Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes

A genome-wide comparison of transposable elements reveals evidence for unexpectedly high rates of horizontal transfer between three species of Drosophil

On local cross sections in topological abelian groups

Versión aceptada de https://doi.org/10.1007/s13398-018-0599-4[Abstract:] We introduce the notion of local pseudo-homomorphism between two topological abelian groups. We prove that it is closely related with the widely studied notions of local cross sections and splitting extensions in the category of topological abelian groups. In the final section we present an example of a non-splitting extension of (R, τν ) by R, where τν is a metrizable group topology on R weaker than the usual one. This extension admits a local cross section.The authors acknowledge the financial support of the Spanish AEI and FEDER UE funds. Grant: MTM2016-79422-P. They also acknowledge the support of the Asociación de Amigos of the University of Navarra. A portion of this research was conducted while the fourth author was a Fulbright Senior Scholar

Civil society and international governance: the role of non-state actors in the EU, Africa, Asia and Middle East

Structures and processes occurring within and between states are no longer the only – or even the most important - determinants of those political, economic and social developments and dynamics that shape the modern world. Many issues, including the environment, health, crime, drugs, migration and terrorism, can no longer be contained within national boundaries. As a result, it is not always possible to identify the loci for authority and legitimacy, and the role of governments has been called into question. \ud \ud Civil Society anf International Governance critically analyses the increasing impact of nongovernmental organisations and civil society on global and regional governance. Written from the standpoint of advocates of civil society and addressing the role of civil society in relation to the UN, the IMF, the G8 and the WTO, this volume assess the role of various non-state actors from three perspectives: theoretical aspects, civil society interaction with the European Union and civil society and regional governance outside Europe, specifically Africa, East Asia and the Middle East. It demonstrates that civil society’s role has been more complex than one defined in terms, essentially, of resistance and includes actual participation in governance as well as multi-facetted contributions to legitimising and democratising global and regional governance

Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders

The human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the major pandemic of the twenty-first century. We analyzed more than 4700 SARS-CoV-2 genomes and associated metadata retrieved from public repositories. SARS-CoV-2 sequences have a high sequence identity (>99.9%), which drops to >96% when compared to bat coronavirus genome. We built a mutation-annotated reference SARS-CoV-2 phylogeny with two main macro-haplogroups, A and B, both of Asian origin, and more than 160 sub-branches representing virus strains of variable geographical origins worldwide, revealing a rather uniform mutation occurrence along branches that could have implications for diagnostics and the design of future vaccines. Identification of the root of SARS-CoV-2 genomes is not without problems, owing to conflicting interpretations derived from either using the bat coronavirus genomes as an outgroup or relying on the sampling chronology of the SARS-CoV-2 genomes and TMRCA estimates; however, the overall scenario favors haplogroup A as the ancestral node. Phylogenetic analysis indicates a TMRCA for SARS-CoV-2 genomes dating to November 12, 2019, thus matching epidemiological records. Sub-haplogroup A2 most likely originated in Europe from an Asian ancestor and gave rise to subclade A2a, which represents the major non-Asian outbreak, especially in Africa and Europe. Multiple founder effect episodes, most likely associated with super-spreader hosts, might explain COVID-19 pandemic to a large extentThis study received support from the Instituto de Salud Carlos III: project GePEM (Instituto de Salud Carlos III(ISCIII)/PI16/01478/ Cofinanciado FEDER), DIAVIR (Instituto de Salud Carlos III(ISCIII)/DTS19/00049/Cofinanciado FEDER; Proyecto de Desarrollo Tecnológico en Salud) and Resvi-Omics (Instituto de Salud Carlos III(ISCIII)/PI19/01039/Cofinanciado FEDER) and project BI-BACVIR (PRIS-3; Agencia de Conocimiento en Salud (ACIS)—Servicio Gallego de Salud (SERGAS)—Xunta de Galicia; Spain) given to A.S.; and projects ReSVinext (Instituto de Salud Carlos III(ISCIII)/PI16/01569/Cofinanciado FEDER), and Enterogen (Instituto de Salud Carlos III(ISCIII)/ PI19/01090/ Cofinanciado FEDER) given to F.M.-TS

Ancestry patterns inferred from massive RNA-seq data

There is a growing body of evidence suggesting that patterns of gene expression vary within and between human populations. However, the impact of this variation in human diseases has been poorly explored, in part owing to the lack of a standardized protocol to estimate biogeographical ancestry from gene expression studies. Here we examine several studies that provide new solid evidence indicating that the ancestral background of individuals impacts gene expression patterns. Next, we test a procedure to infer genetic ancestry from RNA-seq data in 25 data sets where information on ethnicity was reported. Genome data of reference continental populations retrieved from The 1000 Genomes Project were used for comparisons. Remarkably, only eight out of 25 data sets passed FastQC default filters. We demonstrate that, for these eight population sets, the ancestral background of donors could be inferred very efficiently, even in data sets including samples with complex patterns of admixture (e.g., American-admixed populations). For most of the gene expression data sets of suboptimal quality, ancestral inference yielded odd patterns. The present study thus brings a cautionary note for gene expression studies highlighting the importance to control for the potential confounding effect of ancestral genetic background

A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus

Respiratory syncytial virus (RSV) is one of the major causes of acute lower respiratory tract infection worldwide. The absence of a commercial vaccine and the limited success of current therapeutic strategies against RSV make further research necessary. We used a multi-cohort analysis approach to investigate host transcriptomic biomarkers and shed further light on the molecular mechanism underlying RSV-host interactions. We meta-analyzed seven transcriptome microarray studies from the public Gene Expression Omnibus (GEO) repository containing a total of 922 samples, including RSV, healthy controls, coronaviruses, enteroviruses, influenzas, rhinoviruses, and coinfections, from both adult and pediatric patients. We identified > 1500 genes differentially expressed when comparing the transcriptomes of RSV-infected patients against healthy controls. Functional enrichment analysis showed several pathways significantly altered, including immunologic response mediated by RSV infection, pattern recognition receptors, cell cycle, and olfactory signaling. In addition, we identified a minimal 17-transcript host signature specific for RSV infection by comparing transcriptomic profiles against other respiratory viruses. These multi-genic signatures might help to investigate future drug targets against RSV infectionThis study received support from the Instituto de Salud Carlos III: project GePEM (Instituto de Salud Carlos III(ISCIII)/PI16/01478/Cofinanciado FEDER), DIAVIR (Instituto de Salud Carlos III(ISCIII)/DTS19/00049/Cofinanciado FEDER; Proyecto de Desarrollo Tecnológico en Salud) and Resvi-Omics (Instituto de Salud Carlos III(ISCIII)/PI19/0103; 9/Cofinanciado FEDER) given to A.S.; and project ReSVinext (Instituto de Salud Carlos III(ISCIII)/PI16/01569/Cofinanciado FEDER), and Enterogen (Instituto de Salud Carlos III(ISCIII)/ PI19/01090/Cofinanciado FEDER) given to F.M.-T.S

Striking structural dynamism and nucleotide sequence variation of the transposon Galileo in the genome of Drosophila mojavensis

Background: Galileo is a transposable element responsible for the generation of three chromosomal inversions in natural populations of Drosophila buzzatii. Although the most characteristic feature of Galileo is the long internally-repetitive terminal inverted repeats (TIRs), which resemble the Drosophila Foldback element, its transposase-coding sequence has led to its classification as a member of the P-element superfamily (Class II, subclass 1, TIR order). Furthermore, Galileo has a wide distribution in the genus Drosophila, since it has been found in 6 of the 12 Drosophila sequenced genomes. Among these species, D. mojavensis, the one closest to D. buzzatii, presented the highest diversity in sequence and structure of Galileo elements. Results: In the present work, we carried out a thorough search and annotation of all the Galileo copies present in the D. mojavensis sequenced genome. In our set of 170 Galileo copies we have detected 5 Galileo subfamilies (C, D, E, F, and X) with different structures ranging from nearly complete, to only 2 TIR or solo TIR copies. Finally, we have explored the structural and length variation of the Galileo copies that point out the relatively frequent rearrangements within and between Galileo elements. Different mechanisms responsible for these rearrangements are discussed. Conclusions: Although Galileo is a transposable element with an ancient history in the D. mojavensis genome, our data indicate a recent transpositional activity. Furthermore, the dynamism in sequence and structure, mainly affecting the TIRs, suggests an active exchange of sequences among the copies. This exchange could lead to new subfamilies of the transposon, which could be crucial for the long-term survival of the element in the genome

GUANIN: an all-in-one GUi-driven analyzer for NanoString interactive normalization

GUANIN can be installed with pip install GUANIN and it is available at https://pypi.org/project/guanin/. Source code, documentation, and case studies are available at https://github.com/julimontoto/guanin under the GPLv3 license.[Abstract]: Most tools for normalizing NanoString gene expression data, apart from the default NanoString nCounter software, are R packages that focus on technical normalization and lack configurable parameters. However, content normalization is the most sensitive, experiment-specific, and relevant step to preprocess NanoString data. Currently this step requires the use of multiple tools and a deep understanding of data management by the researcher. We present GUANIN, a comprehensive normalization tool that integrates both new and well-established methods, offering a wide variety of options to introduce, filter, choose, and evaluate reference genes for content normalization. GUANIN allows the introduction of genes from an endogenous subset as reference genes, addressing housekeeping-related selection problems. It performs a specific and straightforward normalization approach for each experiment, using a wide variety of parameters with suggested default values. GUANIN provides a large number of informative output files that enable the iterative refinement of the normalization process. In terms of normalization, GUANIN matches or outperforms other available methods. Importantly, it allows researchers to interact comprehensively with the data preprocessing step without programming knowledge, thanks to its easy-to-use Graphical User Interface (GUI).The supercomputer FinisTerrae III and its permanent data storage system have been funded by the Spanish Ministry of Science and Innovation, the Galician Government, and the European Regional Development Fund (ERDF). This study also received support by (i) ISCIII: TRINEO: PI22/00162; DIAVIR: DTS19/00049; Resvi-Omics: PI19/01039 (A.S.), ReSVinext: PI16/01569, Enterogen: PI19/01090 (F.M.-T.), cofinanciados FEDER, (ii) GAIN: IN607B 2020/08 and IN607A 2023/02 (A.S.), GEN-COVID: IN845D 2020/23 (F.M.-T.), IIN607A2021/05 (F.M.-T.); (iii) ACIS: BI-BACVIR (PRIS-3, to A.S.), CovidPhy (SA 304 C, to A.S.); and (iv) consorcio Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CB21/06/00103; to A.S. and F.M.-T.). In addition, this study has been funded by ISCIII through the project “CP23/00080” and co-funded by the European Union. The funders were not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication.Xunta de Galicia; IN607B 2020/08Xunta de Galicia; IN607A 2023/02Xunta de Galicia; IN845D 2020/23Xunta de Galicia; IIN607A2021/05Centro de Investigación Biomédica en Red de Enfermedades Respiratorias; CB21/06/0010