Functional study of the Hap4-like genes suggests that the key regulators of carbon metabolism HAP4 and oxidative stress response YAP1 in yeast diverged from a common ancestor.

The transcriptional regulator HAP4, induced by respiratory substrates, is involved in the balance between fermentation and respiration in S. cerevisiae. We identified putative orthologues of the Hap4 protein in all ascomycetes, based only on a conserved sixteen amino acid-long motif.

A head and neck cancer tumor response-specific gene signature for cisplatin, 5-fluorouracil induction chemotherapy fails with added taxanes.

Background: It is a major clinical challenge to predict which patients, with advanced stage head and neck squamous cell carcinoma, will not exhibit a reduction in tumor size following induction chemotherapy in order to avoid toxic effects of ineffective chemotherapy and delays for instituting other therapeutic options. Further, it is of interest to know to what extent a gene signature, which identifies patients with tumors that will not respond to a particular induction chemotherapy, is applicable when additional chemotherapeutic agents are added to the regimen.

Methodology/principal Findings: To identify genes that predict tumor resistance to induction with cisplatin/5-fluorouracil (PF) or PF and a taxane, we analyzed patient tumor biopsies with whole genome microarrays and quantitative reverse transcriptase-PCR (TLDA) cards.

Ventral hippocampal molecular pathways and impaired neurogenesis associated with 5-HT₁A and 5-HT₁B receptors disruption in mice.

The serotonergic system has been widely implicated in stress related psychiatric disorders such as depression and anxiety. Generation of receptor knockout mice has offered a new approach to study processes underlying anxiety. For instance, knockout mice for both 5-HT(1A) and 5-HT(1B) receptors (5-HT(1A/1B)(-/-)) display an anxious phenotype, associated with robust physiological and neurochemical changes related to brain serotonin function.

Comparative transcriptomic analysis of salt adaptation in roots of contrasting Medicago truncatula genotypes.

Evolutionary diversity can be driven by the interaction of plants with different environments. Molecular bases involved in ecological adaptations to abiotic constraints can be explored using genomic tools. Legumes are major crops worldwide and soil salinity is a main stress affecting yield in these plants.

Genome-wide gene expression profiling of fertilization competent mycelium in opposite mating types in the heterothallic fungus Podospora anserina.

Background: Mating-type loci in yeasts and ascomycotan filamentous fungi (Pezizomycotina) encode master transcriptional factors that play a critical role in sexual development. Genome-wide analyses of mating-type-specification circuits and mating-type target genes are available in Saccharomyces cerevisiae and Schizosaccharomyces pombe; however, no such analyses have been performed in heterothallic (self-incompatible) Pezizomycotina. The heterothallic fungus Podospora anserina serves as a model for understanding the basic features of mating-type control.

Functional study of genes essential for autogamy and nuclear reorganization in Paramecium.

Like all ciliates, Paramecium tetraurelia is a unicellular eukaryote that harbors two kinds of nuclei within its cytoplasm. At each sexual cycle, a new somatic macronucleus (MAC) develops from the germ line micronucleus (MIC) through a sequence of complex events, which includes meiosis, karyogamy, and assembly of the MAC genome from MIC sequences. The latter process involves developmentally programmed genome rearrangements controlled by noncoding RNAs and a specialized RNA interference machinery.

A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina.

Background: The development of new microarray technologies makes custom long oligonucleotide arrays affordable for many experimental applications, notably gene expression analyses. Reliable results depend on probe design quality and selection. Probe design strategy should cope with the limited accuracy of de novo gene prediction programs, and annotation up-dating.

Variation in gene expression profiles of human monocytic U937 cells exposed to various fluxes of nitric oxide.

We examined early and late alterations in gene expression patterns and phosphorylation levels of key regulators of selected signaling pathways in U937 cells exposed to various (*)NO fluxes. cDNA microarray analysis and real-time quantitative PCR identified 45 NO-sensitive genes (>or=2-fold change), among which KLF2, KLF6, TSC22D3, DDIT4, MKP-5 (up-regulated), KIF23, histone H4, ARL6IP2, CLNS1A, SLC7A6, CDKN3, SRP19, and BCL11A (down-regulated) have not been reported before. For two selected genes, KLF2 and DDIT4, the sensitivity to (.

Genomic consequences of cytochrome P450 2C9 overexpression in human hepatoma cells.

Cytochrome P450 2C9 (P450 2C9) is one of the most important P450 isoforms in the human liver, as it metabolizes numerous exogenous and endogenous substrates. Moreover, it is inducible by several compounds, such as rifampicin, phenobarbital, and NSAIDs (nonsteroidal anti-inflammatories). The aim of this study was to investigate the global cellular consequences of P450 2C9 overexpression at the transcriptional level using an untargeted approach: pangenomic microarrays.

Characterisation and correction of signal fluctuations in successive acquisitions of microarray images.

Background: There are many sources of variation in dual labelled microarray experiments, including data acquisition and image processing. The final interpretation of experiments strongly relies on the accuracy of the measurement of the signal intensity. For low intensity spots in particular, accurately estimating gene expression variations remains a challenge as signal measurement is, in this case, highly subject to fluctuations.

PPIDD: an extraction and visualisation method of biological protein-protein interfaces.

Today, the information for generating reliable protein-protein complex datasets is not directly accessible from PDB structures. Moreover, in X-ray protein structures, different types of contacts can be observed between proteins: contacts in homodimers or inside heterocomplexes considered to be specific, and contacts induced by crystallogenesis processes, considered to be non-specific. However, none of the databases giving access to protein-protein complexes allows the crystallographic interfaces to be distinguished from the biological interfaces.

Expression ratio evaluation in two-colour microarray experiments is significantly improved by correcting image misalignment.

Motivation: Two-colour microarrays are widely used to perform transcriptome analysis. In most cases, it appears that the 'red' and 'green' images resulting from the scan of a microarray slide are slightly shifted one with respect to the other. To increase the robustness of the measurement of the fluorescent emission intensities, multiple acquisitions with the same or different PMT gains can be used.

MAnGO: an interactive R-based tool for two-colour microarray analysis.

Unlabelled: MAnGO (Microarray Analysis at the Gif/Orsay platform) is an interactive R-based tool for the analysis of two-colour microarray experiments. It is a compilation of various methods, which allows the user (1) to control data quality by detecting biases with a large number of visual representations, (2) to pre-process data (filtering and normalization) and (3) to carry out differential analyses. MAnGO is not only a 'turn-key' tool, oriented towards biologists but also a flexible and adaptable R script oriented towards bioinformaticians.

Genomewide and biochemical analyses of DNA-binding activity of Cdc6/Orc1 and Mcm proteins in Pyrococcus sp.

The origin of DNA replication (oriC) of the hyperthermophilic archaeon Pyrococcus abyssi contains multiple ORB and mini-ORB repeats that show sequence similarities to other archaeal ORB (origin recognition box). We report here that the binding of Cdc6/Orc1 to a 5 kb region containing oriC in vivo was highly specific both in exponential and stationary phases, by means of chromatin immunoprecipitation coupled with hybridization on a whole genome microarray (ChIP-chip). The oriC region is practically the sole binding site for the Cdc6/Orc1, thereby distinguishing oriC in the 1.

Birth and growth kinetics of brome mosaic virus microcrystals.

The early steps of crystal nucleation and growth in Brome Mosaïc virus and polyethylene glycol mixtures were analyzed using time-resolved x-ray scattering (at the European Synchrotron Radiation Facility, Grenoble, France). The system was chosen as a crystallization model since the phase diagram of the macromolecule/polymer mixture was known to present, at high polymer concentration, a solid, precipitated phase made of the synchronized formation of a large number of microcrystals. The precipitation and crystallization of the samples was induced by the controlled mixing of virus and polymer using a stopped-flow device.

Use of cryo-negative staining in tomographic reconstruction of biological objects: application to T4 bacteriophage.

Recent advances in electron microscopy and image analysis techniques have resulted in the development of tomography, which makes possible the study of structures neither accessible to X-ray crystallography nor nuclear magnetic resonance. However, the use of tomography to study biological structures, ranging from 100 to 500 nm, requires developments in sample preparation and image analysis. Indeed, cryo-electron tomography present two major drawbacks: the low contrast of recorded images and the sample radiation damage.

Structural analysis and evidence for dynamic emergence of Bacillus anthracis S-layer networks.

Surface layers (S-layers), which form the outermost layers of many Bacteria and Archaea, consist of protein molecules arranged in two-dimensional crystalline arrays. Bacillus anthracis, a gram-positive, spore-forming bacterium, responsible for anthrax, synthesizes two abundant surface proteins: Sap and EA1. Regulatory studies showed that EA1 and Sap appear sequentially at the surface of the parental strain.