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Stobbe M.D.,Netherlands Bioinformatics Center | Houten S.M.,Metabolic | Van Kampen A.H.C.,Swammerdam Institute for Life science | Van Kampen A.H.C.,University of Amsterdam | And 3 more authors.
FASEB Journal | Year: 2012

To collect the ever-increasing yet scattered knowledge on metabolism, multiple pathway databases like the Kyoto Encyclopedia of Genes and Genomes have been created. A complete and accurate description of the metabolic network for human and other organisms is essential to foster new biological discoveries. Previous research has shown, however, that the level of agreement among pathway databases is surprisingly low. We investigated whether the lack of consensus among databases can be explained by an inaccurate representation of the knowledge described in scientific literature. As an example, we focus on the well-known tricarboxylic acid (TCA) cycle and evaluated the description of this pathway as found in a comprehensive selection of 10 human metabolic pathway databases. Remarkably, none of the descriptions given by these databases is entirely correct. Moreover, consensus exists on only 3 reactions. Mistakes in pathway databases might lead to the propagation of incorrect knowledge, misinterpretation of high-throughput molecular data, and poorly designed follow-up experiments. We provide an improved description of the TCA cycle via the community-curated database WikiPathways. We review various initiatives that aim to improve the description of the human metabolic network and discuss the importance of the active involvement of biological experts in these. © FASEB.


Scinches J.M.,University of Lisbon | Branco M.P.,University of Lisbon | Da Silva F.L.,Swammerdam Institute for Life science
Proceedings - International Symposium on Biomedical Imaging | Year: 2016

Intentions of specific motor movements are known to generate event-related (de)synchronization (ERD/ERS) patterns which may be interpreted as changes in the degree of synchronization of underlying neuronal networks. When activated, the neural populations in a certain region of the brain de-synchronize, leading to a decrease in the EEG power signal. Notably, this phenomena happens not only in time but also in space. Here, we propose a novel method to detect brain activity based on this spatial desynchronization effect. The electrical activity at the scalp is described by a finite dimension continuous 2D field estimated from the EEG data acquired at the discrete locations of the electrodes and analyzed using the monogenic framework. The method was tested with synthetic data and the results are compared with other methods, namely, the traditional power-based ERD/ERS estimation method. It is shown that the proposed approach yields more space-specific and less blurred results than traditional approaches. © 2016 IEEE.


Colquhoun T.A.,University of Florida | Kim J.Y.,University of Florida | Wedde A.E.,University of Florida | Levin L.A.,University of Florida | And 3 more authors.
Journal of Experimental Botany | Year: 2011

In Petunia×hybrida cv 'Mitchell Diploid' (MD), floral volatile benzenoid/phenylpropanoid (FVBP) biosynthesis is controlled spatially, developmentally, and daily at molecular, metabolic, and biochemical levels. Multiple genes have been shown to encode proteins that either directly catalyse a biochemical reaction yielding FVBP compounds or are involved in metabolite flux prior to the formation of FVBP compounds. It was hypothesized that multiple transcription factors are involved in the precise regulation of all necessary genes, resulting in the specific volatile signature of MD flowers. After acquiring all available petunia transcript sequences with homology to Arabidopsis thaliana R2R3-MYB transcription factors, PhMYB4 (named for its close identity to AtMYB4) was identified, cloned, and characterized. PhMYB4 transcripts accumulate to relatively high levels in floral tissues at anthesis and throughout open flower stages, which coincides with the spatial and developmental distribution of FVBP production and emission. Upon RNAi suppression of PhMYB4 (ir-PhMYB4) both petunia CINNAMATE-4-HYDROXYLASE (PhC4H1 and PhC4H2) gene transcript levels were significantly increased. In addition, ir-PhMYB4 plants emit higher levels of FVBP compounds derived from p-coumaric acid (isoeugenol and eugenol) compared with MD. Together, these results indicate that PhMYB4 functions in the repression of C4H transcription, indirectly controlling the balance of FVBP production in petunia floral tissue (i.e. fine-tunes). © 2010 The Author(s).


Scala A.,Swammerdam Institute for Life science | Allmann S.,Swammerdam Institute for Life science | Mirabella R.,Swammerdam Institute for Life science | Haring M.A.,Swammerdam Institute for Life science | Schuurink R.C.,Swammerdam Institute for Life science
International Journal of Molecular Sciences | Year: 2013

Plants cannot avoid being attacked by an almost infinite number of microorganisms and insects. Consequently, they arm themselves with molecular weapons against their attackers. Plant defense responses are the result of a complex signaling network, in which the hormones jasmonic acid (JA), salicylic acid (SA) and ethylene (ET) are the usual suspects under the magnifying glass when researchers investigate host-pest interactions. However, Green Leaf Volatiles (GLVs), C6 molecules, which are very quickly produced and/or emitted upon herbivory or pathogen infection by almost every green plant, also play an important role in plant defenses. GLVs are semiochemicals used by insects to find their food or their conspecifics. They have also been reported to be fundamental in indirect defenses and to have a direct effect on pests, but these are not the only roles of GLVs. These volatiles, being probably one of the fastest weapons exploited, are also able to directly elicit or prime plant defense responses. Moreover, GLVs, via crosstalk with phytohormones, mostly JA, can influence the outcome of the plant's defense response against pathogens. For all these reasons GLVs should be considered as co-protagonists in the play between plants and their attackers. © 2013 by the authors; licensee MDPI, Basel, Switzerland.


Schwabe A.,Center for Mathematics and Computer Science Centrum Wiskunde and Informatica | Schwabe A.,Netherlands Institute for Systems Biology | Rybakova K.N.,VU University Amsterdam | Bruggeman F.J.,Center for Mathematics and Computer Science Centrum Wiskunde and Informatica | And 3 more authors.
Biophysical Journal | Year: 2012

Transcription is regulated by a multitude of factors that concertedly induce genes to switch between activity states. Eukaryotic transcription involves a multitude of complexes that sequentially assemble on chromatin under the influence of transcription factors and the dynamic state of chromatin. Prokaryotic transcription depends on transcription factors, sigma-factors, and, in some cases, on DNA looping. We present a stochastic model of transcription that considers these complex regulatory mechanisms. We coarse-grain the molecular details in such a way that the model can describe a broad class of gene-regulation mechanisms. We solve this model analytically for various measures of stochastic transcription and compare alternative gene-regulation designs. We find that genes with complex multiprotein regulation can have peaked burst-size distributions in contrast to the geometric distributions found for simple models of transcription regulation. Burst-size distributions are, in addition, shaped by mRNA degradation during transcription bursts. We derive the stochastic properties of genes in the limit of deterministic switch times. These genes typically have reduced transcription noise. Severe timescale separation between gene regulation and transcription initiation enhances noise and leads to bimodal mRNA copy number distributions. In general, complex mechanisms for gene regulation lead to nonexponential waiting-time distributions for gene switching and transcription initiation, which typically reduce noise in mRNA copy numbers and burst size. Finally, we discuss that qualitatively different gene regulation models can often fit the same experimental data on single-cell mRNA abundance even though they have qualitatively different burst-size statistics and regulatory parameters. © 2012 Biophysical Society.


Schaefer A.,Swammerdam Institute for Life science | Reinhard N.R.,Swammerdam Institute for Life science | Hordijk P.L.,Swammerdam Institute for Life science
Small GTPases | Year: 2014

Cell adhesion and migration are regulated through the concerted action of cytoskeletal dynamics and adhesion proteins, the activity of which is governed by RhoGTPases. Specific RhoGTPase signaling requires spatio-temporal activation and coordination of subsequent protein-protein and protein-lipid interactions. The nature, location and duration of these interactions are dependent on polarized extracellular triggers, such as cell-cell contact, and intracellular modifying events, such as phosphorylation. RhoA, RhoB, and RhoC are highly homologous GTPases that, however, succeed in generating specific intracellular responses. Here, we discuss the key features that contribute to this specificity. These not only include the well-studied switch regions, the conformation of which is nucleotide- dependent, but also additional regions and seemingly small differences in primary sequence that also contribute to specific interactions. These differences translate into differential surface charge distribution, local exposure of amino acid side-chains and isoform-specific post-translational modifications. The available evidence supports the notion that multiple regions in RhoA/B/C cooperate to provide specificity in binding to regulators and effectors. These specific interactions are highly regulated in time and space. We therefore subsequently discuss current approaches means to visualize and analyze localized GTPase activation using biosensors that allow imaging of isoform-specific, localized regulation. © 2014 Taylor & Francis Group, LLC.


Ament K.,Swammerdam Institute for Life science | Krasikov V.,Swammerdam Institute for Life science | Allmann S.,Max Planck Institute for Chemical Ecology | Rep M.,Swammerdam Institute for Life science | And 2 more authors.
Plant Journal | Year: 2010

The role of methyl salicylate (MeSA) production was studied in indirect and direct defence responses of tomato (Solanum lycopersicum) to the spider mite Tetranychus urticae and the root-invading fungus Fusarium oxysporum f. sp. lycopersici, respectively. To this end, we silenced the tomato gene encoding salicylic acid methyl transferase (SAMT). Silencing of SAMT led to a major reduction in SAMT expression and MeSA emission upon herbivory by spider mites, without affecting the induced emission of other volatiles (terpenoids). The predatory mite Phytoseiulus persimilis, which preys on T. urticae, could not discriminate between infested and non-infested SAMT-silenced lines, as it could for wild-type tomato plants. Moreover, when given the choice between infested SAMT-silenced and infested wild-type plants, they preferred the latter. These findings are supportive of a major role for MeSA in this indirect defence response of tomato. SAMT-silenced tomato plants were less susceptible to a virulent strain of F. oxysporum f. sp. lycopersici, indicating that the direct defense responses in the roots are also affected in these plants. Our studies show that the conversion of SA to MeSA can affect both direct and indirect plant defence responses. © 2010 Blackwell Publishing Ltd.


Diezel C.,Max Planck Institute for Chemical Ecology | Allmann S.,Max Planck Institute for Chemical Ecology | Allmann S.,Swammerdam Institute for Life science | Baldwin I.T.,Max Planck Institute for Chemical Ecology
Journal of Integrative Plant Biology | Year: 2011

To defend themselves against herbivore attack, plants produce secondary metabolites, which are variously inducible and constitutively deployed, presumably to optimize their fitness benefits in light of their fitness costs. Three phytohormones, jasmonates (JA) and their active forms, the JA-isoleucine (JA-Ile) and ethylene (ET), are known to play central roles in the elicitation of induced defenses, but little is known about how this mediation changes over ontogeny. The Optimal Defense Theory (ODT) predicts changes in the costs and benefits of the different types of defenses and has been usefully extrapolated to their modes of deployment. Here we studied whether the herbivore-induced accumulation of JA, JA-Ile and ET changed over ontogeny in Nicotiana attenuata, a native tobacco in which inducible defenses are particularly well studied. Herbivore-elicited ET production changed dramatically during six developmental stages, from rosette through flowering, decreasing with the elongation of the first corollas during flower development. This decrease was largely recovered within a day after flower removal by decapitation. A similar pattern was found for the herbivore-induced accumulation of JA and JA-Ile. These results are consistent with ODT predictions and suggest that the last steps in floral development control the inducibility of at least three plant hormones, optimizing defense-growth tradeoffs. © 2011 Institute of Botany, Chinese Academy of Sciences.


Allmann S.,Max Planck Institute for Chemical Ecology | Halitschke R.,Max Planck Institute for Chemical Ecology | Halitschke R.,Cornell University | Schuurink R.C.,Max Planck Institute for Chemical Ecology | And 2 more authors.
Plant, Cell and Environment | Year: 2010

Lipoxygenases (LOXs) are key enzymes in the biosynthesis of oxylipins, and catalyse the formation of fatty acid hydroperoxides (HPs), which represent the first committed step in the synthesis of metabolites that function as signals and defences in plants. HPs are the initial substrates for different branches of the oxylipin pathway, and some plant species may express different LOX isoforms that supply specific branches. Here, we compare isogenic lines of the wild tobacco Nicotiana attenuata with reduced expression of NaLOX2 (irlox2) or NaLOX3 (irlox3) to determine the role of these different LOX isoforms in supplying substrates for two different pathways: green leaf volatiles (GLVs) and jasmonic acid (JA). Reduced NaLOX2 expression strongly decreased the production of GLVs without influencing the formation of JA and JA-related secondary metabolites. Conversely, reduced NaLOX3 expression strongly decreased JA biosynthesis, without influencing GLV production. The temporal expression of NaLOX2 and NaLOX3 also differed after elicitation; NaLOX3 was rapidly induced, attaining highest transcript levels within 1 h after elicitation, whereas NaLOX2 transcripts reached maximum levels after 14 h. These results demonstrate that N. attenuata channels the flux of HPs through the activities of different LOXs, leading to different direct and indirect defence responses mediating the plant's herbivore resistance. © 2010 Blackwell Publishing Ltd.


Allmann S.,Max Planck Institute for Chemical Ecology | Allmann S.,Swammerdam Institute for Life science | Spathe A.,Max Planck Institute for Chemical Ecology | Bisch-Knaden S.,Max Planck Institute for Chemical Ecology | And 6 more authors.
eLife | Year: 2013

The ability to decrypt volatile plant signals is essential if herbivorous insects are to optimize their choice of host plants for their offspring. Green leaf volatiles (GLVs) constitute a widespread group of defensive plant volatiles that convey a herbivory-specific message via their isomeric composition: feeding of the tobacco hornworm Manduca sexta converts (Z)-3- to (E)-2-GLVs thereby attracting predatory insects. Here we show that this isomer-coded message is monitored by ovipositing M. sexta females. We detected the isomeric shift in the host plant Datura wrightii and performed functional imaging in the primary olfactory center of M. sexta females with GLV structural isomers. We identified two isomer-specific regions responding to either (Z)-3- or (E)-2-hexenyl acetate. Field experiments demonstrated that ovipositing Manduca moths preferred (Z)-3-perfumed D. wrightii over (E)-2-perfumed plants. These results show that (E)-2-GLVs and/or specific (Z)-3/(E)-2-ratios provide information regarding host plant attack by conspecifics that ovipositing hawkmoths use for host plant selection. Copyright Allmann et al.

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