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Microbial communities in agricultural soils are fundamental for plant growth and in vineyard ecosystems contribute to defining regional wine quality. Managing soil microbes towards beneficial outcomes requires knowledge of how community assembly processes vary across taxonomic groups, spatial scales, and through time. However, our understanding of microbial assembly remains limited. To quantify the contributions of stochastic and deterministic processes to bacterial and fungal assembly across spatial scales and through time, we used 16 s rRNA gene and ITS sequencing in the soil of an emblematic wine-growing region of Italy.Combining null- and neutral-modelling, we found that assembly processes were consistent through time, but bacteria and fungi were governed by different processes. At the within-vineyard scale, deterministic selection and homogenising dispersal dominated bacterial assembly, while neither selection nor dispersal had clear influence over fungal assembly. At the among-vineyard scale, the influence of dispersal limitation increased for both taxonomic groups, but its contribution was much larger for fungal communities. These null-model-based inferences were supported by neutral modelling, which estimated a dispersal rate almost two orders-of-magnitude lower for fungi than bacteria.This indicates that while stochastic processes are important for fungal assembly, bacteria were more influenced by deterministic selection imposed by the biotic and/or abiotic environment. Managing microbes in vineyard soils could thus benefit from strategies that account for dispersal limitation of fungi and the importance of environmental conditions for bacteria. Our results are consistent with theoretical expectations whereby larger individual size and smaller populations can lead to higher levels of stochasticity.

Amino acids (AA) and IGF1 have been demonstrated to play essential roles in protein synthesis and fish muscle growth. The myoblast cell culture is useful for studying muscle regulation, and omics data have contributed enormously to understanding its molecular biology. However, to our knowledge, no study has performed the large-scale sequencing of fish-cultured muscle cells stimulated with pro-growth signals. In this work, we obtained the transcriptome and microRNAome of pacu (

Fish are widely exposed to higher microbial loads compared to land and air animals. It is known that the microbiome plays an essential role in the health and development of the host. The oral microbiome is vital in females of different organisms, including the maternal mouthbrooding species such as Nile tilapia (Oreochromis niloticus). The present study reports for the first time the microbial composition in the buccal cavity of female and male Nile tilapia reared in a recirculating aquaculture system. Mucus samples were collected from the buccal cavity of 58 adult fish (∼1 kg), and 16S rRNA gene amplicon sequencing was used to profile the microbial communities in females and males. The analysis revealed that opportunistic pathogens such as Streptococcus sp. were less abundant in the female buccal cavity. The power play of certain bacteria such as Acinetobacter, Acidobacteria (GP4 and GP6), and Saccharibacteria that have known metabolic advantages was evident in females compared to males. Association networks inferred from relative abundances showed few microbe–microbe interactions of opportunistic pathogens in female fish. The findings of opportunistic bacteria and their interactions with other microbes will be valuable for improving Nile tilapia rearing practices. The presence of bacteria with specific functions in the buccal cavity of female fish points to their ability to create a protective microbial ecosystem for the offspring.

Made available in DSpace on 2021-06-25T10:27:54Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-12-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Background: Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu) are good fish species for aquaculture. The tambacu, individuals originating from the induced hybridization of the female tambaqui with the male pacu, present rapid growth and robustness, characteristics which have made the tambacu a good choice for Brazilian fish farms. Here, we used small RNA sequencing to examine global miRNA expression in the genotypes pacu (PC), tambaqui (TQ), and hybrid tambacu (TC), (Juveniles, n = 5 per genotype), to better understand the relationship between tambacu and its parental species, and also to clarify the mechanisms involved in tambacu muscle growth and maintenance based on miRNAs expression. Results: Regarding differentially expressed (DE) miRNAs between the three genotypes, we observed 8 upregulated and 7 downregulated miRNAs considering TC vs. PC; 14 miRNAs were upregulated and 10 were downregulated considering TC vs. TQ, and 15 miRNAs upregulated and 9 were downregulated considering PC vs. TQ. The majority of the miRNAs showed specific regulation for each genotype pair, and no miRNA were shared between the 3 genotype pairs, in both up- and down-regulated miRNAs. Considering only the miRNAs with validated target genes, we observed the miRNAs miR-144-3p, miR-138-5p, miR-206-3p, and miR-499-5p. GO enrichment analysis showed that the main target genes for these miRNAs were grouped in pathways related to oxygen homeostasis, blood vessel modulation, and oxidative metabolism. Conclusions: Our global miRNA analysis provided interesting DE miRNAs in the skeletal muscle of pacu, tambaqui, and the hybrid tambacu. In addition, in the hybrid tambacu, we identified some miRNAs controlling important molecular muscle markers that could be relevant for the farming maximization. Department of Structural and Functional Biology Institute of Biosciences São Paulo State University – UNESP Ninth of July University – UNINOVE Department of Cellular Computational and Integrative Biology – CIBIO University of Trento University of Western Sao Paulo – UNOESTE Department of Structural and Functional Biology Institute of Biosciences São Paulo State University – UNESP FAPESP: 2015/19985-2 FAPESP: 2016/05009-4 FAPESP: 2017/15708-0 CNPq: 302656/2015-4

The taxonomic identification of organisms based on the amplification of specific genetic markers (metabarcoding) implicitly requires adequate discriminatory information and taxonomic coverage of environmental DNA sequences in taxonomic databases. These requirements were quantitatively examined by comparing the determination of cyanobacteria and microalgae obtained by metabarcoding and light microscopy. We used planktic and biofilm samples collected in 37 lakes and 22 rivers across the Alpine region. We focused on two of the most used and best represented genetic markers in the reference databases, namely the 16S rRNA and 18S rRNA genes. A sequence gap analysis using blastn showed that, in the identity range of 99-100%, approximately 30% (plankton) and 60% (biofilm) of the sequences did not find any close counterpart in the reference databases (NCBI GenBank). Similarly, a taxonomic gap analysis showed that approximately 50% of the cyanobacterial and eukaryotic microalgal species identified by light microscopy were not represented in the reference databases. In both cases, the magnitude of the gaps differed between the major taxonomic groups. Even considering the species determined under the microscope and represented in the reference databases, 22% and 26% were still not included in the results obtained by the blastn at percentage levels of identity ≥95% and ≥97%, respectively. The main causes were the absence of matching sequences due to amplification and/or sequencing failure and potential misidentification in the microscopy step. Our results quantitatively demonstrated that in metabarcoding the main obstacles in the classification of 16S rRNA and 18S rRNA sequences and interpretation of high-throughput sequencing biomonitoring data were due to the existence of important gaps in the taxonomic completeness of the reference databases and the short length of reads. The study focused on the Alpine region, but the extent of the gaps could be much greater in other less investigated geographic areas.

The microbial communities associated to the rhizosphere (the rhizomicrobiome) have a substantial impact on plant growth and yield. Understanding the effects of agricultural management on the rhizomicrobiome is very important for selecting efficient practices. By sequencing the V4 region of 16S rRNA for bacteria and the ITS1 regions and fungi, we investigated the influences of agronomic practices, including cucumber grafting on cucurbit hybrid (Cucurbita moschata × C. maxima), cucumber-garlic intercropping, and treatment with fungicide iprodione-carbendazim on cucumber rhizosphere microbial communities during plant growth. Soil dehydrogenase activity (DHA) and plant vegetative parameters were assessed as an indicator of overall soil microbial activity. We found that both treatments and growth stage induced significant shifts in microbial community structure. Grafting had the highest number of differentially abundant OTUs compared to control samples, followed by intercropping and fungicide treatment, while plant development stage affected both alpha and beta diversities indices and composition of the rhizomicrobiome. DHA was more dependent on plant growth stages than on treatments. Among the assessed factors, grafting and plant developmental stage resulted in the greatest changes in the microbial community composition. Grafting also increased the plant growth parameters, suggesting that this method should be further investigated in vegetable production systems.

We describe three new parastenocaridid: Cottarellicaris sanctiangeli Bruno & Cottarelli sp. nov., Stammericaris vincentimariae Bruno & Cottarelli sp. nov. and Proserpinicars specincola Bruno & Cottarelli sp. nov., collected in the pools of five different caves located in Calabria (Southern Italy). We conducted a phylogenetic analysis based on the mitochondrial COI and ribosomal 18S sequences of C. sanctiangeli sp. nov. and S. vincentimariae sp. nov., and of four more species of Stammericaris and one Proserpinicaris available from literature. Based on the molecular study, the specimens of C. sanctiangeli sp. nov. are clearly separated from the species belonging to the closely-related genus Stammericaris. The morphological and molecular data indicate that the genera belonging to the two subfamilies Parastenocaridinae and Fontinalicaridinae form two monophyletic and distinct clades, thus supporting their status. We also provide insights on the genus Proserpinicaris based on morphological data only; in particular, the most important synapomorphic character of the genus, i.e., the taxonomic value of the hyaline structure inserted on the anterior surface of the male leg 4 basis, is discussed based on the development of the P4 endopod, as observed in the last copepodid stage of some species of this genus. Finally, we widen the biogeographic and ecological knowledge of the three genera.

10 pages, 5 figures, 1 table, The common octopus (Octopus vulgaris) is a species of great interest to the aquaculture industry. However, the high mortalities registered during different phases of the octopus lifecycle, particularly the paralarvae stage, present a challenge for commercial aquaculture. Improvement of diet formulation is seen as one way to reduce mortality and improve growth. Molecular growth-markers could help to improve rearing protocols and increase survival and growth performance; therefore, over a hundred orthologous genes related to protein balance and muscle growth in vertebrates were identified for the common octopus and their suitability as molecular markers for growth in octopus paralarvae explored. We successfully amplified 14 of those genes and studied their transcription in paralarvae either fed with artemia, artemia + zoea diets or submitted to a short fasting-refeeding procedure. Paralarvae fed with artemia + zoea had higher growth rates compared to those fed only with artemia, as well as a significant increase in octopus mtor (mtor-L) and hsp90 (hsp90-L) transcription, with both genes also up-regulated during refeeding. Our results suggest that at least mtor-L and hsp90-L are likely linked to somatic growth in octopus paralarvae. Conversely, ckip1-L, crk-L, src-L and srf-L had expression patterns that did not match to periods of growth as would be expected based on similar studies in vertebrates, indicating that further research is needed to understand their function during growth and in a muscle specific context, This work has been carried out with financial support from the European Union under grant project AQUAEXCEL2020 (652831, TNA AE050063- Octogrowth) to DGS and MP. DGS is a Serra Húnter Fellow at the University of Barcelona. JHU is supported by a Juan de la Cierva’s post-doc research grant (# FJCI-2016-30990) funded by the Spanish Ministry of Science, Innovation and Universities

Background Although the most common path of infection for fire blight, a severe bacterial disease on apple, is via host plant flowers, quantitative trait loci (QTLs) for fire blight resistance to date have exclusively been mapped following shoot inoculation. It is not known whether the same mechanism underlies flower and shoot resistance. Results We report the detection of a fire blight resistance QTL following independent artificial inoculation of flowers and shoots on two F1 segregating populations derived from crossing resistant Malus ×robusta 5 (Mr5) with susceptible ‘Idared’ and ‘Royal Gala’ in experimental orchards in Germany and New Zealand, respectively. QTL mapping of phenotypic datasets from artificial flower inoculation of the ‘Idared’ × Mr5 population with Erwinia amylovora over several years, and of the ‘Royal Gala’ × Mr5 population in a single year, revealed a single major QTL controlling floral fire blight resistance on linkage group 3 (LG3) of Mr5. This QTL corresponds to the QTL on LG3 reported previously for the ‘Idared’ × Mr5 and an ‘M9’ × Mr5 population following shoot inoculation in the glasshouse. Interval mapping of phenotypic data from shoot inoculations of subsets from both flower resistance populations re-confirmed that the resistance QTL is in the same position on LG3 of Mr5 as that for flower inoculation. These results provide strong evidence that fire blight resistance in Mr5 is controlled by a major QTL on LG3, independently of the mode of infection, rootstock and environment. Conclusions This study demonstrates for the first time that resistance to fire blight caused by Erwinia amylovora is independent of the mode of inoculation at least in Malus ×robusta 5.

Objetivo: Describir las estrategias de adaptación de los padres en la crianza de niños con Síndrome de Down que acuden al Centro de Educación Básica Especial “Los Pinos” de San Juan de Lurigancho, 2017. Materiales y Métodos: El estudio fue observacional, de nivel descriptivo, de diseño no experimental. La muestra estuvo constituida por 38 padres de familia. Resultados: En relación a la estrategia del área afectiva, el 55.3 % manifestaron que se vincularon con otros padres que tienen hijos con síndrome de Down, mientras que el 18.4% refirieron que buscaron apoyo espiritual, 13.2% padres se informaron sobre el síndrome de Down y con mismo porcentaje de 13.2% corresponde a los padres que buscaron apoyo emocional. En las estrategias de área de la salud, 81.6% de padres afirman que sus hijos actualmente reciben terapias, y el 18.4% que no recibe terapias. Referente a los niños con SD que reciben terapias el 71% opta por la terapia de lenguaje, el 29% por la terapia de lenguaje junto con la psicomotriz. En cuanto a la estrategia del área social, el 76.3% de padres manifestaron que sí tuvieron el apoyo de su familia, y el 23.7% refieren que no tuvieron apoyo familiar. Dentro del grupo de padres que tuvieron apoyo familiar el 44.8% menciono que tuvieron aceptación de su persona y de su hijo, y el 13.8% refieren que los familiares ayudaron a cuidar al niño. Y n la estrategia del área educativa, en el inicio de la vida escolar del niño con SD se evidencia que el 73.7% de los padres optaron que sus hijos inicien su vida escolar en un colegio de educación especial, y en menor porcentaje 26,3% corresponde a los padres que optaron por el colegio de educación regular. Conclusión: Los niños se integran en las actividades ordinarias dentro del entorno social y familiar. Se ha de resaltar la conducta favorable frente a las actividades del entorno. Inicialmente los padres muestran cierto grado de preocupación debido a la dificultad para asimilar la situación respecto al estado de sus hijos.

Made available in DSpace on 2022-05-01T06:31:27Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-07-01 Fish muscle growth is a complex process regulated by multiple pathways, resulting on the net accumulation of proteins and the activation of myogenic progenitor cells. Around 350–320 million years ago, teleost fish went through a specific whole genome duplication (WGD) that expanded the existent gene repertoire. Duplicated genes can be retained by different molecular mechanisms such as subfunctionalization, neofunctionalization or redundancy, each one with different functional implications. While the great majority of ohnolog genes have been identified in the teleost genomes, the effect of gene duplication in the fish physiology is still not well characterized. In the present study we studied the effect of WGD on the transcription of the duplicated components controlling muscle growth. We compared the expression of lineage-specific ohnologs related to myogenesis and protein balance in the fast-skeletal muscle of pacus (Piaractus mesopotamicus—Ostariophysi) and Nile tilapias (Oreochromis niloticus—Acanthopterygii) fasted for 4 days and refed for 3 days. We studied the expression of 20 ohnologs and found that in the great majority of cases, duplicated genes had similar expression profiles in response to fasting and refeeding, indicating that their functions during growth have been conserved during the period after the WGD. Our results suggest that redundancy might play a more important role in the retention of ohnologs of regulatory pathways than initially thought. Also, comparison to non-duplicated orthologs showed that it might not be uncommon for the duplicated genes to gain or loss new regulatory elements simultaneously. Overall, several of duplicated ohnologs have similar transcription profiles in response to pro-growth signals suggesting that evolution tends to conserve ohnolog regulation during muscle development and that in the majority of ohnologs related to muscle growth their functions might be very similar. Department of Histology Embryology and Cell Biology Institute of Biological Sciences Federal University of Goiás (UFG), Goiás Department of Structural and Functional Biology Institute of Biosciences São Paulo State University (UNESP), Botucatu Department of Cell Biology Physiology and Immunology Faculty of Biology University of Barcelona University of Western São Paulo (UNOESTE), Presidente Prudente Fisheries Institute (IP-APTA) Department of Structural and Functional Biology Institute of Biosciences São Paulo State University (UNESP), Botucatu

Objectives: Describe the strategies of adaptation of parents in the upbringing of children with Down syndrome that go to the Special Basic Education Center "Los Pinos" of San Juan de Lurigancho, 2017. Materials and Methods: The study was observational, descriptive level, non-experimental design. The sample consisted of 38 parents. Results: In relation to the strategy of the affective area, 55.3% stated that they were linked with other parents who have children with Down syndrome, while 18.4% reported that they sought spiritual support, 13.2% parents were informed about Down syndrome and with the same percentage of 13.2% corresponds to parents who sought emotional support. In health area strategies, 81.6% of parents affirm that their children currently receive therapies, and 18.4% do not receive therapies. Regarding children with SD who receive therapies 71% choose language therapy, 29% for language therapy along with the psychomotor. Regarding the strategy of the social area, 76.3% of parents stated that they did have the support of their family, and 23.7% report that they did not have family support. Within the group of parents who had family support, 44.8% mentioned that they had accepted their person and their child, and 13.8% said that family members helped take care of the child. And in the strategy of the educational area, in the beginning of the school life of the child with SD it is evident that 73.7% of the parents opted for their children to start their school life in a special education school, and in a lower percentage 26.3 % corresponds to parents who opted for the regular education college. Conclusion: Children are integrated into ordinary activities within the social and family environment. We must highlight the favorable behavior against the surrounding activities. Initially the parents show some degree of concern due to the difficulty to assimilate the situation regarding the status of their children. Objetivo: Describir las estrategias de adaptación de los padres en la crianza de niños con Síndrome de Down que acuden al Centro de Educación Básica Especial “Los Pinos” de San Juan de Lurigancho, 2017. Materiales y Métodos: El estudio fue observacional, de nivel descriptivo, de diseño no experimental. La muestra estuvo constituida por 38 padres de familia. Resultados: En relación a la estrategia del área afectiva, el 55.3 % manifestaron que se vincularon con otros padres que tienen hijos con síndrome de Down, mientras que el 18.4% refirieron que buscaron apoyo espiritual, 13.2% padres se informaron sobre el síndrome de Down y con mismo porcentaje de 13.2% corresponde a los padres que buscaron apoyo emocional. En las estrategias de área de la salud, 81.6% de padres afirman que sus hijos actualmente reciben terapias, y el 18.4% que no recibe terapias. Referente a los niños con SD que reciben terapias el 71% opta por la terapia de lenguaje, el 29% por la terapia de lenguaje junto con la psicomotriz. En cuanto a la estrategia del área social, el 76.3% de padres manifestaron que sí tuvieron el apoyo de su familia, y el 23.7% refieren que no tuvieron apoyo familiar. Dentro del grupo de padres que tuvieron apoyo familiar el 44.8% menciono que tuvieron aceptación de su persona y de su hijo, y el 13.8% refieren que los familiares ayudaron a cuidar al niño. Y n la estrategia del área educativa, en el inicio de la vida escolar del niño con SD se evidencia que el 73.7% de los padres optaron que sus hijos inicien su vida escolar en un colegio de educación especial, y en menor porcentaje 26,3% corresponde a los padres que optaron por el colegio de educación regular. Conclusión: Los niños se integran en las actividades ordinarias dentro del entorno social y familiar. Se ha de resaltar la conducta favorable frente a las actividades del entorno. Inicialmente los padres muestran cierto grado de preocupación debido a la dificultad para asimilar la situación respecto al estado de sus hijos.

We present a draft assembly of the genome of European pear (Pyrus communis) 'Bartlett'. Our assembly was developed employing second generation sequencing technology (Roche 454), from single-end, 2 kb, and 7 kb insert paired-end reads using Newbler (version 2.7). It contains 142,083 scaffolds greater than 499 bases (maximum scaffold length of 1.2 Mb) and covers a total of 577.3 Mb, representing most of the expected 600 Mb Pyrus genome. A total of 829,823 putative single nucleotide polymorphisms (SNPs) were detected using re-sequencing of 'Louise Bonne de Jersey' and 'Old Home'. A total of 2,279 genetically mapped SNP markers anchor 171 Mb of the assembled genome. Ab initio gene prediction combined with prediction based on homology searching detected 43,419 putative gene models. Of these, 1219 proteins (556 clusters) are unique to European pear compared to 12 other sequenced plant genomes. Analysis of the expansin gene family provided an example of the quality of the gene prediction and an insight into the relationships among one class of cell wall related genes that control fruit softening in both European pear and apple (Malus × domestica). The 'Bartlett' genome assembly v1.0 (http://www.rosaceae.org/species/pyrus/pyrus_communis/genome_v1.0) is an invaluable tool for identifying the genetic control of key horticultural traits in pear and will enable the wide application of marker-assisted and genomic selection that will enhance the speed and efficiency of pear cultivar development.