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Pig swine intestine culturomics sequences
<p>The culturomics sequences here presented are part of the manuscript entitled "<em>Salmonella enterica</em> serovar Typhimurium Temporally Modulates the Enteric Microbiota and Host Responses to Overcome Colonization Resistance in Swine".</p> <p>The sequence headers in the FASTA file contain the following information:</p> <ul> <li>Species assigned (might include strain and GenBank accession number)</li> <li>Treatment</li> <li>Isolation method / Environment / Tissue</li> <li>Animal number identifier</li> </ul>
Figure 1 in Swimming and bipedal bottom-running in the pig-nosed turtle Carettochelys insculpta Ramsay, 1886
Figure 1. Large Carettochelys insculpta bipedal bottom-running. Intervals of 10 fields (0.33 s) between numbered fields. Note that, at fields 4 and 5, the two foreflipper tips are both flipped downwards and posteriorly.
Figure 3 in Swimming and bipedal bottom-running in the pig-nosed turtle Carettochelys insculpta Ramsay, 1886
Figure 3. Images of large Carettochelys insculpta. (A) Turtle gliding towards camera. (B) Moving bipedally on substratum away from camera; forelimbs are stippled. Short horizontal lines indicate substratum beneath hindlimbs.
Figure 5 from: Kadinov B, Itzev D (2020) Influence between NO and CO in guinea pig stomach fundus. Pharmacia 67(3): 161-168. https://doi.org/10.3897/pharmacia.67.e52474
Figure 5 FES-evoked relaxations in non-treated and treated guinea pigs in presence of VitE (100 µmol L-1). (a) Effect of Hemin (10 µmol L-1) on 2 Hz (n = 5) evoked relaxations. (b) Effect of Hemin (10 µmol L-1) on 5 Hz (n = 5) induced relaxatory responses of the strips. Data are the means ±SEM of experiments (* p < 0.5).
Figure 3 from: Kadinov B, Itzev D (2020) Influence between NO and CO in guinea pig stomach fundus. Pharmacia 67(3): 161-168. https://doi.org/10.3897/pharmacia.67.e52474
Figure 3 (a) Original trace representing the effect of hemin (0.01 µmol.L-1) on the FES-evoked relaxation in non-treated guinea-pig gastric fundus strips. (b) Original trace representing the effect of hemin (0.01 µmol.L-1) on the FES-evoked relaxation in treated guinea-pig gastric fundus strips. – adding PgF2α (0.5 ηmol.L-1) to evoke contractile response. Incubation with hemin is for 20 min., with Vitamin E – 10 min. before hemin application. The responses of the strips to EFS were registered in the presence of atropine (1 µmol.L-1).
Figure 4 from: Kadinov B, Itzev D (2020) Influence between NO and CO in guinea pig stomach fundus. Pharmacia 67(3): 161-168. https://doi.org/10.3897/pharmacia.67.e52474
Figure 4 FES-evoked relaxations in non-treated and treated guinea pigs. (a) Effect of Hemin (10 µmol.L-1) on 2 Hz (n = 5) evoked relaxations. (b) Effect of Hemin (10 µmol.L-1) on 5 Hz (n = 5) induced relaxatory responses of the strips. Data are the means ±SEM of experiments (* p < 0.5).
Figure 2 from: Kadinov B, Itzev D (2020) Influence between NO and CO in guinea pig stomach fundus. Pharmacia 67(3): 161-168. https://doi.org/10.3897/pharmacia.67.e52474
Figure 2 Immunohistochemistry of HO-1 and HO-2. Immunohistochemically stained 30 µm thick sections of the guinea pig stomach fundus for non-treated and treated animals.
Data from: Genome-wide association analysis for blood lipid traits measured in three pig populations revealed a substantial level of genetic heterogeneity
Serum lipids are associated with myocardial infarction and cardiovascular disease in humans. Here we dissected the genetic architecture of blood lipid traits by applying genome-wide association studies (GWAS) in 1,256 pigs from Laiwu, Erhualian and Duroc × (Landrace × Yorkshire) populations, and a meta-analysis of GWAS in more than 2,400 pigs from five diverse populations. A total of 22 genomic loci surpassing the suggestive significance level were detected on 11 pig chromosomes (SSC) for six blood lipid traits. Meta-analysis of GWAS identified 5 novel loci associated with blood lipid traits. Comparison of GWAS loci across the tested populations revealed a substantial level of genetic heterogeneity for porcine blood lipid levels. We further evaluated the causality of nine polymorphisms nearby or within the APOB gene on SSC3 for serum LDL-C and TC levels. Of the 9 polymorphisms, an indel showed the most significant association with LDL-C and TC in Laiwu pigs. But the significant association was not identified in the White Duroc × Erhualian F2 resource population, in which the QTL for LDL-C and TC was also detected on SSC3. This indicates that population-specific signals may exist for the SSC3 QTL. Further investigations are warranted to validate this assumption.
Data from: Comparative analyses of QTLs influencing obesity and metabolic phenotypes in pigs and humans
The pig is a well-known animal model used to investigate genetic and mechanistic aspects of human disease biology. They are particularly useful in the context of obesity and metabolic diseases because other widely used models (e.g. mice) do not completely recapitulate key pathophysiological features associated with these diseases in humans. Therefore, we established a F2 pig resource population (n = 564) designed to elucidate the genetics underlying obesity and metabolic phenotypes. Segregation of obesity traits was ensured by using breeds highly divergent with respect to obesity traits in the parental generation. Several obesity and metabolic phenotypes were recorded (n = 35) from birth to slaughter (242 ± 48 days), including body composition determined at about two months of age (63 ± 10 days) via dual-energy x-ray absorptiometry (DXA) scanning. All pigs were genotyped using Illumina Porcine 60k SNP Beadchip and a combined linkage disequilibrium-linkage analysis was used to identify genome-wide significant associations for collected phenotypes. We identified 229 QTLs which associated with adiposity- and metabolic phenotypes at genome-wide significant levels. Subsequently comparative analyses were performed to identify the extent of overlap between previously identified QTLs in both humans and pigs. The combined analysis of a large number of obesity phenotypes has provided insight in the genetic architecture of the molecular mechanisms underlying these traits indicating that QTLs underlying similar phenotypes are clustered in the genome. Our analyses have further confirmed that genetic heterogeneity is an inherent characteristic of obesity traits most likely caused by segregation or fixation of different variants of the individual components belonging to cellular pathways in different populations. Several important genes previously associated to obesity in human studies, along with novel genes were identified. Altogether, this study provides novel insight that may further the current understanding of the molecular mechanisms underlying human obesity.
Data from: Familiarity to a feed additive modulates its effects on brain responses in reward and memory regions in the pig model
Brain responses to feed flavors with or without a feed additive (FA) were investigated in piglets familiarized or not with this FA. Sixteen piglets were allocated to 2 dietary treatments from weaning until d 37: the naive group (NAI) received a standard control feed and the familiarized group (FAM) received the same feed added with a FA mainly made of orange extracts. Animals were subjected to a feed transition at d 16 post-weaning, and to 2-choice feeding tests at d 16 and d 23. Production traits of the piglets were assessed up to d 28 post-weaning. From d 26 onwards, animals underwent 2 brain imaging sessions (positron emission tomography of 18FDG) under anesthesia to investigate the brain activity triggered by the exposure to the flavors of the feed with (FA) or without (C) the FA. Images were analyzed with SPM8 and a region of interest (ROI)-based small volume correction (p < 0.05, k ≥ 25 voxels per cluster). The brain ROI were selected upon their role in sensory evaluation, cognition and reward, and included the prefrontal cortex, insular cortex, fusiform gyrus, limbic system and corpus striatum. The FAM animals showed a moderate preference for the novel post-transition FA feed compared to the C feed on d 16, i.e., day of the feed transition (67% of total feed intake). The presence or absence of the FA in the diet from weaning had no impact on body weight, average daily gain, and feed efficiency of the animals over the whole experimental period (p ≥ 0.10). Familiar feed flavors activated the prefrontal cortex. The amygdala, insular cortex, and prepyriform area were only activated in familiarized animals exposed to the FA feed flavor. The perception of FA feed flavor in the familiarized animals activated the dorsal striatum differently than the perception of the C feed flavor in naive animals. Our data demonstrated that the perception of FA in familiarized individuals induced different brain responses in regions involved in reward anticipation and/or perception processes than the familiar control feed flavor in naive animals. Chronic exposure to the FA might be necessary for positive hedonic effects, but familiarity only cannot explain them.
Data from: Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs
Early pig farmers in Europe imported Asian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds. We propose that the Asian variants are still present because they affect phenotypes that were important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes that were historically under selection. We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs.
Genome Data Uncover Conservation Status, Historical Relatedness and Candidate Genes under Selection in Chinese Indigenous Pigs in the Taihu Lake Region
<p>Chinese indigenous pig breeds in the Taihu Lake region (TH) of Eastern China are well-recognized for their exceptional prolificacy. These breeds including Meishan (MS), Erhualian (EHL), Jiaxing Black (JXB), Fengjing (FJ), Shawutou (SWT), Mi (MI) and Hongdenglong (HDL). At present, these breeds are facing a great threaten of population decline, lineage admixture and inbreeding depression since Western commercial pigs have dominated Chinese pig industry. To provide better conservation schemes and identify candidate genes under selection for these breeds, we explored genome-wide SNP markers to unravel genetic variability and relatedness, population structure, historical admixture and genomic signatures of selection of 440 pigs representing the most comprehensive lineages of these breeds in TH in a context of 1228 pig from 45 Eurasian breeds.<b> </b>We showed that these breeds were more closely related among each other as compared to other Eurasian breeds, defining one of the main ancestral lineages of Chinese indigenous pigs. These breeds can be divided into two regional subgroups, one including JXB and FJ pigs, and the other comprising EHL, MI, HDL, MS and SWT pigs. In additional, HDL pigs were highly inbred, whereas EHL and MS pigs had more abundant genetic diversity. This is attributable to multiple conservation populations of the two breeds. Moreover, we identified a list of candidate genes for body size and prolificacy at the loci putatively under selection. our results would benefit the sustainable conservation of these valuable breeds and improve our understanding of the genetic mechanisms of body size and fecundity in pigs.</p>
Data from: Paternal intergenerational epigenetic response to heat exposure in male Wild guinea pigs
Epigenetic modifications, of which DNA methylation is the best studied one, can convey environmental information through generations via parental germ lines. Past studies have focused on the maternal transmission of epigenetic information to the offspring of isogenic mice and rats in response to external changes, whereas heterogeneous wild mammals as well as paternal epigenetic effects have been widely neglected. In most wild mammal species, males are the dispersing sex and have to cope with differing habitats and thermal changes. As temperature is a major environmental factor we investigated if genetically heterogeneous Wild guinea pig (Cavia aperea) males can adapt epigenetically to an increase in temperature and if that response will be transmitted to the next generation(s). Five adult male guinea pigs (F0) were exposed to an increased ambient temperature for 2 months, i.e. the duration of spermatogenesis. We studied the liver (as the main thermoregulatory organ) of F0 fathers and F1 sons, and testes of F1 sons for paternal transmission of epigenetic modifications across generation(s). Reduced representation bisulphite sequencing revealed shared differentially methylated regions in annotated areas between F0 livers before and after heat treatment, and their sons' livers and testes, which indicated a general response with ecological relevance. Thus, paternal exposure to a temporally limited increased ambient temperature led to an 'immediate' and 'heritable' epigenetic response that may even be transmitted to the F2 generation. In the context of globally rising temperatures epigenetic mechanisms may become increasingly relevant for the survival of species.
Data from: The role of plasma and urine metabolomics in identifying new biomarkers in severe newborn asphyxia: a study of asphyxiated newborn pigs following cardiopulmonary resuscitation
Background: Optimizing resuscitation is important to prevent morbidity and mortality from perinatal asphyxia. The metabolism of cells and tissues is severely disturbed during asphyxia and resuscitation, and metabolomic analyses provide a snapshot of many small molecular weight metabolites in body fluids or tissues. In this study metabolomics profiles were studied in newborn pigs that were asphyxiated and resuscitated using different protocols to identify biomarkers for subject characterization, intervention effects and possibly prognosis. Methods: A total of 125 newborn Noroc pigs were anesthetized, mechanically ventilated and inflicted progressive asphyxia until asystole. Pigs were randomized to resuscitation with a FiO2 0.21 or 1.0, different duration of ventilation before initiation of chest compressions (CC), and different CC to ventilation ratios. Plasma and urine samples were obtained at baseline, and 2 h and 4 h after return of spontaneous circulation (ROSC, heart rate > = 100 bpm). Metabolomics profiles of the samples were analyzed by nuclear magnetic resonance spectroscopy. Results: Plasma and urine showed severe metabolic alterations consistent with hypoxia and acidosis 2 h and 4 h after ROSC. Baseline plasma hypoxanthine and lipoprotein concentrations were inversely correlated to the duration of hypoxia sustained before asystole occurred, but there was no evidence for a differential metabolic response to the different resuscitation protocols or in terms of survival. Conclusions: Metabolic profiles of asphyxiated newborn pigs showed severe metabolic alterations. Consistent with previously published reports, we found no evidence of differences between established and alternative resuscitation protocols. Lactate and pyruvate may have a prognostic value, but have to be independently confirmed.
Data from: Establishment of a refined oral glucose tolerance test in pigs, and assessment of insulin, glucagon and glucagon-like peptide-1 responses
Diabetes mellitus is increasing worldwide and reliable animal models are important for progression of the research field. The pig is a commonly used large animal model in diabetes research and the present study aimed to refine a model for oral glucose tolerance test (OGTT) in young growing pigs, as well as describing intravenous glucose tolerance test (IVGTT) in the same age group. The refined porcine OGTT will reflect that used in children and adolescents. Eighteen pigs were obtained one week after weaning and trained for two weeks to bottle-feed glucose solution, mimicking the human OGTT. The pigs subsequently underwent OGTT (1.75 g/kg BW) and IVGTT (0.5 g/kg BW). Blood samples were collected from indwelling vein catheters for measurements of glucose and the diabetes related hormones insulin, glucagon and active glucagon-like peptide-1. The study confirmed that pigs can be trained to bottle-feed glucose dissolved in water and thereby undergo an OGTT more similar to the human standard OGTT than previously described methods in pigs. With the refined method for OGTT, oral intake only consists of glucose and water, which is an advantage over previously described methods in pigs where glucose is given together with feed which will affect glucose absorption. Patterns of hormonal secretion in response to oral and intravenous glucose were similar to those in humans; however, the pigs were more glucose tolerant with lower insulin levels than humans. In translational medicine, this refined OGTT and IVGTT methods provide important tools in diabetes research when pigs are used as models for children and adolescents in diabetes research.
Data from: Genome data from a 16th century pig illuminate modern breed relationships
Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds.
Data from: Metabolomic perfusate analysis during kidney machine perfusion: the pig provides an appropriate model for human studies
Introduction: Hypothermic machine perfusion offers great promise in kidney transplantation and experimental studies are needed to establish the optimal conditions for this to occur. Pig kidneys are considered to be a good model for this purpose and share many properties with human organs. However it is not established whether the metabolism of pig kidneys in such hypothermic hypoxic conditions is comparable to human organs. Methods: Standard criteria human (n = 12) and porcine (n = 10) kidneys underwent HMP using the LifePort Kidney Transporter 1.0 (Organ Recovery Systems) using KPS-1 solution. Perfusate was sampled at 45 minutes and 4 hours of perfusion and metabolomic analysis performed using 1-D 1H-NMR spectroscopy. Results: There was no inter-species difference in the number of metabolites identified. Of the 30 metabolites analysed, 16 (53.3%) were present in comparable concentrations in the pig and human kidney perfusates. The rate of change of concentration for 3-Hydroxybutyrate was greater for human kidneys (p<0.001). For the other 29 metabolites (96.7%), there was no difference in the rate of change of concentration between pig and human samples. Conclusions: Whilst there are some differences between pig and human kidneys during HMP they appear to be metabolically similar and the pig seems to be a valid model for human studies.
Datasets: Integrative Multi-omics Profiling in Human Decedents Receiving Pig Heart Xenografts
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Feral Pig Networks and Disease Trasmission
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Population genomic, olfactory, dietary, and gut microbiota analyses demonstrate the unique evolutionary trajectory of feral pigs
<p><span><span><span><span><span><span><span><span><span><span><span>Domestication is an intriguing evolutionary process. Many domestic populations are subjected to strong human-mediated selection, and when some individuals return to the wild, they are again subjected to selective forces associated with new environments. Generally, these feral populations evolve into something different from their wild predecessors and their members typically possess a combination of both wild and human selected traits. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>Feralisation can manifest in different forms on a spectrum from a wild to a domestic phenotype. This depends on how the re-wilded domesticated populations can re-adapt to natural environments based on how much potential and flexibility the ancestral genome retains after its domestication signature. Whether feralisation leads to the evolution of new traits that do not exist in the wild or to convergence with wild forms, however, remains unclear. To address this question, we performed population genomic, olfactory, dietary, and gut microbiota analyses on different populations of <i>Sus scrofa </i>(wild boar, hybrid, feral and several domestic pig breeds). Porcine Single Nucleotide Polymorphisms (SNPs) analysis shows that the feral population represents a cluster distinctly separate from all others. Its members display signatures of past artificial selection, as demonstrated by values of <i>F</i><sub>ST</sub> in specific regions of the genome and bottleneck signature, such as the number and length of runs of homozygosity. Generalised <i>F</i><sub>ST</sub> values, re-acquired olfactory abilities, diet, and gut microbiota variation show current responses to natural selection. Our results suggest that feral pigs are an independent evolutionary unit which can persist so long as levels of human intervention remain unchanged.</span></span></span></span></span></span></span></span></span></span></span></p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.