Pig proteomics: a review of a species in the crossroad between biomedical and food sciences

The pig (Sus scrofa) is one of the most important animal species used for meat production worldwide, playing a fundamental role in numerous cultures from Southern Europe to the Pacific Islands. Additionally, it is broadly used as an experimental animal for several purposes, from physiological studies to drug testing and surgical training. Proteomics studies have covered both physiological and biomedical application studies of pig to a much greater extent than for any other farm animal. Despite this fact, no review seems to be available on the application of proteomics to production aspects in pig. The aim of this article is to provide a review on such applications of proteomics to the pig species. The article is divided in three parts. The first is dedicated to productive characterization and includes aspects related to reproduction and meat science. The second concerns the management of health and disease in production. Finally, the third part concerns the use of the pig as a model organism in biomedical research.     

Unravelling the complexity of domestication: a case study using morphometrics and ancient DNA analyses of archaeological pigs from Romania

Current evidence suggests that pigs were first domesticated in Eastern Anatolia during the ninth millennium cal BC before dispersing into Europe with Early Neolithic farmers from the beginning of the seventh millennium. Recent ancient DNA (aDNA) research also indicates the incorporation of European wild boar into domestic stock during the Neolithization process. In order to establish the timing of the arrival of domestic pigs into Europe, and to test hypotheses regarding the role European wild boar played in the domestication process, we combined a geometric morphometric analysis (allowing us to combine tooth size and shape) of 449 Romanian ancient teeth with aDNA analysis. Our results firstly substantiate claims that the first domestic pigs in Romania possessed the same mtDNA signatures found in Neolithic pigs in west and central Anatolia. Second, we identified a significant proportion of individuals with large molars whose tooth shape matched that of archaeological (likely) domestic pigs. These large ‘domestic shape’ specimens were present from the outset of the Romanian Neolithic (6100–5500 cal BC) through to later prehistory, suggesting a long history of admixture between introduced domestic pigs and local wild boar. Finally, we confirmed a turnover in mitochondrial lineages found in domestic pigs, possibly coincident with human migration into Anatolia and the Levant that occurred in later prehistory.     

Effects of human perturbation on the genetic make-up of an island population: the case of the Sardinian wild boar

Game species are often manipulated by human beings, whose activities can deeply affect their genetic make-up and population structure. We focused on a geographically isolated wild boar population (Sardinia, Italy), which is classified, together with the Corsican population, as a separate subspecies (Sus scrofa meridionalis). Two hundred and ten wild boars collected across Sardinia were analysed with a set of 10 microsatellites and compared with 296 reference genotypes from continental wild populations and to a sample of domestic pigs. The Sardinian population showed remarkable diversity and a high proportion of private alleles, and strongly deviated from the equilibrium. A Bayesian cluster analysis of only the Sardinian sample revealed a partition into five subpopulations. However, two different Bayesian approaches to the assignment of individuals, accounting for different possible source populations, produced consistent results and proved the admixed nature of the Sardinian population. Indeed, introgressive hybridization with boars from multiple sources (Italian peninsula, central Europe, domestic stocks) was detected, although poor evidence of crossbreeding with free-ranging domestic pigs was unexpectedly found. After excluding individuals who carried exotic genes, the population re-entered Hardy-Weinberg proportions and a clear population structure with three subpopulations emerged. Therefore, the inclusion of introgressed animals in the Bayesian analysis implied an overestimation of the number of clusters. Nonetheless, two of them were consistent between analyses and corresponded to highly pure stocks, located, respectively, in north-west and south-west Sardinia. This work shows the critical importance of including adequate reference samples when studying the genetic structure of managed wild populations.     

Fruit flies learn to avoid odours associated with virulent infection

While learning to avoid toxic food is common in mammals and occurs in some insects, learning to avoid cues associated with infectious pathogens has received little attention. We demonstrate that Drosophila melanogaster show olfactory learning in response to infection with their virulent intestinal pathogen Pseudomonas entomophila. This pathogen was not aversive to taste when added to food. Nonetheless, flies exposed for 3 h to food laced with P. entomophila, and scented with an odorant, became subsequently less likely to choose this odorant than flies exposed to pathogen-laced food scented with another odorant. No such effect occurred after an otherwise identical treatment with an avirulent mutant of P. entomophila, indicating that the response is mediated by pathogen virulence. These results demonstrate that a virulent pathogen infection can act as an aversive unconditioned stimulus which flies can associate with food odours, and thus become less attracted to pathogen-contaminated food.     

Coordinating cell polarity and cell cycle progression: what can we learn from flies and worms?

Spatio-temporal coordination of events during cell division is crucial for animal development. In recent years, emerging data have strengthened the notion that tight coupling of cell cycle progression and cell polarity in dividing cells is crucial for asymmetric cell division and ultimately for metazoan development. Although it is acknowledged that such coupling exists, the molecular mechanisms linking the cell cycle and cell polarity machineries are still under investigation. Key cell cycle regulators control cell polarity, and thus influence cell fate determination and/or differentiation, whereas some factors involved in cell polarity regulate cell cycle timing and proliferation potential. The scope of this review is to discuss the data linking cell polarity and cell cycle progression, and the importance of such coupling for asymmetric cell division. Because studies in model organisms such as Caenorhabditis elegans and Drosophila melanogaster have started to reveal the molecular mechanisms of this coordination, we will concentrate on these two systems. We review examples of molecular mechanisms suggesting a coupling between cell polarity and cell cycle progression.     

Annual and seasonal space use of different age classes of female wild boar Sus scrofa L.

In a radiotelemetric study, we analysed space use of 24 female specimens (14 family groups and 14 nonreproductive yearling females) out of 23 wild boar groups for periods between 3 and 39 months. Generally, wild boar used relatively small areas, showed high site fidelity but also a strong individual variation of home ranges, indicating a high flexibility in space use. Although age-specific differences were not statistically significant, female yearlings tended to have larger mean annual home ranges (1,185 ha MCP) than animals ranging in family groups (771 ha). Yearlings also showed a stronger shifting from spring to summer home ranges (2,345 m) and a tendency towards larger home range sizes in summer (791 ha MCP), compared to family groups (shift 1,766 m, MCP 461 ha). Yearlings displayed a dislocation of about 1 km of the annual centre in the first year after dividing from the mother. In contrast, in adults older than 2 years, the dislocation of the annual center was only 240 m.     

Seasonality of reproduction in wild boar (Sus scrofa) assessed by fecal and plasmatic steroids

The collection of biological samples through non-invasive techniques represents one way of monitoring in vivo physiological changes associated with reproductive activity. Such techniques are particularly important for the study of animal species in the wild.The goals of this study were 1) to evaluate fecal progestogen (P), estrogen (E), and androgen (A) by means of radioimmunoassays, in male and female wild boars culled in the Piedmont, Italy area; 2) to compare them with plasmatic concentrations and the animals’ reproductive status; and 3) to assess variations in reproductive seasonality between two populations of wild boars living in a mountainous vs. a plain habitat in Piedmont.The results demonstrate a positive correlation between fecal and plasmatic steroid concentrations (r = 0.46, 0.58, and 0.45 for plasma P₄ and P, E₂ and E, and T and A; P < 0.05). Moreover, high fecal levels of both P and E (>170 ng/g and >100 pg/g respectively) were found in 70.6% of pregnant sows and in none of the non-pregnant animals, thus supporting the use of this technique for detecting pregnancy status in wild boar.Similar birth patterns were displayed by the mountain and plain populations, but births peaked significantly only in the mountain population, in the spring (46%, P < 0.05, vs. other seasons). A corresponding autumnal peak of plasma testosterone concentrations in males was displayed only by the mountain population (7.4 vs. < 2.0 ng/mL in the other seasons, P < 0.05).The correlation between fecal and plasmatic steroid concentrations obtained in this study supports the applicability of this non-invasive sampling technique for monitoring reproductive status in wild boar, thus enabling a more informed and correct management of the species.     

Annotation of hypothetical proteins orthologous in Pongo abelii and Sus scrofa

A hypothetical protein is predicted to be expressed from an open reading frame without known experimental evidence of translation. They constitute a substantial fraction of proteomes. Domain extraction from these hypothetical sequences helps to search for protein coding genes for protein structural and functional annotation. We describe the analysis of prediction data in a sequence dataset of hypothetical protein orthologs of Pongo abelii (orangutan) and Sus scrofa (pig). It should be noted that these orangutan-pig orthologs are also non-homologous to human proteins. These predicted data find application in the genome wide annotation of proteins in poorly understood genomes.

Abbreviations

PDB - Protein Data Bank, DEG - Database of Essential Genes, CDD - Conserved Domain Database, IUCN - International Union for Conservation of Nature.     

Temporal Changes in Native and Exotic Vegetation and Soil Characteristics following Disturbances by Feral Pigs in a California Grassland

Invasive species that increase prevailing disturbance regimes can profoundly alter the composition and structure of ecosystems they invade. Using both comparative and manipulative approaches, we investigated how native and exotic vegetation and soil characteristics at a coastal grassland site in northern California changed through time following disturbances by feral pigs (Sus scrofa). We quantified these successional changes by comparing pig disturbances of varying ages (2, 14, 26+, and 60+ months) during the spring and early summer of 2001. Our results indicate that species richness of native plants increased slowly but steadily through time following disturbances, whereas richness of exotic species rebounded much more rapidly. Percent cover of native perennial grasses also increased steadily through time after pig disturbance, whereas the cover of exotic perennial grasses, annual grasses and forbs initially increased rapidly after disturbance and then remained the same or subsided slightly with time. The cover of native forbs and bulbs either increased weakly through time following disturbance or did not change substantially. Pools of ammonium and nitrate in the soil did not change greatly through time following pig disturbance. Net mineralization rates for ammonium and nitrate also varied little with age since disturbance, although we did find that nitrate mineralization was greater at intermediate ages in one study. Neither organic matter content or particle size varied significantly with disturbance age. In summary, we have shown that native and exotic plants from different functional groups vary greatly in how they recovered from pig disturbances. Exotic taxa were generally able to rapidly colonize and persist in pig disturbances, whereas native taxa usually exhibited a slow but steady rebounding following pig disturbance. Given our results, and those of others from nearby sites, we suggest that the health of coastal grasslands may be enhanced substantially by eliminating or greatly reducing the size of feral pig populations.     

Toxoplasma gondii: A morphometric analysis of the wall and epithelial cells of pigs intestine

The aim of this study was to perform a morphometric analysis of the different layers of the jejunal wall and epithelial cells of pigs with toxoplasmosis. Experiments were conducted using 10, 88-day-old crossbred (Pietran × Wessex) pigs divided into two groups: control (n = 5) and experimental (n = 5). The experimental group consisted of animals inoculated orally with 5000 sporulated oocysts of a genotype III strain of Toxoplasma gondii. At 30 and 60 days following inoculation, the animals were anaesthetised for jejunal biopsy. The intestinal segments were processed routinely for histology. Transverse cuts (4 μm thick) were stained with haematoxylin and eosin (HE), Periodic Acid Schiff (PAS), Alcian Blue (AB), pH 2.5, and Alcian Blue (AB), pH 1.0. We observed hypertrophy of the jejunal wall, increased enterocyte height, and a decreased number of intraepithelial lymphocytes in the infected animals. There were no changes in the number of goblet cells.     

Cryptosporidium suis Infection in Post-Weaned and Adult Pigs in Shaanxi Province,Northwestern China

Cryptosporidium spp., ubiquitous enteric parasitic protozoa of vertebrates, recently emerged as an important cause of economic loss and zoonosis. The present study aimed to determine the distribution and species of Cryptosporidium in post-weaned and adult pigs in Shaanxi province, northwestern China. A total of 1,337 fresh fecal samples of post-weaned and adult pigs were collected by sterile disposable gloves from 8 areas of Shaanxi province. The samples were examined by Sheather’s sugar flotation technique and microscopy at×400 magnification for Cryptosporidium infection, and the species in positive samples was further identified by PCR amplification of the small subunit (SSU) rRNA gene. A total of 44 fecal samples were successfully amplified by the nested PCR of the partial SSU rRNA, with overall prevalence of 3.3%. The average prevalence of Cryptosporidium infection in each pig farms ranged from 0 to 14.4%. Species identification by sequencing of SSU rRNA gene revealed that 42 (3.1%) samples were Cryptosporidium suis and 2 (0.15%) were Cryptosporidium scrofarum. C. suis had the highest prevalence (7.5%) in growers and the lowest in breeding pigs (0.97%). C. suis was the predominant species in pre-weaned and adult pigs, while C. scrofarum infected pigs older than 3 months only. A season-related difference of C. suis was observed in this study, with the highest prevalence in autumn (5.5%) and the lowest (1.7%) in winter. The present study provided basic information for control of Cryptosporidium infection in pigs and assessment of zoonotic transmission of pigs in Shaanxi province, China.     

Colour learning when foraging for nectar and pollen: bees learn two colours at once

Bees are model organisms for the study of learning and memory, yet nearly all such research to date has used a single reward, nectar. Many bees collect both nectar (carbohydrates) and pollen (protein) on a single foraging bout, sometimes from different plant species. We tested whether individual bumblebees could learn colour associations with nectar and pollen rewards simultaneously in a foraging scenario where one floral type offered only nectar and the other only pollen. We found that bees readily learned multiple reward–colour associations, and when presented with novel floral targets generalized to colours similar to those trained for each reward type. These results expand the ecological significance of work on bee learning and raise new questions regarding the cognitive ecology of pollination.     

Hydatid control in Australia: where it began, what we have achieved and where to from here

Echinococcus granulosus was imported into Australia with domestic livestock about 200 years ago. It spread rapidly through domestic animals and quickly became a public health problem in the new colony. Control was hampered by ignorance of the transmission pattern. The association between metacestodes and tapeworms was not elucidated until 63 years after the arrival of the First Fleet. Australian wildlife were highly susceptible to infection with E. granulosus and wildlife/domestic animal interaction facilated rapid infiltration of wildlife by E. granulosus. The wildlife reservoir has hampered hydatid control campaigns on mainland Australia but successful eradication has been achieved in the island state of Tasmania where there was no wildlife reservoir. The application of a new recombinant vaccine for sheep in control campaigns and the use of praziquantel baits for controlling infection in dingoes around bush campsites and picnic areas is discussed.