Why Toll-Like Receptors genes are so polymorphic?

Toll-like receptors (TLRs) are pattern recognition receptors (PRRs) considered to be the primary sensors of pathogens in innate immunity. Genetic variants could be associated to differences in breed innate immune response to pathogens and thus to susceptibility to infections or autoimmune diseases. TLRs are encoded by a multigene family and are conserved through evolution, from Drosophila to mammals, because of its essential role in innate immunity. Ten TLRs have been identified in most mammals. TLRs can be classified into groups, depending on the PAMPs detected and their cellular location. There are significant distinctions between intracellular and extracellular TLRs. Intracellular TLRs theoretically can't accept much variability, because they have evolved under strong purifying selection. Viruses can only be detected through their nucleic acids; therefore, intracellular TLRs have an essential non-redundant role in host survival. Moreover, mutations in those TLRs could end up with an autoimmune disease against own nucleic acids or with high susceptibility to some viral infections. On the other hand, membrane or extracellular TLRs have evolved under less evolutionary pressure, due to they can recognize one pathogen through different PAMPs (immunological redundancy). So they show a higher rate of damaging non-synonymous and STOP mutations. Although infective pressure that has reached these molecules is one of the main mechanisms of evolution, it is not the only one. In some domestic species non-adaptative evolution has also an important role, through genetic drift, bottlenecks and migratory routes. Genetic variation in canine and porcine TLRs characterized in our laboratory using massive parallel sequencing will be presented and results discussed

La Reacció en cadena de la polimerasa (PCR)

La reacció en cadena de la polimerasa —coneguda coma PCR per les seves sigles en anglès, polymerase chain reaction— és un mètode d'anàlisi d'àcids nucleics desenvolupat per Kary Mullis a mitjan anys vuitanta per produir grans quantitats d'un fragment específic d'ADN de seqüència i longitud definides a partir d'una petita quantitat de material inicial. La tècnica permet amplificar selectivament una molècula d'ADN o ARN diversos milions de vegades en poques hores. Mitjançant la PCR, podem realitzar la detecció i l'anàlisi de seqüències específiques d'un gen sense la necessitat d'aïllar-lo prèviament per tècniques de clonació d'ADN. Les anàlisis poden realitzar-se a partir d'unes poques cèl·lules o d'una mínima quantitat de mostra biològica sense la necessitat d'aïllar prèviament grans quantitats d'àcids nucleics. La PCR ha revolucionat el camp del dagnòstic molecular i s'ha convertit en una tècnica de rutina en l'àmbit de la genètica, la microbiologia i la biotecnologia.The chain reaction of polymerase-PCR as known for their singles in English, Polymerase chain reaction is a method of analysis of nucleic acids developed by Kary Mullis in themid eighties to produce large quantities of a specific DNA fragment of defined sequence and length from a small amount of starting material. The technique allows a molecule selectively amplifies DNA or RNA various million times more. By PCR, we performed the detection and analysis of specific sequences of a gene without the need to insulate it from previous techniques for DNA cloning. The analysis can be performed from a few stem cells or minimum amount of biological sample without the need for pre-Amentia isolate large quantities of nucleic acids. The PCR has revolutionized the field of molecular diagnostics and has become a routine technique in the field of genetics, microbiology and biotechnology

Time course differential gene expression in response to porcine circovirus type 2 subclinical infection

This study was aimed at characterizing the potential differences in gene expression in piglets inoculated with Porcine circovirus type 2 (PCV2), the essential causative agent of postweaning multisystemic wasting syndrome. Seven-day-old caesarean-derived, colostrum-deprived piglets were distributed into two groups: control (n = 8) and pigs inoculated with 105.2 TCID50 of the Burgos PCV2 isolate (n = 16). One control and three inoculated pigs were necropsied on days 1, 2, 5, and 8 post-infection (p.i.). The remaining pigs (four of each group) were sequentially bled on days 0, 7, 14, 21, and 29 p.i. (necropsy). Total RNA from the mediastinal lymph node (MLN) and lysed whole blood (LWB) samples were hybridized to Affymetrix Porcine GeneChip®. Forty-three probes were differentially expressed (DE) in MLN samples (FDR < 0.1, fold change > 2) and were distributed into three clusters: globally down-regulated genes, and up-regulated genes at early (first week p.i.) and late (day 29 p.i.) stages of infection. In LWB samples, maximal differences were observed at day 7 p.i., with 54 probes DE between control and inoculated pigs. Main Gene Ontology biological processes assigned to up-regulated genes were related to the immune response. Six common genes were found in both types of samples, all of which belonged to the interferon signaling antiviral effector pathway. Down-regulated genes were mainly related to cell adhesion and migration in MLN, and cellular organization and biogenesis in LWB. Microarray results were validated by quantitative real-time PCR. This study provides, for the first time, the characterization of the early and late molecular events taking place in response to a subclinical PCV2 infection

Short Communication: Characterization of a New Genetic Variant in the Caprine k-casein Gene

A new polymorphism has been identified in the goat kappa-casein gene by evaluating genomic DNA from the Montefalcone breed in Italy. The polymorphic site consists of a single nucleotide substitution A to G at position 242 of the exon 4 and produces an amino acid substitution Asp/Gly. A polymerase chain reaction-restriction fragment length polymorphism protocol for rapid genotyping of the variant has been developed, using the HaeIII enzyme. Animals from Italian, Spanish, and French breeds have been analyzed to investigate the occurrence of the allele in other populations. The allele appears to be exclusive to the Montefalcone breed

Coherent generation of nonclassical light on chip via detuned photon blockade

The on-chip generation of non-classical states of light is a key-requirement for future optical quantum hardware. In solid-state cavity quantum electrodynamics, such non-classical light can be generated from self-assembled quantum dots strongly coupled to photonic crystal cavities. Their anharmonic strong light-matter interaction results in large optical nonlinearities at the single photon level, where the admission of a single photon into the cavity may enhance (photon-tunnelling) or diminish (photon-blockade) the probability for a second photon to enter the cavity. Here, we demonstrate that detuning the cavity and QD resonances enables the generation of high-purity non-classical light from strongly coupled systems. For specific detunings we show that not only the purity but also the efficiency of single-photon generation increases significantly, making high-quality single-photon generation by photon-blockade possible with current state-of-the-art samples.Comment: Phys. Rev. Lett. in pres

Breeding farm, level of feeding and presence of antibiotics in the feed influence rabbit cecal microbiota

Background The effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the breeding farm and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance. Results Four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes (ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rRNA gene-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at slaughter. Different univariate and multivariate approaches were conducted to unravel the influence of the different factors on microbial alpha diversity and composition at phylum, genus and OTU taxonomic levels. The animals raised in the facility harboring the most stable environmental conditions had greater, and less variable, microbial richness and diversity. Bootstrap univariate analyses of variance and sparse partial least squares-discriminant analyses endorsed that farm conditions exerted an important influence on rabbit microbiota since the relative abundances of many taxa were found differentially represented between both facilities at all taxonomic levels characterized. Furthermore, only five OTUs were needed to achieve a perfect classification of samples according to the facility where animals were raised. The level of feeding and the presence of antibiotics did not modify the global alpha diversity but had an impact on some bacteria relative abundances, albeit in a small number of taxa compared with farm, which is consistent with the lower sample classification power according to these factors achieved using microbial information. Conclusions This study reveals that factors associated with the farm effect and other management factors, such as the presence of antibiotics in the diet or the feeding level, modify cecal microbial communities. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be responsible for different animal performance.info:eu-repo/semantics/publishedVersio

A systems biology framework integrating GWAS and RNA-seq to shed light on the molecular basis of sperm quality in swine

Background Genetic pressure in animal breeding is sparking the interest of breeders for selecting elite boars with higher sperm quality to optimize ejaculate doses and fertility rates. However, the molecular basis of sperm quality is not yet fully understood. Our aim was to identify candidate genes, pathways and DNA variants associated to sperm quality in swine by analysing 25 sperm-related phenotypes and integrating genome-wide association studies (GWAS) and RNA-seq under a systems biology framework. Results By GWAS, we identified 12 quantitative trait loci (QTL) associated to the percentage of head and neck abnormalities, abnormal acrosomes and motile spermatozoa. Candidate genes included CHD2, KATNAL2, SLC14A2 and ABCA1. By RNA-seq, we identified a wide repertoire of mRNAs (e.g. PRM1, OAZ3, DNAJB8, TPPP2 and TNP1) and miRNAs (e.g. ssc-miR-30d, ssc-miR-34c, ssc-miR-30c-5p, ssc-miR-191, members of the let-7 family and ssc-miR-425-5p) with functions related to sperm biology. We detected 6128 significant correlations (P-value ≤ 0.05) between sperm traits and mRNA abundances. By expression (e)GWAS, we identified three trans-expression QTL involving the genes IQCJ, ACTR2 and HARS. Using the GWAS and RNA-seq data, we built a gene interaction network. We considered that the genes and interactions that were present in both the GWAS and RNA-seq networks had a higher probability of being actually involved in sperm quality and used them to build a robust gene interaction network. In addition, in the final network we included genes with RNA abundances correlated with more than four semen traits and miRNAs interacting with the genes on the network. The final network was enriched for genes involved in gamete generation and development, meiotic cell cycle, DNA repair or embryo implantation. Finally, we designed a panel of 73 SNPs based on the GWAS, eGWAS and final network data, that explains between 5% (for sperm cell concentration) and 36% (for percentage of neck abnormalities) of the phenotypic variance of the sperm traits. Conclusions By applying a systems biology approach, we identified genes that potentially affect sperm quality and constructed a SNP panel that explains a substantial part of the phenotypic variance for semen quality in our study and that should be tested in other swine populations to evaluate its relevance for the pig breeding sector.info:eu-repo/semantics/publishedVersio

Short communication: Effect of αS1-casein (CSN1S1) and κ-casein (CSN3) genotypes on milk composition in Murciano-Granadina goats

The effects of the caprine alpha(S1)-casein (CSN1S1) polymorphisms on milk quality have been widely demonstrated. However, much less is known about the consequences of the kappa-casein (CSN3) genotype on milk composition in goats. Moreover, the occurrence of interactions between CSN3 and CSN1S1 genotypes has not been investigated. In this study, an association analysis between CSN1S1 and CSN3 genotypes and milk quality traits was performed in 89 Murciano-Granadina goats. Total milk yield as well as total protein, fat, solids-not-fat, lactose, alpha(S1)-casein (CSN1S1), and alpha(S2)-casein (CSN1S2) contents were recorded every other month during a whole lactation (316 observations). Data analysis using a linear mixed model for repeated observations revealed no interaction between the CSN1S1 and CSN3 genotypes. With regard to the effect of the CSN3 locus, AB and BB genotypes were significantly associated with higher levels of total casein and protein content compared with the AA CSN3 genotype. In strong contrast with French breeds, the CSN1S1 genotype did not affect protein, casein, and fat concentrations in Murciano-Granadina goats. These results highlight the importance of taking into consideration the CSN3 genotype when performing selection for milk composition in dairy goats

A pilot RNA-seq study in 40 pietrain ejaculates to characterize the porcine sperm microbiome

The microbiome plays a key role in homeostasis and health and it has been also linked to fertility and semen quality in several animal species including swine. Despite the more than likely importance of sperm bacteria on the boar's reproductive ability and the dissemination of pathogens and antimicrobial resistance genes, the high throughput characterization of the swine sperm microbiome remains scarce. We carried RNA-seq on 40 ejaculates each from a different Pietrain boar and found that a proportion of the sequencing reads did not map to the Sus scrofa genome. The current study aimed at using these reads not belonging to pig to carry a pilot study to profile the boar sperm bacterial population and its relation with 7 semen quality traits. We found that the boar sperm contains a broad population of bacteria. The most abundant phyla were Proteobacteria (39.1%), Firmicutes (27.5%), Actinobacteria (14.9%) and Bacteroidetes (5.7%). The predominant species contaminated sperm after ejaculation from soil, faeces and water sources (Bacillus megaterium, Brachybacterium faecium, Bacillus coagulans). Some potential pathogens were also found but at relatively low levels (Escherichia coli, Clostridioides difficile, Clostridium perfringens, Clostridium botulinum and Mycobacterium tuberculosis). We also identified 3 potential antibiotic resistant genes from E. coli against chloramphenicol, Neisseria meningitidis against spectinomycin and Staphylococcus aureus against linezolid. None of these genes were highly abundant. Finally, we classified the ejaculates into categories according to their bacterial features and semen quality parameters and identified two categories that significantly differed for 5 semen quality traits and 13 bacterial features including the genera Acinetobacter, Stenotrophomonas and Rhodobacter. Our results show that boar semen contains a bacterial community, including potential pathogens and putative antibiotic resistance genes, and that these bacteria may affect its reproductive performance.info:eu-repo/semantics/acceptedVersio

Studying the impact of the Full-Network embedding on multimodal pipelines

The current state of the art for image annotation and image retrieval tasks is obtained through deep neural network multimodal pipelines, which combine an image representation and a text representation into a shared embedding space. In this paper we evaluate the impact of using the Full-Network embedding (FNE) in this setting, replacing the original image representation in four competitive multimodal embedding generation schemes. Unlike the one-layer image embeddings typically used by most approaches, the Full-Network embedding provides a multi-scale discrete representation of images, which results in richer characterisations. Extensive testing is performed on three different datasets comparing the performance of the studied variants and the impact of the FNE on a levelled playground, i.e., under equality of data used, source CNN models and hyper-parameter tuning. The results obtained indicate that the Full-Network embedding is consistently superior to the one-layer embedding. Furthermore, its impact on performance is superior to the improvement stemming from the other variants studied. These results motivate the integration of the Full-Network embedding on any multimodal embedding generation scheme.This work is partially supported by the Joint Study Agreement no. W156463 under the IBM/BSC Deep Learning Center agreement, by the Spanish Government through Programa Severo Ochoa (SEV-2015- 0493), by the Spanish Ministry of Science and Technology through TIN2015-65316-P project and by the Generalitat de Catalunya (contracts 2014-SGR-1051), and by the Core Research for Evolutional Science and Technology (CREST) program of Japan Science and Technology Agency (JST).Peer ReviewedPostprint (author's final draft