Effective temperature in stochastic kinetics and gene networks

The fluctuation-dissipation theorem, one of the central theorems in thermal dynamics, breaks down in out-of-equilibrium systems. The idea of effective temperature coming from the extensions of that theorem has been recently introduced to study glasses and has proved to be a key concept for out-of-equilibrium systems. Gene networks involve stochastic chemical kinetics and are far from equilibrium. This leads us to try to use the notion of effective temperature to study them. To develop this idea, we study a simple birth-death process and a general two-species interacting process using the language of effective temperature. Furthermore, a model of a nonregulatory gene is studied as an example. The effective temperature may serves as an alternative and somewhat more fundamental language to describe the intrinsic-extrinsic noise distinction that has already provided a tool for qualifying gene networks.     

Study of the inheritance of seed primary dormancy and the ability to enter secondary dormancy in Petunia: influence of temperature, light and gibberellic acid on dormancy

Abstract. The germination behaviour of two Petunia hybrida lines. M₃₀ and Th₇, and their reciprocal hybrids was studied. Two sets of experimental conditions appeared helped to distinguish between dormant and non-dormant parental lines: (1) 25 and 35 °C in the dark, in the latter case after 2 months of dry storage at 20 °C; (2) 35 and 40 °C in the light. Photosensitivity was tested in the first case and sensitivity to GA₃ in the second case. The predominance of paternal control over dormancy was evident. A maternal or tegumentary control of photosensitivity and of sensitivity to GA₃ was also shown. Transferring the seeds, originally imbibed in conditions expressing primary dormancy, to conditions which previously supported their germination, allowed us to show that secondary dormancy could be easily induced when a deeper primary dormancy had already developed in the seeds.     

Stamen development and winter dormancy in apricot (Prunus armeniaca)

Background and Aims

In temperate woody perennials, flower bud development is halted during the winter, when the buds enter dormancy. This dormant period is a prerequisite for adequate flowering, is genetically regulated, and plays a clear role in possibly adapting species and cultivars to climatic areas. However, information on the biological events underpinning dormancy is lacking. Stamen development, with clear differentiated stages, appears as a good framework to put dormancy in a developmental context. Here, stamen developmental changes are characterized in apricot (Prunus armeniaca) and are related to dormancy.

Methods

Stamen development was characterized cytochemically from the end of August to March, over 4 years. Developmental changes were related to dormancy, using the existing empirical information on chilling requirements.

Key Results

Stamen development continued during the autumn, and the flower buds entered dormancy with a fully developed sporogenous tissue. Although no anatomical changes were observed during dormancy, breaking of dormancy occurred following a clear sequence of events. Starch accumulated in particular places, pre-empting further development in those areas. Vascular bundles developed and pollen mother cells underwent meiosis followed by microspore development.

Conclusions

Dormancy appears to mark a boundary between the development of the sporogenous tissue and the occurrence of meiosis for further microspore development. Breaking of dormancy occurs following a clear sequence of events, providing a developmental context in which to study winter dormancy and to evaluate differences in chilling requirements among genotypes.     

Soil temperature affects carbon allocation within arbuscular mycorrhizal networks and carbon transport from plant to fungus

How soil carbon balance will be affected by plant–mycorrhizal interactions under future climate scenarios remains a significant unknown in our ability to forecast ecosystem carbon storage and fluxes. We examined the effects of soil temperature (14, 20, 26 °C) on the structure and extent of a multispecies community of arbuscular mycorrhizal (AM) fungi associated with Plantago lanceolata. To isolate fungi from roots, we used a mesh‐divided pot system with separate hyphal compartments near and away from the plant. A ¹³C pulse label was then used to trace the flow of recently fixed photosynthate from plants into belowground pools and respiration. Temperature significantly altered the structure and allocation of the AM hyphal network, with a switch from more vesicles (storage) in cooled soils to more extensive extraradical hyphal networks (growth) in warmed soils. As soil temperature increased, we also observed an increase in the speed at which plant photosynthate was transferred to and respired by roots and AM fungi coupled with an increase in the amount of carbon respired per unit hyphal length. These differences were largely independent of plant size and rates of photosynthesis. In a warmer world, we would therefore expect more carbon losses to the atmosphere from AM fungal respiration, which are unlikely to be balanced by increased growth of AM fungal hyphae.     

Responses of stomatal conductance to light, humidity and temperature in winter wheat and barley grown at three concentrations of carbon dioxide in the field

Responses of leaf stomatal conductance to light, humidity and temperature were characterized for winter wheat and barely grown at ambient (about 350 μmol mol^?1 in the daytime), ambient + 175 and ambient + 350 μmol mol^?1 concentrations of carbon dioxide in open‐topped chambers in field plots over a three year period. Stomatal responses to environment were determined by direct manipulation of single environmental factors, and those results were compared with responses derived from natural day to day variation in mid‐day stomatal conductance. The purpose of these experiments was to determine the magnitude of reduction in stomatal conductance at elevated [CO₂], and to assess whether the relative response of conductance to elevated [CO₂] was constant across light, humidity and temperature conditions. The results indicated that light, humidity and temperature all significantly affected the relative decrease in stomatal conductance at elevated [CO₂]. The relative decrease in conductance with elevated [CO₂] was greater at low light, low water vapour pressure difference, and high temperature in both species. For measurements made at saturating light near mid‐day, the ratio of mid‐day stomatal conductances at doubled [CO₂] to that at ambient [CO₂] ranged from 0.42 to 0.86, with a mean of 0.66 in barley, and from 0.33 to 0.80, with a mean of 0.56 in wheat. Day‐to‐day variation in the relative effect of elevated [CO₂] on conductance was correlated with the relative stimulation of [CO₂] assimilation rate and with temperature. Some limitations of multiple linear regression, multiplicative, and ‘Ball–Berry' models as summaries of the data are discussed. In barley, a better fit to the models occurred in individual years than for the combined data, and in wheat a better fit to the models occurred when data from near the end of the season were removed.     

Responses of succulents to plant water stress

Experiments were performed to test the hypothesis that succulents “shift” their method of photosynthetic metabolism in response to environmental change. Our data showed that there were at least three different responses of succulents to plant water status. When plant water status of Portulacaria afra (L.) Jacq. was lowered either by withholding water or by irrigating with 2% NaCl, a change from C₃-photosynthesis to Crassulacean acid metabolism (CAM) occurred. Fluctuation of titratable acidity and nocturnal CO₂ uptake was induced in the stressed plants. Stressed Peperomia obtusifolia A. Dietr. plants showed a change from C₃-photosynthesis to internal cycling of CO₂. Acid fluctuation commenced in response to stress but exogenous CO₂ uptake did not occur. Zygocactus truncatus Haworth plants showed a pattern of acid fluctuation and nocturnal CO₂ uptake typical of CAM even when well irrigated. The cacti converted from CAM to an internal CO₂ cycle similar to Peperomia when plants were water-stressed. Reverse phase gas exchange in succulents results in low water loss to carbon gain. Water is conserved and low levels of metabolic activity are maintained during drought periods by complete stomatal closure and continual fluctuation of organic acids.     

Conjugated plant hormones: Structure,metabolism and function

Book reviews

Conjugated plant hormones: Structure, metabolism and functionK. Schreiber, H.R. Schütte and G. Sembdner (Eds.), proceedings of the international symposium on conjugated plant hormones. Structure, metabolism and function. Berlin: VEB Deutscher Verlag der Wissenschaften, 1987. 405 pages     

Coordinated gene networks regulating Arabidopsis plant metabolism in response to various stresses and nutritional cues

The expression pattern of any pair of genes may be negatively correlated, positively correlated, or not correlated at all in response to different stresses and even different progression stages of the stress. This makes it difficult to identify such relationships by classical statistical tools such as the Pearson correlation coefficient. Hence, dedicated bioinformatics approaches that are able to identify groups of cues in which there is a positive or negative expression correlation between pairs or groups of genes are called for. We herein introduce and discuss a bioinformatics approach, termed Gene Coordination, that is devoted to the identification of specific or multiple cues in which there is a positive or negative coordination between pairs of genes and can further incorporate additional coordinated genes to form large coordinated gene networks. We demonstrate the utility of this approach by providing a case study in which we were able to discover distinct expression behavior of the energy-associated gene network in response to distinct biotic and abiotic stresses. This bioinformatics approach is suitable to a broad range of studies that compare treatments versus controls, such as effects of various cues, or expression changes between a mutant and the control wild-type genotype.     

Protein complexes mediate signalling in plant responses to hormones,light, sucrose and pathogens

Living organisms use complex pathways of signal perception and transduction to respond to stimuli in their environments. In plants, putative signal transduction components have been identified through mutant screens and comparative analysis of genome sequences of model eukaryotes. Several pieces in a large series of puzzles have now been identified and a current challenge is to determine how these pieces interconnect. Functional analysis of the encoded proteins has necessitated a change from genetic to biochemical approaches. In recent years, the application of techniques such as two-hybrid screening and epitope tagging has facilitated the study of protein-protein interactions and has increased our understanding of cellular signalling mechanisms. One focus of present research is the ubiquitin/proteasome-mediated degradation of proteins. Increasing evidence suggests this is a control common to many plant signalling pathways including development and responsiveness to hormones, light and sucrose. A central challenge in the study of plant disease resistance has been to identify protein complexes that contain host defence proteins and pathogenicity factors. In this review we summarize the latest developments in these areas where the existence of protein complexes has been demonstrated to be of fundamental importance in plant signalling.     

Responses of tree fine roots to temperature

Soil temperature can influence the functioning of roots in many ways. If soil moisture and nutrient availability are adequate, rates of root length extension and root mortality increase with increasing soil temperature, at least up to an optimal temperature for root growth, which seems to vary among taxa. Root growth and root mortality are highly seasonal in perennial plants, with a flush of growth in spring and significant mortality in the fall. At present we do not understand whether root growth phenology responds to the same temperature cues that are known to control shoot growth. We also do not understand whether the flush of root growth in the spring depends on the utilization of stored nonstructural carbohydrates, or if it is fueled by current photosynthate. Root respiration increases exponentially with temperature, but Q ₁₀ values range widely from c . 1.5 to > 3.0. Significant questions yet to be resolved are: whether rates of root respiration acclimate to soil temperature, and what mechanisms control acclimation if it occurs. Limited data suggest that fine roots depend heavily on the import of new carbon (C) from the canopy during the growing season. We hypothesize that root growth and root respiration are tightly linked to whole-canopy assimilation through complex source–sink relationships within the plant. Our understanding of how the whole plant responds to dynamic changes in soil temperature, moisture and nutrient availability is poor, even though it is well known that multiple growth-limiting resources change simultaneously through time during a typical growing season. We review the interactions between soil temperature and other growth-limiting factors to illustrate how simple generalizations about temperature and root functioning can be misleading.     

Genetic loci associated with stem elongation and winter dormancy release in wheat

In winter wheat (Triticum aestivum L.), the stem begins to elongate after the vernalization requirement is satisfied during winter and when favorable temperature and photoperiod conditions are attained in spring. In this study, we precisely measured elongation of the first extended internode on 96 recombinant inbred lines of a population that was generated from a cross between two winter wheat cultivars, Jagger (early stem elongation) and 2174 (late stem elongation). We mapped a major locus for stem elongation to the region where VRN-A1 resides in chromosome 5A. Visible assessment of winter dormancy release was concomitantly associated with this locus. VRN1 was previously cloned based on variation in vernalization requirement between spring wheat carrying a dominant Vrn-1 allele and winter wheat carrying a recessive vrn-1 allele. Both of two winter wheat cultivars in this study carry a recessive vrn-A1 allele; therefore, our results suggest that either VRN-A1 might invoke a new regulatory mechanism or a new gene residing close to VRN-A1 plays a regulatory role in winter wheat development. Phenotypic expression of the vrn-A1a allele of Jagger was more sensitive to the year of measurement of stem elongation than that of the vrn-A1b allele of 2174. In addition to QSte.osu.5A, several loci were also found to have minor effects on initial stem elongation of winter wheat. Seventeen of nineteen locally adapted cultivars in the southern Great Plaints contained the vrn-A1b allele. Hence, breeders in this area have inadvertently selected this allele, contributing to later stem elongation and more conducive developmental patterns for grain production.