Bacterial diversity using metagenomics of 16s rDNA in water kefir, an innovative source of probiotics for bee nutrition.

Water kefir is a sparkling, slightly acidic fermented beverage made from sugar, water, and water kefir grains, which are a mixture of yeast and bacteria. These grains produce a variety of fermentation compounds such as lactic acid, acetaldehyde, acetoin, ethanol and carbon dioxide. In this study, a high-throughput sequencing technique was used to characterize the bacterial composition of the original water kefir from which potential probiotics were obtained. We studied the bacterial diversity of both water kefir grains and beverages. DNA was extracted from three replicate samples of both grains and beverages using the Powerlyzer Microbial Kit. The hypervariable V1-V2 region of the bacterial 16S ribosomal RNA gene was amplified to prepare six DNA libraries. Between 1.4M and 2.4M base-pairs were sequenced for the library. In total, 28721971 raw reads were obtained from all the samples. Estimated species richness was higher in kefir beverage samples compared to grain samples. Moreover, a higher level of microbial alpha diversity was observed in the beverage samples. Particularly, the predominant bacteria in beverages were Anaerocolumna and Ralstonia, while in grains Liquorilactobacillus dominated, with lower levels of Leuconostoc and Oenococcus. Although the bacterial diversity in kefir grains was low because only three genera were the most represented, all of them are LAB bacteria with the potential to serve as probiotics in the artificial feeding of bees.

From tetraploid to diploid, a pangenomic approach to identify genes lost during synthetic diploidization of Eragrostis curvula.

Introduction: In Eragrostis curvula, commonly known as weeping lovegrass, a synthetic diploidization event of the facultative apomictic tetraploid Tanganyika INTA cv. originated from the sexual diploid Victoria cv. Apomixis is an asexual reproduction by seeds in which the progeny is genetically identical to the maternal plant. Methods: To assess the genomic changes related to ploidy and to the reproductive mode occurring during diploidization, a mapping approach was followed to obtain the first E. curvula pangenome assembly. In this way, gDNA of Tanganyika INTA was extracted and sequenced in 2x250 Illumina pair-end reads and mapped against the Victoria genome assembly. The unmapped reads were used for variant calling, while the mapped reads were assembled using Masurca software. Results: The length of the assembly was 28,982,419 bp distributed in 18,032 contigs, and the variable genes annotated in these contigs rendered 3,952 gene models. Functional annotation of the genes showed that the reproductive pathway was differentially enriched. PCR amplification in gDNA and cDNA of Tanganyika INTA and Victoria was conducted to validate the presence/absence variation in five genes related to reproduction and ploidy. The polyploid nature of the Tanganyika INTA genome was also evaluated through the variant calling analysis showing the single nucleotide polymorphism (SNP) coverage and allele frequency distribution with a segmental allotetraploid pairing behavior. Discussion: The results presented here suggest that the genes were lost in Tanganyika INTA during the diploidization process that was conducted to suppress the apomictic pathway, affecting severely the fertility of Victoria cv.

Respuestas psicológicas a la cuarentena por pandemia de COVID-19 en población colombiana / Psychological responses to the COVID-19 pandemic quarantine in Colombian population

Resumen Introducción: el presente estudio analiza el estrés percibido, las estrategias de afrontamiento, su regulación emocional, impacto y malestar psicológico, durante la cuarentena por la pandemia de COVID-19 en la población colombiana. Método: muestra no probabilística de 356 adultos que respondieron un cuestionario en línea. Resultados: se encontraron puntuaciones medias y altas en estrategias de afrontamiento y regulación emocional activas y puntuaciones bajas en estrés, malestar psicológico e impacto de la cuarentena. El 38.76 % presentó puntuaciones que indican riesgo de trastorno por estrés postraumático. Las mujeres, los menores de 35 años, los bachilleres, los estudiantes y las personas que viven solas presentan mayores afectaciones. Se encontraron relaciones estadísticamente significativas de estrés con todas las variables, excepto con apoyo social y convivientes durante la cuarentena. Por último, se encontró asociación positiva del estrés con desahogo, supresión expresiva, impacto de la cuarentena y malestar psicológico; y asociación negativa con planificación, aceptación, revaluación cognitiva y edad mayor de 25 años. Conclusiones: los resultados contribuyen a comprender las respuestas ante la cuarentena e identificar factores de vulnerabilidad para diseñar programas de prevención e intervención.

Abstract Introduction: The aim of this study was to analyze the perceived stress, coping strategies, emotional regulation, impact of the event, and psychological distress during quarantine due to COVID-19 pandemic in the Colombian population. Method: Non-probabilistic sample made up of 356 adults who answered an online questionnaire. Results: It was found medium and high scores in active coping strategies and emotional regulation, and low scores in stress, psychological distress and impact of quarantine. The 38.76 % presented scores that indicate risk of post-traumatic stress disorder. Women, people under 35 years of age, high school graduates, students, and living alone during the quarantine showed higher affectation. Statistically significant correlations of stress with all variables except with social support and cohabitants during quarantine were found. Finally, it was found a positive association of stress with venting, expressive suppression, the impact of quarantine, and psychological distress, and negative association with planning, acceptance, cognitive reappraisal, and age over 25 years. Conclusions: These results contribute to understanding responses to quarantine and to identify vulnerability factors to design prevention and intervention programs.

Geriatric co-management and interdisciplinary transitional care reduced hospital readmissions in frail older patients in Argentina: results from a randomized controlled trial.

BACKGROUND: Hospitalization is a moment of extreme vulnerability for frail older adults. There is scarce evidence on the effectiveness of geriatric co-management or transitional care interventions in Latin America. AIMS: To assess whether geriatric co-management combined with an interdisciplinary transitional care intervention could reduce 30-day hospital readmission rate compared to usual care in hospitalized frail older patients in a tertiary hospital in Argentina. METHODS: Single-blinded randomized controlled trial. Usual care treatment arm: all procedures performed during hospitalization were overseen by a senior internal medicine specialist and complied with pre-defined protocols. Patients had access to specialist care if needed, as well as hospital-at-home or home-based primary care services after discharge. Intervention treatment arm: in addition to usual care, a geriatric co-management team performed a comprehensive geriatric assessment during hospitalization, provided tailored recommendations to minimize geriatric syndromes and planned transition of care. A health and social care counselor oversaw continuity of care in patients' homes after discharge. RESULTS: We included 120 participants in each of the intervention and usual care (control) arms. Thirty-day hospital readmissions were 47.7% lower in the intervention arm (18.3% vs 35.0%; P = 0.040); and emergency room visits within the first 6 months after discharge were 27.8% lower (43.3% vs 60.0%; P = 0.010). There was a non-statistically significant decrease in 6-month mortality in the intervention arm (25.0% vs 35.0%; P = 0.124). CONCLUSION: Geriatric co-management of frail older patients during hospitalization combined with an interdisciplinary transitional care intervention reduced 30-day hospital readmissions and emergency visits 6 months after discharge. TRIAL REGISTRATION NUMBER: Trial registration number: RENIS IS003081.

Phylogenomics, CAZyome and core secondary metabolome of Streptomyces albus species.

A phylogenomic study conducted with different bioinformatic tools such as TYGS, REALPHY and AAI comparisons revealed a high rate of misidentified Streptomyces albus genomes in GenBank. Only 9 of the 18 annotated genomes available in the public database were correctly identified as S. albus species. The pangenome of the nine in silico confirmed S. albus genomes was almost closed. Lignocellulosic agroresidues were a common niche among strains of the S. albus clade while carbohydrate active enzymes (CAZymes) were highly conserved. Relevant enzymes for cellulose degradation such as beta glucosidases belonging to the GH1 family, a GH6 cellulase and a monooxygenase AA10-CBM2 were encoded by all S. albus genomes. Among them, one GH1 glycosidase would be regulated by CebR. However, this regulatory mechanism was not confirmed for other genes related to cellulose degradation. Based on AntiSMASH predictions, the core secondary metabolome of S. albus encompassed a total of 23 biosynthetic gene clusters (BGCs), where 4 were related to common metabolites within Streptomyces genus. Species specific BGCs included those related to pseudouridimycin and xantholipin. Additionally, four BGCs encoded putative derivatives of ibomycin, the lasso peptide SSV-2086, the lanthipeptide SapB and the terpene isorenieratene. Known metabolites could not be assigned to ten BGCs and three clusters did not match with any previously described BGC. The core genome of S. albus retrieved from nine closely related genomes revealed a high potential for the discovery of novel bioactive metabolites and underexplored regulatory genomic elements related to lignocellulose deconstruction.

Differential Methylation Patterns in Apomictic vs. Sexual Genotypes of the Diplosporous Grass Eragrostis curvula.

DNA methylation is an epigenetic mechanism by which a methyl group is added to a cytosine or an adenine. When located in a gene/regulatory sequence it may repress or de-repress genes, depending on the context and species. Eragrostis curvula is an apomictic grass in which facultative genotypes increases the frequency of sexual pistils triggered by epigenetic mechanisms. The aim of the present study was to look for correlations between the reproductive mode and specific methylated genes or genomic regions. To do so, plants with contrasting reproductive modes were investigated through MCSeEd (Methylation Context Sensitive Enzyme ddRad) showing higher levels of DNA methylation in apomictic genotypes. Moreover, an increased proportion of differentially methylated positions over the regulatory regions were observed, suggesting its possible role in regulation of gene expression. Interestingly, the methylation pathway was also found to be self-regulated since two of the main genes (ROS1 and ROS4), involved in de-methylation, were found differentially methylated between genotypes with different reproductive behavior. Moreover, this work allowed us to detect several genes regulated by methylation that were previously found as differentially expressed in the comparisons between apomictic and sexual genotypes, linking DNA methylation to differences in reproductive mode.

Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes.

BACKGROUND: Durum wheat (Triticum turgidum L. ssp. durum Desf. Husn) is the main staple crop used to make pasta products worldwide. Under the current climate change scenarios, genetic variability within a crop plays a crucial role in the successful release of new varieties with high yields and wide crop adaptation. In this study we evaluated a durum wheat collection consisting of 197 genotypes that mainly comprised a historical set of Argentinian germplasm but also included worldwide accessions. RESULTS: We assessed the genetic diversity, population structure and linkage disequilibrium (LD) patterns in this collection using a 35 K SNP array. The level of polymorphism was considered, taking account of the frequent and rare allelic variants. A total of 1547 polymorphic SNPs was located within annotated genes. Genetic diversity in the germplasm collection increased slightly from 1915 to 2010. However, a reduction in genetic diversity using SNPs with rare allelic variants was observed after 1979. However, larger numbers of rare private alleles were observed in the 2000-2009 period, indicating that a high reservoir of rare alleles is still present among the recent germplasm in a very low frequency. The percentage of pairwise loci in LD in the durum genome was low (13.4%) in our collection. Overall LD and the high (r2 > 0.7) or complete (r2 = 1) LD presented different patterns in the chromosomes. The LD increased over three main breeding periods (1915-1979, 1980-1999 and 2000-2020). CONCLUSIONS: Our results suggest that breeding and selection have impacted differently on the A and B genomes, particularly on chromosome 6A and 2A. The collection was structured in five sub-populations and modern Argentinian accessions (cluster Q4) which were clearly differentiated. Our study contributes to the understanding of the complexity of Argentinian durum wheat germplasm and to derive future breeding strategies enhancing the use of genetic diversity in a more efficient and targeted way.

Genes Modulating the Increase in Sexuality in the Facultative Diplosporous Grass Eragrostis curvula under Water Stress Conditions.

Eragrostis curvula presents mainly facultative genotypes that reproduce by diplosporous apomixis, retaining a percentage of sexual pistils that increase under drought and other stressful situations, indicating that some regulators activated by stress could be affecting the apomixis/sexual switch. Water stress experiments were performed in order to associate the increase in sexual embryo sacs with the differential expression of genes in a facultative apomictic cultivar using cytoembryology and RNA sequencing. The percentage of sexual embryo sacs increased from 4 to 24% and 501 out of the 201,011 transcripts were differentially expressed (DE) between control and stressed plants. DE transcripts were compared with previous transcriptomes where apomictic and sexual genotypes were contrasted. The results point as candidates to transcripts related to methylation, ubiquitination, hormone and signal transduction pathways, transcription regulation and cell wall biosynthesis, some acting as a general response to stress and some that are specific to the reproductive mode. We suggest that a DNA glycosylase EcROS1-like could be demethylating, thus de-repressing a gene or genes involved in the sexuality pathways. Many of the other DE transcripts could be part of a complex mechanism that regulates apomixis and sexuality in this grass, the ones in the intersection between control/stress and apo/sex being the strongest candidates.

A High-Density Linkage Map of the Forage Grass Eragrostis curvula and Localization of the Diplospory Locus.

Eragrostis curvula (Schrad.) Nees (weeping lovegrass) is an apomictic species native to Southern Africa that is used as forage grass in semiarid regions of Argentina. Apomixis is a mechanism for clonal propagation through seeds that involves the avoidance of meiosis to generate an unreduced embryo sac (apomeiosis), parthenogenesis, and viable endosperm formation in a fertilization-dependent or -independent manner. Here, we constructed the first saturated linkage map of tetraploid E. curvula using both traditional (AFLP and SSR) and high-throughput molecular markers (GBS-SNP) and identified the locus controlling diplospory. We also identified putative regulatory regions affecting the expressivity of this trait and syntenic relationships with genomes of other grass species. We obtained a tetraploid mapping population from a cross between a full sexual genotype (OTA-S) with a facultative apomictic individual of cv. Don Walter. Phenotypic characterization of F1 hybrids by cytoembryological analysis yielded a 1:1 ratio of apomictic vs. sexual plants (34:27, X 2 = 0.37), which agrees with the model of inheritance of a single dominant genetic factor. The final number of markers was 1,114 for OTA-S and 2,019 for Don Walter. These markers were distributed into 40 linkage groups per parental genotype, which is consistent with the number of E. curvula chromosomes (containing 2 to 123 markers per linkage group). The total length of the OTA-S map was 1,335 cM, with an average marker density of 1.22 cM per marker. The Don Walter map was 1,976.2 cM, with an average marker density of 0.98 cM/marker. The locus responsible for diplospory was mapped on Don Walter linkage group 3, with other 65 markers. QTL analyses of the expressivity of diplospory in the F1 hybrids revealed the presence of two main QTLs, located 3.27 and 15 cM from the diplospory locus. Both QTLs explained 28.6% of phenotypic variation. Syntenic analysis allowed us to establish the groups of homologs/homeologs for each linkage map. The genetic linkage map reported in this study, the first such map for E. curvula, is the most saturated map for the genus Eragrostis and one of the most saturated maps for a polyploid forage grass species.

Crosstalk pathway inference using topological information and biclustering of gene expression data.

Detection of crosstalks among pathways is a challenging task, which requires the identification of different types of interactions associated with cellular processes. A common strategy used in bioinformatics consists in extrapolating pathway associations from the pairwise analysis of some genes related to them, using gene expression data and topological information. PET, the method proposed in this paper, goes a step further by incorporating a strategy for the detection of correlation across conditions between differentially expressed genes based on biclustering analysis. In order to evaluate the performance of this new approach, a comparison with two recently published algorithms was carried out. The methods were contrasted in the inference of pathway associations from Alzheimer disease datasets, where the new proposal presents a higher crosstalk discoveries' rate. Finally, the analysis of the biological relevance of the pathway associations inferred by PET has shown the soundness of the extracted knowledge.

Discovering time-lagged rules from microarray data using gene profile classifiers.

BACKGROUND: Gene regulatory networks have an essential role in every process of life. In this regard, the amount of genome-wide time series data is becoming increasingly available, providing the opportunity to discover the time-delayed gene regulatory networks that govern the majority of these molecular processes. RESULTS: This paper aims at reconstructing gene regulatory networks from multiple genome-wide microarray time series datasets. In this sense, a new model-free algorithm called GRNCOP2 (Gene Regulatory Network inference by Combinatorial OPtimization 2), which is a significant evolution of the GRNCOP algorithm, was developed using combinatorial optimization of gene profile classifiers. The method is capable of inferring potential time-delay relationships with any span of time between genes from various time series datasets given as input. The proposed algorithm was applied to time series data composed of twenty yeast genes that are highly relevant for the cell-cycle study, and the results were compared against several related approaches. The outcomes have shown that GRNCOP2 outperforms the contrasted methods in terms of the proposed metrics, and that the results are consistent with previous biological knowledge. Additionally, a genome-wide study on multiple publicly available time series data was performed. In this case, the experimentation has exhibited the soundness and scalability of the new method which inferred highly-related statistically-significant gene associations. CONCLUSIONS: A novel method for inferring time-delayed gene regulatory networks from genome-wide time series datasets is proposed in this paper. The method was carefully validated with several publicly available data sets. The results have demonstrated that the algorithm constitutes a usable model-free approach capable of predicting meaningful relationships between genes, revealing the time-trends of gene regulation.