The Pig PeptideAtlas: A resource for systems biology in animal production and biomedicine

Biological research of Sus scrofa, the domestic pig, is of immediate relevance for food production sciences, and for developing pig as a model organism for human biomedical research. Publicly available data repositories play a fundamental role for all biological sciences, and protein data repositories are in particular essential for the successful development of new proteomic methods. Cumulative proteome data repositories, including the PeptideAtlas, provide the means for targeted proteomics, system‐wide observations, and cross‐species observational studies, but pigs have so far been underrepresented in existing repositories. We here present a significantly improved build of the Pig PeptideAtlas, which includes pig proteome data from 25 tissues and three body fluid types mapped to 7139 canonical proteins. The content of the Pig PeptideAtlas reflects actively ongoing research within the veterinary proteomics domain, and this article demonstrates how the expression of isoform‐unique peptides can be observed across distinct tissues and body fluids. The Pig PeptideAtlas is a unique resource for use in animal proteome research, particularly biomarker discovery and for preliminary design of SRM assays, which are equally important for progress in research that supports farm animal production and veterinary health, as for developing pig models with relevance to human health research.     

小型猪在肾脏疾病研究中的应用

随着对小型猪研究的不断深入,其作为人类疾病模型的优势日益明显,在生物医学研究中的应用也日趋增多。比较解剖学和生理学研究表明,小型猪的诸多生物学特性均与人类极为相似,尤其在肾脏的解剖和功能方面几乎是人类的复制品,使其在复制肾脏疾病模型,研究疾病发病机制和评估治疗策略等中具有无可替代的作用。本文将综述小型猪作为疾病动物模型在肾脏疾病研究中的应用。     

Recent advances in the use of Sus scrofa (pig) as a model system for proteomic studies

Of the numerous animal models available for proteomic studies only a small number have been successfully used in understanding human biology. To date, rodents have been widely employed in proteomic and genomic studies but often these models do not truly mimic the relevant human conditions. On the other hand, the pig shows similarity in size, shape and physiology to human and has been used as a major mammalian model for many studies concerning xenotransplantation, cardiovascular diseases, blood dynamics, nutrition, general metabolic functions, digestive-related disorders, respiratory diseases, diabetes, kidney and bladder diseases, organ-specific toxicity, dermatology and neurological sequelae. With the substantially improved knowledge of the structure and function of the pig genome in the last two decades it has been found that this animal shares a high sequence and chromosomal structure homology with humans. Nevertheless, in comparison to other available model organisms, very little work has been devoted to pig proteomics until recently. Keeping this in mind, the present review will highlight some of the advantages and disadvantages of pig as a model system for proteomic studies.     

Plant proteome changes under abiotic stress--contribution of proteomics studies to understanding plant stress response

Plant acclimation to stress is associated with profound changes in proteome composition. Since proteins are directly involved in plant stress response, proteomics studies can significantly contribute to unravel the possible relationships between protein abundance and plant stress acclimation. In this review, proteomics studies dealing with plant response to a broad range of abiotic stress factors--cold, heat, drought, waterlogging, salinity, ozone treatment, hypoxia and anoxia, herbicide treatments, inadequate or excessive light conditions, disbalances in mineral nutrition, enhanced concentrations of heavy metals, radioactivity and mechanical wounding are discussed. Most studies have been carried out on model plants Arabidopsis thaliana and rice due to large protein sequence databases available; however, the variety of plant species used for proteomics analyses is rapidly increasing. Protein response pathways shared by different plant species under various stress conditions (glycolytic pathway, enzymes of ascorbate-glutathione cycle, accumulation of LEA proteins) as well as pathways unique to a given stress are discussed. Results from proteomics studies are interpreted with respect to physiological factors determining plant stress response. In conclusion, examples of application of proteomics studies in search for protein markers underlying phenotypic variation in physiological parameters associated with plant stress tolerance are given.     

Cultured meat: creative solutions for a cell biological problem

Cultured meat is an emerging technology that could address environmental, health, and animal welfare concerns associated with meat production. Development of cultured meat represents an exciting challenge for cell biologists and engineers, but it requires effective, open approaches for knowledge sharing to establish a fertile scientific field alongside a competitive industry.     

Proteomics and transcriptomics investigation on longissimus muscles in Large White and Casertana pig breeds

Consumer complaints against the blandness of modern lean meat and the frequent reference to the more strongly flavored meat that was available years ago have prompted reconsideration of high fat-depositing typical pig breeds. Casertana and Large White pig breeds are characterized by a different tendency toward fat accumulation as they exhibit opposite genetic and physiological traits with respect to the energy metabolism. These physiological differences were investigated in longissimus lumborum muscles through proteomics (2-DE, MS/MS) and microarray approaches. Data were analyzed for pathway and network analyses, as well as GO term enrichment of biological functions. As a result, Casertana showed a greater amount of proteins involved in glycolitic metabolism and mainly rely on fast-mobilizable energy sources. Large White overexpressed cell cycle and skeletal muscle growth related genes. Metabolic behavior and other implications are discussed.     

Sex-sorting sperm by flow cytometry in pigs: issues and perspectives

Several hundred thousand offspring of preselected sex of various species have been born since sperm sexing technology based on flow cytometric sorting of X- and Y-chromosome-bearing sperm and DNA was first demonstrated in 1989. The advantages derived from application of sexing technology to commercial dairy cattle production have been demonstrated worldwide. Utilizing sex-sorting technology for pig production systems offers many similar advantages. However, several factors currently limit implementation of sexing technology in pigs. Anatomical and physiological features inherent to the female pig, together with the relatively low sperm output of a flow sorter, are the main limitations to widespread use of this technology in pig production systems. This review analyzes the factors that limit the efficiency of sperm sorting technology for commercial swine production. In addition, this review discusses recent innovations in technical instrumentation and applied reproductive techniques that may help to overcome some of these limitations.     

The Application of Biotechnical and Epidemiologic Tools for Pig Health

Health maximization is a farm essential because of its implications for animal well-being and for production. Health care in all livestock species is a dynamic, technologically-limited, and resource-constrained enterprise. As in any health endeavor, challenges abound. Fundamentally, the cornerstones of animal health are good husbandry and good housing. Effective health systems, however, incorporate other management aspects, including biotechnology and epidemiology. The degree to which each affects the incidence and severity of pig disease is not fully appreciated. Shortfalls in management, resource allocation, available tools, and/or understanding are not uncommon. This article reviews the dynamics of pig health emphasizing how technology and management marginally affect the course of disease. Further, management techniques that incorporate technology in disease control, elimination, and eradication are reviewed. Antimicrobials are a key biotechnical tool for maximizing pig health.     

Proteomics and peptidomics in fundamental and applied medical studies

The review is focused on current issues of biomedical proteomics and peptidomics. The main attention is paid to modem proteomics technologies applied in medical research--extraction, detection and data analysis techniques. The use of chromatography, mass spectrometry and chromato mass spectrometry in proteogenomic, biomedical studies and biomarker discovery is discussed in detail.     

The application of biotechnical and epidemiologic tools for pig health

Health maximization is a farm essential because of its implications for animal well-being and for production. Health care in all livestock species is a dynamic, technologically-limited, and resource-constrained enterprise. As in any health endeavor, challenges abound. Fundamentally, the cornerstones of animal health are good husbandry and good housing. Effective health systems, however, incorporate other management aspects, including biotechnology and epidemiology. The degree to which each affects the incidence and severity of pig disease is not fully appreciated. Shortfalls in management, resource allocation, available tools, and/or understanding are not uncommon. This article reviews the dynamics of pig health emphasizing how technology and management marginally affect the course of disease. Further, management techniques that incorporate technology in disease control, elimination, and eradication are reviewed. Antimicrobials are a key biotechnical tool for maximizing pig health.     

Proteome changes underpin improved meat quality and yield of chickens (Gallus gallus) fed the probiotic Enterococcus faecium

Background

Supplementation of broiler chicken diets with probiotics may improve carcass characteristics and meat quality. However, the underlying molecular mechanism remains unclear. In the present study, 2D-DIGE-based proteomics was employed to investigate the proteome changes associated with improved carcass traits and meat quality of Arbor Acres broilers (Gallus gallus) fed the probiotic Enterococcus faecium.

Results

The probiotic significantly increased meat colour, water holding capacity and pH of pectoral muscle but decreased abdominal fat content. These meat quality changes were related to the altered abundance of 22 proteins in the pectoral muscle following E. faecium feeding. Of these, 17 proteins have central roles in regulating meat quality due to their biological interaction network. Altered cytoskeletal and chaperon protein expression also contribute to improved water holding capacity and colour of meat, which suggests that upregulation of chaperon proteins maintains cell integrity and prevents moisture loss by enhancing folding and recovery of the membrane and cytoskeletal proteins. The down-regulation of β-enolase and pyruvate kinase muscle isozymes suggests roles in increasing the pH of meat by decreasing the production of lactic acid. The validity of the proteomics results was further confirmed by qPCR.

Conclusions

This study reveals that improved meat quality of broilers fed probiotics is triggered by proteome alterations (especially the glycolytic proteins), and provides a new insight into the mechanism by which probiotics improve poultry production.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1167) contains supplementary material, which is available to authorized users.     

Outlook for development of high-throughput cryopreservation for small-bodied biomedical model fishes

With the development of genomic research technologies, comparative genome studies among vertebrate species are becoming commonplace for human biomedical research. Fish offer unlimited versatility for biomedical research. Extensive studies are done using these fish models, yielding tens of thousands of specific strains and lines, and the number is increasing every day. Thus, high-throughput sperm cryopreservation is urgently needed to preserve these genetic resources. Although high-throughput processing has been widely applied for sperm cryopreservation in livestock for decades, application in biomedical model fishes is still in the concept-development stage because of the limited sample volumes and the biological characteristics of fish sperm. High-throughput processing in livestock was developed based on advances made in the laboratory and was scaled up for increased processing speed, capability for mass production, and uniformity and quality assurance. Cryopreserved germplasm combined with high-throughput processing constitutes an independent industry encompassing animal breeding, preservation of genetic diversity, and medical research. Currently, there is no specifically engineered system available for high-throughput of cryopreserved germplasm for aquatic species. This review is to discuss the concepts and needs for high-throughput technology for model fishes, propose approaches for technical development, and overview future directions of this approach.     

Outlook for development of high-throughput cryopreservation for small-bodied biomedical model fishes

With the development of genomic research technologies, comparative genome studies among vertebrate species are becoming commonplace for human biomedical research. Fish offer unlimited versatility for biomedical research. Extensive studies are done using these fish models, yielding tens of thousands of specific strains and lines, and the number is increasing every day. Thus, high-throughput sperm cryopreservation is urgently needed to preserve these genetic resources. Although high-throughput processing has been widely applied for sperm cryopreservation in livestock for decades, application in biomedical model fishes is still in the concept-development stage because of the limited sample volumes and the biological characteristics of fish sperm. High-throughput processing in livestock was developed based on advances made in the laboratory and was scaled up for increased processing speed, capability for mass production, and uniformity and quality assurance. Cryopreserved germplasm combined with high-throughput processing constitutes an independent industry encompassing animal breeding, preservation of genetic diversity, and medical research. Currently, there is no specifically engineered system available for high-throughput of cryopreserved germplasm for aquatic species. This review is to discuss the concepts and needs for high-throughput technology for model fishes, propose approaches for technical development, and overview future directions of this approach.     

动物细胞培养技术在人造肉研究中的应用

人造肉作为2018年全球十大突破和新兴科技之一,因其来源可追溯、食品安全性和绿色可持续等优势得到广泛的关注。欧美等国家已经投入大量资源开展细胞培养人造肉研究,未来将对我国的肉制品及食品市场造成一定的冲击。现阶段,细胞培养人造肉生产的挑战在于如何高效模拟动物肌肉组织生长环境,并在生物反应器中实现大规模的生产。尽管动物细胞组织培养技术已经得到深入的研究,并取得了不同程度的成功应用,但由于现有动物细胞组织培养成本与技术要求较高,仍不能实现大规模的产业化培养。因此,对于人造肉的生产来说,开发高效、安全的大规模细胞培养技术是亟需解决的问题,可以有效降低生产成本,实现产业化应用。文中通过介绍基于人造肉生物制造的动物细胞组织培养技术研究现状,具体阐述了目前的挑战和关键技术问题,并初步探讨了其可能的解决策略和应用前景。     

Pigs taking wing with transposons and recombinases

Swine production has been an important part of our lives since the late Mesolithic or early Neolithic periods, and ranks number one in world meat production. Pig production also contributes to high-value-added medical markets in the form of pharmaceuticals, heart valves, and surgical materials. Genetic engineering, including the addition of exogenous genetic material or manipulation of the endogenous genome, holds great promise for changing pig phenotypes for agricultural and medical applications. Although the first transgenic pigs were described in 1985, poor survival of manipulated embryos; inefficiencies in the integration, transmission, and expression of transgenes; and expensive husbandry costs have impeded the widespread application of pig genetic engineering. Sequencing of the pig genome and advances in reproductive technologies have rejuvenated efforts to apply transgenesis to swine. Pigs provide a compelling new resource for the directed production of pharmaceutical proteins and the provision of cells, vascular grafts, and organs for xenotransplantation. Additionally, given remarkable similarities in the physiology and size of people and pigs, swine will increasingly provide large animal models of human disease where rodent models are insufficient. We review the challenges facing pig transgenesis and discuss the utility of transposases and recombinases for enhancing the success and sophistication of pig genetic engineering. 'The paradise of my fancy is one where pigs have wings.' (GK Chesterton).