Complexity of the effects of pre-fermentation oxygenation, skin contact and use of pectolytic enzymes in white winemaking as revealed by comprehensive proteomics and volatilomics analysis

Ion exchange chromatography and SDS-PAGE followed by identification by MALDI-TOF/TOF, and two-dimensional gas chromatography with time-of-flight mass spectrometry (GC × GC-TOF-MS) were used for comprehensive proteomics and volatilomics evaluation of the effects of pre-fermentative oxygenation, skin contact and use of pectolytic enzymes in production of Malvazija istarska white wine, respectively. Many protein species and an unprecedented number of volatiles have been identified and (semi)quantified, revealing high complexity of the observed effects. Compared to a standard control wine, oxygenation treatment modulated the protein composition and resulted with a volatilome characterized by decreased levels of several important volatiles. Skin contact treatments, especially in combination with pectolytic enzymes, significantly increased the levels of a large number of proteins, but were also deprived of particular protein species found in other wines. Wines obtained by skin contact with exogenous enzymes exhibited the most complex volatile composition with increased levels of many key monoterpenoids, alcohols and esters.

In vitro aging alters the gene expression and secretome composition of canine adipose-derived mesenchymal stem cells

Introduction

Canine adipose-derived mesenchymal stem cells (cAD-MSCs) hold therapeutic promise due to their regenerative potential, particularly within their secretome. However, concerns arise regarding the impact of in vitro cultivation necessitated for storing therapeutic doses, prompting this study to comprehensively explore the impact of in vitro aging on gene expression and secretome composition.

Methods

The study involved collecting abdominal adipose tissue samples from nine healthy female dogs, from which cAD-MSCs were extracted and cultured. Stem cells were validated through trilineage differentiation assays and flow cytometry immunophenotyping. Gene expression profiling using RT-qPCR array, and cAD-MSCs secretome LC-MS/MS analysis, were conducted at passages 3 and 6 to reveal gene expression and protein composition alterations during in vitro culture.

Results and Discussion

The results demonstrate that the gene expression and secretome composition of cAD-MSCs were impacted by in vitro aging. Among many alterations in gene expression between two passages, two significant downregulations were noted in the MSC-associated PTPRC and IL10 genes. While the majority of proteins and their functional characteristics were shared between passages, the influence of cell aging on secretome composition is highlighted by 10% of proteins being distinctively expressed in each passage, along with 21 significant up- and downregulations. The functional attributes of proteins detected in passage 3 demonstrated a greater inclination towards supporting the regenerative capacity of cAD-MSCs. Moreover, proteins in passage 6 exhibited a noteworthy correlation with the blood coagulation pathway, suggesting an elevated likelihood of coagulation events. To the best of our knowledge, this study presents the first original perspective on the changes in secretome composition that occur when cAD-MSCs age in vitro. Furthermore, it contributes to broadening the currently restricted knowledge base concerning the secretome of cAD-MSCs. In conclusion, our findings show that the regenerative potential of cAD-MSCs, as well as their secretome, may be compromised by in vitro aging. Therefore, our study suggests a preference for earlier passages when considering these cells for therapeutic applications.

An Integrated Comprehensive Peptidomics and In Silico Analysis of Bioactive Peptide-Rich Milk Fermented by Three Autochthonous Cocci Strains

Bioactive peptides (BPs) are molecules of paramount importance with great potential for the development of functional foods, nutraceuticals or therapeutics for the prevention or treatment of various diseases. A functional BP-rich dairy product was produced by lyophilisation of bovine milk fermented by the autochthonous strains Lactococcus lactis subsp. lactis ZGBP5-51, Enterococcus faecium ZGBP5-52 and Enterococcus faecalis ZGBP5-53 isolated from the same artisanal fresh cheese. The efficiency of the proteolytic system of the implemented strains in the production of BPs was confirmed by a combined high-throughput mass spectrometry (MS)-based peptidome profiling and an in silico approach. First, peptides released by microbial fermentation were identified via a non-targeted peptide analysis (NTA) comprising reversed-phase nano-liquid chromatography (RP nano-LC) coupled with matrix-assisted laser desorption/ionisation-time-of-flight/time-of-flight (MALDI-TOF/TOF) MS, and then quantified by targeted peptide analysis (TA) involving RP ultrahigh-performance LC (RP-UHPLC) coupled with triple-quadrupole MS (QQQ-MS). A combined database and literature search revealed that 10 of the 25 peptides identified in this work have bioactive properties described in the literature. Finally, by combining the output of MS-based peptidome profiling with in silico bioactivity prediction tools, three peptides (75QFLPYPYYAKPA86, 40VAPFPEVFGK49, 117ARHPHPHLSF126), whose bioactive properties have not been previously reported in the literature, were identified as potential BP candidates.

Alternative methods for RuBisCO extraction from sugar beet waste: A comparative approach of ultrasound and high voltage electrical discharge

Ultrasound (US) and high voltage electric discharge (HVED) with water as a green solvent represent promising novel non-thermal techniques for protein extraction from sugar beet (Beta vulgaris subsp. vulgaris var. altissima) leaves. Compared to HVED, US proved to be a better alternative method for total soluble protein extraction with the aim of obtaining high yield of ribulose-1,5-bisphosphate carboxylase-oxygenase enzyme (RuBisCO). Regardless of the solvent temperature, the highest protein yields were observed at 100% amplitude and 9 min treatment time (84.60 ± 3.98 mg/gd.m. with cold and 96.75 ± 4.30 mg/gd.m. with room temperature deionized water). US treatments at 75% amplitude and 9 min treatment time showed the highest abundance of RuBisCO obtained by immunoblotting assay. The highest protein yields recorded among HVED-treated samples were observed at a voltage of 20 kV and a treatment time of 3 min, disregarding the used gas (33.33 ± 1.06 mg/gd.m. with argon and 34.89 ± 1.59 mg/gd.m. with nitrogen as injected gas), while the highest abundance of the RuBisCO among HVED-treated samples was noticed at 25 kV voltage and 3 min treatment time. By optimizing the US and HVED parameters, it is possible to affect the solubility and improve the isolation of RuBisCO, which could then be purified and implemented into new or already existing functional products.

Loss of thermotolerance in antibiotic-resistant Acinetobacter baumannii

Bacterium Acinetobacter baumannii is a leading cause of nosocomial infections. The occurrence of antibiotic-resistant A. baumannii isolates outside hospitals suggests that monitoring of this pathogen in environmental samples is needed. Survival of pandrug-resistant A. baumannii was followed on selective plates with and without carbapenems in water and soil. After a few days of starvation, A. baumannii lost the ability to be cultivated at 44°C on plates supplemented with carbapenems. Once cultivated on plates without carbapenems and/or at 36°C, A. baumannii could grow again at 44°C in the presence of carbapenems. Comparative proteomic analysis revealed that impaired membrane integrity and reduced function of efflux pumps due to elevated temperature combined with antibiotic exposure were the main reasons for this phenomenon. Loss of thermotolerance in the presence of antibiotics points to the need for temperature adjustment in long-term monitoring of A. baumannii in environmental samples, to avoid the underestimation of viable bacteria.

Proteome changes in human bladder T24 cells induced by hydroquinone derived from Arctostaphylos uva-ursi herbal preparation

ETHNOPHARMACOLOGICAL RELEVANCE

Arctostaphylos uva-ursi (L.) Spreng. (bearberry) is a well-known traditional herbal plant used as a urinary tract disinfectant. Its antiseptic and diuretic properties can be attributed to hydroquinone, obtained by hydrolysis of arbutin.

AIM OF THE STUDY

This study aimed to determine the toxic profile of free hydroquinone on urinary bladder cells (T24) as a target of therapeutic action.

MATERIALS AND METHODS

Quantitative and qualitative analysis of the extract and the digestive stability and bioavailability of arbutin and hydroquinone were performed by HPLC assay and simulated in vitro digestion, respectively. Cytotoxic effect, reactive oxygen species induction and proteome changes in T24 cells after hydroquinone treatment were determined using Neutral red assay, 2',7'-dichlorofluorescein-diacetate (DCFH-DA) assay and mass spectrometry, respectively.

RESULTS

Through in vitro digestion, arbutin was stable, but hydroquinone increased after pepsin treatment (109.6%) and then decreased after the small intestine phase (65.38%). The recommended doses of Uva-ursi had a cytotoxic effect on T24 cells only when all hydroquinone conjugates were converted to free hydroquinone (320 and 900 μg/mL) and the toxic effect was enhanced by recovery. One cup of the therapeutic dose had a prooxidative effect after 4 h of incubation. Shorter time of cell exposure (2 h) to hydroquinone did not have any impact on reactive oxygen species induction. Proteomic analysis found 17 significantly up-regulated proteins compared to control. Hydroquinone activated proteins related to oxidative stress response, stress-adaptive signalling, heat shock response and initiation of translation.

CONCLUSIONS

Despite the therapeutic properties of bearberry, up-regulated T24 cell proteins are evidence that plant compounds, although from a natural source, may exhibit negative properties.

Formulation and characterization of liposomal encapsulated systems of bioactive ingredients from traditional plant mountain germander (Teucrium montanum L.) for the incorporation into coffee drinks

Conventional and innovative (microwave-assisted and subcritical water extraction) techniques were applied to investigate the bioactive content of traditional plant - Teucrium montanum. Verbascoside and echinacoside, identified and quantified using LC-MS/MS and HPLC-PAD, were found to be the predominant phenolics in all extracts. Infusion (30 °C, 30 min) was characterized with the highest total phenolic content and antioxidant capacity and was further used for encapsulation into liposomes. Formulation of liposomes with a high encapsulation efficiency of echinacoside (68.27%) and verbascoside (80.60%), satisfactory physical properties, including size (326.2 nm) and polydispersity index (0.34), was achieved, although determined zeta potential (-23.03 mV) indicated their instability. Formulated liposomes were successfully coated with pectin and alginate that was also proved by FTIR analysis. Liposomes coated with pectin showed the most desirable in vitro digestion release of verbascoside and echinacoside, while alginate as liposome surface layer proved to be more appropriate for their retention during storage time.

Comparison of Traditional and Industrial Sausages - Baranjski Kulen and Kulenova Seka Using Comprehensive Proteome, Peptidome and Metabolome Techniques

Research background

Baranjski kulen is one of the most popular fermented meat sausages originating from Croatia. It has protected geographical indication, and is traditionally produced in the Baranja region of Croatia. Kulenova seka is a fermented sausage very similar to baranjski kulen, but it has a different calibre and consequently, a shorter time of production. In recent decades, due to the high demand and popularity of these products, industrially produced baranjski kulen and kulenova seka have become available on the market. This work aims to identify specific characteristics of traditional and industrial sausages baranjski kulen and kulenova seka on proteome, peptidome and metabolome level, which could potentially lead to better optimization of the industrial production process in order to obtain an equivalent to the traditional product.

Experimental approach

Protein profiles of baranjski kulen and kulenova seka (traditional and industrial) were analysed using two-dimensional gel electrophoresis followed by differential display analysis and protein identification by mass spectrometry. Peptidomic profile was analysed via liquid chromatography-tandem mass spectrometry. Furthermore, aroma profiles were investigated via headspace solid phase microextraction and gas chromatography-mass spectrometry.

Results and conclusions

The major identified characteristics of each product were: industrial baranjski kulen: specific degradation of myosin-1 and titin, overabundance of stress-related proteins and increased phenylalanine degradation; traditional baranjski kulen: decreased concentration of phenylalanine and overabundance of fructose-bisphosphate aldolase A and carbonic anhydrase 3; industrial kulenova seka - specific myosin-4 and haemoglobin subunit alpha degradation process; traditional kulenova seka - overabundance of dihydropyrimidine dehydrogenase [NADP(+)] and myosin light chain 1/3, skeletal muscle isoform, degradation of albumin and myoglobin, decreased concentrations of almost all free amino acids and increased amounts of smoke-derived volatile compounds. Presented results showed that potential product type-specific quality markers for each sausage could be found.

Novelty and scientific contribution

In this preliminary communication, the first insights into protein degradation processes and generation of peptides, free amino acids and aroma compounds of industrial and traditional baranjski kulen and kulenova seka are presented. Although further research is needed to draw general conclusions, the specific profile of proteins, peptides, amino acids and volatile compounds represents the first step in the industrial production of sausages that meet the characteristics of traditional flavour.

A Lactic Acid Bacteria Consortium Impacted the Content of Casein-Derived Biopeptides in Dried Fresh Cheese

This study aimed to define a consortium of lactic acid bacteria (LAB) that will bring added value to dried fresh cheese through specific probiotic properties and the synthesis of bioactive peptides (biopeptides). The designed LAB consortium consisted of three Lactobacillus strains: S-layer carrying Levilactobacillus brevis D6, exopolysaccharides producing Limosilactobacillus fermentum D12 and plantaricin expressing Lactiplantibacillus plantarum D13, and one Enterococcus strain, Enterococcus faecium ZGZA7-10. Chosen autochthonous LAB strains exhibited efficient adherence to the Caco-2 cell line and impacted faecal microbiota biodiversity. The cheese produced by the LAB consortium showed better physicochemical, textural and sensory properties than the cheese produced by a commercial starter culture. Liquid chromatography coupled with matrix-assisted laser desorption/ionization-time of flight tandem mass spectrometry (LC-MALDI-TOF/TOF) showed the presence of 18 specific biopeptides in dried fresh cheeses. Their identification and relative quantification was confirmed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) using multiple reaction monitoring (MRM). The results also showed that their synthesis resulted mainly from β-casein and also α-S1 casein degradation by proteolytic activities of the LAB consortium. The designed LAB consortium enhanced the functional value of the final product through impact on biopeptide concentrations and specific probiotic properties.

Proteomic analysis of Saccharomyces cerevisiae response to plasma treatment

Food safety is one of the main issues for the food industry. Regarding the increased reports of food-associated infections new non-thermal technologies are rapidly developing and improving. The aim of this research was to define the inactivation, recovery and stress response of Saccharomyces cerevisiae ATCC 204508 cells after the treatment by high voltage gas phase plasma and liquid phase plasma discharges in bubbles. Variations of the plasma frequency (60, 90 and 120 Hz), input gas (air or argon) and processing time (5 and 10 min) have been used to define plasma effects on S. cerevisiae cells. Complete inactivation's by liquid plasma in bubbles were determined as well as recovery of treated samples. Transmission electron microscopy figures showed cells with the normal cell shape and intact inner and outer membrane after the plasma treatments. Proteomic analyses indicated overexpressed proteins which contributed in cell defense mechanisms to overcome stress conditions. S. cerevisiae ATCC 204508 cells were under the stress, but with the proven ability to recover its metabolic activity.

Differentiation between Pseudomonas and Stenotrophomonas Species Isolated from Fish Using Molecular and MALDI-TOF Method

For the purpose of precise antibiotic susceptibility testing it is necessary to clearly distinguish Pseudomonas and Stenotrophomonas genera, considering acquired resistance of Pseudomonas species, as well as the intrinsic resistance of Stenotrophomonas species. This is why in the identification of the 51 isolates originated from fish, the following methods were used: standard PCR, 16S rRNA gene sequencing, and MALDI-TOF.

The results of the standard PCR test, 16S rRNA gene sequencing and MALDI-TOF analysis confirmed 35 strains to belong to the Pseudomonas genus. Standard PCR test and VITEK MS device confirmed that 10 strains belong to Stenotrophomonas maltophilia species.

Three strains were positive in both standard PCR tests for Pseudomonas and Stenotrpohomonas. 16S rRNA gene sequencing identified these 3 strains to be 99% Pseudomonas sp. and 99% Stenotrophomonas sp. VITEK MS first identified these three strains as 99% Stenotrophomonas, and in the repeated identification it identified them as 99% Pseudomonas. MALDI TOF/TOF 4800 Plus device identified these strains as Stenotrophomonas.

Three strains were negative in both standard PCR tests for Pseudomonas and Stenotrpohomonas. 16S rRNA gene sequencing identified these 3 strains to be 99% Pseudomonas sp. and 99% Stenotrophomonas sp. VITEK MS first identified these three strains as 99% Stenotrophomonas, and in the repeated identification it identified them as 99% Pseudomonas. MALDI TOF/TOF 4800 Plus device identified these strains as Stenotrophomonas.

Although modern test methods that have very high specificity (PCR, 16S rRNA gene sequencing, MALDI TOF) were used in this study, precise differentiation between Pseudomonas and Stenotrophomonas species for 6 isolates could not be reached using the above mentioned methods.

Characterization of a S-adenosyl-l-methionine (SAM)-accumulating strain of Scheffersomyces stipitis

S-adenosyl-l-methionine (SAM) is an important molecule in the cellular metabolism of mammals. In this study, we examined several of the physiological characteristics of a SAM-accumulating strain of the yeast Scheffersomyces stipitis (M12), including SAM production, ergosterol content, and ethanol tolerance. S. stipitis M12 accumulated up to 52.48 mg SAM/g dry cell weight. Proteome analyses showed that the disruption of C-24 methylation in ergosterol biosynthesis, a step mediated by C-24 sterol methyltransferase (Erg6p), results in greater SAM accumulation by S. stipitis M12 compared to the wild-type strain. A comparative proteome-wide analysis identified 25 proteins that were differentially expressed by S. stipitis M12. These proteins are involved in ribosome biogenesis, translation, the stress response, ubiquitin-dependent catabolic processes, the cell cycle, ethanol tolerance, posttranslational modification, peroxisomal membrane stability, epigenetic regulation, the actin cytoskeleton and cell morphology, iron and copper homeostasis, cell signaling, and energy metabolism.

Sub-emetic toxicity of Bacillus cereus toxin cereulide on cultured human enterocyte-like Caco-2 cells

Cereulide (CER) intoxication occurs at relatively high doses of 8 µg/kg body weight. Recent research demonstrated a wide prevalence of low concentrations of CER in rice and pasta dishes. However, the impact of exposure to low doses of CER has not been studied before. In this research, we investigated the effect of low concentrations of CER on the behavior of intestinal cells using the Caco-2 cell line. The MTT (mitochondrial 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) and the SRB (sulforhodamine B) reactions were used to measure the mitochondrial activity and cellular protein content, respectively. Both assays showed that differentiated Caco-2 cells were sensitive to low concentrations of CER (in a MTT reaction of 1 ng/mL after three days of treatment; in an SRB reaction of 0.125 ng/mL after three days of treatment). Cell counts revealed that cells were released from the differentiated monolayer at 0.5 ng/mL of CER. Additionally, 0.5 and 2 ng/mL of CER increased the lactate presence in the cell culture medium. Proteomic data showed that CER at a concentration of 1 ng/mL led to a significant decrease in energy managing and H2O2 detoxification proteins and to an increase in cell death markers. This is amongst the first reports to describe the influence of sub-emetic concentrations of CER on a differentiated intestinal monolayer model showing that low doses may induce an altered enterocyte metabolism and membrane integrity.

The effect of starvation stress on Lactobacillus brevis L62 protein profile determined by de novo sequencing in positive and negative mass spectrometry ion mode

RATIONALE

We describe a novel negative chemically activated fragmentation/positive chemically activated fragmentation (CAF-/CAF+) technique for protein identification. The technique was used to investigate Lactobacillus brevis adaptation to nutrient deprivation.

METHODS

The CAF-/CAF+ method enables de novo sequencing of derivate peptides with negative and positive ion mode matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry (MS/MS). Peptide sequences obtained from MS/MS spectra were matched against the National Center for Biotechnology Information (NCBI) non-redundant (nr) database and confirmed by the mass spectrometry data of elucidated peptide mass sequences derived from the annotated genome. This improved protein identification method highlighted 36 differentially expressed proteins in the proteome of L. brevis after 75 days of starvation.

RESULTS

The results revealed the key differences in the metabolic pathways that are responsible for the survival of L. brevis in a hostile environment. Proteomics analysis demonstrated that numerous proteins engaged in glucose and amino-acid catabolizing pathways, glycerolipid metabolizing pathways, and stress-response mechanisms are differentially expressed after long-term starvation. Amino acid and proteomics analysis indicated that starved L. brevis metabolized arginine, glycine, and histidine from dead cells as alternative nutrient sources. The production of lactic acid also varied between the parent cells and the starved cells.

CONCLUSIONS

Differentially expressed proteins identified exclusively by peptide sequence reading provided promising results for CAF-/CAF+ implementation in a standard proteomics workflow (e.g., biomarker and mutation discovery and biotyping). The practical performance of a reliable de novo sequencing technique in routine proteomics analysis is emphasized in this article.

Characterization of Lactobacillus brevis L62 strain, highly tolerant to copper ions

Lactic acid bacteria (LAB) as starter culture in food industry must be suitable for large-scale industrial production and possess the ability to survive in unfavorable processes and storage conditions. Approaches taken to address these problems include the selection of stress-resistant strains. In food industry, LAB are often exposed to metal ions induced stress. The interactions between LAB and metal ions are very poorly investigated. Because of that, the influence of non-toxic, toxic and antioxidant metal ions (Zn, Cu, and Mn) on growth, acid production, metal ions binding capacity of wild and adapted species of Leuconostoc mesenteroides L3, Lactobacillus brevis L62 and Lactobacillus plantarum L73 were investigated. The proteomic approach was applied to clarify how the LAB cells, especially the adapted ones, protect themselves and tolerate high concentrations of toxic metal ions. Results have shown that Zn and Mn addition into MRS medium in the investigated concentrations did not have effect on the bacterial growth and acid production, while copper ions were highly toxic, especially in static conditions. Leuc. mesenteroides L3 was the most efficient in Zn binding processes among the chosen LAB species, while L. plantarum L73 accumulated the highest concentration of Mn. L. brevis L62 was the most copper resistant species. Adaptation had a positive effect on growth and acid production of all species in the presence of copper. However, the adapted species incorporated less metal ions than the wild species. The exception was adapted L. brevis L62 that accumulated high concentration of copper ions in static conditions. The obtained results showed that L. brevis L62 is highly tolerant to copper ions, which allows its use as starter culture in fermentative processes in media with high concentration of copper ions.