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Scientific Reports Jan 2021Contrary to spontaneous yawning-an ancient phenomenon common to vertebrates-contagious yawning (elicited by others' yawns) has been found only in highly social species...
Contrary to spontaneous yawning-an ancient phenomenon common to vertebrates-contagious yawning (elicited by others' yawns) has been found only in highly social species and may reflect an emotional inter-individual connection. We investigated yawn contagion in the domestic pig, Sus scrofa. Owing to the complex socio-emotional and cognitive abilities of Sus scrofa, we posited that yawn contagion could be present in this species (Prediction 1) and influenced by individual/social factors (Prediction 2). In June-November 2018, on 104 semi-free ranging adolescent/adult pigs, 224 videos were recorded for video analysis on yawning. Kinship information was refined via genetic analyses. Statistical elaboration was conducted via GLMMs and non-parametric/randomization/cross-tabulation tests. We found yawn contagion in Sus scrofa, as it was more likely that pigs yawned when perceiving rather than not perceiving (yawning/control condition) others' yawns (response peak in the first out of three minutes). Yawn contagion was more likely: (1) in response to males' yawns; (2) as the age increased; (3) within short distance (1 m); (4) between full siblings, with no significant association between kinship and distance. The influence of kinship suggests that-as also hypothesized for Homo sapiens-yawn contagion might be linked with emotional communication and possibly contagion.
Topics: Animals; Animals, Domestic; Imitative Behavior; Male; Sus scrofa; Yawning
PubMed: 33473157
DOI: 10.1038/s41598-020-80545-1 -
Epigenetics & Chromatin Apr 2022Mitochondrial DNA (mtDNA) copy number in oocytes correlates with oocyte quality and fertilisation outcome. The introduction of additional copies of mtDNA through...
BACKGROUND
Mitochondrial DNA (mtDNA) copy number in oocytes correlates with oocyte quality and fertilisation outcome. The introduction of additional copies of mtDNA through mitochondrial supplementation of mtDNA-deficient Sus scrofa oocytes resulted in: (1) improved rates of fertilisation; (2) increased mtDNA copy number in the 2-cell stage embryo; and (3) improved development of the embryo to the blastocyst stage. Furthermore, a subset of genes showed changes in gene expression. However, it is still unknown if mitochondrial supplementation alters global and local DNA methylation patterns during early development.
RESULTS
We generated a series of embryos in a model animal, Sus scrofa, by intracytoplasmic sperm injection (ICSI) and mitochondrial supplementation in combination with ICSI (mICSI). The DNA methylation status of ICSI- and mICSI-derived blastocysts was analysed by whole genome bisulfite sequencing. At a global level, the additional copies of mtDNA did not affect nuclear DNA methylation profiles of blastocysts, though over 2000 local genomic regions exhibited differential levels of DNA methylation. In terms of the imprinted genes, DNA methylation patterns were conserved in putative imprint control regions; and the gene expression profile of these genes and genes involved in embryonic genome activation were not affected by mitochondrial supplementation. However, 52 genes showed significant differences in expression as demonstrated by RNAseq analysis. The affected gene networks involved haematological system development and function, tissue morphology and cell cycle. Furthermore, seven mtDNA-encoded t-RNAs were downregulated in mICSI-derived blastocysts suggesting that extra copies of mtDNA affected tRNA processing and/or turnover, hence protein synthesis in blastocysts. We also showed a potential association between differentially methylated regions and changes in expression for 55 genes due to mitochondrial supplementation.
CONCLUSIONS
The addition of just an extra ~ 800 copies of mtDNA into oocytes can have a significant impact on both gene expression and DNA methylation profiles in Sus scrofa blastocysts by altering the epigenetic programming established during oogenesis. Some of these changes may affect specific tissue-types later in life. Consequently, it is important to determine the longitudinal effect of these molecular changes on growth and development before considering human clinical practice.
Topics: Animals; Blastocyst; DNA Methylation; DNA, Mitochondrial; Dietary Supplements; Embryonic Development; Metaphase; Oocytes; Sus scrofa; Swine; Transcriptome
PubMed: 35428319
DOI: 10.1186/s13072-022-00442-x -
International Journal of Biological... Feb 2007The pig, a representative of the artiodactyla clade, is one of the first animals domesticated, and has become an important agriculture animal as one of the major human... (Review)
Review
The pig, a representative of the artiodactyla clade, is one of the first animals domesticated, and has become an important agriculture animal as one of the major human nutritional sources of animal based protein. The pig is also a valuable biomedical model organism for human health. The pig's importance to human health and nutrition is reflected in the decision to sequence its genome (3X). As an animal species with its wild ancestors present in the world, the pig provides a unique opportunity for tracing mammalian evolutionary history and defining signatures of selection resulting from both domestication and natural selection. Completion of the pig genome sequencing project will have significant impacts on both agriculture and human health. Following the pig whole genome sequence drafts, along with large-scale polymorphism data, it will be possible to conduct genome sweeps using association mapping, and identify signatures of selection. Here, we provide a description of the pig genome sequencing project and perspectives on utilizing genomic technologies to exploit pig genome evolution and the molecular basis for phenotypic traits for improving pig production and health.
Topics: Alternative Splicing; Animals; Biodiversity; Breeding; Chromosome Mapping; Evolution, Molecular; Genetic Variation; Genomics; Phylogeny; Selection, Genetic; Sus scrofa
PubMed: 17384734
DOI: 10.7150/ijbs.3.153 -
Nature Biomedical Engineering Feb 2021The clinical applicability of porcine xenotransplantation-a long-investigated alternative to the scarce availability of human organs for patients with organ failure-is...
The clinical applicability of porcine xenotransplantation-a long-investigated alternative to the scarce availability of human organs for patients with organ failure-is limited by molecular incompatibilities between the immune systems of pigs and humans as well as by the risk of transmitting porcine endogenous retroviruses (PERVs). We recently showed the production of pigs with genomically inactivated PERVs. Here, using a combination of CRISPR-Cas9 and transposon technologies, we show that pigs with all PERVs inactivated can also be genetically engineered to eliminate three xenoantigens and to express nine human transgenes that enhance the pigs' immunological compatibility and blood-coagulation compatibility with humans. The engineered pigs exhibit normal physiology, fertility and germline transmission of the 13 genes and 42 alleles edited. Using in vitro assays, we show that cells from the engineered pigs are resistant to human humoral rejection, cell-mediated damage and pathogenesis associated with dysregulated coagulation. The extensive genome engineering of pigs for greater compatibility with the human immune system may eventually enable safe and effective porcine xenotransplantation.
Topics: Animals; CRISPR-Associated Protein 9; CRISPR-Cas Systems; Cells, Cultured; Galactosyltransferases; Gene Knockout Techniques; Genetic Engineering; Germ Cells; Mixed Function Oxygenases; N-Acetylgalactosaminyltransferases; Sus scrofa; Transplantation, Heterologous
PubMed: 32958897
DOI: 10.1038/s41551-020-00613-9 -
Scientific Reports Jun 2021Epipaleolithic hunter-gatherers from the Near East introduced wild boars (Sus scrofa) to Cyprus, with the Early Pre-Pottery Neolithic (PPN) settlers hunting the wild...
Epipaleolithic hunter-gatherers from the Near East introduced wild boars (Sus scrofa) to Cyprus, with the Early Pre-Pottery Neolithic (PPN) settlers hunting the wild descendants of these boars. However, the geographic origin of the Cypriot boar and how they were integrated into the earliest forms of pig husbandry remain unsolved. Here, we present data on 11,000 to 9000 cal. BP Sus scrofa from the PPN sites of Klimonas and Shillourokambos. We compared them to contemporaneous populations from the Near East and to Neolithic and modern populations in Corsica, exploring their origin and evolution using biosystematic signals from molar teeth and heel bones (calcanei), using 2D and 3D geometric morphometrics. We found that the Cypriot PPN lineage of Sus scrofa originates from the Northern Levant. Yet, their phenotypic idiosyncrasy suggest that they evolved into an insular sub-species that we named Sus scrofa circeus, referring to Circe, the metamorphosis goddess that changed Ulysses companions into pigs. The phenotypic homogeneity among PPNA Klimonas wild boars and managed populations of PPNB Shillourokambos suggests that local domestication has been undertaken on the endemic S. s. circeus, strengthening the idea that Cyprus was integrated into the core region of animal domestication.
Topics: Animal Husbandry; Animals; Domestication; History, Ancient; Sus scrofa
PubMed: 34075126
DOI: 10.1038/s41598-021-90933-w -
DNA Research : An International Journal... Jun 2019Adenosine-to-inosine (A-to-I) RNA editing meditated by adenosine deaminases acting on RNA (ADARs) enzymes is a widespread post-transcriptional event in mammals. However,...
Adenosine-to-inosine (A-to-I) RNA editing meditated by adenosine deaminases acting on RNA (ADARs) enzymes is a widespread post-transcriptional event in mammals. However, A-to-I editing in skeletal muscle remains poorly understood. By integrating strand-specific RNA-seq, whole genome bisulphite sequencing, and genome sequencing data, we comprehensively profiled the A-to-I editome in developing skeletal muscles across 27 prenatal and postnatal stages in pig, an important farm animal and biomedical model. We detected 198,892 A-to-I editing sites and found that they occurred more frequently at prenatal stages and showed low conservation among pig, human, and mouse. Both the editing level and frequency decreased during development and were positively correlated with ADAR enzymes expression. The hyper-edited genes were functionally related to the cell cycle and cell division. A co-editing module associated with myogenesis was identified. The developmentally differential editing sites were functionally enriched in genes associated with muscle development, their editing levels were highly correlated with expression of their host mRNAs, and they potentially influenced the gain/loss of miRNA binding sites. Finally, we developed a database to visualize the Sus scrofa RNA editome. Our study presents the first profile of the dynamic A-to-I editome in developing animal skeletal muscle and provides evidences that RNA editing is a vital regulator of myogenesis.
Topics: Adenosine Deaminase; Animals; Databases, Genetic; Gene Expression Regulation, Developmental; Male; Muscle, Skeletal; RNA Editing; RNA, Messenger; Sequence Analysis, RNA; Sus scrofa; Whole Genome Sequencing
PubMed: 31231762
DOI: 10.1093/dnares/dsz006 -
Scientific Reports May 2021The wild boar Sus scrofa is one of the widely spread ungulate species in Europe, yet the origin and genetic structure of the population inhabiting Central and Eastern...
The wild boar Sus scrofa is one of the widely spread ungulate species in Europe, yet the origin and genetic structure of the population inhabiting Central and Eastern Europe are not well recognized. We analysed 101 newly obtained sequences of complete mtDNA genomes and 548 D-loop sequences of the species and combined them with previously published data. We identified five phylogenetic clades in Europe with clear phylogeographic pattern. Two of them occurred mainly in western and central part of the continent, while the range of the third clade covered North-Eastern, Central and South-Eastern Europe. The two other clades had rather restricted distribution. In Central Europe, we identified a contact zone of three mtDNA clades. Population genetic structure reflected clear phylogeographic pattern of wild boar in this part of Europe. The contribution of lineages originating from the southern (Dinaric-Balkan) and eastern (northern cost of the Black Sea) areas to the observed phylogeographic pattern of the species in Central and Eastern Europe was larger than those from the regions located in southern France, Iberian, and Italian Peninsulas. The present work was the first mitogenomic analysis conducted in Central and Eastern Europe to study genetic diversity and structure of wild boar population.
Topics: Animals; Demography; Europe; Genetic Variation; Genome, Mitochondrial; Phylogeography; Sus scrofa
PubMed: 33958636
DOI: 10.1038/s41598-021-88991-1 -
Mitochondrial DNA. Part A, DNA Mapping,... Sep 2016In this study, we report the complete mitochondrial genome sequence of the European wild boar, Sus scrofa scrofa for the first time. The genome is found to be...
In this study, we report the complete mitochondrial genome sequence of the European wild boar, Sus scrofa scrofa for the first time. The genome is found to be 16,770 bp in length and has a base composition of A (34.63%), G (13.38%), C (26.21%), and T (25.78%), indicating that the percentage of A + T (60.41%) was higher than G + C (39.59%). Similar to other pigs, it contains a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region (D-loop). Most of the genes were located on the H-strand except for the ND6 gene and eight tRNA genes. The complete mitochondrial genome sequence provided here would add a new genetic resource and new study on the evolution of the genus Sus.
Topics: Animals; Base Composition; Codon; Gene Rearrangement; Genes, Mitochondrial; Genome Size; Genome, Mitochondrial; Open Reading Frames; Regulatory Sequences, Nucleic Acid; Sequence Analysis, DNA; Sus scrofa; Whole Genome Sequencing
PubMed: 25693697
DOI: 10.3109/19401736.2015.1007366 -
DNA Research : An International Journal... Aug 2018Alternative splicing (AS) and fusion transcripts produce a vast expansion of transcriptomes and proteomes diversity. However, the reliability of these events and the...
Alternative splicing (AS) and fusion transcripts produce a vast expansion of transcriptomes and proteomes diversity. However, the reliability of these events and the extend of epigenetic mechanisms have not been adequately addressed due to its limitation of uncertainties about the complete structure of mRNA. Here we combined single-molecule real-time sequencing, Illumina RNA-seq and DNA methylation data to characterize the landscapes of DNA methylation on AS, fusion isoforms formation and lncRNA feature and further to unveil the transcriptome complexity of pig. Our analysis identified an unprecedented scale of high-quality full-length isoforms with over 28,127 novel isoforms from 26,881 novel genes. More than 92,000 novel AS events were detected and intron retention predominated in AS model, followed by exon skipping. Interestingly, we found that DNA methylation played an important role in generating various AS isoforms by regulating splicing sites, promoter regions and first exons. Furthermore, we identified a large of fusion transcripts and novel lncRNAs, and found that DNA methylation of the promoter and gene body could regulate lncRNA expression. Our results significantly improved existed gene models of pig and unveiled that pig AS and epigenetic modify were more complex than previously thought.
Topics: Alternative Splicing; Animals; DNA Methylation; Epigenesis, Genetic; Gene Expression Profiling; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA; Sequence Analysis, RNA; Sus scrofa; Transcriptome
PubMed: 29850846
DOI: 10.1093/dnares/dsy014 -
Scientific Reports Aug 2021Hunting can easily be linked to stress in wildlife. Drive hunts performed two to three times in one area during the respective hunting period, are thought to decrease...
Hunting can easily be linked to stress in wildlife. Drive hunts performed two to three times in one area during the respective hunting period, are thought to decrease the pressure hunting places on wildlife. Nevertheless, the expression of cortisol-one of the main mammalian stress hormones-is considered to have negative impacts on animals' well-being if expressed excessively, which may occur during some (especially repeated) hunting events. We explored the effect of drive hunts on cortisol levels in wild boar in Lower Saxony, Germany, compared these cortisol levels to reference values given by a similar study, and investigated the effect of age, sex, and pregnancy. Blood collected from wild boar shot on drive hunts was analysed using a radioimmunoassay. As expected, we observed elevated cortisol levels in all samples, however, we still found significant differences between age groups and sexes, as well as an influence of pregnancy on cortisol levels. The effect of drive hunts on cortisol levels appears to be weaker than predicted, while the effects of other variables, such as sex, are distinct. Only half of the evaluated samples showed explicitly increased cortisol levels and no significant differences were found between sampling months and locations. Group living animals and pregnant females showed significantly higher cortisol levels. The impact of hunting is measurable but is masked by natural effects such as pregnancy. Thus, we need more information on stress levels in game species.
Topics: Animals; Animals, Wild; Female; Germany; Hydrocortisone; Male; Stress, Physiological; Sus scrofa
PubMed: 34385546
DOI: 10.1038/s41598-021-95927-2