TY - JOUR TI - Methanocella conradii sp. nov., a Thermophilic, Obligate Hydrogenotrophic Methanogen, Isolated from Chinese Rice Field Soil AB - Methanocellales contributes significantly to anthropogenic methane emissions that cause global warming, but few pure cultures for Methanocellales are available to permit subsequent laboratory studies (physiology, biochemistry, etc.).By combining anaerobic culture and molecular techniques, a novel thermophilic methanogen, strain HZ254(T) was isolated from a Chinese rice field soil located in Hangzhou, China. The phylogenetic analyses of both the 16S rRNA gene and mcrA gene (encoding the α subunit of methyl-coenzyme M reductase) confirmed its affiliation with Methanocellales, and Methanocella paludicola SANAE(T) was the most closely related species. Cells were non-motile rods, albeit with a flagellum, 1.4-2.8 µm long and by 0.2-0.3 µm in width. They grew at 37-60 °C (optimally at 55 °C) and salinity of 0-5 g NaCl l(-1) (optimally at 0-1 g NaCl l(-1)). The pH range for growth was 6.4-7.2 (optimum 6.8). Under the optimum growth condition, the doubling time was 6.5-7.8 h, which is the shortest ever observed in Methanocellales. Strain HZ254(T) utilized H(2)/CO(2) but not formate for growth and methane production. The DNA G+C content of this organism was 52.7 mol%. The sequence identities of 16S rRNA gene and mcrA gene between strain HZ254(T) and SANAE(T) were 95.0 and 87.5% respectively, and the genome based Average Nucleotide Identity value between them was 74.8%. These two strains differed in phenotypic features with regard to substrate utilization, possession of a flagellum, doubling time (under optimal conditions), NaCl and temperature ranges. Taking account of the phenotypic and phylogenetic characteristics, we propose strain HZ254(T) as a representative of a novel species, Methanocella conradii sp. nov. The type strain is HZ254(T) ( = CGMCC 1.5162(T) = JCM 17849(T) = DSM 24694(T)).Strain HZ254(T) could potentially serve as an excellent laboratory model for studying Methanocellales due to its fast growth and consistent cultivability. DA - 2012/// PY - 2012/// DO - 10.1371/journal.pone.0035279 ER - TY - JOUR TI - Complete Genome Sequence of a Thermophilic Methanogen, Methanocella conradii HZ254, Isolated from Chinese Rice Field Soil AU - Lu, Z. AU - Lu, Y. T2 - Journal of Bacteriology AB - ABSTRACT Members of the order Methanocellales play a key role in methane emissions in paddy fields. Because of their slow growth and fastidious culture conditions, pure cultures are difficult to isolate and have been unavailable until recently. Here we report the complete genome sequence of a novel isolate in this group, Methanocella conradii strain HZ254. DA - 2012/// PY - 2012/// DO - 10.1128/jb.00207-12 VL - 194 IS - 9 SP - 2398-2399 ER - TY - JOUR TI - Grappling with Proteus: population level approaches to understanding microbial diversity AU - Choudoir, Mallory J AU - Campbell, Ashley N AU - Buckley, Daniel H T2 - Frontiers in microbiology DA - 2012/// PY - 2012/// VL - 3 SP - 336 ER - TY - JOUR TI - Meiotic prophase requires proteolysis of m phase regulators mediated by the meiosis-specific APC/CAma1 AU - Okaz, E. AU - Argüello-Miranda, O. AU - Bogdanova, A. AU - Vinod, P.K. AU - Lipp, J.J. AU - Markova, Z. AU - Zagoriy, I. AU - Novak, B. AU - Zachariae, W. T2 - Cell AB - Whereas proliferating cells enter M phase shortly after DNA replication, the first M phase of meiosis is preceded by an extended prophase in which homologous chromosomes undergo recombination. Exit from prophase I is controlled by the recombination checkpoint (RC), which, in yeast, represses the meiosis-specific transcription factor Ndt80 required for the expression of B-type cyclins and other M phase regulators. We show that an extended prophase I additionally requires the suppression of latent, mitotic cell-cycle controls by the anaphase-promoting complex (APC/C) and its meiosis-specific activator Ama1, which trigger the degradation of M phase regulators and Ndd1, a subunit of a mitotic transcription factor. ama1Δ mutants exit from prophase I prematurely and independently of the RC, which results in recombination defects and chromosome missegregation. Thus, control of prophase I by meiotic mechanisms depends on the suppression of the alternative, mitotic mechanisms by a meiosis-specific form of the APC/C. DA - 2012/// PY - 2012/// DO - 10.1016/j.cell.2012.08.044 VL - 151 IS - 3 SP - 603-618 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84868033744&partnerID=MN8TOARS ER - TY - CONF TI - Investigation of sclerotial morphogenesis in the soil fungus Rhizoctonia solani AU - Thomas, E. AU - Taylor, N. AU - Figueroa-Contreras, M. AU - Zhang, Z. AU - Ivors, K.L. AU - Cubeta, M.A. T2 - Mycological Society Annual Meeting C2 - 2012/// CY - Yale University, New Haven, CT DA - 2012/// PY - 2012/// ER - TY - JOUR TI - Self-pollinated Artemisia annua plants form a new platform to understand artemisinin biosynthesis AU - Xie, D.Y. AU - Alejos-Gonzalez, F. AU - Qu, G. T2 - Pharmaceutical Biology DA - 2012/// PY - 2012/// VL - 50 IS - 5 SP - 662–662 ER - TY - JOUR TI - Discovery of Hydrocotyle bowlesioides (Araliaceae) in Louisiana AU - Thornhill, R.W. AU - Krings, A. T2 - Journal of the Botanical Research Institute of Texas DA - 2012/// PY - 2012/// VL - 6 IS - 1 SP - 283–285 ER - TY - CONF TI - Programming and reprogramming of gene expression: Mechanisms of cellular specific metabolisms? AU - Xie, D.Y. AU - Shi, M.Z. T2 - 51st Annual Meeting of the Phytochemical Society of North America C2 - 2012/// C3 - Pharmaceutical Biology CY - University of Western Ontario, London, Ontario, Canada DA - 2012/// PY - 2012/8/11/ VL - 50 SP - 1356–1356 M1 - 11 ER - TY - CHAP TI - Comparative Metabolomics of Transgenic Tobacco Plants (Nicotiana tabacum var. Xanthi) Reveals Differential Effects of Engineered Complete and Incomplete Flavonoid Pathways on the Metabolome AU - Broeckling, Corey D. AU - Li, Ke-Gang AU - Xie, De-Yu T2 - Transgenic Plants - Advances and Limitations A2 - Çiftçi, Yelda Ozden AB - Anthocyanins and proanthocyanidins (PAs) are two groups of end products of the plant flavonoid pathway (Fig. 1). Biochemical and genetic evidences have demonstrated that they share the same upstream pathway beginning with phenylalanine through a series of enzymatic reaction to anthocyanidins. Anthocyanidins are either modified by glycosylation, methylation, or other reactions to form diverse anthocyanins (Springob et al. 2003) or catalyzed into flavan-3-ols by an anthocyanidin reductase (ANR) (Xie et al. 2003; Xie et al. 2006). In addition, leucoanthocyanidin reductase (LAR) has been enzymatically demonstrated to catalyze leucoanthocyanidins into catechin (Tanner et al. 2003). To date, whether or not this branch catalyzed by LAR exists in plants still remains open to genetic studies. PY - 2012/3/7/ DO - 10.5772/32872 PB - InTech SN - 9789535101819 UR - http://dx.doi.org/10.5772/32872 ER - TY - JOUR TI - Plant Sex and Induced Responses Independently Influence Herbivore Performance, Natural Enemies and Aphid-Tending Ants AU - Mooney, Kailen A. AU - Fremgen, Aleshia AU - Petry, William K. T2 - Arthropod-Plant Interactions DA - 2012/12// PY - 2012/12// DO - 10.1007/s11829-012-9204-5 VL - 6 IS - 4 SP - 553-560 KW - Ant-aphid interactions KW - Dioecy KW - Indirect defense KW - Induced defense KW - Natural enemies KW - Parasitoids KW - Slow-growth/high-mortality hypothesis KW - Sexual dimorphism KW - Valeriana edulis ER - TY - JOUR TI - Influence of Macronutrient Imbalance on Native Ant Foraging and Interspecific Interactions in the Field AU - Petry, William K. AU - Perry, Kayla I. AU - Mooney, Kailen A. T2 - Ecological Entomology AB - 1. Ants interact with a diversity of organisms. These interactions, coupled with their abundance, cause ants to have ecologically important effects across multiple trophic levels. 2. Empirical study of ant nutritional ecology has led to the prediction that a macronutrient imbalance will affect ant behaviour and interspecific interactions that underlie these broad‐scale effects. Excess carbohydrate relative to protein is predicted to increase ant aggressiveness, predatory tendency and foraging activity, and to decrease collection of hemipteran honeydew and plant nectar. 3. In field experiments conducted in 2009 and 2010, captive colony fragments of a native ant, Formica podzolica (Hymenoptera: Formicidae), were provided with either simulated prey or carbohydrate solution ad libitum . Foraging behaviours and interactions with flowers, myrmecophilous aphids and aphid natural enemies on wild‐grown plants were documented. 4. Strong effects of macronutrient imbalance on foraging manifested quickly and consistently across colonies; in accordance with predictions, prey‐fed foragers collected both honeydew and floral nectar, whereas carbohydrate‐fed ants ceased collecting these resources. Counter to predictions, carbohydrate‐fed ants dramatically lowered their activity levels and did not prey upon aphids. 5. Ants had no effect on aphid enemies in 2009, when the latter were relatively rare, but decreased their abundance in 2010. Despite this protection, the net effect of ants on aphids was negative (measured only in 2009). Prey‐fed ants demonstrated a strong preference for honeydew over floral nectar, thus demonstrating that a macronutrient imbalance may lead to different interactions with similar resources. 6. This study links ant nutrition and community ecology by demonstrating the rapid, asymmetric and multitrophic consequences of nutritionally mediated behaviour. DA - 2012/6// PY - 2012/6// DO - 10.1111/j.1365-2311.2012.01349.x VL - 37 IS - 3 SP - 175-183 KW - Ant-aphid interaction KW - ant behaviour KW - Aphis valerianae KW - Formica podzolica KW - nutrient imbalance KW - nutritional ecology KW - Valeriana edulis ER - TY - JOUR TI - Integration of GC-MS Based Non-Targeted Metabolic Profiling with Headspace Solid Phase Microextraction Enhances the Understanding of Volatile Differentiation in Tobacco Leaves from North Carolina, India and Brazil AU - Ma, Dong-Ming AU - Gandra, Saiprasad V. S. AU - Sharma, Navin AU - Xie, De-Yu T2 - American Journal of Plant Sciences AB - In this report, gas chromatography-mass spectrometry (GC-MS) based non-targeted metabolomics is used to develop appropriate headspace solid phase microextractions (HS-SPME) to enhance the understanding of volatile complexity of flue-cured tobacco leaves. Non-targeted metabolic profiling of GC-MS shows that the extraction condition of HS-SPME at 100?C for 30 min provides a better metabolite profile than other extraction conditions tested. GC-MS and principal component analyses (PCA) show that among five types of fibers tested, 100 μm polydimethylsiloxane (PMDS), 65 μm polydimethylsiloxane/divinylbenzene (PMDS/DVB) and 75 μm carboxen/polydimethylsiloxane (CAR/ PMS) provide a better reproducible metabolite profile. Based on an appropriate PDMS extraction condition optimized, we use GC-MS analysis and PCA to compare metabolite profiles in flue-cured leaves of tobacco plants grown in North Carolina, India and Brazil, respectively. The resulting data of PCA show that the global metabolic profiles in North Carolina samples are separated from those in Brazil and India samples, two groups of which are characterized by a partially overlapped pattern. Several peaks that were differentially accumulated in samples were annotated to known metabolites by deconvolution analysis, such as norsolanadione, solavetivone and rishtin. Norsolanadione is detected only in Brazil samples. Solavetivone is detected in samples of India and Brazil but not in those of North Carolina. Rishtin is detected in samples of North Carolina and India but not in Brazil samples. These data indicate that not only can a non-targeted metabolic profiling approach enhance the understanding of volatile complexity, but also can identify marker volatile metabolites in tobacco leaves produced in different growth regions. DA - 2012/// PY - 2012/// DO - 10.4236/ajps.2012.312215 VL - 03 IS - 12 SP - 1759-1769 J2 - AJPS OP - SN - 2158-2742 2158-2750 UR - http://dx.doi.org/10.4236/ajps.2012.312215 DB - Crossref ER - TY - JOUR TI - Differentiation of programmed Arabidopsis cells AU - Xie, De-Yu AU - Shi, Ming-Zhu T2 - Bioengineered AB - Plants express genes that encode enzymes that catalyse reactions to form plant secondary metabolites in specific cell types. However, the mechanisms of how plants decide their cellular metabolic fate and how cells diversify and specialise their specific secondary metabolites remains largely unknown. Additionally, whether and how an established metabolic program impacts genome-wide reprogramming of plant gene expression is unclear. We recently isolated PAP1-programmed anthocyanin-producing (red) and -free (white) cells from Arabidopsis thaliana; our previous studies have indicated that the PAP1 expression level is similar between these two different cell types. Transcriptional analysis showed that the red cells contain the TTG1-GL3/TT8-PAP1 regulatory complex, which controls anthocyanin biosynthesis; in contrast, the white cells and the wild-type cells lack this entire complex. These data indicate that different regulatory programming underlies the different metabolic states of these cells. In addition, our previous transcriptomic comparison indicated that there is a clear difference in the gene expression profiles of the red and wild-type cells, which is probably a consequence of cell-specific reprogramming. Based on these observations, in this report we discuss the potential mechanisms that underlie the programming and reprogramming of gene expression involved in anthocyanin biosynthesis. DA - 2012/1// PY - 2012/1// DO - 10.4161/bbug.3.1.17786 VL - 3 IS - 1 SP - 54-59 J2 - Bioengineered LA - en OP - SN - 2165-5979 2165-5987 UR - http://dx.doi.org/10.4161/bbug.3.1.17786 DB - Crossref KW - Arabidopsis thaliana KW - anthocyanin KW - PAP1 KW - metabolic KW - engineering KW - metabolic fate KW - plant secondary metabolism ER - TY - JOUR TI - Convergent and divergent evolution of metabolism in sulfur-oxidizing symbionts and the role of horizontal gene transfer AU - Kleiner, Manuel AU - Petersen, Jillian M AU - Dubilier, Nicole T2 - Current Opinion in Microbiology AB - Symbioses between marine invertebrates and autotrophic sulfur-oxidizing bacteria have evolved from multiple lineages within the Gammaproteobacteria in a striking example of convergent evolution. These GammaSOX symbionts all perform the same basic function: they provide their hosts with nutrition through the fixation of CO2 into biomass using reduced sulfur compounds as an energy source. However, our review of recent –omics based studies and genome mining for this study revealed that the GammaSOX symbionts diverge in many other metabolic capabilities and functions, and we show how these divergences could reflect adaptations to different hosts and habitat conditions. Our phylogenetic analyses of key metabolic genes in GammaSOX symbionts revealed that these differed markedly from 16S rRNA phylogenies. We hypothesize that horizontal gene transfer (HGT) would explain many of these incongruencies, and conclude that HGT may have played a significant role in shaping the metabolic evolution of GammaSOX symbionts. DA - 2012/10// PY - 2012/10// DO - 10.1016/j.mib.2012.09.003 VL - 15 IS - 5 SP - 621-631 J2 - Current Opinion in Microbiology LA - en OP - SN - 1369-5274 UR - http://dx.doi.org/10.1016/j.mib.2012.09.003 DB - Crossref ER - TY - JOUR TI - Epistasis dominates the genetic architecture of Drosophila quantitative traits AU - Huang, W. AU - Richards, S. AU - Carbone, M. A. AU - Zhu, D. AU - Anholt, R. R. H. AU - Ayroles, J. F. AU - Duncan, L. AU - Jordan, K. W. AU - Lawrence, F. AU - Magwire, M. M. AU - Warner, C. B. AU - Blankenburg, K. AU - Han, Y. AU - Javaid, M. AU - Jayaseelan, J. AU - Jhangiani, S. N. AU - Muzny, D. AU - Ongeri, F. AU - Perales, L. AU - Wu, Y.-Q. AU - Zhang, Y. AU - Zou, X. AU - Stone, E. A. AU - Gibbs, R. A. AU - Mackay, T. F. C. T2 - Proceedings of the National Academy of Sciences AB - Epistasis-nonlinear genetic interactions between polymorphic loci-is the genetic basis of canalization and speciation, and epistatic interactions can be used to infer genetic networks affecting quantitative traits. However, the role that epistasis plays in the genetic architecture of quantitative traits is controversial. Here, we compared the genetic architecture of three Drosophila life history traits in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and a large outbred, advanced intercross population derived from 40 DGRP lines (Flyland). We assessed allele frequency changes between pools of individuals at the extremes of the distribution for each trait in the Flyland population by deep DNA sequencing. The genetic architecture of all traits was highly polygenic in both analyses. Surprisingly, none of the SNPs associated with the traits in Flyland replicated in the DGRP and vice versa. However, the majority of these SNPs participated in at least one epistatic interaction in the DGRP. Despite apparent additive effects at largely distinct loci in the two populations, the epistatic interactions perturbed common, biologically plausible, and highly connected genetic networks. Our analysis underscores the importance of epistasis as a principal factor that determines variation for quantitative traits and provides a means to uncover genetic networks affecting these traits. Knowledge of epistatic networks will contribute to our understanding of the genetic basis of evolutionarily and clinically important traits and enhance predictive ability at an individualized level in medicine and agriculture. DA - 2012/9/4/ PY - 2012/9/4/ DO - 10.1073/pnas.1213423109 VL - 109 IS - 39 SP - 15553-15559 J2 - Proceedings of the National Academy of Sciences LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.1213423109 DB - Crossref KW - chill coma recovery KW - genetic interaction networks KW - genome-wide association studies KW - startle response KW - starvation resistance ER - TY - JOUR TI - The Drosophila melanogaster Genetic Reference Panel AU - Mackay, Trudy F. C. AU - Richards, Stephen AU - Stone, Eric A. AU - Barbadilla, Antonio AU - Ayroles, Julien F. AU - Zhu, Dianhui AU - Casillas, Sònia AU - Han, Yi AU - Magwire, Michael M. AU - Cridland, Julie M. AU - Richardson, Mark F. AU - Anholt, Robert R. H. AU - Barrón, Maite AU - Bess, Crystal AU - Blankenburg, Kerstin Petra AU - Carbone, Mary Anna AU - Castellano, David AU - Chaboub, Lesley AU - Duncan, Laura AU - Harris, Zeke AU - Javaid, Mehwish AU - Jayaseelan, Joy Christina AU - Jhangiani, Shalini N. AU - Jordan, Katherine W. AU - Lara, Fremiet AU - Lawrence, Faye AU - Lee, Sandra L. AU - Librado, Pablo AU - Linheiro, Raquel S. AU - Lyman, Richard F. AU - Mackey, Aaron J. AU - Munidasa, Mala AU - Muzny, Donna Marie AU - Nazareth, Lynne AU - Newsham, Irene AU - Perales, Lora AU - Pu, Ling-Ling AU - Qu, Carson AU - Ràmia, Miquel AU - Reid, Jeffrey G. AU - Rollmann, Stephanie M. AU - Rozas, Julio AU - Saada, Nehad AU - Turlapati, Lavanya AU - Worley, Kim C. AU - Wu, Yuan-Qing AU - Yamamoto, Akihiko AU - Zhu, Yiming AU - Bergman, Casey M. AU - Thornton, Kevin R. AU - Mittelman, David AU - Gibbs, Richard A. T2 - Nature AB - A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype–phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype–phenotype mapping using the power of Drosophila genetics. A new resource for the analysis of population genomics and quantitative traits, the Drosophila melanogaster Genetic Reference Panel is presented. The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource charting the molecular and phenotypic variation in 168 fully sequenced fruitfly strains derived from a single outbred natural population. The first set of analyses of DGRP data provides insights into the genomic landscape of genetic variation, positive and negative selection, and rapid evolution of the X chromosome. The results also reveal many low frequency variants in novel loci that are associated with quantitative traits, and explain a large fraction of the phenotypic variance. DA - 2012/2// PY - 2012/2// DO - 10.1038/nature10811 VL - 482 IS - 7384 SP - 173-178 J2 - Nature LA - en OP - SN - 0028-0836 1476-4687 UR - http://dx.doi.org/10.1038/nature10811 DB - Crossref ER - TY - JOUR TI - Advanced Oxidation of Toluene Using Ni-Olivine Catalysts: Part 1. Synthesis, Characterization, and Evaluation of Ni-Olivine Catalysts for Toluene Oxidation AU - Smith, V. M. AU - Kolar, P. AU - Boyette, M. D. AU - Chinn, M. AU - Smith, C. AU - Gangadharan, R. AU - Zhang, G. T2 - Transactions of the ASABE AB - This research focused on advanced oxidation of toluene by evaluating Ni-olivine catalysts in combination with ozone. Specifically, our objectives were to: (1) synthesize catalysts via electroless plating (ELP) and thermal impregnation (TI) techniques to impregnate nickel onto the olivine surface; (2) characterize Ni-olivine catalysts by Brunauer-Emmett-Teller specific surface area, electron microscopy, energy dispersive spectroscopy, and x-ray photoelectron spectroscopy to understanding the mechanisms of toluene oxidation; (3) determine the catalytic activity of the newly synthesized Ni-olivine catalysts in the oxidation of toluene; and (4) evaluate the influence of varying toluene and ozone concentrations on Ni-olivine oxidation efficiencies. Testing was performed in a continuous packed bed reactor (200C). Toluene (200 to 600 ppmv) and ozone (70 to 800 ppmv) were injected into the heated reactor, while inlet and outlet concentrations were measured using gas chromatography. Results indicated that 90% of toluene was oxidized within a 1 s residence time using ELP and TI catalyst synthesis techniques and 70 ppmv ozone. Microscopic and spectroscopic analyses revealed porous structures and a nickel film uniformly coating the electroless plated olivine surface, mostly comprised of Ni-P-O, while the thermally impregnated Ni-olivine possessed sparingly deposited Ni2O3 compounds on the surface. An increase in ozone concentrations increased toluene oxidation efficiencies, whereas an increase in toluene concentrations temporarily decreased toluene oxidation efficiencies. Knowledge obtained from this research can be used for synthesizing advanced catalysts for toluene oxidation at significantly lower temperature. DA - 2012/// PY - 2012/// DO - 10.13031/2013.41499 VL - 55 IS - 3 SP - 1013-1024 LA - en OP - SN - 2151-0040 UR - http://dx.doi.org/10.13031/2013.41499 DB - Crossref ER - TY - JOUR TI - Consolidated Bioprocessing of Lignocellulosic Feedstocks for Ethanol Fuel Production AU - Schuster, Brian G. AU - Chinn, Mari S. T2 - BioEnergy Research DA - 2012/12/4/ PY - 2012/12/4/ DO - 10.1007/s12155-012-9278-z VL - 6 IS - 2 SP - 416-435 J2 - Bioenerg. Res. LA - en OP - SN - 1939-1234 1939-1242 UR - http://dx.doi.org/10.1007/s12155-012-9278-z DB - Crossref KW - Bio-ethanol KW - Fuel KW - Consolidated bioprocessing KW - Simultaneous saccharification and fermentation KW - Co-cultures KW - Enzyme hydrolysis KW - Pretreatment ER - TY - JOUR TI - A Role for Phosphoinositides in Regulating Plant Nuclear Functions AU - Dieck, Catherine B. AU - Boss, Wendy F. AU - Perera, Imara Y. T2 - Frontiers in Plant Science AB - REVIEW article Front. Plant Sci., 16 March 2012Sec. Plant Physiology Volume 3 - 2012 | https://doi.org/10.3389/fpls.2012.00050 DA - 2012/// PY - 2012/// DO - 10.3389/fpls.2012.00050 VL - 3 J2 - Front. Plant Sci. OP - SN - 1664-462X UR - http://dx.doi.org/10.3389/fpls.2012.00050 DB - Crossref KW - nucleus KW - phosphoinositide KW - inositol phosphate KW - phosphatidylinositol KW - plant KW - signaling KW - chromatin remodeling ER - TY - JOUR TI - AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during Arabidopsis development AU - Péret, Benjamin AU - Swarup, Kamal AU - Ferguson, Alison AU - Seth, Malvika AU - Yang, Yaodong AU - Dhondt, Stijn AU - James, Nicholas AU - Casimiro, Ilda AU - Perry, Paula AU - Syed, Adnan T2 - The Plant Cell Online AB - Auxin transport, which is mediated by specialized influx and efflux carriers, plays a major role in many aspects of plant growth and development. AUXIN1 (AUX1) has been demonstrated to encode a high-affinity auxin influx carrier. In Arabidopsis thaliana, AUX1 belongs to a small multigene family comprising four highly conserved genes (i.e., AUX1 and LIKE AUX1 [LAX] genes LAX1, LAX2, and LAX3). We report that all four members of this AUX/LAX family display auxin uptake functions. Despite the conservation of their biochemical function, AUX1, LAX1, and LAX3 have been described to regulate distinct auxin-dependent developmental processes. Here, we report that LAX2 regulates vascular patterning in cotyledons. We also describe how regulatory and coding sequences of AUX/LAX genes have undergone subfunctionalization based on their distinct patterns of spatial expression and the inability of LAX sequences to rescue aux1 mutant phenotypes, respectively. Despite their high sequence similarity at the protein level, transgenic studies reveal that LAX proteins are not correctly targeted in the AUX1 expression domain. Domain swapping studies suggest that the N-terminal half of AUX1 is essential for correct LAX localization. We conclude that Arabidopsis AUX/LAX genes encode a family of auxin influx transporters that perform distinct developmental functions and have evolved distinct regulatory mechanisms. DA - 2012/// PY - 2012/// DO - 10.1105/tpc.112.097766 VL - 24 IS - 7 SP - 2874-2885 ER - TY - JOUR TI - The temporal development and additivity of plant-soil feedback in perennial grasses AU - Hawkes, Christine V. AU - Kivlin, Stephanie N. AU - Du, Jennifer AU - Eviner, Valerie T. T2 - Plant Soil DA - 2012/// PY - 2012/// DO - 10.1007/s11104-012-1557-0 VL - 369 IS - 1-2 SP - 141-150 KW - Bothriochloa KW - Exotic KW - Native KW - Panicum KW - Plant-soil feedback KW - Temporal variation ER - TY - JOUR TI - Biogeochemical and Microbial Legacies of Non-Native Grasses Can Affect Restoration Success AU - Hamman, Sarah T. AU - Hawkes, Christine V. T2 - Restoration Ecology AB - The restoration of disturbed ecosystems is challenging and often unsuccessful, particularly when non‐native plants are abundant. Ecosystem restoration may be hindered by the effects of non‐native plants on soil biogeochemical characteristics and microbial communities that persist even after plants are removed. To examine the importance of soil legacy effects, we used experimental restorations of Florida shrubland habitat that had been degraded by the introduction of non‐native grasses coupled with either mechanical disturbance or pasture conversion. We removed non‐native grasses and inoculated soils with native microbial communities at each degraded site, then examined how habitat structure, soil nitrogen, soil microbial abundances, and native seed germination responded over two years compared to undisturbed native sites. Grass removal treatments effectively restored some aspects of native habitat structure, including decreased exotic grass cover, increased bare ground, and reduced litter cover. Soil fungal abundance was also somewhat restored by grass removals, but soil algal abundance was unaffected. In addition, grass removal and microbial inoculation improved seed germination rates in degraded sites, but these remained quite low compared to native sites. High soil nitrogen persisted throughout the experiment regardless of treatment. Many treatment effects were site‐specific, however, with legacies in the more degraded vegetation type tending to be more difficult to overcome. These results support the need for context‐dependent restoration approaches and suggest that the degree of soil legacy effects may be a good indicator of restoration potential. DA - 2012/4// PY - 2012/4// DO - 10.1111/j.1526-100x.2011.00856.x VL - 21 IS - 1 SP - 58-66 KW - algae KW - biological soil crusts KW - disturbance KW - exotic KW - Florida scrub KW - fungi KW - Melinis repens KW - nitrogen KW - Paspalum notatum KW - pasture ER - TY - JOUR TI - Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes AU - Ibarra, C. A. AU - Feng, X. AU - Schoft, V. K. AU - Hsieh, T.-F. AU - Uzawa, R. AU - Rodrigues, J. A. AU - Zemach, A. AU - Chumak, N. AU - Machlicova, A. AU - Nishimura, T. AU - Rojas, D. AU - Fischer, R. L. AU - Tamaru, H. AU - Zilberman, D. T2 - Science AB - Intergenerational Transposable Shutdown Transposable elements (TEs) are a potential threat, especially to the germline genome. In many eukaryotes, TEs are shut down by DNA methylation and/or small-RNA–mediated silencing. Therefore, it seems counterintuitive that results obtained by Ibarra et al. (p. 1360 ) on Arabidopsis showed that in the cells of this plant's sexual apparatus, many small TEs are demethylated by DEMETER (DME) DNA glycosylase and become activated. But it turns out that activation of the TEs triggers the formation of small-interfering RNAs, which in these experiments were seen to travel from the surrounding cells to the egg. Thus, activation of TEs in the companion cells “immunizes” the gametes via the interfering RNAs that shutdown the TEs in the gametes permanently. DA - 2012/9/13/ PY - 2012/9/13/ DO - 10.1126/science.1224839 VL - 337 IS - 6100 SP - 1360-1364 J2 - Science LA - en OP - SN - 0036-8075 1095-9203 UR - http://dx.doi.org/10.1126/science.1224839 DB - Crossref ER - TY - JOUR TI - Two new species in the Matelea stenopetala complex (Apocynaceae, Asclepiadoideae) from the Guiana Shield and Amazonian Brazil AU - Krings, Alexander AU - Morillo, Gilberto T2 - PhytoKeys AB - Two new species in the Matelea stenopetala complex (Apocynaceae, Asclepiadoideae) are described from the Guiana Shield and Amazonian Brazil: Matelea brevistipitata Krings & Morillo, sp. nov. and Matelea trichopedicellataKrings & Morillo, sp. nov. The new species belong to a small group of adaxially-pubescent-flowered taxa within the complex, including Matelea hildegardiana and Matelea pakaraimensis. The new species are described and a dichotomous key is provided. DA - 2012/9/26/ PY - 2012/9/26/ DO - 10.3897/phytokeys.17.3485 VL - 17 IS - 0 SP - 27-39 J2 - PHYTOKEYS OP - SN - 1314-2003 1314-2011 UR - http://dx.doi.org/10.3897/phytokeys.17.3485 DB - Crossref ER - TY - JOUR TI - Thermostable invertases from Paecylomyces variotii produced under submerged and solid-state fermentation using agroindustrial residues AU - Giraldo, M.A. AU - Silva, T.M. AU - Salvato, F. AU - Terenzi, H.F. AU - Jorge, J.A. AU - Guimarães, L.H.S. T2 - World Journal of Microbiology and Biotechnology DA - 2012/// PY - 2012/// DO - 10.1007/s11274-011-0837-9 VL - 28 IS - 2 SP - 463-472 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84856480074&partnerID=MN8TOARS KW - Invertase KW - beta-Fructofuranosidase KW - Sucrose KW - Paecylomyces KW - Fungi ER - TY - JOUR TI - Strategies for Protein Separation AU - Salvato, Fernanda AU - Carvalho, Mayra Costa AU - Lima Leite, Aline T2 - Integrative Proteomics AB - The proteome of a cell or tissue depends on cellular and environmental conditions, showing a dynamic system subject to large variations. To study these large changes of variability and quantity, proteomics has emerged, providing techniques dedicated to global characterization of all proteins simultaneously. The expectation is that this information will produce new insights into the biological function of proteins in different physiological states of a cell or tissue. The proteome has a dynamic and complex nature that is the result of many posttranslational modifications, molecular interactions, and a variety of proteins arising from alternative mRNA splicing. With this in mind, the number of modified and unmodified proteins found in any biological system is much bigger than the number of genes (Anderson et al., 2004), which is why mRNA expression may not correlate with protein content (Rogers et. al, 2008). In addition, not all proteins are expressed in the same or similar level in the proteome. For example, the enzyme Rubisco comprises 3050% of leaf proteome (Feller et al., 2008), which is a big issue in the proteomic assessment of low-abundance proteins. In fact, the majority of proteins are in the low-abundance level. To overcome these challenges, the proteome must be fractionated for effective detection and quantification by mass spectrometry (MS). Consequently, the analysis of proteins on the large or small scale is dependent on separation methods. As the ultimate goal in proteomics is to resolve all individual proteins in the cell, although it is quite difficult to find a separation method that could accommodate the diversity of proteins equally, protein separation methods directly affect the achievement of reliable results. Such methods are based on the physical or chemical properties of different proteins, such as their mass or net charge. The combination of sequential methods exploiting different properties can provide highresolution analysis of very complex protein mixtures. Then, current analytical strategies can reach different levels of resolution depending on the platform used. Two-dimensional gel electrophoresis (2DGE) and multidimensional liquid chromatography (MDLC) are the two methods that dominate the separation steps in proteomics. The differences of each strategy are basically related to sensitivity, automation, and high-throughput possibilities. In this chapter, the limitations and principles of these techniques will be discussed. DA - 2012/2// PY - 2012/2// DO - 10.5772/29363 ER - TY - JOUR TI - Large-Scale Proteome Comparative Analysis of Developing Rhizomes of the Ancient Vascular Plant Equisetum Hyemale AU - Balbuena, Tiago Santana AU - He, Ruifeng AU - Salvato, Fernanda AU - Gang, David R. AU - Thelen, Jay J. T2 - Frontiers in Plant Science AB - ORIGINAL RESEARCH article Front. Plant Sci., 26 June 2012Sec. Plant Proteomics and Protein Structural Biology Volume 3 - 2012 | https://doi.org/10.3389/fpls.2012.00131 DA - 2012/// PY - 2012/// DO - 10.3389/fpls.2012.00131 VL - 3 KW - rough horsetail KW - ferns KW - label-free proteomics KW - spectral counting ER - TY - JOUR TI - Plant regeneration and genetic transformation of C. canadensis: a non-model plant appropriate for investigation of flower development in Cornus (Cornaceae) AU - Liu, Xiang AU - Feng, Chun-Miao AU - Franks, Robert AU - Qu, Rongda AU - Xie, De-Yu AU - Xiang, Qiu-Yun Jenny T2 - Plant Cell Reports DA - 2012/10/31/ PY - 2012/10/31/ DO - 10.1007/s00299-012-1341-x VL - 32 IS - 1 SP - 77-87 J2 - Plant Cell Rep LA - en OP - SN - 0721-7714 1432-203X UR - http://dx.doi.org/10.1007/s00299-012-1341-x DB - Crossref ER - TY - JOUR TI - Integrative systems biology: an attempt to describe a simple weed AU - Liberman, Louisa M. AU - Sozzani, Rosangela AU - Benfey, Philip N. T2 - Current Opinion in Plant Biology AB - Genome-scale studies hold great promise for revealing novel plant biology. Because of the complexity of these techniques, numerous considerations need to be made before embarking on a study. Here we focus on the Arabidopsis model system because of the wealth of available genome-scale data. Many approaches are available that provide genome-scale information regarding the state of a given organism (e.g. genomics, epigenomics, transcriptomics, proteomics, metabolomics interactomics, ionomics, phenomics, etc.). Integration of all of these types of data will be necessary for a comprehensive description of Arabidopsis. In this review we propose that 'triangulation' among transcriptomics, proteomics and metabolomics is a meaningful approach for beginning this integrative analysis and uncovering a systems level perspective of Arabidopsis biology. C2 - PMC3435099 DA - 2012/4// PY - 2012/4// DO - 10.1016/j.pbi.2012.01.004 VL - 15 IS - 2 SP - 162-167 J2 - Curr. Opin. Plant Biol. LA - eng SN - 1879-0356 ST - Integrative systems biology DB - PubMed ER - TY - JOUR TI - A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division AU - Cruz-Ramírez, Alfredo AU - Díaz-Triviño, Sara AU - Blilou, Ikram AU - Grieneisen, Verônica A. AU - Sozzani, Rosangela AU - Zamioudis, Christos AU - Miskolczi, Pál AU - Nieuwland, Jeroen AU - Benjamins, René AU - Dhonukshe, Pankaj AU - Caballero-Pérez, Juan AU - Horvath, Beatrix AU - Long, Yuchen AU - Mähönen, Ari Pekka AU - Zhang, Hongtao AU - Xu, Jian AU - Murray, James A. H. AU - Benfey, Philip N. AU - Bako, Laszlo AU - Marée, Athanasius F. M. AU - Scheres, Ben T2 - Cell AB - In plants, where cells cannot migrate, asymmetric cell divisions (ACDs) must be confined to the appropriate spatial context. We investigate tissue-generating asymmetric divisions in a stem cell daughter within the Arabidopsis root. Spatial restriction of these divisions requires physical binding of the stem cell regulator SCARECROW (SCR) by the RETINOBLASTOMA-RELATED (RBR) protein. In the stem cell niche, SCR activity is counteracted by phosphorylation of RBR through a cyclinD6;1-CDK complex. This cyclin is itself under transcriptional control of SCR and its partner SHORT ROOT (SHR), creating a robust bistable circuit with either high or low SHR-SCR complex activity. Auxin biases this circuit by promoting CYCD6;1 transcription. Mathematical modeling shows that ACDs are only switched on after integration of radial and longitudinal information, determined by SHR and auxin distribution, respectively. Coupling of cell-cycle progression to protein degradation resets the circuit, resulting in a "flip flop" that constrains asymmetric cell division to the stem cell region. C2 - PMC3500399 DA - 2012/8/31/ PY - 2012/8/31/ DO - 10.1016/j.cell.2012.07.017 VL - 150 IS - 5 SP - 1002-1015 J2 - Cell LA - eng SN - 1097-4172 DB - PubMed ER - TY - JOUR TI - Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use AU - Kleiner, Manuel AU - Wentrup, Cecilia AU - Lott, Christian AU - Teeling, Hanno AU - Wetzel, Silke AU - Young, Jacque AU - Chang, Yun-Juan AU - Shah, Manesh AU - VerBerkmoes, Nathan C. AU - Zarzycki, Jan AU - Fuchs, Georg AU - Markert, Stephanie AU - Hempel, Kristina AU - Voigt, Birgit AU - Becher, Doerte AU - Liebekeh, Manuel AU - Lalk, Michael AU - Albrecht, Dirk AU - Hecker, Michael AU - Schweder, Thomas AU - Dubilier, Nicole T2 - Proceedings of the National Academy of Sciences of the United States of America AB - Low nutrient and energy availability has led to the evolution of numerous strategies for overcoming these limitations, of which symbiotic associations represent a key mechanism. Particularly striking are the associations between chemosynthetic bacteria and marine animals that thrive in nutrient-poor environments such as the deep sea because the symbionts allow their hosts to grow on inorganic energy and carbon sources such as sulfide and CO 2 . Remarkably little is known about the physiological strategies that enable chemosynthetic symbioses to colonize oligotrophic environments. In this study, we used metaproteomics and metabolomics to investigate the intricate network of metabolic interactions in the chemosynthetic association between Olavius algarvensis , a gutless marine worm, and its bacterial symbionts. We propose previously undescribed pathways for coping with energy and nutrient limitation, some of which may be widespread in both free-living and symbiotic bacteria. These pathways include ( i ) a pathway for symbiont assimilation of the host waste products acetate, propionate, succinate and malate; ( ii ) the potential use of carbon monoxide as an energy source, a substrate previously not known to play a role in marine invertebrate symbioses; ( iii ) the potential use of hydrogen as an energy source; ( iv ) the strong expression of high-affinity uptake transporters; and ( v ) as yet undescribed energy-efficient steps in CO 2 fixation and sulfate reduction. The high expression of proteins involved in pathways for energy and carbon uptake and conservation in the O . algarvensis symbiosis indicates that the oligotrophic nature of its environment exerted a strong selective pressure in shaping these associations. DA - 2012/// PY - 2012/// DO - 10.1073/pnas.1121198109 VL - 109 IS - 19 SP - E1173-E1182 UR - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000304090600007&KeyUID=WOS:000304090600007 KW - 3-hydroxypropionate bi-cycle KW - Calvin cycle KW - proton-translocating pyrophosphatase KW - pyrophosphate dependent phosphofructokinase KW - metagenomics ER - TY - JOUR TI - Convergent and divergent evolution of metabolism in sulfur-oxidizing symbionts and the role of horizontal gene transfer AU - Kleiner, Manuel AU - Petersen, Jillian M. AU - Dubilier, Nicole T2 - Current Opinion in Microbiology DA - 2012/// PY - 2012/// DO - 10.1016/j.mlb.2012.09.003 VL - 15 IS - 5 SP - 621-631 UR - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000311181000012&KeyUID=WOS:000311181000012 ER - TY - JOUR TI - Understanding bias in geographic range size estimates AU - Sheth, S.N. AU - Lohmann, L.G. AU - Distler, T. AU - Jiménez, I. T2 - Global Ecology and Biogeography AB - ABSTRACT Aim Estimates of geographic range size derived from natural history museum specimens are probably biased for many species. We aim to determine how bias in these estimates relates to range size. Location We conducted computer simulations based on herbarium specimen records from localities ranging from the southern United States to northern Argentina. Methods We used theory on the sampling distribution of the mean and variance to develop working hypotheses about how range size, defined as area of occupancy (AOO), was related to the inter‐specific distribution of: (1) mean collection effort per area across the range of a species (MC); (2) variance in collection effort per area across the range of a species (VC); and (3) proportional bias in AOO estimates (PBias: the difference between the expected value of the estimate of AOO and true AOO, divided by true AOO). We tested predictions from these hypotheses using computer simulations based on a dataset of more than 29,000 herbarium specimen records documenting occurrences of 377 plant species in the tribe Bignonieae (Bignoniaceae). Results The working hypotheses predicted that the mean of the inter‐specific distribution of MC, VC and PBias were independent of AOO, but that the respective variance and skewness decreased with increasing AOO. Computer simulations supported all but one prediction: the variance of the inter‐specific distribution of VC did not decrease with increasing AOO. Main conclusions Our results suggest that, despite an invariant mean, the dispersion and symmetry of the inter‐specific distribution of PBias decreases as AOO increases. As AOO increased, range size was less severely underestimated for a large proportion of simulated species. However, as AOO increased, range size estimates having extremely low bias were less common. DA - 2012/// PY - 2012/// DO - 10.1111/j.1466-8238.2011.00716.x VL - 21 IS - 7 SP - 732-742 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84862325044&partnerID=MN8TOARS KW - Area of occupancy KW - bias KW - collection effort KW - geographic range size KW - herbarium data KW - sampling intensity ER - TY - JOUR TI - Preparing Science-Trained Professionals for the Biotechnology Industry: A Ten-Year Perspective on a Professional Science Master’s Program AU - Hamilton, Paul T. AU - Luginbuhl, Sarah C. AU - Hyman, Michael T2 - Journal of Microbiology & Biology Education : JMBE AB - The biotechnology industry has a need for business-savvy scientists; however, this is not the way scientists are traditionally trained at universities and colleges. To address this need, universities have developed Professional Science Master’s (PSM) degree programs that offer advanced training in a technical field along with professional skills development through team-based projects and internships. Nearly ten years ago, the Department of Microbiology at NCSU started a PSM program in Microbial Biotechnology (MMB). This article provides an overview of the MMB program, and shares some of the lessons that we have learned. C2 - PMC3577309 DA - 2012/5/3/ PY - 2012/5/3/ DO - 10.1128/jmbe.v13i1.375 VL - 13 IS - 1 SP - 39-44 J2 - J Microbiol Biol Educ SN - 1935-7877 ST - Preparing Science-Trained Professionals for the Biotechnology Industry UR - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577309/ DB - PubMed Central Y2 - 2019/2/1/ ER - TY - BOOK TI - Molecular biology techniques: a classroom laboratory manual AU - Carson, S. AU - Miller, H. AU - Witherow, D. S. DA - 2012/// PY - 2012/// PB - New York: Academic ER - TY - JOUR TI - Advanced oxidation of toluene using Ni-olivine catalysts: part 2. Toluene oxidation kinetics and mechanism of Ni-olivine catalysts synthesized via electroless deposition and thermal impregnation AU - Smith, V. M. AU - Kolar, P. AU - Boyette, M. D. AU - Chinn, Mari AU - Smith, C. AU - Gangadharan, R. AU - Zhang, G. T2 - Transactions of the ASABE AB - The production of synthesis gas (syngas) involves the gasification of biomass under oxygen-limited conditions, which also produces tars. Tars pose significant problems for mechanical devices by depositing on piping, resulting in clogging and engine fouling. While recent research has shown that thermally impregnated Ni-olivine has been effective in reforming tars into H2 and CO, this technique possessed limited economic feasibility due to high input energy requirements. Thus, stable, active, and inexpensive catalysts are required for effective and efficient conditioning of syngas. This research compared the activity of Ni-olivine catalysts synthesized via electroless plating (ELP) (35C) and thermal impregnation (TI) (1400C) for oxiding toluene in a flow-through reactor. The objectives were to (1) determine the kinetics of toluene oxidation, (2) propose a reaction mechanism for toluene oxidation, and (3) investigate the effect of syngas on toluene oxidation. Conversion of toluene using Ni-olivine catalysts increased with increasing ozone concentration and temperature, as well as decreasing toluene molar flow rate, and facilitated the complete oxidation of toluene. The information obtained from this research is expected to provide opportunities for efficient cleanup of tars from biomass gasification facilities at lower temperatures. DA - 2012/// PY - 2012/// DO - 10.13031/2013.42485 VL - 55 IS - 6 SP - 2273–2283 ER - TY - JOUR TI - Student Learning Outcomes and Attitudes When Biotechnology Lab Partners Are of Different Academic Levels AU - Miller, Heather B. AU - Witherow, D. Scott AU - Carson, Susan T2 - CBE-LIFE SCIENCES EDUCATION AB - The North Carolina State University Biotechnology Program offers laboratory-intensive courses to both undergraduate and graduate students. In "Manipulation and Expression of Recombinant DNA," students are separated into undergraduate and graduate sections for the laboratory, but not the lecture, component. Evidence has shown that students prefer pairing with someone of the same academic level. However, retention of main ideas in peer learning environments has been shown to be greater when partners have dissimilar abilities. Therefore, we tested the hypothesis that there will be enhanced student learning when lab partners are of different academic levels. We found that learning outcomes were met by both levels of student, regardless of pairing. Average undergraduate grades on every assessment method increased when undergraduates were paired with graduate students. Many of the average graduate student grades also increased modestly when graduate students were paired with undergraduates. Attitudes toward working with partners dramatically shifted toward favoring working with students of different academic levels. This work suggests that offering dual-level courses in which different-level partnerships are created does not inhibit learning by students of different academic levels. This format is useful for institutions that wish to offer "boutique" courses in which student enrollment may be low, but specialized equipment and faculty expertise are needed. DA - 2012/9// PY - 2012/9// DO - 10.1187/cbe.11-10-0094 VL - 11 IS - 3 SP - 323-332 SN - 1931-7913 ER - TY - JOUR TI - Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa AU - Li, Quanzi AU - Lin, Ying-Chung AU - Sun, Ying-Hsuan AU - Song, Jian AU - Chen, Hao AU - Zhang, Xing-Hai AU - Sederoff, Ronald R. AU - Chiang, Vincent L. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Secondary Wall-Associated NAC Domain 1s (SND1s) are transcription factors (TFs) known to activate a cascade of TF and pathway genes affecting secondary cell wall biosynthesis (xylogenesis) in Arabidopsis and poplars. Elevated SND1 transcriptional activation leads to ectopic xylogenesis and stunted growth. Nothing is known about the upstream regulators of SND1 . Here we report the discovery of a stem-differentiating xylem (SDX)-specific alternative SND1 splice variant, PtrSND1 - A2 IR , that acts as a dominant negative of SND1 transcriptional network genes in Populus trichocarpa . PtrSND1 - A2 IR derives from PtrSND1-A2 , one of the four fully spliced PtrSND1 gene family members ( PtrSND1 - A1 , - A2 , - B1 , and - B2 ). Each full-size PtrSND1 activates its own gene, and all four full-size members activate a common MYB gene ( PtrMYB021 ). PtrSND1-A2 IR represses the expression of its PtrSND1 member genes and PtrMYB021 . Repression of the autoregulation of a TF family by its only splice variant has not been previously reported in plants. PtrSND1-A2 IR lacks DNA binding and transactivation abilities but retains dimerization capability. PtrSND1-A2 IR is localized exclusively in cytoplasmic foci. In the presence of any full-size PtrSND1 member, PtrSND1-A2 IR is translocated into the nucleus exclusively as a heterodimeric partner with full-size PtrSND1s. Our findings are consistent with a model in which the translocated PtrSND1-A2 IR lacking DNA-binding and transactivating abilities can disrupt the function of full-size PtrSND1s, making them nonproductive through heterodimerization, and thereby modulating the SND1 transcriptional network. PtrSND1-A2 IR may contribute to transcriptional homeostasis to avoid deleterious effects on xylogenesis and plant growth. DA - 2012/9/4/ PY - 2012/9/4/ DO - 10.1073/pnas.1212977109 VL - 109 IS - 36 SP - 14699-14704 SN - 0027-8424 ER - TY - JOUR TI - Prolidase function in proline metabolism and its medical and biotechnological applications AU - Kitchener, R. L. AU - Grunden, A. M. T2 - JOURNAL OF APPLIED MICROBIOLOGY AB - Prolidase is a multifunctional enzyme that possesses the unique ability to degrade imidodipeptides in which a proline or hydroxyproline residue is located at the C-terminal end. Prolidases have been isolated from archaea and bacteria, where they are thought to participate in proline recycling. In mammalian species, prolidases are found in the cytoplasm and function primarily to liberate proline in the final stage of protein catabolism, particularly during the biosynthesis and degradation of collagen. Collagen comprises nearly one-third of the total protein in the body, and it is essential in maintaining tissue structure and integrity. Prolidase deficiency (PD), a rare autosomal recessive disorder in which mutations in the PEPD gene affect prolidase functionality, tends to have serious and sometimes life-threatening clinical symptoms. Recombinant prolidases have many applications and have been investigated not only as a possible treatment for PD, but also as a part of anti-cancer strategies, a component of biodecontamination cocktails and in the dairy industry. This review will serve to discuss the many in vivo functions of procaryotic and eucaryotic prolidases, as well as the most recent advances in therapeutic and biotechnological application of prolidases. DA - 2012/8// PY - 2012/8// DO - 10.1111/j.1365-2672.2012.05310.x VL - 113 IS - 2 SP - 233-247 SN - 1365-2672 KW - biotechnology KW - degradation KW - diagnosis KW - enzymes KW - peptides ER - TY - JOUR TI - Phosphoinositide Signaling AU - Boss, Wendy F. AU - Im, Yang Ju T2 - ANNUAL REVIEW OF PLANT BIOLOGY, VOL 63 AB - "All things flow and change…even in the stillest matter there is unseen flux and movement." Attributed to Heraclitus (530-470 BC), from The Story of Philosophy by Will Durant. Heraclitus, a Greek philosopher, was thinking on a much larger scale than molecular signaling; however, his visionary comments are an important reminder for those studying signaling today. Even in unstimulated cells, signaling pathways are in constant metabolic flux and provide basal signals that travel throughout the organism. In addition, negatively charged phospholipids, such as the polyphosphorylated inositol phospholipids, provide a circuit board of on/off switches for attracting or repelling proteins that define the membranes of the cell. This template of charged phospholipids is sensitive to discrete changes and metabolic fluxes-e.g., in pH and cations-which contribute to the oscillating signals in the cell. The inherent complexities of a constantly fluctuating system make understanding how plants integrate and process signals challenging. In this review we discuss one aspect of lipid signaling: the inositol family of negatively charged phospholipids and their functions as molecular sensors and regulators of metabolic flux in plants. DA - 2012/// PY - 2012/// DO - 10.1146/annurev-arplant-042110-103840 VL - 63 SP - 409-429 SN - 1545-2123 KW - phosphatidylinositol KW - inositol lipids KW - plant KW - PIP modulin KW - flux KW - networking ER - TY - JOUR TI - Method: low-cost delivery of the cotton leaf crumple virus-induced gene silencing system AU - Tuttle, John Richard AU - Haigler, Candace H. AU - Robertson, Dominique T2 - PLANT METHODS AB - We previously developed a virus-induced gene silencing (VIGS) vector for cotton from the bipartite geminivirusCotton leaf crumple virus (CLCrV). The original CLCrV VIGS vector was designed for biolistic delivery by a gene gun. This prerequisite limited the use of the system to labs with access to biolistic equipment. Here we describe the adaptation of this system for delivery by Agrobacterium (Agrobacterium tumefaciens). We also describe the construction of two low-cost particle inflow guns. The biolistic CLCrV vector was transferred into two Agrobacterium binary plasmids. Agroinoculation of the binary plasmids into cotton resulted in silencing and GFP expression comparable to the biolistic vector. Two homemade low-cost gene guns were used to successfully inoculate cotton (G. hirsutum) and N. benthamiana with either the CLCrV VIGS vector or the Tomato golden mosaic virus (TGMV) VIGS vector respectively. These innovations extend the versatility of CLCrV-based VIGS for analyzing gene function in cotton. The two low-cost gene guns make VIGS experiments affordable for both research and teaching labs by providing a working alternative to expensive commercial gene guns. DA - 2012/8/1/ PY - 2012/8/1/ DO - 10.1186/1746-4811-8-27 VL - 8 SP - SN - 1746-4811 KW - Cotton KW - VIGS KW - Virus-induced gene silencing KW - Cotton leaf crumple virus KW - Agroinoculation KW - Particle inflow gun KW - Bombardment KW - Gossypium ER - TY - JOUR TI - Interactions between fungal growth, substrate utilization and enzyme production during shallow stationary cultivation of Phanerochaete chrysosporium on cotton stalks AU - Shi, Jian AU - Sharma-Shivappa, Ratna R. AU - Chinn, Mari S. T2 - ENZYME AND MICROBIAL TECHNOLOGY AB - Microbial pretreatment of lignocellulosic feedstocks is an environment friendly alternative to physio-chemical pretreatment methods. A better understanding of the interactive fungal mechanisms in biological systems is essential for enhancing performance and facilitating scale-up and commercialization of this pretreatment technique. In this study, mathematical models were developed for describing cellulose and hemicellulose consumption, lignin degradation, cellulase and ligninolytic enzyme production and oxygen uptake associated with the growth of Phanerochaete chrysosporium during a 14-day shallow stationary submerged fungal pretreatment process on cotton stalks. Model parameters were estimated and validated by Statistics Toolbox in MatLab 7.1. Models yielded sufficiently accurate predictions for cellulose and hemicellulose consumption (R²=0.9772 and 0.9837), lignin degradation (R²=0.9879 and 0.8682) and ligninolytic enzyme production (R²=0. 8135 and 0.9693) under both 1-day and 3-day oxygen flushing conditions, respectively. The predictabilities for fungal growth (R²=0.6397 and 0.5750) and cellulase production (R²=0.0307 and 0.3046) for 1-day and 3-day oxygen flushing, respectively, and oxygen uptake (R²=0.5435) for 3-day oxygen flushing were limited. DA - 2012/6/10/ PY - 2012/6/10/ DO - 10.1016/j.enzmictec.2012.03.006 VL - 51 IS - 1 SP - 1-8 SN - 1879-0909 KW - Bioethanol KW - Phanerochaete chrysosporium KW - Kinetics KW - Pretreatment ER - TY - JOUR TI - Increasing phosphatidylinositol (4,5) bisphosphate biosynthesis affects plant nuclear lipids and nuclear functions AU - Dieck, Catherine B. AU - Wood, Austin AU - Brglez, Irena AU - Rojas-Pierce, Marcela AU - Boss, Wendy F. T2 - PLANT PHYSIOLOGY AND BIOCHEMISTRY AB - In order to characterize the effects of increasing phosphatidylinositol(4,5)bisphosphate (PtdIns(4,5)P2) on nuclear function, we expressed the human phosphatidylinositol (4)-phosphate 5-kinase (HsPIP5K) 1α in Nicotiana tabacum (NT) cells. The HsPIP5K-expressing (HK) cells had altered nuclear lipids and nuclear functions. HK cell nuclei had 2-fold increased PIP5K activity and increased steady state PtdIns(4,5)P2. HK nuclear lipid classes showed significant changes compared to NT (wild type) nuclear lipid classes including increased phosphatidylserine (PtdSer) and phosphatidylcholine (PtdCho) and decreased lysolipids. Lipids isolated from protoplast plasma membranes (PM) were also analyzed and compared with nuclear lipids. The lipid profiles revealed similarities and differences in the plasma membrane and nuclei from the NT and transgenic HK cell lines. A notable characteristic of nuclear lipids from both cell types is that PtdIns accounts for a higher mol% of total lipids compared to that of the protoplast PM lipids. The lipid molecular species composition of each lipid class was also analyzed for nuclei and protoplast PM samples. To determine whether expression of HsPIP5K1α affected plant nuclear functions, we compared DNA replication, histone 3 lysine 9 acetylation (H3K9ac) and phosphorylation of the retinoblastoma protein (pRb) in NT and HK cells. The HK cells had a measurable decrease in DNA replication, histone H3K9 acetylation and pRB phosphorylation. DA - 2012/8// PY - 2012/8// DO - 10.1016/j.plaphy.2012.05.011 VL - 57 SP - 32-44 SN - 1873-2690 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84861821133&partnerID=MN8TOARS KW - Plant nuclei KW - Phospholipids KW - Histone KW - Phosphatidylinositol (4,5) bisphosphate KW - Plasma membrane ER - TY - JOUR TI - Evolution of bract development and B‐class MADS box gene expression in petaloid bracts of Cornus s. l. (Cornaceae) AU - Feng, Chun‐Miao AU - Liu, Xiang AU - Yu, Yi AU - Xie, Deyu AU - Franks, Robert G. AU - Xiang, Qiu‐Yun (Jenny) T2 - New Phytologist AB - • Despite increasing interest in the molecular mechanisms of floral diversity, few studies have investigated the developmental and genetic bases of petaloid bracts. This study examined morphological patterns of bract initiation and expression patterns of B-class MADS-box genes in bracts of several Cornus species. We suggest that petaloid bracts in this genus may not share a single evolutionary origin. • Developmental pathways of bracts and spatiotemporal expression of B-class genes in bracts and flowers were examined for four closely related dogwood species. • Divergent morphological progressions and gene expression patterns were found in the two sister lineages with petaloid bracts, represented by Cornus florida and Cornus canadensis. Phylogeny-based analysis identified developmental and gene expression changes that are correlated with the evolution of petaloid bracts in C. florida and C. canadensis. • Our data support the existence of independent evolutionary origins of petaloid bracts in C. canadensis and C. florida. Additionally, we suggest that functional transference within B-class gene families may have contributed to the origin of bract petaloidy in C. florida. However, the underlying mechanisms of petaloid bract development likely differ between C. florida and C. canadensis. In the future this hypothesis can be tested by functional analyses of Cornus B-class genes. DA - 2012/8/16/ PY - 2012/8/16/ DO - 10.1111/j.1469-8137.2012.04255.x VL - 196 IS - 2 SP - 631-643 J2 - New Phytol LA - en OP - SN - 0028-646X 1469-8137 UR - http://dx.doi.org/10.1111/j.1469-8137.2012.04255.x DB - Crossref KW - APETALA3 KW - B-class gene expression KW - Cornus KW - development KW - Evo-Devo KW - evolution of petaloid bracts KW - heterotopic petaloidy KW - PISTILLATA ER - TY - JOUR TI - AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during arabidopsis development AU - Peret, B. AU - Swarup, K. AU - Ferguson, A. AU - Seth, M. AU - Yang, Y. D. AU - Dhondt, S. AU - James, N. AU - Casimiro, I. AU - Perry, P. AU - Syed, A. AU - Yang, H. B. AU - Reemmer, J. AU - Venison, E. AU - Howells, C. AU - Perez-Amador, M. A. AU - Yun, J. G. AU - Alonso, J. AU - Beemster, G. T. S. AU - Laplaze, L. T2 - Plant Cell DA - 2012/// PY - 2012/// VL - 24 IS - 7 SP - 2874-2885 ER - TY - JOUR TI - Special Issue on Metabolic Plant Biology AU - Xie, De-Yu AU - Melis, Anastasios T2 - PLANTA DA - 2012/9// PY - 2012/9// DO - 10.1007/s00425-012-1700-4 VL - 236 IS - 3 SP - 763-764 SN - 0032-0935 ER - TY - JOUR TI - Regulation of anthocyanin biosynthesis by nitrogen in TTG1-GL3/TT8-PAP1-programmed red cells of Arabidopsis thaliana AU - Zhou, Li-Li AU - Shi, Ming-Zhu AU - Xie, De-Yu T2 - PLANTA DA - 2012/9// PY - 2012/9// DO - 10.1007/s00425-012-1674-2 VL - 236 IS - 3 SP - 825-837 SN - 1432-2048 KW - Arabidopsis thaliana KW - Anthocyanin biosynthesis KW - Production of anthocyanin pigmentation 1 KW - Nitrogen ER - TY - JOUR TI - Pollination biology and seed production of a federally endangered perennial, Echinacea laevigata (Asteraceae:Heliantheae) AU - Stucky, J. M. AU - Gadd, L. E. AU - Arellano, C. T2 - American Midland Naturalist AB - Pollination biology and factors affecting reproductive success of the federally endangered Echinacea laevigata (coneflower) were studied in one large and five small populations. Insect visitor exclusion from flowering heads and pollination treatments showed that seed production was 10x higher in open-pollinated treatments compared to bagged flowers that were not pollinated and 20x higher than flower heads receiving self pollen suggesting that cross-pollination was responsible for most seed production. Peak flowering occurred the 2nd–4th wk of Jun. 2004 and the large population contributed 50–68% of the flowering individuals in its plant community. During this period, Bombus (Apidae, bumblebees), Hesperiidae (skippers), and Megachile (Megachilidae, leaf-cutter bees) accounted for 73%, 12%, and 11% of the observed visits to coneflower, respectively. Species richness of coneflower flower visitors and number of flower visits was lower in each small population than in the large population. However, comparison of seed production between heads receiving supplemental pollen and open-pollination heads indicated that seed production was not pollen limited. In addition, over 93% of pollen grains stained normally in cotton blue-lactophenol in all six populations suggesting that pollen viability was high in small and large populations. However, seed production in the large population exceeded that in each of three small populations during 2005, and seedling size was larger in the large population compared to seedlings from one of the small populations. Comparison of soil cation concentrations among populations suggested that cations did not limit seed production. We suggest that genetic factors, such as inbreeding or low S allele variation, may limit seed production in the small populations. DA - 2012/// PY - 2012/// DO - 10.1674/0003-0031-168.1.93 VL - 168 IS - 1 SP - 93-111 ER - TY - JOUR TI - Fuels or microclimate? Understanding the drivers of fire feedbacks at savanna-forest boundaries AU - Hoffmann, William A. AU - Jaconis, Susany. AU - Mckinley, Kristen L. AU - Geiger, Erika L. AU - Gotsch, Sybil G. AU - Franco, Augusto C. T2 - AUSTRAL ECOLOGY AB - Abstract The higher flammability of tropical savanna, compared with forest, plays a critical role in mediating vegetation‐environment feedbacks, alternate stable states, and ultimately, the distribution of these two biomes. Multiple factors contribute to this difference in flammability, including microclimate, fuel amount and fuel type. To understand this transition in flammability, we studied fuel characteristics and microclimate across eight savanna–forest boundaries in south‐central Brazil. At each boundary, the environment was monitored for one week with automated measurements of near‐surface wind speed, air temperature, relative humidity and presence of dew. Manual measurements were performed to quantify fuel amounts and fuel moisture. These data were used to parameterize the fire behaviour model BehavePlus5 in order to simulate fire behaviour over the savanna–forest boundary. There were strong gradients across the boundary in all variables with the exception of total fuel load. During the day, savannas had higher wind speed and air temperature, and lower relative humidity and fuel moisture than forests. Although fuel loads were similar in savanna and forest, savanna was characterized by lower fuel bulk density, largely because of the presence of grasses. Based on these measurements, the fire behaviour model predicted savanna fires to be faster, more intense, and with greater flame lengths, relative to forest. A sensitivity analysis indicated that the primary cause of these differences was the low fuel bulk density characteristic of grassy fuels, with lesser contributions from wind speed, fuel moisture and total fuel load. These results indicate that the dominance of grassy fuels is the primary cause of the high flammability of savanna. DA - 2012/9// PY - 2012/9// DO - 10.1111/j.1442-9993.2011.02324.x VL - 37 IS - 6 SP - 634-643 SN - 1442-9985 KW - C4 grass KW - Cerrado KW - fire behaviour KW - fire intensity KW - positive feedback ER - TY - JOUR TI - An integrated approach to demonstrating the ANR pathway of proanthocyanidin biosynthesis in plants AU - Peng, Qing-Zhong AU - Zhu, Yue AU - Liu, Zhong AU - Du, Ci AU - Li, Ke-Gang AU - Xie, De-Yu T2 - PLANTA DA - 2012/9// PY - 2012/9// DO - 10.1007/s00425-012-1670-6 VL - 236 IS - 3 SP - 901-918 SN - 1432-2048 KW - ANR pathway KW - Anthocyanidin reductase KW - Leucoanthocyanidin reductase KW - Flavan-3-ols KW - Catechin KW - Epicatechin KW - Proanthocyanidins ER - TY - JOUR TI - Demographic effects of fire on two endemic plant species in the longleaf pine-wiregrass ecosystem AU - Wall, Wade A. AU - Hoffmann, William A. AU - Wentworth, Thomas R. AU - Gray, Janet B. AU - Hohmann, Matthew G. T2 - PLANT ECOLOGY DA - 2012/7// PY - 2012/7// DO - 10.1007/s11258-012-0068-7 VL - 213 IS - 7 SP - 1093-1104 SN - 1385-0237 KW - Astragalus KW - Demography KW - Endemism KW - Fire KW - Matrix models KW - Pinus palustris KW - Pyxidanthera ER - TY - JOUR TI - A versatile method for preparation of hydrated microbial–latex biocatalytic coatings for gas absorption and gas evolution AU - Gosse, Jimmy L. AU - Chinn, Mari S. AU - Grunden, Amy M. AU - Bernal, Oscar I. AU - Jenkins, Jessica S. AU - Yeager, Chris AU - Kosourov, Sergey AU - Seibert, Michael AU - Flickinger, Michael C. T2 - Journal of Industrial Microbiology & Biotechnology AB - Abstract We describe a latex wet coalescence method for gas-phase immobilization of microorganisms on paper which does not require drying for adhesion. This method reduces drying stresses to the microbes. It is applicable for microorganisms that do not tolerate desiccation stress during latex drying even in the presence of carbohydrates. Small surface area, 10–65 μm thick coatings were generated on chromatography paper strips and placed in the head-space of vertical sealed tubes containing liquid to hydrate the paper. These gas-phase microbial coatings hydrated by liquid in the paper pore space demonstrated absorption or evolution of H2, CO, CO2 or O2. The microbial products produced, ethanol and acetate, diffuse into the hydrated paper pores and accumulate in the liquid at the bottom of the tube. The paper provides hydration to the back side of the coating and also separates the biocatalyst from the products. Coating reactivity was demonstrated for Chlamydomonas reinhardtii CC124, which consumed CO2 and produced 10.2 ± 0.2 mmol O2 m−2 h−1, Rhodopseudomonas palustris CGA009, which consumed acetate and produced 0.47 ± 0.04 mmol H2 m−2 h−1, Clostridium ljungdahlii OTA1, which consumed 6 mmol CO m−2 h−1, and Synechococcus sp. PCC7002, which consumed CO2 and produced 5.00 ± 0.25 mmol O2 m−2 h−1. Coating thickness and microstructure were related to microbe size as determined by digital micrometry, profilometry, and confocal microscopy. The immobilization of different microorganisms in thin adhesive films in the gas phase demonstrates the utility of this method for evaluating genetically optimized microorganisms for gas absorption and gas evolution. DA - 2012/5/17/ PY - 2012/5/17/ DO - 10.1007/s10295-012-1135-8 VL - 39 IS - 9 SP - 1269-1278 J2 - J Ind Microbiol Biotechnol LA - en OP - SN - 1367-5435 1476-5535 UR - http://dx.doi.org/10.1007/S10295-012-1135-8 DB - Crossref KW - Latex coating immobilization on chromatography paper KW - Chlamydomonas KW - Rhodopseudomonas KW - Clostridium KW - Synechococcus ER - TY - JOUR TI - Matelea sanojana (Apocynaceae, Asclepiadoideae), a new species in the Matelea squiresii complex from Venezuela AU - Krings, A. AU - Morillo, G. T2 - Systematic Botany AB - Abstract A new species from Venezuela, Matelea sanojana (Apocynaceae, Asclepiadoideae, Gonolobinae), is described and illustrated. The species has affinities to the M. squiresii complex in Matelea s. l., but is easily distinguished by its lanceolate leaves and densely pubescentringed gynostegium. The new species is currently only known from Municipio Caroni, Estado Bolivar. A key and illustrations to identify the pubescent-flowered members of the complex are provided. DA - 2012/// PY - 2012/// DO - 10.1600/036364412x656572 VL - 37 IS - 4 SP - 992–994 KW - Asclepiadoideae KW - climbing milkweeds KW - Gonolobinae KW - Guiana Shield KW - South America ER - TY - JOUR TI - Matelea gilbertoana (Apocynaceae), a New Species from Venezuela AU - Krings, Alexander T2 - SYSTEMATIC BOTANY AB - Abstract A new species from Venezuela, Matelea gilbertoana (Apocynaceae, Asclepiadoideae, Gonolobinae), is described and illustrated. The species has affinities to the ocellate complex in Matelea s. 1., but is easily distinguished by its involute corolla lobes. A key to identify the continental species of the ocellate complex is provided. DA - 2012/// PY - 2012/// DO - 10.1600/036364412x656473 VL - 37 IS - 4 SP - 989-991 SN - 1548-2324 KW - Asclepiadoideae KW - climbing milkweeds KW - Gonolobinae KW - ocellate KW - South America ER - TY - JOUR TI - Chloroplast DNA phylogenomics of Monocots – Insights into the placement of Liliales and influences of gene partitions AU - Liu, J. AU - Qi, Z.C. AU - Zhao, Y.P. AU - Fu, C.X. AU - Xiang, Q.-Y. T2 - Molecular Phylogenetics and Evolution AB - The complete nucleotide sequence of the chloroplast genome (cpDNA) of Smilax china L. (Smilacaceae) is reported. It is the first complete cp genome sequence in Liliales. Genomic analyses were conducted to examine the rate and pattern of cpDNA genome evolution in Smilax relative to other major lineages of monocots. The cpDNA genomic sequences were combined with those available for Lilium to evaluate the phylogenetic position of Liliales and to investigate the influence of taxon sampling, gene sampling, gene function, natural selection, and substitution rate on phylogenetic inference in monocots. Phylogenetic analyses using sequence data of gene groups partitioned according to gene function, selection force, and total substitution rate demonstrated evident impacts of these factors on phylogenetic inference of monocots and the placement of Liliales, suggesting potential evolutionary convergence or adaptation of some cpDNA genes in monocots. Our study also demonstrated that reduced taxon sampling reduced the bootstrap support for the placement of Liliales in the cpDNA phylogenomic analysis. Analyses of sequences of 77 protein genes with some missing data and sequences of 81 genes (all protein genes plus the rRNA genes) support a sister relationship of Liliales to the commelinids-Asparagales clade, consistent with the APG III system. Analyses of 63 cpDNA protein genes for 32 taxa with few missing data, however, support a sister relationship of Liliales (represented by Smilax and Lilium) to Dioscoreales-Pandanales. Topology tests indicated that these two alignments do not significantly differ given any of these three cpDNA genomic sequence data sets. Furthermore, we found no saturation effect of the data, suggesting that the cpDNA genomic sequence data used in the study are appropriate for monocot phylogenetic study and long-branch attraction is unlikely to be the cause to explain the result of two well-supported, conflict placements of Liliales. Further analyses using sufficient nuclear data remain necessary to evaluate these two phylogenetic hypotheses regarding the position of Liliales and to address the causes of signal conflict among genes and partitions. DA - 2012/// PY - 2012/// DO - 10.1016/j.ympev.2012.05.010 VL - 64 IS - 3 SP - 545–562 SN - 1095-9513 KW - Smilax KW - Chloroplast genoine KW - Monocot phylogeny KW - cpDNA phylogenomics KW - Taxon sampling KW - Gene sampling KW - Phylogenetic effect of natural selection and nucleotide substitution rate ER - TY - JOUR TI - Caught in a fire trap: Recurring fire creates stable size equilibria in woody resprouters AU - Grady, John M. AU - Hoffmann, William A. T2 - ECOLOGY AB - Globally, fire maintains many mesic habitats in an open canopy state by killing woody plants while reducing the size of those able to resprout. Where fire is frequent, tree saplings are often suppressed by a “fire trap” of repeated topkill (death of aerial biomoass) and resprouting, preventing them from reaching adult size. The ability to tolerate repeated topkill is an essential life‐history trait that allows a sapling to persist until it experiences a long fire‐free interval, during which it can escape the fire trap. We hypothesized that persistence in the fire trap results from a curvilinear relationship between pre‐burn size and resprout size, which causes a plant to approach an equilibrial size in which post‐fire biomass recovery is equal to fire‐induced biomass loss. We also predicted that the equilibrial stem size is positively related to resource availability. To test these hypotheses, we collected data on pre‐burn and resprout size of five woody plant species at wetland ecotones in longleaf pine savanna subjected to frequent burning. As expected, all species exhibited similar curvilinear relationships between pre‐burn size and resprout size. The calculated equilibrial sizes were strong predictors of mean plant size across species and growing conditions, supporting the persistence equilibrium model. An alternative approach using matrix models yielded similar results. Resprouting was less vigorous in dry sites than at wet sites, resulting in smaller equilibrial stem sizes in drier sites; extrapolating these results provides an explanation for the absence of these species in xeric uplands. This new framework offers a straightforward approach to guide data collection for experimental, comparative, and modeling studies of plant persistence and community dynamics in frequently burned habitats. DA - 2012/9// PY - 2012/9// DO - 10.1890/12-0354.1 VL - 93 IS - 9 SP - 2052-2060 SN - 1939-9170 KW - fire KW - fire trap KW - Fort Bragg, North Carolina, USA KW - longleaf pine savanna, southeastern USA KW - persistence equilibrium model KW - persistence niche KW - resprouting KW - shrub KW - topkill KW - tree KW - wetland-savanna ecotone KW - woody-plant dynamics ER - TY - JOUR TI - A contemporary, laboratory-intensive course on messenger RNA transcription and processing AU - Carson, Sue AU - Miller, Heather T2 - BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION AB - Abstract Messenger ribonucleic acid (mRNA) plays a pivotal role in the central dogma of molecular biology. Importantly, molecular events occurring during and after mRNA synthesis have the potential to create multiple proteins from one gene, leading to some of the remarkable protein diversity that genomes hold. The North Carolina State University Biotechnology Program developed and implemented a new, laboratory‐intensive course to provide students with a contemporary view of mRNA entitled “mRNA: Transcription and Processing.” This course, offered at both the undergraduate and graduate levels, aimed to introduce students to the many functions of RNA, with an emphasis on mRNA. In addition to fundamental aspects of these processes, students were exposed to cutting‐edge techniques used to analyze mRNA in both lecture and laboratory components. We evaluated this course over two semesters and found that learning outcomes were met by both undergraduate and graduate students, based on assessments such as laboratory reports, pre‐lab assignments, a final exam, and successful results in the laboratory. We also examined student perceptions through anonymous surveys, where students reported gains in confidence in both conceptual knowledge and technical skill after completing this course. DA - 2012/// PY - 2012/// DO - 10.1002/bmb.20580 VL - 40 IS - 2 SP - 89-99 SN - 1470-8175 KW - mRNA KW - transcription KW - processing KW - laboratory ER - TY - JOUR TI - A Small Molecule Inhibitor Partitions Two Distinct Pathways for Trafficking of Tonoplast Intrinsic Proteins in Arabidopsis AU - Rivera-Serrano, Efrain E. AU - Rodriguez-Welsh, Maria F. AU - Hicks, Glenn R. AU - Rojas-Pierce, Marcela T2 - PLOS ONE AB - Tonoplast intrinsic proteins (TIPs) facilitate the membrane transport of water and other small molecules across the plant vacuolar membrane, and members of this family are expressed in specific developmental stages and tissue types. Delivery of TIP proteins to the tonoplast is thought to occur by vesicle-mediated traffic from the endoplasmic reticulum to the vacuole, and at least two pathways have been proposed, one that is Golgi-dependent and another that is Golgi-independent. However, the mechanisms for trafficking of vacuolar membrane proteins to the tonoplast remain poorly understood. Here we describe a chemical genetic approach to unravel the mechanisms of TIP protein targeting to the vacuole in Arabidopsis seedlings. We show that members of the TIP family are targeted to the vacuole via at least two distinct pathways, and we characterize the bioactivity of a novel inhibitor that can differentiate between them. We demonstrate that, unlike for TIP1;1, trafficking of markers for TIP3;1 and TIP2;1 is insensitive to Brefeldin A in Arabidopsis hypocotyls. Using a chemical inhibitor that may target this BFA-insensitive pathway for membrane proteins, we show that inhibition of this pathway results in impaired root hair growth and enhanced vacuolar targeting of the auxin efflux carrier PIN2 in the dark. Our results indicate that the vacuolar targeting of PIN2 and the BFA-insensitive pathway for tonoplast proteins may be mediated in part by common mechanisms. DA - 2012/9/5/ PY - 2012/9/5/ DO - 10.1371/journal.pone.0044735 VL - 7 IS - 9 SP - SN - 1932-6203 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84866026793&partnerID=MN8TOARS ER - TY - JOUR TI - Evaluation of a quantitative H2S MPN test for fecal microbes analysis of water using biochemical and molecular identification AU - McMahan, Lanakila AU - Grunden, Amy M. AU - Devine, Anthony A. AU - Sobsey, Mark D. T2 - WATER RESEARCH AB - The sensitivity and specificity of the H2S test to detect fecal bacteria in water has been variable and uncertain in previous studies, partly due to its presence–absence results. Furthermore, in groundwater samples false-positive results have been reported, with H2S-positive samples containing no fecal coliforms or Escherichia coli. False-negative results also have been reported in other studies, with H2S-negative samples found to contain E. coli. Using biochemical and molecular methods and a novel quantitative test format, this research identified the types and numbers of microbial community members present in natural water samples, including fecal indicators and pathogens as well as other bacteria. Representative water sources tested in this study included cistern rainwater, a protected lake, and wells in agricultural and forest settings. Samples from quantitative H2S tests of water were further cultured for fecal bacteria by spread plating onto the selective media for detection and isolation of Aeromonas spp., E. coli, Clostridium spp., H2S-producers, and species of Salmonella and Shigella. Isolates were then tested for H2S production, and identified to the genus and species level using biochemical methods. Terminal Restriction Fragment Length Polymorphisms (TRFLP) was the molecular method employed to quantitatively characterize microbial community diversity. Overall, it was shown that water samples testing positive for H2S bacteria also had bacteria of likely fecal origin and waters containing fecal pathogens also were positive for H2S bacteria. Of the microorganisms isolated from natural water, greater than 70 percent were identified using TRFLP analysis to reveal a relatively stable group of organisms whose community composition differed with water source and over time. These results further document the validity of the H2S test for detecting and quantifying fecal contamination of water. DA - 2012/4/15/ PY - 2012/4/15/ DO - 10.1016/j.watres.2011.12.037 VL - 46 IS - 6 SP - 1693-1704 SN - 0043-1354 KW - Quantitative H2S test KW - Microbial water quality KW - TRFLP KW - Fecal indicator ER - TY - JOUR TI - Ecological thresholds at the savanna-forest boundary: how plant traits, resources and fire govern the distribution of tropical biomes AU - Hoffmann, William A. AU - Geiger, Erika L. AU - Gotsch, Sybil G. AU - Rossatto, Davi R. AU - Silva, Lucas C. R. AU - Lau, On Lee AU - Haridasan, M. AU - Franco, Augusto C. T2 - ECOLOGY LETTERS AB - Abstract Fire shapes the distribution of savanna and forest through complex interactions involving climate, resources and species traits. Based on data from central Brazil, we propose that these interactions are governed by two critical thresholds. The fire‐resistance threshold is reached when individual trees have accumulated sufficient bark to avoid stem death, whereas the fire‐suppression threshold is reached when an ecosystem has sufficient canopy cover to suppress fire by excluding grasses. Surpassing either threshold is dependent upon long fire‐free intervals, which are rare in mesic savanna. On high‐resource sites, the thresholds are reached quickly, increasing the probability that savanna switches to forest, whereas low‐resource sites are likely to remain as savanna even if fire is infrequent. Species traits influence both thresholds; saplings of savanna trees accumulate bark thickness more quickly than forest trees, and are more likely to become fire resistant during fire‐free intervals. Forest trees accumulate leaf area more rapidly than savanna trees, thereby accelerating the transition to forest. Thus, multiple factors interact with fire to determine the distribution of savanna and forest by influencing the time needed to reach these thresholds. Future work should decipher multiple environmental controls over the rates of tree growth and canopy closure in savanna. DA - 2012/7// PY - 2012/7// DO - 10.1111/j.1461-0248.2012.01789.x VL - 15 IS - 7 SP - 759-768 SN - 1461-0248 KW - Alternate stable states KW - critical thresholds KW - forest KW - savanna KW - tipping point ER - TY - JOUR TI - An ER-targeted calcium-binding peptide confers salt and drought tolerance mediated by CIPK6 in Arabidopsis AU - Tsou, Pei-Lan AU - Lee, Sang Yoon AU - Allen, Nina Stromgren AU - Winter-Sederoff, Heike AU - Robertson, Dominique T2 - PLANTA DA - 2012/3// PY - 2012/3// DO - 10.1007/s00425-011-1522-9 VL - 235 IS - 3 SP - 539-552 SN - 1432-2048 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84857634774&partnerID=MN8TOARS KW - ER calcium KW - Calcium-binding peptide (CBP) KW - CBL-interacting protein kinase (CIPK6) KW - Drought KW - Salt ER - TY - JOUR TI - Processing of materials derived from sweet sorghum for biobased products AU - Whitfield, Matthew B. AU - Chinn, Mari S. AU - Veal, Matthew W. T2 - INDUSTRIAL CROPS AND PRODUCTS AB - Sweet sorghum (Sorghum bicolor (L.) Moench) is particularly suitable as a feedstock for a variety of bioprocesses, largely because of its high yields of both lignocellulosic biomass and fermentable saccharides. Sweet sorghum is less economically important for refined sugar production than other sugar crops, e.g., sugar beet and sugarcane, but can produce more raw fermentable sugar under marginal conditions than those crops. In this review, the agronomic requirements of sorghum (viz., water, soil, and nutrient requirements), cultural practices, and plant morphology are discussed from a bioprocessing perspective. Historically, sugar extraction from the plant in the form of juice has been of primary interest; these methods, along with modern developments are presented. Recently, the direct yeast fermentation of sorghum juice for ethanol production has been studied. Additionally, the bagasse resulting from the juice extraction has been used for a variety of potential products: forage, silage, combustion energy, synthesis gas, and paper. The bagasse contains high levels of relatively low crystallinity cellulose, along with relatively labile lignin, and so is itself of interest as a fermentation feedstock. Whole sorghum stalk, and its bagasse, have been subjected to studies of a wide array of pretreatment, enzymatic hydrolysis, and fermentation processes. The potential fermentation products of sweet sorghum are wide ranging; those demonstrated include ethanol, acetone, butanol, various lipids, lactic acid, hydrogen, and methane. Several potential native products of the plant, in addition to cellulose for paper production, are also identified: waxes, proteins, and allelopathic compounds, such as sorgoleone. DA - 2012/5// PY - 2012/5// DO - 10.1016/j.indcrop.2011.12.011 VL - 37 IS - 1 SP - 362-375 SN - 1872-633X KW - Sorghum bicolor (L.) Moench KW - Sweet sorghum KW - Fermentation KW - Lignocellulosic bagasse KW - Biofuel KW - Natural products ER - TY - JOUR TI - Where has all the message gone? AU - Davies, Eric AU - Stankovic, Bratislav AU - Vian, Alain AU - Wood, Andrew J. T2 - PLANT SCIENCE AB - We provide a brief history of polyribosomes, ergosomes, prosomes, informosomes, maternal mRNA, stored mRNA, and RNP particles. Even though most published research focuses on total mRNA rather than polysomal mRNA and often assumes they are synonymous - i.e., if a functional mRNA is present, it must be translated - results from our laboratories comparing polysomal RNA and total mRNA in a range of "normal" issues show that some transcripts are almost totally absent from polysomes while others are almost entirely associated with polysomes. We describe a recent model from yeast showing various destinies for polysomal mRNA once it has been released from polysomes. The main points we want to emphasize are; a) when mRNA leaves polysomes to go to prosomes, P-bodies, stress granules, etc., it is not necessarily destined for degradation - it can be re-utilized; b) "normal" tissue, not just seeds and stressed tissue, contains functional non-polysomal mRNA; c) association of mRNA with different classes of polysomes affects their sub-cellular location and translatability; and d) drawbacks, misinterpretations, and false hopes arise from analysis of total mRNA rather than polysomal mRNA and from presuming that all polysomes are "created equal". DA - 2012/4// PY - 2012/4// DO - 10.1016/j.plantsci.2011.08.001 VL - 185 SP - 23-32 SN - 0168-9452 KW - mRNP KW - Polysome KW - P-bodies KW - RNA KW - Ribosome KW - Translation ER - TY - JOUR TI - Triallelic SNP-mediated genotyping of regenerated protoplasts of the heterokaryotic fungus Rhizoctonia solani AU - Thomas, Elizabeth AU - Pakala, Suman AU - Fedorova, Natalie D. AU - Nierman, William C. AU - Cubeta, Marc A. T2 - JOURNAL OF BIOTECHNOLOGY AB - The aneuploid and heterokaryotic nuclear condition of the soil fungus Rhizoctonia solani have provided challenges in obtaining a complete genome sequence. To better aid in the assembly and annotation process, a protoplast and single nucleotide polymorphism (SNP)-based method was developed to identify regenerated protoplasts with a reduced nuclear genome. Protocol optimization experiments showed that enzymatic digestion of mycelium from a 24 h culture of R. solani increased the proportion of protoplasts with a diameter of ≤7.5 μm and 1–4 nuclei. To determine whether strains regenerated from protoplasts with a reduced number of nuclei were genetically different from the parental strain, triallelic SNPs identified from variance records of the genomic DNA sequence reads of R. solani were used in PCR-based genotyping assays. Results from 16 of the 24 SNP-based PCR assays provided evidence that one of the three alleles was missing in the 11 regenerated protoplast strains, suggesting that these strains represent a reduced genomic complement of the parental strain. The protoplast and triallelic SNP-based method used in this study may be useful in strain development and analysis of other basidiomycete fungi with complex nuclear genomes. DA - 2012/4/15/ PY - 2012/4/15/ DO - 10.1016/j.jbiotec.2012.01.024 VL - 158 IS - 3 SP - 144-150 SN - 1873-4863 KW - Rhizoctonia solani KW - Heterokaryon KW - Protoplast KW - Strain development KW - SNP KW - Triallelic variant ER -