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A Guide to Biology Resources

Publications from WU Biology Department - 2019

A live version of this list, including links to more information and full-text access, is available on PubMed.

  1. Zelle K, Vernier C, Liang X, Halloran S, Millar J, Ben-Shahar Y. A pleiotropic chemoreceptor facilitates the coupling of pheromonal signal perception and production. bioRxiv. 2019:124305.

  2. Zarrouk A, Smach MA, Hafsa J, Sghaier R, Majdoub H, Hammami M, et al. Effects of Carpobrotus edulis Extract on Oxidative Stress and 158N Oligodendrocyte Death. Biomed Environ Sci. 2019;32(4):291-9.

  3. Yan LL, Zaher HS. How do cells cope with RNA damage and its consequences? J Biol Chem. 2019;294(41):15158-71.

  4. Wolf BM, Blankenship RE. Far-red light acclimation in diverse oxygenic photosynthetic organisms. Photosynth Res. 2019;142(3):349-59.

  5. Wendt KE, Pakrasi HB. Genomics Approaches to Deciphering Natural Transformation in Cyanobacteria. Frontiers in Microbiology. 2019;10(1259).

  6. Weisz DA, Johnson VM, Niedzwiedzki DM, Shinn MK, Liu H, Klitzke CF, et al. A novel chlorophyll protein complex in the repair cycle of photosystem II. Proc Natl Acad Sci U S A. 2019;116(43):21907-13.

  7. Wedger MJ, Topp CN, Olsen KM. Convergent evolution of root system architecture in two independently evolved lineages of weedy rice. New Phytol. 2019;223(2):1031-42.

  8. Wang SH, Elgin SCR. The impact of genetic background and cell lineage on the level and pattern of gene expression in position effect variegation. Epigenetics Chromatin. 2019;12(1):70.

  9. Walker LM, Cedeno-Sanchez M, Carbonero F, Herre EA, Turner BL, Wright SJ, et al. The Response of Litter-Associated Myxomycetes to Long-Term Nutrient Addition in a Lowland Tropical Forest. J Eukaryot Microbiol. 2019;66(5):757-70.

  10. Walck-Shannon EM, Cahill MJ, McDaniel MA, Frey RF. Participation in Voluntary Re-quizzing Is Predictive of Increased Performance on Cumulative Assessments in Introductory Biology. CBE Life Sci Educ. 2019;18(2):ar15.

  11. Vernier CL, Krupp JJ, Marcus K, Hefetz A, Levine JD, Ben-Shahar Y. The cuticular hydrocarbon profiles of honey bee workers develop via a socially-modulated innate process. eLife. 2019;8:e41855.

  12. Ungerer J, Wendt KE, Hendry JI, Maranas CD, Pakrasi HB. Reply to Zhou and Li: Plasticity of the genomic haplotype of Synechococcus elongatus leads to rapid strain adaptation under laboratory conditions. Proc Natl Acad Sci U S A. 2019;116(10):3946-7.

  13. Thomas EN, Simms CL, Keedy HE, Zaher HS. Insights into the base-pairing preferences of 8-oxoguanosine on the ribosome. Nucleic Acids Res. 2019;47(18):9857-70.

  14. Taylor I, Baer J, Calcutt R, Walker JC. Hypermorphic SERK1 Mutations Function via a SOBIR1 Pathway to Activate Floral Abscission Signaling. Plant Physiol. 2019;180(2):1219-29.

  15. Stroud JT, Giery ST, Outerbridge M, Feeley KJ. Ecological character displacement alters the outcome of priority effects during community assembly. Ecology. 2019;100(8):e02727.

  16. Strassmann JE, Queller DC. ECOLOGICAL DETERMINANTS OF SOCIAL. The Genetics Of Social Evolution. 2019:81.

  17. Stingaciu LR, O'Neill HM, Liberton M, Pakrasi HB, Urban VS. Influence of Chemically Disrupted Photosynthesis on Cyanobacterial Thylakoid Dynamics in Synechocystis sp. PCC 6803. Sci Rep. 2019;9(1):5711.

  18. Stella J, Croney C. Coping Styles in the Domestic Cat (Animals (Basel). 2019;9(6).

  19. Squires AH, Dahlberg PD, Liu H, Magdaong NCM, Blankenship RE, Moerner WE. Single-molecule trapping and spectroscopy reveals photophysical heterogeneity of phycobilisomes quenched by Orange Carotenoid Protein. Nat Commun. 2019;10(1):1172.

  20. Snyder AE, Harmon-Threatt AN. Reduced water-availability lowers the strength of negative plant-soil feedbacks of two Asclepias species. Oecologia. 2019;190(2):425-32.

  21. Simms CL, Yan LL, Qiu JK, Zaher HS. Ribosome Collisions Result in +1 Frameshifting in the Absence of No-Go Decay. Cell Rep. 2019;28(7):1679-89.e4.

  22. Si F, Le Treut G, Sauls JT, Vadia S, Levin PA, Jun S. Mechanistic Origin of Cell-Size Control and Homeostasis in Bacteria. Curr Biol. 2019;29(11):1760-70.e7.

  23. Segev O, Pezaro N, Rovelli V, Rybak O, Templeton AR, Blaustein L. Phenotypic plasticity and local adaptations to dissolved oxygen in larvae fire salamander (Salamandra infraimmaculata). Oecologia. 2019;190(4):737-46.

  24. Scott TJ, Queller DC. Long-term evolutionary conflict, Sisyphean arms races, and power in Fisher's geometric model. Ecology and Evolution. 2019;9(19):11243-53.

  25. Sarkar D, Mueller TJ, Liu D, Pakrasi HB, Maranas CD. A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism. PLOS Computational Biology. 2019;15(1):e1006692.

  26. Saer RG, Schultz RL, Blankenship RE. The influence of quaternary structure on the stability of Fenna-Matthews-Olson (FMO) antenna complexes. Photosynth Res. 2019;140(1):39-49.

  27. Reznick DN, Losos J, Travis J. From low to high gear: there has been a paradigm shift in our understanding of evolution. Ecol Lett. 2019;22(2):233-44.

  28. Ranaivoarisoa TO, Singh R, Rengasamy K, Guzman MS, Bose A. Towards sustainable bioplastic production using the photoautotrophic bacterium Rhodopseudomonas palustris TIE-1. J Ind Microbiol Biotechnol. 2019;46(9-10):1401-17.

  29. Queller DC. Pleiotropy and synergistic cooperation. PLOS Biology. 2019;17(6):e3000320.

  30. Queller D. What life is for: a commentary on Fromhage and Jennions. Proc Biol Sci. 2019;286(1905):20191060.

  31. Powers SK, Holehouse AS, Korasick DA, Schreiber KH, Clark NM, Jing H, et al. Nucleo-cytoplasmic Partitioning of ARF Proteins Controls Auxin Responses in Arabidopsis thaliana. Mol Cell. 2019;76(1):177-90.e5.

  32. Porath HT, Hazan E, Shpigler H, Cohen M, Band M, Ben-Shahar Y, et al. RNA editing is abundant and correlates with task performance in a social bumblebee. Nat Commun. 2019;10(1):1605.

  33. Pizano C, Kitajima K, Graham JH, Mangan SA. Negative plant-soil feedbacks are stronger in agricultural habitats than in forest fragments in the tropical Andes. Ecology. 2019:e02850.

  34. Peng Z, Ben-Shahar Y. Codon clusters with biased synonymous codon usage represent hidden functional domains in protein-coding DNA sequences. bioRxiv. 2019:530345.

  35. Papandreou C, Bulló M, Díaz-López A, Martínez-González MA, Corella D, Castañer O, et al. High sleep variability predicts a blunted weight loss response and short sleep duration a reduced decrease in waist circumference in the PREDIMED-Plus Trial. Int J Obes (Lond). 2019.

  36. Niedzwiedzki DM, Wolf BM, Blankenship RE. Excitation energy transfer in the far-red absorbing violaxanthin/vaucheriaxanthin chlorophyll a complex from the eustigmatophyte alga FP5. Photosynth Res. 2019;140(3):337-54.

  37. Niedzwiedzki DM, Bar-Zvi S, Blankenship RE, Adir N. Mapping the excitation energy migration pathways in phycobilisomes from the cyanobacterium Acaryochloris marina. Biochim Biophys Acta Bioenerg. 2019;1860(4):286-96.

  38. Neik TX, Chai JY, Tan SY, Sudo MPS, Cui Y, Jayaraj J, et al. When West Meets East: The Origins and Spread of Weedy Rice Between Continental and Island Southeast Asia. G3 (Bethesda). 2019;9(9):2941-50.

  39. Nagarajan A, Zhou M, Nguyen AY, Liberton M, Kedia K, Shi T, et al. Proteomic Insights into Phycobilisome Degradation, A Selective and Tightly Controlled Process in The Fast-Growing Cyanobacterium Synechococcus elongatus UTEX 2973. Biomolecules. 2019;9(8).

  40. Michniewicz M, Ho CH, Enders TA, Floro E, Damodaran S, Gunther LK, et al. TRANSPORTER OF IBA1 Links Auxin and Cytokinin to Influence Root Architecture. Dev Cell. 2019;50(5):599-609.e4.

  41. McLoughlin F, Kim M, Marshall RS, Vierstra RD, Vierling E. HSP101 Interacts with the Proteasome and Promotes the Clearance of Ubiquitylated Protein Aggregates. Plant Physiol. 2019;180(4):1829-47.

  42. Marshall RS, Hua Z, Mali S, McLoughlin F, Vierstra RD. ATG8-Binding UIM Proteins Define a New Class of Autophagy Adaptors and Receptors. Cell. 2019;177(3):766-81.e24.

  43. Mandakova T, Pouch M, Brock JR, Al-Shehbaz IA, Lysak MA. Origin and Evolution of Diploid and Allopolyploid Camelina Genomes Were Accompanied by Chromosome Shattering. Plant Cell. 2019;31(11):2596-612.

  44. Ma Z, Turrigiano GG, Wessel R, Hengen KB. Cortical Circuit Dynamics Are Homeostatically Tuned to Criticality In Vivo. Neuron. 2019;104(4):655-64.e4.

  45. Lu X, Selvaraj B, Ghimire-Rijal S, Orf GS, Meilleur F, Blankenship RE, et al. Neutron and X-ray analysis of the Fenna-Matthews-Olson photosynthetic antenna complex from Prosthecochloris aestuarii. Acta Crystallogr F Struct Biol Commun. 2019;75(Pt 3):171-5.

  46. Lou W, Wolf BM, Blankenship RE, Liu H. Cu(+) Contributes to the Orange Carotenoid Protein-Related Phycobilisome Fluorescence Quenching and Photoprotection in Cyanobacteria. Biochemistry. 2019;58(28):3109-15.

  47. Liu PY, Cheng AC, Huang SW, Chang HW, Oshida T, Yu HT. Variations in Gut Microbiota of Siberian Flying Squirrels Correspond to Seasonal Phenological Changes in Their Hokkaido Subarctic Forest Ecosystem. Microb Ecol. 2019;78(1):223-31.

  48. Liu H, Weisz DA, Zhang MM, Cheng M, Zhang B, Zhang H, et al. Phycobilisomes Harbor FNR<sub>L</sub> in Cyanobacteria. mBio. 2019;10(2):e00669-19.

  49. Liu H, Blankenship RE. On the interface of light-harvesting antenna complexes and reaction centers in oxygenic photosynthesis. Biochim Biophys Acta Bioenerg. 2019;1860(11):148079.

  50. Lin PC, Pakrasi HB. Engineering cyanobacteria for production of terpenoids. Planta. 2019;249(1):145-54.

  51. Lin CG, Chao JL, Tsai HK, Chalker D, Yao MC. Setting boundaries for genome-wide heterochromatic DNA deletions through flanking inverted repeats in Tetrahymena thermophile. Nucleic Acids Res. 2019;47(13):7143-4.

  52. Lin CG, Chao JL, Tsai HK, Chalker D, Yao MC. Setting boundaries for genome-wide heterochromatic DNA deletions through flanking inverted repeats in Tetrahymena thermophila. Nucleic Acids Res. 2019;47(10):5181-92.

  53. Liberton M, Bandyopadhyay A, Pakrasi HB. Enhanced Nitrogen Fixation in a <em>glgX</em>-Deficient Strain of <em>Cyanothece</em> sp. Strain ATCC 51142, a Unicellular Nitrogen-Fixing Cyanobacterium. Applied and Environmental Microbiology. 2019;85(7):e02887-18.

  54. Levin PA, Taheri-Araghi S. One is Nothing without the Other: Theoretical and Empirical Analysis of Cell Growth and Cell Cycle Progression. J Mol Biol. 2019;431(11):2061-7.

  55. Leitner N, Ben‐Shahar Y. The neurogenetics of sexually dimorphic behaviors from a post‐developmental perspective. Genes, Brain and Behavior. 2019.

  56. Lee SG, Salomon E, Yu O, Jez JM. Molecular basis for branched steviol glucoside biosynthesis. Proc Natl Acad Sci U S A. 2019;116(26):13131-6.

  57. Kumar R, Lee SG, Augustine R, Reichelt M, Vassao DG, Palavalli MH, et al. Molecular Basis of the Evolution of Methylthioalkylmalate Synthase and the Diversity of Methionine-Derived Glucosinolates. Plant Cell. 2019;31(7):1633-47.

  58. Ko B, D'Alessandro J, Douangkeomany L, Stumpf S, deButts A, Blodgett J. Construction of a new integrating vector from actinophage varphiOZJ and its use in multiplex Streptomyces transformation. J Ind Microbiol Biotechnol. 2019.

  59. Knoot CJ, Pakrasi HB. Diverse hydrocarbon biosynthetic enzymes can substitute for olefin synthase in the cyanobacterium Synechococcus sp. PCC 7002. Sci Rep. 2019;9(1):1360.

  60. Knoot CJ, Khatri Y, Hohlman RM, Sherman DH, Pakrasi HB. Engineered Production of Hapalindole Alkaloids in the Cyanobacterium Synechococcus sp. UTEX 2973. ACS Synth Biol. 2019;8(8):1941-51.

  61. Karthikeyan R, Singh R, Bose A. Microbial electron uptake in microbial electrosynthesis: a mini-review. J Ind Microbiol Biotechnol. 2019;46(9-10):1419-26.

  62. Kapheim KM, Jones BM, Søvik E, Stolle E, Waterhouse RM, Bloch G, et al. Changes in brain microRNAs are associated with social evolution in bees. bioRxiv. 2019:730317.

  63. Jing H, Strader LC. Interplay of Auxin and Cytokinin in Lateral Root Development. Int J Mol Sci. 2019;20(3).

  64. Jez JM. Plant nitrilase: a new job for an old enzyme. Biochem J. 2019;476(7):1105-7.

  65. Jassas M, Goodson C, Blankenship RE, Jankowiak R, Kell A. On Excitation Energy Transfer within the Baseplate BChl a-CsmA Complex of Chloroflexus aurantiacus. J Phys Chem B. 2019;123(46):9786-91.

  66. Jaspan VN, Taye ME, Carle CM, Chung JJ, Chalker DL. Boundaries of eliminated heterochromatin of Tetrahymena are positioned by the DNA-binding protein Ltl1. Nucleic Acids Res. 2019;47(14):7348-62.

  67. Itakura AK, Chan KX, Atkinson N, Pallesen L, Wang L, Reeves G, et al. A Rubisco-binding protein is required for normal pyrenoid number and starch sheath morphology in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A. 2019;116(37):18445-54.

  68. Huang H, McLoughlin KE, Sorkin ML, Burgie ES, Bindbeutel RK, Vierstra RD, et al. PCH1 regulates light, temperature, and circadian signaling as a structural component of phytochrome B-photobodies in Arabidopsis. Proc Natl Acad Sci U S A. 2019;116(17):8603-8.

  69. Hu Y, Qi Y, Stumpf SD, D'Alessandro JM, Blodgett JAV. Bioinformatic and Functional Evaluation of Actinobacterial Piperazate Metabolism. ACS Chem Biol. 2019;14(4):696-703.

  70. Holland CK, Westfall CS, Schaffer JE, De Santiago A, Zubieta C, Alvarez S, et al. Brassicaceae-specific Gretchen Hagen 3 acyl acid amido synthetases conjugate amino acids to chorismate, a precursor of aromatic amino acids and salicylic acid. J Biol Chem. 2019;294(45):16855-64.

  71. Hill A, Jain P, Ben-Shahar Y. The Drosophila ERG channel seizure plays a role in the neuronal homeostatic stress response. bioRxiv. 2019:521005.

  72. Hendry JI, Gopalakrishnan S, Ungerer J, Pakrasi HB, Tang YJ, Maranas CD. Genome-Scale Fluxome of Synechococcus elongatus UTEX 2973 Using Transient (13)C-Labeling Data. Plant Physiol. 2019;179(2):761-9.

  73. Hendry JI, Bandyopadhyay A, Srinivasan S, Pakrasi HB, Maranas CD. Metabolic model guided strain design of cyanobacteria. Curr Opin Biotechnol. 2019;64:17-23.

  74. Hayama R, Yang P, Valverde F, Mizoguchi T, Furutani-Hayama I, Vierstra RD, et al. Ubiquitin carboxyl-terminal hydrolases are required for period maintenance of the circadian clock at high temperature in Arabidopsis. Sci Rep. 2019;9(1):17030.

  75. Haselkorn TS, DiSalvo S, Miller JW, Bashir U, Brock DA, Queller DC, et al. The specificity of Burkholderia symbionts in the social amoeba farming symbiosis: Prevalence, species, genetic and phenotypic diversity. Molecular Ecology. 2019;28(4):847-62.

  76. Guzman MS, Rengasamy K, Binkley MM, Jones C, Ranaivoarisoa TO, Singh R, et al. Phototrophic extracellular electron uptake is linked to carbon dioxide fixation in the bacterium Rhodopseudomonas palustris. Nat Commun. 2019;10(1):1355.

  77. Gillespie MAK, Alfredsson M, Barrio IC, Bowden JJ, Convey P, Culler LE, et al. Status and trends of terrestrial arthropod abundance and diversity in the North Atlantic region of the Arctic. Ambio. 2019.

  78. Gemperline DC, Marshall RS, Lee KH, Zhao Q, Hu W, McLoughlin F, et al. Proteomic analysis of affinity-purified 26S proteasomes identifies a suite of assembly chaperones in Arabidopsis. J Biol Chem. 2019;294(46):17570-92.

  79. Geist KS, Strassmann JE, Queller DC. Family quarrels in seeds and rapid adaptive evolution in Arabidopsis. Proc Natl Acad Sci U S A. 2019;116(19):9463-8.

  80. Garcia-Porta J, Irisarri I, Kirchner M, Rodriguez A, Kirchhof S, Brown JL, et al. Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards. Nat Commun. 2019;10(1):4077.

  81. Garcia-Pichel F, Zehr JP, Bhattacharya D, Pakrasi HB. What's in a name? The case of cyanobacteria. J Phycol. 2019.

  82. Garcia JR, Larsen TJ, Queller DC, Strassmann JE. Fitness costs and benefits vary for two facultative Burkholderia symbionts of the social amoeba, Dictyostelium discoideum. Ecology and Evolution. 2019;9(17):9878-90.

  83. Gadagkar R, Gordon D, Keller L, Michod R, Queller D, Robinson GE, et al. Insights and opportunities in insect social behavior. Current Opinion in Insect Science. 2019;34:ix-xx.

  84. Fristoe TS, Botero CA. Alternative ecological strategies lead to avian brain size bimodality in variable habitats. Nat Commun. 2019;10(1):3818.

  85. Eck JL, Stump SM, Delavaux CS, Mangan SA, Comita LS. Evidence of within-species specialization by soil microbes and the implications for plant community diversity. Proc Natl Acad Sci U S A. 2019;116(15):7371-6.

  86. Cloyed CS, Dell AI. Resource distribution and internal factors interact to govern movement of a freshwater snail. Proc Biol Sci. 2019;286(1911):20191610.

  87. Butman JA, Suga N. Inhibitory mechanisms shaping delay-tuned combination-sensitivity in the auditory cortex and thalamus of the mustached bat. Hear Res. 2019;373:71-84.

  88. Burkart GM, Dixit R. Microtubule bundling by MAP65-1 protects against severing by inhibiting the binding of katanin. Mol Biol Cell. 2019;30(13):1587-97.

  89. Brock JR, Mandakova T, Lysak MA, Al-Shehbaz IA. Camelinaneglecta (Brassicaceae, Camelineae), a new diploid species from Europe. PhytoKeys. 2019(115):51-7.

  90. Blanco L, Lago J, González V, Paz B, Rambla-Alegre M, Cabado AG. Occurrence of Tetrodotoxin in Bivalves and Gastropods from Harvesting Areas and Other Natural Spaces in Spain. Toxins (Basel). 2019;11(6).

  91. Balkunde R, Foroughi L, Ewan E, Emenecker R, Cavalli V, Dixit R. Mechanism of microtubule plus-end tracking by the plant-specific SPR1 protein and its development as a versatile plus-end marker. J Biol Chem. 2019;294(44):16374-84.