Quantitative milk proteomics - Host responses to lipopolysaccharide-mediated inflammation of bovine mammary gland

Analysis of milk with liquid chromatography–mass spectrometry: a review

As a widely consumed foodstuff, milk and dairy products are increasingly studied over the years. At the present time, milk profiling is used as a benchmark to assess the properties of milk. Modern biomolecular mass spectrometers have become invaluable to fully characterize the milk composition. This review reports the analysis of milk and its components using liquid chromatography coupled with mass spectrometry (LC–MS). LC–MS analysis as a whole will be discussed subdivided into the major constituents of milk, namely, lipids, proteins, sugars and the mineral fraction.

Interrogating the role of the milk microbiome in mastitis in the multi-omics era

There is growing interest in a functional understanding of milk-associated microbiota as there is ample evidence that host-associated microbial communities play an active role in host health and phenotype. Mastitis, characterized by painful inflammation of the mammary gland, is prevalent among lactating humans and agricultural animals and is associated with significant clinical and economic consequences. The etiology of mastitis is complex and polymicrobial and correlative studies have indicated alterations in milk microbial community composition. Recent evidence is beginning to suggest that a causal relationship may exist between the milk microbiota and host phenotype in mastitis. Multi-omic approaches can be leveraged to gain a mechanistic, molecular level understanding of how the milk microbiome might modulate host physiology, thereby informing strategies to prevent and ameliorate mastitis. In this paper, we review existing studies that have utilized omics approaches to investigate the role of the milk microbiome in mastitis. We also summarize the strengths and challenges associated with the different omics techniques including metagenomics, metatranscriptomics, metaproteomics, metabolomics and lipidomics and provide perspective on the integration of multiple omics technologies for a better functional understanding of the milk microbiome.

Milk proteins as a feed restriction signature indicating the metabolic adaptation of dairy cows

Milk production in dairy cows is affected by numerous factors, including diet. Feed restriction is known to have little impact on milk total protein content but its effect on the fine protein composition is still poorly documented. The objective of this study was to describe the effects of two feed restriction trials of different intensities on the milk protein composition of Holstein cows. One restriction trial was of high intensity (H: 8 mid-lactation Holstein cows) and the second of moderate intensity (M: 19 peak lactation Holstein cows). Feed restriction decreased the milk protein yield for caseins under the M trial and of all six major milk proteins under the H trial. These decreased yields lead to lower concentrations of αs1-, αs2- and β-caseins during the H trial. The milk proteome, analyzed on 32 milk samples, was affected as a function of restriction intensity. Among the 345 proteins identified eight varied under the M trial and 160 under the H trial. Ontology analyses revealed their implication in carbohydrate, lipid and protein metabolisms as well as in the immune system. These proteins reflected adaptations of the animal and mammary gland physiology to feed restriction and constituted a signature of this change.

Comparative Analysis of Saliva and Plasma Proteins Patterns in Pregnant Cows—Preliminary Studies

Simple Summary

One of the most crucial topics about cattle breeding is pregnancy. During this state, there are many changes in protein expression and abundance. These changes find reflection not only in plasma protein patterns but also in saliva, which is easier to obtain than blood. The aim of this study was the analysis of plasma and salivary protein profiles in pregnant cows in order to search for valuable markers of pregnancy status. In this study, the presence of apolipoproteins possibly related to bovine pregnancy was confirmed both in plasma and saliva. This means that saliva can be considered a good source of information about the condition of the organism, including during pregnancy. It is possible that the comparison of salivary and plasma proteomes can be a helpful tool to assess the pregnancy status of cattle, and can be useful for developing rapid tests from saliva.

Abstract

Pregnancy is a physiological state that can be described, from a biochemical point of view, using protein patterns. The present study focused on the comparison of protein patterns between the saliva and plasma of pregnant cows to search for possible markers which are present both in plasma and saliva. Saliva and plasma were collected from healthy, pregnant (3–4 months) and non-pregnant (C; n = 4) cows aged between 4 and 8 years (P; n = 8) from the same farm. Biological material was analyzed using 2D electrophoresis and MS identification. Among identified spots, there were those which could be related to pregnancy (e.g., apolipoproteins I and II in all examined matrices or transforming growth factor-beta-induced protein ig-h3 in albumin-free plasma) as well as those which are responsible for regulating of cellular processes (e.g., pyruvate kinase and aspartate aminotransferase in all examined matrices, or lactate dehydrogenase, phosphoglycerate kinase, and NADH dehydrogenase in plasma). Further identification of common spots and those only specific to saliva as well as the comparison between other periods of pregnancy are necessary; it is already clear that saliva can be considered a valuable diagnostic matrix containing potential markers of physiological and pathological status.

Complement component 3 haplotypes influence serum complement activity and milk production traits in Chinese Holstein cattle

Complement component 3 (C3) is the key molecule of the three pathways of complement activation (alternative, classical, and lectin pathways), which are involved in phagocytosis, inflammation, and immunoregulation processes to destroy infectious microorganisms. In this study, three novel single-nucleotide polymorphisms (SNPs) (g.-1293C>G located in the 5′-flanking region, g.56T>C in exon I, and g.7017C>T in exon XII) of the C3 gene were detected using created restriction site polymerase chain reaction, restriction fragment length polymorphism, and DNA sequencing in 952 cattle from three Chinese breeds. The genotypes and haplotypes were analyzed to investigate the polymorphisms and their possible implications, with particular investigative focus on their associations with serum C3 level, complement hemolytic activity (CH50 and ACH50), and milk production traits. The g.56T>C SNP in exon I affected the serum ACH50 (P<0.01) and the milk somatic cell score (SCS) (P<0.05), and the g.7017C>T SNP in exon XII significantly affected the serum ACH50 values (P<0.01). Moreover, statistical analyses revealed that individuals with genotypic combination CCC/GCC showed significantly lower SCS and the lowest C3 concentration in serum compared with cows with CCC/GTT (P = 0.0007) and CTT/CTT (P = 0.0021); the individuals with CCC/CCT had significantly higher ACH50 values than those with CCC/CTC (P = 0.0008) and CTC/GTC (P = 0.001); cows with CCT/CTT had higher values of CH50 and 305-day milk yield (P>0.05). The C3 expression levels were significantly increased in lung and mammary tissues (P<0.05), while significantly decreased in heart, spleen, liver, and kidney tissues in mastitis cows compared with those in healthy animals (P<0.01), respectively. Bacterial counts of serum antibacterial activities were also completed to verify the effect of SNPs on resistance to mastitis pathogens. Genetically resistant cows (CCC/GCC) had serum with noticeably higher antibacterial activity against S. aureus and E. coli in vitro than the genetically susceptible CCC/GTT cows (P<0.05). Results from this study imply that the C3 gene plays a role in resistance to bacterial infection and that it can be used as a molecular marker for complement activity and traits related to milk production.

Milk and serum proteomes in subclinical and clinical mastitis in Simmental cows

Bovine mastitis causes changes in the milk and serum proteomes. Here changes in both proteomes caused by naturally occurring subclinical and clinical mastitis have been characterised and quantified. Milk and serum samples from healthy dairy cows (n = 10) were compared to those of cows with subclinical (n = 12) and clinical mastitis (n = 10) using tandem mass tag (TMT) proteomics. Proteins that significantly increased or decreased in milk (n = 237) or serum (n = 117) were quantified and classified by the type of change in subclinical and clinical mastitis. A group of the proteins (n = 38) showed changes in both milk and serum a number of which decreased in the serum but increased in milk, suggesting a particular role in host defence for maintaining and restoring homeostasis during the disease. Proteins affected by bovine mastitis included proteins in host defence and coagulation pathways. Investigation of the modified proteomes in milk and serum was assessed by assays for haptoglobin, serum amyloid A and α₁ acid glycoprotein validating the results obtained by quantitative proteomics. Alteration of abundance patterns of milk and serum proteins, together with pathway analysis reveal multiple interactions related to proteins affected by mastitis. Data are available via ProteomeXchange with identifier PXD022595. SIGNIFICANCE: Mastitis is the most serious condition to affect dairy cows and leads to reduced animal welfare as well as having a negative economic effect for the dairy industry. Proteomics has previously identified changes in abundance of milk proteins during mastitis, but there have been few investigations addressing changes that may affect proteins in the blood during the infection. In this study, changes in the abundance of proteins of milk and serum, caused by naturally occurring mastitis have been characterised by proteomics using a quantitative approach and both subclinical and clinical cases of mastitis have been investigated. In both milk and serum, change in individual proteins was determined and classified into varying types of altering abundance, such as increasing in subclinical mastitis, but showing no further increase in clinical mastitis. Of special interest were the proteins that altered in abundance in both milk and serum which either showed similar trends - increasing or decreasing in both biological fluids or showed reciprocal change decreasing in serum but increasing in milk. As well as characterising proteins as potential markers of mastitis and the severity of the disease, these results provide insight into the pathophysiology of the host response to bovine mastitis.

Influence of Dry Period Length of Swedish Dairy Cows on the Proteome of Colostrum

The aim of this study was to evaluate the influence of applying a 4-week instead of an 8-week dry period to dairy cows on the proteome of colostrum (first sample) and of transition milk (the fifth postpartum milk sample). Individual milk serum samples of colostrum and transition milk were analysed from 12 Swedish Holstein (SH) and 12 Swedish Red (SR) cows. Samples were prepared by filter-aided sample preparation and dimethyl labelling and analysed by liquid chromatography tandem mass spectrometry. Shortening the dry period resulted in upregulation of 18 proteins in colostrum and transition milk of SR, whereas no statistical differences were found for SH colostrum and transition milk. These upregulated proteins may reflect a specific immune response in the SR samples that was reflected in colostrum as well as in transition milk. Upregulated proteins in colostrum seemed to reflect increased mammary epithelial cell proliferation in the periparturient period when a 4-week dry period was applied. The proteome data indicate that a dry period of 4 weeks to SR cows may not be sufficient for complete regeneration of the mammary epithelium.

Proteomic 2D-DIGE Analysis of Milk Whey from Dairy Cows with Staphylococcus aureus Mastitis Reveals Overexpression of Host Defense Proteins

Bovine mastitis remains a primary focus of dairy cattle disease research due to its considerable negative economic impact on the dairy industry. Subclinical mastitis (SCM), commonly caused by Staphylococcus aureus, lacks overt clinical signs and the diagnosis is based on bacteriological culture and somatic cell counts of milk, both of which have limitations. The main objective of this study was to identify, characterize and quantify the differential abundance of milk whey proteins from cows with S. aureus SCM compared to whey from healthy cows. Using two-dimensional differential gel electrophoresis (2D-DIGE) coupled with liquid chromatography and tandem mass spectrometry, 28 high-abundant proteins were detected in whey from mastitic milk, 9 of which had host defense functions. These included acute phase proteins involved in innate immunity and antimicrobial functions (e.g., serotransferrin, complement C3, fibrinogen gamma-B chain and cathepsin B), and proteins associated with the immune response to pathogens (e.g., polymeric immunoglobulin receptor-like protein, MHC class I antigen and beta-2-microglobulin). These results provide a unique 2D map of the modulated milk proteome during S. aureus mastitis. The broader importance is that the identified proteins, particularly those with host-defense biological functions, represent potential candidate biomarkers of subclinical mastitis in dairy cows.

High-Resolution Mass Spectrometer-Based Ultra-Deep Profile of Milk Whey Proteome in Indian Zebu (Sahiwal) Cattle

Milk serves as a mode of protection to neonate through transferring the host defense proteins from mother to offspring. It also guards the mammary gland against various types of infections. Along with the presence of six vital proteins, bovine milk (whey) contains a massive class of minor proteins, not all of which have been comprehensively reported. In this study, we performed an LC-MS/MS-based ultra-deep identification of the milk whey proteome of Indian zebu (Sahiwal) cattle. Three independent search engines that are Comet, Tandem, and Mascot-based analysis resulted in the discovery of over 6,210 non-redundant proteins commonly identified. Genome-wise mapping revealed that chromosome 1 showed a minimum expression of 14 proteins, whereas chromosome 19 expressed 250 maximum proteins in milk whey. These results demonstrate that milk proteome in Sahiwal cattle is quite complicated, and minor milk fractions play a significant role in host defense.

Novel Biomarkers of Mastitis in Goat Milk Revealed by MALDI-TOF-MS-Based Peptide Profiling

Mastitis is the most common infection of dairy goats impairing milk production and quality, which is usually recognized by mammary gland visual inspection and palpation. Subclinical forms of the disease are also widely represented, which lack the typical signs of the clinical ones but are still associated with reduced production and safety for human consumption of milk, generally presenting a high bacterial count. In order to obtain novel analytical tools for rapid and non-invasive diagnosis of mastitis in goats, we analyzed milk samples from healthy, subclinical and clinical mastitic animals with a MALDI-TOF-MS-based peptidomic platform, generating disease group-specific spectral profiles whose signal intensity and mass values were analyzed by statistics. Peculiar spectral signatures of mastitis with respect to the control were identified, while no significant spectral differences were observed between clinical and subclinical milk samples. Discriminant signals were assigned to specific peptides through nanoLC-ESI-Q-Orbitrap-MS/MS experiments. Some of these molecules were predicted to have an antimicrobial activity based on their strong similarity with homolog bioactive compounds from other mammals. Through the definition of a panel of peptide biomarkers, this study provides a very rapid and low-cost method to routinely detect mastitic milk samples even though no evident clinical signs in the mammary gland are observed.

Technological interventions and advances in the diagnosis of intramammary infections in animals with emphasis on bovine population-a review

Mastitis, an inflammation of the udder, is a challenging problem in dairy animals accounting for high economic losses. Disease complexity, degree of economic losses and increasing importance of the dairy industries along with public health concerns envisages devising appropriate diagnostics of mastitis, which can offer rapid, accurate and confirmatory diagnosis. The various diagnostic tests of mastitis have been divided into general or phenotypic and specific or genotypic tests. General or phenotypic tests are those that identify general alterations, which are not specific to any pathogen. Genotypic tests are specific, hence confirmatory for diagnosis of mastitis and include specific culture, polymerase chain reaction (PCR) and its various versions (e.g. qRT-PCR), loop-mediated isothermal amplification, lateral flow assays, nucleotide sequencing, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, and other molecular diagnostic methods. However, for highly specific and confirmatory diagnosis, pure cultures still provide raw materials for more sophisticated diagnostic technological interventions like PCR and nucleotide sequencing. Diagnostic ability of like infra-red thermography (IRT) has been shown to be similar to California mastitis test and also differentiates clinical mastitis from subclinical mastitis cases. As such, IRT can become a convenient and portable diagnostic tool. Of note, magnetic nanoparticles-based colorimetric biosensor assay was developed by using for instance proteolytic activity of plasmin or anti-S. aureus antibody. Last but not least, microRNAs have been suggested to be potential biomarkers for diagnosing bovine mastitis. This review summarizes the various diagnostic tests available for detection of mastitis including diagnosis through general and specific technological interventions and advances.

Dataset reporting 4654 cow milk proteins listed according to lactation stages and milk fractions

Milk contains numerous proteins including bioactive molecules that may be important in human nutrition. Thanks to improvements in proteomic methods, hundreds of proteins identified in milk are available through open data from different publications. We gathered these public data to produce an atlas reporting the cow milk proteins. We aggregated data from 20 publications reporting milk proteome and produced an atlas of 4654 unique proteins detected in milk from healthy cows. In this atlas, proteins are categorized according to four milk fractions: skimmed milk, whey, milk fat globule membranes (MFGM) and exosomes; and five lactation stages: colostrum period, early lactation, peak of lactation, mid-lactation and drying-off. These 9 protein lists were compared and annotated by Gene Ontology (GO) terms to identify the pathways they contribute to, the molecular signatures of different milk fractions and lactation stages. This data article compiles the 4654 cow milk proteins. This atlas may be used by researchers on human nutrition interested in milk protein allergy and/or digestibility in humans, and for milk processing industry. The atlas may be useful to i) find molecular signatures of physiological adaptations of dairy cows, ii) facilitate the isolation of proteins of interest, thanks to the knowledge on their presence in milk fractions and their period of secretion during lactation.

Milk proteome from in silico data aggregation allows the identification of putative biomarkers of negative energy balance in dairy cows

A better knowledge of the bovine milk proteome and its main drivers is a prerequisite for the modulation of bioactive proteins in milk for human nutrition, as well as for the discovery of biomarkers that are useful in husbandry and veterinary medicine. Milk composition is affected by lactation stage and reflects, in part, the energy balance of dairy cows. We aggregated the cow milk proteins reported in 20 recent proteomics publications to produce an atlas of 4654 unique proteins. A multistep assessment was applied to the milk proteome datasets according to lactation stages and milk fractions, including annotations, pathway analysis and literature mining. Fifty-nine proteins were exclusively detected in milk from early lactation. Among them, we propose six milk proteins as putative biomarkers of negative energy balance based on their implication in metabolic adaptative pathways. These proteins are PCK2, which is a gluconeogenic enzyme; ACAT1 and IVD, which are involved in ketone metabolism; SDHA and UQCRC1, which are related to mitochondrial oxidative metabolism; and LRRC59, which is linked to mammary gland cell proliferation. The cellular origin of these proteins warrants more in-depth research but may constitute part of a molecular signature for metabolic adaptations typical of early lactation.

Anti-inflammatory mechanism of ginsenoside Rg1: Proteomic analysis of milk from goats with mastitis induced with lipopolysaccharide

Previous investigation showed that intravenous injection of ginsenoside Rg1 had a therapeutic effect on Escherichia coli lipopolysaccharide-induced mastitis in lactating goats and it protected animals from lipopolysaccharide challenge via toll-like receptor 4 signaling pathway. The present study was to use proteomic approach to explore the anti-inflammatory mechanisms of Rg1. Nine dairy goats were randomly divided into three groups with 3 animals in each: groups 1 and 2 received intra-mammary infusion of lipopolysaccharide and then intravenously injected with saline or Rg1 solution; animals in group 3 were first intramammarily and then intravenously administered saline solution, and served as a control group. Milk whey at 6 h post lipopolysaccharide challenge was prepared for tandem mass tags based quantitative proteomic analysis. The results showed that 791 proteins were totally identified from the whey. Of them, 98 proteins between groups 1 (lipopolysaccharide + Saline) and 3 (Saline + Saline), and 34 proteins between groups 2 (lipopolysaccharide + Rg1) and 1 were significantly different. Group 1 than group 3 had significantly more inflammatory factors such as interleukin 6, acute phase proteins, blood coagulation factors, complement proteins, and oxidative stress markers while these factors were reduced in group 2 treated with Rg1. In addition, proteins in group 2 associated with peroxisome-proliferator-activated receptor γ activation and recovery of milk fat and production were upregulated compared to group 1. Therefore, Rg1 may exert its anti-inflammatory effect on lipopolysaccharide-induced mastitis in goats via modulating expression of proteins relating to peroxisome-proliferator-activated receptor γ and toll-like receptor 4 signaling pathway.

Reference 1D and 2D electrophoresis maps for potential disease related proteins in milk whey from lactating buffaloes and blood serum from buffalo calves (Water buffalo, Bubalus bubalis)

The aim of this study was to identify potential disease related proteins in milk whey of lactating buffaloes and blood serum of buffalo calves, in order to define a reference electrophoresis map for 1-DE and 2-DE. Additionally, changes in some protein patterns from buffalo calves during salmonellosis and lactating buffaloes during mastitis are presented. Milk samples were collected and distributed into groups: Milk samples from healthy buffaloes (SCC < 100.000 cells/ml, negative microbiology and CMT) (G1, n = 5) and buffaloes with subclinical mastitis (SCC > 500.000 cells/ml, positive microbiology and CMT) (G2, n = 5). Blood samples from buffalo calves (n = 6) were collected, and three calves were experimentally infected with Salmonella Dublin and samples analyzed before (M0) and 72 h after inoculation (M1). 1-DE was accomplished by loading 10 μg of TP into SDS-PAGE, stained with Coomassie blue. 2-DE was accomplished by loading 200 μg of TP into 11 cm, pH 3-10 non-linear IPG strips, followed by SDS-PAGE, stained with Coomassie blue. Protein bands/spots were excised, subjected to tryptic in-gel digestion and analyzed by LC/ESI-MS/MS. Protein identity was assigned using NCBI databases. After bands/spots from 1-DE and 2-DE were analyzed, a protein map with 35 and 40 different identified proteins in blood serum and milk whey, respectively, was generated. Significant changes in patterns of haptoglobin were observed in buffalo calves with salmonellosis and in patterns of IgLC, β-lactoglobulin and α-lactalbumin of lactating buffaloes during mastitis. The establishment of a protein map for 1-DE and 2-DE, identifying potential disease related proteins, can help to address alterations during diseases in buffaloes.

Selected reaction monitoring mass spectrometry of mastitis milk reveals pathogen-specific regulation of bovine host response proteins

Mastitis is a major challenge to bovine health. The detection of sensitive markers for mastitis in dairy herds is of great demand. Suitable biomarkers should be measurable in milk and should report pathogen-specific changes at an early stage to support earlier diagnosis and more efficient treatment. However, the identification of sensitive biomarkers in milk has remained a challenge, in part due to their relatively low concentration in milk. In the present study, we used a selected reaction monitoring (SRM) mass spectrometry approach, which allowed the absolute quantitation of 13 host response proteins in milk for the first time. These proteins were measured over a 54-h period upon an in vivo challenge with cell wall components from either gram-negative (lipopolysaccharide from Escherichia coli; LPS) or gram-positive bacteria (peptidoglycan from Staphylococcus aureus; PGN). Whereas our data clearly demonstrate that all challenged animals have consistent upregulation of innate immune response proteins after both LPS and PGN challenge, the data also reveal clearly that LPS challenge unleashes faster and shows a more intense host response compared with PGN challenge. Biomarker candidates that may distinguish between gram-negative and gram-positive bacteria include α-2 macroglobulin, α-1 antitrypsin, haptoglobin, serum amyloid A3, cluster of differentiation 14, calgranulin B, cathepsin C, vanin-1, galectin 1, galectin 3, and IL-8. Our approach can support further studies of large cohorts of animals with natural occurring mastitis, to validate the relevance of these suggested biomarkers in dairy production.

Host defense cathelicidins in cattle: types, production, bioactive functions and potential therapeutic and diagnostic applications

Cathelicidins are a primitive class of host defense peptides and are known for their broad-spectrum antimicrobial activity against bacteria, fungi, and enveloped viruses. These small, cationic, proteolytically-activated peptides are diverse in structure, encompassing a wide range of activities on host immune and inflammatory cell responses. The dual capacity of cathelicidins to directly control infection and regulate host defenses highlights the potential use of these peptides as alternatives to antibiotics and immunomodulators. Cathelicidins are found in many mammalian species; this review focuses on bovine cathelicidins. Eight naturally and two synthetically occurring bovine cathelicidins are described in detail, with a focus on recent advances in their expression, location and biological roles. This review also presents an overview of the bioactive functions of cathelicidins in bovine mastitis, a disease causing economic losses in cattle dairy production. Comparison of the structural, antimicrobial, cytotoxic and mechanistic properties of bovine cathelicidins advances the knowledge needed for the development of these peptides as potential identifiers of infectious diseases (e.g., bovine mastitis) and as novel therapeutic alternatives to antibiotics.

Structure, chaperone-like activity and allergenicity profile of bovine caseins upon peroxynitrite modification: New evidences underlying mastitis pathomechanisms

Mastitis, an inflammatory reaction frequently develops in response to intra-mammary bacterial infection‌‌, may induce the generation of peroxynitrite (PON)‌ which is a highly potent reactive oxygen and nitrogen species. Caseins as the intrinsically unfolded proteins seem feasible substrates to react with PON. Therefore, in the current study, structural and functional aspects of both β-casein (β-CN) and whole casein fraction (WCF) were evaluated after PON modification, using a variety of techniques. Modification of the bovine caseins with PON results in an important enhancement in the carbonyl, nitrotryptophan, nitrotyrosine and dityrosine content of these proteins‌. The results of fluorescence and far UV-CD assessments suggested significant structural alteration of caseins upon PON-modification. The chaperone-like activity of β-casein was significantly altered after PON modification. The results of scanning electron microscopy suggest that bovine caseins display unique morphological features after treatment with PON. Also, the PON-modified caseins preserved their allergenicity profile and displayed partial resistance against digestion by the pancreatic proteases. Ascorbic acid, an important antioxidant component of milk, was also capable to significantly prevent the PON-induced structural damages in bovine milk caseins. In conclusion, our results suggest that PON may have significant role in the structural and functional alteration of milk caseins. Also, the PON-induced structural damaging effects of caseins might be effectively prevented by a sufficient level of milk antioxidant components particularly by ascorbic acid.

Differential Ability of Bovine Antimicrobial Cathelicidins to Mediate Nucleic Acid Sensing by Epithelial Cells

Cathelicidins encompass a family of cationic peptides characterized by antimicrobial activity and other functions, such as the ability to enhance the sensing of nucleic acids by the innate immune system. The present study aimed to investigate the ability of the bovine cathelicidins indolicidin, bactenecin (Bac)1, Bac5, bovine myeloid antimicrobial peptide (BMAP)-27, BMAP-28, and BMAP-34 to inhibit the growth of bacteria and to enhance the sensing of nucleic acid by the host’s immune system. BMAP-27 was the most effective at killing Staphylococcus aureus, Streptococcus uberis, and Escherichia coli, and this was dependent on its amphipathic structure and cationic charge. Although most cathelicidins possessed DNA complexing activity, only the alpha-helical BMAP cathelicidins and the cysteine-rich disulfide-bridged Bac1 were able to enhance the sensing of nucleic acids by primary epithelial cells. We also compared these responses with those mediated by neutrophils. Activation of neutrophils with phorbol myristate acetate resulted in degranulation and release of cathelicidins as well as bactericidal activity in the supernatants. However, only supernatants from unstimulated neutrophils were able to promote nucleic acid sensing in epithelial cells. Collectively, the present data support a role for certain bovine cathelicidins in helping the innate immune system to sense nucleic acids. The latter effect is observed at concentrations clearly below those required for direct antimicrobial functions. These findings are relevant in development of future strategies to promote protection at mucosal surfaces against pathogen invasion.

Lipopolysaccharide derived from the digestive tract activates inflammatory gene expression and inhibits casein synthesis in the mammary glands of lactating dairy cows

To meet the nutrition requirements of lactation, dairy cows are usually fed a high concentrate diet (HC). However, high-grain feeding causes subacute ruminal acidosis (SARA), a metabolic disorder that causes milk protein depression. This study aimed to investigate the effect of lipopolysaccharide (LPS) released in the rumen on inflammatory gene expression and casein synthesis in mammary glands of lactating dairy cows fed a HC diet. We found that milk protein was significantly decreased in the HC group after 15 weeks of feeding. Overall, LPS concentrations in the rumen fluid, lacteal artery and vein were increased in the HC group. Transcriptome microarray was used to evaluate alterations in the signaling pathway in mammary glands. Signaling pathways involved in inflammatory responses were activated, whereas those involved in protein synthesis were inhibited in the HC group. mRNA expression involved in inflammatory responses, including that of TLR4, NF-кB and pro-inflammatory genes, was increased in the HC group, while αs1-casein (CSN1S1), β-casein (CSN2), mTOR and S6K gene expression were decreased. Moreover, protein expression was consistent with the corresponding gene expression. After feeding with an HC diet, LPS derived from the rumen increased inflammatory gene expression and inhibited casein synthesis in the mammary glands of lactating dairy cows fed a HC diet.

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.

Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 1. High abundance proteins, acute phase proteins and peptidomics

A peptidomic investigation of milk from an experimental model of Streptococcus uberis mastitis in dairy cows has incorporated a study of milk high abundance and acute phase (APP) proteins as well as analysis of low molecular weight peptide biomarkers. Intramammary infection (IMI) with S. uberis caused a shift in abundance from caseins, β-lactoglobulin and α-lactalbumin to albumin, lactoferrin and IgG with the increase in lactoferrin occurring last. The APP response of haptoglobin, mammary associated serum amyloid A3 and C-reactive protein occurred between 30-48 hours post challenge with peak concentrations of APPs at 72-96 hours post challenge and declined thereafter at a rate resembling the fall in bacterial count rather than the somatic cell count. A peptide biomarker panel for IMI based on capillary electrophoresis and mass spectrometry was developed. It comprised 77 identified peptides (IMI77) composed mainly of casein derived peptides but also including peptides of glycosylation dependent cell adhesion molecule and serum amyloid A. The panel had a biomarker classification score that increased from 36 hour to 81 hour post challenge, significantly differentiating infected from non-infected milk, thus suggesting potential as a peptide biomarker panel of bovine mastitis and specifically that of S. uberis origin. The use of omic technology has shown a multifactorial cross system reaction in high and low abundance proteins and their peptide derivatives with changes of over a thousand fold in analyte levels in response to S. uberis infection.

Challenges and opportunities of bovine milk analysis by mass spectrometry

Bovine milk and its products (e.g. cheese, yoghurt) are an important part of human diet with beneficial effects for all ages. Although analyses of different milk components (e.g. proteins, lipids) pose huge challenges, the use of mass spectrometric (MS)-based techniques is steadily improving our understanding of the complexity of the biological traits that effect milk yield and its components to meet the global demand arising from population growth. In addition, different milk constituents have various applications in veterinary research and medicine, including early disease diagnosis. The aim of the review is to present an overview of the progress made in MS-based analysis of milk, and suggest a multi-pronged MS strategy to better explore different milk components for translational and clinical utilities.

Milk Bottom-Up Proteomics: Method Optimization

Milk is a complex fluid whose proteome displays a diverse set of proteins of high abundance such as caseins and medium to low abundance whey proteins such as ß-lactoglobulin, lactoferrin, immunoglobulins, glycoproteins, peptide hormones, and enzymes. A sample preparation method that enables high reproducibility and throughput is key in reliably identifying proteins present or proteins responding to conditions such as a diet, health or genetics. Using skim milk samples from Jersey and Holstein-Friesian cows, we compared three extraction procedures which have not previously been applied to samples of cows' milk. Method A (urea) involved a simple dilution of the milk in a urea-based buffer, method B (TCA/acetone) involved a trichloroacetic acid (TCA)/acetone precipitation, and method C (methanol/chloroform) involved a tri-phasic partition method in chloroform/methanol solution. Protein assays, SDS-PAGE profiling, and trypsin digestion followed by nanoHPLC-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS/MS) analyses were performed to assess their efficiency. Replicates were used at each analytical step (extraction, digestion, injection) to assess reproducibility. Mass spectrometry (MS) data are available via ProteomeXchange with identifier PXD002529. Overall 186 unique accessions, major and minor proteins, were identified with a combination of methods. Method C (methanol/chloroform) yielded the best resolved SDS-patterns and highest protein recovery rates, method A (urea) yielded the greatest number of accessions, and, of the three procedures, method B (TCA/acetone) was the least compatible of all with a wide range of downstream analytical procedures. Our results also highlighted breed differences between the proteins in milk of Jersey and Holstein-Friesian cows.

Determination of changes in bovine plasma and milk proteins during naturally occurring Escherichia coli mastitis by comparative proteomic analysis

The aim of this study was to investigate changes in plasma and milk proteins in response to Escherichia coli infection in cows. Plasma and milk were collected from healthy cows, cows suffering from mild E. coli mastitis, and cows suffering from severe E. coli mastitis. Protein composition was examined by two-dimensional gel electrophoresis coupled with mass spectrometry. Plasma haptoglobin and α-1 acid glycoprotein demonstrated greater expression in mastitic cows compared with controls, but there were no difference between mildly and severely mastitic cows. Milk from mildly mastitic cows showed increased albumin and casein variants. Severely mastitic cows showed lower casein levels and increased anti-microbial and acute phase proteins. Milk α-1 acid glycoprotein and cathelicidins were associated with severe mastitis. A greater number of β-casein fragments that corresponded to β-casein isoforms were found in milk from mildly mastitic cows. These results suggest that caseins levels decreased and the concentrations of anti-microbial and acute phase proteins increased corresponding to the degree of E. coli mastitis. Nevertheless, further studies are needed to determine whether cathelicidin could serve as a diagnostic marker for mastitis.

Proteomics and the search for welfare and stress biomarkers in animal production in the one-health context

Stress and welfare are important factors in animal production in the context of growing production optimization and scrutiny by the general public.

Animal board invited review: advances in proteomics for animal and food sciences

Animal production and health (APH) is an important sector in the world economy, representing a large proportion of the budget of all member states in the European Union and in other continents. APH is a highly competitive sector with a strong emphasis on innovation and, albeit with country to country variations, on scientific research. Proteomics (the study of all proteins present in a given tissue or fluid - i.e. the proteome) has an enormous potential when applied to APH. Nevertheless, for a variety of reasons and in contrast to disciplines such as plant sciences or human biomedicine, such potential is only now being tapped. To counter such limited usage, 6 years ago we created a consortium dedicated to the applications of Proteomics to APH, specifically in the form of a Cooperation in Science and Technology (COST) Action, termed FA1002--Proteomics in Farm Animals: www.cost-faproteomics.org. In 4 years, the consortium quickly enlarged to a total of 31 countries in Europe, as well as Israel, Argentina, Australia and New Zealand. This article has a triple purpose. First, we aim to provide clear examples on the applications and benefits of the use of proteomics in all aspects related to APH. Second, we provide insights and possibilities on the new trends and objectives for APH proteomics applications and technologies for the years to come. Finally, we provide an overview and balance of the major activities and accomplishments of the COST Action on Farm Animal Proteomics. These include activities such as the organization of seminars, workshops and major scientific conferences, organization of summer schools, financing Short-Term Scientific Missions (STSMs) and the generation of scientific literature. Overall, the Action has attained all of the proposed objectives and has made considerable difference by putting proteomics on the global map for animal and veterinary researchers in general and by contributing significantly to reduce the East-West and North-South gaps existing in the European farm animal research. Future activities of significance in the field of scientific research, involving members of the action, as well as others, will likely be established in the future.

The use of liquid chromatography tandem mass spectrometry to detect proteins in saliva from horses with and without systemic inflammation

The objective of the study was to assess global expression of proteins in equine saliva using liquid chromatography tandem mass spectrometry (LC-MS/MS). Saliva was obtained from seven horses with and six horses without evidence of systemic inflammatory disease. Tryptic peptides from saliva were analysed by LC-MS/MS. Of 195 unique proteins identified, 57 were detected only in saliva samples from horses with systemic inflammation (in two to six of the seven horses). Among the differentially expressed proteins were several acute phase proteins (APPs) such as serum amyloid A, fibrinogen, haptoglobin, and alpha1-acid glycoprotein. The study is the first to describe detection of inflammatory proteins in horse saliva. The proteins detected were similar to those described in saliva from cattle, small ruminants and pigs. Detection of APPs in horses with systemic inflammation suggests that saliva may be used for non-invasive disease monitoring in horses as in humans, pigs and dogs.

Host defence related responses in bovine milk during an experimentally induced Streptococcus uberis infection

BACKGROUND

Milk contains a range of proteins of moderate or low abundance that contribute to host defence. Characterisation of these proteins, the extent to which their abundance is regulated by pathogenic stimuli, and the variability of their response between and within individual animals would facilitate a better understanding of the molecular basis for this important function of milk.

RESULTS

We have characterised the host defence proteins in bovine milk and their responses to intra-mammary infection by a common Gram positive mastitis pathogen, Streptococcus uberis, using a combination of 2D gel electrophoresis and GeLC mass spectrometry. In total, 68 host defence-associated proteins were identified, 18 of which have a direct antimicrobial function, 23 of which have a pathogen-recognition function, and 27 of which have a role in modulating inflammatory or immune signalling. The responsiveness of seven proteins was quantified by western blotting; validating the proteomic analyses, quantifying the within- and between animal variability of the responses, and demonstrating the complexity and specificity of the responses to this pathogen.

CONCLUSIONS

These data provide a foundation for understanding the role of milk in host-microbe interaction. Furthermore they provide candidate biomarkers for mastitis diagnosis, and will inform efforts to develop dairy products with improved health-promoting properties.

The mammary gland in domestic ruminants: a systems biology perspective

Milk and dairy products are central elements in the human diet. It is estimated that 108kg of milk per year are consumed per person worldwide. Therefore, dairy production represents a relevant fraction of the economies of many countries, being cattle, sheep, goat, water buffalo, and other ruminants the main species used worldwide. An adequate management of dairy farming cannot be achieved without the knowledge on the biological mechanisms behind lactation in ruminants. Thus, understanding the morphology, development and regulation of the mammary gland in health, disease and production is crucial. Presently, innovative and high-throughput technologies such as genomics, transcriptomics, proteomics and metabolomics allow a much broader and detailed knowledge on such issues. Additionally, the application of a systems biology approach to animal science is vastly growing, as new advances in one field of specialization or animal species lead to new lines of research in other areas or/and are expanded to other species. This article addresses how modern research approaches may help us understand long-known issues in mammary development, lactation biology and dairy production.

BIOLOGICAL SIGNIFICANCE

Dairy production depends upon the knowledge of the morphology and regulation of the mammary gland and lactation. High-throughput technologies allow a much broader and detailed knowledge on the biology of the mammary gland. This paper reviews the major contributions that genomics, transcriptomics, metabolomics and proteomics approaches have provided to understand the regulation of the mammary gland in health, disease and production. In the context of mammary gland "omics"-based research, the integration of results using a Systems Biology Approach is of key importance.

Proteomics in Veterinary Medicine

Advancement in electrophoresis and mass spectrometry techniques along with the recent progresses in genomics, culminating in bovine and pig genome sequencing, widened the potential application of proteomics in the field of veterinary medicine. The aim of the present review is to provide an in-depth perspective about the application of proteomics to animal disease pathogenesis, as well as its utilization in veterinary diagnostics. After an overview on the various proteomic techniques that are currently applied to veterinary sciences, the article focuses on proteomic approaches to animal disease pathogenesis. Included as well are recent achievements in immunoproteomics (ie, the identifications through proteomic techniques of antigen involved in immune response) and histoproteomics (ie, the application of proteomics in tissue processed for immunohistochemistry). Finally, the article focuses on clinical proteomics (ie, the application of proteomics to the identification of new biomarkers of animal diseases).

Detection of casein phosphopeptides in goat milk

The aims of this study were to profile casein phosphopeptides in goat milk, to accurately determine the site of phosphorylation, and to evaluate whether or not any of the casein phosphorylation patterns were specific to a given physiological condition. Goat milk, collected before and after experimental induction of endotoxin mastitis, was separated by SDS-PAGE. Casein bands were digested with trypsin and the resulting peptides were analyzed by nLC-MS/MS. Eight out of nine predicted tryptic phosphopeptides corresponding to 18 different phosphorylation sites were detected in αS1-, αS2-, and β-casein. Characterization of the phosphorylation sites illustrated the capability of tandem MS to accurately localize phosphorylated residues among a number of other putative sites. Despite an apparent lower abundance, almost all of the phosphopeptides were also detected in milk samples obtained from the goats following experimental induction of endotoxin mastitis. However, a tetra-phosphopeptide in αS2-casein was only observed in the milk samples obtained from healthy animals. The absence of this multiphosphopeptide in the mastitic goat milk samples could indicate changes in phosphorylation as a result of disease and potentially be used as a marker for milk quality. This study represents the first comprehensive analysis of casein phosphoproteome and reveals a much higher level of phosphorylation than previously demonstrated in goat milk.

A peptidomic approach to biomarker discovery for bovine mastitis

Bovine mastitis is usually caused by either Gram positive or Gram negative bacteria, reducing the quantity and quality of milk produced. This investigation using capillary electrophoresis and mass spectroscopy, studied peptides in milk from cows with clinical mastitis in comparison to milk from healthy cows to identify biomarkers for mastitis. In addition, the milk peptidome from udders infected with Gram positive Staphylococcus aureus (S. aureus) or with Gram negative Escherichia coli (E. coli), was examined to assess differential diagnosis between the causative agent. Comparison of the peptidome between healthy (n=10) and mastitic milk (n=27) identified 154 peptides for a biomarker panel which in a model for diagnosis of mastitis showed 100% sensitivity and specificity. β-casein and α(s1) casein provided the majority of peptides identified in this model. The peptidome comparison of milk from mastitis cases caused by S. aureus (n=8) or E. coli (n=11) revealed a biomarker panel of 47 peptides which discriminated between cause of infection with a sensitivity of 75% and a specificity of 100%. β-casein fragments were the most common of the peptides in this model. Peptide biomarkers of milk could be used in the diagnosis of mastitis and can discriminate between these two bacterial causes.

BIOLOGICAL SIGNIFICANCE

The paper describes an innovative approach to the use of gel free proteomics to identify the peptides that are present in milk during clinical mastitis, which is a major cause of loss of production to dairy farmers worldwide. The use of capillary electrophoresis, liquid chromatography and mass spectrometry has been able to identify panels of peptides which can be used for disease diagnosis and for differential diagnosis of the causative bacteria of the infections of the mammary gland. As well as contributing to our knowledge of the pathophysiology of bovine mastitis the results could be the basis of improved detection and differential diagnosis of the disease.

Large pore dermal microdialysis and liquid chromatography-tandem mass spectroscopy shotgun proteomic analysis: a feasibility study

BACKGROUND/AIMS

The purpose of the present pilot study was to investigate the feasibility of combining large pore dermal microdialysis with shotgun proteomic analysis in human skin.

METHODS

Dialysate was recovered from human skin by 2000 kDa microdialysis membranes from one subject at three different phases of the study; trauma due to implantation of the dialysis device, a post implantation steady-state period, and after induction of vasodilatation and plasma extravasation. For shotgun proteomics, the proteins were extracted and digested with trypsin. Peptides were separated by capillary and nanoflow HPLC systems, followed by tandem mass spectrometry (MS/MS) on a Quadrupole-TOF hybrid instrument. The MS/MS spectra were merged and mapped to a human target protein database to achieve peptide identification and protein inference.

RESULTS

Results showed variation in protein amounts and profiles for each of the different sampling phases. The total protein concentration was 1.7, 0.6, and 1.3 mg/mL during the three phases, respectively. A total of 158 different proteins were identified. Immunoglobulins and the major classes of plasma proteins, including proteases, coagulation factors, apolipoproteins, albumins, and complement factors, make up the major load of proteins in all three test conditions.

CONCLUSION

Shotgun proteomics allowed the identification of more than 150 proteins in microdialysis samples from human skin. This highlights the opportunities of LC-MS/MS to study the complex molecular interactions in the skin.

Bovine milk proteome: quantitative changes in normal milk exosomes, milk fat globule membranes and whey proteomes resulting from Staphylococcus aureus mastitis

Milk protein expression in healthy cows and cows with mastitis will provide information important for the dairy food industry and immune function in the mammary gland. To facilitate protein discovery, milk was fractioned into whey, milk fat globule membranes (MFGM) and exosomes from healthy and Staphylococcus aureus infected cows. Amine-reactive isobaric tags (iTRAQ) were used to quantify protein changes between milk fractions isolated from healthy and S. aureus infected cows. 2971 milk proteins were identified with a false discovery rate of 0.1%. Greater than 300 milk proteins associated with host defense were identified and 94 were significantly differentially regulated in S. aureus infected milk compared to their uninfected controls. These differentially regulated host defense proteins were selectively segregated in the 3 milk compartments examined. An example of this segregation of host defense proteins was the partitioning and high concentration of proteins indicative of neutrophil extracellular traps (NETs) formation in the MFGM preparations from S. aureus infected milk as compared to exosomes or whey. Protein composition changes found in milk exosomes, MFGM and whey during an infection provides new and comprehensive information on milk protein composition in general as well as changes occurring during an infection.

BIOLOGICAL SIGNIFICANCE

The significance of this study is the identification and quantification of the individual components of the neutrophil extracellular traps (NET) functional proteome in an apparent stable complex with MFGM and/or milk fat globules during an intra-mammary infection. NETs could be functionally relevant in intra-mammary infection, as it is known that during an infection neutrophils ingest large amounts of milk fat that down regulates many of their traditional immune functions. Thus the presence of NETs in milk fat provides new insights to mammary immune function and suggests a role for NETs in clinical mastitis. These in vivo NETs can now be tested to determine if they retain functional antimicrobial activity when primarily associated with milk fat. Then we can estimate their real world functional relevance during an intra-mammary infection, which is one key to understanding clinical mastitis in dairy cows.

A Bovine PeptideAtlas of milk and mammary gland proteomes

Proteome information resources of farm animals are lagging behind those of the classical model organisms despite their important biological and economic relevance. Here, we present a Bovine PeptideAtlas, representing a first collection of Bos taurus proteome data sets within the PeptideAtlas framework. This database was built primarily as a source of information for designing selected reaction monitoring assays for studying milk production and mammary gland health, but it has an intrinsic general value for the farm animal research community. The Bovine PeptideAtlas comprises 1921 proteins at 1.2% false discovery rate (FDR) and 8559 distinct peptides at 0.29% FDR identified in 107 samples from six tissues. The PeptideAtlas web interface has a rich set of visualization and data exploration tools, enabling users to interactively mine information about individual proteins and peptides, their prototypic features, genome mappings, and supporting spectral evidence.

The initiative on Model Organism Proteomes (iMOP) Session September 6, 2011, Geneva, Switzerland

iMOP--the Initiative on Model Organism Proteomes--was accepted as a new HUPO initiative at the Ninth HUPO meeting in Sydney in 2010. A goal of iMOP is to integrate research groups working on a great diversity of species into a model organism community. At the Tenth HUPO meeting in Geneva this variety was reflected in the iMOP session on Tuesday September 6, 2011. The presentations covered the quantitative proteome database PaxDb, proteomics projects studying farm animals, Arabidopsis thaliana, as well as host-pathogen interactions.

Farm animal milk proteomics

Milk is one of the most important nutrients for humans during lifetime. Farm animal milk in all its products like cheese and other fermentation and transformation products is a widespread nutrient for the entire life of humans. Proteins are key molecules of the milk functional component repertoire and their investigation represents a major challenge. Proteins in milk, such as caseins, contribute to the formation of micelles that are different from species to species in dimension and casein-type composition; they are an integral part of the MFGM (Milk Fat Globule Membrane) that has being exhaustively studied in recent years. Milk proteins can act as enzymes or have an antimicrobial activity; they could act as hormones and, last but not least, they have a latent physiological activity encoded in their primary structure that turns active when the protein is cleaved by fermentation or digestion processes. In this review we report the last progress in proteomics, peptidomics and bioinformatics. These new approaches allow us to better characterize the milk proteome of farm animal species, to highlight specific PTMs, the peptidomic profile and even to predict the potential nutraceutical properties of the analyzed proteins.