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1.  Independent Control of Organogenesis and Shoot Tip Abortion are Key Factors to Developmental Plasticity in Kiwifruit (Actinidia) 
Annals of Botany  2007;100(3):471-481.
Background and Aims
In kiwifruit (Actinidia), the number of nodes per shoot is highly variable and is influenced by genotype and environmental conditions. To understand this developmental plasticity, three key processes were studied: organogenesis by the shoot apical meristem during shoot growth; expansion of phytomers; and shoot tip abortion.
Methods
Studies were made of organogenesis and shoot tip abortion using light and scanning electron microscopy. The effect of temperature on shoot growth cessation was investigated using temperature indices over the budbreak period, and patterns of shoot tip abortion were quantified using stochastic modelling.
Key Results
All growing buds began organogenesis before budbreak. During shoot development, the number of phytomers initiated by the shoot apical meristem is correlated with the number of expanding phytomers and the mean internode length. Shoot tip abortion is preceded by growth cessation and is not brought about by the death of the shoot apical meristem, but occurs by tissue necrosis in the sub-apical zone. For most genotypes studied, the probability of shoot tip abortion is higher during expansion of the preformed part of the shoot. Lower temperatures during early growth result in a higher probability of shoot tip abortion.
Conclusions
Organogenesis and shoot tip abortion are controlled independently. All buds have the potential to become long shoots. Conditions that increase early growth rate postpone shoot tip abortion.
doi:10.1093/aob/mcm140
PMCID: PMC2533607  PMID: 17650513
Actinidia; kiwifruit; shoot fate; neoformation; organogenesis; shoot tip abortion; developmental plasticity; temperature
2.  Are the common assimilate pool and trophic relationships appropriate for dealing with the observed plasticity of grapevine development? 
Annals of Botany  2009;105(2):233-247.
Background and Aims
Models based on the consideration of plant development as the result of source–sink relationships between organs suffer from an inherent lack of quantification of the effect of trophic competition on organ growth processes. The ‘common assimilate pool theory’ underlying many such models is highly debatable.
Methods
Six experiments were carried out in a greenhouse and outdoors with two grapevine cultivars and with 12 management systems, resulting in different types of plant architecture. Ten variables were used to quantify the impact of variations in assimilate supply and topological distances between sources and sinks on organogenesis, morphogenesis and biomass growth.
Key Results
A hierarchy of the responses of these processes to variations in assimilate supply was identified. Organ size seemed to be independent of assimilate supply, whereas both organogenesis and biomass growth were affected by variations in assimilate supply. Lower levels of organ biomass growth in response to the depletion of assimilate supplies seemed to be the principal mechanism underlying the plasticity of plant development in different environments. Defoliation or axis ablation resulted in changes in the relationship between growth processes and assimilate supply, highlighting the influence of non-trophic determinants. The findings cast doubt on the relevance of ‘the common assimilate pool theory’ for modelling the development of grapevine.
Conclusions
The results of this study suggest new formalisms for increasing the ability of models to take plant plasticity into account. The combination of an ecophysiological model for morphogenesis taking environmental signals into account and a biomass driven model for organogenesis and biomass allocation taking the topological distances between the sources and the sinks into account appears to be a promising approach. Moreover, in order to simulate the impact of agronomic practices, it will be necessary to take into account the non-trophic determinants of plant development such as hormonal signaletics.
doi:10.1093/aob/mcp278
PMCID: PMC2814752  PMID: 19946042
Biomass growth; branching system; common assimilate pool; morphogenesis; organogenesis; source–sink; grapevine; Vitis vinifera
3.  Branch Development Controls Leaf Area Dynamics in Grapevine (Vitis vinifera) Growing in Drying Soil 
Annals of Botany  2006;98(1):175-185.
• Background and Aims Soil water deficit is a major abiotic stress with severe consequences for the development, productivity and quality of crops. However, it is considered a positive factor in grapevine management (Vitis vinifera), as it has been shown to increase grape quality. The effects of soil water deficit on organogenesis, morphogenesis and gas exchange in the shoot were investigated.
• Methods Shoot organogenesis was analysed by distinguishing between the various steps in the development of the main axis and branches. Several experiments were carried out in pots, placed in a greenhouse or outside, in southern France. Soil water deficits of various intensities were imposed during vegetative development of the shoots of two cultivars (‘Syrah’ and ‘Grenache N’).
• Key Results All developmental processes were inhibited by soil water deficit, in an intensity-dependent manner, and sensitivity to water stress was process-dependent. Quantitative relationships with soil water were established for all processes. No difference was observed between the two cultivars for any criterion. The number of leaves on branches was particularly sensitive to soil water deficit, which rapidly and strongly reduced the rate of leaf appearance on developing branches. This response was not related to carbon availability, photosynthetic activity or the soluble sugar content of young expanding leaves. The potential number of branches was not a limiting factor for shoot development.
• Conclusions The particularly high sensitivity to soil water deficit of leaf appearance on branches indicates that this process is a major determinant of the adaptation of plant leaf area to soil water deficit. The origin of this particular developmental response to soil water deficit is unclear, but it seems to be related to constitutive characteristics of branches rather than to competition for assimilates between axes differing in sink strength.
doi:10.1093/aob/mcl085
PMCID: PMC2803536  PMID: 16679414
Shoot; organogenesis; morphogenesis; branching; leaf area; stomatal conductance; photosynthesis; carbon availability; soil water deficit; Vitis vinifera L
4.  The problem of morphogenesis: unscripted biophysical control systems in plants 
Protoplasma  2013;251:25-36.
The relative simplicity of plant developmental systems, having evolved within the universal constraints imposed by the plant cell wall, may allow us to outline a consistent developmental narrative that is not currently possible in the animal kingdom. In this article, I discuss three aspects of the development of the mature form in plants, approaching them in terms of the role played by the biophysics and mechanics of the cell wall during growth. First, I discuss axis extension in terms of a loss of stability-based model of cell wall stress relaxation and I introduce the possibility that cell wall stress relaxation can be modeled as a binary switch. Second, I consider meristem shape and surface conformation as a controlling element in the morphogenetic circuitry of plant organogenesis at the apex. Third, I approach the issue of reproductive differentiation and propose that the multicellular sporangium, a universal feature of land plants, acts as a stress–mechanical lens, focusing growth-induced stresses to create a geometrically precise mechanical singularity that can serve as an inducing developmental signal triggering the initiation of reproductive differentiation. Lastly, I offer these three examples of biophysically integrated control processes as entry points into a narrative that provides an independent, nongenetic context for understanding the evolution of the apoplast and the morphogenetic ontogeny of multicellular land plants.
doi:10.1007/s00709-013-0522-y
PMCID: PMC3893470  PMID: 23846861
Morphogenesis; Loss of stability; Axis extension; Meristem shape; Surface conformation; Reproductive differentiation
5.  A dynamic model of plant growth with interactions between development and functional mechanisms to study plant structural plasticity related to trophic competition 
Annals of Botany  2009;103(8):1173-1186.
Background and Aims
The strong influence of environment and functioning on plant organogenesis has been well documented by botanists but is poorly reproduced in most functional–structural models. In this context, a model of interactions is proposed between plant organogenesis and plant functional mechanisms.
Methods
The GreenLab model derived from AMAP models was used. Organogenetic rules give the plant architecture, which defines an interconnected network of organs. The plant is considered as a collection of interacting ‘sinks’ that compete for the allocation of photosynthates coming from ‘sources’. A single variable characteristic of the balance between sources and sinks during plant growth controls different events in plant development, such as the number of branches or the fruit load.
Key Results
Variations in the environmental parameters related to light and density induce changes in plant morphogenesis. Architecture appears as the dynamic result of this balance, and plant plasticity expresses itself very simply at different levels: appearance of branches and reiteration, number of organs, fructification and adaptation of ecophysiological characteristics.
Conclusions
The modelling framework serves as a tool for theoretical botany to explore the emergence of specific morphological and architectural patterns and can help to understand plant phenotypic plasticity and its strategy in response to environmental changes.
doi:10.1093/aob/mcp054
PMCID: PMC2685317  PMID: 19297366
Trophic plasticity; plant growth; functional–structural models; dynamic system; interactions; GreenLab
6.  Cessation of Tillering in Spring Wheat in Relation to Light Interception and Red : Far-red Ratio 
Annals of Botany  2006;97(4):649-658.
• Background and Aims The production of axillary shoots (tillering) in spring wheat (Triticum aestivum) depends on intraspecific competition. The mechanisms that underlie this competition are complex, but light within the wheat canopy plays a key role. The main objectives of this paper are to analyse the effects of plant population density and shade on tillering dynamics of spring wheat, to assess the canopy conditions quantitatively at the time of tillering cessation, and to analyse the relationship between the tiller bud and the leaf on the same phytomer.
• Methods Spring wheat plants were grown at three plant population densities and under two light regimes (25 % and 100 % light). Tiller appearance, fraction of the light intercepted, and red : far-red ratio at soil level were recorded. On six sampling dates the growth status of axillary buds was analysed.
• Key Results Tillering ceased earlier at high population densities and ceased earlier in the shade than in full sunlight. At cessation of tillering, both the fraction of light intercepted and the red : far-red ratio at soil level were similar in all treatments. Leaves on the same phytomer of buds that grew out showed more leaf mass per unit area than those on the same phytomer of buds that remained dormant.
• Conclusions Tillering ceases at specific light conditions within the wheat canopy, independent of population density, and to a lesser extent independent of light intensity. It is suggested that cessation of tillering is induced when the fraction of PAR intercepted by the canopy exceeds a specific threshold (0·40–0·45) and red : far-red ratio drops below 0·35–0·40.
doi:10.1093/aob/mcl020
PMCID: PMC2803660  PMID: 16464875
Triticum aestivum; wheat; tiller; bud; plant population density; shade; PAR; red : far-red ratio; functional–structural model
7.  Alignment between PIN1 Polarity and Microtubule Orientation in the Shoot Apical Meristem Reveals a Tight Coupling between Morphogenesis and Auxin Transport 
PLoS Biology  2010;8(10):e1000516.
Imaging and computational modeling of the Arabidopsis shoot meristem epidermis suggests that biomechanical signals coordinately regulate auxin efflux carrier distribution and microtubule patterning to orchestrate the extent and directionality of growth.
Morphogenesis during multicellular development is regulated by intercellular signaling molecules as well as by the mechanical properties of individual cells. In particular, normal patterns of organogenesis in plants require coordination between growth direction and growth magnitude. How this is achieved remains unclear. Here we show that in Arabidopsis thaliana, auxin patterning and cellular growth are linked through a correlated pattern of auxin efflux carrier localization and cortical microtubule orientation. Our experiments reveal that both PIN1 localization and microtubule array orientation are likely to respond to a shared upstream regulator that appears to be biomechanical in nature. Lastly, through mathematical modeling we show that such a biophysical coupling could mediate the feedback loop between auxin and its transport that underlies plant phyllotaxis.
Author Summary
The proper development of plant organs such as leaves or flowers depends both on localized growth, which can be controlled by the plant hormone auxin, and directional growth, which is dependent on each cell's microtubule cytoskeleton. In this paper we show that at the shoot apex where organs initiate the orientation of the microtubule cytoskeleton is correlated with the orientation of the auxin transporter PIN1, suggesting coordination between growth patterning at the tissue level and directional growth at the cellular level. Recent work has indicated that mechanical signals play a role in orienting the plant microtubule network, and here we show that such signals can also orient PIN1. In addition, we demonstrate through mathematical modeling that an auxin transport system that is coordinated by mechanical signals akin to those we observed in vivo is sufficient to give rise to the patterns of organ outgrowth found in the plant Arabidopsis thaliana.
doi:10.1371/journal.pbio.1000516
PMCID: PMC2957402  PMID: 20976043
8.  Genetic approach towards the identification of auxin–cytokinin crosstalk components involved in root development 
Phytohormones are important plant growth regulators that control many developmental processes, such as cell division, cell differentiation, organogenesis and morphogenesis. They regulate a multitude of apparently unrelated physiological processes, often with overlapping roles, and they mutually modulate their effects. These features imply important synergistic and antagonistic interactions between the various plant hormones. Auxin and cytokinin are central hormones involved in the regulation of plant growth and development, including processes determining root architecture, such as root pole establishment during early embryogenesis, root meristem maintenance and lateral root organogenesis. Thus, to control root development both pathways put special demands on the mechanisms that balance their activities and mediate their interactions. Here, we summarize recent knowledge on the role of auxin and cytokinin in the regulation of root architecture with special focus on lateral root organogenesis, discuss the latest findings on the molecular mechanisms of their interactions, and present forward genetic screen as a tool to identify novel molecular components of the auxin and cytokinin crosstalk.
doi:10.1098/rstb.2011.0233
PMCID: PMC3321684  PMID: 22527389
auxin; cytokinin; forward genetic screen; lateral roots
9.  Genetic chimerism of Vitis vinifera cv. Chardonnay 96 is maintained through organogenesis but not somatic embryogenesis 
BMC Plant Biology  2005;5:20.
Background
Grapevine can be a periclinal chimera plant which is composed at least of two distinct cell layers (L1, L2). When the cell layers of this plant are separated by passage through somatic embryogenesis, regenerated plants could show distinct DNA profiles and a novel phenotype which proved different from that of the parent plant.
Results
Genetically Chardonnay clone 96 is a periclinal chimera plant in which is L1 and L2 cell layers are distinct. Plants obtained via organogenesis through meristematic bulks are shown to be composed of both cell layers. However, plants regenerated through somatic embryogenesis starting from anthers or nodal explants are composed only of L1 cells. These somaclones do not show phenotypic differences to the parental clone up to three years after regeneration. Interestingly, the only somaclone showing an atypical phenotype (asymmetric leave) shows a genotypic modification.
Conclusion
These results suggest that the phenotype of Chardonnay 96 does not result from an interaction between the two distinct cell layers L1 and L2. If phenotype conformity is further confirmed, somatic embryogenesis will result in true-to-type somaclones of Chardonnay 96 and would be well suitable for gene transfer.
doi:10.1186/1471-2229-5-20
PMCID: PMC1285365  PMID: 16194273
10.  Going with the wind – Adaptive dynamics of plant secondary meristems 
Mechanisms of Development  2013;130(1):34-44.
Highlights
► We discuss the role of secondary meristems in the adaptation of plant growth forms. ► We highlight the integration of environmental inputs into plant growth regulation. ► Branching and secondary growth shape the plant body. ► Plant’s phenotypic plasticity can be used to dissect the evolution of growth forms.
The developmental plasticity of organisms is a natural consequence of adaptation. Classical approaches targeting developmental processes usually focus on genetics as the essential factor underlying phenotypic differences. However, such differences are often based on the inherent plasticity of developmental programs. Due to their dependence on environmental stimuli, plants represent ideal experimental systems in which to dissect the contribution of genetic and environmental variation to phenotypic plasticity. An evident example is the vast repertoire of growth forms observed in plant shoot systems. A fundamental factor underlying the broadness of this repertoire is the activity of secondary meristems, namely the axillary meristems that give rise to side shoots, and the cambium essential for stem thickening. Differential activities of both meristem types are crucial to the tremendous variation seen in higher plant architecture. In this review, we discuss the role of secondary meristems in the adaptation of plant growth forms, and the ways in which they integrate environmental input. In particular, we explore potential approaches for dissecting the degree to which this flexibility and its consequences for plant architecture is genetically predetermined and how much it represents an adaptive value.
doi:10.1016/j.mod.2012.05.011
PMCID: PMC3560032  PMID: 22691403
Phenotypic plasticity; Adaptation; Plant meristems; Branching; Cambium; Natural variation
11.  Organ regeneration does not require a functional stem cell niche in plants 
Nature  2009;457(7233):1150-1153.
Plants rely on the maintenance of stem cell niches at their apices for the continuous growth of roots and shoots. However, while the developmental plasticity of plant cells has been demonstrated1, it is not known whether the stem cell niche is required for organogenesis. Here we explore the capacity of a broad range of differentiating cells to regenerate an organ without the activity of a stem cell niche. Using a root-tip regeneration system in Arabidopsis to track the molecular and functional recovery of cell fates, we show that re-specification of lost cell identities begins within hours of excision and that the function of specialized cells is restored within one day. Critically, regeneration proceeds in plants with mutations that fail to maintain the stem cell niche. These results show that stem cell-like properties that mediate complete organ regeneration are dispersed in plant meristems and are not restricted to niches, which nonetheless appear necessary for indeterminate growth. This regenerative reprogramming of an entire organ without transition to a stereotypical stem cell environment has intriguing parallels to recent reports of induced transdifferentiation of specific cell types in the adult organs of animals2,3.
doi:10.1038/nature07597
PMCID: PMC2649681  PMID: 19182776
12.  Regulation of shoot meristem integrity during Arabidopsis vegetative development 
Plant Signaling & Behavior  2011;6(8):1250-1252.
Shoot growth and development is mediated by the activity of the shoot meristem, which initiates leaves and axillary meristems. Meristem maintenance is achieved by a poorly understood process that functions to sustain the balance of stem cell perpetuation in the central zone (CZ) and organogenesis in the peripheral zone (PZ). A recent study showed that two related homeodomain transcription factors, PENNYWISE (PNY) and POUND-FOOLISH (PNF), regulate meristem maintenance by controlling the integrity of the CZ. The non-flower producing phenotype displayed by pny pnf plants can be rescued by genetically increasing the size of the shoot meristem. In this addendum, we show that augmenting the size of the central region of pny pnf shoot meristems partially rescues the meristem termination phenotype that occurs during early stages of vegetative development. Thus, regulation of CZ integrity by PNY and PNF is crucial for vegetative and reproductive development.
doi:10.4161/psb.6.8.16462
PMCID: PMC3260737  PMID: 21822063
development; shoot growth; meristem; homeodomain; stem cells
13.  Plant Nitrogen Dynamics and Nitrogen-use Strategies under Altered Nitrogen Seasonality and Competition 
Annals of Botany  2007;100(4):821-830.
Background and Aims
Numerous studies have examined the effects of climatic factors on the distribution of C3 and C4 grasses in various regions throughout the world, but the role of seasonal fluctuations in temperature, precipitation and soil N availability in regulating growth and competition of these two functional types is still not well understood. This report is about the effects of seasonality of soil N availability and competition on plant N dynamics and N-use strategies of one C3 (Leymus chinensis) and one C4 (Chloris virgata) grass species.
Methods
Leymus chinensis and C. virgata, two grass species native to the temperate steppe in northern China, were planted in a monoculture and a mixture under three different N seasonal availabilities: an average model (AM) with N evenly distributed over the growing season; a one-peak model (OM) with more N in summer than in spring and autumn; and a two-peak model (TM) with more N in spring and autumn than in summer.
Key Results
The results showed that the altered N seasonality changed plant N concentration, with the highest value of L. chinensis under the OM treatment and C. virgata under the TM treatment, respectively. N seasonality also affected plant N content, N productivity and N-resorption efficiency and proficiency in both the C3 and C4 species. Interspecific competition influenced N-use and resorption efficiency in both the C3 and C4 species, with higher N-use and resorption efficiency in the mixture than in monoculture. The C4 grass had higher N-use efficiency than the C3 grass due to its higher N productivity, irrespective of the N treatment or competition.
Conclusions
The observations suggest that N-use strategies in the C3 and C4 species used in the study were closely related to seasonal dynamics of N supply and competition. N seasonality might be involved in the growth and temporal niche separation between C3 and C4 species observed in the natural ecosystems.
doi:10.1093/aob/mcm178
PMCID: PMC2749635  PMID: 17704500
Competition; C3 and C4 grasses; nitrogen seasonality; nitrogen productivity; mean residence time; temperate steppe
14.  NO VEIN facilitates auxin-mediated development in Arabidopsis 
Plant Signaling & Behavior  2010;5(10):1249-1251.
Local, efflux-dependent auxin gradients and maxima mediate organ and tissue development in plants. The auxin-efflux pattern is regulated by dynamic expression and asymmetric subcellular localization of PIN auxin-efflux proteins during plant organogenesis. Thus, the question of how the expression and subcellular localization of PIN proteins are controlled goes to the heart of plant development. It has been shown that PIN expression and polarity are established not only through a self-organizing auxin-mediated polarization mechanism, but also through other means such as cell-fate determination. We found that the Arabidopsis NO VEIN (NOV) gene, encoding a novel, plant-specific nuclear factor, is required for leaf vascular development, cellular patterning and stem-cell maintenance in the root meristem and cotyledon outgrowth and separation. NOV function underlies cell-fate decisions associated with auxin gradients and maxima, thereby establishing cell type-specific PIN expression and polarity. We propose that NOV mediates cell acquisition of the competence to undergo auxin-dependent coordinated cell specification and patterning, thereby educing context-dependent auxin-mediated developmental responses.
doi:10.4161/psb.5.10.12948
PMCID: PMC3115359  PMID: 20729639
Arabidopsis; auxin; PIN; organ development; vascular development; stem-cell maintenance; NO VEIN
15.  Accumulation of Biomass and Mineral Elements with Calendar Time by Corn: Application of the Expanded Growth Model 
PLoS ONE  2011;6(12):e28515.
The expanded growth model is developed to describe accumulation of plant biomass (Mg ha−1) and mineral elements (kg ha−1) in with calendar time (wk). Accumulation of plant biomass with calendar time occurs as a result of photosynthesis for green land-based plants. A corresponding accumulation of mineral elements such as nitrogen, phosphorus, and potassium occurs from the soil through plant roots. In this analysis, the expanded growth model is tested against high quality, published data on corn (Zea mays L.) growth. Data from a field study in South Carolina was used to evaluate the application of the model, where the planting time of April 2 in the field study maximized the capture of solar energy for biomass production. The growth model predicts a simple linear relationship between biomass yield and the growth quantifier, which is confirmed with the data. The growth quantifier incorporates the unit processes of distribution of solar energy which drives biomass accumulation by photosynthesis, partitioning of biomass between light-gathering and structural components of the plants, and an aging function. A hyperbolic relationship between plant nutrient uptake and biomass yield is assumed, and is confirmed for the mineral elements nitrogen (N), phosphorus (P), and potassium (K). It is concluded that the rate limiting process in the system is biomass accumulation by photosynthesis and that nutrient accumulation occurs in virtual equilibrium with biomass accumulation.
doi:10.1371/journal.pone.0028515
PMCID: PMC3237438  PMID: 22194842
16.  Field-Scale Transplantation Experiment To Investigate Structures of Soil Bacterial Communities at Pioneering Sites▿† 
Applied and Environmental Microbiology  2011;77(23):8241-8248.
Studies on the effect of environmental conditions on plants and microorganisms are a central issue in ecology, and they require an adequate experimental setup. A strategy often applied in geobotanical studies is based on the reciprocal transplantation of plant species at different sites. We adopted a similar approach as a field-based tool to investigate the relationships of soil bacterial communities with the environment. Soil samples from two different (calcareous and siliceous) unvegetated glacier forefields were reciprocally transplanted and incubated for 15 months between 2009 and 2010. Controls containing local soils were included. The sites were characterized over time in terms of geographical (bedrock, exposition, sunlight, temperature, and precipitation) and physicochemical (texture, water content, soluble and nutrients) features. The incubating local (“home”) and transplanted (“away”) soils were monitored for changes in extractable nutrients and in the bacterial community structure, defined through terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA gene. Concentrations of soluble ions in most samples were more significantly affected by seasons than by the transplantation. For example, NO3− showed a seasonal pattern, increasing from 1 to 3 μg NO3− (g soil dry weight)−1 after the melting of snow but decreasing to <1 μg NO3− (g soil dry weight)−1 in autumn. Seasons, and in particular strong precipitation events occurring in the summer of 2010 (200 to 300 mm of rain monthly), were also related to changes of bacterial community structures. Our results show the suitability of this approach to compare responses of bacterial communities to different environmental conditions directly in the field.
doi:10.1128/AEM.05778-11
PMCID: PMC3233051  PMID: 21965395
17.  Auxin gradients trigger de novo formation of stem cells during somatic embryogenesis 
Plant Signaling & Behavior  2009;4(7):574-576.
Single or a group of somatic cells could give rise to the whole plant, which require hormones, or plant growth regulators. Although many studies have been done during past years, how hormones specify cell fate during in vitro organogenesis is still unknown. To uncover this mechanism, Arabidopsis somatic embryogenesis has been recognized as a model for studying in vitro plant organogenesis. In this paper, we showed that establishment of auxin gradients within embryonic callus is essential for inducing stem cell formation via PIN1 regulation. This study sheds new light on how hormone regulates stem cell formation during in vitro organogenesis.
PMCID: PMC2710545  PMID: 19820347
auxin gradients; PIN proteins; stem cell; somatic embryogenesis
18.  Water and heat transport in hilly red soil of southern China: I. Experiment and analysis*  
Studies on coupled transfer of soil moisture and heat have been widely carried out for decades. However, little work has been done on red soils, widespread in southern China. The simultaneous transfer of soil moisture and heat depends on soil physical properties and the climate conditions. Red soil is heavy clay and high content of free iron and aluminum oxide. The climate conditions are characterized by the clear four seasons and the serious seasonal drought. The great annual and diurnal air temperature differences result in significant fluctuation in soil temperature in top layer. The closed and evaporating columns experiments with red soil were conducted to simulate the coupled transfer of soil water and heat under the overlaying and opening fields’ conditions, and to analyze the effects of soil temperature gradient on the water transfer and the effects of initial soil water contents on the transfer of soil water and heat. The closed and evaporating columns were designed similarly with about 18 °C temperatures differences between the top and bottom boundary, except of the upper end closed or exposed to the air, respectively. Results showed that in the closed column, water moved towards the cold end driven by temperature gradient, while the transported water decreased with the increasing initial soil water content until the initial soil water content reached to field capacity equivalent, when almost no changes for the soil moisture profile. In the evaporating column, the net transport of soil water was simultaneously driven by evaporation and temperature gradients, and the drier soil was more influenced by temperature gradient than by evaporation. In drier soil, it took a longer time for the temperature to reach equilibrium, because of more net amount of transported water.
doi:10.1631/jzus.2005.B0331
PMCID: PMC1389746  PMID: 15822143
Red soil; Coupled transfer of water and heat; Evaporation; Initial soil moisture
19.  Ad Hoc Modeling of Root Zone Soil Water with Landsat Imagery and Terrain and Soils Data 
Sensors (Basel, Switzerland)  2008;8(1):314-326.
Agricultural producers require knowledge of soil water at plant rooting depths, while many remote sensing studies have focused on surface soil water or mechanistic models that are not easily parameterized. We developed site-specific empirical models to predict spring soil water content for two Montana ranches. Calibration data sample sizes were based on the estimated variability of soil water and the desired level of precision for the soil water estimates. Models used Landsat imagery, a digital elevation model, and a soil survey as predictor variables. Our objectives were to see whether soil water could be predicted accurately with easily obtainable calibration data and predictor variables and to consider the relative influence of the three sources of predictor variables. Independent validation showed that multiple regression models predicted soil water with average error (RMSD) within 0.04 mass water content. This was similar to the accuracy expected based on a statistical power test based on our sample size (n = 41 and n = 50). Improved prediction precision could be achieved with additional calibration samples, and range managers can readily balance the desired level of precision with the amount of effort to collect calibration data. Spring soil water prediction effectively utilized a combination of land surface imagery, terrain data, and subsurface soil characterization data. Ranchers could use accurate spring soil water content predictions to set stocking rates. Such management can help ensure that water, soil, and vegetation resources are used conservatively in irrigated and non-irrigated rangeland systems.
PMCID: PMC3681134
empirical models; precision agriculture; rangeland; site-specific agriculture; soil survey
20.  Accumulation of Biomass and Mineral Elements with Calendar Time by Cotton: Application of the Expanded Growth Model 
PLoS ONE  2013;8(9):e72810.
Accumulation of plant biomass (Mg ha−1) with calendar time (wk) occurs as a result of photosynthesis for green land-based plants. A corresponding accumulation of mineral elements (kg ha−1) such as nitrogen, phosphorus, and potassium occurs from the soil through plant roots. Field data from literature for the warm-season annual cotton (Gossypium hirsutum L.) are used in this analysis. The expanded growth model is used to describe accumulation of biomass and mineral elements with calendar time. The growth model predicts a simple linear relationship between biomass yield and the growth quantifier, which is confirmed with the data. The growth quantifier incorporates the unit processes of distribution of solar energy which drives biomass accumulation by photosynthesis, partitioning of biomass between light-gathering and structural components of the plants, and an aging function. A hyperbolic relationship between plant nutrient uptake and biomass yield is assumed, and is confirmed for the mineral elements nitrogen, phosphorus, and potassium. It is concluded that the rate limiting process in the system is biomass accumulation by photosynthesis and that nutrient accumulation occurs in virtual equilibrium with biomass accumulation. The expanded growth model describes field data from California and Alabama rather well. Furthermore, all model parameters were common for the two sites with the exception of the yield factor A which accounts for differences in soil types, environmental conditions, fertilizer levels, and plant population.
doi:10.1371/journal.pone.0072810
PMCID: PMC3767794  PMID: 24039802
21.  The Forkhead Transcription Factor, Foxd1, Is Necessary for Pituitary Luteinizing Hormone Expression in Mice 
PLoS ONE  2012;7(12):e52156.
The pituitary gland regulates numerous physiological functions including growth, reproduction, temperature and metabolic homeostasis, lactation, and response to stress. Pituitary organogenesis is dependent on signaling factors that are produced in and around the developing pituitary. The studies described in this report reveal that the forkhead transcription factor, Foxd1, is not expressed in the developing mouse pituitary gland, but rather in the mesenchyme surrounding the pituitary gland, which is an essential source of signaling factors that regulate pituitary organogenesis. Loss of Foxd1 causes a morphological defect in which the anterior lobe of the pituitary gland protrudes through the cartilage plate that is developing ventral to the pituitary at embryonic days (e)14.5, e16.5, and e18.5. The number of proliferating pituitary cells is increased at e14.5 and e16.5. Loss of Foxd1 also results in significantly decreased levels of Lhb expression at e18.5. This decrease in Lhb expression does not appear to be due to a change in the number of gonadotrope cells in the pituitary gland. Previous studies have shown that loss of the LIM homeodomain factor, Lhx3, which is activated by the FGF signaling pathway, results in loss of LH production. Although there is a difference in Lhb expression in Foxd1 null mice, the expression pattern of LHX3 is not altered in Foxd1 null mice. These studies suggest that Foxd1 is indirectly required for normal Lhb expression and cartilage formation.
doi:10.1371/journal.pone.0052156
PMCID: PMC3526578  PMID: 23284914
22.  The effects of water regime on phosphorus responses of rainfed lowland rice cultivars 
Annals of Botany  2008;103(2):211-220.
Background and Aims
Soil phosphorus (P) solubility declines sharply when a flooded soil drains, and an important component of rice (Oryza sativa) adaptation to rainfed lowland environments is the ability to absorb and utilize P under such conditions. The aim of this study was to test the hypothesis that rice cultivars differ in their P responses between water regimes because P uptake mechanisms differ.
Methods
Six lowland rice cultivars (three considered tolerant of low P soils, three sensitive) were grown in a factorial experiment with three water regimes (flooded, moist and flooded-then-moist) and four soil P levels, and growth and P uptake were measured. Small volumes of soil were used to maximize inter-root competition and uptake per unit root surface. The results were compared with the predictions of a model allowing for the effects of water regime on P solubility and diffusion.
Key Results
The plants were P stressed but not water stressed in all the water regimes at all P levels except the higher P additions in the flooded soil. The cultivar rankings scarcely differed between the water regimes and P additions. In all the treatments, the soil P concentrations required to explain the measured uptake were several times the concentration of freely available P in the soil.
Conclusions
The cultivar rankings were driven more by differences in growth habit than specific P uptake mechanisms, so the hypothesis cannot be corroborated with these data. Evidently all the plants could tap sparingly soluble forms of P by releasing a solubilizing agent or producing a greater root length than measured, or both. However, any cultivar differences in this were not apparent in greater net P uptake, possibly because the restricted rooting volume meant that additional P uptake could not be converted into new root growth to explore new soil volumes.
doi:10.1093/aob/mcn199
PMCID: PMC2707314  PMID: 18945744
Oryza sativa; rainfed lowland; phosphorus efficiency; root morphology; solubilization; rice cultivar
23.  Statistical Modeling of Spatio-Temporal Variability in Monthly Average Daily Solar Radiation over Turkey 
Sensors (Basel, Switzerland)  2007;7(11):2763-2778.
Though one of the most significant driving forces behind ecological processes such as biogeochemical cycles and energy flows, solar radiation data are limited or non-existent by conventional ground-based measurements, and thus, often estimated from other meteorological data through (geo)statistical models. In this study, spatial and temporal patterns of monthly average daily solar radiation on a horizontal surface at the ground level were quantified using 130 climate stations for the entire Turkey and its conventionally-accepted seven geographical regions through multiple linear regression (MLR) models as a function of latitude, longitude, altitude, aspect, distance to sea; minimum, maximum and mean air temperature and relative humidity, soil temperature, cloudiness, precipitation, pan evapotranspiration, day length, maximum possible sunshine duration, monthly average daily extraterrestrial solar radiation, and time (month), and universal kriging method. The resulting 20 regional best-fit MLR models (three MLR models for each region) based on parameterization datasets had R2adj values of 91.5% for the Central Anatolia region to 98.0% for the Southeast Anatolia region. Validation of the best-fit MLR models for each region led to R2 values of 87.7% for the Mediterranean region to 98.5% for the Southeast Anatolia region. The best-fit anisotropic semi-variogram models for universal kriging as a result of one-leave-out cross-validation gave rise to R2 values of 10.9% in July to 52.4% in November. Surface maps of monthly average daily solar radiation were generated over Turkey, with a grid resolution of 500 m × 500 m.
PMCID: PMC3965217
Solar radiation; Spatio-temporal modeling; Universal kriging; Multiple linear regression; Turkey
24.  The unique relationship between tsh4 and ra2 in patterning floral phytomers 
Plant Signaling & Behavior  2010;5(8):979-981.
Phytomers are developmental compartments that display stereotypical patterns dependent on whether they are initiated during the vegetative phase or the floral phases. Differences in appearance result from differential partitioning mechanisms responsible for allocation of cells to different components of the phytomer. The tasselsheath loci of maize control cell partitioning within the phytomer, indirectly influencing growth and development of its individual components. The tasselsheath4 (tsh4) gene accomplishes this through regulation of the ramosa2 (ra2) meristem determinacy gene, whereas tasselsheath1 (tsh1) appears to function differently.
doi:10.4161/psb.5.8.12220
PMCID: PMC3115173  PMID: 20622509
meristem; SBP box; bract; maize; ramosa; tasselsheath; phytomer
25.  Complex Responses of Intertidal Molluscan Embryos to a Warming and Acidifying Ocean in the Presence of UV Radiation 
PLoS ONE  2013;8(2):e55939.
Climate change and ocean acidification will expose marine organisms to synchronous multiple stressors, with early life stages being potentially most vulnerable to changing environmental conditions. We simultaneously exposed encapsulated molluscan embryos to three abiotic stressors—acidified conditions, elevated temperate, and solar UV radiation in large outdoor water tables in a multifactorial design. Solar UV radiation was modified with plastic filters, while levels of the other factors reflected IPCC predictions for near-future change. We quantified mortality and the rate of embryonic development for a mid-shore littorinid, Bembicium nanum, and low-shore opisthobranch, Dolabrifera brazieri. Outcomes were consistent for these model species with embryos faring significantly better at 26°C than 22°C. Mortality sharply increased at the lowest temperature (22°C) and lowest pH (7.6) examined, producing a significant interaction. Under these conditions mortality approached 100% for each species, representing a 2- to 4-fold increase in mortality relative to warm (26°C) non-acidified conditions. Predictably, development was more rapid at the highest temperature but this again interacted with acidified conditions. Development was slowed under acidified conditions at the lowest temperature. The presence of UV radiation had minimal impact on the outcomes, only slowing development for the littorinid and not interacting with the other factors. Our findings suggest that a warming ocean, at least to a threshold, may compensate for the effects of decreasing pH for some species. It also appears that stressors will interact in complex and unpredictable ways in a changing climate.
doi:10.1371/journal.pone.0055939
PMCID: PMC3566103  PMID: 23405238

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