Impact of a cognitive stimulation program on the reading comprehension of children in primary education

Introduction: At present, numerous studies can be found in which influences and relationships between the principal executive functions, reading comprehension, and academic performance associated with reading are reported. However, there is still a lack of convergence regarding the impact of computerized cognitive training on children’s executive development and its transfer in academic reading performance and comprehension of written texts. Methods: This study analyzes the effect of implementing a cognitive stimulation program on the performance of reading comprehension and academic performance in the subject of Spanish Language and Literature. To this end, a total sample of 196 children from 23 educational centers received the cognitive intervention for 8 weeks, with three weekly sessions of between 15 and 20 min each occurring on non-consecutive days. Pre-test and posttest measurements were collected and analyzed. Results: The results demonstrate a significant increase in the reading comprehension scores. In addition, a significant impact of the training on the participants’ academic performance in the subject Spanish Language and Literature was found. Discussion: These results highlight the usefulness of computerized cognitive stimulation programs for reading comprehension enhancement

spongeScan: A web for detecting microRNA binding elements in lncRNA sequences.

Non-coding RNA transcripts such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are important genetic regulators. However, the functions of many of these transcripts are still not clearly understood. Recently, it has become apparent that there is significant crosstalk between miRNAs and lncRNAs and that this creates competition for binding between the miRNA, a lncRNA and other regulatory targets. Indeed, various competitive endogenous RNAs (ceRNAs) have already been identified where a lncRNA acts by sequestering miRNAs. This implies the down-regulation in the interaction of the miRNAs with their mRNA targets, what has been called a sponge effect. Multiple approaches exist for the prediction of miRNA targets in mRNAs. However, few methods exist for the prediction of miRNA response elements (MREs) in lncRNAs acting as ceRNAs (sponges). Here, we present spongeScan (http://spongescan.rc.ufl.edu), a graphical web tool to compute and visualize putative MREs in lncRNAs, along with different measures to assess their likely behavior as ceRNAs

A survey of best practices for RNA-seq data analysis.

RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.This is the final published version. It first appeared at http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8

Quality criteria of physiotherapy grade (diploma): report provided by the Spanish Association and Physiotherapists

[Resumen] El informe sobre criterios de calidad específicos de recursos materiales y profesorado para el título de grado de Fisioterapia ha sido elaborado por la Asociación Española de Fisioterapeutas que convocó, con tal finalidad, a una comisión de expertos en Educación en Fisioterapia. El documento, realizado a propuesta de la Dirección General de Universidades en diciembre de 2004, tiene por objetivo el establecer los criterios mínimos de recursos materiales y humanos derivados de la especificidad de la titulación de Fisioterapia, que permita cubrir las nuevas demandas de la sociedad. En relación a los recursos materiales, se ha procurado darle un suficiente grado de especificación cuantitativa y cualitativa a los instrumentos que constituyen los recursos materiales específicos. La intención es, así mismo, facilitar su valoración en el momento de acreditar la titulación. Se abordan, por una parte, los recursos específicos de la titulación para la docencia teórico-práctica en el centro, dentro de los laboratorios destinados a tal efecto. Por otra parte, se definen las características o perfil de los centros sociosanitarios donde debe impartirse la formación clínica del alumno. En relación a los recursos humanos, se hace especial hincapié en el perfil y la experiencia del profesorado para la docencia, así como en el ratio profesor-alumno en la formación práctica y en la formación clínica.[Abstract] The report about specific quality criteria of resources material (items) and teaching profession to obtain the Physiotherapy Grade, has been elaborated by the Spanish Association of Physiotherapists, which aimed to convoke a Physiotherapy Education experts commission. The document was carried out on Universities General Chairmene’s proposal, aiming to establish the minimum criteria of human and Material (Items) resources, derived from the specific Physical Therapy Grade (Diploma), Which may cover the latest Society requirements. According to the Material resources, there has been a serious attempt to give the instruments, which constitute the specific material resources, an appropriate degree, quantitative and qualitative specification. The main intention by itself, consists of providing its assessment when the time to accredit the title comes. On the one hand the specific resources of the Physiotherapy Grade for the Theoric-practical Teaching in the Centre are taken up even in the laboratories aimed to get such goal. On the other hand we define the characteristics or the profile of the social. Health centres, where Pupils’ Clinical Education, must be carried out. Relating to the Human Resources, we do underline the Teaching Profession experience and profile, as well as the rate Teacher-Pupil, both in the practical Training and the Clinical Education, too

First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.)

[EN] Background: Zucchini fruit set can be limited due to unfavourable environmental conditions in off-seasons crops that caused ineffective pollination/fertilization. Parthenocarpy, the natural or artificial fruit development without fertilization, has been recognized as an important trait to avoid this problem, and is related to auxin signalling. Nevertheless, differences found in transcriptome analysis during early fruit development of zucchini suggest that other complementary pathways could regulate fruit formation in parthenocarpic cultivars of this species. The development of next-generation sequencing technologies (NGS) as RNA-sequencing (RNA-seq) opens a new horizon for mapping and quantifying transcriptome to understand the molecular basis of pathways that could regulate parthenocarpy in this species. The aim of the current study was to analyze fruit transcriptome of two cultivars of zucchini, a non-parthenocarpic cultivar and a parthenocarpic cultivar, in an attempt to identify key genes involved in parthenocarpy. Results: RNA-seq analysis of six libraries (unpollinated, pollinated and auxin treated fruit in a non-parthenocarpic and parthenocarpic cultivar) was performed mapping to a new version of C. pepo transcriptome, with a mean of 92% success rate of mapping. In the non-parthenocarpic cultivar, 6479 and 2186 genes were differentially expressed (DEGs) in pollinated fruit and auxin treated fruit, respectively. In the parthenocarpic cultivar, 10,497 in pollinated fruit and 5718 in auxin treated fruit. A comparison between transcriptome of the unpollinated fruit for each cultivar has been performed determining that 6120 genes were differentially expressed. Annotation analysis of these DEGs revealed that cell cycle, regulation of transcription, carbohydrate metabolism and coordination between auxin, ethylene and gibberellin were enriched biological processes during pollinated and parthenocarpic fruit set. Conclusion: This analysis revealed the important role of hormones during fruit set, establishing the activating role of auxins and gibberellins against the inhibitory role of ethylene and different candidate genes that could be useful as markers for parthenocarpic selection in the current breeding programs of zucchini.Research worked is supported by the project RTA2014-00078 from the Spanish Institute of Agronomy Research INIA (Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria) and also PP.AVA.AVA201601.7, FEDER y FSE (Programa Operativo FSE de Andalucia 2007-2013 "Andalucia se mueve con Europa"). TPV is supported by a FPI scholarship from RTA2011-00044-C02-01/02 project of INIA. 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Cellular responses to auxin: division versus expansion. Cold Spring Harb Perspect Biol. 2010;2(5):a001446.De Veylder L, Beeckman T, Beemster GT, Krols L, Terras F, Landrieu I, et al. Functional analysis of cyclin-dependent kinase inhibitors of Arabidopsis. Plant Cell. 2001;13:1653–68.Nieuwland J, Menges M, Murray JAH. The plant cyclins. In: Inze D, editor. Cell cycle control and plant development, vol. 2007. Oxford: Wiley-Blackwell Publishing; 2007. p. 33–61.Menges M, Samland AK, Planchais S, Murray JA. The D-type cyclin CYCD3;1 is limiting for the G1-to-S-phasetransition in Arabidopsis. Plant Cell. 2006;18:893–906.Boruc J, Mylle E, Duda M, De Clercq R, Rombauts S, Geelen D, et al. Systematic localization of the Arabidopsis core cell cycle proteins reveals novel cell division complexes. Plant Physiol. 2010;152(2):553–65.Sampedro J, Cosgrove DJ. The expansin superfamily. Genome Biol. 2005;6:242.Esmon CA, Tinsley AG, Ljung K, Sandberg G, Hearne LB, Liscum E. A gradient of auxin and auxin-dependent transcription precedes tropic growth responses. Proc Natl Acad Sci. 2006;103:236–41.De Folter S, Busscher J, Colombo L, Losa A, Angenent GC. Transcript profiling of transcription factors genes during siliques development in Arabidopsis. Plant Mol Bio. 2004;56:351–3662004.Son O, Cho HY, Kim MR, Lee H, Lee MS, Song E, et al. Induction of a homeodomain-leucine zipper gene by auxin is inhibited by cytokinin in Arabidopsis roots. Biochem Biophys Res Commun. 2005;326(1):203–9.Olsson ASB, Engstroem P, Seoderman E. The homeobox genes ATHB12 and ATHB7 encode potential regulators of growth in response to water deficit in Arabidopsis. Plant Mol Biol. 2004;55:663–77.Merrow SB, Hopp RJ. Storage effects on winter squashes. Associations between the sugar and starch content of and the degree of preference for winter squashes. J Agric Food Chem. 1961;9:321–6.Berg JM, Tymoczko JL, Stryer L. Carbohydrates. In: Freeman WH, editor. Biochemistry. 5th ed. New York: W H Freeman; 2002.Prabhakar V, Löttgert T, Gigolashvili T, Bell K, Flügge UI, Häusler RE. Molecular and functional characterization of the plastid-localized phosphoenolpyruvate enolase (ENO1) from Arabidopsis thaliana. FEBS Lett. 2009;583(6):983–91.Rius SP, Casati P, Iglesias AA, Gomez-Casati DF. Characterization of Arabidopsis lines deficient in GAPC-1, a cytosolic NAD-dependent glyceraldehyde-3-phosphate dehydrogenase. Plant Physiol. 2008;148(3):1655–67.Van der Linde K, Gutsche N, Leffers HM, Lindermayr C, Müller B, Holtgrefe S, et al. Regulation of plant cytosolic aldolase functions by redox-modifications. Plant Physiol Biochem. 2011;49(9):946–57.Lim H, Cho MH, Jeon JS, Bhoo SH, Kwon YK, Hahn TR. Altered expression of pyrophosphate: fructose-6-phosphate 1-phosphotransferase affects the growth of transgenic Arabidopsis plants. Mol Cells. 2009;27(6):641–9.Baud S, Wuillème S, Dubreucq B, De Almeida A, Vuagnat C, Lepiniec L, et al. Function of plastidial pyruvate kinases in seeds of Arabidopsis thaliana. Plant J. 2007;52:405–19.De Jong M, Mariani C, Vriezen WH. The role of auxin and gibberellin in tomato fruit set. J Exp Bot. 2009;60(5):1523–32.Martínez C, Manzano S, Megías Z, Garrido D, Picó B, Jamilena M. Involvement of ethylene biosynthesis and signalling in fruit set and early fruit development in zucchini squash (Cucurbita pepo L.). BMC Plant Biol. 2013;13:139.Serrani JC, Fos M, Atarés A, Garcia-martinez JL. Effect of gibberellin and auxin on parthenocarpic fruit growth induction in the cv. micro-tom of tomato. J Plant Growth Regul. 2007;26:211–21.Mapelli S. Changes in cytokinin in the fruits of parthenocarpic and normal tomatoes. Plant Sci Lett. 1981;22:227–33.Ulmasov T, Hagen G, Guilfoyle TJ. Activation and repression of transcription by auxin-response factors. Proc Natl Acad Sci U S A. 1999;96:5844–9.Ulmasov T, Hagen G, Guilfoyle TJ. Dimerization and DNA binding of auxin response factors. Plant J. 1999;19:309–19.Tiwari SB, Hagen G, Guilfoyle TJ. Aux/IAA proteins contain a potent transcriptional repression domain. Plant Cell. 2004;16:533–43.Switzenberg JA, Beaudry RM, Grumet R. Effect of CRC:: etr1-1 transgene expression on ethylene production, sex expression, fruit set and fruit ripening in transgenic melon (Cucumis melo L.). Transgenic Res. 2015;24(3):497-507.Nitsch LM, Oplaat C, Feron R, Ma Q, Wolters-Arts M, Hedden P, et al. Abscisic acid levels in tomato ovaries are regulated by LeNCED1 and SlCYP707A1. Planta. 2009;229(6):1335–46.Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods. 2008;5(7):621–8.Robinson MD, McCarthy DJ, Smyth GK. Edger: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2008;26(1):139–40.Raza K, Mishra A. A novel anticlustering filtering algorithm for the prediction of genes as a drug target. 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Catalysis for industrial production and of energy resources

Peer reviewe

PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data

[EN] The increasing availability of multi-omic platforms poses new challenges to data analysis. Joint visualization of multi-omics data is instrumental in better understanding interconnections across molecular layers and in fully utilizing the multi-omic resources available to make biological discoveries. We present here PaintOmics 3, a web-based resource for the integrated visualization of multiple omic data types onto KEGG pathway diagrams. PaintOmics 3 combines server-end capabilities for data analysis with the potential of modern web resources for data visualization, providing researchers with a powerful framework for interactive exploration of their multi-omics information. Unlike other visualization tools, PaintOmics 3 covers a comprehensive pathway analysis workflow, including automatic feature name/identifier conversion, multi-layered feature matching, pathway enrichment, network analysis, interactive heatmaps, trend charts, and more. It accepts a wide variety of omic types, including transcriptomics, proteomics and metabolomics, as well as region-based approaches such as ATAC-seq or ChIP-seq data. The tool is freely available at www.paintomics.orgEuropean Union Seventh Framework Programme [FP7/2007-2013] under the grant agreement [306000-STATegra]; Marie Curie International Research Staff Exchange Scheme under grant agreement [612583-DEANN]; Spanish MINECO [BIO2012-40244]. INB Grant [PT17/0009/0015 - ISCIII-SGEFI / ERDF]. Funding for open access charge: MINECO [BIO2012-40244].Hernandez-De Diego, R.; Tarazona Campos, S.; Martínez-Mira, C.; Balzano-Nogueira, L.; Furió-Tarí, P.; Conesa, A.; Pappas, G. (2018). PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data. Nucleic Acids Research. 46(W1):503-509. https://doi.org/10.1093/nar/gky466S50350946W

Enchytraeus albidus Microarray: Enrichment, Design, Annotation and Database (EnchyBASE)

Enchytraeus albidus (Oligochaeta) is an ecologically relevant species used as standard test organisms for risk assessment. Effects of stressors in this species are commonly determined at the population level using reproduction and survival as endpoints. The assessment of transcriptomic responses can be very useful e.g. to understand underlying mechanisms of toxicity with gene expression fingerprinting. In the present paper the following is being addressed: 1) development of suppressive subtractive hybridization (SSH) libraries enriched for differentially expressed genes after metal and pesticide exposures; 2) sequencing and characterization of all generated cDNA inserts; 3) development of a publicly available genomic database on E. albidus. A total of 2100 Expressed Sequence Tags (ESTs) were isolated, sequenced and assembled into 1124 clusters (947 singletons and 177 contigs). From these sequences, 41% matched known proteins in GenBank (BLASTX, e-value≤10-5) and 37% had at least one Gene Ontology (GO) term assigned. In total, 5.5% of the sequences were assigned to a metabolic pathway, based on KEGG. With this new sequencing information, an Agilent custom oligonucleotide microarray was designed, representing a potential tool for transcriptomic studies. EnchyBASE (http://bioinformatics.ua.pt/enchybase/) was developed as a web freely available database containing genomic information on E. albidus and will be further extended in the near future for other enchytraeid species. The database so far includes all ESTs generated for E. albidus from three cDNA libraries. This information can be downloaded and applied in functional genomics and transcription studies

Maritime-oriented foragers during the Late Pleistocene on the eastern costa del sol (Southeast Iberia): Cueva Victoria (Málaga, Spain)

The Mediterranean coast of Spain is marked by several clusters of Palaeolithic sites: to the south of the Pyrenees, in the area around the Ebro River, in the central part, and on the south coast, one of the southernmost regions in Europe. The number of sites is small compared with northern Iberia, but like that region, the Palaeolithic occupations are accompanied by several rock art ensembles. The archaeological material (both biotic and abiotic resources) and radiocarbon dates presented here were obtained during archaeological fieldwork of professor J. Fortea in the Late Pleistocene deposits in Cueva Victoria, located near the modern coastline and about 150 km north of the Strait of Gibraltar. In the three occupation phases, marine resources were acquired by shell-fishing (focusing almost exclusively on the clam Ruditapes decussatus), fishing, and the use of beached marine mammals. This contrasts with the limited data about the exploitation of terrestrial resources by hunting and gathering animals and plants. The study is completed by the study of artefacts (lithic and bone industry and objects of adornment) that help to understand the subsistence strategies of the cave occupants and enable a comparison with other groups inhabiting the Mediterranean coasts of the Iberian Peninsula during Greenland Interstadial 1, between ca. 15.1 and 13.6 cal BP.This work was supported by the University of Salamanca GIR PREHUSAL, the Ministry of Science and Innovation-Spanish Government (PaleontheMove-PID2020-114462GB-I00), the Universidad Nacional de Educación a Distancia (Madrid) and Dirección General de Universitat, Investigacio i Ciencia of the Valencian Regional Government (Project Aico/2020/97).Peer reviewe

Phytoremediation of heavy metal-contaminated sites: Eco-environmental concerns, field studies, sustainability issues and future prospects

Environmental contamination due to heavy metals (HMs) is of serious ecotoxicological concern worldwide because of their increasing use at industries. Due to non-biodegradable and persistent nature, HMs cause serious soil/water pollution and severe health hazards in living beings upon exposure. HMs can be genotoxic, carcinogenic, mutagenic, and teratogenic in nature even at low concentration. They may also act as endocrine disruptors and induce developmental as well as neurological disorders and thus, their removal from our natural environment is crucial for the rehabilitation of contaminated sites. To cope with HM pollution, phytoremediation has emerged as a low-cost and eco-sustainable solution to conventional physico-chemical cleanup methods that require high capital investment and labor alter soil properties and disturb soil microflora. Phytoremediation is a green technology wherein plants and associated microbes are used to remediate HM-contaminated sites to safeguard the environment and protect public health. Hence, in view of the above, the present paper aims to examine the feasibility of phytoremediation as a sustainable remediation technology for the management of metals-contaminated sites. Therefore, this paper provides an in-depth review on both the conventional and novel phytoremediation approaches, evaluate their efficacy to remove toxic metals from our natural environment, explore current scientific progresses, field experiences and sustainability issues and revise world over trends in phytoremediation research for its wider recognition and public acceptance as a sustainable remediation technology for the management of contaminated sites in 21st century