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PubMed2005

Using L-systems for modeling source-sink interactions, architecture and physiology of growing trees: the L-PEACH model.

Functional-structural plant models simulate the development of plant structure, taking into account plant physiology and environmental factors. The L-PEACH model is based on the development of peach trees. It demonstrates the usefulness of L-systems in constructing functional-structural models. L-PEACH uses L-systems both to simulate the development of tree structure and to solve differential equations for carbohydrate flow and allocation. New L-system-based algorithms are devised for simulating the behavior of dynamically changing structures made of hundreds of interacting, time-varying, nonlinear components. L-PEACH incorporates a carbon-allocation model driven by source-sink interactions between tree components. Storage and mobilization of carbohydrates during the annual life cycle of a tree are taken into account. Carbohydrate production in the leaves is simulated based on the availability of water and light. Apices, internodes, leaves and fruit grow according to the resulting local carbohydrate supply. L-PEACH outputs an animated three-dimensional visual representation of the growing tree and user-specified statistics that characterize selected stages of plant development. The model is applied to simulate a tree's response to fruit thinning and changes in water stress. L-PEACH may be used to assist in horticultural decision-making processes after being calibrated to specific trees.

Biological Transport, Active↗
PubMed2006

Effect of a copper gradient on plant community structure.

Vegetation data including plant cover, biomass, species richness, and vegetation height was sampled on a copper-contaminated field with total copper contents varying from 50 to almost 3,000 mg/kg soil. The field was covered by early succession grassland dominated by Agrostis stolonifera. Plant cover, biomass, species richness, and vegetation height generally decreased with increasing copper content, although the highest biomass was reached at intermediate copper concentrations. Multivariate statistical analyses showed that plant community composition was significantly correlated with soil copper concentration and that community composition at soil copper concentrations above 200 mg/kg differed significantly from community composition at lower copper levels. Comparison of single-species (Black Bindweed, Fallopia convolvulus) performance at the field site and in laboratory tests involving field soil and spiked soil indicates that the laboratory tests conventionally applied for risk assessment purposes do not overestimate copper effects. Interaction between copper and other stressors operating only in the field probably balance the higher bioavailability in spiked soil.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed1998

A multiscale model of plant topological structures

In applications dealing with plant growth modeling, increasing attention is being devoted to the topological structure of plants. Different models, based on tree-graphs, have been introduced to represent plants. These models assume that the scale of description is fixed. However, this hypothesis is too restrictive for new modeling applications that aim to tackle analysis or simulation of plant growth at different time and space scales. In order to make such multiscale descriptions available to computer applications, we have defined a general methodology for measuring and representing multiscale plant topological structures. This paper discusses the design of a model of plant topological structures and sketches out its general formal properties. The model supports multiscale, attributed and time-varying descriptions of plants. It is intended to be used for plant analysis methodologies and plant growth simulations.Copyright 1998 Academic Press Limited

Journal Article↗
PubMed2001

Modeling of branching structures of plants.

Previous studies of branching structures generally focused on arteries. Four cost models minimizing total surface area, total volume, total drag and total power losses at a junction point have been proposed to study branching structures. In this paper, we highlight the branching structures of plants and examine which model fits data of branching structures of plants the best. Though the effect of light (e.g. phototropism) and other possible factors are not included in these cost models, a simple cost model with physiological significance, needs to be verified before further research on modeling of branching structures is conducted. Therefore, data are analysed in this paper to determine the best cost model. Branching structures of plants are studied by measuring branching angles and diameters of 234 junctions from four species of plants. The sample includes small junctions, large junctions, two- and three-dimensional junctions, junctions with three branches joining at a point and those with four branches joining at a point. First, junction exponents (x) were determined. Second, log-log plots indicate that model of volume minimization fits data better than other models. Third, one-sided t -tests were used to compare the fitness of four models. It is found that model of volume minimization fits data better than other cost models.

Models, Biological↗
PubMed1973

The Structure of Plant Cell Walls: IV. A Structural Comparison of the Wall Hemicellulose of Cell Suspension Cultures of Sycamore (Acer PseudoPlatAnus) and of Red Kidney Bean (Phaseolus Vulgaris).

The molecular structure and chemical properties of the hemicellulose present in the isolated cell walls of suspension cultures of sycamore (Acer pseudoplatanus) cells has recently been described by Bauer et al. (Plant Physiol. 51: 174-187). The hemicellulose of the sycamore primary cell wall is a xyloglucan. This polymer functions as an important cross-link in the structure of the cell wall; the xyloglucan is hydrogen-bonded to cellulose and covalently attached to the pectic polymers.The present paper describes the structure of a xyloglucan present in the walls and in the extracellular medium of suspension-cultured Red Kidney bean (Phaseolus vulgaris) cells and compares the structure of the bean xyloglucan with the structure of the sycamore xyloglucan. Although some minor differences were found, the basic structure of the xyloglucans in the cell walls of these distantly related species is the same. The structure is based on a repeating heptasaccharide unit which consists of four residues of beta-1, 4-linked glucose and three residues of terminal xylose linked to the 6 position of three of the glucosyl residues.

Journal Article↗
PubMed2003

Bottom-up control of carabid beetle communities in early successional wetlands: mediated by vegetation structure or plant diversity?

Two hypotheses of bottom-up control that predict that the species richness of Carabidae will depend either on the taxonomic diversity of plants ("taxonomic diversity hypothesis") or on the structural heterogeneity of the vegetation ("structural heterogeneity hypothesis") were tested. Plant species were classified into nine plant structural groups through cluster analysis of morphological traits (e.g. total height) at 30 early successional temporary wetlands in the east-German agricultural landscape. In a linear regression analysis, the heterogeneity of vegetation structures explained 55% of the variation in carabid beetle diversity. According to a partial correlation analysis, plant taxonomic diversity did not have a significant effect, consistent with the "structural heterogeneity hypothesis," and contradicting previous studies which concluded that plant taxonomic diversity would be the most important factor in early successional habitats. An experimental study was used to test hypotheses on the processes underlying this bottom-up control by vegetation structure: the "hunting efficiency hypothesis," the "enemy-free space hypothesis," and the "microhabitat specialization hypothesis." The composition of plant structural groups in 15 vegetation plots (1 m(2)) was manipulated, creating a gradient from dense vegetation to open plots. Subsequent pitfall catches revealed significant differences in the activity-abundances of the carabid species. Large species preferred dense vegetation plots, consistent with the enemy-free space hypothesis that large species are more vulnerable to predation on the open plots and prefer dense vegetation to escape from natural enemies. The results indicate that bottom-up control is not mediated only by plant taxonomic or functional group diversity and that vegetation structures may be more important than previously suggested.

Agriculture↗
PubMed1992

Small repeated sequences and the structure of plant mitochondrial genomes.

The structure of plant mitochondrial genomes has proven to be complex and difficult to study. Recombination across large and small repeated sequences can result in genome diversity within individual plants, as well as rapid evolutionary change in genome structure. The role of these repeats is becoming more obvious as mitochondrial genomes are examined in detail.

DNA, Mitochondrial↗
PubMed2002

Insect antifeedants from tropical plants II: structure of zumsin.

A novel A-seco limonoid was isolated from methanolic extract of Croton jatrophoides and designated as zumsin. This compound showed potent antifeedant activity against two lepidopteran larvae, pink bollworm, Pectinophora gossypiella (PC(50) = 1 microg/cm(2), PC(95) = 8 microg/cm(2)), and fall armyworm, Spodoptera frugiperda (PC(50) = 2 microg/cm(2), PC(95) = 16 microg/cm(2)). The structure of zumsin was determined as 1 using a variety of spectroscopic methods including nuclear magnetic resonance, mass spectrometry, and circular dichroism. The structure consists of an A'-B trans-fused ring while dumsin (2), a constituent of the same source, maintains an A'-B cis-fused ring, and suggests two unique biosynthetic processes after A ring oxidative expansion.

Animals↗
PubMed2003

Crystal structure of chloroplastic ascorbate peroxidase from tobacco plants and structural insights into its instability.

Ascorbate peroxidase (APX) is a heme-containing protein that plays a central role in scavenging H(2)O(2) in higher plants. The structure of stromal APX (sAPX) was determined at 1.6 A to an R-factor of 19.1% and an R-free-factor of 22.3%. The electrostatic potential of the gamma-channel that connects the molecular surface of sAPX to the gamma-edge of heme was more positive than that of cytosolic APX (cAPX) from pea, so sAPX might bind more easily with ascorbate than cAPX. The overall structure of sAPX was similar to those of cAPX from pea and cytochrome c peroxidase (CCP) from yeast, with a substantial difference in a loop structure located in the vicinity of the heme. The side chain of Arg169 in sAPX corresponding to His169 in cAPX and His181 in CCP extended in the opposite direction from the heme, forming two hydrogen bonds with carbonyl groups in the loop structure. The rapid inactivation of sAPX might be due to the characteristic conformation of Arg169 owing to the loop structure of sAPX.

Ascorbate Peroxidases↗
PubMed2007

Plant architecture: a dynamic, multilevel and comprehensive approach to plant form, structure and ontogeny.

BACKGROUND AND AIMS: The architecture of a plant depends on the nature and relative arrangement of each of its parts; it is, at any given time, the expression of an equilibrium between endogenous growth processes and exogenous constraints exerted by the environment. The aim of architectural analysis is, by means of observation and sometimes experimentation, to identify and understand these endogenous processes and to separate them from the plasticity of their expression resulting from external influences. SCOPE: Using the identification of several morphological criteria and considering the plant as a whole, from germination to death, architectural analysis is essentially a detailed, multilevel, comprehensive and dynamic approach to plant development. Despite their recent origin, architectural concepts and analysis methods provide a powerful tool for studying plant form and ontogeny. Completed by precise morphological observations and appropriated quantitative methods of analysis, recent researches in this field have greatly increased our understanding of plant structure and development and have led to the establishment of a real conceptual and methodological framework for plant form and structure analysis and representation. This paper is a summarized update of current knowledge on plant architecture and morphology; its implication and possible role in various aspects of modern plant biology is also discussed.

Body Patterning↗
PubMedDate not supplied

[Molecular structure of plant genomes].

The genome structure of several species of Graminea and Drosophila was investigated by DNA renaturation method. Kinetics of DNA reassociation was studied by direct optical scanning and the data obout Cot curve were analized by an improved computer programm "Finger". Differences between structure DNA animals and plants are shown. Plant genomes have no unique fraction which exists in animal genomes. Slowly reassociating fraction in plants comprises about 20% DNA as compared with more than 60% in animal DNA. An analysis of kinetic complexity indicates that the relative content of the slowly reassociating fraction in the genome both of animal and of plants is much higher than that of the highly repeated DNA fraction.

DNA↗
PubMed1990

Nuclear architecture in plants.

Structure within the nucleus of plants is becoming increasingly clear in both metaphase and interphase nuclei, although there are conflicting data about the relative positions of individual and pairs of chromosomes. At interphase, individual chromosomes may generally occupy discrete domains that are not intermixed with other chromosomes. Aspects of mechanical chromosome behaviour and even of gene expression may correlate with interphase chromosome position, and imply that a better understanding of nuclear architecture is required.

Cell Nucleus↗
PubMed2004

Differential antifungal and calcium channel-blocking activity among structurally related plant defensins.

Plant defensins are a family of small Cys-rich antifungal proteins that play important roles in plant defense against invading fungi. Structures of several plant defensins share a Cys-stabilized alpha/beta-motif. Structural determinants in plant defensins that govern their antifungal activity and the mechanisms by which they inhibit fungal growth remain unclear. Alfalfa (Medicago sativa) seed defensin, MsDef1, strongly inhibits the growth of Fusarium graminearum in vitro, and its antifungal activity is markedly reduced in the presence of Ca(2+). By contrast, MtDef2 from Medicago truncatula, which shares 65% amino acid sequence identity with MsDef1, lacks antifungal activity against F. graminearum. Characterization of the in vitro antifungal activity of the chimeras containing portions of the MsDef1 and MtDef2 proteins shows that the major determinants of antifungal activity reside in the carboxy-terminal region (amino acids 31-45) of MsDef1. We further define the active site by demonstrating that the Arg at position 38 of MsDef1 is critical for its antifungal activity. Furthermore, we have found for the first time, to our knowledge, that MsDef1 blocks the mammalian L-type Ca(2+) channel in a manner akin to a virally encoded and structurally unrelated antifungal toxin KP4 from Ustilago maydis, whereas structurally similar MtDef2 and the radish (Raphanus sativus) seed defensin Rs-AFP2 fail to block the L-type Ca(2+) channel. From these results, we speculate that the two unrelated antifungal proteins, KP4 and MsDef1, have evolutionarily converged upon the same molecular target, whereas the two structurally related antifungal plant defensins, MtDef2 and Rs-AFP2, have diverged to attack different targets in fungi.

Amino Acid Sequence↗
PubMed1992

Satellite RNAs of plant viruses: structures and biological effects.

Plant viruses often contain parasites of their own, referred to as satellites. Satellite RNAs are dependent on their associated (helper) virus for both replication and encapsidation. Satellite RNAs vary from 194 to approximately 1,500 nucleotides (nt). The larger satellites (900 to 1,500 nt) contain open reading frames and express proteins in vitro and in vivo, whereas the smaller satellites (194 to 700 nt) do not appear to produce functional proteins. The smaller satellites contain a high degree of secondary structure involving 49 to 73% of their sequences, with the circular satellites containing more base pairing than the linear satellites. Many of the smaller satellites produce multimeric forms during replication. There are various models to account for their formation and role in satellite replication. Some of these smaller satellites encode ribozymes and are able to undergo autocatalytic cleavage. The enzymology of satellite replication is poorly understood, as is the replication of their helper viruses. In many cases the coreplication of satellites suppresses the replication of the helper virus genome. This is usually paralleled by a reduction in the disease induced by the helper virus; however, there are notable exceptions in which the satellite exacerbates the pathogenicity of the helper virus, albeit on only a limited number of hosts. The ameliorative satellites are being assessed as biocontrol agents of virus-induced disease. In greenhouse studies, satellites have been known to "spontaneously" appear in virus cultures. The possible origin of satellites will be briefly considered.

Base Sequence↗
PubMed1980

Structure of Plant Cell Walls: X. RHAMNOGALACTURONAN I, A STRUCTURALLY COMPLEX PECTIC POLYSACCHARIDE IN THE WALLS OF SUSPENSION-CULTURED SYCAMORE CELLS.

The purification and characterization of a pectic polymer, rhamnogalacturonan I, present in the primary cell walls of dicots is described. Rhamnogalacturonan I accounts for approximately 7% of the mass of the walls isolated from suspension-cultured sycamore cells. As purified, rhamnogalacturonan I has a molecular weight of approximately 200,000 and is composed primarily of l-rhamnosyl, d-galacturonosyl, l-arabinosyl, and d-galactosyl residues. The backbone of rhamnogalacturonan I is thought to be composed predominantly of d-galacturonosyl and l-rhamnosyl residues in a ratio of approximately 2:1. About half of the l-rhamnosyl residues are 2-linked and are glycosidically attached to C(4) of a d-galacturonosyl residue. The other half of the l-rhamnosyl residues are 2,4-linked and have a d-galacturonosyl residue glycosidically attached at C(2). Sidechains averaging 6 residues in length are attached to C(4) of the l-rhamnosyl residues. There are many different sidechains, containing variously linked l-arabinosyl, and/or d-galactosyl residues.

Journal Article↗
PubMed2005

Solving the structure of plant photosystem I--biochemistry is vital.

The recently determined structure of plant photosystem I (PSI) provides the first relatively high-resolution structural model of a supercomplex containing a reaction center and its peripheral antenna. Large amounts of highly purified PSI were required to get enough crystals amenable for structural determination by X-ray crystallography. In addition, a deep biochemical understanding of the large supercomplex was vital for achieving the goal. The stability of PSI was analyzed by sucrose gradient centrifugation and gel electrophoresis. Small amounts of LHCI were detached from PSI following a 12 day incubation under crystallization conditions. The interaction between the reaction center and the peripheral antenna of PSI (LHCI) as well as the interactions among the LHCI monomers are flexible. Nevertheless, the pure and homogeneous preparation of PSI allows for relatively tight crystal packing, which holds promise for obtaining atomic resolution in the future.

Chromatography, DEAE-Cellulose↗