Showing papers by "Technical University of Denmark published in 2008"

Hierarchical zeolites: enhanced utilisation of microporous crystals in catalysis by advances in materials design.

Abstract: The introduction of synthetic zeolites has led to a paradigm shift in catalysis, separations, and adsorption processes, due to their unique properties such as crystallinity, high-surface area, acidity, ion-exchange capacity, and shape-selective character. However, the sole presence of micropores in these materials often imposes intracrystalline diffusion limitations, rendering low utilisation of the zeolite active volume in catalysed reactions. This critical review examines recent advances in the rapidly evolving area of zeolites with improved accessibility and molecular transport. Strategies to enhance catalyst effectiveness essentially comprise the synthesis of zeolites with wide pores and/or with short diffusion length. Available approaches are reviewed according to the principle, versatility, effectiveness, and degree of reality for practical implementation, establishing a firm link between the properties of the resulting materials and the catalytic function. We particularly dwell on the exciting field of hierarchical zeolites, which couple in a single material the catalytic power of micropores and the facilitated access and improved transport consequence of a complementary mesopore network. The carbon templating and desilication routes as examples of bottom-up and top-down methods, respectively, are reviewed in more detail to illustrate the benefits of hierarchical zeolites. Despite encircling the zeolite field, this review stimulates intuition into the design of related porous solids (116 references).

Environmental behavior and ecotoxicity of engineered nanoparticles to algae, plants, and fungi

Abstract: Developments in nanotechnology are leading to a rapid proliferation of new materials that are likely to become a source of engineered nanoparticles (ENPs) to the environment, where their possible ecotoxicological impacts remain unknown. The surface properties of ENPs are of essential importance for their aggregation behavior, and thus for their mobility in aquatic and terrestrial systems and for their interactions with algae, plants and, fungi. Interactions of ENPs with natural organic matter have to be considered as well, as those will alter the ENPs aggregation behavior in surface waters or in soils. Cells of plants, algae, and fungi possess cell walls that constitute a primary site for interaction and a barrier for the entrance of ENPs. Mechanisms allowing ENPs to pass through cell walls and membranes are as yet poorly understood. Inside cells, ENPs might directly provoke alterations of membranes and other cell structures and molecules, as well as protective mechanisms. Indirect effects of ENPs depend on their chemical and physical properties and may include physical restraints (clogging effects), solubilization of toxic ENP compounds, or production of reactive oxygen species. Many questions regarding the bioavailability of ENPs, their uptake by algae, plants, and fungi and the toxicity mechanisms remain to be elucidated.

USEtox—the UNEP-SETAC toxicity model: recommended characterisation factors for human toxicity and freshwater ecotoxicity in life cycle impact assessment

Abstract: In 2005, a comprehensive comparison of life cycle impact assessment toxicity characterisation models was initiated by the United Nations Environment Program (UNEP)–Society for Environmental Toxicology and Chemistry (SETAC) Life Cycle Initiative, directly involving the model developers of CalTOX, IMPACT 2002, USES-LCA, BETR, EDIP, WATSON and EcoSense. In this paper, we describe this model comparison process and its results—in particular the scientific consensus model developed by the model developers. The main objectives of this effort were (1) to identify specific sources of differences between the models’ results and structure, (2) to detect the indispensable model components and (3) to build a scientific consensus model from them, representing recommended practice. A chemical test set of 45 organics covering a wide range of property combinations was selected for this purpose. All models used this set. In three workshops, the model comparison participants identified key fate, exposure and effect issues via comparison of the final characterisation factors and selected intermediate outputs for fate, human exposure and toxic effects for the test set applied to all models. Through this process, we were able to reduce inter-model variation from an initial range of up to 13 orders of magnitude down to no more than two orders of magnitude for any substance. This led to the development of USEtox, a scientific consensus model that contains only the most influential model elements. These were, for example, process formulations accounting for intermittent rain, defining a closed or open system environment or nesting an urban box in a continental box. The precision of the new characterisation factors (CFs) is within a factor of 100–1,000 for human health and 10–100 for freshwater ecotoxicity of all other models compared to 12 orders of magnitude variation between the CFs of each model, respectively. The achieved reduction of inter-model variability by up to 11 orders of magnitude is a significant improvement. USEtox provides a parsimonious and transparent tool for human health and ecosystem CF estimates. Based on a referenced database, it has now been used to calculate CFs for several thousand substances and forms the basis of the recommendations from UNEP-SETAC’s Life Cycle Initiative regarding characterisation of toxic impacts in life cycle assessment. We provide both recommended and interim (not recommended and to be used with caution) characterisation factors for human health and freshwater ecotoxicity impacts. After a process of consensus building among stakeholders on a broad scale as well as several improvements regarding a wider and easier applicability of the model, USEtox will become available to practitioners for the calculation of further CFs.

The minimum information about a genome sequence (MIGS) specification.

Abstract: With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.

Identification of non-precious metal alloy catalysts for selective hydrogenation of acetylene

Abstract: The removal of trace acetylene from ethylene is performed industrially by palladium hydrogenation catalysts (often modified with silver) that avoid the hydrogenation of ethylene to ethane. In an effort to identify catalysts based on less expensive and more available metals, density functional calculations were performed that identified relations in heats of adsorption of hydrocarbon molecules and fragments on metal surfaces. This analysis not only verified the facility of known catalysts but identified nickel-zinc alloys as alternatives. Experimental studies demonstrated that these alloys dispersed on an oxide support were selective for acetylene hydrogenation at low pressures.

Ammonia for hydrogen storage: challenges and opportunities

Abstract: The possibility of using ammonia as a hydrogen carrier is discussed. Compared to other hydrogen storage materials, ammonia has the advantages of a high hydrogen density, a well-developed technology for synthesis and distribution, and easy catalytic decomposition. Compared to hydrocarbons and alcohols, it has the advantage that there is no CO2 emission at the end user. The drawbacks are mainly the toxicity of liquid ammonia and the problems related to trace amounts of ammonia in the hydrogen after decomposition. Storage of ammonia in metal ammine salts is discussed, and it is shown that this maintains the high volumetric hydrogen density while alleviating the problems of handling the ammonia. Some of the remaining challenges for research in ammonia as a hydrogen carrier are outlined.

Why chronic wounds will not heal: a novel hypothesis.

Abstract: The present paper presents a hypothesis aimed at explaining why venous leg ulcers, pressure ulcers, and diabetic foot ulcers develop into a chronic state. We propose that the lack of proper wound healing is at least in part caused by inefficient eradication of infecting, opportunistic pathogens, a situation reminiscent of chronic Pseudomonas aeruginosa infections found in patients suffering from cystic fibrosis (CF). We have analyzed sections from chronic wounds by fluorescence in situ hybridization and found distinct microcolonies--the basal structures of bacterial biofilms. Several researchers have previously reported that another important hallmark of biofilm formation is development of increased tolerance to various antimicrobial measures and treatments. Furthermore, the immune response to infecting bacteria in the cystic fibrosis lung is dominated by polymorphonuclear neutrophils (PMNs), and we have recently shown that in vitro biofilms of P. aeruginosa produce a shielding mechanism that offers protection from the phagocytic activity of PMNs. We hypothesize that the presence of P. aeruginosa in biofilms, and the lack of concomitant elimination by attended PMNs, are the main causes of inefficient eradication by antibiotic treatment and antimicrobial activity of the innate immune system, respectively.

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11

Abstract: NetMHC-30 is trained on a large number of quantitative peptide data using both affinity data from the Immune Epitope Database and Analysis Resource (IEDB) and elution data from SYFPEITHI The method generates high-accuracy predictions of major histocompatibility complex (MHC): peptide binding The predictions are based on artificial neural networks trained on data from 55 MHC alleles (43 Human and 12 non-human), and position-specific scoring matrices (PSSMs) for additional 67 HLA alleles As only the MHC class I prediction server is available, predictions are possible for peptides of length 8-11 for all 122 alleles artificial neural network predictions are given as actual IC(50) values whereas PSSM predictions are given as a log-odds likelihood scores The output is optionally available as download for easy post-processing The training method underlying the server is the best available, and has been used to predict possible MHC-binding peptides in a series of pathogen viral proteomes including SARS, Influenza and HIV, resulting in an average of 75-80% confirmed MHC binders Here, the performance is further validated and benchmarked using a large set of newly published affinity data, non-redundant to the training set The server is free of use and available at: http://wwwcbsdtudk/services/NetMHC

Ecotoxicity of engineered nanoparticles to aquatic invertebrates: a brief review and recommendations for future toxicity testing.

Abstract: Based on a literature review and an overview of toxic effects of engineered nanoparticles in aquatic invertebrates, this paper proposes a number of recommendations for the developing field of nanoecotoxicology by highlighting the importance of invertebrates as sensitive and relevant test organisms. Results show that there is a pronounced lack of data in this field (less than 20 peer-reviewed papers are published so far), and the most frequently tested engineered nanoparticles in invertebrate tests are C(60), carbon nanotubes, and titanium dioxide. In addition, the majority of the studies have used Daphnia magna as the test organism. To date, the limited number of studies has indicated acute toxicity in the low mg l(-1) range and higher of engineered nanoparticles to aquatic invertebrates, although some indications of chronic toxicity and behavioral changes have also been described at concentrations in the high microg l(-1) range. Nanoparticles have also been found to act as contaminant carriers of co-existing contaminants and this interaction has altered the toxicity of specific chemicals towards D. magna. We recommend that invertebrate testing is used to advance the level of knowledge in nanoecotoxicology through standardized short-term (lethality) tests with invertebrates as a basis for investigating behaviour and bioavailability of engineered nanoparticles in the aquatic environment. Based on this literature review, we further recommend that research is directed towards invertebrate tests employing long-term low exposure with chronic endpoints along with more research in bioaccumulation of engineered nanoparticles in aquatic invertebrates.

The nature of the active site in heterogeneous metal catalysis.

Abstract: This tutorial review, of relevance for the surface science and heterogeneous catalysis communities, provides a molecular-level discussion of the nature of the active sites in metal catalysis. Fundamental concepts such as “Bronsted–Evans–Polanyi relations” and “volcano curves” are introduced, and are used to establish a strict partitioning between the so-called “electronic” and “geometrical” effects. This partitioning is subsequently employed as the basis for defining the concept “degree of structure sensitivity” which can be used when analyzing the structure sensitivity of catalytic reactions.

Templating mesoporous zeolites

Abstract: The application of templating methods to produce zeolite materials with hierarchical bi- or trimodal pore size distributions is reviewed with emphasis on mesoporous materials. Hierarchical zeolite materials are categorized into three distinctly different types of materials: hierarchical zeolite crystals, nanosized zeolite crystals, and supported zeolite crystals. For the pure zeolite materials in the first two categories, the additional meso- or macroporosity can be classified as being either intracrystalline or intercrystalline, whereas for supported zeolite materials, the additional porosity originates almost exclusively from the support material. The methods for introducing mesopores into zeolite materials are discussed and categorized. In general, mesopores can be templated in zeolite materials by use of solid templating, supramolecular templating, or indirect templating. In this categorization of templating methods, the nature of the interface between the zeolite crystal and the mesopore exactly when...

A review on the young history of the wind power short-term prediction

Abstract: This paper makes a brief review on 30 years of history of the wind power short-term prediction, since the first ideas and sketches on the theme to the actual state of the art on models and tools, giving emphasis to the most significant proposals and developments. The two principal lines of thought on short-term prediction (mathematical and physical) are indistinctly treated here and comparisons between models and tools are avoided, mainly because, on the one hand, a standard for a measure of performance is still not adopted and, on the other hand, it is very important that the data are exactly the same in order to compare two models (this fact makes it almost impossible to carry out a quantitative comparison between a huge number of models and methods). In place of a quantitative description, a qualitative approach is preferred for this review, remarking the contribution (and innovative aspect) of each model. On the basis of the review, some topics for future research are pointed out.

Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq.

Abstract: Recent advances in high-throughput pyrosequencing (HTPS) technology now allow a thorough analysis of RNA bound to cellular proteins, and, therefore, of post-transcriptional regulons. We used HTPS to discover the Salmonella RNAs that are targeted by the common bacterial Sm-like protein, Hfq. Initial transcriptomic analysis revealed that Hfq controls the expression of almost a fifth of all Salmonella genes, including several horizontally acquired pathogenicity islands (SPI-1, -2, -4, -5), two sigma factor regulons, and the flagellar gene cascade. Subsequent HTPS analysis of 350,000 cDNAs, derived from RNA co-immunoprecipitation (coIP) with epitope-tagged Hfq or control coIP, identified 727 mRNAs that are Hfq-bound in vivo. The cDNA analysis discovered new, small noncoding RNAs (sRNAs) and more than doubled the number of sRNAs known to be expressed in Salmonella to 64; about half of these are associated with Hfq. Our analysis explained aspects of the pleiotropic effects of Hfq loss-of-function. Specifically, we found that the mRNAs of hilD (master regulator of the SPI-1 invasion genes) and flhDC (flagellar master regulator) were bound by Hfq. We predicted that defective SPI-1 secretion and flagellar phenotypes of the hfq mutant would be rescued by overexpression of HilD and FlhDC, and we proved this to be correct. The combination of epitope-tagging and HTPS of immunoprecipitated RNA detected the expression of many intergenic chromosomal regions of Salmonella. Our approach overcomes the limited availability of high-density microarrays that have impeded expression-based sRNA discovery in microorganisms. We present a generic strategy that is ideal for the systems-level analysis of the post-transcriptional regulons of RNA-binding proteins and for sRNA discovery in a wide range of bacteria.

Avoided crossing of rattler modes in thermoelectric materials

Abstract: Engineering of materials with specific physical properties has recently focused on the effect of nano-sized ‘guest domains’ in a ‘host matrix’ that enable tuning of electrical, mechanical, photo-optical or thermal properties. A low thermal conductivity is a prerequisite for obtaining effective thermoelectric materials, and the challenge is to limit the conduction of heat by phonons, without simultaneously reducing the charge transport. This is named the ‘phonon glass–electron crystal’ concept and may be realized in host–guest systems. The guest entities are believed to have independent oscillations, so-called rattlermodes,which scatter the acoustic phonons and reduce the thermal conductivity. We have investigated the phonon dispersion relation in the phonon glass–electron crystal material Ba8Ga16Ge30 using neutron triple-axis spectroscopy. The results disclose unambiguously the theoretically predicted avoided crossing of the rattler modes and the acoustic-phonon branches. The observed phonon lifetimes are longer than expected, and a new explanation for the low L is provided.

Analysis of a power grid using a Kuramoto-like model

Abstract: We show that there is a link between the Kuramoto paradigm and another system of synchronized oscillators, namely an electrical power distribution grid of generators and consumers. The purpose of this work is to show both the formal analogy and some practical consequences. The mapping can be made quantitative, and under some necessary approximations a class of Kuramoto-like models, those with bimodal distribution of the frequencies, is most appropriate for the power-grid. In fact in the power-grid there are two kinds of oscillators: the “sources" delivering power to the “consumers".

Methodologies for social life cycle assessment

Abstract: Goal, Scope and Background. In recent years several different approaches towards Social Life Cycle Assessment (SLCA) have been developed. The purpose of this review is to compare these approaches in order to highlight methodological differences and general shortcomings. SLCA has several similarities with other social assessment tools, although, in order to limit the expanse of the review, only claims to address social impacts from an LCA-like framework are considered. Main Features. The review is to a large extent based on conference proceedings and reports, which are not all easily accessible, since very little has been published on SLCA in the open literature. The review follows the methodological steps of the environmental LCA (ELCA) known from the ISO 14044 standard. Results. The review reveals a broad variety in how the approaches address the steps of the ELCA methodology, particularly in the choice and formulation of indicators. The indicators address a wide variety of issues; some approaches focus on impacts created in the very close proximity of the processes included in the product system, whereas others focus on the more remote societal consequences. Only very little focus has been given to the use stage in the product life cycle. Another very important difference among the proposals is their position towards the use of generic data. Several of the proposals argue that social impacts are connected to the conduct of the company leading to the conclusion that each individual company in the product chain has to be assessed, whereas others claim that generic data can give a sufficiently accurate picture of the associated social impacts. Discussion. The SLCA approaches show that the perception of social impacts is very variable. An assessment focusing on social impacts created in the close proximity of the processes included in the product system will not necessarily point in the same direction as an assessment that focuses on the more societal consequences. This points toward the need to agree on the most relevant impacts to include in the SLCA in order to include the bulk of the situation. Regarding the use of generic data as a basis for the assessment, this obviously has an advantage over using site specific data in relation to practicality, although many authors behind the SLCA ESS-Submission Editor: Dr. David Hunkeler

Phytate: impact on environment and human nutrition. A challenge for molecular breeding

Abstract: Phytic acid (PA) is the primary storage compound of phosphorus in seeds accounting for up to 80% of the total seed phosphorus and contributing as much as 1.5% to the seed dry weight. The negatively charged phosphate in PA strongly binds to metallic cations of Ca, Fe, K, Mg, Mn and Zn making them insoluble and thus unavailable as nutritional factors. Phytate mainly accumulates in protein storage vacuoles as globoids, predominantly located in the aleurone layer (wheat, barley and rice) or in the embryo (maize). During germination, phytate is hydrolysed by endogenous phytase(s) and other phosphatases to release phosphate, inositol and micronutrients to support the emerging seedling. PA and its derivatives are also implicated in RNA export, DNA repair, signalling, endocytosis and cell vesicular trafficking. Our recent studies on purification of phytate globoids, their mineral composition and dephytinization by wheat phytase will be discussed. Biochemical data for purified and characterized phytases isolated from more than 23 plant species are presented, the dephosphorylation pathways of phytic acid by different classes of phytases are compared, and the application of phytase in food and feed is discussed.

Protein abundance profiling of the Escherichia coli cytosol

Abstract: Knowledge about the abundance of molecular components is an important prerequisite for building quantitative predictive models of cellular behavior. Proteins are central components of these models, since they carry out most of the fundamental processes in the cell. Thus far, protein concentrations have been difficult to measure on a large scale, but proteomic technologies have now advanced to a stage where this information becomes readily accessible. Here, we describe an experimental scheme to maximize the coverage of proteins identified by mass spectrometry of a complex biological sample. Using a combination of LC-MS/MS approaches with protein and peptide fractionation steps we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100. A measure of abundance is presented for each of the identified proteins, based on the recently developed emPAI approach which takes into account the number of sequenced peptides per protein. The values of abundance are within a broad range and accurately reflect independently measured copy numbers per cell. As expected, the most abundant proteins were those involved in protein synthesis, most notably ribosomal proteins. Proteins involved in energy metabolism as well as those with binding function were also found in high copy number while proteins annotated with the terms metabolism, transcription, transport, and cellular organization were rare. The barrel-sandwich fold was found to be the structural fold with the highest abundance. Highly abundant proteins are predicted to be less prone to aggregation based on their length, pI values, and occurrence patterns of hydrophobic stretches. We also find that abundant proteins tend to be predominantly essential. Additionally we observe a significant correlation between protein and mRNA abundance in E. coli cells. Abundance measurements for more than 1000 E. coli proteins presented in this work represent the most complete study of protein abundance in a bacterial cell so far. We show significant associations between the abundance of a protein and its properties and functions in the cell. In this way, we provide both data and novel insights into the role of protein concentration in this model organism.

Graphene antidot lattices: designed defects and spin qubits.

Abstract: Antidot lattices, defined on a two-dimensional electron gas at a semiconductor heterostructure, are a well-studied class of man-made structures with intriguing physical properties. We point out that a closely related system, graphene sheets with regularly spaced holes ("antidots"), should display similar phenomenology, but within a much more favorable energy scale, a consequence of the Dirac fermion nature of the states around the Fermi level. Further, by leaving out some of the holes one can create defect states, or pairs of coupled defect states, which can function as hosts for electron spin qubits. We present a detailed study of the energetics of periodic graphene antidot lattices, analyze the level structure of a single defect, calculate the exchange coupling between a pair of spin qubits, and identify possible avenues for further developments.

Distribution, Organization, and Ecology of Bacteria in Chronic Wounds

Abstract: Between 1 and 2% of the population in the developed world experiences a nonhealing or chronic wound characterized by an apparent arrest in a stage dominated by inflammatory processes. Lately, research groups have proposed that bacteria might be involved in and contribute to the lack of healing of these wounds. To investigate this, we collected and examined samples from chronic wounds obtained from 22 different patients, all selected because of suspicion of Pseudomonas aeruginosa colonization. These wound samples were investigated by standard culturing methods and peptide nucleic acid-based fluorescence in situ hybridization (PNA FISH) for direct identification of bacteria. By means of the culturing methods, Staphylococcus aureus was detected in the majority of the wounds, whereas P. aeruginosa was observed less frequently. In contrast, using PNA FISH, we found that a large fraction of the wounds contained P. aeruginosa. Furthermore, PNA FISH revealed the structural organization of bacteria in the samples. It appeared that P. aeruginosa aggregated as microcolonies imbedded in the matrix component alginate, which is a characteristic hallmark of the biofilm mode of growth. The present investigation suggests that bacteria present within these wounds tend to be aggregated in microcolonies imbedded in a self-produced matrix, characteristic of the biofilm mode of growth. Additionally, we must conclude that there exists no good correlation between bacteria detected by standard culturing methods and those detected by direct detection methods such as PNA FISH. This strongly supports the development of new diagnostic and treatment strategies for chronic wounds.

Linear Motif Atlas for Phosphorylation-Dependent Signaling

Abstract: Systematic and quantitative analysis of protein phosphorylation is revealing dynamic regulatory networks underlying cellular responses to environmental cues. However, matching these sites to the kinases that phosphorylate them and the phosphorylation-dependent binding domains that may subsequently bind to them remains a challenge. NetPhorest is an atlas of consensus sequence motifs that covers 179 kinases and 104 phosphorylation-dependent binding domains [Src homology 2 (SH2), phosphotyrosine binding (PTB), BRCA1 C-terminal (BRCT), WW, and 14-3-3]. The atlas reveals new aspects of signaling systems, including the observation that tyrosine kinases mutated in cancer have lower specificity than their non-oncogenic relatives. The resource is maintained by an automated pipeline, which uses phylogenetic trees to structure the currently available in vivo and in vitro data to derive probabilistic sequence models of linear motifs. The atlas is available as a community resource (http://netphorest.info).

Amide Synthesis from Alcohols and Amines by the Extrusion of Dihydrogen

Abstract: An environmentally friendly method for synthesis of amides is presented where a simple ruthenium catalyst mediates the direct coupling between an alcohol and an amine with the liberation of two molecules of dihydrogen. The active catalyst is generated in situ from an easily available ruthenium complex, an N-heterocyclic carbene and a phosphine. The reaction allows primary alcohols to be coupled with primary alkylamines to afford the corresponding secondary amides in good yields. The amide formation presumably proceeds through a catalytic cycle where the intermediate aldehyde and hemiaminal are both coordinated to the metal catalyst.

The prevalence of plant food allergies: a systematic review.

Abstract: Background There is uncertainty regarding the prevalence of allergies to plant food. Objective To assess the prevalence of allergies to plant food according to the different subjective and objective assessment methods. Methods Our systematic search of population-based studies (since 1990) in the literature database MEDLINE focused on fruits, vegetables/legumes, tree nuts, wheat, soy, cereals, and seeds. Prevalence estimates were categorized by food item and method used (food challenges, skin prick test, serum IgE, parent/self-reported symptoms), complemented by appropriate meta-analyses. Results We included 36 studies with data from a total of over 250,000 children and adults. Only 6 studies included food challenge tests with prevalences ranging from 0.1% to 4.3% each for fruits and tree nuts, 0.1% to 1.4% for vegetables, and Conclusion Population-based prevalence estimates for allergies to plant products determined by the diagnostic gold standard are scarce. There was considerable heterogeneity in the prevalence estimates of sensitization or perceived allergic reactions to plant food.

Arabidopsis MAP kinase 4 regulates gene expression through transcription factor release in the nucleus

Abstract: Plant and animal perception of microbes through pathogen surveillance proteins leads to MAP kinase signalling and the expression of defence genes. However, little is known about how plant MAP kinases regulate specific gene expression. We report that, in the absence of pathogens, Arabidopsis MAP kinase 4 (MPK4) exists in nuclear complexes with the WRKY33 transcription factor. This complex depends on the MPK4 substrate MKS1. Challenge with Pseudomonas syringae or flagellin leads to the activation of MPK4 and phosphorylation of MKS1. Subsequently, complexes with MKS1 and WRKY33 are released from MPK4, and WRKY33 targets the promoter of PHYTOALEXIN DEFICIENT3 (PAD3) encoding an enzyme required for the synthesis of antimicrobial camalexin. Hence, wrky33 mutants are impaired in the accumulation of PAD3 mRNA and camalexin production upon infection. That WRKY33 is an effector of MPK4 is further supported by the suppression of PAD3 expression in mpk4–wrky33 double mutant backgrounds. Our data establish direct links between MPK4 and innate immunity and provide an example of how a plant MAP kinase can regulate gene expression by releasing transcription factors in the nucleus upon activation.