Regulation of cellular adhesion molecule expression in murine oocytes, peri-implant ation and post-implantation embryos

Expression of the adhesion molecules, ICAM-1, VCAM-1, NCAM, CD44, CD49d (VLA-4, a chain), and CDlla (LFA-1, a chain) on mouse oocytes, and pre- and peri-implantation stage embryos was examined by quantitative indirect immunofluorescence microscopy. ICAM-1 was most strongly expressed at the oocyte stage, gradually declining almost to undetectable levels by the expanded blastocyst stage. NCAM, also expressed maximally on the oocyte, declined to undetectable levels beyond the morula stage. On the other hand, CD44 declined from highest expression at the oocyte stage to show a second maximum at the compacted 8-cell/morula. This molecule exhibited high expression around contact areas between trophecto-derm and zona pellucida during blastocyst hatching. CD49d was highly expressed in the oocyte, remained significantly expressed throughout and after blastocyst hatching was expressed on the polar trophecto-derm. Like CD44, CD49d declined to undetectable levels at the blastocyst outgrowth stage. Expression of both     

Species Diversity of Edible Plants Grown in Homegardens of Chibchan Amerindians from Costa Rica

We studied edible crop species diversity at homegardens of two Chibchan Amerindian Reserves in Costa Rica: Talamanca and Coto Brus. We visited six settlements at Talamanca and five at Coto Brus. We recorded the number of edible crop species growing homegardens; we found 46 edible plant species at Talamanca and 27 at Coto Brus. The mean number of species per homegarden ranged between 3.80 and 6.80 at Coto Brus and 4.50 and 8.63 at Talamanca. We identified species that were common, i.e., found in most households and all settlements, and species that were rare. We estimated diversity indexes for each settlement and each Reserve. Also, we compared crop species composition between both Reserves and among settlements within each Reserve, using the Jaccard coefficient of community similarity. Settlements from the same Reserve were grouped together, with the exception of Villa Palacios from the Coto Brus Reserve.     

ATP stimulates human placental 11beta-hydroxysteroid dehydrogenase type 2 activity by a novel mechanism independent of phosphorylation.

The human placental 11beta-hydroxysteroid dehydrogenase type 2 (11beta-HSD2) is believed to play a key role in fetal development since this enzyme protects the fetus from exposure to high levels of maternal cortisol by virtue of converting maternal cortisol to its inert metabolite cortisone. The present study was undertaken to examine the effect of ATP on 11beta-HSD2 activity in human placental microsomes. Enzyme activity, reflected by the rate of conversion of cortisol to cortisone, was stimulated more than six-fold by 0.5 mM ATP (EC(50) = 0.2 mM). Such stimulation appears to be mediated through a novel mechanism independent of ATP-induced phosphorylation of the reaction components since AMP-PNP, a non-hydrolyzable analogue of ATP, was equally effective. The ATP-induced stimulation of 11beta-HSD2 activity is adenine nucleotide specific in that a similar stimulation was observed with ADP and AMP but not with CTP, GTP, or UTP. Furthermore, ATP increased the maximal velocity (V(max)) of the 11beta-HSD2 catalyzed conversion of cortisol to cortisone without altering the apparent K(m) of 11beta-HSD2 for cortisol, suggesting that ATP may stimulate enzyme activity by interacting with the enzyme at a site other than that involved in substrate binding. In conclusion, the present study has identified ATP as a novel regulator of human placental 11beta-HSD2 in vitro. It is conceivable that intracellular ATP may have a profound effect on 11beta-HSD2 function in vivo.     

Geographic variation in reef-fish assemblages along the Brazilian coast

The species composition of reef‐fish assemblages from nine Brazilian major coastal sites and four oceanic islands are compared. Canonical correspondence analysis (CCA) was utilized to identify groups of sites based on similarity of composition, and to correlate environmental trends with such groups. Five distinct groups of sites were recognized: (1) the South and South‐eastern coastal reefs (from Guarapari Islands to Santa Catarina, the southernmost Brazilian reefs); (2) the North‐eastern coast (extending from the Manuel Luis Reefs to Abrolhos Archipelago); (3) Trindade Island; (4) Fernando de Noronha and Atol das Rocas; and (5) St Paul’s Rocks. Water temperature, coral richness, distance from mainland, primary production and shelf width strongly correlated with the diversity and composition of the reef sites.     

Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis.

We analysed the Bacillus subtilis protein coding sequences termini, and compared it to other genomes. The analysis focused on signals, com-positional biases of nucleotides, oligonucleotides, codons and amino acids and mRNA secondary structure. AUG is the preferred start codon in all genomes, independent of their G+C content, and seems to induce less stable mRNA structures. However, it is not conserved between homologous genes neither is it preferred in highly expressed genes. In B.subtilis the ribosome binding site is very strong. We found that downstream boxes do not seem to exist either in Escherichia coli or in B.subtilis. UAA stop codon usage is correlated with the G+C content and is strongly selected in highly expressed genes. We found less stable mRNA structures at both termini, which we related to mRNA-ribosome and mRNA-release-factor interactions. This pattern seems to impose a peculiar A-rich nucleotide and codon usage bias in these regions. Finally the analysis of all proteins from B.subtilis revealed a similar amino acid bias near both termini of proteins consisting of over-representation of hydrophilic residues. This bias near the stop codon is partially release-factor specific.     

The past,present and future of genomics and bioinformatics: A survey of Brazilian scientists

Brazil has one of the highest rates of scientific production, occupying the ninth position among countries with genome-sequencing projects. Considering the rapid development of this research area and the diversity of professionals involved, the present study aims to understand the expectations, past experiences and the current scenario of Brazilian research in bioinformatics and genomics. The present research was carried out by analyzing the perceptions of 576 researchers in genomics and bioinformatics in Brazil through content and sentiment analysis techniques. This group of participants is equivalent to 48% of the members of the research community. The results suggest that most researchers have a positive perception of the potential of this research area. However, there is concern about the lack of funding for investing in equipment and professional training. As part of a wish list for the future, researchers highlighted the need for higher funding, formal education, and collaboration among research networks. When asked about genomics and bioinformatics in other countries, the participants recognize that sequencing technologies and infrastructure are more accessible, allowing better data volume expansion.     

The VarA-CsrA regulatory pathway influences cell shape in Vibrio cholerae

Despite extensive studies on the curve-shaped bacterium Vibrio cholerae, the causative agent of the diarrheal disease cholera, its virulence-associated regulatory two-component signal transduction system VarS/VarA is not well understood. This pathway, which mainly signals through the downstream protein CsrA, is highly conserved among gamma-proteobacteria, indicating there is likely a broader function of this system beyond virulence regulation. In this study, we investigated the VarA-CsrA signaling pathway and discovered a previously unrecognized link to the shape of the bacterium. We observed that varA-deficient V. cholerae cells showed an abnormal spherical morphology during late-stage growth. Through peptidoglycan (PG) composition analyses, we discovered that these mutant bacteria contained an increased content of disaccharide dipeptides and reduced peptide crosslinks, consistent with the atypical cellular shape. The spherical shape correlated with the CsrA-dependent overproduction of aspartate ammonia lyase (AspA) in varA mutant cells, which likely depleted the cellular aspartate pool; therefore, the synthesis of the PG precursor amino acid meso-diaminopimelic acid was impaired. Importantly, this phenotype, and the overall cell rounding, could be prevented by means of cell wall recycling. Collectively, our data provide new insights into how V. cholerae use the VarA-CsrA signaling system to adjust its morphology upon unidentified external cues in its environment.