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When yeast cells enter into quiescence in response to nutrient limitation, the adenine deaminase Aah1p is specifically degraded via a process requiring the F-box protein Saf1p and components of the Skp1-Cullin-F-box complex. In this paper, we show that Saf1p interacts with both Aah1p and Skp1p. Interaction with Skp1p, but not with Aah1p, requires the F-box domain of Saf1p. Based on deletion and point mutations, we further demonstrate that the F-box domain of Saf1p is critical for degradation of Aah1p. We also establish that overexpression of Saf1p in proliferating cells is sufficient to trigger the degradation of Aah1p. Using this property and a two-dimensional protein gel approach, we found that Saf1p has a small number of direct targets. Finally, we isolated and characterized several point mutations in Aah1p, which increase its stability during quiescence. The majority of the mutated residues are located in two distinct exposed regions in the Aah1p three-dimensional model structure. Two hybrid experiments strongly suggest that these domains are directly involved in interaction with Saf1p. Importantly, we obtained a mutation in Aah1p that does not affect the protein interaction with Saf1p but abolishes Aah1p degradation. Because this mutated residue is an exposed lysine in the Aah1p three-dimensional model, we propose that it is likely to be a major ubiquitylation site. All together, our data strongly argue for Saf1p being a bona fide Skp1-Cullin-F-box subunit. [ABSTRACT FROM AUTHOR]

[Display omitted] • Brewer's spent grain (BSG) fermentation improved its soluble sugars greatly. • The soluble protein in fermented BSG was also improved effectively. • High cellulase activity was obtained in BSG, especially CMCase and FPase. • Ultrasonic pretreatment was beneficial to protease secretion but not to cellulase. • Genome analyse showed that Bacillus velezensis K8 preferred protein to sugars. Low nutritional value and digestive efficiency restrict the feeding application of brewer's spent grain (BSG). Bacillus velezensis has been increasingly considered a promising fermenting agent in feed production. This study aimed to investigate the fermentative characteristics of Bacillus velezensis K8 on degrading lignocellulose and increasing soluble sugar and protein in BSG. The lignocellulose contents (including cellulose, hemicellulose and lignin) decreased by 36.85 % and 27.68 % in BSG and ultrasonic-pretreated BSG (UBSG), respectively. The reducing sugar contents increased by 226.8 % and 198.1 %, and the soluble protein contents increased by 260.7 % and 258.3 % in BSG and UBSG, respectively. The arabinose, cellobiose, xylose, glucose, fructose, and xylooligosaccharides contents were significantly increased, indicating effective conversion of cellulose and hemicellulose into soluble sugars. High cellulase activity was obtained in BSG fermentation, especially CMCase and filter paper activities. Protease secretion increased but cellulase decreased, and the activities of xylanase and fructofuranosidase remained stable in UBSG fermentation. Genome analysis revealed that B. velezensis K8 possessed more amino acid-metabolism genes than carbohydrate-metabolism genes, illustrating that B. velezensis K8 preferentially utilized protein nutrients but left more sugars. These results provide a promising strategy for improving the value of grain residue in food and feed industrial applications. [ABSTRACT FROM AUTHOR]

Recombinant therapeutic proteins are a broad class of biological products used to replace dysfunctional human proteins in individuals with genetic defects (e.g., factor VIII for hemophilia) or, in the case of monoclonal antibodies, bind to disease targets involved in cancers, autoimmune disorders, or other conditions. Unfortunately, immunogenicity (immune response to the drug) remains a key impediment, potentially affecting the safety and efficacy of these therapeutics. Immunogenicity risk is routinely evaluated during the licensure of therapeutic proteins. However, despite eliciting anti-drug immune responses in at least some patients, most protein drugs are nevertheless licensed as they address unmet medical needs. The pre-licensure immunogenicity assessments of therapeutic proteins are the subject of numerous reviews and white papers. However, observation and clinical management of the immunogenicity of approved therapeutic proteins face additional challenges. We survey the immunogenicity of approved therapeutic proteins, discuss the clinical management of immunogenicity, and identify the challenges to establishing clinically relevant immunogenicity assays for use in routine clinical practice. Immunogenicity can compromise the safety and/or efficacy of therapeutic protein products, and is a priority issue for regulatory agencies. In addition to poor patient outcomes, the social and economic costs associated with neutralizing antibodies are considerable. Reliable assays for monitoring anti-drug antibodies (ADAs) and neutralizing antibodies post-licensure are lacking for most therapeutic proteins. [ABSTRACT FROM AUTHOR]

• A new benchmark of protein surfaces equipped with three physicochemical properties. • Protein surfaces are retrieved and classified with respect to different ground truths. • Analysis of the retrieval and classification performances of the methods that participated in SHREC 2021. • A thorough Investigation of how different physicochemical properties impact the performance of retrieval methods. [Display omitted] This paper presents the methods that have participated in the SHREC 2021 contest on retrieval and classification of protein surfaces on the basis of their geometry and physicochemical properties. The goal of the contest is to assess the capability of different computational approaches to identify different conformations of the same protein, or the presence of common sub-parts, starting from a set of molecular surfaces. We addressed two problems: defining the similarity solely based on the surface geometry or with the inclusion of physicochemical information, such as electrostatic potential, amino acid hydrophobicity, and the presence of hydrogen bond donors and acceptors. Retrieval and classification performances, with respect to the single protein or the existence of common sub-sequences, are analysed according to a number of information retrieval indicators. [ABSTRACT FROM AUTHOR]

Papain is a cysteine protease from papaya, with many applications due to its broad specificity. This paper reviews for first time the immobilization of papain on different supports (organic, inorganic or hybrid supports) presenting some of the features of the utilized immobilization strategies (e.g., epoxide, glutaraldehyde, genipin, glyoxyl for covalent immobilization). Special focus is placed on the preparation of magnetic biocatalysts, which will permit the simple recovery of the biocatalyst even if the medium is a suspension. Problems specific to the immobilization of proteases (e.g., steric problems when hydrolyzing large proteins) are also defined. The benefits of a proper immobilization (enzyme stabilization, widening of the operation window) are discussed, together with some artifacts that may suggest an enzyme stabilization that may be unrelated to enzyme rigidification. • Advantages and problems of proteases immobilization are discussed. • Immobilization of papain in organic, inorganic and hydroid materials is discussed. • Most used groups to get covalent immobilization are presented. • Magnetic supports advantages are discussed. [ABSTRACT FROM AUTHOR]

The influence of different wastewater compositions on the extracellular polymer substances (EPS) (protein, polysaccharide and DNA) and physicochemical properties (surface charge, bound water and contact angle) were studied in continuous fed completely stirred tank reactor (CSTR). Five laboratory-scale activated sludge reactors were operated under steady-state conditions. Protein was the predominant polymer followed by polysaccharide and DNA. Lower amounts of protein and higher DNA levels were found in the extracellular substances from flocs grown on more complex organics and substrates. A high level of protein (nearly 70 mg g−1 VSS) and a low DNA content (nearly 6 mg g−1 VSS) were measured in the EPS of the winery industry and municipal activated sludge while lower levels of protein (approximately 38–42 mg g−1 VSS) and higher levels of DNA content (approximately 11–17 mg g−1 VSS) were measured in the pulp-paper, textile (cotton knit fabrics) and petrochemical floc EPSs under steady-state conditions. Flocs with small (36 μm) and large (nearly 130 μm) diameters were observed in the pulp-paper, textile and petrochemical industries, respectively, associating with high SVI values. Larger contact angles (between 37 and 42°), low negatively charged surface values (between −0.11 and −0.25 meq g−1 VSS) and high amounts of bound water (between 20 and 24 g g−1 TSS) were determined in the pulp-paper, textile and petrochemical industry activated sludge samples. However, floc samples from the municipal and winery industry activated sludge had small contact angles (between 7 and 9°) and low bound water content (7–9 g g−1 TSS) together with high surface charge values (between −0.55 and −0.61 meq g−1 VSS), indicating good settleability. Since the reactor design of the five laboratory-scale reactor were similar and different wastewater were compared, it can be said that the EPS composition depends more on wastewater type rather than operating conditions. [Copyright &y& Elsevier]

Prediction of protein structural class plays an important role in protein structure and function analysis, drug design and many other biological applications. Prediction of protein structural class for low-similarity sequences is still a challenging task. Based on the theory of wavelet denoising, this paper presents a novel method of prediction of protein structural class for the first time. Firstly, the features of the protein sequence are extracted by using Chou’s pseudo amino acid composition (PseAAC). Then the extracted feature information is denoised by two-dimensional (2D) wavelet. Finally, the optimal feature vectors are input to support vector machine (SVM) classifier to predict protein structural classes. We obtained significant predictive results using jackknife test on three low-similarity protein structural class datasets 25PDB, 1189 and 640, and compared our method with previous methods The results indicate that the method proposed in this paper can effectively improve the prediction accuracy of protein structural class, which will be a reliable tool for prediction of protein structural class, especially for low-similarity sequences. [ABSTRACT FROM AUTHOR]

Purpose: By 2050 it is projected that 115 million people worldwide will have Alzheimer's Disease (AD) [1]. Recent attempts have been made to redefine the diagnostic criteria of AD to include markers of neurodegeneration - measurable by FDG-PET - and markers of amyloid accumulation - measurable by amyloid-PET.Materials and Methods: A systematic review of the literature was performed to examine the current diagnostic use of amyloid and FDG PET. MEDLINE and EMBASE databases and the Cochrane Database were searched for relevant papers RESULTS AND DISCUSSION: This search resulted in twenty-nine papers on amyloid imaging, twenty-three papers on FDG-PET and eight papers which utilized both techniques. Both modalities are considered in turn with regards to their diagnostic accuracy, their role in mild cognitive impairment (MCI) and prognostication, their use in the differential diagnosis of AD and their clinical application. As evidenced from the current literature, both amyloid and FDG-PET meet criteria for suitable biomarkers for the diagnosis of AD. They both indicate pathophysiological processes, albeit at different stages of the Alzheimer's process, and are distinct from normal patterns of aging.Conclusion: Both techniques have been shown to detect AD with high sensitivity and specificity compared to other neurodegenerative processes and cognitively normal age-matched individuals. However, future studies with standardised, uniform thresholds and a lengthier longitudinal follow-up need to be conducted to allow us to make surer conclusions about the future role of PET in clinical practice. In addition, comparison with post-mortem diagnosis, rather than clinical diagnosis with its acknowledged flaws, would result in more powerful statistical outcomes - which is becoming increasingly important given that several disease-modifying AD drugs are now in phase 3 trials. [ABSTRACT FROM AUTHOR]

Water soluble polymers and their derivatives bound to proteins can dramatically favor the biological activity of new drugs and vaccines. Quantification of the modification degree of the protein is crucial during the development and licensing phase and later in order to monitor the industrial production process and to match product specification. In this work, we describe an innovative way to measure directly the modification degree of polysialylated proteins using proton NMR (Nuclear Magnetic Resonance) spectroscopy. Following a calibration step, the modification degree can be easily deduced by the integration ratio of a separate signal from the polymer and selected signals from the protein. In fact, the upfield-shifted signals of methyl groups from Valine, Leucine and Isoleucine can be used as an internal calibration reference for the integration. In this paper recombinant factor VIII (rFVIII) and recombinant factor IX (rFIX) proteins modified by polysialic acid (PSA) are used to illustrate the accuracy, reproducibility and ease of the method that may replace or complement wet-chemistry approaches. [ABSTRACT FROM AUTHOR]

Over the course of a few decades, the concern of environmental damages of fossil fuels, an increase in CO 2 emission and a decrease of hydrogen have been growing more and more. Accordingly, hydrogen production is a crucial issue nowadays. Different polymers are applied to attain the purpose. Among all polymers, biodegradables polymers are the best choices to develop the main aim. Polysaccharides and proteins are biodegradable polymers with unique places and advantages with regards to their ecofriendly properties. There are different techniques to apply and achieve the foremost purpose. It is worthwhile to mention that green and facile methods are always attracting attention in different aspects and fields. The three non-polluting and economical techniques, that is, electrochemical hydrogen evolution reaction (HER), photocatalytic technique, and hydrolysis of hydrides, are reviewed in this paper. This review helps researchers, who are environment supporters, to evaluate and choose the most ecological biopolymers and processes in their work. [Display omitted] • Developments in hydrogen evolution by biopolymer-derived (nano)catalysts have been described. • Summary of synthetic procedures to obtain biopolymer-derived (nano)catalysts. • Future challenges of hydrogen evolution using biopolymer-derived (nano)catalysts have been discussed. [ABSTRACT FROM AUTHOR]

Renewable resources including polycarbohydrates, lignin, proteins, and polyacids are the intrinsically valuable class of materials that are naturally available in great quantities. Their utilization as green additives and reinforcing bio-fillers, in substitution of environmentally perilous petroleum-based fillers, for developing high-performance green rubber blends and composites is presently a highly tempting option. Blending of these renewable materials with elastomers is not straight-forward and research needs to exploit the high functionality of carbohydrates and other natural materials as proper physicochemical interactions are essential. Correlating and understanding the structural properties of lignin, carbohydrates, polyacids, and other biopolymers, before their incorporation in elastomers, is a potential approach towards the development of green elastomers for value-added applications. Promising properties i.e., biodegradability, biocompatibility, morphological characteristics, high mechanical properties, thermal stability, sustainability, and various other characteristics along with recent advancements in the development of green elastomers are reviewed in this paper. Structures, viability, interactions, properties, and use of most common natural polycarbohydrates (chitosan and starch), lignin, and proteins (collagen and gelatin) for elastomer modification are extensively reviewed. Challenges in commercialization, applications, and future perspectives of green elastomers are also discussed. Sustainability analysis of green elastomers is accomplished to elaborate their cost-effectiveness and environmental friendliness. • Structural performance and interaction of carbohydrates, lignin, proteins, and polyacids with an elastomeric material • Potential approaches to the development of green technology based on biobased macromolecules • Promising high-performance properties of green elastomers material comprised of proteins, lignin, and polysaccharides • High morphological performance of green rubber blends with biological macromolecules • Cradle-to-grave life cycle model of green elastomers [ABSTRACT FROM AUTHOR]

Post-translational transformation of cysteine residues to persulfides, known as protein S-sulfhydration or persulfidation, is a beneficial H 2 S signaling mechanism. In this paper, we found that GSH is bound to active cysteine sites of protein by S-desulfurization, which is a new covalent modification mechanism of protein, thus regulating catalytic activity. Here, we provide direct evidence that GSH modifies the reactive cysteine residues of four enzymes (alliinase/ D -LDH/ADH/G6PD) and generates protein-SG or protein-SSG derivatives by S-desulfurization. S-desulfurization, α-carbon nucleophilic substitution or thiol-disulfide exchange occurs and H 2 S is released as a by-product. S-desulfurization is the opposite of persulfidation in terms of H 2 S production/consumption and enzyme inhibition/mitigation. Here, we elucidated the GSH mechanisms and H 2 S mechanisms in the enzyme-metabolite system and the beneficial roles of persulfidation and S-desulfurization. These theoretical findings are now shedding light on understanding GSH and H 2 S molecular functions and providing new theoretical basis for them in cell signaling pathways. [Display omitted] • GSH-modified proteins forming protein-SG derivatives is named S-desulfurization. • S-desulfurization is a protein modification mechanism with a sulfur atom minus. • Moderate GSH concentrations alleviate inactivation against persulfidation. • Persulfidation of DADS/DATS/allicin is an enzyme-metabolite protection. [ABSTRACT FROM AUTHOR]

Current parenteral containers used for the storage and delivery of protein-based drugs, contain silicone oil which may seep into the protein solution and can result in adsorption, aggregation and denaturation of the protein. Tightly adherent surface coatings prepared by radio frequency glow-discharge (RFGD) plasma polymerization are described in this paper. Using this robust technique, methacrylic acid (MA) (hydrophilic), hexamethyldisiloxane (HMDSO) (hydrophobic), tetraglyme (TG) (hydrophilic) were plasma polymerized onto glass. In addition, HMDSO and MA were copolymerized to create a plasma polymerized HMDSO-MA (hydrophobic) surface. Untreated glass and glass dip-coated in PDMS were used as controls. TG and MA plasma coatings adsorbed the least amount of protein in all pH conditions. Interestingly HMDSO-MA retained significantly lesser protein compared to HMDSO and dip-coated PDMS samples. In the presence of Polysorbate 80 (PS80) all plasma polymerized coatings adsorbed and retained negligible amounts of protein, compared to controls. Furthermore, the peak glide force of plasma coated syringes did not significantly increase compared to syringes without plasma coating. Due to the versatility of RFGD plasma, this process is scalable and could potentially be used for the treatment of hypodermic syringes used for the storage and delivery of protein-based therapeutics. [ABSTRACT FROM AUTHOR]

Autophagy is a catabolic process in which a double-membrane organelle, the autophagosome (AP), engulfs cellular components that will be degraded in the lysosomes. ATG8 protein family members participate at various stages of AP formation. The present study compares the capacity to induce lipid-vesicle tethering and fusion of two ATG8 family members, LC3B and LC3C, with model membranes. LC3B is the most thoroughly studied ATG8 protein. It is generally considered as an autophagosomal marker and a canonical representative of the LC3 subfamily. LC3C is less studied, but recent data have reported its implication in various processes, crucial to cellular homeostasis. The results in this paper show that LC3C induces higher levels of tethering and of intervesicular lipid mixing than LC3B. As the N-terminus of LC3C is different from that of the other family members, various mutants of the N-terminal region of both LC3B and LC3C were designed, and their activities compared. It was concluded that the N-terminal region of LC3C was responsible for the enhanced vesicle tethering, membrane perturbation and vesicle-vesicle fusion activities of LC3C as compared to LC3B. The results suggest a specialized function of LC3C in the AP expansion process. [ABSTRACT FROM AUTHOR]

The stability of food emulsions is the basis for other properties. During their production and processing, emulsions tend to become unstable due to their thermodynamic instability, and it is usually necessary to add emulsifiers and proteins to stabilize emulsions. It becomes crucial to study the intrinsic mechanisms of emulsifiers and proteins and their joint stabilization of food emulsions. This paper summarizes the research on intrinsic mechanisms of food emulsions stabilized by emulsifiers and proteins in recent years. The destabilization and stabilization of emulsions are related to the added surfactants. The properties, type, and concentration of emulsifiers determine the stability of emulsions, and the emulsifiers can be classified into different types (e.g., ionic or nonionic, solid or liquid) according to their properties and sources. The physicochemical properties of proteins (e.g., spatial conformation, hydrophobicity) and the composition of proteins can also determine the stability of emulsions, and emulsions stabilized by emulsifiers and proteins together not only depend on these factors but also have a great relationship with the mutual combination and competition between the two. The instability and stability of emulsions are related to factors such as interfacial interaction forces, the rheological nature of the interface, and the added surfactant. [ABSTRACT FROM AUTHOR]

Polymer-based pH-responsive fluorescent materials have the characteristics of fast response, real-time monitoring, visualisation, and easy forming. Consequently, they have attracted widespread attention in wound healing, sweat monitoring, security and anti-counterfeiting, freshness detection of aquatic products, metal-ion sensing and bioimaging. This paper analyses the preparation principles and characteristics of pH-responsive fluorescent materials based on cellulose, chitosan and proteins. It then outlines the fluorescence properties, environmental response mechanisms and applications of various luminescent materials. Next, the research indicates that amines, N -heterocyclic rings, carboxyl groups and amino plasmonic groups on the fluorescent molecule structure and polymer skeleton appear to change the degree of ionisation under acid or alkali stimulation, which affects the light absorption ability of chromophore electrons, thus producing fluorescence changes in fluorescent materials under different pH stimuli. On this basis, the challenges and growth encountered in the development of proteins and polysaccharides–based pH-responsive fluorescent materials were prospected to provide theoretical references and technical support for constructing pH-responsive fluorescent materials with high stability, high sensitivity, long-lasting pH-response and wide detection range. [ABSTRACT FROM AUTHOR]

The use of raw materials from natural sources as substitutes for petrochemical monomers is of high interest in the polymer science, to comply with the increasing social awareness of pollution and environmental regulations. Natural proteins emerge as particularly promising candidates to be combine with synthetic polymers, offering the prospect of enhancing the product sustainability. Nonetheless, protein-based hybrid materials still present some drawbacks such as high susceptibility to water, due to the incorporation of hydrophilic protein and the resulting morphology of hybrid particles. In the present study, we propose a novel approach for synthesizing biphasic hybrid particles with a controlled morphology that tend to optimize the synergy between both phases. Here, protein phase forms the core of hybrid particles, which is surrounded by an acrylic polymer phase. To achieve this particular morphology, a seeded semibatch emulsion polymerization strategy was designed by employing preformed zein-casein bioparticles (BPs) as seed. This paper encompassed a comprehensive exploration of the key variables impacting on both the synthesis of BPs and the subsequent formation of hybrid latex particles. The outcomes of this research not only contribute to a deeper understanding of the synthesis process but also broaden the potential applications of acrylic-protein hybrid films, particularly as coatings. [Display omitted] • Hybrid latex produced by emulsion polymerization using protein bioparticles as seed • Acrylic-protein particles exhibiting a non-equilibrium multi-lobular morphology • Hybrid films with improved water resistance for coating applications [ABSTRACT FROM AUTHOR]

Although rare earth element (REE) complexes are often utilized in bioimaging due to their photo- and redox stability, magnetic and optical characteristics, they are also applied for pharmaceutical applications due to their interaction with macromolecules namely proteins. The possible implications induced by REEs through modification in the function or regulatory activity of the proteins trigger a variety of applications for these elements in biomedicine and biotechnology. Lanthanide complexes have particularly been applied as anti-biofilm agents, cancer inhibitors, potential inflammation inhibitors, metabolic elicitors, and helper agents in the cultivation of unculturable strains, drug delivery, tissue engineering, photodynamic, and radiation therapy. This paper overviews emerging applications of REEs in biotechnology, especially in biomedical imaging, tumor diagnosis, and treatment along with their potential toxic effects. Although significant advances in applying REEs have been made, there is a lack of comprehensive studies to identify the potential of all REEs in biotechnology since only four elements, Eu, Ce, Gd, and La, among 17 REEs have been mostly investigated. However, in depth research on ecotoxicology, environmental behavior, and biological functions of REEs in the health and disease status of living organisms is required to fill the vital gaps in our understanding of REEs applications. [ABSTRACT FROM AUTHOR]

• Ιonic liquids as resolution-enhancing background electrolyte additives in CE. • Utilization of ionic liquids as capillary coating materials. • CE and CEC analysis of proteins using regular and polymeric ionic liquids. • Ιonic liquid-mediated capillary electrophoresis analysis of carbohydrates. Ionic liquids (ILs), as non-molecular type solvents, possess excellent physical-chemical properties, which make them useful in important separation applications in gas chromatography, liquid chromatography, and capillary electrophoresis. Among a plethora of potential uses of ionic liquids in separation science, capillary electrophoresis can utilize its resolution-enhancing effect in the analysis of proteins and carbohydrates, via the formation of intermolecular interactions, e.g., hydrophobic, hydrogen bonding, or electrostatic. ILs and polymeric ionic liquids (PIL) also represent an excellent choice as background electrolyte (BGE) additives for capillary coatings in CE, which is especially important in protein analysis. Another interesting utilization of ILs is the fabrication of monoliths for capillary electrochromatography in which instance the mechanism of retention is based on ion exclusion interactions. Carbohydrates can also be readily analyzed by CE with the help of ionic liquids without the need for an extra derivatization step. One of the future perspectives on the use of ILs is their utilization in the recently emerging biopharmaceutical industry exploiting the increased resolution of proteins and carbohydrates, two of the important components of glycoprotein therapeutics. In this paper, we address the so-far not-reviewed ionic liquid-mediated analysis of proteins and carbohydrates by capillary electrophoresis-based techniques also addressing their impact on the separation mechanism. [ABSTRACT FROM AUTHOR]

Fish swim bladder (FSB) protein possesses inherent health and nutritional value. Recent studies have shown that its pharmacological, biomedical, and nutritional benefits can be enhanced through extraction, purification and concentration processes. Additionally, research indicates that modifications such as cross-linking, decellularization, doping, glycation, and hydrolysis can further enhance the utility of FSB protein in various applications. This paper provides a comprehensive review on FSB protein products, focusing on modifications, functionalities, bioactivities, and mechanisms uncovered through various techniques, including in vitro , ex vivo , in vivo , and in silico methods. FSB protein and its products exhibit various biological activities including antioxidant, anti-inflammatory, wound healing, anti-aging, and others. While drying FSB to fish maw (FM) remains popular, recent trends, including producing FM-related products, enzymatic hydrolysis, extracting collagen and gelatin, and decellularization are rising. The results indicate the significant potential of FSB protein products as nutraceuticals, biomedicals, and therapeutics to alleviate health concerns. Clinical safety, the fate of ingested and absorbed compounds, nutrient-nutrient interactions, and changes in structure post-absorption are gaps that require further research. [Display omitted] • Fish swim bladder (FSB) proteins exhibit a variety of biological activities. • FSB is consumed fresh or is dried to fish maw. • FSB proteins are used to extract multiple functional and high-value products. • Further research is needed on clinical safety and fate of ingested FSB peptides. [ABSTRACT FROM AUTHOR]

This paper presents a comprehensive analysis of deep transfer learning methods, supervised methods, and semi-supervised methods in the context of protein fitness prediction, with a focus on small datasets. The analysis includes the exploration of the combination of different data sources to enhance the performance of the models. While deep learning and deep transfer learning methods have shown remarkable performance in situations with abundant data, this study aims to address the more realistic scenario faced by wet lab researchers, where labeled data is often limited. The novelty of this work lies in its examination of deep transfer learning in the context of small datasets and its consideration of semi-supervised methods and multi-view strategies. While previous research has extensively explored deep transfer learning in large dataset scenarios, little attention has been given to its efficacy in small dataset settings or its comparison with semi-supervised approaches. Our findings suggest that deep transfer learning, exemplified by ProteinBERT, shows promising performance in this context compared to the rest of the methods across various evaluation metrics, not only in small dataset contexts but also in large dataset scenarios. This highlights the robustness and versatility of deep transfer learning in protein fitness prediction tasks, even with limited labeled data. The results of this study shed light on the potential of deep transfer learning as a state-of-the-art approach in the field of protein fitness prediction. By leveraging pre-trained models and fine-tuning them on small datasets, researchers can achieve competitive performance surpassing traditional supervised and semi-supervised methods. These findings provide valuable insights for wet lab researchers who face the challenge of limited labeled data, enabling them to make informed decisions when selecting the most effective methodology for their specific protein fitness prediction tasks. Additionally, the study investigated the combination of two different sources of information (encodings) through our enhanced semi-supervised methods, yielding noteworthy results improving their base model and providing valuable insights for further research. The presented analysis contributes to a better understanding of the capabilities and limitations of different learning approaches in small dataset scenarios, ultimately aiding in the development of improved protein fitness prediction methods. • Deep transfer learning excels in small dataset protein fitness prediction. • We explore labeled-unlabeled data combination through semi-supervised learning. • We developed enhanced semi-supervised methods for regression and multi-view tasks. • Information combination from different encodings holds potential for future research. • Insights can aid wet lab researchers in selecting protein fitness prediction methods. [ABSTRACT FROM AUTHOR]

[Display omitted] • Maximal VFAs and hydrogen yields reached 0.66 g/g-VS and 109 mL/g-VS, respectively. • SCG-derived VFAs offer a potential feedstock for microbial protein production. • Candida maltosa KKU-ARY2, a newly isolated yeast, accumulated protein of 43%. • Recycled solid residue after VFAs separation showed a promising methane production. Recovering nutrients from waste for biological processes aligns with sustainability principles. This study aimed to convert spent coffee grounds (SCG) into valuable products, including fermentable sugars, volatile fatty acids (VFAs), yeast-based single-cell protein and biofuels. Alkaline pretreatment was conducted before enzymatic hydrolysis, in which the pretreated SCG was hydrolyzed with varying enzyme loadings (20–60 filter paper units (FPU)/g-solid) and solid loadings (3–15 % w/v). The hydrolyzed slurry was utilized for VFAs and hydrogen production, yielding high values of 0.66 g/g-volatile solids (VS) and 109 mL/g-VS, respectively, using an enzyme loading of 50 FPU/g-solid and a solid loading of 3 % (w/v). The derived VFAs were used to cultivate a newly isolated yeast, Candida maltosa KKU-ARY2, resulting in an accumulated protein content of 43.7 % and a biomass concentration of 4.6 g/L. This study highlights the conversion of SCG into essential components, emphasizing the benefits of waste utilization through cascade bioprocesses. [ABSTRACT FROM AUTHOR]

Nano drug delivery systems offer several benefits, including enhancing drug solubility, regulating drug release, prolonging drug circulation time, and minimized toxicity and side effects. However, upon entering the bloodstream, nanoparticles (NPs) encounter a complex biological environment and get absorbed by various biological components, primarily proteins, leading to the formation of a 'Protein Corona'. The formation of the protein corona is affected by the characteristics of NPs, the physiological environment, and experimental design, which in turn affects of the immunotoxicity, specific recognition, cell uptake, and drug release of NPs. To improve the abundance of a specific protein on NPs, researchers have explored pre-coating, modifying, or wrapping NPs with the cell membrane to reduce protein adsorption. This paper, we have reviewed studies of the protein corona in recent years, summarized the formation and detection methods of the protein corona, the effect of the protein corona composition on the fate of NPs, and the design of new drug delivery systems based on the optimization of protein corona to provide a reference for further study of the protein corona and a theoretical basis for the clinical transformation of NPs. [Display omitted] • Mechanism of protein corona formation • Formation of protein corona affects the fate of nanoparticles in vivo • Using protein corona to facilitate the research of nanodistribution system [ABSTRACT FROM AUTHOR]

• GCP and glucose play a synergistic role in preparing the freeze–thaw stable HIPE. • The synergistic effect is related to GCP grafting degree and residual sugar level. • Using GCP reduce the amount of glucose used in preparing freeze–thaw stable HIPE. Nowadays, glycosylated protein seems to be one of the most effective stabilizers for preparing freeze–thaw stabile emulsion; nevertheless, few papers mentioned the relationship between the residual free sugars after the glycosylation reaction and the freeze–thaw stability of high internal phase emulsions (HIPEs). Herein, glucose was used to prepare glycosylated cod proteins (GCPs). The synergistic effect was related to the grafting degree of GCP, and the amount of glucose added to prepare freeze–thaw stable HIPEs was reduced from 20% to 4% when the grafting degree of GCP increased from 0% to 31.58% (i.e. 12% GCP). This might be due to fewer ice crystals forming in water phase or less destruction of emulsion droplets by ice crystals. The obtained results in this study will allow developing freeze–thaw stable HIPEs or new frozen ingredients. [ABSTRACT FROM AUTHOR]

Erigeron breviscapus is a common medicine of eight ethnic minorities, including Miao, Naxi, and Yi. As early as the Ming Dynasty (AD 1368–1644), Lanmao's Materia Medica of Southern Yunnan (AD 1436) recorded that the medicine is used for the treatment of "Zuo tan you huan." In modern pharmacological research, Erigeron breviscapus injection is the most commonly used preparation in the treatment of ischemic stroke caused by acute cerebral infarction, but its mechanism of action in the treatment of ischemic stroke is not well understood. In this study, a metabonomics study based on ultraperformance liquid chromatography–quadrupole time-of-flight tandem mass spectrometry (UPLC-QTOF-MS) was used in investigating the effect of a traditional Chinese medicine preparation Erigeron breviscapus injection on the rat model of focal cerebral ischemia-reperfusion and the affinity of its main components with the targets of mitochondrial apoptotic pathways. This study used molecular docking technology to verify the effective binding ability of main effective components of Erigeron breviscapus injection to target proteins related to mitochondrial apoptosis pathway. This study developed a metabonomics method based on the ultra-performance liquid chromatography combined with quadrupole time-of-flight tandem mass spectrometry (UPLC Q-TOF MS) to evaluate the efficacy and study the mechanism of traditional Chinese medicine preparation. With pattern recognition analysis (principal component analysis and partial least squares-discriminate analysis) of urinary metabolites, a clear separation of focal cerebral ischemia-reperfusion model group and healthy control group was achieved. Erigeron breviscapus injection can significantly reduce the area of cerebral infarction, improve tissue morphological lesion in rats, and can increase the number of Nissl bodies. It may be a promoting factor by inhibiting hippocampal nerve cell apoptosis and Bax protein expression and by exerting effects against ischemia reperfusion after the induction of apoptosis. Thus, it plays a role in brain protection. Moreover, it can considerably promote the recovery of neurological deficiency signs in advance. Meanwhile, Erigeron breviscapus decreased malondialdehyde content and T-NOS activity. Its curative effect from strong to weak order: low dose > high dose > medium dose. The representative components of Erigeron breviscapus have good affinity with the active sites of mitochondrial apoptosis-related proteins. Metabolomics found that the potential biomarkers regulated by breviscapine are kynurequinolinic acid, succinylornithine, and leucine proline. It is speculated that it may participate in TRP–kynurequinolinic acid and succinylornithine–urea cycle–NO metabolic pathways. This paper revealed the potential biomarkers and metabolic pathways regulated by Erigeron breviscapus. It was speculated that the mechanism is related to its inhibition of mitochondrion-mediated apoptosis. Erigeron breviscapus could restore the metabolic profiles of the model animals to normal animal levels. The mechanism may be related to the potential biomarkers of quinolinic acid, succinylornithine, and leucine proline and the metabolic pathways involved. However, the exact mechanism by which Erigeron breviscapus inhibits mitochondrion-mediated apoptosis remains to be further explored. [Display omitted] • The metabolic profile of cerebral ischemia-reperfusion injury model rats regulated by Breviscapus injection were revealed. • A new method of metabolomics combined with pharmacodynamics to evaluate the effectiveness of ethnomedicine was explored. • Erigeron breviscapus has high research value. • Erigeron breviscapus is a common medicine of eight ethnic minorities, such as the Miao, Naxi and Yi nationalities. [ABSTRACT FROM AUTHOR]

• Modifications in Fc and VH3 binding region of ProA ligand can allow mild elution pH. • Jetted A50 HipH can elute Fc-containing proteins at or above pH 4.6. • Mild elution pH can be achieved with high yield and >50 % HMW reduction. • pH-sensitive proteins can elute within stable pH region and stay stable over time. • Jetted A50 HipH is a flexible platform ProA resin for stable and labile proteins. Protein A affinity chromatography is widely used as a capture step for monoclonal antibodies (mAb) and molecules that possess an Fc-domain, such as fusion proteins and bispecific antibodies. However, the use of low pH (3.0–4.0) to elute the molecule and achieve acceptable yield (>85 %) can lead to product degradation (e.g. fragmentation, aggregation) for molecules sensitive to low pH. In this paper, we describe a comprehensive evaluation of two protein A resins with ligands designed to elute at a milder pH as a result of modified sequences in their Fc and VH3 binding regions. One of the evaluated resins has been made commercially available by Purolite and named Praesto Jetted A50 HipH. Results demonstrated that Jetted A50 HipH could elute the Fc-fusion protein and most mAbs evaluated with an elution pH at or above 4.6. Elution and wash optimization determined run conditions for high recovery (>90 % monomer yield), reduction of high molecular weight (HMW) species (>50 %), and significant host cell protein (HCP) clearance at the mildest elution pH possible. For a pH-stable mAb and a pH-sensitive fusion protein, cell culture material was purified with optimized conditions and demonstrated the mild elution pH resins' ability to purify product with acceptable yield, comparable or better impurity clearance, and significantly milder native eluate pH compared to traditional resins. The benefits of the mild elution pH resins were clearly exemplified for the pH-sensitive protein, where a milder elution buffer and native eluate pH resulted in only 2 % HMW in the eluate that remained stable over 48 h. In contrast, a traditional protein A resin requiring low pH elution led to eluate HMW levels of 8 %, which increased to 16 % over the same hold time. Additionally, these resins have high dynamic binding capacity and allow the use of traditional HCP washes. Therefore, Jetted A50 HipH is an ideal candidate for a platform protein A resin and provides flexibility for pH-sensitive proteins and stable mAbs, while preserving product quality, recovery, and seamless integration into a downstream process. [ABSTRACT FROM AUTHOR]

Amyloid fibers formed by the aggregation of amyloid proteins can lead to various neurological diseases. Accurate prediction of amyloid proteins can provide scientific basis for exploring the pathogenesis of related neurological diseases, and developing targeted treatment plans. In view of the limitations of the synthetic minority over-sampling technique (SMOTE), an improved SMOTE method based on density clustering is proposed in this paper, and combined with multi-view features to construct an amyloid protein prediction model. The benefits of this enhanced SMOTE method include eliminating problematic samples, accomplishing an evenly distributed minority sample pool, and utilizing all available boundary sample information. Compared with other over-sampling methods, this method can effectively improve the authenticity and representativeness of the synthesized samples, and has a strong ability to process imbalanced data. After the dataset is over-sampling, different prediction algorithms are trained respectively to construct the baseline models. To fully characterize proteins, the probability and category features are extracted from the baseline models and combined with the sequence features selected by CFS-GSSS (Correlation-based Feature Selection Combined with Greedy Stepwise Search Strategy) to generate the multi-view features. Experimental results demonstrate the complementarity and feasibility of the multi-view features. On the independent test set, compared with the existing best model (ECAmyloid), the proposed amyloid protein prediction model improved the sensitivity and geometric mean by 0.0706 and 0.0129, respectively, far superior to other existing methods. • Sequence composition, evolutionary, structural and physicochemical properties are extracted. • Correlation-based Feature Selection is performed to remove redundancy features. • A density-based minority over-sampling technique is proposed to balance the dataset. • Multi-view features are proposed to fully characterize the proteins. • Compared with existing methods, the proposed predictor exhibits superior performance. [ABSTRACT FROM AUTHOR]

Atomic Force Microscope (AFM) is a widely used tool in force spectroscopy studies. Presently, this instrument is accessible from numerous vendors, albeit commercial solutions are expensive and almost always hardware and software closed. Approaches for open setups were published, as with modern low cost and readily available piezoelectric actuators, data acquisition interfaces and optoelectronic components building such force spectroscopy AFM is relatively easy. However, suitable software to control such laboratory made instrument was not released. Developing it in the lab requires significant time and effort. Our Nanopuller software described in this paper is intended to eliminate this obstacle. With only minimum adjustments this program can be used to control and acquire data with any suitable National Instruments universal digital/analog interface and piezoelectric actuator analog controller, giving significant freedom and flexibility in designing force spectroscopy experiment. Since the full code, written in a graphical LabVIEW environment is available, our Nanopuller can be easily customized. In this paper we describe the program and test its performance in controlling different setups. Successful and accurate force curve acquisition for standard samples (single molecules of I27O reference titin polyprotein and DNA as well as red blood cells) is shown. [ABSTRACT FROM AUTHOR]

Chronic diseases are becoming more prevalent, and the complexities of managing patients continue to escalate, since their care must be balanced between the home and clinical settings. Diabetes is the most advanced example, where self-monitoring has been shown to be necessary. Glucometers are point-of-care (POC) devices that have become standard platforms at home and clinical settings. Similarly, many other POC biosensors have also been developed. Enzymes are often used in these sensors because of their specificity and the reaction products can be electrochemically transduced for the measurement. When enzymes are immobilized to an electronically active substrate, enzymatic reactions can be transduced by direct electron transport. This paper describes an approach for the development of graphene-based POC devices. This includes modifying enzymes for improved performance, developing methods to bind them to the graphene surface, incorporation of the functionalized graphene on a field-effect transistor (FET), and integration into a microfluidic device suitable for home use. This paper describes an approach for the development of a graphene-based POC biosensor platform using glucose as an example of target molecule. [ABSTRACT FROM AUTHOR]

Hydrophilisation of polyethersulfone (PES) based membrane is often achieved by addition of polyvinylpyrrolidone (PVP) leading to a physical blend of the two polymers. This paper shows that the most commonly used membrane for UF in dairy industry is a PES/PVP based one. Nevertheless if hydrophilisation limits the organic fouling, PVP is also the Achilles heel of these membranes. It is particularly true when membranes are exposed to hypochlorite as it is the case for cleaning/disinfection steps. Evidencing the disappearance of PVP from a pristine PES/PVP membrane can be easily achieved by FTIR-ATR analyses. But when one wants to study the ageing of a membrane used in UF it gets more complicated: regardless of the cleaning efficiency the membrane always remains fouled by some proteins. As both PVP and proteins own chemical bounds leading to absorption at the same wavenumber in FTIR-ATR, it thereby prevents the easy highlighting of the PVP degradation. The aim of this paper is to propose a simple treatment of raw FTIR-ATR spectra to dissociate these two contributions, allowing consequently the study of the degradation of a fouled membrane. Then the procedure is applied to a real case study on a spiral membrane. [ABSTRACT FROM AUTHOR]

Ethylene oxide (EtO) is widely used in sterilization of drug product primary containers and medical devices. The impact of residual EtO on protein therapeutics is of significant interest in the biopharmaceutical industry. The potential for EtO to modify individual amino acids in proteins has been previously reported. However, specific identification of EtO adducts in proteins and the effect of residual EtO on the stability of therapeutic proteins has not been reported to date. This paper describes studies of residual EtO with two therapeutic proteins, a PEGylated form of the recombinant human granulocyte colony-stimulating factor (Peg- GCSF) and recombinant human erythropoietin ( EPO) formulated with human serum albumin ( HSA). Peg- GCSF was filled in an EtO sterilized delivery device and incubated at accelerated stress conditions. Glu-C peptide mapping and LC- MS analyses revealed residual EtO reacted with Peg- GCSF and resulted in EtO modifications at two methionine residues (Met-127 and Met-138). In addition, tryptic peptide mapping and LC- MS analyses revealed residual EtO in plastic vials reacted with HSA in EPO formulation at Met-328 and Cys-34. This paper details the work conducted to understand the effects of residual EtO on the chemical stability of protein therapeutics. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 104:731-739, 2015 [ABSTRACT FROM AUTHOR]

The analysis of the 3D structures of proteins is a very important problem in life sciences, since the geometric set-up of proteins has a deep relevance in many biological processes. The complexity of the analysis and the continuous increase in the number of proteins whose 3D structure is known, call for efficient and quick algorithms. Parallel processing is becoming an enabling tool for such research. A key component in the geometric description of a protein is the structural motif, a 3D element which appears in a variety of molecules and is usually made of just a few simpler structures, the secondary structures elements (SSEs). This paper is an extended version of Ferretti and Musci (2013), and presents the Cross Motif Search (CMS) and the Complete CMS (CCMS) algorithms, two highly optimized and efficient parallel methods to detect the presence and location of all common motifs of secondary structures in a given protein pair (CMS) or across an arbitrary large dataset of proteins (CCMS). The analysis builds on existing approaches, such as Secondary Structure Co-Occurrences (SSC), based on the General Hough Transform (GHT) technique. The main difference between our proposal and the state of the art is the innovative focus that CMS puts on the geometric description of the structural motifs, which could be simply viewed as vectors in a 3D space, rather than on the topological/biological description employed by competing algorithms, such as ProSMoS, PROMOTIF or MASS. The advantage of a geometrical approach is that it enables to retrieve the exact location of the common substructures in a protein pair. The paper analyzes all possible forms of serial and parallelism optimization of the proposed algorithms, both shared memory and message passing. It introduces a complete parallel implementation of CMS, based on OpenMP, and discusses its scalability on shared-memory architectures. Both small-scale and medium-scale testing shows that the methods produces very interesting results in real applications, and scales nicely up to the eight-processor limit. More in-depth testing also shows that the scalability limit is due to the inner structure of the problem, and that the similarities among proteins and the chosen tolerance for the analysis highly affect the overall performance. [ABSTRACT FROM AUTHOR]

A protein coat, termed the protein corona, assembles around the nanocarriers´ surface once it gets in contact with a biological environment. We show that the media used for the washing of protein corona can be crucial. This is true for the downstream analysis as well as for the pre-coating used in in vitro or in vivo. This has been widely overlooked so far. In this paper we focus on eight different washing media and analyze how they influence the composition of the hard protein corona of several nanocarriers incubated with human blood plasma and serum. SDS-PAGE and LC-MS analysis showed major differences in protein corona profiles when using diverse washing media. While plasma and serum proteins already have different complexities, each washing media changes the composition of proteins detected by downstream methods with different key proteins bound to the nanocarriers´ surface. Furthermore, the protein structure of the most abundant blood proteins incubated in the different media was analyzed with nanoDSF. This also emphasized the importance of the washing media, which had a significant influence on the protein adsorption stability. Lastly, cell uptake experiments for HeLa and RAW 264.7 macrophages also indicated an influence of the washing media. In conclusion, picking a specific washing media is on the one hand an important factor for downstream detection of protein compositions and may on the other hand be used to deliberately tune the protein corona for pre-adsorbed proteins from complex protein compositions. This might further support a guided delivery of the nanocarrier to a desired location within a physiological environment. The successfully application of nanocarriers as drug delivery vehicles is currently hampered by a limited understanding of the nanocarriers´ behavior in a complex biological environment. Once the nanocarrier comes into contact with blood plasma or serum, biomolecules rapidly adsorb onto their surface, covering the nanocarriers and forming a protein corona, which then dictates their biological identity. Analyzing the composition of this dynamic network of bound molecules, has already been shown to be influenced by various factors. However, the impact of the washing media used for the protein corona preparation has so far been neglected. In the present study, we demonstrate a quantitative influence of the washing media on the composition of the hard corona of different nanocarrier systems, which additionally affects protein stability and cellular uptake behavior. Image, graphical abstract [ABSTRACT FROM AUTHOR]

Emulsion formation is a major concern when dealing with multiphasic fermentations. Floc- culants can be used together with other demulsification techniques to improve oil recovery in multiphasic fermentations. In this paper, the impact of adding flocculants during a mul- tiphasic fermentation with 10 wt% dodecane, to destabilize the broth emulsion, improve creaming formation and enhance oil recovery is studied. Flocculants, CaCl2 and (NH4)2SO4 were shown to be the most promising flocculants. Flocculant addition, their time of addition, and its impact on multiphasic fermentations has been evaluated by comparing fermentation performance against reference fermentations and three oil recovery methods: gravity settling, gas enhanced oil recovery and centrifugation. When adding 75 mM of (NH4)2SO4 during fermentation, the creaming rate during gravity settling increased 3-fold and the oil recovery by gas enhanced oil recovery was 35%, without altering fermentation performance. Addition of CaCl2 during fermentation resulted in 88% and 67% oil recovery for early and late addition, which is a 4 and 3-fold increase in comparison with the reference. Yet, CaCl2 deviated from standard fermentation performance when added immediately after second phase addition. In conclusion, flocculant addition during multiphasic fermentation can be used to destabilize microbial emulsions and potentially improve in situ oil recovery. [ABSTRACT FROM AUTHOR]

Proteins are essential macronutrients of the human diet. Currently, major dietary sources in developed countries are of animal origin. However, the association of red meat consumption to the increased risks of some health conditions and its unsustainable pressure on the environment have increased the interest in plant proteins as healthier and sustainable alternatives. Of these, legumes have a great potential, but part of their proteins are indigestible due to interaction with other components such as phytate and polyphenols. As such, the quest to improve protein accessibility has become of interest to many researchers. Germination is proposed to be a bioprocess method to improve protein digestibility and protein biological properties. This review discusses the importance of plant proteins and the hindrance of protein digestibility. This paper also highlights the role of germination in the deactivation of antinutritional factors, hydrolysis of indigestible proteins, and improvement of properties and content of proteins of different legume seeds. Protein digestibility is dependent on the nature of antinutritional factors (e.g. trypsin inhibitors and phytate) in the food matrix. Germination represses the activity of trypsin inhibitors and removes the phytate-related inhibition through hydrolysis. Protein content increases in germinated seeds when compared to non-germinated ones, suggesting that proteins were either hydrolysed or dissociated from antinutritional factors. Germination seems like an adequate bioprocessing method to improve the content and nutritional quality of legume seed proteins. • Legumes have high protein content but some of the proteins are not highly digestible. • Legume seed germination degrades antinutritional factors to enhance protein digestibility. • Germination also disrupts the seed microstructure to release proteins from complexes. • Protease activity during germination partially hydrolyses seed proteins to enhance digestibility. • This sustainable bioprocess enhances legume seed protein quality and nutritional prospects. [ABSTRACT FROM AUTHOR]

3- Iso butyl-2-methoxypyrazine (IBMP) is an important odor compound that revives unripe grapes or poor-quality wine. The biosynthesis of IBMP in grape berries is under the catalysis of Vitis vinifera O-methyltranferase 3 (VvOMT3). The homologous verification in this paper was carried out with the transient overexpression technique. The results showed that both the expression levels of the VvOMT3 gene and the IBMP concentration in 'Red globe' grapes increased significantly, which suggested that VvOMT3 could function in the biosynthesis of IBMP. Based on β -glucuronidase (GUS) staining results, blue color was only observed in grape pulp, not in grape skin, which indicated that VvOMT3 was expressed in grape pulp. The outcomes of the subcellular location examination performed on the protoplasts of Arabidopsis thaliana showed that the VvOMT3 protein was located on the inner surface of the cytoplasmic membrane. In summary, the VvOMT3 enzyme may function at the inner surface of the cytoplasmic membrane of pulp cells during grape development. These results will provide a background for future research on the catalytic mechanisms of VvOMT3. • Pulp is the major site where IBMP is synthesized in grape berries. • The VvOMT3 enzyme functions at the inner surface of the cytoplasmic membrane. • The function of VvOMT3 enzyme was confirmed in 'Red globe' berries. [ABSTRACT FROM AUTHOR]

Senescence is a complex cellular state, which can be considered as a stress response phenotype. However, the mechanisms through which cells acquire and maintain this phenotype are not fully understood. In this paper, it is argued that the unfolded protein response (UPR) may represent a signalling platform that is associated with the major senescence hallmarks. [ABSTRACT FROM AUTHOR]

Skin and soft tissue infections are major concerns with respect to wound repair. Recently, anti-bacterial wound dressings have been emerging as promising candidates to reduce infection, thus accelerating the wound healing process. This paper presents our work to develop and characterize poly(vinyl alcohol) (PVA)/chitosan (CS)/silk sericin (SS)/tetracycline (TCN) porous nanofibers, with diameters varying from 305 to 425 nm, both in vitro and in vivo for potential applications as wound dressings. The fabricated nanofibers possess a considerable capacity to take up water through swelling (~325–650%). Sericin addition leads to increased hydrophilicity and elongation at break while decreasing fiber diameter and mechanical strength. Moreover, fibroblasts (L929) cultured on the nanofibers with low sericin content (PVA/CS/1-2SS) displayed greater proliferation compared to those on nanofibers without sericin (PVA/CS). Nanofibers loaded with high sericin and tetracycline content significantly inhibited the growth of Escherichia coli and Staphylococcus aureus. In vivo examination revealed that PVA/CS/2SS-TCN nanofibers enhance wound healing, re-epithelialization, and collagen deposition compared to traditional gauze and nanofibers without sericin. The results of this study demonstrate that the PVA/CS/2SS-TCN nanofiber creates a promising alternative to traditional wound dressing materials. Unlabelled Image • Functional PVA/CS/TCN/SS nanofibers were prepared using the electrospinning method. • Incorporation of sericin into nanofiber results in superior cytocompatibility than PVA/CS/TCN. • Antibacterial performance of nanofiber mats increases with increasing sericin content. • Antibacterial mechanism of the nanofiber-containing sericin is proposed. [ABSTRACT FROM AUTHOR]

Both human telomere and proto-oncogene c-MYC can form G-quadruplex (G4) with various conformations. Porphyrin derivative (TMPyP4) could stabilize G4, and thus is considered as a potential drug for anticancer therapeutics. In this paper, the translocation behaviors of three typical G4s (telomere basket, telomere hybrid-1 and c-MYC Pu22 parallel) and their interaction with TMPyP4 were investigated with a single protein nanopore sensing interface with the same main electrolyte of 0.5 M tetramethylammonium chloride. As observed by the statistics of the dwell time of the current pulses, in the presence of K+, the parallel G4 is more stable than the hybrid-1 G4, while the basket G4 in the presence of Na+ exhibited shortest duration. The dwell time of all of the G4s increased as the result of interaction with TMPyP4, indicating an obvious stabilizing effect. This study demonstrated that the single nanopore sensing interface not only reveal the stability of various G4 conformations at a single-molecule level, but also provide the interaction information of a ligand, which could be useful in the drug design. Image 1 • The translocation behaviors of three G4s G4 were examined, and compared for the first time with nanopore sensing interface. • Interaction of porphyrin derivative TMPyP4 with G4s was investigated and compared with the proposed method. • This work provides a new method for obtaining knowledge about the stability of G4 itself and its interaction with ligand. [ABSTRACT FROM AUTHOR]

• Cold-active enzymes (CAEs) and ice-binding proteins (IBPs) can be industrially exploited. • In food industry CAEs are useful for processing of heat-labile products. • CAEs thermolability is fundamental for sequential molecular biology reactions. • IBPs can preserve the quality of frozen food. • IBPs are "safe" cryoprotectants for cryopreservation of biological materials. Psychrophilic organisms adapted to cold environments produce molecules of relevance for biotechnological application, in particular enzymes active at low temperatures and ice-binding proteins that control the growth of ice crystals. The use of cold-active enzymes supports low temperature processes that preserve heat labile compounds and can result, in some circumstances, in energy saving. Among the several possible applications in biotransformations, this paper focuses on reactions of relevance for the food industry and in molecular biology, representative of different market segments. Ice-binding proteins reduce tissues damage provoked by ice crystals and are therefore of relevance for frozen foods and for the cryopreservation of organs and tissues in the biomedical sector. [ABSTRACT FROM AUTHOR]

Biologics represent the fastest growing sector of the pharmaceutical industry, yet their manufacture lags significantly behind that of small molecule drugs. This paper discusses the main product-related and process-related challenges during the development and production of therapeutic proteins, with particular focus on product heterogeneity and process monitoring and analytics. Emphasis is placed on novel contributions from the field of computational research that aim to enable the application of model-based process control strategies or are working towards the development of a digital twin of bioprocesses. Lastly, we review promising developments in the paradigm shift from batch to continuous processing. [ABSTRACT FROM AUTHOR]

Cell theory, as formulated by Theodor Schwann in 1839, introduced the idea that the cell is the main structural unit of living nature. Later, in solving the problem of cell multiplication, Rudolf Virchow expanded the cell theory with a postulate: all cells only arise from pre-existing cells. But what did the very first cell arise from? This paper proposes extending the Virchow's law by the assumption that between the nonliving protocell and the first living cell the continuity of fundamental physical properties (the principle of invariance of physical properties) is preserved. The protocell is understood here as a cell-shaped physical system on the basis of the self-organized biologically significant prebiotic macromolecules, primarily peptides, having a potential to transform into the living cell. Biophase is considered as the physical basis of the membraneless protocell, the internal environment of which is separated from the external environment due to the phase of adsorbed water. The evidence is given that the first protocells may have been formed on the basis of intrinsically disordered peptides. Data on the similarity of the physical properties of living cells and the following model systems are given: protein and artificial polymer solutions, coacervate droplets, and ion-exchange resin granules. Available data on the similarity of the physical properties of cell models and living cells allow us to rephrase the Virchow's postulate as follows: the physical properties of a living cell could only arise from pre-existing physical properties of the protocell. Image 105 [ABSTRACT FROM AUTHOR]

Plant resistance proteins play a key role in detecting pathogen infection and activating plant defense. Two recent papers by Horsefield et al. and Wan et al. revealed that the TIR domain in resistance (R) proteins functions as an NAD+-cleaving enzyme. This enzymatic activity is induced by pathogen recognition and is indispensable for the R protein-dependent cell death response. [ABSTRACT FROM AUTHOR]

Mussel (Mytilus edulis) by-products consist of materials including byssus threads, shell and discarded whole mussels containing meat. Mussels are a rich source of lipids, proteins, carbohydrates, minerals and other bioactives. This nutrient rich waste can be effectively exploited for high value applications including as functional food and feed ingredients, feed supplements, enzymes and other fine chemicals. The present review paper collates data on (i) the total global production of Mytilus edulis and fractionated by-products available for processing and (ii) potential treatment and extraction strategies used to obtain value-added products. The review also discusses other macromolecules besides proteins including lipids, carbohydrates and minerals and possible uses of these in food packaging, as food preservation agents or as bio-adhesives. Mussel by-products represent a reserve of valuable components like bioactive proteins, polyunsaturated fatty acids, mineral compounds, pigments, enzymes and much more. Though researchers have explored various mussel fractions for target applications, a holistic approach using bioprocessing techniques needs to be employed at a commercial scale. Unless researchers, primary manufacturers and technologists develop an integrated approach to utilize mussel by-products, there will be negative environmental and economic impact. Sustainable by-products supply and scalable technologies will ensure successful bioconversion of by-products into high value end products. • Highlights of the review. • Potential uses of by-products blue mussels are detailed. • Bioprocessing techniques for conversion of mussels to bioactives are shown. • Feed, food, functional food and application as materials are described. [ABSTRACT FROM AUTHOR]

Intrinsic disorder in proteins, a widely distributed phenomenon in nature, is related to many crucial biological processes and various diseases. Traditional determination methods tend to be costly and labor-intensive, therefore it is desirable to seek an accurate identification method of intrinsically disordered proteins (IDPs). In this paper, we proposed a novel D eep learning model for Intrinsically D isordered R egions in P roteins named DeepDRP. DeepDRP employed an innovative TimeDistributed strategy and Bi-LSTM architecture to predict IDPs and is driven by integrated view features of PSSM, Energy-based encoding, AAindex, and transformer-enhanced embeddings including DR-BERT, OntoProtein, Prot-T5, and ESM-2. The comparison of different feature combinations indicates that the transformer-enhanced features contribute far more than traditional features to predict IDPs and ESM-2 accounts for a larger contribution in the pre-trained fusion vectors. The ablation test verified that the TimeDistributed strategy surely increased the model performance and is an efficient approach to the IDP prediction. Compared with eight state-of-the-art methods on the DISORDER723, S1, and DisProt832 datasets, the Matthews correlation coefficient of DeepDRP significantly outperformed competing methods by 4.90 % to 36.20 %, 11.80 % to 26.33 %, and 4.82 % to 13.55 %. In brief, DeepDRP is a reliable model for IDP prediction and is freely available at https://github.com/ZX-COLA/DeepDRP. • The combined use of integrated-view features can enhance the prediction of intrinsically disordered regions. • The transformer-enhanced embeddings are of paramount importance to the IDP prediction. • The TimeDistributed strategy enables information propagation across time steps which is useful for IDP prediction. • DeepDRP utilizes Bi-LSTM to capture the bidirectional contextual information of proteins. [ABSTRACT FROM AUTHOR]

The appropriateness of animal by-product proteins as emulsifiers is barely explored compared to their meat counterparts. This paper focused on improving interfacial and emulsifying properties of modified goose liver protein using three structurally relevant polyphenols either enhanced by pH shifting (P-catechin, P-quercetin and P-rutin) or not (catechin, quercetin and rutin). Due to its high hydrophobicity and limited steric hindrance, quercetin was more sufficient to hydrophobically interact (ΔH > 0, ΔS > 0) with MGLP than catechin and rutin. Results showed that polyphenol interactive affinity was positively correlated to surface hydrophobicity but negatively to size and aggregation extent of MGLP. Interfacial pressure and dilatational elastic modulus implied that synergistic polyphenol interaction and pH shifting favored the interfacial adsorption and macromolecular association of MGLP, particularly for P-quercetin with the values reached to 19.9 ± 2.0 mN/m and 22.9 ± 1.2 mN/m, respectively. Emulsion stabilized by P-quercetin also maintained highest physical and oxidative stabilities regarding the lowest D [4,3] (3.78 ± 0.27 μm) and creaming index (8.38 ± 0.43 %), together with highest mono- (19.51 %) and polyunsaturated fatty acid content (29.39 %) during storage. Overall, chemical structure of polyphenols may be determining in fabricating MGLP-polyphenol complexes with improved emulsion stabilization efficiency. [Display omitted] • Different phenolic modifications of modified goose liver protein were compared. • The complexation of quercetin was most obvious after pH shifting treatment. • Interfacial behaviors of products depended on the chemical structure of polyphenols. • Physicochemical stability of emulsions via MGLP-polyphenol complexation was studied. [ABSTRACT FROM AUTHOR]

Inspired by protein post-translational modification (PTM), post-imprinting modification (PIM) has been proposed and developed to prepare novel molecularly imprinted polymers (MIPs), which are similar to functionalized biosynthetic proteins. The PIM involves site-directed modifications in the imprinted cavity of the MIP, such as introducing high-affinity binding sites and introducing fluorescent signal molecules. This modification makes the MIP further functionalized and improves the shortcomings of general molecular imprinting, such as single function, low selectivity, low sensitivity, and inability to fully restore the complex function of natural antibodies. This paper describes the characteristics of PIM strategies, reviews the latest research progress in the recognition and detection of protein biomarkers such as lysozyme, prostate-specific antigen, alpha-fetoprotein, human serum albumin, and peptides, and further discusses the importance, main challenges, and development prospects of PIM. The PIM technology has the potential to develop a new generation of biomimetic recognition materials beyond natural antibodies. It can be used in bioanalysis and other multitudinous fields for its unique features in molecule recognition. • A post-imprinting modification (PIM) strategy was highlighted. • PIM can improve the function of molecularly imprinted polymers (MIPs). • MIPs prepared by PIM can surpass natural antibodies. • Applications of PIM in biomakers recognition detection were focused. [ABSTRACT FROM AUTHOR]

[Display omitted] • The critical pH of the structural unfolding of cod protein was pH 10 during pH-shift. • The electrostatic, hydrogen bond and hydrophobic interaction operated in unfolding. • The cod protein at critical pH could indeed improve the encapsulation ability. Hydrophobic polyphenols, with a variety of physiological activities, are often practically limited due to their low water solubility and chemical instability, among which curcumin (Cur) is a representative hydrophobic polyphenol. To improve Cur, the cod protein (CP)-Cur composite particles (CP-Cur) were successfully prepared using the pH-shift method, but this pH-shift method (7-12-7) required a higher pH, which limited application and increased cost. The critical pH of CP structure unfolding during pH-shift and its encapsulation effect on Cur were investigated in this paper. During the pH-shift process, the critical pH of the structural unfolding of CP was pH 10, and the degree of protein structure unfolding was higher, which was attributed to the increasing electrostatic repulsion, and the weakened hydrogen bond and hydrophobic interaction. The encapsulation efficiency of CP-Cur formed after pH 10-shift was higher than that formed after pH 9.8-shift, which increased by 22.17 %. At pH 9.8, the binding sites in CP reached saturation at the molar ratio of 10, while at pH 10 and 10.2, the binding sites in CP both reached saturation at the molar ratio of 14, also indicating that the protein treated with critical pH could bind more Cur. The binding between Cur and CP was mostly hydrophobic interaction, accompanied by hydrogen bonding and electrostatic interactions. The above results verified the necessity of critical pH in the experiment, indicating that critical pH could indeed improve the encapsulation effect and obtain a higher encapsulation efficiency. This work will help improve the large-scale application of hydrophobic functional substances in production. [ABSTRACT FROM AUTHOR]