Motivation: A number of available program packages determine the significant enrichments and/or depletions of GO categories among a class of genes of interest. Whereas a correct formulation of the problem leads to a single exact null distribution, these GO tools use a large variety of statistical tests whose denominations often do not clarify the underlying P-value computations. Summary: We review the different formulations of the problem and the tests they lead to: the binomial, χ², equality of two probabilities, Fisher's exact and hypergeometric tests. We clarify the relationships existing between these tests, in particular the equivalence between the hypergeometric test and Fisher's exact test. We recall that the other tests are valid only for large samples, the test of equality of two probabilities and the χ²-test being equivalent. We discuss the appropriateness of one- and two-sided P-values, as well as some discreteness and conservatism issues. Contact:isabelle.rivals@espci.fr Supplementary information: Supplementary data are available at Bioinformatics online.

The electrochemical reduction of hematite with various particle sizes by metallic lithium has been studied by means of X-ray diffraction (XRD) Mössbauer and extended X-ray absorption fine structure (EXAFS) spectroscopy. Previous in situ XRD analysis coupled with electrochemical data showed that lithium can be inserted in the nanosized sample up to 1 Li per Fe2O3 whereas bulk material undergoes an irreversible Li-driven transformation from an hexagonal anionic packing to a close cubic packed framework as soon as 0.03 Li is inserted in the corundum structure. The present data show that only 0.6 Li per formula unit are actually inserted in the structure of small particles. The remaining lithium (0.4) is engaged in irreversible reduction of surface groups, or capacitive behavior. Beyond the solid solution domains, both samples are multiphase, and consist of Li2Fe2O3, Fe0 clusters (10-15 Å) and inserted α-Fe2O3, which proportions are used to calculate the mean iron oxidation state in the electrode as the reaction proceeds. From these data, we found that electrolyte decomposition can occur at very different steps of the reduction depending on the texture of the active materials. In addition, during the reduction process, we evidenced a reaction of disproportionation (3Fe2+ → 2Fe3 + Fe0), an intense electrochemical grinding of the hematite particles and the formation of extremely fine metallic surface clusters. For the first time, the EXAFS/X-ray absorption near-edge structure signature of the divalent intermediate Li2Fe2O3 phase is obtained

Individuals with partial HSA21 trisomies and mice with partial MMU16 trisomies containing an extra copy of the DYRK1A gene present various alterations in brain morphogenesis. They present also learning impairments modeling those encountered in Down syndrome. Previous MRI and histological analyses of a transgenic mice generated using a human YAC construct that contains five genes including DYRK1A reveal that DYRK1A is involved, during development, in the control of brain volume and cell density of specific brain regions. Gene dosage correction induces a rescue of the brain volume alterations. DYRK1A is also involved in the control of synaptic plasticity and memory consolidation. Increased gene dosage results in brain morphogenesis defects, low BDNF levels and mnemonic deficits in these mice. Epigallocatechin gallate (EGCG) — a member of a natural polyphenols family, found in great amount in green tea leaves — is a specific and safe DYRK1A inhibitor. We maintained control and transgenic mice overexpressing DYRK1A on two different polyphenol-based diets, from gestation to adulthood. The major features of the transgenic phenotype were rescued in these mice.

Enlarged early endosomes have been observed in neurons and fibroblasts in Down syndrome (DS). These endosome abnormalities have been implicated in the early development of Alzheimer's disease (AD) pathology in these subjects. Here, we show the presence of enlarged endosomes in blood mononuclear cells and lymphoblastoid cell lines (LCLs) from individuals with DS using immunofluorescence and confocal microscopy. Genotype–phenotype correlations in LCLs carrying partial trisomies 21 revealed that triplication of a 2.56 Mb locus in 21q22.11 is associated with the endosomal abnormalities. This locus contains the gene encoding the phosphoinositide phosphatase synaptojanin 1 (SYNJ1), a key regulator of the signalling phospholipid phosphatidylinositol-4,5-biphosphate that has been shown to regulate clathrin-mediated endocytosis. We found that SYNJ1 transcripts are increased in LCLs from individuals with DS and that overexpression of SYNJ1 in a neuroblastoma cell line as well as in transgenic mice leads to enlarged endosomes. Moreover, the proportion of enlarged endosomes in fibroblasts from an individual with DS was reduced after silencing SYNJ1 expression with RNA interference. In LCLs carrying amyloid precursor protein (APP) microduplications causing autosomal dominant early-onset AD, enlarged endosomes were absent, suggesting that APP overexpression alone is not involved in the modification of early endosomes in this cell type. These findings provide new insights into the contribution of SYNJ1 overexpression to the endosomal changes observed in DS and suggest an attractive new target for rescuing endocytic dysfunction and lipid metabolism in DS and in AD.