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Biology

Publications from WU Biology Department - 2016 - first author M-Z

WU faculty names are in bold

  1. McDaniel SL, Zweifel E, Harris PK, Yao MC, Cole ES, Chalker DL. 2016. DRH1, a p68-related RNA helicase, is required for chromosome breakage in Tetrahymena. Biol Open 2016 : doi: 10.1242/bio.021576. PubMed abstract & open access fulltext.
  2. McDonnell MM, Burkhart SE, Stoddard JM, Wright ZJ, Strader LC, Bartel B. 2016. The Early-Acting Peroxin PEX19 Is Redundantly Encoded, Farnesylated, and Essential for Viability in Arabidopsis thaliana. PLoS One 11(1):e0148335. PubMed abstract & open access fulltext.
  3. Machingura M, Salomon E, Jez JM, Ebbs SD. 2016. The ß-Cyanoalanine Synthase Pathway: Beyond Cyanide Detoxification. Plant Cell Environ 39(10):2329-41. PubMed abstract & fulltext for subscribers.
  4. Mackinder LC, Meyer MT, Mettler-Altmann T, Chen VK, Mitchell MC, Caspari O, Freeman Rosenzweig ES, Pallesen L, Reeves G, Itakura A, Roth R, Sommer F, Geimer S, Mühlhaus T, Schroda M, Goodenough U, Stitt M, Griffiths H, Jonikas MC. 2016. A repeat protein links Rubisco to form the eukaryotic carbon-concentrating organelle. Proc Natl Acad Sci U S A 113(21):5958-63. PubMed abstract & fulltext for subscribers.
  5. McLoughlin F, Basha E, Fowler ME, Kim M, Bordowitz J, Katiyar-Agarwal S, Vierling E. 2016. Class I and II Small Heat Shock Proteins Together with HSP101 Protect Protein Translation Factors during Heat Stress. Plant Physiol 172(2):1221-1236. PubMed abstract & freely available fulltext.
  6. Magdaong NC, Niedzwiedzki DM, Goodson C, Blankenship RE. 2016. Carotenoid-to-Bacteriochlorophyll Energy Transfer in the LH1-RC Core Complex of a Bacteriochlorophyll b-Containing Purple Photosynthetic Bacterium Blastochloris viridis. J Phys Chem B 120(23):5159-71. PubMed abstract & fulltext for subscribers.
  7. Majumder EL, Olsen JD, Qian P, Collins AM, Hunter CN, Blankenship RE. 2016. Supramolecular organization of photosynthetic complexes in membranes of Roseiflexus castenholzii. Photosynth Res 127(1):117-30. PubMed abstract & fulltext for subscribers.
  8. Marshall RS, McLoughlin F. Vierstra RD. 2016. Autophagic Turnover of Inactive 26S Proteasomes in Yeast Is Directed by the Ubiquitin Receptor Cue5 and the Hsp42 Chaperone. Cell Rep 16(6):1717-32. PubMed abstract & open access fulltext |In the news: Big trash pickup.
  9. Melo D, Porto A, Cheverud JM, Marroig G. 2016. Modularity: Genes, Development, and Evolution. Annual Review of Ecology, Evolution, and Systematics 47:463-486. dx.doi.org/10.1146/annurev-ecolsys-121415-032409.
  10. Meyer JR, Dobias DT, Medina SJ, Servilio L, Gupta A, Lenski RE. 2016. Ecological speciation of bacteriophage lambda in allopatry and sympatry. Science 354(6317):1301-1304. PubMed abstract & fulltext for subscribers.
  11. Mueller TJ, Welsh EA, Pakrasi HB, Maranas CD. 2016. Identifying regulatory changes to facilitate nitrogen fixation in the non-diazotroph Synechocystis sp. PCC 6803. ACS Synth Biol 5(3):250-8. PubMed abstract & fulltext for subscribers.
  12. Murthy AC, Fristoe TS, Burger JR. 2016. Homogenizing effects of cities on North American winter bird diversity. Ecosphere 7(1):10.1002/ecs2.1216. Open access fulltext.
  13. Muto C, Ishikawa R, Olsen KM, Kawano K, Bounphanousay C, Matoh T, Sato YI. 2016. Genetic diversity of the wx flanking region in rice landraces in northern Laos. Breed Sci 66(4):580-590. PubMed abstract & freely available fulltext.
  14. Myers JA, LaManna JA. The promise and pitfalls of beta diversity in ecology and conservation. Journal of Vegetation Science 27(6):1081–1083. dx.doi.org/10.1111/jvs.12482.
  15. Niedzwiedzki DM, Tronina T, Liu H, Staleva H, Komenda J, Sobotka R, Blankenship RE, Polívka T. 2016. Carotenoid-induced non-photochemical quenching in the cyanobacterial chlorophyll synthase-HliC/D complex. Biochim Biophys Acta 1857(9):1430-1439. PubMed abstract & fulltext for subscribers.
  16. Niedzwiedzki DM, Hunter CN, Blankenship RE. 2016. Evaluating the Nature of So-Called S*-State Feature in Transient Absorption of Carotenoids in Light Harvesting Complex 2 (LH2) From Purple Photosynthetic Bacteria. J Phys Chem B 120(43):11123-11131. PubMed abstract & fulltext for subscribers.
  17. Noh S, Marshall JL. 2016. Sorted gene genealogies and species- specific nonsynonymous substitutions point to putative postmating prezygotic isolation genes in Allonemobius crickets.Peer J 4:e1678. Open access fulltext.
  18. Oberle B, Milo AM, Myers JA, Walton ML, Young DF, Zanne AE. 2016. Direct estimates of downslope deadwood movement over 30 years in a temperature forest illustrate impacts of treefall on forest ecosystem dynamics. Canadian Journal of Forest Research 46(3):351-361. dx.doi.org/10.1139/cjfr-2015-0348. [WU does not have access]
  19. Orf GS, Saer RG, Niedzwiedzki DM, Zhang H, McIntosh CL, Schultz JW, Mirica LM, Blankenship RE. 2016. Evidence for a cysteine-mediated mechanism of excitation energy regulation in a photosynthetic antenna complex. Proc Natl Acad Sci U S A 113(31):E4486-93. PubMed abstract & fulltext for subscribers | In the news: Controlling light: New protection for photosynthetic organisms.
  20. Paliulis LV, Laakso MM, Santisteban MS, Leung W, Elgin SC. 2016. A bioinformatics curriculum that teaches gene structure is associated with learning gains in beginning college students. Molecular Biology of the Cell 27:meeting abstract P27. Open PDF and scroll to P27.
  21. Palmer JL, Blake S, Wellehan JF Jr, Childress AL, Deem SL. 2016. Clinical Mycoplasma sp. Infections in Free-living Three-toed Box Turtles ( Terrapene carolina triunguis) in Missouri, USA. J Wildl Dis 52(2):378-82. PubMed abstract & fulltext for subscribers.
  22. Pan J, Saer R, Lin S, Beatty JT, Woodbury NW. 2016. Electron Transfer in Bacterial Reaction Centers with the Photoactive Bacteriopheophytin Replaced by a Bacteriochlorophyll through Coordinating Ligand Substitution. Biochemistry 55(35):4909-18. PubMed abstract & fulltext for subscribers.
  23. Pierson WE, Hoffer ED, Keedy HE, Simms CL, Dunham CM, Zaher HS. 2016. Uniformity of Peptide Release Is Maintained by Methylation of Release Factors. Cell Rep 17(1):11-8. PubMed abstract & open access fulltext.
  24. Plavskin Y, Nagashima A, Perroud PF, Hasebe M, Quatrano RS, Atwal GS, Timmermans MC. 2016. Ancient trans-Acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response. Dev Cell 36(3):276-289. PubMed abstract & fulltext for subscribers.
  25. Porto A, Schmelter R, VandeBerg JL, Marroig G, Cheverud JM. 2016. Evolution of the Genotype-to-Phenotype Map and the Cost of Pleiotropy in Mammals. Genetics 204(4):1601-1612. PubMed abstract & fulltext for subscribers.
  26. Powers SK, Strader LC. 2016. Up in the air: Untethered Factors of Auxin Response. F1000Res 5:133 PubMed abstract & open access fulltext.
  27. Prigge M, Greenham K, Zhang Y, Santner A, Castillejo C, Mutka AM, O'Malley RC, Ecker JR, Kunkel BN, Estelle M. 2016. The Arabidopsis Auxin Receptor F-box proteins AFB4 and AFB5 are Required for Response to the Synthetic Auxin Picloram. G3 (Bethesda) 6(5):1383-1390. PubMed abstract & open access fulltext.
  28. Pusadee T, Jamjod S, Rerkasem B, Schaal BA. 2016. Life-history traits and geographical divergence in wild rice (Oryza rufipogon) gene pool in Indochina Peninsula region. Annals of Applied Biology 168(1):52–65. dx.doi.org/10.1111/aab.12242. [WU does not subscribe]
  29. Queller DC. 2016. Kin Selection and Its Discontents. Philosophy of Science 83(5):861-872. dx.doi.org/10.1086/687870.
  30. Queller DC, Strassmann JE. 2016. Problems of multi-species organisms: endosymbionts to holobionts. Biology & Philosophy 31(6):855–873 dx.doi.org/10.1007/s10539-016-9547-x.
  31. Queller DC. 2016. The Theory of Inclusive Fitness: A review of Social Evolution and Inclusive Fitness Theory: An Introduction. Quarterly Review of Biology 91(3):343-347. Abstract & fulltext for subscribers.
  32. Raven PH. 2016. I. Our World and Pope Francis’ Encyclical, Laudato si’ (part of Four Commentaries on the Pope’s Message on Climate Change and Income Inequality) Quarterly Review of Biology 91(3):247-260. Freely available fulltext.
  33. Rinaldi MA, Patel AB, Park J, Lee K, Strader LC, Bartel B. 2016. The Roles of ß-Oxidation and Cofactor Homeostasis in Peroxisome Distribution and Function in Arabidopsis thaliana. Genetics 204(3):1089-1115. PubMed abstract & fulltext for subscribers.
  34. Rosenwald AG, Pauley MA, Welch L, Elgin SCR, Wright R, Blum J. 2016. The CourseSource Bioinformatics Learning Framework. [letter to editor] CBE-Life Sciences Education 15(1):10.1187/cbe.15-10-0217. Open access fulltext.
  35. Ross TG, Barrett CF, Soto Gomez M, Lam VKY, Henriquez CL, Les DH, Davis JI, Cuenca A, Petersen G, Seberg O, Thadeo M, Givnish TJ, Conran J, Stevenson DW, Graham SW. 2016. Plastid phylogenomics and molecular evolution of Alismatales. Cladistics 32(2):160-178. dx.doi.org/10.1111/cla.12133.
  36. Rubenstein DR, Botero CA, Lacey EA. 2016. Discrete but variable structure of animal societies leads to the false perception of a social continuum. R Soc Open Sci 3(5):160147. PubMed abstract & open access fulltext.
  37. Ryals R, Eviner VT, Stein C, Suding KN, Silver WL. 2016. Grassland compost amendments increase plant production without changing plant communities. Ecosphere 7(3):10.1002/ecs2.1270. Open access fulltext.
  38. Rytz TC, Miller MJ, Vierstra RD. 2016. Purification of SUMO Conjugates from Arabidopsis for Mass Spectrometry Analysis. Methods Mol Biol 1475:257-281. Abstract & fulltext for subscribers.
  39. Saer R, Orf GS, Lu X, Zhang H, Cuneo MJ, Myles DA, Blankenship RE. 2016. Perturbation Of Bacteriochlorophyll Molecules In Fenna-Matthews-Olson Protein Complexes Through Mutagenesis Of Cysteine Residues. Biochim Biophys Acta 1857(9):1455-1463. PubMed abstract & fulltext for subscribers.
  40. Saha R, Liu D, Hoynes-O'Connor A, Liberton M, Yu J, Bhattacharyya-Pakrasi M, Balassy A, Zhang F, Moon TS, Maranas CD, Pakrasi HB. 2016. Diurnal Regulation of Cellular Processes in the Cyanobacterium Synechocystis sp. Strain PCC 6803: Insights from Transcriptomic, Fluxomic, and Physiological Analyses. MBio 7(3):pii e00464-16. PubMed abstract & open access fulltext.
  41. Saward-Arav D, Sadeh A, Mangel M, Templeton AR, Blaustein L. 2016. Oviposition responses of two mosquito species to pool size and predator presence: varying trade-offs between desiccation and predation risks. Israel Journal of Ecology & Evolution 62(3-4):143-148. dx.doi.org/10.1080/15659801.2015.1069113. [WU does not subscribe]
  42. Shi W, Zeng Q, Kunkel BN, Running MP. 2016. Arabidopsis Rab Geranylgeranyltransferases Demonstrate Redundancy and Broad Substrate Specificity in vitro. J Biol Chem 291(3):1398-410. PubMed abstract & fulltext for subscribers.
  43. Shu LF, Laurila A, Suter JF, Rasanen K. 2016. Molecular phenotyping of maternally mediated parallel adaptive divergence within Rana arvalis and Rana temporaria. Molecular Ecology 25(18):4564-4579. dx.doi.org/10.1111/mec.13786.
  44. Simms CL, Zaher HS. 2016. Quality control of chemically damaged RNA. Cell Mol Life Sci 73(19):3639-53. PubMed abstract & fulltext for subscribers.
  45. Smith J, Strassmann JE, Queller DC. 2016. Fine-scale spatial ecology drives kin selection relatedness among cooperating amoebae. Evolution 70(4):848-859. PubMed abstract & fulltext for subscribers.
  46. Song F, Li J, Fan X, Zhang Q, Chang W, Yang F, Geng G. 2016. Transcriptome analysis of Glomus mosseae/Medicago sativa mycorrhiza on atrazine stress. Sci Rep 6:20245. PubMed abstract & open access fulltext.
  47. Søvik E, Plath JA, Devaud JM, Barron AB. 2016. Neuropharmacological Manipulation of Restrained and Free-flying Honey Bees, Apis mellifera. J Vis Exp (117). PubMed abstract & fulltext for subscribers.
  48. Spasojevic MJ, Bahlai CA, Bradley BA, Butterfield BJ, Tuanmu MN, Sistla S, Wiederholt R, Suding KN. 2015. Scaling up the diversity-resilience relationship with trait databases and remote sensing data: the recovery of productivity after wildfire. Glob Chang Biol 222(4):1421-32. PubMed abstract & fulltext for subscribers.
  49. Spasojevic MJ, Turner BL, Myers JA. 2016. When does intraspecific trait variation contribute to functional beta-diversity? Journal of Ecology 104(2):487-496. dx.doi.org/10.1111/1365-2745.12518.
  50. Stein C, Harpole WS, Suding KN. 2016. Transitions and invasion along a grazing gradient in experimental California grasslands. Ecology 97(9):2319-2330. dx.doi.org/10.1002/ecy.1478.
  51. Stein PS, Daniels-McQueen S, Lai J, Liu Z, Corman TS. 2016. Modular organization of the multipartite central pattern generator for turtle rostral scratch: knee-related interneurons during deletions. J Neurophysiol 115(6):3130-9. PubMed abstract & fulltext for subscribers.
  52. Stingaciu LR, O'Neill H, Liberton M, Urban VS, Pakrasi HB, Ohl M. 2016. Revealing the Dynamics of Thylakoid Membranes in Living Cyanobacterial Cells. Sci Rep 6:19627. PubMed abstract & open access fulltext.
  53. Strader LC, Zhao Y. 2016. Auxin perception and downstream events. Curr Opin Plant Biol 33:8-14. PubMed abstract & fulltext for subscribers.
  54. Strassmann JE. 2016. Kin Discrimination in Dictyostelium Social Amoebae. J Eukaryot Microbiol 63(3):378-383. PubMed abstract & fulltext for subscribers.
  55. Sudianto E, Neik TX, Tam SM, Chuah TS, Idris AA, Olsen KM, Song BK. 2016 Morphology of Malaysian Weedy Rice (Oryza sativa): Diversity, Origin and Implications for Weed Management. Weed Science 64(3):501-512. dx.doi.org/10.1614/WS-D-15-00168.1.
  56. Sukhum KV, Freiler MK, Wang R, Carlson BA. 2016. The costs of a big brain: extreme encephalization results in higher energetic demand and reduced hypoxia tolerance in weakly electric African fishes. Proc Biol Sci 283(1845):pii: 20162157. PubMed abstract & fulltext for subscribers > | In the news: Why big brains are rare.
  57. Sutherland MC, Rankin JA, Kranz RG. 2016 Heme trafficking and modifications during system I cytochrome c biogenesis: insights from heme redox potentials of Ccm proteins. Biochemistry 55(22):3150-6. PubMed abstract & fulltext for subscribers.
  58. Tiosano D, Audi L, Climer S, Zhang W, Templeton AR, Fernández-Cancio M, Gershoni-Baruch R, Sánchez-Muro JM, El Kholy M, Hochberg Z. 2016. Latitudinal Clines of the Human Vitamin D Receptor and Skin Color Genes. G3 (Bethesda) 6(5):1251-66. PubMed abstract & open access fulltext.
  59. Ungerer J, Pakrasi HB. 2016. Cpf1 Is A Versatile Tool for CRISPR Genome Editing Across Diverse Species of Cyanobacteria. Sci Rep 6:39681. PubMed abstract & open access fulltext.
  60. Vélez A, Carlson BA. 2016. Detection of transient synchrony across oscillating receptors by the central electrosensory system of mormyrid fish. Elife 5. pii: e16851. PubMed abstract & open access fulltext.
  61. Vigueira CC, Small LL, Olsen KM. 2016. Long-term balancing selection at the Phosphorus Starvation Tolerance 1 (PSTOL1) locus in wild, domesticated and weedy rice (Oryza). BMC Plant Biol 16(1):101. PubMed abstract & open access fulltext.
  62. Vizcaychipi KA, Rinas M, Irazu L, Miyagi A, Arguelles CF, DeMatteo KE. 2016. Neotropical Zoonotic Parasites in Bush Dogs (Speothos venaticus) from Upper Parana Atlantic Forests in Misiones, Argentina. Vector-Borne and Zoonotic Diseases 16(10):664-672. dx.doi.org/10.1089/vbz.2015.1929.
  63. Wang X, Zhang H, Li Y, Zhang Z, Li L, Liu B. 2016. Transcriptome asymmetry in synthetic and natural allotetraploid wheats, revealed by RNA-sequencing. New Phytol. 209(3):1264-77. PubMed abstract & fulltext for subscribers.
  64. Weisz DA, Gross ML, Pakrasi HB. 2016. The Use of Advanced Mass Spectrometry to Dissect the Life-Cycle of Photosystem II. Frontiers in Plant Science 7:no.00617. Open access fulltext.
  65. Wendt KE, Ungerer J, Cobb RE, Zhao H, Pakrasi HB. 2016. CRISPR/Cas9 mediated targeted mutagenesis of the fast growing cyanobacterium Synechococcus elongatus UTEX 2973. Microb Cell Fact 15(1):115. PubMed abstract & fulltext.
  66. Westfall CS, Sherp AM, Zubieta C, Alvarez S, Schraft E, Marcellin R, Ramirez L, Jez JM. 2016. Arabidopsis thaliana GH3.5 acyl acid amido synthetase mediates metabolic crosstalk in auxin and salicylic acid homeostasis. Proc Natl Acad Sci U S A 113(48):13917–13922. PubMed abstract & fulltext for subscribers | In the news: Single enzyme controls two plant hormones.
  67. Wilson ME, Mixdorf M, Berg RH, Haswell ES. 2016. Plastid osmotic stress influences cell differentiation at the plant shoot apex. Development 143(18):3382-3393. PubMed abstract & fulltext for subscribers.
  68. Woods LM, Biro EG, Yang MX, Smith KG. 2016. Does regional diversity recover after disturbance? A field experiment in constructed ponds. PeerJ 4:e2455. doi.org/10.7717/peerj.2455 [open access].
  69. Xia J, Wang X, Perroud PF, He Y, Quatrano R, Zhang W. 2016. Endogenous Small-Noncoding RNAs and Potential Functions in Desiccation Tolerance in Physcomitrella Patens. Sci Rep 6:30118. PubMed abstract & open access fulltext.
  70. Yoneda A, Wittmann BJ, King JD, Blankenship RE, Dantas G. 2016. Transcriptomic analysis illuminates genes involved in chlorophyll synthesis after nitrogen starvation in Acaryochloris sp. CCMEE 5410. Photosynth Res 129(2):171-182. PubMed abstract & fulltext for subscribers.
  71. Yotsui I, Serada S, Naka T, Saruhashi M, Taji T, Hayashi T, Quatrano RS, Sakata Y. 2016. Large-scale proteome analysis of abscisic acid and ABSCISIC ACID INSENSITIVE3-dependent proteins related to desiccation tolerance in Physcomitrella patens. Biochem Biophys Res Commun 471(4):589-95. PubMed abstract & fulltext for subscribers.
  72. Zhang H, Liu H, Blankenship RE, Gross ML. 2016. Isotope-Encoded Carboxyl Group Footprinting for Mass Spectrometry-Based Protein Conformational Studies. J Am Soc Mass Spectrom 27(1):178-81. PubMed abstract & fulltext for subscribers.
  73. Zhang H, Liu H, Lu Y, Wolf NR, Gross ML, Blankenship RE. 2016. Native Mass Spectrometry and Ion Mobility Characterize the Orange Carotenoid Protein Functional Domains. Biochim Biophys Acta 1857(6):734-739. PubMed abstract & fulltext for subscribers.
  74. Zhang H, Gou X, Zhang A, Wang X, Zhao N, Dong Y, Li L, Liu B. 2016. Transcriptome shock invokes disruption of parental expression-conserved genes in tetraploid wheat. Sci Rep 6:26363. PubMed abstract & open access fulltext.
  75. Zhu Y, Liberton M, Pakrasi HB. 2016. A Novel Redoxin in the Thylakoid Membrane Regulates the Titer of Photosystem I. J Biol Chem 291(36):18689-99. PubMed abstract & fulltext for subscribers.