Gravity-directed calcium current in germinating spores of Ceratopteris richardii

Polarized distribution of extracellular nucleotides promotes gravity-directed polarization of development in spores of Ceratopteris richardii

Gravity directs the polarization of Ceratopteris fern spores. This process begins with the uptake of calcium through channels at the bottom of the spore, a step necessary for the gravity response. Data showing that extracellular ATP (eATP) regulates calcium channels led to the hypothesis that extracellular nucleotides could play a role in the gravity-directed polarization of Ceratopteris spores. In animal and plant cells ATP can be released from mechanosensitive channels. This report tests the hypothesis that the polarized release of ATP from spores could be activated by gravity, preferentially along the bottom of the spore, leading to an asymmetrical accumulation of eATP. In order to carry out this test, an ATP biosensor was used to measure the [eATP] at the bottom and top of germinating spores during gravity-directed polarization. The [eATP] along the bottom of the spore averaged 7-fold higher than the concentration at the top. All treatments that disrupted eATP signaling resulted in a statistically significant decrease in the gravity response. In order to investigate the source of ATP release, spores were treated with Brefeldin A (BFA) and gadolinium trichloride (GdCl3). These treatments resulted in a significant decrease in gravity-directed polarization. An ATP biosensor was also used to measure ATP release after treatment with both BFA and GdCl3. Both of these treatments caused a significant decrease in [ATP] measured around spores. These results support the hypothesis that ATP could be released from mechanosensitive channels and secretory vesicles during the gravity-directed polarization of Ceratopteris spores.

Gravi-Sensitivity of Mosses and Their Gravity-Dependent Ontogenetic Adaptations

Gravi-morphoses affect the variability of plants and are the morphogenetic adaptation to different environmental conditions. Gravity-dependent phenotypic plasticity of gametophytes as well as gravi-sensitivity of moss protonemata in microgravity and simulated microgravity conditions are discussed. The moss protonema, a filamentous multicellular system, representing a juvenile stage of moss development, develops as a result of the elongation and division of the apical cell. This apical cell of the protonema is a unique object for research on moss gravi-sensitivity, as graviperception and gravitropic growth occur within the same single cell. Attention is focused on the influence of gravity on bryophyte ontogenesis, including the gravitropic reactivity of moss protonemata, gravi-sensitivity at the stage of leafy shoot development and sporogonium formation, gravity-influenced morphogenesis of apical cell budding, and gravity-dependent spiral growth patterns. The role of gravireceptors in the growth processes of mosses at the cellular level under microgravity conditions are being discussed, as well as the involvement of auxin transport, Ca2+-induced gravitropism and the cytoskeleton in gravitropic reactions.

Spore Preparation and Protoplast Isolation to Study Gravity Perception and Response in Ceratopteris richardii

Early studies revealed a highly predictable pattern of gravity-directed growth and development in Ceratopteris richardii spores. This makes the spore a valuable model system for the study of how a single-cell senses and responds to the force of gravity. Gravity regulates both the direction and magnitude of a trans-cell calcium current in germinating spores, and the orientation of this current predicts the polarization of spore development. In order to make Ceratopteris richardii cells easier to transform and image during this developmental process, a procedure for isolating protoplasts from Ceratopteris richardii gametophytes has been developed and optimized. These protoplasts follow the same developmental pattern as Ceratopteris richardii spores and can be used to monitor the molecular and developmental processes during single-cell polarization. Here, we describe this optimized procedure, along with protocols for sterilizing the spores, sowing them in solid or liquid growth media, and evaluating germination and polarization.

The change of gravity vector induces short-term phosphoproteomic alterations in Arabidopsis

Plants can sense the gravitational force. When plants perceive a change in this natural force, they tend to reorient their organs with respect to the direction of the gravity vector, i.e., the shoot stem curves up. In the present study, we performed a 4C quantitative phosphoproteomics to identify those altered protein phosphosites resulting from 150 s of reorientation of Arabidopsis plants on earth. A total of 5556 phosphopeptides were identified from the gravistimulated Arabidopsis. Quantification based on the ¹⁵N-stable isotope labeling in Arabidopsis (SILIA) and computational analysis of the extracted ion chromatogram (XIC) of phosphopeptides showed eight and five unique PTM peptide arrays (UPAs) being up- and down-regulated, respectively, by gravistimulation. Among the 13 plant reorientation-responsive protein groups, many are related to the cytoskeleton dynamic and plastid movement. Interestingly, the most gravistimulation-responsive phosphosites are three serine residues, S350, S376, and S410, of a blue light receptor Phototropin 1 (PHOT1). The immunoblots experiment confirmed that the change of gravity vector indeed affected the phosphorylation level of S410 in PHOT1. The functional role of PHOT1 in gravitropic response was further validated with gravicurvature measurement in the darkness of both the loss-of-function double mutant phot1phot2 and its complementary transgenic plant PHOT1/phot1phot2. SIGNIFICANCE: The organs of sessile organisms, plants, are able to move in response to environmental stimuli, such as gravity vector, touch, light, water, or nutrients, which is termed tropism. For instance, the bending of plant shoots to the light source is called phototropism. Since all plants growing on earth are continuously exposed to the gravitational field, plants receive the mechanical signal elicited by the gravity vector change and convert it into plant morphogenesis, growth, and development. Past studies have resulted in various hypotheses for gravisensing, but our knowledge about how the signal of gravity force is transduced in plant cells is still minimal. In the present study, we performed a SILIA-based 4C quantitative phosphoproteomics on 150-s gravistimulated Arabidopsis seedlings to explore the phosphoproteins involved in the gravitropic response. Our data demonstrated that such a short-term reorientation of Arabidopsis caused changes in phosphorylation of cytoskeleton structural proteins like Chloroplast Unusual Positioning1 (CHUP1), Patellin3 (PATL3), and Plastid Movement Impaired2 (PMI2), as well as the blue light receptor Phototropin1 (PHOT1). These results suggested that protein phosphorylation plays a crucial role in gravisignaling, and two primary tropic responses of plants, gravitropism and phototropism, may share some common components and signaling pathways. We expect that the phosphoproteins detected from this study will facilitate the subsequent molecular and cellular studies on the mechanism underlying the signal transduction in plant gravitropic response.

Systems, variation, individuality and plant hormones

Inter-individual variation in plants and particularly in hormone content, figures strongly in evolution and behaviour. Homo sapiens and Arabidopsis exhibit similar and substantial phenotypic and molecular variation. Whereas there is a very substantial degree of hormone variation in mankind, reports of inter-individual variation in plant hormone content are virtually absent but are likely to be as large if not larger than that in mankind. Reasons for this absence are discussed. Using an example of inter-individual variation in ethylene content in ripening, the article shows how biological time is compressed by hormones. It further resolves an old issue of very wide hormone dose response that result directly from negative regulation in hormone (and light) transduction. Negative regulation is used because of inter-individual variability in hormone synthesis, receptors and ancillary proteins, a consequence of substantial genomic and environmental variation. Somatic mosaics have been reported for several plant tissues and these too contribute to tissue variation and wide variation in hormone response. The article concludes by examining what variation exists in gravitropic responses. There are multiple sensing systems of gravity vectors and multiple routes towards curvature. These are an aspect of the need for reliability in both inter-individual variation and unpredictable environments. Plant hormone inter-individuality is a new area for research and is likely to change appreciation of the mechanisms that underpin individual behaviour.

An autonomous lab on a chip for space flight calibration of gravity-induced transcellular calcium polarization in single-cell fern spores

This report describes the development of lab-on-a-chip device designed to measure changes in cellular ion gradients that are induced by changes in gravitational (g) forces. The bioCD presented here detects differential calcium ion concentrations outside of individual cells. The device includes sufficient replicates for statistical analysis of the gradients around multiple single cells and around control wells that are empty or include dead cells. In the data presented, the degree of the cellular response correlates with the magnitude of the g-force applied via rotation of the bioCD. The experiments recorded the longest continuous observation of a cellular response to hypergravity made to date, and they demonstrate the potential utility of this device for assaying the threshold of cells' g-force responses in spaceflight conditions.

A Bird's-Eye View of Molecular Changes in Plant Gravitropism Using Omics Techniques

During evolution, plants have developed mechanisms to adapt to a variety of environmental stresses, including drought, high salinity, changes in carbon dioxide levels and pathogens. Central signaling hubs and pathways that are regulated in response to these stimuli have been identified. In contrast to these well studied environmental stimuli, changes in transcript, protein and metabolite levels in response to a gravitational stimulus are less well understood. Amyloplasts, localized in statocytes of the root tip, in mesophyll cells of coleoptiles and in the elongation zone of the growing internodes comprise statoliths in higher plants. Deviations of the statocytes with respect to the earthly gravity vector lead to a displacement of statoliths relative to the cell due to their inertia and thus to gravity perception. Downstream signaling events, including the conversion from the biophysical signal of sedimentation of distinct heavy mass to a biochemical signal, however, remain elusive. More recently, technical advances, including clinostats, drop towers, parabolic flights, satellites, and the International Space Station, allowed researchers to study the effect of altered gravity conditions - real and simulated micro- as well as hypergravity on plants. This allows for a unique opportunity to study plant responses to a purely anthropogenic stress for which no evolutionary program exists. Furthermore, the requirement for plants as food and oxygen sources during prolonged manned space explorations led to an increased interest in the identi-fication of genes involved in the adaptation of plants to microgravity. Transcriptomic, proteomic, phosphoproteomic, and metabolomic profiling strategies provide a sensitive high-throughput approach to identify biochemical alterations in response to changes with respect to the influence of the gravitational vector and thus the acting gravitational force on the transcript, protein and metabolite level. This review aims at summarizing recent experimental approaches and discusses major observations.

Cytological and Proteomic Analyses of Osmunda cinnamomea Germinating Spores Reveal Characteristics of Fern Spore Germination and Rhizoid Tip Growth

Fern spore is a good single-cell model for studying the sophisticated molecular networks in asymmetric cell division, differentiation, and polar growth. Osmunda cinnamomea L. var. asiatica is one of the oldest fern species with typical separate-growing trophophyll and sporophyll. The chlorophyllous spores generated from sporophyll can germinate without dormancy. In this study, the spore ultrastructure, antioxidant enzyme activities, as well as protein and gene expression patterns were analyzed in the course of spore germination at five typical stages (i.e. mature spores, rehydrated spores, double-celled spores, germinated spores, and spores with protonemal cells). Proteomic analysis revealed 113 differentially expressed proteins, which were mainly involved in photosynthesis, reserve mobilization, energy supplying, protein synthesis and turnover, reactive oxygen species scavenging, signaling, and cell structure modulation. The presence of multiple proteoforms of 25 differentially expressed proteins implies that post-translational modification may play important roles in spore germination. The dynamic patterns of proteins and their encoding genes exhibited specific characteristics in the processes of cell division and rhizoid tip growth, which include heterotrophic and autotrophic metabolisms, de novo protein synthesis and active protein turnover, reactive oxygen species and hormone (brassinosteroid and ethylene) signaling, and vesicle trafficking and cytoskeleton dynamic. In addition, the function skew of proteins in fern spores highlights the unique and common mechanisms when compared with evolutionarily divergent spermatophyte pollen. These findings provide an improved understanding of the typical single-celled asymmetric division and polar growth during fern spore germination.

Cytological and proteomic analyses of horsetail (Equisetum arvense L.) spore germination

Spermatophyte pollen tubes and root hairs have been used as single-cell-type model systems to understand the molecular processes underlying polar growth of plant cells. Horsetail (Equisetum arvense L.) is a perennial herb species in Equisetopsida, which creates separately growing spring and summer stems in its life cycle. The mature chlorophyllous spores produced from spring stems can germinate without dormancy. Here we report the cellular features and protein expression patterns in five stages of horsetail spore germination (mature spores, rehydrated spores, double-celled spores, germinated spores, and spores with protonemal cells). Using 2-DE combined with mass spectrometry, 80 proteins were found to be abundance changed upon spore germination. Among them, proteins involved in photosynthesis, protein turnover, and energy supply were over-represented. Thirteen proteins appeared as proteoforms on the gels, indicating the potential importance of post-translational modification. In addition, the dynamic changes of ascorbate peroxidase, peroxiredoxin, and dehydroascorbate reductase implied that reactive oxygen species homeostasis is critical in regulating cell division and tip-growth. The time course of germination and diverse expression patterns of proteins in photosynthesis, energy supply, lipid and amino acid metabolism indicated that heterotrophic and autotrophic metabolism were necessary in light-dependent germination of the spores. Twenty-six proteins were involved in protein synthesis, folding, and degradation, indicating that protein turnover is vital to spore germination and rhizoid tip-growth. Furthermore, the altered abundance of 14-3-3 protein, small G protein Ran, actin, and caffeoyl-CoA O-methyltransferase revealed that signaling transduction, vesicle trafficking, cytoskeleton dynamics, and cell wall modulation were critical to cell division and polar growth. These findings lay a foundation toward understanding the molecular mechanisms underlying fern spore asymmetric division and rhizoid polar growth.

Live cell and immuno-labeling techniques to study gravitational effects on single plant cells

The constant force of gravity plays a primordial role in the ontogeny of all living organisms. Plants, for example, develop their roots and shoots in accordance with the direction of the gravitational vector. Any change in the magnitude and/or the direction of gravity has an important impact on the development of tissues and cells. In order to understand how the gravitational force affects plant cell growth and differentiation, we established two complementary experimental procedures with which the effect of hyper-gravity on single plant cell development can be assessed. The single model cell system we used is the pollen tube or male gametophyte which, because of its rapid growth behavior, is known for its instant response to external stresses. The physiological response of the pollen tube can be assessed in a quantitative manner based on changes in the composition and spatial distribution of its cell wall components and in the precisely defined pattern of its very dynamic cytoplasmic streaming. Here, we provide a detailed description of the steps required for the immuno-localization of various cell wall components using microwave-assisted techniques and we explain how live imaging of the intracellular traffic can be achieved under hyper-gravity conditions.

Structure and function of CrACA1, the major PM-type Ca2+-ATPase, expressed at the peak of the gravity-directed trans-cell calcium current in spores of the fern Ceratopteris richardii

Spores of the fern Ceratopteris richardii have proven to be a valuable single-cell system for studying gravity responses. The earliest cellular change directed by gravity in these cells is a trans-cell calcium current, which peaks near 10 h after the spores are induced to germinate. This current is needed for gravity-directed axis alignment, and its peak is coincident with the time period when gravity polarises the direction of subsequent nuclear migration and rhizoid growth. Transcriptomic analysis of genes expressed at the 10-h time point revealed several that encode proteins likely to be key components that either drive the current or regulate it. Notable among these is a plasma membrane (PM)-type Ca(2+) ATPase, CrACA1, whose activity pumping Ca(2+) out of cells is regulated by gravity. This report provides an initial characterisation of the structure and expression of this protein, and demonstrates its heterologous function complementing the K616 mutant of yeast, which is deficient in PM-type Ca(2+) pump activity. Gravity-induced changes in the trans-cell Ca(2+) current occur within seconds, a result consistent with the hypothesis that the force of gravity can rapidly alter the post-translational state of the channels and pumps that drive this current across spore cells. This report identifies a transporter likely to be a key driver of the current, CrACA1, and characterises the role of this protein in early germination and gravity-driven polarity fixation through analysis of expression levels, functional complementation and pharmacological treatments. These data, along with newly available transcriptomic data obtained at the 10-h time point, indicate that CrACA1 is present, functional and likely a major contributing component of the trans-cell Ca(2+) efflux. CrACA1 is not necessary for polar axis alignment, but pharmacological perturbations of it disrupt rhizoid development. These data support and help refine the post-translational modification model for gravity responses.

Analyses of a gravistimulation-specific Ca2+ signature in Arabidopsis using parabolic flights

Gravity is a critical environmental factor affecting the morphology and functions of organisms on the Earth. Plants sense changes in the gravity vector (gravistimulation) and regulate their growth direction accordingly. In Arabidopsis (Arabidopsis thaliana) seedlings, gravistimulation, achieved by rotating the specimens under the ambient 1g of the Earth, is known to induce a biphasic (transient and sustained) increase in cytoplasmic calcium concentration ([Ca(2+)]c). However, the [Ca(2+)]c increase genuinely caused by gravistimulation has not been identified because gravistimulation is generally accompanied by rotation of specimens on the ground (1g), adding an additional mechanical signal to the treatment. Here, we demonstrate a gravistimulation-specific Ca(2+) response in Arabidopsis seedlings by separating rotation from gravistimulation by using the microgravity (less than 10(-4)g) conditions provided by parabolic flights. Gravistimulation without rotating the specimen caused a sustained [Ca(2+)]c increase, which corresponds closely to the second sustained [Ca(2+)]c increase observed in ground experiments. The [Ca(2+)]c increases were analyzed under a variety of gravity intensities (e.g. 0.5g, 1.5g, or 2g) combined with rapid switching between hypergravity and microgravity, demonstrating that Arabidopsis seedlings possess a very rapid gravity-sensing mechanism linearly transducing a wide range of gravitational changes (0.5g-2g) into Ca(2+) signals on a subsecond time scale.

RNA-seq analysis identifies potential modulators of gravity response in spores of Ceratopteris (Parkeriaceae): evidence for modulation by calcium pumps and apyrase activity

PREMISE OF THE STUDY

Gravity regulates the magnitude and direction of a trans-cell calcium current in germinating spores of Ceratopteris richardii. Blocking this current with nifedipine blocks the spore's downward polarity alignment, a polarization that is fixed by gravity ∼10 h after light induces the spores to germinate. RNA-seq analysis at 10 h was used to identify genes potentially important for the gravity response. The data set will be valuable for other developmental and phylogenetic studies.

METHODS

De novo Newbler assembly of 958 527 reads from Roche 454 sequencing was executed. The sequences were identified and analyzed using in silico methods. The roles of endomembrane Ca(2+)-ATPase pumps and apyrases in the gravity response were further tested using pharmacological agents.

KEY RESULTS

Transcripts related to calcium signaling and ethylene biosynthesis were identified as notable constituents of the transcriptome. Inhibiting the activity of endomembrane Ca(2+)-ATPase pumps with 2,5-di-(t-butyl)-1,4-hydroquinone diminished the trans-cell current, but increased the orientation of the polar axis to gravity. The effects of applied nucleotides and purinoceptor antagonists gave novel evidence implicating extracellular nucleotides as regulators of the gravity response in these fern spores.

CONCLUSIONS

In addition to revealing general features of the transcriptome of germinating spores, the results highlight a number of calcium-responsive and light-receptive transcripts. Pharmacologic assays indicate endomembrane Ca(2+)-ATPases and extracellular nucleotides may play regulatory roles in the gravity response of Ceratopteris spores.

Fundamental plant biology enabled by the space shuttle

The relationship between fundamental plant biology and space biology was especially synergistic in the era of the Space Shuttle. While all terrestrial organisms are influenced by gravity, the impact of gravity as a tropic stimulus in plants has been a topic of formal study for more than a century. And while plants were parts of early space biology payloads, it was not until the advent of the Space Shuttle that the science of plant space biology enjoyed expansion that truly enabled controlled, fundamental experiments that removed gravity from the equation. The Space Shuttle presented a science platform that provided regular science flights with dedicated plant growth hardware and crew trained in inflight plant manipulations. Part of the impetus for plant biology experiments in space was the realization that plants could be important parts of bioregenerative life support on long missions, recycling water, air, and nutrients for the human crew. However, a large part of the impetus was that the Space Shuttle enabled fundamental plant science essentially in a microgravity environment. Experiments during the Space Shuttle era produced key science insights on biological adaptation to spaceflight and especially plant growth and tropisms. In this review, we present an overview of plant science in the Space Shuttle era with an emphasis on experiments dealing with fundamental plant growth in microgravity. This review discusses general conclusions from the study of plant spaceflight biology enabled by the Space Shuttle by providing historical context and reviews of select experiments that exemplify plant space biology science.

Parabolic flight induces changes in gene expression patterns in Arabidopsis thaliana

Our primary objective was to evaluate gene expression changes in Arabidopsis thaliana in response to parabolic flight as part of a comprehensive approach to the molecular biology of spaceflight-related adaptations. In addition, we wished to establish parabolic flight as a tractable operations platform for molecular biology studies. In a succession of experiments on NASA's KC-135 and C-9 parabolic aircraft, Arabidopsis plants were presented with replicated exposure to parabolic flight. Transcriptome profiling revealed that parabolic flight caused changes in gene expression patterns that stood the statistical tests of replication on three different flight days. The earliest response, after 20 parabolas, was characterized by a prominence of genes associated with signal transduction. After 40 parabolas, this prominence was largely replaced by genes associated with biotic and abiotic stimuli and stress. Among these responses, three metabolic processes stand out in particular: the induction of auxin metabolism and signaling, the differential expression of genes associated with calcium-mediated signaling, and the repression of genes associated with disease resistance and cell wall biochemistry. Many, but not all, of these responses are known to be involved in gravity sensing in plants. Changes in auxin-related gene expression were also recorded by reporter genes tuned to auxin signal pathways. These data demonstrate that the parabolic flight environment is appropriate for molecular biology research involving the transition to microgravity, in that with replication, proper controls, and analyses, gene expression changes can be observed in the time frames of typical parabolic flight experiments.

Gravity research on plants: use of single-cell experimental models

Future space missions and implementation of permanent bases on Moon and Mars will greatly depend on the availability of ambient air and sustainable food supply. Therefore, understanding the effects of altered gravity conditions on plant metabolism and growth is vital for space missions and extra-terrestrial human existence. In this mini-review we summarize how plant cells are thought to perceive changes in magnitude and orientation of the gravity vector. The particular advantages of several single-celled model systems for gravity research are explored and an overview over recent advancements and potential use of these systems is provided.

Changes in gravity rapidly alter the magnitude and direction of a cellular calcium current

In single-celled spores of the fern Ceratopteris richardii, gravity directs polarity of development and induces a directional, trans-cellular calcium (Ca(2+)) current. To clarify how gravity polarizes this electrophysiological process, we measured the kinetics of the cellular response to changes in the gravity vector, which we initially estimated using the self-referencing calcium microsensor. In order to generate more precise and detailed data, we developed a silicon microfabricated sensor array which facilitated a lab-on-a-chip approach to simultaneously measure calcium currents from multiple cells in real time. These experiments revealed that the direction of the gravity-dependent polar calcium current is reversed in less than 25 s when the cells are inverted, and that changes in the magnitude of the calcium current parallel rapidly changing g-forces during parabolic flight on the NASA C-9 aircraft. The data also revealed a hysteresis in the response of cells in the transition from 2g to micro-g in comparison to cells in the micro-g to 2-g transition, a result consistent with a role for mechanosensitive ion channels in the gravity response. The calcium current is suppressed by either nifedipine (calcium-channel blocker) or eosin yellow (plasma membrane calcium pump inhibitor). Nifedipine disrupts gravity-directed cell polarity, but not spore germination. These results indicate that gravity perception in single plant cells may be mediated by mechanosensitive calcium channels, an idea consistent with some previously proposed models of plant gravity perception.

Construction, theory, and practical considerations for using self-referencing of Ca(2+)-selective microelectrodes for monitoring extracellular Ca(2+) gradients

Ca(2+) signaling in the extra- and intracellular domains is linked to Ca(2+) transport across the plasma membrane. Noninvasive monitoring of these resulting extracellular Ca(2+) gradients with self-referencing of Ca(2+)-selective microelectrodes is used for studying Ca(2+) signaling across Kingdoms. The quantitated Ca(2+) flux enables comparison with changes to intracellular [Ca(2+)] measured with other methods and determination of Ca(2+) transport stoichiometry. Here, we review the construction of Ca(2+)-selective microelectrodes, their physical characteristics, and their use in self-referencing mode to calculate Ca(2+) flux. We also discuss potential complications when using them to measure Ca(2+) gradients near the boundary layers of single cells and tissues.

Gene expression changes induced by space flight in single-cells of the fern Ceratopteris richardii

This work describes a rare high-throughput evaluation of gene expression changes induced by space flight in a single plant cell. The cell evaluated is the spore of the fern Ceratopteris richardii, which exhibits both perception and response to gravity. cDNA microarray and Q RT-PCR analysis of spores germinating in microgravity onboard NASA space shuttle flight STS-93 revealed changes in the mRNA expression of roughly 5% of genes analyzed. These gene expression changes were compared with gene expression changes that occur during gravity perception and response in animal cells and multicellular plants. Our data contribute to a better understanding of the impact of space flight conditions, including microgravity, on cellular growth and development, and provide insights into the adaptive strategies of individual cells in response to these conditions.

Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient

Background

Currently, clustering with some form of correlation coefficient as the gene similarity metric has become a popular method for profiling genomic data. The Pearson correlation coefficient and the standard deviation (SD)-weighted correlation coefficient are the two most widely-used correlations as the similarity metrics in clustering microarray data. However, these two correlations are not optimal for analyzing replicated microarray data generated by most laboratories. An effective correlation coefficient is needed to provide statistically sufficient analysis of replicated microarray data.

Results

In this study, we describe a novel correlation coefficient, shrinkage correlation coefficient (SCC), that fully exploits the similarity between the replicated microarray experimental samples. The methodology considers both the number of replicates and the variance within each experimental group in clustering expression data, and provides a robust statistical estimation of the error of replicated microarray data. The value of SCC is revealed by its comparison with two other correlation coefficients that are currently the most widely-used (Pearson correlation coefficient and SD-weighted correlation coefficient) using statistical measures on both synthetic expression data as well as real gene expression data from Saccharomyces cerevisiae. Two leading clustering methods, hierarchical and k-means clustering were applied for the comparison. The comparison indicated that using SCC achieves better clustering performance. Applying SCC-based hierarchical clustering to the replicated microarray data obtained from germinating spores of the fern Ceratopteris richardii, we discovered two clusters of genes with shared expression patterns during spore germination. Functional analysis suggested that some of the genetic mechanisms that control germination in such diverse plant lineages as mosses and angiosperms are also conserved among ferns.

Conclusion

This study shows that SCC is an alternative to the Pearson correlation coefficient and the SD-weighted correlation coefficient, and is particularly useful for clustering replicated microarray data. This computational approach should be generally useful for proteomic data or other high-throughput analysis methodology.

Nitric oxide and cGMP signaling in calcium-dependent development of cell polarity in Ceratopteris richardii

Single-celled spores of the fern Ceratopteris richardii undergo gravity-directed cell polarity development that is driven by polar calcium currents. Here we present results that establish a role for nitric oxide (NO)/cGMP signaling in transducing the stimulus of gravity to directed polarization of the spores. Application of specific NO donors and scavengers inhibited the calcium-dependent gravity response in a dose-dependent manner. The effects of NO donor exposure were antagonized by application of NO scavenger compounds. Similarly, the guanylate cyclase inhibitors 6-anilino-5,8-quinolinedione and 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin, and the phosphodiesterase inhibitor Viagra, which modulate NO-dependent cGMP levels in the cells, disrupted gravity-directed cell polarity in a dose-dependent manner. Viagra effects were antagonized by application of NO scavengers, consistent with the postulate that NO and cGMP are linked in the signaling pathway. To identify other components of the signaling system we analyzed gene expression changes induced by Viagra treatment using microarrays and quantitative real-time reverse transcription-polymerase chain reaction. Preliminary microarray analysis revealed several genes whose expression was significantly altered by Viagra treatment. Three of these genes had strong sequence similarity to key signal transduction or stress response genes and quantitative real-time reverse transcription-polymerase chain reaction was used to more rigorously quantify the effects of Viagra on their expression in spores and to test how closely these effects could be mimicked by treatment with dibutyryl cGMP. Taken together our results implicate NO and cGMP as downstream effectors that help link the gravity stimulus to polarized growth in C. richardii spores. Sequence data from this article can be found in the GenBank/EMBL data libraries under accession numbers BE 640669 to BE 643506, BQ 086920 to BQ 087668, and CV 734654 to CV 736151.

Profile and analysis of gene expression changes during early development in germinating spores of Ceratopteris richardii

Analysis of an expressed sequence tag library with more than 5,000 sequences from spores of the fern Ceratopteris richardii reveals that more than 3,900 of them represent distinct genes, and almost 70% of these have significant similarity to Arabidopsis (Arabidopsis thaliana) genes. Eight genes are common between three very different dormant plant systems, Ceratopteris spores, Arabidopsis seeds, and Arabidopsis pollen. We evaluated the pattern of mRNA abundance over the first 48 h of spore development using a microarray of cDNAs representing 3,207 distinct genes of C. richardii and determined the relative levels of RNA abundance for 3,143 of these genes using a Bayesian method of statistical analysis. More than 900 of them (29%) show a significant change between any of the five time points analyzed, and these have been annotated based on their sequence similarity with the Arabidopsis proteome. Novel data arising from these analyses identify genes likely to be critical for the germination and subsequent early development of diverse cells and tissues emerging from dormancy.

RNA silencing in plants: a shortcut to functional analysis

RNA silencing is a rapidly expanding research field, not only because it is a fundamental biological issue but also because its application in the control of gene expression is highly promising. Post-transcriptional gene silencing in plants is a form of RNA silencing by which target RNA is degraded in a sequence-specific manner. Findings regarding the central role that double-stranded RNA plays in triggering RNA silencing have prompted the development of many modified methods for RNA silencing. These methods, in combination with the development of genomic resources, have provided rapid and efficient means by which to investigate gene function in a wide range of plant species. This review addresses the technical aspects of RNA silencing in plants by introducing the principles of several methods of RNA silencing, as well as the advantages and disadvantages of each method.

Calcium signaling in plant cells in altered gravity

Changes in the intracellular Ca2+ concentration in altered gravity (microgravity and clinostating) evidence that Ca2+ signaling can play a fundamental role in biological effects of microgravity. Calcium as a second messenger is known to play a crucial role in stimulus-response coupling for many plant cellular signaling pathways. Its messenger functions are realized by transient changes in the cytosolic ion concentration induced by a variety of internal and external stimuli such as light, hormones, temperature, anoxia, salinity, and gravity. Although the first data on the changes in the calcium balance in plant cells under the influence of altered gravity have appeared in 80th, a review highlighting the performed research and the possible significance of such Ca2+ changes in the structural and metabolic rearrangements of plant cells in altered gravity is still lacking. In this paper, an attempt was made to summarize the available experimental results and to consider some hypotheses in this field of research. It is proposed to distinguish between cell gravisensing and cell graviperception; the former is related to cell structure and metabolism stability in the gravitational field and their changes in microgravity (cells not specialized to gravity perception), the latter is related to active use of a gravitational stimulus by cells presumebly specialized to gravity perception for realization of normal space orientation, growth, and vital activity (gravitropism, gravitaxis) in plants. The main experimental data concerning both redistribution of free Ca2+ ions in plant cell organelles and the cell wall, and an increase in the intracellular Ca2+ concentration under the influence of altered gravity are presented. Based on the gravitational decompensation hypothesis, the consequence of events occurring in gravisensing cells not specialized to gravity perception under altered gravity are considered in the following order: changes in the cytoplasmic membrane surface tension --> alterations in the physicochemical properties of the membrane --> changes in membrane permeability, ion transport, membrane-bound enzyme activity, etc. --> metabolism rearrangements --> physiological responses. An analysis of data available on biological effects of altered gravity at the cellular level allows one to conclude that microgravity environment appears to affect cytoskeleton, carbohydrate and lipid metabolism, cell wall biogenesis via changes in enzyme activity and protein expression, with involvement of regulatory Ca2+ messenger system. Changes in Ca2+ influx/efflux and possible pathways of Ca2+ signaling in plant cell biochemical regulation in altered gravity are discussed.

Plants in space

Virtually all scenarios for the long-term habitation of spacecraft and other extraterrestrial structures involve plants as important parts of the contained environment that would support humans. Recent experiments have identified several effects of spaceflight on plants that will need to be more fully understood before plant-based life support can become a reality. The International Space Station (ISS) is the focus for the newest phase of space-based research, which should solve some of the mysteries of how spaceflight affects plant growth. Research carried out on the ISS and in the proposed terrestrial facility for Advanced Life Support testing will bring the requirements for establishing extraterrestrial plant-based life support systems into clearer focus.

Reorientation of seedlings in the earth's gravitational field induces cytosolic calcium transients

The gravitational field controls plant growth, morphology, and development. However, the underlying transduction mechanisms are not well understood. Much indirect evidence has implicated the cytoplasmic free calcium concentration ([Ca(2+)](c)) as an important factor, but direct evidence for changes in [Ca(2+)](c) is currently lacking. We now have made measurements of [Ca(2+)](c) in groups of young seedlings of Arabidopsis expressing aequorin in the cytoplasm and reconstituted in vivo with cp-coelenterazine, a synthetic high-affinity luminophore. Distinct [Ca(2+)](c) signaling occurs in response to gravistimulation with kinetics very different from [Ca(2+)](c) transients evoked by other mechanical stimuli (e.g. movement and wind). [Ca(2+)](c) changes produced in response to gravistimulation are transient but with a duration of many minutes and dependent on stimulus strength (i.e. the angle of displacement). The auxin transport blockers 2,3,5-tri-iodo benzoic acid and N-(1-naphthyl) phthalamic acid interfere with gravi-induced [Ca(2+)](c) responses and addition of methyl indole-3-acetic acid to whole seedlings induces long-lived [Ca(2+)](c) transients, suggesting that changes in auxin transport may interact with [Ca(2+)](c). Permanent nonaxial rotation of seedlings on a two-dimensional clinostat, however, produced a sustained elevation of the [Ca(2+)](c) level. This probably reflects permanent displacement of gravity-sensing cellular components and/or disturbance of cytoskeletal tension. It is concluded that [Ca(2+)](c) is part of the gravity transduction mechanism in young Arabidopsis seedlings.

Calmodulin as a versatile calcium signal transducer in plants

The complexity of Ca²⁺ patterns observed in eukaryotic cells, including plants, has led to the hypothesis that specific patterns of Ca²⁺ propagation, termed Ca²⁺ signatures, encode information and relay it to downstream elements (effectors) for translation into appropriate cellular responses. Ca²⁺ -binding proteins (sensors) play a key role in decoding Ca²⁺ signatures and transducing signals by activating specific targets and pathways. Calmodulin is a Ca²⁺ sensor known to modulate the activity of many mammalian proteins, whose targets in plants are now being actively characterized. Plants possess an interesting and rapidly growing list of calmodulin targets with a variety of cellular roles. Nevertheless, many targets appear to be unique to plants and remain uncharacterized, calling for a concerted effort to elucidate their functions. Moreover, the extended family of calmodulin-related proteins in plants consists of evolutionarily divergent members, mostly of unknown function, although some have recently been implicated in stress responses. It is hoped that advances in functional genomics, and the research tools it generates, will help to explain themultiplicity of calmodulin genes in plants, and to identify their downstream effectors. This review summarizes current knowledge of the Ca²⁺ -calmodulin messenger system in plants and presents suggestions for future areas of research. Contents I. Introduction 36 II. CaM isoforms and CaM-like proteins 37 III. CaM-target proteins 42 IV. CaM and nuclear functions 46 V. Regulation of ion transport 49 VI. CaM and plant responses to environmental stimuli 52 VII. Conclusions and future studies 58 Acknowledgements 59 References 59.

Transgene expression patterns indicate that spaceflight affects stress signal perception and transduction in arabidopsis

The use of plants as integral components of life support systems remains a cornerstone of strategies for long-term human habitation of space and extraterrestrial colonization. Spaceflight experiments over the past few decades have refined the hardware required to grow plants in low-earth orbit and have illuminated fundamental issues regarding spaceflight effects on plant growth and development. Potential incipient hypoxia, resulting from the lack of convection-driven gas movement, has emerged as a possible major impact of microgravity. We developed transgenic Arabidopsis containing the alcohol dehydrogenase (Adh) gene promoter linked to the beta-glucuronidase (GUS) reporter gene to address specifically the possibility that spaceflight induces the plant hypoxia response and to assess whether any spaceflight response was similar to control terrestrial hypoxia-induced gene expression patterns. The staining patterns resulting from a 5-d mission on the orbiter Columbia during mission STS-93 indicate that the Adh/GUS reporter gene was activated in roots during the flight. However, the patterns of expression were not identical to terrestrial control inductions. Moreover, although terrestrial hypoxia induces Adh/GUS expression in the shoot apex, no apex staining was observed in the spaceflight plants. This indicates that either the normal hypoxia response signaling is impaired in spaceflight or that spaceflight inappropriately induces Adh/GUS activity for reasons other than hypoxia.