Design and Performance of a Turbot (Scophthalmus maximus) Oligo-microarray Based on ESTs from Immune Tissues

An expressed sequence tag database from immune tissues was used to design the first high-density turbot (Scophthalmus maximus) oligo-microarray with the aim of identifying candidate genes for tolerance to pathogens. Specific oligonucleotides (60 mers) were successfully designed for 2,716 out of 3,482 unique sequences of the database. An Agilent custom oligo-microarray 8 × 15 k (five replicates/gene; eight microarrays/slide) was constructed. The performance of the microarray and the sources of variation along microarray analysis were examined on spleen pools of controls and Aeromonas salmonicida-challenged fish at 3 days postinfection. Only 48 out of 2,716 probes did not show signal of hybridization on the 32 microarrays employed, thus demonstrating the consistency of the bioinformatic applications of our database. An asymmetric hierarchical design was employed to ascertain the noise associated with biological and technical (RNA extraction, labeling, hybridization, slide, and dye bias) factors using 1C and 2C labeling approaches. The high correlation coefficient between replicates at most factors tested demonstrated the high reproducibility of the signal. An analysis of random-effects variance revealed that technical variation was mostly negligible, and biological variation represented the main factor, even using pooled samples. One-color approach performed at least as well as 2C, suggesting their usefulness due to its higher design flexibility and lower cost. A relevant proportion of genes turn out to be differentially labeled depending on fluorophore, which alerts for the likely need of swapping replication in 2C experiments. A set of differentially expressed genes and enriched functions related to immune/defense response were detected at 3 days postchallenging.     

Mutagenesis of specific amino acids converts carnitine acetyltransferase into carnitine palmitoyltransferase

Carnitine acyltransferases catalyze the exchange of acyl groups between carnitine and CoA. The members of the family can be classified on the basis of their acyl-CoA selectivity. Carnitine acetyltransferases (CrATs) are very active toward short-chain acyl-CoAs but not toward medium- or long-chain acyl-CoAs. Previously, we identified an amino acid residue (Met(564) in rat CrAT) that was critical to fatty acyl-chain-length specificity. M564G-mutated CrAT behaved as if its natural substrates were medium-chain acyl-CoAs, similar to that of carnitine octanoyltransferase (COT). To extend the specificity of rat CrAT to other substrates, we have performed new mutations. Using in silico molecular modeling procedures, we have now identified a second putative amino acid involved in acyl-CoA specificity (Asp(356) in rat CrAT). The double CrAT mutant D356A/M564G showed 6-fold higher activity toward palmitoyl-CoA than that of the single CrAT mutant M564G and a new activity toward stearoyl-CoA. We show that by performing two amino acid replacements a CrAT can be converted into a pseudo carnitine palmitoyltransferase (CPT) in terms of substrate specificity. To change CrAT specificity from carnitine to choline, we also prepared a mutant CrAT that incorporates four amino acid substitutions (A106M/T465V/T467N/R518N). The quadruple mutant shifted the catalytic discrimination between l-carnitine and choline in favor of the latter substrate and showed a 9-fold increase in catalytic efficiency toward choline compared with that of the wild-type. Molecular in silico docking supports kinetic data for the positioning of substrates in the catalytic site of CrAT mutants.     

Development and characterization of twelve microsatellite markers for <Emphasis Type="Italic">Porphyra linearis</Emphasis> Greville

The genus Porphyra (and its sister genus Pyropia) contains important red algal species that are cultivated and/or harvested for human consumption, sustaining a billion-dollar aquaculture industry. A vast amount of research has been focused on species of this genus, including studies on genetics and genomics among other areas. Twelve novel microsatellite markers were developed here for Porphyra linearis. Markers were characterized using 32 individuals collected from four natural populations of P. linearis with total heterozygosity varying from 0.098 to 0.916. The number of alleles per locus ranged from 2 to 18. All markers showed cross amplification with Porphyra umbilicalis and/or Porphyra dioica. These polymorphic microsatellite markers are useful for investigating population genetic diversity and differentiation in P. linearis and may become useful for other genetic research on the reproductive biology of this important species.     

Frequency shift in topography of spontaneous brain rhythms from childhood to adulthood

It has been described that the frequency ranges at which theta, mu and alpha rhythms oscillate is increasing with age. The present report, by analyzing the spontaneous EEG, tries to demonstrate whether there is an increase with age in the frequency at which the cortical structures oscillate. A topographical approach was followed. The spontaneous EEG of one hundredand seventy subjects was recorded. The spectral power (from 0.5 to 45.5 Hz) was obtained by means of the Fast Fourier Transform. Correlations of spatial topographies among the different age groups showed that older groups presented the same topographical maps as younger groups, but oscillating at higher frequencies. The results suggest that the same brain areas oscillate at lower frequencies in children than in older groups, for a broad frequency range. This shift to a higher frequency with age would be a trend in spontaneous brain rhythm development.     

Computer assisted simulations and molecular graphics methods in molecular design. 1. Theory and applications to enzyme active-site directed drug design

A survey is presented of model building techniques, computer-assisted molecular dynamics simulations and a new theory of enzyme catalysis. Some aspects of the theoretical formalism are given. Enzyme active-site directed drug design is illustrated with examples taken from molecular modeling studies using FAD-containing disulphide oxidoreductases, proteinases and carbonic anhydrases.     

High within-stream replication is needed to predict litter fluxes in wet–dry tropical streams

1. Streams draining forested landscapes are fuelled by terrestrial plant litter, which can be transported downstream or retained and broken down locally. However, fluxes of plant litter in streams can vary at multiple spatio-temporal scales, affecting the availability of this key resource in heterotrophic stream food webs.
2. To explore this question we quantified several processes related to litter dynamics (i.e. litter inputs, storage, losses by transport and losses by breakdown) by sampling litter at multiple sites in three streams of the Brazilian Cerrado biome (which has a tropical wet–dry climate) for 2 years. We assessed the relative contribution of different spatial (among and within streams) and temporal scales (annual, seasonal and monthly) to total variability of these processes (hereafter fluxes).
3. Spatial and temporal variability of fluxes were both high, but spatial variation was 1.67-fold greater than temporal variation (61 versus 37%, respectively), especially at the within-stream scale (50% overall); an exception was litterfall, which varied less spatially than temporally (24 versus 76%). Temporal variation of litter storage (and hence availability to consumers) was mostly seasonal and due to differences in net transport.
4. Inputs and transport were higher in the wet than the dry season (wet versus dry season, 1.45 versus 0.92 and 1.43 versus 0.06 g litter m⁻² day⁻¹), while breakdown was similar between both seasons (0.88 versus 0.94 g litter m⁻² day⁻¹). Storage (i.e. accumulation) rate was positive and negative in the dry and wet season, respectively, indicating that litter was stored in the dry season and exported in the wet season. The transitional dry–wet season showed the highest inputs, breakdown and storage (3.21, 1.63 g litter m⁻² day⁻¹ and 145 g litter m⁻²), while the wet–dry season showed lower inputs (as in the dry season), higher transport (as in the wet season) and lower breakdown and storage than the other seasons (0.93, 0.65, 0.31 g litter m⁻² day⁻¹ and 24 g litter m⁻²).
5. Our results underscore the role of variation in biophysical drivers of litter fluxes within streams (e.g. pool–riffle configuration, substrate features, biological communities), and suggest that high within-stream replication is necessary to study litter fluxes at larger scales and over time. The seasonal patterns suggested potential changes in litter dynamics under future climate scenarios in the tropics, including increased storage due to reduced transport in a drier climate.

     

Systematics of spiny‐backed treefrogs (Hylidae: Osteocephalus): an Amazonian puzzle

Spiny‐backed tree frogs of the genus Osteocephalus are conspicuous components of the tropical wet forests of the Amazon and the Guiana Shield. Here, we revise the phylogenetic relationships of Osteocephalus and its sister group Tepuihyla, using up to 6134 bp of DNA sequences of nine mitochondrial and one nuclear gene for 338 specimens from eight countries and 218 localities, representing 89% of the 28 currently recognized nominal species. Our phylogenetic analyses reveal (i) the paraphyly of Osteocephalus with respect to Tepuihyla, (ii) the placement of ‘Hyla’ warreni as sister to Tepuihyla, (iii) the non‐monophyly of several currently recognized species within Osteocephalus and (iv) the presence of low (<1%) and overlapping genetic distances among phenotypically well‐characterized nominal species (e.g. O. taurinus and O. oophagus) for the 16S gene fragment used in amphibian DNA barcoding. We propose a new taxonomy, securing the monophyly of Osteocephalus and Tepuihyla by rearranging and redefining the content of both genera and also erect a new genus for the sister group of Osteocephalus. The colouration of newly metamorphosed individuals is proposed as a morphological synapomorphy for Osteocephalus. We recognize and define five monophyletic species groups within Osteocephalus, synonymize three species of Osteocephalus (O. germani, O. phasmatus and O. vilmae) and three species of Tepuihyla (T. celsae, T. galani and T. talbergae) and reallocate three species (Hyla helenae to Osteocephalus, O. exophthalmus to Tepuihyla and O. pearsoni to Dryaderces gen. n.). Furthermore, we flag nine putative new species (an increase to 138% of the current diversity). We conclude that species numbers are largely underestimated, with most hidden diversity centred on widespread and polymorphic nominal species. The evolutionary origin of breeding strategies within Osteocephalus is discussed in the light of this new phylogenetic hypothesis, and a novel type of amplexus (gular amplexus) is described.