High-pressure microfluidisation positively impacts structural properties and improves functional characteristics of almond proteins obtained from almond meal

Almond protein isolate (API) obtained from almond meal was processed using dynamic high-pressure microfluidisation (0, 40, 80, 120, and 160 MPa pressure; single pass). Microfluidisation caused significant reductions in the particle size and increased absolute zeta potential. SDS-PAGE analysis indicated reduction in band intensity and the complete disappearance of bands beyond 80 MPa. Structural analysis (by circular dichroism, UV-Vis, and intrinsic-fluorescence spectra) of the API revealed disaggregation (up to 80 MPa) and then re-aggregation beyond 80 MPa. Significant increments in protein digestibility (1.16-fold) and the protein digestibility corrected amino acid score (PDCAAS; 1.15-fold) were observed for the API (80 MPa) than control. Furthermore, significant improvements (P < 0.05) in the functional properties were observed, viz., the antioxidant activity, protein solubility, and emulsifying properties. Overall, the results revealed that moderate microfluidisation treatment (80 MPa) is an effective and sustainable technique for enhancing physico-chemical and functional attributes of API, thus potentially enabling its functional food/nutraceuticals application.

"Exotic" seeds from Southern Africa as potential Novel Foods? - Chemical composition of manketti nuts (Schinziophyton rautanenii) and ushivi beans (Guibourtia coleosperma)

Various species of Southern African plants and their edible seeds have gained huge importance due to positive health aspects, and there is increasing interest to introduce such seeds as Novel Food on the international market. Especially the seeds of Schinziophyton rautanenii (manketti) and Guibourtia coleosperma (ushivi) could have great potential as a food and food ingredient. Hence, extensive analyses on the chemical composition of manketti nuts and ushivi beans including the analysis of total solids, protein and fat content, soluble carbohydrates, ash, total and free amino acids, biogenic amines and polyamines, fatty acid profile as well as the content of certain B-vitamins and tocopherols were performed. Results obtained showed a valuable nutritional composition, e.g., a true protein content of 22.6% with a ratio of essential amino acids to total amino acid composition of 48% in manketti nuts, while ushivi beans had a true protein content of 8.2% with a similar ratio of essential to total amino acids (45%). Lipid content was 54.1% in manketti nuts, ushivi beans had a value of 7.7%. In both, linoleic acid was the most abundant. Furthermore, ushivi beans had high amounts of vitamin B1 and B2.

Reversal of Valproate-Induced Major Salivary Gland Changes By Moringa Oleifera Extract in Rats

This study aimed to explore the potential protective impacts of Moringa oleifera extract on major alteration in salivary glands of rats exposed to sodium valproate (VA). Groups were defined as control, control+moringa extract, sodium valproate, and sodium valproate+moringa extract. Antioxidant and oxidant status, activities of digestive and metabolic enzymes were examined. VA treatment led to various biochemical changes in the salivary glands, including decreased levels of antioxidants like glutathione, glutathione-S-transferase, and superoxide dismutase (except for sublingual superoxide dismutase). Conversely, a decrease in alpha-amylase, alkaline and acid phosphatase, lactate dehydrogenase, protease, and maltase activities were observed. The study also demonstrated that VA induces oxidative stress, increases lipid peroxidation, sialic acid, and nitric oxide levels in the salivary glands. Total oxidant capacity was raised in all glands except in the sublingual gland. The electrophoretic patterns of proteins were similar. Moringa oleifera extract exhibited protective properties, reversing these VA-induced biochemical changes due to its antioxidant and therapeutic attributes. This research suggests that moringa extract might serve as an alternative treatment approach for individuals using VA and experiencing salivary gland issues, although further research is necessary to confirm these findings in human subjects.

An Evaluation of the Physicochemical Properties of Sesame Paste Produced by Ball Milling Compared against Conventional Colloid Milling

The physicochemical characteristics and general food quality were greatly impacted by milling. In order to investigate the effect of milling technique for physicochemical properties of sesame paste of sesame paste, samples were prepared using ball mill and colloid mill by varying grinding times. The samples prepared by ball milling had the higher moisture contents (0.07% - 0.14%) than colloid milling (p < 0.05), except for colloid milling for one cycle (0.11%). The particle size curves showed the multimodal distributions. Compared to colloid milled samples, ball milled samples have smaller particle sizes and more uniform particle distribution. The L* values of samples prepared by ball milling were higher than colloid milling. The ball mill produced sesame paste with a wider range of hardness and silkier texture, and the samples made by ball milling for 30 min had the highest hardness. And the hardness of both CMS and BMS showed a decreasing trend with increasing grinding time. During ball milling, high-speed cutting and collision caused breakage of disulfide bonds, and the sesame proteins were decomposed to their subunits. In conclusions, ball milling may be an alternative and promising process for the preparation of sesame paste.

Creating a novel genetic diversity of Trichoderma afroharzianum by γ-radiation for xylanase-cellulase production

Creating novel sources of a microbial strain using induced mutation can increase enzyme production for industrial use. According to this, we have developed a mutant strain of Trichoderma afroharzianum by Co60 gamma irradiation. Trichoderma mutants were isolated from an optimum dose of 250 Gy. The qualitative and quantitative screening were used for evaluating their enzyme production and the DNA barcoding method was used to identify the best Trichoderma mutant isolates. The highest cellulase (exo-glucanase, endoglucanase, β-glucosidase, and total cellulase) and xylanase activities were observed in superior mutant isolates of Trichoderma afroharzianum NAS107-M44 and Trichoderma afroharzianum NAS107-M82, which is approximately 1.6-2.5 times higher than its parent strain, respectively. The electrophoretic pattern of proteins showed that the exo-glucanase I, endo-glucanase III, and the xylanase I enzymes hydrolyzed the corn bran, synergistically. Overall, gamma irradiation-induced mutation could be an expedient technique to access such superior mutants for the bioconversion of corn bran wastes.

Whey protein dynamics in goat mammary secretions during colostrum and early lactation periods

The protein composition in goat milk undergoes changes throughout the different lactation periods, displaying distinct characteristics that are influenced by the dynamic nature of protein composition and concentration during the transition from colostrum secretion to mature milk. To evaluate the dynamics of whey proteins of Saanen goats during the colostral phase and the first month of lactation, 110 milk samples from 11 healthy mammary halves of seven Saanen goats were selected through a clinical evaluation. Whey was obtained by rennet coagulation of the mammary secretion. The biuret method determined total protein concentration, and their fractions were identified by 12% dodecyl sulfate-polyacrylamide gel electrophoresis. Maximum concentrations of all protein fractions were observed in the first 12 h of lactation, reducing throughout the study. Modification of the protein predominance was also observed. The transition from colostrum secretion to milk occurred 5 or 7 d postpartum.

Development of a fast and simple method for the isolation of superparamagnetic iron oxide nanoparticles protein corona from protein-rich matrices

The adsorption of proteins onto the surface of nanoparticle (NP) leads to the formation of the so-called "protein corona" as consisting both loosely and tightly bound proteins. It is well established that the biological identity of NPs that may be acquired after exposure to a biological matrix is mostly provided by the components of the hard corona as the pristine surface is generally less accessible for binding. For that reason, the isolation and the characterisation of the NP-corona complexes and identification of the associated biomolecules can help in understanding its biological behaviour. Established methods for the isolation of the NP-HC complexes are time-demanding and can lead to different results based on the isolation method applied. Herein, we have developed a fast and simple method using ferromagnetic beads isolated from commercial MACS column and used for the isolation of superparamagnetic NP following exposure to different types of biological milieu. We first demonstrated the ability to easily isolate superparamagnetic iron oxide NPs (IONPs) from different concentrations of human blood plasma, and also tested the method on the corona isolation using more complex biological matrices, such as culture medium containing pulmonary mucus where the ordinary corona methods cannot be applied. Our developed method showed less than 20% difference in plasma corona composition when compared with centrifugation. It also showed effective isolation of NP-HC complexes from mucus-containing culture media upon comparing with centrifugation and MACS columns, which failed to wash out the unbound proteins. Our study was supported with a full characterisation profile including dynamic light scattering, nanoparticle tracking analysis, analytical disk centrifuge, and zeta potentials. The biomolecules/ proteins composing the HC were separated by vertical gel electrophoresis and subsequently analysed by liquid chromatography-tandem mass spectrometry. In addition to our achievements in comparing different isolation methods to separate IONPs with corona from human plasma, this is the first study that provides a complete characterisation profile of particle protein corona after exposure in vitro to pulmonary mucus-containing culture media.

Keratin as an effective coating material for in vitro stem cell culture, induced differentiation and wound healing assays

The utilization of stem cells in tissue engineering holds great promise as efficient tools for tissue regeneration and in treating numerous musculoskeletal diseases. However, several limiting factors, such as precise delivery and control of differentiation of these stem cells as well as mimicking the microenvironment required to modulate stem cell behaviour in-vivo, have given rise to an urgent need for the development of new biomaterials which could be tailored to enhance cell renewal and/or direct cell fates. Keratin-rich biological materials offer several advantages, such as biocompatibility, tailorable mechanical properties, huge bioavailability, non-toxicity, non-immunogenic, and intrinsic tissue repair and/or regeneration capabilities, which makes them highly valued. In the present work, we report the preparation of keratin-based bio-materials from goat hair waste and its effectiveness as a coating material for in vitro culture and induced differentiation of mesenchymal stem cells (MSC's) and primary goat fibroblast cells. Since no known keratinase enzymes are expressed as such in human and/or animal systems, these keratin biomaterials could be used to slow the rate of degradation and deliver keratin-loaded stem cell scaffolds to induce their directed differentiation in vivo. The generated keratin materials have been characterized for surface morphology, protein structures, size and other properties using SDS-PAGE, LC/MS-MS, SEM, FTIR etc. Also, in vitro cell culture assays such as cell adhesion, viability using MTT, live dead assays, differentiation assays and in vitro scratch/wound healing assays were performed. Our results provide important data supporting tissue engineering applications of these keratinous biomaterials by combining the unique biological characteristics of goat hair-derived keratin material with the regenerative power of stem cells and their combinatorial use in applications such as disease treatment and injury repair as well as their use in the preparation of wound healing products, such as dressings and bandages, for management of clinical care in animals.

An efficient protocol for extracting thylakoid membranes and total leaf proteins from Posidonia oceanica and other polyphenol-rich plants

BACKGROUND

The extraction of thylakoids is an essential step in studying the structure of photosynthetic complexes and several other aspects of the photosynthetic process in plants. Conventional protocols have been developed for selected land plants grown in controlled conditions. Plants accumulate defensive chemical compounds such as polyphenols to cope with environmental stresses. When the polyphenol levels are high, their oxidation and cross-linking properties prevent thylakoid extraction.

RESULTS

In this study, we developed a method to counteract the hindering effects of polyphenols by modifying the grinding buffer with the addition of both vitamin C (VitC) and polyethylene glycol (PEG4000). This protocol was first applied to the marine plant Posidonia oceanica and then extended to other plants synthesizing substantial amounts of polyphenols, such as Quercus pubescens (oak) and Vitis vinifera (grapevine). Native gel analysis showed that photosynthetic complexes (PSII, PSI, and LHCII) can be extracted from purified membranes and fractionated comparably to those extracted from the model plant Arabidopsis thaliana. Moreover, total protein extraction from frozen P. oceanica leaves was also efficiently carried out using a denaturing buffer containing PEG and VitC.

CONCLUSIONS

Our work shows that the use of PEG and VitC significantly improves the isolation of native thylakoids, native photosynthetic complexes, and total proteins from plants containing high amounts of polyphenols and thus enables studies on photosynthesis in various plant species grown in natural conditions.

Minimizing Shear Stress in Cell Signaling Studies

Cellular signal transduction comprises a complex series of biochemical reactions by which extracellular signals such as growth factors, hormones, cytokines, and neurotransmitters are translated into specific intracellular responses. Signal transduction is mediated by protein kinase phosphorylation cascades that culminate in the regulation of numerous cellular responses, including division, differentiation, migration, and survival. Importantly, signal relay pathways are dysregulated in human diseases, making the study of signal transduction important for both uncovering basic biology and understanding pathophysiology. Established laboratory cell culture models are useful for studying signal transduction mechanisms, but differences in sample handling procedures can introduce unwanted variability in experimental outcomes and conclusions. One such potential source of experimental variability is the introduction of fluid shear stress upon handling of tissue culture cells. Fluid shear stress triggers a wide range of cellular responses in adherent cell culture, including stimulating the production of cyclic AMP, potentiating the activation of extracellular signal-regulated kinases 1 and 2 (ERK1/2), and ultimately inducing changes in the gene expression of growth and remodeling factors. Further, mechanical stress on cells is physiologically relevant to the development of many pathologies. Here, we describe a detailed protocol for cell lysis and protein extraction that minimizes shear stress induced by classical cell harvest protocols. We also highlight the impact of fluid shear stress by using immunoblotting to assess ERK pathway activation as a readout for this protocol. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Gentle cell lysis and protein extraction Basic Protocol 2: Immunoblotting for cell signaling readouts by SDS-PAGE.

Influence of Roasting Temperature on the Detectability of Potentially Allergenic Lupin by SDS-PAGE, ELISAs, LC-MS/MS, and Real-Time PCR

Seeds of "sweet lupins" have been playing an increasing role in the food industry. Lupin proteins may be used for producing a variety of foods, including pasta, bread, cookies, dairy products, and coffee substitutes. In a small percentage of the population, lupin consumption may elicit allergic reactions, either due to primary sensitization to lupin or due to cross-allergy with other legumes. Thus, lupin has to be declared on commercial food products according to EU food regulations. In this study, we investigated the influence of roasting seeds of the L. angustifolius cultivar "Boregine" on the detectability of lupin by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), ELISAs, LC-MS/MS, and real-time PCR. Seeds were roasted by fluidized bed roasting, and samples were drawn at seed surface temperatures ranging from 98 °C to 242 °C. With increasing roasting temperature, the extractability of proteins and DNA decreased. In addition, roasting resulted in lower detectability of lupin proteins by ELISAs and LC-MS/MS and lower detectability of DNA by real-time PCR. Our results suggest reduced allergenicity of roasted lupin seeds used for the production of "lupin coffee"; however, this has to be confirmed in in vivo studies.

Technological and Safety Characterization of Coagulase-Negative Staphylococci Isolated from Sardinian Fermented Sausage Made by Ovine Meat

Ripened sheep sausages are widely consumed in Italy, particularly in Sardinia. Despite their driving role in flavor and color development, coagulase-negative staphylococci in these products have been rarely investigated. A total of 70 CoNS cultures isolated from Sardinian sheep sausages were characterized by rep-PCR and M13-RAPD typing and identified by 16S rDNA sequencing. S. xylosus and S. equorum accounted for more than 70% of the total isolates, whilst S. pasteuri (8.5%), S. succinus (2.8%), and S. haemolyticus (2.8%) were less represented. The genes encoding the synthesis of putrescine, tyramine, cadaverine, and histamine were evaluated by PCR. None of the strains hosted genes for decarboxylases, except one S. pasteuri strain that was potentially a tyramine-producer. Antibiotic resistance was evaluated, along with nitrate reductase, lipolytic, and proteolytic activity, in a pool of selected cultures. Resistance to the primary antibiotics was rather widespread. S. xylosus, S. equorum, and S. pasteuri strains were all resistant to amoxicillin and kanamycin. S. equorum strains were sensitive to all tested antibiotics. S. xylosus strains were all resistant to penicillin B. Conversely, all S. pasteuri strains were resistant to both ampicillin and penicillin B, and four out of five strains exhibited tetracycline resistance. The high variability in the production of sheep sausages makes the search for adjunct cultures of crucial relevance. According to this perspective, the characterization of the autochthonous CSN population represents the first step to approach a starter selection.

Isolation, characterization, and cloning of thermostable pullulanase from Geobacillus stearothermophilus ADM-11

This study aimed to identify thermo-stable pullulanase-producing bacteria in soil samples of potato fields and food-producing companies. Pullulan agar medium was used to screen 17 bacterial strains, which were incubated at 65 °C. The isolate with the maximum activity (375U/ml) was selected and recognized as Geobacillus stearothermophilus ADM-11 by morphological, biochemical characterization, and 16S rRNA gene sequencing. The pullulanase production required optimum pH of 7 and temperature of 75 °C, respectively. The electrophoresis of purified pullulanase on SDS-polyacrylamide gel revealed 83 kDa of a molecular weight that is active at 70 °C and pH 7.0. It was also stable at 90 °C but its activity was decreased by 10 % at 100 °C. The action of pullulanase was increased and stabilized by Ca+2 among the metal ions. Beta and gamma-cyclodextrins inhibited enzyme activity while ethylenediaminetetraacetate (EDTA) and phenylmethylsulfonyl fluoride (PMSF) have no significant effect on pullulanase activity. A full-length pullulanase gene was amplified from G. stearothermophilus ADM-11 using genomic DNA 2.1 kb of PCR product which was then purified and ligated in the cloning vector pTZ57R using the TA cloning technique. Colony PCR confirmed cloning on the positive clones after the pullulanase gene had been ligated and subjected to restriction digestion. It revealed 74 % similarity with the reported pullulanase gene from Geobacillus sp. 44C. The thermostability of pullulanase and its ability to degrade raw pullulan may therefore have wide-scale applications in starch processing, the detergent business, and new biotechnological applications.

Development and qualification of an automated capillary Western method for the identification of polysaccharide serotypes in pneumococcal conjugate vaccine (PCV)

Streptococcus pneumoniae bacterial infection causes mortality in both adults and infants. To mitigate the impact of the disease, several Pneumococcal conjugate vaccines (PCVs) have been manufactured for the U.S. market, including the recent approval of the 15-valent PCV Vaxneuvance™ from MSD. These vaccines demonstrate high efficacy for both the adult and pediatric dose. These PCVs contain multiple unique serotypes in the final, formulated vaccine product, and identifying a specific polysaccharide, in the presence of other serotypes, is a critical quality attribute that must be demonstrated through analytical testing. Here we describe the development and qualification of an identity assay using an automated capillary western system, called Simple Western, implementing a multi-valent system suitability sample (SSS) to determine individual polysaccharide components. The assay was optimized through rigorous analytical development and was successfully qualified for use in the clinical release of the PCV.

Allergen Diversity and Abundance in Different Tissues of the Redclaw Crayfish (Cherax quadricarinatus)

Shellfish allergy affects ~2.5% of the global population and is a type I immune response resulting from exposure to crustacean and/or molluscan proteins. The Australian Redclaw crayfish (Cherax quadricarinatus) is a freshwater species endemic to and farmed in northern Australia and is becoming an aquaculture species of interest globally. Despite being consumed as food, allergenic proteins from redclaw have not been identified or characterised. In addition, as different body parts are often consumed, it is conceivable that redclaw tissues vary in allergenicity depending on tissue type and function. To better understand food-derived allergenicity, this study characterised allergenic proteins in various redclaw body tissues (the tail, claw, and cephalothorax) and how the stability of allergenic proteins was affected through cooking (raw vs. cooked tissues). The potential of redclaw allergens to cross-react and cause IgE-binding in patients allergic to other shellfish (i.e., shrimp) was also investigated. Raw and cooked extracts were prepared from each body part. SDS-PAGE followed by immunoblotting was performed to determine allergen-specific antibody reactivity to sarcoplasmic calcium-binding protein and hemocyanin, as well as to identify redclaw proteins binding to IgE antibodies from individual and pooled sera of shrimp-allergic patients. Liquid chromatography-mass spectrometry (LC/MS) was utilised to identify proteins and to determine the proportion within extracts. Known crustacean allergens were found in all tissues, with a variation in tissue distribution (e.g., higher levels of hemocyanin in the claw and cephalothorax than in the tail). The proportion of some allergens as a percentage of remaining heat-stable proteins increased in cooked tissues. Previously described heat-stable allergens (i.e., hemocyanin and sarcoplasmic calcium-binding protein) were found to be partially heat-labile. Immunoblotting indicated that shrimp-allergic patients cross-react to redclaw allergens. IgE-binding bands, analysed by LC/MS, identified up to 11 known shellfish allergens. The findings of this study provide fundamental knowledge into the diagnostic and therapeutic field of shellfish allergy.

Growth and protein response of rice plant with plant growth-promoting rhizobacteria inoculations under salt stress conditions

Soil salinity has been one of the significant barriers to improving rice production and quality. According to reports, Bacillus spp. can be utilized to boost plant development in saline soil, although the molecular mechanisms behind the interaction of microbes towards salt stress are not fully known. Variations in rice plant protein expression in response to salt stress and plant growth-promoting rhizobacteria (PGPR) inoculations were investigated using a proteomic method and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Findings revealed that 54 salt-responsive proteins were identified by mass spectrometry analysis (LC-MS/MS) with the Bacillus spp. interaction, and the proteins were functionally classified as gene ontology. The initial study showed that all proteins were labeled by mass spectrometry analysis (LC-MS/MS) with Bacillus spp. interaction; the proteins were functionally classified into six groups. Approximately 18 identified proteins (up-regulated, 13; down-regulated, 5) were involved in the photosynthetic process. An increase in the expression of eight up-regulated and two down-regulated proteins in protein synthesis known as chaperones, such as the 60 kDa chaperonin, the 70 kDa heat shock protein BIP, and calreticulin, was involved in rice plant stress tolerance. Several proteins involved in protein metabolism and signaling pathways also experienced significant changes in their expression. The results revealed that phytohormones regulated the manifestation of various chaperones and protein abundance and that protein synthesis played a significant role in regulating salt stress. This study also described how chaperones regulate rice salt stress, their different subcellular localizations, and the activity of chaperones.

Type I Lipoteichoic Acid (LTA) Detection by Western Blot

Type I lipoteichoic acid (LTA) is a glycerol phosphate polymer found in the cell envelope of diverse Gram-positive bacteria including Staphylococcus aureus, Bacillus subtilis, and Listeria monocytogenes. The polymer is linked by a lipid anchor to the outer leaflet of the bacterial membrane and in some bacteria can also be shed and detected in the culture supernatant. Here, we describe a simple and rapid western blot method for the detection of Type I LTA in bacterial cell extracts and culture supernatant fractions using a polyglycerol phosphate specific monoclonal LTA antibody.

Detection of Ligand-Induced Receptor Kinase and Signaling Component Phosphorylation with Mn2+-Phos-Tag SDS-PAGE

Plasma membrane-resident receptor kinases (RKs) are crucial for plants to sense endogenous and exogenous signals in regulating growth, development, and stress response. Upon perception of ligands by the extracellular domain, RKs are usually activated by auto- and/or trans-phosphorylation of the cytoplasmic kinase domain, which in turn phosphorylates downstream substrates to relay the signaling. Therefore, monitoring ligand-induced in vivo phosphorylation dynamics of RKs and their associated proteins provides mechanistic insight into RK activation and downstream signal transduction. Phos-tag specifically binds phosphomonoester dianions of phosphorylated serine, threonine, and tyrosine residues, which enables Phos-tag-containing SDS-PAGE gels to separate phosphorylated proteins from non-phosphorylated form. Here, we describe a detailed method of Mn2+-Phos-tag SDS-PAGE analysis to detect the ligand-induced in vivo phosphorylation of RKs and associated proteins.

Current Trends in Validating Antibody Specificities for ELISpot by Western Blotting

The enzyme-linked immunospot (ELISpot) assay is a highly useful and sensitive method to detect total immunoglobulin and antigen-specific antibody-secreting cells. In addition, this method can measure biological activity and immunological secretions from immune cells. In general, membrane-bound antigen allows binding of antibody secreted by B cells, or a membrane-bound analyte-specific antibody binds to the specific analyte (e.g., cytokines) elicited from cells added to the well containing the bound antibody. The response from added cells is then detected by using an anti-Ig antibody and a colorimetric substrate, while in the case of non-B cells, the elicited antigen is detected with appropriate antibodies and enzyme-conjugated antibodies. Specificity of antibodies binding the protein of interest is necessary to achieve correct results. Western blotting can be used for this with/without siRNA knockdown of proteins of interest or with the use of peptide inhibitors to inhibit the binding of specific antibodies to the target protein. Despite its general simplicity, western blotting is a powerful technique for immunodetection of proteins (notably low abundance proteins) as it provides simultaneous resolution of multiple immunogenic antigens within a sample for detection by specific antibodies. Now, we have plethora of immunoblotting methods to validate antibodies for ELISpot.

Two-Dimensional Gel Electrophoresis in Studies of Flower and Leaf Proteome of Common Buckwheat

Two-dimensional gel electrophoresis (2-DE) is a proteomic tool used for the separation of protein mixtures according to protein isoelectric point and molecular mass. Although gel-free quantitative and qualitative proteomic study techniques are now available, 2-DE remains a useful analytical tool. The presented protocol was performed to analyze the flower and leaf proteome of common buckwheat using 24 cm immobilized pH gradient strips (pH 4-7) and visualization of proteins on gels via colloidal Coomassie G-250 staining.

Two-Dimensional Gel Electrophoresis for Protein Separation of Plant Samples

This chapter provides a description of the procedure for two-dimensional electrophoresis that can be performed for any given gel size and isoelectric focusing range. This will enable the operator to recognize critical steps and gain sufficient information to generate 2D images suitable for computer-assisted analysis of 2D-gel, as well as mass spectrometry analysis for protein identification and characterization.

Effector Translocation Assay: Differential Solubilization

The identification of effector proteins delivered into mammalian host cells by bacterial pathogens possessing syringe-like nanomachines is an important step towards an understanding of the mechanisms underlying virulence of these pathogens. In this chapter, we describe a method based on mammalian tissue culture infection models where incubation with a non-ionic detergent (Triton X-100) enables solubilization of host cell membranes but not of bacterial membranes. This allows the isolation of a Triton-soluble fraction lacking bacteria but enriched in proteins present in the host cell cytoplasm, nucleus, and plasma membrane. Using appropriate controls, this fraction can be probed by immunoblotting for the presence of bacterial effector proteins delivered into host cells.

A Chromogenic Quantification of Protein Expression in Zebrafish Larvae

Western blot is a versatile and widely used technique in many areas of molecular biology and biotechnology for studying different protein characteristics. In general, the Western blot technique involves the extraction of proteins from the samples such as cells or tissues, which, after denaturation, are separated by molecular size using electrophoresis. The protein is then transferred to a membrane, typically PVDF or nitrocellulose, which, after blocking, is probed with specific antibodies labeled with a detection agent. Overall, this allows the recognition and binding to the target protein allowing the visualization of bands, a step called immunodetection. Over the years, new approaches to the Western blotting technique have been proposed to overcome performance limitations.This chapter describes a routine procedure for protein evaluation in zebrafish (Danio rerio) larvae, a widely used animal model for predicting the toxicity of drugs, by using a chromogenic substrate and allowing the proper execution of the technique without the costly equipment needed for detection.

In-house CHO HCPs platform: A promising approach for HCPs ELISA monitoring

A key aspect that must be supervised during the development of recombinant therapeutic products is the potential presence of impurities. Residual host cell proteins (HCPs) are a major class of process-related impurities derived from the host organism that even in trace amount have the potential to affect product quality, safety, and efficacy. Therefore, the product purification processes must be optimized to consistently remove as many HCPs as feasible, with the goal of making the product as pure as possible. The workhorse of HCP monitoring and quantitation during bioprocessing manufacturing is sandwich ELISA (enzyme-linked immunosorbent assay), which employs polyclonal anti-HCP antibodies for both capture and detection. Commercial ELISA kits developed from Chinese Hamster Ovary (CHO) cell lines are widely applied in early drug development stages (preclinical, phase I, and phase II), but are not specifically designed for a given manufacturer's proprietary cell line, and users do not have control over reagent availability and lot-to-lot consistency. For later development stages, the upstream process-specific method is preferred to guarantee an improved sensitivity and coverage. In agreement with the USP General Chapter 〈1132〉, a platform assay can be used in place of the commercial one through all stages of product development, if already available when product development starts. This proof-of-concept study was carried out to demonstrate the feasibility and the advantages of the development of a proprietary CHO HCPs platform ELISA. Different proprietary mock materials have been characterized and compared by orthogonal bidimensional electrophoresis techniques (SDS-PAGE coupled to SS/WB and 2D DIGE) with the scope of selecting the best antigen-antibody couple for setting up the in-house ELISA. A preliminary evaluation of the in-house method performance has been done in comparison with the commercial assay, demonstrating that the platform method is promising for an accurate and precise CHO HCPs quantification during the early phase product and process development.

Germplasm characterization and SDS-PAGE analysis of caper (Capparis spinosa L.) from different provenances

BACKGROUND

Capparis spinosa L. is a typical desert plant that is resistant to high temperatures and drought, and at the same time is rich in medicinal and food values. The objective of this study is to explore the variations in nutrient composition, morphological characteristics, and SDS-PAGE patterns of caper seeds from different provenances, aiming to provide insights for the selection of superior seed provenances.

RESULTS

In this experiment, there were significant differences in the morphological characteristics and major nutritional components of caper seeds from different provenances. Seeds from the YKL (Karayagaqi Township, Yining County) and YKG (G218, KashiTown, Yining County) regions were larger in size compared to seeds from other regions. Among the four measured nutritional components, crude fat had the highest content, especially in the YKL and YKG region. The results of correlation analysis showed that crude fat was negatively correlated with soluble sugar and soluble protein but significantly positively correlated with starch content. As longitude increased from east to west, the morphological characteristics gradually increased. Based on the principal component analysis of all the parameters of the seeds, the eight provenances could be classified into three groups. HM (Hami), TGS (S202, Gaochang District, Turpan), HYW (Wubao Town, Yizhou District, Hami), TQQ (Qiquanhu Town, Turpan), and TLF (Turpan) were a group with higher soluble protein, soluble sugar, and water content. YKL and YKG were in one group, which had larger seed grains with high crude fat and starch content. AKS (Aksu) was in a separate group. The protein fractions from seeds of eight regions were extracted using Osborne fractionation method, it was found that glutelin content was the highest, while albumin content was the lowest. After these proteins were analyzed by SDS-PAGE, the electrophoretic patterns showed that the protein molecular weights were relatively small, and there were differences in protein bands among different provenances.

CONCLUSION

According to the PCA results, the eight seed provenances could be divided into three groups. There were both geographically distant ones clustered into one group, and those close to each other were also divided into one group. There were differences in seed morphology, nutrient content and SDS-PAGE profiles among the different seed sources. This difference might be caused by a combination of geographic and climatic factors. In addition, YKL and YKG were roughly selected as good seed provenances, which provided a theoretical basis for the development of C. spinosa L. germplasm resources.

Alkaline Thermo- and Oxidant-Stable Protease from Bacillus pumilus Strain TNP93: Laundry Detergent Formulations

The study aims to produce a detergent-compatible and alkaline thermophilic protease from a Bacillus strain and to investigate its usability as a detergent bio-additive. The protease-producing bacterium was identified as Bacillus pumilus strain TNP93 according to the 16S rRNA sequence. The bacterium optimally synthesized the protease at 40 °C and pH 10 in 40 h. The raw protease displayed its optimum activity at pH 10 and 60 °C and its stability between pH 6-13 and 30-100 °C for 24 h. The molecular mass of the proteolytic band was estimated to be about 85 kDa. The protease was not inhibited by any of the metal ions used (Ba2+, Ca2+, Co2+, Cu2+, Mg2+, Mn2+, Zn2+). 97 and 90% of its original activity with 5 mM PMSF and EDTA remained. The activity was measured as 84, 124, and 95%, respectively, in the presence of 1% concentrations of Tween 20, Tween 80, and Triton X-100. In addition, all of its activity was preserved when the enzyme was exposed to 5% H2O2. The end products of casein were detected as tyrosine, aspartic acid, glycine, and cysteine by thin-layer chromatography. Considering the wash performance analysis, the mix of 1% commercial detergent and enzyme almost removed all of the protein-based stains (blood and egg yolk albumin). These remarkable findings indicate that the alkaline, thermo-, and oxidant-stable TNP93 protease is a valuable candidate for usage as a biological additive in various laundry detergents.

Analysis of commercial fetal bovine serum (FBS) and its substitutes in the development of cultured meat

Fetal bovine serum (FBS) is an extremely important culture growth supplement, accounting for approximately 60 % of cell-culture-media costs; therefore, lowering FBS-acquisition costs for the industrialization of cultured meat is imperative. This study attempted to produce an FBS substitute using discarded livestock by-products, with particular focus on formulating a product with a composition similar to that of FBS to improve effectiveness. However, to date, no study has precisely analyzed the commercial components of FBS, and this study is the first to compare the chemical composition of FBS and commercially available horse serum purchased from the United States or Europe with that of FBS substitutes developed by our team. This study analyzed the chemical composition of the FBS products purchased by our team over the past 3 years via blood, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and independent composition analyses. While the composition and quality of commercial FBS products are known to vary, the FBS composition of our purchased products was relatively uniform regardless of company, brand, or country of origin. In contrast, FBS substitutes obtained from three major livestock species (cattle, pig, and chicken) clearly exhibited differences in composition, a phenomenon that was also observed upon comparing with FBS as well as among different species. Therefore, to replace commercial FBS entirely, the production of a proportionately effective substitute product comprising an equal or similar composition is required, and the results of this study can be a steppingstone to achieving this. In addition, FBS substitutes manufactured using inexpensive slaughter by-products as raw materials are expected to ultimately reduce the unit cost of cultured meat production.

Effect of High-Hydrostatic-Pressure Treatment on the Physicochemical Properties of Kafirin

The kafirin derived from Jin Nuo 3 sorghum underwent a high-hydrostatic-pressure (HHP) treatment of 100, 300, and 600 MPa for 10 min to investigate alterations in its physicochemical attributes. The findings exhibited a reduction in protein solubility, declining from 83% to 62%, consequent to the application of the HHP treatment. However, this treatment did not lead to subunit-specific aggregation. The absorption intensity of UV light diminished, and the peak fluorescence absorption wavelength exhibited a shift from 342 nm to 344 nm, indicating an increased polarity within the amino acid microenvironment. In an aqueous solution, the specific surface area expanded from 294.2 m2/kg to 304.5 m2/kg, while the average particle-size value in a 70% ethanol solution rose to 26.3 nm. Conversely, the zeta-potential value decreased from 3.4 mV to 1.3 mV, suggesting a propensity for aggregation in ethanol solutions. A notable rise in the intermolecular β-sheet content to 21.06% was observed, along with a shift in the peak denaturation temperature from 76.33 °C to 86.33 °C. Additionally, the content of disulfide bonds increased to 14.5 μmol/g. Collectively, the application of the HHP treatment not only enhanced the thermal stability but also induced a more ordered secondary structure within the kafirin.

Assessment of intra- and inter-genetic diversity in tetraploid and hexaploid wheat genotypes based on omega, gamma and alpha-gliadin profiles

Durum and bread wheat are well adapted to the Mediterranean Basin. Twenty-three genotypes of each species were grown to evaluate the intra- and inter-genetic diversity based on omega (ω), gamma (γ) and alpha (α)-gliadin profiles. To achieve this purpose, the endosperm storage proteins (both gliadins and glutenins) were extracted from wheat grains and electrophoresed on sodium dodecyl sulfate (SDS)-polyacrylamide gels. The results of SDS-Polyacrylamide Gel Electrophoresis (SDS-PAGE) revealed nine polymorphic loci out of 16 loci with durum wheat genotypes and nine polymorphic loci out of 18 loci with bead wheat genotypes. The polymorphisms revealed by the SDS-PAGE were 56% and 50% in durum and bread wheat genotypes, respectively. Using the cluster analysis, the durum wheat genotypes were clustered into five groups, while the bread wheat genotypes were grouped into six clusters using un-weighed pair group mean analyses based on ω, γ, and α-gliadins profiles. The 46 durum and bread wheat genotypes were grouped into seven clusters based on the combined ω, γ, and α-gliadins profiles revealed by the SDS-PAGE. The in silico analysis determined the intra-genetic diversity between bread and durum wheat based on the sequences of ω, γ, and α-gliadins. The alignment of ω-gliadin revealed the highest polymorphism (52.1%) between bread and durum wheat, meanwhile, the alignment of γ and α-gliadins revealed very low polymorphism 6.6% and 15.4%, respectively. According to computational studies, all gliadins contain a lot of glutamine and proline residues. The analysis revealed that the bread wheat possessed ω and γ -gliadins with a lower content of proline and a higher content of glutamine than durum wheat. In contrast, durum wheat possessed α-gliadin with a lower content of proline and a higher content of glutamine than bread wheat. In conclusion, the SDS-PAGE, in silico and computational analyses are effective tools to determine the intra- and inter-genetic diversity in tetraploid and hexaploid wheat genotypes based on ω, γ, and α-gliadins profiles.

Protein carbonylation and structural changes in porcine myofibrillar protein exposed to metal ion-H2O2-ascorbate and linoleic acid-lipoxidase oxidizing systems

The present study aimed to compare two oxidizing systems commonly present in meat for their influence on protein oxidation patterns, with emphasis on the specific lysine-derived markers for protein carbonylation (α-aminoadipic semialdehyde, AAS; lysinonorlucine, LNL) and their relationships with the common markers for protein oxidation. For this purpose, pork myofibrillar proteins (MFP, 5 mg/mL) were suspended in 0.6 M NaCl (pH 7.5) and incubated at 4 ℃ for 24 h with two oxidizing systems: (1) a metal-catalyzed oxidizing system (MOS: 10 µM FeCl3, 100 µM ascorbic acid, and 0-10 mmol/L H2O2), (2) a linoleic acid - lipoxidase oxidizing system (LOS: 7500 units of lipoxidase/mL, and 0-10 mM linoleic acid). Results showed that the amounts of AAS and LNL in both MOS- and LOS-oxidized MFP was proportional to the oxidant concentrations (H2O2 or linoleic acid), while the formation of total carbonyl and total thiol also exhibited similar oxidant-dose-dependent patterns. Meanwhile, the α-helix contents of MFP declined with oxidant concentrations irrespective of the oxidizing systems. The reducing SDS-PAGE revealed that the myosin heavy chain band started to diminish at high H2O2 concentration (5 and 10 mM) in MOS whereas at low level of linoleic acid (0.5 mM) in LOS. Overall, these results demonstrated both oxidizing systems could be involved in the formation of AAS and LNL, and that the generation of AAS and LNL can be used as reliable markers for protein oxidation, but also might be directly involved in protein structural changes and then contribute to the alternations of protein functionality.

Bactericidal role of epidermal mucus of freshwater fish treated with Aeromonas hydrophila

This study explored the bactericidal role of the epidermal mucus (EM) of five freshwater Cyprinid fish species namely Ctenopharyngodon idella, Labeo rohita, Catla catla, Hypophthalmichthys molitrix, and Cirrhinus mrigala after treatment with Aeromonas hydrophila. Extracts of EM (crude and acidic) of each species showed bactericidal activity against various Gram -ve (Pseudomonas aeruginosa, Escherichia coli, Aeromonas hydrophila, Edwardsiella tarda, Salmonella enterica, Klebsiella pneumonia, Serratia marcescens, and Enterobacter cloacae) and Gram +ve (Bacillus wiedmannii and Staphylococcus aureus) bacteria compared with standard antibiotics (Fosfomycin). The zone of inhibition (ZOI) was measured in millimetres against antibiotics (Fosfomycin). Variations in bactericidal activity of EM were observed against bacteria from the same and different fish species. The acidic extract was more effective than the crude extract and showed significantly higher ZOI values against various bacteria and Fosfomycin antibiotics. This result shows that fish EM may perform an important role in fish defence against bacteria. Therefore, this study may hint towards the substitution of synthetic antibiotics with fish EM that may be used as a novel 'bactericidal' in aquaculture as well as in humans against bacterial infections.

Agro-morphological, biochemical, and molecular markers of barley genotypes grown under salinity stress conditions

The aim of this study was to evaluate the impact of salt stress on morphological, yield, biochemical, and molecular attributes of different barley genotypes. Ten genotypes were cultivated at Fayoum Research Station, El-Fayoum Governorate, Egypt, during two seasons (2020-2021 and 2021-2022), and they were exposed to two different salt concentrations (tap water as a control and 8000 ppm). The results showed that genotypes and salt stress had a significant impact on all morphological and physiological parameters. The morphological parameters (plant height) and yield attributes (spike length, number of grains per spike, and grain yield per plant) of all barley genotypes were significantly decreased under salt stress as compared to control plants. Under salt stress, the total soluble sugars, proline, total phenol, total flavonoid, ascorbic acid, malondialdehyde, hydrogen peroxide, and sodium contents of the shoots of all barley genotypes significantly increased while the potassium content decreased. L1, which is considered a sensitive genotype was more affected by salinity stress than the tolerance genotypes L4, L6, L9, and Giza 138. SDS-PAGE of seed proteins demonstrated high levels of genetic variety with a polymorphism rate of 42.11%. All genotypes evaluated revealed significant variations in the seed protein biochemical markers, with new protein bands appearing and other protein bands disappearing in the protein patterns of genotypes cultivated under various conditions. Two molecular marker techniques (SCoT and ISSR primers) were used in this study. Ten Start Codon Targeted (SCoT) primers exhibited a total of 94 fragments with sizes ranging from 1800 base pairs to 100 base pairs; 29 of them were monomorphic, and 65 bands, with a polymorphism of 62.18%, were polymorphic. These bands contained 21 unique bands (9 positive specific markers and 12 negative specific markers). A total of 54 amplified bands with molecular sizes ranging from 2200 to 200 bp were produced using seven Inter Simple Sequence Repeat (ISSR) primers; 31 of them were monomorphic bands and 23 polymorphic bands had a 40.9% polymorphism. The techniques identified molecular genetic markers associated with salt tolerance in barley crop and successfully marked each genotype with distinct bands. The ten genotypes were sorted into two main groups by the unweighted pair group method of arithmetic averages (UPGMA) cluster analysis based on molecular markers and data at a genetic similarity coefficient level of 0.71.

Effect of Gluten Composition in Low-Allergy O-Free Wheat Flour on Cookie-Making Performance Compared with Flours with Different Gluten Strengths

The increasing demand for allergen-free and reduced-allergen foods has led to an investigation into the potential use of O-free wheat, a low-allergy wheat cultivar, in cookie production. This study focused on assessing the gluten composition of O-free flour and comparing its suitability for cookie making in comparison to flours with varying gluten strengths. Several analyses were conducted, including gluten composition, solvent retention capacity (SRC), thermal and pasting properties, dough-mixing characteristics, and cookie-making performance. The gluten composition of O-free flour by SDS-PAGE confirmed the absence of ω-gliadins and the reduced levels of low-molecular-weight glutenins and γ-gliadins. The SRC values of O-free flour fell between the flours with weak and medium gluten strengths. While thermal and pasting properties showed significant differences in sucrose solution but not across flour types, indicating similar starch structures, mixograms displayed distinct variations influenced by both sucrose solution and flour type, highlighting the importance of gluten quality and composition. Cookies made with O-free flour demonstrated similarities to those produced with weak gluten flour, known for their favorable cookie characteristics. This study emphasizes the significant influence of flour gluten composition on cookie-making performance and advocates for the adoption of O-free flour in the development of allergy-friendly cookies.

Green synthesis of silver nanoparticles derived from lemon and pomegranate peel extracts to combat multidrug-resistant bacterial isolates

BACKGROUND

Multidrug-resistant (MDR) bacteria are acknowledged as one of the main factors contributing to chronic illnesses and fatalities globally. Numerous diseases, including bloodstream infections, pneumonia, urinary tract infections, and surgical site infections, can be brought on by MDR bacteria. Therefore, a crucial topic of continuing research is the development of a novel and different treatment for MDR microbial pathogens. This work is introduce an alternative method for elimination of MDR bacterial isolates which are causative agents of urinary tract infection among people in Egypt. In our study, we need a novel strategy to combat MDR bacteria by green-synthesized metal nanoparticles (MNPs). That is due to the ability of MNPs to penetrate the cell wall and the cell membrane of gram-positive and gram-negative bacteria.

METHODS

Clinical isolates of MDR bacteria had their antibiotic susceptibility assessed before being molecularly identified using 16 s rRNA, sequencing, and phylogenetic analysis. Also, genetic profiles of isolated strains were performed using ISSR and SDS-PAGE. Finally, characterized plant-mediated silver nanoparticles derived from lemon and pomegranate peel extracts were evaluated against isolated multidrug-resistant bacterial stains.

RESULTS

In our present trial, one-hundred urine samples were collected from 71 females and 29 males complaining of UTI (urinary tract infection) symptoms. One-hundred microbial isolates were isolated, including 88-g negative and only 8-g positive bacteria in addition to four yeast isolates (Candida species). A total of 72% of the isolated bacteria showed MDR activity. The most prevalent MDR bacterial isolates (Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii, Enterococcus faecalis, and Klebsiella pneumoniae) were identified through 16S rDNA PCR sequencing as with accession numbers OP741103, OP741104, OP741105, OP741106, and OP741107, respectively. Lemon and pomegranate-mediated silver nanoparticles [Ag-NPs] were characterized by UV spectroscopy, FTIR, XRD, and TEM with average size 32 and 28 nm, respectively. Lemon and pomegranate-mediated silver nanoparticles [Ag-NPs] showed an inhibitory effect on the selected five MDR isolates at MIC 50 and 30 µg/mL, respectively. These common bacterial isolates were also genetically examined using ISSR PCR, and their total protein level was evaluated using SDS-PAGE, showing the presence of distinct genetic and protein bands for each bacterial species and emphasizing their general and protein composition as a crucial and essential tool in understanding and overcoming MDR behavior in UTI patients.

CONCLUSIONS

Lemon and pomegranate-mediated silver nanoparticles [Ag-NPs] were found to have an inhibitory effect on MDR isolates. Therefore, the study suggests that [Ag-NPs] could be a potential treatment for MDR UTI infections caused by the identified bacterial species.

Purification and characterization of extracellular lipase from a thermotolerant strain: Bacillus subtilis TTP-06

In current study, lipase from a thermotolerant Bacillus subtilis TTP-06 was purified in a stepwise manner by using ammonium sulfate precipitation and column chromatography. Thenceforth, it was subjected to sodium dodecyl sulfate- and native-polyacrylamide gel electrophoresis to check the homogeneity of the purified enzyme. The ideal substrate concentration, pH, temperature, reaction duration and lipase specificity were identified. With a yield of 11.02%, purified lipase displayed activity of 8.51 U/mg. Thenceforward, the homogeneously purified enzyme was considered to be a homo-dimer of 30 kDa subunits. Enzyme had Km and Vmax value of 9.498 mM and 19.92 mol mg-1 min-1, respectively. Additionally, the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) method was used to investigate the purified lipase and estimate its 3-D structure, which revealed a catalytic triad of serine, aspartate and histidine.

Effect of environmental factors on expression of staphylococcal enterotoxin genes

Staphylococcal enterotoxins (SEs) secreted by Staphylococcus aureus (S. aureus) can cause foodborne disease, nausea, vomiting and diarrhea, and even death. Regulation of SE expression is related to accessory gene regulators (Agr). It is important to reveal which environmental factors influence regulation of SE expression to prevent SE food poisoning outbreak. Hence, natural environmental factors which may have an impact on SE expression were selected, such as temperature, food types, strains, and competing strains. Seven strains of S. aureus carrying different SE genes were collected from the Chinese Academy of Inspection and Quarantine (CAIQ) strain bank for study. Strains were cultured with different conditions. Temperature was 8 °C, 22 °C, and 30 °C. Food type was milk powder and nutrient broth. Competing strains were Vibrio parahaemolyticus (V. parahaemolyticus), Escherichia coli (E. coli), and Bacillus cereus (B. cereus). The expression culture solution was pretreated by centrifugation, then determined by using SDS-PAGE, and distinguished SEs apart from each other by HPLC-ESI-TOF. There are 168 samples collected from SE expression culture; the result of SDS-PAGE suggests 23 samples were positive for SEs, and the other 145 samples were negative for SEs. The result of HPLC-ESI-TOF suggests that SEs with similar molecular weight can be distinguished in terms of m/z. The most important factor contributing to regulate expression of SEs was estimated by logistic regressive analysis. The result shows that McFadden R2 is 0.213; p value is 0.000 (p < 0.05); this result illustrates that the model is valid and meaningful. Strains, food types, temperature, and competing strands can explain the 21% change in SE expression. Temperature (z = 3.029, p = 0.002 < 0.01), strains (z =  - 3.132, p = 0.002 < 0.01), and food types (z =  - 2.415, p = 0.016 < 0.05) have significant impact on SE expression, and the competing strains (z = 1.230, p = 0.219 > 0.05) have no impact on the SE expression. More important impact on SE expression was estimated by OR value; the result shows that strength of temperature influencing on SE expression is bigger than strains and food types in terms of values of OR, temperature (OR = 2.862), strains (OR = 0.641), and food types (OR = 0.561); consequently, temperature is a key factor for stimulating SE expression and had high expression at 30 °C. Therefore, food easily contaminated with S. aureus should be monitored intensively at early and late summer, when proper temperature for expressing SEs may result in S. aureus food poisoning prevalence.

Development of a concise and reliable method for quantifying the antibody loaded onto lipid nanoparticles modified with Herceptin

Antibodies are essential components of the immune system with a wide range of molecular targets. They have been recognized as modalities for treating several diseases and more than 130 approved antibody-based therapeutics are available for clinical use. However, limitations remain associated with its efficacy, tissue permeability, and safety, especially in cancer treatment. Nanoparticles, particularly those responsive to external stimuli, have shown promise in improving the efficacy of antibody-based therapeutics and tissue-selective delivery. In this study, we developed a reliable and accurate method for quantifying the amount of antibody loaded onto lipid nanoparticles modified with Herceptin® (Trastuzumab), an antibody-based therapeutic used to treat HER2-positive cancers, using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) followed by silver staining. This method proved to be a suitable alternative to commonly used protein quantification techniques, which are limited by lipid interference present in the samples. Furthermore, the amount of Herceptin modified on the liposomes, measured by this method, was confirmed by Herceptin's antibody-dependent cell-mediated cytotoxicity activity. Our results demonstrate the potential of this method as a critical tool for developing tissue-selective antibody delivery systems, leading to improved efficacy and reduced side effects of antibody-based therapeutics.

Seminal plasma protein profiles and testosterone levels as biomarker semen quality of candidate Madura bulls

Objective

This study aims to determine the protein profile based on molecular weight (MW) and testosterone levels in seminal plasma (SP) that correlates to the semen quality of candidate Madura bulls.

Material and Methods

A total of 10 male candidate madura bulls underwent semen evaluation (motility, viability, membrane plasma integrity (MPI), and sperm concentration). The centrifuge was run at 1,200 rpm (4°C) for 20 min to collect SP. SP testosterone levels were measured using an Enzyme-linked immunosorbent assay. The characterization of SP proteins in Madura bulls was done using 1D sodium dodecyl-sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. All parameters were analyzed using Pearson correlation analysis.

Result

The results of the SDS-PAGE analysis found eight protein bands with the highest MW of 110 kDa and the lowest of 12 kDa. The mean and SD of SP testosterone levels were 20.58 ± 8.56 ng/ml, motility 59.32% ± 20.14%, viability 67.45% ± 20.22%, MPI 32.77% ± 16.52%, and sperm concentration 1,002.64 ± 429.33 106/mm3. Proteins with MWs of 110 and 91 kDa significantly correlated with MPI, and 110 kDa negatively correlated with sperm concentration (p < 0.05). Proteins with MWs of 73 and 36 kDa significantly correlated with SP testosterone levels, while proteins with MWs of 29 kDa significantly correlated with sperm viability (p < 0.05).

Conclusion

The expressed protein fraction based on MW is closely related to the quality of semen, so it has the potential to be a biomarker of semen quality. Further research is needed to determine the specific proteins in certain fractions.

Recombinant protein production for structural and kinetic studies: A case study using M. tuberculosis α-methylacyl-CoA racemase (MCR)

Modern drug discovery is a target-driven approach in which a particular protein such as an enzyme is implicated in the disease process. Commonly, small-molecule drugs are identified using screening, rational design, and structural biology approaches. Drug screening, testing and optimization is typically conducted in vitro, and copious amounts of protein are required. The advent of recombinant DNA technologies has resulted in a rise in proteins purified by affinity techniques, typically by incorporating an "affinity tag" at the N- or C-terminus. Use of these tagged proteins and affinity techniques comes with a host of issues. This chapter describes the production of an untagged enzyme, α-methylacyl-CoA racemase (MCR) from Mycobacterium tuberculosis, using a recombinant E. coli system. Purification of the enzyme on a 100 mg scale using tandem anion-exchange chromatographies (DEAE-sepharose and RESOURCE-Q columns), and size-exclusion chromatographies is described. A modified protocol allowing the purification of cationic proteins is also described, based on tandem cation-exchange chromatographies (using CM-sepharose and RESOURCE-S columns) and size-exclusion chromatographies. The resulting MCR protein is suitable for biochemical and structural biology applications. The described protocols have wide applicability to the purification of other recombinant proteins and enzymes without using affinity chromatography.

Speeding up SDS-PAGE: Theory and experiment

In order to accelerate Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), here we propose an optimized version of the technique enabled by experimental tuning reinforced by theoretical description. In the resulting system, the gel buffer was diluted twofold and supplemented with glycine at a low concentration, whereas a higher voltage was applied. This approach reduced runtime from 90 to 18 min. It is important to emphasize that, despite the high voltage applied to the gel, the resolution of the bands did not decrease compared to the original Laemmli method. The proposed acceleration approach can be used in other variants of SDS-PAGE.

Western Blotting with Fast SDS-PAGE and Semi-Dry Protein Transfer

Western blotting is a method widely used in cell and molecular biology for the specific detection of proteins in biological samples. It is time-consuming and normally takes up to 2 days to complete. This protocol introduces a more time-efficient method to complete western blots, covering the preparation of protein extracts (including strategies for solubilization), electrophoretic separation of proteins, transfer of proteins to the membrane, and probing with antibodies. We describe an SDS-PAGE protocol that achieves a gradient-like separation of proteins (10-400 kDa) on a single-percentage polyacrylamide gel in only 45 min. Additionally, we present a rapid (10-14 min) semi-dry transfer of proteins from standard Tris/glycine polyacrylamide gels onto a membrane using homemade Tris/HEPES- or Tris/EPPS-based buffers. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) Support Protocol 1: Cell lysis and protein extraction Support Protocol 2: Protein quantification with BCA assay and sample preparation for loading on gel Basic Protocol 2: Protein transfer with a fast semi-dry transfer (FSDT) buffer Basic Protocol 3: Immunoprobing, chemiluminescent visualization, stripping, and reuse of membranes.

Isolation and Characterization of Protein Fractions for Valorization of Sacha Inchi Oil Press-Cake

The growing interest in plant-based food protein sources has provided opportunities for the valorization of agri-food by-products, driving the food industry towards more sustainable development. In this study, three extraction procedures (varying the pH value (7.0 and 11.0) and the addition of salt (0 and 5%)) were investigated to obtain seven different protein fractions (SIPF) from Sacha Inchi oil press-cake (SIPC), which were characterized in terms of their protein content, electrophoretic profile, secondary structure, and techno-functional properties. Extractions at pH 11.0 without salt addition produced the highest values of protein content, extraction yield, protein recovery, and protein concentration increase (84.0%, 24.7%, 36.5%, and 1.5-fold, respectively). Under these extraction conditions, the electrophoretic analysis indicated that most of the SIPC proteins were extracted. SIPF displayed an excellent oil absorption capacity (4.3-9.0 w/w), and interesting foam activity (36.4-133.3%). The solubility and emulsifying activity of the albumin fractions were significantly higher than those of the other fractions (~87 vs. <15.8%, and 280-370 vs. <140 m²/g, respectively). Correlation analysis showed that the secondary structure of the SIPF significantly influences their techno-functional properties. These results indicate that SIPC is a by-product of great potential for protein extraction processes, and as a valorization strategy for technical cycle solutions for the Sacha Inchi productive chain in the circular economy context.

The Internal Structure of the Velvet Worm Projectile Slime: A Small-Angle Scattering Study

For prey capture and defense, velvet worms eject an adhesive slime which has been established as a model system for recyclable complex liquids. Triggered by mechanical agitation, the liquid bio-adhesive rapidly transitions into solid fibers. In order to understand this mechanoresponsive behavior, here, the nanostructural organization of slime components are studied using small-angle scattering with neutrons and X-rays. The scattering intensities are successfully described with a three-component model accounting for proteins of two dominant molecular weight fractions and nanoscale globules. In contrast to the previous assumption that high molecular weight proteins-the presumed building blocks of the fiber core-are contained in the nanoglobules, it is found that the majority of slime proteins exist freely in solution. Only less than 10% of the slime proteins are contained in the nanoglobules, necessitating a reassessment of their function in fiber formation. Comparing scattering data of slime re-hydrated with light and heavy water reveals that the majority of lipids in slime are contained in the nanoglobules with homogeneous distribution. Vibrating mechanical impact under exclusion of air neither leads to formation of fibers nor alters the bulk structure of slime significantly, suggesting that interfacial phenomena and directional shearing are required for fiber formation.

Ethrel-induced release of fresh seed dormancy causes remodelling of amylase activity, proteomics, phytohormone and fatty acid profile of groundnut (Arachis hypogaea L.)

It is important to have a short period of fresh seed dormancy in some of the groundnut species to counter pre-harvest sprouting (PHS). One of the main causes of PHS is the activation of ethylene-mediated pathways. To determine the effect of ethylene, the study was conducted and alterations in amylase, proteins and fatty acids were observed at the 0, 6, 12, and 24 h stages after ethrel administration. The result showed an increase in amylase activity, and the fatty acids profile showed a unique alteration pattern at different germination stages. Two-dimensional gel electrophoresis (2DGE) revealed differential expression of proteins at each stage. The trypsin digestion following spectral development through UPLC-MS/MS enabled identification of number of differentially expressed proteins. A total of 49 proteins were identified from 2DGE excised spots. The majority were belonged to seed storage-related proteins like Arah1, Arah2, AAI- domain containing protein, conglutin, Arah3/4, arachin, glycinin. Expression of lipoxygenase1, lipoxygenase9 and Arah2 genes were further confirmed by qRT-PCR which showed its involvement at transcript level. Up-regulation of lipoxygenase9 is correlated with decreased content of fatty acids during germination. Phytohormone detection revealed decrease in ABA, SA and JA content which are generally inhibitor of seed germination while GA, IAA and kinetin concentration increased revealing positive regulation of seed germination. We present an integrated view of proteomics, phytohormone profile, carbohydrate and lipid metabolism to unravel mechanism of fresh seed dormancy.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01332-6.

Honey Quality Control: Review of Methodologies for Determining Entomological Origin

Honey is a widely consumed natural product, and its entomological origin can significantly influence its market value. Therefore, traceability of the entomological origin of honey should also be considered in honey quality control protocols. Although several methods exist, such as physicochemical characterization and bioactivity profiling of honey of different entomological origins, the most promising three methods for entomological authentication of honey include protein-based identification, chemical profiling, and a DNA-based method. All of these methods can be applied for reliable identification of the entomological origin of honey. However, as the honey is a complex matrix, the inconsistency of the results obtained by these methods is a pragmatic challenge, and therefore, the use of each method in all the cases is questionable. Most of these methodologies can be used for authentication of newly harvested honey and it is worth understanding the possibility of using these methods for authentication of relatively old samples. Most probably, using DNA-based methods targeting small fragments of DNA can provide the best result in old samples, however, the species-specific primers targeting short fragments are limited and not available for all species. Therefore, using universal primers in combination with a DNA metabarcoding approach can be a good solution that requires further investigation. This present article describes the applications of different methods, their pros, and their cons to identify honey based on entomological origin.

Complete genome sequence analysis, morphology and structural protein identification of two Bacillus subtilis phages, BSTP4 and BSTP6, which may form a new species in the genus Salasvirus

In the present study, two new Bacillus subtilis phages, BSTP4 and BSTP6, were isolated and studied further. Morphologically, BSTP4 and BSTP6 are podoviruses with complete genome of 19,145 (39.9% G + C content) and 19,367 bp (39.8% G + C content), respectively, which became among the smallest Bacillus phages. Three most prominent structural proteins were separated and identified as pre-neck appendage, major head, and head fiber proteins using LC-MS/MS. Both phages encode putative terminal proteins (TP) and contain short inverted terminal repeats (ITRs) which may be important for their replication. In addition, non-coding RNA (pRNA) and parS sites were identified which may be required for DNA packaging and their maintenance inside the host, respectively. Furthermore, the phage genome sequences show significant similarity to B. subtilis group species genome sequences. Finally, phylogenomic and phylogenetic analyses suggest that BSTP4 and BSTP6 may form a new species in the genus Salasvirus, subfamily Picovirinae of family Salasmaviridae. Considering the small numbers of ICTV-accepted B. subtilis phages and the importance of the host in the food industry and biotechnology, the current study helps to improve our understanding of the diversity of B. subtilis phages and shed light on the phage-host relationships.

Identification of Major and Cross-reactive Allergens of Local Freshwater Snail (Pila polita) and the Impact of Thermal and Non-thermal Food Processing on Allergen Stability

BACKGROUND

Snail allergy is rare but can be fatal. Pila polita, a freshwater snail was considered as a popular exotic food particularly in tropical countries and consumed in processed forms. Thus, the purpose of this study was to identify the major and cross-reactive allergens of P. polita and determine the impact of food processing on the allergen stability.

RESULTS

SDS-PAGE fractionated raw snail extract to approximately 24 protein bands, between 9 to 245 kDa. The prominent band at 33 kDa was detected in all raw and processed snail extracts. Immunoblotting tests of the raw extract demonstrated 19 IgE-binding proteins and four of them at 30, 35, 42 and 49 kDa were revealed as the major IgE-binding proteins of P. polita. MALDI-TOF identified the 49 kDa and 42 kDa major allergens as actin, while the 30 and 35 kDa major allergens were identified as tropomyosin. Immunoblotting revealed that the raw snail had more allergenic proteins than the processed snail. The degree of allergenicity in the decreasing order was: raw > brine pickled> boiled > roasted > fried > vinegar pickled. The presence of cross-reactivity between P. polita and the shellfish tested was exhibited, with either none, complete or partial inhibitions.

CONCLUSION

Actin and tropomyosin were identified as the major and cross-reactive allergens of P. polita among local patients with snail allergy. Those major allergens are highly stable to high temperatures, acidic pH and high salt, which might played a crucial role in snail allergy in this country. This article is protected by copyright. All rights reserved.

Precooking treatments affect the sensory and tensile properties of autoclaved recooked noodles via moisture distribution and protein structure

To improve the quality of autoclaved recooked noodles (ARNs), this study explored the effects of precooking on the sensory and tensile properties of ARNs from the perspectives of changes in protein structure and water distribution. The results showed that the ARNs of two kinds of pretreatments (Boiling 2 min, Boiling 1 min + Steaming 2 min) presented the best sensory quality (average score ≥ 7.50) and high tensile properties (tensile distance ≥ 45.24 mm). After autoclaving and recooking, the proportion of tightly bound water increased by 11.30%-12.52%, resulting in stronger water-solid interaction. The results of laser confocal microscopy (CLSM) proved that a strengthened gluten network (protein percentage area ≥ 40.28%; junction density ≥ 10.96 × 10^-4) appeared. Therefore, appropriate precooking treatment could effectively improve the sensory quality and tensile properties of ARNs by enhancing the tightly bound water ratio and strengthening the gluten network.

Grain Characteristics, Moisture, and Specific Peptides Produced by Ustilaginoidea virens Contribute to False Smut Disease in Rice (Oryza sativa L.)

The fungus Ustilaginoidea virens, the causative agent of false smut in rice (Oryza sativa L.), is responsible for one of the severe grain diseases that lead to significant losses worldwide. In this research, microscopic and proteomic analyses were performed by comparing U. virens infected and non-infected grains of the susceptible and resistant rice varieties to provide insights into the molecular and ultrastructural factors involved in false smut formation. Prominent differentially expressed peptide bands and spots were detected due to false smut formation as revealed by sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional gel electrophoresis (2-DE) SDS-PAGE profiles and were identified using liquid chromatography-mass spectrometry (LC-MS/MS). The proteins identified from the resistant grains were involved in diverse biological processes such as cell redox homeostasis, energy, stress tolerance, enzymatic activities, and metabolic pathways. It was found that U. virens produces diverse degrading enzymes such as β-1, 3-endoglucanase, subtilisin-like protease, putative nuclease S1, transaldolase, putative palmitoyl-protein thioesterase, adenosine kinase, and DNase 1 that could discretely alter the host morphophysiology resulting in false smut. The fungus also produced superoxide dismutase, small secreted proteins, and peroxidases during the smut formation. This study revealed that the dimension of rice grain spikes, their elemental composition, moisture content, and the specific peptides produced by the grains and the fungi U. virens play a vital role in the formation of false smut.

Preparation of Bacillus subtilis cell samples and generation of an SDS-PAGE

Bacillus subtilis is a critical host for producing recombinant proteins. However, the SDS-PAGE process, including the sample preparation steps, varies among B. subtilis-related studies, making it impossible to compare findings. Hence, this paper provides a simple guide to culture and collect B. subtilis cells through an OD₆₀₀ measurement and a protocol for SDS-PAGE. These techniques were applied to check the expression of a BgaB, a reporter protein and LukF-PV, a potential vaccine candidate against S. aureus, in the cytoplasm of B. subtilis under the control of a strong promoter, P_grac212. This protocol could be helpful for scientists in preparing samples and generating an SDS-PAGE experiment, as well as favoring the unification of research about protein expression in B. subtilis.