Insight on the heterocyte patterning and the proheterocyte division in the toxic cyanobacterium Kaarinaea lacus gen. nov., sp. nov., and its genomic potential for natural products.

Nostoc sp. 152 (= PCC 9237), a toxic cyanobacterium, isolated from mixed cyanobacterial bloom in a Finnish freshwater lake was reassessed using phylogenetic, morphological and genomic analyses. Multilocus and 16S rRNA gene phylogenetic analyses confirmed that this strain represents a novel Nostocalean genus for which we propose the name Kaarinaea lacus gen.

Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis.

Numerous statistical pipelines are now available for the differential analysis of gene expression measured with RNA-sequencing technology. Most of them are based on similar statistical frameworks after normalization, differing primarily in the choice of data distribution, mean and variance estimation strategy and data filtering. We propose an evaluation of the impact of these choices when few biological replicates are available through the use of synthetic data sets.

A TILLING Platform for Functional Genomics in Brachypodium distachyon.

The new model plant for temperate grasses, Brachypodium distachyon offers great potential as a tool for functional genomics. We have established a sodium azide-induced mutant collection and a TILLING platform, called "BRACHYTIL", for the inbred line Bd21-3. The TILLING collection consists of DNA isolated from 5530 different families.

Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants.

Nitrate is both an important nutrient and a signalling molecule for plants. Although several components of the nitrate signalling pathway have been identified, their hierarchical organization remains unclear. Here we show that the localization of NLP7, a member of the RWP-RK transcription factor family, is regulated by nitrate via a nuclear retention mechanism.

Disruption of Bcchs4, Bcchs6 or Bcchs7 chitin synthase genes in Botrytis cinerea and the essential role of class VI chitin synthase (Bcchs6).

Chitin synthases play critical roles in hyphal development and fungal pathogenicity. Previous studies on Botrytis cinerea, a model organism for necrotrophic pathogens, have shown that disruption of Bcchs1 and more particularly Bcchs3a genes have a drastic impact on virulence (Soulié et al., 2003, 2006).

Histone H2B monoubiquitination facilitates the rapid modulation of gene expression during Arabidopsis photomorphogenesis.

Profiling of DNA and histone modifications has recently allowed the establishment of reference epigenomes from several model organisms. This identified a major chromatin state for active genes that contains monoubiquitinated H2B (H2Bub), a mark linked to transcription elongation. However, assessment of dynamic chromatin changes during the reprogramming of gene expression in response to extrinsic or developmental signals has been more difficult.

Transcriptome analysis of ein3 eil1 mutants in response to iron deficiency.

Multiple transcriptome and proteome studies indicated that the micronutrient deficiency stress caused by lack of iron results in increased molecular responses for the mobilization and uptake of iron and also in altered metabolic adaptation and stress responses. Recently, we identified the ethylene-regulated transcription factors ETHYLENE INSENSITIVE3 (EIN3) and EIN3-LIKE1 (EIL1) as protein interaction partners of the Fe deficiency response regulator and transcription factor FER-LIKE FE DEFINCY-INDUCED TRANSCRPTION FACTOR1 (FIT). EIN3/EIL1 contribute to high level gene expression of FIT downstream genes and also promote FIT protein abundance.

Interaction between the bHLH transcription factor FIT and ETHYLENE INSENSITIVE3/ETHYLENE INSENSITIVE3-LIKE1 reveals molecular linkage between the regulation of iron acquisition and ethylene signaling in Arabidopsis.

Understanding the regulation of key genes involved in plant iron acquisition is of crucial importance for breeding of micronutrient-enriched crops. The basic helix-loop-helix protein FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT), a central regulator of Fe acquisition in roots, is regulated by environmental cues and internal requirements for iron at the transcriptional and posttranscriptional levels. The plant stress hormone ethylene promotes iron acquisition, but the molecular basis for this remained unknown.

Disruption of LACCASE4 and 17 results in tissue-specific alterations to lignification of Arabidopsis thaliana stems.

Peroxidases have been shown to be involved in the polymerization of lignin precursors, but it remains unclear whether laccases (EC 1.10.3.