Costantini M.,Stazione Zoologica Anton Dohrn |
Greif G.,Instituto Pasteur Of Montevideo |
Alvarez-Valin F.,University of the Republic of Uruguay |
Bernardi G.,Stazione Zoologica Anton Dohrn
Genome biology and evolution | Year: 2016
Two articles published 5 years ago concluded that the genome of the lizard Anolis carolinensis is an amniote genome without isochores. This claim was apparently contradicting previous results on the general presence of an isochore organization in all vertebrate genomes tested (including Anolis). In this investigation, we demonstrate that the Anolis genome is indeed heterogeneous in base composition, since its macrochromosomes comprise isochores mainly from the L2 and H1 families (a moderately GC-poor and a moderately GC-rich family, respectively), and since the majority of the sequenced microchromosomes consists of H1 isochores. These families are associated with different features of genome structure, including gene density and compositional correlations (e.g., GC3 vs flanking sequence GC and intron GC), as in the case of mammalian and avian genomes. Moreover, the assembled Anolis chromosomes have an enormous number of gaps, which could be due to sequencing problems in GC-rich regions of the genome. In conclusion, the Anolis genome is no exception to the general rule of an isochore organization in the genomes of vertebrates (and other eukaryotes). © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Gonzalez-Recio O.,Instituto Nacional Of Investigaciones Agrarias |
Weigel K.A.,University of Wisconsin - Madison |
Gianola D.,University of Wisconsin - Madison |
Gianola D.,Norwegian University of Life Sciences |
And 2 more authors.
Genetics Research | Year: 2010
The L2-Boosting algorithm is one of the most promising machine-learning techniques that has appeared in recent decades. It may be applied to high-dimensional problems such as whole-genome studies, and it is relatively simple from a computational point of view. In this study, we used this algorithm in a genomic selection context to make predictions of yet to be observed outcomes. Two data sets were used: (1) productive lifetime predicted transmitting abilities from 4702 Holstein sires genotyped for 32 611 single nucleotide polymorphisms (SNPs) derived from the Illumina BovineSNP50 BeadChip, and (2) progeny averages of food conversion rate, pre-corrected by environmental and mate effects, in 394 broilers genotyped for 3481 SNPs. Each of these data sets was split into training and testing sets, the latter comprising dairy or broiler sires whose ancestors were in the training set. Two weak learners, ordinary least squares (OLS) and non-parametric (NP) regression were used for the L2-Boosting algorithm, to provide a stringent evaluation of the procedure. This algorithm was compared with BL [Bayesian LASSO (least absolute shrinkage and selection operator)] and BayesA regression. Learning tasks were carried out in the training set, whereas validation of the models was performed in the testing set. Pearson correlations between predicted and observed responses in the dairy cattle (broiler) data set were 065 (033), 053 (037), 066 (026) and 063 (027) for OLS-Boosting, NP-Boosting, BL and BayesA, respectively. The smallest bias and mean-squared errors (MSEs) were obtained with OLS-Boosting in both the dairy cattle (008 and 108, respectively) and broiler (0011 and 0006) data sets, respectively. In the dairy cattle data set, the BL was more accurate (bias=010 and MSE=110) than BayesA (bias=126 and MSE=281), whereas no differences between these two methods were found in the broiler data set. L2-Boosting with a suitable learner was found to be a competitive alternative for genomic selection applications, providing high accuracy and low bias in genomic-assisted evaluations with a relatively short computational time. © 2010 Cambridge University Press.
PubMed | Laboratory of Genomics, State Laboratory of Public Health, University of Los Andes, Venezuela, Cayetano Heredia Peruvian University and 24 more.
Type: Journal Article | Journal: The Journal of molecular diagnostics : JMD | Year: 2015
An international study was performed by 26 experienced PCR laboratories from 14 countries to assess the performance of duplex quantitative real-time PCR (qPCR) strategies on the basis of TaqMan probes for detection and quantification of parasitic loads in peripheral blood samples from Chagas disease patients. Two methods were studied: Satellite DNA (SatDNA) qPCR and kinetoplastid DNA (kDNA) qPCR. Both methods included an internal amplification control. Reportable range, analytical sensitivity, limits of detection and quantification, and precision were estimated according to international guidelines. In addition, inclusivity and exclusivity were estimated with DNA from stocks representing the different Trypanosoma cruzi discrete typing units and Trypanosoma rangeli and Leishmania spp. Both methods were challenged against 156 blood samples provided by the participant laboratories, including samples from acute and chronic patients with varied clinical findings, infected by oral route or vectorial transmission. kDNA qPCR showed better analytical sensitivity than SatDNA qPCR with limits of detection of 0.23 and 0.70 parasite equivalents/mL, respectively. Analyses of clinical samples revealed a high concordance in terms of sensitivity and parasitic loads determined by both SatDNA and kDNA qPCRs. This effort is a major step toward international validation of qPCR methods for the quantification of T. cruzi DNA in human blood samples, aiming to provide an accurate surrogate biomarker for diagnosis and treatment monitoring for patients with Chagas disease.
PubMed | Childrens Hospital Oakland Research Institute, University of California at San Francisco, Institute Of Recherches Cliniques Of Montreal and Instituto Pasteur Of Montevideo
Type: Journal Article | Journal: European journal of immunology | Year: 2015
Activation induced deaminase (AID) initiates somatic hypermutation and class switch recombination of the Ig genes in antigen-activated B cells, underpinning antibody affinity maturation and isotype switching. AID can also be pathogenic by contributing to autoimmune diseases and oncogenic mutations. Moreover, AID can exert noncanonical functions when aberrantly expressed in epithelial cells. The lack of specific inhibitors prevents therapeutic applications to modulate AID functions. Here, we have exploited our previous finding that the HSP90 molecular chaperoning pathway stabilizes AID in B cells, to test whether HSP90 inhibitors could target AID in vivo. We demonstrate that chronic administration of HSP90 inhibitors decreases AID protein levels and isotype switching in immunized mice. HSP90 inhibitors also reduce disease severity in a mouse model of acute B-cell lymphoblastic leukemia in which AID accelerates disease progression. We further show that human AID protein levels are sensitive to HSP90 inhibition in normal and leukemic B cells, and that HSP90 inhibition prevents AID-dependent epithelial to mesenchymal transition in a human breast cancer cell line in vitro. Thus, we provide proof-of-concept that HSP90 inhibitors indirectly target AID in vivo and that endogenous human AID is widely sensitive to them, which could have therapeutic applications.
PubMed | University of the Republic of Uruguay, University of Buenos Aires, Instituto Pasteur Of Montevideo and University of Sao Paulo
Type: Journal Article | Journal: PLoS neglected tropical diseases | Year: 2017
The larva of cestodes belonging to the Echinococcus granulosus sensu lato (s.l.) complex causes cystic echinococcosis (CE). It is a globally distributed zoonosis with significant economic and public health impact. The most immunogenic and specific Echinococcus-genus antigen for human CE diagnosis is antigen B (AgB), an abundant lipoprotein of the hydatid cyst fluid (HF). The AgB protein moiety (apolipoprotein) is encoded by five genes (AgB1-AgB5), which generate mature 8 kDa proteins (AgB8/1-AgB8/5). These genes seem to be differentially expressed among Echinococcus species. Since AgB immunogenicity lies on its protein moiety, differences in AgB expression within E. granulosus s.l. complex might have diagnostic and epidemiological relevance for discriminating the contribution of distinct species to human CE. Interestingly, AgB2 was proposed as a pseudogene in E. canadensis, which is the second most common cause of human CE, but proteomic studies for verifying it have not been performed yet. Herein, we analysed the protein and lipid composition of AgB obtained from fertile HF of swine origin (E. canadensis G7 genotype). AgB apolipoproteins were identified and quantified using mass spectrometry tools. Results showed that AgB8/1 was the major protein component, representing 71% of total AgB apolipoproteins, followed by AgB8/4 (15.5%), AgB8/3 (13.2%) and AgB8/5 (0.3%). AgB8/2 was not detected. As a methodological control, a parallel analysis detected all AgB apolipoproteins in bovine fertile HF (G1/3/5 genotypes). Overall, E. canadensis AgB comprised mostly AgB8/1 together with a heterogeneous mixture of lipids, and AgB8/2 was not detected despite using high sensitivity proteomic techniques. This endorses genomic data supporting that AgB2 behaves as a pseudogene in G7 genotype. Since recombinant AgB8/2 has been found to be diagnostically valuable for human CE, our findings indicate that its use as antigen in immunoassays could contribute to false negative results in areas where E. canadensis circulates. Furthermore, the presence of anti-AgB8/2 antibodies in serum may represent a useful parameter to rule out E. canadensis infection when human CE is diagnosed.
Botti H.,Instituto Pasteur Of Montevideo |
Botti H.,Center for Free Radical and Biomedical Research |
Moller M.N.,Center for Free Radical and Biomedical Research |
Moller M.N.,University of the Republic of Uruguay |
And 9 more authors.
Journal of Physical Chemistry B | Year: 2010
The fast reaction of •NO and O2 •- to give ONOO- has been extensively studied at irreversible conditions, but the reasons for the wide variations in observed forward rate constants (3.8 ≥ kf ≥ 20 × 109 M-1 s-1) remain unexplained. We characterized the diffusion-dependent aqueous (pH > 12) chemical equilibrium of the form •NO + O2 •- = ONOO- with respect to its dependence on temperature, viscosity, and [ONOO-] eq by determining [ONOO-]eq and [ •NO]eq. The equilibrium forward reaction rate constant (kf eq) has negative activation energy, in contrast to that found under irreversible conditions. In contradiction to the law of mass action, we demonstrate that the equilibrium constant depends on ONOO- concentration. Therefore, a wide range of kf eq values could be derived (7.5-21 × 109 M -1 s-1). Of general interest, the variations in k f can thus be explained by its dependence on the distance between ONOO- particles (sites of generation of •NO and O2 •-). © 2010 American Chemical Society.
PubMed | University of the Republic of Uruguay, Stazione Zoologica Anton Dohrn and Instituto Pasteur Of Montevideo
Type: Journal Article | Journal: Genome biology and evolution | Year: 2016
Two articles published 5 years ago concluded that the genome of the lizard Anolis carolinensis is an amniote genome without isochores. This claim was apparently contradicting previous results on the general presence of an isochore organization in all vertebrate genomes tested (including Anolis). In this investigation, we demonstrate that the Anolis genome is indeed heterogeneous in base composition, since its macrochromosomes comprise isochores mainly from the L2 and H1 families (a moderately GC-poor and a moderately GC-rich family, respectively), and since the majority of the sequenced microchromosomes consists of H1 isochores. These families are associated with different features of genome structure, including gene density and compositional correlations (e.g., GC3 vs flanking sequence GC and intron GC), as in the case of mammalian and avian genomes. Moreover, the assembled Anolis chromosomes have an enormous number of gaps, which could be due to sequencing problems in GC-rich regions of the genome. In conclusion, the Anolis genome is no exception to the general rule of an isochore organization in the genomes of vertebrates (and other eukaryotes).
Obal G.,University of the Republic of Uruguay |
Obal G.,CNR Institute of Biophysics |
Ramos A.L.,University of the Republic of Uruguay |
Silva V.,University of the Republic of Uruguay |
And 6 more authors.
PLoS Neglected Tropical Diseases | Year: 2012
Antigen B (EgAgB) is the most abundant and immunogenic antigen produced by the larval stage (metacestode) of Echinococcus granulosus. It is a lipoprotein, the structure and function of which have not been completely elucidated. EgAgB apolipoprotein components have been well characterised; they share homology with a group of hydrophobic ligand binding proteins (HLBPs) present exclusively in cestode organisms, and consist of different isoforms of 8-kDa proteins encoded by a polymorphic multigene family comprising five subfamilies (EgAgB1 to EgAgB5). In vitro studies have shown that EgAgB apolipoproteins are capable of binding fatty acids. However, the identity of the native lipid components of EgAgB remains unknown. The present work was aimed at characterising the lipid ligands bound to EgAgB in vivo. EgAgB was purified to homogeneity from hydatid cyst fluid and its lipid fraction was extracted using chloroform:methanol mixtures. This fraction constituted approximately 40-50% of EgAgB total mass. High-performance thin layer chromatography revealed that the native lipid moiety of EgAgB consists of a variety of neutral (mainly triacylglycerides, sterols and sterol esters) and polar (mainly phosphatidylcholine) lipids. Gas-liquid chromatography analysis showed that 16:0, 18:0 and 18:1(n-9) are the most abundant fatty acids in EgAgB. Furthermore, size exclusion chromatography coupled to light scattering demonstrated that EgAgB comprises a population of particles heterogeneous in size, with an average molecular mass of 229 kDa. Our results provide the first direct evidence of the nature of the hydrophobic ligands bound to EgAgB in vivo and indicate that the structure and composition of EgAgB lipoprotein particles are more complex than previously thought, resembling high density plasma lipoproteins. Results are discussed considering what is known on lipid metabolism in cestodes, and taken into account the Echinococcus spp. genomic information regarding both lipid metabolism and the EgAgB gene family. © 2012 Obal et al.
Leon I.E.,National University of La Plata |
Di Virgilio A.L.,National University of La Plata |
Porro V.,Instituto Pasteur Of Montevideo |
Muglia C.I.,National University of La Plata |
And 4 more authors.
Dalton Transactions | Year: 2013
Flavonoids, a polyphenolic compound family, and the vanadium compounds have interesting biological, pharmacological, and medicinal properties. We report herein the antitumor actions of the complex [VO(chrysin)2EtOH] 2 (VOchrys) on the MG-63 human osteosarcoma cell line. Oxovanadium(iv), chrysin and VOchrys caused a concentration-dependent inhibition of cell viability. The complex was the strongest antiproliferative agent (p < 0.05). Cytotoxicity and genotoxicity studies also showed a concentration effect. Reactive oxygen species (ROS) and the alterations in the GSH/GSSG ratio underlie the main mechanisms of action of VOchrys. Additions of ROS scavengers (vitamin C plus vitamin E) or GSH to the viability experiments demonstrated beneficial effects (p < 0.01). Besides, the complex triggered apoptosis, disruption of the mitochondria membrane potential (MMP), increased levels of caspase 3 and DNA fragmentation measured by the sub-G1 peak in cell cycle arrest experiments (p < 0.01). Collectively, VOchrys is a cell death modulator and a promissory complex to be used in cancer treatments. This journal is © The Royal Society of Chemistry.
Peloso E.F.,University of Campinas |
Gonalves C.C.,University of Campinas |
Silva T.M.,University of Campinas |
Ribeiro L.H.G.,University of Campinas |
And 3 more authors.
Archives of Biochemistry and Biophysics | Year: 2012
Trypanosoma cruzi's antioxidant system is unique and relevant to the parasite. In this study, quantitative assays were performed to determine cytosolic and mitochondrial tryparedoxin peroxidases and superoxide dismutases expression (TcCPx, TcMPx, SODB and SODA) in correlation to H 2O 2 release and O2- production. Differences were observed regarding H 2O 2 release and O2- production between strains and along the growth curve. All of the enzymes studied exhibited varied expression as a function of time in culture. Although at lower levels, the Y strain exhibited the same pattern of Tulahuen 2 enzyme expression for all of the proteins studied, except SODA. In the stationary phase, the degree of expression of all of the enzymes in the Y strain returned to similar levels as those detected in the log phase with the exception of TcCPx and SODA. In Tulahuen 2, a higher expression of TcMPx, SODA and SODB was detected in the early stationary phase, and a slight decrease was observed in the late stationary phase for each enzyme, excluding TcMPx, which exhibited a marked decrease, and TcCPx, which increased its level. Because of the significance of ROS in redox signaling, these differences in enzyme expression underscore the importance of these parameters for epimastigote proliferation. © 2012 Elsevier Inc. All rights reserved.