Fundacion Institute Estudios Avanzados IDEA

Caracas, Venezuela

Fundacion Institute Estudios Avanzados IDEA

Caracas, Venezuela

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Moraes Barros R.R.,University of Sao Paulo | Marini M.M.,University of Sao Paulo | Antonio C.R.,University of Sao Paulo | Cortez D.R.,University of Sao Paulo | And 6 more authors.
BMC Genomics | Year: 2012

Background: The subtelomeres of many protozoa are highly enriched in genes with roles in niche adaptation. T. cruzi trypomastigotes express surface proteins from Trans-Sialidase (TS) and Dispersed Gene Family-1 (DGF-1) superfamilies which are implicated in host cell invasion. Single populations of T. cruzi may express different antigenic forms of TSs. Analysis of TS genes located at the telomeres suggests that chromosome ends could have been the sites where new TS variants were generated. The aim of this study is to characterize telomeric and subtelomeric regions of T. cruzi available in TriTrypDB and connect the sequences of telomeres to T. cruzi working draft sequence.Results: We first identified contigs carrying the telomeric repeat (TTAGGG). Of 49 contigs identified, 45 have telomeric repeats at one end, whereas in four contigs the repeats are located internally. All contigs display a conserved telomeric junction sequence adjacent to the hexamer repeats which represents a signature of T. cruzi chromosome ends. We found that 40 telomeric contigs are located on T. cruzi chromosome-sized scaffolds. In addition, we were able to map several telomeric ends to the chromosomal bands separated by pulsed-field gel electrophoresis.The subtelomeric sequence structure varies widely, mainly as a result of large differences in the relative abundance and organization of genes encoding surface proteins (TS and DGF-1), retrotransposon hot spot genes (RHS), retrotransposon elements, RNA-helicase and N-acetyltransferase genes. While the subtelomeric regions are enriched in pseudogenes, they also contain complete gene sequences matching both known and unknown expressed genes, indicating that these regions do not consist of nonfunctional DNA but are instead functional parts of the expressed genome. The size of the subtelomeric regions varies from 5 to 182 kb; the smaller of these regions could have been generated by a recent chromosome breakage and telomere healing event.Conclusions: The lack of synteny in the subtelomeric regions suggests that genes located in these regions are subject to recombination, which increases their variability, even among homologous chromosomes. The presence of typical subtelomeric genes can increase the chance of homologous recombination mechanisms or microhomology-mediated end joining, which may use these regions for the pairing and recombination of free ends. © 2012 Moraes Barros et al.; licensee BioMed Central Ltd.


Romay G.,French National Institute for Agricultural Research | Romay G.,Fundacion Institute Estudios Avanzados IDEA | Lecoq H.,French National Institute for Agricultural Research | Desbiez C.,French National Institute for Agricultural Research
Journal of Plant Pathology | Year: 2014

Cucurbit crops are cultivated throughout the world. Melon (Cucumis melo L.), cucumber (Cucumis sativus L.), watermelon (Citrullus lanatus (Thumb.) Mat. et Nak.), squash and pumpkin (Cucurbita spp.) are the major crops. In Latin America and the Caribbean islands (LAC) cucurbits are consumed as a part of the daily diet since pre-Columbian times, when some species such as Cucurbita pepo L., Cucurbita moschata Duch. and Cucurbita maxima Duch. were domesticated by American Indians. In LAC, cucurbit crops have become export commodities and a source of income for several countries, in addition to their role in local consumption. The increase of area devoted to cucurbit crops and the intensification of production has led to the emergence of severe viral epidemics that threaten the sustainability of these cultures. This paper reviews the cucurbit viruses described in the region and their impact. In addition, the potential of different measures to control the most frequent cucurbit viruses in LAC is discussed.


Romay G.,French National Institute for Agricultural Research | Romay G.,Fundacion Institute Estudios Avanzados IDEA | Lecoq H.,French National Institute for Agricultural Research | Geraud-Pouey F.,University of Zulia | And 2 more authors.
Plant Pathology | Year: 2014

In Venezuela, cucurbit viruses have been associated with important yield losses. Therefore, an extensive survey was conducted to determine the major cucurbit viruses in this country. Leaf samples from 284 cucurbit plants exhibiting virus-like symptoms were collected mainly in 2009-2010 from several states of Venezuela. They were assessed for viral infection by polymerase chain reaction (PCR) for Melon chlorotic mosaic virus (MeCMV) and reverse transcriptase (RT)-PCR for Papaya ringspot virus (PRSV), Zucchini yellow mosaic virus (ZYMV), Watermelon mosaic virus (WMV), Cucumber mosaic virus (CMV), Squash mosaic virus (SqMV) and Cucurbit aphid-borne yellows virus (CABYV). The most common virus in cucurbit fields, MeCMV, was present in 65·8% of samples. Its associated alphasatellite was found in 78% of samples positive for MeCMV. PRSV, ZYMV and WMV were found with different prevalence: 34·2, 32·4 and 1·1% respectively. CMV was also detected (6·7%) but SqMV and CABYV were not found. Single infections were more frequent than mixed infections (56·4 and 38·6%, respectively). For ZYMV, comparison and phylogenetic analyses of either polymerase and coat protein (NIb-CP) partial sequences or CP complete sequences revealed a low genetic diversity within Venezuelan isolates. Thirty-four ZYMV isolates were used for serological and biological analysis. Thirteen monoclonal antibodies showed a major group of isolates spread in several states and two groups located in Zulia only. Venezuelan ZYMV isolates showed biological variability on cucurbit cultivars susceptible, tolerant or resistant to ZYMV. Resistance to ZYMV in cucumber appears potentially durable, whereas resistance or tolerance in zucchini and melon may be easily overcome. © 2013 British Society for Plant Pathology.


Torres-Alruiz M.D.,Fundacion Institute Estudios Avanzados IDEA | Rodriguez D.J.,Central University of Venezuela
Ecological Modelling | Year: 2013

Topological studies of trophic webs have shown that a community's extinction risk can be influenced by the positional properties of its species. For example, networks are more robust after the deletion of high degree species, than after the deletion of species with high values of other centrality indexes. The effects of other positional attributes of the species, such as betweenness and closeness, have not been explored as deeply. There is also an evidence that community dynamics is affected by properties such as geometry, connectance, and the connection patterns between species. Most publications on community network models have analyzed the importance of species based on the number of species left unconnected after species deletions (topological criterion). However it is also important to analyze this importance in terms of community dynamics resulting after the deletion (dynamical criterion). To answer these questions we studied the importance of species for indirect interactions and the persistence of the community in network models with various levels of species number, connectance and geometries. We used a topo-dynamical criterion using two new indexes proposed in the present work: (a) the Index of importance of species i, Ii, which is a combined measure of centrality and the consequence in terms of secondary extinctions of the species' deletion; and (b) the species deletion resistance, SDR, which measures the resistance of the whole community to species deletions. We found that: (a) the mean index of importance of species in a community increases with connectance and/or species richness; (b) in webs with high connectance and/or high species richness, keystone species are less frequent; (c) the SDR of a community decreases with connectance and species richness; (d) communities with rectangular geometry do not behave differently than those with triangular geometry; (e) the number of tri-trophic chains and/or trophic loops increases with connectance and/or species richness. The possible effect of these last two modules is discussed. © 2012 Elsevier B.V.


Lander N.,Fundacion Institute Estudios Avanzados IDEA | Lander N.,University of Georgia | Bernal C.,Fundacion Institute Estudios Avanzados IDEA | Diez N.,Fundacion Institute Estudios Avanzados IDEA | And 3 more authors.
Infection and Immunity | Year: 2010

The dispersed gene family 1 (DGF-1) is the fifth largest gene family in the Trypanosoma cruzi genome, with over 500 members (11). Many of the predicted DGF-1 protein products have several transmembrane domains and N-glycosylation and phosphorylation sites and were thought to localize in the plasma membrane. Here, we report that affinity-purified antibodies against a region of one of these proteins (DGF-1.2) localized it intracellularly in different stages of the parasite. DGF-1.2 is more abundant in the amastigote stage than in trypomastigotes and epimastigotes, as detected by immunofluorescence and Western blot analyses. The protein changed localization during intracellular or extracellular differentiation from the trypomastigote to the amastigote stage, where it finally localized to small bodies in close contact with the inner side of the amastigote plasma membrane. DGF-1.2 did not colocalize with markers of other subcellular organelles, such as acidocalcisomes, glycosomes, reservosomes, lipid droplets, or endocytic vesicles. During extracellular differentiation, the protein was detected in the culture medium from 0 to 22 h, peaking at 14 h. The presence of DGF-1.2 in the differentiation culture medium was confirmed by mass spectrometry analysis. Finally, when epimastigotes were subjected to starvation, there was a decrease in the labeling of the cells and, in Western blots, the appearance of bands of lower molecular mass, suggesting its cleavage. These results represent the first report of direct immunodetection and developmental expression and secretion of a DGF-1 protein. Copyright © 2010, American Society for Microbiology. All Rights Reserved.


Strubinger A.,Simon Bolivar University of Venezuela | Ehrmann U.,Simon Bolivar University of Venezuela | Leon V.,Fundacion Institute Estudios Avanzados IDEA
Energy and Fuels | Year: 2012

In the petroleum industry, the implementation of new methodologies requires a validation procedure in order to guarantee compliance with the specifications. This study presents a comparison between the methodology proposed for the determination of the API gravity using a gas pycnometer with a standard and an internationally recognized method such as the one described in ASTM D1298. One of the main advantages of the gas pycnometer technique is related to the use of a hydrometer, which requires a minimum amount of sample. This makes it an ideal method to monitor API gravity in research laboratory-scale processes. In addition, it is a simple and reasonably fast methodology for small samples and therefore attractive for processes with limited sample availability like biotechnological applications. Although the validation parameters reported in the literature are varied, only the results obtained by using the new method as compared with those obtained by using the standard methodology, such as those related to precision and accuracy, are presented. For the API gravity values obtained by using gas pycnometer to be equivalent to the results obtained by using the ASTM D1298 standard method, which would allow the use of both methodologies without this resulting in a deviation of the API gravity specification value of the sample, it is necessary to carry out a correction using the linear correlation data obtained. However, taking into account the precision data, reproducibility limits specifically, both methodologies are comparable. © 2012 American Chemical Society.


Strubinger A.,Simon Bolivar University of Venezuela | Ehrmann U.,Simon Bolivar University of Venezuela | Leon V.,Fundacion Institute Estudios Avanzados IDEA | DeSisto A.,Fundacion Institute Estudios Avanzados IDEA | Gonzalez M.,Fundacion Institute Estudios Avanzados IDEA
Journal of Petroleum Science and Engineering | Year: 2015

Heavy crude oils from Venezuelan Orinoco belt needs special and costly handling processes due to its high viscosity, sulfur and metals content. Different biotechnological applications have been aimed to improve these properties. However, emulsified systems have not been assessed to increase the bioavailability of crude oil for microorganisms. In the present study were evaluated changes induced in two extra heavy crude oils by bacterial consortium using oil in water emulsified systems. For 5 day incubation period, larger detectable changes were observed for Boscán than Carabobo crude oil. The changes were an increase of the initial boiling point, decrease of the light fractions content, as well as a decrease of total sulfur. These changes were mainly observed after treatment with consortia grown in naphthalene. A 45 day incubation period of Carabobo crude oil treated with consortia grown in naphthalene exhibited an increase of the initial boiling point, CH2 and CH3 groups and partial loss of the lighter crude oil components. A relevant change was found after subsequent thermal treatment, it was a slight decrease of the 550°C+ residues; also an important biodesulfurization was found under the same conditions. Finally, the study shows that bacterial degradation of extra heavy crude oils using emulsions is a sensitive procedure. The changes could depend on the heavy crude oil, bacterial consortium, culture medium, incubation time and temperature; as well as the implementation of thermal treatments. © 2015 Elsevier B.V.


Today it is estimated that half world population can be infected by malaria and there is not an available vaccine, however, there is hope with vaccine RTS,S/AS02. For this reason, we must continue to develop computer methodologies and strategies that will allow the rational design of potentially effective vaccines. We propose a new computational approach to predict linear B-cell epitopes from the whole genome sequencing of Plasmodium falciparum 3D7, obtained from IEDB database. Those that were repeated were discarded and were grouped into blocks according to the obtained results by Redundancy and Nomad programs. Subsequently, the possible antigenic character was predicted using the programs BepiPred, BcePred and BCPred. Three potentially antigenic sequences out of the 45 predicted were obtained with this methodology, but it is not possible to say which one the most antigenic without experimental evidence.


Alvarez-Barreto J.F.,University of Oklahoma | Landy B.,University of Oklahoma | Vangordon S.,University of Oklahoma | Place L.,University of Oklahoma | And 3 more authors.
Journal of Tissue Engineering and Regenerative Medicine | Year: 2011

The present study combines chemical and mechanical stimuli to modulate the osteogenic differentiation of mesenchymal stem cells (MSCs). Arg-Gly-Asp (RGD) peptides incorporated into biomaterials have been shown to upregulate MSC osteoblastic differentiation. However, these effects have been assessed under static culture conditions, while it has been reported that flow perfusion also has an enhancing effect on MSC osteoblastic differentiation. It is clear that there is a need to combine RGD modification of biomaterials with mechanical stimulation of MSCs via flow perfusion and evaluate its effects on MSC differentiation down the osteogenic lineage. In this study, the effect of different levels of RGD modification of poly(L-lactic acid) scaffolds on MSC osteogenesis was evaluated under conditions of flow perfusion. It was found that there is a synergistic enhancement of different osteogenic markers, due to the combination of flow perfusion and RGD surface modification when compared to their individual effects. Furthermore, under conditions of flow perfusion, there is an RGD surface concentration optimal for differentiation, and it is flow rate-dependent. This report underlines the significance of incorporating combined biomimesis via biochemical and mechanical microenvironments that modulate in vivo cell behaviour and tissue function for more efficient tissue-engineering strategies. © 2010 John Wiley & Sons, Ltd.


PubMed | Fundacion Institute Estudios Avanzados IDEA and Simon Bolivar University of Venezuela
Type: Journal Article | Journal: Journal of immunoassay & immunochemistry | Year: 2016

Polyclonal immunoglobulin Y (IgY) antibodies were produced in chicken eggs against the purified R(II)-subunit of the cAMP-dependent protein kinase (PKA) from pig heart, which corresponds to the Sus scrofa R(II) isoform. In order to evaluate whether Trypanosoma equiperdum possessed PKA R-like proteins, parasites from the Venezuelan TeAp-N/D1 strain were examined using the generated anti-R(II) IgY antibodies. Western blot experiments revealed a 57-kDa polypeptide band that was distinctively recognized by these antibodies. Likewise, polyclonal antibodies raised in mice ascites against the recombinant T. equiperdum PKA R-like protein recognized the PKA R(II)-subunit purified from porcine heart and the recombinant human PKA R(I)-subunit by immunoblotting. However, a partially purified fraction of the parasite PKA R-like protein was not capable of binding cAMP, implying that this protein is not a direct downstream cAMP effector in T. equiperdum. Although the function of the S. scrofa PKA R(II) and the T. equiperdum PKA R-like protein appear to be different, their cross-reactivity together with results obtained by bioinformatics techniques corroborated the high level of homology exhibited by both proteins. Moreover, its presence in other trypanosomatids suggests an important cellular role of PKA R-like proteins in parasite physiology.

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