TY - JOUR TI - Helping Educational Reforms To Succeed in a Microbiology Department T2 - Microbe Magazine AB - During the past decade, a rising chorus has called for major reforms in how we teach science, technology, engineering, and mathematics. Part of the impetus for those reforms comes from concerns over growing numbers of students leaving the sciences, the eroding stature of the United States in the sciences compared with countries such as China and India, and also losses of personnel to fields such as biotechnology. DA - 2009/5/1/ PY - 2009/5/1/ DO - 10.1128/microbe.4.219.1 UR - http://dx.doi.org/10.1128/microbe.4.219.1 ER - TY - JOUR TI - Correlation between transcript abundance of the RB gene and the level of the RB-mediated late blight resistance in potato AU - Kramer, Lara C AU - Choudoir, Mallory J AU - Wielgus, Susan M AU - Bhaskar, Pudota B AU - Jiang, Jiming T2 - Molecular Plant-Microbe Interactions DA - 2009/// PY - 2009/// VL - 22 IS - 4 SP - 447-455 ER - TY - JOUR TI - Clarification of the typification of Michaux names in eastern North American Vitis (Vitaceae) AU - Fisk, C. AU - Krings, A. T2 - Journal of the Botanical Research Institute of Texas DA - 2009/// PY - 2009/// VL - 3 IS - 2 SP - 739–740 ER - TY - JOUR TI - Introduced lesser celandine (Ranunculus ficaria, Ranunculaceae) and its putative subspecies in the United States: A morphometric analysis AU - Post, A.R. AU - Krings, A. AU - Wall, W.A. AU - Neal, J.C. T2 - Journal of the Botanical Research Institute of Texas DA - 2009/// PY - 2009/// VL - 3 IS - 1 SP - 193–209 ER - TY - JOUR TI - Lectotypification of Cardamine flexuosa (Brassicaceae) AU - Post, A.R. AU - Krings, A. AU - Xiang, Q.-Y. AU - Sosinski, B.R. AU - Neal, J.C. T2 - Journal of the Botanical Research Institute of Texas DA - 2009/// PY - 2009/// VL - 3 IS - 1 SP - 227–230 ER - TY - CONF TI - Extraction of Essential Oil and Anatomical Characterization of Oil Cell from Leaves of Litsea Euosma AU - Liu, Shibiao AU - Liu, Zhu-Xiang AU - Zhang, Hui AU - Cai, Shi-Jian AU - Chen, Gong-Xi AU - Xie, De-Yu T2 - 2009 International Conference of Natural Products and Traditional Medicine C2 - 2009/// C3 - Proceedings of 2009 International Conference of Natural Products and Traditional Medicine DA - 2009/// PY - 2009/10/16/ SP - 737–744 ER - TY - JOUR TI - Caracterización de aceites, tortas y harinas de frutos de ungurahui (Jessenia polycarpa) y aguaje (Mauritia flexuosa L.) de la amazonía peruana. T2 - Revista de la Sociedad Química del Perú DA - 2009/// PY - 2009/// UR - https://www.redalyc.org/articulo.oa?id=371937613012 ER - TY - JOUR TI - Antocianinas, fenoles totales y actividad antioxidante de las corontas del maíz morado (Zea mays L.): Método de extracción T2 - Boletín Latinoamericano y del Caribe de Plantas Medicinales y Aromáticas DA - 2009/// PY - 2009/// UR - https://www.redalyc.org/articulo.oa?id=85617461006 ER - TY - JOUR TI - Integrating Modern Biology into the ChE Biomolecular Engineering Concentration through a Campus-Wide Core Laboratory Education Program AU - Carson, S. AU - Chisnell, J. AU - Kelly, R. T2 - Chemical Engineering Education DA - 2009/// PY - 2009/// VL - 43 IS - 4 SP - 257–264 ER - TY - JOUR TI - Erratum to: Characterization of two proline dipeptidases (prolidases) from the hyperthermophilic archaeon Pyrococcus horikoshii AU - Theriot, Casey M. AU - Tove, Sherry R. AU - Grunden, Amy M. T2 - Applied Microbiology and Biotechnology DA - 2009/10/27/ PY - 2009/10/27/ DO - 10.1007/s00253-009-2300-5 VL - 86 IS - 1 SP - 393-393 J2 - Appl Microbiol Biotechnol LA - en OP - SN - 0175-7598 1432-0614 UR - http://dx.doi.org/10.1007/s00253-009-2300-5 DB - Crossref ER - TY - CHAP TI - InsP3 in Plant Cells AU - Im, Yang Ju AU - Phillippy, Brian Q. AU - Perera, Imara Y. T2 - Lipid Signaling in Plants AB - D-myo-Inositol 1,4,5-trisphosphate (InsP3) is an important second messenger in eukaryotic cells. Although the phosphoinositide (PI) pathway has been well studied in plants, there is much that is not understood about PI-mediated signaling and there are fundamental differences between the plant and animal models. Many researchers have shown that plants produce InsP3 in response to multiple stimuli and that InsP3-mediated Ca2+ release is a component of plant signaling, although the candidate intracellular target of InsP3 in plants remains elusive. As plants are sessile organisms with multiple back-up systems, the InsP3-mediated signaling pathway may be one of the many signaling pathways in plants and its role may be more significant in specialized cells. This chapter provides an overview of InsP3 metabolism in plants, the current methods of analysis, and a review of the role of InsP3 in plants gathered from recent studies using mutants or transgenic plants with altered PI metabolism. PY - 2009/10/29/ DO - 10.1007/978-3-642-03873-0_10 SP - 145-160 OP - PB - Springer Berlin Heidelberg SN - 9783642038723 9783642038730 UR - http://dx.doi.org/10.1007/978-3-642-03873-0_10 DB - Crossref ER - TY - JOUR TI - Effects of mechanized pine straw raking on population densities of longleaf pine seedlings AU - Kelly, Lisa A. AU - Wentworth, Thomas R. T2 - Forest Ecology and Management AB - Longleaf pine communities occupy a small fraction of their original extent in the southeastern United States and are in great need of restoration and conservation management. Recent anthropogenic disturbances, such as pine straw raking, may interfere with seedling survival and, hence, restoration efforts. We examined the effects of mechanized straw raking on longleaf pine (Pinus palustris Mill.) seedlings (pre-grass stage, or <3-yr-old) in natural, fire-maintained plant communities in Croatan National Forest, North Carolina, by testing the effects of number of rakings (0–4 times during a 2-yr period (1992–1994)) and community type (pine-turkey oak, dry savanna, and mesic savanna) on seedling densities in 1-m2 quadrats. Despite initial differences in densities of seedlings among communities, analyses of variance did not detect significant differences among communities as averaged over time and raking treatment. Both raked and unraked quadrats exhibited declines in seedling density during the study, but the declines were greater for raked quadrats. After 2 yr, initial densities were, on average, reduced by 34% in unraked quadrats and by 47%, 63%, 78%, and 77% in quadrats raked one, two, three, and four times, respectively. In quadrats raked four times, censuses performed after each raking indicated significant declines in densities in response to all but the first raking. Raking either injures pine seedlings directly and/or modifies microsite conditions in ways unfavorable for seedling survival. Having established a link between raking and mortality, we now recommend additional work to reveal the causal mechanisms. Land management decisions should accommodate the potential adverse effects of mechanized raking on pine regeneration. DA - 2009/12// PY - 2009/12// DO - 10.1016/j.foreco.2009.09.029 VL - 259 IS - 1 SP - 1-7 J2 - Forest Ecology and Management LA - en OP - SN - 0378-1127 UR - http://dx.doi.org/10.1016/j.foreco.2009.09.029 DB - Crossref KW - Pine straw KW - Litter raking KW - Restoration KW - Longleaf pine seedlings KW - Pinus palustris KW - Litter ER - TY - JOUR TI - Effects of gasoline components on MTBE and TBA cometabolism by Mycobacterium austroafricanum JOB5. T2 - Biodegradation DA - 2009/12/10/ PY - 2009/12/10/ DO - 10.1007/s10532-009-9321-8 UR - https://doi.org/10.1007/s10532-009-9321-8 KW - Cometabolism KW - MTBE KW - TBA KW - Gasoline hydrocarbons KW - Alkanes KW - BTEX ER - TY - JOUR TI - Development rooted in interwoven networks AU - Benfey, Philip N. AU - Cui, Hongchang AU - Twigg, Richard AU - Long, Terri AU - Iyer-Pascuzzi, Anjali AU - Tsukagoshi, Hironaka AU - Sozzani, Rosangela AU - Jackson, Terry AU - Van Norman, Jaimie AU - Moreno-Risueno, Miguel T2 - Developmental Biology AB - Freshwater planarians appear to utilize inductive signals to specify their germ cell lineage: germ cells are believed to form post-embryonically from the pluripotent somatic stem cells, known as neoblasts. Previously, we identified a planarian homolog of nanos (Smed-nanos) and demonstrated by RNA interference (RNAi) that this gene is required for the development, maintenance, and regeneration of planarian germ cells. We have performed microarray analyses to compare gene expression profiles between planarians with early germ cells and those without them. We identified ∼300 genes that are significantly down-regulated in animals lacking early germ cells. This data set contains genes implicated in germ cell development in other organisms, conserved genes not yet reported to have germ cell-related functions, and novel genes. Analysis using putative domain functions (Clusters of Orthologous Groups) suggested diverse molecular functions, including cytoskeletal components, metabolism, RNA processing and modification, transcription, as well as signal transduction. Top hits have been validated by in situ hybridization. Functional analyses of these genes via RNA interference are being carried out. Thus far, we have identified several genes that, when knocked down by RNAi, cause various defects in germ cell development, including: impaired testes development; loss of spermatogonial stem cells; meiotic failure; and defects in sperm elongation. This work will contribute to our knowledge of conserved regulators of germ cell differentiation. (Supported by NIH-NICHD R01-HD043403.) DA - 2009/7// PY - 2009/7// DO - 10.1016/j.ydbio.2009.05.012 VL - 331 IS - 2 SP - 386 J2 - Developmental Biology LA - en OP - SN - 0012-1606 UR - http://dx.doi.org/10.1016/j.ydbio.2009.05.012 DB - Crossref ER - TY - CHAP TI - Isolation of Peptide Aptamers to Target Protein Function AU - Lopez-Ochoa, Luisa AU - Nash, Tara E. AU - Ramirez-Prado, Jorge AU - Hanley-Bowdoin, Linda T2 - Methods in Molecular Biology AB - Peptide aptamers are small recombinant proteins typically inserted into a supportive protein scaffold. These short peptide domains can bind to their target proteins with high specificity and affinity, often resulting in an altered target protein. We describe high-throughput protocols that facilitate the selection and characterization of peptide aptamers from yeast dihybrid libraries. These protocols include the preparation and evaluation of the bait fusion and the peptide aptamer screen. They also include confirmation of interaction specificity as well as isolation and sequencing of peptide inserts. Once the amino acid sequence is determined, we describe a protocol for aligning and comparing short peptide sequences and assessing the statistical significance of the alignments. PY - 2009/// DO - 10.1007/978-1-59745-557-2_19 SP - 333-360 OP - PB - Humana Press SN - 9781934115893 9781597455572 UR - http://dx.doi.org/10.1007/978-1-59745-557-2_19 DB - Crossref ER - TY - JOUR TI - A combinatorial interplay among the 1-aminocyclopropane-1-carboxylate isoforms regulates ethylene biosynthesis in Arabidopsis thaliana AU - Tsuchisaka, Atsunari AU - Yu, Guixia AU - Jin, Hailing AU - Alonso, Jose M. AU - Ecker, Joseph R. AU - Zhang, Xiaoming AU - Gao, Shang AU - Theologis, Athanasios T2 - Genetics AB - Ethylene (C(2)H(4)) is a unique plant-signaling molecule that regulates numerous developmental processes. The key enzyme in the two-step biosynthetic pathway of ethylene is 1-aminocyclopropane-1-carboxylate synthase (ACS), which catalyzes the conversion of S-adenosylmethionine (AdoMet) to ACC, the precursor of ethylene. To understand the function of this important enzyme, we analyzed the entire family of nine ACS isoforms (ACS1, ACS2, ACS4-9, and ACS11) encoded in the Arabidopsis genome. Our analysis reveals that members of this protein family share an essential function, because individual ACS genes are not essential for Arabidopsis viability, whereas elimination of the entire gene family results in embryonic lethality. Phenotypic characterization of single and multiple mutants unmasks unique but overlapping functions of the various ACS members in plant developmental events, including multiple growth characteristics, flowering time, response to gravity, disease resistance, and ethylene production. Ethylene acts as a repressor of flowering by regulating the transcription of the FLOWERING LOCUS C. Each single and high order mutant has a characteristic molecular phenotype with unique and overlapping gene expression patterns. The expression of several genes involved in light perception and signaling is altered in the high order mutants. These results, together with the in planta ACS interaction map, suggest that ethylene-mediated processes are orchestrated by a combinatorial interplay among ACS isoforms that determines the relative ratio of homo- and heterodimers (active or inactive) in a spatial and temporal manner. These subunit isoforms comprise a combinatorial code that is a central regulator of ethylene production during plant development. The lethality of the null ACS mutant contrasts with the viability of null mutations in key components of the ethylene signaling apparatus, strongly supporting the view that ACC, the precursor of ethylene, is a primary regulator of plant growth and development. DA - 2009/// PY - 2009/// DO - 10.1534/genetics.109.107102 VL - 183 IS - 3 SP - 979-1003 ER - TY - JOUR TI - Why do we fly? Ecologists' sins of emission AU - Fox, Helen E AU - Kareiva, Peter AU - Silliman, Brian AU - Hitt, Jessica AU - Lytle, David A AU - Halpern, Benjamin S AU - Hawkes, Christine V AU - Lawler, Joshua AU - Neel, Maile AU - Olden, Julian D AU - Schlaepfer, Martin A AU - Smith, Katherine AU - Tallis, Heather T2 - Frontiers in Ecology and the Environment AB - Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. DA - 2009/8// PY - 2009/8// DO - 10.1890/09.wb.019 VL - 7 IS - 6 SP - 294-296 ER - TY - JOUR TI - Plant neighborhood control of arbuscular mycorrhizal community composition AU - Hausmann, Natasha Teutsch AU - Hawkes, Christine V. T2 - New Phytologist AB - • Arbuscular mycorrhizal fungi (AMF) are important root symbionts that can provide benefits to plant hosts, yet we understand little about how neighboring hosts in a plant community contribute to the composition of the AMF community. We hypothesized that the composition of the plant neighborhood, including the identities of both host and neighbor, would alter AMF community composition. • We tested this in a glasshouse experiment in which a native perennial grass (Nassella pulchra) and three annual grasses (Avena barbata, Bromus hordeaceaous and Vulpia microstachys) were grown in two neighborhoods: conspecific monocultures and heterospecific perennial–annual mixtures. To identify AMF taxa colonizing plant roots, we used a combination of terminal restriction fragment length polymorphism and cloning. • Both host and neighbor were important in structuring AMF communities. Unique AMF communities were associated with each plant host in monoculture. In heterospecific neighborhoods, the annual neighbors V. microstachys, A. barbata, and B. hordeaceus influenced N. pulchra AMF in different ways (synergistic, controlling, or neutral) and the reciprocal effect was not always symmetric. • Our findings support a community approach to AMF studies, which can be used to increase our understanding of processes such as invasion and succession. DA - 2009/9// PY - 2009/9// DO - 10.1111/j.1469-8137.2009.02882.x VL - 183 IS - 4 SP - 1188-1200 KW - arbuscular mycorrhizal fungi (AMF) KW - Avena barbata KW - Bromus hordeaceus KW - grassland KW - Nassella pulchra KW - neighborhood KW - plant community KW - Vulpia microstachys ER - TY - JOUR TI - Origin, local experience, and the impact of biotic interactions on native and introduced Senecio species AU - Hawkes, Christine V. AU - Douglas, Angela E. AU - Fitter, Alastair H. T2 - Biol Invasions DA - 2009/2/6/ PY - 2009/2/6/ DO - 10.1007/s10530-009-9435-2 VL - 12 IS - 1 SP - 113-124 KW - Enemy release KW - Mutualist facilitation KW - Herbivory KW - Invasion KW - Pathogens ER - TY - JOUR TI - Genome-Wide Demethylation of Arabidopsis Endosperm AU - Hsieh, T.-F. AU - Ibarra, C. A. AU - Silva, P. AU - Zemach, A. AU - Eshed-Williams, L. AU - Fischer, R. L. AU - Zilberman, D. T2 - Science AB - Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here, we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA-targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo. DA - 2009/6/11/ PY - 2009/6/11/ DO - 10.1126/science.1172417 VL - 324 IS - 5933 SP - 1451-1454 J2 - Science LA - en OP - SN - 0036-8075 1095-9203 UR - http://dx.doi.org/10.1126/science.1172417 DB - Crossref ER - TY - JOUR TI - Anthocyanins, total phenolic compounds and antioxidant activity of purple corn (Zea mays L) cobs: Extraction method,Antocianinas, fenoles totales y actividad antioxidante de las corontas del maíz morado (Zea mays L.): Método de extracción AU - Gorriti Gutierrez, A. AU - Arroyo Acevedo, J. AU - Negron Ballarte, L. AU - Jurado Teixeira, B. AU - Purizaca Llajaruna, H. AU - Santiago Aquise, I. AU - Taype Espinoza, E. AU - Quispe Jacobo, F. T2 - Boletin Latinoamericano y del Caribe de Plantas Medicinales y Aromaticas DA - 2009/// PY - 2009/// VL - 8 IS - 6 SP - 509-518 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-76649104783&partnerID=MN8TOARS ER - TY - JOUR TI - Synopsis of Gonolobus s.s. (Apocynaceae, Asclepiadoideae) in Trinidad and Tobago AU - Krings, A. T2 - Journal of the Botanical Research Institute of Texas DA - 2009/// PY - 2009/// VL - 3 SP - 77–83 ER - TY - CHAP TI - Plant Genome Engineering Using Zinc Finger Nucleases AU - Kumar, Sandeep AU - Thompson, William F. T2 - Molecular Techniques in Crop Improvement PY - 2009/10/12/ DO - 10.1007/978-90-481-2967-6_24 SP - 579-590 OP - PB - Springer Netherlands SN - 9789048129669 9789048129676 UR - http://dx.doi.org/10.1007/978-90-481-2967-6_24 DB - Crossref ER - TY - JOUR TI - The Arabidopsis MCM2 gene is essential to embryo development and its over-expression alters root meristem function AU - Ni, Di An AU - Sozzani, Rosangela AU - Blanchet, Sophie AU - Domenichini, Séverine AU - Reuzeau, Christophe AU - Cella, Rino AU - Bergounioux, Catherine AU - Raynaud, Cécile T2 - The New Phytologist AB - • Minichromosome maintenance (MCM) proteins are subunits of the pre-replication complex that probably function as DNA helicases during the S phase of the cell cycle. Here, we investigated the function of AtMCM2 in Arabidopsis. • To gain an insight into the function of AtMCM2, we combined loss- and gain-of-function approaches. To this end, we analysed two null alleles of AtMCM2, and generated transgenic plants expressing AtMCM2 downstream of the constitutive 35S promoter. • Disruption of AtMCM2 is lethal at a very early stage of embryogenesis, whereas its over-expression results in reduced growth and inhibition of endoreduplication. In addition, over-expression of AtMCM2 induces the formation of additional initials in the columella root cap. In the plt1,2 mutant, defective for root apical meristem maintenance, over-expression of AtMCM2 induces lateral root initiation close to the root tip, a phenotype not reported in the wild-type or in plt1,2 mutants, even when cell cycle regulators, such as AtCYCD3;1, were over-expressed. • Taken together, our results provide evidence for the involvement of AtMCM2 in DNA replication, and suggest that it plays a crucial role in root meristem function. DA - 2009/10// PY - 2009/10// DO - 10.1111/j.1469-8137.2009.02961.x VL - 184 IS - 2 SP - 311-322 J2 - New Phytol. LA - eng SN - 1469-8137 DB - PubMed KW - AtMCM3 KW - DNA replication KW - lateral root initiation KW - minichromosome maintenance KW - root meristem function ER - TY - JOUR TI - Helping educational reforms to succeed in a Microbiology Department AU - Lee, V.S. AU - M, Hyman T2 - Microbe DA - 2009/// PY - 2009/// VL - 4 SP - 219–223 ER - TY - JOUR TI - Phylogenetic constraints on fine-scale patterns of habitat use by eight primate species in eastern Ecuador AU - Sheth, S.N. AU - Loiselle, B.A. AU - Blake, J.G. T2 - Journal of Tropical Ecology AB - Abstract: Lowland forests of western Amazonia contain the most species-rich primate communities in the Neotropics, which begs the question of what mechanisms operate to promote species coexistence. This study examines habitat occupancy and its relationship to phylogeny in a primate community in Amazonian Ecuador. First, as potential factors that shape community structure, we determined whether (1) mean height in the forest canopy differed among species; (2) within each species, habitat occupancy was disproportional to habitat availability; and (3) species diverged in habitat occupancy. We then tested hypotheses regarding ecological distance and its relationship to phylogenetic distance among species pairs within this community. We tested these hypotheses primarily with data derived from 15 censuses of primate species on two 100-ha plots in eastern Ecuador. In these censuses, we observed eight primate species over nearly 200 encounters. We observed larger species at greater heights in the forest canopy than smaller ones. Although they occupied habitat types at frequencies proportionate to their availability in the study area, species diverged in habitat occupancy. Although a clear relationship was not observed between phylogenetic and ecological distances among species pairs, this study suggests that ecological differences among the species in this community facilitate their coexistence. DA - 2009/// PY - 2009/// DO - 10.1017/S0266467409990216 VL - 25 IS - 6 SP - 571-582 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-74049151075&partnerID=MN8TOARS KW - Amazon KW - Atelidae KW - Cebidae KW - community structure KW - habitat use KW - neotropical primates KW - niche conservatism KW - Pitheciidae KW - species coexistence ER - TY - JOUR TI - An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III AU - GROUP, THE ANGIOSPERM PHYLOGENY T2 - Botanical Journal of the Linnean Society AB - A revised and updated classification for the families of flowering plants is provided. Many recent studies have yielded increasingly detailed evidence for the positions of formerly unplaced families, resulting in a number of newly adopted orders, including Amborellales, Berberidopsidales, Bruniales, Buxales, Chloranthales, Escalloniales, Huerteales, Nymphaeales, Paracryphiales, Petrosaviales, Picramniales, Trochodendrales, Vitales and Zygophyllales. A number of previously unplaced genera and families are included here in orders, greatly reducing the number of unplaced taxa; these include Hydatellaceae (Nymphaeales), Haptanthaceae (Buxales), Peridiscaceae (Saxifragales), Huaceae (Oxalidales), Centroplacaceae and Rafflesiaceae (both Malpighiales), Aphloiaceae, Geissolomataceae and Strasburgeriaceae (all Crossosomatales), Picramniaceae (Picramniales), Dipentodontaceae and Gerrardinaceae (both Huerteales), Cytinaceae (Malvales), Balanophoraceae (Santalales), Mitrastemonaceae (Ericales) and Boraginaceae (now at least known to be a member of lamiid clade). Newly segregated families for genera previously understood to be in other APG-recognized families include Petermanniaceae (Liliales), Calophyllaceae (Malpighiales), Capparaceae and Cleomaceae (both Brassicales), Schoepfiaceae (Santalales), Anacampserotaceae, Limeaceae, Lophiocarpaceae, Montiaceae and Talinaceae (all Caryophyllales) and Linderniaceae and Thomandersiaceae (both Lamiales). Use of bracketed families is abandoned because of its unpopularity, and in most cases the broader circumscriptions are retained; these include Amaryllidaceae, Asparagaceace and Xanthorrheaceae (all Asparagales), Passifloraceae (Malpighiales), Primulaceae (Ericales) and several other smaller families. Separate papers in this same volume deal with a new linear order for APG, subfamilial names that can be used for more accurate communication in Amaryllidaceae s.l., Asparagaceace s.l. and Xanthorrheaceae s.l. (all Asparagales) and a formal supraordinal classification for the flowering plants. DA - 2009/10// PY - 2009/10// DO - 10.1111/j.1095-8339.2009.00996.x VL - 161 IS - 2 SP - 105-121 LA - en SN - 00244074, 10958339 ST - An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants UR - https://academic.oup.com/botlinnean/article-lookup/doi/10.1111/j.1095-8339.2009.00996.x DB - Crossref Y2 - 2019/1/29/ ER - TY - JOUR TI - Phylogeny of Abies (Pinaceae) inferred from ITS sequence data AU - Xiang, Q.P. AU - Qy, Xiang AU - Guo, Y.Y. AU - Zhang, X.C. T2 - TAXON DA - 2009/2// PY - 2009/2// VL - 58 IS - 1 SP - 141–152 ER - TY - JOUR TI - Molecular and morphological inference of the phylogeny, origin, and biogeographic History of Aesculus L. (Sapindaceae or Hippocastanaceae). AU - Harris, A.J. AU - Xiang, Q.Y. AU - Thomas, D.T. T2 - TAXON DA - 2009/// PY - 2009/// VL - 58 SP - 1-19 ER - TY - JOUR TI - Lectotypification of Cardamine flexuosa (Brassicaceae). AU - Post, A.R. AU - Krings, A. AU - Xiang, Q.Y. AU - Sosinski, B.R. AU - Neal, J.C. T2 - J. Bot. Res. Inst. Texas DA - 2009/7/15/ PY - 2009/7/15/ VL - 3 IS - 1 SP - 227–230 UR - https://www.jstor.org/stable/41972157 ER - TY - CHAP TI - Cornaceae AU - Xiang, Q.-Y. T2 - China Checklist of Higher Plants, In the Biodiversity Committeee of Chinese Academy of Sciences A2 - Qin, H.N. T3 - Catalogue of Life, China: 2009 Annual Checklist PY - 2009/// PB - Species 2000 China Node UR - http://www.sp2000.cn/ ER - TY - JOUR TI - Directed Assembly of PEGylated-Peptide Coatings for Infection-Resistant Titanium Metal AU - Khoo, Xiaojuan AU - Hamilton, Paul AU - O’Toole, George A. AU - Snyder, Brian D. AU - Kenan, Daniel J. AU - Grinstaff, Mark W. T2 - J. Am. Chem. Soc. AB - Appropriate surface chemistry between a material and its surrounding biological environment is crucial to the eventual integration and performance of any implant, whether metal, plastic, or ceramic. A robust peptide-based coating technology capable of easily modifying the surface of titanium (Ti) metal through noncovalent binding is described. A short peptide possessing affinity for Ti was identified using a phage display screening process and subjected to an amino acid substitution exercise using solid-phase chemical synthesis. Through these studies, the HKH tripeptide motif was elucidated as an important contributor to Ti binding within the Ti-binding peptide. This peptide spontaneously and selectively adsorbs onto a Ti surface from dilute aqueous solution with submicromolar binding affinities as determined by ELISA and quartz crystal microbalance with dissipation monitoring (QCM-D), through a process largely dominated by electrostatic interactions. Atomic force microscopy (AFM) reveals a densely packed peptide adlayer with an average height of ∼0.5 nm. Subsequently, a PEGylated analogue of the peptide was shown to rapidly coat Ti to afford a nonfouling surface that efficiently blocked the adsorption of fibronectin and significantly reduced the extent of Staphylococcus aureus attachment and biofilm formation in vitro. These PEGylated-peptide coatings show promise in terms of resolving two major hurdles common to implanted metals: (i) nonspecific protein adsorption and (ii) bacterial colonization. At the same time, the facile one-step modification process will facilitate the point-of-care application of these coatings in the surgical suite. DA - 2009/8// PY - 2009/8// DO - 10.1021/ja9020827 VL - 131 IS - 31 SP - 10992-10997 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-68249136655&partnerID=MN8TOARS ER - TY - JOUR TI - Immunohistochemical localization of apyrase during initial differentiation and germination of pea seeds AU - Yoneda, Motohito AU - Davies, Eric AU - Morita, Eugene Hayato AU - Abe, Shunnosuke T2 - PLANTA DA - 2009/12// PY - 2009/12// DO - 10.1007/s00425-009-1025-0 VL - 231 IS - 1 SP - 47-56 SN - 1432-2048 KW - Apyrase KW - APY1 KW - Lateral root primordium KW - Immunohistochemistry KW - Pea KW - Seed germination ER - TY - JOUR TI - Blue light induced changes in inositol 1,4,5-trisphosphate in Cuscuta campestris seedlings AU - Haidar, M. A. AU - Boss, W. F. T2 - WEED RESEARCH AB - Summary Previous studies revealed that blue light stimulates and red light inhibits prehaustoria development in young seedlings of the parasitic weed Cuscuta campestris (field dodder). This study showed a positive correlation between blue light induced increases in inositol 1,4,5‐trisphosphate (IP 3 ) and blue light‐mediation of prehaustoria development, prior to host attachment. Blue light induced a significant increase in the level of IP 3 , with a peak at about 30 min. Thereafter, the level of IP 3 declined to the resting value after 2 h of blue light. Irradiation with 10 min red light pulse applied directly at the end of each 0.05, 0.1, 0.15, 0.2, 0.3, 1, 2 and 4 h blue light significantly reduced IP 3 , while high levels of IP 3 were observed after 10 min far‐red pulse. The G‐protein inhibitor pertussis toxin inhibited prehaustoria developed under blue light, suggesting that receptor‐coupled G‐proteins are likely to be involved in prehaustoria development. These results are the first in vivo demonstration of a possible role for IP 3 as a second messenger in the blue light signal transduction process in prehaustoria development in Cuscuta . DA - 2009/12// PY - 2009/12// DO - 10.1111/j.1365-3180.2009.00732.x VL - 49 IS - 6 SP - 628-633 SN - 1365-3180 KW - blue light KW - field dodder KW - inositol 1 KW - 4 KW - 5-trisphosphate KW - IP3 KW - cryptochromes KW - G-proteins KW - phytochromes ER - TY - JOUR TI - Plant cell calcium-rich environment enhances thermostability of recombinantly produced alpha-amylase from the hyperthermophilic bacterium Thermotoga maritime AU - Santa-Maria, Monica C. AU - Chou, Chung-Jung AU - Yencho, G. Craig AU - Haigler, Candace H. AU - Thompson, William F. AU - Kelly, Robert M. AU - Sosinski, Bryon T2 - Biotechnology and Bioengineering AB - Abstract In the industrial processing of starch for sugar syrup and ethanol production, a liquefaction step is involved where starch is initially solubilized at high temperature and partially hydrolyzed with a thermostable and thermoactive α‐amylase. Most amylases require calcium as a cofactor for their activity and stability, therefore calcium, along with the thermostable enzyme, are typically added to the starch mixture during enzymatic liquefaction, thereby increasing process costs. An attractive alternative would be to produce the enzyme directly in the tissue to be treated. In a proof of concept study, tobacco cell cultures were used as model system to test in planta production of a hyperthermophilic α‐amylase from Thermotoga maritima . While comparable biochemical properties to recombinant production in Escherichia coli were observed, thermostability of the plant‐produced α‐amylase benefited significantly from high intrinsic calcium levels in the tobacco cells. The plant‐made enzyme retained 85% of its initial activity after 3 h incubation at 100°C, whereas the E. coli ‐produced enzyme was completely inactivated after 30 min under the same conditions. The addition of Ca 2+ or plant cell extracts from tobacco and sweetpotato to the E. coli ‐produced enzyme resulted in a similar stabilization, demonstrating the importance of a calcium‐rich environment for thermostability, as well as the advantage of producing this enzyme directly in plant cells where calcium is readily available. Biotechnol. Bioeng. 2009; 104: 947–956. © 2009 Wiley Periodicals, Inc. DA - 2009/12/1/ PY - 2009/12/1/ DO - 10.1002/bit.22468 VL - 104 IS - 5 SP - 947-956 J2 - Biotechnol. Bioeng. LA - eng SN - 1097-0290 DB - PubMed KW - hyperthermophilic enzymes KW - starch processing KW - transgenic plants KW - tobacco NT1 Cell cultures KW - biofuel ER - TY - JOUR TI - A Laboratory-intensive Course on RNA Interference and Model Organisms AU - Miller, Joanna A. AU - Witherow, D. Scott AU - Carson, Susan T2 - CBE-LIFE SCIENCES EDUCATION AB - RNA interference (RNAi) is a powerful method to silence gene expression in a variety of organisms and is generating interest not only as a useful tool for research scientists but also as a novel class of therapeutics in clinical trials. Here, we report that undergraduate and graduate students with a basic molecular biology background were able to demonstrate conceptual knowledge and technical skills for using RNAi as a research tool upon completion of an intensive 8-wk RNAi course with a 2-h lecture and 5-h laboratory per week. Students were instructed on design of RNAi experiments in model organisms and perform multiweek laboratory sessions based on journal articles read and discussed in class. Using Nicotiana benthamiana, Caenorhabditis elegans, and mammalian cell culture, students analyzed the extent of silencing using both qualitative assessment of phenotypic variations and quantitative measurements of RNA levels or protein levels. We evaluated the course over two semesters, each with a separate instructor. In both semesters, we show students met expected learning outcomes as demonstrated by successful laboratory experiment results, as well as positive instructor assessments of exams and lab reports. Student self-assessments revealed increased confidence in conceptual knowledge and practical skills. Our data also suggest that the course is adaptable to different instructors with varying expertise. DA - 2009/// PY - 2009/// DO - 10.1187/cbe.09-02-0012 VL - 8 IS - 4 SP - 316-325 SN - 1931-7913 ER - TY - JOUR TI - New Zealand Bittercress (Cardamine corymbosa; Brassicaceae): New to the United States AU - Post, A. R. AU - Neal, J. C. AU - Krings, A. AU - Sosinski, B. R. AU - Xiang, Q. T2 - WEED TECHNOLOGY AB - New Zealand bittercress is reported as new to the United States. While collecting specimens to determine what Cardamine species occur in the nursery trade, New Zealand bittercress was discovered in a container nursery in Wilkes County, North Carolina. The nursery tracked the shipment of contaminated plants to a wholesale nursery in Washington County, Oregon. It was subsequently confirmed that New Zealand bittercress also occurs in a nursery in Clackamas County, Oregon, and has likely been distributed throughout the United States as a contaminant in container grown ornamental plants. Thus far there have been no reports of naturalized populations outside of container nursery crop production facilities. DA - 2009/// PY - 2009/// DO - 10.1614/WT-09-017.1 VL - 23 IS - 4 SP - 604-607 SN - 1550-2740 KW - Bittercress KW - Cardamine KW - new species KW - weed ER - TY - JOUR TI - Alcohol Sensitivity in Drosophila: Translational Potential of Systems Genetics AU - Morozova, Tatiana V. AU - Ayroles, Julien F. AU - Jordan, Katherine W. AU - Duncan, Laura H. AU - Carbone, Mary Anna AU - Lyman, Richard E. AU - Stone, Eric A. AU - Govindaraju, Diddahally R. AU - Ellison, R. Curtis AU - Mackay, Trudy F. C. AU - Anholt, Robert R. H. T2 - GENETICS AB - Identification of risk alleles for human behavioral disorders through genomewide association studies (GWAS) has been hampered by a daunting multiple testing problem. This problem can be circumvented for some phenotypes by combining genomewide studies in model organisms with subsequent candidate gene association analyses in human populations. Here, we characterized genetic networks that underlie the response to ethanol exposure in Drosophila melanogaster by measuring ethanol knockdown time in 40 wild-derived inbred Drosophila lines. We associated phenotypic variation in ethanol responses with genomewide variation in gene expression and identified modules of correlated transcripts associated with a first and second exposure to ethanol vapors as well as the induction of tolerance. We validated the computational networks and assessed their robustness by transposon-mediated disruption of focal genes within modules in a laboratory inbred strain, followed by measurements of transcript abundance of connected genes within the module. Many genes within the modules have human orthologs, which provides a stepping stone for the identification of candidate genes associated with alcohol drinking behavior in human populations. We demonstrated the potential of this translational approach by identifying seven intronic single nucleotide polymorphisms of the Malic Enzyme 1 (ME1) gene that are associated with cocktail drinking in 1687 individuals of the Framingham Offspring cohort, implicating that variation in levels of cytoplasmic malic enzyme may contribute to variation in alcohol consumption. DA - 2009/10// PY - 2009/10// DO - 10.1534/genetics.109.107490 VL - 183 IS - 2 SP - 733-745 SN - 1943-2631 ER - TY - JOUR TI - Phylogeny and biogeography of Alangiaceae (Cornales) inferred from DNA sequences, morphology, and fossils AU - Feng, Chun-Miao AU - Manchester, Steven R. AU - Xiang, Qiu-Yun T2 - MOLECULAR PHYLOGENETICS AND EVOLUTION AB - Alangiaceae, in the basal Asterid clade Cornales, consists of only one genus, Alangium. The genus has approximately 24 species distributed mainly in tropical and subtropical regions of the Old World and is well represented in the Tertiary fossil record of the northern hemisphere. We conducted phylogenetic and biogeographic analyses for Alangium by integrating data from DNA sequences, morphology, and fossils to evaluate systematic and biogeographic hypotheses. The results largely agree with the traditional classification of four sections within the genus, and suggest sects. Conostigma and Rhytidandra are successive sister taxa to a clade containing sects. Marlea and Alangium. Our results also indicate that the widespread species A. chinense consists of at least two lineages meriting recognition as distinct species. Biogeographic analysis using DIVA and divergence time dating with the Bayesian method (MULTIDIVTIME) resolved the ancestor of Alangium as being in S.E. Asia in the Late Cretaceous. Several intercontinental migrations involving the margin of the Tethys seaway (TESW), the North Atlantic land bridge (NALB) or the Bering land bridge (BLB), and long-distance dispersals are suggested. The results support TESW for plant migration of thermophilic (including evergreen) taxa in the early Tertiary. DA - 2009/5// PY - 2009/5// DO - 10.1016/j.ympev.2009.01.017 VL - 51 IS - 2 SP - 201-214 SN - 1095-9513 KW - Alangiaceae KW - Biogeography KW - Divergence time KW - Morphology KW - Fossils KW - Phylogeny ER - TY - JOUR TI - Microbial pretreatment of cotton stalks by submerged cultivation of Phanerochaete chrysosporium AU - Shi, Jian AU - Sharma-Shivappa, Ratna R. AU - Chinn, Mari S. T2 - BIORESOURCE TECHNOLOGY AB - This study used the fungus, Phanerochaete chrysosporium, to pretreat cotton stalks with two methods, shallow stationary and agitated cultivation, at three supplemental salt concentrations. Pretreatment efficiencies were compared by evaluating lignin degradation, solid recovery and carbohydrate availability over a 14-day period. Shallow stationary cultivation with no salts gave 20.7% lignin degradation along with 76.3% solid recovery and 29.0% carbohydrate availability. The highest lignin degradation of 33.9% at a corresponding solid recovery and carbohydrate availability of 67.8% and 18.4%, respectively, was obtained through agitated cultivation with Modified NREL salts. Cultivation beyond 10 days did not significantly increase lignin degradation during 14 days of pretreatment. Manganese addition during shallow stationary and agitated cultivation resulted in higher solid recoveries of over 80% but lower lignin degradation. Although agitated cultivation resulted in better delignification, results indicate that pretreatment under submerged shallow stationary conditions provides a better balance between lignin degradation and carbohydrate availability. DA - 2009/10// PY - 2009/10// DO - 10.1016/j.biortech.2008.10.060 VL - 100 IS - 19 SP - 4388-4395 SN - 1873-2976 KW - Fungal pretreatment KW - Biofuel KW - Phanerochaete chrysosporium KW - Cotton residue KW - Delignification ER - TY - JOUR TI - A New Species in the Ibatia Species Complex in Matelea s. l. (Apocynaceae: Asclepiadoideae: Asclepiadeae) from Colombia AU - Krings, Alexander T2 - SYSTEMATIC BOTANY AB - A new species of Matelea s.l. (Apocynaceae: Asclepiadoideae, Asclepiadeae, Gonolobinae) is described from coastal Colombia: Matelea dugandii . The species belongs to the Ibatia species complex in Matelea s.l., but exhibits distinct differences in floral characters from previously known taxa, particularly in the terminal style-head appendage. An updated key to members of the complex in northern South America and the West Indies is provided, including M. cumanensis , M. fontana , M. maritima , M. pacifica , and M. rubra . DA - 2009/// PY - 2009/// DO - 10.1600/036364409788606280 VL - 34 IS - 2 SP - 429-433 SN - 0363-6445 KW - Apocynaceae KW - Gonolobinae KW - Matelea KW - morphology KW - systematics ER - TY - JOUR TI - Local auxin biosynthesis modulates gradient-directed planar polarity in Arabidopsis AU - Ikeda, Yoshihisa AU - Men, Shuzhen AU - Fischer, Urs AU - Stepanova, Anna N. AU - Alonso, Jose M. AU - Ljung, Karin AU - Grebe, Markus T2 - NATURE CELL BIOLOGY AB - Arabidopsis root-hair position and orientation in epithelial cells is directed by an auxin gradient maximum at the root tip. The Raf-like kinase CTR1 negatively regulates local auxin biosynthesis in the root to determine root hair position. The coordination of cell polarity within the plane of a single tissue layer (planar polarity) is a crucial task during development of multicellular organisms. Mechanisms underlying establishment of planar polarity, however, differ substantially between plants and animals1,2,3. In Arabidopsis thaliana, planar polarity of root-hair positioning along epidermal cells is coordinated towards maximum concentration of an auxin gradient in the root tip3,4,5. This gradient has been hypothesized to be sink-driven6 and computational modelling suggests that auxin efflux carrier activity may be sufficient to generate the gradient in the absence of auxin biosynthesis in the root7. Here, we demonstrate that the Raf-like kinase CONSTITUTIVE TRIPLE RESPONSE1 (CTR1; Refs 8, 9) acts as a concentration-dependent repressor of a biosynthesis-dependent auxin gradient that modulates planar polarity in the root tip. We analysed auxin biosynthesis and concentration gradients in a variety of root-hair-position mutants affected in CTR1 activity, auxin biosynthesis and transport. Our results reveal that planar polarity relies on influx- and efflux-carrier-mediated auxin redistribution from a local biosynthesis maximum. Thus, a local source of auxin biosynthesis contributes to gradient homeostasis during long-range coordination of cellular morphogenesis. DA - 2009/6// PY - 2009/6// DO - 10.1038/ncb1879 VL - 11 IS - 6 SP - 731-U70 SN - 1476-4679 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-67349090679&partnerID=MN8TOARS ER - TY - JOUR TI - Intercontinental and intracontinental biogeography-patterns and methods AU - Wen, Jun AU - Xiang, Qiu-Yun Jenny AU - Qian, Hong AU - Li, Jianhua AU - Wang, Xiao-Quan AU - Ickert-Bond, Stefanie M. T2 - Journal of Systematics and Evolution AB - The study of biogeography has benefited from the exponential increase of DNA sequence data from recent molecular systematic studies, the development of analytical methods in the last decade concerning divergence time estimation and geographic area analyses, and the availability of large-scale distribution data of species in many groups of organisms. The underlying principle of divergence time estimation from DNA and protein data is that sequence divergence depends on the product of evolutionary rate and time. With their molecular clock hypothesis, Zuckerkandl and Pauling (1965) separated rates of molecular evolution from time by incorporating fossil evidence. Originally, a constant rate of sequence evolution was assumed, but soon it became evident that many data sets do not obey the constant rate assumption of a strict molecular clock. In fact, many studies have revealed extreme heterogeneity of nucleotide substitution rates over time. To account for the heterogeneity, relaxed molecular clock approaches have been developed (Thorne et al., 1998; Sanderson, 2002; Yang & Yoder, 2003; Drummond et al., 2006) with the availability of computer programs such as r8s, multidivtime, and BEAST (Thorne & Kishino, 2002; Sanderson, 2003; Drummond & Rambaut, 2007; see reviews by Renner, 2005 and by Rutschmann, 2006). Area relationships were primarily inferred using methods in phylogenetic biogeography (Brundin, 1988), cladistic biogeography (Humphries & Parenti, 1999), and panbiogeography (Craw et al., 1999) in the 1980's and 1990's. These different biogeographic methods all have some limitations. The cladistic biogeographic approach emphasizes vicariance in forming biogeographic patterns, but underestimates the impact of processes such as dispersal and extinction (Ronquist, 1996, 1997). Different groups of organisms may respond differently to biogeographic barriers, which complicate the inference of general area relationship from taxon cladograms. In response to these limitations, Ronquist (1997) proposed the dispersal-vicariance (DIVA) analysis as an alternative approach of quantification of historical biogeography. This method reconstructs the ancestral distribution in a phylogeny using a three-dimensional step matrix, while allowing for dispersal and extinction to occur. The optimal ancestral distributions are inferred by minimizing the number of dispersal and extinction events (see review by Lamm & Redelings, this issue). Many studies have employed DIVA for inferring historical biogeography in a wide range of organisms (e.g., Sanmartín & Ronquist, 2004; also see Harris & Xiang, this issue). Recent advances in ancestral area reconstruction have brought forward additional approaches, such as the Bayes-DIVA method (Nylander et al., 2008), as well as the dispersal-extinction-cladogenesis (DEC) analysis (Ree et al., 2005; Ree & Smith, 2008; also see review by Lamm & Redelings, this issue). DEC analysis uses a phylogenetic model of geographic range evolution to infer ancestral ranges and biogeographic events given rates of stochastic dispersal and local extinction estimated by maximum likelihood, and can be implemented in Lagrange version 2.0.1. (available at: http://lagrange.googlecode.com). The newly developed methods have stimulated strong interests in reconstructing the intercontinental disjunctions and intracontinental patterns of biogeography. The results on the divergence times and area relationships have stimulated debates on the significance of vicariance and dispersal. In many cases, dispersal has been validated as an important hypothesis of the origin of many disjunctions (De Queiroz, 2005; Posadas et al., 2006; Wen & Ickert-Bond, this issue). Several important biogeographic patterns especially at the intercontinental level have been examined and reviewed, such as the northern hemisphere disjunctions (see Xiang et al., 1998; Wen, 1999; Manos & Donoghue, 2001; Donoghue & Smith, 2004), the tropical disjunctions (Givnish & Renner, 2004), and the southern hemisphere patterns (Sanmartín & Ronquist, 2004). This special issue of Journal of Systematics and Evolution includes 12 papers, which examine the current intercontinental and intracontinental patterns and explore new analytical methods. Specifically, Wen and Ickert-Bond review two major patterns of intercontinental disjunctions (the Madrean-Tethyan and the North and South American amphitropical disjunctions). Harris and Xiang propose a statistical approach for analyses using DIVA without fully bifurcating trees. Lamm and Redelings provide a review of newly developed methods for reconstructing ancestral ranges. Milne explores the effects of taxon sampling on dating within-genus divergence using deep fossils. Yue et al. examine the geographic assembly of the flora of the Hengduan Mountains using the brassicaceous genus Solms-laubachia as a case study. Nie et al. employ Toxicodendron as a model genus for analyzing the biogeographic interaction of the temperate and tropical elements. Simpson et al. reconstruct the biogeographic pattern in the Andes. Ickert-Bond et al. infer the intercontinental biogeographic disjunctions between the Old and the New World in Ephedra. Dillon et al. explore the biogeographic patterns and diversification of the Atacama and the Peruvian deserts. Fiaschi and Pirani review biogeographic patterns and studies of Brazil. Heinrichs et al. provide an updated summary of the biogeographic disjunctions in bryophytes and the impact of molecular work on bryophyte taxonomy. Qian succinctly compares the global patterns of beta diversity among mammals, birds, reptiles and amphibians. We hope this collection of papers will stimulate future biogeographic analyses on intercontinental and intracontinental patterns and facilitate collaborations of colleagues from different continents. It is important to explore new analytical methods, which may bring better synthesis of data from different fields such as phylogenetics, paleontology and ecology (Donoghue & Moore, 2003; Crisci, 2006). More model-based techniques are needed for rigorous statistical test of hypotheses pertaining to historical biogeography (Ree & Sanmartín, 2009). Robust data using multiple loci including cytoplasmic and nuclear markers are needed in molecular biogeographic studies, especially for groups with frequent interspecific hybridization (Peng & Wang, 2008). Many intercontinental disjunct patterns are particular to either the northern hemisphere or the southern hemisphere. It is nevertheless important to characterize the biogeographic interactions between the northern and the southern hemispheres. Comprehensive biogeographic analyses at the global scale are clearly needed in the future. Recent biogeographic analyses have provided important insights into intercontinental patterns, yet we need to rigorously explore the intracontinental patterns of different regions using comparative phylogeographic and ecological approaches (Soltis et al., 2006). In particular, phylogeographic studies are helpful for understanding intracontinental disjunctions (Yang et al., 2008). It is an exciting period for biogeography, and we hope to see important syntheses that will lead to better understanding of both intracontinental and intercontinental biogeographic dynamics. Acknowledgements We thank Jeff Thorne for helpful comments and edits on this editorial. DA - 2009/9// PY - 2009/9// DO - 10.1111/j.1759-6831.2009.00052.x VL - 47 IS - 5 SP - 327-330 LA - en SN - 16744918 UR - http://doi.wiley.com/10.1111/j.1759-6831.2009.00052.x DB - Crossref Y2 - 2019/1/29/ ER - TY - JOUR TI - Evapotranspiration and energy balance of Brazilian savannas with contrasting tree density AU - Giambelluca, Thomas W. AU - Scholz, Fabian G. AU - Bucci, Sandra J. AU - Meinzer, Frederick C. AU - Goldstein, Guillermo AU - Hoffmann, William A. AU - Franco, Augusto C. AU - Buchert, Martin P. T2 - AGRICULTURAL AND FOREST METEOROLOGY AB - Tropical savannas including those of central Brazil (Cerrado) serve as an important regulator of energy and mass exchange with the atmosphere. However, the effects of interactions between grasses and deeply rooted trees and shrubs on energy and water fluxes of savannas are not well understood. In this study, eddy-covariance measurements were used to observe and compare the energy balance and evapotranspiration at two adjacent Cerrado sites differing in woody plant density. Latent energy flux (LE) and evapotranspiration (ET) for Cerrado Denso (8–10-m trees with a cover density of approximately 50% and an understory of grass and shrubs) were generally similar to or greater than for Campo Cerrado (widely scattered 3–4-m trees with a cover density of about 5% and an understory of grasses, shrubs, and sedges), with the greatest difference between the sites occurring during the dry season. Mean annual ET was 823 and 689 mm yr−1, and LE averaged 63.9 ± 11.7 and 53.5 ± 14.3 W m−2 at Cerrado Denso and Campo Cerrado, respectively. At both sites, ET reached a minimum at near the end of the dry season, indicating that reduced water availability constrained dry season ET at both sites. The Bowen ratio at both sites increased as soil moisture decreased, but with a stronger dependency at the Campo Cerrado site, presumably due to the dominance of shallow-rooted plants and the larger contribution of soil evaporation there. Energy partitioning, as indicated by the Bowen ratio, was also strongly influenced by variations in leaf area index (LAI). The strong similarity in the Bowen ratio–LAI relationship for the two sites suggests that LAI can be used to explain much of the observed temporal and spatial ET variability across seasons and variations in woody plant density in the Cerrado. DA - 2009/8/3/ PY - 2009/8/3/ DO - 10.1016/j.agrformet.2009.03.006 VL - 149 IS - 8 SP - 1365-1376 SN - 1873-2240 KW - Tropical savannas KW - Land-atmosphere interaction KW - Leaf area index KW - Soil moisture ER - TY - JOUR TI - Estimating ancestral distributions of lineages with uncertain sister groups: a statistical approach to Dispersal-Vicariance Analysis and a case using Aesculus L. (Sapindaceae) including fossils AU - Harris, A.J. AU - Xiang, Qiu-Yun Jenny T2 - Journal of Systematics and Evolution AB - Abstract We propose a simple statistical approach for using Dispersal–Vicariance Analysis (DIVA) software to infer biogeographic histories without fully bifurcating trees. In this approach, ancestral ranges are first optimized for a sample of Bayesian trees. The probability P of an ancestral range r at a node is then calculated as where Y is a node, and F ( r Y ) is the frequency of range r among all the optimal solutions resulting from DIVA optimization at node Y , t is one of n topologies optimized, and Pt is the probability of topology t . Node Y is a hypothesized ancestor shared by a specific crown lineage and the sister of that lineage “ x ”, where x may vary due to phylogenetic uncertainty (polytomies and nodes with posterior probability <100%). Using this method, the ancestral distribution at Y can be estimated to provide inference of the geographic origins of the specific crown group of interest. This approach takes into account phylogenetic uncertainty as well as uncertainty from DIVA optimization. It is an extension of the previously described method called Bayes‐DIVA, which pairs Bayesian phylogenetic analysis with biogeographic analysis using DIVA. Further, we show that the probability P of an ancestral range at Y calculated using this method does not equate to pp* F ( r Y ) on the Bayesian consensus tree when both variables are <100%, where pp is the posterior probability and F ( r Y ) is the frequency of range r for the node containing the specific crown group. We tested our DIVA‐Bayes approach using Aesculus L., which has major lineages unresolved as a polytomy. We inferred the most probable geographic origins of the five traditional sections of Aesculus and of Aesculus californica Nutt. and examined range subdivisions at parental nodes of these lineages. Additionally, we used the DIVA‐Bayes data from Aesculus to quantify the effects on biogeographic inference of including two wildcard fossil taxa in phylogenetic analysis. Our analysis resolved the geographic ranges of the parental nodes of the lineages of Aesculus with moderate to high probabilities. The probabilities were greater than those estimated using the simple calculation of pp* F ( r y ) at a statistically significant level for two of the six lineages. We also found that adding fossil wildcard taxa in phylogenetic analysis generally increased P for ancestral ranges including the fossil's distribution area. The Δ P was more dramatic for ranges that include the area of a wildcard fossil with a distribution area underrepresented among extant taxa. This indicates the importance of including fossils in biogeographic analysis. Exmination of range subdivision at the parental nodes revealed potential range evolution (extinction and dispersal events) along the stems of A. californica and sect. Parryana . DA - 2009/9// PY - 2009/9// DO - 10.1111/j.1759-6831.2009.00044.x VL - 47 IS - 5 SP - 349-368 LA - en SN - 16744918 ST - Estimating ancestral distributions of lineages with uncertain sister groups UR - http://doi.wiley.com/10.1111/j.1759-6831.2009.00044.x DB - Crossref Y2 - 2019/1/29/ KW - Aesculus KW - biogeography KW - DIVA KW - fossil wildcards KW - MrBayes KW - phylogenetic uncertainty ER - TY - JOUR TI - Dynamic Localization of the DNA Replication Proteins MCM5 and MCM7 in Plants AU - Shultz, Randall W. AU - Lee, Tae-Jin AU - Allen, George C. AU - Thompson, William F. AU - Hanley-Bowdoin, Linda T2 - PLANT PHYSIOLOGY AB - Abstract Genome integrity in eukaryotes depends on licensing mechanisms that prevent loading of the minichromosome maintenance complex (MCM2-7) onto replicated DNA during S phase. Although the principle of licensing appears to be conserved across all eukaryotes, the mechanisms that control it vary, and it is not clear how licensing is regulated in plants. In this work, we demonstrate that subunits of the MCM2-7 complex are coordinately expressed during Arabidopsis (Arabidopsis thaliana) development and are abundant in proliferating and endocycling tissues, indicative of a role in DNA replication. We show that endogenous MCM5 and MCM7 proteins are localized in the nucleus during G1, S, and G2 phases of the cell cycle and are released into the cytoplasmic compartment during mitosis. We also show that MCM5 and MCM7 are topologically constrained on DNA and that the MCM complex is stable under high-salt conditions. Our results are consistent with a conserved replicative helicase function for the MCM complex in plants but not with the idea that plants resemble budding yeast by actively exporting the MCM complex from the nucleus to prevent unauthorized origin licensing and rereplication during S phase. Instead, our data show that, like other higher eukaryotes, the MCM complex in plants remains in the nucleus throughout most of the cell cycle and is only dispersed in mitotic cells. DA - 2009/6// PY - 2009/6// DO - 10.1104/pp.109.136614 VL - 150 IS - 2 SP - 658-669 SN - 1532-2548 ER - TY - JOUR TI - Are rare species less shade tolerant than common species in fire-prone environments? A test with seven Amorpha (Fabaceae) species AU - Marchin, Renee M. AU - Bhandari, Rohit K. AU - Wall, Wade A. AU - Hohmann, Matthew G. AU - Gray, Janet B. AU - Hoffmann, William A. T2 - PLANT ECOLOGY DA - 2009/12// PY - 2009/12// DO - 10.1007/s11258-009-9614-3 VL - 205 IS - 2 SP - 249-260 SN - 1573-5052 KW - Amorpha KW - Growth analysis KW - Shade tolerance KW - Conservation biology KW - Rare species ER - TY - JOUR TI - Arabidopsis Protein Kinases GRIK1 and GRIK2 Specifically Activate SnRK1 by Phosphorylating Its Activation Loop AU - Shen, Wei AU - Reyes, Maria Ines AU - Hanley-Bowdoin, Linda T2 - PLANT PHYSIOLOGY AB - SNF1-related kinases (SnRK1s) play central roles in coordinating energy balance and nutrient metabolism in plants. SNF1 and AMPK, the SnRK1 homologs in budding yeast (Saccharomyces cerevisiae) and mammals, are activated by phosphorylation of conserved threonine residues in their activation loops. Arabidopsis (Arabidopsis thaliana) GRIK1 and GRIK2, which were first characterized as geminivirus Rep interacting kinases, are phylogenetically related to SNF1 and AMPK activating kinases. In this study, we used recombinant proteins produced in bacteria to show that both GRIKs specifically bind to the SnRK1 catalytic subunit and phosphorylate the equivalent threonine residue in its activation loop in vitro. GRIK-mediated phosphorylation increased SnRK1 kinase activity in autophosphorylation and peptide substrate assays. These data, together with earlier observations that GRIKs could complement yeast mutants lacking SNF1 activation activities, established that the GRIKs are SnRK1 activating kinases. Given that the GRIK proteins only accumulate in young tissues and geminivirus-infected mature leaves, the GRIK-SnRK1 cascade may function in a developmentally regulated fashion and coordinate the unique metabolic requirements of rapidly growing cells and geminivirus-infected cells that have been induced to reenter the cell cycle. DA - 2009/6// PY - 2009/6// DO - 10.1104/pp.108.132787 VL - 150 IS - 2 SP - 996-1005 SN - 1532-2548 ER - TY - JOUR TI - Use of long-term data and multivariate ordination techniques to identify environmental factors governing estuarine phytoplankton species dynamics AU - Rothenberger, Meghan B. AU - Burkholder, JoAnn M. AU - Wentworth, Thomas R. T2 - LIMNOLOGY AND OCEANOGRAPHY AB - A continuous, 13‐yr record of environmental data and phytoplankton species and assemblage structure in the mesohaline Neuse River Estuary (biweekly, April‐October; monthly, November‐March) was used to evaluate phytoplankton assemblage responses to changing environmental conditions. Ordination techniques including nonmetric multidimensional scaling, indicator species analysis, and BIO‐ENV software were used to investigate potential environmental predictors of phytoplankton assemblage patterns under chronic eutrophication. Phytoplankton assemblages were strongly related to temperature and total nitrogen : total phosphorus ratios, with expected seasonal changes in species composition. Interannual changes in river discharge influenced whether phytoplankton assemblages were dominated by diatoms and phototrophic flagellates or by mixotrophic and heterotrophic dinoflagellates. Increasing ammonium concentrations also have been an important influence on phytoplankton assemblages. Raphidophytes (including the potentially toxic species Heterosigma akashiwo ), haptophytes, chlorophytes, and the bloom‐forming dinoflagellate Heterocapsa rotundata have increased in more recent years (2000–2006), concomitant with increasing ammonium concentrations. Abundance of the potentially toxic dinoflagellates Prorocentrum minimum and the grouping Pfiesteria spp., “pfiesteria‐like” dinoflagellates, and Karlodinium veneficum remained stationary over time and rarely exceeded 103 cells mL −1 . Abundance of P. minimum was positively related to dissolved organic nitrogen and suspended solids concentrations, whereas the highest abundance of the grouping Pfiesteria spp., “pfiesteria‐like” dinoflagellates, and K. veneficum occurred during summer and fall, related to high total phosphorus concentrations, temperature, and salinity. Overall, this study provides new species‐level insights to advance understanding about anthropogenic influences on phytoplankton assemblages. The data suggest an increasingly important role of ammonium in controlling phytoplankton assemblage structure, including increased abundance of some harmful species, in eutrophic estuaries. DA - 2009/11// PY - 2009/11// DO - 10.4319/lo.2009.54.6.2107 VL - 54 IS - 6 SP - 2107-2127 SN - 1939-5590 ER - TY - JOUR TI - Tree topkill, not mortality, governs the dynamics of savanna-forest boundaries under frequent fire in central Brazil AU - Hoffmann, William A. AU - Adasme, Ryan AU - Haridasan, M. AU - Carvalho, Marina T. AU - Geiger, Erika L. AU - Pereira, Mireia A. B. AU - Gotsch, Sybil G. AU - Franco, Augusto C. T2 - ECOLOGY AB - Tropical savanna and forest are recognized to represent alternate stable states, primarily determined by feedbacks with fire. Vegetation-fire dynamics in each of these vegetation types are largely determined by the influence of the vegetation on fire behavior, as well as the effects of fire behavior on tree mortality, topkill (defined here as complete death of the aerial biomass, regardless of whether the plant recovers by resprouting), and rate of growth of resprouts. We studied the effect of fire on three savanna-forest boundaries in central Brazil. Fire intensity was greater in savanna than forest, as inferred by a twofold greater height of stem charring. Despite lower fire intensity, forest tree species exhibited higher rates of topkill, which was best explained by their thinner bark, relative to savanna species. Following topkill, there was no tendency for sprouts of savanna trees to grow faster than those of forest species, contrary to expectations, nor was whole-plant mortality higher in forest than in savanna. This contrasts with observations of high rates of postburn mortality in many other tropical forests. The low tree mortality in these transitional forests suggests that the dynamic of these natural savanna-forest boundaries is fundamentally different from that of forest boundaries originating from deforestation in the humid tropics. The forests studied here appear to be much more resilient to occasional incursion of fire from the savanna, despite being unable to invade frequently burned savanna. The thin bark of forest species makes them particularly susceptible to the "fire trap," whereby repeated topkill of small trees prevents recruitment into adult size classes. Rapid growth will be particularly important for forest species to escape the fire trap, so we predict that, where fire is frequent, forests should be restricted to high-resource sites. Here, Mg2+ and Ca2+ concentrations had particularly strong effects on postburn growth rates, suggesting that these elements may most strongly limit the distribution of forest in these fire-prone savannas. DA - 2009/5// PY - 2009/5// DO - 10.1890/08-0741.1 VL - 90 IS - 5 SP - 1326-1337 SN - 1939-9170 KW - alternate stable states KW - Cerrado, Brazil KW - evergreen forest KW - fire ecology KW - gallery forest KW - hysteresis KW - positive feedback KW - riparian forest KW - savanna KW - topkill ER - TY - JOUR TI - Overexpression of a directed mutant of 14-3-3 omega in Arabidopsis leaves affects phosphorylation and protein content of nitrate reductase AU - Oh, Man-Ho AU - Huber, Joan L. AU - Shen, Wei AU - Athwal, Gurdeep S. AU - Wu, Xia AU - Huber, Steven C. T2 - BOTANY AB - The 14-3-3 family of proteins are highly conserved signaling proteins in eukaryotes that bind to their client proteins, usually through specific phosphorylated target sequences. While the 14-3-3 proteins are thought to interact with a wide array of cellular proteins, there have been few studies addressing the in-vivo role of 14-3-3. As one approach to study this in-vivo role, we generated transgenic Arabidopsis plants constitutively overexpressing a directed mutant of 14-3-3 isoform ω that inhibits phosphorylated nitrate reductase (pNR) in a largely divalent-cation-independent manner in vitro. The transgenic plants had increased relative phosphorylation of NR at the regulatory Ser-534 site and decreased NR activity measured in the presence of 5 mmol·L –1 MgCl 2 relative to nontransgenic plants. In addition, total NR protein was increased and the protein half-life was increased about two-fold. Two-dimensional difference gel electrophoresis analysis of proteins extracted from leaves of plants expressing the mutant 14-3-3 identified numerous cellular proteins that were altered in abundance. In particular, several β-glucosidase and glutathione S-transferase isoforms were decreased in abundance relative to wild type plants suggesting a possible alteration in stress or defense responses. DA - 2009/7// PY - 2009/7// DO - 10.1139/b09-003 VL - 87 IS - 7 SP - 691-701 SN - 1916-2804 KW - Arabidopsis thaliana KW - 14-3-3 protein KW - beta-glucosidase KW - glutathione S-transferase KW - two-dimensional difference gel electrophoresis KW - site-directed mutagenesis ER - TY - JOUR TI - Metabolism and Cometabolism of Cyclic Ethers by a Filamentous Fungus, a Graphium sp. AU - Skinner, Kristin AU - Cuiffetti, Lynda AU - Hyman, Michael T2 - Appl. Environ. Microbiol. AB - The filamentous fungus Graphium sp. (ATCC 58400) grows on gaseous n-alkanes and diethyl ether. n-Alkane-grown mycelia of this strain also cometabolically oxidize the gasoline oxygenate methyl tert-butyl ether (MTBE). In this study, we characterized the ability of this fungus to metabolize and cometabolize a range of cyclic ethers, including tetrahydrofuran (THF) and 1,4-dioxane (14D). This strain grew on THF and other cyclic ethers, including tetrahydropyran and hexamethylene oxide. However, more vigorous growth was consistently observed on the lactones and terminal diols potentially derived from these ethers. Unlike the case in all previous studies of microbial THF oxidation, a metabolite, gamma-butyrolactone, was observed during growth of this fungus on THF. Growth on THF was inhibited by the same n-alkenes and n-alkynes that inhibit growth of this fungus on n-alkanes, while growth on gamma-butyrolactone or succinate was unaffected by these inhibitors. Propane and THF also behaved as mutually competitive substrates, and propane-grown mycelia immediately oxidized THF, without a lag phase. Mycelia grown on propane or THF exhibited comparable high levels of hemiacetal-oxidizing activity that generated methyl formate from mixtures of formaldehyde and methanol. Collectively, these observations suggest that THF and n-alkanes may initially be oxidized by the same monooxygenase and that further transformation of THF-derived metabolites involves the activity of one or more alcohol dehydrogenases. Both propane- and THF-grown mycelia also slowly cometabolically oxidized 14D, although unlike THF oxidation, this reaction was not sustainable. Specific rates of THF, 14D, and MTBE degradation were very similar in THF- and propane-grown mycelia. DA - 2009/9/1/ PY - 2009/9/1/ DO - 10.1128/AEM.00078-09 VL - 75 IS - 17 SP - 5514-5522 J2 - Appl. Environ. Microbiol. LA - en SN - 0099-2240, 1098-5336 UR - https://aem.asm.org/content/75/17/5514 DB - aem.asm.org Y2 - 2019/2/1/ ER - TY - JOUR TI - Expression of Pyrococcus furiosus Superoxide Reductase in Arabidopsis Enhances Heat Tolerance AU - Im, Yang Ju AU - Ji, Mikyoung AU - Lee, Alice AU - Killens, Rushyannah AU - Grunden, Amy M. AU - Boss, Wendy F. T2 - PLANT PHYSIOLOGY AB - Plants produce reactive oxygen species (ROS) in response to environmental stresses sending signaling cues, which, if uncontrolled, result in cell death. Like other aerobic organisms, plants have ROS-scavenging enzymes, such as superoxide dismutase (SOD), which removes superoxide anion radical (O(2)(-)) and prevents the production and buildup of toxic free radicals. However, increasing the expression of cytosolic SODs is complex, and increasing their production in vivo has proven to be challenging. To avoid problems with endogenous regulation of gene expression, we expressed a gene from the archaeal hyperthermophile Pyrococcus furiosus that reduces O(2)(-). P. furiosus uses superoxide reductase (SOR) rather than SOD to remove superoxide. SOR is a thermostable enzyme that reduces O(2)(-) in a one-electron reduction without producing oxygen. We show that P. furiosus SOR can be produced as a functional enzyme in planta and that plants producing SOR have enhanced tolerance to heat, light, and chemically induced ROS. Stress tolerance in the SOR-producing plants correlates positively with a delayed increase in ROS-sensitive transcripts and a decrease in ascorbate peroxidase activity. The SOR plants provide a good model system to study the impact of cytosolic ROS on downstream signaling in plant growth and development. Furthermore, this work demonstrates that this synthetic approach for reducing cytosolic ROS holds promise as a means for improving stress tolerance in crop plants. DA - 2009/10// PY - 2009/10// DO - 10.1104/pp.109.145409 VL - 151 IS - 2 SP - 893-904 SN - 1532-2548 ER - TY - JOUR TI - Ethylene signaling and response: where different regulatory modules meet AU - Stepanova, Anna N. AU - Alonso, Jose M. T2 - CURRENT OPINION IN PLANT BIOLOGY AB - The structural simplicity of the gaseous hormone ethylene stands in contrast with the complexity of the physiological processes ethylene regulates. Initial studies suggested a simple linear arrangement of signaling molecules leading from the ethylene receptors to the EIN3 family of transcription factors. Recent discoveries have substantially changed this view. Current models suggest existence of a complex signaling pathway composed of several phosphorylation cascades, feedback-regulated transcriptional networks, and protein and mRNA turnover regulatory modules. Interactions between ethylene and other signals determine which of the ethylene-mediated responses get activated in a particular cell at a particular time. Tissue-specific regulation of auxin biosynthesis, transport, and response by ethylene is emerging as a key element in this signal integration process. DA - 2009/10// PY - 2009/10// DO - 10.1016/j.pbi.2009.07.009 VL - 12 IS - 5 SP - 548-555 SN - 1879-0356 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-70349554136&partnerID=MN8TOARS ER - TY - JOUR TI - Analysis of isolation and expression analysis of ItCYP79B2 during rust infection of dyer's woad (Isatis tinctoria) by Puccinia thlaspeos AU - Thomas, E. AU - Kropp, B. R. T2 - CANADIAN JOURNAL OF PLANT PATHOLOGY AB - Dyer's woad (Isatis tinctoria) has been shown to have unusually high quantities of indole glucosinolates. It is known that production of glucosinolates and their hydrolysis products is part of a plant's defense response to pathogens and insects. In Arabidopsis thaliana, which, like dyer's woad, is in the family Brassicaceae, the gene sequences encoding CYP79B2 and CYP79B3 catalyze the conversion of tryptophan to indole-3-acetaldoxime during the biosynthesis of indole glucosinolates. In this study, a sequence encoding CYP79B2 was isolated from dyer's woad. ItCYP79B2 from I. tinctoria shows 97% sequence identity with CYP79B2 and 89% sequence identity with CYP79B3 from A. thaliana. Thus, it can be inferred that the I. tinctoria sequence, like that of A. thaliana, is involved in the biosynthesis of indole glucosinolates. The kinetics and amplitude of ItCYP79B2 expression during the first 72 h after infection by the pathogenic rust fungus Puccinia thlaspeos were also studied. There was a significant down-regulation of ItCYP79B2 during the first 8 h after infection of the host that coincides with fungal penetration. This was followed by induction of ItCYP79B2, coinciding with the formation of haustoria. However, after haustoria formation, ItCYP9B2 was again suppressed during the time period coinciding with successful asymptomatic systemic colonization of the host. The results of this study indicates that suppression of a gene involved in indole glucosinolate production during the penetration and post-haustorial phases of infection plays a role in pathogen establishment. They also imply that the pathogen possesses mechanisms for circumventing the elevated expression of this gene during the haustorial phase DA - 2009/// PY - 2009/// DO - 10.1080/07060660909507578 VL - 31 IS - 1 SP - 103-107 SN - 1715-2992 KW - biological control KW - gene expression analysis KW - glucosinolate KW - Isatis tinctoria KW - plant defense response KW - Puccinia thlaspeos ER - TY - JOUR TI - Stomatal traits of cerrado and gallery forest congeneric pairs growing in a transitional region in Central Brazil AU - Rossatto, Davi Rodrigo AU - Hoffmann, William Arthur AU - Franco, Augusto Cesar T2 - ACTA BOTANICA BRASILICA AB - Em áreas protegidas do fogo, espécies arbóreas predominantemente florestais conseguem se estabelecer no cerrado e crescer lado a lado com espécies do mesmo gênero que são características destas formações savânicas. Devido às condições ambientais diferenciadas encontradas nas formações de cerrado e de mata, estas espécies congenéricas podem se comportar como grupos funcionais distintos. Neste trabalho foi realizado um estudo comparativo da anatomia dos estômatos e da condutância estomática e taxas de transpiração foliar em 10 pares de espécies congenéricas do cerrado e de mata de galeria e das relações entre as características estomáticas selecionadas e a condutância estomática, já que a morfologia dos estômatos e sua densidade afetam a área para difusão dos gases e sua trajetória através dos poros estomáticos. Cada par foi de uma família diferente. Para a maioria das espécies, a área do poro estomático foi o fator de maior influencia no processo de trocas gasosas, pela sua correlação com a condutância estomática, enquanto a densidade estomática mostrou uma correlação negativa significativa tanto com o comprimento da célula-guarda quanto com a área do poro estomático. As espécies do cerrado apresentaram valores significativamente maiores do comprimento da célula-guarda e do poro estomático. No entanto, para a maioria dos outros parâmetros estomáticos examinados, a maior parte da variação pode ser atribuída a diferenças entre os gêneros, sendo que a variação entre as espécies dos dois ambientes parece ser um produto da historia evolutiva de cada grupo e não reflete uma especialização ao ambiente de cerrado ou de mata de galeria. DA - 2009/// PY - 2009/// DO - 10.1590/S0102-33062009000200021 VL - 23 IS - 2 SP - 499-508 SN - 1677-941X KW - stomata KW - stomatal conductance KW - stomatal pore KW - transpiration ER - TY - JOUR TI - Size-dependent mortality in a Neotropical savanna tree: the role of height-related adjustments in hydraulic architecture and carbon allocation AU - Zhang, Yong-Jiang AU - Meinzer, Frederick C. AU - Hao, Guang-You AU - Scholz, Fabian G. AU - Bucci, Sandra J. AU - Takahashi, Frederico S. C. AU - Villalobos-Vega, Randol AU - Giraldo, Juan P. AU - Cao, Kun-Fang AU - Hoffmann, William A. AU - Goldstein, Guillermo T2 - PLANT CELL AND ENVIRONMENT AB - ABSTRACT Size‐related changes in hydraulic architecture, carbon allocation and gas exchange of Sclerolobium paniculatum (Leguminosae), a dominant tree species in Neotropical savannas of central Brazil (Cerrado), were investigated to assess their potential role in the dieback of tall individuals. Trees greater than ∼6‐m‐tall exhibited more branch damage, larger numbers of dead individuals, higher wood density, greater leaf mass per area, lower leaf area to sapwood area ratio (LA/SA), lower stomatal conductance and lower net CO 2 assimilation than small trees. Stem‐specific hydraulic conductivity decreased, while leaf‐specific hydraulic conductivity remained nearly constant, with increasing tree size because of lower LA/SA in larger trees. Leaves were substantially more vulnerable to embolism than stems. Large trees had lower maximum leaf hydraulic conductance ( K leaf ) than small trees and all tree sizes exhibited lower K leaf at midday than at dawn. These size‐related adjustments in hydraulic architecture and carbon allocation apparently incurred a large physiological cost: large trees received a lower return in carbon gain from their investment in stem and leaf biomass compared with small trees. Additionally, large trees may experience more severe water deficits in dry years due to lower capacity for buffering the effects of hydraulic path‐length and soil water deficits. DA - 2009/10// PY - 2009/10// DO - 10.1111/j.1365-3040.2009.02012.x VL - 32 IS - 10 SP - 1456-1466 SN - 1365-3040 KW - carbon balance KW - hydraulic conductivity KW - population dynamics KW - tree dieback KW - xylem cavitation ER - TY - JOUR TI - Effects of antibiotics and oil on microbial profiles and fermentation in mixed cultures of ruminal microorganisms AU - Johnson, M. C. AU - Devine, A. A. AU - Ellis, J. C. AU - Grunden, A. M. AU - Fellner, V. T2 - JOURNAL OF DAIRY SCIENCE AB - Ionophores and supplemental fat are fed to lactating cows to improve feed efficiency. Their effect on rumen fermentation is similar, but less is known about their impact on rumen microbes. The objective of this study was to determine the effects of monensin (M), bacitracin (B), and soybean oil (O) on microbial populations. Mixed cultures of rumen microbes were incubated in 5 dual-flow continuous fermentors and fed 13.8 g of alfalfa hay pellets daily (DM basis) for 16 d. All fermentors were allowed to stabilize for 4 d. From d 5 to 10, two fermentors received O (5% of diet DM), one fermentor received M (22 mg/kg), and one received B (22 mg/kg). From d 11 to 16, the 2 fermentors receiving O also received either M (OM) or B (OB) and O was included in the fermentors receiving M (MO) and B (BO). One fermentor served as the control and received 100% alfalfa pellets throughout the experiment. Each run was replicated 3 times. Samples were taken at 2 h after the morning feeding on d 4, 10, and 16 and were analyzed for bacterial populations using terminal restriction fragment length polymorphism. Volatile fatty acid concentration, methane production, and pH in the control cultures were not affected by time and remained similar during the entire experiment. The M and O treatments reduced molar concentration of acetate, increased concentration of propionate, and decreased methane production. Bacitracin did not alter acetate or propionate concentration, but reduced methane production. All 3 treatments (M, B, and O) altered the fragment patterns of microbial profiles. In contrast, treatments MO, OM, BO, and OB had little effect on culture fermentation despite differences in the patterns of microbial fragments. The terminal restriction fragment length polymorphism data suggest that microbial adaptation to the in vitro system in the control fermentor occurred within 4 d. DA - 2009/9// PY - 2009/9// DO - 10.3168/jds.2008-1841 VL - 92 IS - 9 SP - 4467-4480 SN - 1525-3198 KW - ionophore KW - soybean oil KW - rumen microbial diversity KW - continuous culture ER - TY - JOUR TI - biotechnological applications of recombinant microbial prolidases AU - Theriot, C. M. AU - Tove, S. R. AU - Grunden, A. M. T2 - Advances in applied microbiology, vol 68 DA - 2009/// PY - 2009/// VL - 68 SP - 99- ER - TY - JOUR TI - Vascular Flora, Plant Communities, and Soils of a Significant Natural Area in the Middle Atlantic Coastal Plain (Craven County, North Carolina) AU - Elam, Caitlin E. AU - Stucky, Jon M. AU - Wentworth, Thomas R. AU - Gregory, James D. T2 - CASTANEA AB - Abstract Cool Springs Environmental Education Center (CSEEC), owned by Weyerhaeuser Company, includes a 591 ha State Significant Natural Area. It is located in Craven County, North Carolina, in the floristically rich Atlantic Coastal Plain. A vascular flora inventory documented the occurrences of 567 species and sub-specific taxa and 303 genera in 118 plant families, including populations of the Atlantic Coastal Plain endemics Pondspice (Litsea aestivalis) and LeBlond's Coastal Goldenrod (Solidago villosicarpa). We identified twenty plant community types, including the uncommon Longleaf Pine (Pinus palustris) Woodland, Bald Cypress–Tupelo Gum (Taxodium distichum – Nyssa aquatica) Swamp, a number of small depression wetland communities, and the novel Sand Laurel Oak-Loblolly Pine (Quercus hemisphaerica – Pinus taeda) Woodland. Soils ranged from excessively drained sands to very poorly drained organics. The order of the soil mapping units according to the number of plant taxa they supported per unit area wa... DA - 2009/3// PY - 2009/3// DO - 10.2179/08-07.1 VL - 74 IS - 1 SP - 53-77 SN - 1938-4386 ER - TY - JOUR TI - Species Diversity and Composition in Old Growth and Second Growth Rich Coves of the Southern Appalachian Mountains AU - Jackson, B. Clay AU - Pittillo, J. Dan AU - Allen, H. Lee AU - Wentworth, Thomas R. AU - Bullock, Bronson P. AU - Loftis, David L. T2 - CASTANEA AB - Because of ongoing debate over the long term impacts of logging, we conducted a study to assess if second growth (70 ± 10 years) rich coves differ from old growth rich coves (> 125 years) in species diversity or composition. We sampled twenty-six 0.1 ha plots, representing these two age classes. We distributed the plots amongst three randomly selected mountain ranges in the southern Appalachians of North Carolina, and sampled each mountain range in separate years. We used nested subplots of 0.01 m2, 0.1 m2, 1 m2, 10 m2, 100 m2, and 1000 m2 to establish species-area relationships (SARs) for each age class. We found no significant differences between the SARs for the two age classes, nor did we find significant differences between age classes using the Simpson, Shannon-Wiener, or Sorensen indices of species diversity. However, we found that total cover of all plant species was greater in old growth rich coves, and that 10% of the tested species had lower abundance in second growth. No species were present in old growth and absent in second growth, but species with lower second growth abundance may warrant future study. DA - 2009/3// PY - 2009/3// DO - 10.2179/07-017.1 VL - 74 IS - 1 SP - 27-38 SN - 1938-4386 ER - TY - JOUR TI - Proteomics of Pyrococcus furiosus, a Hyperthermophilic Archaeon Refractory to Traditional Methods AU - Lee, Alice M. AU - Sevinsky, Joel R. AU - Bundy, Jonathan L. AU - Grunden, Amy M. AU - Stephenson, James L., Jr. T2 - JOURNAL OF PROTEOME RESEARCH AB - Pyrococcus furiosus is one of the most extensively studied hyperthermophilic archaea. Proteins from this hyperthemophile organism are extremely thermostable and are highly resistant to chemical denaturants, organic solvents and proteolytic digestion. This thermostability makes it difficult to apply traditional methods of enzymatically digesting a complex mixture of proteins, commonly a first step in peptide generation in most shotgun proteomics methods. Here, we have developed a simple shotgun proteomics approach for the global identification of the P. furiosus proteome. This methodology uses a detergent-based microwave assisted acid hydrolysis (MAAH) step coupled with an overnight trypsin digest to obtain peptides. Subsequent peptide fractionation by isoelectric focusing in immobilized pH gradients (IPG-IEF), followed by chromatographic separation with reverse phase nano-HPLC and electrospray ionization tandem mass spectrometry (ESI-MS/MS) of peptides enabled the identification of over 900 proteins representing over 44% of the proteome. In most functional classes, over 50% of the predicted proteins were identified, including a number of membrane proteins. This new sample preparation technique will enable extensive proteomics data to be obtained for this organism, thereby enabling the reconstruction of metabolic pathways and promoting a systems biology based understanding of this important extremophile. DA - 2009/8// PY - 2009/8// DO - 10.1021/pr801119h VL - 8 IS - 8 SP - 3844-3851 SN - 1535-3907 KW - Pyrococcus furiosus KW - shotgun proteomics KW - archaea KW - hyperthermophile KW - high throughput KW - IPG-IEF KW - LC-MS/MS KW - archaeal proteins KW - microwave assisted acid hydrolysis ER - TY - JOUR TI - Influence of process parameters on growth of Clostridium ljungdahlii and Clostridium autoethanogenum on synthesis gas AU - Cotter, Jacqueline L. AU - Chinn, Mari S. AU - Grunden, Amy M. T2 - ENZYME AND MICROBIAL TECHNOLOGY AB - Effects of initial medium pH and gas flow rate on Clostridium ljungdahlii and Clostridium autoethanogenum in liquid batch, continuous gas fermentations were investigated. Synthesis gas components were supplied at varying flow rates (5, 7.5 and 10 mL/min) for C. ljungdahlii (pH 6.8 and 5.5) and C. autoethanogenum (pH 6.0). Growth on synthesis gas was slower than growth on sugars. For C. ljungdahlii, higher cell densities were achieved at pH 6.8 (579 mg/L) compared to pH 5.5 (378 mg/L). The ethanol concentration at pH 6.8 was also 110% greater than that at pH 5.5. The interaction of flow rate and pH was statistically significant with the greatest acetate production in the 10 mL/min, pH 6.8 treatment. The ethanol to acetate ratios were smaller at lower pH levels and higher flow rates. In C. autoethanogenum fermentations, higher flow rates resulted in greater end product formation with no significant effect on product ratios. DA - 2009/5/6/ PY - 2009/5/6/ DO - 10.1016/j.enzmictec.2008.11.002 VL - 44 IS - 5 SP - 281-288 SN - 1879-0909 KW - Clostridium ljungdahlii KW - Clostridium autoethanaogenum KW - Synthesis gas fermentation KW - Ethanol KW - Acetate ER - TY - JOUR TI - Differences in growth patterns between co-occurring forest and savanna trees affect the forest-savanna boundary AU - Rossatto, Davi Rodrigo AU - Hoffmann, William Arthur AU - Franco, Augusto Cesar T2 - FUNCTIONAL ECOLOGY AB - Summary Patterns of growth, activity and renewal of stems and branches are primary determinants of ecosystem function and strongly influence net primary productivity, water and energy balance. Here we compare patterns of leaf phenology, stem radial growth and branch growth of co‐occurring savanna and forest trees in the Cerrado region of central Brazil to gain insight into the influence of these parameters in forest–savanna boundary dynamics. We hypothesized that forest species would have higher radial growth rates but later leaf flush than savanna species. We studied 12 congeneric species pairs, each containing one savanna species and one forest species. All individuals were growing in savanna conditions under full sun. We measured specific leaf area (SLA), light‐saturated photosynthesis and monthly increments in stem circumference, branch length, leaf flush and leaf fall. Relative to savanna species, forest species had 68% higher diameter growth rates, 38% higher SLA, and displayed a greater crown area for a given basal area. Across species, radial growth was positively correlated with SLA ( r 2 = 0·31), but not with CO 2 assimilation. Peak leaf production of savanna species was in the late dry season, 1 month earlier than for forest species, which suggests a strategy to avoid nutrient losses during leaf expansion due to herbivory or leaching. However, savanna and forest species did not differ in annual branch growth, number of leaves produced per branch, or in timing of leaf fall. Radial growth was tightly coupled to monthly rainfall in forest species whereas the growth of savanna species ceased before the end of the wet season. The cessation of above‐ground growth at a time of active photosynthesis may reflect a shift in allocation to roots and reserves. These results contribute to recent studies showing that savanna and forest species represent different functional types and that despite the limiting resources in savanna environments, forest trees that invade the savanna tend to present higher growth rates and larger and denser crowns, which enhance shading and could promote changes in equilibrium of forest–savanna boundaries. DA - 2009/8// PY - 2009/8// DO - 10.1111/j.1365-2435.2009.01568.x VL - 23 IS - 4 SP - 689-698 SN - 1365-2435 KW - cerrado KW - ecosystem dynamics KW - forest-savanna boundaries KW - leaf phenology KW - photosynthesis KW - specific leaf area ER - TY - JOUR TI - Isotopic Fractionation of Methyl tert-Butyl Ether Suggests Different Initial Reaction Mechanisms during Aerobic Biodegradation AU - McKelvie, Jennifer R. AU - Hyman, Michael R. AU - Elsner, Martin AU - Smith, Christy AU - Aslett, Denise M. AU - Lacrampe-Couloume, Georges AU - Sherwood Lollar, Barbara T2 - Environmental Science & Technology AB - Carbon isotopic enrichment factors (εC) measured during cometabolic biodegradation of methyl tert-butyl ether (MTBE), ethyl tert-butyl ether (ETBE), and tert-amyl methyl ether (TAME) by Pseudonocardia tetrahydrofuranoxydans strain K1 were −2.3 ± 0.2‰, −1.7 ± 0.2‰, and −1.7 ± 0.3‰, respectively. The measured carbon apparent kinetic isotope effect was 1.01 for all compounds, consistent with the expected kinetic isotope effects for both oxidation of the methoxy (or ethoxy) group and enzymatic SN1 biodegradation mechanisms. Significantly, δ13C measurements of the tert-butyl alcohol and tert-amyl alcohol products indicated that the tert-butyl and tert-amyl groups do not participate in the reaction and confirmed that ether biodegradation by strain K1 involves oxidation of the methoxy (or ethoxy) group. Measured hydrogen isotopic enrichment factors (εH) were −100 ± 10‰, −73 ± 7‰, and −72 ± 2‰ for MTBE, ETBE, and TAME respectively. Previous results reported for aerobic biodegradation of MTBE by Methylibium petroleiphilum PM1 and Methylibium R8 showed smaller εH values (−35‰ and −42‰, respectively). Plots of Δ2H/ Δ13C show different slopes for strain K1 compared with strains PM1 and R8, suggesting that different mechanisms are utilized by K1 and PM1/R8 during aerobic MTBE biodegradation. DA - 2009/4/15/ PY - 2009/4/15/ DO - 10.1021/es803307y VL - 43 IS - 8 SP - 2793-2799 J2 - Environ. Sci. Technol. SN - 0013-936X UR - https://doi.org/10.1021/es803307y DB - ACS Publications Y2 - 2019/2/1/ ER - TY - JOUR TI - Systems genetics of complex traits in Drosophila melanogaster AU - Ayroles, Julien F. AU - Carbone, Mary Anna AU - Stone, Eric A. AU - Jordan, Katherine W. AU - Lyman, Richard F. AU - Magwire, Michael M. AU - Rollmann, Stephanie M. AU - Duncan, Laura H. AU - Lawrence, Faye AU - Anholt, Robert R. H. AU - Mackay, Trudy F. C. T2 - NATURE GENETICS AB - Determining the genetic architecture of complex traits is challenging because phenotypic variation arises from interactions between multiple, environmentally sensitive alleles. We quantified genome-wide transcript abundance and phenotypes for six ecologically relevant traits in D. melanogaster wild-derived inbred lines. We observed 10,096 genetically variable transcripts and high heritabilities for all organismal phenotypes. The transcriptome is highly genetically intercorrelated, forming 241 transcriptional modules. Modules are enriched for transcripts in common pathways, gene ontology categories, tissue-specific expression and transcription factor binding sites. The high degree of transcriptional connectivity allows us to infer genetic networks and the function of predicted genes from annotations of other genes in the network. Regressions of organismal phenotypes on transcript abundance implicate several hundred candidate genes that form modules of biologically meaningful correlated transcripts affecting each phenotype. Overlapping transcripts in modules associated with different traits provide insight into the molecular basis of pleiotropy between complex traits. DA - 2009/3// PY - 2009/3// DO - 10.1038/ng.332 VL - 41 IS - 3 SP - 299-307 SN - 1546-1718 ER - TY - JOUR TI - Shoot regeneration of dwarf dogwood (Cornus canadensis L.) and morphological characterization of the regenerated plants AU - Feng, Chun-Miao AU - Qu, Rongda AU - Zhou, Li-Li AU - Xie, De-Yu AU - Xiang, Qiu-Yun T2 - PLANT CELL TISSUE AND ORGAN CULTURE DA - 2009/4// PY - 2009/4// DO - 10.1007/s11240-009-9495-0 VL - 97 IS - 1 SP - 27-37 SN - 1573-5044 KW - Cornus canadensis KW - Organogenesis KW - Regeneration KW - Rhizomes KW - Tissue culture ER - TY - JOUR TI - Molecular characterization of the recombinant iron-containing alcohol dehydrogenase from the hyperthermophilic Archaeon, Thermococcus strain ES1 AU - Ying, Xiangxian AU - Grunden, Amy M. AU - Nie, Lin AU - Adams, Michael W. W. AU - Ma, Kesen T2 - EXTREMOPHILES DA - 2009/3// PY - 2009/3// DO - 10.1007/s00792-008-0217-z VL - 13 IS - 2 SP - 299-311 SN - 1433-4909 KW - Iron-containing alcohol dehydrogenase KW - Heterologous expression KW - Hyperthermophile KW - Archaea KW - Thermococcus ER - TY - JOUR TI - Ethanol and acetate production by Clostridium ljungdahlii and Clostridium autoethanogenum using resting cells AU - Cotter, Jacqueline L. AU - Chinn, Mari S. AU - Grunden, Amy M. T2 - BIOPROCESS AND BIOSYSTEMS ENGINEERING DA - 2009/4// PY - 2009/4// DO - 10.1007/s00449-008-0256-y VL - 32 IS - 3 SP - 369-380 SN - 1615-7591 KW - Clostridium ljungdahlii KW - Clostridium autoethanaogenum KW - Ethanol KW - Acetate KW - Resting cells KW - Non-growing cells ER - TY - JOUR TI - Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep AU - Harbison, Susan T. AU - Carbone, Mary Anna AU - Ayroles, Julien F. AU - Stone, Eric A. AU - Lyman, Richard F. AU - Mackay, Trudy F. C. T2 - NATURE GENETICS AB - Sleep disorders are common in humans, and sleep loss increases the risk of obesity and diabetes. Studies in Drosophila have revealed molecular pathways and neural tissues regulating sleep; however, genes that maintain genetic variation for sleep in natural populations are unknown. Here, we characterized sleep in 40 wild-derived Drosophila lines and observed abundant genetic variation in sleep architecture. We associated sleep with genome-wide variation in gene expression to identify candidate genes. We independently confirmed that molecular polymorphisms in Catsup (Catecholamines up) are associated with variation in sleep and that P-element mutations in four candidate genes affect sleep and gene expression. Transcripts associated with sleep grouped into biologically plausible genetically correlated transcriptional modules. We confirmed co-regulated gene expression using P-element mutants. Quantitative genetic analysis of natural phenotypic variation is an efficient method for revealing candidate genes and pathways. DA - 2009/3// PY - 2009/3// DO - 10.1038/ng.330 VL - 41 IS - 3 SP - 371-375 SN - 1546-1718 ER - TY - JOUR TI - The ABC transporter ATR1 is necessary for efflux of the toxin cercosporin in the fungus Cercospora nicotianae AU - Amnuaykanjanasin, Alongkom AU - Daub, Margaret E. T2 - FUNGAL GENETICS AND BIOLOGY AB - The Cercospora nicotianae mutant deficient for the CRG1 transcription factor has marked reductions in both resistance and biosynthesis of the toxin cercosporin. We cloned and sequenced full-length copies of two genes, ATR1 and CnCFP, previously identified from a subtractive library between the wild type (WT) and a crg1 mutant. ATR1 is an ABC transporter gene and has an open reading frame (ORF) of 4368 bp with one intron. CnCFP encodes a MFS transporter with homology to Cercospora kikuchii CFP, previously implicated in cercosporin export, and has an ORF of 1975 bp with three introns. Disruption of ATR1 indicated atr1-null mutants had dramatic reductions in cercosporin production (25% and 20% of WT levels) in solid and liquid cultures, respectively. The ATR1 disruptants also showed moderately higher sensitivity to cercosporin. Constitutive expression of ATR1 in the crg1 mutant restored cercosporin biosynthesis and moderately increased resistance. In contrast, CnCFP overexpression in the mutant did not restore toxin production, however, it moderately enhanced toxin resistance. The results together indicate ATR1 acts as a cercosporin efflux pump in this fungus and plays a partial role in resistance. DA - 2009/2// PY - 2009/2// DO - 10.1016/j.fgb.2008.11.007 VL - 46 IS - 2 SP - 146-158 SN - 1096-0937 KW - ABC transporter KW - Cercospora nicotianae KW - Cercosporin KW - Efflux pump KW - MFS transporter KW - Polyketide KW - Cercosporin production KW - Cercosporin resistance ER - TY - JOUR TI - Phylogeny, origin, and biogeographic history of Aesculus L. (Sapindales) - an update from combined analysis of DNA sequences, morphology, and fossils AU - Harris, AJ AU - Xiang, Qiu-Yunjenny AU - Thomas, David T. T2 - TAXON AB - Abstract Conflicting phylogenies and biogeographic hypotheses for Aesculus L. were reevaluated using data integrating morphology, fossils, and DNA sequences. A more robust phylogeny of Aesculus was constructed by increasing taxon and character sampling to include 42 morphological characters and five DNA regions including rps16, trnHK, matK , ITS, and part of the LEAFY gene. Our analyses revealed three well‐supported major lineages in Aesculus . These are sect. Calothyrsus excluding A. californica , sect. Macrothyrsus + A. californica , and sect. Aesculus + sect. Pavia + sect. Parryana . The relationship of sect. Aesculus to sect. Parryana + sect. Pavia is strongly supported and previously unreported. Relationships among the three major clades remained incompletely resolved. Biogeographic and divergence time analyses using DIVA and Multidivtime support a Paleocene origin of Aesculus in eastern Asia and western North America, and showed that the genus subsequently dispersed into eastern North America, Central America, and Europe. Our results support that Aesculus originated as an element of the Paleogene mesophilic flora in the Beringian region with multiple eastward migrations characterizing the early spatial history of this genus. This biogeographic history supports Trans‐Beringian migration of plants in the very early Paleogene. DA - 2009/2// PY - 2009/2// DO - 10.1002/TAX.581012 VL - 58 IS - 1 SP - 108–126 SN - 0040-0262 UR - http://dx.doi.org/10.1002/TAX.581012 KW - Aesculus KW - biogeography KW - Divergence time dating KW - Hippocastanaceae KW - Laurasia KW - phylogeny KW - Sapindaceae KW - Sapindales ER - TY - JOUR TI - Phylogeny of Abies (Pinaceae) inferred from nrITS sequence data AU - Xiang, Q. P. AU - Xiang, Q. Y. AU - Guo, Y. Y. AU - Zhang, X. C. T2 - Taxon DA - 2009/// PY - 2009/// VL - 58 IS - 1 SP - 141-152 ER - TY - JOUR TI - Phosphatidylinositol (4,5)Bisphosphate Inhibits K+-Efflux Channel Activity in NT1 Tobacco Cultured Cells AU - Ma, Xiaohong AU - Shor, Oded AU - Diminshtein, Sofia AU - Yu, Ling AU - Im, Yang Ju AU - Perera, Imara AU - Lomax, Aaron AU - Boss, Wendy F. AU - Moran, Nava T2 - PLANT PHYSIOLOGY AB - In the animal world, the regulation of ion channels by phosphoinositides (PIs) has been investigated extensively, demonstrating a wide range of channels controlled by phosphatidylinositol (4,5)bisphosphate (PtdInsP2). To understand PI regulation of plant ion channels, we examined the in planta effect of PtdInsP2 on the K+-efflux channel of tobacco (Nicotiana tabacum), NtORK (outward-rectifying K channel). We applied a patch clamp in the whole-cell configuration (with fixed "cytosolic" Ca2+ concentration and pH) to protoplasts isolated from cultured tobacco cells with genetically manipulated plasma membrane levels of PtdInsP2 and cellular inositol (1,4,5)trisphosphate: "Low PIs" had depressed levels of these PIs, and "High PIs" had elevated levels relative to controls. In all of these cells, K channel activity, reflected in the net, steady-state outward K+ currents (IK), was inversely related to the plasma membrane PtdInsP2 level. Consistent with this, short-term manipulations decreasing PtdInsP2 levels in the High PIs, such as pretreatment with the phytohormone abscisic acid (25 microM) or neutralizing the bath solution from pH 5.6 to pH 7, increased IK (i.e. NtORK activity). Moreover, increasing PtdInsP2 levels in controls or in abscisic acid-treated high-PI cells, using the specific PI-phospholipase C inhibitor U73122 (2.5-4 microM), decreased NtORK activity. In all cases, IK decreases stemmed largely from decreased maximum attainable NtORK channel conductance and partly from shifted voltage dependence of channel gating to more positive potentials, making it more difficult to activate the channels. These results are consistent with NtORK inhibition by the negatively charged PtdInsP2 in the internal plasma membrane leaflet. Such effects are likely to underlie PI signaling in intact plant cells. DA - 2009/2// PY - 2009/2// DO - 10.1104/pp.108.129007 VL - 149 IS - 2 SP - 1127-1140 SN - 1532-2548 ER - TY - JOUR TI - Effect of microbial pretreatment on enzymatic hydrolysis and fermentation of cotton stalks for ethanol production AU - Shi, Jian AU - Sharma-Shivappa, Ratna R. AU - Chinn, Mari AU - Howell, Noura T2 - BIOMASS & BIOENERGY AB - The potential of microbial pretreatment of cotton stalks by Phanerochaete chrysosporium to degrade lignin and facilitate fuel ethanol production was investigated under two culture conditions: submerged cultivation (SmC) and solid state (SSC) cultivation. Although microbial pretreatments showed significant lignin degradation (LD) (19.38% and 35.53% for SmC and SSC, respectively), a study on hydrolysis and fermentation of the microbial-pretreated cotton stalks showed no increase in cellulose conversion (10.98% and 3.04% for SmC and SSC pretreated samples, respectively) compared to untreated cotton stalks (17.93%). Solid state cultivation demonstrated better selectivity of 0.82 than 0.70 with submerged pretreatment. Washing of pretreated cotton stalks did not significantly increase cellulose conversion. However, heating and washing remarkably improved (P<0.05) cellulose conversion to 14.94% and 17.81% for SmC and SSC 14 day pretreatment, respectively. Ethanol yields, up to 0.027 g ethanol g−1 initial cotton stalks, were low for all untreated and pretreated samples mainly due to the low cellulose conversion. Although potential and some critical aspects of fungal pretreatment using P. chrysosporium have been explored in this study, additional investigation is still required especially to improve the selectivity for preferential LD and to optimize hydrolysis efficiency. The mechanism of catalytic binding of cellulolytic enzymes to cotton stalks as affected by the presence of fungal mycelia also warrants further study. DA - 2009/1// PY - 2009/1// DO - 10.1016/j.biombioe.2008.04.016 VL - 33 IS - 1 SP - 88-96 SN - 1873-2909 KW - Gossypium hirsutum L KW - Pretreatment KW - Phanerochaete chrysosporium KW - Lignin KW - Fuel ethanol KW - Cellobiose KW - Submerged cultivation KW - Solid state cultivation ER - TY - JOUR TI - X-ray structure of ILL2, an auxin-conjugate amidohydrolase from Arabidopsis thaliana AU - Bitto, Eduard AU - Bingman, Craig A. AU - Bittova, Lenka AU - Houston, Norma L. AU - Boston, Rebecca S. AU - Fox, Brian G. AU - Phillips, George N., Jr. T2 - PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS AB - The plant hormone indole-3-acetic acid (IAA) is the most abundant natural auxin involved in many aspects of plant development and growth. The IAA levels in plants are modulated by a specific group of amidohydrolases from the peptidase M20D family that release the active hormone from its conjugated storage forms. Here, we describe the X-ray crystal structure of IAA-amino acid hydrolase IAA-leucine resistantlike gene 2 (ILL2) from Arabidopsis thaliana at 2.0 A resolution. ILL2 preferentially hydrolyses the auxin-amino acid conjugate N-(indol-3-acetyl)-alanine. The overall structure of ILL2 is reminiscent of dinuclear metallopeptidases from the M20 peptidase family. The structure consists of two domains, a larger catalytic domain with three-layer alpha beta alpha sandwich architecture and aminopeptidase topology and a smaller satellite domain with two-layer alphabeta-sandwich architecture and alpha-beta-plaits topology. The metal-coordinating residues in the active site of ILL2 include a conserved cysteine that clearly distinguishes this protein from previously structurally characterized members of the M20 peptidase family. Modeling of N-(indol-3-acetyl)-alanine into the active site of ILL2 suggests that Leu175 serves as a key determinant for the amino acid side-chain specificity of this enzyme. Furthermore, a hydrophobic pocket nearby the catalytic dimetal center likely recognizes the indolyl moiety of the substrate. Finally, the active site of ILL2 harbors an absolutely conserved glutamate (Glu172), which is well positioned to act as a general acid-base residue. Overall, the structure of ILL2 suggests that this enzyme likely uses a catalytic mechanism that follows the paradigm established for the other enzymes of the M20 peptidase family. DA - 2009/1// PY - 2009/1// DO - 10.1002/prot.22124 VL - 74 IS - 1 SP - 61-71 SN - 1097-0134 KW - M20D peptidase family KW - auxin homeostasis KW - metalloenzyme KW - X-ray structure ER - TY - JOUR TI - Invasion of a West Everglades wetland by Melaleuca quinquenervia countered by classical biological control AU - Tipping, Philip W. AU - Martin, Melissa R. AU - Nimmo, Kayla R. AU - Pierce, Ryan M. AU - Smart, Matthew D. AU - White, Emily AU - Madeira, Paul T. AU - Center, Ted D. T2 - BIOLOGICAL CONTROL AB - The population dynamics of Melaleuca quinquenervia were monitored over a 5-year period in a cypress-pine wetland while subjected to two levels of herbivory. The trees had been recruited during 1998–1999 after a destructive crown fire. Half of 26 experimental plots were sprayed every 4–6 weeks with an insecticide to reduce herbivory by the biological control agents Oxyops vitiosa and Boreioglycaspis melaleucae. After only 1-year melaleuca density increased by 26% in sprayed plots and by 7% in unsprayed plots. However, over the entire 5-year period melaleuca density increased in sprayed plots by 0.1% while decreasing by 47.9% in unsprayed plots when compared to initial densities. Annual mortality of melaleuca never exceeded 6% in any year in sprayed plots but ranged from 11% to 25% in unsprayed plots. There was a significant year by treatment interaction indicating the importance of the environment on tree mortality. Limited seed production occurred on sprayed trees but never on unsprayed trees. Mean tree height increased by 19.6% in sprayed plots while declining by 30.6% in unsprayed plots. Coverage by native vegetation did not increase with decreasing melaleuca density. This is the first study with controls that quantifies the population level regulation of melaleuca by introduced biological control agents and corroborates other correlative studies that documented significant changes in melaleuca communities after the introduction and establishment of biological control agents. DA - 2009/1// PY - 2009/1// DO - 10.1016/j.biocontrol.2008.08.018 VL - 48 IS - 1 SP - 73-78 SN - 1090-2112 KW - Weed biological control KW - Melaleuca KW - Florida Everglades KW - Community level impacts ER - TY - JOUR TI - Genetic analyses of the federally endangered Echinacea laevigata using amplified fragment length polymorphisms (AFLP)—Inferences in population genetic structure and mating system AU - Peters, Melinda D. AU - Xiang, Qiu-Yun (Jenny) AU - Thomas, David T. AU - Stucky, Jon AU - Whiteman, Noah K. T2 - Conservation Genetics AB - Echinacea laevigata (Boynton and Beadle) Blake is a federally endangered flowering plant species restricted to four states in the southeastern United States. To determine the population structure and outcrossing rate across the range of the species, we conducted AFLP analysis using four primer combinations for 22 populations. The genetic diversity of this species was high based on the level of polymorphic loci (200 of 210 loci; 95.24%) and Nei’s gene diversity (ranging from 0.1398 to 0.2606; overall 0.2611). There was significant population genetic differentiation (GST = 0.294; ӨII = 0.218 from the Bayesian f = 0 model). Results from the AMOVA analysis suggest that a majority of the genetic variance is attributed to variation within populations (70.26%), which is also evident from the PCoA. However, 82% of individuals were assigned back to the original population based on the results of the assignment test. An isolation by distance analysis indicated that genetic differentiation among populations was a function of geographic distance, although long-distance gene dispersal between some populations was suggested from an analysis of relatedness between populations using the neighbor-joining method. An estimate of the outcrossing rate based on genotypes of progenies from six of the 22 populations using the multilocus method from the program MLTR ranged from 0.780 to 0.912, suggesting that the species is predominantly outcrossing. These results are encouraging for conservation, signifying that populations may persist due to continued genetic exchange sustained by the outcrossing mating system of the species. DA - 2009/2// PY - 2009/2// DO - 10.1007/s10592-008-9509-1 VL - 10 IS - 1 SP - 1-14 LA - en SN - 1566-0621, 1572-9737 UR - http://link.springer.com/10.1007/s10592-008-9509-1 DB - Crossref Y2 - 2019/1/29/ KW - Echinacea laevigata KW - Genetic structure KW - Outcrossing rate KW - AFLP ER - TY - JOUR TI - LEAVES OF CORNUS (CORNACEAE) FROM THE PALEOCENE OF NORTH AMERICA AND ASIA CONFIRMED BY TRICHOME CHARACTERS AU - Manchester, Steven R. AU - Xiang, Qiu-Yun AU - Kodrul, Tatiana M. AU - Akhmetiev, Mikhail A. T2 - INTERNATIONAL JOURNAL OF PLANT SCIENCES AB - The identification of Cornus foliage in the fossil record previously has relied primarily on similarities in venation, particularly the eucamptodromous secondary veins and widely spaced, transversely oriented tertiary veins. These features, while consistent with Cornus, are not by themselves diagnostic for the genus. Double‐armed, acicular trichomes mineralized with calcium carbonate are an additional characteristic feature found in all extant species of the genus. The presence of such trichomes provides a means of confirming leaf impression fossils attributed to Cornus. Reexamination of previously described Cornus leaves from the Paleocene of the Rocky Mountains and Great Plains region leads us to reject Cornus nebrascensis Schimper (=Cornus newberryi Hollick) from the genus. Another species, Cornus hyperborea Heer, is provisionally accepted as Cornus based on its venation, although we were unable to confirm the trichomes in the type material from Greenland or in the assigned specimens from North Dakota. We also review other Eurasian Paleocene Cornus‐like leaf remains, including Cornus platyphylla Saporta and Cornophyllum hebridicum (Johnson) Boulter and Kvaček. We recognize two new Paleocene species, whose identity as Cornus is confirmed by the presence of characteristic trichomes and venation: Cornus swingii sp. n., from the Paleocene of Wyoming, Montana, and North Dakota, and Cornus krassilovii sp. n., from the Paleocene Tsagayan flora of Russia. These occurrences, along with fruit records, indicate that the extant genus was well established in the Northern Hemisphere early in the Tertiary. DA - 2009/1// PY - 2009/1// DO - 10.1086/593040 VL - 170 IS - 1 SP - 132-142 SN - 1537-5315 KW - Cornus KW - fossil KW - leaves KW - trichomes KW - North America KW - Greenland KW - Europe KW - Russia KW - Paleocene ER - TY - JOUR TI - Simultaneous excision of two transgene flanking sequences and resolution of complex integration loci AU - Kumar, Sandeep AU - Thompson, William F. T2 - PLANT MOLECULAR BIOLOGY DA - 2009/1// PY - 2009/1// DO - 10.1007/s11103-008-9402-9 VL - 69 IS - 1-2 SP - 23-32 SN - 1573-5028 KW - Site specific recombination KW - Sequence excision KW - Complex transgene locus resolution KW - Transgene expression KW - Plant transformation ER -