsky Lab

Crawshaw, L.I., Podrabsky, JE. (2011). Temperature Preference - BehavioralResponses to Temperature in Fishes. In: Encyclopedia of Fish Physiology. From Genome to Environment. (ed. A.P. Farrell). Academic Press.

Pri-Tal, B. M., Blue, S., Pau F. K.-Y., Podrabsky, JE. (2011). Hormonal componentsof altered developmental pathways in the annual killifish, Autrofundulus limnaeus. DOI:10.1016/jgcen.2011.08.016.

Carey, H.V., Martin, S.L., Horowitz, B.A., Yan, L., Bailey, S.M., Podrabsky, JE, Storz, J.F.,Ortiz, R.M., Wong, R.P., Lathrop, D.A. (2012). Elucidating Nature's Solutions to Heart, Lung, and Blood Diseases and Sleep Disorders. Circ Res. 110: 915-921.

Meller, CL, Meller R, Simon RP, Culpepper KM, & Podrabsky JE. Cell cycle arrest associated with anoxia-induced quiescence, anoxic preconditioning, and embryonic diapause in embryos of the annual killifish Austrofundulus limnaeus.  J. Comp. Physiol. B.  (2012).

Podrabsky JE & Culpepper KM.  Cell cycle regulation during development and dormancy in embryos of the annual killifish Austrofundulus limnaeus.  Cell Cycle 11(9): 1697-1794 (2012).

Podrabsky, JE, Menze, MA, Hand, SC. (2012). Long-Term Survival of AnoxiaDespite Rapid ATP Decline in Embryos of the Annual Killifish Austrofundulus imnaeusJ Exp Zool A. 317: 524–532.

Podrabsky, JE, Riggs, CL, and Duerr, JM. (2012). Anoxia Tolerance During Vertebrate Development - Insights from Studies on the Annual Killifish Austrofundulus limnaeus, In: Anoxia, Pamela Padilla (Ed.), ISBN: 978-953-307-664-5.

  

Reysenbach Lab

Reysenbach, A-L, I. Wagner, Y. Liu, C. Sislak and S. Schouten. (Accepted). Laodiceanella acidophila gen. nov., sp. nov., a moderate thermoacidophilic Thermotogales from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol.

Podar MK, S Makarova, DE Graham, Y Wolf, E Koonin and A-L Reysenbach (Submitted). Insights into archaeal evolution and symbiosis from the genomes of a Nanoarchaeon and its crenarchaeal host from Yellowstone National Park. Biology Direct

Gibson RA, MTJ van der Meer, EC Hopmans, A-L Reysenbach, S Schouten, JS Sinninghe Damsté (2013). Comparison of intact polar lipid with microbial community composition of vent deposits of the Rainbow and Lucky Strike hydrothermal fields. Geobiology. 11: 72–85.

Hamamura N, J Meneghin, and A-L Reysenbach. (2013).  Comparative community gene expression analysis of Aquificales-dominant geothermal springs. Environ. Microbiol. DOI: 10.1111/1462-2920.12061

Slobodkin AI, A-L. Reysenbach, GB Slobodkina, TV Kolganova, NA Kostrikina, EA Bonch-Osmolovskaya. 2012. Dissulfuribacter thermophilus gen. nov., sp. nov. a novel thermophilic autotrophic sulfur-disproportionating deeply-branching delta-proteobacterium from a deep-sea hydrothermal vent of the Eastern Lau Spreading Center Int J Syst Evol Microbiol ijs.0.046938-0; published ahead of print September 28, 2012, doi:10.1099/ijs.0.046938-0

Tivey MK, E Becker, R Beinart, CR Fisher, PR. Girguis, CH Langmuir, PJ Michael, A-L Reysenbach. .(2012).  Links from mantle to microbe at the Lau Integrated Study Site: Insights from a back-arc spreading center. Oceanography. 25(1):62–77.

Flores, GE, ID Wagner, Y Liu and A-L Reysenbach (2012) Distribution, abundance, and diversity patterns of the thermoacidophilic “Deep-sea Hydrothermal Vent Euryarchaeota 2” (DHVE2) Frontiers in Extreme Microbiology. doi: 10.3389/fmicb.2012.00047

Flores, GE, Shakya M, Meneghin J, Yang ZK, Seewald JS, Wheat CG, Podar, M and Reysenbach, A-L. (2012). Inter-field variability in the microbial communities of hydrothermal vent deposits from a back-arc basin. Geobiology 10: 333-346.

Resing J, A-L Reysenbach et al., 2011. Active submarine eruption of boninite in the northeastern Lau Basin. Nature Geoscience 4:799–806.

Maddison DR, R Guralnick, A Hill, A-L Reysenbach and LA McDade. 2011. Ramping up biodiversity discovery via online quantum contributions. Trends  in Ecology and Evolution 27, 72-77.

Slobodkin, AI, A-L. Reysenbach, GA Slobodkina, RV. Baslerov, N Kostrikina, I Wagner, and E Bonch-Osmolovskaya. 2011. Thermosulfurimonas dismutans gen. nov., sp. nov. a novel extremely thermophilic sulfur-disproportionating bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol doi:10.1099/ijs.0.034397-0

Slobodkina, GB,  A-L Reysenbach, A Panteleeva, N Kostrikina, I Wagner, E Bonch-Osmolovskaya, AI Slobodkin. 2011. Deferrisoma camini gen. nov., sp. nov. a novel moderately thermophilic dissimilatory Fe(III)-reducing bacterium from a deep-sea hydrothermal vent that forms a distinct phylogenetic branch in Deltaproteobacteria. Int J Syst Evol Microbiol doi:10.1099/ijs.0.038372-0

Flores GE, Hunter RC, Liu Y and Reysenbach, A-L. 2011. Hippea jasoniae sp. nov. and Hippea alviniae sp. nov., Thermoacidophilic Deltaproteobacteria Isolated From Deep-Sea Hydrothermal Vent Deposits. Int J Syst Evol Microbiol doi:10.1099/ijs.0.033001-0

Flores GE and Reysenbach, A.-L. (2011) Hydrothermal environments, marine. In Encyclopedia of Earth Science Series: Encyclopedia of Geobiology, J. Reitner, and V. Thiel (ed.), Springer, Dordrecht, The Netherlands, p. 456-466.

Podosokorskaya OA,  IV Kublanov, A-L Reysenbach, TV Kolganova, and EA Bonch-Osmolovskaya. 2010. Thermosipho affectus sp. nov., a novel thermophilic anaerobic cellulolytic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent. Int J Syst Evol Microbiol, doi:10.1099/ijs.0.025197-0

Flores GE,  JH Campbell, JD Kirshtein, J Meneghin, M Podar, J. Steinberg, JS Seewald, MK Tivey, MA Voytek, ZK Yang, and A-L Reysenbach. (2011). Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge. Environ Microbiol 13. no. doi: 10.1111/j.1462-2920.2011.02463.x.

Inskeep, W. P., D. B. Rusch, Z. J. Jay, M. J. Herrgard, M. A. Kozubal, T. H. Richardson, R. E. Macur, N. Hamamura, R. Jennings, B. W. Fouke, A. L. Reysenbach, F. Roberto, M. Young, A. Schwartz, E. S. Boyd, J. H. Badger, E. J. Mathur, A. C. Ortmann, M. Bateson, G. Geesey, and M. Frazier. (2011) Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. PLoS One 5:e9773.

Caldwell S, Y Liu, I Ferrera, TJ Beveridge, A-L Reysenbach. (2010). Thermocrinis minervae sp. nov., a hydrogen- and sulfur-oxidizing, thermophilic member of the Aquificales from a Costa Rican terrestrial hot spring. Int J Syst Evol Microbiol 60: 338 – 343.

 

Stedman Lab 

Stedman, K (2013).  Mechanisms for RNA capture by ssDNA viruses: Grand Theft RNA!  J. Mol. Evol. 76(6): 359-364/ doi: 10.1007/s00239-01309569-9.

Laidler, J, Shugart, A, Cady, S, Bahjat, KS, Stedman, KM (2013).  Reversible Inactivation and Desiccation Tolerance of Silicified Viruses.  J. Virology, 87(24): 13927-13929.  doi: 10.1128/JVI.02825-13. 

KM Stedman, Kosmicki N, and Diemer, GS (2013.  Codon usage frequency of RNA virus genomes from high temperature acidic envirnment metagenomes. J. Virology 87/3 1919  doi: 10.1128/JVI.02610-12

Diemer, J and Stedman, KM (2012).  A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses. Biology Direct, 2012; 7 (1): 13 DOI: 10.1186/1745-6150-7-13.

Ceballos, RM, Marceau, CD, Marceau, JO, Morris, S, Clore, AJ, Stedman, KM (2012).  Differential Virus Host-Ranges of the Fuselloviridae of Hyperthermophilic Archaea: Implications for Evolution in Extreme Environments. Frontiers in Microbiology. 3: 295 doi:10.3389/fmicb.2012.00295

Iverson, E, and Stedman, KM (2012). A genetic study of SSV1, the prototypical fusellovirus. Frontiers in Microbiology. 3: 200. doi: 10.3389/fmicb.2012.00200.

Stedman, KM (2012).  Fusellovirus, Fuselloviridae. In The Springer Index of Viruses, Second Edition. Editors: C. Tidona and G. Darai. Springer Verlag, Heidelberg. (doi:10.1007/978-0-387-95919-1) 

DeYoung, M., Thayer, M., van der Oost, J, Stedman, KM (2011). Growth phase dependent gene regulation in vivo in Sulfolobus solfataricus. FEMS Microbiology Letters, 321/2, 92-99. Published online 6 June 2011. (doi: 10.1111/j.1574-6968.2011.02313.x)

Stedman, KM (2011).  Virus – Long Entry. In: Encyclopedia of Astrobiology (M.Gargaud, R. Amils, J. Cernicharo Quintanilla, H.J. Cleaves II, W.M. Irvine, D.L. Pinti, and M. Viso. Eds). 1745-1748, Springer, Heidelberg.

J. Laidler & Stedman, KM (2010) Virus Silicification under Simulated Hot Spring Conditions. Astrobiology10/6. 569-576. (On the Cover).  Editor’s “key” selection

Stedman, M, Porter, R, and Dyall-Smith, M (2010) The isolation of viruses infecting Archaea, pp57-64. In: S.W. Wilhelm, M.G. Weinbauer and C.A. Suttle [eds], Manual of Aquatic Viral Ecology. Waco, American Society for Limnology and Oceanography doi:10.4319/mave.2010.978-0-9845591-0-7