Biology Department Publications, April 2018

| Publications

April 2018

  • Allen GE, Baker JJW. 2017. Scientific process and social issues in biology education. Switzerland : Springer.More book info.
  • Arp J, Götze S, Mukherji R, Mattern DJ, García-Altares M, Klapper M, Brock DA, Brakhage AA, Strassmann JE, Queller DC, Bardl B, Willing K, Peschel G, Stallforth P. 2018. Synergistic activity of cosecreted natural products from amoebae-associated bacteria. Proc Natl Acad Sci U S A 115(15):3758-3763. PubMed abstract & fulltext for subscribers.
  • Chen H-YS, Bandyopadhyay A, Pakrasi HB. 2018. Function, regulation and distribution of IsiA, a membrane-bound chlorophyll a-antenna protein in cyanobacteria. Photosynthetica 56(1):322–333. doi.org/10.1007/s11099-018-0787-7.
  • Gopalakrishnan S, Pakrasi HB, Maranas CD. 2018. Elucidation of Photoautotrophic Carbon Flux Topology in Synechocystis PCC 6803 using Genome-scale Carbon Mapping Models. Metab Eng 47:190-199. PubMed abstract & fulltext for subscribers.
  • Haswell E, Basu D, Hamilton ES, Maksaev G, Mixdorf M, Radin I, Richardson R, Schlegel AM, Schultz E, Wang Y. 2017. MscS-like Mechanosensitive Ion Channels: Modular Sensors and Reporters of Membrane Tension. Biophysical Journal 112(3):Supplement 1, p38a. doi.org/10.1016/j.bpj.2016.11.240 [free to read].
  • Hill NS, Zuke JD, Buske PJ, Chien AC, Levin PA. 2018. A nutrient-dependent division antagonist is regulated post-translationally by the Clp proteases in Bacillus subtilis. BMC Microbiol. 18(1):29. PubMed abstract & open access fulltext.
  • Holland CK, Berkovich DA, Kohn ML, Maeda H, Jez JM. 2018. Structural Basis for Substrate Recognition and Inhibition of Prephenate Aminotransferase from Arabidopsis. Plant J 94(2):304-314. PubMed abstract & fulltext for subscribers.
  • Hovanes KA, Harms KE, Gagnon PR, Myers JA, Elderd BD. 2018. Overdispersed Spatial Patterning of Dominant Bunchgrasses in Southeastern Pine Savannas. Am Nat 191(5):658-667. PubMed abstract & open access fulltext.
  • Jez JM. 2018. Introduction to the thematic minireview series: green biological chemistry. J Biol Chem293(14):5016-5017. PubMed abstract & fulltext for subscribers.
  • Kass JM, Vilela B, Aiello-Lammens ME, Muscarella R, Merow C, Anderson RP. 2018. WALLACE: A flexible platform for reproducible modeling of species niches and distributions built for community expansion. Methods in Ecology and Evolution 9(4):1151-1156. doi.org/10.1111/2041-210X.12945.
  • Khmelnitskiy A, Kell A, Reinot T, Saer RG, Blankenship RE, Jankowiak R. 2018. Corrigendum to “energy landscape of the intact and destabilized FMO antennas from C. tepidum and the L122Q mutant: Low temperature spectroscopy and modeling study” [Biochim. Biophys. Acta Bioenerg. 1859 (2018) 165-173].Biochim Biophys Acta 1859(5):409. PubMed citation & fulltext for subscribers.
  • Khmelnitskiy A, Saer RG, Blankenship RE, Jankowiak RJ. 2018. Excitonic Energy Landscape of the Y16F Mutant of the Chlorobium tepidum Fenna-Matthews-Olson (FMO) Complex: High Resolution Spectroscopic and Modeling Studies. J Phys Chem B 122(14):3734-3743. PubMed abstract & fulltext for subscribers.
  • Knoot CJ, Ungerer JL, Wangikar PP, Pakrasi HB. 2018. Cyanobacteria: promising biocatalysts for sustainable chemical production. J Biol Chem 293(14):5044-5052. PubMed abstract & fulltext for subscribers.
  • Lu Y, Goodson C, Blankenship RE, Gross ML. 2018. Primary and higher order structure of the reaction center from the purple phototrophic bacterium Blastochloris viridis: A test for native mass spectrometry. J Proteome Res 17(4):1615-1623. PubMed abstract & fulltext for subscribers.
  • Magdaong NCM, Blankenship RE. 2018. Photoprotective, excited-state quenching mechanisms in diverse photosynthetic organisms. J Biol Chem 293(14):5018-5025. PubMed abstract & fulltext for subscribers.
  • Ogren JI, Tong AL, Gordon SC, Chenu A, Lu Y, Blankenship RE, Cao JS, Schlau-Cohen GS. 2018. Impact of the lipid bilayer on energy transfer kinetics in the photosynthetic protein LH2. Chemical Science 9(12):3095-3104. doi.org/10.1039/c7sc04814a [open access]
  • Olsen KM, Li L-F. 2018. Rooting for new sources of natural rubber. National Science Review 5(1):89-89. doi.org/10.1093/nsr/nwx101c [open access].
  • Pant B, Park M, Ojha GP, Park J, Kuk YS, Lee EJ, Kim HY, Park SJ. 2018. Carbon nanofibers wrapped with zinc oxide nano-flakes as promising electrode material for supercapacitors. J Colloid Interface Sci 522:40-47. PubMed abstract & fulltext for subscribers.
  • Rengasamy K, Ranaivoarisoa T, Singh R, Bose A. 2018. An insoluble iron complex coated cathode enhances direct electron uptake by Rhodopseudomonas palustris TIE-1. Bioelectrochemistry 122:164-173. PubMed abstract & fulltext for subscribers.
  • Stadnytskyi V, Orf GS, Blankenship RE, Savikhin S. 2018. Near shot-noise limited time-resolved circular dichroism pump-probe spectrometer. Rev Sci Instrum 89(3):033104. PubMed abstract & fulltext for subscribers.
  • Sutherland MC, Jarodsky JM, Ovchinnikov S, Baker D, Kranz RG. 2018. Structurally Mapping Endogenous Heme in the CcmCDE Membrane Complex for Cytochrome c Biogenesis. J Mol Biol 430(8):1065-1080. PubMed abstract & fulltext for subscribers.
  • Üstün S, Hafrén A, Liu Q, Marshall RS, Minina EA, Bozhkov P, Vierstra RD, Hofius D. 2018. Bacteria exploit autophagy for proteasome degradation and enhanced virulence in plants. Plant Cell 30(3):668-685. PubMed abstract & fulltext for subscribers.
  • Vallone A, D’Alessandro S, Brogi S, Brindisi M, Chemi G, Alfano G, Lamponi S, Lee SG, Jez JM, Koolen KJM, Dechering KJ, Saponara S, Fusi F, Gorelli B, Taramelli D, Parapini S, Caldelari R, Campiani G, Gemma S, Butini S. 2018. Antimalarial agents against both sexual and asexual parasites stages: structure-activity relationships and biological studies of the Malaria Box compound 1-[5-(4-bromo-2-chlorophenyl)furan-2-yl]-N-[(piperidin-4-yl)methyl]methanamine (MMV019918) and analogues. Eur J Med Chem 150:698-718. PubMed abstract & fulltext for subscribers.
  • Wang X, Wiegand T, Anderson-Teixeira KJ, Bourg TA, Hao Z, Howe R, Jin G, Orwig DA, Spasojevic MJ, Wang S, Wolf A, Myers JA. 2018. Ecological drivers of spatial community dissimilarity, species replacement and species nestedness across temperate forests. Global Ecology and Biogeography 27(5):581-592. doi.org/10.1111/geb.12719.
  • Xin Y, Shi Y, Niu T, Wang Q, Niu W, Huang X, Ding W, Yang L, Blankenship RE, Xu X, Sun F. 2018. Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote. Nat Commun9(1):1568. PubMed abstract & open access fulltext.
  • Zheng XM, Gong T, Ou HL, Xue D, Qiao W, Wang J, Liu S, Yang Q, Olsen KM. 2018. Genome-wide association study of rice grain width variation. Genome 61(4):233-240. PubMed abstract & fulltext for subscribers.
  • Allen GE, Baker JJW. 2017. Scientific process and social issues in biology education. Switzerland : Springer.More book info.
  • Arp J, Götze S, Mukherji R, Mattern DJ, García-Altares M, Klapper M, Brock DA, Brakhage AA, Strassmann JE, Queller DC, Bardl B, Willing K, Peschel G, Stallforth P. 2018. Synergistic activity of cosecreted natural products from amoebae-associated bacteria. Proc Natl Acad Sci U S A 115(15):3758-3763. PubMed abstract & fulltext for subscribers.
  • Chen H-YS, Bandyopadhyay A, Pakrasi HB. 2018. Function, regulation and distribution of IsiA, a membrane-bound chlorophyll a-antenna protein in cyanobacteria. Photosynthetica 56(1):322–333. doi.org/10.1007/s11099-018-0787-7.
  • Gopalakrishnan S, Pakrasi HB, Maranas CD. 2018. Elucidation of Photoautotrophic Carbon Flux Topology in Synechocystis PCC 6803 using Genome-scale Carbon Mapping Models. Metab Eng 47:190-199. PubMed abstract & fulltext for subscribers.
  • Haswell E, Basu D, Hamilton ES, Maksaev G, Mixdorf M, Radin I, Richardson R, Schlegel AM, Schultz E, Wang Y. 2017. MscS-like Mechanosensitive Ion Channels: Modular Sensors and Reporters of Membrane Tension. Biophysical Journal 112(3):Supplement 1, p38a. doi.org/10.1016/j.bpj.2016.11.240 [free to read].
  • Hill NS, Zuke JD, Buske PJ, Chien AC, Levin PA. 2018. A nutrient-dependent division antagonist is regulated post-translationally by the Clp proteases in Bacillus subtilis. BMC Microbiol. 18(1):29. PubMed abstract & open access fulltext.
  • Holland CK, Berkovich DA, Kohn ML, Maeda H, Jez JM. 2018. Structural Basis for Substrate Recognition and Inhibition of Prephenate Aminotransferase from Arabidopsis. Plant J 94(2):304-314. PubMed abstract & fulltext for subscribers.
  • Hovanes KA, Harms KE, Gagnon PR, Myers JA, Elderd BD. 2018. Overdispersed Spatial Patterning of Dominant Bunchgrasses in Southeastern Pine Savannas. Am Nat 191(5):658-667. PubMed abstract & open access fulltext.
  • Jez JM. 2018. Introduction to the thematic minireview series: green biological chemistry. J Biol Chem293(14):5016-5017. PubMed abstract & fulltext for subscribers.
  • Kass JM, Vilela B, Aiello-Lammens ME, Muscarella R, Merow C, Anderson RP. 2018. WALLACE: A flexible platform for reproducible modeling of species niches and distributions built for community expansion. Methods in Ecology and Evolution 9(4):1151-1156. doi.org/10.1111/2041-210X.12945.
  • Khmelnitskiy A, Kell A, Reinot T, Saer RG, Blankenship RE, Jankowiak R. 2018. Corrigendum to “energy landscape of the intact and destabilized FMO antennas from C. tepidum and the L122Q mutant: Low temperature spectroscopy and modeling study” [Biochim. Biophys. Acta Bioenerg. 1859 (2018) 165-173].Biochim Biophys Acta 1859(5):409. PubMed citation & fulltext for subscribers.
  • Khmelnitskiy A, Saer RG, Blankenship RE, Jankowiak RJ. 2018. Excitonic Energy Landscape of the Y16F Mutant of the Chlorobium tepidum Fenna-Matthews-Olson (FMO) Complex: High Resolution Spectroscopic and Modeling Studies. J Phys Chem B 122(14):3734-3743. PubMed abstract & fulltext for subscribers.
  • Knoot CJ, Ungerer JL, Wangikar PP, Pakrasi HB. 2018. Cyanobacteria: promising biocatalysts for sustainable chemical production. J Biol Chem 293(14):5044-5052. PubMed abstract & fulltext for subscribers.
  • Lu Y, Goodson C, Blankenship RE, Gross ML. 2018. Primary and higher order structure of the reaction center from the purple phototrophic bacterium Blastochloris viridis: A test for native mass spectrometry. J Proteome Res 17(4):1615-1623. PubMed abstract & fulltext for subscribers.
  • Magdaong NCM, Blankenship RE. 2018. Photoprotective, excited-state quenching mechanisms in diverse photosynthetic organisms. J Biol Chem 293(14):5018-5025. PubMed abstract & fulltext for subscribers.
  • Ogren JI, Tong AL, Gordon SC, Chenu A, Lu Y, Blankenship RE, Cao JS, Schlau-Cohen GS. 2018. Impact of the lipid bilayer on energy transfer kinetics in the photosynthetic protein LH2. Chemical Science 9(12):3095-3104. doi.org/10.1039/c7sc04814a [open access]
  • Olsen KM, Li L-F. 2018. Rooting for new sources of natural rubber. National Science Review 5(1):89-89. doi.org/10.1093/nsr/nwx101c [open access].
  • Pant B, Park M, Ojha GP, Park J, Kuk YS, Lee EJ, Kim HY, Park SJ. 2018. Carbon nanofibers wrapped with zinc oxide nano-flakes as promising electrode material for supercapacitors. J Colloid Interface Sci 522:40-47. PubMed abstract & fulltext for subscribers.
  • Rengasamy K, Ranaivoarisoa T, Singh R, Bose A. 2018. An insoluble iron complex coated cathode enhances direct electron uptake by Rhodopseudomonas palustris TIE-1. Bioelectrochemistry 122:164-173. PubMed abstract & fulltext for subscribers.
  • Stadnytskyi V, Orf GS, Blankenship RE, Savikhin S. 2018. Near shot-noise limited time-resolved circular dichroism pump-probe spectrometer. Rev Sci Instrum 89(3):033104. PubMed abstract & fulltext for subscribers.
  • Sutherland MC, Jarodsky JM, Ovchinnikov S, Baker D, Kranz RG. 2018. Structurally Mapping Endogenous Heme in the CcmCDE Membrane Complex for Cytochrome c Biogenesis. J Mol Biol 430(8):1065-1080. PubMed abstract & fulltext for subscribers.
  • Üstün S, Hafrén A, Liu Q, Marshall RS, Minina EA, Bozhkov P, Vierstra RD, Hofius D. 2018. Bacteria exploit autophagy for proteasome degradation and enhanced virulence in plants. Plant Cell 30(3):668-685. PubMed abstract & fulltext for subscribers.
  • Vallone A, D’Alessandro S, Brogi S, Brindisi M, Chemi G, Alfano G, Lamponi S, Lee SG, Jez JM, Koolen KJM, Dechering KJ, Saponara S, Fusi F, Gorelli B, Taramelli D, Parapini S, Caldelari R, Campiani G, Gemma S, Butini S. 2018. Antimalarial agents against both sexual and asexual parasites stages: structure-activity relationships and biological studies of the Malaria Box compound 1-[5-(4-bromo-2-chlorophenyl)furan-2-yl]-N-[(piperidin-4-yl)methyl]methanamine (MMV019918) and analogues. Eur J Med Chem 150:698-718. PubMed abstract & fulltext for subscribers.
  • Wang X, Wiegand T, Anderson-Teixeira KJ, Bourg TA, Hao Z, Howe R, Jin G, Orwig DA, Spasojevic MJ, Wang S, Wolf A, Myers JA. 2018. Ecological drivers of spatial community dissimilarity, species replacement and species nestedness across temperate forests. Global Ecology and Biogeography 27(5):581-592. doi.org/10.1111/geb.12719.
  • Xin Y, Shi Y, Niu T, Wang Q, Niu W, Huang X, Ding W, Yang L, Blankenship RE, Xu X, Sun F. 2018. Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote. Nat Commun9(1):1568. PubMed abstract & open access fulltext.
  • Zheng XM, Gong T, Ou HL, Xue D, Qiao W, Wang J, Liu S, Yang Q, Olsen KM. 2018. Genome-wide association study of rice grain width variation. Genome 61(4):233-240. PubMed abstract & fulltext for subscribers.
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