TY - JOUR TI - Dynamics of the Methanogenic Archaeal Community during Plant Residue Decomposition in an Anoxic Rice Field Soil AU - Peng, J. AU - Lu, Z. AU - Rui, J. AU - Lu, Y. T2 - Applied and Environmental Microbiology AB - Incorporation of plant residues strongly enhances the methane production and emission from flooded rice fields. Temperature and residue type are important factors that regulate residue decomposition and CH(4) production. However, the response of the methanogenic archaeal community to these factors in rice field soil is not well understood. In the present experiment, the structure of the archaeal community was determined during the decomposition of rice root and straw residues in anoxic rice field soil incubated at three temperatures (15 degrees C, 30 degrees C, and 45 degrees C). More CH(4) was produced in the straw treatment than root treatment. Increasing the temperature from 15 degrees C to 45 degrees C enhanced CH(4) production. Terminal restriction fragment length polymorphism analyses in combination with cloning and sequencing of 16S rRNA genes showed that Methanosarcinaceae developed early in the incubations, whereas Methanosaetaceae became more abundant in the later stages. Methanosarcinaceae and Methanosaetaceae seemed to be better adapted at 15 degrees C and 30 degrees C, respectively, while the thermophilic Methanobacteriales and rice cluster I methanogens were significantly enhanced at 45 degrees C. Straw residues promoted the growth of Methanosarcinaceae, whereas the root residues favored Methanosaetaceae. In conclusion, our study revealed a highly dynamic structure of the methanogenic archaeal community during plant residue decomposition. The in situ concentration of acetate (and possibly of H(2)) seems to be the key factor that regulates the shift of methanogenic community. DA - 2008/// PY - 2008/// DO - 10.1128/aem.00070-08 VL - 74 IS - 9 SP - 2894-2901 ER - TY - JOUR TI - Interchromatidal central ridge and transversal symmetry in early metaphasic human chromosome one AU - Argüello-Miranda, O. AU - Sáenz-Arce, G. T2 - Journal of Molecular Recognition AB - The topographic structure of Giemsa-banded (G-banded) early metaphase human chromosomes adsorbed on glass was analyzed by atomic force microscope using amplitude modulation mode (AM-AFM). Longitudinal height measurements for early metaphasic human chromosomes showed a central ridge that was further characterized by transversal height measurements. The heterochromatic regions displayed a high level of transversal symmetry, while the euchromatic ones presented several peaks across the transversal height measurements. We suggest that this central ridge and symmetry patterns point out a transitional arrangement of the early metaphase chromosome and support evidence for interchromatidal interactions prior to disjunction. DA - 2008/// PY - 2008/// DO - 10.1002/jmr.884 VL - 21 IS - 3 SP - 184-189 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-44949128921&partnerID=MN8TOARS ER - TY - JOUR TI - Revision of Gonolobus s.s. (Apocynaceae, Asclepiadoideae) in the West Indies AU - Krings, A. T2 - Journal of the Botanical Research Institute of Texas DA - 2008/// PY - 2008/// VL - 2 IS - 1 SP - 95–138 ER - TY - JOUR TI - Index of names and types in West Indian Gonolobinae (Apocynaceae, Asclepiadoideae), including fourteen new lectotypifications, one neotypification, and a new combination AU - Krings, A. T2 - Journal of the Botanical Research Institute of Texas DA - 2008/// PY - 2008/// VL - 2 IS - 1 SP - 139–163 ER - TY - JOUR TI - In vitro studies of tropical woody species AU - Bhatnagar, S. AU - Chandrasekharan, S. AU - Xie, D.Y. AU - Hong, Y. T2 - In Vitro Cellular & Developmental Biology - Animal DA - 2008/// PY - 2008/// VL - 44 IS - Supplement SP - S54 ER - TY - CHAP TI - Plan(t)s for Space Exploration AU - Brown, C.S. AU - Sederoff, H.W. AU - Davies, E. AU - Ferl, R.J. AU - Stankovic, B. T2 - Plant Tropisms AB - This chapter contains section titled: Introduction Human Missions to Space Life Support Genomics and Space Exploration Nanotechnology Sensors, Biosensors, and Intelligent Machines Plan(t)s for Space Exploration Imagine… Literature Cited PY - 2008/// DO - 10.1002/9780470388297.ch9 SP - 183-195 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84889307727&partnerID=MN8TOARS ER - TY - JOUR TI - Arabidopsis P-Glycoprotein19 Participates in the Inhibition of Gravitropism by Gravacin AU - Rojas-Pierce, Marcela AU - Titapiwatanakun, Boosaree AU - Sohn, Eun Ju AU - Fang, Fang AU - Larive, Cynthia K. AU - Blakeslee, Joshua AU - Cheng, Yan AU - Cuttler, Sean AU - Peer, Wendy A. AU - Murphy, Angus S. AU - Raikhel, Natasha V. T2 - Chemistry & Biology DA - 2008/1// PY - 2008/1// DO - 10.1016/j.chembiol.2008.01.004 VL - 15 IS - 1 SP - 87 J2 - Chemistry & Biology LA - en OP - SN - 1074-5521 UR - http://dx.doi.org/10.1016/j.chembiol.2008.01.004 DB - Crossref ER - TY - JOUR TI - Systems Approaches to Identifying Gene Regulatory Networks in Plants AU - Long, T.A. AU - Brady, S.M. AU - Benfey, P.N. T2 - Annual Review of Cell and Developmental Biology AB - Complex gene regulatory networks are composed of genes, noncoding RNAs, proteins, metabolites, and signaling components. The availability of genome-wide mutagenesis libraries; large-scale transcriptome, proteome, and metabalome data sets; and new high-throughput methods that uncover protein interactions underscores the need for mathematical modeling techniques that better enable scientists to synthesize these large amounts of information and to understand the properties of these biological systems. Systems biology approaches can allow researchers to move beyond a reductionist approach and to both integrate and comprehend the interactions of multiple components within these systems. Descriptive and mathematical models for gene regulatory networks can reveal emergent properties of these plant systems. This review highlights methods that researchers are using to obtain large-scale data sets, and examples of gene regulatory networks modeled with these data. Emergent properties revealed by the use of these network models and perspectives on the future of systems biology are discussed. DA - 2008/11// PY - 2008/11// DO - 10.1146/annurev.cellbio.24.110707.175408 VL - 24 SP - 81-103 UR - http://dx.doi.org/10.1146/annurev.cellbio.24.110707.175408 KW - systems biology KW - Arabidopsis KW - transcription factors KW - emergent properties KW - modeling KW - genomics ER - TY - JOUR TI - Conserved role of PROTON GRADIENT REGULATION 5 in the regulation of PSI cyclic electron transport AU - Long, Terri A. AU - Okegawa, Yuki AU - Shikanai, Toshiharu AU - Schmidt, Gregory W. AU - Covert, Sarah F. T2 - Planta DA - 2008/7/29/ PY - 2008/7/29/ DO - 10.1007/s00425-008-0789-y VL - 228 IS - 6 SP - 907-918 J2 - Planta LA - en OP - SN - 0032-0935 1432-2048 UR - http://dx.doi.org/10.1007/s00425-008-0789-y DB - Crossref KW - Arabidopsis KW - Cyclic electron transport KW - Nonphotochemical quenching KW - Photosynthesis KW - PGR5 KW - Stress tolerance ER - TY - JOUR TI - Cell Identity Mediates the Response of Arabidopsis Roots to Abiotic Stress AU - Dinneny, J.R. AU - Long, T.A. AU - Wang, J.Y. AU - Jung, J.W. AU - Mace, D. AU - Pointer, S. AU - Barron, C. AU - Brady, S.M. AU - Schiefelbein, J. AU - Benfey, P.N. T2 - Science AB - Little is known about the way developmental cues affect how cells interpret their environment. We characterized the transcriptional response to high salinity of different cell layers and developmental stages of the Arabidopsis root and found that transcriptional responses are highly constrained by developmental parameters. These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell layers, several of which correspond to observable physiological changes. We showed that known stress pathways primarily control semiubiquitous responses and used mutants that disrupt epidermal patterning to reveal cell-layer-specific and inter-cell-layer effects. By performing a similar analysis using iron deprivation, we identified common cell-type-specific stress responses and revealed the crucial role the environment plays in defining the transcriptional outcome of cell-fate decisions. DA - 2008/5/16/ PY - 2008/5/16/ DO - 10.1126/science.1153795 VL - 320 IS - 5878 SP - 942-945 UR - http://dx.doi.org/10.1126/science.1153795 ER - TY - JOUR TI - Independent origins of syringyl lignin in vascular plants AU - Weng, J.-K. AU - Li, X. AU - Stout, J. AU - Chapple, C. T2 - Proceedings of the National Academy of Sciences AB - Lycophytes arose in the early Silurian ( approximately 400 Mya) and represent a major lineage of vascular plants that has evolved in parallel with the ferns, gymnosperms, and angiosperms. A hallmark of vascular plants is the presence of the phenolic lignin heteropolymer in xylem and other sclerified cell types. Although syringyl lignin is often considered to be restricted in angiosperms, it has been detected in lycophytes as well. Here we report the characterization of a cytochrome P450-dependent monooxygenase from the lycophyte Selaginella moellendorffii. Gene expression data, cross-species complementation experiments, and in vitro enzyme assays indicate that this P450 is a ferulic acid/coniferaldehyde/coniferyl alcohol 5-hydroxylase (F5H), and is capable of diverting guaiacyl-substituted intermediates into syringyl lignin biosynthesis. Phylogenetic analysis indicates that the Selaginella F5H represents a new family of plant P450s and suggests that it has evolved independently of angiosperm F5Hs. DA - 2008/5/27/ PY - 2008/5/27/ DO - 10.1073/pnas.0801696105 VL - 105 IS - 22 SP - 7887-7892 J2 - Proceedings of the National Academy of Sciences LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.0801696105 DB - Crossref KW - convergent evolution KW - DFRC KW - F5H KW - P450 KW - Selaginella ER - TY - JOUR TI - Emerging strategies of lignin engineering and degradation for cellulosic biofuel production AU - Weng, Jing-Ke AU - Li, Xu AU - Bonawitz, Nicholas D AU - Chapple, Clint T2 - Current Opinion in Biotechnology AB - Ethanol and other biofuels produced from lignocellulosic biomass represent a renewable, more carbon-balanced alternative to both fossil fuels and corn-derived or sugarcane-derived ethanol. Unfortunately, the presence of lignin in plant cell walls impedes the breakdown of cell wall polysaccharides to simple sugars and the subsequent conversion of these sugars to usable fuel. Recent advances in the understanding of lignin composition, polymerization, and regulation have revealed new opportunities for the rational manipulation of lignin in future bioenergy crops, augmenting the previous successful approach of manipulating lignin monomer biosynthesis. Furthermore, recent studies on lignin degradation in nature may provide novel resources for the delignification of dedicated bioenergy crops and other sources of lignocellulosic biomass. DA - 2008/4// PY - 2008/4// DO - 10.1016/j.copbio.2008.02.014 VL - 19 IS - 2 SP - 166-172 J2 - Current Opinion in Biotechnology LA - en OP - SN - 0958-1669 UR - http://dx.doi.org/10.1016/j.copbio.2008.02.014 DB - Crossref ER - TY - JOUR TI - Improvement of biomass through lignin modification AU - Li, Xu AU - Weng, Jing-Ke AU - Chapple, Clint T2 - The Plant Journal AB - Lignin, a major component of the cell wall of vascular plants, has long been recognized for its negative impact on forage quality, paper manufacturing, and, more recently, cellulosic biofuel production. Over the last two decades, genetic and biochemical analyses of brown midrib mutants of maize, sorghum and related grasses have advanced our understanding of the relationship between lignification and forage digestibility. This work has also inspired genetic engineering efforts aimed at generating crops with altered lignin, with the expectation that these strategies would enhance forage digestibility and/or pulping efficiency. The knowledge gained from these bioengineering efforts has greatly improved our understanding of the optimal lignin characteristics required for various applications of lignocellulosic materials while also contributing to our understanding of the lignin biosynthetic pathway. The recent upswing of interest in cellulosic biofuel production has become the new focus of lignin engineering. Populus trichocarpa and Brachypodium distachyon are emerging as model systems for energy crops. Lignin research on these systems, as well as on a variety of proposed energy crop species, is expected to shed new light on lignin biosynthesis and its regulation in energy crops, and lead to rational genetic engineering approaches to modify lignin for improved biofuel production. DA - 2008/5// PY - 2008/5// DO - 10.1111/j.1365-313x.2008.03457.x VL - 54 IS - 4 SP - 569-581 J2 - Plant J LA - en OP - SN - 0960-7412 1365-313X UR - http://dx.doi.org/10.1111/j.1365-313x.2008.03457.x DB - Crossref KW - biofuel KW - brown midrib KW - digestibility KW - cell wall KW - pulping ER - TY - JOUR TI - Preserving Accuracy in GenBank T2 - Science AB - GenBank, the public repository for nucleotide and protein sequences, is a critical resource for molecular biology, evolutionary biology, and ecology. While some attention has been drawn to sequence errors ([1][1]), common annotation errors also reduce the value of this database. In fact, for DA - 2008/3/21/ PY - 2008/3/21/ DO - 10.1126/science.319.5870.1616a UR - http://dx.doi.org/10.1126/science.319.5870.1616a ER - TY - JOUR TI - The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels AU - Leivar, Pablo AU - Monte, Elena AU - Al-Sady, Bassem AU - Carle, Christine AU - Storer, Alyssa AU - Alonso, Jose M. AU - Ecker, Joseph R. AU - Quail, Peter H. T2 - The Plant Cell Online AB - Abstract We show that a previously uncharacterized Arabidopsis thaliana basic helix-loop-helix (bHLH) phytochrome interacting factor (PIF), designated PIF7, interacts specifically with the far-red light–absorbing Pfr form of phyB through a conserved domain called the active phyB binding motif. Similar to PIF3, upon light exposure, PIF7 rapidly migrates to intranuclear speckles, where it colocalizes with phyB. However, in striking contrast to PIF3, this process is not accompanied by detectable light-induced phosphorylation or degradation of PIF7, suggesting that the consequences of interaction with photoactivated phyB may differ among PIFs. Nevertheless, PIF7 acts similarly to PIF3 in prolonged red light as a weak negative regulator of phyB-mediated seedling deetiolation. Examination of pif3, pif4, and pif7 double mutant combinations shows that their moderate hypersensitivity to extended red light is additive. We provide evidence that the mechanism by which these PIFs operate on the phyB signaling pathway under prolonged red light is through maintaining low phyB protein levels, in an additive or synergistic manner, via a process likely involving the proteasome pathway. These data suggest that the role of these phyB-interacting bHLH factors in modulating seedling deetiolation in prolonged red light may not be as phy-activated signaling intermediates, as proposed previously, but as direct modulators of the abundance of the photoreceptor. DA - 2008/// PY - 2008/// DO - 10.1105/tpc.107.052142 VL - 20 IS - 2 SP - 337-352 ER - TY - JOUR TI - Potential sites of bioactive gibberellin production during reproductive growth in Arabidopsis AU - Hu, Jianhong AU - Mitchum, Melissa G. AU - Barnaby, Neel AU - Ayele, Belay T. AU - Ogawa, Mikihiro AU - Nam, Edward AU - Lai, Wei-Chu AU - Hanada, Atsushi AU - Alonso, Jose M. AU - Ecker, Joseph R. T2 - The Plant Cell Online AB - Gibberellin 3-oxidase (GA3ox) catalyzes the final step in the synthesis of bioactive gibberellins (GAs). We examined the expression patterns of all four GA3ox genes in Arabidopsis thaliana by promoter-beta-glucuronidase gene fusions and by quantitative RT-PCR and defined their physiological roles by characterizing single, double, and triple mutants. In developing flowers, GA3ox genes are only expressed in stamen filaments, anthers, and flower receptacles. Mutant plants that lack both GA3ox1 and GA3ox3 functions displayed stamen and petal defects, indicating that these two genes are important for GA production in the flower. Our data suggest that de novo synthesis of active GAs is necessary for stamen development in early flowers and that bioactive GAs made in the stamens and/or flower receptacles are transported to petals to promote their growth. In developing siliques, GA3ox1 is mainly expressed in the replums, funiculi, and the silique receptacles, whereas the other GA3ox genes are only expressed in developing seeds. Active GAs appear to be transported from the seed endosperm to the surrounding maternal tissues where they promote growth. The immediate upregulation of GA3ox1 and GA3ox4 after anthesis suggests that pollination and/or fertilization is a prerequisite for de novo GA biosynthesis in fruit, which in turn promotes initial elongation of the silique. DA - 2008/// PY - 2008/// DO - 10.1105/tpc.107.057752 VL - 20 IS - 2 SP - 320-336 ER - TY - JOUR TI - Soil temperature affects carbon allocation within arbuscular mycorrhizal networks and carbon transport from plant to fungus AU - HAWKES, CHRISTINE V. AU - HARTLEY, IAIN P. AU - INESON, PHIL AU - FITTER, ALASTAIR H. T2 - Global Change Biol AB - Abstract How soil carbon balance will be affected by plant–mycorrhizal interactions under future climate scenarios remains a significant unknown in our ability to forecast ecosystem carbon storage and fluxes. We examined the effects of soil temperature (14, 20, 26 °C) on the structure and extent of a multispecies community of arbuscular mycorrhizal (AM) fungi associated with Plantago lanceolata . To isolate fungi from roots, we used a mesh‐divided pot system with separate hyphal compartments near and away from the plant. A 13 C pulse label was then used to trace the flow of recently fixed photosynthate from plants into belowground pools and respiration. Temperature significantly altered the structure and allocation of the AM hyphal network, with a switch from more vesicles (storage) in cooled soils to more extensive extraradical hyphal networks (growth) in warmed soils. As soil temperature increased, we also observed an increase in the speed at which plant photosynthate was transferred to and respired by roots and AM fungi coupled with an increase in the amount of carbon respired per unit hyphal length. These differences were largely independent of plant size and rates of photosynthesis. In a warmer world, we would therefore expect more carbon losses to the atmosphere from AM fungal respiration, which are unlikely to be balanced by increased growth of AM fungal hyphae. DA - 2008/5// PY - 2008/5// DO - 10.1111/j.1365-2486.2007.01535.x VL - 14 IS - 5 SP - 1181-1190 KW - C-13 pulse label KW - carbon cycle KW - climate change KW - extraradical mycelia KW - Plantago lanceolata KW - root length colonization KW - soil respiration ER - TY - JOUR TI - Embracing Variability in the Application of Plant-Soil Interactions to the Restoration of Communities and Ecosystems AU - Eviner, Valerie T. AU - Hawkes, Christine V. T2 - Restoration Ecology AB - Abstract Plant–soil interactions are the foundation of effective and sustained restoration of terrestrial communities and ecosystems. Recent advances in ecological science have greatly contributed to our understanding of the effects of soil conditions on plant community dynamics and our understanding of plant composition impacts on almost every aspect of soil structure and function. Although these theories provide important guidelines for the practice of restoration, they often fall short of providing the level of information required to make effective site‐specific management decisions. This is largely because of ecology’s search for simple unifying theories and the resulting tendency to generalize from studies at one or only a few sites. An average effect or broad‐scale simple relationship tends to provide a “one‐size‐fits‐all” (or none) prescription for managers. Plant–soil interactions can vary greatly depending on their context (e.g., environmental conditions, management practices, time, neighboring community, interaction with other organisms). The ability to predict these context‐dependent interactions between plants and soils can be developed by building upon existing general frameworks for understanding plant–soil interactions. Collaborations between researchers and managers can develop conceptual tools that allow us to understand and manage the variability and complexity of plant–soil interactions, simultaneously advancing theory and applicability. DA - 2008/// PY - 2008/// DO - 10.1111/j.1526-100x.2008.00482.x VL - 16 IS - 4 SP - 713-729 KW - context dependence KW - microbial communities KW - plant-soil interactions KW - plant traits KW - restoration KW - soil nutrients KW - species effects ER - TY - JOUR TI - Arabidopsis LEAFY COTYLEDON2 induces maturation traits and auxin activity: Implications for somatic embryogenesis AU - Stone, S. L. AU - Braybrook, S. A. AU - Paula, S. L. AU - Kwong, L. W. AU - Meuser, J. AU - Pelletier, J. AU - Hsieh, T.-F. AU - Fischer, R. L. AU - Goldberg, R. B. AU - Harada, J. J. T2 - Proceedings of the National Academy of Sciences AB - LEAFY COTYLEDON2 (LEC2) is a central regulator of embryogenesis sufficient to induce somatic cells to form embryos when expressed ectopically. Here, we analyze the cellular processes induced by LEC2, a B3 domain transcription factor, that may underlie its ability to promote somatic embryogenesis. We show auxin-responsive genes are induced after LEC2 activation in seedlings. Genes encoding enzymes involved in auxin biosynthesis, YUC2 and YUC4, are activated within 1 h after induction of LEC2 activity, and YUC4 appears to be a direct transcriptional target of LEC2. We also show ectopic LEC2 expression induces accumulation of seed storage protein and oil bodies in vegetative and reproductive organs, events that normally occur during the maturation phase of embryogenesis. Furthermore, LEC2 activates seed protein genes before an increase in RNAs encoding LEC1 or FUS3 is observed. Thus, LEC2 causes rapid changes in auxin responses and induces cellular differentiation characteristic of the maturation phase. The relevance of these changes to the ability of LEC2 to promote somatic embryogenesis is discussed. DA - 2008/2/19/ PY - 2008/2/19/ DO - 10.1073/pnas.0712364105 VL - 105 IS - 8 SP - 3151-3156 J2 - Proceedings of the National Academy of Sciences LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.0712364105 DB - Crossref KW - seed development KW - totipotency ER - TY - JOUR TI - Cellular Programming of Plant Gene Imprinting AU - Huh, Jin Hoe AU - Bauer, Matthew J. AU - Hsieh, Tzung-Fu AU - Fischer, Robert L. T2 - Cell AB - Gene imprinting, the differential expression of maternal and paternal alleles, independently evolved in mammals and in flowering plants. A unique feature of flowering plants is a double-fertilization event in which the sperm fertilize not only the egg, which forms the embryo, but also the central cell, which develops into the endosperm (an embryo-supporting tissue). The distinctive mechanisms of gene imprinting in the endosperm, which involve DNA demethylation and histone methylation, begin in the central cell and sperm prior to fertilization. Flowering plants might have coevolved double fertilization and imprinting to prevent parthenogenetic development of the endosperm. DA - 2008/3// PY - 2008/3// DO - 10.1016/j.cell.2008.02.018 VL - 132 IS - 5 SP - 735-744 J2 - Cell LA - en OP - SN - 0092-8674 UR - http://dx.doi.org/10.1016/j.cell.2008.02.018 DB - Crossref ER - TY - JOUR TI - Synopsis of Gonolobus S. L. (Apocynaceae, Asclepiadoideae) in the United States and its Territories, Including Lectotypification of Lachnostoma Arizonicum AU - Krings, Alexander T2 - Harvard Papers in Botany AB - Recent evidence supports the recognition of Gonolobus (Apocynaceae, Asclepiadoideae), a genus of 100–150 species of vines endemic to the NewWorld, as distinct from Matelea. Synapomorphies of Gonolobus s.l. include two indels in LEAFY, as well as winged follicles. Laminar dorsal anther appendages are exclusive to the Gonolobus s.l. clade, though lacking or reduced in some species. Given this evidence and in light of past controversies regarding circumscription, this study presents a synopsis of the three species of Gonolobus recognized in the United States and its territories: G. arizonicus, G. stephanotrichus, and G. suberosus. Lachnostoma arizonicum is lectotypified. DA - 2008/12// PY - 2008/12// DO - 10.3100/1043-4534-13.2.209 VL - 13 IS - 2 SP - 209-218 J2 - Harvard Papers in Botany LA - en OP - SN - 1043-4534 UR - http://dx.doi.org/10.3100/1043-4534-13.2.209 DB - Crossref ER - TY - JOUR TI - Feeling the Pulse in Maya Medicine: An Endangered Traditional Tool for Diagnosis, Therapy, and Tracking Patients’ Progress AU - Balick, Michael J. AU - De Gezelle, Jillian M. AU - Arvigo, Rosita T2 - EXPLORE AB - Throughout history, diagnostic tools utilizing the human senses, such as pulse diagnosis, have developed all over the world. In many areas where medical technology is limited or absent, they persist, whereas in other areas these skills are in danger of extinction. The practice of pulse diagnosis by the accomplished Maya healer, Don Elijio Panti, who lived in Belize, Central America, was observed over the final decade of his life and work. Don Elijio used pulse palpation as a diagnostic tool, therapeutic tool, and as a means for tracking patients’ progress. He could diagnose a wide array of both physical and spiritual afflictions and was observed diagnosing 42 different conditions or states throughout this period by feeling the pulse. He recognized at least 28 distinct pulse types. Herein, the authors report the detailed system of an endangered diagnostic tradition as practiced by the late, acclaimed Maya healer, including pulse-type descriptions and corresponding diagnoses. Pulse diagnosis is still practiced today among some of Belize’s diminishing population of traditional healers, although no practice appears to be as developed as that of the previous generation of Maya healers. Furthermore, it is unlikely that there are new practitioners of pulse diagnosis in the Maya community to maintain and build on the disappearing tradition. Given the unfortunate paucity of data on Maya pulse diagnosis, the practice of pulse diagnosis in Traditional Chinese Medicine (TCM) is used as an illustrative framework for documenting Don Elijio’s practice. Corresponding diagnoses from TCM and Don Elijio’s system are compared, elucidating similarities between the two disparate medical systems. DA - 2008/3// PY - 2008/3// DO - 10.1016/j.explore.2007.12.002 VL - 4 IS - 2 SP - 113-119 J2 - EXPLORE LA - en OP - SN - 1550-8307 UR - http://dx.doi.org/10.1016/j.explore.2007.12.002 DB - Crossref KW - ethnomedicine KW - pulse diagnosis KW - Belize KW - Maya ER - TY - JOUR TI - Epigenomic Consequences of Immortalized Plant Cell Suspension Culture AU - Tanurdzic, Milos AU - Vaughn, Matthew W AU - Jiang, Hongmei AU - Lee, Tae-Jin AU - Slotkin, R. Keith AU - Sosinski, Bryon AU - Thompson, William F AU - Doerge, R. W AU - Martienssen, Robert A T2 - PLoS Biology AB - Plant cells grown in culture exhibit genetic and epigenetic instability. Using a combination of chromatin immunoprecipitation and DNA methylation profiling on tiling microarrays, we have mapped the location and abundance of histone and DNA modifications in a continuously proliferating, dedifferentiated cell suspension culture of Arabidopsis. We have found that euchromatin becomes hypermethylated in culture and that a small percentage of the hypermethylated genes become associated with heterochromatic marks. In contrast, the heterochromatin undergoes dramatic and very precise DNA hypomethylation with transcriptional activation of specific transposable elements (TEs) in culture. High throughput sequencing of small interfering RNA (siRNA) revealed that TEs activated in culture have increased levels of 21-nucleotide (nt) siRNA, sometimes at the expense of the 24-nt siRNA class. In contrast, TEs that remain silent, which match the predominant 24-nt siRNA class, do not change significantly in their siRNA profiles. These results implicate RNA interference and chromatin modification in epigenetic restructuring of the genome following the activation of TEs in immortalized cell culture. DA - 2008/12/9/ PY - 2008/12/9/ DO - 10.1371/journal.pbio.0060302 VL - 6 IS - 12 SP - e302 J2 - PLoS Biol LA - en OP - SN - 1545-7885 UR - http://dx.doi.org/10.1371/journal.pbio.0060302 DB - Crossref ER - TY - JOUR TI - Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection AU - Ascencio-Ibáñez, José Trinidad AU - Sozzani, Rosangela AU - Lee, Tae-Jin AU - Chu, Tzu-Ming AU - Wolfinger, Russell D. AU - Cella, Rino AU - Hanley-Bowdoin, Linda T2 - Plant Physiology AB - Geminiviruses are small DNA viruses that use plant replication machinery to amplify their genomes. Microarray analysis of the Arabidopsis (Arabidopsis thaliana) transcriptome in response to cabbage leaf curl virus (CaLCuV) infection uncovered 5,365 genes (false discovery rate <0.005) differentially expressed in infected rosette leaves at 12 d postinoculation. Data mining revealed that CaLCuV triggers a pathogen response via the salicylic acid pathway and induces expression of genes involved in programmed cell death, genotoxic stress, and DNA repair. CaLCuV also altered expression of cell cycle-associated genes, preferentially activating genes expressed during S and G2 and inhibiting genes active in G1 and M. A limited set of core cell cycle genes associated with cell cycle reentry, late G1, S, and early G2 had increased RNA levels, while core cell cycle genes linked to early G1 and late G2 had reduced transcripts. Fluorescence-activated cell sorting of nuclei from infected leaves revealed a depletion of the 4C population and an increase in 8C, 16C, and 32C nuclei. Infectivity studies of transgenic Arabidopsis showed that overexpression of CYCD3;1 or E2FB, both of which promote the mitotic cell cycle, strongly impaired CaLCuV infection. In contrast, overexpression of E2FA or E2FC, which can facilitate the endocycle, had no apparent effect. These results showed that geminiviruses and RNA viruses interface with the host pathogen response via a common mechanism, and that geminiviruses modulate plant cell cycle status by differentially impacting the CYCD/retinoblastoma-related protein/E2F regulatory network and facilitating progression into the endocycle. C2 - PMC2528102 DA - 2008/9// PY - 2008/9// DO - 10.1104/pp.108.121038 VL - 148 IS - 1 SP - 436-454 J2 - Plant Physiol. LA - eng SN - 0032-0889 DB - PubMed ER - TY - JOUR TI - Effects of detectability on estimates of geographic range size in Bignonieae AU - Sheth, S.N. AU - Lohmann, L.G. AU - Consiglio, T. AU - Jiménez, I. T2 - Conservation Biology AB - Extinction risk has not been evaluated for 96% of all described plant species. Given that the Global Strategy for Plant Conservation proposes preliminary conservation assessments of all described plant species by 2010, herbarium specimens (i.e., primary occurrence data) are increasingly being used to infer threat components from estimates of geographic range size. Nevertheless, estimates of range size based on herbarium data may be inaccurate due to collection bias associated with interspecific variation in detectability. We used data on 377 species of Bignonieae to test the hypothesis that there is a positive relationship between detectability and estimates of geographic range size derived from herbarium specimens. This relationship is expected if the proportion of the true geographic range size of a species that is documented by herbarium specimens is given by the product of the true geographic range size and the detectability of the species, assuming no relationship between true geographic range size and detectability. We developed 4 measures of detectability that can be estimated from herbarium data and examined the relationship between detectability and 2 types of estimates of geographic range size: area of occupancy and extent of occurrence. Our results from regressing estimates of extent of occurrence and area of occupancy on detectability across genera provided no support for this hypothesis. The same was true for regressions of estimated extent of occurrence on detectability across species within genera. Nevertheless, regressions of estimated area of occupancy on detectability across species within genera provided partial support for our hypothesis. We considered 3 possible explanations for this mixed outcome: violation of the assumption of no relationship between true geographic range size and detectability; the relationships between estimated geographic range size and detectability may be an artifact of a negative relationship between estimated area of occupancy and the sampling variance of detectability; detectability may have had 2 opposite effects on estimated species range sizes: one determines the proportion of the true range of a species documented by herbarium specimens and the other determines the distribution of true range size for the species actually observed with herbarium data. Our findings should help improve understanding of the potential biases incurred with the use of herbarium data. DA - 2008/// PY - 2008/// DO - 10.1111/j.1523-1739.2007.00858.x VL - 22 IS - 1 SP - 200-211 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-38849091349&partnerID=MN8TOARS KW - area of occupancy KW - Bignoniaceae KW - Bignonieae KW - collection bias KW - extent of occurrence KW - geographic range size KW - herbarium specimens KW - species detectabilit ER - TY - CONF TI - Growth factor coated sutures for improved tendon repair AU - Hamilton, P.T. AU - Buehrer, B. AU - Juzumiene, D. C2 - 2008/// C3 - 8th World Biomaterials Congress 2008 DA - 2008/// VL - 1 SP - 179 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84869010182&partnerID=MN8TOARS ER - TY - CONF TI - A peptide coating for the endothelialization of intravascular devices AU - Hamilton, P.T. AU - Solan, A. C2 - 2008/// C3 - 8th World Biomaterials Congress 2008 DA - 2008/// VL - 1 SP - 200 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84869012621&partnerID=MN8TOARS ER - TY - JOUR TI - Tracking character evolution and biogeographic history through time in Cornaceae – Does choice of methods matter? AU - Qy, Xiang AU - Thomas, D.T. T2 - Journal of Systematics and Evolution DA - 2008/// PY - 2008/// VL - 46 IS - 3 SP - 349–374 ER - TY - JOUR TI - Preparation of methyl ester precursors of biologically active agents AU - Zou, Yunfan AU - Rojas-Pierce, Marcela AU - Raikhel, Natasha AU - Pirrung, Michael T2 - BioTechniques AB - This method enables scientists to easily convert biologically active carboxylic acids into their methyl esters ("pro-drugs" generally having improved ability to penetrate cell membranes) using only equipment commonly found in a biology laboratory. An ion-exchange resin is used to convert the acid into its salt, which is thereby sequestered on the resin. The addition of methyl iodide converts the salt to the ester, which has no affinity for the resin and is readily eluted. Evaporation of the liquid phase provides the pure methyl ester. The preparation in good chemical yields of methyl esters of bioactive agents in excellent purity and 10–20 mg quantities can be achieved using this method. The method can be completed in 1 day. DA - 2008/3// PY - 2008/3// DO - 10.2144/000112704 VL - 44 IS - 3 SP - 377-384 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-41849117739&partnerID=MN8TOARS ER - TY - BOOK TI - Creating effective undergraduate research programs in science the transformation from student to scientist DA - 2008/// PY - 2008/// PB - New York: Teachers College Press ER - TY - JOUR TI - Effect of vegetation management on bird habitat in Riparian buffer zones AU - Smith, Timothy A. AU - Osmond, Deanna L. AU - Moorman, Christopher E. AU - Stucky, Jon M. AU - Gilliam, J. Wendell T2 - SOUTHEASTERN NATURALIST AB - Riparian buffers can be valuable refuge areas for wildlife in otherwise homogeneous agricultural landscapes. Government sponsored programs like the Cropland Reserve Program generally require the planting of specific vegetative species during buffer restoration, although the effectiveness of such an approach when compared to restoration by volunteer species is unknown. We studied the effect of differences in vegetation structure on avian habitat in riparian buffer zones. A 25 m (82 ft) wide planted woodland buffer, 30 m (98 ft) wide grass, shrub, and woodland three-zone buffer, and a 9 m (30 ft) wide shrub buffer were evaluated for habitat potential using breeding-bird counts and vegetation surveys. Bird density and species richness varied with the structure of the vegetative communities present at the three sites. Avian species richness and total detections were higher in the three-zone buffer than in both the shrub and planted buffer, likely a result of the diversity of vegetation at the site. These data suggest that restoration of riparian areas by allowing fallow vegetation to recolonize is at the very least equally beneficial to avian wildlife as is restoration by planting specific grass, shrub, and tree species. Buffer restoration by natural revegetation using this method could be recommended as an alternative to implementation by planting riparian species due to its simplicity and cost effectiveness. DA - 2008/// PY - 2008/// DO - 10.1656/1528-7092(2008)7[277:EOVMOB]2.0.CO;2 VL - 7 IS - 2 SP - 277-288 SN - 1938-5412 ER - TY - JOUR TI - Epigenomic consequences of immortalized plant cell suspension culture AU - Tanurdzic, M. AU - Vaughn, M. W. AU - Jiang, H. AU - Lee, T. J. AU - Slotkin, R. K. AU - Sosinski, B. AU - Thompson, W. F. AU - Doerge, R. W. AU - Martienssen, R. A. T2 - PLoS Biology DA - 2008/// PY - 2008/// VL - 6 IS - 12 SP - 2880-2895 ER - TY - JOUR TI - Development of tobacco callus cultures over expressing Arabidopsis PAP1/MYB75 transcription factor and characterization of anthocyanin biosynthesis AU - Zhou, Li-Li AU - Zeng, Hai-Nian AU - Shi, Ming-Zhu AU - Xie, De-Yu T2 - Planta DA - 2008/9/3/ PY - 2008/9/3/ DO - 10.1007/s00425-008-0809-y VL - 229 IS - 1 SP - 37-51 J2 - Planta LA - en OP - SN - 0032-0935 1432-2048 UR - http://dx.doi.org/10.1007/s00425-008-0809-y DB - Crossref KW - Anthocyanin KW - Callus KW - HPLC-mass spectrum KW - Metabolic profiling KW - Nicotiana tabacum KW - PAP1 KW - Tobacco KW - Transgene ER - TY - JOUR TI - Transgenic Arabidopsis Plants Expressing the Type 1 Inositol 5-Phosphatase Exhibit Increased Drought Tolerance and Altered Abscisic Acid Signaling AU - Perera, Imara Y. AU - Hung, Chiu-Yueh AU - Moore, Candace D. AU - Stevenson-Paulik, Jill AU - Boss, Wendy F. T2 - PLANT CELL AB - The phosphoinositide pathway and inositol-1,4,5-trisphosphate (InsP(3)) are implicated in plant responses to stress. To determine the downstream consequences of altered InsP(3)-mediated signaling, we generated transgenic Arabidopsis thaliana plants expressing the mammalian type I inositol polyphosphate 5-phosphatase (InsP 5-ptase), which specifically hydrolyzes soluble inositol phosphates and terminates the signal. Rapid transient Ca(2+) responses to a cold or salt stimulus were reduced by approximately 30% in these transgenic plants. Drought stress studies revealed, surprisingly, that the InsP 5-ptase plants lost less water and exhibited increased drought tolerance. The onset of the drought stress was delayed in the transgenic plants, and abscisic acid (ABA) levels increased less than in the wild-type plants. Stomatal bioassays showed that transgenic guard cells were less responsive to the inhibition of opening by ABA but showed an increased sensitivity to ABA-induced closure. Transcript profiling revealed that the drought-inducible ABA-independent transcription factor DREB2A and a subset of DREB2A-regulated genes were basally upregulated in the InsP 5-ptase plants, suggesting that InsP(3) is a negative regulator of these DREB2A-regulated genes. These results indicate that the drought tolerance of the InsP 5-ptase plants is mediated in part via a DREB2A-dependent pathway and that constitutive dampening of the InsP(3) signal reveals unanticipated interconnections between signaling pathways. DA - 2008/10// PY - 2008/10// DO - 10.1105/tpc.108.061374 VL - 20 IS - 10 SP - 2876-2893 SN - 1040-4651 ER - TY - JOUR TI - Rates of nucleotide substitution in Cornaceae (Cornales)—Pattern of variation and underlying causal factors AU - Xiang, Qiu-Yun (Jenny) AU - Thorne, Jeffrey L. AU - Seo, Tae-Kun AU - Zhang, Wenheng AU - Thomas, David T. AU - Ricklefs, Robert E. T2 - Molecular Phylogenetics and Evolution AB - Identifying causes of genetic divergence is a central goal in evolutionary biology. Although rates of nucleotide substitution vary among taxa and among genes, the causes of this variation tend to be poorly understood. In the present study, we examined the rate and pattern of molecular evolution for five DNA regions over a phylogeny of Cornus, the single genus of Cornaceae. To identify evolutionary mechanisms underlying the molecular variation, we employed Bayesian methods to estimate divergence times and to infer how absolute rates of synonymous and nonsynonymous substitutions and their ratios change over time. We found that the rates vary among genes, lineages, and through time, and differences in mutation rates, selection type and intensity, and possibly genetic drift all contributed to the variation of substitution rates observed among the major lineages of Cornus. We applied independent contrast analysis to explore whether speciation rates are linked to rates of molecular evolution. The results showed no relationships for individual genes, but suggested a possible localized link between species richness and rate of nonsynonymous nucleotide substitution for the combined cpDNA regions. Furthermore, we detected a positive correlation between rates of molecular evolution and morphological change in Cornus. This was particularly pronounced in the dwarf dogwood lineage, in which genome-wide acceleration in both molecular and morphological evolution has likely occurred. DA - 2008/10// PY - 2008/10// DO - 10.1016/j.ympev.2008.07.010 VL - 49 IS - 1 SP - 327-342 LA - en SN - 10557903 UR - https://linkinghub.elsevier.com/retrieve/pii/S1055790308003606 DB - Crossref Y2 - 2019/1/29/ KW - Comus KW - Cornaceae KW - Divergence time KW - Rate of molecular evolution KW - Rate of morphological evolution KW - Speciation ER - TY - JOUR TI - Endoplasmic reticulum quality control and the unfolded protein response: Insights from plants AU - Vitale, Alessandro AU - Boston, Rebecca S. T2 - TRAFFIC AB - Protein quality control (QC) within the endoplasmic reticulum and the related unfolded protein response (UPR) pathway of signal transduction are major regulators of the secretory pathway, which is involved in virtually any aspect of development and reproduction. The study of plant‐specific processes such as pathogen response, seed development and the synthesis of seed storage proteins and of particular toxins is providing novel insights, with potential implications for the general recognition events and mechanisms of action of QC and UPR. DA - 2008/10// PY - 2008/10// DO - 10.1111/j.1600-0854.2008.00780.x VL - 9 IS - 10 SP - 1581-1588 SN - 1398-9219 KW - endoplasmic reticulum KW - molecular chaperones KW - protein bodies KW - protein degradation KW - protein folding ER - TY - JOUR TI - Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection AU - Ascencio-Ibanez, J. T. AU - Sozzani, R. AU - Lee, T. J. AU - Chu, T. M. AU - Wolfinger, R. D. AU - Cella, R. AU - Hanley-Bowdoin, L. T2 - Plant Physiology DA - 2008/// PY - 2008/// VL - 148 IS - 1 SP - 436-454 ER - TY - JOUR TI - Gene-environment contributions to the development of infant vagal reactivity: The interaction of dopamine and maternal sensitivity AU - Propper, Cathi AU - Moore, Ginger A. AU - Mills-Koonce, W. Roger AU - Halpern, Carolyn Tucker AU - Hill-Soderlund, Ashley L. AU - Calkins, Susan D. AU - Carbone, Mary Anna AU - Cox, Martha T2 - CHILD DEVELOPMENT AB - This study investigated dopamine receptor genes ( DRD2 and DRD4 ) and maternal sensitivity as predictors of infant respiratory sinus arrhythmia (RSA) and RSA reactivity, purported indices of vagal tone and vagal regulation, in a challenge task at 3, 6, and 12 months in 173 infant–mother dyads. Hierarchical linear modeling (HLM) revealed that at 3 and 6 months, RSA withdrawal in response to maternal separation was greater (suggesting expected physiological regulation) in infants without the DRD2 risk allele than those with the risk allele. At 12 months, infants with the risk allele who were also exposed to maternal sensitivity showed levels of RSA withdrawal comparable to infants who were not at genetic risk. Findings demonstrate the importance of developmental analysis of gene–environment interaction. DA - 2008/// PY - 2008/// DO - 10.1111/j.1467-8624.2008.01194.x VL - 79 IS - 5 SP - 1377-1394 SN - 1467-8624 ER - TY - JOUR TI - Geminivirus-mediated gene silencing from Cotton leaf crumple virus is enhanced by low temperature in cotton AU - Tuttle, John R. AU - Idris, A. M. AU - Brown, Judith K. AU - Haigler, Candace H. AU - Robertson, Dominique T2 - PLANT PHYSIOLOGY AB - A silencing vector for cotton (Gossypium hirsutum) was developed from the geminivirus Cotton leaf crumple virus (CLCrV). The CLCrV coat protein gene was replaced by up to 500 bp of DNA homologous to one of two endogenous genes, the magnesium chelatase subunit I gene (ChlI) or the phytoene desaturase gene (PDS). Cotyledons of cotton cultivar 'Deltapine 5415' bombarded with the modified viral vectors manifested chlorosis due to silencing of either ChlI or PDS in approximately 70% of inoculated plants after 2 to 3 weeks. Use of the green fluorescence protein gene showed that replication of viral DNA was restricted to vascular tissue and that the viral vector could transmit to leaves, roots, and the ovule integument from which fibers originate. Temperature had profound effects on vector DNA accumulation and the spread of endogenous gene silencing. Consistent with reports that silencing against viruses increases at higher temperatures, plants grown at a 30 degrees C/26 degrees C day/night cycle had a greater than 10-fold reduction in viral DNA accumulation compared to plants grown at 22 degrees C/18 degrees C. However, endogenous gene silencing decreased at 30 degrees C/26 degrees C. There was an approximately 7 d delay in the onset of gene silencing at 22 degrees C/18 degrees C, but silencing was extensive and persisted throughout the life of the plant. The extent of silencing in new growth could be increased or decreased by changing temperature regimes at various times following the onset of silencing. Our experiments establish the use of the CLCrV silencing vector to study gene function in cotton and show that temperature can have a major impact on the extent of geminivirus-induced gene silencing. DA - 2008/9// PY - 2008/9// DO - 10.1104/pp.108.123869 VL - 148 IS - 1 SP - 41-50 SN - 1532-2548 ER - TY - JOUR TI - Expansion of gallery forests into central Brazilian savannas AU - Silva, Lucas C. R. AU - Sternberg, Leonel AU - Haridasan, Mundayatan AU - Hoffmann, William A. AU - Miralles-Wilhelm, Fernando AU - Franco, Augusto C. T2 - GLOBAL CHANGE BIOLOGY AB - Abstract Upland tropical forests have expanded and contracted in response to past climates, but it is not clear whether similar dynamics were exhibited by gallery (riparian) forests within savanna biomes. Because such forests generally have access to ample water, their extent may be buffered against changing climates. We tested the long‐term stability of gallery forest boundaries by characterizing the border between gallery forests and savannas and tracing the presence of gallery forest through isotopic analysis of organic carbon in the soil profile. We measured leaf area index, grass vs. shrub or tree coverage, the organic carbon, phosphorus, nitrogen and calcium concentrations in soils and the carbon isotope ratios of soil organic matter in two transitions spanning gallery forests and savanna in a Cerrado ecosystem. Gallery forests without grasses typically show a greater leaf area index in contrast to savannas, which show dense grass coverage. Soils of gallery forests have significantly greater concentrations of organic carbon, phosphorus, nitrogen and calcium than those of savannas. Soil organic carbon of savannas is significantly more enriched in 13 C compared with that of gallery forests. This difference in enrichment is in part caused by the presence of C 4 grasses in savanna ecosystem and its absence in gallery forests. Using the 13 C abundance as a signature for savanna and gallery forest ecosystems in 1 m soil cores, we show that the borders of gallery forests have expanded into the savanna and that this process initiated at least 3000–4000 bp based on 14 C analysis. Gallery forests, however, may be still expanding as we found more recent transitions according to 14 C activity measurements. We discuss the possible mechanisms of gallery forest expansion and the means by which nutrients required for the expansion of gallery forest might accumulate. DA - 2008/9// PY - 2008/9// DO - 10.1111/j.1365-2486.2008.01637.x VL - 14 IS - 9 SP - 2108-2118 SN - 1365-2486 KW - carbon isotope ratios KW - carbon sink KW - carbon stocks KW - climate change KW - gallery forest KW - leaf area index KW - nutrients KW - savanna KW - tropical ecosystems KW - vegetation dynamics ER - TY - JOUR TI - SEUSS and AINTEGUMENTA mediate patterning and ovule initiation during gynoecium medial domain development AU - Azhakanandam, Sridevi AU - Nole-Wilson, Staci AU - Bao, Fang AU - Franks, Robert G. T2 - PLANT PHYSIOLOGY AB - The Arabidopsis (Arabidopsis thaliana) gynoecium, the female floral reproductive structure, requires the action of genes that specify positional identities during its development to generate an organ competent for seed development and dispersal. Early in gynoecial development, patterning events divide the primordium into distinct domains that will give rise to specific tissues and organs. The medial domain of the gynoecium gives rise to the ovules, and several other structures critical for reproductive competence. Here we report a synergistic genetic interaction between seuss and aintegumenta mutants resulting in a complete loss of ovule initiation and a reduction of the structures derived from the medial domain. We show that patterning events are disrupted early in the development of the seuss aintegumenta gynoecia and we identify PHABULOSA (PHB), REVOLUTA, and CRABS CLAW (CRC) as potential downstream targets of SEUSS (SEU) and AINTEGUMENTA (ANT) regulation. Our genetic data suggest that SEU additionally functions in pathways that are partially redundant and parallel to PHB, CRC, and ANT. Thus, SEU and ANT are part of a complex and robust molecular system that coordinates patterning cues and cellular proliferation along the three positional axes of the developing gynoecium. DA - 2008/3// PY - 2008/3// DO - 10.1104/pp.107.114751 VL - 146 IS - 3 SP - 1165-1181 SN - 0032-0889 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-48949120198&partnerID=MN8TOARS ER - TY - JOUR TI - On the Generic Circumscription of Gonolobus (Apocynaceae, Asclepiadoideae): Evidence from Molecules and Morphology AU - Krings, Alexander AU - Thomas, David T. AU - Xiang, Qiu-Yun T2 - Systematic Botany AB - Abstract Gonolobus (Apocynaceae, Asclepiadoideae) is a New World genus comprising an estimated 100–150 species. Variation in estimated species numbers is largely the result of still poorly known tropical taxa and differences regarding generic limits. Characters historically used to delimit genera such as Gonolobus within Gonolobinae—such as laminar dorsal anther appendages and various follicle morphologies—have been controversial and their evolution remains unknown, not having been explored in a phylogenetic framework. The primary objectives of the current study were to (1) test the monophyly of Gonolobus sensu Woodson in the context of a phylogeny of New World Asclepiadeae and (2) explore the evolution of laminar dorsal anther appendages and winged follicles with respect to their potential utility in generic circumscription. Chloroplast (trnL–F, rpsl6) data are newly presented for sixty-three taxa of Gonolobinae, representing an increased sampling of the subtribe from a maximum of seven taxa in prior stu... DA - 2008/4/1/ PY - 2008/4/1/ DO - 10.1600/036364408784571527 VL - 33 IS - 2 SP - 403-415 LA - en SN - 03636445, 15482324 ST - On the Generic Circumscription of Gonolobus (Apocynaceae, Asclepiadoideae) UR - http://openurl.ingenta.com/content/xref?genre=article&issn=0363-6445&volume=33&issue=2&spage=403 DB - Crossref Y2 - 2019/1/29/ KW - delimitation KW - dorsal anther appendages KW - Gonolobinae KW - winged follicles ER - TY - JOUR TI - Microsatellite analysis of a broad hybrid zone in Aesculus (Sapindales) – Inferences in genetic structure and evolution AU - Thomas, D.T. AU - Ahedor, A.R. AU - Williams, C.F. AU - DePamphilis, C. AU - Crawford, D.J. AU - Xiang, Q.Y. T2 - International Journal of Plant Sciences AB - The genetic structure of a broad hybrid zone involving three hybridizing Aesculus species, Aesculus flava, Aesculus pavia, and Aesculus sylvatica, was examined. The objectives were to assess genetic variability, to test previously reported hypotheses on patterns of gene flow, and to infer the genetic structure and evolutionary processes in the hybrid zone. Samples from 24 populations within parental ranges and the hybrid zone were analyzed for variation at microsatellite and intersimple sequence repeat loci. The results indicated that genetic variability was similar among parental and hybrid populations, indicating no evident increased diversity in the hybrid zone. Most hybrid individuals were genetically more similar to A. sylvatica than to the other two species, and the overall genetic structure of the hybrid zone is asymmetrically biased toward A. sylvatica. Our analyses supported occasional recurrent long‐distant gene flow from A. pavia and frequent gene flow from A. sylvatica into the hybrid zone, agreeing with results of a previous allozyme study. Collectively, the data from our study and previous allozyme and chloroplast DNA studies indicate that both historical localized gene flow and recurrent long‐distant gene flow have contributed to the existence of the hybrid zone, that is, its origin via historical localized gene flow, while its maintenance involves ongoing long‐distance pollen dispersal. DA - 2008/// PY - 2008/// DO - 10.1086/533605 VL - 169 IS - 5 SP - 647–657 SN - 1537-5315 KW - aesculus KW - hybrid zone KW - ISSR KW - long-distance gene flow KW - microsatellites ER - TY - JOUR TI - Tracking character evolution and biogeographic history through time in Cornaceae - Does choice of methods matter? AU - Xiang, Qiu-Yun AU - Thomas, David T. T2 - JOURNAL OF SYSTEMATICS AND EVOLUTION DA - 2008/5// PY - 2008/5// DO - 10.3724/SP.J.1002.2008.08056 VL - 46 IS - 3 SP - 349-374 SN - 1759-6831 KW - AReA KW - BAYESTRAITS KW - BEAST KW - biogeography KW - chromosome evolution KW - Cornaceae KW - fruit and inflorescence evolution KW - LAGRANGE KW - MESQUITE KW - divergence time ER - TY - JOUR TI - Resin flow responses to fertilization, wounding and fungal inoculation in loblolly pine (Pinus taeda) in North Carolina AU - Knebel, Larissa AU - Robison, Daniel J. AU - Wentworth, Thomas R. AU - Klepzig, Kier D. T2 - TREE PHYSIOLOGY AB - Resin flow is the primary means of natural defense against southern pine beetle (Dendroctonus frontalis Zimm.), the most important insect pest of Pinus spp. in the southern United States. As a result, factors affecting resin flow are of interest to researchers and forest managers. We examined the influence of fertilization, artificial wounding and fungal inoculation on resin flow in 6- and 12-year-old stands of loblolly pine (Pinus taeda L.) and determined the extent of that influence within and above the wounded stem area and through time. Fertilization increased constitutive resin flow, but only the younger trees sustained increased resin flow after wounding and inoculation treatments. An induced resin flow response occurred between 1 and 30 days after wounding and inoculation treatments. Wounding with inoculation resulted in greater resin flow than wounding alone, but increasing amounts of inoculum did not increase resin flow. Increased resin flow (relative to controls) lasted for at least 90 days after wounding and inoculation. This increase appeared to be limited to the area of treatment, at least in younger trees. The long-lasting effects of fungal inoculation on resin flow, as well as the response to fertilization, suggest that acquired resistance through induced resin flow aids in decreasing susceptibility of loblolly pine to southern pine beetle. DA - 2008/6// PY - 2008/6// DO - 10.1093/treephys/28.6.847 VL - 28 IS - 6 SP - 847-853 SN - 1758-4469 KW - Dendroctonus frontalis KW - hypersensitive response KW - Ophiostoma minus KW - southern pine beetle ER - TY - JOUR TI - Phenotypic plasticity and genotype by environment interaction for olfactory behavior in Drosophila melanogaster AU - Sambandan, Deepa AU - Carbone, Mary Anna AU - Anholt, Robert R. H. AU - Mackay, Trudy E. C. T2 - GENETICS AB - Abstract Genotype by environment interactions (GEI) play a major part in shaping the genetic architecture of quantitative traits and are confounding factors in genetic studies, for example, in attempts to associate genetic variation with disease susceptibility. It is generally not known what proportion of phenotypic variation is due to GEI and how many and which genes contribute to GEI. Behaviors are complex traits that mediate interactions with the environment and, thus, are ideally suited for studies of GEI. Olfactory behavior in Drosophila melanogaster presents an opportunity to systematically dissect GEI, since large numbers of genetically identical individuals can be reared under defined environmental conditions and the olfactory system of Drosophila and its behavioral response to odorants have been well characterized. We assessed variation in olfactory behavior in a population of 41 wild-derived inbred lines and asked to what extent different larval-rearing environments would influence adult olfactory behavior and whether GEI is a minor or major contributing source of phenotypic variation. We found that ∼50% of phenotypic variation in adult olfactory behavior is attributable to GEI. In contrast, transcriptional analysis revealed that only 20 genes show GEI at the level of gene expression [false discovery rate (FDR) &lt; 0.05], some of which are associated with physiological responses to environmental chemicals. Quantitative complementation tests with piggyBac-tagged mutants for 2 of these genes (CG9664 and Transferrin 1) demonstrate that genes that show transcriptional GEI are candidate genes for olfactory behavior and that GEI at the level of gene expression is correlated with GEI at the level of phenotype. DA - 2008/6// PY - 2008/6// DO - 10.1534/genetics.108.086769 VL - 179 IS - 2 SP - 1079-1088 SN - 0016-6731 ER - TY - JOUR TI - Molecular evolution of PISTILLATA-like genes in the dogwood genus Cornus (Cornaceae) AU - Zhang, Wenheng AU - Xiang, Qiu-Yun AU - Thomas, David T. AU - Wiegmann, Brian M. AU - Frohlich, Michael W. AU - Soltis, Douglas E. T2 - MOLECULAR PHYLOGENETICS AND EVOLUTION AB - The MADS-box gene family encodes critical regulators determining floral organ development. Understanding evolutionary patterns and processes of MADS-box genes is an important step toward unraveling the molecular basis of floral morphological evolution. In this study, we investigated the evolution of PI-like genes of the MADS-box family in the dogwood genus Cornus (Cornaceae). Cornus is a eudicot lineage in the asterids clade, and is intriguing in evolving petaloid bract morphology in two major lineages within the genus. The gene genealogy reconstructed using genomic DNA and cDNA sequences suggests multiple PI-like gene duplication events in Cornus. An ancient duplication event resulted in two ancient paralogs, CorPI-A and CorPI-B, which have highly diverged intron regions. Duplication of CorPI-A further resulted in two paralogs in one subgroup of Cornus, the BW group that does not produce modified bracts. Most species analyzed were found to contain more than one copy of the PI-like gene with most copies derived recently within species. Estimation and comparison of dN/dS ratios revealed relaxed selection in the PI-like gene in Cornus in comparison with the gene in the closely related outgroups Alangium and Davidia, and in other flowering plants. Selection also differed among major gene copies, CorPI-A and CorPI-B, and among different morphological subgroups of Cornus. Variation in selection pressures may indicate functional changes in PI-like genes after gene duplication and among different lineages. Strong positive selection at three amino acid sites of CorPI was also detected from a region critical for dimerization activity. Total substitution rates of the CorPI gene also differ among lineages of Cornus, showing a trend similar to that found in dN/dS ratios. We also found that the CorPI-A copy contains informative phylogenetic information when compared across species of Cornus. DA - 2008/4// PY - 2008/4// DO - 10.1016/j.ympev.2007.12.022 VL - 47 IS - 1 SP - 175-195 SN - 1095-9513 KW - adaptive evolution KW - Cornus KW - gene duplication KW - MADS-box genes KW - PISTILLATA-like genes KW - regulatory gene evolution ER - TY - JOUR TI - Microbial pretreatment of cotton stalks by solid state cultivation of Phanerochaete chrysosporium AU - Shi, Jian AU - Chinn, Mari S. AU - Sharma-Shivappa, Ratna R. T2 - BIORESOURCE TECHNOLOGY AB - White rot fungi degrade lignin and have biotechnological applications in conversion of lignocellulose to valuable products. Pretreatment is an important processing step to increase the accessibility of cellulosic material in plant biomass, impacting efficiency of subsequent hydrolysis and fermentation. This study investigated microbial pretreatment of cotton stalks by solid state cultivation (SSC) using Phanerochaete chrysosporium to facilitate the conversion into ethanol. The effects of substrate moisture content (M.C.; 65%, 75% and 80% wet-basis), inorganic salt concentration (no salts, modified salts without Mn(2+), modified salts with Mn(2+)) and culture time (0-14 days) on lignin degradation (LD), solids recovery (SR) and availability of carbohydrates (AOC) were examined. Moisture content significantly affected lignin degradation, with 75% and 80% M.C. degrading approximately 6% more lignin than 65% M.C. after 14 days. Within the same moisture content, treatments supplemented with salts were not statistically different than those without salts for LD and AOC. Within the 14day pretreatment, additional time resulted in greater lignin degradation, but indicated a decrease in SR and AOC. Considering cost, solid state cultivation at 75% M.C. without salts was the most preferable pretreatment resulting in 27.6% lignin degradation, 71.1% solids recovery and 41.6% availability of carbohydrates over a period of 14 days. Microbial pretreatment by solid state cultivation has the potential to be a low cost, environmentally friendly alternative to chemical approaches. Moisture relationships will be significant to the design of an effective microbial pretreatment process using SSC technology. DA - 2008/9// PY - 2008/9// DO - 10.1016/j.biortech.2007.11.069 VL - 99 IS - 14 SP - 6556-6564 SN - 1873-2976 KW - cotton stalk KW - pretreatment KW - phanerochaete chrysosporium KW - bioethanol KW - lignin ER - TY - JOUR TI - Mannitol biosynthesis is required for plant pathogenicity by Alternaria alternata AU - Veleaz, Heriberto AU - Glassbrook, Norman J. AU - Daub, Margaret E. T2 - FEMS MICROBIOLOGY LETTERS AB - Mannitol has been hypothesized to play a role in antioxidant defense. In previous work, we confirmed the presence of the two mannitol biosynthetic enzymes, mannitol dehydrogenase (MtDH) and mannitol 1-phosphate 5-dehydrogenase (MPDH), in the fungus Alternaria alternata and created disruption mutants for both enzymes. These mutants were used to investigate the role of mannitol in pathogenicity of A. alternata on its host, tobacco. Conidia of all mutants were viable and germinated normally. GC-MS analysis demonstrated elevated levels of trehalose in the mutants, suggesting that trehalose may substitute for mannitol as a storage compound for germination. Tobacco inoculation showed no reduction in lesion severity caused by the MtDH mutant as compared with wild type; however, the MPDH mutant and a mutant in both enzymes caused significantly less disease. Microscopy analysis indicated that the double mutant was unaffected in the ability to germinate and produce appressoria on tobacco leaves and elicited a defense response from the host, indicating that it was able to penetrate and infect the host. We conclude that mannitol biosynthesis is required for pathogenesis of A. alternata on tobacco, but is not required for spore germination either in vitro or in planta or for initial infection. DA - 2008/8// PY - 2008/8// DO - 10.1111/j.1574-6968.2008.01224.x VL - 285 IS - 1 SP - 122-129 SN - 0378-1097 KW - mannitol metabolism KW - reactive oxygen species KW - antioxidant KW - plant disease ER - TY - JOUR TI - Controls on stand transpiration and soil water utilization along a tree density gradient in a Neotropical savanna AU - Bucci, Sandra J. AU - Scholz, Fabian G. AU - Goldstein, Guillermo AU - Hoffmann, William A. AU - Meinzer, Frederick C. AU - Franco, Augusto C. AU - Giambelluca, Thomas AU - Miralles-Wilhelm, Fernando T2 - AGRICULTURAL AND FOREST METEOROLOGY AB - Environmental controls of stand-level tree transpiration (E) and seasonal patterns of soil water utilization were studied in five central Brazilian savanna (Cerrado) sites differing in tree density. Tree density of Cerrado vegetation in the study area consistently changes along topographic gradients from ∼1000 trees ha−1 in open savannas (campo sujo) at the lower end of the topographic gradient to >3000 trees ha−1 in woodlands (cerradão) at the upper end of the gradient. Tree canopy resistance (rC) increased linearly with increasing daily mean air saturation deficit (D) at all sites, but cerradão and cerrado denso sites with higher tree density and higher tree leaf area index (LAI) had lower rC values at all values of D compared to physiognomies with lower tree density, suggesting that rC was less sensitive to changes in D in physiognomies with high tree density and LAI. During the peak of the dry season, mean soil water potential at 0.20 m depth was most negative in the sites with the lowest tree basal area and increased linearly with basal area across sites. In contrast, soil water storage in the 0.10–2.50 m layer decreased exponentially with increasing basal area, consistent with trees in higher density sites utilizing a larger proportion of available soil water at depth during the dry season. Maximum tree transpiration was highest in the cerradão and cerrado denso (∼0.81 mm day−1). Despite higher evaporative demand during the dry season, E was similar between the dry and wet seasons within each study site, which was associated with lower LAI and canopy conductance (gC) during the dry season compared to the wet season. Leaf area index was a good predictor of E and gC. For both dry and wet season data combined, E increased asymptotically with increasing LAI across all physiognomic types, allowing LAI to be used as a predictor of spatial variation of E. The lack of seasonality in E across the Cerrado physiognomies studied could not be explained by individual constraining variables such as D or soil water potential near the surface, but was consistent with the influence of multiple regulatory effects of D and soil water potential on seasonal changes in leaf area and gC. DA - 2008/6/30/ PY - 2008/6/30/ DO - 10.1016/j.agrformet.2007.11.013 VL - 148 IS - 6-7 SP - 839-849 SN - 1873-2240 KW - canopy resistance KW - Cerrado KW - leaf area index KW - sap flow KW - soil water potential ER - TY - JOUR TI - A new branch of endoplasmic reticulum stress signaling and the osmotic signal converge on plant-specific asparagine-rich proteins to promote cell death AU - Costa, Maximiller D. L. AU - Reis, Pedro A. B. AU - Valente, Maria Anete S. AU - Irsigler, Andre S. T. AU - Carvalho, Claudine M. AU - Loureiro, Marcelo E. AU - Aragao, Francisco J. L. AU - Boston, Rebecca S. AU - Fietto, Luciano G. AU - Fontes, Elizabeth P. B. T2 - JOURNAL OF BIOLOGICAL CHEMISTRY AB - NRPs (N-rich proteins) were identified as targets of a novel adaptive pathway that integrates endoplasmic reticulum (ER) and osmotic stress signals based on coordinate regulation and synergistic up-regulation by tunicamycin and polyethylene glycol treatments. This integrated pathway diverges from the molecular chaperone-inducing branch of the unfolded protein response (UPR) in several ways. While UPR-specific targets were inversely regulated by ER and osmotic stresses, NRPs required both signals for full activation. Furthermore, BiP (binding protein) overexpression in soybean prevented activation of the UPR by ER stress inducers, but did not affect activation of NRPs. We also found that this integrated pathway transduces a PCD signal generated by ER and osmotic stresses that result in the appearance of markers associated with leaf senescence. Overexpression of NRPs in soybean protoplasts induced caspase-3-like activity and promoted extensive DNA fragmentation. Furthermore, transient expression of NRPs in planta caused leaf yellowing, chlorophyll loss, malondialdehyde production, ethylene evolution, and induction of the senescence marker gene CP1. This phenotype was alleviated by the cytokinin zeatin, a potent senescence inhibitor. Collectively, these results indicate that ER stress induces leaf senescence through activation of plant-specific NRPs via a novel branch of the ER stress response. NRPs (N-rich proteins) were identified as targets of a novel adaptive pathway that integrates endoplasmic reticulum (ER) and osmotic stress signals based on coordinate regulation and synergistic up-regulation by tunicamycin and polyethylene glycol treatments. This integrated pathway diverges from the molecular chaperone-inducing branch of the unfolded protein response (UPR) in several ways. While UPR-specific targets were inversely regulated by ER and osmotic stresses, NRPs required both signals for full activation. Furthermore, BiP (binding protein) overexpression in soybean prevented activation of the UPR by ER stress inducers, but did not affect activation of NRPs. We also found that this integrated pathway transduces a PCD signal generated by ER and osmotic stresses that result in the appearance of markers associated with leaf senescence. Overexpression of NRPs in soybean protoplasts induced caspase-3-like activity and promoted extensive DNA fragmentation. Furthermore, transient expression of NRPs in planta caused leaf yellowing, chlorophyll loss, malondialdehyde production, ethylene evolution, and induction of the senescence marker gene CP1. This phenotype was alleviated by the cytokinin zeatin, a potent senescence inhibitor. Collectively, these results indicate that ER stress induces leaf senescence through activation of plant-specific NRPs via a novel branch of the ER stress response. The unfolded protein response (UPR) 5The abbreviations used are: UPR, unfolded protein response; AZC, l-azetidine-2-carboxylic acid; BAP, 6-benzylaminopurine; BiP, binding protein; CNX, calnexin; CRT, calreticulin; DCD, development and cell death; ER, endoplasmic reticulum; MDA, malondialdehyde; NIG, NSP-interacting GTPase; NRPs, N-rich proteins; PCD, programmed cell death; PDI, protein-disulfide isomerase; PEG, polyethylene glycol; SMP, seed maturation protein; MES, 4-morpholineethanesulfonic acid; GFP, green fluorescent protein; TUNEL, terminal deoxynucleotidyltransferase-mediated dUTP nick end-labeling; WT, wild type; RACE, rapid amplification of cDNA ends. 5The abbreviations used are: UPR, unfolded protein response; AZC, l-azetidine-2-carboxylic acid; BAP, 6-benzylaminopurine; BiP, binding protein; CNX, calnexin; CRT, calreticulin; DCD, development and cell death; ER, endoplasmic reticulum; MDA, malondialdehyde; NIG, NSP-interacting GTPase; NRPs, N-rich proteins; PCD, programmed cell death; PDI, protein-disulfide isomerase; PEG, polyethylene glycol; SMP, seed maturation protein; MES, 4-morpholineethanesulfonic acid; GFP, green fluorescent protein; TUNEL, terminal deoxynucleotidyltransferase-mediated dUTP nick end-labeling; WT, wild type; RACE, rapid amplification of cDNA ends. is activated by stress conditions that disrupt the endoplasmic reticulum (ER) homeostasis and the proper folding and maturation of secretory proteins. This complex signaling cascade is conserved in eukaryotes, although the mechanism of signal transduction differs across species. The central transducer of the UPR is IRE1, a transmembrane kinase that appears to be the only means of signal transduction in yeast, but is part of a tripartite signaling response in animals, which also includes the ER-transmembrane transducers PERK and ATF6 (1Maa Y. Hendershot L.M. J. Chem. Neuroanatomy. 2004; 28: 51-65Crossref PubMed Scopus (313) Google Scholar). In plants, there is compelling evidence that the UPR operates through IRE1 (2Buzeli R.A.A. Cascardo J.C.M. Rodrigues L.A.Z. Andrade M.O. Loureiro M.E. Otoni W.C. Fontes E.P.B. Plant Mol. Biol. 2002; 50: 757-771Crossref PubMed Scopus (37) Google Scholar, 3Denecke J. Carlsson L.E. Vidal S. Hoglund A.-S. Ek B. van Zeiji M.J. Sinjorgo K.M.C. Palva E.T. Plant Cell. 1995; 7: 391-406Crossref PubMed Scopus (184) Google Scholar, 4Irsigler A.S. Costa M.D. Zhang P. Reis P.A.B. Dewey R.E. Boston R.S. Fontes E.P.B. BMC Genomics. 2007; 8: 431Crossref PubMed Scopus (84) Google Scholar, 5Kamauchi S. Nakatani H. Nakano C. Urade R. Febs. J. 2005; 272: 3461-3476Crossref PubMed Scopus (163) Google Scholar, 6Kirst M.E. Meyer D.J. Gibbon B.C. Jung R. Boston R.S. Plant Physiol. 2005; 138: 218-231Crossref PubMed Scopus (52) Google Scholar, 7Martinez I.M. Chrispeels M.J. Plant Cell. 2003; 15: 561-576Crossref PubMed Scopus (331) Google Scholar), but characterization of this cytoprotective signaling pathway is still incipient. The only known components of plant UPR are the putative proximal sensors that include two Arabidopsis Ire1p homologues and two ATF6-related proteins, designated AtbZIP28 and AtbZIP60 (8Koizumi N. Martinez I.M. Kimata Y. Kohno K. Sano H. Chrispeels M.J. Plant Physiol. 2001; 127: 949-962Crossref PubMed Scopus (186) Google Scholar, 9Iwata Y. Koizumi N. Proc. Natl. Acad. Sci. U. S. A. 2005; 102: 5280-5285Crossref PubMed Scopus (266) Google Scholar, 10Liu J.-X. Srivastava R. Che P. Howell S.H. Plant Cell. 2007; 19: 4111-4119Crossref PubMed Scopus (323) Google Scholar). Although the N-terminal domain of plant IRE1 homologues can replace functionally the yeast IRE1, downstream components of the IRE1 signaling are yet to be identified (8Koizumi N. Martinez I.M. Kimata Y. Kohno K. Sano H. Chrispeels M.J. Plant Physiol. 2001; 127: 949-962Crossref PubMed Scopus (186) Google Scholar). AtbZIP60 and AtbZIP28 have been described as ER stress-induced leucine zipper (bZIP) transcription factor genes that are anchored to the ER membrane under normal conditions and may serve as ER stress sensors and transducers (9Iwata Y. Koizumi N. Proc. Natl. Acad. Sci. U. S. A. 2005; 102: 5280-5285Crossref PubMed Scopus (266) Google Scholar, 10Liu J.-X. Srivastava R. Che P. Howell S.H. Plant Cell. 2007; 19: 4111-4119Crossref PubMed Scopus (323) Google Scholar). Upon sensing the ER stress, AtbZIP28 is proteolytically released from the membrane and translocated to the nucleus by a mechanism that is predicted to be similar to that acting on mammalian ATF6 transducer (10Liu J.-X. Srivastava R. Che P. Howell S.H. Plant Cell. 2007; 19: 4111-4119Crossref PubMed Scopus (323) Google Scholar). Expression of a truncated form of either AtbZIP28 or AtbZIP60, harboring the bZIP domain, up-regulates UPR target genes under normal conditions (9Iwata Y. Koizumi N. Proc. Natl. Acad. Sci. U. S. A. 2005; 102: 5280-5285Crossref PubMed Scopus (266) Google Scholar, 10Liu J.-X. Srivastava R. Che P. Howell S.H. Plant Cell. 2007; 19: 4111-4119Crossref PubMed Scopus (323) Google Scholar). The UPR up-regulated chaperone BiP (binding protein) is central to this cytoprotective response as the indirect sensor of alterations in the ER environment. In addition to this role as molecular chaperone, in mammalian cells, BiP has been shown to regulate the UPR by controlling the activation status of the three transducers, IRE1, PERK, and ATF6 (11Malhotra J.D. Kaufman R.J. Semin. Cell Dev. Biol. 2007; 18: 716-731Crossref PubMed Scopus (759) Google Scholar). Under normal conditions, the luminal domains of these sensors are occupied with BiP, which is recruited by unfolded proteins upon ER stress. The dissociation of BiP promotes oligomerization and phosphorylation of IRE1 and PERK, as well as relocalization of ATF6 to the Golgi where its transcriptional domain is proteolytically released from the membrane into the nucleus. Although the UPR has not been extensively characterized in plants, conserved aspects between mammalian and plant UPR include its negative regulation by BiP, possibly through interaction with the putative proximal sensors, and the BiP cytoprotective role (12Leborgne-Castel N. Jelitto-Van Dooren E. Crofts A.J. Denecke J. Plant Cell. 1999; 11: 459-469Crossref PubMed Scopus (152) Google Scholar). In fact, we have previously demonstrated that BiP confers tolerance to water deficit in transgenic plants (13Alvim F.C. Carolino S.M.B. Cascardo J.C.M. Nunes C.C. Martinez C.A. Otoni W.C. Fontes E.P.B. Plant Physiol. 2001; 126: 1042-1054Crossref PubMed Scopus (185) Google Scholar). Constant challenges by adverse conditions and environmental stresses pose major constraints for development, growth, and productivity of plants. Our knowledge about stress-specific adaptive responses and cross-talk between signaling cascades has advanced considerably with genome-wide analyses and expression-profiling studies in different plant species under different stress conditions (14Denekamp M. Smeekens S.C. Plant Physiol. 2003; 132: 1415-1423Crossref PubMed Scopus (158) Google Scholar, 15Kreps J.A. Wu Y.J. Chang H.S. Zhu T. Wang X. Harper J.F. Plant Physiol. 2002; 130: 2129-2141Crossref PubMed Scopus (1190) Google Scholar, 16Seki M. Narusaka M. Ishida J. Nanjo T. Fujita M. Oono Y. Kamiya A. Nakajima M. Enju A. Sakurai T. Satou M. Akiyama K. Taji T. Yamaguchi-Shinozaki K. Carninci P. Kawai J. Hayashizaki Y. Shinozaki K. Plant J. 2002; 31: 279-292Crossref PubMed Scopus (1613) Google Scholar). A common theme that has emerged is that plants transduce environmental signals through integrated networks between different stress-induced adaptive responses. Despite the potential of ER stress response to accommodate adaptive pathways, its integration with environmental-induced responses is poorly understood in plants. Recently, we performed global expression profiling on soybean leaves exposed to polyethylene glycol (PEG) treatment or to UPR inducers to identify integrated networks between osmotic and ER stress-induced adaptive responses (4Irsigler A.S. Costa M.D. Zhang P. Reis P.A.B. Dewey R.E. Boston R.S. Fontes E.P.B. BMC Genomics. 2007; 8: 431Crossref PubMed Scopus (84) Google Scholar). In addition to uncovering specific responses to ER stress and osmotically regulated changes, a small proportion (5.5%) of the up-regulated genes represented a shared response that seemed to integrate the two signaling pathways. These co-regulated genes had similar induction kinetics and a synergistic response to the combination of osmotic- and ER stress-inducing treatments. Thus, they were considered to be downstream targets of the integrating pathway. Two ESTs (N-richI and N-richII), which showed the strongest synergistic induction, were homologous to genes encoding asparagine-rich proteins that have a plant-specific development and cell death (DCD) domain. Here we investigated the possibility that the integrated pathway might transduce a programmed cell death (PCD) signal generated by ER and osmotic stress. We demonstrated that induction of target genes, such as N-richI and N-richII ESTs, by ER stress-inducing agents occurs via a pathway distinct from the UPR. We also found that the N-rich proteins are critical mediators of osmotic- and ER stress-induced cell death in plants. Plant Growth, Soybean Suspension Cells, and Stress Treatments—Soybean (Glycine max) seeds (cultivar Conquista) were germinated in soil and grown under greenhouse conditions (avg: 21 °C, max: 31 °C, min: 15 °C) under natural conditions of light, 70% relative humidity, and approximately equal day and night length. Two weeks after germination, the seedlings were transferred to a 2-ml 10 μg/ml tunicamycin (Sigma) solution (DMSO, as control). After 12 and 24 h of treatment, the leaves were harvested, immediately frozen in liquid N2, and stored at -80 °C until use. Alternatively, the aerial portions of 3-week-old plants were excised below the cotyledons and directly placed into 15 ml of 10% (w/v) polyethylene glycol (PEG; MW 8000, Sigma), 10 μg/ml tunicamycin (Sigma), or 50 mm l-azetidine-2-carboxylic acid (AZC, Sigma) solutions. The first trifoliate leaves were harvested after 4, 10, or 16 h of PEG and tunicamycin treatments, then immediately frozen in liquid N2, and stored at -80 °C until use. Each stress treatment and RNA extraction were replicated in three independent experiments. Cotyledons cells from the soybean variety Conquista were cultured as described previously (17Cascardo J.C.M. Almeida R.S. Buzeli R.A.A. Carolino S.M.B. Otoni W.C. Fontes E.P.B. J. Biol. Chem. 2000; 275: 14494-14500Abstract Full Text Full Text PDF PubMed Scopus (62) Google Scholar). Cells were subcultured every 10 days by diluting the culture 1:10 in fresh MS medium. All treatments were performed on 5-day-old subcultures. Tunicamycin was added to cultures by dilution of a 5 mg/ml stock in DMSO into normal growth medium to 10 μg/ml and incubated for the intervals indicated in the figure legends. For PEG-induced dehydration, the cells were washed and then cultured with normal growth medium containing 10% (w/v) PEG-8000 for the indicated intervals. Suspension cells were directly treated with 0.5 μg/ml cycloheximide, 10 μm BAP (6-benzylaminopurine), and 10 μm zeatin for the intervals indicated in the figure legends. After treatments, the cells were filtrated under vacuum, washed with 0.25 m NaCl, and immediately frozen in liquid N2. Rapid Amplification of 3′-cDNA Ends (3′-RACE) and NRP-B cDNA Cloning—3′-RACE was performed using the GeneRacer kit (Invitrogen). Total RNA isolated from PEG-treated soybean leaves was used for reverse transcription, and an N-richI EST-specific primer (FwNRich1, TACAGGCATCCAATTTGGCGAACC) and oligo dT primer from the kit were used in the polymerase chain reaction. The amplified fragment was cloned in pCR4 to generate pCR4-NRPB, which harbors the full-length NRP-B cDNA. Plasmid Construction—For transient expression in protoplasts, NRP-B and NRP-A (gi:57898928) cDNAs were amplified and inserted into the BglII and EcoRI sites of pMON921 (18Fontes E.P.B. Eagle P.A. Sipe P.S. Luckow V.A. Hanley-Bowdoin L. J. Biol. Chem. 1994; 269: 8459-8465Abstract Full Text PDF PubMed Google Scholar). The resulting clones pUFV967 and pUFV849 contain NRP-B or NRP-A cDNAs, respectively, under the control of the cauliflower mosaic virus 35S promoter and the 3′-end of the pea E9 rbcS gene. For agroinfiltration in tobacco leaves, NRP-A and NRP-B cDNAs were amplified by PCR and introduced by recombination into the entry vector pCR8/GW/TOPO (Invitrogen) to generate pUFV908 and pUFV874, respectively. NRP-A and NRP-B cDNAs were then transferred by recombination to the plant transformation binary vector 35S-YFP-cassetteA-Nos-pCAMBIA1300 yielding pUFV937 (35S:NRP-B) and pUFV938 (35S:NRP-A), which contain NRP-B or NRP-A cDNA, respectively, under the control of the 35S promoter and 3′-ends of nos. For subcellular localization, NRP-A and NRP-B cDNAs were amplified by PCR with appropriate extensions and introduced by recombination into the entry vector pDONR201 (Invitrogen) and then transferred to the binary vector pK7FWG2 to generate pK7F-NRP-B and pK7F-NRP-A, which contain the GFP gene fused in-frame after the last codon of the respective cDNAs. The U16322 plasmid harboring a full-length NIG (NSP-interacting GTPase, Ref. 19Carvalho, C. M., Fontenelle, M. R., Florentino, L. H., Santos, A. A., Zerbini, F. M., and Fontes, E. P. B. (2008) Plant J., in pressGoogle Scholar). cDNA was obtained from the Arabidopsis Biological Resource Center (ABRC) and used as a control. For this purpose, the full-length NIG cDNA was amplified by PCR from U16322 cDNA, cloned into pDONR201 and then transferred to the binary vector pK7WG2 to obtain pK7-NIG, which contains NIG cDNA under the control of the CaMV 35S promoter. Real-time RT-PCR Analysis—For quantitative RT-PCR, total RNA was extracted from frozen leaves or cells with TRIzol (Invitrogen) according to the instructions from the manufacturer. The RNA was treated with 2 units of RNase-free DNase (Promega) and further purified through RNeasy Mini kit (Qiagen) columns. First-strand cDNA was synthesized from 4 μg of total RNA using oligo-dT(18) and Transcriptase Reversa M-MLV (Invitrogen), according to the manufacturer's instructions. Real-time RT-PCR reactions were performed on an ABI7500 instrument (Applied Biosystems), using SYBR® Green PCR Master Mix (Applied Biosystems). The amplification reactions were performed as follows: 2 min at 50 °C, 10 min at 95 °C, and 40 cycles of 94 °C for 15 s and 60 °C for 1 min. To confirm quality and primer specificity, we verified the size of amplification products after electrophoresis through a 1.5% agarose gel, and analyzed the Tm (melting temperature) of amplification products in a dissociation curve, performed by the ABI7500 instrument. The primers used are listed in supplemental Table S1. For quantitation of gene expression in soybean protoplasts and seedlings, we used RNA helicase (4Irsigler A.S. Costa M.D. Zhang P. Reis P.A.B. Dewey R.E. Boston R.S. Fontes E.P.B. BMC Genomics. 2007; 8: 431Crossref PubMed Scopus (84) Google Scholar) as the endogenous control gene for data normalization in real-time RT-PCR analysis. For quantitation of gene expression in tobacco leaves, we used actin as a control gene. Fold variation, which is based on the comparison of the target gene expression (normalized to the endogenous control) between experimental and control samples, was quantified using the comparative Ct method: 2−^ - (ΔCtTreatment - ΔCtControl). The absolute gene expression was quantified using the 2-ΔCT method, and values were normalized to the endogenous control. Soybean Transformation—A plant expression cassette containing the BiPD gene was constructed by insertion of the 2.0-kb XbaI cDNA insert of pUFV24 (17Cascardo J.C.M. Almeida R.S. Buzeli R.A.A. Carolino S.M.B. Otoni W.C. Fontes E.P.B. J. Biol. Chem. 2000; 275: 14494-14500Abstract Full Text Full Text PDF PubMed Scopus (62) Google Scholar) into the pBS35SdAMVNOS2 vector. The resulting clone pBS35SdAMVNOS2-BiP contains the BiP cDNA under control of a duplicated cauliflower mosaic virus 35S promoter with an enhancer region from the alfalfa mosaic virus and the polyadenylation signal of the nos gene. The Arabidopsis thaliana ahas gene (that confers tolerance to the herbicide imazapyr) was removed from the vector pAC321 (20Aragão F.J.L. Sarokin L. Vianna G.R. Rech E.L. Theor. Appl. Genet. 2000; 101: 1-6Crossref Scopus (111) Google Scholar) with XbaI and inserted into the vector pFACM1 to generate pFACMahas. The BiPD expression cassette was released with SalI and NotI from pBS35SdAMVNOS2-BiP and cloned into the vector pFACMahasm to yield pahasBip. The vector pahasBip was used to transform soybean (cv. Conquista) as previously described (20Aragão F.J.L. Sarokin L. Vianna G.R. Rech E.L. Theor. Appl. Genet. 2000; 101: 1-6Crossref Scopus (111) Google Scholar). Primary transformants were selected by PCR using the primers bipsoy235 (5′-GAGAGACTAATTGGAGAGGCTG-3′) and bipsoy645c (5′-ATAGGCAATGGCAGCAGCAGTG-3′), which amplify a 410-bp sequence from the BiPD gene coding region and cover an intron region from the genomic BiPD sequence. Segregation analyses of independently transformed soybean lines were performed by PCR, and accumulation of BiP was monitored in each subsequent generation by immunoblotting. RNA Gel Blotting—Total RNA was extracted from frozen leaves of control and tunicamycin-treated wild type and soybean transgenic seedlings, which were treated with tunicamycin or control DMSO for 24 h, with TRIzol (Invitrogen) according to the instructions from the manufacturer. Equal amounts of total RNA were denatured by formamide/formaldehyde and resolved on 1% agarose gels containing formaldehyde. The RNA was transferred to a nylon membrane by capillary transfer and immobilized by UV cross-linking (Stratalinker, Stratagene). The membrane was hybridized at high stringency conditions using the soyBiPD cDNA (17Cascardo J.C.M. Almeida R.S. Buzeli R.A.A. Carolino S.M.B. Otoni W.C. Fontes E.P.B. J. Biol. Chem. 2000; 275: 14494-14500Abstract Full Text Full Text PDF PubMed Scopus (62) Google Scholar) as probe. The hybridization probe was radiolabeled with [α-32P]dCTP by random primed labeling (Amersham Biosciences). Autoradiography was performed at -80 °C using a Lightning-Plus intensifying screen. The amount of RNA and the integrity of ribosomal RNA were monitored by rehybridizing the membranes with an 18 S rDNA probe. Immunoblot Analysis—Total protein was extracted from control and tunicamycin-treated leaves of wild-type and soybean transgenic seedlings as previously described (17Cascardo J.C.M. Almeida R.S. Buzeli R.A.A. Carolino S.M.B. Otoni W.C. Fontes E.P.B. J. Biol. Chem. 2000; 275: 14494-14500Abstract Full Text Full Text PDF PubMed Scopus (62) Google Scholar). SDS-PAGE was carried out, and the proteins were transferred from 10% SDS-polyacrylamide gels to nitrocellulose membranes by electroblotting. Immunoblot analyses were performed using polyclonal anti-BiP-carboxyl antibodies (2Buzeli R.A.A. Cascardo J.C.M. Rodrigues L.A.Z. Andrade M.O. Loureiro M.E. Otoni W.C. Fontes E.P.B. Plant Mol. Biol. 2002; 50: 757-771Crossref PubMed Scopus (37) Google Scholar), an anti-calreticulin serum (21Pagny S. Cabanes-Macheteau M. Gillikin J. Leborgne-Castel N. Lerouge P. Boston R.S. Faye L. Gomord V. Plant Cell. 2000; 12: 739-755Crossref PubMed Scopus (96) Google Scholar) or an anti-GmSBP2 serum (22Delú-Filho N. Pirovani C.P. Pedra J.H.F. Matrangolo F.S.V. Macêdo J.N.A. Otoni W.C. Fontes E.P.B. Plant Physiol. Biochem. 2000; 38 (353): 353Crossref Scopus (20) Google Scholar) at a 1:1000 dilution and a goat anti-rabbit IgG alkaline phosphatase conjugate (Sigma) at a 1:5000 dilution. Alkaline phosphatase activity was assayed using 5-bromo-4-chloro-3-indolyl phosphate (Sigma) and p-nitro blue tetrazolium (Sigma). Transient Expression in Soybean Protoplasts—Protoplasts were prepared from soybean suspension cells as essentially described by Fontes et al. (18Fontes E.P.B. Eagle P.A. Sipe P.S. Luckow V.A. Hanley-Bowdoin L. J. Biol. Chem. 1994; 269: 8459-8465Abstract Full Text PDF PubMed Google Scholar). The protoplasts were isolated 5 days after subculture by digestion for 3 h, under agitation at 40 rpm, with 0.5% cellulase, 0,5% macerozyme R-10, 0.1% pectolyase Y23, 0.6 m mannitol, 20 mm MES, pH 5.5. The extent of digestion was monitored by examining the cells microscopically at each 30-min interval. After filtration through nylon mesh of 65 μm, protoplasts were recovered by centrifugation, resuspended in 2 ml of 0.6 m mannitol, 20 mm MES, pH 5.5, separated by centrifugation in a sucrose gradient (20% (w/v) sucrose, 0.6 m mannitol, 20 mm MES, pH 5.5), and diluted into 2 ml of electroporation buffer (25 mm Hepes-KOH, pH 7.2, 10 mm KCl, 15 mm MgCl2, 0.6 m mannitol). Transient expression assays were performed by electroporation (250 V, 250 μF) of 10 μg of expression cassette DNA, and 30 μg of sheared salmon sperm DNA into 2 × 105 - 5 × 106 protoplasts in a final volume of 0.8 ml. Protoplasts were diluted into 8 ml of MS medium supplemented with 0.2 mg/ml 2,4-dichlorophenoxyacetic acid and 0.6 m mannitol, pH 5.5. After 36 h of incubation in the dark, the protoplasts were washed with 0.6 m mannitol, 20 mm MES, pH 5.5, and frozen in liquid N2 until use. Caspase-3-like Activity and in Situ Labeling of DNA Fragmentation (TUNEL)—Total protein was extracted from soybean cells 36-h post-electroporation. Caspase-3-like activity was determined using the ApoAlert® Caspase-3 Colorimetric Assay kit (Clontech) according to the manufacturer's instructions. The substrate was DEVD-pNA, and the inhibitor of caspase-3 activity was the synthetic tetrapeptide DEVD-fmk supplied by the kit. Free 3′-OH in the DNA was labeled by the terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) assay using the ApoAlert DNA Fragmentation Assay kit (Clontech) as instructed by the manufacturer. Samples were observed with a Zeiss LSM 410 inverted confocal laser scanning microscope fitted with the configuration: excitation at 488 nm and emission at 515 nm. As a positive control, samples were treated with DNase1. Transient Overexpression in Nicotiana tabacum by Agrobacterium Infiltration—N. tabacum plants were grown in a greenhouse with natural day length illumination. Three weeks after germination, the plants were transferred to a growth chamber at 21 °C with a 16-hour light and 8-hour dark cycle. Agrobacterium infiltration was performed in the leaves of N. tabacum with Agrobacterium strain GV3101 carrying pUFV937 (35S: NRP-B) or pUFV938 (35S:NRP-A), NIG (35S:NIG), rpl10 (35S: rpL10) as previously described (23Batoko H. Zheng H.Q. Hawes C. Moore I. Plant Cell. 2000; 12: 2201-2218Crossref PubMed Scopus (462) Google Scholar). Subcellular Localization of Proteins—For subcellular localization of proteins, N. tabacun leaves were agroinoculated with pK7F-NRP-B and pK7F-NRP-A. About 72-h post-agroinfiltration, 1-cm2 leaf explants were excised incubated with 0.6 m mannitol for 10 min, and GFP fluorescence patterns were examined in epidermal cells with ×40 oil immersion objective and a Zeiss LSM510 META inverted laser scanning microscope equipped with an argon laser as excitation source. For imaging GFP, the 455-nm excitation line and the 500–530-nm band pass filter were used. The pinhole was usually set to give a 1–1.5-μm optical slice. Post-acquisition image processing was done using the LSM 5 Browser software (Carl-Zeiss) and Adobe Photoshop (Adobe Systems). Microsomal fractions were prepared from agroinoculated leaves, as described (24Pirovani C.P. Macêdo J.N.A. Contim L.A.S. Matrangolo F.S.V. Loureiro M.E. Fontes E.P.B. Eur. J. Biochem. 2002; 269: 3998-4008Crossref PubMed Scopus (16) Google Scholar), and immunoblotted with an anti-GFP serum. Determination of Chlorophyll Content and Lipid Peroxidation—Total chlorophyll content was determined spectrophotometrically at 663 and 646 nm after quantitative extraction from individual leaves with 80% (v/v) acetone in the presence of ∼1 mg of Na2CO3 (25Lichtenthaler H.K. Methods Enzymol. 1987; 148: 350-382Crossref Scopus (8704) Google Scholar). The extent of lipid peroxidation in leaves was estimated by measuring the amount of MDA (malondialdehyde, a decomposition product of the oxidation of polyunsaturated fatty acids). MDA content was determined by the reaction of thiobarbituric acid (TBA) as described by Cakmak and Horst (26Cakmak I. Horst W.J. Physiol. Plantarum. 1991; 83: 463-468Crossref Scopus (1301) Google Scholar). Ethylene Determination—For ethylene measurements as a function of NRP-A and NRP-B expression, whole leaves of 3-week-old tobacco plants were agroinoculated with pK7-NRP-A, pK7-NRP-B, or control binary vector. Agroinfiltrated tobacco plants were placed in 25-ml flasks containing a Petri dish with 3 ml of 1 m HgClO4·4H2O and sealed with rubber serum caps. After 5 days, the solution was collected into a sealed assay tube, and ethylene was released with the injection of 1 ml of 1 m KCl. 1 ml of gas was collected with a syringe, and ethylene was measured on a model 5840A gas chromatography system (Hewlett-Packard Canada Ltda) equipped with a flame ionization detector. A Porapak N (80–100 mesh, 100 cm × 6 mm) column was used at 60 °C. The injection port and detector temperatures were 100 and 150 °C, respectively. The flow of nitrogen, air, and hydrogen was at 30, 130, and 20 ml min-1, respectively. N-richI and N-richII ESTs Are Both Encoded by the NRP-B Gene—The N-richI and N-richII ESTs correspond to different regions of a contiguous soybean genomic sequence (scaffold_78:2951370.2949024). To determine if both ESTs corresponded to the same mRNAs, we obtained the full sequences of N-richI and N-richII cDNAs through RACE. A comparison of the cDNA sequences revealed that these ESTs represented the same gene which we designated NRP-B (N-rich protein B; supplemental Fig. S1A). The deduced NRP-B protein has an estimated Mr of 37092 and pI 7.05 and is most closely related to the previously identified NRP from soybean (27Ludwig A.A. Tenhaken R. Eur. J. Plant Pathol. 2001; 107: 323-336Crossref Scopus (24) Google Scholar), here designated NRP-A. The two NRPs share a highly conserved C-terminal DCD domain in addition to a high content of asparagine residues at their more divergent N termini. This structural organization places NRP-A and NRP-B in the subgroup I of plant-specific DCD-containing proteins (28Tenhaken R. Doerks T. Bork P. BMC Bioinformatics. 2005; 6: 169Crossref PubMed Scopus (33) Google Scholar). Analysis of several subgroup I DCD domain-containing proteins by ClustalW showed that NRP-A and NRP-B form a subgroup with the Arabidopsis protein of unknown function encoded by At5g42050 (gi 231 18422167, supplemental Fig. S1B). An examination of available microarray data indicated that the At5g42050 locus is induced by cycloheximide, osmotic stress, salt stress, and during senescence (GeneInvestigator). Integration of ER Stress and Osmotic Signals Leads to Maximal Express DA - 2008/7/18/ PY - 2008/7/18/ DO - 10.1074/jbc.M802654200 VL - 283 IS - 29 SP - 20209-20219 SN - 1083-351X ER - TY - JOUR TI - Water economy of Neotropical savanna trees: six paradigms revisited AU - Goldstein, Guillermo AU - Meinzer, Frederick C. AU - Bucci, Sandra J. AU - Scholz, Fabian G. AU - Franco, Augusto C. AU - Hoffmann, William A. T2 - TREE PHYSIOLOGY AB - Biologists have long been puzzled by the striking morphological and anatomical characteristics of Neotropical savanna trees which have large scleromorphic leaves, allocate more than half of their total biomass to belowground structures and produce new leaves during the peak of the dry season. Based on results of ongoing interdisciplinary projects in the savannas of central Brazil (cerrado), we reassessed the validity of six paradigms to account for the water economy of savanna vegetation. (1) All savanna woody species are similar in their ability to take up water from deep soil layers where its availability is relatively constant throughout the year. (2) There is no substantial competition between grasses and trees for water resources during the dry season because grasses exclusively explore upper soil layers, whereas trees access water in deeper soil layers. (3) Tree species have access to abundant groundwater, their stomatal control is weak and they tend to transpire freely. (4) Savanna trees experience increased water deficits during the dry season despite their access to deep soil water. (5) Stomatal conductance of savanna species is low at night to prevent nocturnal transpiration, particularly during the dry season. (6) Savanna tree species can be classified into functional groups according to leaf phenology. We evaluated each paradigm and found differences in the patterns of water uptake between deciduous and evergreen tree species, as well as among evergreen tree species, that have implications for regulation of tree water balance. The absence of resource interactions between herbaceous and woody plants is refuted by our observation that herbaceous plants use water from deep soil layers that is released by deep-rooted trees into the upper soil layer. We obtained evidence of strong stomatal control of transpiration and show that most species exhibit homeostasis in maximum water deficit, with midday water potentials being almost identical in the wet and dry seasons. Although stomatal control is strong during the day, nocturnal transpiration is high during the dry season. Our comparative studies showed that the grouping of species into functional categories is somewhat arbitrary and that ranking species along continuous functional axes better represents the ecological complexity of adaptations of cerrado woody species to their seasonal environment. DA - 2008/3// PY - 2008/3// DO - 10.1093/treephys/28.3.395 VL - 28 IS - 3 SP - 395-404 SN - 1758-4469 KW - cerrado KW - nighttime transpiration KW - tropical savannas KW - water deficit KW - water uptake ER - TY - JOUR TI - TAA1-Mediated Auxin Biosynthesis Is Essential for Hormone Crosstalk and Plant Development AU - Stepanova, Anna N. AU - Robertson-Hoyt, Joyce AU - Yun, Jeonga AU - Benavente, Larissa M. AU - Xie, De-Yu AU - Doležal, Karel AU - Schlereth, Alexandra AU - Jürgens, Gerd AU - Alonso, Jose M. T2 - Cell AB - Plants have evolved a tremendous ability to respond to environmental changes by adapting their growth and development. The interaction between hormonal and developmental signals is a critical mechanism in the generation of this enormous plasticity. A good example is the response to the hormone ethylene that depends on tissue type, developmental stage, and environmental conditions. By characterizing the Arabidopsis wei8 mutant, we have found that a small family of genes mediates tissue-specific responses to ethylene. Biochemical studies revealed that WEI8 encodes a long-anticipated tryptophan aminotransferase, TAA1, in the essential, yet genetically uncharacterized, indole-3-pyruvic acid (IPA) branch of the auxin biosynthetic pathway. Analysis of TAA1 and its paralogues revealed a link between local auxin production, tissue-specific ethylene effects, and organ development. Thus, the IPA route of auxin production is key to generating robust auxin gradients in response to environmental and developmental cues. DA - 2008/4// PY - 2008/4// DO - 10.1016/j.cell.2008.01.047 VL - 133 IS - 1 SP - 177-191 J2 - Cell LA - en OP - SN - 0092-8674 UR - http://dx.doi.org/10.1016/j.cell.2008.01.047 DB - Crossref ER - TY - JOUR TI - Stem and leaf hydraulics of congeneric tree species from adjacent tropical savanna and forest ecosystems AU - Hao, Guang-You AU - Hoffmann, William A. AU - Scholz, Fabian G. AU - Bucci, Sandra J. AU - Meinzer, Frederick C. AU - Franco, Augusto C. AU - Cao, Kun-Fang AU - Goldstein, Guillermo T2 - OECOLOGIA AB - Leaf and stem functional traits related to plant water relations were studied for six congeneric species pairs, each composed of one tree species typical of savanna habitats and another typical of adjacent forest habitats, to determine whether there were intrinsic differences in plant hydraulics between these two functional types. Only individuals growing in savanna habitats were studied. Most stem traits, including wood density, the xylem water potential at 50% loss of hydraulic conductivity, sapwood area specific conductivity, and leaf area specific conductivity did not differ significantly between savanna and forest species. However, maximum leaf hydraulic conductance (K (leaf)) and leaf capacitance tended to be higher in savanna species. Predawn leaf water potential and leaf mass per area were also higher in savanna species in all congeneric pairs. Hydraulic vulnerability curves of stems and leaves indicated that leaves were more vulnerable to drought-induced cavitation than terminal branches regardless of genus. The midday K (leaf) values estimated from leaf vulnerability curves were very low implying that daily embolism repair may occur in leaves. An electric circuit analog model predicted that, compared to forest species, savanna species took longer for their leaf water potentials to drop from predawn values to values corresponding to 50% loss of K (leaf) or to the turgor loss points, suggesting that savanna species were more buffered from changes in leaf water potential. The results of this study suggest that the relative success of savanna over forest species in savanna is related in part to their ability to cope with drought, which is determined more by leaf than by stem hydraulic traits. Variation among genera accounted for a large proportion of the total variance in most traits, which indicates that, despite different selective pressures in savanna and forest habitats, phylogeny has a stronger effect than habitat in determining most hydraulic traits. DA - 2008/3// PY - 2008/3// DO - 10.1007/s00442-007-0918-5 VL - 155 IS - 3 SP - 405-415 SN - 1432-1939 KW - plant water relations KW - embolism KW - vulnerability KW - phylogenetic inertia ER - TY - JOUR TI - Influence of moisture content and cultivation duration on Clostridium thermocellum 27405 end-product formation in solid substrate cultivation on Avicel AU - Chinn, Mari S. AU - Nokes, Sue E. AU - Strobel, Herbert J. T2 - BIORESOURCE TECHNOLOGY AB - Avicel serves as a model microcrystalline cellulose substrate for investigations of cellulolytic microbial performance and cellulase enzyme systems in submerged liquid cultures. Clostridium thermocellum is a thermophilic, anaerobic bacterium capable of degrading lignocellulose and fermenting it to ethanol and other products, suggesting the native growth environment is similar to that supported by solid substrate cultivation. Few studies have examined the effects of process parameters on the metabolism of thermophilic anaerobes in solid substrate cultivation, however. The effects of solid substrate cultivation (SSC) substrate moisture content (30%, 50% and 70% wet-basis) and cultivation duration (2, 4 and 8 days) on the metabolic activity of C. thermocellum 27405 on Avicel was studied. The 70% substrate moisture content SSC culture yielded total end-product concentrations that were comparable to submerged liquid cultures. The SSC cultivation conditions with the highest end-product formation on Avicel were the combination of 70% substrate moisture content and cultivation duration period of 4 days, producing approximately 100 mM of total end-products. The ethanol and lactate concentrations were fairly constant and did not change significantly over time in SSC. Acetate production was more dependent on the cultivation conditions in SSC and was significant for both the 70% substrate moisture content SSC and liquid cultivation experiments, making up on average 56% and 86% of total end-products, respectively. Performance of C. thermocellum 27405 in SSC was more dependent on the kinetic properties rather than the thermodynamic properties of substrate moisture content. High substrate loadings in C. thermocellum cultivation affected product ratios, resulting in the higher observed acetate production. In addition, cessation of metabolism was observed prior to complete Avicel conversion; the mechanisms involved need further investigation. DA - 2008/5// PY - 2008/5// DO - 10.1016/j.biortech.2007.04.052 VL - 99 IS - 7 SP - 2664-2671 SN - 0960-8524 KW - C. thermocellum KW - Avicel KW - solid substrate cultivation (SSC) KW - moisture content KW - thermophilic ER - TY - JOUR TI - Diverse inhibitors of aflatoxin biosynthesis AU - Holmes, Robert A. AU - Boston, Rebecca S. AU - Payne, Gary A. T2 - APPLIED MICROBIOLOGY AND BIOTECHNOLOGY DA - 2008/3// PY - 2008/3// DO - 10.1007/s00253-008-1362-0 VL - 78 IS - 4 SP - 559-572 SN - 1432-0614 KW - aspergillus KW - secondary metabolism KW - oxidative stress KW - host resistance ER - TY - JOUR TI - High frequency (900 MHz) low amplitude (5 V m(-1)) electromagnetic field: a genuine environmental stimulus that affects transcription, translation, calcium and energy charge in tomato AU - Roux, David AU - Vian, Alain AU - Girard, Sebastien AU - Bonnet, Pierre AU - Paladian, Francoise AU - Davies, Eric AU - Ledoigt, Gerard T2 - PLANTA DA - 2008/3// PY - 2008/3// DO - 10.1007/s00425-007-0664-2 VL - 227 IS - 4 SP - 883-891 SN - 1432-2048 KW - mode stirred reverberation chamber KW - radiofrequency electromagnetic field KW - stress KW - tomato KW - wound-like responses ER - TY - JOUR TI - The invasive grass, Melinis minutiflora, inhibits tree regeneration in a Neotropical savanna AU - Hoffmann, William A. AU - Haridasan, M. T2 - AUSTRAL ECOLOGY AB - Abstract Exotic grasses are becoming increasingly abundant in Neotropical savannas, with Melinis minutiflora Beauv. being particularly invasive. To better understand the consequences for the native flora, we performed a field study to test the effect of this species on the establishment, survival and growth of seedlings of seven tree species native to the savannas and forests of the Cerrado region of Brazil. Seeds of the tree species were sown in 40 study plots, of which 20 were sites dominated by M. minutiflora , and 20 were dominated by native grasses. The exotic grass had no discernable effect on initial seedling emergence, as defined by the number of seedlings present at the end of the first growing season. Subsequent seedling survival in plots dominated by M. minutiflora was less than half that of plots dominated by native species. Consequently, at the end of the third growing season, invaded plots had only 44% as many seedlings as plots with native grasses. Above‐ground grass biomass of invaded plots was more than twice that of uninvaded plots, while seedling survival was negatively correlated with grass biomass, suggesting that competition for light may explain the low seedling survival where M. minutiflora is dominant. Soils of invaded plots had higher mean Ca, Mg and Zn, but these variables did not account for the higher grass biomass or the lower seedling survival in invaded plots. The results indicate that this exotic grass is having substantial effects on the dynamics of the tree community, with likely consequences for ecosystem structure and function. DA - 2008/2// PY - 2008/2// DO - 10.1111/j.1442-9993.2007.01787.x VL - 33 IS - 1 SP - 29-36 SN - 1442-9985 KW - alien KW - Cerrado KW - competition KW - exotic species KW - invasive species KW - savanna ER - TY - JOUR TI - Pathway, inhibition and regulation of methyl tertiary butyl ether oxidation in a filamentous fungus, Graphium sp AU - Skinner, Kristin M. AU - Martinez-Prado, Adriana AU - Hyman, Michael R. AU - Williamson, Kenneth J. AU - Ciuffetti, Lynda M. T2 - APPLIED MICROBIOLOGY AND BIOTECHNOLOGY DA - 2008/1// PY - 2008/1// DO - 10.1007/s00253-007-1268-2 VL - 77 IS - 6 SP - 1359-1365 SN - 1432-0614 KW - methyl tertiary butyl alcohol KW - cometabolism KW - Graphium sp KW - tertiary butyl alcohol KW - tertiary butyl formate KW - alkane monooxygenase ER - TY - JOUR TI - Characterization of a new family of protein kinases from Arabidopsis containing phosphoinositide 3/4-kinase and ubiquitin-like domains AU - Galvao, Rafaelo M. AU - Kota, Uma AU - Soderblom, Erik J. AU - Goshe, Michael B. AU - Boss, Wendy F. T2 - BIOCHEMICAL JOURNAL AB - At least two of the genes predicted to encode type II PI4K (phosphoinositide 4-kinase) in Arabidopsis thaliana (thale cress), namely AtPI4Kγ4 and AtPI4Kγ7, encode enzymes with catalytic properties similar to those of members of the PIKK (phosphoinositide kinase-related kinase) family. AtPI4Kγ4 and AtPI4Kγ7 undergo autophosphorylation and phosphorylate serine/threonine residues of protein substrates, but have no detectable lipid kinase activity. AtPI4Kγ4 and AtPI4Kγ7 are members of a subset of five putative AtPI4Ks that contain N-terminal UBL (ubiquitin-like) domains. In vitro analysis of AtPI4Kγ4 indicates that it interacts directly with, and phosphorylates, two proteins involved in the ubiquitin–proteasome system, namely UFD1 (ubiquitin fusion degradation 1) and RPN10 (regulatory particle non-ATPase 10). On the basis of the present results, we propose that AtPI4Kγ4 and AtPI4Kγ7 should be designated UbDKγ4 and UbDKγ7 (ubiquitin-like domain kinases γ4 and γ7). These UBL-domain-containing AtPI4Ks correspond to a new PIKK subfamily of protein kinases. Furthermore, UFD1 and RPN10 phosphorylation represents an additional mechanism by which their function can be regulated. DA - 2008/1/1/ PY - 2008/1/1/ DO - 10.1042/bj20070959 VL - 409 SP - 117-127 SN - 1470-8728 KW - phosphoinositide kinase (PIK) KW - phosphorylation KW - proteasome regulatory particle non-ATPase 10 subunit (proteasome RPN10 subunit) KW - protein kinase KW - ubiquitin fusion degradation (UFD) KW - ubiquitin-like domain (UBL domain) ER - TY - JOUR TI - Expression of the bacteriophage T4 lysozyme gene in tall fescue confers resistance to gray leaf spot and brown patch diseases AU - Dong, Shujie AU - Shew, H. David AU - Tredway, Lane P. AU - Lu, Jianli AU - Sivamani, Elumalai AU - Miller, Eric S. AU - Qu, Rongda T2 - TRANSGENIC RESEARCH DA - 2008/2// PY - 2008/2// DO - 10.1007/s11248-007-9073-3 VL - 17 IS - 1 SP - 47-57 SN - 1573-9368 KW - fungal resistance KW - Magnaporthe grisea KW - Rhizoctonia solani KW - T4 lysozyme KW - tall fescue ER -