TY - JOUR TI - Response of a paddy soil methanogen to syntrophic growth as revealed by transcriptional analyses AU - Liu, P. AU - Yang, Y. AU - Lu, Z. AU - Lu, Y. T2 - Applied and Environmental Microbiology AB - ABSTRACT Members of Methanocellales are widespread in paddy field soils and play the key role in methane production. These methanogens feature largely in these organisms' adaptation to low H 2 and syntrophic growth with anaerobic fatty acid oxidizers. The adaptive mechanisms, however, remain unknown. In the present study, we determined the transcripts of 21 genes involved in the key steps of methanogenesis and acetate assimilation of Methanocella conradii HZ254, a strain recently isolated from paddy field soil. M. conradii was grown in monoculture and syntrophically with Pelotomaculum thermopropionicum (a propionate syntroph) or Syntrophothermus lipocalidus (a butyrate syntroph). Comparison of the relative transcript abundances showed that three hydrogenase-encoding genes and all methanogenesis-related genes tested were upregulated in cocultures relative to monoculture. The genes encoding formylmethanofuran dehydrogenase (Fwd), heterodisulfide reductase (Hdr), and the membrane-bound energy-converting hydrogenase (Ech) were the most upregulated among the evaluated genes. The expression of the formate dehydrogenase (Fdh)-encoding gene also was significantly upregulated. In contrast, an acetate assimilation gene was downregulated in cocultures. The genes coding for Fwd, Hdr, and the D subunit of F 420 -nonreducing hydrogenase (Mvh) form a large predicted transcription unit; therefore, the Mvh/Hdr/Fwd complex, capable of mediating the electron bifurcation and connecting the first and last steps of methanogenesis, was predicted to be formed in M. conradii . We propose that Methanocella methanogens cope with low H 2 and syntrophic growth by (i) stabilizing the Mvh/Hdr/Fwd complex and (ii) activating formate-dependent methanogenesis. DA - 2014/// PY - 2014/// DO - 10.1128/AEM.01259-14 VL - 5 UR - http://aem.asm.org/content/early/2014/05/12/AEM.01259-14.abstract ER - TY - CONF TI - Engineering Cercospora disease-resistant plants using fungal resistance genes AU - Baumgardner, A. AU - Thomas, E. AU - Daub, M.E. T2 - 13th Annual NC State University Summer Undergraduate Research Symposium C2 - 2014/// CY - Raleigh, NC DA - 2014/// PY - 2014/// ER - TY - JOUR TI - Draft Genome Sequence of the Plant-Pathogenic Soil Fungus Rhizoctonia solani Anastomosis Group 3 Strain Rhs1AP AU - Cubeta, Marc A. AU - Thomas, Elizabeth AU - Dean, Ralph A. AU - Jabaji, Suha AU - Neate, Stephen M. AU - Tavantzis, Stellos AU - Toda, Takeshi AU - Vilgalys, Rytas AU - Bharathan, Narayanaswamy AU - Fedorova-Abrams, Natalie AU - Pakala, Suman B. AU - Pakala, Suchitra M. AU - Zafar, Nikhat AU - Joardar, Vinita AU - Losada, Liliana AU - Nierman, William C. T2 - Genome Announcements AB - ABSTRACT The soil fungus Rhizoctonia solani is a pathogen of agricultural crops. Here, we report on the 51,705,945 bp draft consensus genome sequence of R. solani strain Rhs1AP. A comprehensive understanding of the heterokaryotic genome complexity and organization of R. solani may provide insight into the plant disease ecology and adaptive behavior of the fungus. DA - 2014/10/30/ PY - 2014/10/30/ DO - 10.1128/genomeA.01072-14 VL - 2 IS - 5 J2 - Genome Announc LA - en OP - SN - 2169-8287 UR - http://dx.doi.org/10.1128/genomeA.01072-14 DB - Crossref ER - TY - JOUR TI - The Arabidopsis 14-3-3 Protein RARE COLD INDUCIBLE 1A Links Low-Temperature Response and Ethylene Biosynthesis to Regulate Freezing Tolerance and Cold Acclimation   AU - Catalá, Rafael AU - López-Cobollo, Rosa AU - Mar Castellano, M. AU - Angosto, Trinidad AU - Alonso, José M. AU - Ecker, Joseph R. AU - Salinas, Julio T2 - The Plant Cell AB - In plants, the expression of 14-3-3 genes reacts to various adverse environmental conditions, including cold, high salt, and drought. Although these results suggest that 14-3-3 proteins have the potential to regulate plant responses to abiotic stresses, their role in such responses remains poorly understood. Previously, we showed that the RARE COLD INDUCIBLE 1A (RCI1A) gene encodes the 14-3-3 psi isoform. Here, we present genetic and molecular evidence implicating RCI1A in the response to low temperature. Our results demonstrate that RCI1A functions as a negative regulator of constitutive freezing tolerance and cold acclimation in Arabidopsis thaliana by controlling cold-induced gene expression. Interestingly, this control is partially performed through an ethylene (ET)-dependent pathway involving physical interaction with different ACC SYNTHASE (ACS) isoforms and a decreased ACS stability. We show that, consequently, RCI1A restrains ET biosynthesis, contributing to establish adequate levels of this hormone in Arabidopsis under both standard and low-temperature conditions. We further show that these levels are required to promote proper cold-induced gene expression and freezing tolerance before and after cold acclimation. All these data indicate that RCI1A connects the low-temperature response with ET biosynthesis to modulate constitutive freezing tolerance and cold acclimation in Arabidopsis. DA - 2014/8/1/ PY - 2014/8/1/ DO - 10.1105/tpc.114.127605 VL - 26 IS - 8 SP - 3326-3342 LA - en OP - SN - 1532-298X 1040-4651 UR - http://dx.doi.org/10.1105/tpc.114.127605 DB - Crossref ER - TY - JOUR TI - Trade-Offs between Constitutive and Induced Defences Drive Geographical and Climatic Clines in Pine Chemical Defences T2 - Ecology Letters AB - Abstract There is increasing evidence that geographic and climatic clines drive the patterns of plant defence allocation and defensive strategies. We quantified early growth rate and both constitutive and inducible chemical defences of 18 Pinaceae species in a common greenhouse environment and assessed their defensive allocation with respect to each species' range across climatic gradients spanning 31 o latitude and 2300 m elevation. Constitutive defences traded‐off with induced defences, and these defensive strategies were associated with growth rate such that slow‐growing species invested more in constitutive defence, whereas fast‐growing species invested more in inducible defence. The position of each pine species along this trade‐off axis was in turn associated with geography; moving poleward and to higher elevations, growth rate and inducible defences decreased, while constitutive defence increased. These geographic patterns in plant defence were most strongly associated with variation in temperature. Climatic and geographical clines thus act as drivers of defence profiles by mediating the constraints imposed by trade‐offs, and this dynamic underlays global patterns of defence allocation. DA - 2014/5// PY - 2014/5// DO - 10.1111/ele.12253 VL - 17 IS - 5 SP - 537-546 KW - latitude KW - salicylic acid KW - temperature KW - precipitation KW - jasmonic acid KW - Altitude KW - growth rate KW - non-volatile resin KW - Pinus KW - total phenolics ER - TY - JOUR TI - Exploiting Natural Variation of Secondary Metabolism Identifies a Gene Controlling the Glycosylation Diversity of Dihydroxybenzoic Acids in Arabidopsis thaliana AU - Li, Xu AU - Svedin, Elisabeth AU - Mo, Huaping AU - Atwell, Susanna AU - Dilkes, Brian P. AU - Chapple, Clint T2 - Genetics AB - Abstract Plant secondary metabolism is an active research area because of the unique and important roles the specialized metabolites have in the interaction of plants with their biotic and abiotic environment, the diversity and complexity of the compounds and their importance to human medicine. Thousands of natural accessions of Arabidopsis thaliana characterized with increasing genomic precision are available, providing new opportunities to explore the biochemical and genetic mechanisms affecting variation in secondary metabolism within this model species. In this study, we focused on four aromatic metabolites that were differentially accumulated among 96 Arabidopsis natural accessions as revealed by leaf metabolic profiling. Using UV, mass spectrometry, and NMR data, we identified these four compounds as different dihydroxybenzoic acid (DHBA) glycosides, namely 2,5-dihydroxybenzoic acid (gentisic acid) 5-O-β-D-glucoside, 2,3-dihydroxybenzoic acid 3-O-β-D-glucoside, 2,5-dihydroxybenzoic acid 5-O-β-D-xyloside, and 2,3-dihydroxybenzoic acid 3-O-β-D-xyloside. Quantitative trait locus (QTL) mapping using recombinant inbred lines generated from C24 and Col-0 revealed a major-effect QTL controlling the relative proportion of xylosides vs. glucosides. Association mapping identified markers linked to a gene encoding a UDP glycosyltransferase gene. Analysis of Transfer DNA (T-DNA) knockout lines verified that this gene is required for DHBA xylosylation in planta and recombinant protein was able to xylosylate DHBA in vitro. This study demonstrates that exploiting natural variation of secondary metabolism is a powerful approach for gene function discovery. DA - 2014/8/29/ PY - 2014/8/29/ DO - 10.1534/genetics.114.168690 VL - 198 IS - 3 SP - 1267-1276 SN - 0016-6731 1943-2631 UR - http://dx.doi.org/10.1534/genetics.114.168690 ER - TY - BOOK TI - Messages from the Gods: A Guide to the Useful Plants of Belize AU - Balick, M.J. AU - Arvigo, R. A3 - De Gezelle, J.M. DA - 2014/// PY - 2014/// PB - Oxford University Press/The New York Botanical Garden ER - TY - JOUR TI - Biosynthesis and Metabolic Engineering of Anthocyanins in Arabidopsis thaliana AU - Shi, Ming-Zhu AU - Xie, De-Yu T2 - Recent Patents on Biotechnology AB - Arabidopsis thaliana is the first model plant, the genome of which has been sequenced. In general, intensive studies on this model plant over the past nearly 30 years have led to many new revolutionary understandings in every single aspect of plant biology. Here, we review the current understanding of anthocyanin biosynthesis in this model plant. Although the investigation of anthocyanin structures in this model plant was not performed until 2002, numerous studies over the past three decades have been conducted to understand the biosynthesis of anthocyanins. To date, it appears that all pathway genes of anthocyanins have been molecularly, genetically and biochemically characterized in this plant. These fundamental accomplishments have made Arabidopsis an ideal model to understand the regulatory mechanisms of anthocyanin pathway. Several studies have revealed that the biosynthesis of anthocyanins is controlled by WD40-bHLH-MYB (WBM) transcription factor complexes under lighting conditions. However, how different regulatory complexes coordinately and specifically regulate the pathway genes of anthocyanins remains unclear. In this review, we discuss current progresses and findings including structural diversity, regulatory properties and metabolic engineering of anthocyanins in Arabidopsis thaliana. Keywords: Anthocyanins, Arabidopsis thaliana, biosynthetic pathway, structural diversity, transcriptional regulation. DA - 2014/4// PY - 2014/4// DO - 10.2174/1872208307666131218123538 VL - 8 IS - 1 SP - 47-60 J2 - BIOT LA - en OP - SN - 1872-2083 UR - http://dx.doi.org/10.2174/1872208307666131218123538 DB - Crossref ER - TY - JOUR TI - Complete Genome Sequence of Solvent-Tolerant Clostridium beijerinckii Strain SA-1 T2 - Microbiology Resource Announcements DA - 2014/// PY - 2014/// DO - 10.1128/GENOMEA.01310-14.COPYRIGHT UR - https://publons.com/publon/274767/ ER - TY - JOUR TI - Making Heads or Tails: Planarian Stem Cells in the Classroom † AU - Srougi, Melissa C. AU - Carson, Susan AU - Thomas-Swanik, Jackie AU - Marchant, Jonathan S. AU - Chan, John D. T2 - Journal of Microbiology & Biology Education AB - Stem cells hold great promise in the treatment of diseases ranging from cancer to dementia. However, as rapidly as the field of stem cell biology has emerged, heated political debate has followed, scrutinizing the ethical implications of stem cell use. It is therefore imperative to promote scientific literacy by educating students about stem cell biology. Yet, there is a definite lack of material to engage students in this subject at the basic science level. Therefore, we have developed and implemented a hands-on introductory laboratory module that introduces students to stem cell biology and can be easily incorporated into existing curricula. Students learn about stem cell biology using an in vivo planarian model system in which they down-regulate two genes important in stem cell differentiation using RNA interference and then observe the regenerative phenotype. The module was piloted at the high school, community college, and university levels. Here, we report that introductory biology students enrolled at a community college were able to demonstrate gains in learning after completion of a one-hour lecture and four 45-minute laboratory sessions over the course of three weeks. These gains in learning outcomes were objectively evaluated both before and after its execution using a student quiz and experimental results. Furthermore, students’ self-assessments revealed increases in perceived knowledge as well as a general interest in stem cells. Therefore, these data suggest that this module is a simple, useful way to engage and to teach students about stem cell biology. DA - 2014/5/1/ PY - 2014/5/1/ DO - 10.1128/jmbe.v15i1.692 VL - 15 IS - 1 SP - 18-25 LA - en OP - SN - 1935-7877 1935-7885 UR - http://dx.doi.org/10.1128/jmbe.v15i1.692 DB - Crossref ER - TY - JOUR TI - Do phosphoinositides regulate membrane water permeability of tobacco protoplasts by enhancing the aquaporin pathway? AU - Ma, Xiaohong AU - Shatil-Cohen, Arava AU - Ben-Dor, Shifra AU - Wigoda, Noa AU - Perera, Imara Y. AU - Im, Yang Ju AU - Diminshtein, Sofia AU - Yu, Ling AU - Boss, Wendy F. AU - Moshelion, Menachem AU - Moran, Nava T2 - Planta DA - 2014/12/9/ PY - 2014/12/9/ DO - 10.1007/s00425-014-2216-x VL - 241 IS - 3 SP - 741-755 J2 - Planta LA - en OP - SN - 0032-0935 1432-2048 UR - http://dx.doi.org/10.1007/s00425-014-2216-x DB - Crossref KW - BY2 KW - Lipid KW - Osmotic water permeability coefficient KW - P-f KW - Signaling KW - Synthetic-biology ER - TY - CONF TI - Modeling ribosome dynamics to optimize heterologous protein production in escherichia coli AU - Vu, S. K. AU - Belloti, A. A. AU - Gabriel, C. J. AU - Brochu, H. N. AU - Miller, E. S. AU - Bitzer, D. L. AU - Vouk, M. A. T2 - 2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP) AB - Ineffective heterologous protein synthesis has often been ascribed to codon bias and rare codons. New experimental evidence suggests that codon bias alone may not be the sole cause of poor translation. In this paper we present a free-energy based model of translation elongation to predict and optimize genes for expression in E. coli. The model takes into account second order free energy effects from the binding between the anti-Shine-Dalgarno sequence of the 3' terminal 16S rRNA tail and the mRNA, tRNA abundance, and ribosome displacement. The model and software allow optimization of genes for increased (or decreased) protein yield. The model's predictive and optimization accuracy was assessed by optimizing and expressing three model genes and multiple mRNA variants coding for GST (26 kDa Glutathion S-Transferase from Schistosomajaponicum). Protein yield of optimized genes showed increase from their wildtype levels. Optimization of Glutathion S-Transferase from Schistosoma japonicum and Alcohol Dehydrogenase from Clostridium ljungdahlii DSM 13528 are discussed as examples. Corresponding author, S. K Vu, can be reached at skvu@ncsu.edu. C2 - 2014/12// C3 - 2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP) DA - 2014/12// DO - 10.1109/GlobalSIP.2014.7032363 PB - IEEE SN - 9781479970889 UR - http://dx.doi.org/10.1109/GlobalSIP.2014.7032363 DB - Crossref ER - TY - BOOK TI - Arabidopsis transformation with large bacterial artificial chromosomes AU - Alonso, J.M. AU - Stepanova, A.N. AB - The study of a gene’s function requires, in many cases, the ability to reintroduce the gene of interest or its modified version back into the organism of choice. One potential caveat of this approach is that not only the coding region but also the regulatory sequences of a gene should be included in the corresponding transgenic construct. Even in species with well-annotated genomes, such as Arabidopsis, it is nearly impossible to predict which sequences are responsible for the proper expression of a gene. One way to circumvent this problem is to utilize a large fragment of genomic DNA that contains the coding region of the gene of interest and at least 5–10 kb of flanking genomic sequences. To facilitate these types of experiments, libraries harboring large genomic DNA fragments in binary vectors have been constructed for Arabidopsis and several other plant species. Working with these large clones, however, requires some special precautions. In this chapter, we describe the experimental procedures and extra cautionary measures involved in the identification of the clone containing the gene of interest, its transfer from E. coli to Agrobacterium, and the generation, verification, and analysis of the corresponding transgenic plants. DA - 2014/// PY - 2014/// DO - 10.1007/978-1-62703-580-4_15 VL - 1062 SE - 271-283 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84934439816&partnerID=MN8TOARS ER - TY - CHAP TI - A recombineering-based gene tagging system for Arabidopsis AU - Alonso, J.M. AU - Stepanova, A.N. T2 - Bacterial Artificial Chromosomes: Second Edition AB - Many of the experimental approaches aimed at studying gene function heavily rely on the ability to make precise modifications in the gene’s DNA sequence. Homologous recombination (HR)-based strategies provide a convenient way to create such types of modifications. HR-based DNA sequence manipulations can be enormously facilitated by expressing in E. coli a small set of bacteriophage proteins that make the exchange of DNA between a linear donor and the target DNA molecules extremely efficient. These in vivo recombineering techniques have been incorporated as essential components of the molecular toolbox in many model organisms. In this chapter, we describe the experimental procedures involved in recombineering-based tagging of an Arabidopsis gene contained in a plant transformation-ready bacterial artificial chromosome (TAC). PY - 2014/// DO - 10.1007/978-1-4939-1652-8_11 SP - 233-243 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84954591851&partnerID=MN8TOARS KW - Recombineering KW - Arabidopsis KW - Fluorescent protein KW - Lambda RED ER - TY - CHAP TI - Arabidopsis Transformation with Large Bacterial Artificial Chromosomes AU - Alonso, Jose M. AU - Stepanova, Anna N. T2 - Arabidopsis Protocols PY - 2014/// SP - 271-283 PB - SE - ER - TY - JOUR TI - Resilience in ecology: Abstraction, distraction, or where the action is? AU - Standish, Rachel J. AU - Hobbs, Richard J. AU - Mayfield, Margaret M. AU - Bestelmeyer, Brandon T. AU - Suding, Katherine N. AU - Battaglia, Loretta L. AU - Eviner, Valerie AU - Hawkes, Christine V. AU - Temperton, Vicky M. AU - Cramer, Viki A. AU - Harris, James A. AU - Funk, Jennifer L. AU - Thomas, Peter A. T2 - Biological Conservation AB - Increasingly, the success of management interventions aimed at biodiversity conservation are viewed as being dependent on the ‘resilience’ of the system. Although the term ‘resilience’ is increasingly used by policy makers and environmental managers, the concept of ‘resilience’ remains vague, varied and difficult to quantify. Here we clarify what this concept means from an ecological perspective, and how it can be measured and applied to ecosystem management. We argue that thresholds of disturbance are central to measuring resilience. Thresholds are important because they offer a means to quantify how much disturbance an ecosystem can absorb before switching to another state, and so indicate whether intervention might be necessary to promote the recovery of the pre-disturbance state. We distinguish between helpful resilience, where resilience helps recovery, and unhelpful resilience where it does not, signalling the presence of a threshold and the need for intervention. Data to determine thresholds are not always available and so we consider the potential for indices of functional diversity to act as proxy measures of resilience. We also consider the contributions of connectivity and scale to resilience and how to incorporate these factors into management. We argue that linking thresholds to functional diversity indices may improve our ability to predict the resilience of ecosystems to future, potentially novel, disturbances according to their spatial and temporal scales of influence. Throughout, we provide guidance for the application of the resilience concept to ecosystem management. In doing so, we confirm its usefulness for improving biodiversity conservation in our rapidly changing world. DA - 2014/9// PY - 2014/9// DO - 10.1016/j.biocon.2014.06.008 VL - 177 SP - 43-51 KW - Biodiversity conservation KW - Ecological resilience KW - Environmental policy KW - Recovery KW - Restoration goals KW - Threshold ER - TY - JOUR TI - Short-Term Precipitation Exclusion Alters Microbial Responses to Soil Moisture in a Wet Tropical Forest AU - Waring, Bonnie G. AU - Hawkes, Christine V. T2 - Microb Ecol DA - 2014/6/3/ PY - 2014/6/3/ DO - 10.1007/s00248-014-0436-z VL - 69 IS - 4 SP - 843-854 ER - TY - JOUR TI - Environmental Controls on Fungal Community Composition and Abundance Over 3 Years in Native and Degraded Shrublands AU - Glinka, Clare AU - Hawkes, Christine V. T2 - Microb Ecol DA - 2014/6// PY - 2014/6// DO - 10.1007/s00248-014-0443-0 VL - 68 IS - 4 SP - 807-817 ER - TY - JOUR TI - Guide to the Vascular Flora of the Savannas and Flatwoods of Shaken Creek Preserve and Vicinity (Pender & Onslow Counties, North Carolina, U.S.A.) AU - Thornhill, Robert AU - Krings, Alexander AU - Lindbo, David AU - Stucky, Jon T2 - Biodiversity Data Journal AB - Shaken Creek Preserve ("SCP") is a 2,448 ha (6,050 ac) natural area in Pender and Onslow Counties, North Carolina (U.S.A). Best known for its high-quality longleaf pine savanna habitat, the site contains seven savanna or savanna-like plant community types (i.e., flatwoods or sandhills), three of which are globally critically imperiled (G1): Sandy Pine Savanna (Rush Featherling subtype), Wet Loamy Pine Savanna, and Very Wet Loamy Pine Savanna. SCP hosts three Federally Endangered plant species and six Federal Species of Concern. Formerly a private hunting club, the site was virtually unknown to scientists until the 1990s; consequently, few biological inventories of SCP have been conducted. In particular, no systematic floristic inventories of the species-rich savannas have been undertaken, despite the fact that floristic data is critical to the effective management of any natural area. The goals of this study were to (1) inventory the vascular flora of the savannas, flatwoods, and sandhill community types on site through the collection of voucher specimens; (2) provide a comprehensive checklist of the flora based on collections and reports made from the site and from the same or similar habitats in the vicinity (i.e., within 2 miles of SCP); and (3) create an illustrated guide based on the checklist. In order to increase the usefulness of the guide, taxa not currently known from SCP but collected or reported from the same or similar habitats within two miles of SCP, are included in the guide. Eighty-three families containing 450 taxa, including thirty-two Significantly Rare and thirty-eight Watch List taxa, were collected or reported from SCP; an additional seven families containing a total of 102 taxa, including eighteen Significantly Rare and seven Watch List taxa, were collected or reported from the vicinity. In total, ninety families containing 552 taxa, including fifty Significantly Rare and forty-five Watch List taxa, are treated in the guide. Dichotomous keys are provided to all vouchered or reported families, genera, and species. The following features are provided for all species and infraspecific taxa: flowering and fruiting phenology; synonymy with Manual of the Vascular Flora of the Carolinas, the Flora of North America, and Flora of the Southern and Mid-Atlantic States; relevant voucher information; and, for most taxa, line drawings and/or photographs. For taxa collected from SCP, community types in which the taxa occur and estimates of abundance on site are also provided. DA - 2014/5/16/ PY - 2014/5/16/ DO - 10.3897/BDJ.2.e1099 VL - 2 SP - e1099 J2 - BDJ OP - SN - 1314-2828 1314-2836 UR - http://dx.doi.org/10.3897/BDJ.2.e1099 DB - Crossref ER - TY - BOOK TI - Q’eqchi’ Maya Reproductive Ethnomedicine AU - De Gezelle, Jillian DA - 2014/// PY - 2014/// DO - 10.1007/978-3-319-10744-8 OP - PB - Springer International Publishing SN - 9783319107431 9783319107448 UR - http://dx.doi.org/10.1007/978-3-319-10744-8 DB - Crossref ER - TY - JOUR TI - The potato tuber mitochondrial proteome AU - Salvato, F. AU - Havelund, J.F. AU - Chen, M. AU - Shyama Prasad Rao, R. AU - Rogowska-Wrzesinska, A. AU - Jensen, O.N. AU - Gang, D.R. AU - Thelen, J.J. AU - M?ller, I.M. T2 - Plant Physiology AB - Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum 'Folva') and their proteome investigated. Proteins were resolved by one-dimensional gel electrophoresis, and tryptic peptides were extracted from gel slices and analyzed by liquid chromatography-tandem mass spectrometry using an Orbitrap XL. Using four different search programs, a total of 1,060 nonredundant proteins were identified in a quantitative manner using normalized spectral counts including as many as 5-fold more "extreme" proteins (low mass, high isoelectric point, hydrophobic) than previous mitochondrial proteome studies. We estimate that this compendium of proteins represents a high coverage of the potato tuber mitochondrial proteome (possibly as high as 85%). The dynamic range of protein expression spanned 1,800-fold and included nearly all components of the electron transport chain, tricarboxylic acid cycle, and protein import apparatus. Additionally, we identified 71 pentatricopeptide repeat proteins, 29 membrane carriers/transporters, a number of new proteins involved in coenzyme biosynthesis and iron metabolism, the pyruvate dehydrogenase kinase, and a type 2C protein phosphatase that may catalyze the dephosphorylation of the pyruvate dehydrogenase complex. Systematic analysis of prominent posttranslational modifications revealed that more than 50% of the identified proteins harbor at least one modification. The most prominently observed class of posttranslational modifications was oxidative modifications. This study reveals approximately 500 new or previously unconfirmed plant mitochondrial proteins and outlines a facile strategy for unbiased, near-comprehensive identification of mitochondrial proteins and their modified forms. DA - 2014/// PY - 2014/// DO - 10.1104/pp.113.229054 VL - 164 IS - 2 SP - 637-653 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84893484597&partnerID=MN8TOARS ER - TY - JOUR TI - A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement AU - He, R. AU - Salvato, F. AU - Park, J.-J. AU - Kim, M.-J. AU - Nelson, W. AU - Balbuena, T.S. AU - Willer, M. AU - Crow, J.A. AU - May, G.D. AU - Soderlund, C.A. AU - Thelen, J.J. AU - Gang, D.R. T2 - BMC Plant Biology AB - The rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. Red rice (Oryza longistaminata) is a perennial wild rice species with many valuable traits that could be used to improve cultivated rice cultivars, including rhizomatousness, disease resistance and drought tolerance. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and function in this plant.We used an integrated approach to compare the transcriptome, proteome and metabolome of the rhizome to other tissues of red rice. 116 Gb of transcriptome sequence was obtained from various tissues and used to identify rhizome-specific and preferentially expressed genes, including transcription factors and hormone metabolism and stress response-related genes. Proteomics and metabolomics approaches identified 41 proteins and more than 100 primary metabolites and plant hormones with rhizome preferential accumulation. Of particular interest was the identification of a large number of gene transcripts from Magnaportha oryzae, the fungus that causes rice blast disease in cultivated rice, even though the red rice plants showed no sign of disease.A significant set of genes, proteins and metabolites appear to be specifically or preferentially expressed in the rhizome of O. longistaminata. The presence of M. oryzae gene transcripts at a high level in apparently healthy plants suggests that red rice is resistant to this pathogen, and may be able to provide genes to cultivated rice that will enable resistance to rice blast disease. DA - 2014/// PY - 2014/// DO - 10.1186/1471-2229-14-46 VL - 14 IS - 1 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84893701507&partnerID=MN8TOARS KW - Transcriptomics KW - Proteomics KW - Metabolomics KW - Rhizome KW - Invasive species KW - Disease resistance KW - Rice blast KW - Rice ER - TY - JOUR TI - Isolation of Mitochondria from Potato Tubers AU - Havelund, Jesper AU - Salvato, Fernanda AU - Chen, Mingjie AU - Rao, R.S.P. AU - Rogowska-Wrzesinska, Adelina AU - Jensen, Ole AU - Gang, David AU - Thelen, Jay AU - Ian, M�ller T2 - BIO-PROTOCOL AB - One way to study the function of plant mitochondria is to extract them from plant tissues in an uncontaminated, intact and functional form. The reductionist assumption is that the components present in such a preparation and the in vitro measurable functions or activities reliably reflect the in vivo properties of the organelle inside the plant cell. Here, we describe a method to isolate mitochondria from a relatively homogeneous plant tissue, the dormant potato tuber. The homogenization is done using a juice extractor, which is a relatively gentle homogenization procedure where the mitochondria are only exposed to strong shearing forces once. After removal of starch and large tissue pieces by filtration, differential centrifugation is used to remove residual starch as well as larger organelles. The crude mitochondria are then first purified by using a step Percoll gradient. The mitochondrial band from the step gradient is further purified by using a continuous Percoll gradient. The gradients remove contaminating amyloplasts and peroxisomes as well as ruptured mitochondria. The result is a highly purified, intact and functional mitochondrial preparation, which can be frozen and stored in liquid nitrogen in the presence of 5% (v/v) dimethylsulfoxide to preserve integrity and functionality for months. DA - 2014/// PY - 2014/// DO - 10.21769/bioprotoc.1226 VL - 4 IS - 17 ER - TY - JOUR TI - Complete Genome Sequence of Solvent-Tolerant Clostridium beijerinckii Strain SA-1. AU - Noar, J. AU - Makwana, S.T. AU - Bruno-Bárcena, J.M. T2 - Genome announcements AB - ABSTRACT We report the complete genome sequence of Clostridium beijerinckii SA-1, derived by directed evolution from C. beijerinckii NCIMB 8052, selecting for enhanced solvent tolerance. This sequence allows for accurate placement of SA-1 as C. beijerinckii , permits functional analyses of mutant phenotypes, and suggests methods for distinguishing SA-1 from its parent. DA - 2014/// PY - 2014/// DO - 10.1128/genomea.01310-14 VL - 2 IS - 6 UR - http://europepmc.org/abstract/med/25523769 ER - TY - THES TI - Determinants of geographic distribution in western North American monkeyflowers AU - Sheth, Seema Nayan DA - 2014/// PY - 2014/// SP - 146 LA - English M3 - Ph.D. PB - Colorado State University UR - https://search.proquest.com/docview/1614530607/abstract/1D0947DD4E2F42F7PQ/1 DB - ProQuest Y2 - 2019/2/22/ ER - TY - JOUR TI - Identification and activity of acetate-assimilating bacteria in diffuse fluids venting from deep-sea hydrothermal systems AU - Winkel, M. AU - Pjevac, P. AU - Kleiner, M. AU - Littmann, S. AU - Meyerdierks, A. AU - Amann, R. AU - Mußmann, M. T2 - FEMS Microbiology Ecology AB - Diffuse hydrothermal fluids often contain organic compounds such as hydrocarbons, lipids, and organic acids. Microorganisms consuming these compounds at hydrothermal sites are so far only known from cultivation-dependent studies. To identify potential heterotrophs without prior cultivation, we combined microbial community analysis with short-term incubations using (13)C-labeled acetate at two distinct hydrothermal systems. We followed cell growth and assimilation of (13)C into single cells by nanoSIMS combined with fluorescence in situ hybridization (FISH). In 55 °C-fluids from the Menez Gwen hydrothermal system/Mid-Atlantic Ridge, a novel epsilonproteobacterial group accounted for nearly all assimilation of acetate, representing the first aerobic acetate-consuming member of the Nautiliales. In contrast, Gammaproteobacteria dominated the (13) C-acetate assimilation in incubations of 37 °C-fluids from the back-arc hydrothermal system in the Manus Basin/Papua New Guinea. Here, 16S rRNA gene sequences were mostly related to mesophilic Marinobacter, reflecting the high content of seawater in these fluids. The rapid growth of microorganisms upon acetate addition suggests that acetate consumers in diffuse fluids are copiotrophic opportunists, which quickly exploit their energy sources, whenever available under the spatially and temporally highly fluctuating conditions. Our data provide first insights into the heterotrophic microbial community, catalyzing an under-investigated part of microbial carbon cycling at hydrothermal vents. DA - 2014/// PY - 2014/// DO - 10.1111/1574-6941.12429 VL - 90 IS - 3 SP - 731–746 UR - http://europepmc.org/abstract/med/25244359 KW - Epsilonproteobacteria KW - Gammaproteobacteria KW - heterotrophy KW - 16S rRNA gene KW - nanoSIMS KW - stable isotopes ER - TY - JOUR TI - The evolution of environmental tolerance and range size: A comparison of geographically restricted and widespread mimulus AU - Sheth, S.N. AU - Angert, A.L. T2 - Evolution AB - The geographic ranges of closely related species can vary dramatically, yet we do not fully grasp the mechanisms underlying such variation. The niche breadth hypothesis posits that species that have evolved broad environmental tolerances can achieve larger geographic ranges than species with narrow environmental tolerances. In turn, plasticity and genetic variation in ecologically important traits and adaptation to environmentally variable areas can facilitate the evolution of broad environmental tolerance. We used five pairs of western North American monkeyflowers to experimentally test these ideas by quantifying performance across eight temperature regimes. In four species pairs, species with broader thermal tolerances had larger geographic ranges, supporting the niche breadth hypothesis. As predicted, species with broader thermal tolerances also had more within-population genetic variation in thermal reaction norms and experienced greater thermal variation across their geographic ranges than species with narrow thermal tolerances. Species with narrow thermal tolerance may be particularly vulnerable to changing climatic conditions due to lack of plasticity and insufficient genetic variation to respond to novel selection pressures. Conversely, species experiencing high variation in temperature across their ranges may be buffered against extinction due to climatic changes because they have evolved tolerance to a broad range of temperatures. DA - 2014/// PY - 2014/// DO - 10.1111/evo.12494 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84906531223&partnerID=MN8TOARS KW - Climatic variability hypothesis KW - geographic range size KW - genetic variation KW - niche breadth KW - specialist-generalist trade-offs KW - thermal performance curve ER - TY - JOUR TI - Identifying the paths leading to variation in geographical range size in western North American monkeyflowers AU - Sheth, S.N. AU - Jiménez, I. AU - Angert, A.L. T2 - Journal of Biogeography AB - Abstract Aim Closely related species can vary tremendously in size of geographical range, yet the causes of such variation are poorly understood. Prominent hypotheses about range size emphasize effects of niche properties and habitat connectivity via the amount and occupancy of suitable habitat, respectively. Previous studies have examined single hypotheses in isolation; however, we assessed the relative importance of these effects along with their potential interactions, using monkeyflower species (genus Mimulus ) as a study system. Location Western North America. Methods We used primary occurrence data and climatic layers to estimate climatic niche breadth and position (relative to average regional climate), connectivity of climatically suitable habitat, and geographical range size of 72 monkeyflower species. Using path analysis, we then assessed the relative importance of climatic niche properties and connectivity of climatically suitable habitat in explaining variation in the amount and occupancy of climatically suitable habitat, respectively, and in turn, variation in geographical range size. Results We documented strong support for the hypothesized effects of climatic niche breadth, but not niche position and connectivity of climatically suitable habitat. Amount of climatically suitable habitat explained more variation in range size than occupancy of climatically suitable habitat, with amount and occupancy of suitable habitat together explaining c. 83% of the variation in range size. Main conclusions To our knowledge, this is the first study to show that climatic niche breadth, via its effects on the amount of climatically suitable habitat, is a strong predictor of geographical range size, thereby improving our understanding of the mechanisms driving species rarity. DA - 2014/// PY - 2014/// DO - 10.1111/jbi.12378 VL - 41 IS - 12 SP - 2344-2356 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84939252863&partnerID=MN8TOARS KW - Extent of occurrence KW - geographical range size KW - habitat connectivity KW - Mimulus KW - niche breadth KW - niche position KW - North America KW - range occupancy KW - rarity ER - TY - JOUR TI - Multiple vacuoles inimpaired tonoplast trafficking3mutants are independent organelles AU - Zheng, Jiameng AU - Han, Sang Won AU - Munnik, Teun AU - Rojas-Pierce, Marcela T2 - Plant Signaling & Behavior AB - Plant vacuoles are essential and dynamic organelles, and mechanisms of vacuole biogenesis and fusion are not well characterized. We recently demonstrated that Wortmannin, an inhibitor of Phosphatidylinositol 3-Kinase (PI3K), induces the fusion of plant vacuoles both in roots of itt3/vti11 mutant alleles and in guard cells of wild type Arabidopsis and Fava bean. Here we used Fluorescence Recovery After Photobleaching (FRAP) to demonstrate that the vacuoles in itt3/vti11 are independent organelles. Furthermore, we used fluorescent protein reporters that bind specifically to Phosphatidylinositol 3-Phosphate (PtdIns(3)P) or PtdIns(4)P to show that Wortmannin treatments that induce the fusion of vti11 vacuoles result in the loss of PtdIns(3)P from cellular membranes. These results provided supporting evidence for a critical role of PtdIns(3)P in vacuole fusion in roots and guard cells. DA - 2014/10/3/ PY - 2014/10/3/ DO - 10.4161/psb.29783 VL - 9 IS - 10 SP - e972113 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84922263982&partnerID=MN8TOARS KW - vacuoles KW - phosphoinositides KW - SNARE KW - Wortmannin KW - membrane fusion ER - TY - JOUR TI - The arabidopsis thaliana GRF-interacting factor gene family plays an essential role in control of male and female reproductive development AU - Lee, B.H. AU - Wynn, A.N. AU - Franks, R.G. AU - Hwang, Y.-S. AU - Lim, J. AU - Kim, J.H. T2 - Developmental Biology AB - Reproductive success of angiosperms relies on the precise development of the gynoecium and the anther, because their primary function is to bear and to nurture the embryo sac/female gametophyte and pollen, in which the egg and sperm cells, respectively, are generated. It has been known that the GRF-INTERACTING FACTOR (GIF) transcription co-activator family of Arabidopsis thaliana (Arabidopsis) consists of three members and acts as a positive regulator of cell proliferation. Here, we demonstrate that GIF proteins also play an essential role in development of reproductive organs and generation of the gamete cells. The gif1 gif2 gif3 triple mutant, but not the single or double mutants, failed to establish normal carpel margin meristem (CMM) and its derivative tissues, such as the ovule and the septum, resulting in a split gynoecium and no observable embryo sac. The gif triple mutant also displayed severe structural and functional defects in the anther, producing neither microsporangium nor pollen grains. Therefore, we propose that the GIF family of Arabidopsis is a novel and essential component required for the cell specification maintenance during reproductive organ development and, ultimately, for the reproductive competence. DA - 2014/// PY - 2014/// DO - 10.1016/j.ydbio.2013.12.009 VL - 386 IS - 1 SP - 12-24 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84892481215&partnerID=MN8TOARS KW - Arabidopsis thaliana KW - GRF-INTERACTING FACTOR KW - Carpel KW - Anther KW - Cell specification ER - TY - BOOK TI - Scanning Electron Microscopy analysis of floral development AU - Franks, R.G. AB - Scanning Electron Microscopy (SEM) allows the morphological characterization of the surface features of floral and inflorescence structures in a manner that retains the topography or three-dimensional appearance of the structure. Even at relatively low magnification levels it is possible to characterize early developmental stages. Using medium to high power magnification at later stages of development, cell surface morphology can be visualized allowing the identification of specific epidermal cell types. The analysis of the altered developmental progressions of mutant plants can provide insight into the developmental processes that are disrupted in that mutant background. DA - 2014/// PY - 2014/// DO - 10.1007/978-1-4614-9408-9_13 VL - 1110 SE - 263-273 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84934439650&partnerID=MN8TOARS ER - TY - BOOK TI - Flower development: Open questions and future directions DA - 2014/// PY - 2014/// DO - 10.1007/978-1-4614-9408-9-5 VL - 1110 SE - 103-124 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84898771360&partnerID=MN8TOARS ER - TY - JOUR TI - OMICS applications in crop science foreword AU - Davies, E. T2 - Omics Applications in Crop Science DA - 2014/// PY - 2014/// SP - IX- ER - TY - BOOK TI - Plant-plant allelopathic interactions II: Laboratory bioassays for water-soluble compounds with an emphasis on phenolic acids AU - Blum, U. DA - 2014/// PY - 2014/// PB - New York: Springer Verlag ER - TY - BOOK TI - Exploring Southern Appalachian forests: An ecological guide to 30 great hikes in the Carolinas, Georgia, Tennessee, and Virginia A3 - Jeffries, S. B. A3 - Wentworth, T. R. DA - 2014/// PY - 2014/// PB - Chapel Hill: University of North Carolina Press ER - TY - JOUR TI - Polar Auxin Transport Is Essential for Medial versus Lateral Tissue Specification and Vascular-Mediated Valve Outgrowth in Arabidopsis Gynoecia[W] AU - Larsson, Emma AU - Roberts, Christina J. AU - Claes, Andrea R. AU - Franks, Robert G. AU - Sundberg, Eva T2 - PLANT PHYSIOLOGY AB - Although it is generally accepted that auxin is important for the patterning of the female reproductive organ, the gynoecium, the flow as well as the temporal and spatial actions of auxin have been difficult to show during early gynoecial development. The primordium of the Arabidopsis (Arabidopsis thaliana) gynoecium is composed of two congenitally fused, laterally positioned carpel primordia bisected by two medially positioned meristematic regions that give rise to apical and internal tissues, including the ovules. This organization makes the gynoecium one of the most complex plant structures, and as such, the regulation of its development has remained largely elusive. By determining the spatiotemporal expression of auxin response reporters and localization of PINFORMED (PIN) auxin efflux carriers, we have been able to create a map of the auxin flow during the earliest stages of gynoecial primordium initiation and outgrowth. We show that transient disruption of polar auxin transport (PAT) results in ectopic auxin responses, broadened expression domains of medial tissue markers, and disturbed lateral preprocambium initiation. Based on these results, we propose a new model of auxin-mediated gynoecial patterning, suggesting that valve outgrowth depends on PIN1-mediated lateral auxin maxima as well as subsequent internal auxin drainage and provascular formation, whereas the growth of the medial domains is less dependent on correct PAT. In addition, PAT is required to prevent the lateral domains, at least in the apical portion of the gynoecial primordium, from obtaining medial fates. DA - 2014/12// PY - 2014/12// DO - 10.1104/pp.114.245951 VL - 166 IS - 4 SP - 1998-U1237 SN - 1532-2548 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84914129165&partnerID=MN8TOARS ER - TY - JOUR TI - Intercellular Protein Movement: Deciphering the Language of Development AU - Gallagher, Kimberly L. AU - Sozzani, Rosangela AU - Lee, Chin-Mei T2 - ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 30 AB - Development in multicellular organisms requires the coordinated production of a large number of specialized cell types through sophisticated signaling mechanisms. Non-cell-autonomous signals are one of the key mechanisms by which organisms coordinate development. In plants, intercellular movement of transcription factors and other mobile signals, such as hormones and peptides, is essential for normal development. Through a combination of different approaches, a large number of non-cell-autonomous signals that control plant development have been identified. We review some of the transcriptional regulators that traffic between cells, as well as how changes in symplasmic continuity affect and are affected by development. We also review current models for how mobile signals move via plasmodesmata and how movement is inhibited. Finally, we consider challenges in and new tools for studying protein movement. DA - 2014/// PY - 2014/// DO - 10.1146/annurev-cellbio-100913-012915 VL - 30 SP - 207-233 SN - 1530-8995 KW - Arabidopsis development KW - plasmodesmata KW - non-cell-autonomous proteins KW - cell-to-cell signaling ER - TY - JOUR TI - Environmental Controls of Reproduction and Early Growth of Lindera melissifolia (Lauraceae) AU - Unks, Ryan R. AU - Shear, Theodore H. AU - Krings, Alexander AU - Braham, Richard R. T2 - CASTANEA AB - Lindera melissifolia is a federally endangered endemic shrub of the southeastern United States. Numerous populations are gender-biased. The goal of this study was to determine environmental conditions most appropriate for establishment and growth of seedlings and adult females. Seedlings were grown under varied moisture and light to compare growth rates and morphological ratios. Seedlings were clipped to simulate two levels of disturbance, and their shoot sprouting ability was assessed. Densities of adult flowering stems, co-occurring species, and solar transmittance were analyzed within two North Carolina populations. The lowest levels of light resulted in decreased growth, but light and moisture did not interact to affect seedling growth rate significantly. Morphological ratios and growth responses followed patterns expected for plants exhibiting plasticity in response to varied light levels, but not to moisture. Clipping immature plants below root collars decreased survivorship to 31%. Growth rates of new shoots when clipped below and above the root collar were 40% and 58% percent lower, respectively (p < 0.001). Percent cover of Lindera melissifolia explained 52% of the variation in the number of male flowering stems per plot and 14% of the variation in female stems per plot. No relation of stem density to percent transmittance was found. Indicator species analysis revealed association of males with facultative wetland species and a weak association of females with wetland obligates, but overall difference in vegetation composition between plots with or without females present was slight (MRPP: A = 0.02, p = 0.016). We concluded hydrology should be a primary concern for future studies. DA - 2014/12// PY - 2014/12// DO - 10.2179/14-034 VL - 79 IS - 4 SP - 266-277 SN - 1938-4386 KW - Carolina Bays KW - indicator species KW - Lindera melissifolia KW - male-bias ER - TY - JOUR TI - Interactions between fungal growth, substrate utilization, and enzyme production during solid substrate cultivation of Phanerochaete chrysosporium on cotton stalks AU - Shi, Jian AU - Chinn, Mari S. AU - Sharma-Shivappa, Ratna R. T2 - Bioprocess and Biosystems Engineering DA - 2014/6/8/ PY - 2014/6/8/ DO - 10.1007/s00449-014-1224-3 VL - 37 IS - 12 SP - 2463-2473 J2 - Bioprocess Biosyst Eng LA - en OP - SN - 1615-7591 1615-7605 UR - http://dx.doi.org/10.1007/s00449-014-1224-3 DB - Crossref KW - Cotton stalk KW - Pretreatment KW - Bioethanol KW - Phanerochaete chrysosporium KW - Kinetics KW - Solid substrate cultivation ER - TY - JOUR TI - Corrigendum: [Novel functional roles for PERIANTHIA and SEUSS during floral organ identity specification, floral meristem termination and gynoecial development] AU - Franks, Robert G. T2 - FRONTIERS IN PLANT SCIENCE AB - The gynoecium is the female reproductive structure of angiosperm flowers. In Arabidopsis thaliana the gynoecium is composed of two carpels that are fused into a tube-like structure. As the gynoecial primordium arises from the floral meristem, a specialized meristematic structure, the carpel margin meristem (CMM), develops from portions of the medial gynoecial domain. The CMM is critical for reproductive competence because it gives rise to the ovules, the precursors of the seeds. Here we report a functional role for the transcription factor PERIANTHIA (PAN) in the development of the gynoecial medial domain and the formation of ovule primordia. This function of PAN is revealed in pan aintegumenta (ant) as well as seuss (seu) pan double mutants that form reduced numbers of ovules. Previously, PAN was identified as a regulator of perianth organ number and as a direct activator of AGAMOUS (AG) expression in floral whorl four. However, the seu pan double mutants display enhanced ectopic AG expression in developing sepals and the partial transformation of sepals to petals indicating a novel role for PAN in the repression of AG in floral whorl one. These results indicate that PAN functions as an activator or repressor of AG expression in a whorl-specific fashion. The seu pan double mutants also display enhanced floral indeterminacy, resulting in the formation of "fifth whorl" structures and disruption of WUSCHEL (WUS) expression patterns revealing a novel role for SEU in floral meristem termination. DA - 2014/8/29/ PY - 2014/8/29/ DO - 10.3389/fpls.2014.00434 VL - 5 SP - SN - 1664-462X UR - http://europepmc.org/abstract/med/25221562 KW - corrigendum KW - hoyers KW - chloral hydrate KW - PERIANTHIA KW - SEUSS ER - TY - JOUR TI - Characterization of a thermophilic bacteriophage of Geobacillus kaustophilus AU - Marks, Timothy J. AU - Hamilton, Paul T. T2 - ARCHIVES OF VIROLOGY DA - 2014/10// PY - 2014/10// DO - 10.1007/s00705-014-2101-8 VL - 159 IS - 10 SP - 2771-2775 SN - 1432-8798 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84907692380&partnerID=MN8TOARS ER - TY - JOUR TI - The farm to biorefinery continuum: A techno-economic and LCA analysis of ethanol production from sweet sorghum juice AU - Caffrey, Kevin R. AU - Veal, Matthew W. AU - Chinn, Mari S. T2 - Agricultural Systems AB - This paper describes the economic, environmental, and energy issues of the farm to biorefinery continuum related to production of ethanol from soluble sugars recovered from sweet sorghum using the BE3 (bioenergy economics, energy, and environmental) model methodology. A comparative analysis of five process configurations was conducted to determine how process decentralization affects the total production system. An increased integration of on-farm processing resulted in a moderate increase in the breakeven sales price of ethanol ($0.08/L), however the substantial increase in value-added agricultural practices (approximately 180%) can offer greater returns to the farm operation. Benefits outside the scope of this analysis related to decentralized processing include: increased rural development, reductions in transportation requirements, additional income to farmers, and dissipation of some environmental impacts. Using a single parameter sensitivity analysis for those process configurations the greatest economic impacts were found to be related to conversion efficiency, crop yield, and press efficiency. Conservative values were used throughout the process modeling procedure (e.g. crop yield, Brix level of juice, conversion efficiency, and by-product usage), yet with system optimization, breakeven sales price could be significantly decreased. DA - 2014/9// PY - 2014/9// DO - 10.1016/j.agsy.2014.05.016 VL - 130 SP - 55-66 J2 - Agricultural Systems LA - en OP - SN - 0308-521X UR - http://dx.doi.org/10.1016/j.agsy.2014.05.016 DB - Crossref KW - Value-added agriculture KW - Bioenergy KW - Life cycle assessment KW - Techno-economic evaluation KW - Energy audit ER - TY - JOUR TI - The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes AU - Mérai, Zsuzsanna AU - Chumak, Nina AU - García-Aguilar, Marcelina AU - Hsieh, Tzung-Fu AU - Nishimura, Toshiro AU - Schoft, Vera K. AU - Bindics, János AU - Ślusarz, Lucyna AU - Arnoux, Stéphanie AU - Opravil, Susanne AU - Mechtler, Karl AU - Zilberman, Daniel AU - Fischer, Robert L. AU - Tamaru, Hisashi T2 - Proceedings of the National Academy of Sciences AB - Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48A(NPL4) complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction. DA - 2014/10/24/ PY - 2014/10/24/ DO - 10.1073/pnas.1418564111 VL - 111 IS - 45 SP - 16166-16171 J2 - Proc Natl Acad Sci USA LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.1418564111 DB - Crossref KW - centromere disassembly KW - heterochromatin decondensation KW - chromosome dynamics KW - rDNA activation KW - pollen tip growth ER - TY - JOUR TI - Molecular cloning and functional characterization of the anthocyanidin reductase gene from Vitis bellula AU - Zhu, Yue AU - Peng, Qing-Zhong AU - Li, Ke-Gang AU - Xie, De-Yu T2 - PLANTA DA - 2014/8// PY - 2014/8// DO - 10.1007/s00425-014-2094-2 VL - 240 IS - 2 SP - 381-398 SN - 1432-2048 KW - Anthocyanidin reductase KW - Flavan-3-ols KW - (-)-Epicatechin KW - (-)-Catechin KW - (-)-Epigallocatechin KW - (-)-Gallocatechin KW - Proanthocyanidins KW - Vitis bellula ER - TY - JOUR TI - Alien species pool influences the level of habitat invasion in intercontinental exchange of alien plants AU - Kalusova, Veronika AU - Chytry, Milan AU - Peet, Robert K. AU - Wentworth, Thomas R. T2 - GLOBAL ECOLOGY AND BIOGEOGRAPHY AB - Abstract Aim We hypothesize that the level of plant invasion at the scale of vegetation plots is affected by the different sizes of regional species pools of alien plants adapted to particular habitats. We test these species‐pool effects in the context of alien species exchange between analogous habitats on two continents. Location N orth and S outh C arolina, and the C zech R epublic (both as native and invaded range). Methods We identified native and alien vascular plant species within 6059 vegetation plots from 27 habitats of eastern N orth A merica and C entral E urope. We compared the habitats’ level of invasion, expressed as the proportion of alien species in a representative sample of vegetation plots from each habitat, with the contribution of each habitat to the alien species pool, calculated as the proportion of species of this habitat that are native to one continent and donated as aliens to the other. Results A habitat's level of invasion on one continent increases with the proportion of alien species donated to its regional species pools by analogous habitats on the other continent, i.e. the more of its native species a habitat contributes as aliens, the more of them establish in analogous recipient habitats (direct species‐pool effect). The habitat's level of invasion on the same continent also increases with the proportion of native species that those habitats themselves donate to regional species pools on the other continent, i.e. a habitat that gives many aliens also receives many aliens (reciprocal species‐pool effect). Main conclusions We demonstrate that when a habitat on one continent donates more of its native species to the alien species pool, the analogous habitat on the recipient continent also contains a greater number of aliens. The same donor habitat is itself also the recipient of more alien species invading from the analogous habitats of other continents. DA - 2014/12// PY - 2014/12// DO - 10.1111/geb.12209 VL - 23 IS - 12 SP - 1366-1375 SN - 1466-8238 KW - Alien species pool KW - exotic species KW - habitat level of invasion KW - invaded range KW - native range KW - plant invasions ER - TY - JOUR TI - Two inositol hexakisphosphate kinases drive inositol pyrophosphate synthesis in plants AU - Desai, Mintu AU - Rangarajan, Padma AU - Donahue, Janet L. AU - Williams, Sarah P. AU - Land, Eric S. AU - Mandal, Mihir K. AU - Phillippy, Brian Q. AU - Perera, Imara Y. AU - Raboy, Victor AU - Gillaspy, Glenda E. T2 - The Plant Journal AB - Inositol pyrophosphates are unique cellular signaling molecules with recently discovered roles in energy sensing and metabolism. Studies in eukaryotes have revealed that these compounds have a rapid turnover, and thus only small amounts accumulate. Inositol pyrophosphates have not been the subject of investigation in plants even though seeds produce large amounts of their precursor, myo-inositol hexakisphosphate (InsP6 ). Here, we report that Arabidopsis and maize InsP6 transporter mutants have elevated levels of inositol pyrophosphates in their seed, providing unequivocal identification of their presence in plant tissues. We also show that plant seeds store a little over 1% of their inositol phosphate pool as InsP7 and InsP8 . Many tissues, including, seed, seedlings, roots and leaves accumulate InsP7 and InsP8 , thus synthesis is not confined to tissues with high InsP6 . We have identified two highly similar Arabidopsis genes, AtVip1 and AtVip2, which are orthologous to the yeast and mammalian VIP kinases. Both AtVip1 and AtVip2 encode proteins capable of restoring InsP7 synthesis in yeast mutants, thus AtVip1 and AtVip2 can function as bonafide InsP6 kinases. AtVip1 and AtVip2 are differentially expressed in plant tissues, suggesting non-redundant or non-overlapping functions in plants. These results contribute to our knowledge of inositol phosphate metabolism and will lay a foundation for understanding the role of InsP7 and InsP8 in plants. DA - 2014/10/27/ PY - 2014/10/27/ DO - 10.1111/tpj.12669 VL - 80 IS - 4 SP - 642-653 J2 - Plant J LA - en OP - SN - 0960-7412 UR - http://dx.doi.org/10.1111/tpj.12669 DB - Crossref KW - Arabidopsis thaliana KW - At3g01310 KW - At5g15070 KW - inositol pyrophosphate KW - inositol kinase KW - InsP(6) ER - TY - JOUR TI - SnRK1 Phosphorylation of AL2 Delays Cabbage Leaf Curl Virus Infection in Arabidopsis AU - Shen, Wei AU - Dallas, Mary Beth AU - Goshe, Michael B. AU - Hanley-Bowdoin, Linda T2 - JOURNAL OF VIROLOGY AB - Geminivirus AL2/C2 proteins play key roles in establishing infection and causing disease in their plant hosts. They are involved in viral gene expression, counter host defenses by suppressing transcriptional gene silencing, and interfere with the host signaling involved in pathogen resistance. We report here that begomovirus and curtovirus AL2/C2 proteins interact strongly with host geminivirus Rep-interacting kinases (GRIKs), which are upstream activating kinases of the protein kinase SnRK1, a global regulator of energy and nutrient levels in plants. We used an in vitro kinase system to show that GRIK-activated SnRK1 phosphorylates recombinant AL2/C2 proteins from several begomoviruses and to map the SnRK1 phosphorylation site to serine-109 in the AL2 proteins of two New World begomoviruses: Cabbage Leaf Curl Virus (CaLCuV) and Tomato mottle virus. A CaLCuV AL2 S109D phosphomimic mutation did not alter viral DNA levels in protoplast replication assays. In contrast, the phosphomimic mutant was delayed for symptom development and viral DNA accumulation during infection of Arabidopsis thaliana, demonstrating that SnRK1 contributes to host defenses against CaLCuV. Our observation that serine-109 is not conserved in all AL2/C2 proteins that are SnRK1 substrates in vitro suggested that phosphorylation of viral proteins by plant kinases contributes to the evolution of geminivirus-host interactions.Geminiviruses are single-stranded DNA viruses that cause serious diseases in many crops. Dicot-infecting geminiviruses carry genes that encode multifunctional AL2/C2 proteins that are essential for infection. However, it is not clear how AL2/C2 proteins are regulated. Here, we show that the host protein kinase SnRK1, a central regulator of energy balance and nutrient metabolism in plants, phosphorylates serine-109 in AL2 proteins of three subgroups of New World begomoviruses, resulting in a delay in viral DNA accumulation and symptom appearance. Our results support SnRK1's antiviral role and reveal a novel mechanism underlying this function. Phylogenetic analysis suggested that AL2 S109 evolved as begomoviruses migrated from the Old World to the New World and may have provided a selective advantage as begomoviruses adapted to a different environment and different plant hosts. This study provides new insights into the interaction of viral pathogens with their plant hosts at the level of viral protein modification by the host. DA - 2014/9// PY - 2014/9// DO - 10.1128/jvi.00761-14 VL - 88 IS - 18 SP - 10598-10612 SN - 1098-5514 ER - TY - JOUR TI - Recommendations to Mitigate Potential Sources of Error in Preparation of Biomass Sorghum Samples for Compositional Analyses Used in Industrial and Forage Applications AU - Whitfield, Matthew B. AU - Chinn, Mari S. AU - Veal, Matthew W. T2 - BioEnergy Research DA - 2014/6/3/ PY - 2014/6/3/ DO - 10.1007/s12155-014-9476-y VL - 7 IS - 4 SP - 1561-1570 J2 - Bioenerg. Res. LA - en OP - SN - 1939-1234 1939-1242 UR - http://dx.doi.org/10.1007/s12155-014-9476-y DB - Crossref KW - Sweet sorghum KW - Forage sorghum KW - Physical properties KW - Fermentable sugars KW - Biofuel KW - Lignocellulose ER - TY - JOUR TI - Phosphoinositide-signaling is one component of a robust plant defense response AU - Hung, Chiu-Yueh AU - Aspesi Jr, Peter AU - Hunter, Melissa R. AU - Lomax, Aaron W. AU - Perera, Imara Y. T2 - Frontiers in Plant Science AB - The phosphoinositide pathway and inositol-1,4,5-triphosphate (InsP3) have been implicated in plant responses to many abiotic stresses; however, their role in response to biotic stress is not well characterized. In the current study, we show that both basal defense and systemic acquired resistance responses are affected in transgenic plants constitutively expressing the human type I inositol polyphosphate 5-phosphatase (InsP 5-ptase) which have greatly reduced InsP3 levels. Flagellin induced Ca2+-release as well as the expressions of some flg22 responsive genes were attenuated in the InsP 5-ptase plants. Furthermore, the InsP 5-ptase plants were more susceptible to virulent and avirulent strains of Pseudomonas syringae pv. tomato (Pst)DC3000. The InsP 5-ptase plants had lower basal salicylic acid (SA) levels and the induction of SAR in systemic leaves was reduced and delayed. Reciprocal exudate experiments showed that although the InsP 5-ptase plants produced equally effective molecules that could trigger PR-1 gene expression in wild type plants, exudates collected from either wild type or InsP 5-ptase plants triggered less PR-1 gene expression in InsP 5-ptase plants. Additionally, expression profiles indicated that several defense genes including PR-1, PR-2, PR-5 and AIG1 were basally down regulated in the InsP 5-ptase plants compared with wild type. Upon pathogen attack, expression of these genes was either not induced or showed delayed induction in systemic leaves. Our study shows that phosphoinositide signaling is one component of the plant defense network and is involved in both basal and systemic responses. The dampening of InsP3-mediated signaling affects Ca2+ release, modulates defense gene expression and compromises plant defense responses. DA - 2014/6/11/ PY - 2014/6/11/ DO - 10.3389/fpls.2014.00267 VL - 5 SP - J2 - Front. Plant Sci. OP - SN - 1664-462X UR - http://dx.doi.org/10.3389/fpls.2014.00267 DB - Crossref KW - Arabidopsis KW - Ca2+ KW - salicylic acid KW - phosphoinositides KW - InsP(3) KW - plant defense signaling KW - SAR ER - TY - JOUR TI - PLASTID MOVEMENT IMPAIRED1 mediates ABA sensitivity during germination and implicates ABA in, light-mediated Chloroplast movements AU - Rojas-Pierce, Marcela AU - Whippo, Craig W. AU - Davis, Phillip A. AU - Hangarter, Roger P. AU - Springer, Patricia S. T2 - PLANT PHYSIOLOGY AND BIOCHEMISTRY AB - The plant hormone abscisic acid (ABA) controls many aspects of plant growth and development, including seed development, germination and responses to water-deficit stress. A complex ABA signaling network integrates environmental signals including water availability and light intensity and quality to fine-tune the response to a changing environment. To further define the regulatory pathways that control water-deficit and ABA responses, we carried out a gene-trap tagging screen for water-deficit-regulated genes in Arabidopsis thaliana. This screen identified PLASTID MOVEMENT IMPAIRED1 (PMI1), a gene involved in blue-light-induced chloroplast movement, as functioning in ABA-response pathways. We provide evidence that PMI1 is involved in the regulation of seed germination by ABA, acting upstream of the intersection between ABA and low-glucose signaling pathways. Furthermore, PMI1 participates in the regulation of ABA accumulation during periods of water deficit at the seedling stage. The combined phenotypes of pmi1 mutants in chloroplast movement and ABA responses indicate that ABA signaling may modulate chloroplast motility. This result was further supported by the detection of altered chloroplast movements in the ABA mutants aba1-6, aba2-1 and abi1-1. DA - 2014/10// PY - 2014/10// DO - 10.1016/j.plaphy.2014.07.014 VL - 83 SP - 185-193 SN - 0981-9428 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84907306226&partnerID=MN8TOARS KW - ABA KW - Arabidopsis KW - Chloroplast movement KW - Seed germination KW - Water deficit ER - TY - JOUR TI - Experimental data and computational modeling link auxin gradient and development in the Arabidopsis root AU - Clark, N. M. AU - Balaguer, M. A. D. AU - Sozzani, R. T2 - Frontiers in Plant Science DA - 2014/// PY - 2014/// VL - 5 ER - TY - JOUR TI - Chromate alters root system architecture and activates expression of genes involved in iron homeostasis and signaling in Arabidopsis thaliana AU - Martinez-Trujillo, M. AU - Mendez-Bravo, A. AU - Ortiz-Castro, R. AU - Hernandez-Madrigal, F. AU - Ibarra-Laclette, E. AU - Ruiz-Herrera, L. F. AU - Long, Terri A. AU - Cervantes, C. AU - Herrera-Estrella, L. AU - Lopez-Bucio, J. AU - al. T2 - PLANT MOLECULAR BIOLOGY DA - 2014/9// PY - 2014/9// DO - 10.1007/s11103-014-0210-0 VL - 86 IS - 1-2 SP - 35-50 SN - 1573-5028 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84906088354&partnerID=MN8TOARS KW - Chromium KW - Root development KW - Gene expression KW - Iron homeostasis KW - Arabidopsis ER - TY - JOUR TI - Simultaneous saccharification and fermentation of industrial sweetpotatoes for ethanol production and anthocyanins extraction AU - Diaz, Joscelin T. AU - Chinn, Mari S. AU - Truong, Van-Den T2 - INDUSTRIAL CROPS AND PRODUCTS AB - A simultaneous saccharification fermentation (SSF) system was studied for ethanol production in flour industrial sweetpotato (ISP) feedstocks (lines: white DM02-180 and purple NC-413) as an integrated cost saving process, and to examine the feasibility of extracting anthocyanins from flour purple ISPs under a simultaneous extraction and fermentation (SEF) system. Furthermore, a separate hydrolysis fermentation (SHF) configuration was carried out to establish a baseline in sugar consumption and ethanol production from the ISP lines. The thermotolerant ethanol producing yeast strain Kluyveromyces marxianus NCYC 851 and the mesophilic Saccharomyces cerevisiae Ethanol Red were evaluated, using commercial alpha amylases for hydrolysis of available ISP starch to sugars. Fermentation by S. cerevisiae during SHF had an ethanol yield of 0.32 g/g dry ISP, a 1.1-fold increase above that produced by K. marxianus. Subsequent studies showed that ethanol yield could be increased in a SSF system with a maximum ethanol yield of 0.39 g/g dry ISP achieved, a 15% increase compared with using a SHF system when S. cerevisiae was used. Simultaneous extraction and fermentation of flour purple-fleshed NC-413 ISPs was studied to evaluate the effect of pH on extraction of total monomeric anthocyanins (TMA) and ethanol production. On average, maximum ethanol yield ranged from 0.31 to 0.34 g/g dry ISP and TMA concentration ranged from 45 to 64 mg cyanidin-3-glu/100 g dry powder (10–22 mg/100 g fresh weight) with the greatest ethanol production coming from non-adjusted pH fermentations. The highest anthocyanin recovery, 64 mg cyanidin-3-glu/100 g dry powder was obtained at 35 °C and pH 4.5 using S. cerevisiae Ethanol Red. This study showed the feasibility of extracting anthocyanins and producing ethanol simultaneously in one unit operation without the need of purified solvents. DA - 2014/12// PY - 2014/12// DO - 10.1016/j.indcrop.2014.07.032 VL - 62 SP - 53-60 SN - 1872-633X KW - Ipomoea batatas KW - Kluyveromyces marxianus KW - Saccharomyces cerevisiae KW - Antioxidants KW - Fermentation KW - Starch KW - Sweet potato ER - TY - JOUR TI - Omics and modelling approaches for understanding regulation of asymmetric cell divisions in arabidopsis and other angiosperm plants AU - Kajala, Kaisa AU - Ramakrishna, Priya AU - Fisher, Adam AU - Bergmann, Dominique C. AU - De Smet, Ive AU - Sozzani, Rosangela AU - Weijers, Dolf AU - Brady, Siobhan M. T2 - ANNALS OF BOTANY AB - Asymmetric cell divisions are formative divisions that generate daughter cells of distinct identity. These divisions are coordinated by either extrinsic (‘niche-controlled’) or intrinsic regulatory mechanisms and are fundamentally important in plant development. This review describes how asymmetric cell divisions are regulated during development and in different cell types in both the root and the shoot of plants. It further highlights ways in which omics and modelling approaches have been used to elucidate these regulatory mechanisms. For example, the regulation of embryonic asymmetric divisions is described, including the first divisions of the zygote, formative vascular divisions and divisions that give rise to the root stem cell niche. Asymmetric divisions of the root cortex endodermis initial, pericycle cells that give rise to the lateral root primordium, procambium, cambium and stomatal cells are also discussed. Finally, a perspective is provided regarding the role of other hormones or regulatory molecules in asymmetric divisions, the presence of segregated determinants and the usefulness of modelling approaches in understanding network dynamics within these very special cells. Asymmetric cell divisions define plant development. High-throughput genomic and modelling approaches can elucidate their regulation, which in turn could enable the engineering of plant traits such as stomatal density, lateral root development and wood formation. DA - 2014/6// PY - 2014/6// DO - 10.1093/aob/mcu065 VL - 113 IS - 7 SP - 1083-1105 SN - 1095-8290 KW - Asymmetric cell division KW - embryo KW - root KW - stomata KW - lateral root KW - cortex endodermis initial KW - omics KW - Arabidopsis thaliana KW - Zea mays KW - maize ER - TY - JOUR TI - Immunological Tools: Engaging Students in the Use and Analysis of Flow Cytometry and Enzyme-Linked Immunosorbent Assay (ELISA) AU - Ott, Laura E. AU - Carson, Susan T2 - BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION AB - Abstract Flow cytometry and enzyme‐linked immunosorbent assay (ELISA) are commonly used techniques associated with clinical and research applications within the immunology and medical fields. The use of these techniques is becoming increasingly valuable in many life science and engineering disciplines as well. Herein, we report the development and evaluation of a novel half‐semester course that focused on introducing undergraduate and graduate students to advance conceptual and technical skills associated with flow cytometry and ELISA, with emphasis on applications, experimental design, and data analysis. This course was offered in the North Carolina State University Biotechnology Program over three semesters and consisted of weekly lectures and laboratories. Students performed and/or analyzed flow cytometry and ELISA in three separate laboratory exercises: (1) identification of transgenic zebrafish hematopoietic cells, (2) analysis of transfection efficiency, and (3) analysis of cytokine production upon lipopolysaccharide stimulation. Student learning outcomes were achieved as demonstrated by multiple means of assessment, including three laboratory reports, a data analysis laboratory practicum, and a cumulative final exam. Further, anonymous student self‐assessment revealed increased student confidence in the knowledge and skill sets defined in the learning outcomes. © 2014 by The International Union of Biochemistry and Molecular Biology, 42(5):382–397, 2014. DA - 2014/// PY - 2014/// DO - 10.1002/bmb.20808 VL - 42 IS - 5 SP - 382-397 SN - 1539-3429 KW - flow cytometry KW - enzyme-linked immunosorbent assay (ELISA) KW - laboratory KW - undergraduate students KW - graduate students KW - data analysis ER - TY - JOUR TI - Are winter-active species vulnerable to climate warming? A case study with the wintergreen terrestrial orchid, Tipularia discolor AU - Marchin, Renee M. AU - Dunn, Robert R. AU - Hoffmann, William A. T2 - OECOLOGIA DA - 2014/12// PY - 2014/12// DO - 10.1007/s00442-014-3074-8 VL - 176 IS - 4 SP - 1161-1172 SN - 1432-1939 KW - Experimental warming KW - Vapor pressure deficit KW - Reproduction KW - Photosynthesis KW - Temperate forest understory ER - TY - JOUR TI - Advanced imaging techniques for the study of plant growth and development AU - Sozzani, Rosangela AU - Busch, Wolfgang AU - Spalding, Edgar P. AU - Benfey, Philip N. T2 - TRENDS IN PLANT SCIENCE AB - •Integration of imaging tools with genome-wide approaches and modeling. •Quantitative measurements to describe biological systems at cellular resolution over time. •Recent developments in the field of imaging. •Vision-based methods (2D high-throughput and non-destructive methods). A variety of imaging methodologies are being used to collect data for quantitative studies of plant growth and development from living plants. Multi-level data, from macroscopic to molecular, and from weeks to seconds, can be acquired. Furthermore, advances in parallelized and automated image acquisition enable the throughput to capture images from large populations of plants under specific growth conditions. Image-processing capabilities allow for 3D or 4D reconstruction of image data and automated quantification of biological features. These advances facilitate the integration of imaging data with genome-wide molecular data to enable systems-level modeling. A variety of imaging methodologies are being used to collect data for quantitative studies of plant growth and development from living plants. Multi-level data, from macroscopic to molecular, and from weeks to seconds, can be acquired. Furthermore, advances in parallelized and automated image acquisition enable the throughput to capture images from large populations of plants under specific growth conditions. Image-processing capabilities allow for 3D or 4D reconstruction of image data and automated quantification of biological features. These advances facilitate the integration of imaging data with genome-wide molecular data to enable systems-level modeling. laser microscopy that allows image acquisition of fluorescent molecules producing images with high horizontal resolution and depth selectivity. technique in which the sample is illuminated perpendicular to the direction of observation. 3D image computed from multiple 2D projections from different angles obtained by interaction of matter and X-rays. apparatus in which small volumes of liquid can be controlled. integrated and automated approach to track cell lineages over time, in which images of organs are acquired from multiple angles, computationally merged and segmented. 3D image computed from multiple 2D projections from different angles obtained by optical microscopy. genome regions that underlie the quantitative variation of a trait. collection of lines, each containing chromosomes which constitute a genetic mosaic of two parental lines. light sheet illumination-based microscopy allowing for image acquisition with high-spatial and temporal resolution. microscopy technique that can yield images with a resolution higher than the diffraction limit would allow. DA - 2014/5// PY - 2014/5// DO - 10.1016/j.tplants.2013.12.003 VL - 19 IS - 5 SP - 304-310 SN - 1878-4372 KW - imaging techniques KW - plant growth and development KW - systems-level modeling. ER - TY - JOUR TI - A simple improved-throughput xylem protoplast system for studying wood formation AU - Lin, Ying-Chung AU - Li, Wei AU - Chen, Hao AU - Li, Quanzi AU - Sun, Ying-Hsuan AU - Shi, Rui AU - Lin, Chien-Yuan AU - Wang, Jack P. AU - Chen, Hsi-Chuan AU - Chuang, Ling AU - Qu, Guan-Zheng AU - Sederoff, Ronald R. AU - Chiang, Vincent L. T2 - NATURE PROTOCOLS DA - 2014/9// PY - 2014/9// DO - 10.1038/nprot.2014.147 VL - 9 IS - 9 SP - 2194-2205 SN - 1750-2799 ER - TY - JOUR TI - A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue AU - Li, Wei AU - Lin, Ying-Chung AU - Li, Quanzi AU - Shi, Rui AU - Lin, Chien-Yuan AU - Chen, Hao AU - Chuang, Ling AU - Qu, Guan-Zheng AU - Sederoff, Ronald R. AU - Chiang, Vincent L. T2 - NATURE PROTOCOLS DA - 2014/9// PY - 2014/9// DO - 10.1038/nprot.2014.146 VL - 9 IS - 9 SP - 2180-2193 SN - 1750-2799 ER - TY - JOUR TI - Tropical grassy biomes: misunderstood, neglected, and under threat AU - Parr, Catherine L. AU - Lehmann, Caroline E. R. AU - Bond, William J. AU - Hoffmann, William A. AU - Andersen, Alan N. T2 - TRENDS IN ECOLOGY & EVOLUTION AB - Tropical grassy biomes (TGBs) are globally extensive, provide critical ecosystem services, and influence the earth-atmosphere system. Yet, globally applied biome definitions ignore vegetation characteristics that are critical to their functioning and evolutionary history. Hence, TGB identification is inconsistent and misinterprets the ecological processes governing vegetation structure, with cascading negative consequences for biodiversity. Here, we discuss threats linked to the definition of TGB, the Clean Development Mechanism (CDM) and Reducing Emissions from Deforestation and Forest Degradation schemes (REDD+), and enhanced atmospheric CO2, which may facilitate future state shifts. TGB degradation is insidious and less visible than in forested biomes. With human reliance on TGBs and their propensity for woody change, ecology and evolutionary history are fundamental to not only the identification of TGBs, but also their management for future persistence. DA - 2014/4// PY - 2014/4// DO - 10.1016/j.tree.2014.02.004 VL - 29 IS - 4 SP - 205-213 SN - 1872-8383 KW - savanna KW - grassland KW - forest KW - REDD KW - CDM KW - atmospheric CO2 KW - biome shift ER - TY - JOUR TI - Size-dependent enhancement of water relations during post-fire resprouting AU - Schafer, Jennifer L. AU - Breslow, Bradley P. AU - Hollingsworth, Stephanie N. AU - Hohmann, Matthew G. AU - Hoffmann, William A. T2 - TREE PHYSIOLOGY AB - In resprouting species, fire-induced topkill causes a reduction in height and leaf area without a comparable reduction in the size of the root system, which should lead to an increase in the efficiency of water transport after fire. However, large plants undergo a greater relative reduction in size, compared with small plants, so we hypothesized that this enhancement in hydraulic efficiency would be greatest among large growth forms. In the ecotone between long-leaf pine (Pinus palustris Mill.) savannas and wetlands, we measured stomatal conductance (gs), mid-day leaf water potential (Ψleaf), leaf-specific whole-plant hydraulic conductance (KL.p), leaf area and height of 10 species covering a range of growth forms in burned and unburned sites. As predicted, KL.p was higher in post-fire resprouts than in unburned plants, and the post-fire increase in KL.p was positively related to plant size. Specifically, large-statured species tended to undergo the greatest relative reductions in leaf area and height, and correspondingly experienced the greatest increases in KL.p. The post-fire increase in KL.p was smaller than expected, however, due to a decrease in absolute root hydraulic conductance (i.e., not scaled to leaf area). The higher KL.p in burned sites was manifested as an increase in gs rather than an increase in Ψleaf. Post-fire increases in gs should promote high rates of photosynthesis for recovery of carbohydrate reserves and aboveground biomass, which is particularly important for large-statured species that require more time to recover their pre-fire size. DA - 2014/4// PY - 2014/4// DO - 10.1093/treephys/tpu015 VL - 34 IS - 4 SP - 404-414 SN - 1758-4469 KW - leaf area KW - leaf-specific whole-plant hydraulic conductance KW - mid-day leaf water potential KW - root hydraulic conductance KW - stem height KW - stomatal conductance ER - TY - JOUR TI - Novel functional roles for PERIANTHIA and SEUSS during floral organ identity specification, floral meristem termination, and gynoecial development AU - Wynn, A.N. AU - Seaman, A.A. AU - Jones, A.L. AU - Franks, Robert G. T2 - Frontiers in Plant Science AB - The gynoecium is the female reproductive structure of angiosperm flowers. In Arabidopsis thaliana the gynoecium is composed of two carpels fused into a tube-like structure. As the gynoecial primordium arises from the floral meristem, a specialized meristematic structure, the carpel margin meristem (CMM), develops from portions of the medial gynoecial domain. The CMM is critical for reproductive competence because it gives rise to the ovules, the precursors of the seeds. Here we report a functional role for the transcription factor PERIANTHIA (PAN) in the development of the gynoecial medial domain and the formation of ovule primordia that is revealed in aintegumenta (ant) pan and seuss (seu) pan double mutants. Additionally, enhanced disruptions of gynoecial morphology suggest that gynoecial patterning processes are disrupted in the seu pan double mutant. Previously, PAN was identified as a regulator of perianth organ number and as a direct activator of AGAMOUS expression in floral whorl four. However, the seu pan double mutants display enhanced ectopic AG expression in developing sepals and the partial transformation of sepals to petals indicating a novel role for PAN in the repression of AG in floral whorl 1. These results indicate that PAN functions as an activator or repressor of AG expression in a whorl specific fashion. The seu pan double mutants also display enhanced floral indeterminacy, resulting in the formation of “fifth whorl” structures and disruption of WUS expression patterns revealing a novel role for SEU in floral meristem termination. DA - 2014/// PY - 2014/// DO - 10.3389/fpls.2014.00130 VL - 5 IS - APR UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84901002654&partnerID=MN8TOARS KW - ovule KW - gynoecium KW - flowers KW - agamous KW - wuschel KW - organ identity KW - indeterminate growth ER - TY - JOUR TI - Methods for Cercospora coffeicola protoplast isolation and genetic transformation with the green fluorescent protein AU - Coelho Souza, Andre Gomes AU - Herrero, Sonia AU - Maffia, Luiz Antonio AU - Daub, Margaret Elizabeth T2 - EUROPEAN JOURNAL OF PLANT PATHOLOGY AB - Cercospora coffeicola is the causal agent of brown eye spot on coffee leaves. Although the disease has significant importance, few molecular studies have been done with C. coffeicola. Here we report a protocol for isolating protoplasts as well as development of a genetic transformation system using Green Fluorescent Protein. High yields of protoplasts (≈108/ml) were obtained from mycelial cultures from five isolates of C. coffeicola. One isolate was transformed with a vector encoding hygromycin resistance and Green Fluorescent Protein. Out of 43 hygromycin-resistant transformants obtained, Green Fluorescent Protein was highly expressed in one (2.3 %). DA - 2014/6// PY - 2014/6// DO - 10.1007/s10658-013-0301-9 VL - 139 IS - 2 SP - 235-238 SN - 1573-8469 KW - Brown eye spot KW - Coffea arabica L. KW - Leaf spot ER - TY - JOUR TI - Genetic aspects of auxin biosynthesis and its regulation AU - Brumos, Javier AU - Alonso, Jose M. AU - Stepanova, Anna N. T2 - PHYSIOLOGIA PLANTARUM AB - Auxin is an essential plant hormone that controls nearly every aspect of a plant's life, from embryo development to organ senescence. In the last decade the key genes involved in auxin transport, perception, signaling and response have been identified and characterized, but the elucidation of auxin biosynthesis has proven to be especially challenging. In plants, a significant amount of indole‐3‐acetic acid ( IAA ), the predominant biologically active form of auxin, is synthesized via a simple two‐step route where indole‐3‐pyruvic acid ( IPyA ) produced from l ‐tryptophan by tryptophan aminotransferases ( TAA1 / TAR ) is converted to IAA by the YUC family of flavin monooxygenases. The TAA1 / TAR and YUC gene families constitute the first complete auxin biosynthetic pathway described in plants. Detailed characterization of these genes' expression patterns suggested a key role of local auxin biosynthesis in plant development. This has prompted an active search for the molecular mechanisms that regulate the spatiotemporal activity of the IPyA route. In addition to the TAA1 / TAR and YUC ‐mediated auxin biosynthesis, several alternative routes of IAA production have been postulated to function in plants, but their biological significance is yet to be demonstrated. Herein, we take a genetic perspective to describe the current view of auxin biosynthesis and its regulation in plants, focusing primarily on Arabidopsis. DA - 2014/5// PY - 2014/5// DO - 10.1111/ppl.12098 VL - 151 IS - 1 SP - 3-12 SN - 1399-3054 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84898468296&partnerID=MN8TOARS ER - TY - JOUR TI - A maize root tip system to study DNA replication programmes in somatic and endocycling nuclei during plant development AU - Bass, Hank W. AU - Wear, Emily E. AU - Lee, Tae-Jin AU - Hoffman, Gregg G. AU - Gumber, Hardeep K. AU - Allen, George C. AU - Thompson, William F. AU - Hanley-Bowdoin, Linda T2 - JOURNAL OF EXPERIMENTAL BOTANY AB - The progress of nuclear DNA replication is complex in both time and space, and may reflect several levels of chromatin structure and 3-dimensional organization within the nucleus. To understand the relationship between DNA replication and developmental programmes, it is important to examine replication and nuclear substructure in different developmental contexts including natural cell-cycle progressions in situ. Plant meristems offer an ideal opportunity to analyse such processes in the context of normal growth of an organism. Our current understanding of large-scale chromosomal DNA replication has been limited by the lack of appropriate tools to visualize DNA replication with high resolution at defined points within S phase. In this perspective, we discuss a promising new system that can be used to visualize DNA replication in isolated maize (Zea mays L.) root tip nuclei after in planta pulse labelling with the thymidine analogue, 5-ethynyl-2'-deoxyuridine (EdU). Mixed populations of EdU-labelled nuclei are then separated by flow cytometry into sequential stages of S phase and examined directly using 3-dimensional deconvolution microscopy to characterize spatial patterns of plant DNA replication. Combining spatiotemporal analyses with studies of replication and epigenetic inheritance at the molecular level enables an integrated experimental approach to problems of mitotic inheritance and cellular differentiation. DA - 2014/6// PY - 2014/6// DO - 10.1093/jxb/ert470 VL - 65 IS - 10 SP - 2747-2756 SN - 1460-2431 KW - DNA replication KW - EdU KW - endocycle KW - flow cytometry KW - high-resolution microscopy KW - maize KW - mitotic cell cycle KW - root development KW - S phase ER - TY - JOUR TI - Regulation of anthocyanin biosynthesis in Arabidopsis thaliana red pap1-D cells metabolically programmed by auxins AU - Liu, Zhong AU - Shi, Ming-Zhu AU - Xie, De-Yu T2 - PLANTA DA - 2014/4// PY - 2014/4// DO - 10.1007/s00425-013-2011-0 VL - 239 IS - 4 SP - 765-781 SN - 1432-2048 KW - Anthocyanin biosynthesis KW - Arabidopsis thaliana KW - Auxins KW - Metabolic engineering KW - pap1-D cells KW - WBM complex KW - Regulation route ER - TY - JOUR TI - Isolation of Paenibacillus glucanolyticus from pulp mill sources with potential to deconstruct pulping waste AU - Mathews, Stephanie L. AU - Pawlak, Joel J. AU - Grunden, Amy M. T2 - BIORESOURCE TECHNOLOGY AB - Black liquor is a pulping waste generated by the kraft process that has potential for downstream bioconversion. A microorganism was isolated from a black liquor sample collected from the Department of Forest Biomaterials at North Carolina State University. The organism was identified as Paenibacillus glucanolyticus using 16S rRNA sequence analysis and was shown to be capable of growth on black liquor as the sole carbon source based on minimal media growth studies. Minimal media growth curves demonstrated that this facultative anaerobic microorganism can degrade black liquor as well as cellulose, hemicellulose, and lignin. Gas chromatography-mass spectrometry was used to identify products generated by P. glucanolyticus when it was grown anaerobically on black liquor. Fermentation products which could be converted into high-value chemicals such as succinic, propanoic, lactic, and malonic acids were detected. DA - 2014/7// PY - 2014/7// DO - 10.1016/j.biortech.2014.04.093 VL - 164 SP - 100-105 SN - 1873-2976 KW - Biodegradation (bacterial degradation) KW - Pulp mill waste KW - Black liquor KW - Lignin KW - Paenibacillus glucanolyticus ER - TY - JOUR TI - Evidence of population bottleneck in Astragalus michauxii (Fabaceae), a narrow endemic of the southeastern United States AU - Wall, W. A. AU - Douglas, N. A. AU - Hoffmann, W. A. AU - Wentworth, T. R. AU - Gray, J. B. AU - Xiang, Q. Y. J. AU - Knaus, B. K. AU - Hohmann AU - G., M. T2 - Conservation Genetics DA - 2014/2// PY - 2014/2// DO - 10.1007/s10592-013-0527-2 VL - 15 IS - 1 SP - 153-164 LA - en SN - 1566-0621, 1572-9737 UR - http://link.springer.com/10.1007/s10592-013-0527-2 DB - Crossref Y2 - 2019/1/29/ KW - Astragalus KW - Bottleneck KW - Endemism KW - Genetic diversity KW - Microsatellites KW - Pinus palustris ER - TY - JOUR TI - Development of NIRS models to predict composition of enzymatically processed sweetpotato AU - Diaz, Joscelin T. AU - Veal, Matthew W. AU - Chinn, Mari S. T2 - Industrial Crops and Products AB - This study was conducted to develop calibration models to predict the major constituents (moisture, protein, fiber, alcohol insoluble solids (AIS), and starch) of enzymatically processed sweetpotatoes using a non-destructive near-infrared spectroscopy (NIRS) technique. Prediction of these constituents is of interest since starch content can be used to estimate crop potential and efficiency of processing enzymes used to convert starch into valuable products needed for industrial applications. Wet chemistry procedures are expensive, laborious, and time consuming; however, NIRS is a reliable and fast tool that can be used to quantify components and identify composition changes occurring during sweetpotato processing. Freeze-dried samples of sweetpotato roots (clones: NC-413, DM02-180, and Covington) were scanned over the near infrared wavelengths at different stages of processing (unprocessed material, wet samples after liquefaction, and wet samples after saccharification) and chemically analyzed. Calibration models were established by Multiple Linear Regression (MLR) analysis and developed to predict moisture, AIS, protein, fiber, and starch content. Spectral range and the number of MLR factors were examined in a stepwise manner that yielded the lowest standard error of calibration (SEC) and highest correlation coefficient of determination (R2). Calibration models based on all sweetpotato clones adequately predicted moisture, AIS, and starch compounds in unprocessed and processed treatments. Protein was successfully predicted with 99% confidence for unprocessed material and an approximate quantitative prediction in processed treatments (R2 = 0.69). Fiber was predicted with 85% confidence for Covington sweetpotato and with 65% for both NC-413 and DM02-180 sweetpotato clones. Starch was successfully predicted with 91% and 97% confidence for unprocessed and processed treatments, respectively. Our results indicated that NIRS technique is a tool able to rapidly predict with reasonable accuracy the composition of different constituents present in sweetpotato samples before and during its processing to value-added products. DA - 2014/8// PY - 2014/8// DO - 10.1016/j.indcrop.2014.05.012 VL - 59 SP - 119-124 J2 - Industrial Crops and Products LA - en OP - SN - 0926-6690 UR - http://dx.doi.org/10.1016/j.indcrop.2014.05.012 DB - Crossref KW - Near-infrared spectroscopy (NIRS) KW - Ipomoea batatas KW - Hydrolysis KW - Starch KW - Protein KW - Fiber ER - TY - JOUR TI - Carbon accumulation and nitrogen pool recovery during transitions from savanna to forest in central Brazil AU - Pellegrini, Adam F. A. AU - Hoffmann, William A. AU - Franco, Augusto C. T2 - ECOLOGY AB - The expansion of tropical forest into savanna may potentially be a large carbon sink, but little is known about the patterns of carbon sequestration during transitional forest formation. Moreover, it is unclear how nutrient limitation, due to extended exposure to fire‐driven nutrient losses, may constrain carbon accumulation. Here, we sampled plots that spanned a woody biomass gradient from savanna to transitional forest in response to differential fire protection in central Brazil. These plots were used to investigate how the process of transitional forest formation affects the size and distribution of carbon (C) and nitrogen (N) pools. This was paired with a detailed analysis of the nitrogen cycle to explore possible connections between carbon accumulation and nitrogen limitation. An analysis of carbon pools in the vegetation, upper soil, and litter shows that the transition from savanna to transitional forest can result in a fourfold increase in total carbon (from 43 to 179 Mg C/ha) with a doubling of carbon stocks in the litter and soil layers. Total nitrogen in the litter and soil layers increased with forest development in both the bulk (+68%) and plant‐available (+150%) pools, with the most pronounced changes occurring in the upper layers. However, the analyses of nitrate concentrations, nitrate : ammonium ratios, plant stoichiometry of carbon and nitrogen, and soil and foliar nitrogen isotope ratios suggest that a conservative nitrogen cycle persists throughout forest development, indicating that nitrogen remains in low supply relative to demand. Furthermore, the lack of variation in underlying soil type (>20 cm depth) suggests that the biogeochemical trends across the gradient are driven by vegetation. Our results provide evidence for high carbon sequestration potential with forest encroachment on savanna, but nitrogen limitation may play a large and persistent role in governing carbon sequestration in savannas or other equally fire‐disturbed tropical landscapes. In turn, the link between forest development and nitrogen pool recovery creates a framework for evaluating potential positive feedbacks on savanna–forest boundaries. DA - 2014/2// PY - 2014/2// DO - 10.1890/13-0290.1 VL - 95 IS - 2 SP - 342-352 SN - 1939-9170 KW - Carbon sequestration KW - cerrado KW - fire KW - nitrogen limitation KW - savanna biogeochemistry KW - savanna-forest boundary KW - tropical ecosystem recovery ER - TY - JOUR TI - Biotechnological applications of halophilic lipases and thioesterases AU - Schreck, Steven D. AU - Grunden, Amy M. T2 - APPLIED MICROBIOLOGY AND BIOTECHNOLOGY DA - 2014/2// PY - 2014/2// DO - 10.1007/s00253-013-5417-5 VL - 98 IS - 3 SP - 1011-1021 SN - 1432-0614 KW - Lipase KW - Thioesterase KW - Halophilic KW - Halotolerant KW - Biofuel KW - Algae KW - Dunaliella ER - TY - JOUR TI - A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students AU - Jordan, T.C. AU - Burnett, S.H. AU - Carson, S. AU - Caruso, S.M. AU - Clase, K AU - DeJong, R.J. AU - Dennehy, J.J. AU - Denver, D.R. AU - Dunbar, D. AU - Elgin, S.R. AU - Findley, A.M. AU - Gissendanner, C.R. AU - Golebiewska, U.P. AU - Guild, N. AU - Hartzog, G.A. AU - Grillo, W.H. AU - Hollowell, G.P. AU - Hughes, L.E. AU - Johnson, A. AU - King, R.A. AU - Lewis, L.O. AU - Li, W. AU - Rosenzweig, F. AU - Rubin, M.R. AU - Saha, M.S. AU - Sandoz, J. AU - Shaffer, C.D. AU - Taylor, B. AU - Temple, L. AU - Vazquez, E. AU - Ware, V.C. AU - Barker, L.P. AU - Bradley, K.W. AU - Jacobs-Sera, D. AU - Pope, W.H. AU - Russell, D.A. AU - Cresawn, S.G. AU - Lopatto, D. AU - Bailey, C.P. AU - Hatfull, G.F. T2 - mBio AB - Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students' interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training.Engagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome annotation, and comparative genomics, with strong impacts on bacteriophage research, increased persistence in STEM fields, and student self-identification with learning gains, motivation, attitude, and career aspirations. DA - 2014/// PY - 2014/// DO - 10.1128/mbio.01051-13 VL - 5 IS - 1 SP - e01051–13 SN - 2150-7511 ER - TY - JOUR TI - Vegetative Impact of Feral Horses, Feral Pigs, and White-tailed Deer on the Currituck National Wildlife Refuge, North Carolina AU - Porter, Kimberly M. AU - DePerno, Christopher S. AU - Krings, Alexander AU - Krachey, Matthew AU - Braham, Richard T2 - CASTANEA AB - The Currituck National Wildlife Refuge (CNWR) in North Carolina is inhabited by feral horses (Equus caballus), feral pigs (Sus scrofa), and white-tailed deer (Odocoileus virginianus). The impact of these species on the vegetation of CNWR is unknown. To assess impact, we created two replicate exclosure plots within maritime forests, brackish marshes, and maritime grasslands. An electric fence divided each habitat into two sections: including or excluding horses. On each side of the electric fence within each habitat, we sampled three different 5 × 5 m plots (i.e., 36 plots). The first was a fenced exclosure 3 m high, the second a fenced exclosure raised 1 m above the ground and extended to 3 m, and the third, a control, was not fenced. Within plots, we created two 1 m transects, and randomly selected and tagged grasses, forbs, shrubs, and trees. We measured the distances from base to tip of herbs and from branching point to terminal bud in shrubs. We used a linear model to analyze plant growth rate. We used a length ratio adjusted by the number of days as the response variable. Out of 1,105 tagged plants, we detected 87 disturbances; 80 where horses were present and 7 where horses were excluded. Overall, horses were responsible for 84% of disturbances. Most disturbances occurred in brackish marshes on Schoenoplectus pungens. We detected a significant effect of exclosure treatment on plant growth rate where horses were present (p = 0.035), but not where they were excluded (p = 0.32). DA - 2014/3// PY - 2014/3// DO - 10.2179/13-037 VL - 79 IS - 1 SP - 8-17 SN - 1938-4386 KW - Currituck National Wildlife Refuge KW - feral horses KW - feral pigs KW - habitat conservation KW - normative wildlife KW - vegetation impacts KW - white-tailed deer KW - wildlife conservation ER - TY - JOUR TI - Systems analysis of auxin transport in the arabidopsis root apex AU - Band, L. R. AU - Wells, D. M. AU - Fozard, J. A. AU - Ghetiu, T. AU - French, A. P. AU - Pound, M. P. AU - Wilson, M. H. AU - Yu, L. AU - Li, W. D. AU - Hijazi, H. I. AU - Oh, J. AU - Pearce, S. P. AU - Perez-Amador, M. A. AU - Yun, J. AU - Kramer, E. AU - Alonso, J. M. AU - Godin, C. AU - Vernoux, T. AU - Hodgman, T. C. T2 - Plant Cell DA - 2014/// PY - 2014/// VL - 26 IS - 3 SP - 862-875 ER - TY - JOUR TI - Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines AU - Huang, W. AU - Massouras, A. AU - Inoue, Y. AU - Peiffer, J. AU - Ramia, M. AU - Tarone, A. M. AU - Turlapati, L. AU - Zichner, T. AU - Zhu, D. H. AU - Lyman, R. F. AU - Magwire, M. M. AU - Blankenburg, K. AU - Carbone, M. A. AU - Chang, K. AU - Ellis, L. L. AU - Fernandez, S. AU - Han, Y. AU - Highnam, G. T2 - Genome Research DA - 2014/// PY - 2014/// VL - 24 IS - 7 SP - 1193-1208 ER - TY - JOUR TI - In Vivo Mapping of Arabidopsis Scaffold/Matrix Attachment Regions Reveals Link to Nucleosome-Disfavoring Poly(dA:dT) Tracts AU - Pascuzzi, Pete E. AU - Flores-Vergara, Miguel A. AU - Lee, Tae-Jin AU - Sosinski, Bryon AU - Vaughn, Matthew W. AU - Hanley-Bowdoin, Linda AU - Thompson, William F. AU - Allen, George C. T2 - PLANT CELL AB - Scaffold or matrix attachment regions (S/MARs) are found in all eukaryotes. The pattern of distribution and genomic context of S/MARs is thought to be important for processes such as chromatin organization and modulation of gene expression. Despite the importance of such processes, much is unknown about the large-scale distribution and sequence content of S/MARs in vivo. Here, we report the use of tiling microarrays to map 1358 S/MARs on Arabidopsis thaliana chromosome 4 (chr4). S/MARs occur throughout chr4, spaced much more closely than in the large plant and animal genomes that have been studied to date. Arabidopsis S/MARs can be divided into five clusters based on their association with other genomic features, suggesting a diversity of functions. While some Arabidopsis S/MARs may define structural domains, most occur near the transcription start sites of genes. Genes associated with these S/MARs have an increased probability of expression, which is particularly pronounced in the case of transcription factor genes. Analysis of sequence motifs and 6-mer enrichment patterns show that S/MARs are preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation, and the majority of S/MARs contain at least one nucleosome-depleted region. This global view of S/MARs provides a framework to begin evaluating genome-scale models for S/MAR function. DA - 2014/1// PY - 2014/1// DO - 10.1105/tpc.113.121194 VL - 26 IS - 1 SP - 102-120 SN - 1532-298X ER - TY - JOUR TI - A new species and a new combination in Phaeostemma (Apocynaceae, Asclepiadoideae, Gonolobinae) AU - Morillo, Gilberto AU - Krings, Alexander T2 - PHYTOKEYS AB - Phaeostemma surinamensis Morillo & Krings, sp. nov., anew species of Apocynaceae (Asclepiadoideae, Gonolobinae) is described and illustrated, and the new combination Phaeostemma fucata (Woodson) Morillo & Krings, comb. nov., is made. The new species, known only from a lowland wet forest of Suriname, seems to be closely related to Phaeostemma fucata, which is an endemic to Ptari-tepui, a sandstone mountain in the southeastern edge of the Venezuelan Guayana. DA - 2014/// PY - 2014/// DO - 10.3897/phytokeys.33.6453 VL - 33 SP - 41-50 SN - 1314-2003 KW - Climbing milkweeds KW - Matelea KW - Suriname KW - Venezuela ER - TY - JOUR TI - RNAi silencing of a cytochrome P450 monoxygenase disrupts the ability of a filamentous fungus, Graphium sp., to grow on short-chain gaseous alkanes and ethers AU - Trippe, Kristin M. AU - Wolpert, Thomas J. AU - Hyman, Michael R. AU - Ciuffetti, Lynda M. T2 - Biodegradation DA - 2014/2// PY - 2014/2// DO - 10.1007/s10532-013-9646-1 VL - 25 IS - 1 SP - 137-151 J2 - Biodegradation LA - eng SN - 1572-9729 DB - PubMed KW - Fungi KW - Alkane oxidation KW - Tetrahydrofuran KW - Cometabolism KW - Cytochrome P450 ER - TY - JOUR TI - Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3 AU - Losada, Liliana AU - Pakala, Suman B. AU - Fedorova, Natalie D. AU - Joardar, Vinita AU - Shabalina, Svetlana A. AU - Hostetler, Jessica AU - Pakala, Suchitra M. AU - Zafar, Nikhat AU - Thomas, Elizabeth AU - Rodriguez-Carres, Marianela AU - Dean, Ralph AU - Vilgalys, Rytas AU - Nierman, William C. AU - Cubeta, Marc A. T2 - FEMS MICROBIOLOGY LETTERS AB - The soil fungus Rhizoctonia solani is an economically important pathogen of agricultural and forestry crops. Here, we present the complete sequence and analysis of the mitochondrial genome of R. solani, field isolate Rhs1AP. The genome (235 849 bp) is the largest mitochondrial genome of a filamentous fungus sequenced to date and exhibits a rich accumulation of introns, novel repeat sequences, homing endonuclease genes, and hypothetical genes. Stable secondary structures exhibited by repeat sequences suggest that they comprise functional, possibly catalytic RNA elements. RNA-Seq expression profiling confirmed that the majority of homing endonuclease genes and hypothetical genes are transcriptionally active. Comparative analysis suggests that the mitochondrial genome of R. solani is an example of a dynamic history of expansion in filamentous fungi. DA - 2014/3// PY - 2014/3// DO - 10.1111/1574-6968.12387 VL - 352 IS - 2 SP - 165-173 SN - 1574-6968 KW - Basidiomycota KW - homing endonucleases KW - repetitive elements ER - TY - JOUR TI - Homotypic Vacuole Fusion Requires VTI11 and Is Regulated by Phosphoinositides AU - Zheng, Jiameng AU - Han, Sang Won AU - Rodriguez-Welsh, Maria Fernanda AU - Rojas-Pierce, Marcela T2 - MOLECULAR PLANT AB - Most plant cells contain a large central vacuole that is essential to maintain cellular turgor. We report a new mutant allele of VTI11 that implicates the SNARE protein VTI11 in homotypic fusion of protein storage and lytic vacuoles. Fusion of the multiple vacuoles present in vti11 mutants could be induced by treatment with Wortmannin and LY294002, which are inhibitors of Phosphatidylinositol 3-Kinase (PI3K). We provide evidence that Phosphatidylinositol 3-Phosphate (PtdIns(3)P) regulates vacuole fusion in vti11 mutants, and that fusion of these vacuoles requires intact microtubules and actin filaments. Finally, we show that Wortmannin also induced the fusion of guard cell vacuoles in fava beans, where vacuoles are naturally fragmented after ABA-induced stomata closure. These results suggest a ubiquitous role of phosphoinositides in vacuole fusion, both during the development of the large central vacuole and during the dynamic vacuole remodeling that occurs as part of stomata movements. DA - 2014/6// PY - 2014/6// DO - 10.1093/mp/ssu019 VL - 7 IS - 6 SP - 1026-1040 SN - 1752-9867 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84907579328&partnerID=MN8TOARS KW - vacuole KW - SNARE KW - phosphoinositides KW - membrane fusion KW - Wortmannin ER - TY - JOUR TI - Fixating on metals: new insights into the role of metals in nodulation and symbiotic nitrogen fixation AU - Gonzalez-Guerrero, Manuel AU - Matthiadis, Anna AU - Saez, Angela AU - Long, Terri A. T2 - FRONTIERS IN PLANT SCIENCE AB - Symbiotic nitrogen fixation is one of the most promising and immediate alternatives to the overuse of polluting nitrogen fertilizers for improving plant nutrition. At the core of this process are a number of metalloproteins that catalyze and provide energy for the conversion of atmospheric nitrogen to ammonia, eliminate free radicals produced by this process, and create the microaerobic conditions required by these reactions. In legumes, metal cofactors are provided to endosymbiotic rhizobia within root nodule cortical cells. However, low metal bioavailability is prevalent in most soils types, resulting in widespread plant metal deficiency and decreased nitrogen fixation capabilities. As a result, renewed efforts have been undertaken to identify the mechanisms governing metal delivery from soil to the rhizobia, and to determine how metals are used in the nodule and how they are recycled once the nodule is no longer functional. This effort is being aided by improved legume molecular biology tools (genome projects, mutant collections, and transformation methods), in addition to state-of-the-art metal visualization systems. DA - 2014/2/13/ PY - 2014/2/13/ DO - 10.3389/fpls.2014.00045 VL - 5 IS - FEB SP - SN - 1664-462X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84901021951&partnerID=MN8TOARS KW - symbiotic nitrogen fixation (SNF) KW - metals KW - legume KW - rhizobia KW - nodule KW - iron KW - zinc KW - copper ER - TY - JOUR TI - Adaptive and nonadaptive genome size evolution in Karst endemic flora of China AU - Kang, Ming AU - Tao, Junjie AU - Wang, Jing AU - Ren, Chen AU - Qi, Qingwen AU - Xiang, Qiu-Yun AU - Huang, Hongwen T2 - New Phytologist AB - Summary Genome size variation is of fundamental biological importance and has been a longstanding puzzle in evolutionary biology. Several hypotheses for genome size evolution including neutral, maladaptive, and adaptive models have been proposed, but the relative importance of these models remains controversial. Primulina is a genus that is highly diversified in the Karst region of southern China, where genome size variation and the underlying evolutionary mechanisms are poorly understood. We reconstructed the phylogeny of Primulina using DNA sequences for 104 species and determined the genome sizes of 101 species. We examined the phylogenetic signal in genome size variation, and tested the fit to different evolutionary models and for correlations with variation in latitude and specific leaf area ( SLA ). The results showed that genome size, SLA and latitudinal variation all displayed strong phylogenetic signals, but were best explained by different evolutionary models. Furthermore, significant positive relationships were detected between genome size and SLA and between genome size and latitude. Our study is the first to investigate genome size evolution on such a comprehensive scale and in the Karst region flora. We conclude that genome size in Primulina is phylogenetically conserved but its variation among species is a combined outcome of both neutral and adaptive evolution. DA - 2014/2/17/ PY - 2014/2/17/ DO - 10.1111/nph.12726 VL - 202 IS - 4 SP - 1371-1381 J2 - New Phytol LA - en OP - SN - 0028-646X UR - http://dx.doi.org/10.1111/nph.12726 DB - Crossref KW - chromosome number KW - correlated evolution KW - flow cytometry KW - genome size evolution KW - Karst flora KW - phylogeny-based comparative analysis KW - Primulina KW - specific leaf area ER - TY - JOUR TI - Chemically Induced Conditional Rescue of the Reduced Epidermal Fluorescence8 Mutant of Arabidopsis Reveals Rapid Restoration of Growth and Selective Turnover of Secondary Metabolite Pools AU - Kim, Jeong Im AU - Ciesielski, Peter N. AU - Donohoe, Bryon S. AU - Chapple, Clint AU - Li, Xu T2 - PLANT PHYSIOLOGY AB - The phenylpropanoid pathway is responsible for the biosynthesis of diverse and important secondary metabolites including lignin and flavonoids. The reduced epidermal fluorescence8 (ref8) mutant of Arabidopsis (Arabidopsis thaliana), which is defective in a lignin biosynthetic enzyme p-coumaroyl shikimate 3′-hydroxylase (C3′H), exhibits severe dwarfism and sterility. To better understand the impact of perturbation of phenylpropanoid metabolism on plant growth, we generated a chemically inducible C3′H expression construct and transformed it into the ref8 mutant. Application of dexamethasone to these plants greatly alleviates the dwarfism and sterility and substantially reverses the biochemical phenotypes of ref8 plants, including the reduction of lignin content and hyperaccumulation of flavonoids and p-coumarate esters. Induction of C3′H expression at different developmental stages has distinct impacts on plant growth. Although early induction effectively restored the elongation of primary inflorescence stem, application to 7-week-old plants enabled them to produce new rosette inflorescence stems. Examination of hypocotyls of these plants revealed normal vasculature in the newly formed secondary xylem, presumably restoring water transport in the mutant. The ref8 mutant accumulates higher levels of salicylic acid than the wild type, but depletion of this compound in ref8 did not relieve the mutant’s growth defects, suggesting that the hyperaccumulation of salicylic acid is unlikely to be responsible for dwarfism in this mutant. DA - 2014/2// PY - 2014/2// DO - 10.1104/pp.113.229393 VL - 164 IS - 2 SP - 584-595 SN - 1532-2548 ER - TY - JOUR TI - Savanna vegetation-fire-climate relationships differ among continents AU - Lehmann, C. E. R. AU - Anderson, T. M. AU - Sankaran, M. AU - Higgins, S. I. AU - Archibald, S. AU - Hoffmann, W. A. AU - Hanan, N. P. AU - Williams, R. J. AU - Fensham, R. J. AU - Felfili, J. AU - Hutley, L. B. AU - Ratnam, J. AU - San Jose, J. AU - Montes, R. AU - Franklin, D. AU - Russell-Smith, J. T2 - Science DA - 2014/// PY - 2014/// VL - 343 IS - 6170 SP - 548-552 ER - TY - JOUR TI - Postembryonic control of root meristem growth and development AU - Sozzani, Rosangela AU - Iyer-Pascuzzi, Anjali T2 - CURRENT OPINION IN PLANT BIOLOGY AB - Organ development in multicellular organisms is dependent on the proper balance between cell proliferation and differentiation. In the Arabidopsis root apical meristem, meristem growth is the result of cell divisions in the proximal meristem and cell differentiation in the elongation and differentiation zones. Hormones, transcription factors and small peptides underpin the molecular mechanisms governing these processes. Computer modeling has aided our understanding of the dynamic interactions involved in stem cell maintenance and meristem activity. Here we review recent advances in our understanding of postembryonic root stem cell maintenance and control of meristem size. DA - 2014/2// PY - 2014/2// DO - 10.1016/j.pbi.2013.10.005 VL - 17 SP - 7-12 SN - 1879-0356 ER -