Bioinformatic Analysis of Ixodes ricinus Long Non-Coding RNAs Predicts Their Binding Ability of Host miRNAs

Ixodes ricinus ticks are distributed across Europe and are a vector of tick-borne diseases. Although I. ricinus transcriptome studies have focused exclusively on protein coding genes, the last decade witnessed a strong increase in long non-coding RNA (lncRNA) research and characterization. Here, we report for the first time an exhaustive analysis of these non-coding molecules in I. ricinus based on 131 RNA-seq datasets from three different BioProjects. Using this data, we obtained a consensus set of lncRNAs and showed that lncRNA expression is stable among different studies. While the length distribution of lncRNAs from the individual data sets is biased toward short length values, implying the existence of technical artefacts, the consensus lncRNAs show a more homogeneous distribution emphasizing the importance to incorporate data from different sources to generate a solid reference set of lncRNAs. KEGG enrichment analysis of host miRNAs putatively targeting lncRNAs upregulated upon feeding showed that these miRNAs are involved in several relevant functions for the tick-host interaction. The possibility that at least some tick lncRNAs act as host miRNA sponges was further explored by identifying lncRNAs with many target regions for a given host miRNA or sets of host miRNAs that consistently target lncRNAs together. Overall, our findings suggest that lncRNAs that may act as sponges have diverse biological roles related to the tick–host interaction in different tissues.European Commission CZ.02.2.69/0.0/0.0/20_079/0017809FEDER (Fondo Europeo De Desarrollo Regional-European Regional Development Fund) A-BIO-481-UGR18Grant Agency of the Czech Republic 19-382 07247SERD Fundsproject CePaVip OPVVV 384 CZ.02.1.01/0.0/0.0/16_019/000075

Genome-Wide Analysis of microRNA Expression Profile in Roots and Leaves of Three Wheat Cultivars under Water and Drought Conditions

The following are available online at https://www.mdpi.com/article/ 10.3390/biom13030440/s1. Figure S1: Fraction of different RNA species. Figure S2: Read length distribution of all genome mapped reads (a) from total reads (redundant reads) and (b) from unique reads (non-redundant reads. Figure S3: Library normalized RPM values distribution per sample of novel miRNAs. Figure S4: qRT-PCR analysis of the expression of novel miRNA Tae-mir-novel54-5p and known miRNA Tae-miR827c in 10 samples. Figure S5: Network analysis of (a) target genes by drought downregulated miRNAs and (b) drought upregulated miRNAs in leaves. Table S1: Quality and read mapping report. Table S2: Fraction of different RNA species. Table S3: Read length distribution of all genome mapped reads from total reads (redundant reads). Table S4: Read length distribution of all genome mapped reads from unique reads (non-redundant reads. Table S5: All miRNAs expression matrix. Table S6: Expression matrix of all the miRNAs in the SRA datasets. Table S7: miRNA expression matrix of all miRNAs in the Zea mays SRA datasets. Table S8: Degradome based target-gene predicted interactions. Table S9: qRT-PCR assay information. Table S10: Enrichment of functional annotations in miRNA target genes. Table S11: Mature and hairpin sequences of predicted miRNAs. Table S12: Degradome miRNA-target interaction predictions using CleaveLand4.Wheat is one of the most important food sources on Earth. MicroRNAs (miRNAs) play important roles in wheat productivity. To identify wheat miRNAs as well as their expression profiles under drought condition, we constructed and sequenced small RNA (sRNA) libraries from the leaves and roots of three wheat cultivars (Kukri, RAC875 and Excalibur) under water and drought conditions. A total of 636 known miRNAs and 294 novel miRNAs were identified, of which 34 miRNAs were tissue- or cultivar-specific. Among these, 314 were significantly regulated under drought conditions. miRNAs that were drought-regulated in all cultivars displayed notably higher expression than those that responded in a cultivar-specific manner. Cultivar-specific drought response miRNAs were mainly detected in roots and showed significantly different drought regulations between cultivars. By using wheat degradome library, 6619 target genes were identified. Many target genes were strongly enriched for protein domains, such as MEKHLA, that play roles in drought response. Targeting analysis showed that drought-downregulated miRNAs targeted more genes than drought- upregulated miRNAs. Furthermore, such genes had more important functions. Additionally, the genes targeted by drought-downregulated miRNAs had multiple interactions with each other, while the genes targeted by drought-upregulated miRNAs had no interactions. Our data provide valuable information on wheat miRNA expression profiles and potential functions in different tissues, cultivars and drought conditions

Transcriptomic analysis of the tick midgut and salivary gland responses upon repeated blood-feeding on a vertebrate host

Ticks are blood-feeding arthropods that use the components of their salivary glands to counter the host’s hemostatic, inflammatory, and immune responses. The tick midgut also plays a crucial role in hematophagy. It is responsible for managing blood meals (storage and digestion) and protecting against host immunity and pathogen infections. Previous transcriptomic studies revealed the complexity of tick sialomes (salivary gland transcriptomes) and mialomes (midgut transcriptomes) which encode for protease inhibitors, lipocalins (histamine-binding proteins), disintegrins, enzymes, and several other tickspecific proteins. Several studies have demonstrated that mammalian hosts acquire tick resistance against repeated tick bites. Consequently, there is an urgent need to uncover how tick sialomes and mialomes respond to resistant hosts, as they may serve to develop novel tick control strategies and applications. Here, we mimicked natural repeated tick bites in a laboratory setting and analyzed gene expression dynamics in the salivary glands and midguts of adult female ticks. Rabbits were subjected to a primary (feeding on a naive host) and a secondary infestation of the same host (we re-exposed the hosts but to other ticks). We used single salivary glands and midguts dissected from individual siblings adult pathogen-free female Ixodes ricinus to reduce genetic variability between individual ticks. The comprehensive analysis of 88 obtained RNA-seq data sets allows us to provide high-quality annotated sialomes and mialomes from individual ticks. Comparisons between fed/ unfed, timepoints, and exposures yielded as many as 3000 putative differentially expressed genes (DEG). Interestingly, when classifying the exposure DEGs by means of a clustering approach we observed that the majority of these genes show increased expression at early feeding timepoints in the mid-gut of re-exposed ticks. The existence of clearly defined groups of genes with highly similar responses to re-exposure suggests the existence of molecular swiches. In silico functional analysis shows that these early feeding reexposure response genes form a dense interaction network at protein level being related to virtually all aspects of gene expression regulation and glycosylation. The processed data is available through an easy-to-use database-associated webpage (https://arn.ugr.es/IxoriDB/) that can serve as a valuable resource for tick research.Grant Agency of the Czech Republic 19-382 07247SERD Funds 384 CZ.02.1.01/0.0/0.0/16_019/0000759Programa Operativo FEDER de Andalucia A-BIO-481-UGR18European Union within ESIF in frame of Operational Programme Research, Development and Education CZ.02.2.69/0.0/0.0/20_079/001780

The Kramer sampling theorem revisited

The classical Kramer sampling theorem provides a method for obtaining orthogonal sampling formulas. Besides, it has been the cornerstone for a significant mathematical literature on the topic of sampling theorems associated with differential and difference problems. In this work we provide, in an unified way, new and old generalizations of this result corresponding to various different settings; all these generalizations are illustrated with examples. All the different situations along the paper share a basic approach: the functions to be sampled are obtaining by duality in a separable Hilbert space H through an H -valued kernel K defined on an appropriate domain

The Kramer sampling theorem revisited

The classical Kramer sampling theorem provides a method for obtaining orthogonal sampling formulas. Besides, it has been the cornerstone for a significant mathematical literature on the topic of sampling theorems associated with differential and difference problems. In this work we provide, in an unified way, new and old generalizations of this result corresponding to various different settings; all these generalizations are illustrated with examples. All the different situations along the paper share a basic approach: the functions to be sampled are obtaining by duality in a separable Hilbert space through an -valued kernel K defined on an appropriate domain.This work has been supported by the grant MTM2009–08345 from the Spanish Ministerio de Ciencia e Innovación (MICNN).Publicad

A multidisciplinary Final Project in Civil engineering. UEM experience

[ES] En el Departamento de Ingeniería Civil de la UEM se ha tratado de aproximar la experiencia del Proyecto Fin de Carrera a la realidad profesional, mediante la creación de equipos multidisciplinares que resuelvan un “proyecto global” de desarrollo de una zona determinada mediante obras civiles que dependen unas de otras. Este proyecto se realiza en dos fases. La primera fase es un “Anteproyecto multidisciplinar en grupo” (que constituye el enfoque innovador). Cada alumno se constituye en experto de una de las disciplinas implicadas y, entre todos, estudian un conjunto de alternativas interrelacionadas que respondan de forma óptima a las necesidades del problema, eligiendo la mejor. La solución elegida para cada disciplina se desarrolla ya individualmente en una segunda fase, constituyendo esta la redacción del proyecto de construcción clásico. Como ejemplo, se han proyectado puertos deportivos incluyendo una playa como medida compensatoria al impacto en la costa, con el correspondiente desarrollo urbanístico, con accesos mediante una carretera que salva un cauce con un viaducto. Esta innovación ha presentado sus fortalezas obvias, pero también debilidades (muchas relacionadas con la implementación práctica), ofreciendo en conjunto una gran oportunidad de aprendizaje mucho más completa,en la opinión de los autores,que el concepto clásico.[EN] Real practice in Engineering Project development is tried to be implemented at the Civil Engineering Department of the Engineering School in UEM. Multidisciplinary teams have been defined to develop certain geographical areas by a complex, civil engineering project, where different constructions are inter‐dependent. The student’s project is made in two different phases. The first one is a Multidisciplinary Preliminary Project (which is the more innovative part). Each student becomes an “expert” in a particular civil engineering discipline involved in the Project. All together should study a number of choices for the different constructions in order to select the better in a global sense. The final choice in each discipline is later developed as a classic Construction Project in the second phase. As an example, one project may content a marina, including the coastal rehabilitation, the urban development with different road access and the corresponding structures, as a bridge, to cross a a river. This new proce dure for the final Project has many strengths but also weaknesses(many of them related to the practical implementation),offering a great chance for the student to learnin a globa lway, in the authors’ opinion, than using the classic procedure.[FR] Dans le département de génie civil de l'UEM nous avons essayé de rapprocher l'expérience du mémoire à la réalité professionnelle grâce à la création d'équipes multidisciplinaires visant à résoudre un projet global de développement d'une zone à travers des constructions civiles qui dépendent les unes des autres. Ce projet est réalisé en deux phases. La première est un avant‐projet pluridisciplinaire en groupe(approche innovante).Chaque étudiant est un expert dans l'une des disciplines impliquées dans le projet global et ils analysent un ensemble de solutions corrélées quirépondent de façon optimale aux besoins du problème, en choisissant la meilleure. La solution retenue pour chaque discipline est développée individuellement dans une deuxième phase, et devient la rédaction du mémoire. À titre d’exemple, on a projeté des ports de plaisance qui incluent une plage comme mesure compensatoire à l'impact sur la côte, avec le développement urbain correspondant,dont les accès sont résolus avec une route qui sauve une voie fluviale au moyen d'un viaduc. Cette innovation a évidemment présenté ses atouts, mais aussi ses faiblesses (certaines d’entre‐elles sont liées à l'application pratique),ce qui donne dans l’ensemble, d’après les auteurs,une excellente occasion d'apprendre beaucoup plus complète que la notion classique.Millán Muñoz, MÁ.; Medina Villaverde, JM. (2011). Nuevo enfoque multidisciplinar en el el proyecto fin de carrera en ingeniería civil. Experiencia en la UEM. REDU. Revista de Docencia Universitaria. 8(2):117-130. https://doi.org/10.4995/redu.2010.6198OJS11713082BAIN, K. (2005) Lo que hacen los mejores profesores universitarios. Publicaciones de la Universidad de Valencia.BENITO, A y CRUZ, A. (2007), Nuevas claves para la docencia universitaria en el Espacio Europeo de Educación Superior, Ed. Narcea.RUE, J. (2007), Enseñar en la Universidad. Ed. NarceaRUE, J (2009) El aprendizaje autónomo en Educación Superior. Ed. NarceaBARKLEY, E. (2007) Técnicas de aprendizaje colaborativo: manual para el profesorado universitario Madrid: Ministerio de Educación y Ciencia: Morata, D.L. 2007KATZENBACH, J. (2000) El trabajo en equipo: ventajas y dificultades. Ed: Granica

Generalized sampling: from shift-invariant to U-invariant spaces

The aim of this article is to derive a sampling theory in U-invariant subspaces of a separable Hilbert space ℋ where U denotes a unitary operator defined on ℋ. To this end, we use some special dual frames for L2(0, 1), and the fact that any U-invariant subspace with stable generator is the image of L2(0, 1) by means of a bounded invertible operator. The used mathematical technique mimics some previous sampling work for shift-invariant subspaces of L2(ℝ). Thus, sampling frame expansions in U-invariant spaces are obtained. In order to generalize convolution systems and deal with the time-jitter error in this new setting we consider a continuous group of unitary operators which includes the operator U

On Some Sampling-Related Frames in U-Invariant Spaces

This paper is concerned with the characterization as frames of some sequences in -invariant spaces of a separable Hilbert space H where U denotes an unitary operator defined on H ; besides, the dual frames having the same form are also found. This general setting includes, in particular, shift-invariant or modulation-invariant subspaces in L2(R) , where these frames are intimately related to the generalized sampling problem. We also deal with some related perturbation problems. In doing so, we need the unitary operator to belong to a continuous group of unitary operators

La irrigación en la Bética romana: las fuentes escritas para el estudio de los humedales

[EN] This paper is part of the studies of the Research Project “Riparia. Conceptualization, management, exploitation and function of Wetlands and the lacustrine spaces in the Roman Baetica”. Through analysis of the diverse documentary sources, particularly from the epigraphic and legal ones, it tries the conceptual definition of lacustrine and wetland spaces and its reflection in those who integrate the riverside areas of the Roman Baetica. This Roman region was a space that counted on diversity of wetlands and lacustrine areas, as much in the coast as in the interior, and had to be organized, to be regularized and to be used by the Roman power from its inception in the territory after the creation in 197 BC of the Ulterior Baetica province, to the object of its correct exploitation and economic advantage taking into account the resources that it provided.[ES] La presente comunicación forma parte de los estudios del Proyecto de Investigación “Riparia. Conceptualización, gestión, explotación y función de los espacios lacustres en la Bética romana” y pretende la definición conceptual, a través del análisis de las diversas fuentes documentales, particularmente de las epigráficas y jurídicas, de los espacios lacustres y humedales y su reflejo en aquellos que integran los medios ribereños de la Bética romana. Esta región romana fue un espacio que contó con diversidad de zonas humedales y lacustres, tanto en la costa como en el interior, y hubo de ser organizado, regularizado y utilizado por el poder romano desde su aparición en el territorio tras la creación en el 197 a.C. de la provincia Ulterior Baetica, al objeto de su correcta explotación y aprovechamiento económico habida cuenta de los recursos que suministraba.Cañizar Palacios, JL.; Fornell Muñoz, A.; López Medina, MJ. (2015). La irrigación en la Bética romana: las fuentes escritas para el estudio de los humedales. En Irrigation, Society and Landscape. Tribute to Tom F. Glick. Editorial Universitat Politècnica de València. 212-232. https://doi.org/10.4995/ISL2014.2014.161OCS21223

GC gene polymorphism and unbound serum retinol-binding protein 4 are related to the risk of insulin resistance in patients with chronic hepatitis c: A prospective cross-sectional study

Insulin resistance (IR) is found in chronic hepatitis C (CHC) more frequently than in other chronic liver diseases. Prospective cross-sectional study to evaluate a wide multitest panel to identify factors related with IR in CHC and their possible interactions. In 76 patients with CHC we performed a series of routine laboratory analysis as well as specifically designed serum biochemical tests [retinol, retinol-binding protein 4 (RBP4), 25-OH vitamin D, Vitamin E, lipopolysaccharide-binding protein (LBP), interleukin-6 (IL-6), and cystatin C]. The single nucleotide polymorphisms rs7041 and rs4588 GC-DBP (group-specific component-Vitamin D-binding protein), rs738409 PNPLA3 (patatin-like phospholipase domain containing 3), and rs12979860 IL28B (interleukin-28 B) genes were determined. Insulin sensitivity was established with the HOMA-IR and IR was diagnosed when HOMA-IR>3. Fibrosis staging was assessed with liver biopsy or transient elastography. After backward logistic regression analysis, independent variables associated with IR were Gc1s/Gc1s DBP phenotype, that results from the homozygous carriage of the rs7041G/rs4588Chaplotype (P¼0.033); low retinol/RBP4 ratio, reflecting a greater rate of unboundRBP4 (P¼0.005); older age (P¼0.01); high serum tryglicerides (P¼0.026); and advanced (F3–F4) fibrosis stage. The AUROC provided by the multivariate model was 0.950 (95% CI¼0.906–0.993). In addition to previously known ones, the Gc1s/Gc1s phenotype variant of DBP and the unbound fraction of plasma RBP4 may be considered as factors related with the incidence, and possibly the risk, of IR in CHC patients.• Instituto de Salud Carlos III, Fondo de Investigación Sanitari: Ayudas PI12/00241 y PI12/00324 • Junta de Extremadura: Ayuda GR15026 • Fondos FEDERpeerReviewe