Contacts in the last 90,000 years over the Strait of Gibraltar evidenced by genetic analysis of wild boar (Sus scrofa)

[EN] Contacts across the Strait of Gibraltar in the Pleistocene have been studied in different research papers, which have demonstrated that this apparent barrier has been permeable to human and fauna movements in both directions. Our study, based on the genetic analysis of wild boar (Sus scrofa), suggests that there has been contact between Africa and Europe through the Strait of Gibraltar in the Late Pleistocene (at least in the last 90,000 years), as shown by the partial analysis of mitochondrial DNA. Cytochrome b and the control region from North African wild boar indicate a close relationship with European wild boar, and even some specimens belong to a common haplotype in Europe. The analyses suggest the transformation of the wild boar phylogeography in North Africa by the emergence of a natural communication route in times when sea levels fell due to climatic changes, and possibly through human action, since contacts coincide with both the Last Glacial period and the increasing human dispersion via the strait.This study was supported by The Emirates Centre for Wildlife Propagation (Morocco). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Soria-Boix, C.; Donat-Torres, MP.; Urios, V. (2017). Contacts in the last 90,000 years over the Strait of Gibraltar evidenced by genetic analysis of wild boar (Sus scrofa). PLoS ONE. 12(7). doi:10.1371/journal.pone.0181929S12

Transient Reversal of Episome Silencing Precedes VP16-Dependent Transcription during Reactivation of Latent HSV-1 in Neurons

Herpes simplex virus type-1 (HSV-1) establishes latency in peripheral neurons, creating a permanent source of recurrent infections. The latent genome is assembled into chromatin and lytic cycle genes are silenced. Processes that orchestrate reentry into productive replication (reactivation) remain poorly understood. We have used latently infected cultures of primary superior cervical ganglion (SCG) sympathetic neurons to profile viral gene expression following a defined reactivation stimulus. Lytic genes are transcribed in two distinct phases, differing in their reliance on protein synthesis, viral DNA replication and the essential initiator protein VP16. The first phase does not require viral proteins and has the appearance of a transient, widespread de-repression of the previously silent lytic genes. This allows synthesis of viral regulatory proteins including VP16, which accumulate in the cytoplasm of the host neuron. During the second phase, VP16 and its cellular cofactor HCF-1, which is also predominantly cytoplasmic, concentrate in the nucleus where they assemble an activator complex on viral promoters. The transactivation function supplied by VP16 promotes increased viral lytic gene transcription leading to the onset of genome amplification and the production of infectious viral particles. Thus regulated localization of de novo synthesized VP16 is likely to be a critical determinant of HSV-1 reactivation in sympathetic neurons

Porcine Y-chromosome variation is consistent with the occurrence of paternal gene flow from non-Asian to Asian populations

Altres ajuts: CERCA Programme/Generalitat de Catalunya.Pigs (Sus scrofa) originated in Southeast Asia and expanded to Europe and North Africa approximately 1 MYA. Analyses of porcine Y-chromosome variation have shown the existence of two main haplogroups that are highly divergent, a result that is consistent with previous mitochondrial and autosomal data showing that the Asian and non-Asian pig populations remained geographically isolated until recently. Paradoxically, one of these Y-chromosome haplogroups is extensively shared by pigs and wild boars from Asia and Europe, an observation that is difficult to reconcile with a scenario of prolonged geographic isolation. To shed light on this issue, we genotyped 33 Y-linked SNPs and one indel in a worldwide sample of pigs and wild boars and sequenced a total of 9903 nucleotide sites from seven loci distributed along the Y-chromosome. Notably, the nucleotide diversity per site at the Y-linked loci (0.0015 in Asian pigs) displayed the same order of magnitude as that described for autosomal loci (~0.0023), a finding compatible with a process of sustained and intense isolation. We performed an approximate Bayesian computation analysis focused on the paternal diversity of wild boars and local pig breeds in which we compared three demographic models: two isolation models (I models) differing in the time of isolation and a model of isolation with recent unidirectional migration (IM model). Our results suggest that the most likely explanation for the extensive sharing of one Y-chromosome haplogroup between non-Asian and Asian populations is a recent and unidirectional (non-Asian > Asian) paternal migration event

Detection and replication of QTL underlying resistance to gastrointestinal nematodes in adult sheep using the ovine 50K SNP array

16 p.Persistence of gastrointestinal nematode (GIN) infection and the related control methods have major impacts on the sheep industry worldwide. Based on the information generated with the Illumina OvineSNP50 BeadChip (50 K chip), this study aims at confirming quantitative trait loci (QTL) that were previously identified by microsatellite ‑ based genome scans and identifying new QTL and allelic variants that are associated with indicator traits of parasite resistance in adult sheep. We used a commercial half ‑ sib population of 518 Spanish Churra ewes with available data for fecal egg counts (FEC) and serum levels of immunoglobulin A (IgA) to perform different genome scan QTL mapping analyses based on classical linkage analysis (LA), a combined linkage disequilibrium and linkage analysis (LDLA) and a genome ‑ wide association study (GWAS)This work was supported by a competitive grant from the Castilla and León regional government (Junta de Castilla y León) (Ref. LE245A12-2) and the AGL2012-34437 project funded by the Spanish Ministry of Economy and Competitiveness (MINECO). M Atlija is a grateful grantee of a Marie Curie fellowship funded by the EC-funded Initial Training Network (ITN) NematodeSystemHealth (FP7-PEOPLE-2010-ITN Ref. 264639). B Gutiérrez-Gil is funded through the Spanish “Ramón y Cajal” Programme (RYC-2012-10230) from the MINECO.S

Analysis of the non-recombining Y chromosome defines polymorphisms in domestic pig breeds: ancestral bases identified by comparative sequencing.

Sequences from 20 amplicons representing nine different loci and 11369bp from the short arm of the pig Y chromosome were compared using pools of DNA from different European and Chinese breeds. A total of 33 polymorphic sites were identified, including five indels and 28 single nucleotide polymorphisms (SNPs). Three high frequency SNPs within the coding regions of SRY were further analysed across 889 males representing 25 European and 25 Asian breeds or Lines, plus a European Line of Meishan. Two haplotypes seen to be associated with 'European' or 'Chinese' origin in the initial SNP discovery phase were found to be the most common in their respective groups of breeds in a more detailed genotyping study. Two further SRY haplotypes are relatively rare. One was found exclusively within Tamworth, at low frequency in Retinto, and in three Chinese breeds (Huai, Sahwutou and Xiaomeishan). The other uncommon haplotype is found exclusively in Bamajiang, two further Chinese breeds (Hangjiang Black and Longling) and two European rare breeds (Mangalica and Linderödssvin), but appears based on comparison with other suids to represent an ancestral sequence

Analysis of the non-recombining Y chromosome defines polymorphisms in domestic pig breeds: ancestral bases identified by comparative sequencing

Sequences from 20 amplicons representing nine different loci and 11369bp from the short arm of the pig Y chromosome were compared using pools of DNA from different European and Chinese breeds. A total of 33 polymorphic sites were identified, including five indels and 28 single nucleotide polymorphisms (SNPs). Three high frequency SNPs within the coding regions of SRY were further analysed across 889 males representing 25 European and 25 Asian breeds or Lines, plus a European Line of Meishan. Two haplotypes seen to be associated with 'European' or 'Chinese' origin in the initial SNP discovery phase were found to be the most common in their respective groups of breeds in a more detailed genotyping study. Two further SRY haplotypes are relatively rare. One was found exclusively within Tamworth, at low frequency in Retinto, and in three Chinese breeds (Huai, Sahwutou and Xiaomeishan). The other uncommon haplotype is found exclusively in Bamajiang, two further Chinese breeds (Hangjiang Black and Longling) and two European rare breeds (Mangalica and Linderödssvin), but appears based on comparison with other suids to represent an ancestral sequence

Human intellectual disability genes form conserved functional modules in Drosophila

Contains fulltext : 124936.pdf (publisher's version ) (Open Access)Intellectual Disability (ID) disorders, defined by an IQ below 70, are genetically and phenotypically highly heterogeneous. Identification of common molecular pathways underlying these disorders is crucial for understanding the molecular basis of cognition and for the development of therapeutic intervention strategies. To systematically establish their functional connectivity, we used transgenic RNAi to target 270 ID gene orthologs in the Drosophila eye. Assessment of neuronal function in behavioral and electrophysiological assays and multiparametric morphological analysis identified phenotypes associated with knockdown of 180 ID gene orthologs. Most of these genotype-phenotype associations were novel. For example, we uncovered 16 genes that are required for basal neurotransmission and have not previously been implicated in this process in any system or organism. ID gene orthologs with morphological eye phenotypes, in contrast to genes without phenotypes, are relatively highly expressed in the human nervous system and are enriched for neuronal functions, suggesting that eye phenotyping can distinguish different classes of ID genes. Indeed, grouping genes by Drosophila phenotype uncovered 26 connected functional modules. Novel links between ID genes successfully predicted that MYCN, PIGV and UPF3B regulate synapse development. Drosophila phenotype groups show, in addition to ID, significant phenotypic similarity also in humans, indicating that functional modules are conserved. The combined data indicate that ID disorders, despite their extreme genetic diversity, are caused by disruption of a limited number of highly connected functional modules