Representative sampling and adequate sample preparation are key factors for successful performance of further steps in foodomic analyses, as well as for correct data interpretation. Incorrect ...sampling and improper sample preparation can be sources of severe bias in foodomic analyses. It is well known that both wrong sampling and sample treatment cannot be corrected anymore. These, in the past frequently neglected facts, are now taken into consideration, and the progress in sampling and sample preparation in foodomics is reviewed here. We report the use of highly sophisticated instruments for both high‐performance and high‐throughput analyses, as well as miniaturization and the use of laboratory robotics in metabolomics, proteomics, peptidomics, and genomics.
► Sample displacement chromatography is a method for separation of complex mixtures. ► This method can be performed in different chromatographic modes. ► SDC in analytical and micro-analytical scale ...opens new perspectives in proteomics. ► In preparative scale, SDC is a method for isolation of low abundance proteins.
Sample displacement chromatography (SDC) in reversed-phase and ion-exchange modes was introduced approximately twenty years ago. This method takes advantage of relative binding affinities of components in a sample mixture. During loading, there is a competition among different sample components for the sorption on the surface of the stationary phase. SDC was first used for the preparative purification of proteins. Later, it was demonstrated that this kind of chromatography can also be performed in ion-exchange, affinity and hydrophobic-interaction mode. It has also been shown that SDC can be performed on monoliths and membrane-based supports in both analytical and preparative scale. Recently, SDC in ion-exchange and hydrophobic interaction mode was also employed successfully for the removal of trace proteins from monoclonal antibody preparations and for the enrichment of low abundance proteins from human plasma. In this review, the principals of SDC are introduced, and the potential for separation of proteins and peptides in micro-analytical, analytical and preparative scale is discussed.
A distinct feature of human prostate cancer (PCa) is the development of osteoblastic (bone-forming) bone metastases. Metastatic growth in the bone is supported by factors secreted by PCa cells that ...activate signaling networks in the tumor microenvironment that augment tumor growth. To better understand these signaling networks and identify potential targets for therapy of bone metastases, we characterized the secretome of a patient-derived xenograft, MDA-PCa-118b (PCa-118b), generated from osteoblastic bone lesion. PCa-118b induces osteoblastic tumors when implanted either in mouse femurs or subcutaneously. To study signaling molecules critical to these unique tumor/microenvironment-mediated events, we performed mass spectrometry on conditioned media of isolated PCa-118b tumor cells, and identified 26 secretory proteins, such as TGF-β2, GDF15, FGF3, FGF19, CXCL1, galectins, and β2-microglobulin, which represent both novel and previously published secreted proteins. RT-PCR using human versus mouse-specific primers showed that TGFβ2, GDF15, FGF3, FGF19, and CXCL1 were secreted from PCa-118b cells. TGFβ2, GDF15, FGF3, and FGF19 function as both autocrine and paracrine factors on tumor cells and stromal cells, that is, endothelial cells and osteoblasts. In contrast, CXCL1 functions as a paracrine factor through the CXCR2 receptor expressed on endothelial cells and osteoblasts. Thus, our study reveals a complex PCa bone metastasis secretome with paracrine and autocrine signaling functions that mediate cross-talk among multiple cell types within the tumor microenvironment.
Mannose Ligands for Mannose Receptor Targeting Paurević, Marija; Šrajer Gajdošik, Martina; Ribić, Rosana
International journal of molecular sciences,
02/2024, Letnik:
25, Številka:
3
Journal Article
Recenzirano
Odprti dostop
The mannose receptor (MR, CD 206) is an endocytic receptor primarily expressed by macrophages and dendritic cells, which plays a critical role in both endocytosis and antigen processing and ...presentation. MR carbohydrate recognition domains (CRDs) exhibit a high binding affinity for branched and linear oligosaccharides. Furthermore, multivalent mannose presentation on the various templates like peptides, proteins, polymers, micelles, and dendrimers was proven to be a valuable approach for the selective and efficient delivery of various therapeutically active agents to MR. This review provides a detailed account of the most relevant and recent aspects of the synthesis and application of mannosylated bioactive formulations for MR-mediated delivery in treatments of cancer and other infectious diseases. It further highlights recent findings related to the necessary structural features of the mannose-containing ligands for successful binding to the MR.
Foodborne pathogens and their toxins Martinović, Tamara; Andjelković, Uroš; Gajdošik, Martina Šrajer ...
Journal of proteomics,
09/2016, Letnik:
147
Journal Article
Recenzirano
Foodborne pathogens, mostly bacteria and fungi, but also some viruses, prions and protozoa, contaminate food during production and processing, but also during storage and transport before consuming. ...During their growth these microorganisms can secrete different components, including toxins, into the extracellular environment. Other harmful substances can be also liberated and can contaminate food after disintegration of food pathogens. Some bacterial and fungal toxins can be resistant to inactivation, and can survive harsh treatment during food processing. Many of these molecules are involved in cellular processes and can indicate different mechanisms of pathogenesis of foodborne organisms. More knowledge about food contaminants can also help understand their inactivation. In the present review the use of proteomics, peptidomics and metabolomics, in addition to other foodomic methods for the detection of foodborne pathogenic fungi and bacteria, is overviewed. Furthermore, it is discussed how these techniques can be used for discovering biomarkers for pathogenicity of foodborne pathogens, determining the mechanisms by which they act, and studying their resistance upon inactivation in food of animal and plant origin.
Comprehensive and comparative view into the genome and proteome of foodborne pathogens of bacterial or fungal origin and foodomic, mostly proteomic, peptidomic and metabolomic investigation of their toxin production and their mechanism of action is necessary in order to get further information about their virulence, pathogenicity and survival under stress conditions. Furthermore, these data pave the way for identification of biomarkers to trace sources of contamination with food-borne microorganisms and their endo- and exotoxins in order to ensure food safety and prevent the outbreak of food-borne diseases. Therefore, detection of pathogens and their toxins during production, transport and before consume of food produce, as well as protection against food spoilage is a task of great social, economic and public health importance.
Display omitted
•Use of foodomics techniques for better and more efficient detection of food pathogens and their toxins•High throughput methods for sample preparation and analysis will promote use of foodomics for routine food analyses.•Technological advances will bring ultra high resolution MS to wider range of users in food analytics.•Already used immunological and chromatographic methods, especially in high throughput mode still have great potential for detection of foodborne microorganisms and their toxins•Identification of biomarkers will result in fast identification of contaminated food.
Image-guided tumor ablation is a technique whereby needle-like applicators are placed directly into solid tumors under guidance typically with computed tomography or ultrasound. Changes in IgG and ...IgM antibody glycosylation were studied during ablation-induced immune response to cancer, and the use of glycosylation as a biomarker for diagnosis, prognosis and disease treatment was examined.
Plasma from 27 tumor patients was collected immediately before, after and for 6months following ablation. IgG and IgM antibodies were isolated by use high-throughput chromatography, and analyzed by hydrophilic liquid chromatography. Thorough identification of glycan structures in each chromatography peak was performed by nano-liquid chromatography electrospray ionization mass spectrometry.
Although antibody glycosylation was found to vary with cancer type, discernable patterns of change based on the successful treatment of tumors by ablation were not identified. One patient with renal clear cell carcinoma and poor disease outcome had unexpectedly high amount of oligomannose IgG glycans during the whole period of monitoring. In contrast, IgM antibodies did not follow the same pattern.
These findings suggest that glycosylation patterns are indicative of an immune system that is unable to prevent different types of cancer, rather than products of the immunostimulatory response to the ablation of tumor itself. Analyses of the outcome effect suggested that IgG glycosylation and IgM glycosylation are not associated with tumor ablation.
Present work opens a new way for parallel determination of glycosylation changes of both IgG and IgM antibodies by use of high-throughput methods, and their future use as biomarkers for disease diagnosis and prognosis. This article is part of a Special Issue entitled "Glycans in personalised medicine" Guest Editor: Professor Gordan Lauc.
The antimicrobial activity of quaternary ammonium salts of pyridinium oxime against four food pathogenic bacteria, the Gram positive Bacillus subtilis and Listeria monocytogenes, as well as the Gram ...negative Escherichia coli and Yersinia enterocolitica, were evaluated. Changes of proteome in these bacteria grown under stress conditions were identified. By the application of a new method for sample preparation, followed by both in-gel and in-solution digestion and LC–MS/MS, both characterization and comparison of proteomes of these food pathogens were achieved. It was shown in all investigated bacteria that some of the proteins of key importance for protein turnover and bacterial metabolism are down regulated. Some stress proteins involved in protein folding and degradation were up regulated. Most of both up- and down-regulated proteins belong to the group of proteins with high abundance. Flagellin is the only protein of lower abundance that was found to be down regulated in two strains, B. subtilis and E. coli. The presented results give the better view into the proteome of food pathogens, and pave the way for further investigation of their virulence, pathogenicity and detection of biomarkers for tracing the ways and sources of food contamination.
► Sample preparation techniques for study of changes of food pathogens proteome. ► Almost all up- or down regulated proteins belong to the group of high abundance. ► Flagelin is the only protein of lower abundance that was found to be down regulated.
Industrial hemp is a fast-growing, short-day plant, characterized by high biomass yields and low demands for cultivation. To manipulate growth, hemp is usually cultivated under prolonged photoperiods ...or continuous light that could cause photooxidative damage and adjustments of photosynthetic reactions. To determine the extent of changes in photosynthetic response caused by prolonged light exposure, we employed chlorophyll a fluorescence measurements accompanied with level of lipid peroxidation (TBARS) and FT-IR spectroscopy on two Cannabis cultivars. Plants were grown under white (W) and purple (P) light at different photoperiods (16/8, 20/4, and 24/0). Our results showed diverse photosynthetic reactions induced by the different light type and by the duration of light exposure in two cultivars. The most beneficial condition was the 16/8 photoperiod, regardless of the light type since it brought the most efficient physiological response and the lowest TBARS contents suggesting the lowest level of thylakoid membrane damage. These findings indicate that different efficient adaptation strategies were employed based on the type of light and the duration of photoperiod. White light, at both photoperiods, caused higher dissipation of excess light causing reduced pressure on PSI. Efficient dissipation of excess energy and formation of cyclic electron transport around PSI suggests that P20/4 initiated an efficient repair system. The P24/0 maintained functional electron transport between two photosystems suggesting a positive effect on the photosynthetic reaction despite the damage to thylakoid membranes.
Foodomics and Food Safety: Where We Are Andjelkovic, Uros; Gajdosik, Ma; Gaso-Sokac, Dajana ...
Food technology and biotechnology,
07/2017, Letnik:
55, Številka:
3
Journal Article
Recenzirano
Odprti dostop
The power of foodomics as a discipline that is now broadly used for quality assurance of food products and adulteration identification, as well as for determining the safety of food, is presented. ...Concerning sample preparation and application, maintenance of highly sophisticated instruments for both high-performance and high-throughput techniques, and analysis and data interpretation, special attention has to be paid to the development of skilled analysts. The obtained data shall be integrated under a strong bioinformatics environment. Modern mass spectrometry is an extremely powerful analytical tool since it can provide direct qualitative and quantitative information about a molecule of interest from only a minute amount of sample. Quality of this information is influenced by the sample preparation procedure, the type of mass spectrometer used and the analyst's skills. Technical advances are bringing new instruments of increased sensitivity, resolution and speed to the market. Other methods presented here give additional information and can be used as complementary tools to mass spectrometry or for validation of obtained results. Genomics and transcriptomics, as well as affinity-based methods, still have a broad use in food analysis. Serious drawbacks of some of them, especially the affinity-based methods, are the cross-reactivity between similar molecules and the influence of complex food matrices. However, these techniques can be used for pre-screening in order to reduce the large number of samples. Great progress has been made in the application of bioinformatics in foodomics. These developments enabled processing of large amounts of generated data for both identification and quantification, and for corresponding modeling.
We examined proteomic profiles of rat liver extracellular vesicles (EVs) shed following treatment with a sub-toxic dose (500 mg/kg) of the pain reliever drug, acetaminophen (APAP). EVs representing ...the entire complement of hepatic cells were isolated after perfusion of the intact liver and analyzed with LC-MS/MS. The investigation was focused on revealing the function and cellular origin of identified EVs proteins shed by different parenchymal and non-parenchymal liver cells and their possible role in an early response of this organ to a toxic environment. Comparison of EV proteomic profiles from control and APAP-treated animals revealed significant differences. Alpha-1-macroglobulin and members of the cytochrome P450 superfamily were highly abundant proteins in EVs shed by the normal liver. In contrast, proteins like aminopeptidase N, metalloreductase STEAP4, different surface antigens like CD14 and CD45, and most members of the annexin family were detected only in EVs that were shed by livers of APAP-treated animals. In EVs from treated livers, there was almost a complete disappearance of members of the cytochrome P450 superfamily and a major decrease in other enzymes involved in the detoxification of xenobiotics. Additionally, there were proteins that predominated in non-parenchymal liver cells and in the extracellular matrix, like fibronectin, receptor-type tyrosine-protein phosphatase C, and endothelial type gp91. These differences indicate that even treatment with a sub-toxic concentration of APAP initiates dramatic perturbation in the function of this vital organ.
PDF
