CLERK is a novel receptor kinase required for sensing of root-active CLE peptides in <i>Arabidopsis</i>.

CLAVATA3/EMBRYO SURROUNDING REGION (CLE) peptides are secreted endogenous plant ligands that are sensed by receptor kinases (RKs) to convey environmental and developmental inputs. Typically, this involves an RK with narrow ligand specificity that signals together with a more promiscuous co-receptor. For most CLEs, biologically relevant (co-)receptors are unknown. The dimer of the receptor-like protein CLAVATA 2 (CLV2) and the pseudokinase CORYNE (CRN) conditions perception of so-called root-active CLE peptides, the exogenous application of which suppresses root growth by preventing protophloem formation in the meristem. &lt;i&gt;clv2&lt;/i&gt; as well as &lt;i&gt;crn&lt;/i&gt; null mutants are resistant to root-active CLE peptides, possibly because CLV2-CRN promotes expression of their cognate receptors. Here, we have identified the &lt;i&gt;CLE-RESISTANT RECEPTOR KINASE&lt;/i&gt; ( &lt;i&gt;CLERK&lt;/i&gt; ) gene, which is required for full sensing of root-active CLE peptides in early developing protophloem. CLERK protein can be replaced by its close homologs, SENESCENCE-ASSOCIATED RECEPTOR-LIKE KINASE (SARK) and NSP-INTERACTING KINASE 1 (NIK1). Yet neither CLERK nor NIK1 ectodomains interact biochemically with described CLE receptor ectodomains. Consistently, &lt;i&gt;CLERK&lt;/i&gt; also acts genetically independently of &lt;i&gt;CLV2-CRN&lt;/i&gt; We, thus, have discovered a novel hub for redundant CLE sensing in the root

Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays

A new approach to detect deletions in divergentgenomes combines short read sequencing and tilling array data. Its utility is demonstrated on Arabidopsis strains

How to create coats for all seasons: elucidating antigenic variation in African trypanosomes

Extracellular parasites of the mammalian bloodstream face considerable challenges including incessant assault by the immune system. African trypanosomes are consummate survivors in this inclement environment and are renowned for their supremely sophisticated strategy of antigenic variation of their protective surface coat during the course of chronic infections. Recent developments are making us realize how complex this antigenic machinery is and are allowing us to tackle previously intractable problems. However, many of the simplest (and arguably the most important) questions still remain unanswered

Bidirectional silencing of RNA polymerase I transcription by a strand switch region in Trypanosoma brucei

The procyclin genes in Trypanosoma brucei are transcribed by RNA polymerase I as part of 5–10 kb long polycistronic transcription units on chromosomes VI and X. Each procyclin locus begins with two procyclin genes followed by at least one procyclin-associated gene (PAG). In procyclic (insect midgut) form trypanosomes, PAG mRNA levels are about 100-fold lower than those of procyclins. We show that deletion of PAG1, PAG2 or PAG3 results in increased mRNA levels from downstream genes in the same transcription unit. Nascent RNA analysis revealed that most of the effects are due to increased transcription elongation in the knockouts. Furthermore, transient and stable transfections showed that sequence elements on both strands of PAG1 can inhibit Pol I transcription. Finally, by database mining we identified 30 additional PAG-related sequences that are located almost exclusively at strand switch regions and/or at sites where a change of RNA polymerase type is likely to occur

The role of genomic location and flanking 3'UTR in the generation of functional levels of variant surface glycoprotein in Trypanosoma brucei

Trypanosoma brucei faces relentless immune attack in the mammalian bloodstream, where it is protected by an essential coat of Variant Surface Glycoprotein (VSG) comprising ∼10% total protein. The active VSG gene is in a Pol I-transcribed telomeric expression site (ES). We investigated factors mediating these extremely high levels of VSG expression by inserting ectopic VSG117 into VSG221 expressing T. brucei. Mutational analysis of the ectopic VSG 3′UTR demonstrated the essentiality of a conserved 16-mer for mRNA stability. Expressing ectopic VSG117 from different genomic locations showed that functional VSG levels could be produced from a gene 60 kb upstream of its normal telomeric location. High, but very heterogeneous levels of VSG117 were obtained from the Pol I-transcribed rDNA. Blocking VSG synthesis normally triggers a precise precytokinesis cell-cycle checkpoint. VSG117 expression from the rDNA was not adequate for functional complementation, and the stalled cells arrested prior to cytokinesis. However, VSG levels were not consistently low enough to trigger a characteristic ‘VSG synthesis block’ cell-cycle checkpoint, as some cells reinitiated S phase. This demonstrates the essentiality of a Pol I-transcribed ES, as well as conserved VSG 3′UTR 16-mer sequences for the generation of functional levels of VSG expression in bloodstream form T. brucei

Régulation du site d'expression du VSG chez Trypanosoma brucei

Doctorat en Sciencesinfo:eu-repo/semantics/nonPublishe

Operation properties: a representation and their role in the propagation of meta-data

To facilitate the sharing and re-use of data in scientific studies we propose an automated technique for annotating operation results. The annotated output has to preserve, as much as possible, the properties of the input annotations. The preservation of properties is achieved by taking into account operation properties. Property preservation is evaluated with information theory metrics

The identification problem: a description

Scientific data are often annotated based on their properties, which are not maintained during further data processing. Not maintaining annotations results in loss of information. Decisions made on such incomplete information may be wrong. In this paper the problem of propagating annotations along a data processing chain is formulated. In particular, an annotation of a data element is an identification that this data element exhibits a specific property. The propagation of this property from the input of an operation to its output is called the identification problem. In this paper the identification problem is described as a clustering problem