Applied Proteomics in 'One Health'

Syndecan-1: a key player in health and disease

Syndecan-1 (SDC-1) is a transmembrane protein localized on the basolateral surface of epithelial cells, encompassing a core protein with heparin sulfate and chondroitin sulfate glycosaminoglycan side chains. SDC-1 is involved in a panoply of cellular mechanisms including cell-to-cell adhesion, extracellular matrix interactions, cell cycle modulation, and lipid clearance. Alterations in the expression and function of SDC-1 are implicated in numerous disease entities, making it an attractive diagnostic and therapeutic target. However, despite its broad involvement in several disease processes, the underlying mechanism contributing to its diverse functions, pathogenesis, and therapeutic uses remains underexplored. Therefore, this review examines the role of SDC-1 in health and disease, focusing on liver pathologies, inflammatory diseases, infectious diseases, and cancer, and sheds light on SDC-1-based therapeutic approaches. Moreover, it delves into the mechanisms through which SDC-1 contributes to these diseases, emphasizing cell-type specific mechanisms. By comprehensively summarizing the significance of SDC-1, its association with several diseases, and its underlying mechanisms of action, the findings of this review could inform future research directions toward the development of targeted therapies and early diagnosis for a multitude of disease entities.

iTRAQ-Based Proteomic Profiling of Skin Aging Protective Effects of Tremella fuciformis-Derived Polysaccharides on D-Galactose-Induced Aging Mice

In the present study, a heteromannan primarily composed of mannose, fucose, xylose, glucose, and arabinose at a molar ratio of 4.78:1.18:1:0.82:0.11 containing a low proportion of glucuronic acid with weight-average molecular weights of 3.6 × 106 Da, named NTP, was prepared from the fruiting body of Tremella fuciformis. The anti-skin-aging effects of NTP on d-Galactose-induced aging mice and the biological mechanisms were investigated by an iTRAQ-based proteomics approach. NTP substantially mitigated skin aging characterized by a decreased loss of hydroxyproline and hyaluronic acid and reduced oxidative stress in the skin. Moreover, 43 differentially expressed proteins (DEPs) were identified in response to NTP, of which 23 were up-regulated and 20 were down-regulated. Bioinformatics analysis revealed that these DEPs were mainly involved in the biological functions of cellular and metabolic regulations, immune system responses, and structural components. The findings provided new insights into the biological mechanisms underlying the anti-skin-aging actions of T. fuciformis-derived polysaccharides and facilitated NTP applications in naturally functional foods.

The Omics Revolution in Understanding Chicken Reproduction: A Comprehensive Review

Omics approaches have significantly contributed to our understanding of several aspects of chicken reproduction. This review paper gives an overview of the use of omics technologies such as genomics, transcriptomics, proteomics, and metabolomics to elucidate the mechanisms of chicken reproduction. Genomics has transformed the study of chicken reproduction by allowing the examination of the full genetic makeup of chickens, resulting in the discovery of genes associated with reproductive features and disorders. Transcriptomics has provided insights into the gene expression patterns and regulatory mechanisms involved in reproductive processes, allowing for a better knowledge of developmental stages and hormone regulation. Furthermore, proteomics has made it easier to identify and quantify the proteins involved in reproductive physiology to better understand the molecular mechanisms driving fertility, embryonic development, and egg quality. Metabolomics has emerged as a useful technique for understanding the metabolic pathways and biomarkers linked to reproductive performance, providing vital insights for enhancing breeding tactics and reproductive health. The integration of omics data has resulted in the identification of critical molecular pathways and biomarkers linked with chicken reproductive features, providing the opportunity for targeted genetic selection and improved reproductive management approaches. Furthermore, omics technologies have helped to create biomarkers for fertility and embryonic viability, providing the poultry sector with tools for effective breeding and reproductive health management. Finally, omics technologies have greatly improved our understanding of chicken reproduction by revealing the molecular complexities that underpin reproductive processes.

Scientometrics Evaluation of Published Scientific Papers on the Use of Proteomics Technologies in Mastitis Research in Ruminants

The objective of this study was the presentation of quantitative characteristics regarding the scientific content and bibliometric details of the relevant publications. In total, 156 papers were considered. Most papers presented original studies (n = 135), and fewer were reviews (n = 21). Most original articles (n = 101) referred to work involving cattle. Most original articles described work related to the diagnosis (n = 72) or pathogenesis (n = 62) of mastitis. Most original articles included field work (n = 75), whilst fewer included experimental (n = 31) or laboratory (n = 30) work. The tissue assessed most frequently in the studies was milk (n = 59). Milk was assessed more frequently in studies on the diagnosis (61.1% of relevant studies) or pathogenesis (30.6%) of the infection, but mammary tissue was assessed more frequently in studies on the treatment (31.0%). In total, 47 pathogens were included in the studies described; most were Gram-positive bacteria (n = 34). The three bacteria most frequently included in the studies were Staphylococcus aureus (n = 55 articles), Escherichia coli (n = 31) and Streptococcus uberis (n = 19). The proteomics technology employed more often in the respective studies was liquid chromatography-tandem mass spectrometry (LC-MS/MS), either on its own (n = 56) or in combination with other technologies (n = 40). The median year of publication of articles involving bioinformatics or LC-MS/MS and bioinformatics was the most recent: 2022. The 156 papers were published in 78 different journals, most frequently in the Journal of Proteomics (n = 16 papers) and the Journal of Dairy Science (n = 12). The median number of cited references in the papers was 48. In the papers, there were 1143 co-authors (mean: 7.3 ± 0.3 co-authors per paper, median: 7, min.-max.: 1-19) and 742 individual authors. Among them, 15 authors had published at least seven papers (max.: 10). Further, there were 218 individual authors who were the first or last authors in the papers. Most papers were submitted for open access (n = 79). The median number of citations received by the 156 papers was 12 (min.-max.: 0-339), and the median yearly number of citations was 2.0 (min.-max.: 0.0-29.5). The h-index of the papers was 33, and the m-index was 2. The increased number of cited references in papers and international collaboration in the respective study were the variables associated with most citations to published papers. This is the first ever scientometrics evaluation of proteomics studies, the results of which highlighted the characteristics of published papers on mastitis and proteomics. The use of proteomics in mastitis research has focused on the elucidation of pathogenesis and diagnosis of the infection; LC-MS/MS has been established as the most frequently used proteomics technology, although the use of bioinformatics has also emerged recently as a useful tool.

Proteomics Applications in Toxoplasma gondii: Unveiling the Host-Parasite Interactions and Therapeutic Target Discovery

Toxoplasma gondii, a protozoan parasite with the ability to infect various warm-blooded vertebrates, including humans, is the causative agent of toxoplasmosis. This infection poses significant risks, leading to severe complications in immunocompromised individuals and potentially affecting the fetus through congenital transmission. A comprehensive understanding of the intricate molecular interactions between T. gondii and its host is pivotal for the development of effective therapeutic strategies. This review emphasizes the crucial role of proteomics in T. gondii research, with a specific focus on host-parasite interactions, post-translational modifications (PTMs), PTM crosstalk, and ongoing efforts in drug discovery. Additionally, we provide an overview of recent advancements in proteomics techniques, encompassing interactome sample preparation methods such as BioID (BirA*-mediated proximity-dependent biotin identification), APEX (ascorbate peroxidase-mediated proximity labeling), and Y2H (yeast two hybrid), as well as various proteomics approaches, including single-cell analysis, DIA (data-independent acquisition), targeted, top-down, and plasma proteomics. Furthermore, we discuss bioinformatics and the integration of proteomics with other omics technologies, highlighting its potential in unraveling the intricate mechanisms of T. gondii pathogenesis and identifying novel therapeutic targets.

Nutrigenomics in livestock sector and its human-animal interface-a review

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Nutrigenomics unfolds the link between nutrition and gene expression for productivity.expression profile of intramuscular.

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Nutrigenomics helps scientists discover genes and DNA in each animal's cell or tissue by assisting them in selecting nutrients.

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It brings out the importance of micronutrition for increasing animal production.

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Nutrigenomics integrates nutrition, molecular biology, genomics, bioinformatics, molecular medicine, and epidemiology.

Noncommunicable diseases such as cardiovascular disease, obesity, diabetes, and cancer now outnumber all other health ailments in humans globally due to abrupt changes in lifestyle following the industrial revolution. The industrial revolution has also intensified livestock farming, resulting in an increased demand for productivity and stressed animals. The livestock industry faces significant challenges from a projected sharp increase in global food and high animal protein demand. Nutrition genomics holds great promise for the future as its advances have opened up a whole new world of disease understanding and prevention. Nutrigenomics is the study of the interactions between genes and diet. It investigates molecular relationships between nutrients and genes to identify how even minor modifications could potentially alter animal and human health/performance by using techniques like proteomics, transcriptomics, metabolomics, and lipidomics. Dietary modifications mostly studied in livestock focus mainly on health and production traits through protein, fat, mineral, and vitamin supplementation changes. Nutrigenomics meticulously selects nutrients for fine-tuning the expression of genes that match animal/human genotypes for better health, productivity, and the environment. As a step forward, nutrigenomics integrates nutrition, molecular biology, genomics, bioinformatics, molecular medicine, and epidemiology to better understand the role of food as an epigenetic factor in the occurrence of these diseases. This review aims to provide a comprehensive overview of the fundamental concepts, latest advances, and studies in the field of nutrigenomics, emphasizing the interaction of diet with gene expression, and how it relates to human and animal health along with its human-animal interphase.

The successful use of -omic technologies to achieve the 'One Health' concept in meat producing animals

Human health and wellbeing are closely linked to healthy domestic animals, a vital wildlife, and an intact ecosystem. This holistic concept is referred to as 'One Health'. In this review, we provide an overview of the potential and the challenges for the use of modern -omics technologies, especially transcriptomics and proteomics, to implement the 'One Health' idea for food-producing animals. These high-throughput studies offer opportunities to find new potential molecular biomarkers to monitor animal health, detect pharmacological interventions and evaluate the wellbeing of farm animals in modern intensive livestock systems.

Saliva changes in composition associated to COVID-19: a preliminary study

The coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV 2), is usually associated with a wide variety of clinical presentations from asymptomatic to severe cases. The use of saliva as a diagnostic and monitoring fluid has gained importance since it can be used to investigate the immune response and to direct quantification of antibodies against COVID-19. Additionally, the use of proteomics in saliva has allowed to increase  our understanding of the underlying pathophysiology of diseases, bringing new perspectives on diagnostics, monitoring, and treatment. In this work, we compared the salivary proteome of 10 patients with COVID-19, (five patients with mild and five patients with severe COVID-19) and ten control healthy patients. Through the application of proteomics, we have identified 30 proteins whose abundance levels differed between the COVID-19 groups and the control group. Two of these proteins (TGM3 and carbonic anhydrase-CA6) were validated by the measurement of gGT and TEA respectively, in 98 additional saliva samples separated into two groups: (1) COVID-19 group, integrated by 66 patients who tested positive for COVID-19 (2) control group, composed of 32 healthy individuals who did not show any sign of disease for at least four weeks and were negative for COVID-19 in RT-PCR. In the proteomic study there were observed upregulations in CAZA1, ACTN4, and ANXA4, which are proteins related to the protective response against the virus disturbance, and the upregulation of TGM3, that is correlated to the oxidative damage in pulmonary tissue. We also showed the downregulation in cystatins and CA6 that can be involved in the sensory response to stimulus and possibly related to the presence of anosmia and dysgeusia during the COVID-19. Additionally, the presence of FGB in patients with severe COVID-19 but not in mild COVID-19 patients could indicate a higher viral aggregation and activation in these cases. In conclusion, the salivary proteome in patients with COVID-19 showed changes in proteins related to the protective response to viral infection, and the altered sensory taste perception that occur during the disease. Moreover, gGT and TEA could be potential biomarkers of respiratory complications that can occurs during COVID 19 although further larger studies should be made to corroborate this.