A distinctive gene expression fingerprint in mentally retarded male patients reflects disease-causing defects in the histone demethylase KDM5C

Background: Mental retardation is a genetically heterogeneous disorder, as more than 90 genes for this disorder has been found on the X chromosome alone. In addition the majority of patients are non-syndromic in that they do not present with clinically recognisable features. This makes it difficult to determine the molecular cause of this disorder on the basis of the phenotype alone. Mutations in KDM5C (previously named SMCX or JARID1C), a gene that encodes a transcriptional regulator with histone demethylase activity specific for dimethylated and trimethylated H3K4, are a comparatively frequent cause of non-syndromic X-linked mental retardation (NS-XLMR). Specific transcriptional targets of KDM5C, however, are still unknown and the effects of KDM5C deficiency on gene expression have not yet been investigated. Results: By whole-mount in situ hybridisation we showed that the mouse homologue of KDM5C is expressed in multiple tissues during mouse development. We present the results of gene expression profiling performed on lymphoblastoid cell lines as well as blood from patients with mutations in KDM5C. Using whole genome expression arrays and quantitative reverse transcriptase polymerase chain reaction (QRT-PCR) experiments, we identified several genes, including CMKOR1, KDM5B and KIAA0469 that were consistently deregulated in both tissues. Conclusions: Our findings shed light on the pathological mechanisms underlying mental retardation and have implications for future diagnostics of this heterogeneous disorder

Rapid niche expansion by selection on functional genomic variation after ecosystem recovery

It is well recognized that environmental degradation caused by human activities can result in dramatic losses of species and diversity. However, comparatively little is known about the ability of biodiversity to re-emerge following ecosystem recovery. Here, we show that a European whitefish subspecies, the gangfisch Coregonus lavaretus macrophthalmus, rapidly increased its ecologically functional diversity following the restoration of Lake Constance after anthropogenic eutrophication. In fewer than ten generations, gangfisch evolved a greater range of gill raker numbers (GRNs) to utilize a broader ecological niche. A sparse genetic architecture underlies this variation in GRN. Several co-expressed gene modules and genes showing signals of positive selection were associated with GRN and body shape. These were enriched for biological pathways related to trophic niche expansion in fishes. Our findings demonstrate the potential of functional diversity to expand following habitat restoration, given a fortuitous combination of genetic architecture, genetic diversity and selection

Répartition des bactéries dans les sédiments du lac de Constance

La répartition des bactéries dans les sédiments du Lac de Constance a été étudiée à l'aide de la méthode de Koch sur milieu peptoné. Trois sédiments typiques ont été choisis pour les prélèvements : l'un dans la zone littorale (Güttingen), les deux autres dans la zone profonde (Centre et Schussen). Les deux sédiments Centre et Güttingen ne sont pas touchés par une pollution directe, tandis que le troisième sédiment Schüssen se trouve sous l'influence d'une rivière polluée. Le nombre de germes trouvés à la surface sédimentaire est sous l'influence de l'apport nutritionnel, qui atteint les sédiments. Cependant un taux réduit en carbone organique et en bactéries ne doit pas faire penser nécessairement à une diminution de l'apport nutritionnel. La diminution du nombre des bactéries à l'intérieur du sédiment est très accentuée dans les cinq premiers centimètres, puis elle se fait graduellement. Elle est très lente dans les sédiments pollués. La plupart des bactéries hétérotrophes rencontrées sont aérobies-anaérobies facultatives. Le nombre de germes à la surface du sédiment dans le Lac de Constance est environ 8000 fois plus élevé que dans l'eau libre du Lac