Plant and Microbial Biology - 2015

Worden, N., Wilkop, T. E., Esteve, V. E., Jeannotte, R., Lathe, R., Vernhettes, S., … Drakakaki, G. (2015). CESA TRAFFICKING INHIBITOR Inhibits Cellulose Deposition and Interferes with the Trafficking of Cellulose Synthase Complexes and Their Associated Proteins KORRIGAN1 and POM2/CELLULOSE SYNTHASE INTERACTIVE PROTEIN. Plant Physiology, 167(2), 381–393. https://doi.org/10.1104/pp.114.249003

Miller, E. S., Whittman, J., Kropinski, A. M., & Areaenssesn, E. M. (2015). Divavirus taxonomic bacteriophage group infecting Paenibacillus larvae. International Committee on the Taxonomy of Viruses.

Olarte, R. A., Worthington, C. J., Horn, B. W., Moore, G. G., Singh, R., Monacell, J. T., … Carbone, I. (2015). Enhanced diversity and aflatoxigenicity in interspecific hybrids ofAspergillus flavusandAspergillus parasiticus. Molecular Ecology, 24(8), 1889–1909. https://doi.org/10.1111/mec.13153

Wang, G.-F., He, Y., Strauch, R., Olukolu, B., Nielsen, D., Li, X., & Balint-Kurti, P. (2015). Maize Homologs of HCT, a Key Enzyme in Lignin Biosynthesis, Bind the NLR Rp1 Proteins to Modulate the Defense Response. Plant Physiology, 169. https://doi.org/10.1104/pp.15.00703

Dembeck, L. M., Huang, W., Carbone, M. A., & Mackay, T. F. C. (2015). Genetic basis of natural variation in body pigmentation in Drosophila melanogaster. Fly, 9(2), 75–81. https://doi.org/10.1080/19336934.2015.1102807

Huang, W., Carbone, M. A., Magwire, M. M., Peiffer, J. A., Lyman, R. F., Stone, E. A., … Mackay, T. F. C. (2015). Genetic basis of transcriptome diversity in Drosophila melanogaster. Proceedings of the National Academy of Sciences, 112(44), E6010–E6019. https://doi.org/10.1073/PNAS.1519159112

Shorter, J., Couch, C., Huang, W., Carbone, M. A., Peiffer, J., Anholt, R. R. H., & Mackay, T. F. C. (2015). Genetic architecture of natural variation in Drosophila melanogaster aggressive behavior. Proceedings of the National Academy of Sciences, 112(27), E3555–E3563. https://doi.org/10.1073/PNAS.1510104112

Koryachko, A., Matthiadis, A., Ducoste, J. J., Tuck, J., Long, T. A., & Williams, C. (2015). Computational approaches to identify regulators of plant stress response using high-throughput gene expression data. Current Plant Biology, 3-4, 20–29. https://doi.org/10.1016/j.cpb.2015.04.001

Chinn, M., & Mbaneme, V. (2015). Consolidated bioprocessing for biofuel production: recent advances. Energy and Emission Control Technologies, 5, 23. https://doi.org/10.2147/eect.s63000

Phillippy, B., Perera, I., Donahue, J., & Gillaspy, G. (2015). Certain Malvaceae Plants Have a Unique Accumulation of  myo-Inositol 1,2,4,5,6-Pentakisphosphate. Plants, 4(2), 267–283. https://doi.org/10.3390/plants4020267

Pope, W. H., Bowman, C. A., Russell, D. A., Jacobs-Sera, D., Asai, D. J., Cresawn, S. G., … Hatfull, G. F. (2015). Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. ELife, 4. https://doi.org/10.7554/eLife.06416

Carson, S., Bruff, E., DeFoor, W., Dums, J., Groth, A., Hatfield, T., … Miller, E. S. (2015). Genome Sequences of Six Paenibacillus larvae Siphoviridae Phages. Genome Announcements, 3(3). https://doi.org/10.1128/genomea.00101-15

Hu, Q., Merchante, C., Stepanova, A. N., Alonso, J. M., & Heber, S. (2015). A Stacking-Based Approach to Identify Translated Upstream Open Reading Frames in Arabidopsis Thaliana. In Bioinformatics Research and Applications (Vol. 9096, pp. 138–149). https://doi.org/10.1007/978-3-319-19048-8_12

Hawkes, C. V. (2015). Short-Term Precipitation Exclusion Alters Microbial Responses to Soil Moisture in a Wet Tropical Forest. Microbial Ecology. https://doi.org/10.1007/s00248-014-0436-z

Hawkes, C. V. (2015). Resilience vs. historical contingency in microbial responses to environmental change. Ecology Letters. https://doi.org/10.1111/ele.12451

Hawkes, C. V. (2015). Microbial-mediated redistribution of ecosystem nitrogen cycling can delay progressive nitrogen limitation. Biogeochemistry. https://doi.org/10.1007/s10533-015-0160-x

Hines, K. M., Krings, A., & Stucky, J. M. (2015). Guide to the vascular flora of Howell Woods (Johnston County, North Carolina, U.S.A.). Ft. Worth, Texas: Botanical Research Institute of Texas Press.

Salvato, F., Balbuena, T. S., Nelson, W., Rao, R. S. P., He, R., Soderlund, C. A., … Thelen, J. J. (2015). Comparative Proteomic Analysis of Developing Rhizomes of the Ancient Vascular PlantEquisetum hyemaleand Different Monocot Species. Journal of Proteome Research, 14(4), 1779–1791. https://doi.org/10.1021/pr501157w

Call, A., Sun, Y.-X., Yu, Y., Pearman, P. B., Thomas, D. T., Trigiano, R. N., … Xiang, Q.-Y. J. (2015). Genetic structure and post-glacial expansion ofCornus floridaL. (Cornaceae): integrative evidence from phylogeography, population demographic history, and species distribution modeling. Journal of Systematics and Evolution, 54(2), 136–151. https://doi.org/10.1111/jse.12171

Utturkar, S. M., Klingeman, D. M., Bruno-Barcena, J. M., Chinn, M. S., Grunden, A. M., Köpke, M., & Brown, S. D. (2015). Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies. Scientific Data, 2(1). https://doi.org/10.1038/SDATA.2015.14

Kottegoda, S., Waligora, E., & Hyman, M. (2015). Isolation and characterization of a 2-methylpropene (isobutylene)-metabolizing bacterium, Mycobacterium sp. ELW1. Applied and Environmental Microbiology, 81, 1966–1976.

Kleiner, M., Hooper, L. V., & Duerkop, B. A. (2015). Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes. BMC Genomics, 16(7), 7. https://doi.org/10.1186/s12864-014-1207-4

Kleiner, M., Wentrup, C., Holler, T., Lavik, G., Harder, J., Lott, C., … Dubilier, N. (2015). Use of carbon monoxide and hydrogen by a bacteria-animal symbiosis from seagrass sediments. Environmental Microbiology, 17(12), 5023–5035. https://doi.org/10.1111/1462-2920.12912

Sayavedra, L., Kleiner, M., Ponnudurai, R., Wetzel, S., Pelletier, E., Barbe, V., … eLife. (2015). Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels. ELife, 4, e07966. https://doi.org/10.7554/eLife.07966

Carlson, R. O., Hyde-DeRuyscher, R., & Hamilton, P. T. (2015). High-throughput and high-content screening using peptides. In Phage Display in Biotechnology and Drug Discovery, Second Edition (pp. 249–274). https://doi.org/10.1201/b18196

Carlson, R., Hyde-DeRuyscher, R., & Hamilton, P. (2015, February). High-Throughput and High-Content Screening Using Peptides. Phage Display In Biotechnology and Drug Discovery, Second Edition, pp. 249–274. https://doi.org/10.1201/b18196-11

Search, C. M. (2015). Molecular basis of fruit development. In Z. Liu & R. G. Franks (Eds.), Frontiers Research Topics. https://doi.org/10.3389/978-2-88919-460-5

Leite, M. C. T., Troxell, B., Bruno-Bárcena, J. M., & Hassan, H. M. (2015). Biology of reactive oxygen species, oxidative stress, and antioxidants in lactic acid bacteria. Probiotics and Prebiotics: Current Research and Future Trends, 205–218. https://doi.org/10.21775/9781910190098.14

Hu, Q., Merchante, C., STEPANOVA, A. N. N. A., Alonso, J., & Heber, S. (2015). Mining transcript features related to translation in Arabidopsis using LASSO and random forest. 2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2015. https://doi.org/10.1109/iccabs.2015.7344713

Dalal, J., Land, E., Vasani, N., He, L., Smith, C., Rodriguez-Welsh, M., … Sederoff, H. (2015). Methods for RNA Profiling of Gravi-Responding Plant Tissues. In Methods in Molecular Biology (Vol. 1309, pp. 91–117). https://doi.org/10.1007/978-1-4939-2697-8_9

Sandoval-Espinola, W. J., Chinn, M., & Bruno-Barcena, J. M. (2015). Inoculum optimization of Clostridium beijerinckii for reproducible growth. FEMS Microbiology Letters, 362(19), fnv164. https://doi.org/10.1093/femsle/fnv164

Hsieh, T.-F. (2015). Whole-Genome DNA Methylation Profiling with Nucleotide Resolution. In Methods in Molecular Biology (Vol. 1284, pp. 27–40). https://doi.org/10.1007/978-1-4939-2444-8_2

Alonso, J., & STEPANOVA, A. N. N. A. (2015). Plant functional genomics: Methods and protocols. In J. M. Alonso & A. N. Stepanova (Eds.), Plant Functional Genomics: Methods and Protocols: Second Edition (2nd ed., pp. 1–526). https://doi.org/10.1007/978-1-4939-2444-8

Alonso, J. M., & Stepanova, A. N. (2015). Plant functional genomics methods and protocols second edition preface. Plant Functional Genomics: Methods and Protocols, 2nd Edition, 1284, V-.

Flores, M. A., Reyes, M. I., Robertson, D., & Kjemtrup, S. (2015). Persistent virus-induced gene silencing in asymptomatic accessions of arabidopsis. Plant Functional Genomics: Methods and Protocols, 2nd Edition, 1284, 305–322. https://doi.org/10.1007/978-1-4939-2444-8_15

Kalusova, V., Chytry, M., Peet, R. K., & Wentworth, T. R. (2015). Intercontinental comparison of habitat levels of invasion between temperate North America and Europe. Ecology, 96(12), 3363–3373. https://doi.org/10.1890/15-0021.1

Tuttle, J. R., Haigler, C. H., & Robertson, D. (2015). Virus-induced gene silencing of fiber-related genes in cotton. Plant Gene Silencing: Methods and Protocols, 1287, 219–234. https://doi.org/10.1007/978-1-4939-2453-0_16

Qi, Z.-C., Yu, Y., Liu, X., Pais, A., Ranney, T., Whetten, R., & Xiang, Q.-Y. J. (2015). Phylogenomics of polyploidy Fothergilla (Hamamelidaceae) by RAD-tag based GBS—Insights into species origin and effects of software pipelines. Journal of Systematics and Evolution, 53(5), 432–447. https://doi.org/10.1111/jse.12176

Wen, J., Liu, J. Q., Ge, S., Xiang, Q.-Y., & Zimmer, E. A. (2015). Phylogenomic approaches to deciphering the tree of life. Journal of Systematics and Evolution, 53(5), 369–370. https://doi.org/10.1111/jse.12175

Whitham, J. M., Tirado-Acevedo, O., Chinn, M. S., Pawlak, J. J., & Grunden, A. M. (2015). Metabolic Response of Clostridium ljungdahlii to Oxygen Exposure. Applied and Environmental Microbiology, 81(24), 8379–8391. https://doi.org/10.1128/aem.02491-15

Beseli, A., Noar, R., & Daub, M. E. (2015). Characterization of Cercospora nicotianae hypothetical proteins in cercosporin resistance. PLoS One, 10(10). https://doi.org/10.1371/journal.pone.0140676

Delaux, P.-M., Radhakrishnan, G. V., Jayaraman, D., Cheema, J., Malbreil, M., Volkening, J. D., … Ane, J.-M. (2015). Algal ancestor of land plants was preadapted for symbiosis. Proceedings of the National Academy of Sciences of the United States of America, 112(43), 13390–13395. https://doi.org/10.1073/pnas.1515426112

Hu, Q. W., Merchante, C., Stepanova, A. N., Alonso, J. M., & Heber, S. (2015). A stacking-based approach to identify translated upstream open reading frames in Arabidopsis thaliana. Bioinformatics research and applications (isbra 2015), 9096, 138–149.

Ma, D. M., Wang, Z. L., Wang, L. J., Alejos-Gonzales, F., Sun, M. A., & DE-YU, X. I. E. (2015). A genome-wide scenario of terpene pathways in self-pollinated Artemisia annua. Molecular Plant, 8(11), 1580–1598. https://doi.org/10.1016/j.molp.2015.07.004

Beseli, A., Amnuaykanjanasin, A., Herrero, S., Thomas, E., & Daub, M. E. (2015). Membrane transporters in self resistance of Cercospora nicotianae to the photoactivated toxin cercosporin. Current Genetics, 61(4), 601–620. https://doi.org/10.1007/s00294-015-0486-x

Strauch, R. C., Svedin, E., Dilkes, B., Chapple, C., & Li, X. (2015). Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America, 112(37), 11726–11731. https://doi.org/10.1073/pnas.1503272112

Koryachko, A., Matthiadis, A., Muhammad, D., Foret, J., Brady, S. M., Ducoste, J., … Williams, C. (2015). Clustering and differential alignment algorithm: Identification of early stage regulators in the Arabidopsis thaliana iron deficiency response. PLoS One, 10(8). https://doi.org/10.1371/journal.pone.0136591

Moreno-Risueno, M. A., Sozzani, R., Yardimici, G. G., Petricka, J. J., Vernoux, T., Blilou, I., … Benfey, P. N. (2015). Bird and Scarecrow proteins organize tissue formation in Arabidopsis roots. Science, 350(6259), 426–430. https://doi.org/10.1126/science.aad1171

Carlson, A. S., Dole, J. M., Matthysse, A. G., Hoffmann, W. A., & Kornegay, J. L. (2015). Bacteria species and solution pH effect postharvest quality of cut Zinnia elegans. Scientia Horticulturae, 194, 71–78. https://doi.org/10.1016/j.scienta.2015.07.044

Dalal, J., Yalamanchili, R., Hovary, C. L., Ji, M., Rodriguez-Welsh, M., Aslett, D., … al. (2015). A novel gateway-compatible binary vector series (PC-GW) for flexible cloning of multiple genes for genetic transformation of plants. Plasmid, 81, 55–62. https://doi.org/10.1016/j.plasmid.2015.06.003

Gkarmiri, K., Finlay, R. D., Alström, S., Thomas, E., Cubeta, M. A., & Högberg, N. (2015). Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica. BMC Genomics, 16(1). https://doi.org/10.1186/s12864-015-1758-z

Merchante, C., Brumos, J., Yun, J., Hu, Q., Spencer, K. R., Enríquez, P., … Alonso, J. (2015). Gene-Specific Translation Regulation Mediated by the Hormone-Signaling Molecule EIN2. Cell, 163(3), 684–697. https://doi.org/10.1016/j.cell.2015.09.036

Bass, H. W., Hoffman, G. G., Lee, T. J., Wear, E. E., Joseph, S. R., Allen, G. C., … Thompson, W. (2015). Defining multiple, distinct, and shared spatiotemporal patterns of DNA replication and endoreduplication from 3D image analysis of developing maize (Zea mays L.) root tip nuclei. Plant Molecular Biology, 89(4-5), 339–351. https://doi.org/10.1007/s11103-015-0364-4

Dalal, J., Lopez, H., Vasani, N. B., Hu, Z. H., Swift, J. E., Yalamanchili, R., … Sederoff, H. (2015). A photorespiratory bypass increases plant growth and seed yield in biofuel crop Camelina sativa. Biotechnology for Biofuels, 8(1). https://doi.org/10.1186/s13068-015-0357-1

Lowder, L. G., Zhang, D. W., Baltes, N. J., Paul, J. W., Tang, X., Zheng, X. L., … al. (2015). A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation. Plant Physiology, 169(2), 971–985. https://doi.org/10.1104/pp.15.00636

Shu, X., Livingston, D. P., Franks, R. G., Boston, R. S., Woloshuk, C. P., & Payne, G. A. (2015). Tissue-specific gene expression in maize seeds during colonization by Aspergillus flavus and Fusarium verticillioides. Molecular Plant Pathology, 16(7), 662–674. https://doi.org/10.1111/mpp.12224

Beseli, A., Silva, M. G., & Daub, M. E. (2015). The role of Cercospora zeae-maydis homologs of Rhodobacter sphaeroides O-1(2)-resistance genes in resistance to the photoactivated toxin cercosporin. FEMS Microbiology Letters, 362(2). https://doi.org/10.1093/femsle/fnu036

Marchin, R. M., Salk, C. F., Hoffmann, W. A., & Dunn, R. R. (2015). Temperature alone does not explain phenological variation of diverse temperate plants under experimental warming. Global Change Biology, 21(8), 3138–3151. https://doi.org/10.1111/gcb.12919

Schafer, J. L., Breslow, B. P., Hohmann, M. G., & Hoffmann, W. A. (2015). Relative bark thickness is correlated with tree species distributions along a fire frequency gradient. Fire Ecology, 11(1), 74–87. https://doi.org/10.4996/fireecology.1101074

Ji, M., Barnwell, C. V., & Grunden, A. (2015). Characterization of recombinant glutathione reductase from the psychrophilic Antarctic bacterium Colwellia psychrerythraea. Extremophiles, 19(4), 863–874. https://doi.org/10.1007/s00792-015-0762-1

Esposito, D., Damsud, T., Wilson, M., Grace, M. H., Strauch, R., Li, X., … Komarnytsky, S. (2015). Black currant anthocyanins attenuate weight gain and improve glucose metabolism in diet-induced obese mice with intact, but not disrupted, gut microbiome. Journal of Agricultural and Food Chemistry, 63(27), 6172–6180. https://doi.org/10.1021/acs.jafc.5b00963

Sehra, B., & Franks, R. G. (2015). Auxin and cytokinin act during gynoecial patterning and the development of ovules from the meristematic medial domain. Wiley Interdisciplinary Reviews: Developmental Biology, 4(6), 555–571. https://doi.org/10.1002/wdev.193

Noar, J., Loveless, T., Navarro-Herrero, J. L., Olson, J. W., & Bruno-Bárcena, J. M. (2015). Aerobic Hydrogen Production via Nitrogenase in Azotobacter vinelandii CA6. Applied and Environmental Microbiology, 7(13), 4507–4516. https://doi.org/10.1128/aem.00679-15

Han, S. W., Alonso, J., & Rojas-Pierce, M. (2015). Regulator of bulb biogenesis1 (RBB1) is involved in vacuole bulb formation in arabidopsis. PLoS One, 10(4), e0125621. https://doi.org/10.1371/journal.pone.0125621

Srirangan, S., Sauer, M. L., Howard, B., Dvora, M., Dums, J., Backman, P., & Sederoff, H. (2015). Interaction of temperature and photoperiod increases growth and oil content in the marine microalgae Dunaliella viridis. PLoS One, 10(5). https://doi.org/10.1371/journal.pone.0127562

Fabregas, N., Formosa-Jordan, P., Confraria, A., Siligato, R., Alonso, J., Swarup, R., … Ibanes, M. (2015). Auxin influx carriers control vascular patterning and xylem differentiation in Arabidopsis thaliana. PLoS Genetics, 11(4). https://doi.org/10.1371/journal.pgen.1005183

Wang, J. P., Chuang, L., Loziuk, P. L., Chen, H., Lin, Y. C., Shi, R., … Chiang, V. L. (2015). Phosphorylation is an on/off switch for 5-hydroxyconiferaldehyde O-methyltransferase activity in poplar monolignol biosynthesis. Proceedings of the National Academy of Sciences of the United States of America, 112(27), 8481–8486. https://doi.org/10.1073/pnas.1510473112

Zhu, Y., Wang, H. Y., Peng, Q. Z., Tang, Y. T., Xia, G. X., Wu, J. H., & DE-YU, X. I. E. (2015). Functional characterization of an anthocyanidin reductase gene from the fibers of upland cotton (Gossypium hirsutum). Planta, 241(5), 1075–1089. https://doi.org/10.1007/s00425-014-2238-4

Sun, W., Chen, H., Wang, J., Sun, H. W., Yang, S. K., Sang, Y. L., … Xu, X. H. (2015). Expression analysis of genes encoding mitogen-activated protein kinases in maize provides a key link between abiotic stress signaling and plant reproduction. Functional & Integrative Genomics, 15(1), 107–120. https://doi.org/10.1007/s10142-014-0410-3

Mathews, S. L., Pawlak, J., & Grunden, A. (2015). Bacterial biodegradation and bioconversion of industrial lignocellulosic streams. Applied Microbiology and Biotechnology, Vol. 99, pp. 2939–2954. https://doi.org/10.1007/s00253-015-6471-y

Liu, Z., & Franks, R. G. (2015). Molecular basis of fruit development. Frontiers in Plant Science, 6(FEB). https://doi.org/10.3389/fpls.2015.00028

Ma, X. H., Shatil-Cohen, A., Ben-Dor, S., Wigoda, N., Perera, I., Im, Y. J., … Moran, N. (2015). Do phosphoinositides regulate membrane water permeability of tobacco protoplasts by enhancing the aquaporin pathway? Planta, 241(3), 741–755. https://doi.org/10.1007/s00425-014-2216-x

Selote, D., Samira, R., Matthiadis, A., Gillikin, J. W., & Long, T. A. (2015). Iron-binding E3 ligase mediates iron response in plants by targeting basic helix-loop-helix transcription factors. Plant Physiology, 167(1), 273-. https://doi.org/10.1104/pp.114.250837

Jeong, C. W., Park, G. T., Yun, H., Hsieh, T.-F., Choi, Y. D., Choi, Y., & Lee, J. S. (2015). Control of Paternally Expressed Imprinted UPWARD CURLY LEAF1, a Gene Encoding an F-Box Protein That Regulates CURLY LEAF Polycomb Protein, in the Arabidopsis Endosperm. PLOS ONE, 10(2), e0117431. https://doi.org/10.1371/journal.pone.0117431

Kottegoda, S., Waligora, E., & Hyman, M. (2015). Metabolism of 2-methylpropene (isobutylene) by the aerobic bacterium mycobacterium sp strain ELW1. Applied and Environmental Microbiology, 81(6), 1966–1976. https://doi.org/10.1128/aem.03103-14

Bruno-Bárcena, J. M., & Azcarate-Peril, M. A. (2015). Galacto-oligosaccharides and Colorectal Cancer: Feeding our Intestinal Probiome. Journal of Functional Foods, 1, 92–108. https://doi.org/10.1016/j.jff.2014.10.029

Williams, S. P., Gillaspy, G. E., & Perera, I. (2015). Biosynthesis and possible functions of inositol pyrophosphates in plants. Frontiers in Plant Science, 6. https://doi.org/10.3389/fpls.2015.00067

Krings, A., & Morillo, G. (2015). A new species in the matelea palustris complex (Apocynaceae, Asclepiadeae) and a synopsis of the complex in the Guianas and Northern Brazil. Systematic Botany, 40(1), 214–219. https://doi.org/10.1600/036364415x686521

Alonso, J., & STEPANOVA, A. N. N. A. (2015). A recombineering-based gene tagging system for Arabidopsis. Methods in Molecular Biology (Clifton, N.J.), 1227, 233–243. https://doi.org/10.1007/978-1-4939-1652-8_11