Consensus scoring has become a commonly used strategy within structure-based virtual screening (VS) workflows with improved performance compared to those based in a single scoring function. However, ...no research has been devoted to analyze the worth of docking scoring functions components in consensus scoring. We implemented and tested a method that incorporates docking scoring functions components into the setting of high performance VS workflows. This method uses genetic algorithms for finding the combination of scoring components that maximizes the VS enrichment for any target. Our methodology was validated using a data set including ligands and decoys for 102 targets that have been widely used in VS validation studies. Results show that our approach outperforms other methods for all targets. It also boosts the initial enrichment performance of the traditional use of whole scoring functions in consensus scoring by an average of 45%. Our methodology showed to be outstandingly predictive when challenged to rescore external (previously unseen) data. Remarkably, CompScore was able not only to retain its performance after redocking with a different software, but also proved that the enrichment obtained was not artificial. CompScore is freely available at: http://bioquimio.udla.edu.ec/compscore/.
Video delivery is exploiting 5G networks to enable higher server consolidation and deployment flexibility. Performance optimization is also a key target in such network systems. We present a ...multi-objective optimization framework for service function chain deployment in the particular context of Live-Streaming in virtualized content delivery networks using deep reinforcement learning. We use an Enhanced Exploration, Dense-reward mechanism over a Dueling Double Deep Q Network (E2-D4QN). Our model assumes to use network function virtualization at the container level. We carefully model processing times as a function of current resource utilization in data ingestion and streaming processes. We assess the performance of our algorithm under bounded network resource conditions to build a safe exploration strategy that enables the market entry of new bounded-budget vCDN players. Trace-driven simulations with real-world data reveal that our approach is the only one to adapt to the complexity of the particular context of Live-Video delivery concerning the state-of-art algorithms designed for general-case service function chain deployment. In particular, our simulation test revealed a substantial QoS/QoE performance improvement in terms of session acceptance ratio against the compared algorithms while keeping operational costs within proper bounds.
Celotno besedilo
Dostopno za:
CEKLJ, DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Mercury (Hg) accumulation capacity was assessed in three plant species (Axonopus compressus, Erato polymnioides, and Miconia zamorensis) that grow on soils polluted by artisanal small-scale gold ...mines in the Ecuadorian rainforest. Individuals of three species were collected at two sampling zones: i) an intensive zone (IZ, 4.8 mg Hg kg−1 of soil) where gold extraction continues to occur, and ii) a natural zone (NZ, 0.19 mg Hg kg−1 of soil). In addition, the percentage of arbuscular mycorrhizal fungi (AMF) colonization was determined in plant roots and seven fungal morphotypes isolated from rhizospheric soil. Results suggest a facilitation role of native and pollution adapted AMF on Hg phytoaccumulation. E.g., E. polymnioides increased Hg accumulation when growing with greater AMF colonization. We concluded that E. polymnioides is a good candidate for the design of microbe-assisted strategies for Hg remediation at gold mining areas. The consortia between E. polymnioides and the AMF isolated in this study could be instrumental to get a deeper understanding of the AMF role in Hg phytoaccumulation.
•Hg accumulation capacity was studied in three plant species.•Hg in acid soil studied is higher than the Ecuadorian threshold (0.1 mg kg−1).•Concentrations of Hg in roots and leaves were higher than in stems.•All plants showed arbuscular mycorrhizal fungi colonization in their roots.•Erato polymnioides showed high potential as an Hg hyperaccumulator.
The emergence of new virulent Vibrio strains resistant to common antibiotics has caused significant economic losses to shrimp farming worldwide. It is mandatory to adopt new strategies to control ...shrimp farming related vibriosis. Essential oils (EOs) have several biological properties among of which the quorum sensing (QS) inhibitory activity is appealing for vibriosis control. In this work, we evaluated QS inhibitory activity of five EOs obtained from oregano (Organum vulgare), tea tree (Melaleuca alternifolia), lemongrass (Cymbopogon citratus), cinnamon (Cinnamomum verum) and thyme (Thymus vulgaris), at sublethal doses. EOs involvement in bioluminescence shutdown, biofilm formation and swarming motility was evaluated in four Vibrio strains of aquaculture interest including V. harveyi, V. campbellii, V. vulnificus, and V. parahaemolyticus. Oregano oil (EOOv) and tea tree oil (EOMa) were further tested in in vivo assays due to their significant effects (P < 0.05) on QS inhibition. EOOv was the most efficient one and exerted a comparable QS inhibitory effect to EOMa at a lower concentration in vivo (2.5 μg mL−1 of EOMa versus 1.0 μg mL−1 of EOOv). The lowest active doses of EOOv and EOMa that inhibited QS had no toxic effects on hemocytes and larvae of P. vannamei. A challenge test was performed in P. vannamei postlarvae (PL8) with V. campbellii, grown previously in the presence of EOOv or EOMa at sublethal active doses. Our results indicated that both EOs affected the virulence of V. campbellii and were able to significantly (P < 0.05) reduce shrimp mortality (EOOv in a 40% while EOMa in a 32%). A field bioassay was also carried in earthen ponds to test two different concentrations of EOOv and EOMa for feed supplementation (2.5 and 5.0 mg kg−1 respectively). EOOv increased significantly (P < 0.05) shrimp survival and yield at both doses, whereas EOMa increased shrimp survival and yield only at the highest dose. In conclusion, EOOv and EOMa constitute suitable alternatives to reduce vibrios virulence and to increase yield in shrimp culture systems.
•Essential oils are virulence inhibitors of pathogenic vibrios in shrimp aquaculture.•Essential oils increased shrimp survival and yield in earthen ponds experiments.•Organum vulgare and Melaleuca alternifolia oils showed the best results.
El avance de la ciencia ha sido impulsado constantemente por la búsqueda de respuestas a preguntas fundamentales, la exploración de nuevos enfoques y la aplicación de metodologías innovadoras1. En el ...Primer Simposio Internacional de Enfoques Innovadores en Ciencias de la Vida, celebrado con entusiasmo y dedicación, se han presentado trabajos que representan un espectro diverso de investigaciones en áreas que van desde la biotecnología hasta la salud humana. A través de un análisis profundo de datos y una perspectiva científica rigurosa, estos trabajos han contribuido a una visión más cuantitativa y esclarecedora del mundo que nos rodea.
The study of type III RNases constitutes an important area in molecular biology. It is known that the pac1 + gene encodes a particular RNase III that shares low amino acid similarity with other genes ...despite having a double-stranded ribonuclease activity. Bioinformatics methods based on sequence alignment may fail when there is a low amino acidic identity percentage between a query sequence and others with similar functions (remote homologues) or a similar sequence is not recorded in the database. Quantitative structure−activity relationships (QSAR) applied to protein sequences may allow an alignment-independent prediction of protein function. These sequences of QSAR-like methods often use 1D sequence numerical parameters as the input to seek sequence-function relationships. However, previous 2D representation of sequences may uncover useful higher-order information. In the work described here we calculated for the first time the spectral moments of a Markov matrix (MMM) associated with a 2D-HP-map of a protein sequence. We used MMMs values to characterize numerically 81 sequences of type III RNases and 133 proteins of a control group. We subsequently developed one MMM-QSAR and one classic hidden Markov model (HMM) based on the same data. The MMM-QSAR showed a discrimination power of RNAses from other proteins of 97.35% without using alignment, which is a result as good as for the known HMM techniques. We also report for the first time the isolation of a new Pac1 protein ( DQ647826 ) from Schizosaccharomyces pombe strain 428-4-1. The MMM-QSAR model predicts the new RNase III with the same accuracy as other classical alignment methods. Experimental assay of this protein confirms the predicted activity. The present results suggest that MMM-QSAR models may be used for protein function annotation avoiding sequence alignment with the same accuracy of classic HMM models.
The repeatome is composed of diverse families of repetitive DNA that keep signatures on the historical events that shaped the evolution of their hosting species. The cold seasonal Loliinae subtribe ...includes worldwide distributed taxa, some of which are the most important forage and lawn species (fescues and ray-grasses). The Loliinae are prone to hybridization and polyploidization. It has been observed a striking two-fold difference in genome size between the broad-leaved (BL) and fine-leaved (FL) Loliinae diploids and a general trend of genome reduction of some high polyploids. We have used genome skimming data to uncover the composition, abundance, and potential phylogenetic signal of repetitive elements across 47 representatives of the main Loliinae lineages. Independent and comparative analyses of repetitive sequences and of 5S rDNA loci were performed for all taxa under study and for four evolutionary Loliinae groups Loliinae, Broad-leaved (BL), Fine-leaved (FL), and Schedonorus lineages. Our data showed that the proportion of the genome covered by the repeatome in the Loliinae species was relatively high (average ∼ 51.8%), ranging from high percentages in some diploids (68.7%) to low percentages in some high-polyploids (30.7%), and that changes in their genome sizes were likely caused by gains or losses in their repeat elements. Ty3-gypsy Retand and Ty1-copia Angela retrotransposons were the most frequent repeat families in the Loliinae although the relatively more conservative Angela repeats presented the highest correlation of repeat content with genome size variation and the highest phylogenetic signal of the whole repeatome. By contrast, Athila retrotransposons presented evidence of recent proliferations almost exclusively in the
Lolium
clade. The repeatome evolutionary networks showed an overall topological congruence with the nuclear 35S rDNA phylogeny and a geographic-based structure for some lineages. The evolution of the Loliinae repeatome suggests a plausible scenario of recurrent allopolyploidizations followed by diploidizations that generated the large genome sizes of BL diploids as well as large genomic rearrangements in highly hybridogenous lineages that caused massive repeatome and genome contractions in the Schedonorus and Aulaxyper polyploids. Our study has contributed to disentangling the impact of the repeatome dynamics on the genome diversification and evolution of the Loliinae grasses.
The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and ...annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T. urticae has the smallest sequenced arthropod genome. Compared with other arthropods, the spider mite genome shows unique changes in the hormonal environment and organization of the Hox complex, and also reveals evolutionary innovation of silk production. We find strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Deep transcriptome analysis of mites feeding on different plants shows how this pest responds to a changing host environment. The T. urticae genome thus offers new insights into arthropod evolution and plant-herbivore interactions, and provides unique opportunities for developing novel plant protection strategies.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Oceanic islands constitute natural laboratories to study plant speciation and biogeographic patterns of island endemics. Juan Fernandez is a southern Pacific archipelago consisting of three small ...oceanic islands located 600-700 km west of the Chilean coastline. Exposed to current cold seasonal oceanic climate, these 5.8-1 Ma old islands harbor a remarkable endemic flora. All known Fernandezian endemic grass species belong to two genera,
and
, of uncertain taxonomic adscription. Classical and modern classifications have placed them either in Bromeae (
), Duthieinae, Aveneae/Poeae, or Loliinae (fine-leaved
); however, none of them have clarified their evolutionary relationships with respect to their closest
relatives.
includes four species, which are endemic to Masatierra (Robinson Crusoe island) (
and
) and to Masafuera (Alejandro Selkirk island) (
and
). The monotypic
is a rare endemic species to Masatierra which is only known from its type locality and is currently considered extinct. We have used museomic approaches to uncover the challenging evolutionary history of these endemic grasses and to infer the divergence and dispersal patterns from their ancestors. Genome skimming data were produced from herbarium samples of
and
, and the 164 years old type specimen of
, as well as for a collection of 33 species representing the main broad- and fine-leaved Loliinae lineages. Paired-end reads were successfully mapped to plastomes and nuclear ribosomal cistrons of reference
species and used to reconstruct phylogenetic trees. Filtered ITS and
TLF sequences from these genomes were further combined with our large Loliinae data sets for accurate biogeographic reconstruction. Nuclear and plastome data recovered a strongly supported fine-leaved Fernandezian clade where
was resolved as sister to
. Bayesian divergence dating and dispersal-extinction-cladogenesis range evolution analyses estimated the split of the Fernandezian clade from its ancestral southern American Pampas-Ventanian Loliinae lineage in the Miocene-Pliocene transition, following a long distance dispersal from the continent to the uplifted volcanic palaeo-island of Santa Clara-Masatierra. Consecutive Pliocene-Pleistocene splits and a Masatierra-to-Masafuera dispersal paved the way for
speciation of
and
taxa.
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