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PubMed2006

ALAMEDA, a structural-functional model for faba bean crops: morphological parameterization and verification.

BACKGROUND: Plant structural (i.e. architectural) models explicitly describe plant morphology by providing detailed descriptions of the display of leaf and stem surfaces within heterogeneous canopies and thus provide the opportunity for modelling the functioning of plant organs in their microenvironments. The outcome is a class of structural-functional crop models that combines advantages of current structural and process approaches to crop modelling. ALAMEDA is such a model. METHODS: The formalism of Lindenmayer systems (L-systems) was chosen for the development of a structural model of the faba bean canopy, providing both numerical and dynamic graphical outputs. It was parameterized according to the results obtained through detailed morphological and phenological descriptions that capture the detailed geometry and topology of the crop. The analysis distinguishes between relationships of general application for all sowing dates and stem ranks and others valid only for all stems of a single crop cycle. RESULTS AND CONCLUSIONS: The results reveal that in faba bean, structural parameterization valid for the entire plant may be drawn from a single stem. ALAMEDA was formed by linking the structural model to the growth model 'Simulation d'Allongement des Feuilles' (SAF) with the ability to simulate approx. 3500 crop organs and components of a group of nine plants. Model performance was verified for organ length, plant height and leaf area. The L-system formalism was able to capture the complex architecture of canopy leaf area of this indeterminate crop and, with the growth relationships, generate a 3D dynamic crop simulation. Future development and improvement of the model are discussed.

Computer Simulation↗
PubMed2004

Photosynthetic pathway alters hydraulic structure and function in woody plants.

Xylem structure and function is proposed to reflect an evolutionary balance between demands for efficient movement of water to the leaf canopy and resistance to cavitation during high xylem tension. Water use efficiency (WUE) affects this balance by altering the water cost of photosynthesis. Therefore species of greater WUE, such as C(4) plants, should have altered xylem properties. To evaluate this hypothesis, we assessed the hydraulic and anatomical properties of 19 C(3) and C(4) woody species from arid regions of the American west and central Asia. Specific conductivity of stem xylem ( K(s) ) was 16%-98% lower in the C(4) than C(3) shrubs from the American west. In the Asian species, the C(3) Nitraria schoberi had similar and Halimodendron halodendron higher K(s) values compared with three C(4) species. Leaf specific conductivity ( K(L); hydraulic conductivity per leaf area) was 60%-98% lower in the C(4) than C(3) species, demonstrating that the presence of the C(4) pathway alters the relationship between leaf area and the ability of the xylem to transport water. C(4) species produced similar or smaller vessels than the C(3) shrubs except in Calligonum, and most C(4) shrubs exhibited higher wood densities than the C(3) species. Together, smaller conduit size and higher wood density indicate that in most cases, the C(4) shrubs exploited higher WUE by altering xylem structure to enhance safety from cavitation. In a minority of cases, the C(4) shrubs maintained similar xylem properties but enhanced the canopy area per branch. By establishing a link between C(4) photosynthesis and xylem structure, this study indicates that other phenomena that affect WUE, such as atmospheric CO(2) variation, may also affect the evolution of wood structure and function.

Carbon Dioxide↗
PubMedDate not supplied

The effects of plant and tooth structure on intake and digestibility in two small mammalian herbivores.

We investigated the interaction between plant structure and animal tooth structure and how it can affect digestive performance in two small mammalian herbivores. Mastacomys fuscus, an exclusively herbivorous rodent, and Rattus lutreolus, a less herbivorous rodent, were fed diets varying in fibre structure and level (18%-45% neutral detergent fibre). On high-fibre whole wheat diets, R. lutreolus was not able to maintain body mass. M. fuscus was able to maintain body mass, and this was related to a much greater intake by M. fuscus on this diet. We attribute this result to more effective physical processing by M. fuscus as a consequence of a highly developed dentition. On a milled-wheat diet, intake by R. lutreolus increased significantly compared with the whole wheat diet, although intake was still not great enough to maintain body mass. On diets that were lower in fibre than the wheat diet, and with different fibre arrangements, R. lutreolus was able to achieve intakes great enough to maintain body mass. This suggests that, in addition to gut constraints, the physical form of the plant diet and dental structure can have a significant effect on digestive performance by animals in feeding trials.

Animals↗
PubMed2003

Experimental analysis of biparental inbreeding in a self-fertilizing plant.

Localized dispersal and mating may genetically structure plant populations, resulting in matings among related individuals. This biparental inbreeding has significant consequences for the evolution of mating systems, yet is difficult to estimate in natural populations. We estimated biparental inbreeding in two populations of the largely self-fertilizing plant Aquilegia canadensis using standard inference as well as a novel experiment comparing apparent selfing between plants that were randomly relocated within populations to experimental control plants. Using two allozyme markers, biparental inbreeding (b) inferred from the difference between single-locus and multilocus estimates of selfing (b = s(s) - s(m)) was low. Less than 3% of matings involved close relatives (mean b = 0.029). In contrast, randomly relocating plants greatly reduced apparent selfing (mean s(s) = 0.674) compared to control plants that had been dug up and replanted in their original locations (s(s) = 0.953, P = 0.002). Based on this difference in s(s), we estimated that approximately 30% of all matings involved close relatives (mean b = 0.279, 95% CL = 0.072-0.428). Inference from s(s) - s(m) underestimated b in these populations by more than an order of magnitude. Biparental inbreeding is thought to influence the evolution of self-fertilization primarily through reducing the genetic cost of outcrossing. This is unlikely to be of much significance in A. canadensis because inbreeding depression (a major cost of selfing) is much stronger than the cost of outcrossing. However, biparental inbreeding combined with strong inbreeding depression may influence selection on dispersal.

Aquilegia↗
PubMed2001

Transcriptional responses in the hemiparasitic plant Triphysaria versicolor to host plant signals.

Parasitic plants in the Scrophulariaceae use chemicals released by host plant roots to signal developmental processes critical for heterotrophy. Haustoria, parasitic plant structures that attach to and invade host roots, develop on roots of the hemiparasitic plant Triphysaria versicolor within a few hours of exposure to either maize (Zea mays) root exudate or purified haustoria-inducing factors. We prepared a normalized, subtractive cDNA library enriched for transcripts differentially abundant in T. versicolor root tips treated with the allelopathic quinone 2,6-dimethoxybenzoquinone (DMBQ). Northern analyses estimated that about 10% of the cDNAs represent transcripts strongly up-regulated in roots exposed to DMBQ. Northern and reverse northern analyses demonstrated that most DMBQ-responsive messages were similarly up-regulated in T. versicolor roots exposed to maize root exudates. From the cDNA sequences we assembled a unigene set of 137 distinct transcripts and assigned functions by homology comparisons. Many of the proteins encoded by the transcripts are predicted to function in quinone detoxification, whereas others are more likely associated with haustorium development. The identification of genes transcriptionally regulated by haustorium-inducing factors provides a framework for dissecting genetic pathways recruited by parasitic plants during the transition to heterotrophic growth.

Benzoquinones↗
PubMed2005

Structural dynamics and resonance in plants with nonlinear stiffness.

Although most biomaterials are characterized by strong stiffness nonlinearities, the majority of studies of plant biomechanics and structural dynamics focus on the linear elastic range of their behavior. In this paper, the effects of hardening (elastic modulus increases with strain) and softening (elastic modulus decreases with strain) nonlinearities on the structural dynamics of plant stems are investigated. A number of recent studies suggest that trees, crops, and other plants often uproot or snap when they are forced by gusting winds or waves at their natural frequency. This can be attributed to the fact that the deflections of the plant, and hence mechanical stresses along the stem and root system, are greatest during resonance. To better understand the effect of nonlinear stiffness on the resonant behavior of plants, plant stems have been modeled here as forced Duffing oscillators with softening or hardening nonlinearities. The results of this study suggest that the resonant behavior of plants with nonlinear stiffness is substantially different from that predicted by linear models of plant structural dynamics. Parameter values were considered over a range relevant to most plants. The maximum amplitudes of deflection of the plant stem were calculated numerically for forcing frequencies ranging from zero to twice the natural frequency. For hardening nonlinearities, the resonant behavior was 'pushed' to higher frequencies, and the maximum deflection amplitudes were lower than for the linear case. For softening nonlinearities, the resonant behavior was pushed to lower frequencies, and the maximum deflection amplitudes were higher than for the linear case. These nonlinearities could be beneficial or detrimental to the stability of the plant, depending on the environment. Damping had the effect of drastically decreasing deflection amplitudes and reducing the effect of the nonlinearities.

Elasticity↗
PubMed2003

Proposed amino acid sequence and the 1.63 A X-ray crystal structure of a plant cysteine protease, ervatamin B: some insights into the structural basis of its stability and substrate specificity.

The crystal structure of a cysteine protease ervatamin B, isolated from the medicinal plant Ervatamia coronaria, has been determined at 1.63 A. The unknown primary structure of the enzyme could also be traced from the high-quality electron density map. The final refined model, consisting of 215 amino acid residues, 208 water molecules, and a thiosulfate ligand molecule, has a crystallographic R-factor of 15.9% and a free R-factor of 18.2% for F > 2sigma(F). The protein belongs to the papain superfamily of cysteine proteases and has some unique properties compared to other members of the family. Though the overall fold of the structure, comprising two domains, is similar to the others, a few natural substitutions of conserved amino acid residues at the interdomain cleft of ervatamin B are expected to increase the stability of the protein. The substitution of a lysine residue by an arginine (residue 177) in this region of the protein may be important, because Lys --> Arg substitution is reported to increase the stability of proteins. Another substitution in this cleft region that helps to hold the domains together through hydrogen bonds is Ser36, replacing a conserved glycine residue in the others. There are also some substitutions in and around the active site cleft. Residues Tyr67, Pro68, Val157, and Ser205 in papain are replaced by Trp67, Met68, Gln156, and Leu208, respectively, in ervatamin B, which reduces the volume of the S2 subsite to almost one-fourth that of papain, and this in turn alters the substrate specificity of the enzyme.

Amino Acid Sequence↗
PubMed2006

3D lidar imaging for detecting and understanding plant responses and canopy structure.

Understanding and diagnosing plant responses to stress will benefit greatly from three-dimensional (3D) measurement and analysis of plant properties because plant responses are strongly related to their 3D structures. Light detection and ranging (lidar) has recently emerged as a powerful tool for direct 3D measurement of plant structure. Here the use of 3D lidar imaging to estimate plant properties such as canopy height, canopy structure, carbon stock, and species is demonstrated, and plant growth and shape responses are assessed by reviewing the development of lidar systems and their applications from the leaf level to canopy remote sensing. In addition, the recent creation of accurate 3D lidar images combined with natural colour, chlorophyll fluorescence, photochemical reflectance index, and leaf temperature images is demonstrated, thereby providing information on responses of pigments, photosynthesis, transpiration, stomatal opening, and shape to environmental stresses; these data can be integrated with 3D images of the plants using computer graphics techniques. Future lidar applications that provide more accurate dynamic estimation of various plant properties should improve our understanding of plant responses to stress and of interactions between plants and their environment. Moreover, combining 3D lidar with other passive and active imaging techniques will potentially improve the accuracy of airborne and satellite remote sensing, and make it possible to analyse 3D information on ecophysiological responses and levels of various substances in agricultural and ecological applications and in observations of the global biosphere.

Biosensing Techniques↗
PubMed2001

Hydroxyproline-rich glycoproteins in plant reproductive tissues: structure, functions and regulation.

The plant reproductive process of pollination involves a series of interactions between the male gametophyte (the pollen grain or pollen tube) and extracellular matrix (ECM) molecules secreted by different cell types along the pollen tube growth pathway in the female organ, the pistil. These interactions are believed to signal and regulate the pollen tube growth process to effect successful delivery of the sperm cells to the ovules where fertilization takes place. Hydroxyproline-rich glycoproteins secreted by plant cells are believed to play a broad range of functions, ranging from providing structural integrity to mediating cell-cell interactions and communication. The pistil and pollen tube ECM is enriched in these highly glycosylated proteins. Our discussions here will focus on a number of these proteins for which most information has been available, from Nicotiana tabacum, its self-incompatible relative N. alata, and Zea mays. In addition, the regulation of the synthesis and glyco-modification of one of these proteins, TTS (transmitting tissue-specific) protein from N. tabacum will be discussed in the light of how differential glycosylation may be used to regulate molecular interactions within the ECM.

Extracellular Matrix↗
PubMed1996

The structures of arabinoxyloglucans produced by solanaceous plants.

Several structural features, most notably the presence of alpha-L-Araf-(1-->2)-alpha-D-Xylp side chains, distinguish the arabinoxyloglucans (AXGs) produced by solanaceous plants from the xyloglucans produced by other dicotyledonous plants. However, previous studies did not establish the exact order of attachment of the various side chains along the backbone of these AXGs. Therefore, oligosaccharide subunits of the AXGs secreted by suspension-cultured tobacco and tomato cells were generated by treatment of the isolated AXGs with a fungal endo-beta-(1-->4)-D-glucanase (EG). The oligosaccharides were reduced with sodium borohydride to the corresponding oligoglycosyl alditol derivatives and purified by a combination of gel-permeation chromatography, reversed-phase HPLC, and HPAE chromatography. The isolated oligoglycosyl alditols were chemically characterized by NMR spectroscopy, matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDITOFMS), fast-atom bombardment mass spectrometry (FABMS), FABMS/MS, and glycosyl-linkage analysis. The results confirmed that the AXGs from these species are composed of a (1-->4)-linked beta-D-Glcp backbone substituted at O-6 with various side chains. Both tobacco and tomato AXG contain alpha-D-Xylp and alpha-L-Araf-(1-->2)-alpha-D-Xylp side chains. However, oligosaccharide fragments of tomato AXG were also shown to contain beta-D-Galp-(1-->2)-alpha-D-Xylp and beta-Araf-(1-->3)-alpha-L-Araf-(1-->2)-alpha-D-Xylp side chains that are not present in the tobacco AXG. This is the first report of beta-Araf residues in a xyloglucan. The primary structures of 20 oligosaccharides generated by EG-treatment of tobacco AXG were determined. The generation of such a large number of oligosaccharides is due in part to the presence of O-acetyl substituents at O-6 of many of the backbone beta-D-Glcp residues of tobacco AXG. The presence of either an O-acetyl or a glycosidic substituent at O-6 of a beta-D-Glc p residue in the AXG backbone protects the glycosidic bond of this residue from cleavage by the EG. Removal of the O-acetyl substituents prior to EG-treatment of the AXG-results in oligosacharide fragments that are smaller than those produced by EG-treatment of the O-acetylated AXG. Therefore, analysis of the complex mixture of oligosaccharides obtained by EG treatment of native tobacco AXGs provides information regarding the distribution of AXG side chains that would be lost if the AXG is de-O-acetylated prior to EG-treatment. Furthermore, the large library of oligosaccharide fragments generated by this approach revealed additional correlations between the structural features of AXGs and diagnosis chemical shift effects in their 1H NMR spectra.

Arabinose↗
PubMed2002

Changes in secondary metabolism and deposition of an unusual lignin in the ref8 mutant of Arabidopsis.

The end products of the phenylpropanoid pathway play important roles in plant structure and development, as well as in plant defense mechanisms against biotic and abiotic stresses. From a human perspective, phenylpropanoid pathway-derived metabolites influence both human health and the potential utility of plants in agricultural contexts. The last known enzyme of the phenylpropanoid pathway that has not been characterized is p-coumarate 3-hydroxylase (C3H). By screening for plants that fail to accumulate soluble fluorescent phenylpropanoid secondary metabolites, we have identified a number of Arabidopsis mutants that display a reduced epidermal fluorescence (ref) phenotype. We have now shown that the ref8 mutant is defective in the gene encoding C3H. Phenotypic characterization of the ref8 mutant has revealed that the lack of C3H activity in the mutant leads to diverse changes in phenylpropanoid metabolism. The ref8 mutant accumulates p-coumarate esters in place of the sinapoylmalate found in wild-type plants. The mutant also deposits a lignin formed primarily from p-coumaryl alcohol, a monomer that is at best a minor component in the lignin of other plants. Finally, the mutant displays developmental defects and is subject to fungal attack, suggesting that phenylpropanoid pathway products downstream of REF8 may be required for normal plant development and disease resistance.

Arabidopsis↗
PubMed2004

Below-ground plant parts emit herbivore-induced volatiles: olfactory responses of a predatory mite to tulip bulbs infested by rust mites.

Although odour-mediated interactions among plants, spider mites and predatory mites have been extensively studied above-ground, belowground studies are in their infancy. In this paper, we investigate whether feeding by rust mites (Aceria tulipae) cause tulip bulbs to produce odours that attract predatory mites (Neoseiulus cucumeris). Since our aim was to demonstrate such odours and not their relevance under soil conditions, the experiments were carried out using a classic Y-tube olfactometer in which the predators moved on a Y-shaped wire in open air. We found that food-deprived female predators can discriminate between odours from infested bulbs and odours from uninfested bulbs or artificially wounded bulbs. No significant difference in attractiveness to predators was found between clean bulbs and bulbs either wounded 30 min or 3 h before the experiment. These results indicate that it may not be simply the wounding of the bulbs, but rather the feeding by rust mites, which causes the bulb to release odours that attract N. cucumeris. Since bulbs are belowground plant structures, the olfactometer results demonstrate the potential for odour-mediated interactions in the soil. However, their importance in the actual soil medium remains to be demonstrated.

Animals↗
PubMed1989

Implications for evolution of nuclear structures of animals, plants, fungi and protoctists.

The evolutionary variations of nuclear structure of animals, plants, fungi and protoctists were studied with electron microscopy by using techniques preferentially staining ribonucleoprotein (RNP) particles and chromatin. A remarkable similarity in the general morphological features of the RNP particles and chromatin arrangement is found in animals, plants and fungi. Important variations of these features were found in protoctists. These observations suggest that major evolutionary changes in the nuclear structure predate the acquisition of plastids by the ancestors of green plants. Once evolved, the nuclear structural pattern is conserved in plants and animals. Among protoctists studied, Kinetoplastida, Cryptomonadida and Volvocida have RNP particles and chromatin arrangement resembling those of plants and animals. These similarities may indicate a common ancestor. Important differences in the nuclear structure among Euglenida, Amebida, Cryptomonadida, Volvocida and Kinetoplastida support the view that Sarcomastigophora is a polyphyletic taxon. For the same reason Kinetoplastida and Euglenida must not be grouped in a monophyletic taxon. We propose that the variations of RNP particles may be related to the initial evolution of post-transcriptional processing.

Animals↗
PubMed1994

Structural features of plant chitinases and chitin-binding proteins.

Structural features of plant chitinases and chitin-binding proteins are discussed. Many of these proteins consist of multiple domains, of which the chitin-binding hevein domain is a predominant one. X-ray and NMR structures of representatives of the major classes of these proteins are available now, and are used to describe the structures of the other ones. Conserved positions of Cys residues can be taken as evidence for identically located disulfide bridges or cysteine residues. The current classification of chitinases is unsatisfactory and needs to be replaced by an evolutionarily more correct one. As the currently known three-dimensional structures of chitinases are those from barley and the rubber tree, Hevea brasiliensis, it is proposed to adopt the designation b-type (classes I, II and IV) and h-type (classes III and V) chitinases, respectively.

Amino Acid Sequence↗
PubMed2005

Microbial community structure at different depths in disturbed and undisturbed semiarid Mediterranean forest soils.

Metabolic abilities and micrfiobial community structure were investigated through three semiarid Mediterranean soils of SE Spain. The soils were (1) a Typic Calcixerept under an adult pine plantation (PP), growing on abandoned agricultural terraces; (2) a Typic Calcixeroll under a native pinewood (NP); and (3) a Typic Haploxerept covered with a grass steppe (GS). PP and NP were similar as regards their genesis, but the former used to be tilled. NP and GS were undisturbed and supported natural and seminatural vegetation, respectively. Seven samples in 10-cm depth increments were taken in triplicate along each soil profile. Community-level physiological profiles based on sole-C-source use were determined to characterize the metabolic abilities. A 16S rDNA polymerase chain reaction-denaturing gradient gel electrophoresis analysis was performed to investigate the microbial genetic structure. Plant cover and land-use history were major determinants of microbial community structure. Microbial communities residing in soils under a native pinewood, the most diverse and stable plant cover, were the most complex both metabolically and genetically. The microbial community structure distinctly changed with depth, related to the quantity and quality of total organic carbon. Both undisturbed soils showed falling gradients of metabolic and genetic complexity, which were invariably of a greater magnitude in the mature woodland than in the grass steppe. In the planted pinewood, however, the substrate-use diversity increased with depth, apparently a response to the depleted metabolic abilities within its upper layer (0-30 cm). Tilling and plant cover removal might be responsible for such a perturbation. In the same profile, molecular fingerprint patterns of the topsoil layer (0-10 cm) indicated a disturbed genetic structure that might underlie the loss of metabolic abilities. However, the genetic structure of the deeper layers of the planted and native pinewoods was not dissimilar, revealing that equivalent genetic resources perform different environmental functions under changing soil scenarios.

Bacteria↗
PubMed1993

Modification of phospholipid membrane structure by the plant toxic peptide Pyrularia thionin.

Pyrularia thionin (P thionin) is a bioactive peptide from the parasitic plant Pyrularia pubera. The structural aspects of its interaction with phospholipid membranes were investigated by measuring the responses of phosphorescence quenching, EPR spin labels, and 1H and 31P NMR at different phospholipid compositions. In phosphatidylcholine bilayers containing cardiolipin or phosphatidylinositol, P thionin induced a pronounced increase in the membrane viscosity, and at higher P thionin concentrations the formation of nonbilayer structures was observed. In phosphatidylcholine bilayers containing phosphatidylserine, P thionin induced a significant transformation of membrane lamellar structure accompanied by a decrease of membrane viscosity. In all investigated lipid systems added P thionin caused an increase in membrane permeability and induced a fusion of sonicated liposomes. The specificity of P thionin interaction with phosphatidylserine-containing membrane is discussed and a model of phospholipid membrane modification by P thionin is suggested.

Antimicrobial Cationic Peptides↗
PubMed2003

Extensive summer water pulses do not necessarily lead to canopy growth of Great Basin and northern Mojave Desert shrubs.

Plant species and functionally related species groups from arid and semi-arid habitats vary in their capacity to take up summer precipitation, acquire nitrogen quickly after summer precipitation, and subsequently respond with ecophysiological changes (e.g. water and nitrogen relations, gas exchange). For species that respond ecophysiologically, the use of summer precipitation is generally assumed to affect long-term plant growth and thus alter competitive interactions that structure plant communities and determine potential responses to climate change. We assessed ecophysiological and growth responses to large short-term irrigation pulses over one to three growing seasons for several widespread Great Basin and northern Mojave Desert shrub species: Chrysothamnus nauseosus, Sarcobatus vermiculatus, Atriplex confertifolia, and A. parryi. We compared control and watered plants in nine case studies that encompassed adults of all four species, juveniles for three of the species, and two sites for two of the species. In every comparison, plants used summer water pulses to improve plant water status or increase rates of functioning as indicated by other ecophysiological characters. Species and life history stage responses of ecophysiological parameters (leaf N, delta15N, delta13C, gas exchange, sap flow) were consistent with several previous short-term studies. However, use of summer water pulses did not affect canopy growth in eight out of nine comparisons, despite the range of species, growth stages, and site conditions. Summer water pulses affected canopy growth only for C. nauseosus adults. The general lack of growth effects for these species might be due to close proximity of groundwater at these sites, co-limitation by nutrients, or inability to respond due to phenological canalization. An understanding of the connections between short-term ecophysiological responses and growth, for different habitats and species, is critical for determining the significance of summer precipitation for desert community dynamics.

Analysis of Variance↗
PubMed2000

Computer simulation of sphenopsid architecture. I. Principles and methodology.

The modelling system AMAP 1 provides morphological models that reproduce the series of shapes developed in a plant structure during its growth. It is applicable to plants that have architectural features consistent with the principles introduced by Hallé et al. (Hallé, F., Oldeman, R.A.A., Tomlinson, P.B., 1978. Tropical Trees and Forest. Springer, Berlin, 441 pp.). We present the main principles of the methodology including the use of an architectural template and the statistical processing of the data collected on sample plants and a description of its components and parameters. We use models of Equisetum telmateia aerial shoots as examples of adaptations of this methodology to plants represented by a limited number of specimens. The main features of this approach that make it especially relevant for modelling incomplete and fragmented fossil plants include the use of architectural templates constructed by adding discrete morphological entities limited to a number of axial components as follows: as many branch orders as are identified in the sample plants, a single extension unit per branch order, and its internodes. This approach is viewed as a means to provide visual representations of plants at different ontogenetical stages, expressing our current knowledge of their growth and branching strategies, and of the parameters that control their geometries.

Journal Article↗