Identification of genetic risk factors for maxillary lateral incisor agenesis.

Tooth agenesis affects 20% of the world population, and maxillary lateral incisors agenesis (MLIA) is one of the most frequent subtypes, characterized by the absence of formation of deciduous or permanent lateral incisors. Odontogenesis is a complex mechanism regulated by sequential and reciprocal epithelial-mesenchymal interactions, controlled by activators and inhibitors involved in several pathways. Disturbances in these signaling cascades can lead to abnormalities in odontogenesis, resulting in alterations in the formation of the normal teeth number. Our aim was to study a large number of genes encoding either transcription factors or key components in signaling pathways shown to be involved in tooth odontogenesis. We selected 8 genes-MSX1, PAX9, AXIN2, EDA, SPRY2, TGFA, SPRY4, and WNT10A-and performed one of the largest case-control studies taking into account the number of genes and variants assessed, aiming at the identification of MLIA susceptibility factors. We show the involvement of PAX9, EDA, SPRY2, SPRY4, and WNT10A as risk factors for MLIA. Additionally, we uncovered 3 strong synergistic interactions between MLIA liability and MSX1-TGFA, AXIN2-TGFA, and SPRY2-SPRY4 gene pairs. We report the first evidence of the involvement of sprouty genes in MLIA susceptibility. This large study results in a better understanding of the genetic components and mechanisms underlying this trait.

Modulation of genes related to specific metabolic pathways in response to cytosolic ascorbate peroxidase knockdown in rice plants.

As a central component of the hydrogen peroxide detoxifying system in plant cells, ascorbate peroxidases (APX) play an essential role in the control of intracellular reactive oxygen species (ROS) levels. To characterise the function of cytosolic APX isoforms (OsAPX1 and OsAPX2) in the mechanisms of plant defence, OsAPX1/2 knockdown rice plants were previously obtained. OsAPX1/2 knockdown plants (APx1/2s) exhibited a normal phenotype and development, even though they showed a global reduction of APX activity and increased hydrogen peroxide accumulation. To understand how rice plants compensate for the deficiency of cytosolic APX, expression and proteomic analyses were performed to characterise the global expression pattern of the APx1/2s mutant line compared with non-transformed plants. Our results strongly suggest that deficiencies in cytosolic APX isoforms markedly alter expression of genes associated with several key metabolic pathways, especially of genes involved in photosynthesis and antioxidant defence. These metabolic changes are compensatory because central physiological processes such as photosynthesis and growth were similar to non-transformed rice plants. Our analyses showed modulation of groups of genes and proteins related to specific metabolic pathways. Among the differentially expressed genes, the largest number corresponded to those with catalytic activity. Genes related to oxidative stress, carbohydrate metabolism, photosynthesis and transcription factor-encoding genes were also modulated. These results represent an important step toward understanding of the role played by cytosolic APX isoforms and hydrogen peroxide in the regulation of metabolism by redox modulation in monocots.

A novel SPRY2 and SPRY4 interaction increases tooth agenesis susceptibility.

Short Communication selected from the Oral Presentations of the 56th Congress of the Groupèment International pour la Recherche Scientifique en Stomatologie et Odontologie, Peñafiel (Portugal) May 2012.

ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility.

Optimizing and monitoring the data flow in high-throughput sequencing facilities is important for data input and output, for tracking the status of results for the users of the facility, and to guarantee a good, high-quality service. In a multi-user system environment with different throughputs, each user wants to access his/her data easily, track his/her sequencing history, analyze sequences and their quality, and apply some basic post-sequencing analysis, without the necessity of installing further software. Recently, Fiocruz established such a core facility as a "technological platform". Infrastructure includes a 48-capillary 3730 DNA Sequence Analyzer (Applied Biosystems) and supporting equipment. The service includes running samples for large-scale users, performing DNA sequencing reactions and runs for medium and small users, and participation in partial or full genome projects. We implemented a workflow that fulfills these requirements for small and high throughput users. Our implementation also includes the monitoring of data for continuous quality improvement (reports by plate, month and user) by the sequencing staff. For the user, different analyses of the chromatograms, such as visualization of good quality regions, as well as processing, such as comparisons or assemblies, are available. So far, 180 users have made use of the service, generating 155,000 sequences, 35% of which were produced for the BCG Moreau-RJ genome project. The pipeline (named ChromaPipe for Chromatogram Pipeline) is available for download by the scientific community at the url http://bioinfo.pdtis.fiocruz.br/ChromaPipe/. The support for assembly is also configured as a web service: http://bioinfo.pdtis.fiocruz.br/Assembly/.

In silico reconstruction of the amino acid metabolic pathways of Trypanosoma cruzi.

Trypanosoma cruzi is the epidemiological agent of Chagas' disease, affecting most of Central and South America, constituting a significant health and socio-economic problem. The parasite has a metabolism largely based on the consumption of amino acids, which participate in a diversity of metabolic pathways, leading to many crucial compounds for the survival of this parasite. Study of its enzymes has the potential to disclose new therapeutic targets and foster the development of new drugs. In this study, we employed computational approaches to reconstruct in silico the amino acid metabolic pathways of T. cruzi, aiming to link genomic information with functional information. For that, protein sequences from 570 EC classes belonging to 25 different pathways in general amino acid metabolism were downloaded from KEGG. A subset of 471 EC classes had at least one sequence deposited. Clustering of the proteins belonging to each EC class was performed using a similarity-based approach implemented in the tool AnEnPi. Reconstruction of the metabolic pathways comprising the amino acid metabolism of T. cruzi was performed by analyzing the output of BLASTP, using as query the dataset of predicted proteins of T. cruzi against all sequences of each individual cluster. This approach allowed us to identify 764 T. cruzi proteins probably involved in the metabolism of amino acids as well as the identification of several putative cases of analogy. Furthermore, we were able to identify several enzymatic activities of T. cruzi that were not previously included in KEGG.

Magnesium-dependent ecto-ATP diphosphohydrolase activity in Herpetomonas muscarum muscarum.

In the present work we characterized the ecto-ATP diphosphohydrolase activity of the trypanosomatid parasite Herpetomonas muscarum muscarum. This parasite hydrolyzed ATP at a rate of 15.52 nmol Pi/mg protein/min and this activity reached a maximum at pH 7.5. Classical inhibitors of acid phosphatases, such as sodium orthovanadate (NaVO3), sodium fluoride (NaF), and ammonium molybdate presented no effect on this activity. MgCl2, ZnCl2, and MnCl2 stimulated the ATP hydrolysis by H. m. muscarum. The ecto-ATPase activity was insensitive to oligomycin and sodium azide, two inhibitors of mitochondrial Mg-ATPase, bafilomycin A1, a V-ATPase inhibitor, ouabain, a Na(+)+K+-ATPase inhibitor and to levamizole, an inhibitor of alkaline phosphatase. An extracellular impermeant inhibitor 4,4'-diisothiocyanostylbene 2',2'-disulfonic acid (DIDS) and a inhibitor of some ecto-ATPases, suramin, which is also a competitive antagonist of P2-purinergic receptors, promoted a great inhibition on the ATP hydrolysis. This enzyme is able to hydrolysis ATP, ADP, UTP, and UDP, but not GTP, GDP, CTP, or CDP. ADP inhibited the enzymatic activity in a concentration dependent manner, reaching 70% inhibition.

Ca(2+)-ATPase from chicken (Gallus domesticus) erythrocyte plasma membrane: effects of calmodulin and taurine on the Ca(2+)-dependent ATPase activity and Ca2+ uptake.

In the present report we describe a method for purifying plasma membranes from chicken erythrocytes using sonication under conditions that facilitate preferential lysis of plasma membrane, followed by centrifugation through a sucrose gradient. The Ca(2+)-dependent ATP hydrolysis by plasma membranes is activated by nanomolar levels of calmodulin, similarly to that from anucleated erythrocytes. Inside-out vesicles display a calmodulin-activated Ca2+ uptake. Purified Ca(2+)-ATPase is obtained from the plasma membrane by Sepharose-calmodulin affinity chromatography, and exhibits an apparent molecular mass of 150 kDa on SDS-polyacrylamide gel electrophoresis, clearly showing that the enzyme is distinct from that described in anucleated erythrocytes (140 kDa). The enzyme is insensitive to physiological concentrations of taurine, a beta-amino acid that has been proposed to be involved in Ca2+ homeostasis of nucleated erythrocytes, suggesting that the effect of taurine is not mediated by the Ca(2+)-ATPase. Taken together, these data suggest that the enzyme may be an isoform that resembles the previously described plasma membrane Ca(2+)-ATPase from anucleated erythrocytes in its regulation by calmodulin, but differs in its apparent molecular weight.

Expression of cell cycle genes during Sesbania rostrata stem nodule development.

Upon infection of Sesbania rostrata with Azorhizobium caulinodans, nodules are formed on roots and stems. Stem nodules develop from abundantly distributed dormant root primordia. To acquire more insight into the meristem organization during stem nodule development, the expression patterns of a mitotic B1-type cyclin gene (Sesro; CycB1;1), a cyclin-dependent kinase gene (Cdc-2-1Sr), and a histone H4 gene (H4-1Sr) of S. rostrata were followed by in situ hybridization. Cdc2-1Sr transcripts were found in all cells of uninfected and infected root primordia. In uninfected root primordia, Sesro;CycB1;1 transcripts were detected in a few cells of the apical root meristem whereas H4-1Sr transcripts were abundant in this region. Interestingly, after inoculation with A. caulinodans, H4-1Sr transcripts disappeared in the root meristem and a patchy pattern of Sesro;CycB1;1 and H4-1Sr expression appeared in the cortex of the root primordium, reflecting the formation of globular nodule primordia. When bacterial invasion started, a distal nodule meristem was delimited wherein Sesro;CycB1;1 and H4-1Sr expression was concentrated. Approximately 1 week after inoculation, meristem activity ceased, indicated by the loss of Sesro;CycB1;1 and H4-1Sr expression.

p-nitrophenylphosphatase activity of plasma membrane H(+)-ATPase from yeast. Implications for the regulation of the catalytic cycle by H+.

The H(+)-ATPase from Schizosaccharomyces pombe belongs to the group of transport ATPases which displays two main conformational states, E1 and E2 (P-type ATPase). In this report, we show that, as in the case of other P-type ATPase, the purified enzyme exhibits a p-nitrophenylphosphatase activity which can be completely inhibited by vanadate. In aqueous medium, p-nitrophenyl phosphate hydrolysis proceeds at only 0.5% of the rate of ATP hydrolysis, and both activities can be stimulated 3- to 4-fold by decreasing the pH from 7.5 to 6.5. Addition of the organic solvent dimethyl sulfoxide (10-40%), which has been shown to favor the E2 conformation, stimulates the p-nitrophenylphosphatase activity but inhibits the ATPase activity. At pH 7.5, the Km for p-nitrophenyl phosphate decreases when dimethyl sulfoxide is present. In the presence of 30% (v/v) dimethyl sulfoxide, the phosphatase activity can be inhibited by ATP (K(i) 300 microM) or by P(i) (K(i) 1 mM). The H(+)-ATPase incorporated into liposomes retains pNPPase activity, but it does not support H+ transport. Gel electrophoresis reveals that the pattern of H(+)-ATPase cleavage by trypsin changes when vanadate, Me2SO, or both compounds are present in the medium, regardless of the pH used during trypsinization. We propose that p-nitrophenyl phosphate is hydrolyzed by a H(+)-ATPase conformation distinct from that which hydrolyzes ATP, most probably an E2-like form. We also suggest that, in addition to the E1-E2 transition, the enzyme activity can be regulated by protons at another step of the catalytic cycle.