The kinome of Phytophthora infestans reveals oomycete-specific innovations and links to other taxonomic groups

<p>Abstract</p> <p>Background</p> <p>Oomycetes are a large group of economically and ecologically important species. Its most notorious member is <it>Phytophthora infestans</it>, the cause of the devastating potato late blight disease. The life cycle of <it>P. infestans </it>involves hyphae which differentiate into spores used for dispersal and host infection. Protein phosphorylation likely plays crucial roles in these stages, and to help understand this we present here a genome-wide analysis of the protein kinases of <it>P. infestans </it>and several relatives. The study also provides new insight into kinase evolution since oomycetes are taxonomically distant from organisms with well-characterized kinomes.</p> <p>Results</p> <p>Bioinformatic searches of the genomes of <it>P. infestans</it>, <it>P. ramorum</it>, and <it>P. sojae </it>reveal they have similar kinomes, which for <it>P. infestans </it>contains 354 eukaryotic protein kinases (ePKs) and 18 atypical kinases (aPKs), equaling 2% of total genes. After refining gene models, most were classifiable into families seen in other eukaryotes. Some ePK families are nevertheless unusual, especially the tyrosine kinase-like (TKL) group which includes large oomycete-specific subfamilies. Also identified were two tyrosine kinases, which are rare in non-metazoans. Several ePKs bear accessory domains not identified previously on kinases, such as cyclin-dependent kinases with integral cyclin domains. Most ePKs lack accessory domains, implying that many are regulated transcriptionally. This was confirmed by mRNA expression-profiling studies that showed that two-thirds vary significantly between hyphae, sporangia, and zoospores. Comparisons to neighboring taxa (apicomplexans, ciliates, diatoms) revealed both clade-specific and conserved features, and multiple connections to plant kinases were observed. The kinome of <it>Hyaloperonospora arabidopsidis</it>, an oomycete with a simpler life cycle than <it>P. infestans</it>, was found to be one-third smaller. Some differences may be attributable to gene clustering, which facilitates subfamily expansion (or loss) through unequal crossing-over.</p> <p>Conclusion</p> <p>The large sizes of the <it>Phytophthora </it>kinomes imply that phosphorylation plays major roles in their life cycles. Their kinomes also include many novel ePKs, some specific to oomycetes or shared with neighboring groups. Little experimentation to date has addressed the biological functions of oomycete kinases, but this should be stimulated by the structural, evolutionary, and expression data presented here. This may lead to targets for disease control.</p

Use of beneficial bacteria and their secondary metabolites to control grapevine pathogen diseases

Grapevine is one of the most important economic crops yielding berries, wine products as well as derivates. However, due to the large array of pathogens inducing diseases on this plant, considerable amounts of pesticides—with possible negative impact on the environment and health—have been used and are currently used in viticulture. To avoid negative impacts of such products and to ensure product quality, a substantial fraction of pesticides needs to be replaced in the near future. One solution can be related to the use of beneficial bacteria inhabiting the rhizo- and/or the endosphere of plants. These biocontrol bacteria and their secondary metabolites can reduce directly or indirectly pathogen diseases by affecting pathogen performance by antibiosis, competition for niches and nutrients, interference with pathogen signaling or by stimulation of host plant defenses. Due to the large demand for biocontrol of grapevine diseases, such biopesticides, their modes of actions and putative consequences of their uses need to be described. Moreover, the current knowledge on new strains from the rhizo- and endosphere and their metabolites that can be used on grapevine plants to counteract pathogen attack needs to be discussed. This is in particular with regard to the control of root rot, grey mould, trunk diseases, powdery and downy mildews, pierce’s disease, grapevine yellows as well as crown gall. Future prospects on specific beneficial microbes and their secondary metabolites that can be used as elicitors of plant defenses and/or as biocontrol agents with potential use in a more sustainable viticulture will be further discussed

Models and data analysis tools for the Solar Orbiter mission

Context. The Solar Orbiter spacecraft will be equipped with a wide range of remote-sensing (RS) and in situ (IS) instruments to record novel and unprecedented measurements of the solar atmosphere and the inner heliosphere. To take full advantage of these new datasets, tools and techniques must be developed to ease multi-instrument and multi-spacecraft studies. In particular the currently inaccessible low solar corona below two solar radii can only be observed remotely. Furthermore techniques must be used to retrieve coronal plasma properties in time and in three dimensional (3D) space. Solar Orbiter will run complex observation campaigns that provide interesting opportunities to maximise the likelihood of linking IS data to their source region near the Sun. Several RS instruments can be directed to specific targets situated on the solar disk just days before data acquisition. To compare IS and RS, data we must improve our understanding of how heliospheric probes magnetically connect to the solar disk.Aims. The aim of the present paper is to briefly review how the current modelling of the Sun and its atmosphere can support Solar Orbiter science. We describe the results of a community-led effort by European Space Agency's Modelling and Data Analysis Working Group (MADAWG) to develop different models, tools, and techniques deemed necessary to test different theories for the physical processes that may occur in the solar plasma. The focus here is on the large scales and little is described with regards to kinetic processes. To exploit future IS and RS data fully, many techniques have been adapted to model the evolving 3D solar magneto-plasma from the solar interior to the solar wind. A particular focus in the paper is placed on techniques that can estimate how Solar Orbiter will connect magnetically through the complex coronal magnetic fields to various photospheric and coronal features in support of spacecraft operations and future scientific studies.Methods. Recent missions such as STEREO, provided great opportunities for RS, IS, and multi-spacecraft studies. We summarise the achievements and highlight the challenges faced during these investigations, many of which motivated the Solar Orbiter mission. We present the new tools and techniques developed by the MADAWG to support the science operations and the analysis of the data from the many instruments on Solar Orbiter.Results. This article reviews current modelling and tool developments that ease the comparison of model results with RS and IS data made available by current and upcoming missions. It also describes the modelling strategy to support the science operations and subsequent exploitation of Solar Orbiter data in order to maximise the scientific output of the mission.Conclusions. The on-going community effort presented in this paper has provided new models and tools necessary to support mission operations as well as the science exploitation of the Solar Orbiter data. The tools and techniques will no doubt evolve significantly as we refine our procedure and methodology during the first year of operations of this highly promising mission.Peer reviewe

Constitutive monocyte-restricted activity of NF-M, a nuclear factor that binds to a C/EBP motif

In a search for monocyte-specific nuclear factors, we analyzed in human cells the promoter of the chicken myelomonocytic growth factor, a gene that, in the chicken, is expressed in myeloid and myelomonocytic cells. Reporter gene constructs were active in monocytic Mono Mac 6 cells and in monoblastic THP-1 cells but not in the hematopoietic stem cell line K562. When a region with homology to the sequence recognized by CAAT enhancer-binding proteins (C/EBP) was inactivated by site-directed mutagenesis, the reporter activity was reduced by a factor of 10. Multimers of this region, termed F, in front of a heterologous promoter were active in Mono Mac 6 and THP-1 cells but not in K562 cells, WIL2 B cells, BT20 mammary carcinoma cells, MelJuso melanoma cells, or SK-Hep-1 hepatoma cells. Gel shift analysis with the F oligonucleotide identified DNA-binding activity in monocytic Mono Mac 6, monoblastic THP-1, and myelomonocytic HL60 cells. No binding was detected in myelomonocytic RC2A cells, in myeloid KG-1 cells, or in the hematopoietic stem cell line K562. Furthermore, a panel of solid tumor cell lines, representing various tissues, were also negative. Stimulation by PMA could not induce this binding factor in any of the negative cell lines. Analysis of primary cells (granulocytes, T cells, monocytes, and alveolar macrophages) revealed binding activity only in monocytes and macrophages. This DNA-binding factor, termed NF-M, was found to consist of two molecules, of 50 and 72 kDa, as determined by affinity cross-linking. Binding of NF-M was competed by the region F oligonucleotide and by the C/EBP motif from the albumin enhancer but not by an AP-2 motif. These data suggest that NF-M is a member of the C/EBP family of nuclear factors. The monocyte-restricted activity of NF-M suggests that this nuclear factor may be involved in regulation of monocyte-specific genes

The PROMISE/Sylt-Roemoe data set - a comprehensive bench-mark data set to test and evaluate numerical models for suspended sediment transport in shallow tidal lagoons. Der PROMISE/Sylt-Roemoe Datensatz - ein umfassender 'bench-mark'-Datensatz zum Pruefen und Bewerten numerischer Schwebstofftransportmodelle in tidebeeinflussten Flachwasserbuchten

In the framework of the MAST III project PROMISE (Pre-Operational Modelling in the Seas of Europe) a data set was assembled which will serve as a comprehensive bench-mark data set for testing and evaluating coupled numerical models to simulate suspended sediment (SPM) transport in shallow tidal lagoons. The data were sampled in the Sylt-Roemoe bight, a semi-enclosed lagoon in the North-Frisian Wadden Sea at the border between Germany and Denmark. The total sampling periods were from April 1996 to October 1996 and during April 1997. Out of these, four periods (three in 1996 and one in 1997) of three weeks lengths were selected and further processed for the PROMISE project. They include significant wind events with wind speeds above 15 m/s. The observational data encompass SPM measurements and all hydrographical and meteorological parameters significant for the SPM transport. Used devices were moored piles with probe packages, moored Acoustical Doppler Current Profilers (ADCP), a wave rider buoy and a vertical multiprobe profiler plus an ADCP from a cruising vessel. In addition, boundary data from other observations and model calculations were added. (orig.)Available from TIB Hannover: RA 3251(99/E/53) / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekSIGLEDEGerman

T cell costimulus-independent and very efficacious inhibition of tumor growth in mice bearing subcutaneous or leukemic human B cell lymphoma xenografts by a CD19-/CD3-bispecific single-chain antibody construct1

We have recently demonstrated that a recombinant single-chain bispecific Ab construct, bscCD19xCD3, in vitro induces rapid B lymphoma-directed cytotoxicity at picomolar concentrations with unstimulated peripheral T cells. In this study, we show that treatment of nonobese diabetic SCID mice with submicrogram doses of bscCD19xCD3 could prevent growth of s.c. human B lymphoma xenografts and essentially cured animals when given at an early tumor stage. The effect was dose dependent, dependent on E:T ratio and the time between tumor inoculation and administration of bscCD19xCD3. No therapeutic effect was seen in the presence of human lymphocytes alone, a vehicle control, or with a bispecific single-chain construct of identical T cell-binding activity but different target specificity. In a leukemic nonobese diabetic SCID mouse model, treatment with bscCD19xCD3 prolonged survival of mice in a dose-dependent fashion. The human lymphocytes used as effector cells in both animal models did not express detectable T cell activation markers at the time of coinoculation with tumor cells. The bispecific Ab therefore showed an in vivo activity comparable to that observed in cell culture with respect to high potency and T cell costimulus independence. These properties make bscCD19xCD3 superior to previously investigated CD19 bispecific Ab-based therapies

Preparation of silica aerogel for Cerenkov counters

SIGLEDEGerman