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Find video protocols related to scientific articles indexed in Pubmed.
Fullerene cyanation does not always increase electron affinity: an experimental and theoretical study.
Phys Chem Chem Phys
PUBLISHED: 11-20-2014
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The electron affinities of C70 derivatives with trifluoromethyl, methyl and cyano groups were studied experimentally and theoretically using low-temperature photoelectron spectroscopy (LT PES) and density functional theory (DFT). The electronic effects of these functional groups were determined and found to be highly dependent on the addition patterns. Substitution of CF3 for CN for the same addition pattern increases the experimental electron affinity by 70 meV per substitution. The synthesis of a new fullerene derivative, C70(CF3)10(CN)2, is reported for the first time.
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An elusive fulvene 1,7,11,24-C60(CF3)4 and its unusual reactivity.
Chem. Commun. (Camb.)
PUBLISHED: 10-15-2014
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The X-ray crystal structure of a trifluoromethylfullerene (TMF), 1,7,11,24-C60(CF3)4, is reported for the first time. This elusive intermediate, while highly air stable as a solid, exhibits highly regioselective reactivity towards molecular oxygen in polar solvents, and only when exposed to light.
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EARLY BUD-BREAK 1 (EBB1) is a regulator of release from seasonal dormancy in poplar trees.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 06-20-2014
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Trees from temperate latitudes transition between growth and dormancy to survive dehydration and freezing stress during winter months. We used activation tagging to isolate a dominant mutation affecting release from dormancy and identified the corresponding gene EARLY BUD-BREAK 1 (EBB1). We demonstrate through positioning of the tag, expression analysis, and retransformation experiments that EBB1 encodes a putative APETALA2/Ethylene responsive factor transcription factor. Transgenic up-regulation of the gene caused early bud-flush, whereas down-regulation delayed bud-break. Native EBB1 expression was highest in actively growing apices, undetectable during the dormancy period, but rapidly increased before bud-break. The EBB1 transcript was localized in the L1/L2 layers of the shoot meristem and leaf primordia. EBB1-overexpressing transgenic plants displayed enlarged shoot meristems, open and poorly differentiated buds, and a higher rate of cell division in the apex. Transcriptome analyses of the EBB1 transgenics identified 971 differentially expressed genes whose expression correlated with the EBB1 expression changes in the transgenic plants. Promoter analysis among the differentially expressed genes for the presence of a canonical EBB1-binding site identified 65 putative target genes, indicative of a broad regulatory context of EBB1 function. Our results suggest that EBB1 has a major and integrative role in reactivation of meristem activity after winter dormancy.
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The floral transcriptome of Eucalyptus grandis.
New Phytol.
PUBLISHED: 06-07-2014
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As a step toward functional annotation of genes required for floral initiation and development within the Eucalyptus genome, we used short read sequencing to analyze transcriptomes of floral buds from early and late developmental stages, and compared these with transcriptomes of diverse vegetative tissues, including leaves, roots, and stems. A subset of 4807 genes (13% of protein-coding genes) were differentially expressed between floral buds of either stage and vegetative tissues. A similar proportion of genes were differentially expressed among all tissues. A total of 479 genes were differentially expressed between early and late stages of floral development. Gene function enrichment identified 158 gene ontology classes that were overrepresented in floral tissues, including 'pollen development' and 'aromatic compound biosynthetic process'. At least 40 floral-dominant genes lacked functional annotations and thus may be novel floral transcripts. We analyzed several genes and gene families in depth, including 49 putative biomarkers of floral development, the MADS-box transcription factors, 'S-domain'-receptor-like kinases, and selected gene family members with phosphatidylethanolamine-binding protein domains. Expanded MADS-box gene subfamilies in Eucalyptus grandis included SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1), SEPALLATA (SEP) and SHORT VEGETATIVE PHASE (SVP) Arabidopsis thaliana homologs. These data provide a rich resource for functional and evolutionary analysis of genes controlling eucalypt floral development, and new tools for breeding and biotechnology.
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Poly(trifluoromethyl)azulenes: structures and acceptor properties.
Chem. Commun. (Camb.)
PUBLISHED: 05-02-2014
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Six new poly(trifluoromethyl)azulenes prepared in a single high-temperature reaction exhibit strong electron accepting properties in the gas phase and in solution and demonstrate the propensity to form regular ?-stacked columns in donor-acceptor crystals when mixed with pyrene as a donor.
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The genome of Eucalyptus grandis.
Nature
PUBLISHED: 04-02-2014
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Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.
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Single-step gas-phase polyperfluoroalkylation of naphthalene leads to thermodynamic products.
Chemistry
PUBLISHED: 03-03-2014
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High-temperature gas-phase, solvent- and catalyst-free reaction of naphthalene with an excess of RF I reagent (RF ?CF3 , C2 F5 , n-C3 F7 , and n-C4 F9 ) was used for the first time to produce a series of highly perfluoroalkylated naphthalene products NAPH(RF )n with n=2-5. Four 95+?% pure 1,3,5,7-NAPH(RF )4 with RF ?CF3 , C2 F5 , n-C3 F7 , and n-C4 F9 were isolated using a simple chromatography-free procedure. These new compounds were fully characterized by (19) F and (1) H?NMR spectroscopy, X-ray crystallography (for RF ?CF3 and C2 F5 ), atmospheric-pressure chemical ionization mass spectrometry, and cyclic and square-wave voltammetry. DFT calculations confirm that the proposed synthesis yields the most stable isomers that have not been accessed by alternative preparation techniques.
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Structure of 7,9,12,15,18,20,39,24,45,57-C60(CF3)10(1,2:3,4-O)2. The first regiospecific diepoxidation of a fullerene derivative.
Acta Chim Slov
PUBLISHED: 10-31-2013
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An unusual regiospecific diepoxidation of an isomer of C60(CF3)10 was discovered to slowly occur in solution while exposed to air. This is the only known example of a perfluoroalkyl fullerene undergoing epoxidation under ambient conditions. This compound was characterized by a variety of analytical methods including 19F NMR spectroscopy, APCI-MS, UV-vis spectroscopy, and X-ray crystallography. Numerous oxidation methods were explored including ozonation, photolysis, thermolysis, and the chemical oxidation by m-chloroperoxobenzoic acid, none of which has yielded the diepoxide. This indicated that the process is kinetically very slow, presumably due to steric crowding around the oxygen addition sites. These findings of spontaneous diepoxidation of the otherwise stable compound have far reaching implications as more fullerenes and fullerene derivatives are being used in organic electronics, and their instability toward oxidation in ambient conditions may alter the performance of the device.
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Duward F. Shriver (1934-2013).
Angew. Chem. Int. Ed. Engl.
PUBLISHED: 09-12-2013
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Duward F. Shriver passed away at the age of 78 on March 6, 2013. He was well-known to generations of inorganic and organometallic chemists from his classic textbooks.
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Fullerene "superhalogen" radicals: the substituent effect on electronic properties of 1,7,11,24,27-C60X5.
Chemistry
PUBLISHED: 04-02-2013
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Hexasubstituted fullerenes with the skew pentagonal pyramid (SPP) addition pattern are predominantly formed in many types of reactions and represent important and versatile building blocks for supramolecular chemistry, biomedical and optoelectronic applications. Regioselective synthesis and characterization of the new SPP derivative, C60(CF3)4(CN)H, in this work led to the experimental identification of the new family of "superhalogen fullerene radicals", species with the gas-phase electron affinity higher than that of the most electronegative halogens, F and Cl. Low-temperature photoelectron spectroscopy and DFT studies of different C60X5 radicals reveal a profound effect of X groups on their electron affinities (EA), which vary from 2.76 eV (X=CH3) to 4.47 eV (X=CN). The measured gas-phase EA of the newly synthesized C60(CF3)4CN equals 4.28(1) eV, which is about 1 eV higher than the EA of Cl atom. An observed remarkable stability of C60(CF3)4CN(-) in solution under ambient conditions opens new venues for design of air-stable molecular complexes and salts for supramolecular structures of electroactive functional materials.
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Regioselective sequential additions of nucleophiles and electrophiles to perfluoroalkylfullerenes: which cage C atoms are the most reactive and why?
Chemistry
PUBLISHED: 02-18-2013
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The sequential addition of CN(-) or CH3(-) and electrophiles to three perfluoroalkylfullerenes (PFAFs), C(s)-C70(CF3)8, C1-C70(CF3)10, and C(s)-p-C60(CF3)2, was carried out to determine the most reactive individual fullerene C atoms (as opposed to the most reactive C=C bonds, which has previously been studied). Each PFAF reacted with CH3(-) or CN(-) to generate metastable PFAF(CN)(-) or PFAF(CH3)2(2-) species with high regioselectivity (i.e., one or two predominant isomers). They were treated with electrophiles E(+) to generate PFAF(CN)(E) or PFAF(CH3)2(E)2 derivatives, also with high regioselectivity (E(+)=CN(+), CH3(+), or H(+)). All of the predominant products, characterized by mass spectrometry and (19)F NMR spectroscopy, are new compounds. Some could be purified by HPLC to give single isomers. Two of them, C70(CF3)8(CN)2 and C70(CF3)10(CH3)2(CN)2, were characterized by single-crystal X-ray diffraction. DFT calculations were used to propose whether a particular reaction is under kinetic or thermodynamic control.
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C20H4(C4F8)3: a fluorine-containing annulated corannulene that is a better electron acceptor than C60.
Angew. Chem. Int. Ed. Engl.
PUBLISHED: 01-29-2013
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At sixes and sevens: The reaction of corannulene with 35 equivalents of 1,4-C4F8I2 is an efficient and a relatively selective process that yields two main products in which six H atoms are substituted with three C4F8 moieties that form six- and seven-membered rings. Low-temperature photoelectron spectroscopy showed the electron affinity of the major isomer (shown) exceeds that of C60 (2.74±0.02 and 2.689±0.008?eV, respectively).
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Poplars with a PtDDM1-RNAi transgene have reduced DNA methylation and show aberrant post-dormancy morphology.
Planta
PUBLISHED: 01-22-2013
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The Arabidopsis thaliana DDM1 (Decreased DNA Methylation) gene is necessary for the maintenance of DNA methylation and heterochromatin assembly. In Arabidopsis, ddm1 mutants exhibit strong but delayed morphological phenotypes. We used RNA interference (RNAi) to suppress transcripts of two orthologous DDM1 paralogs in Populus trichocarpa and examined effects on whole plant phenotypes during perennial growth and seasonal dormancy. The RNAi-PtDDM1 transgenic poplars showed a wide range of DDM1 transcript suppression; the most strongly suppressed line had 37.5 % of the expression of the non-transgenic control. Genomic cytosine methylation (mC %) was 11.1 % in the non-transgenic control, compared with 9.1 % for the transgenic event with lowest mC %, a reduction of 18.1 %. An evaluation of greenhouse growth directly after acclimation of in vitro grown plants showed no developmental or growth rate abnormalities associated with the decrease in PtDDM1 expression. However, after a dormancy cycle and growth outdoors, a mottled leaf phenotype appeared in some of the transgenic insertion events that had strongly reduced PtDDM1 expression and DNA methylation. The phenotypic consequences of reduced DDM1 activity and DNA methylation appears to increase with cumulative plant propagation and growth.
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Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa.
BMC Plant Biol.
PUBLISHED: 01-18-2013
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Cytosine DNA methylation (5mC) is an epigenetic modification that is important to genome stability and regulation of gene expression. Perturbations of 5mC have been implicated as a cause of phenotypic variation among plants regenerated through in vitro culture systems. However, the pattern of change in 5mC and its functional role with respect to gene expression, are poorly understood at the genome scale. A fuller understanding of how 5mC changes during in vitro manipulation may aid the development of methods for reducing or amplifying the mutagenic and epigenetic effects of in vitro culture and plant transformation.
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Epigenetic regulation of adaptive responses of forest tree species to the environment.
Ecol Evol
PUBLISHED: 01-17-2013
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Epigenetic variation is likely to contribute to the phenotypic plasticity and adaptative capacity of plant species, and may be especially important for long-lived organisms with complex life cycles, including forest trees. Diverse environmental stresses and hybridization/polyploidization events can create reversible heritable epigenetic marks that can be transmitted to subsequent generations as a form of molecular "memory". Epigenetic changes might also contribute to the ability of plants to colonize or persist in variable environments. In this review, we provide an overview of recent data on epigenetic mechanisms involved in developmental processes and responses to environmental cues in plant, with a focus on forest tree species. We consider the possible role of forest tree epigenetics as a new source of adaptive traits in plant breeding, biotechnology, and ecosystem conservation under rapid climate change.
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DR5 as a reporter system to study auxin response in Populus.
Plant Cell Rep.
PUBLISHED: 01-03-2013
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KEY MESSAGE : Auxin responsive promoter DR5 reporter system is functional in Populus to monitor auxin response in tissues including leaves, roots, and stems. We described the behavior of the DR5::GUS reporter system in stably transformed Populus plants. We found several similarities with Arabidopsis, including sensitivity to native and synthetic auxins, rapid induction after treatment in a variety of tissues, and maximal responses in root tissues. There were also several important differences from Arabidopsis, including slower time to maximum response and lower induction amplitude. Young leaves and stem sections below the apex showed much higher DR5 activity than did older leaves and stems undergoing secondary growth. DR5 activity was highest in cortex, suggesting high levels of auxin concentration and/or sensitivity in this tissue. Our study shows that the DR5 reporter system is a sensitive and facile system for monitoring auxin responses and distribution at cellular resolution in poplar.
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Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus.
Genome Res.
PUBLISHED: 10-05-2011
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Comparative analysis of multiple angiosperm genomes has implicated gene duplication in the expansion and diversification of many gene families. However, empirical data and theory suggest that whole-genome and small-scale duplication events differ with respect to the types of genes preserved as duplicate pairs. We compared gene duplicates resulting from a recent whole genome duplication to a set of tandemly duplicated genes in the model forest tree Populus trichocarpa. We used a combination of microarray expression analyses of a diverse set of tissues and functional annotation to assess factors related to the preservation of duplicate genes of both types. Whole genome duplicates are 700 bp longer and are expressed in 20% more tissues than tandem duplicates. Furthermore, certain functional categories are over-represented in each class of duplicates. In particular, disease resistance genes and receptor-like kinases commonly occur in tandem but are significantly under-retained following whole genome duplication, while whole genome duplicate pairs are enriched for members of signal transduction cascades and transcription factors. The shape of the distribution of expression divergence for duplicated pairs suggests that nearly half of the whole genome duplicates have diverged in expression by a random degeneration process. The remaining pairs have more conserved gene expression than expected by chance, consistent with a role for selection under the constraints of gene balance. We hypothesize that duplicate gene preservation in Populus is driven by a combination of subfunctionalization of duplicate pairs and purifying selection favoring retention of genes encoding proteins with large numbers of interactions.
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Tissue-specific expression of Populus C19 GA 2-oxidases differentially regulate above- and below-ground biomass growth through control of bioactive GA concentrations.
New Phytol.
PUBLISHED: 08-05-2011
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• Here, we studied the poplar C(19) gibberellin 2-oxidase (GA2ox) gene subfamily. We show that a set of paralogous gene pairs differentially regulate shoot and root development. • PtGA2ox4 and its paralogous gene PtGA2ox5 are primarily expressed in aerial organs, and overexpression of PtGA2ox5 produced a strong dwarfing phenotype characteristic of GA deficiency. Suppression of PtGA2ox4 and PtGA2ox5 led to increased biomass growth, but had no effect on root development. By contrast, the PtGA2ox2 and PtGA2ox7 paralogous pair was predominantly expressed in roots, and when these two genes were RNAi-suppressed it led to a decrease of root biomass. • The morphological changes in the transgenic plants were underpinned by tissue-specific increases in bioactive GAs that corresponded to the predominant native expression of the targeted paralogous gene pair. Although RNAi suppression of both paralogous pairs led to changes in wood development, they were much greater in the transgenics with suppressed PtGA2ox4 and PtGA2ox5. The degree of gene suppression in independent events was strongly associated with phenotypes, demonstrating dose-dependent control of growth by GA2ox RNA concentrations. • The expression and transgenic modifications reported here show that shoot- and leaf-expressed PtGA2ox4 and PtGA2ox5 specifically restrain aerial shoot growth, while root-expressed PtGA2ox2 and PtGA2ox7 promote root development.
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FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 06-08-2011
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Annual plants grow vegetatively at early developmental stages and then transition to the reproductive stage, followed by senescence in the same year. In contrast, after successive years of vegetative growth at early ages, woody perennial shoot meristems begin repeated transitions between vegetative and reproductive growth at sexual maturity. However, it is unknown how these repeated transitions occur without a developmental conflict between vegetative and reproductive growth. We report that functionally diverged paralogs FLOWERING LOCUS T1 (FT1) and FLOWERING LOCUS T2 (FT2), products of whole-genome duplication and homologs of Arabidopsis thaliana gene FLOWERING LOCUS T (FT), coordinate the repeated cycles of vegetative and reproductive growth in woody perennial poplar (Populus spp.). Our manipulative physiological and genetic experiments coupled with field studies, expression profiling, and network analysis reveal that reproductive onset is determined by FT1 in response to winter temperatures, whereas vegetative growth and inhibition of bud set are promoted by FT2 in response to warm temperatures and long days in the growing season. The basis for functional differentiation between FT1 and FT2 appears to be expression pattern shifts, changes in proteins, and divergence in gene regulatory networks. Thus, temporal separation of reproductive onset and vegetative growth into different seasons via FT1 and FT2 provides seasonality and demonstrates the evolution of a complex perennial adaptive trait after genome duplication.
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Repression of gibberellin biosynthesis or signaling produces striking alterations in poplar growth, morphology, and flowering.
Planta
PUBLISHED: 05-10-2011
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We modified gibberellin (GA) metabolism and signaling in transgenic poplars using dominant transgenes and studied their effects for 3 years under field conditions. The transgenes that we employed either reduced the bioactive GAs, or attenuated their signaling. The majority of transgenic trees had significant and in many cases dramatic changes in height, crown architecture, foliage morphology, flowering onset, floral structure, and vegetative phenology. Most transgenes elicited various levels of height reduction consistent with the roles of GA in elongation growth. Several other growth traits were proportionally reduced, including branch length, internode distance, and leaf length. In contrast to elongation growth, stem diameter growth was much less affected, suggesting that semi-dwarf trees in dense stands might provide high levels of biomass production and carbon sequestration. The severity of phenotypic effects was strongly correlated with transgene expression among independent transgenic events, but often in a non-linear manner, the form of which varied widely among constructs. The majority of semi-dwarfed, transgenic plants showed delayed bud flush and early bud set, and expression of a native GAI transgene accelerated first time flowering in the field. All of the phenotypic changes observed in multiple years were stable over the 3 years of field study. Our results suggest that transgenic modification of GA action may be useful for producing semi-dwarf trees with modified growth and morphology for horticulture and other uses.
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In search of fullerene-based superacids: synthesis, X-ray structure, and DFT study of C60(C2F5)(5)H.
Chemistry
PUBLISHED: 05-02-2011
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Simply super! The perfluoroalkylfullerene C(60)(C(2)F(5))(5) H is the first structurally characterized perfluoroalkylated fullerene-based acid and is also predicted to be the first gas-phase fullerene-based superacid.
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Transgenic poplars with reduced lignin show impaired xylem conductivity, growth efficiency and survival.
Plant Cell Environ.
PUBLISHED: 02-11-2011
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We studied xylem anatomy and hydraulic architecture in 14 transgenic insertion events and a control line of hybrid poplar (Populus spp.) that varied in lignin content. Transgenic events had different levels of down-regulation of two genes encoding 4-coumarate:coenzyme A ligase (4CL). Two-year-old trees were characterized after growing either as free-standing trees in the field or as supported by stakes in a greenhouse. In free-standing trees, a 20 to 40% reduction in lignin content was associated with increased xylem vulnerability to embolism, shoot dieback and mortality. In staked trees, the decreased biomechanical demands on the xylem was associated with increases in the leaf area to sapwood area ratio and wood specific conductivity (k(s)), and with decreased leaf-specific conductivity (k(l)). These shifts in hydraulic architecture suggest that the bending stresses perceived during growth can affect traits important for xylem water transport. Severe 4CL-downregulation resulted in the patchy formation of discoloured, brown wood with irregular vessels in which water transport was strongly impeded. These severely 4CL-downregulated trees had significantly lower growth efficiency (biomass/leaf area). These results underscore the necessity of adequate lignification for mechanical support of the stem, water transport, tree growth and survival.
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Poly(perfluoroalkylation) of metallic nitride fullerenes reveals addition-pattern guidelines: synthesis and characterization of a family of Sc3N@C80(CF3)n (n = 2-16) and their radical anions.
J. Am. Chem. Soc.
PUBLISHED: 02-04-2011
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A family of highly stable (poly)perfluoroalkylated metallic nitride cluster fullerenes was prepared in high-temperature reactions and characterized by spectroscopic (MS, (19)F NMR, UV-vis/NIR, ESR), structural and electrochemical methods. For two new compounds, Sc(3)N@C(80)(CF(3))(10) and Sc(3)N@C(80)(CF(3))(12,) single crystal X-ray structures are determined. Addition pattern guidelines for endohedral fullerene derivatives with bulky functional groups are formulated as a result of experimental ((19)F NMR spectroscopy and single crystal X-ray diffraction) studies and exhaustive quantum chemical calculations of the structures of Sc(3)N@C(80)(CF(3))(n) (n = 2-16). Electrochemical studies revealed that Sc(3)N@C(80)(CF(3))(n) derivatives are easier to reduce than Sc(3)N@C(80), the shift of E(1/2) potentials ranging from +0.11 V (n = 2) to +0.42 V (n = 10). Stable radical anions of Sc(3)N@C(80)(CF(3))(n) were generated in solution and characterized by ESR spectroscopy, revealing their (45)Sc hyperfine structure. Facile further functionalizations via cycloadditions or radical additions were achieved for trifluoromethylated Sc(3)N@C(80) making them attractive versatile platforms for the design of molecular and supramolecular materials of fundamental and practical importance.
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Trade-offs between biomass growth and inducible biosynthesis of polyhydroxybutyrate in transgenic poplar.
Plant Biotechnol. J.
PUBLISHED: 01-25-2011
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Polyhydroxybutyrate (PHB) is a bioplastic that can be produced in transgenic plants by the coexpression of three bacterial genes for its biosynthesis. PHB yields from plants have been constrained by the negative impacts on plant health that result from diversion of resources into PHB production; thus, we employed an ecdysone analogue-based system for induced gene expression. We characterized 49 insertion events in hybrid transgenic poplar (Populus tremula x alba) that were produced using Agrobacterium transformation and studied two high-producing events in detail. Regenerated plants contained up to 1-2% PHB (dry weight) in leaves after 6-8 weeks of induction. Strong induction was observed with 1-10 mm Intrepid and limited direct toxicity observed. Confocal fluorescence microscopy was used to visualize PHB granules in chloroplasts after chemical treatment to reduce autofluorescence. A greenhouse study indicated that there were no negative consequences of PHB production on growth unless the PHB content exceeded 1% of leaf weight; at PHB levels above 1%, growth (height, diameter and total mass) decreased by 10%-34%.
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Reduced wood stiffness and strength, and altered stem form, in young antisense 4CL transgenic poplars with reduced lignin contents.
New Phytol.
PUBLISHED: 12-15-2010
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• Reduced lignin content in perennial crops has been sought as a means to improve biomass processability for paper and biofuels production, but it is unclear how this could affect wood properties and tree form. • Here, we studied a nontransgenic control and 14 transgenic events containing an antisense 4-coumarate:coenzyme A ligase (4CL) to discern the consequences of lignin reduction in poplar (Populus sp.). During the second year of growth, trees were grown either free-standing in a field trial or affixed to stakes in a glasshouse. • Reductions in lignin of up to 40% gave comparable losses in wood strength and stiffness. This occurred despite the fact that low-lignin trees had a similar wood density and up to three-fold more tension wood. In free-standing and staked trees, the control line had twice the height for a given diameter as did low-lignin trees. Staked trees had twice the height for a given diameter as free-standing trees in the field, but did not differ in wood stiffness. • Variation in tree morphogenesis appears to be governed by lignin x environment interactions mediated by stresses exerted on developing cells. Therefore our results underline the importance of field studies for assessing the performance of transgenic trees with modified wood properties.
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Chemical tailoring of fullerene acceptors: synthesis, structures and electrochemical properties of perfluoroisopropylfullerenes.
Chem. Commun. (Camb.)
PUBLISHED: 11-09-2010
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High-temperature syntheses of the new C(60)(i-C(3)F(7))(2,4,6) and C(70)(i-C(3)F(7))(2,4) isomers and their characterization by spectroscopic methods, X-ray crystallography, cyclic voltammetry and density functional theory provide compelling evidence that they are superior electron acceptors than trifluoromethylfullerenes.
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Dynamic HPLC study of C70 chlorination reveals a surprisingly selective synthesis of C70Cl8.
Chem. Commun. (Camb.)
PUBLISHED: 09-27-2010
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A dynamic HPLC study of C(70) chlorination led to the discovery, isolation, characterization, and development of the efficient preparatory procedures for two previously unknown soluble chlorofullerenes C(70)Cl(8) and C(70)Cl(6) and for insoluble [C(70)Cl(8)](n). A novel synthesis of 99% pure C(70)Cl(10) with a nearly quantitative yield was also developed. The first stability study of C(70)Cl(10,8,6) in solution showed that these compounds are very light-sensitive.
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Latent porosity in potassium dodecafluoro-closo-dodecaborate(2-). Structures and rapid room temperature interconversions of crystalline K2B12F12, K2(H2O)2B12F12, and K2(H2O)4B12F12 in the presence of water vapor.
J. Am. Chem. Soc.
PUBLISHED: 09-14-2010
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Structures of K(2)(H(2)O)(2)B(12)F(12) and K(2)(H(2)O)(4)B(12)F(12) were determined by X-ray diffraction. They contain [K(?-H(2)O)(2)K](2+) and [(H(2)O)K(?-H(2)O)(2)K(H(2)O)](2+) dimers, respectively, which interact with superweak B(12)F(12)(2-) anions via multiple K···F(B) interactions and (O)H···F(B) hydrogen bonds (the dimers in K(2)(H(2)O)(4)B(12)F(12) are also linked by (O)H···O hydrogen bonds). DFT calculations show that both dimers are thermodynamically stabilized by the lattice of anions: the predicted ?E values for the gas-phase dimerization of two K(H(2)O)(+) or K(H(2)O)(2)(+) cations into [K(?-H(2)O)(2)K](2+) or [(H(2)O)K(?-H(2)O)(2)K(H(2)O)](2+) are +232 and +205 kJ mol(-1), respectively. The calculations also predict that ?E for the gas-phase reaction 2 K(+) + 2 H(2)O ? [K(?-H(2)O)(2)K](2+) is +81.0 kJ mol, whereas ?H for the reversible reaction K(2)B(12)F(12?(s)) + 2 H(2)O((g)) ? K(2)(H(2)O)(2)B(12)F(12?(s)) was found to be -111 kJ mol(-1) by differential scanning calorimetry. The K(2)(H(2)O)(0,2,4)B(12)F(12) system is unusual in how rapidly the three crystalline phases (the K(2)B(12)F(12) structure was reported recently) are interconverted, two of them reversibly. Isothermal gravimetric and DSC measurements showed that the reaction K(2)B(12)F(12?(s)) + 2 H(2)O((g)) ? K(2)(H(2)O)(2)B(12)F(12?(s)) was complete in as little as 4 min at 25 °C when the sample was exposed to a stream of He or N(2) containing 21 Torr H(2)O((g)). The endothermic reverse reaction required as little as 18 min when K(2)(H(2)O)(2)B(12)F(12) at 25 °C was exposed to a stream of dry He. The products of hydration and dehydration were shown to be crystalline K(2)(H(2)O)(2)B(12)F(12) and K(2)B(12)F(12), respectively, by PXRD, and therefore these reactions are reconstructive solid-state reactions (there is also evidence that they may be single-crystal-to-single-crystal transformations when carried out very slowly). The hydration and dehydration reaction times were both particle-size dependent and carrier-gas flow rate dependent and continued to decrease up to the maximum carrier-gas flow rate of the TGA instrument that was used, demonstrating that the hydration and dehydration reactions were limited by the rate at which H(2)O((g)) was delivered to or swept away from the microcrystal surfaces. Therefore, the rates of absorption and desorption of H(2)O from unit cells at the surface of the microcrystals, and the rate of diffusion of H(2)O across the moving K(2)(H(2)O)(2)B(12)F(12?(s))/K(2)B(12)F(12?(s)) phase boundary, are even faster than the fastest rates of change in sample mass due to hydration and dehydration that were measured. The exchange of 21 Torr H(2)O((g)) with either D(2)O or H(2)(18)O in microcrystalline K(2)(D(2)O)(2)B(12)F(12) or K(2)(H(2)(18)O)(2)B(12)F(12) at 25 °C was also facile and required as little as 45 min to go to completion (H(2)O((g)) replaced both types of isotopically labeled water at the same rate for a given starting sample of K(2)B(12)F(12), demonstrating that water molecules were exchanging, not protons. Significant portions of mass (m) vs time (t) plots for the (1,2)H(2)O((g))/K(2)((2,1)H(2)O)(2)B(12)F(12?(s)) exchange reactions fit the equation m ? e(-kt), with 10(3)k = 1.9 s(-1) for one particle size distribution and 10(3)k = 0.50 s(-1) for another. Finally, K(2)(H(2)O)(2)B(12)F(12) was not transformed into K(2)(H(2)O)(4)B(12)F(12) after prolonged exposure to 21 Torr H(2)O((g)) at 25 °C, 37 Torr H(2)O((g)) at 35 °C, or 55 Torr H(2)O((g)) at 45 °C.
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Antisense down-regulation of 4CL expression alters lignification, tree growth, and saccharification potential of field-grown poplar.
Plant Physiol.
PUBLISHED: 08-20-2010
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Transgenic down-regulation of the Pt4CL1 gene family encoding 4-coumarate:coenzyme A ligase (4CL) has been reported as a means for reducing lignin content in cell walls and increasing overall growth rates, thereby improving feedstock quality for paper and bioethanol production. Using hybrid poplar (Populus tremula × Populus alba), we applied this strategy and examined field-grown transformants for both effects on wood biochemistry and tree productivity. The reductions in lignin contents obtained correlated well with 4CL RNA expression, with a sharp decrease in lignin amount being observed for RNA expression below approximately 50% of the nontransgenic control. Relatively small lignin reductions of approximately 10% were associated with reduced productivity, decreased wood syringyl/guaiacyl lignin monomer ratios, and a small increase in the level of incorporation of H-monomers (p-hydroxyphenyl) into cell walls. Transgenic events with less than approximately 50% 4CL RNA expression were characterized by patches of reddish-brown discolored wood that had approximately twice the extractive content of controls (largely complex polyphenolics). There was no evidence that substantially reduced lignin contents increased growth rates or saccharification potential. Our results suggest that the capacity for lignin reduction is limited; below a threshold, large changes in wood chemistry and plant metabolism were observed that adversely affected productivity and potential ethanol yield. They also underline the importance of field studies to obtain physiologically meaningful results and to support technology development with transgenic trees.
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Unraveling the electron spin resonance pattern of nonsymmetric radicals with 30 fluorine atoms: electron spin resonance and vis-near-infrared spectroelectrochemistry of the anion radicals and dianions of C60(CF3)(2n) (2n = 2-10) derivatives and density fu
J. Am. Chem. Soc.
PUBLISHED: 07-30-2010
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The charged states of C(60)(CF(3))(2n) (2n = 2-10) derivatives have been studied by electron spin resonance (ESR) and vis-near-infrared (NIR) spectroelectrochemistry. The anion radicals and diamagnetic dianions were furthermore described by theoretical calculations. The ESR spectra of anion radicals exhibit complex patterns due to multiple CF(3) groups. Their interpretation is accomplished by DFT calculations with B3LYP functional. It is shown that calculations provide reliable results when the extended aug-cc-pCVTZ basis set is used for fluorine atoms; however, specially tailored basis sets such as EPR-III also give very similar results with only a fraction of the computational cost. Absorption spectra of the anions exhibit NIR absorption bands, whose assignment is provided by time-dependent DFT calculations.
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Tyloses and phenolic deposits in xylem vessels impede water transport in low-lignin transgenic poplars: a study by cryo-fluorescence microscopy.
Plant Physiol.
PUBLISHED: 07-16-2010
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Of 14 transgenic poplar genotypes (Populus tremula × Populus alba) with antisense 4-coumarate:coenzyme A ligase that were grown in the field for 2 years, five that had substantial lignin reductions also had greatly reduced xylem-specific conductivity compared with that of control trees and those transgenic events with small reductions in lignin. For the two events with the lowest xylem lignin contents (greater than 40% reduction), we used light microscopy methods and acid fuchsin dye ascent studies to clarify what caused their reduced transport efficiency. A novel protocol involving dye stabilization and cryo-fluorescence microscopy enabled us to visualize the dye at the cellular level and to identify water-conducting pathways in the xylem. Cryo-fixed branch segments were planed in the frozen state on a sliding cryo-microtome and observed with an epifluorescence microscope equipped with a cryo-stage. We could then distinguish clearly between phenolic-occluded vessels, conductive (stain-filled) vessels, and nonconductive (water- or gas-filled) vessels. Low-lignin trees contained areas of nonconductive, brown xylem with patches of collapsed cells and patches of noncollapsed cells filled with phenolics. In contrast, phenolics and nonconductive vessels were rarely observed in normal colored wood of the low-lignin events. The results of cryo-fluorescence light microscopy were supported by observations with a confocal microscope after freeze drying of cryo-planed samples. Moreover, after extraction of the phenolics, confocal microscopy revealed that many of the vessels in the nonconductive xylem were blocked with tyloses. We conclude that reduced transport efficiency of the transgenic low-lignin xylem was largely caused by blockages from tyloses and phenolic deposits within vessels rather than by xylem collapse.
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Bridged heterocyclium dicationic closo-icosahedral perfluoroborane, borane, and carborane salts via aqueous, open-air benchtop synthesis.
Org. Lett.
PUBLISHED: 05-27-2010
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Thirteen bridged triazolium and imidazolium dicationic salts, which uniquely pair closo-icosahedral perfluoroborane [B(12)F(12)](2-), borane [B(12)H(12)](2-), or carborane [CB(11)H(12)](-) anionic species with unsaturated bridged heterocyclium dications, were synthesized using an aqueous benchtop method. This considerably extends the scope of a reported aqueous synthesis of binary [heterocyclium](2)[B(12)H(12)] and [heterocyclium][CB(11)H(12)] salts. Also, the one-step preparation of five new precursor bridged heterocyclium dicationic dihalide salts using conventional procedures and in one case a microwave-assisted method is described.
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Soluble chlorofullerenes C(60)Cl(2,4,6,8,10). Synthesis, purification, compositional analysis, stability, and experimental/theoretical structure elucidation, including the X-ray structure of C(1)-C(60)Cl(10).
J. Am. Chem. Soc.
PUBLISHED: 04-23-2010
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The efficacy of various analytical techniques for the characterization of products of C(60) chlorination reactions were evaluated by (i) using samples of C(60)Cl(6) of known purity and (ii) repeating a number of literature syntheses reported to yield pure C(60)Cl(n) compounds. The techniques were NMR, UV-vis, IR, and Raman spectroscopy, FAB, MALDI, LDI, ESI, and APCI mass spectrometry, HPLC, TGA, elemental analysis, and single-crystal X-ray diffraction. Most of these techniques are shown to give ambiguous or erroneous results, calling into question the composition and/or purity of nearly all C(60)Cl(n) compounds reported to date. The optimum analytical method for chlorofullerenes was found to be a combination of HPLC and either MALDI or APCI mass spectrometry. For the first time, the chlorination of C(60) by ICl, ICl(3), and Cl(2) was studied in detail using dynamic HPLC analysis and APCI mass spectrometry. Suitable conditions were found for the preparation of the new chlorofullerenes 1,7-C(60)Cl(2), 1,9-C(60)Cl(2), 1,6,9,18-C(60)Cl(4), and 1,2,7,10,14,24,25,28,29,31-C(60)Cl(10). The latter compound was also studied by (13)C NMR spectroscopy and X-ray diffraction, which led to the unambiguous determination of its asymmetric addition pattern. The unusual structure of C(60)Cl(10) was compared with other possible isomers using DFT-predicted relative energies. These results, along with additional experimental data and an analysis of the DFT-predicted frontier orbitals of likely intermediates, were used to rationalize the formation of the new compound C(60)Cl(10) from C(60)Cl(6) and excess ICl without the rearrangement of any C-Cl bonds. For the first time, the stability of C(60)Cl(n) compounds under a variety of conditions was studied in detail, leading to the discovery that they are, in general, very light-sensitive in solution. The X-ray structure of C(60)Cl(6) was also redetermined with higher precision.
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Precocious flowering in trees: the FLOWERING LOCUS T gene as a research and breeding tool in Populus.
J. Exp. Bot.
PUBLISHED: 04-20-2010
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Expression of FLOWERING LOCUS T (FT) and its homologues has been shown to accelerate the onset of flowering in a number of plant species, including poplar (Populus spp.). The application of FT should be of particular use in forest trees, as it could greatly accelerate and enable new kinds of breeding and research. Recent evidence showing the extent to which FT is effective in promoting flowering in trees is discussed, and its effectiveness in poplar is reported. Results using one FT gene from Arabidopsis and two from poplar, all driven by a heat-inducible promoter, transformed into two poplar genotypes are also described. Substantial variation in flowering response was observed depending on the FT gene and genetic background. Heat-induced plants shorter than 30 cm failed to flower as well as taller plants. Plants exposed to daily heat treatments lasting 3 weeks tended to produce fewer abnormal flowers than those in heat treatments of shorter durations; increasing the inductive temperature from 37 degrees C to 40 degrees C produced similar benefits. Using optimal induction conditions, approximately 90% of transgenic plants could be induced to flower. When induced FT rootstocks were grafted with scions that lacked FT, flowering was only observed in rootstocks. The results suggest that a considerable amount of species- or genotype-specific adaptation will be required to develop FT into a reliable means for shortening the generation cycle for breeding in poplar.
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Conservation and divergence of methylation patterning in plants and animals.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 04-15-2010
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Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. Although DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here we used shotgun genomic bisulfite sequencing (BS-Seq) to compare DNA methylation in eight diverse plant and animal genomes. We found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals. Vertebrates have methylation throughout the genome except for CpG islands. Gene body methylation is conserved with clear preference for exons in most organisms. Furthermore, genes appear to be the major target of methylation in Ciona and honey bee. Among the eight organisms, the green alga Chlamydomonas has the most unusual pattern of methylation, having non-CG methylation enriched in exons of genes rather than in repeats and transposons. In addition, the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes.
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Gibberellins regulate lateral root formation in Populus through interactions with auxin and other hormones.
Plant Cell
PUBLISHED: 03-30-2010
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The role of gibberellins (GAs) in regulation of lateral root development is poorly understood. We show that GA-deficient (35S:PcGA2ox1) and GA-insensitive (35S:rgl1) transgenic Populus exhibited increased lateral root proliferation and elongation under in vitro and greenhouse conditions, and these effects were reversed by exogenous GA treatment. In addition, RNA interference suppression of two poplar GA 2-oxidases predominantly expressed in roots also decreased lateral root formation. GAs negatively affected lateral root formation by inhibiting lateral root primordium initiation. A whole-genome microarray analysis of root development in GA-modified transgenic plants revealed 2069 genes with significantly altered expression. The expression of 1178 genes, including genes that promote cell proliferation, growth, and cell wall loosening, corresponded to the phenotypic severity of the root traits when transgenic events with differential phenotypic expression were compared. The array data and direct hormone measurements suggested crosstalk of GA signaling with other hormone pathways, including auxin and abscisic acid. Transgenic modification of a differentially expressed gene encoding an auxin efflux carrier suggests that GA modulation of lateral root development is at least partly imparted by polar auxin transport modification. These results suggest a mechanism for GA-regulated modulation of lateral root proliferation associated with regulation of plant allometry during the stress response.
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Electron donor-acceptor interactions in regioselectively synthesized exTTF(2)-C(70)(CF(3))(10) dyads.
Chemistry
PUBLISHED: 03-09-2010
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The decakis(trifluoromethyl)fullerene C(1)-C(70)(CF(3))(10), in which the CF(3) groups are arranged on a para(7)-meta-para ribbon of C(6)(CF(3))(2) edge-sharing hexagons, and which has now been prepared in quantities of hundreds of milligrams, was reacted under standard Bingel-Hirsch conditions with a bis-pi-extended tetrathiafulvalene (exTTF) malonate derivative to afford a single exTTF(2)-C(70)(CF(3))(10) regioisomer in 80 % yield based on consumed starting material. The highly soluble hybrid was thoroughly characterized by using 1D (1)H, (13)C, and (19)F NMR, 2D NMR, and UV/Vis spectroscopy; matrix-assisted laser desorption ionization (MALDI) mass spectrometry; and electrochemistry. The cyclic voltammogram of the exTTF(2)-C(70)(CF(3))(10) dyad revealed an irreversible second reduction process, which is indicative of a typical retro-Bingel reaction; whereas the usual phenomenon of exTTF inverted potentials (E1ox>E2ox), resulting in a single, two-electron oxidation process, was also observed. Steady-state and time-resolved photolytic techniques demonstrated that the C(1)-C(70)(CF(3))(10) singlet excited state is subject to a rapid electron-transfer quenching. The resulting charge-separated states were identified by transient absorption spectroscopy, and radical pair lifetimes of the order of 300 ps in toluene were determined. The exTTF(2)-C(70)(CF(3))(10) dyad represents the first example of exploitation of the highly soluble trifluoromethylated fullerenes for the construction of systems able to mimic the photosynthetic process, and is therefore of interest in the search for new materials for photovoltaic applications.
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Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa.
BMC Genomics
PUBLISHED: 03-04-2010
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With its genome sequence and other experimental attributes, Populus trichocarpa has become the model species for genomic studies of wood development. Wood is derived from secondary growth of tree stems, and begins with the development of a ring of vascular cambium in the young developing stem. The terminal region of the developing shoot provides a steep developmental gradient from primary to secondary growth that facilitates identification of genes that play specialized functions during each of these phases of growth.
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Populus CEN/TFL1 regulates first onset of flowering, axillary meristem identity and dormancy release in Populus.
Plant J.
PUBLISHED: 02-26-2010
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Members of the CENTRORADIALIS (CEN)/TERMINAL FLOWER 1 (TFL1) subfamily control shoot meristem identity, and loss-of-function mutations in both monopodial and sympodial herbaceous plants result in dramatic changes in plant architecture. We studied the degree of conservation between herbaceous and woody perennial plants in shoot system regulation by overexpression and RNA interference (RNAi)-mediated suppression of poplar orthologs of CEN, and the related gene MOTHER OF FT AND TFL 1 (MFT). Field study of transgenic poplars (Populus spp.) for over 6 years showed that downregulation of PopCEN1 and its close paralog, PopCEN2, accelerated the onset of mature tree characteristics, including age of first flowering, number of inflorescences and proportion of short shoots. Surprisingly, terminal vegetative meristems remained indeterminate in PopCEN1-RNAi trees, suggesting the possibility that florigen signals are transported to axillary mersitems rather than the shoot apex. However, the axillary inflorescences (catkins) of PopCEN1-RNAi trees contained fewer flowers than did wild-type catkins, suggesting a possible role in maintaining the indeterminacy of the inflorescence apex. Expression of PopCEN1 was significantly correlated with delayed spring bud flush in multiple years, and in controlled environment experiments, 35S::PopCEN1 and RNAi transgenics required different chilling times to release dormancy. Considered together, these results indicate that PopCEN1/PopCEN2 help to integrate shoot developmental transitions that recur during each seasonal cycle with the age-related changes that occur over years of growth.
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Photoelectron spectroscopy of C60Fn- and C60Fm2- (n = 17, 33, 35, 43, 45, 47; m = 34, 46) in the gas phase and the generation and characterization of C1-C60F47- and D2-C60F44 in solution.
J Phys Chem A
PUBLISHED: 01-12-2010
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A photoelectron spectroscopy investigation of the fluorofullerene anions C(60)F(n)(-) (n = 17, 33, 35, 43, 45, 47) and the doubly charged anions C(60)F(34)(2-) and C(60)F(46)(2-) is reported. The first electron affinities for the corresponding neutral molecules, C(60)F(n), were directly measured and were found to increase as n increased, reaching the extremely high value of 5.66 +/- 0.10 eV for C(60)F(47). Density functional calculations suggest that the experimentally observed species C(60)F(17)(-), C(60)F(35)(-), and C(60)F(47)(-) were each formed by reductive defluorination of the parent fluorofullerene, C(3v)-C(60)F(18), C(60)F(36) (a mixture of isomers), and D(3)-C(60)F(48), respectively, without rearrangement of the remaining fluorine atoms. The DFT-predicted stability of C(60)F(47)(-) was verified by its generation by chemical reduction from D(3)-C(60)F(48) in chloroform solution at 25 degrees C and its characterization by mass spectrometry and (19)F NMR spectroscopy. Further reductive defluorination of C(60)F(47)(-) in solution resulted in the selective generation of a new fluorofullerene, D(2)-C(60)F(44), which was also characterized by mass spectrometry and (19)F NMR spectroscopy.
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Direct perfluorination of K(2)B(12)H(12) in acetonitrile occurs at the gas bubble-solution interface and is inhibited by HF. Experimental and DFT study of inhibition by protic acids and soft, polarizable anions.
J. Am. Chem. Soc.
PUBLISHED: 12-04-2009
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During the optimization of the F(2) perfluorination of K(2)B(12)H(12) in acetonitrile with continuous bubbling of 20/80 F(2)/N(2), it was discovered that (i) HF and other protic acids inhibit each of the 12 fluorination steps (in contradiction to recently published findings) and (ii) the fluorinations appear to take place at the gas bubble-solution interface. Experimental results and DFT calculations suggest that these two phenomena are related by the relative propensities of the various B(12)H(12-x)F(x)(2-) anions to partition from bulk solution to the interface (i.e., their relative polarizabilities or softness; 0
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Sc3N@(C80-Ih7)(CF3)14 and Sc3N@(C80-Ih(7))(CF3)16. Endohedral metallofullerene derivatives with exohedral addends on four and eight triple-hexagon junctions. Does the Sc3N cluster control the addition pattern or vice versa?
J. Am. Chem. Soc.
PUBLISHED: 11-14-2009
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The compounds Sc(3)N@(C(80)-I(h)(7))(CF(3))(14) (1) and Sc(3)N@(C(80)-I(h)(7))(CF(3))(16) (2) were prepared by heating Sc(3)N@C(80)-I(h)(7) and Ag(CF(3)CO(2)) to 350 degrees C in a sealed tube. The structures of 1 and 2 were determined by single-crystal X-ray diffraction. They are the first X-ray structures of any endohedral metallofullerene with more than four cage C(sp(3)) atoms. The structures exhibit several unprecedented features for metallic nitride fullerenes, including multiple cage sp(3) triple-hexagon junctions (four on 1 and eight on 2), no cage disorder and little (2) or no (1) endohedral atom disorder, high-precision (C-C esds are 0.005 A for 1 and 0.002 A for 2), an isolated aromatic C(sp(2))(6) hexagon on 2, and two negatively charged isolated aromatic C(sp(2))(5)(-) pentagons on 2 that are bonded to one of the Sc atoms. DFT calculations are in excellent agreement with the two Sc(3)N conformations observed for 2 (DeltaE(calc) = 0.36 kJ mol(-1); DeltaE(exp) = 0.26(2) kJ mol(-1)).
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Efficient regioselective [4+2] cycloaddition of o-quinodimethane to C(70)(CF(3))(10).
J. Org. Chem.
PUBLISHED: 08-12-2009
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The Diels-Alder reaction of C(1)-C(70)(CF(3))(10) and 3,6-dimethoxy-1,2-quinodimethane leads regioselectively to the formation of a new cycloadduct that has been fully characterized by spectroscopic and electrochemical methods as well as by X-ray diffraction.
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Strangled at birth? Forest biotech and the Convention on Biological Diversity.
Nat. Biotechnol.
PUBLISHED: 06-11-2009
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Against the Cartagena Protocol and widespread scientific support for a case-by-case approach to regulation, the Convention on Biological Diversity has become a platform for imposing broad restrictions on research and development of all types of transgenic trees.
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Pairing heterocyclic cations with closo-icosahedral borane and carborane anions. i. benchtop aqueous synthesis of binary triazolium and imidazolium salts with limited water solubility.
Org. Lett.
PUBLISHED: 05-16-2009
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Ten new salts that pair triazolium and imidazolium cations with closo-icosahedral anions [B(12)H(12)](2-) and [CB(11)H(12)](-) were synthesized in water solvent using an open-air, benchtop method. These unreported [Heterocyclium](2)[B(12)H(12)] and [Heterocyclium][CB(11)H(12)] salts extend reports of [Imidazolium][CB(11)H(12)] and [Pyridinium][CB(11)H(12)] salts that were synthesized in anhydrous organic solvents under an inert atmosphere with glovebox or Schlenk techniques. Spectroscopic data, melting points, and densities are reported for each salt. Single-crystal X-ray structures are provided for the five new [B(12)H(12)](2-) salts.
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Does sodium dodecyl sulfate wash out of detergent-treated bovine pericardium at cytotoxic concentrations?
J. Heart Valve Dis.
PUBLISHED: 03-24-2009
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The ionic detergent sodium dodecyl sulfate (SDS) is a proposed treatment for the removal of antigenic proteins from unfixed biological scaffolds used in tissue engineering. However, questions remain about possible cytotoxic effects of SDS-treated tissues. The study aims were to: (i) develop a sensitive SDS assay for physiological solutions; (ii) measure SDS concentrations in the washing media of SDS-treated tissue; and (iii) determine cytotoxic SDS concentrations in cultured ovine vascular cells.
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Stability of transgenes in trees: expression of two reporter genes in poplar over three field seasons.
Tree Physiol.
PUBLISHED: 02-11-2009
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High stability of transgene expression is essential for functional genomics studies using transformation approaches and for application of genetic engineering to commercial forestry. We quantified expression of two reporter genes, green fluorescent protein (GFP) and the herbicide bialaphos resistance gene (BAR), in 2256 transgenic poplar trees derived from 404 primary events, and in 106 in vitro-redifferentiated subevents, over 3 years in the greenhouse and in the field. No gene silencing (complete breakdown of expression) was observed for GFP or BAR expression in any of the primary transgenic events during the course of the study. Transgenic cassettes were physically eliminated in four subevents (2.5%) derived from three different primary events during re-organogenesis. Transgene copy number was positively correlated with transgene expression level; however, a majority of transformants (85%) carried single-copy transgenes. About one-third of the events containing two-copy inserts had repeats formed at the same chromosomal position, with direct repeats being the main type observed (87%). All events containing more than two transgene copies showed repeat formation at least at one locus, with direct repeats again dominant (77%). Loci with two direct repeats had substantially greater transgene expression level than other types of two-copy T-DNA configurations, but insert organization was not associated with stability of transgene expression. Use of the poplar rbcS promoter, which drove BAR in the transgenic constructs, had no adverse effect on transgene expression levels or stability compared with the heterologous CaMV 35S promoter, which directed GFP expression.
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WUS and STM-based reporter genes for studying meristem development in poplar.
Plant Cell Rep.
PUBLISHED: 02-08-2009
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We describe the development of a reporter system for monitoring meristem initiation in poplar using promoters of poplar homologs to the meristem-active regulatory genes WUSCHEL (WUS) and SHOOTMERISTEMLESS (STM). When ~3 kb of the 5 flanking regions of close homologs were used to drive expression of the GUSPlus gene, 50-60% of the transgenic events showed expression in apical and axillary meristems. However, expression was also common in other organs, including in leaf veins (40 and 46% of WUS and STM transgenic events, respectively) and hydathodes (56% of WUS transgenic events). Histochemical GUS staining of explants during callogenesis and shoot regeneration using in vitro stems as explants showed that expression was detectable prior to visible shoot development, starting 3-15 days after explants were placed onto callus inducing medium. A minority of WUS and STM events also showed expression in the cambium, phloem, or xylem of regenerated, greenhouse grown plants undergoing secondary growth. Based on microarray gene expression data, a paralog of poplar WUS was detectably up-regulated during shoot initiation, but the other paralog was not. Both paralogs of poplar STM were down-regulated threefold to sixfold during early callus initiation. We identified 15-35 copies of cytokinin response regulator binding motifs (ARR1AT) and one copy of the auxin response element (AuxRE) in both promoters. Several of the events recovered may be useful for studying the process of primary and secondary meristem development, including treatments intended to stimulate meristem development to promote clonal propagation and genetic transformation.
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Genome scale transcriptome analysis of shoot organogenesis in Populus.
BMC Plant Biol.
PUBLISHED: 01-12-2009
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Our aim is to improve knowledge of gene regulatory circuits important to dedifferentiation, redifferentiation, and adventitious meristem organization during in vitro regeneration of plants. Regeneration of transgenic cells remains a major obstacle to research and commercial deployment of most taxa of transgenic plants, and woody species are particularly recalcitrant. The model woody species Populus, due to its genome sequence and amenability to in vitro manipulation, is an excellent species for study in this area. The genes recognized may help to guide the development of new tools for improving the efficiency of plant regeneration and transformation.
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PHOTOPERIOD RESPONSE 1 (PHOR1)-like genes regulate shoot/root growth, starch accumulation, and wood formation in Populus.
J. Exp. Bot.
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This study describes functional characterization of two putative poplar PHOTOPERIOD RESPONSE 1 (PHOR1) orthologues. The expression and sequence analyses indicate that the two poplar genes diverged, at least partially, in function. PtPHOR1_1 is most highly expressed in roots and induced by short days, while PtPHOR1_2 is more uniformly expressed throughout plant tissues and is not responsive to short days. The two PHOR1 genes also had distinct effects on shoot and root growth when their expression was up- and downregulated transgenically. PtPHOR1_1 effects were restricted to roots while PtPHOR1_2 had similar effects on aerial and below-ground development. Nevertheless, both genes seemed to be upregulated in transgenic poplars that are gibberellin-deficient and gibberellin-insensitive, suggesting interplay with gibberellin signalling. PHOR1 suppression led to increased starch accumulation in both roots and stems. The effect of PHOR1 suppression on starch accumulation was coupled with growth-inhibiting effects in both roots and shoots, suggesting that PHOR1 is part of a mechanism that regulates the allocation of carbohydrate to growth or storage in poplar. PHOR1 downregulation led to significant reduction of xylem formation caused by smaller fibres and vessels suggesting that PHOR1 likely plays a role in the growth of xylem cells.
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Green revolution trees: semidwarfism transgenes modify gibberellins, promote root growth, enhance morphological diversity, and reduce competitiveness in hybrid poplar.
Plant Physiol.
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Semidwarfism has been used extensively in row crops and horticulture to promote yield, reduce lodging, and improve harvest index, and it might have similar benefits for trees for short-rotation forestry or energy plantations, reclamation, phytoremediation, or other applications. We studied the effects of the dominant semidwarfism transgenes GA Insensitive (GAI) and Repressor of GAI-Like, which affect gibberellin (GA) action, and the GA catabolic gene, GA 2-oxidase, in nursery beds and in 2-year-old high-density stands of hybrid poplar (Populus tremula × Populus alba). Twenty-nine traits were analyzed, including measures of growth, morphology, and physiology. Endogenous GA levels were modified in most transgenic events; GA(20) and GA(8), in particular, had strong inverse associations with tree height. Nearly all measured traits varied significantly among genotypes, and several traits interacted with planting density, including aboveground biomass, root-shoot ratio, root fraction, branch angle, and crown depth. Semidwarfism promoted biomass allocation to roots over shoots and substantially increased rooting efficiency with most genes tested. The increased root proportion and increased leaf chlorophyll levels were associated with changes in leaf carbon isotope discrimination, indicating altered water use efficiency. Semidwarf trees had dramatically reduced growth when in direct competition with wild-type trees, supporting the hypothesis that semidwarfism genes could be effective tools to mitigate the spread of exotic, hybrid, and transgenic plants in wild and feral populations.
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Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa.
New Phytol.
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• Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype-genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination. • We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29,213 single-nucleotide polymorphisms. • Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r(2) dropping below 0.2 within 3-6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N(e) ? 4000-6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features. • Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed.
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A buckybowl with a lot of potential: C5-C20H5(CF3)5.
Angew. Chem. Int. Ed. Engl.
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Lots of potential: a trifluoromethylated corannulene, C(5)-C(20)H(5)(CF(3))(5), has been prepared and characterized spectroscopically and by X-ray crystallography. The structure exhibits a highly ordered bowl stacking that is unusual for corannulenes with acyclic substituents. The first reduction of C(5)-C(20)H(5)(CF(3))(5) is anodically shifted by 0.95 V, making it the strongest corannulene-based electron acceptor to date.
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Halogenated benzene cation radicals.
Chemistry
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The halogenated benzenes C(6)HF(5), 2,4,6-C(6)H(3)F(3), 2,3,5,6-C(6)H(2)F(4), C(6)F(6), C(6)Cl(6), C(6)Br(6), and C(6)I(6) were converted into their corresponding cation radicals by using various strong oxidants. The cation-radical salts were isolated and characterized by electron paramagnetic resonance (EPR) spectroscopy and by single-crystal X-ray diffraction. The thermal stability of the cation radicals increased with decreasing hydrogen content. As expected, the cation radicals [C(6)HF(5)](+) and 2,3,5,6-[C(6)H(2)F(4)](+) had structures with the same geometry as C(6)HF(5) and 2,3,5,6-[C(6)H(2)F(4)]. In contrast, the cation radicals [C(6)F(6)](+), [C(6)Cl(6)](+), and possibly also [C(6)Br(6)](+) exhibited Jahn-Teller-distorted geometries in the crystalline state. In the case of C(6)F(6)(+)Sb(2)F(11)(-), two low-symmetry geometries were observed in the same crystal. Interestingly, the structures of the cation radicals 2,4,6-[C(6)H(3)F(3)](+) and C(6)I(6)(+) did not exhibit Jahn-Teller distortions. DFT calculations showed that the explanation for the lack of distortion of these cations from the D(3h) or D(6h) symmetry of the neutral benzene precursor was different for 2,4,6-[C(6)H(3)F(3)](+) than for [C(6)I(6)](+).
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Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression.
BMC Genomics
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DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood.
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Gene flow and simulation of transgene dispersal from hybrid poplar plantations.
New Phytol.
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Gene flow is a primary determinant of potential ecological impacts of transgenic trees. However, gene flow is a complex process that must be assessed in the context of realistic genetic, management, and environmental conditions. We measured gene flow from hybrid poplar plantations using morphological and genetic markers, and developed a spatially explicit landscape model to simulate pollination, dispersal, establishment, and mortality in the context of historical and projected disturbance and land-use regimes. Most pollination and seed establishment occurred within 450 m of the source, with a very long tail. Modeled transgene flow was highly context-dependent, strongly influenced by the competitive effects of transgenes, transgenic fertility, plantation rotation length, disturbance regime, and spatial and temporal variation in selection. The use of linked infertility genes even if imperfect, substantially reduced transgene flow in a wide range of modeled scenarios. The significance of seed and vegetative dispersal was highly dependent on plantation size. Our empirical and modeling studies suggest that transgene spread can be spatially extensive. However, the amount of spread is highly dependent on ecological and management context, and can be greatly limited or prevented by management or mitigation genes such as those that cause sexual infertility.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.