Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment

Brown algae belong to a phylogenetic lineage distantly related to land plants and animals. They are almost exclusively found in the intertidal zone, a harsh and frequently changing environment where organisms are submitted to marine and terrestrial constraints. In relation with their unique evolutionary history and their habitat, they feature several peculiarities, including at the level of their primary and secondary metabolism. The establishment of Ectocarpus siliculosus as a model organism for brown algae has represented a framework in which several omics techniques have been developed, in particular, to study the response of these organisms to abiotic stresses. With the recent publication of medium to high throughput profiling data, it is now possible to envision integrating observations at the cellular scale to apply systems biology approaches. As a first step, we propose a protocol focusing on integrating heterogeneous knowledge gained on brown algal metabolism. The resulting abstraction of the system will then help understanding how brown algae cope with changes in abiotic parameters within their unique habitat, and to decipher some of the mechanisms underlying their (1) acclimation and (2) adaptation, respectively consequences of (1) the behavior or (2) the topology of the system resulting from the integrative approach.     

Combining P values to improve classification of differential gene expression in the HTself software

HTself is a web-based bioinformatics tool designed to deal with the classification of differential gene expression in low replication microarray studies. It is based on a statistical test that uses self-self experiments to derive intensity-dependent cutoffs. We developed an extension of HTself, originally released in 2005, by calculating P values instead of using a fixed acceptance level α. As before, the statistic used to compute single-spot P values is obtained from the Gaussian kernel density estimator method applied to self-self data. Different spots corresponding to the same biological gene (replicas) give rise to a set of independent P values that can be combined by well-known statistical methods. The combined P value can be used to decide whether a gene can be considered differentially expressed or not. HTself2 is a new version of HTself that uses P values combination. It is implemented as a user-friendly desktop application to help laboratories without a bioinformatics infrastructure.     

Genomes of extremophile crucifers: new platforms for comparative genomics and beyond

ABSTRACT: Recent reports describe the genome sequencing of Thellungiella salsuginea and Thellungiella parvula, two extremophile crucifers closely related to the stress-sensitive model plant Arabidopsis thaliana.     

Down-regulation of GABA(A) receptor via promiscuity with the vasoactive peptide urotensin II receptor. Potential involvement in astrocyte plasticity

GABA(A) receptor (GABA(A)R) expression level is inversely correlated with the proliferation rate of astrocytes after stroke or during malignancy of astrocytoma, leading to the hypothesis that GABA(A)R expression/activation may work as a cell proliferation repressor. A number of vasoactive peptides exhibit the potential to modulate astrocyte proliferation, and the question whether these mechanisms may imply alteration in GABA(A)R-mediated functions and/or plasma membrane densities is open. The peptide urotensin II (UII) activates a G protein-coupled receptor named UT, and mediates potent vasoconstriction or vasodilation in mammalian vasculature. We have previously demonstrated that UII activates a PLC/PIPs/Ca(2+) transduction pathway, via both G(q) and G(i/o) proteins and stimulates astrocyte proliferation in culture. It was also shown that UT/G(q)/IP(3) coupling is regulated by the GABA(A)R in rat cultured astrocytes. Here we report that UT and GABA(A)R are co-expressed in cerebellar glial cells from rat brain slices, in human native astrocytes and in glioma cell line, and that UII inhibited the GABAergic activity in rat cultured astrocytes. In CHO cell line co-expressing human UT and combinations of GABA(A)R subunits, UII markedly depressed the GABA current (β(3)γ(2)>α(2)β(3)γ(2)>α(2)β(1)γ(2)). This effect, characterized by a fast short-term inhibition followed by drastic and irreversible run-down, is not relayed by G proteins. The run-down partially involves Ca(2+) and phosphorylation processes, requires dynamin, and results from GABA(A)R internalization. Thus, activation of the vasoactive G protein-coupled receptor UT triggers functional inhibition and endocytosis of GABA(A)R in CHO and human astrocytes, via its receptor C-terminus. This UII-induced disappearance of the repressor activity of GABA(A)R, may play a key role in the initiation of astrocyte proliferation.     

Belowground carbon allocation and net primary and ecosystem productivities in apple trees (Malus domestica) as affected by soil water availability

Background and aims

Fruit orchards potential as carbon (C) sinks is virtually unknown. Moreover, despite their importance in the Mediterranean area, few data are available about the effect of the reduction in water availability on fruit tree productivity. Here we report the effect of two different irrigation regimes on net primary (NPP) and net ecosystem (NEP) productivities of an apple orchard in northern Italy in 2006.

Methods

Trees productivity and heterotrophic soil respiration were estimated by inventory and root exclusion methods, while belowground allocation with a C mass-balance approach.

Results

The NPP of the control (7.86?±?0.25?Mg?C ha^-1; mean ± SE) was significantly greater than that of water stressed trees (6.53?±?0.12?Mg?C ha^-1), and the ratio between above and below net primary productivity (ANPP/BNPP) was 1.88 and 0.98 respectively. However, the partitioning of ANPP and BNPP among aerial organs and among fine, coarse roots, and root litter was unaffected by the water regime. Although NEP was greater in the control than in stressed trees the C gain of the system after fruit removal (NEP_afr) was unaffected by water availability.

Conclusions

This study indicated an effect of water availability on C partitioning patterns above- and belowground, although there were no significant effects on the C sink potential as NEP_afr.     

Evolving DNA motifs to predict GeneChip probe performance

Background  

Affymetrix High Density Oligonuclotide Arrays (HDONA) simultaneously measure expression of thousands of genes using millions of probes. We use correlations between measurements for the same gene across 6685 human tissue samples from NCBI's GEO database to indicated the quality of individual HG-U133A probes. Low correlation indicates a poor probe.     

Melanotrope secretory cycle is regulated by physiological inputs via the hypothalamus

Previously, it has been shown that background color conditions regulate the overall activity of the frog intermediate lobe by varying the proportions of the two subtypes of melanotropes existing in the gland, the highly active or secretory melanotropes and hormone storage melanotropes, depending on melanocyte-stimulating hormone requirements. However, the factors and mechanisms underlying these background-induced changes are still unknown. In the present study, we investigated whether hypothalamic factors known to regulate melanotrope cell function can induce changes in vitro similar to those caused by background adaptation in vivo. We found that the inhibitors apomorphine (a dopamine receptor agonist) and neuropeptide Y decreased the number of active melanotropes and increased simultaneously that of storage melanotropes. On the other hand, the stimulator TRH increased the number of active cells and concomitantly reduced that of storage cells. Inasmuch as none of these treatments modified the apoptotic and proliferation rates in melanotrope cells, it appears that these hypothalamic factors caused actual interconversions of cells from a subpopulation to its counterpart. Taken together, these findings suggest that the hypothalamus would control melanotrope activity not only through short-term regulation of hormone synthesis and release, but also through a long-term regulation of the secretory phenotype of these cells whereby the activity of the intermediate lobe would be adjusted to fulfill the hormonal requirements imposed by background conditions.     

The octadecaneuropeptide ODN stimulates neurosteroid biosynthesis through activation of central-type benzodiazepine receptors

Neurosteroids may play a major role in the regulation of various neurophysiological and behavioural processes. However, while the biochemical pathways involved in the synthesis of neuroactive steroids in the central nervous system are now elucidated, the mechanisms controlling the activity of neurosteroid-producing cells remain almost completely unknown. In the present study, we have investigated the effect of the octadecaneuropeptide (ODN), an endogenous ligand of benzodiazepine receptors, in the control of steroid biosynthesis in the frog hypothalamus. Glial cells containing ODN-like immunoreactivity were found to send their thick processes in the close vicinity of neurones expressing the steroidogenic enzyme 3 beta-hydroxysteroid dehydrogenase. Exposure of frog hypothalamic explants to graded concentrations of ODN (10(-10)-10(-5) M) produced a dose-dependent increase in the conversion of tritiated pregnenolone into various radioactive steroids, including 17-hydroxypregnenolone, progesterone, 17-hydroxyprogesterone, dehydroepiandrosterone and dihydrotestosterone. The ODN-induced stimulation of neurosteroid biosynthesis was mimicked by the central-type benzodiazepine receptor (CBR) inverse agonists methyl beta-carboline-3-carboxylate (beta-CCM) and methyl 6,7-dimethoxy-4-ethyl-beta-carboline-3-carboxylate (DMCM). The stimulatory effects of ODN, beta-CCM and DMCM on steroid formation was markedly reduced by the CBR antagonist flumazenil. The ODN-evoked stimulation of neurosteroid production was also significantly attenuated by GABA. Collectively, these data indicate that the endozepine ODN, released by glial cell processes in the vicinity of 3 beta-hydroxysteroid dehydrogenase-containing neurones, stimulates the biosynthesis of neurosteroids through activation of central-type benzodiazepines receptors.     

Beta-amyloid peptides stimulate endozepine biosynthesis in cultured rat astrocytes

Accumulation of beta-amyloid peptide (Abeta), which is a landmark of Alzheimer's disease, may alter astrocyte functions before any visible symptoms of the disease occur. Here, we examined the effects of Abeta on biosynthesis and release of diazepam-binding inhibitor (DBI), a polypeptide primarily expressed by astroglial cells in the CNS. Quantitative RT-PCR and specific radioimmunoassay demonstrated that aggregated Abeta(25-35), at concentrations up to 10(-4) m, induced a dose-dependent increase in DBI mRNA expression and DBI-related peptide release from cultured rat astrocytes. These effects were totally suppressed when aggregation of Abeta(25-35) was prevented by Congo red. Measurement of the number of living cells revealed that Abeta(25-35) induced a trophic rather than a toxic effect on astrocytes. Administration of cycloheximide blocked Abeta(25-35)-induced increase of DBI gene expression and endozepine accumulation in astrocytes, indicating that protein synthesis is required for DBI gene expression. Altogether, the present data suggest that Abeta-induced activation of endozepine biosynthesis and release may contribute to astrocyte proliferation associated with Alzheimer's disease.     

Identification of a fatty acid Delta11-desaturase from the microalga Thalassiosira pseudonana

A set of genomic DNA sequences putatively encoding front-end desaturases were identified by in silico analysis of the draft genome of the marine microalga Thalassiosira pseudonana. Among these candidate genes, an open reading frame named TpdesN was found to be full-length, intronless, and constitutively expressed during cell cultivation. The predicted amino acid sequence of the corresponding protein, TpDESN, exhibited typical features of desaturases involved in the production of polyunsaturated fatty acids (PUFAs) in algae, i.e. a cytochrome b5-like domain at the N-terminus and three conserved histidine-rich motifs in the desaturase domain. Expression of TpDESN in Saccharomyces cerevisiae revealed that this enzyme was not involved in PUFA synthesis, but specifically desaturated palmitic acid 16:0 to 16:1Delta11. To our knowledge, until this report, Delta11-desaturase activity had only been detected in insect cells.