GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data

SUMMARY: Genomic Analysis and Rapid Biological ANnotation (GARBAN) is a new tool that provides an integrated framework to analyze simultaneously and compare multiple data sets derived from microarray or proteomic experiments. It carries out automated classifications of genes or proteins according to the criteria of the Gene Ontology Consortium at a level of depth defined by the user. Additionally, it performs clustering analysis of all sets based on functional categories or on differential expression levels. GARBAN also provides graphical representations of the biological pathways in which all the genes/proteins participate. AVAILABILITY: http://garban.tecnun.es.     

Tyrosine hydroxylase activity in the endocrine pancreas: changes induced by short-term dietary manipulation

BACKGROUND: Tyrosine hydroxylase (TH) activity and its possible participation in the control of insulin secretion were studied in pancreatic islets of adult Wistar rats fed a standard commercial diet (SD) or carbohydrates alone (CHD) for one week. TH activity, norepinephrine (NE) content, and glucose-induced insulin secretion were assessed. Blood glucose and insulin levels were measured at the time of sacrifice. RESULTS: CHD rats had significantly higher blood glucose and lower insulin levels than SD rats (114.5 PlusMinus; 6.7 vs 80.7 PlusMinus; 7.25 mg/dl, p < 0.001; 20.25 PlusMinus; 2.45 vs 42.5 PlusMinus; 4.99 &mgr;U/ml, p < 0.01, respectively). Whereas TH activity was significantly higher in CHD isolated islets (600 PlusMinus; 60 vs 330 PlusMinus; 40 pmol/mg protein/h; p < 0.001), NE content was significantly lower (18 PlusMinus; 1 vs 31 PlusMinus; 5 pmol/mg protein), suggesting that TH activity would be inhibited by the end-products of catecholamines (CAs) biosynthetic pathway. A similar TH activity was found in control and solarectomized rats (330 PlusMinus; 40 vs 300 PlusMinus; 80 pmol/mg protein/h), suggesting an endogenous rather than a neural origin of TH activity. CHD islets released significantly less insulin in response to glucose than SD islets (7.4 PlusMinus; 0.9 vs 11.4 PlusMinus; 1.1 ng/islet/h; p < 0.02). CONCLUSIONS: TH activity is present in islet cells; dietary manipulation simultaneously induces an increase in this activity together with a decrease in glucose-induced insulin secretion in rat islets. TH activity - and the consequent endogenous CAs turnover - would participate in the paracrine control of insulin secretion.     

Effects of ageing on allocentric and egocentric spatial strategies in the Wistar rat

This study was designed to assess the effect of ageing on spatial (allocentric and egocentric) strategies in rats. Two different tasks were designed for this purpose: one involving Morris' circular pool (distal extramaze cues) and another using the T water maze (egocentric cues). In the first task, the aged rats showed some difficulty in acquiring allocentric spatial learning skills. After increasing the number of trials in this task, there was no significant improvement in the performance of the aged group of rats compared to the adult group. However, in the second spatial task (using egocentric cues), both age groups gave a similar performance. Therefore, the effect of ageing on spatial learning depends on the strategy required to acquire this learning.     

CD47 engagement inhibits cytokine production and maturation of human dendritic cells

Upon encounter with bacterial products, immature dendritic cells (iDCs) release proinflammatory cytokines and develop into highly stimulatory mature DCs. In the present study, we show that human monocyte-derived DCs functionally express the CD47 Ag, a thrombospondin receptor. Intact or F(ab')2 of CD47 mAb suppress bacteria-induced production of IL-12, TNF-alpha, GM-CSF, and IL-6 by iDCs. 4N1K, a peptide derived from the CD47-binding site of thrombospondin, also inhibits cytokine release. The inhibition of IL-12 and TNF-alpha is IL-10-independent inasmuch as IL-10 production is down-modulated by CD47 mAb and blocking IL-10 mAb fails to restore cytokine levels. CD47 ligation counteracts the phenotypic and functional maturation of iDCs in that it prevents the up-regulation of costimulatory molecules, the loss of endocytic activity, and the acquisition of an increased capacity to stimulate T cell proliferation and IFN-gamma production. Interestingly, regardless of CD47 mAb treatment during DC maturation, mature DC restimulated by soluble CD40 ligand and IFN-gamma, to mimic DC/T interaction, produce less IL-12 and more IL-18 than iDCs. Finally, CD47 ligation on iDCs does not impair their capacity to phagocytose apoptotic cells. We conclude that following exposure to microorganisms, CD47 ligation may limit the intensity and duration of the inflammatory response by preventing inflammatory cytokine production by iDCs and favoring their maintenance in an immature state.     

Carbon dioxide uptake efficiency by outdoor microalgal cultures in tubular airlift photobioreactors

The influence of solar irradiance and carbon dioxide molar fraction of injected CO(2)-air mixtures on the behavior of outdoor continuous cultures of the microalga Phaeodactylum tricornutum in tubular airlift photobioreactors was analyzed. Instantaneous solar irradiance, pH, dissolved oxygen, temperature, biomass concentration, and the mass flow rates of both the inlet and outlet oxygen and carbon with both the liquid and gas phases were measured. In addition, elemental analysis of the biomass and the cell-free culture medium was performed. The oxygen production rate and carbon dioxide consumption rate increased hyperbolically with the incident solar irradiance on the reactor surface. Carbon losses showed a negative correlation with the daily variation of the carbon dioxide consumption rate. The maximum CO(2) uptake efficiency was 63% of the CO(2) supplied when the CO(2) concentration in the gas supplied was 60% v/v. Carbon losses were >100% during the night, due to CO(2) production by respiration, and hyperbolically decreased to values of 10% to 20% in the midday hours. An increase in the carbon fixed in the biomass with the solar cycle was observed. A slight daily decrease of carbon content of the cell-free culture medium indicated the existence of carbon accumulation in the culture. A decrease in CO(2) molar fraction in the injected gas had a double benefit: first, the biomass productivity of the system was enhanced from 2.05 to 2.47 g L(-1) day(-1) by reduction of CO(2) inhibition and/or pH gradients; and second, the carbon losses during the daylight period were reduced by 60%. The fluid dynamics in the reactor also influenced the carbon losses: the higher the liquid flow rate the higher the carbon losses. By using a previous mass transfer model the experimental results were simulated and the usefulness of this method in the evaluation and scale-up of tubular photobioreactors was established.     

Asynchronous accumulation of lettuce infectious yellows virus RNAs 1 and 2 and identification of an RNA 1 trans enhancer of RNA 2 accumulation

Time course and mutational analyses were used to examine the accumulation in protoplasts of progeny RNAs of the bipartite Crinivirus, Lettuce infectious yellow virus (LIYV; family Closteroviridae). Hybridization analyses showed that simultaneous inoculation of LIYV RNAs 1 and 2 resulted in asynchronous accumulation of progeny LIYV RNAs. LIYV RNA 1 progeny genomic and subgenomic RNAs could be detected in protoplasts as early as 12 h postinoculation (p.i.) and accumulated to high levels by 24 h p.i. The LIYV RNA 1 open reading frame 2 (ORF 2) subgenomic RNA was the most abundant of all LIYV RNAs detected. In contrast, RNA 2 progeny were not readily detected until ca. 36 h p.i. Mutational analyses showed that in-frame stop codons introduced into five of seven RNA 2 ORFs did not affect accumulation of progeny LIYV RNA 1 or RNA 2, confirming that RNA 2 does not encode proteins necessary for LIYV RNA replication. Mutational analyses also supported that LIYV RNA 1 encodes proteins necessary for replication of LIYV RNAs 1 and 2. A mutation introduced into the LIYV RNA 1 region encoding the overlapping ORF 1B and ORF 2 was lethal. However, mutations introduced into only LIYV RNA 1 ORF 2 resulted in accumulation of progeny RNA 1 near or equal to wild-type RNA 1. In contrast, the RNA 1 ORF 2 mutants did not efficiently support the trans accumulation of LIYV RNA 2. Three distinct RNA 1 ORF 2 mutants were analyzed and all exhibited a similar phenotype for progeny LIYV RNA accumulation. These data suggest that the LIYV RNA 1 ORF 2 encodes a trans enhancer for RNA 2 accumulation.     

The narA Locus of Synechococcus sp. Strain PCC 7942 Consists of a Cluster of Molybdopterin Biosynthesis Genes

The narA locus required for nitrate reduction in Synechococcus sp. strain PCC 7942 is shown to consist of a cluster of genes, namely, moeA, moaC, moaD, moaE, and moaA, involved in molybdenum cofactor biosynthesis. The product of the moaC gene of strain PCC 7942 shows homology in its N-terminal half to MoaC from Escherichia coli and in its C-terminal half to MoaB or Mog. Overexpression of the Synechococcus moaC gene in E. coli resulted in the synthesis of a polypeptide of 36 kDa, a size that would conform to a protein resembling a fusion of the MoaC and MoaB or Mog polypeptides of E. coli. Insertional inactivation of the moeA, moaC, moaE, and moaA genes showed that the moeA-moa gene cluster is required for growth on nitrate and expression of nitrate reductase activity in strain PCC 7942. The moaCDEA genes constitute an operon which is transcribed divergently from the moeA gene. Expression of the moeA gene and the moa operon was little affected by the nitrogen source present in the culture medium.     

Variation in sclerophylly among Iberian populations of Quercus coccifera L. is associated with genetic differentiation across contrasting environments

Evergreen oaks are an emblematic element of the Mediterranean vegetation and have a leaf phenotype that seems to have remained unchanged since the Miocene. We hypothesise that variation of the sclerophyll phenotype among Iberian populations of Quercus coccifera is partly due to an ulterior process of ecotypic differentiation. We analysed the genetic structure of nine Iberian populations using ISSR fingerprints, and their leaf phenotypes using mean and intracanopy plasticity values of eight morphological (leaf angle, area, spinescence, lobation and specific area) and biochemical traits (VAZ pool, chlorophyll and β-carotene content). Climate and soil were also characterised at the population sites. Significant genetic and phenotypic differences were found among populations and between NE Iberia and the rest of the populations of the peninsula. Mean phenotypes showed a strong and independent correlation with both genetic and geographic distances. Northeastern plants were smaller, less plastic, with smaller, spinier and thicker leaves, a phenotype consistent with the stressful conditions that prevailed in the steppe environments of the refugia within this geographic area during glaciations. These genetic, phenotypic, geographic and environmental patterns are consistent with previously reported palaeoecological and common evidence. Such consistency leads us to conclude that there has been a Quaternary divergence within the sclerophyllous syndrome that was at least partially driven by ecological factors.