PubMed Health⌕ Search

Biomedical subjects

Eladio Barrio

Publications and source records attributed to Eladio Barrio.

13 recordsLinked to original sources
PubMed2006

Natural hybrids from Saccharomyces cerevisiae, Saccharomyces bayanus and Saccharomyces kudriavzevii in wine fermentations.

Several wine isolates of Saccharomyces were analysed for six molecular markers, five nuclear and one mitochondrial, and new natural interspecific hybrids were identified. The molecular characterization of these Saccharomyces hybrids was performed based on the restriction analysis of five nuclear genes (CAT8, CYR1, GSY1, MET6 and OPY1, located in different chromosomes), the ribosomal region encompassing the 5.8S rRNA gene and the two internal transcribed spacers, and sequence analysis of the mitochondrial gene COX2. This method allowed us to identify and characterize new hybrids between Saccharomyces cerevisiae and Saccharomyces kudriavzevii, between S. cerevisiae and Saccharomyces bayanus, as well as a triple hybrid S. bayanusxS. cerevisiaexS. kudriavzevii. This is the first time that S. cerevisiaexS. kudriavzevii hybrids have been described which have been involved in wine fermentation.

DNA, Fungal↗
PubMed2004

GroEL and the maintenance of bacterial endosymbiosis.

Many eukaryotic organisms have symbiotic associations with obligate intracellular bacteria. The clonal transmission of endosymbionts between host generations should lead to the irreversible fixation of slightly deleterious mutations in their non-recombinant genome by genetic drift. However, the stability of endosymbiosis indicates that some mechanism is involved in the amelioration of the effects of these mutations. We propose that the chaperone GroEL was involved in the acquisition of an endosymbiotic lifestyle not only by means of its over-production, as proposed by Moran, but also by its adaptive evolution mediated by positive selection to improve the interaction with the unstable endosymbiont proteome.

Bacterial Physiological Phenomena↗
PubMed2003

Analysis of the genetic variability in the species of the Saccharomyces sensu stricto complex.

Random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) analysis was applied to differentiate the sibling species Saccharomyces bayanus, S. cerevisiae, S. paradoxus and S. pastorianus, which constitute the most common strains of the Saccharomyces sensu stricto complex. Six decamer primers of arbitrary sequences were used to amplify the DNA of 58 strains. Species-specific (diagnostic) bands were obtained for each species. Two phylogenetic trees constructed by the neighbour-joining and maximum parsimony methods clearly showed that the delimitation of these related yeast species is possible by using RAPD analysis. Four groups of strains, corresponding to the species S. bayanus, S. cerevisiae, S. paradoxus and S. pastorianus, were obtained. Within the S. bayanus taxon, two groups of strains were observed. One includes the former type strain of S. uvarum, CECT1969(T), and closely related wine strains (S. bayanus var. uvarum), whilst the other contains S. bayanus type strain CECT1941(T) and strains CECT1991 and 10513 (S. bayanus var. bayanus). The heterogeneous S. paradoxus group was divided into three lineages, corresponding to different geographic origin, American, Japanese and European populations. In addition, due to the multilocus nature of the RAPD-PCR marker, this method is both useful and appropriate for the identification of the hybrid origin of S. pastorianus. The hybrid nature was deduced from the analysis of the fraction of bands shared by each hybrid strain and the parental species. Among the 58 strains analysed, six S. pastorianus strains were hybrids, although the fraction of genome coming from each parent varied depending on the strain.

DNA, Fungal↗
PubMed2003

Adaptive evolution of wine yeast.

Alcoholic fermentation is one of the main phases in wine production. It is usually conducted by yeasts belonging to the species Saccharomyces cerevisiae. Industrial S. cerevisiae strains are highly specialized organisms, which have evolved to utilize to their full potential the different environments or ecological niches. So, during the alcoholic fermentation, the yeast has been adapted to different kinds of stress conditions; this adaptation is call "domestication". In this review, we describe the different mechanisms involved in the adaptive evolution of wine yeast strains.

Adaptation, Physiological↗
PubMed2003

Molecular evolution in yeast of biotechnological interest.

The importance of yeast in the food and beverage industries was only realized about 1860, when the role of these organisms in food manufacture became evident. Since they grow on a wide range of substrates and can tolerate extreme physicochemical conditions, yeasts, especially the genera Saccharomyces and Kluyveromyces, have been applied to many industrial processes, Industrial strains of these genera are highly specialized organisms that have evolved to utilize a range of environments and ecological niches to their full potential. This adaptation is called "domestication". This review describes the phylogenetic relationships among Saccharomyces and Kluyveromyces species and the different mechanisms involved in the adaptive evolution of industrial yeast strains.

Biotechnology↗
PubMed2003

A new PCR-based method for monitoring inoculated wine fermentations.

A new PCR-based method has been developed to monitor inoculated wine fermentations. The method is based on the variation in the number and position of introns in the mitochondrial gene COX1. Oligonucleotide primers homologous to the regions flanking the Saccharomyces cerevisiae COX1 introns have been designed and tested for S. cerevisiae wine yeast strain differentiation. Four primers were selected for their subsequent use in a multiplex PCR reaction and have proved to be very effective in uncovering polymorphism in natural and commercial yeast strains. An important point is that the speed and simplicity of the technique, which does not require the isolation of DNA, allows early detection of the starter yeast strain throughout the fermentation process. The main advantage for the wineries is that the must sample can be used directly for the PCR reaction obtaining very fast results (in approximately 8 h). This allows the wine industries to intervene quickly if necessary.

DNA, Fungal↗
PubMed2003

Patterns of DNA sequence polymorphism at Sod vicinities in Drosophila melanogaster: unraveling the footprint of a recent selective sweep.

We survey DNA sequence polymorphisms at the Sod locus and four neighboring regions of Drosophila melanogaster, spanning 55,513 base pairs (bp), in 15 strains from a natural population, plus one reference laboratory strain and one strain of Drosophila simulans. Our objective is to characterize a proposed selective sweep that occurred at a locus close to Sod in D. melanogaster and to characterize the strength of the selection event, its time, and the size of the hitchhiked region. Two regions, 1819 and 6kbr3r, show a pattern of polymorphism very similar to the one of Sod, implying that they have been affected by the same evolutionary process that impacted Sod. A third fragment, 2021 seems unaffected by the event. A fourth one, 4039, on the opposite flank of Sod in relation to 2021, is only partially affected. We estimate that the length of the chromosomal segment impacted by the selective sweep is 41-54 kb, the age of the selective sweep is 2,600-22,000 years, and the selective advantage is 0.020 < s < 0.103.

Animals↗
PubMed2003

A DNA region of Torulaspora delbrueckii containing the HIS3 gene: sequence, gene order and evolution.

We cloned a genomic DNA fragment of the yeast Torulaspora delbrueckii by complementation of a Saccharomyces cerevisiae his3 mutant strain. DNA sequence analysis revealed that the fragment contained two complete ORFs, which share a high similarity with S. cerevisiae His3p and Mrp51p, respectively. The cloned TdHIS3 gene fully complemented the his3 mutation of S. cerevisiae, confirming that it encodes for the imidazoleglycerol-phosphate dehydrate of T. delbrueckii. Two additional ORFs, with a high homology to S. cerevisiae PET56 and DED1 genes, were mapped upstream and downstream from TdHIS3 and TdMRP51, respectively. This genetic organization is analogous to that previously found in Saccharomyces kluyveri and Zygosaccharomyces rouxii. The evolutionary significance of gene order in this chromosomal region is analysed and discussed.

Amino Acid Sequence↗
PubMed2002

An analysis of inter- and intraspecific genetic variabilities in the Kluyveromyces marxianus group of yeast species for the reconsideration of the K. lactis taxon.

In the present work, we analyse the sequences of the 5.8S rRNA gene and the two internal transcribed spacers 1 and 2 (5.8S-ITS region), obtained from 39 strains belonging to the species Kluyveromyces aestuarii, K. dobzhanskii, K. lactis and K. marxianus, K. nonfermentans and K. wickerhamii, to solve the phylogenetic relationships among these species and also to determine the possible genetic basis for the delimitation of the two currently accepted K. lactis varieties: lactis, including lactose-positive strains isolated from dairy products, and drosophilarum, comprising lactose-negative strains isolated from insects and plant exudates. The determination of the phylogenetic relationships within the species K. lactis, together with the examination of the electrophoretic karyotypes and phenotypic characterization of strains representatives of K. lactis var. lactis and var. drosophilarum, allowed differentiation of two groups of strains. The first, and ancestral, group comprises lactose-negative strains isolated from natural habitats in North America. The second, and derived, group includes both lactose-negative strains isolated from natural habitats in Europe and wine fermentation in South Africa, and lactose-positive strains associated with dairy products. These results suggest that the present taxon K. lactis is a complex of different species, subspecies or, at least, genetically structured populations.

Base Sequence↗
PubMed2002

A sliding window-based method to detect selective constraints in protein-coding genes and its application to RNA viruses.

Here we present a new sliding window-based method specially designed to detect selective constraints in specific regions of a multiple protein-coding sequence alignment. In contrast to previous window-based procedures, our method is based on a nonarbitrary statistical approach to find the appropriate codon-window size to test deviations of synonymous (d(S)) and nonsynonymous (d(N)) nucleotide substitutions from the expectation. The probabilities of d(N) and d(S) are obtained from simulated data and used to detect significant deviations of d(N) and d(S) in a specific window region of the real sequence alignment. The nonsynonymous-to-synonymous rate ratio (w = d(N)/d(S)) was used to highlight selective constraints in any window wherein d(S) or d(N) was significantly different from the expectation. In these significant windows, w and its variance [V(w)] were calculated and used to test the neutral hypothesis. Computer simulations showed that the method is accurate even for highly divergent sequences. The main advantages of the new method are that it (i) uses a statistically appropriate window size to detect different selective patterns, (ii) is computationally less intensive than maximum likelihood methods, and (iii) detects saturation of synonymous sites, which can give deviations from neutrality. Hence, it allows the analysis of highly divergent sequences and the test of different alternative hypothesis as well. The application of the method to different human immunodeficiency virus type 1 and to foot-and-mouth disease virus genes confirms the action of positive selection on previously described regions as well as on new regions.

Base Sequence↗
PubMed2002

The evolution of the heat-shock protein GroEL from Buchnera, the primary endosymbiont of aphids, is governed by positive selection.

The heat-shock protein GroEL is a double-ring-structured chaperonin that assists the folding of many newly synthesized proteins in Escherichia coli and the refolding in vitro, with the cochaperonin GroES, of conformationally damaged proteins. This protein is constitutively overexpressed in the primary symbiotic bacteria of many insects, constituting approximately 10% of the total protein in Buchnera, the primary endosymbiont of aphids. In the present study, we perform a maximum likelihood (ML) analysis to unveil the selective constraints in GroEL. In addition, we apply a new statistical approach to determine the patterns of evolution in this highly interesting protein. The main conclusion derived from our analysis is that GroEL has suffered an accelerated rate of amino acid substitution upon the symbiotic integration of Buchnera into the aphids. It is most interesting that the ML analysis of codon substitutions in the different branches of the phylogenetic tree strongly supports the action of positive selection in the different lineages of BUCHNERA: Additionally, the new sliding window analysis of the complete groEL sequence reveals different regions of the molecule under the action of positive selection, mainly located in the apical domain, that are important for both peptide and GroES binding.

Amino Acid Substitution↗
PubMed2002

Molecular characterization of a chromosomal rearrangement involved in the adaptive evolution of yeast strains.

Wine yeast strains show a high level of chromosome length polymorphism. This polymorphism is mainly generated by illegitimate recombination mediated by Ty transposons or subtelomeric repeated sequences. We have found, however, that the SSU1-R allele, which confers sulfite resistance to yeast cells, is the product of a reciprocal translocation between chromosomes VIII and XVI due to unequal crossing-over mediated by microhomology between very short sequences on the 5' upstream regions of the SSU1 and ECM34 genes. We also show that this translocation is only present in wine yeast strains, suggesting that the use for millennia of sulfite as a preservative in wine production could have favored its selection. This is the first time that a gross chromosomal rearrangement is shown to be involved in the adaptive evolution of Saccharomyces cerevisiae.

Anion Transport Proteins↗