Regulation of tissue growth in plants - A mathematical modeling study on shade avoidance response in Arabidopsis hypocotyls.

Introduction: Plant growth is a plastic phenomenon controlled both by endogenous genetic programs and by environmental cues. The embryonic stem, the hypocotyl, is an ideal model system for the quantitative study of growth due to its relatively simple geometry and cellular organization, and to its essentially unidirectional growth pattern. The hypocotyl of Arabidopsis thaliana has been studied particularly well at the molecular-genetic level and at the cellular level, and it is the model of choice for analysis of the shade avoidance syndrome (SAS), a growth reaction that allows plants to compete with neighboring plants for light. During SAS, hypocotyl growth is controlled primarily by the growth hormone auxin, which stimulates cell expansion without the involvement of cell division. Methods: We assessed hypocotyl growth at cellular resolution in Arabidopsis mutants defective in auxin transport and biosynthesis and we designed a mathematical auxin transport model based on known polar and non-polar auxin transporters (ABCB1, ABCB19, and PINs) and on factors that control auxin homeostasis in the hypocotyl. In addition, we introduced into the model biophysical properties of the cell types based on precise cell wall measurements. Results and Discussion: Our model can generate the observed cellular growth patterns based on auxin distribution along the hypocotyl resulting from production in the cotyledons, transport along the hypocotyl, and general turnover of auxin. These principles, which resemble the features of mathematical models of animal morphogen gradients, allow to generate robust shallow auxin gradients as they are expected to exist in tissues that exhibit quantitative auxin-driven tissue growth, as opposed to the sharp auxin maxima generated by patterning mechanisms in plant development.

Selective, Fast-Response, and Regenerable Metal-Organic Framework for Sampling Excess Fluoride Levels in Drinking Water.

Prolonged consumption of water contaminated with fluoride ions (F-) at concentrations exceeding 1.5 ppm can lead to considerable health implications, particularly in children and developing embryos. With irreversible and potentially severe forms of fluoride (F-) toxicity such as skeletal fluorosis being endemic in at least 25 countries, constructing affordable, remote-access, reliable water-sampling methods for F- contamination is an important goal. In this work, we present a novel lanthanide-based luminescent metal-organic framework, named SION-105, with a boron (B) receptor site whose interactions with F- in aqueous solutions are simultaneously electrostatic and specific in nature because of its carefully designed structural environment. This allows the material to be easily regenerated and used over 10 cycles, setting it apart from most existing molecular and polymeric F- sensors. SION-105 has been combined with a portable prototype sampling device that was designed and built in-house to measure F- concentrations in natural groundwater samples taken from three different countries, with the results showing excellent agreement with ion chromatography analysis.

Mathematical Modeling of the Dynamics of Shoot-Root Interactions and Resource Partitioning in Plant Growth.

Plants are highly plastic in their potential to adapt to changing environmental conditions. For example, they can selectively promote the relative growth of the root and the shoot in response to limiting supply of mineral nutrients and light, respectively, a phenomenon that is referred to as balanced growth or functional equilibrium. To gain insight into the regulatory network that controls this phenomenon, we took a systems biology approach that combines experimental work with mathematical modeling. We developed a mathematical model representing the activities of the root (nutrient and water uptake) and the shoot (photosynthesis), and their interactions through the exchange of the substrates sugar and phosphate (Pi). The model has been calibrated and validated with two independent experimental data sets obtained with Petunia hybrida. It involves a realistic environment with a day-and-night cycle, which necessitated the introduction of a transitory carbohydrate storage pool and an endogenous clock for coordination of metabolism with the environment. Our main goal was to grasp the dynamic adaptation of shoot:root ratio as a result of changes in light and Pi supply. The results of our study are in agreement with balanced growth hypothesis, suggesting that plants maintain a functional equilibrium between shoot and root activity based on differential growth of these two compartments. Furthermore, our results indicate that resource partitioning can be understood as the emergent property of many local physiological processes in the shoot and the root without explicit partitioning functions. Based on its encouraging predictive power, the model will be further developed as a tool to analyze resource partitioning in shoot and root crops.

A novel bioinformatics pipeline to discover genes related to arbuscular mycorrhizal symbiosis based on their evolutionary conservation pattern among higher plants.

BACKGROUND: Genes involved in arbuscular mycorrhizal (AM) symbiosis have been identified primarily by mutant screens, followed by identification of the mutated genes (forward genetics). In addition, a number of AM-related genes has been identified by their AM-related expression patterns, and their function has subsequently been elucidated by knock-down or knock-out approaches (reverse genetics). However, genes that are members of functionally redundant gene families, or genes that have a vital function and therefore result in lethal mutant phenotypes, are difficult to identify. If such genes are constitutively expressed and therefore escape differential expression analyses, they remain elusive. The goal of this study was to systematically search for AM-related genes with a bioinformatics strategy that is insensitive to these problems. The central element of our approach is based on the fact that many AM-related genes are conserved only among AM-competent species. RESULTS: Our approach involves genome-wide comparisons at the proteome level of AM-competent host species with non-mycorrhizal species. Using a clustering method we first established orthologous/paralogous relationships and subsequently identified protein clusters that contain members only of the AM-competent species. Proteins of these clusters were then analyzed in an extended set of 16 plant species and ranked based on their relatedness among AM-competent monocot and dicot species, relative to non-mycorrhizal species. In addition, we combined the information on the protein-coding sequence with gene expression data and with promoter analysis. As a result we present a list of yet uncharacterized proteins that show a strongly AM-related pattern of sequence conservation, indicating that the respective genes may have been under selection for a function in AM. Among the top candidates are three genes that encode a small family of similar receptor-like kinases that are related to the S-locus receptor kinases involved in sporophytic self-incompatibility. CONCLUSIONS: We present a new systematic strategy of gene discovery based on conservation of the protein-coding sequence that complements classical forward and reverse genetics. This strategy can be applied to diverse other biological phenomena if species with established genome sequences fall into distinguished groups that differ in a defined functional trait of interest.

Accession-dependent action potentials in Arabidopsis.

Plant excitability, as measured by the appearance and circulation of action potentials (APs) after biotic and abiotic stress treatments, is a far lesser and more versatile phenomenon than in animals. To examine the genetic basis of plant excitability we used different Arabidopsis thaliana accessions. APs were induced by wounding (W) with a subsequent deposition (D) of 5µL of 1M KCl onto adult leaves. This treatment elicited transient voltage responses (APs) that were detected by 2 extracellular electrodes placed at a distance from the wounding location over an experimental time of 150min. The first electrode (e1) was placed at the end of the petiole and the beginning of the leaf, and the second (e2) electrode was placed on the petiole near the center of the rosette. All accessions (Columbia (Col), Wassilewskija (Ws) and Landsberg erecta (Ler)) responded to the W & D treatment. After W & D treatment was performed on 100 plants for each accession, the number of APs ranged from 0 to 37 (median 8, total 940), 0 to 16 (median 5, total 528) and 0 to 18 (median 2, total 296) in Col, Ws and Ler, respectively. Responding plants (>0 APs) showed significantly different behaviors depending on their accessions of origin (i.e., Col 91, Ws 83 and Ler 76%). Some AP characteristics, such as amplitude and speed of propagation from e1 to e2 (1.28mms(-1)), were the same for all accessions, whereas the average duration of APs was similar in Col and Ws, but different in Ler. Self-sustained oscillations were observed more frequently in Col than Ws and least often in Ler, and the mean oscillation frequency was more rapid in Col, followed by Ws, and was slowest in Ler. In general, Col was the most excitable accession, followed by Ws, and Ler was the least excitable; this corresponded well with voltage elicited action potentials. In conclusion, part of Arabidopsis excitability in AP responses is genetically pre-determined.

Phosphate systemically inhibits development of arbuscular mycorrhiza in Petunia hybrida and represses genes involved in mycorrhizal functioning.

Most terrestrial plants form arbuscular mycorrhiza (AM), mutualistic associations with soil fungi of the order Glomeromycota. The obligate biotrophic fungi trade mineral nutrients, mainly phosphate (P(i) ), for carbohydrates from the plants. Under conditions of high exogenous phosphate supply, when the plant can meet its own P requirements without the fungus, AM are suppressed, an effect which could be interpreted as an active strategy of the plant to limit carbohydrate consumption of the fungus by inhibiting its proliferation in the roots. However, the mechanisms involved in fungal inhibition are poorly understood. Here, we employ a transcriptomic approach to get insight into potential shifts in metabolic activity and symbiotic signalling, and in the defence status of plants exposed to high P(i) levels. We show that in mycorrhizal roots of petunia, a similar set of symbiosis-related genes is expressed as in mycorrhizal roots of Medicago, Lotus and rice. P(i) acts systemically to repress symbiotic gene expression and AM colonization in the root. In established mycorrhizal roots, P(i) repressed symbiotic gene expression rapidly, whereas the inhibition of colonization followed with a lag of more than a week. Taken together, these results suggest that P(i) acts by repressing essential symbiotic genes, in particular genes encoding enzymes of carotenoid and strigolactone biosynthesis, and symbiosis-associated phosphate transporters. The role of these effects in the suppression of symbiosis under high P(i) conditions is discussed.

In-vitro platform to study ultrasound as source for wireless energy transfer and communication for implanted medical devices.

A platform to study ultrasound as a source for wireless energy transfer and communication for implanted medical devices is described. A tank is used as a container for a pair of electroacoustic transducers, where a control unit is fixed to one wall of the tank and a transponder can be manually moved in three axes and rotate using a mechanical system. The tank is filled with water to allow acoustic energy and data transfer, and the system is optimized to avoid parasitic effects due to cables, reflection paths and cross talk problems. A printed circuit board is developed to test energy scavenging such that enough acoustic intensity is generated by the control unit to recharge a battery loaded to the transponder. In the same manner, a second printed circuit board is fabricated to study transmission of information through acoustic waves.

Superheterodyne configuration for two-wavelength interferometry applied to absolute distance measurement.

We present a new superheterodyne technique for long-distance measurements by two-wavelength interferometry (TWI). While conventional systems use two acousto-optic modulators to generate two different heterodyne frequencies, here the two frequencies result from synchronized sweeps of optical and radio frequencies. A distributed feedback laser source is injected in an intensity modulator that is driven at the half-wave voltage mode. A radio-frequency signal is applied to this intensity modulator to generate two optical sidebands around the optical carrier. This applied radio frequency consists of a digital ramp between 13 and 15 GHz, with 1 ms duration and with an accuracy of better than 1 ppm. Simultaneously, the laser source is frequency modulated by a current modulation that is synchronized on the radio-frequency ramp as well as on a triangle waveform. These two frequency-swept optical signals at the output of the modulator illuminate a Michelson interferometer and create two distinct distance-dependent heterodyne frequencies on the photodetector. The superheterodyne signal is then detected and bandpass filtered to retrieve the absolute distance measurement. Experiments between 1 and 15 m confirm the validity of this new concept, leading to a distance accuracy of +/- 50 microm for a 1 ms acquisition time.

Radio frequency controlled synthetic wavelength sweep for absolute distance measurement by optical interferometry.

We present a new technique applied to the variable optical synthetic wavelength generation in optical interferometry. It consists of a chain of optical injection locking among three lasers: first a distributed-feedback laser is used as a master to injection lock an intensity-modulated laser that is directly modulated around 15 GHz by a radio frequency generator on a sideband. A second distributed-feedback laser is injection locked on another sideband of the intensity-modulated laser. The variable synthetic wavelength for absolute distance measurement is simply generated by sweeping the radio frequency over a range of several hundred megahertz, which corresponds to the locking range of the two slave lasers. In this condition, the uncertainty of the variable synthetic wavelength is equivalent to the radio frequency uncertainty. This latter has a relative accuracy of 10(-7) or better, resulting in a resolution of +/-25 microm for distances exceeding tens of meters. The radio frequency generator produces a linear frequency sweep of 1 ms duration (i.e., exactly equal to one absolute distance measurement acquisition time), with frequency steps of about 1 MHz. Finally, results of absolute distance measurements for ranges up to 10 m are presented.

Voltage-dependent action potentials in Arabidopsis thaliana.

Voltage-elicited action potentials (APs) have been reproducibly obtained in Arabidopsis thaliana ecotype col. Excitations pulses (voltage-duration: V-t) were given in the 0- to 18-V and 0- to 35-s ranges, respectively, by two galvanically isolated Pt/Ir small wires inserted trough the main vein in the distal part of the leaf. Conventional liquid junction Ag/AgCl electrodes were placed at the zone between leaf/petiole (e1) and a second one on the petiole, near the central axis of the rosette (e2). A typical hyperbolic V-t relationship was obtained. The most excitable plants did have a chronaxy of 0.1 s and a rheobase of 2 V. Although the amplitude of the APs was highly variable (range 10-80 mV), it was related neither to the intensity nor to the duration of the stimulation pulse: the phenomenon is a typical all-or-none response. The APs were moving away from the excitation zone and could successively be detected at e1 and then at e2: their propagation speed was 1.15 +/- 0.26 mm s(-1). The absolute refractory period was approximately 20 min and the relative one approximately 80 min. The reproducibility of the voltage elicitation was in A. thaliana col ecotype 91%, with 83% of the APs propagating from the leaf to the petiole. In the Wassilewskija ecotype, 45% of the plants were responsive, with 78% of APs transmitted (propagation speed was 0.76 +/- 0.17 mm s(-1)), whereas in the Lansberg erecta ecotype none of the plant tested elicited a voltage-dependent AP.