Leishmania infantum (JPCM5) transcriptome, gene models and resources for an active curation of gene annotations

Leishmania infantum is one of the causative agents of visceral leishmaniases, the most severe form of leishmaniasis. An improved assembly for the L. infantum genome was published five years ago, yet delineation of its transcriptome remained to be accomplished. In this work, the transcriptome annotation was attained by a combination of both short and long RNA-seq reads. The good agreement between the results derived from both methodologies confirmed that transcript assembly based on Illumina RNA-seq and further delimitation according to the positions of spliced leader (SAS) and poly-A (PAS) addition sites is an adequate strategy to annotate the transcriptomes of Leishmania, a procedure previously used for transcriptome annotation in other Leishmania species and related trypanosomatids. These analyses also confirmed that the Leishmania transcripts boundaries are relatively slippery, showing extensive heterogeneity at the 5′- and 3′-ends. However, the use of RNA-seq reads derived from the PacBio technology (referred to as Iso-Seq) allowed the authors to uncover some complex transcription patterns occurring at particular loci that would be unnoticed by the use of short RNA-seq reads alone. Thus, Iso-Seq analysis provided evidence that transcript processing at particular loci would be more dynamic than expected. Another noticeable finding was the observation of a case of allelic heterozygosity based on the existence of chimeric Iso-Seq reads that might be generated by an event of intrachromosomal recombination. In addition, we are providing the L. infantum gene models, including both UTRs and CDS regions, that would be helpful for undertaking whole-genome expression studies. Moreover, we have built the foundations of a communal database for the active curation of both gene/transcript models and functional annotations for genes and proteinsThis research was supported by the Spanish Ministerio de Ciencia, Innovación (MICINN), Agencia Estatal deInvestigación(AEI), grant number PID2020-117916RB-I00, and Instituto de Salud Carlos III, grant CB21/13/00018 (CIBERINFEC). An institutional grant from Fundacion RamonAreces is also acknowledge

Anthropometric failure and geographical altitude in food assisted schoolchildren from Jujuy

Introducción: Alteraciones en el crecimiento y/o el desarrollo de los niños implica el fracaso, no sólo del crecimiento, sino también en otros aspectos del bienestar infantil. La caracterización de este fracaso y una evaluación de la situación nutricional resulta vital para identificar situaciones de riesgo. Objetivo: Analizar el estado nutricional de escolares jujeños, entre 4 y 9 años, evaluados con el Índice de Fracaso Antropométrico Extendido y su relación con la altura geográfica, las diferentes modalidades de asistencia alimentaria escolar y el sexo, en dos momentos del año escolar. Métodos: Estudio transversal. Se evaluaron 5806 escolares entre 4 y 9 años, asistidos alimentariamente por el programa de Comedores Escolares de la provincia de Jujuy. Se registró peso y talla en dos momentos del año escolar y se consideró la altura geográfica y el sexo. Se determinó bajo peso, baja talla, emaciación y exceso ponderal y se construyó el Índice de Fracaso Antropométrico Extendido. Se estimaron estadísticos descriptivos, prevalencias, se realizaron comparaciones y regresiones logísticas para evaluar la relación entre las variables. Resultados: La categoría "sin fracaso" presentó la mayor frecuencia en ambas mediciones, seguida por exceso de peso y acortamiento. Entre mediciones hubo un lapso promedio de 5 meses y en ese tiempo se observó una reducción del fracaso antropométrico total, acortamiento + bajo peso, acortamiento y exceso de peso + acortamiento. Las diferencias por altura geográfica reflejaron que la malnutrición por déficit fue mayor en tierras altas y la malnutrición por exceso en tierras bajas. A su vez, solo el sexo tuvo relación con el fracaso antropométrico, siendo mayor la probabilidad en mujeres. Conclusiones: Este estudio sugiere que la asistencia alimentaria escolar tendría un efecto positivo en la situación nutricional de escolares, ya que reduciría el riesgo de malnutrición por la eventual inseguridad alimentaria de sus hogares.Introduction: Alterations in the growth and/or development of children implies failure, not only on growth, but also in other aspects of child welfare. The characterization of this failure and an assessment of the nutritional situation is vital to identify risk factors. Objective: To analyze the nutritional status of schoolchildren from Jujuy, between 4 and 9 years old, evaluated with the Extended Anthropometric Failure Index and its relationship with geographical altitude, the different modalities of school food assistance and sex, in two moments of the school year Methods: Cross-sectional study. 5806 schoolchildren from Jujuy between 4 and 9 years old were evaluated, food-assisted by the School Dining Program in the province of Jujuy. Weight and height were recorded at two times of the school year and geographic height and gender were considered. Underweight, stunting, wasting and weight excess were determined and the Extended Anthropometric Failure Index was constructed. Descriptive statistics and prevalence were estimated. Comparisons and logistic regressions were made to assess the relationship between the variables. Results: The “no failure” category presented the highest frequency in both measurements, followed by excess weight and stunting. Between measurements there was an average span of 5 months and at that time a reduction in total anthropometric failure, stunting + underweight, stunting and excess weight + stunting was observed. Differences in geographical altitude reflected that deficit malnutrition was higher in the highlands and malnutrition due to excess in the lowlands. In turn, only sex was related to anthropometric failure, being the probability higher in women. Conclusions: This study suggests that school food assistance would have a positive effect on the nutritional status of schoolchildren, since it would reduce the risk of malnutrition due to eventual food insecurity in their homesFil: Bustamante, María José. Universidad Nacional de Jujuy. Instituto de Ecorregiones Andinas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Ecorregiones Andinas; Argentina. Universidad Nacional de Jujuy. Instituto de Biología de la Altura; ArgentinaFil: Martinez, Jorge Ivan. Universidad Nacional de Jujuy. Instituto de Biología de la Altura; Argentina. Universidad Nacional de Jujuy. Instituto de Ecorregiones Andinas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Ecorregiones Andinas; ArgentinaFil: Alfaro Gómez, Emma Laura. Universidad Nacional de Jujuy. Instituto de Biología de la Altura; Argentina. Universidad Nacional de Jujuy. Instituto de Ecorregiones Andinas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Ecorregiones Andinas; ArgentinaFil: Sánchez Alvarez, María Josefina. Universidad Complutense de Madrid; EspañaFil: Dipierri, Jose Edgardo. Universidad Nacional de Jujuy. Instituto de Biología de la Altura; ArgentinaFil: Tabera, Celia. Gobierno de la Provincia de Jujuy. Ministerio de Educacion de Jujuy.; Argentin

Mejora genética de levaduras vínicas mediante la modificación del gen BCY1

Tesis Doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Química Física Aplicada. Fecha de lectura: 19-10-200

Deletion of BCY1 from the Saccharomyces cerevisiae Genome Is Semidominant and Induces Autolytic Phenotypes Suitable for Improvement of Sparkling Wines

Autolysis of Saccharomyces cerevisiae is the main source of molecules that contribute to the quality of sparkling wines made by the traditional method. In this work the possibility of accelerating this slow process in order to improve the quality of sparkling wines by using genetically engineered wine yeast strains was explored. The effect of partial or total deletion of BCY1 (which encodes a regulatory subunit of cAMP-dependent protein kinase A) in haploid and diploid (heterozygous and homozygous) yeast strains was studied. We proved that heterozygous strains having partial or complete BCY1 deletions have a semidominant phenotype for several of the properties studied, including autolysis under simulated second-fermentation conditions, in contrast to previously published reports describing mutations in BCY1 as recessive. Considering the degree of autolysis, ethanol tolerance, and technical feasibility, we propose that deletion of the 3′ end of the open reading frame of a single copy of BCY1 is a way to improve the quality of sparkling wines

Tyramine and Phenylethylamine Biosynthesis by Food Bacteria

Tyramine poisoning is caused by the ingestion of food containing high levels of tyramine, a biogenic amine. Any foods containing free tyrosine are subject to tyramine formation if poor sanitation and low quality foods are used or if the food is subject to temperature abuse or extended storage time. Tyramine is generated by decarboxylation of the tyrosine through tyrosine decarboxylase (TDC) enzymes derived from the bacteria present in the food. Bacterial TDC have been only unequivocally identified and characterized in Gram-positive bacteria, especially in lactic acid bacteria. Pyridoxal phosphate (PLP)-dependent TDC encoding genes (tyrDC) appeared flanked by a similar genetic organization in several species of lactic acid bacteria, suggesting a common origin by a single mobile genetic element. Bacterial TDC are also able to decarboxylate phenylalanine to produce phenylethylamine (PEA), another biogenic amine. The molecular knowledge of the genes involved in tyramine production has led to the development of molecular methods for the detection of bacteria able to produce tyramine and PEA. These rapid and simple methods could be used for the analysis of the ability to form tyramine by bacteria in order to evaluate the potential risk of tyramine biosynthesis in food products. © 2012 Copyright Taylor and Francis Group, LLC.This work was supported by grants AGL2008-01052, AGL2011-22745, and CONSOLIDER INGENIO 2010 CSD2007-00063 FUN-C-FOOD (CICYT), RM2008-00002 (INIA), and S2009/AGR-1469 (ALIBIRD) (CAM). We are grateful to M. V. Santamaría. J. M. Landete was a recipient of a postdoctoral fellowship from the MEC.Peer Reviewe

Cepas vínicas de S. cerevisiae con bajo rendimiento en etanol.

Desde el punto de vista de la microbiología enológica, y asociados al cambio climático, las variaciones previstas en las condiciones ambientales (temperatura, estrés hídrico, etc.), en la composición del sustrato, o incluso en la fisiología de la baya y en las técnicas de cultivo, hacen probable que se modifiquen la ecología, la biodiversidad y el metabolismo de la microbiota de la viña, la uva, el mosto y el vino. Uno de los aspectos de este problema que más inquieta a los productores es que, para alcanzar la madurez fenólica apropiada, el contenido en azúcar de la uva y el grado alcohólico esperado irán probablemente en aumento, dando lugar a dos situaciones potencialmente negativas, en función también de otros factores, como el estilo de vinificación. Por un lado está la posibilidad de fermentaciones incompletas, si se supera el nivel de tolerancia al etanol de las levaduras predominantes durante el proceso de fermentación (que en principio serán células de la cepa utilizada como cultivo iniciador), dando lugar a vinos con exceso de azúcar residual, microbiológicamente inestables y sensorialmente defectuosos. La situación recíproca, en el caso de que la fermentación sea completa, sería una producción excesiva de etanol, que además de constituir una limitación para la calidad sensorial del vino, lo es también para su viabilidad comercial. Como otras muchas cuestiones en vitivinicultura, el problema del excesivo grado alcohólico del vino puede ser abordado desde diferentes puntos de vista y recurriendo a diferentes disciplinas (viticultura, microbiología, tecnología, biotecnología ) de una manera complementaria. En este artículo vamos a discutir fundamentalmente la posibilidad de reducir la producción de etanol durante la fermentación alcohólica, recurriendo a la microbiología y la biotecnología microbianas, en concreto mediante la selección y desarrollo de cepas deSaccharomyces con bajo rendimiento alcohólico.Peer reviewe

Cepas vínicas de Saccharomyces cerevisiae con bajo rendimiento en etanol

Desde la variabilidad natural hasta la ingeniería genética, pasando por la selección clásica de cepas, Saccharomyces es el organismo clave que mejor ejemplifica las posibilidades de conseguir levaduras con bajo rendimiento en etanol

Transgenic wine yeast technology comes of age: is it time for transgenic wine?

Saccharomyces cerevisiae is the main yeast responsible for alcoholic fermentation of grape juice during wine making. This makes wine strains of this species perfect targets for the improvement of wine technology and quality. Progress in winemaking has been achieved through the use of selected yeast strains, as well as genetic improvement of wine yeast strains through the sexual and pararexual cycles, random mutagenesis and genetic engineering. Development of genetically engineered wine yeasts, their potential application, and factors affecting their commercial viability will be discussed in this reviewWork in the laboratory of the authors is sustained by grants from the Spanish Ministry for Science and Education (AGL2003-01762, AGL2006-02558), and Comunidad de Madrid (S-505/AGR-0153). DGR is the recipient of a fellowship from the Government of The Basque Country (Gobierno Vasco-Eusko Jaurlaritza).Peer reviewe

Multi locus sequence typing of oenological Saccharomyces cerevisiae strains

6 páginas -- 2 TablasThis study describes the application of a multilocus sequence typing (MLST) analysis for molecular discrimination at the strain level of Spanish wine yeast strains. The discrimination power of MLST is compared to mitochondrial RFLP analysis. Fragments of the ADP1, ACC1, RPN2, GLN4, and ALA1 genes were amplified by PCR from chromosomal DNA of 18 wine Saccharomyces cerevisiae strains. Ten polymorphic sites were found in the five loci analyzed showing 13 different genotypes, with 11 of them represented by only one strain. RFLP analysis of the same 18 wine yeast strains showed seventeen different mitochondrial patterns. Phylogenetic relationships among the strains analyzed, inferred by MLST data, showed wine isolates of S. cerevisiae as a rather homogeneous group. The discrimination potential of mitochondrial RFLP analysis was superior to the MLST scheme used in this work. However, MLST analysis allowed an easy construction of reliable phylogenetic trees. MLST analysis offers the possibility of typing wine S. cerevisiae strains simultaneously to the study of the genetic relationship among themThis work was supported by the Spanish Ministerio de Educación y Ciencia (Consolider CSD2007-00063); and the Comunidad de Madrid local Government (grant S-505/AGR-0153).Peer reviewe

A new methodology to obtain wine yeast strains overproducing mannoproteins

Yeast mannoproteins are highly glycosylated proteins that are covalently bound to the β-1,3-glucan present in the yeast cell wall. Among their outstanding enological properties, yeast mannoproteins contribute to several aspects of wine quality by protecting against protein haze, reducing astringency, retaining aroma compounds and stimulating growth of lactic-acid bacteria. The development of a non-recombinant method to obtain enological yeast strains overproducing mannoproteins would therefore be very useful. Our previous experience on the genetic determinants of the release of these molecules by Saccharomyces cerevisiae has allowed us to propose a new methodology to isolate and characterize wine yeast that overproduce mannoproteins. The described methodology is based on the resistance of the killer 9 toxin produced by Williopsis saturnus, a feature linked to an altered biogenesis of the yeast cell wall.This work was supported by the Spanish Ministerio de Ciencia e Innovación (grants AGL2006-02558, and ConsoliderCSD2007-00063). D.G.-R was supported by a pre-doctoral fellowship from the Government of The Basque Country (Gobierno Vasco-Eusko Jaurlaritza). The authors are grateful to José María Barcenilla and Laura López Berges for their excellent technical assistance and to Jytte Laursen for kindly reviewing the English expression in this manuscriptPeer reviewe