Sma3s: A three-step modular annotator for large sequence datasets

This is an Open Access article distributed under the terms of the Creative Commons Attribution License.Automatic sequence annotation is an essential component of modern 'omics' studies, which aim to extract information from large collections of sequence data. Most existing tools use sequence homology to establish evolutionary relationships and assign putative functions to sequences. However, it can be difficult to define a similarity threshold that achieves sufficient coverage without sacrificing annotation quality. Defining the correct configuration is critical and can be challenging for non-specialist users. Thus, the development of robust automatic annotation techniques that generate high-quality annotations without needing expert knowledge would be very valuable for the research community. We present Sma3s, a tool for automatically annotating very large collections of biological sequences from any kind of gene library or genome. Sma3s is composed of three modules that progressively annotate query sequences using either: (i) very similar homologues, (ii) orthologous sequences or (iii) terms enriched in groups of homologous sequences. We trained the system using several random sets of known sequences, demonstrating average sensitivity and specificity values of ∼85%. In conclusion, Sma3s is a versatile tool for high-throughput annotation of a wide variety of sequence datasets that outperforms the accuracy of other well-established annotation algorithms, and it can enrich existing database annotations and uncover previously hidden features. Importantly, Sma3s has already been used in the functional annotation of two published transcriptomes.This work has been partially financed by the National Institute for Bioinformatics (www.inab.org), a platform of Genoma España and the EC project ‘Advancing Clinico-Genomic Trials on Cancer’ (contract no. 026996).Peer Reviewe

Early and delayed long-term transcriptional changes and short-term transient responses during cold acclimation in olive leaves

Low temperature severely affects plant growth and development. To overcome this constraint, several plant species from regions having a cool season have evolved an adaptive response, called cold acclimation. We have studied this response in olive tree (Olea europaea L.) cv. Picual. Biochemical stress markers and cold-stress symptoms were detected after the first 24 h as sagging leaves. After 5 days, the plants were found to have completely recovered. Control and cold-stressed plants were sequenced by Illumina HiSeq 1000 paired-end technique. We also assembled a new olive transcriptome comprising 157,799 unigenes and found 6,309 unigenes differentially expressed in response to cold. Three types of response that led to cold acclimation were found: short-term transient response, early long-term response, and late long-term response. These subsets of unigenes were related to different biological processes. Early responses involved many cold-stress-responsive genes coding for, among many other things, C-repeat binding factor transcription factors, fatty acid desaturases, wax synthesis, and oligosaccharide metabolism. After long-term exposure to cold, a large proportion of gene down-regulation was found, including photosynthesis and plant growth genes. Up-regulated genes after long-term cold exposure were related to organelle fusion, nucleus organization, and DNA integration, including retrotransposons.This work was supported by grant AGR-5948 from Junta de Andalucía (Consejería de Economía, Innovación y Ciencia) and Ministerio de Ciencia e Innovación. Funding to pay the Open Access publication charges for this article was provided by the University of Jaén.Peer reviewe

Cold response in olive tree; A RNAseq study

Póster presentado en el COST TD801 StatSeq 5th Workshop, celebrado en Helsinki del 24 al 26 de abril de 2013.Low temperature severely affects plant growth and development. Several plant species have evolved an adaptive response, named cold acclimation. In order to study this response in olive tree (Olea europaea), we maintained twomonths- old vegetative propagated olive trees cv. Picual at low temperature (14h at 10ºC with light, 10h at 4ºC at the dark) for 15 days. Control plants were maintained in field growing conditions. Cold stress symptoms were observed after the first 24h as sagging leaf and biochemical stress markers. After 5 days the plants were observed completely recovered. We extracted RNA from leaves of three control plants and the same number from 24h and 10 days cold stressed plants. We pooled RNA and made two cDNA libraries for sequencing. We used Illumina HiSeq 1000 sequencer.Peer Reviewe

Tailoring basic and acidic properties of MgAl hydrotalcite by fluoride anions: Effect on glycerol oligomerisation

In this work, two families of catalysts based on mixed metal oxides derived from MgAl hydrotalcites were synthesized with a Mg/Al molar ratio of 3. On the one hand, in the first family, the fluoride anion was incorporated in the interlayer space by using ammonium fluoride, exploiting the “memory effect” characteristic of hydrotalcites. In the second family, fluoride anions substituted oxides anions in the layer, incorporating directly them during the precipitation of hydroxides, by using cryolite as a precursor for both fluorine and aluminium. The hydrotalcites were transformed into mixed metal oxides by thermal treatment and tested in the glycerol etherification reaction at 230 ºC, in a batch reactor at atmospheric pressure. The hydrotalcites and the corresponding mixed metal oxides were characterized by different experimental techniques, such as X-ray diffraction (XRD), elemental analysis (CHF), N2 sorption at -196ºC, thermogravimetric analysis (ATD-TG), X-ray photoelectron spectroscopy (XPS), temperature-programmed desorption of CO2 and NH3 (CO2-TPD and NH3-DTP) and solid state nuclear magnetic resonace (ssNMR) of 19F. It was found that the mixed metal oxides prepared from hydrotalcites, where fluorine was incorporated in the synthesis step using cryolite, achieved the maximum conversion values and complete selectivity towards diglycerol. Diglycerols were the unique detected products and, in some cases, the formation of triglycerols was also detected.Funding for open access charge: Universidad de Málaga / CBU

Pervasive hybridization with local wild relatives in Western European grapevine varieties

Grapevine (Vitis vinifera L.) diversity richness results from a complex domestication history over multiple historical periods. Here, we used whole-genome resequencing to elucidate different aspects of its recent evolutionary history. Our results support a model in which a central domestication event in grapevine was followed by postdomestication hybridization with local wild genotypes, leading to the presence of an introgression signature in modern wine varieties across Western Europe. The strongest signal was associated with a subset of Iberian grapevine varieties showing large introgression tracts. We targeted this study group for further analysis, demonstrating how regions under selection in wild populations from the Iberian Peninsula were preferentially passed on to the cultivated varieties by gene flow. Examination of underlying genes suggests that environmental adaptation played a fundamental role in both the evolution of wild genotypes and the outcome of hybridization with cultivated varieties, supporting a case of adaptive introgression in grapevine.info:eu-repo/semantics/publishedVersio

Seed Propagation and Constituents of the Essential Oil of <em>Stevia serrata</em> Cav. from Guatemala

Stevia serrata Cav. (Eupatorieae, Asteraceae) grows in Central America and Mexico usually over 1500 m. In this study, essential oils of aerial parts from three populations of western Guatemala were obtained yielding 0.17–0.27% of oil by hydrodistillation. Chamazulene (42–62%) was the most abundant compound in the oil analyzed GC/MS, also presenting germacrene D (4.4–15.3%), caryophyllene oxide (3.2–11.8%), (E)-nerolidol (3.9–7.1%), spathulenol (2.3–7.9%), and (E)-caryophyllene (2.5–6.6%). Besides, a propagation trial was carried out on seeds of plants collected in Santa Lucía Utatlán, as the first step for the domestication of the plant, obtaining approximately 75% survival in the transplanting of the germinated seedlings. After the flowering of the individuals, a greenish essential oil was obtained from the roots yielding 0.2% of oil. This oil did not present chamazulene, but α-longipinene (23.5%), germacrene D (22.2%), santolina triene (12.6%), and (E)-caryophyllene (8.1%) as major components. As conclusion, it was confirmed that the aerial parts of the essential oil of S. serrata from western Guatemala presents a high content of chamazulene and that there is feasibility for the domestication of the plant through the germination of seeds

Uncovering new indicators to predict stability, maturity and biodiversity of compost on an industrial scale

Currently, the metagenomic study of the composting process has gained great importance since it has allowed the identification of the existence of microorganisms that, until now, had not been isolated during the process by traditional techniques. However, it is still complex to determine which bioindicators could reveal the degree of maturity and stability of a particular compost. Thereby, the main objective of this work was to demonstrate the possible correlation between traditional parameters of maturity and stability of compost, with other indicators of biodiversity in products highly heterogeneous from composting processes on an industrial scale. The results demonstrated the enormous influence of the raw materials in characterizing the products obtained. Even so, important relationships were established between the Chao1 and Shannon indexes, and certain parameters related to the maturity, stability and toxicity of the samples, such as nitrification index, humification rate, phenolic content, germination index or oxygen consumptio

Use of glucocorticoids megadoses in SARS-CoV-2 infection in a spanish registry: SEMI-COVID-19

Objective To describe the impact of different doses of corticosteroids on the evolution of patients with COVID-19 pneumonia, based on the potential benefit of the non-genomic mechanism of these drugs at higher doses. Methods Observational study using data collected from the SEMI-COVID-19 Registry. We evaluated the epidemiological, radiological and analytical scenario between patients treated with megadoses therapy of corticosteroids vs low-dose of corticosteroids and the development of complications. The primary endpoint was all-cause in-hospital mortality according to use of corticosteroids megadoses. Results Of a total of 14,921 patients, corticosteroids were used in 5,262 (35.3%). Of them, 2,216 (46%) specifically received megadoses. Age was a factor that differed between those who received megadoses therapy versus those who did not in a significant manner (69 years [IQR 59-79] vs 73 years [IQR 61-83]; p < .001). Radiological and analytical findings showed a higher use of megadoses therapy among patients with an interstitial infiltrate and elevated inflammatory markers associated with COVID-19. In the univariate study it appears that steroid use is associated with increased mortality (OR 2.07 95% CI 1.91-2.24 p < .001) and megadose use with increased survival (OR 0.84 95% CI 0.75-0.96, p 0.011), but when adjusting for possible confounding factors, it is observed that the use of megadoses is also associated with higher mortality (OR 1.54, 95% CI 1.32-1.80; p < .001). There is no difference between megadoses and low-dose (p.298). Although, there are differences in the use of megadoses versus low-dose in terms of complications, mainly infectious, with fewer pneumonias and sepsis in the megadoses group (OR 0.82 95% CI 0.71-0.95; p < .001 and OR 0.80 95% CI 0.65-0.97; p < .001) respectively. Conclusion There is no difference in mortality with megadoses versus low-dose, but there is a lower incidence of infectious complications with glucocorticoid megadoses