Trichloroacetic acid-induced protein precipitation involves the reversible association of a stable partially structured intermediate

A Review on Bacteriocin Extraction Techniques from Lactic Acid Bacteria

Lactic acid bacteria (LAB) are widely known for the production of secondary metabolites such as organic acids and other bioactive compounds such as bacteriocins. Finding a broad application in food and healthcare, bacteriocins have received increased attention due to their inherent antimicrobial properties. However, the extraction of bacteriocins is often plagued with low yields due to the complexity of the extraction processes and the diversity of bacteriocins themselves. Here, we review the current knowledge related to bacteriocin extraction on the different extraction techniques for isolating bacteriocins from LAB. The advantages and disadvantages of each technique will also be critically appraised, taking into account factors such as extraction efficiency, scalability and cost-effectiveness. This review aims to guide researchers and professionals in selecting the most suitable approach for bacteriocin extraction from LAB by illuminating the respective advantages and limitations of various extraction techniques.

A Cryptococcus neoformans polysaccharide conjugate vaccine made with filtered polysaccharide elicits protective immunity in mice

Diseases caused by the encapsulated fungus Cryptococcus neoformans are major causes of mortality and morbidity in immunocompromised patients. Two important cryptococcal virulence factors are the polysaccharide capsule (CPS) and the secreted exopolysaccharides (EPS), both of which contain predominantly glucuronoxylomannan (GXM) polymers. Here, we evaluated the efficacy of an experimental glycoconjugate vaccine generated by linking minimally processed cryptococcal EPS with the protein carrier CRM197. Two different adjuvants (aluminum hydroxide and Freund's adjuvant) were utilized to increase the immunogenicity and to evaluate the efficiency of vaccine protection in a mouse model of cryptococcosis. After a three-dose vaccination schedule, titers of GXM-specific antibodies and survival following lethal challenge were assessed. The protective efficacy of antibodies from sera of vaccinated mice was also evaluated in vitro, through the characterization of their enhancement of macrophage engulfment and opsonization patterns on cryptococcal cells. Antibodies elicited by the EPS-CRM197 vaccine formulated with Freund's adjuvant showed the best opsonic capabilities as shown by the macrophage engulfment analysis and cryptococcal capsule binding patterns, which was mirrored by longer survival of this vaccine group in our challenge studies. This study confirms that an EPS-protein conjugate vaccine can elicit a protective immune response in mice and provides encouragement for the development of polysaccharide-protein conjugates for the prevention of cryptococcosis.

A simplified optimization approach for sample preparation workflow in LC-MS-based quantitative proteomic analysis: Biological samples to peptides

Quantitative proteomics, an integral subfield within proteomics, is pivotal for elucidating complex biological processes. By integrating with other omics data, quantitative proteomics facilitates system-level analysis and significantly advances our understanding of cellular networks and disease mechanisms. The ongoing advancements in quantitative proteomics technology significantly boost its importance by improving analytical accuracy. This review focuses on quantitative proteomics employing liquid chromatography-mass spectrometry (LC-MS), a cornerstone technique renowned for its sensitivity, selectivity, accuracy, and throughput. The efficacy of LC-MS proteomics is heavily reliant on sample preparation, which encompasses protein extraction, total protein estimation, reduction, alkylation, digestion, and cleanup. For the very first time, this article provides a detailed examination of sample preparation methods offering insights and guidelines that researchers can utilize to refine their experimental protocols which were not critically evaluated before. By optimizing sample preparation workflows, researchers can enhance the robustness and reproducibility of their proteomic studies. By understanding the complexities of sample preparation in quantitative proteomics, researchers can optimize their experimental workflow to improve the robustness and reproducibility of their results. This review provides a comprehensive overview of sample preparation strategies in quantitative proteomics using LC-MS, discussing the underlying principles and key considerations for each step. By delving into the complexities of sample preparation, this article aims to aid researchers in optimizing their workflows to achieve robust and reproducible results, which ultimately drive innovations and breakthroughs in biomedical research and healthcare.

Molecular intricacies of intrinsically disordered proteins and drought stress in plants

Intrinsically Disordered Proteins (IDPs) and Intrinsically Disordered Regions (IDRs) are renowned for their dynamic structural characteristics and conformational adaptability, allowing them to assume diverse conformations in response to prevailing environmental conditions. This inherent flexibility facilitates their interactions with molecular targets, enabling them to engage in numerous cellular processes without any excessive energy consumption. This adaptability is instrumental in shaping cellular complexity and enhancing adaptability. Notably, most investigations into IDPs/IDRs have concentrated on non-plant organisms, while this comprehensive review explores their multifaceted functions with a perspective of plant resilience to drought stress. Furthermore, the impact of IDPs on plant stress is discussed, highlighting their involvement in diverse biological processes extending beyond mere stress adaptation. This review incorporates a broad spectrum of methodological approaches, ranging from computational tools to experimental techniques, employed for the systematic study of IDPs. We also discussed limitations, challenges, and future directions in this dynamic and evolving field, aiming to provide insights into the unexplored facets of IDPs/IDRs in the intricate landscape of plant responses to drought stress.

Sodium Alginate/Poly (Acrylicacid) Hydrogel Composite, Potential Carrier for Fibroblast Growth Factor1 (FGF1) Delivery

Fibroblast growth factor1 is a powerful signaling molecule that plays a critical role in injury repair of diverse tissue by stimulating cell growth and angiogenesis. FGF1 has significant role in the cell fate and regulating inflammation with short half-life and poor in vivo stability. The encapsulation of the growth factor in the hydrogel led to peptide protect from the degradation and/or immune recognition and enable controlled drug delivery over a longer period of time. The aim of this study is to develop and evaluate a hydrogel carrier with adjustable release rate while maintaining bioactivity of FGF1. Here we describe an optimal ratio of sodium alginate and polyacrylic acid without additional cross linker containing optimum amount of FGF1 with the potential of sustained release to be used as a therapeutic agent. The carrier was characterized by FTIR, contact angle and swelling ratio. The activity of FGF1 after release from the hydrogel was confirmed by ELISA and Western blot. Further assessment of genes related to inflammation were evaluated by RTPCR. This hydrogel is able to deliver growth factors by restricting the essential proteins within the matrix to prevent rapid proteolysis and explosive release and is therefore widely applicable.

Comparative analysis of fixation techniques for signal detection in avian embryos

The choice of fixation method significantly impacts tissue morphology and visualization of gene expression and proteins after in situ hybridization chain reaction (HCR) or immunohistochemistry (IHC), respectively. In this study, we compared the effects of paraformaldehyde (PFA) and trichloroacetic acid (TCA) fixation techniques prior to HCR and IHC on chicken embryos. Our findings underscore the importance of optimizing fixation methods for accurate visualization and subsequent interpretation of HCR and IHC results, with implications for probe and antibody validation and tissue-specific protein localization studies. We found that TCA fixation resulted in larger and more circular nuclei and neural tubes compared to PFA fixation. Additionally, TCA fixation altered the subcellular fluorescence signal intensity of various proteins, including transcription factors, cytoskeletal proteins, and cadherins. Notably, TCA fixation revealed protein signals in tissues that may be inaccessible with PFA fixation. In contrast, TCA fixation proved ineffective for mRNA visualization. These results highlight the need for optimization of fixation protocols depending on the target and model system, emphasizing the importance of methodological considerations in biological analyses.

Protein Precipitation by Metal Hydroxides as a Convenient and Alternative Sample Preparation Procedure for Bioanalysis

Protein precipitation is widely used for sample preparation ahead of liquid chromatography. This step is required to analyze small molecules without the interference of proteins contained in the matrix. Organic solvents and acidic chemicals are the two most popular reagents used for this scope. Organic solvents are quite effective precipitating agents, but require a medium-to-large sample dilution. Moreover, a high concentration of organic solvents in sample media can affect reversed phase separations. Therefore, an evaporation step, followed by the resuspension of the analytes in appropriate media, is sometimes required. On the contrary, the addition of acidic compounds is more straightforward, since it keeps the supernatant aqueous and does not require evaporation, but the extreme pH can cause the degradation of analytes and the stationary phase. Herein, an alternative method for protein precipitation using the addition of zinc hydroxide was tested. The main advantages of this method over the other precipitating reagents are the minimal sample dilution required and the maintenance of aqueous media at nearly neutral pH which ensure analyte stability. The protocol ensured an effective protein removal before the analysis of small molecules in biological matrices, resulting in full compatibility with reversed phase chromatography coupled with both UV and mass spectrometric detectors.

Glucose addition and oven-heating of pork stimulate glycoxidation and protein carbonylation, while reducing lipid oxidation during simulated gastrointestinal digestion

In the present study, it was investigated if glucose addition (3 or 5%) to pork stimulates glycoxidation (pentosidine, PEN), glycation (Maillard reaction products, MRP), lipid oxidation (4-hydroxy-2-nonenal, 4-HNE; hexanal, HEX; thiobarbituric acid reactive substances, TBARS), and protein oxidation (protein carbonyl compounds, PCC) during various heating conditions and subsequent in vitro gastrointestinal digestion. An increase in protein-bound PEN level was observed during meat digestion, which was significantly stimulated by glucose addition (up to 3.3-fold) and longer oven-heating time (up to 2.5-fold) of the meat. These changes were accompanied by the distinct formation of MRP during heating and digestion of the meats. Remarkably, stimulated glyc(oxid)ation was accompanied by increased protein oxidation, whereas lipid oxidation was decreased, indicating these reactions are interrelated during gastrointestinal digestion of meat. Glucose addition generally didn't affect these oxidative reactions when pork was packed preventing air exposure and oven-heated until a core temperature of 75 °C was reached.

The impact of complexation or complex coacervation of lactoferrin and osteopontin on simulated infant gastrointestinal digestion, intestinal inflammation, and in vivo bone development

Lactoferrin (LF) and osteopontin (OPN) are bioactive milk proteins which can form heteroprotein complexes and complex coacervates. This research studied the effect of LF-OPN complexation and complex coacervation on the simulated infant gastrointestinal digestion of LF with subsequent examination of gut and bone health bioactivities in preclinical models. In an infant digestion model, the proteolytic profile of LF was unaltered by the pre-association of LF and OPN. Gastric proteolysis of LF was increased when the model gastric pH was reduced from 5.3 to 4.0, but less so when complexed with OPN. In a model of intestinal inflammation, undigested (79% inhibition) and gastric digestates (26% inhibition) of LF, but not gastrointestinal digestates, inhibited lipopolysaccharide (LPS)-induced NF-κB activation in intestinal epithelial cells. LF-OPN complexation sustained the inhibitory effect (21-43% of the undigested effect, depending on the type of complex) of LF after gastrointestinal digestion, suggesting that the peptides produced were different. In a neonatal rodent model used to study bone development, coacervating LF and OPN improved bone structures with a significant increase of trabecular proportion (BV/TV increase by 21.7%). This resulted in an 11.3% increase in stiffness of bones. Feeding the LF and OPN proteins in coacervate format also increased the levels of OPN, P1NP and M-CSF in blood, signifying a more pronounced impact on bone development. This research demonstrated that LF-OPN complexation and complex coacervation can delay simulated infant gastrointestinal digestion of LF and protect or improve the bioactivity of the proteins.

Approaches for the analysis of redox-dependent protein import into mitochondria of mammalian cells

Oxidation of cysteine residues in proteins can take place as part of an enzymatic reaction cycle, during oxidative protein folding or as a consequence of redox signalling or oxidative stress. Following changes in protein thiol redox states allows to investigate the mechanisms underlying thiol-disulphide redox processes. In this book chapter, we provide information and protocols on different methods for redox state determination with a focus on these processes in the context of oxidation-dependent protein import into the mitochondrial intermembrane space. These methods include assessing the cysteine redox state of mature proteins, methods to investigate oxidative protein folding in radioactive pulse chase assays and methods to follow specifically the formation of oxidative folding intermediates between oxidoreductases and substrates.

A combination of generated hydrogen sulfide and nitric oxide activity has a potentiated protectant effect against cisplatin induced nephrotoxicity

Aim

Hydrogen sulfide and nitric oxide possess cytoprotective activity and in vivo, they are generated from exogenous sodium hydrosulfide and L-arginine respectively. Cisplatin is a major chemotherapeutic agent used to treat cancer and has a high incidence of nephrotoxicity as a side effect. The study aim was to explore the effects of NaHS and L-arginine or their combination on cisplatin induced nephrotoxicity in rats.

Methods

Wistar Kyoto rats were given a single intraperitoneal dose of cisplatin (5 mg/kg) followed either by NaHS (56 μmol/kg, i. p.), L-arginine (1.25 g/L in drinking water) or their combination daily for 28-days. Post-mortem plasma, urine and kidney samples were collected for biochemical assays and histopathological analysis.

Results

Cisplatin decreased body weights and increased urinary output, while plasma creatinine and urea levels were elevated, but sodium and potassium concentrations were diminished. The renal function parameters, blood urea nitrogen and creatinine clearance, were raised and decreased respectively. Regarding markers of reactive oxygen species, plasma total superoxide dismutase was reduced, whereas malondiadehyde was augmented.Cisplatin also diminished plasma and urinary H2S as well as plasma NO, while NaHS and L-arginine counteracted this activity on both redox-active molecules. Cisplatin cotreatment with NaHS, and/or L-arginine exhibited a reversal of all other measured parameters.

Conclusion

In current study, NaHS and L-arginine as monotherapy protected the rats from cisplatin-induced nephrotoxicity but the combination of both worked more effectively suggesting the augmented anti-inflammatory and antioxidative potential of test treatments when administered together.

Effectiveness of fixation methods for wholemount immunohistochemistry across cellular compartments in chick embryos

The choice of fixation method significantly impacts tissue morphology and protein visualization after immunohistochemistry (IHC). In this study, we compared the effects of paraformaldehyde (PFA) and trichloroacetic acid (TCA) fixation prior to IHC on chicken embryos. Our findings underscore the importance of validating fixation methods for accurate interpretation of IHC results, with implications for antibody validation and tissue-specific protein localization studies. We found that TCA fixation resulted in larger and more circular nuclei compared to PFA fixation. Additionally, TCA fixation altered the appearance of subcellular localization and fluorescence intensity of various proteins, including transcription factors and cytoskeletal proteins. Notably, TCA fixation revealed protein localization domains that may be inaccessible with PFA fixation. These results highlight the need for optimization of fixation protocols depending on the target epitope and model system, emphasizing the importance of methodological considerations in biological analyses.

Efficient production of fluorophore-labeled CC chemokines for biophysical studies using recombinant enterokinase and recombinant sortase

Chemokines are important immune system proteins, many of which mediate inflammation due to their function to activate and cause chemotaxis of leukocytes. An important anti-inflammatory strategy is therefore to bind and inhibit chemokines, which leads to the need for biophysical studies of chemokines as they bind various possible partners. Because a successful anti-chemokine drug should bind at low concentrations, techniques such as fluorescence anisotropy that can provide nanomolar signal detection are required. To allow fluorescence experiments to be carried out on chemokines, a method is described for the production of fluorescently labeled chemokines. First, a fusion-tagged chemokine is produced in Escherichia coli, then efficient cleavage of the N-terminal fusion partner is carried out with lab-produced enterokinase, followed by covalent modification with a fluorophore, mediated by the lab-produced sortase enzyme. This overall process reduces the need for expensive commercial enzymatic reagents. Finally, we utilize the product, vMIP-fluor, in binding studies with the chemokine binding protein vCCI, which has great potential as an anti-inflammatory therapeutic, showing a binding constant for vCCI:vMIP-fluor of 0.37 ± 0.006 nM. We also show how a single modified chemokine homolog (vMIP-fluor) can be used in competition assays with other chemokines and we report a Kd for vCCI:CCL17 of 14 μM. This work demonstrates an efficient method of production and fluorescent labeling of chemokines for study across a broad range of concentrations.

Enhancing oral bioavailability of Ca-DTPA by self double emulsifying drug delivery system (SDEDDS)

OBJECTIVE

BCS class III drug (highly soluble, poorly permeable) possesses low oral bioavailability. The research work highlights the utility of self-double emulsifying drug delivery system (SDEDDS) which are stable isotropic mixture of w/o primary emulsion and hydrophilic surfactants for improving oral bioavailability of Ca-DTPA (Calcium diethylenetriamine pentaacetate). Upon oral administration, SDEDDS rapidly emulsifies into w/o/w double emulsions in the aqueous gastrointestinal environment, with hydrophilic drugs entrapped inside oil reservoirs.

METHODS

SDEDDS formulation was successfully developed using excipients, that is, medium chain triglycerides, oleic acid, phospholipids, Span 80, Tween 80 using double emulsification technique.

RESULTS

The optimized formulation F4 (Aq. phase: 11.6%w,w; MCT & oleic acid: 70.9%w/w; Span 80:17.5%w/w; Lecithin:16%w/w and Tween 80 (10%w/w)) appeared bright yellow liquid which upon dilution appeared milky white within 2 min, droplet size (501.7 nm), pdi value (0.044), zeta potential (-52 mV), entrapment efficiency (79.6 ± 1.63), viscosity (72.2 ± 1.8 mpA.s), significant high cumulative in vitro drug permeation (CDP) and 2.17-fold increase in apparent permeability coefficient. Pharmacokinetic studies in rats showed 1.17-fold increases in AUC of F4 and comparatively higher plasma levels (Cmax) compared with pure drug administered orally. The Absolute (OF4, OD) and Relative bioavailability was found to be 14.52%, 12.35%, and 117.47%, respectively.

CONCLUSION

The present studies have clearly demonstrated that SDEDDS could readily form w/o/w double emulsions in vivo with enhanced in vitro and in vivo oral bioavailability. Therefore, considerable augmentation in the rate and extent of oral drug absorption ratified the better performance of the SDEDDS in enhancing the bioavailability of Ca-DTPA.

Extraction of Proteins from Soil

Soil metaproteomics could explore the proteins involved in life activities and their abundance in the soils to overcome the difficulty in pure cultures of soil microorganisms and the limitations of proteomics of pure cultures. However, the complexity and heterogeneity of soil composition, the low abundance of soil proteins, and the presence of massive interfering substances (including humic compounds) generally lead to an extremely low extraction efficiency of soil proteins. Therefore, the efficient extraction of soil proteins is a prerequisite and bottleneck problem in soil metaproteomics. In this chapter, a soil protein extraction method suitable for most types of soils with low cost and enabling simple operation (about 150 μg protein can be extracted from 5.0 g soil) is described. The quantity and purity of the extracted soil proteins could meet the requirements for further analysis using routine mass spectrometry-based proteomics.

Stability Studies of Kynurenine Pathway Metabolites in Blood Components Define Optimal Blood Processing Conditions

The kynurenine pathway (KP) is the main pathway of tryptophan (TRP) metabolism that generates energy for multiple cellular processes. The activity of this pathway has been shown to be dysregulated in multiple human diseases. The resultant modulation of metabolites has been suggested to comprise biomarkers to track disease progression or could identify new therapeutic targets. While metabolite changes can be measured readily in blood, there is limited knowledge on the effect of blood matrices and sample processing time may have on the stability of KP metabolites. Understanding the stability of KP metabolites in blood is integral to obtaining accurate KP data to correlate with clinical pathology. Hence, the aim of this study was to assess the concentration of KP metabolites in matched whole blood, plasma and serum. The impact of pre-analytical sample processing time in the various blood matrices was also analysed. Serum and plasma had the higher concentration of KP metabolites compared to whole blood. Furthermore, concentrations of KP metabolites declined when the collected blood was processed after 24 hours storage at 4°C. Our study shows that that type of blood matrix and the time to processing have an impact on the stability of the KP metabolites. Serum or plasma are the preferred choice of matrix and the isolation of these matrices from whole blood is best performed immediately after collection for optimal analytical KP data.

CogiTx1: A novel subtilisin A inhibitor isolated from the sea anemone Condylactis gigantea belonging to the defensin 4 protein family

Subtilisin-like enzymes are recognized as key players in many infectious agents. In this context, its inhibitors are very valuable molecular lead compounds for structure based drug discovery and design. Marine invertebrates offer a great source of bioactive molecules, including protease inhibitors. In this work, we describe a new subtilisin inhibitor, from the sea anemone Condylactis gigantea (CogiTx1). CogiTx1 was purified using a combination of cation exchange chromatography, size exclusion chromatography and RP-HPLC chromatography. CogiTx1 it is a protein with 46 amino acid residues, with 4970.44 Da and three disulfide bridges. Is also able to inhibit subtilisin-like enzymes and pancreatic elastase. According to the amino acid sequence, it belongs to the defensin 4 family of proteins. The sequencing showed that CogiTx1 has an amidated C-terminal end, which was confirmed by the presence of the typical -XGR signal for amidation in the protein sequence deduced from the cDNA. This modification was described at protein level for the first time in this family of proteins. CogiTx1 is the first subtilisin inhibitor from the defensin 4 family and accordingly it has a folding consisting primarily in beta-strands in agreement with the analysis by CD and 3D modelling. Therefore, future in-depth functional studies may allow a more detailed characterization and will shed light on structure-function properties.

Ganoderma lucidum Mycelia Mass and Bioactive Compounds Production through Grape Pomace and Cheese Whey Valorization

Numerous compounds obtained from the medicinal mushroom Ganoderma lucidum have evidenced renowned bioactive characteristics. Controlled fermentation to generate fungal mycelia confers several advantages, specifically when the valorization of agro-industrial streams as fermentation feedstocks is included. Submerged fermentation of a newly isolated Greek strain of G. lucidum was performed using conventional synthetic media and, also, grape pomace extract (GPE) and cheese whey permeate (CWP) under static and shaking conditions. Under shaking conditions, maximum biomass with GPE and supplementation with organic nitrogen reached 17.8 g/L. The addition of an elicitor in CWP resulted in a significant improvement in biomass production that exceeded synthetic media. Overall, agitation demonstrated a positive impact on biomass productivity and, therefore, on process optimization. Crude intracellular and extracellular polysaccharides were extracted and evaluated regarding antioxidant activity and polysaccharide and protein content. FTIR analysis confirmed the preliminary chemical characterization of the crude extracts. This study introduces the design of a bioprocessing scenario to utilize food industry by-products as onset feedstocks for fungal bioconversions to obtain potential bioactive molecules within the concept of bioeconomy.

The effect of manipulating glucuronic acid biosynthetic pathway in Bacillus subtilis strain on hyaluronic acid production

Hyaluronic acid (HA), composed of glucuronic acid (GlcUA) and N-acetyl glucoseamine (GlcNAc), is a versatile biopolymer with high commercial value and innumerous physiological roles and pharmaceutical applications. The hasA gene has main role in HA biosynthesis by Streptococcus strain as a natural producer. The hasB and hasC genes are also mediate GlcUA precursor biosynthesis. In the present study, S. equisimilis hasA gene; B. subtilis tuaD and gtaB genes for GlcUA precursors enhancement, and vgb gene coding bacterial hemoglobin as an oxygen provider were used to construct the B. subtilis strain for HA production. RBSHA (hasA), RBSHA2 (hasA/tuaD/gtaB), and RBSHA3 (hasA/tuaD/gtaB/vgb) strains were developed and confirmed through genotype and phenotype analysis. After HA production and purification, FTIR spectroscopy confirmed the produced HA structures. HA assay showed the highest HA titer for RBSHA3 (2.1 ± 0.18 mg/ml) and then RBSHA2 (1.9 ± 0.03 mg/ml), and RBSHA (0.6 ± 0.14 mg/ml). Statistical analysis indicated there is no significant difference in HA titer between RBSHA2 and RBSHA3 strains (p-value > 0.05), however, these strains produced HA approximately 4-fold higher than that of RBSHA strain. Agarose gel electrophoresis showed the same molecular weight (< 30 kDa) of produced HA by strains. Dynamic light scattering (DLS) revealed all HA polymers had a relatively low polydispersity index (PDI < 0.5). These findings demonstrate the successful GlcUA biosynthetic pathway engineering strategy in improving HA yield by recombinant B. subtilis, metabolically-robust, and industrially potential strain.

High-throughput quantitation of serological dimethylarginines by LC/MS/MS: Potential cardiovascular biomarkers for rheumatoid arthritis

Rheumatoid arthritis (RA) is a chronic autoimmune disorder characterized by systemic inflammation of the joints and extra-articular tissues. The incidence of cardiovascular disease (CVD) remains the main cause of morbidity and mortality in patients with RA. Despite the development of new therapeutics targeting the articular manifestations, the relief of the cardiovascular burden is still an unmet medical need during the management of RA. So, the early prognosis of RA-associated CVD plays a crucial role in improving the clinical outcomes of RA patients. Recently, circulating dimethylarginines have gained attention as potential biomarkers for CVDs. Here, we present the development and validation of a high-throughput liquid chromatography-tandem mass spectrometric (LC/MS/MS) method for simultaneous quantification of creatinine, arginine, and dimethylarginines in human serum within 2 mins by isotope dilution mass spectrometry. This method employed a protein precipitation method for rapid sample preparation, trichloroacetic acid (TCA)-based ion pairing chromatography for fast analyte separation, and multiple reaction monitoring (MRM) with stable isotope-labeled internal standards (ISs) for simultaneous quantitation. To assure the quality, our method was validated against the FDA guidelines for lower limit of quantitation (0.2 µM), linearity (square of coefficient correlation>0.99), precision (intra-&inter-assay imprecision < 10 %), accuracy (intra-&inter-assay inaccuracy < 10 %), sample preparation recovery (recovery ≥ 90 %), stability (instability < 10 %), matrix effect (signal suppression < 55 %), and carryover ( < 0.01 %). Afterward, we applied the validated method to a retrospective cross-sectional study. We aimed to evaluate the utility of serological dimethylarginines as potential cardiovascular biomarkers in the development of RA-associated CVD. Our results revealed that the serological ratio of asymmetric dimethylarginine (ADMA) and symmetric dimethylarginine (SDMA), an indicator of physiological arginine methylation status, was significantly elevated in patients with RA. This finding might provide value in detecting CVD to improve clinical outcomes in RA management.

Solid phase extraction as sample pretreatment method for top-down quantitative analysis of low molecular weight proteins from biological samples using liquid chromatography - triple quadrupole mass spectrometry

Targeting and quantifying intact proteins from biological samples is still a very challenging research area. Several crucial steps exist in the analytical workflow, including development of a reliable sample preparation method. Here, we developed and applied for the first time a non-immunoaffinity sample preparation method based on a generally widely available micro-elution solid phase extraction (μSPE) strategy for the extraction of multiple lower molecular weight intact proteins (<30 kDa) from various biological matrices. Omission of a time-consuming drying and reconstitution step after extraction resulted in a more simple and rapid sample preparation procedure. A model set of eleven intact proteins (molecular weights: 5.5-29 kDa; isoelectric points: 4.5-11.3) were analyzed in multiple biological fluids using reversed-phase liquid chromatography with a triple quadrupole mass spectrometer operated in multiple reaction monitoring mode. Various sample pre-treatment reagents, sorbent types, and washing and elution solvents were experimentally tested and optimized to obtain the μSPE clean-up condition for a broad mixture of intact proteins having variable physicochemical properties. 1% trifluoroacetic acid and 0.2% Triton 100-X were selected as suitable sample pre-treatment reagents for releasing protein-protein interactions in human serum/plasma and human urine, respectively. Hydrophilic lipophilic balanced μSPE sorbent was selected as a high performing stationary phase. Addition of 1% trifluoroacetic acid to all washing and elution solutions showed the most beneficial effect for the extraction recovery of the proteins. Under the optimized conditions, reproducible extraction recoveries >65% for all targeted proteins (up to 30 kDa) in human urine and >50% for most of the proteins in serum/plasma were achieved. The selected conditions were applied also for the analysis of clinical serum and urine samples to demonstrate the feasibility of the developed method to target intact proteins directly by more affordable μSPE sample preparation and triple quadrupole mass spectrometry, which could be beneficial in many application fields.

A simple method to purify intrinsically disordered proteins by adjusting trichloroacetic acid concentration

Late embryogenic abundant proteins (LEA) are a group of proteins that accumulate during the desiccation phase of the seed and in response to water deficit in the plant. Most LEA proteins are highly hydrophilic and have physicochemical characteristics similar to those of intrinsically disordered proteins (IDPs). Although the function of LEA proteins is not fully understood, there is evidence indicating that these proteins have an important role in reducing the effects caused by water limitation. The analysis of the biochemical and physicochemical characteristics of LEA proteins is crucial to determine their function, for which it is necessary to obtain large amounts of pure protein. Within this current work, we have improved our previous TCA purification method used for basic recombinant LEA proteins to obtain acidic IDPs, the method reported here is fast and simple and is based on the enrichment of the protein of interest by boiling of the bacterial extract followed by a precipitation with different concentrations of TCA and salt. This protocol was applied to acidic and basic IDPs, represented by eight recombinant LEAs, resulting in milligram quantities of highly enriched proteins, which keep their in vitro functionality.

TRICIN: A Phase II Trial on the Efficacy of Topical TRIchloroacetic Acid in Patients with Cervical Intraepithelial Neoplasia

Data on non-surgical treatment approaching persistent cervical intraepithelial neoplasia (CIN) are scarce. Retrospective analysis suggest high efficacy of topical treatment with trichloroacetic acid (TCA). This prospective phase II study set out to investigate the efficacy of a single application of 85% TCA in the treatment of CIN I/II. Patients with CIN I/II were treated a single time with 85% TCA. After three and six months colposcopic, histologic, and HPV evaluation was performed. The primary endpoint was treatment efficacy defined as complete histologic remission six months after treatment. The secondary endpoint was HPV clearance six months after treatment. A total of 102 patients with CIN I/II were included into this trial. Complete histologic remission rates were 75.5% and 78.4% three and six months after TCA treatment, respectively. Clearance rates of HPV 16, 18 and other high risk types were 76.5%, 91.7%, 68.7% after six months, respectively. Side effects of TCA were mild and lasted usually less than 30 min. This is the first prospective trial reporting high histologic complete remission rates in patients with CIN I/II after a single 85% TCA treatment. In the future, TCA may represent an effective and feasible non-surgical treatment approach for CIN.

Study on Tissue Homogenization Buffer Composition for Brain Mass Spectrometry-Based Proteomics

Mass spectrometry-based proteomics aims to study the proteome both qualitatively and quantitatively. A key step in proteomic analysis is sample preparation, which is crucial for reliable results. We investigated the effect of the composition of the homogenization buffer used to extract proteins from brain tissue on the yield of protein extraction and the number and type of extracted proteins. Three different types of buffers were compared—detergent-based buffer (DB), chaotropic agent-based buffer (CAB) and buffer without detergent and chaotropic agent (DFB). Based on label-free quantitative protein analysis, detergent buffer was identified as the most suitable for global proteomic profiling of brain tissue. It allows the most efficient extraction of membrane proteins, synaptic and synaptic membrane proteins along with ribosomal, mitochondrial and myelin sheath proteins, which are of particular interest in the field of neurodegenerative disorders research.

A heterotypic assembly mechanism regulates CHIP E3 ligase activity

CHIP (C-terminus of Hsc70-interacting protein) and its worm ortholog CHN-1 are E3 ubiquitin ligases that link the chaperone system with the ubiquitin-proteasome system (UPS). CHN-1 can cooperate with UFD-2, another E3 ligase, to accelerate ubiquitin chain formation; however, the basis for the high processivity of this E3s set has remained obscure. Here, we studied the molecular mechanism and function of the CHN-1-UFD-2 complex in Caenorhabditis elegans. Our data show that UFD-2 binding promotes the cooperation between CHN-1 and ubiquitin-conjugating E2 enzymes by stabilizing the CHN-1 U-box dimer. However, HSP70/HSP-1 chaperone outcompetes UFD-2 for CHN-1 binding, thereby promoting a shift to the autoinhibited CHN-1 state by acting on a conserved residue in its U-box domain. The interaction with UFD-2 enables CHN-1 to efficiently ubiquitylate and regulate S-adenosylhomocysteinase (AHCY-1), a key enzyme in the S-adenosylmethionine (SAM) regeneration cycle, which is essential for SAM-dependent methylation. Our results define the molecular mechanism underlying the synergistic cooperation of CHN-1 and UFD-2 in substrate ubiquitylation.

Trichloroacetic acid fueled practical amine purifications

Amine purification have for long been dominated by tedious stepwise processes involving the generation of large amounts of undesired waste. Inspired by recent work on out of equilibrium molecular machinery, using trichloroacetic acid (TCA), we disclose a purification technique considerably decreasing the number of operations and the waste generation required for such purifications. At first, TCA triggers the precipitation of the amines through their protonated salt formation, enabling the separation with the impurities. From these amine salts, simple decarboxylation of TCA liberates volatile CO2 and chloroform affording directly the pure amines. Through this approach, a broad range of diversely substituted amines could be isolated with success.

On-line 'protein shaker': A multicommutated flow analysis system for fluorometric creatinine determination in deproteinized serum

A fully mechanized multicommutated flow analysis (MCFA) system for fluorometric determination of creatinine in serum samples is introduced in this paper. The flow system was constructed with microsolenoid pumps and valves and with a 3D-printed flow cell. Fluorometric assay relied on creatinine reaction with 3,5-dinitrobenzoic acid and hydrogen peroxide in an alkaline environment. To overcome significant interference from protein, a flow reactor for serum deproteinization was designed and implemented in the flow system. The deproteinization was carried out by precipitation with trichloroacetic acid and the addition of sodium chloride facilitated the precipitate sedimentation. The supernatant representative sample was pumped out and subjected to fluorometric creatinine assay. The obtained linear range was from 1.6 to 500 μmol L^-1 and the precision, expressed as RSD, was below 3%. The proposed MCFA system was used to determine creatinine concentration in control serum samples. The results obtained with flow deproteinization correlated well with results obtained with conventional deproteinization (y = (0.91 ± 0.09) x + (37 ± 28)) with Pearson's r 0.979.

Menthol-assisted homogenous liquid-liquid microextraction for HPLC/UV determination of favipiravir as an antiviral for COVID-19 in human plasma

Favipiravir is a promising antiviral agent that has been recently approved for treatment of COVID-19 infection. In this study, a menthol-assisted homogenous liquid–liquid microextraction method has been developed for favipiravir determination in human plasma using HPLC/UV. The different factors that could affect the extraction efficiency were studied, including extractant type, extractant volume, menthol amount and vortex time. The optimum extraction efficiency was achieved using 300 µL of tetrahydrofuran, 30 mg of menthol and vortexing for 1 min before centrifuging the sample for 5 min at 3467g. Addition of menthol does not only induce phase separation, but also helps to form reverse micelles to facilitate extraction. The highly polar favipiravir molecules would be incorporated into the hydrophilic core of the formed reverse micelle to be extracted by the non-polar organic extractant. The method was validated according to the FDA bioanalytical method guidelines. The developed method was found linear in the concentration range of 0.1 to 100 µg/mL with a coefficient of determination of 0.9992. The method accuracy and precision were studied by calculating the recovery (%) and the relative standard deviation (%), respectively. The recovery (%) was in the range of 97.1–103.9%, while the RSD (%) values ranged between 2.03 and 8.15 %. The developed method was successfully applied in a bioequivalence study of Flupirava® 200 mg versus Avigan® 200 mg, after a single oral dose of favipiravir administered to healthy adult volunteers. The proposed method was simple, cheap, more eco-friendly and sufficiently sensitive for biomedical application.

Interaction of proteins and amino acids with iso-α-acids during wort preparation in the brewhouse

This paper investigates the binding behavior of iso-α-acids from hops on free wort amino acids and proteins concerning the wort production process in breweries. The studies were carried out with different amino acids, bovine serum albumin and wort. To identify the nature of reaction between iso-α-acids and these substances, analyses of free amino nitrogen, HPLC and isothermal titration calorimetry were performed. According to the results, the iso-α-acids do not form covalent bonds with free amino acids of wort. However, iso-α-acids, especially isohumulone and isoadhumulone, form ionic bonds with wort proteins. A distinction must be made between proteins that are present in the hot trub, and those that are still dissolved in the hot wort. Proteins that are already coagulated and precipitated no longer react with iso-α-acids. Future experiments will investigate whether the established ionic bonds between iso-α-acids and proteins from the wort preparation process are maintained during fermentation until the finished beer or beer foam. If this is the case, which is induced by the experiments, there is a measurable loss of iso-α-acids in the hot wort, but at the same time, a gain for the later beer foam retention, as the iso-α-acids will stabilize it.

Latest Advances in Protein-Recovery Technologies from Agricultural Waste

In recent years, downstream bioprocessing industries are venturing into less tedious, simple, and high-efficiency separation by implementing advanced purification and extraction methods. This review discusses the separation of proteins, with the main focus on amylase as an enzyme from agricultural waste using conventional and advanced techniques of extraction and purification via a liquid biphasic system (LBS). In comparison to other methods, such as membrane extraction, precipitation, ultrasonication, and chromatography, the LBS stands out as an efficient, cost-effective, and adaptable developing method for protein recovery. The two-phase separation method can be water-soluble polymers, or polymer and salt, or alcohol and salt, which is a simpler and lower-cost method that can be used at a larger purification scale. The comparison of different approaches in LBS for amylase purification from agricultural waste is also included. Current technology has evolved from a simple LBS into microwave-assisted LBS, liquid biphasic flotation (LBF), thermoseparation (TMP), three-phase partitioning (TPP), ultrasound-assisted LBS, and electrically assisted LBS. pH, time, temperature, and concentration are some of the significant research parameters considered in the review of advanced techniques.

Genotoxicity of advanced glycation end products in vitro is influenced by their preparation temperature, purification, and cell exposure time

Advanced glycation end products (AGEs) are formed via non-enzymatic reactions between amino groups of proteins and the carbonyl groups of reducing sugars. Previous studies have shown that highly glycated albumin prepared using a glucose-bovine serum albumin (Glu-BSA) model system incubated at 60°C for 6 weeks induces genotoxicity in WIL2-NS cells at 9 days of exposure measured by the cytokinesis-block micronucleus cytome (CBMNcyt) assay. However, this AGE model system is not physiologically relevant as normal body temperature is 37°C and the degree of glycation may exceed the extent of albumin modification in vivo. We hypothesised that the incubation temperature and purification method used in these studies may cause changes to the chemical profile of the glycated albumin and may influence the extent of genotoxicity observed at 3, 6 and 9 days of exposure. We prepared AGEs generated using Glu-BSA model systems incubated at 60°C or 37°C purified using trichloroacetic acid (TCA) precipitation or ultrafiltration (UF) and compared their chemical profile (glycation, oxidation, and aggregation) and genotoxicity in WIL2-NS cells using the CBMNcyt assay after 3, 6, and 9 days of exposure. The number of micronuclei (MNi) was significantly higher for cells treated with Glu-BSA incubated at 60°C and purified via TCA (12 ± 1 MNi/1000 binucleated cells) compared to Glu-BSA incubated at 37°C and purified using UF (6 ± 1 MNi/1000 binucleated cells) after 9 days (p < 0.0001). The increase in genotoxicity observed could be explained by a higher level of protein glycation, oxidation, and aggregation of the Glu-BSA model system incubated at 60°C relative to 37°C. This study highlighted that the incubation temperature, purification method and cell exposure time are important variables to consider when generating AGEs in vitro and will enable future studies to better reflect in vivo situations of albumin glycation.

Metaproteomic Insights Into the Microbial Community in Pozol

Pozol is an acidic, refreshing, and non-alcoholic traditional Mayan beverage made with nixtamalized corn dough that is fermented spontaneously. The extensive analysis of the microbiology, biochemistry and metaproteomics of pozol allowed the construction of a comprehensive image of the fermentation system. The main changes in both the substrate and the microbiota occurred in the first 9 h of fermentation. The increase in microorganisms correlated with the drop in pH and with the decrease in the contents of carbohydrates, lipids, and nitrogen, which shows that this stage has the highest metabolic activity. Bacterial proteins were mainly represented by those of lactic acid bacteria, and among them, the proteins from genus Streptococcus was overwhelmingly the most abundant. Yeast proteins were present in all the analyzed samples, while proteins from filamentous fungi increased up to 48 h. The metaproteomic approach allowed us to identify several previously unknown enzyme complexes in the system. Additionally, enzymes for hydrolysis of starch, hemicellulose and cellulose were found, indicating that all these substrates can be used as a carbon source by the microbiota. Finally, enzymes related to the production of essential intermediates involved in the synthesis of organic acids, acetoin, butanediol, fatty acids and amino acids important for the generation of compounds that contribute to the sensorial quality of pozol, were found.

Potential role of lysine succinylation in the response of moths to artificial light at night stress

Artificial light at night (ALAN) is a widespread environmental pollutant and stressor. Many nocturnal insects have been shown to experience ALAN stress. However, few studies have been conducted to uncover the mechanism by which nocturnal insects respond to ALAN stress. Previous studies suggest that lysine succinylation (Ksuc) is a potential mechanism that coordinates energy metabolism and antioxidant activity under stressful conditions. Mythimna separata (Walker) (M. separata) is a nocturnal insect that has been stressed by ALAN. In this study, we quantified the relative proteomic Ksuc levels in ALAN-stressed M. separata. Of the 466 identified Ksuc-modified proteins, 103 were hypersuccinylated/desuccinylated in ALAN-stressed moths. The hypersuccinylated/desuccinylated proteins were shown to be involved in various biological processes. In particular, they were enriched in metabolic processes, reactive oxygen species (ROS) homeostasis and the neuromuscular system. Furthermore, we demonstrated that Ksuc might affect moth locomotion by intervening with and coordinating these systems under ALAN stress. These findings suggest that Ksuc plays a vital role in the moth response to ALAN stress and moth locomotion behavior and provide a new perspective on the impact of ALAN on nocturnal insect populations and species communities.

In vitro protein and starch digestion kinetics of individual chickpea cells: from static to more complex in vitro digestion approaches

Attention has been given to more (semi-)dynamic in vitro digestion approaches ascertaining the consequences of dynamic in vivo aspects on in vitro digestion kinetics. As these often come with time and economical constraints, evaluating the consequence of stepwise increasing the complexity of static in vitro approaches using easy-to-handle digestion set-ups has been the center of our interest. Starting from the INFOGEST static in vitro protocol, we studied the influence of static gastric pH versus gradual gastric pH change (pH 6.3 to pH 2.5 in 2 h) on macronutrient digestion in individual cotyledon cells derived from chickpeas. Little effect on small intestinal proteolysis was observed comparing the applied digestion conditions. Contrary, the implementation of a gradual gastric pH change, with and without the addition of salivary α-amylase, altered starch digestion kinetics rates, and extents by 25%. The evaluation of starch and protein digestion, being co-embedded in cotyledon cells, did not only confirm but account for the interdependent digestion behavior. The insights generated in this study demonstrate the possibility of using a hypothesis-based approach to introduce dynamic factors to in vitro models while sticking to simple and cost-efficient set-ups.

Comparative Analysis of Universal Protein Extraction Methodologies for Screening of Lipase Activity from Agricultural Products

Protein extraction techniques are absolutely required for the research of biological catalysts. The present study compared four universal protein extraction methodologies (ammonium sulfate precipitation, TCA/acetone precipitation, and two commercial kits) to provide practical information on protein extraction in order to discover a novel lipase in agricultural products. Yields of protein extraction from 24 domestic agricultural products and their specific activities were evaluated and compared with each other. TCA/acetone precipitation showed a relatively higher extraction yield (on average, 3.41 ± 1.08 mg protein/0.1 g sample) in crude protein extraction, whereas the Pierce™ Plant Total Protein Extraction Kit showed the highest specific lipase activity on average in both spectrophotometric (266.61 ± 235.78 μU/mg protein) and fluorometric (41.52 ± 32.63 μU/mg protein) assays. Our results suggest that commercial kits for the rapid extraction of soluble functional proteins would be a better choice than conventional precipitation techniques to perform the high-throughput screening of enzyme activity from plant sources. Finally, several agricultural products such as cordyceps, pepper, bracken, and hemp, all of which exhibited an excellent specific lipase activity, were proposed as promising candidates for a source of novel lipases.

Simplification of the purification of heat stable recombinant low molecular weight proteins and peptides from GST-fusion products

The synthesis and purification of peptides of importance in the fields of research and medicine continue to be a challenging task. Chemical synthesis of oligopeptides, especially those greater than 25 amino acids, is cost prohibitive. On the other hand, several bottlenecks exist in the production of recombinant short peptides in heterologous expression hosts such as Escherichia coli (E. coli). In this study, a rapid, cost-effective, and reliable method for the production and single-step-purification of peptides and small proteins was developed. Five peptides and small proteins were overexpressed in E. coli as GST-fusion products in high yields. The recombinant peptides or proteins were successfully purified after enzymatic cleavage with selective heat-induced precipitation of the GST-affinity tag. Qualitative and quantitative analysis using SDS-PAGE and mass spectrometric methods suggest that the recombinant peptides/ proteins were purified to greater than 95% homogeneity. Results of biophysical experiments, including multi-dimensional NMR spectroscopy, show that the purified proteins/ peptides retain their native conformation. Isothermal titration calorimetry studies indicate no significant change in the binding affinity of the heat-treated purified product to their interacting partner(s) compared to the recombinant peptides purified by conventional chromatographic procedures without subjecting to heat treatment. In our opinion, the results reported render the purification of recombinant proteins/ peptides of biomedical relevance using our proposed method easy and reliable.

A method to improve quantitative radiotracing-based analysis of the in vivo biodistribution of drug carriers

Biodistribution studies are essential in drug carrier design and translation, and radiotracing provides a sensitive quantitation for this purpose. Yet, for biodegradable formulations, small amounts of free-label signal may arise prior to or immediately after injection in animal models, causing potentially confounding biodistribution results. In this study, we refined a method to overcome this obstacle. First, we verified free signal generation in animal samples and then, mimicking it in a controllable setting, we injected mice intravenously with a radiolabeled drug carrier formulation (125I-antibody/3DNA) containing a known amount of free radiolabel (125I), or free 125I alone as a control. Corrected biodistribution data were obtained by separating the free radiolabel from blood and organs postmortem, using trichloroacetic acid precipitation, and subtracting the confounding signal from each tissue measurement. Control free 125I-radiolabel was detected at ≥85% accuracy in blood and tissues, validating the method. It biodistributed very heterogeneously among organs (0.6-39 %ID/g), indicating that any free 125I generated in the body or present in an injected formulation cannot be simply corrected to the free-label fraction in the original preparation, but the free label must be empirically measured in each organ. Application of this method to the biodistribution of 125I-antibody/3DNA, including formulations directed to endothelial target ICAM-1, showed accurate classification of free 125I species in blood and tissues. In addition, this technique rendered data on the in vivo degradation of the traced agents over time. Thus, this is a valuable technique to obtain accurate measurements of biodistribution using 125I and possibly other radiotracers.

Nanobody-Based Quantification of GTP-Bound RHO Conformation Reveals RHOA and RHOC Activation Independent from Their Total Expression in Breast Cancer

As key regulators of the actin cytoskeleton, RHO GTPase expression and/or activity are deregulated in tumorigenesis and metastatic progression. Nevertheless, the vast majority of experiments supporting this conclusion was conducted on cell lines but not on human tumor samples that were mostly studied at the expression level only. Up to now, the activity of RHO proteins remains poorly investigated in human tumors. In this article, we present the development of a robust nanobody-based ELISA assay, with a high selectivity that allows an accurate quantification of RHO protein GTP-bound state in the nanomolar range (1 nM; 20 μg/L), not only in cell lines after treatment but also in tumor samples. Of note, we present here a fine analysis of RHOA-like and RAC1 active state in tumor samples with the most comprehensive study of RHOA-GTP and RHOC-GTP levels performed on human breast tumor samples. We revealed increased GTP-bound RHOA and RHOC protein activities in tumors compared to normal tissue counterparts, and demonstrated that the RHO active state and RHO expression are two independent parameters among different breast cancer subtypes. Our results further highlight the regulation of RHO protein activation in tumor samples and the relevance of directly studying RHO GTPase activities involvement in molecular pathways.

Bioanalysis of plasma acetate levels without derivatization by LC-MS/MS

Background: The acetate ion has important physiological functions and important therapeutic applications. A rapid LC-MS/MS method is described to measure acetate ions in human plasma without chemical derivatization. Materials & methods: A 200 μl sample was spiked with the internal standard 1,2-¹³C-acetate and proteins precipitated with trichloroacetic acid. The supernatant was recovered and separated under acidic conditions on a C18-column. The eluent was alkalinized by post-column infusion of methanolic ammonium hydroxide. Acetate ions were monitored on a low resolution mass spectrometer in negative ion mode. Results: Method was validated for accuracy and precision with a lower limit of quantitation of 9.7 μM and linear dynamic range up to 339.6 μM. Conclusion: The method is open for analytical improvement and adapts with metabolomic and pharmacometabolomic studies on chemicals of similar nature.

New procedure for separation and analysis of the main components of cyanobacterial EPS

Phototrophic biofilms produce a matrix of extracellular polymeric substances (EPS), which holds the cells together and functions inter alia as nutrient storage and protection layer. EPS mainly consist of water, polysaccharides, proteins, lipids and nucleic acids as well as lysis and hydrolysis products which makes the composition very complex. Thus, rough simplifications are used and commonly one or at most two components of the EPS are examined. In this work a new procedure for separation and analysis of EPS in the main components (i) polysaccharides, (ii) proteins and (iii) lipids is presented with recovery rates of nearly 100 %. The method was established with synthetic EPS, which based on the composition of real EPS described in literature. Afterwards, the method was transferred to real EPS samples allowing a deeper insight in the composition of EPS from only one sample. The composition of EPS-extracts from Nostoc spec, cultivated under heterotrophic and mixotrophic batch and fed-batch conditions, was analysed during a cultivation period of 14 days. It was observed that mixotrophic cultivation led to higher amounts of carbohydrates, lipids and proteins than heterotrophic cultivation respectively, regardless of batch or fed-batch culture. While the amount of proteins in the EPS increased during the cultivation period, carbohydrates and lipids were dominant in the beginning and decreased afterwards.

Characterization of glycan determinants that mediate recognition of the major Wuchereria bancrofti circulating antigen by diagnostic antibodies

The Global Program to Eliminate Lymphatic Filariasis (GPELF) relies heavily on a rapid diagnostic test (RDT) to a Wuchereria bancrofti circulating filarial antigen (Wb-CFA) to identify endemic areas and for determining when mass drug administration can stop. The antigen contains a carbohydrate epitope that is recognized by monoclonal antibody AD12. Og4C3, a monoclonal antibody that is used in a commercial ELISA for Wb-CFA recognizes the same moiety. Despite its diagnostic importance, little is known about the structure and function of this "AD12 epitope". It is also present on other W. bancrofti glycoproteins and on glycoproteins of other filarial worms, but such antigens are not detected in the sera of individuals with most other filarial infections. We report here functional and biochemical analyses that shed light on the interaction between filarial glycoproteins and AD12 and/or Og4C3. Binding of these monoclonal antibodies to a mammalian glycan array suggests the reactive moiety has structural similarity to terminal β-d-glucuronic acid in a 1-3 linkage to other hexoses. However, sera collected from individuals with patent W. bancrofti infection had very low or undetectable serum antibodies to the GlcA-containing array glycans. Unlike other filarial glycoproteins, the Wb-CFA is relatively resistant to protease digestion by pronase and trypsin and completely resistant to the mucinase O-sialoglycoprotein endopeptidase (OSGE). The protease resistance of the Wb-CFA may contribute to its consistent detection in Wb-infected sera.

Systematic examination of protein extraction, proteolytic glycopeptide enrichment and MS/MS fragmentation techniques for site-specific profiling of human milk N-glycoproteins

Human milk contains numerous N-glycoproteins with functions that provide protection to the infant. Increasing understanding of the functional role of human milk glycoproteins within the infant requires toolsets to comprehensively profile their site-specific glycosylation patterns. However, optimized methods for site-specific glycosylation analysis across the entire human milk proteome are not available. Therefore, we performed a systematic analysis of techniques for profiling the sites and compositions of N-glycans in human milk using liquid chromatography/mass spectrometry. To decrease interference from non-target molecules, we compared techniques for protein extraction, including ethanol (EtOH) precipitation, trichloroacetic acid precipitation, molecular weight cut-off filtration and techniques for tryptic glycopeptide enrichment, including C18-, porous graphitized carbon and hydrophilic interaction liquid chromatography (HILIC)-solid phase extraction (SPE) and acetone precipitation. We compared the capacity of higher-energy collision dissociation, electron-transfer dissociation and electron-transfer/higher-energy collision dissociation (EThcD) to produce fragment ions that would enable effective identification of the glycan composition, peptide sequence and glycosylation site. Of these methods, a combination of EtOH precipitation, HILIC-SPE and EThcD-fragmentation was the most effective for human milk N-glycopeptide profiling. This optimized approach significantly increased the number of N-glycopeptides and precursor N-glycoproteins (246 N-glycopeptides from 29 glycoproteins) compared with a more common extraction approach with no protein extraction and C18 clean-up (62 N-glycopeptides from 11 glycoproteins). The advancement in methods for human milk N-glycoproteins provided by this study represents a key step for better understanding the function of glycoproteins within the breast milk-fed infant.

Analysis of multiple protein detection methods in human osteoporotic bone extracellular matrix: From literature to practice

The punctual analysis of bone Extracellular Matrix (ECM) proteins represents a pivotal point for medical research in bone diseases like osteoporosis. Studies in this field, historically done to appreciate bone biology, were mainly conducted on animal samples and, up to today, only a few studies on protein detection in human bone are present. The challenges in bone ECM protein extraction and quantitation protocols are related to both the separation of proteins from the mineral content (i.e. hydroxyapatite) and the difficulty of avoiding protein denaturation during the extraction processes. The aim of the present work was to define appropriate protocol(s) for bone ECM protein extraction that could be applied to investigate both normal and pathological conditions. We compared and optimised some of the most used protocols present in the literature, modifying the protein precipitation method, the buffer used for resuspension and/or the volume of reagent used. Bradford and BCA assays and Western Blotting were used to evaluate the variations in the total protein recovery and the amount of selected proteins (Type I Collagen, TGF-β, IGF-1, Decorin, Osteopontin, Bone Sialoprotein-2 and Osteocalcin). Collectively, we were capable to draw-up two single-extract protocols with optimal recovery and ideal protein content, that can be used for a detailed analysis of ECM proteins in pathological bone samples. Time-consuming multi-extract procedures, optimised in their precipitation methods, are however crucial for a precise detection of specific proteins, like osteocalcin. As the matter of fact, also the demineralization processes, commonly suggested and performed in several protocols, could hinder an accurate protein detection, thus inherently affecting the study of a pathological bone ECM. This study represents a starting point for the definition of appropriate strategies in the study of bone extracellular matrix proteins involved in the onset and maintenance of bone diseases, as well as a tool for the development of customized scaffolds capable to modulate a proper feedback loop in bone remodelling, altered in case of diseases like osteoporosis.

Production of Intrinsically Disordered Proteins for Biophysical Studies: Tips and Tricks

Intrinsically disordered proteins (IDPs) have no single, fixed tertiary structure, yet they take on many vital functions in biology. In recent years, considerable effort has been put into the structural characterization of their conformational ensembles, to understand the link between the transient, short- and long-range organizations of IDPs and their functions. Such biophysical studies require substantial amounts of pure protein, representing a major bottleneck in the studies of IDPs. However, the unique physicochemical properties resulting from their compositional bias may be exploited for simple yet effective purification strategies. In this chapter, we provide tips and tricks for IDP production and describe the most important analyses to carry out before bringing an IDP of interest to the laboratory. We outline four purification protocols utilizing the unique properties of IDPs as well as some commonly encountered challenges and pitfalls.