The face value of ion fluxes: the challenge of determining influx in the low-affinity transport range.
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The existence of distinct high- and low-affinity transport systems (HATS and LATS) is well established for major nutrient ions. However, influx mediated by these systems is usually estimated using uniformly simple tracer protocols. Two (42)K radiotracer methods to measure potassium influxes in the HATS and LATS ranges in intact barley (Hordeum vulgare L.) roots are compared here: a direct influx (DI) method, and an integrated flux analysis (IFA), which is designed to account for tracer efflux from labelled roots and differential tracer accumulation along the plant axis. Methods showed only minor discrepancies for influx values in the HATS range, but large discrepancies in the LATS range, revealing striking distinctions in the cellular exchange properties dominated by the operation of the two transport systems. It is shown that accepted DI protocols are associated with very large errors in the high-conductance LATS range, underestimating influx at least 6-fold due to four characteristics of this transport mode: (i) accelerated cellular (42)K exchange; (ii) a greatly increased ratio of efflux to influx; (iii) increased (42)K loss during the removal of water from roots in preweighing centrifugation or blotting protocols; and (iv) increased (42)K retention at the root-shoot interface, a region of the plant frequently disregarded in DI determinations. The findings warrant a re-evaluation of a large body of literature reporting influx in the LATS range, and are of fundamental importance to ion flux experimentation in plant physiology. (+info)
Whole-plant growth stage ontology for angiosperms and its application in plant biology.
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Plant growth stages are identified as distinct morphological landmarks in a continuous developmental process. The terms describing these developmental stages record the morphological appearance of the plant at a specific point in its life cycle. The widely differing morphology of plant species consequently gave rise to heterogeneous vocabularies describing growth and development. Each species or family specific community developed distinct terminologies for describing whole-plant growth stages. This semantic heterogeneity made it impossible to use growth stage description contained within plant biology databases to make meaningful computational comparisons. The Plant Ontology Consortium (http://www.plantontology.org) was founded to develop standard ontologies describing plant anatomical as well as growth and developmental stages that can be used for annotation of gene expression patterns and phenotypes of all flowering plants. In this article, we describe the development of a generic whole-plant growth stage ontology that describes the spatiotemporal stages of plant growth as a set of landmark events that progress from germination to senescence. This ontology represents a synthesis and integration of terms and concepts from a variety of species-specific vocabularies previously used for describing phenotypes and genomic information. It provides a common platform for annotating gene function and gene expression in relation to the developmental trajectory of a plant described at the organismal level. As proof of concept the Plant Ontology Consortium used the plant ontology growth stage ontology to annotate genes and phenotypes in plants with initial emphasis on those represented in The Arabidopsis Information Resource, Gramene database, and MaizeGDB. (+info)
Progress and challenges in studies of the evolution of development.
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Plant evolutionary developmental genetics (EDG) has made considerable progress over the last decade. This is in part due to the accumulation of large amounts of sequence data that have provided robust organismal phylogenies and, increasingly, broad assessments of molecular evolution. Attempts to use primary sequence data to identify genes that have changed function in evolutionary time have not been as successful as initially hoped. The coding sequences of most genes, which are more amenable to statistical analysis than are regulatory sequences, are generally under purifying selection, as would be expected if much evolutionary change is the result of changes in cis-regulatory sequences. Sequence-based analysis of the regulatory sequences themselves remains difficult. Comparative studies of gene expression have been useful to identify genes whose developmental role may have changed in evolutionary time and will be critical to the future development of EDG. Such studies can be used to test hypotheses of gene function. Transformation experiments are often illuminating, but can be hard to interpret, particularly if genes from multiple species are all placed into a single heterologous system such as Arabidopsis. The ideal experiment would be a gene swap or promoter swap between two species, but this awaits development of good transformation systems. The immediate need for EDG is studies of gene expression on a massive scale, far broader than any studies undertaken to date. (+info)
Morphological and molecular phylogenetic context of the angiosperms: contrasting the 'top-down' and 'bottom-up' approaches used to infer the likely characteristics of the first flowers.
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Recent attempts to address the long-debated 'origin' of the angiosperms depend on a phylogenetic framework derived from a matrix of taxa versus characters; most assume that empirical rigour is proportional to the size of the matrix. Sequence-based genotypic approaches increase the number of characters (nucleotides and indels) in the matrix but are confined to the highly restricted spectrum of extant species, whereas morphology-based approaches increase the number of phylogenetically informative taxa (including fossils) at the expense of accessing only a restricted spectrum of phenotypic characters. The two approaches are currently delivering strongly contrasting hypotheses of relationship. Most molecular studies indicate that all extant gymnosperms form a natural group, suggesting surprisingly early divergence of the lineage that led to angiosperms, whereas morphology-only phylogenies indicate that a succession of (mostly extinct) gymnosperms preceded a later angiosperm origin. Causes of this conflict include: (i) the vast phenotypic and genotypic lacuna, largely reflecting pre-Cenozoic extinctions, that separates early-divergent living angiosperms from their closest relatives among the living gymnosperms; (ii) profound uncertainty regarding which (a) extant and (b) extinct angiosperms are most closely related to gymnosperms; and (iii) profound uncertainty regarding which (a) extant and (b) extinct gymnosperms are most closely related to angiosperms, and thus best serve as 'outgroups' dictating the perceived evolutionary polarity of character transitions among the early-divergent angiosperms. These factors still permit a remarkable range of contrasting, yet credible, hypotheses regarding the order of acquisition of the many phenotypic characters, reproductive and vegetative, that distinguish 'classic' angiospermy from 'classic' gymnospermy. The flower remains ill-defined and its mode (or modes) of origin remains hotly disputed; some definitions and hypotheses of evolutionary relationships preclude a role for the flower in delimiting the angiosperms. We advocate maintenance of parallel, reciprocally illuminating programmes of morphological and molecular phylogeny reconstruction, respectively supported by homology testing through additional taxa (especially fossils) and evolutionary-developmental genetic studies that explore genes potentially responsible for major phenotypic transitions. (+info)
Germanium-68 as an adequate tracer for silicon transport in plants. Characterization of silicon uptake in different crop species.
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A basic problem in silicon (Si) uptake studies in biology is the lack of an appropriate radioactive isotope. Radioactive germanium-68 ((68)Ge) has been used previously as a Si tracer in biological materials, but its suitability for the study of Si transport in higher plants is still untested. In this study, we investigated (68)Ge-traced Si uptake by four crop species differing widely in uptake capacity for Si, including rice (Oryza sativa), barley (Hordeum vulgare), cucumber (Cucumis sativus), and tomato (Lycopersicon esculentum). Maintenance of a (68)Ge:Si molar ratio that was similar in the plant tissues of all four plant species to that supplied in the nutrient solution over a wide range of Si concentrations demonstrated the absence of discrimination between (68)Ge and Si. Further, using the (68)Ge tracer, a typical Michaelis-Menten uptake kinetics for Si was found in rice, barley, and cucumber. Compared to rice, the relative proportion of root-to-shoot translocated Si was lower in barley and cucumber and especially in tomato (only 30%). Uptake and translocation of Si in rice, barley, and cucumber (Si accumulators) were strongly inhibited by 2,4-dinitrophenol and HgCl(2), but in tomato, as a Si-excluding species, both inhibitors produced the opposite effect. In conclusion, our results suggest the use of the (68)Ge tracer method as an appropriate choice for future studies of Si transport in plants. Our findings also indicate that the restriction of Si from symplast to apoplast in the cortex of Si excluders is a metabolically active process. (+info)
Spatial variation of deuterium enrichment in bulk water of snowgum leaves.
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Deuterium enrichment of bulk water was measured and modeled in snowgum (Eucalyptus pauciflora Sieber ex Sprengel) leaves grown under contrasting air and soil humidity in arid and wet conditions in a glasshouse. A map of the enrichment was constructed with a resolution of 4 mm by using a newly designed cryodistillation method. There was progressively increasing enrichment in both longitudinal (along the leaf midrib) and transversal (perpendicular to the midrib) directions, most pronounced in the arid-grown leaf. The whole-leaf average of the enrichment was well below the value estimated by the Craig-Gordon model. The discrepancy between model and measurements persisted when the estimates were carried out separately for the leaf base and tip, which differed in temperature and stomatal conductance. The discrepancy was proportional to the transpiration rate, indicating the significance of diffusion-advection interplay (Peclet effect) of deuterium-containing water molecules in small veins close to the evaporating sites in the leaf. Combined Craig-Gordon and desert-river models, with or without the Peclet number, P, were used for predicting the leaf longitudinal enrichment. The predictions without P overestimated the measured values of deltadeuterium. Fixed P value partially improved the coincidence. We suggest that P should vary along the leaf length l to reconcile the modeled data with observations of longitudinal enrichment. Local values of P, P(l), integrating the upstream fraction of water used or the leaf area, substantially improved the model predictions. (+info)
A multi-treatment experimental system to examine photosynthetic differentiation in the maize leaf.
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BACKGROUND: The establishment of C4 photosynthesis in maize is associated with differential accumulation of gene transcripts and proteins between bundle sheath and mesophyll photosynthetic cell types. We have physically separated photosynthetic cell types in the leaf blade to characterize differences in gene expression by microarray analysis. Additional control treatments were used to account for transcriptional changes induced by cell preparation treatments. To analyse these data, we have developed a statistical model to compare gene expression values derived from multiple, partially confounded, treatment groups. RESULTS: Differential gene expression in the leaves of wild-type maize seedlings was characterized using the latest release of a maize long-oligonucleotide microarray produced by the Maize Array Project consortium. The complete data set is available through the project web site. Data is also available at the NCBI GEO website, series record GSE3890. Data was analysed with and without consideration of cell preparation associated stress. CONCLUSION: Empirical comparison of the two analyses suggested that consideration of stress helped to reduce the false identification of stress responsive transcripts as cell-type enriched. Using our model including a stress term, we identified 8% of features as differentially expressed between bundle sheath and mesophyll cell types under control of false discovery rate of 5%. An estimate of the overall proportion of differentially accumulating transcripts (1-pi0) suggested that as many as 18% of the genes may be differentially expressed between B and M. The analytical model presented here is generally applicable to gene expression data and demonstrates the use of statistical elimination of confounding effects such as stress in the context of microarray analysis. We discuss the implications of the high degree of differential transcript accumulation observed with regard to both the establishment and engineering of the C4 syndrome. (+info)
Occurrence of Platypus mutatus Chapuis (Coleoptera: Platypodidae) in a brazilwood experimental plantation in Southeastern Brazil.
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The hardwood of Caesalpinia echinata Lam. (brazilwood, Pernambuco, ibirapitanga) is currently the most profitable material used for violin bow due to the unique vibrational properties and dimensional stability. Although this species is resistant to the wood decay caused by termites and rot fungi, an experimental plantation in Southeastern Brazil has been attacked by the ambrosia beetle Platypus mutatus Chapuis (= Megaplatypus mutatus and P. sulcatus). This species invaded ca. 3% of the individuals, mainly in the central part of the plantation. Infestation by larvae and adults was higher during the dry season (winter) when compared to the rainy period (spring and summer). (+info)