Fernando Alvarez-Valin

Universidad de la República de Uruguay | UdelaR · Seccion Biomatematica

Vitis vinifera Tannat was introduced in Uruguay in 1870 from the Basque Pyrenees, and within several grapevines it became the variety best adapted to our viticultural conditions. Recently, through genetic analysis it was demonstrated that Manseng Noir, in addition to originate from the same region of Tannat, is the only natural sister identified wi...

Apiculate yeasts belonging to the genus Hanseniaspora are predominant on grapes and other fruits. While some species, such as Hanseniaspora uvarum, are well known for their abundant presence in fruits, they are generally characterized by their detrimental effect on fermentation quality because the excessive production of acetic acid. However, the s...

Trypanosomatids belong to a remarkable group of unicellular, parasitic organisms of the order Kinetoplastida, an early diverging branch of the phylogenetic tree of eukaryotes, exhibiting intriguing biological characteristics affecting gene expression (intronless polycistronic transcription, trans-splicing, and RNA editing), metabolism, surface mole...

We sequenced maxicircles from T . cruzi strains representative of the species evolutionary diversity by using long-read sequencing, which allowed us to uncollapse their repetitive regions, finding that their real lengths range from 35 to 50 kb. T . cruzi maxicircles have a common architecture composed of four regions: coding region (CR), AT-rich re...

We sequenced maxicircles from T. cruzi strains representative of the species evolutionary diversity by using long-read sequencing, which allowed us to uncollapse their repetitive regions, finding that their real lengths range from 35 to 50 kb. T. cruzi maxicircles have a common architecture composed of four regions: coding region (CR), AT-rich regi...

We analyzed the kinetoplast (mitochondrial genome) of Trypanosoma vivax strains from America and Africa to determine their precise architecture and to understand their adaptive response to mechanical transmission. Using long-read based assemblies that retain individuality of tandem repeats, without erasing inter-copy variability, allowed us to inve...

We herein present the first reliable record of Lepidosira from Neotropical Region. Lepidosira neotropicalis sp. n. from Brazil is described and illustrated in detail, including its complete mitochondrial genome. We perform a Bayesian phylogenetic analysis to place the new species within the Entomobryidae, and at the same time to test previous contr...

Although the genome of Trypanosoma cruzi, the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (the abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This...

Although the genome of Trypanosoma cruzi , the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This al...

American trypanosomiasis is a chronic and endemic disease which affects millions of people. Trypanosoma cruzi, its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post-t...

Slider turtles are the only known amniotes with self-repair mechanisms of the spinal cord that lead to substantial functional recovery. Their strategic phylogenetic position makes them a relevant model to investigate the peculiar genetic programs that allow anatomical reconnection in some vertebrate groups but are absent in others. Here, we analyze...

American trypanosomiasis is a chronic and endemic disease, which affects millions of people. Trypanosoma cruzi , its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post...

American trypanosomiasis is a chronic and endemic disease, which affects millions of people. Trypanosoma cruzi , its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post...

Two papers published five 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...

Premise of the study: We developed a bioinformatic strategy to recover and assemble a chloroplast genome using data derived from low-coverage 454 GS FLX/Roche whole-genome sequencing. Methods: A comparative genomics approach was applied to obtain the complete chloroplast genome from a weedy biotype of rice from Uruguay. We also applied appropria...

We present a novel model that describes the within-host evolutionary dynamics of parasites undergoing antigenic variation. The approach uses a multi-type branching process with two types of entities defined according to their relationship with the immune system: clans of resistant parasitic cells (i.e. groups of cells sharing the same antigen not y...

The article presents an application of Hidden Markov Models (HMMs) for pattern recognition on genome sequences. We apply HMM for identifying genes encoding the Variant Surface Glycoprotein (VSG) in the genomes of Trypanosoma brucei (T. brucei) and other African trypanosomes. These are parasitic protozoa causative agents of sleeping sickness and sev...

Cystic fibrosis is an inherited chronic disease that affects the lungs and digestive system, with a prevalence of about 1:3000 people. Cystic fibrosis is caused by mutations in CFTR gene, which lead to a defective function of the chloride channel, the cystic fibrosis transmembrane conductance regulator (CFTR). Up-to-date, more than 1900 mutations h...

Tunicates have been extensively studied because their crucial phylogenetic location (the closest living relatives of vertebrates) and particular developmental plan. Recent genome efforts have disclosed that tunicates are also remarkable in their genome organization and molecular evolutionary patterns. Here we review these latter aspects, comparing...

For this report, we analyzed protein secondary structures in relation to the statistics of three nucleotide codon positions. The purpose of this investigation was to find which properties of the ribosome, tRNA or protein level, could explain the purine bias (Rrr) as it is observed in coding DNA. We found that the Rrr pattern is the consequence of a...

The genomes of multicellular eukaryotes are compartmentalized in mosaics of isochores, large and fairly homogeneous stretches of DNA that belong to a small number of families characterized by different average GC levels, by different gene concentration (that increase with GC), different chromatin structures, different replication timing in the cell...

Background Trypanosoma vivax is the earliest branching African trypanosome. This crucial phylogenetic position makes T. vivax a fascinating model to tackle fundamental questions concerning the origin and evolution of several features that characterize African trypanosomes, such as the Variant Surface Glycoproteins (VSGs) upon which antibody clearin...

The tumor suppressor TP53 gene is one of the most frequently mutated in different types of human cancer. Particularly in colorectal cancer (CRC), it is believed that TP53 mutations play a role in the adenoma-carcinoma transition of tumors during pathological process. In order to analyze TP53 expressed alleles in CRC, we examined TP53 mRNA in tumor...

We analyze the patterns and rates of amino acid evolution in tunicates with special interest on the extremely fast evolving Oikopleura dioica. We show that this species, on average, is twice as fast as the already fast evolving Ciona intestinalis. The acceleration in both species seems to be affected by similar evolutionary forces yet to different...

The common liver fluke Fasciola hepatica is the agent of a zoonosis with significant economic consequences in livestock production worldwide, and increasing relevance to human health in developing countries. Although flukicidal drugs are available, re-infection and emerging resistance are demanding new efficient and inexpensive control strategies....

The influence of the environment on two congeneric fishes, Gillichthys mirabilis and Gillichthys seta, that live in the Gulf of California at temperatures of 10–25 °C, and up to 42–44 °C, respectively, was addressed by analyzing their genomes. Compared with G. mirabilis, G. seta showed some striking features. Substitution rates in the mitochondrial...

Genomewide analyses of distances between orthologous gene pairs from the ascidian species Ciona intestinalis and Ciona savignyi were compared with those of vertebrates. Combining this data with a detailed and careful use of vertebrate fossil records, we estimated the time of divergence between the two ascidians nearly 180 My. This estimation was ob...

The availability of complete genome sequences has allowed the study of genic and nucleotide content changes during the evolution of pathogenic and symbiont bacterial lineages. Here we present the comparative genomics between four strains belonging to two species, Leptospira interrogans (L.interrogans Lai str. 56601 and L. interrogans Copenhageni st...

Two years ago, we showed that positive correlations between optimal growth temperature (T(opt)) and genome GC are observed in 15 out of the 20 families of prokaryotes we analyzed, thus indicating that "T(opt) is one of the factors that influence genomic GC in prokaryotes". Our results were disputed, but these criticisms were demonstrated to be mist...

The last release of p53 somatic mutation database contains more than 20,000 of mutation among which 951 are silent (synonymous). This striking amount of silent mutations is much more than what would be expected if synonymous mutations were effectively neutral. The prevalent explanation to reconcile this vast amount of silent mutations with the neut...

We have recently shown that optimal growth temperature (T(opt)) is one of the factors that influence genomic GC in prokaryotes. Our results have been disputed by Marashi and Ghalanbor, who claim that the correlations we show are not "robust" because the elimination of some points (arbitrarily chosen) leads, in some families, to variations in the co...

In prokaryotes, GC levels range from 25% to 75%, and Topt from approximately 0 degrees C to >100 degrees C. When all species are considered together, no correlation is found between the two variables. Correlations are found, however, when Families of prokaryotes are analysed. Indeed, when Families comprising at least 10 species were studied (a set...

It has recently been proposed, based on an analysis of orthologous gene sequences from closely related species, that GC-rich regions of primate and cetartiodactyl genomes are becoming GC-poorer, i.e., that GC-rich isochores are now vanishing in these lineages. We review an artefact of parsimony-based ancestor reconstruction in GC-rich DNA, and show...

The pampas deer, Ozotoceros bezoarticus, was, until the recent past, widespread in South America from 5°S to 41°S; however, it is now considered to be one of the most endangered South American cervids because of habitat destruction and fragmentation. A comparative craniometrical study using univariate and multivariate analyses was performed to dete...

In this work we re-examined the hypothesis that the variation in GC content in the human genome is due to different regional mutational biases. For this purpose we inferred the mutational pattern by using mutation databases that are available for many genes associated with human genetic diseases. The assumption of this approach is that such mutatio...

The genus Cynolebias (Cyprinodontiformes: Rivulidae) is a locally endemic and speciose group of Neotropical fishes with an annual life cycle. Members of the genus vary greatly in morphology and behaviour, and extensive interspecific karyotypic divergence has been documented among species from Uruguay, Argentina and Rio Grande do Sul, Brazil. We pre...

Bioinformatics is increasingly recognised as a crucial field for research and development in the biological sciences, and forms an integral part of genomics, proteomics and modern biotechnology. Worldwide participation is important, and scientists in developing countries can contribute to this field. Regional networks for bioinformatics are highly...

The nucleotide frequencies in the second codon positions of genes are remarkably different for the coding regions that correspond to different secondary structures in the encoded proteins, namely, helix, β-strand and aperiodic structures. Indeed, hydrophobic and hydrophilic amino acids are encoded by codons having U or A, respectively, in their sec...

In this work we analyze the variability in substitution rates in the GP63 gene from Leishmania. By using a sliding window to estimate substitution rates along the gene, we found that the rate of synonymous substitutions along the GP63 gene is highly correlated with both the rate of amino acid substitution and codon bias. Furthermore, we show that c...

For the purpose of investigating the evolutionary relationships among strains of the human parasite Trypanosoma cruzi, we have determined the nucleotide sequence, in 16 T. cruzi stocks, of a DNA fragment having approximately 1030 nucleotides in length. Phylogenetic analyses show the presence of at least three major groups of T. cruzi strains, a res...

Mycobacterium tuberculosis and Mycobacterium leprae are the ethiological agents of tuberculosis and leprosy, respectively. After performing extensive comparisons between genes from these two GC-rich bacterial species, we were able to construct a set of 275 homologous genes. Since these two bacterial species also have a very low growth rate, transla...

In this work, we have investigated the relationships between synonymous and nonsynonymous rates and base composition in coding sequences from Gramineae to analyze the factors underlying the variation in substitutional rates. We have shown that in these genes the rates of nucleotide divergence, both synonymous and nonsynonymous, are, to some extent,...

We investigated the relationships between the nucleotide substitution rates and the predicted secondary structures in the three states representation (α-helix, β-sheet, and coil). The analysis was carried out on 34 alignments, each of which comprised sequences belonging to at least four different mammalian orders. The rates of synonymous substituti...

The discovery that the vertebrate genomes of warm-blooded vertebrates are mosaics of isochores, long DNA segments homogeneous in base composition, yet belonging to families covering a broad spectrum of GC levels, has led to two major observations. The first is that gene density is strikingly non-uniform in the genome of all vertebrates, gene concen...

In this work, we have investigated the relationships between synonymous and nonsynonymous rates and base composition in coding sequences from Gramineae to analyze the factors underlying the variation in substitutional rates. We have shown that in these genes the rates of nucleotide divergence, both synonymous and nonsynonymous, are, to some extent,...

Previous investigations indicated that synonymous and nonsynonymous substitution rates are correlated in mammalian genes. In the present work, this correlation has been studied at the intragenic level using a dataset of 48 orthologous genes from species belonging to at least four different mammalian orders. The results obtained show that the intrag...

We analyze evolutionary relationships among members of the family Trypanosomatidae, with particular emphasis on whether protein coding genes support paraphyly of the genus Trypanosoma. Phylogenetic reconstruction based on three different protein coding genes (glyceraldehyde-3-phosphate dehydrogenase, trypanothione reductase, and alpha-tubulin) sugg...

C-banded karyotypes, DNA content and the male meiiotic process of Triatoma platensis and Triatoma delpontei are compared with those of Triatoma infestans, the main vector of Chagas disease in South America. These three species present the same diploid chromosome number 2n = 22 (20 autosomes + XX male/XY female). They also have several cytogenetic t...

We have investigated the genome organization in the flatworm Schistosoma mansoni. First, we analyzed the compositional distributions of the three codon positions. Second, we investigated the correlations that exist between (1) the GC levels of exons against flanking regions, (2) the GC levels of third codon positions against flanking regions, (3) t...

In this study we analyze and compare the trends in codon usage in five representative species of kinetoplastid protozoans (Crithidia fasciculata, Leishmania donovani, L. major, Trypanosoma cruzi and T. brucei), with the purpose of investigating the processes underlying these trends. A principal component analysis shows that the G+C content at the t...

Dinucleotide biases in the platyhelminth Schistosoma mansoni. International Journal for Parasitology 24: 277-283. The analysis of dinucleotide biases in coding and flanking regions, introns, rDNA and repetitive sequences, in the flatwonn Schistosoma mansoni is reported. Except for rDNA, all regions display CpG avoidance and TpG plus CpA excess, whi...

We report the analysis of the biases of CpG, TpG, and CpA of all the DNA sequences data from the Trematode Schistosoma mansoni. Our results show CpG avoidance whereas TpG and CpA frequencies are over the expected values. These characteristics are similar to the biases displayed by methylated genomes, but in platyhelminths 5mC has not been detected...

This is the first report of intraspecific variation of C-bands in Heteroptera, described in natural populations of Triatoma infestans (Hemiptera: Reduviidae), the main vector of Chagas disease in Uruguay. Marked variation in number, position, and size of C-heterochromatic bands was found in the three large autosomal pairs. A geographical pattern of...