Proteomic differences between Listeria monocytogenes isolates from food and clinical environments

Listeria monocytogenes is an organism associated with a wide range of foods. It causes listeriosis, a severe illness that mainly affects people with weakened immune systems. Proteomic profiles of three different L. monocytogenes isolates were studied using 1D SDS PAGE, 2DE and mass spectrometry. The protein banding patterns generated by 1D SDS PAGE of three strains of L. monocytogenes were found to be similar. Visual observations from 2DE gel maps revealed that certain spots appeared to have intensity differences. Key differences in proteins synthesis of three strains of L. monocytogenes were found using the PDQest TM 2DE Analysis software. Comparison showed that the clinical isolate (strain SB92/844) had 53.4% and 53.9% protein profile similarity with dairy isolate (strain V7) and seafood isolate (SB92/870), respectively. The identity of selected protein spots was achieved using MALDI-TOF and ion trap mass spectrometry. It was found that certain identified proteins (i.e., a major cold shock protein and superoxide dismutase) were expressed differently between two local strains of L. monocytogenes (SB92/844, SB92/870) and one strain from overseas (V7)

Predictive potential of MALDI-TOF analyses for wine and brewing yeast

The potential of MALDI-TOF profiling for predicting potential applications of yeast strains in the beverage sector was assessed. A panel of 59 commercial yeasts (47 wine and 12 brewing yeasts) was used to validate the concept whereby 2 culture media (YPD agar and YPD broth), as well as two mass ranges m/z 500–4000 and m/z 2000–20,000, were evaluated for the best fit. Three machine learning-based algorithms, PCA, MDS, and UMAP, in addition to a hierarchical clustering method, were employed. Profiles derived from broth cultures yielded more peaks, but these were less well-defined compared with those from agar cultures. Hierarchical clustering more clearly resolved different species and gave a broad overview of potential strain utility, but more nuanced insights were provided by MDS and UMAP analyses. PCA-based displays were less informative. The potential of MALDI-TOF proteomics in predicting the utility of yeast strains of commercial benefit is supported in this study, provided appropriate approaches are used for data generation and analysis

The wool proteome and fibre characteristics of three distinct genetic ovine breeds from Portugal

Wool properties and commodity value vary considerably between breeds. In Portugal, three major ovine groups exist: Churros, Bordaleiros and Merinos. This work studies the effect of the ovine genotype on the wool proteome of such groups. Wool was collected from 15 ewes/breed and genetic groups: Churra da Terra Quente (CTQ) or Churro, Serra da Estrela (SE) or Bordaleiro and Merino Branco (MB) or Merino. Proteins were extracted and subjected to label-free proteomics analysis. A total of 50 keratinous protein groups were identified in all the samples, divided into type I and II keratins and the keratin associated proteins: high-glycine-tyrosine proteins, ultra-high sulphur proteins and high-sulphur proteins. Major differences were found between MB and CTQ with respect to K75 and K38, both medullar proteins and to a lesser extent between SE and CTQ suggesting that these might be good markers for this trait in wool. Partial least squares discriminatory analysis proved MB to be readily distinguishable from the other two breeds. Further differences were noted in keratin associated protein levels between the three breeds, normally an indicator of higher levels of orthocortex and also their relationship to high curvature, high crimp fibres like Merinoinfo:eu-repo/semantics/acceptedVersio

Provenancing Archaeological Wool Textiles from Medieval Northern Europe by Light Stable Isotope Analysis (δ13C, δ15N, δ2H)

We investigate the origin of archaeological wool textiles preserved by anoxic waterlogging from seven medieval archaeological deposits in north-western Europe (c. 700-1600 AD), using geospatial patterning in carbon (δ13C), nitrogen (δ15N) and non-exchangeable hydrogen (δ2H) composition of modern and ancient sheep proteins. δ13C, δ15N and δ2H values from archaeological wool keratin (n = 83) and bone collagen (n = 59) from four sites were interpreted with reference to the composition of modern sheep wool from the same regions. The isotopic composition of wool and bone collagen samples clustered strongly by settlement; inter-regional relationships were largely parallel in modern and ancient samples, though landscape change was also significant. Degradation in archaeological wool samples, examined by elemental and amino acid composition, was greater in samples from Iceland (Reykholt) than in samples from north-east England (York, Newcastle) or northern Germany (Hessens). A nominal assignment approach was used to classify textiles into local/non-local at each site, based on maximal estimates of isotopic variability in modern sheep wool. Light element stable isotope analysis provided new insights into the origins of wool textiles, and demonstrates that isotopic provenancing of keratin preserved in anoxic waterlogged contexts is feasible. We also demonstrate the utility of δ2H analysis to understand the location of origin of archaeological protein samples

Bioinformatics and molecular modeling in glycobiology

The field of glycobiology is concerned with the study of the structure, properties, and biological functions of the family of biomolecules called carbohydrates. Bioinformatics for glycobiology is a particularly challenging field, because carbohydrates exhibit a high structural diversity and their chains are often branched. Significant improvements in experimental analytical methods over recent years have led to a tremendous increase in the amount of carbohydrate structure data generated. Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology. In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and data mining, and tools to support experimental glycan analysis are presented. Finally, the field of structural glycoinformatics and molecular modeling of carbohydrates, glycoproteins, and protein–carbohydrate interaction are reviewed

Method developments to extract proteins from oil palm chromoplast for proteomic analysis

Proteins from the plant chromoplast are essential for many physiological processes such as fatty acid biosynthesis. Different protein extraction methods were tested to find the most robust method to obtain oil palm chromoplast proteins for mass spectrometry analysis. Initially, two different solvents were employed to reduce the fruit lipids. Then, two plant cell wall digestive enzymes were used to acquire the protoplasts to increase the protein extraction effectiveness. A two-stage centrifugation-based fractionation approach enhanced the number of identified proteins, particularly the fatty acid biosynthetic enzymes. The effectiveness of each extraction method was assessed using protein yields and 2DE gel profiles. The ideal method was successfully used to establish the 2DE chromoplast proteome maps of low and high oleic acid mesocarps of oil palm. Further nanoLC–MS/MS analysis of the extracted chromoplast proteins led to the identification of 162 proteins, including some of the main enzymes involved in the fatty acid biosynthesis. The established procedures would provide a solid foundation for further functional studies, including fatty acid biosynthetic expression profiling and evaluation of regulatory function

Cooking-induced protein modifications in meat

Food ingredients commonly undergo heat treatment. Meat, in particular, is typically consumed after some form of heating, such as boiling or roasting. Heating of meat can introduce a wide range of structural changes in its proteinaceous components. At the 3-dimensional structural level, meat proteins may denature and form aggregates upon heating. At the molecular level, primary structure (amino acid residue) alterations reported in cooked meat include protein carbonylation, modification of aromatic residues, and the formation of Maillard reaction products. Identification of these modifications is essential for determining the mechanism of thermal processing of meat and allowing better control of the nutritional and functional properties of products. This article reviews and summarizes the current state of understanding of protein modifications at the molecular level in commonly consumed mammalian food. In addition, relevant case studies relating to characterization of heat-induced amino acid residue-level modifications in other biological materials such as milk and wool are discussed to provide complementary insights

Proteomic investigation of protein profile changes and amino acid residue-level modification in cooked lamb longissimus thoracis et lumborum: The effect of roasting

Protein modifications of meat cooked by typical dry-heat methods (e.g., roasting) are currently not well understood. The present study utilised a shotgun proteomic approach to examine the molecular-level effect of roasting on thin lamb longissimus thoracis et lumborum patties, in terms of changes to both the protein profile and amino acid residue side-chain modifications. Cooking caused aggregation of actin, myosin heavy chains and sarcoplasmic proteins. Longer roasting time resulted in significantly reduced protein extractability as well as protein truncation involving particularly a number of myofibrillar and sarcoplasmic proteins, e.g., 6-phosphofructokinase, beta-enolase, l-lactate dehydrogenase A chain, alpha-actinin-3, actin and possibly myosin heavy chains. Modifications that have potential influence on nutritional properties, including carboxyethyllysine and a potentially glucose-derived N-terminal Amadori compound, were observed in actin and myoglobin after roasting. This study provided new insights into molecular changes resulting from the dry-heat treatment of meat, such as commonly used in food preparation

Application of MALDI-TOF analysis to reveal diversity and dynamics of winemaking yeast species in wild-fermented, organically produced, New Zealand Pinot Noir wine

Rapid yeast identification is of particular importance in monitoring wine fermentation and assessing strain application in winemaking. We used MALDI-TOF MS analysis supported by 26 S rRNA gene sequence analysis and Saccharomyces-specific PCR testing to differentiate reference and field strains recovered from organic wine production facilities in Waipara, New Zealand, in which Pinot Noir wine was produced by spontaneous fer-mentations in the vineyard and in the winery. Strains were isolated from each of four key stages of each ferment to evaluate changes in taxonomic diversity. MALDI-TOF MS analysis was confirmed as an excellent yeast identification method, with even closely related Saccharomyces species readily distinguished. A total of 13 indigenous species belonging to eight genera were identified from Pinot Noir ferments, with taxonomic diversity generally reducing as fermentation progressed. However, differences between the taxa recovered were observed between the vineyard and winery ferments, despite the grapes used being from the same batch. Furthermore, some consistent proteomic differences between strains of S. cerevisiae, Hanseniasporum uvarum, Candida cal-ifornica, Pichia membranifaciens and Starmerella bacillaris correlated with the different fermentation systems used. The high speed, low cost, taxonomic resolution and ability to characterise subtle changes in phenotype that may result from variations in environmental conditions makes MALDI-TOF analysis an attractive tool for further and wider applications in the wine industry. Such applications may include monitoring wine fermentation to actively support the consistency of high-quality wine products, and potentially for the development of such products too

The influence of growth conditions on MALDI-TOF MS spectra of winemaking yeast: Implications for industry applications

Previous studies have shown MALDI-TOF MS to be a powerful tool in wine yeast identification and potential prediction of application. However, it is also established that substrate composition influences protein expression, but the degree to which this may affect MALDI-TOF spectra (and analytical results thereof) has not been fully explored. To further inform assay optimisation, the influence on MALDI-TOF spectra was determined using eight Saccharomyces strains of diverse origins cultivated on grape juices from Pinot Noir and Chardonnay varieties, synthetic grape juice, and laboratory-grade artificial culture media (YPD broth and agar). Our results demonstrated significant influences of culture media on strain MALDI-TOF spectra. Yeast culture on YPD agar is recommended for taxonomic studies, with YPD broth culture of S. cerevisiae offering improved intra-subspecific differentiation Furthermore, our data supported a correlation between MALDI spectra and the potential industrial application of individual yeast strains