Signal Modification Research Articles

Neuropeptide F neurons modulate sugar reward during associative olfactory learning of Drosophila larvae.

All organisms continuously have to adapt their behavior according to changes in the environment in order to survive. Experience-driven changes in behavior are usually mediated and maintained by modifications in signaling within defined brain circuits. Given the simplicity of the larval brain of Drosophila and its experimental accessibility on the genetic and behavioral level, we analyzed if Drosophila neuropeptide F (dNPF) neurons are involved in classical olfactory conditioning. dNPF is an ortholog of the mammalian neuropeptide Y, a highly conserved neuromodulator that stimulates food-seeking behavior. We provide a comprehensive anatomical analysis of the dNPF neurons on the single-cell level. We demonstrate that artificial activation of dNPF neurons inhibits appetitive olfactory learning by modulating the sugar reward signal during acquisition. No effect is detectable for the retrieval of an established appetitive olfactory memory. The modulatory effect is based on the joint action of three distinct cell types that, if tested on the single-cell level, inhibit and invert the conditioned behavior. Taken together, our work describes anatomically and functionally a new part of the sugar reinforcement signaling pathway for classical olfactory conditioning in Drosophila larvae.

EVALUATING THE POTENTIAL OF MULTISPECTRAL AIRBORNE LIDAR FOR TOPOGRAPHIC MAPPING AND LAND COVER CLASSIFICATION

Abstract. Recently multispectral LiDAR became a promising research field for enhanced LiDAR classification workflows and e.g. the assessment of vegetation health. Current analyses on multispectral LiDAR are mainly based on experimental setups, which are often limited transferable to operational tasks. In late 2014 Optech Inc. announced the first commercially available multispectral LiDAR system for airborne topographic mapping. The combined system makes synchronic multispectral LiDAR measurements possible, solving time shift problems of experimental acquisitions. This paper presents an explorative analysis of the first airborne collected data with focus on class specific spectral signatures. Spectral patterns are used for a classification approach, which is evaluated in comparison to a manual reference classification. Typical spectral patterns comparable to optical imagery could be observed for homogeneous and planar surfaces. For rough and volumetric objects such as trees, the spectral signature becomes biased by signal modification due to multi return effects. However, we show that this first flight data set is suitable for conventional geometrical classification and mapping procedures. Additional classes such as sealed and unsealed ground can be separated with high classification accuracies. For vegetation classification the distinction of species and health classes is possible.

Abstract 2209: Deregulation of the Ras-Erk signaling axis modulates the enhancer landscape

Abstract Unrestrained activation of receptor tyrosine kinase (RTK) pathways drives tumorigenesis through the persistent activation of critical signaling pathways, including the Ras-ERK axis. This aberrant signaling is unleashed by mutations in signaling effectors such as Ras, as well as through disruption of feedback control by regulatory proteins such as the Sprouty family. Mutations in epigenetic regulators also commonly occur during cancer progression, modulating chromatin architecture and gene expression. While unrestrained signaling and epigenetic deregulation are root causes of tumorigenesis, the relationship between aberrant RTK signaling and chromatin modifications at cis-regulatory elements remains to be fully elucidated. We establish linkage between these processes by examining the effects of oncogenic HRasG12V or loss of feedback regulation by Sprouty on global changes in gene expression and enhancer-associated chromatin modifications. Using RNA-sequencing and ChIP-sequencing, we demonstrate that aberrant RTK signaling unleashed by oncogenic HRasG12V or Sprouty gene deletion disrupts gene expression programs and remodels histone modifications associated with active enhancers, including histone 3 lysine 27 acetylation (H3K27ac). Abolishing persistent Ras-Erk signaling through chemical inhibition of MEK activity reverses the aberrant transcriptional program and H3K27ac remodeling at deregulated enhancers. While both lesions disrupt the Ras-Erk axis, the specific target genes and enhancers modulated upon HRasG12V-transformation or Sprouty deletion are largely distinct. Specifically, oncogenic HRasG12V significantly elevates the expression and H3K27ac levels near key target genes encoding the transcription factor Gata4 and the kinase Prkcb. Gata4 is necessary for the HRasG12V expression program and coordinates H3K27ac marking at enhancers of deregulated target genes. We further show that HRasG12V-driven cells are sensitive to chemical inhibition of Prkcb, which reduces the viability and clonogenicity of HRasG12V-transformed cells. These oncogenic effects upon HRasG12V-transformation are also reduced by chemical inhibition of the chromatin regulators BET bromodomain proteins and p300/CBP, which recognize and deposit H3K27ac, respectively. Taken together, our data support a model in which dynamic reprogramming of the cellular enhancer landscape is a key effect of oncogenic RTK signaling. Furthermore, our study shows that identification of enhancers regulated by oncogenic Ras yields insight into targeting key epigenetic regulators and downstream factors that promote Ras-driven malignancies. Citation Format: Behnam Nabet, Pilib O Broin, Jaime Reyes, Kevin Shieh, Charles Y. Lin, Christine M. Will, Relja Popovic, Teresa Ezponda, James E. Bradner, Aaron A. Golden, Jonathan D. Licht. Deregulation of the Ras-Erk signaling axis modulates the enhancer landscape. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2209. doi:10.1158/1538-7445.AM2015-2209

Achieving tissue specific levels of angiogenesis: Not(ch) a big deal!

Our understanding of the molecular mechanisms regulating endothelial cell behavior in bone vs. other organs has been challenging to date given the inaccessibility of blood vessels deep within the bone mineral and the difficulties associated with bone endothelial cell isolation. A recent study published by Ramasamy et al. , combined postnatal modification of endothelial cell specific Notch signals with improved immunohistochemical approaches and bone endothelial cell isolation, to highlight for the first time the presence of clear bone endothelial cell heterogeneity.

Working memory and intelligibility of hearing-aid processed speech.

Previous work suggested that individuals with low working memory capacity may be at a disadvantage in adverse listening environments, including situations with background noise or substantial modification of the acoustic signal. This study explored the relationship between patient factors (including working memory capacity) and intelligibility and quality of modified speech for older individuals with sensorineural hearing loss. The modification was created using a combination of hearing aid processing [wide-dynamic range compression (WDRC) and frequency compression (FC)] applied to sentences in multitalker babble. The extent of signal modification was quantified via an envelope fidelity index. We also explored the contribution of components of working memory by including measures of processing speed and executive function. We hypothesized that listeners with low working memory capacity would perform more poorly than those with high working memory capacity across all situations, and would also be differentially affected by high amounts of signal modification. Results showed a significant effect of working memory capacity for speech intelligibility, and an interaction between working memory, amount of hearing loss and signal modification. Signal modification was the major predictor of quality ratings. These data add to the literature on hearing-aid processing and working memory by suggesting that the working memory-intelligibility effects may be related to aggregate signal fidelity, rather than to the specific signal manipulation. They also suggest that for individuals with low working memory capacity, sensorineural loss may be most appropriately addressed with WDRC and/or FC parameters that maintain the fidelity of the signal envelope.

A generalizable platform for interrogating target- and signal-specific consequences of electrophilic modifications in redox-dependent cell signaling.

Despite the known propensity of small-molecule electrophiles to react with numerous cysteine-active proteins, biological actions of individual signal inducers have emerged to be chemotype-specific. To pinpoint and quantify the impacts of modifying one target out of the whole proteome, we develop a target-protein-personalized "electrophile toolbox" with which specific intracellular targets can be selectively modified at a precise time by specific reactive signals. This general methodology, T-REX (targetable reactive electrophiles and oxidants), is established by (1) constructing a platform that can deliver a range of electronic and sterically different bioactive lipid-derived signaling electrophiles to specific proteins in cells; (2) probing the kinetics of targeted delivery concept, which revealed that targeting efficiency in cells is largely driven by initial on-rate of alkylation; and (3) evaluating the consequences of protein-target- and small-molecule-signal-specific modifications on the strength of downstream signaling. These data show that T-REX allows quantitative interrogations into the extent to which the Nrf2 transcription factor-dependent antioxidant response element (ARE) signaling is activated by selective electrophilic modifications on Keap1 protein, one of several redox-sensitive regulators of the Nrf2-ARE axis. The results document Keap1 as a promiscuous electrophile-responsive sensor able to respond with similar efficiencies to discrete electrophilic signals, promoting comparable strength of Nrf2-ARE induction. T-REX is also able to elicit cell activation in cases in which whole-cell electrophile flooding fails to stimulate ARE induction prior to causing cytotoxicity. The platform presents a previously unavailable opportunity to elucidate the functional consequences of small-molecule-signal- and protein-target-specific electrophilic modifications in an otherwise unaffected cellular background.

Tumorigenesis and peritoneal colonization from fallopian tube epithelium.

Ovarian cancer is the most lethal gynecological malignancy, primarily because its origin and initiation factors are unknown. A secretory murine oviductal epithelial (MOE) model was generated to address the hypothesis that the fallopian tube is an origin for high-grade serous cancer. MOE cells were stably altered to express mutation in p53, silence PTEN, activate AKT, and amplify KRAS alone and in combination, to define if this cell type gives rise to tumors and what genetic alterations are required to drive malignancy. Cell lines were characterized in vitro and allografted into mice. Silencing PTEN formed high-grade carcinoma with wide spread tumor explants including metastasis into the ovary. Addition of p53 mutation to PTEN silencing did not enhance this phenotype, whereas addition of KRAS mutation reduced survival. Interestingly, PTEN silencing and KRAS mutation originating from ovarian surface epithelium generated endometrioid carcinoma, suggesting that different cellular origins with identical genetic manipulations can give rise to distinct cancer histotypes. Defining the roles of specific signaling modifications in tumorigenesis from the fallopian tube/oviduct is essential for early detection and development of targeted therapeutics. Further, syngeneic MOE allografts provide an ideal model for pre-clinical testing in an in vivo environment with an intact immune system.

The Early Metazoan Trichoplax adhaerens Possesses a Functional O-GlcNAc System

Protein O-GlcNAcylation is a reversible post-translational signaling modification of nucleocytoplasmic proteins that is essential for embryonic development in bilateria. In a search for a reductionist model to study O-GlcNAc signaling, we discovered the presence of functional O-GlcNAc transferase (OGT), O-GlcNAcase (OGA), and nucleocytoplasmic protein O-GlcNAcylation in the most basal extant animal, the placozoan Trichoplax adhaerens. We show via enzymatic characterization of Trichoplax OGT/OGA and genetic rescue experiments in Drosophila melanogaster that these proteins possess activities/functions similar to their bilaterian counterparts. The acquisition of O-GlcNAc signaling by metazoa may have facilitated the rapid and complex signaling mechanisms required for the evolution of multicellular organisms.

3-iodothyronamine differentially modulates α-2A-adrenergic receptor-mediated signaling.

Most in vivo effects of 3-iodothyronamine (3-T1AM) have been thus far thought to be mediated by binding at the trace amine-associated receptor 1 (TAAR1). Inconsistently, the 3-T1AM-induced hypothermic effect still persists in Taar1 knockout mice, which suggests additional receptor targets. In support of this general assumption, it has previously been reported that 3-T1AM also binds to the α-2A-adrenergic receptor (ADRA2A), which modulates insulin secretion. However, the mechanism of this effect remains unclear. We tested two different scenarios that may explain the effect: the sole action of 3-T1AM at ADRA2A and a combined action of 3-T1AM at ADRA2A and TAAR1, which is also expressed in pancreatic islets. We first investigated a potential general signaling modification using the label-free EPIC technology and then specified changes in signaling by cAMP inhibition and MAPKs (ERK1/2) determination. We found that 3-T1AM induced Gi/o activation at ADRA2A and reduced the norepinephrine (NorEpi)-induced MAPK activation. Interestingly, in ADRA2A/TAAR1 hetero-oligomers, application of NorEpi resulted in uncoupling of the Gi/o signaling pathway, but it did not affect MAPK activation. However, 3-T1AM application in mice over a period of 6 days at a daily dose of 5 mg/kg had no significant effects on glucose homeostasis. In summary, we report an agonistic effect of 3-T1AM on the ADRA2A-mediated Gi/o pathway but an antagonistic effect on MAPK induced by NorEpi. Moreover, in ADRA2A/TAAR1 hetero-oligomers, the capacity of NorEpi to stimulate Gi/o signaling is reduced by co-stimulation with 3-T1AM. The present study therefore points to a complex spectrum of signaling modification mediated by 3-T1AM at different G protein-coupled receptors.

Accounting for linear transformations of EEG and MEG data in source analysis.

Analyses of electro- and magnetoencephalography (EEG, MEG) data often involve a linear modification of signals at the sensor level. Examples include re-referencing of the EEG, computation of synthetic gradiometer in MEG, or the removal of artifactual independent components to clean EEG and MEG data. A question of practical relevance is, if such modifications must be accounted for by adapting the physical forward model (leadfield) before subsequent source analysis. Here, we show that two scenarios need to be differentiated. In the first scenario, which corresponds to re-referencing the EEG and synthetic gradiometer computation in MEG, the leadfield must be adapted before source analysis. In the second scenario, which corresponds to removing artifactual components to ‘clean’ the data, the leadfield must not be changed. We demonstrate and discuss the consequences of wrongly modifying the leadfield in the latter case for an example. Future EEG and MEG studies employing source analyses should carefully consider whether and, if so, how the leadfield must be modified as explicated here.

Cell signaling: principles and mechanisms

Table of Contents 1.Overview of Signal Transduction 2.Principles and Mechanisms of Protein Interactions 3.Signaling Enzymes and Their Allosteric Regulation 4.Role of Post-Translational Modifications in Signaling 5.Subcellular Localization of Signaling Molecules 6.Small Soluble Signaling Mediators 7.Lipids and Enzymes that Modify Them 8.Information Transfer Across the Membrane 9.Regulated Protein Degradation 10.Modular Architecture and Evolution of Signaling Proteins 11.Signaling Devices in Networks 12.How Cells Make Decisions 13.Methods for Studying Signaling Proteins and Networks

New G protein coupled receptor targets for 3-iodotyronamine

So far most in vivo effects of 3-iodothyronamine (3-T1AM) are thought to be mediated by binding at the trace amine-associated receptor 1 (TAAR1). Inconsistently, 3-T1AM effects still persist in Taar1 knockout mice, suggesting additional receptor targets. It has previously been reported that 3-T1AM also binds to the alpha-2A-adrenergic receptor (ADRA2A) modulating insulin secretion. We speculated that this effect is mediated by interaction with ADRA2A or with a ADRA2A/TAAR1 complex. To unravel the signaling properties of ADRA2A in interplay with 3-T1AM we first investigated on a potential general signaling modification by the label-free EPIC-technology and then specified changes in signaling by cAMP inhibition and MAPK (ERK1/2) assays. We found that 3-T1AM induces Gi/o activation at ADRA2A. In contrast to nor-epinephrine (NorEpi), 3-T1AM did not activate the MAPK pathway but reduced the NorEpi-induced MAPK activation. Interestingly, co-expression of TAAR1 and ADRA2A as it occurs e.g. in pancreatic β-cells, abolished NorEpi-induced Gi/o signaling at ADRA2A. In addition, in ADRA2A/TAAR1 hetero-oligomers application of NorEpi results in uncoupling of Gi/o signaling pathway, not affecting MAPK activation. RNA sequencing analyses showed significant co-expression of ADRA2A and TAAR1 in mouse pancreatic islets but chronical 3-T1AM application in mice over a period of six days had no significant effects on glucose homeostasis. Our study provides important insights into the 3-T1AM-mediated signaling spectrum. It revealed a direct influence of 3-T1AM on ADRA2A function activating Gi/o pathway and 3-T1AM-induced uncoupling of NorEpi-mediated ADRA2A signaling in ADRA2A/TAAR1 hetero-oligomers.

Nonlinear analysis of EEG in chess players

The chess game is a good example of cognitive task which needs a lot of training and experience. The aim of this work is to compare applicability of two nonlinear methods - Higuchi Fractal Dimension and Empirical Mode Decomposition - in analysis of EEG data recorded during chess match. We analyzed data of three master chess players registered during their matches with computer program. We used two nonlinear methods: Higuchi Fractal Dimension that is a good and fast tool for analyzing signal complexity and modification of Empirical Mode Decomposition, called Sliding Window Empirical Mode Decomposition, that breaks down a signal into its monocomponents. Obtained results are compared with the resting state i.e. EEG during relax witch closed eyes. The analysis shows higher values of Higuchi Fractal Dimension during the thinking over chess moves than in the players’ rest state. There are no statistically significant differences in contribution of EEG bands to total power of EEG calculated with Sliding Window Empirical Mode Decomposition. Our results show beter applicability of Higuchi Fractal Dimension method for analysis of EEG signals related to chess tasks than that of Sliding Window Empirical Mode Decomposition.

Duox1-derived H2O2 modulates Cxcl8 expression and neutrophil recruitment via JNK/c-JUN/AP-1 signaling and chromatin modifications.

DUOX1-derived hydrogen peroxide (H2O2) and CXCL8 are two key neutrophil chemoattractants. H2O2 is critical at the early phase, whereas CXCL8 plays a key role in the late phases of recruitment, but the crosstalks between the two phases in vivo remain unknown. In this study using zebrafish, we report that H2O2 also contributes to neutrophil recruitment to injuries at the late phase as it induces Cxcl8 expression in vivo through a JNK/c-JUN/AP-1 signaling pathway. However, Erk and NF-κB signaling were not involved in this crosstalk. Strikingly, H2O2 also promotes cxcl8 expression through modulation of histone 3 lysine 4 trimethylation, histone 3 lysine 9 acetylation, and histone 3 lysine 9 trimethylation levels at its promoter. These results explain how early H2O2 signal regulates neutrophil recruitment at all phases, directly via Lyn oxidation or indirectly by modulating cxcl8 gene expression, via the activation of redox-sensitive signaling pathways, and further point out H2O2/DUOX1 as a key drug target for anti-inflammatory therapies.

Enhanced auditory evoked activity to self-generated sounds is mediated by primary and supplementary motor cortices.

Accumulating evidence demonstrates that responses in auditory cortex to auditory consequences of self-generated actions are modified relative to the responses evoked by identical sounds generated by an external source. Such modifications have been suggested to occur through a corollary discharge sent from the motor system, although the exact neuroanatomical origin is unknown. Furthermore, since tactile input has also been shown to modify responses in auditory cortex, it is not even clear whether the source of such modifications is motor output or somatosensory feedback. We recorded functional magnetic resonance imaging (fMRI) data from healthy human subjects (n = 11) while manipulating the rate at which they performed sound-producing actions with their right hand. In addition, we manipulated the amount of tactile feedback to examine the relative roles of motor and somatosensory cortices in modifying evoked activity in auditory cortex (superior temporal gyrus). We found an enhanced fMRI signal in left auditory cortex during perception of self-generated sounds relative to passive listening to identical sounds. Moreover, the signal difference between active and passive conditions in left auditory cortex covaried with the rate of sound-producing actions and was invariant to the amount of tactile feedback. Together with functional connectivity analysis, our results suggest motor output from supplementary motor area and left primary motor cortex as the source of signal modification in auditory cortex during perception of self-generated sounds. Motor signals from these regions could represent a predictive signal of the expected auditory consequences of the performed action.

Les dyskinésies L-dopa induites dans la maladie de Parkinson

Involuntary movements, or dyskinesia, represent a debilitating complication of levodopa (L-dopa) therapy for Parkinson's disease (PD). L-dopa-induced dyskinesia (LID) is ultimately experienced by the vast majority of parkinsonian patients. Loss of dopamine in PD induces complex modifications in cellular signaling with numerous pathways showing altered responses to dopaminergic stimulation. Chronic L-dopa treatment further enhances the signaling alterations. The dopamine D1 receptor (D1R) signaling pathway has consistently been shown to be critically involved in LID genesis and manifestation in the striatum, the basal ganglia input structure. Interestingly, recent studies suggest an impact of structures outside of the basal ganglia in LID expression. The present attempts to provide an overview of our current understanding of LID pathophysiology.

Whole transcriptome responses among females of the filariasis and arbovirus vector mosquito Culex pipiens implicate TGF-β signaling and chromatin modification as key drivers of diapause induction.

Culex pipiens mosquitoes are important disease vectors inhabiting temperate zones, worldwide. The seasonal reduction in temperature and photoperiod accompanying late summer and early fall prompts female mosquitoes to enter diapause, a stage of developmental arrest and physiological conditioning that enhances survival during the winter months. To investigate the molecular mechanisms underlying diapause induction, we used custom whole transcriptome microarrays to identify differences in gene expression following exposure to nondiapause (long days, 25 °C) and diapause-inducing (short days, 18 °C) environmental conditions. Using a two-way ANOVA, we identified 1130 genes that were differentially expressed. We used the expression of these genes across three time points to construct a gene co-expression network comprising five modules. Genes in modules 1, 2, and 3 were largely up-regulated, while genes in modules 4 and 5 were down-regulated when compared to nondiapause conditions. Pathway enrichment analysis of the network modules revealed some potential regulatory mechanisms driving diapause induction. Module 1 was enriched for genes in the TGF-ß and Wnt signaling pathways; module 2 was enriched for genes involved in insect hormone biosynthesis, specifically, ecdysone synthesis; module 3 was enriched for genes involved in chromatin modification; and module 5 was enriched for genes in the circadian rhythm pathway. Our results suggest that TGF-β signaling and chromatin modification are key drivers for the integration of environmental signals into the diapause induction phase in C. pipiens mosquitoes.

Acetylation and phosphorylation of STAT3 are involved in the responsiveness of microglia to beta amyloid

Microglia are macrophages within the central nervous system playing a central role in neurodegenerative disorders. Although the initial engagement of microglia seems to be neuroprotective, many lines of evidence indicate that its persistent activation contributes to dismantle neuronal activity and to induce neuronal loss. The molecular pathways that lead from amyloid interaction with membrane receptors to the microglial activation have been extensively investigated, although a definitive picture is not yet at hand. In this work, primary and immortalized microglial cells were treated with a synthetic form of Aβ peptides, and relative abundance of acetylated and phosphorylated STAT3 were assayed. Results highlight, for the first time, three distinctive sequential events: i) an earlier event marked by the increase in the level of STAT3 acetylated species, followed by ii) a later increase in the level of STAT3 phosphorylated form, and finally iii) an involvement of phosphorylated STAT3 in the increase in expression of the 14-3-3 epsilon, a protein frequently associated with neurodegenerative diseases and known to be a marker of Aβ-activated microglia. These data outline a complex, time-dependent modification of STAT3 signalling triggered by amyloid in the microglial compartments, that once confirmed by in vivo experiments will broaden the knowledge of the molecular basis of amyloid neurotoxicity.

Redox signalling and cardioprotection: translatability and mechanism.

The morbidity and mortality from coronary artery disease (CAD) remain significant worldwide. The treatment for acute myocardial infarction has improved over the past decades, including early reperfusion of culprit coronary arteries. Although it is mandatory to reperfuse the ischaemic territory as soon as possible, paradoxically this leads to additional myocardial injury, namely ischaemia/reperfusion (I/R) injury, in which redox stress plays a pivotal role and for which no effective therapy is currently available. In this review, we report evidence that the redox environment plays a pivotal role not only in I/R injury but also in cardioprotection. In fact, cardioprotective strategies, such as pre- and post-conditioning, result in a robust reduction in infarct size in animals and the role of redox signalling is of paramount importance in these conditioning strategies. Nitrosative signalling and cysteine redox modifications, such as S-nitrosation/S-nitrosylation, are also emerging as very important mechanisms in conditioning cardioprotection. The reasons for the switch from protective oxidative/nitrosative signalling to deleterious oxidative/nitrosative/nitrative stress are not fully understood. The complex regulation of this switch is, at least in part, responsible for the diminished or lack of cardioprotection induced by conditioning protocols observed in ageing animals and with co-morbidities as well as in humans. Therefore, it is important to understand at a mechanistic level the reasons for these differences before proposing a safe and useful transition of ischaemic or pharmacological conditioning. Indeed, more mechanistic novel therapeutic strategies are required to protect the heart from I/R injury and to improve clinical outcomes in patients with CAD.

Phosphorylation site prediction in plants.

Protein phosphorylation events on serine, threonine, and tyrosine residues are the most pervasive protein covalent bond modifications in plant signaling. Both low and high throughput studies reveal the importance of phosphorylation in plant molecular biology. Although becoming more and more common, the proteome-wide screening on phosphorylation by experiments remains time consuming and costly. Therefore, in silico prediction methods are proposed as a complementary analysis tool to enhance the phosphorylation site identification, develop biological hypothesis, or help experimental design. These methods build statistical models based on the experimental data, and they do not have some of the technical-specific bias, which may have advantage in proteome-wide analysis. More importantly computational methods are very fast and cheap to run, which makes large-scale phosphorylation identifications very practical for any types of biological study. Thus, the phosphorylation prediction tools become more and more popular. In this chapter, we will focus on plant specific phosphorylation site prediction tools, with essential illustration of technical details and application guidelines. We will use Musite, PhosPhAt and PlantPhos as the representative tools. We will present the results on the prediction of the Arabidopsis protein phosphorylation events to give users a general idea of the performance range of the three tools, together with their strengths and limitations. We believe these prediction tools will contribute more and more to the plant phosphorylation research community.