Recent Developments in Bioprocessing of Recombinant Proteins: Expression Hosts and Process Development

Cost and supply considerations for antibody therapeutics

Monoclonal antibodies (mAbs) and mAb-derived biologics have achieved substantial success across various therapeutic areas over recent decades. Their widespread adoption, however, remains constrained due to high prices and challenges in supply. Here, we examine the general price and cost structure of mAbs and mAb-derived therapeutics and identify directions to improve affordability and strategies to ensure supply. Mainstream and emerging biomanufacturing formats and their implications on cost and supply are discussed. We also summarize modeling tools used across industry for process economics analysis, emphasizing the importance of this assessment throughout the product development lifecycle. A comprehensive understanding of cost and supply scenarios will empower industry players to thrive despite competition, navigate supply challenges, and broaden access to mAb therapeutics for more patients.

Biomimetic peptide conjugates as emerging strategies for controlled release from protein-based materials

Biopolymers, such as collagens, elastin, silk fibroin, spider silk, fibrin, keratin, and resilin have gained significant interest for their potential biomedical applications due to their biocompatibility, biodegradability, and mechanical properties. This review focuses on the design and integration of biomimetic peptides into these biopolymer platforms to control the release of bioactive molecules, thereby enhancing their functionality for drug delivery, tissue engineering, and regenerative medicine. Elastin-like polypeptides (ELPs) and silk fibroin repeats, for example, demonstrate how engineered peptides can mimic natural protein domains to modulate material properties and drug release profiles. Recombinant spider silk proteins, fibrin-binding peptides, collagen-mimetic peptides, and keratin-derived structures similarly illustrate the ability to engineer precise interactions and to design controlled release systems. Additionally, the use of resilin-like peptides showcases the potential for creating highly elastic and resilient biomaterials. This review highlights current achievements and future perspectives in the field, emphasizing the potential of biomimetic peptides to transform biopolymer-based biomedical applications.

Insulin fibrillation under physicochemical parameters of bioprocessing and intervention by peptides and surface-active agents

Even after the centenary celebration of insulin discovery, there prevail challenges concerning insulin aggregation, not only after repeated administration but also during industrial production, storage, transport, and delivery, significantly impacting protein quality, efficacy, and effectiveness. The aggregation reduces insulin bioavailability, increasing the risk of heightened immunogenicity, posing a threat to patient health, and creating a dent in the golden success story of insulin therapy. Insulin experiences various physicochemical and mechanical stresses due to modulations in pH, temperature, ionic strength, agitation, shear, and surface chemistry, during the upstream and downstream bioprocessing, resulting in insulin unfolding and subsequent fibrillation. This has fueled research in the pharmaceutical industry and academia to unveil the mechanistic insights of insulin aggregation in an attempt to devise rational strategies to regulate this unwanted phenomenon. The present review briefly describes the impacts of environmental factors of bioprocessing on the stability of insulin and correlates with various intermolecular interactions, particularly hydrophobic and electrostatic forces. The aggregation-prone regions of insulin are identified and interrelated with biophysical changes during stress conditions. The quest for novel additives, surface-active agents, and bioderived peptides in decelerating insulin aggregation, which results in overall structural stability, is described. We hope this review will help tackle the real-world challenges of insulin aggregation encountered during bioprocessing, ensuring safer, stable, and globally accessible insulin for efficient management of diabetes.

Design and application of expression constructs for FMDV serotype O structural proteins

Design and validate flexible constructs for recombinant expression of FMDV serotype O structural proteins of the circulating topotypes using newly designed degenerate primers. The designed degenerate primers targeting diverse topotypes enabled the successful amplification of VP0, VP1, and VP3 genes. Integration of the essential transcriptional and translational regulatory elements including T7 promoter, leader g10 sequence, and T7 terminator, as well as ribosome binding site (RBS), start and stop codons, respectively via overlap extension PCR empowered efficient expression of these proteins in E. coli. Cloned constructs expressed the target proteins of expected molecular weights: VP0 (34 kDa), VP1 (24 kDa), and VP3 (22 kDa). SDS-PAGE and Western blotting confirmed high protein yield and purity. This platform demonstrated adaptability for diagnostic and vaccine development applications. The workflow offers a robust tool for producing FMDV structural proteins concerning the circulating strains attempting to improve control measures including diagnosis and vaccinations.

Escherichia coli in the production of biopharmaceuticals

Escherichia coli has shouldered a massive workload with the discovery of recombinant DNA technology. A new era began in the biopharmaceutical industry with the production of insulin, the first recombinant protein, in E. coli and its use in treating diabetes. After insulin, many biopharmaceuticals produced from E. coli have been approved by the US Food and Drug Administration and the European Medicines Agency to treat various human diseases. Although E. coli has some disadvantages, such as lack of post-translational modifications and toxicity, it is an important host with advantages such as being a well-known bacterium in recombinant protein production, cheap, simple production system, and high yield. This study examined biopharmaceuticals produced and approved in E. coli under the headings of peptides, hormones, enzymes, fusion proteins, antibody fragments, vaccines, and other pharmaceuticals. The topics on which these biopharmaceuticals were approved for treating human diseases, when and by which company they were produced, and their use and development in the field are included.

Trends and challenges in bispecific antibody production

Bispecific antibodies (bsAbs) represent a rapidly growing field of therapeutic agents. More bsAbs are being approved worldwide and are in various stages of clinical trials. However, the discovery and production of novel bsAbs presents significant challenges due to their complex structure. Thus, precise control of assembly and stability is required, given the many formats developed. This review examines recent trends in bsAb production, focusing on advancements in engineering platforms, production strategies, and challenges in large-scale manufacturing. Key developments include improvements in modular antibody design, novel expression systems, and optimization of bioprocessing techniques to enhance stability, yield, and efficacy. Additionally, the article explores the future potential of bsAbs as next-generation therapeutics, underscoring the growing impact of these innovations on expanding treatment options for patients with unmet medical needs.

Recent perspectives on biotechnological production, modulation and applications of glycerophosphoryl diester phosphodiesterases

Organophosphate (OP) compounds have been extensively employed as pesticides, insecticides and nerve agents. Stockpiles of chemical warfare agents must be destroyed as recommended by Chemical Weapon Convention (CWC). Toxicity of OP compounds to insects and mammals is due to their ability to inhibit the activity of acetylcholinesterase. Accumulation of acetylcholine leads to overstimulation of nerves, leading to convulsion, paralysis or even death. There is a dire need to decontaminate OP contaminated sites by using inexpensive and eco-friendly agents. Recently, OP hydrolyzing enzymes such as glycerophosphoryl diester phosphodiesterases (GDPDs) emerged as appealing agents to clean-up OP contaminated environmental sites. GDPDs are well known for enzymatic generation of glycerol 3-phosphate and corresponding alcoholic moiety from glycerophosphodiesters. Additionally, they are also involved in hydrolysis of OP compounds and degradative products of nerve agents. In the current review, structural and functional characteristics of GDPDs have been elaborated. Production of GDPDs from natural sources is quiet low so the current study aims at recombinant production of GDPDs from various sources. Comparative analysis of biochemical characteristics of various GDPDs indicated that thermostable GDPDs are active over broad temperature and pH range. In addition, thermostable GDPDs are resistant to high concentrations of organic solvents as well as metal ions. In order to enhance their practical utility, different engineering approaches (directed evolution, rational design and site-saturation mutagenesis) as well as immobilization strategies can be utilized to improve catalytic properties of GDPDs. Thus, the current review highlights the utilization of recombinant engineered free or immobilized GDPDs as tools in OP bioremediation.

A comprehensive review of recombinant technology in the food industry: Exploring expression systems, application, and future challenges

Biotechnology has significantly advanced the production of recombinant proteins (RPs). This review examines the latest advancements in protein production technologies, including CRISPR, genetic engineering, vector integration, and fermentation, and their implications for the food industry. This review delineates the merits and shortcomings of prevailing host systems for RP production, underscoring molecular and process strategies pivotal for amplifying yields and purity. It traverses the spectrum of RP applications, challenges, and burgeoning trends, highlighting the imperative of employing robust hosts and cutting-edge genetic engineering to secure high-quality, high-yield outputs while circumventing protein aggregation and ensuring correct folding for enhanced activity. Recombinant technology has paved the way for the food industry to produce alternative proteins like leghemoglobin and cytokines, along with enzyme preparations such as proteases and lipases, and to modify microbial pathways for synthesizing beneficial compounds, including pigments, terpenes, flavonoids, and functional sugars. However, scaling microbial production to industrial scales presents economic, efficiency, and environmental challenges that demand innovative solutions, including high-throughput screening and CRISPR/Cas9 systems, to bolster protein yield and quality. Although recombinant technology holds much promise, it must navigate high costs and scalability to satisfy the escalating global demand for RPs in therapeutics and food. The variability in ethical and regulatory hurdles across regions further complicates market acceptance, underscoring an urgent need for robust regulatory frameworks for genetically modified organisms. These frameworks are essential for safeguarding the production process, ensuring product safety, and upholding the efficacy of RPs in industrial applications.

Recent trends in biotechnological production, engineering, and applications of lysophospholipases

Oil degumming process involves the removal of gums, which is required to improve the physicochemical and storage properties of the vegetable oils. Degumming of oils can be carried out by using chemicals, membranes (polymeric, inorganic, and ceramic), or enzymes, for example, phospholipases. Phospholipases are enzymes of tremendous significance in the degumming process as they convert gums to fatty acids and lipophilic substances. They provide a cost-effective and safe alternative to other degumming processes without affecting the oil yield. Lysophospholipases (LPLs) are highly valuable tools for degumming vegetable oils. LPLs can hydrolyze fatty acyl ester bonds of phosphatidylcholine at the sn-1 and sn-2 positions of glycerol moiety. In addition, they have the ability to catalyze hydrolysis lysophospholipids' ester bond either at sn-1 or sn-2 position. In this review, biotechnological production and biochemical characteristics of LPLs from three domains of life are highlighted. In comparison to bacterial and eukaryotic LPLs, archaeal LPLs were found to be active at high temperatures. Broad substrate specificity and thermostability of archaeal LPLs make them ideal candidates for the industrial degumming of oils. However, improvement of activity and substrate specificity of archaeal LPLs is required for enhancing their industrial utility. In the current review, various protein-engineering approaches (directed evolution, rational design, site-saturation mutagenesis, and fusion technology) as well as in silico tools have been discussed to increase the commercial significance of LPLs.

Application of Pseudoinfectious Viruses in Transient Gene Expression in Mammalian Cells: Combining Efficient Expression with Regulatory Compliance

Transient gene expression (TGE) is commonly employed for protein production, but its reliance on plasmid transfection makes it challenging to scale up. In this paper, an alternative TGE method is presented, utilizing pseudoinfectious alphavirus as an expression vector. Pseudoinfectious viruses (PIV) and a replicable helper construct were derived from the genome of the Venezuelan equine encephalitis virus. The PIV carries a mutant capsid protein that prevents packaging into infectious particles, while the replicable helper encodes a wild-type capsid protein but lacks other viral structural proteins. Although PIV and the helper cannot independently spread infection, their combination results in increased titers in cell cultures, enabling easier scale-up of producing cultures. The PIV-driven production of a model protein outperforms that of alphavirus replicon vectors or simple plasmid vectors. Another described feature of the expression system is the modification to immobilized metal affinity chromatography (IMAC), allowing purification of His-tagged recombinant proteins from a conditioned medium in the presence of substances that can strip metal from the IMAC columns. The PIV-based expression system allows for the production of milligram quantities of recombinant proteins in static cultures, without the need for complex equipment such as bioreactors, and complies with regulatory requirements due to its distinction from common recombinant viruses.

Innovations and challenges in collagen and gelatin production through precision fermentation

Collagen and gelatin are essential biomaterials widely used in industries such as food, cosmetics, healthcare, and pharmaceuticals. Traditionally derived from animal tissues, these proteins are facing growing demand for more sustainable and ethical production methods. Precision fermentation (PF) offers a promising alternative by using genetically engineered microorganisms to produce recombinant collagen and gelatin. This technology not only reduces environmental impact but also ensures consistent quality and higher yields. In this review, we provide a comprehensive overview of collagen and gelatin production through PF destined for the food sector, exploring key advances in recombinant technologies, synthetic biology, and bioprocess optimization. Challenges such as scaling production, cost-efficiency, and market integration are addressed, alongside emerging solutions for enhancing industrial competitiveness. We also highlight leading companies leveraging PF to drive innovation in the food industry. As PF continues to evolve, future developments are expected to improve efficiency, reduce costs, and expand the applications of recombinant collagen and gelatin, particularly in the food and supplement sectors.

From Cell Clones to Recombinant Protein Product Heterogeneity in Chinese Hamster Ovary Cell Systems

Chinese hamster ovary (CHO) cells are commonly used to produce recombinant therapeutic proteins (RTPs). The yield of RTPs in CHO cells has been greatly improved through cell editing and optimization of culture media, cell culture processes, and expression vectors. However, the heterogeneity of cell clones and product aggregation considerably affect the yield and quality of RTPs. Recently, novel technologies such as semi-targeted and site-specific transgene integration, endoplasmic reticulum-residents, and cell culture process optimization have been used to address these issues. In this review, novel developments in the field of CHO cell expression system heterogeneity are summarized. Moreover, the advantages and limitations of the new strategies are discussed, and important methods for the control of RTP quality are outlined.

Design and assessment of two broad-spectrum multi-epitope vaccine candidates against bovine viral diarrhea virus based on the E0 or E2 envelope glycoprotein

Bovine viral diarrhea virus (BVDV) is a significant pathogen that exerts substantial economic influence on the global cattle industry. Developing a safe and effective novel vaccine targeting various BVDV subtypes is critical for controlling BVDV infection. In the study, we created two distinct multi-epitope vaccines by linking highly conserved and dominant cytotoxic T-lymphocytes (CTL), helper T-lymphocytes (HTL), and B-cell epitopes from either the E0 or E2 envelope glycoprotein of diverse BVDV subtypes. To enhance immunogenicity, β-defensin-3 was fused to the N-terminus of these constructs as an adjuvant. Using multiple immunoinformatics tools, we conducted an analysis and assessment of the vaccine constructs' physicochemical properties and immunological features. Consequently, two prospective vaccine candidates named BVDV-M1 and BVDV-M2 were successfully designed and shown to be stable, antigenic, non-allergenic, and non-toxic. The optimized vaccine 3D models exhibit excellent structural quality. Molecular docking revealed a strong interaction between the vaccines with bovine TLR2 and TLR4. The stability of the docked vaccine-TLR complexes was confirmed through molecular dynamics simulation. Immune simulation analyses indicated that both vaccines have the potential to induce high levels of antibodies IgM, IgG and the cytokines IFN-γ and IL-2. Furthermore, the vaccine's efficient expression in the E.coli system was secured through codon optimization coupled with in silico cloning. Summarily, the designed multi-epitope vaccines have the potential to elicit robust humoral and cellular immune responses, positioning them as hopeful broad-spectrum vaccine candidates against the currently prevalent BVDV subtypes.

mRNA-LM: full-length integrated SLM for mRNA analysis

The success of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) messenger RNA (mRNA) vaccine has led to increased interest in the design and use of mRNA for vaccines and therapeutics. Still, selecting the most appropriate mRNA sequence for a protein remains a challenge. Several recent studies have shown that the specific mRNA sequence can have a significant impact on the translation efficiency, half-life, degradation rates, and other issues that play a major role in determining vaccine efficiency. To enable the selection of the most appropriate sequence, we developed mRNA-LM, an integrated small language model for modeling the entire mRNA sequence. mRNA-LM uses the contrastive language-image pretraining integration technology to combine three separate language models for the different mRNA segments. We trained mRNA-LM on millions of diverse mRNA sequences from several different species. The unsupervised model was able to learn meaningful biology related to evolution and host-pathogen interactions. Fine-tuning of mRNA-LM allowed us to use it in several mRNA property prediction tasks. As we show, using the full-length integrated model led to accurate predictions, improving on prior methods proposed for this task.

Metabolomics of Chinese Hamster Ovary Cells

Increasing demand of protein biotherapeutics produced using Chinese hamster ovary (CHO) cell lines necessitates improvement in the production yield of the bioprocess. Various cell engineering, improved media formulation and process-design based approaches utilizing the power of OMICS technologies, specifically, genomics and proteomics, have been employed; however, the potential of metabolomics largely remains unexplored. Metabolomics enables the detection, identification, and/or quantitation of small molecules, commonly known as metabolites, in and around the cells and may help to unlock the cellular molecular mechanism(s) that regulates cell growth and productivity in the bioprocess and improves cellular performance during the bioprocess. Currently, liquid chromatography (LC)/gas chromatography (CG)- coupled with mass-spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy are the most commonly used approaches for metabolomics. Therefore, in this chapter, we have discussed the standard procedures of investigating CHO metabolites using LC/GC-MS and/or NMR-based approaches.

Assessment of membrane-based downstream purification processes as a replacement to traditional resin bead for monoclonal antibody purification

Membrane chromatography devices are a viable alternative to packed-bed resins and enable highly productive purification cascades for monoclonal antibodies and Fc-fusion proteins. In this study, ion exchange and protein A membrane chromatography performances were assessed and compared with their resin counterparts. Protein A dynamic binding capacities were higher than 50 g/L for two of the tested membranes and with a residence time of 0.2 min. For polishing, it was observed that aggregate clearance was generally less performant with membrane separation when compared to resins with similar ligands. However, the comparable yield and increased productivity of membranes could be enough to consider their implementation. In addition, lifetime studies demonstrated that the performance of membranes remained robust over cycles. One hundred cycles were reached for most of the tested membranes with no impact on the process performance nor product quality. Finally, purification cascades were fully operated with membranes, from capture to polishing, reaching good levels of host cells proteins (less than 50 ppm) and aggregates (equal to or less than 1%). The outcome of this study demonstrated that resin chromatography could be fully replaced by membranes for monoclonal antibody and Fc-fusion protein purification processes.

A review on computational models for predicting protein solubility

Protein solubility is a critical factor in the production of recombinant proteins, which are widely used in various industries, including pharmaceuticals, diagnostics, and biotechnology. Predicting protein solubility remains a challenging task due to the complexity of protein structures and the multitude of factors influencing solubility. Recent advances in computational methods, particularly those based on machine learning, have provided powerful tools for predicting protein solubility, thereby reducing the need for extensive experimental trials. This review provides an overview of current computational approaches to predict protein solubility. We discuss the datasets, features, and algorithms employed in these models. The review aims to bridge the gap between computational predictions and experimental validations, fostering the development of more accurate and reliable solubility prediction models that can significantly enhance recombinant protein production.

Cell Adhesion and Local Cytokine Control on Protein-Functionalized PNIPAM-co-AAc Hydrogel Microcarriers

Achieving adequate cell densities remains a major challenge in establishing economic biotechnological and biomedical processes. A possible remedy is microcarrier-based cultivation in stirred-tank bioreactors (STBR), which offers a high surface-to-volume ratio, appropriate process control, and scalability. However, despite their potential, commercial microcarriers are currently limited to material systems featuring unnatural mechanical properties and low adaptability. Because matrix stiffness and ligand presentation impact phenotypical attributes, differentiation potential, and genetic stability, biotechnological processes can significantly benefit from microcarrier systems tailorable toward cell-type specific requirements. This study introduces hydrogel particles co-polymerized from poly(N-isopropylacrylamide) (PNIPAM) and acrylic acid (AAc) as a platform technology for cell expansion. The resulting microcarriers exhibit an adjustable extracellular matrix-like softness, an adaptable gel charge, and functional carboxyl groups, allowing electrostatic and covalent coupling of cell adhesive and cell fate-modulating proteins. These features enable the attachment and growth of L929 mouse fibroblast cells in static microtiter plates and dynamic STBR cultivations while also providing vital growth factors, such as interleukin-3, to myeloblast-like 32D cells over 20 days of cultivation. The study explores the effects of different educt compositions on cell-particle interactions and reveals that PNIPAM-co-AAc microcarriers can provide both covalently coupled and diffusively released cytokine to adjacent cells.

Design and optimization of IgG avidity test for differentiating acute from chronic human toxoplasmosis: A systematic review and meta-analysis

Toxoplasmosis which is caused by T. gondii, is common among humans and animals. T. gondii is a threat to the fetus and individuals with immune disorders, especially patients with acquired immunodeficiency syndrome (AIDS) and individuals who undergo organ transplants. Therefore, quick diagnosis and accurate differentiation of acute and chronic stages are essential. One of the important serological methods in differentiating stages of the disease and the time of acquiring the infection is evaluating the IgG avidity. In this systematic review and meta-analysis, keywords were searched in databases including PubMed, Science Direct, ProQuest, Scopus, and Google Scholar. Included studies were collected after checking the inclusion and exclusion criteria, and according to the PRISMA flow chart. Finally, the data were analyzed by StatsDirect statistical software and random-effects model. A total of 10 studies (26 datasets) were eligible for analysis. The random effects model estimated the prevalence of low IgG avidity in acute toxoplasmosis using in-house IgG avidity tests of 84% and chronic toxoplasmosis infection using in-house IgG avidity of 91%. The IgG avidity test can be a helpful diagnostic tool in differentiating between acute and chronic stages. Also, this review emphasizes that the use of recombinant or chimeric proteins is preferable to TLA in differentiating acute and chronic stages. It can be concluded that choosing more effective antigens (multi-epitope and multi-stage) and performing more detailed studies on the design of an avidity kit to differentiate the stage of infection is required.

Screening microorganisms with robust and stable protein expression and secretion capacity

Robust and stable protein secretion is crucial for efficient recombinant protein production. Here, a novel and powerful platform using split GFP activated droplet sorting (SGADS) has been developed to significantly boost the yields of the protein of interest (POI). The SGADS platform leverages solubilizing peptide P17 and secretory expression in Bacillus subtilis to optimize two split GFP sensors: the P17-GFP1-9/GFP10-POI-GFP11 sensor for assessing protease activity and the P17-GFP1-10/GFP11-POI sensor for measuring secretion capacity. This innovative platform has demonstrated its effectiveness by successfully screening high-performance mutant strains capable of producing collagen, amylase, and protein glutaminase across a range of host organisms, including Escherichia coli, Bacillus subtilis, and Pichia pastoris. The substantial increases in production achieved with the SGADS platform highlight its broad applicability and potential in enhancing recombinant protein production.

A comparative guide to expression systems for phage lysin production

Phage lysins, bacteriophage-encoded enzymes tasked with degrading their host's cell wall, are increasingly investigated and engineered as novel antibacterials across diverse applications. Their rapid action, tuneable specificity, and low likelihood of resistance development make them particularly interesting. Despite numerous application-focused lysin studies, the art of their recombinant production remains relatively undiscussed. Here, we provide an overview of the available expression systems for phage lysin production and discuss key considerations guiding the choice of a suitable recombinant host. We systematically surveyed recent literature to evaluate the hosts used in the lysin field and cover various recombinant systems, including the well-known bacterial host Escherichia coli or yeast Saccharomyces cerevisiae, as well as plant, mammalian, and cell-free systems. Careful analysis of the limited studies expressing lysins in various hosts suggests a host-dependent effect on activity. Nonetheless, the multitude of available expression systems should be further leveraged to accommodate the growing interest in phage lysins and their expanding range of applications.

Circumventing the Impossible: Cell-Free Synthesis of Protein Toxins for Medical and Diagnostic Applications

Naturally occurring protein toxins can derive from bacteria, fungi, plants, and animal venom. Traditionally, toxins are known for their destructive effects on host cells. Despite, and sometimes even because of, these harmful effects, toxins have been used for medical benefits. The prerequisite for the development of toxin-based medications or treatments against toxins is thorough knowledge about the toxin and its underlying mechanism of action. Thus, the toxin of interest must be synthesized. Traditional cell-based production requires high laboratory safety standards and often results in a low total protein yield due to the toxin's harmful, cytotoxic nature. These drawbacks can be circumvented by using cell-free protein synthesis (CFPS), a highly adaptable platform technology relying on cell lysates rather than living cells. This review discusses the current advances in cell-free synthesis of protein toxins as well as their uses and applications for pharmaceutical and diagnostic purposes.

Construction of Pseudomonas aeruginosa SDK-6 with synthetic lipase gene cassette and optimization of different parameters using response surface methodology for over-expression of recombinant lipase

Lipases are industrially important enzymes having vast applications in various fields. Cloning and expression of lipase enzyme-encoding genes in suitable host lead to their widespread use in different fields. The present study represents the first attempt towards the expression of the synthetic lipase gene in Pseudomonas aeruginosa. An alkalophilic lipase gene (GenBank accession number: NP_388152) from Bacillus subtilis was synthetically designed and introduced in the pJN105 vector and subsequently cloned in Pseudomonas aeruginosa SDK-6. Agarose gel electrophoresis confirmed the transformation of SDK-6, exhibiting a band difference of ~ 700 bp between native and recombinant pJN105. Further amplification of cloned lipase gene was confirmed using PCR amplification with Lip 1 and Lip 2 primers respectively, followed by restriction analysis. Approximately 15-fold increase in lipase production was observed in recombinant Pseudomonas as compared to the native strain. One factor at a time (OFAT) analysis revealed L-arabinose, inoculum size (0.5%; v/v), and agitation (120 rpm) as significant factors affecting the over-expression of lipase enzyme. Optimization of enzyme induction conditions by central composite design (CCD) led to 1.60-fold increase in the production of lipase at 0.65% (w/v) inducer concentration, OD600-1.075 before induction and 35 °C post induction temperature with overall lipase production of 50.50 IU/mL. Statistical validation of observed value via ANOVA showed an F-value of 138.70 at p < 0.01 with R2 of 0.9921.

Designing a multi-epitope subunit vaccine against Orf virus using molecular docking and molecular dynamics

Orf virus (ORFV) is an acute contact, epitheliotropic, zoonotic, and double-stranded DNA virus that causes significant economic losses in the livestock industry. The objective of this study is to design an immunoinformatics-based multi-epitope subunit vaccine against ORFV. Various immunodominant cytotoxic T lymphocytes (CTL), helper T lymphocytes (HTL), and B-cell epitopes from the B2L, F1L, and 080 protein of ORFV were selected and linked by short connectors to construct a multi-epitope subunit vaccine. Immunogenicity was enhanced by adding an adjuvant β-defensin to the N-terminal of the vaccine using the EAAAK linker. The vaccine exhibited a significant degree of antigenicity and solubility, without allergenicity or toxicity. The 3D formation of the vaccine was subsequently anticipated, improved, and verified. The optimized model exhibited a lower Z-score of -4.33, indicating higher quality. Molecular docking results demonstrated that the vaccine strongly binds to TLR2 and TLR4. Molecular dynamics results indicated that the docked vaccine-TLR complexes were stable. Immune simulation analyses further confirmed that the vaccine can induce a marked increase in IgG and IgM antibody titers, and elevated levels of IFN-γ and IL-2. Finally, the optimized DNA sequence of the vaccine was cloned into the vector pET28a (+) for high expression in the E.coli expression system. Overall, the designed multi-epitope subunit vaccine is highly stable and can induce robust humoral and cellular immunity, making it a promising vaccine candidate against ORFV.

Soluble expression of hMYDGF was improved by strain engineering and optimizations of fermentation strategies in Escherichia coli

Myeloid-derived growth factor (MYDGF) is a cytokine that exhibits a variety of biological functions. This study focused on utilizing BL21(DE3) strain engineering and fermentation strategies to achieve high-level expression of soluble human MYDGF (hMYDGF) in Escherichia coli. Initially, the E. coli expressing strain BL21(DE3) was engineered by deleting the IpxM gene and inserting the GROEL/S and Trigger factor genes. The engineered E. coli strain BL21(TG)/pT-MYDGF accumulated 3557.3 ± 185.6 μg/g and 45.7 ± 6.7 mg/L of soluble hMYDGF in shake flask fermentation, representing a 15.6-fold increase compared to the control strain BL21(DE3)/pT-MYDGF. Furthermore, the yield of hMYDGF was significantly enhanced by optimizing the fermentation conditions. Under optimized conditions, the 5L bioreactor yielded up to 2665.8 ± 164.3 μg/g and 407.6 ± 42.9 mg/L of soluble hMYDGF. The results indicate that the implementation of these optimization strategies could enhance the ratio and yield of soluble proteins expressed by E.coli, thereby meeting the demands of industrial production. This study employed sophisticated strategies to lay a solid foundation for the industrial application of hMYDGF.

External Bleeding and Advanced Biomacromolecules for Hemostasis

Hemorrhage is a significant medical problem that has been an active area of research over the past few decades. The human body has a complex response to bleeding that leads to blood clot formation and hemostasis. Many biomaterials based on various biomacromolecules have been developed to either accelerate or improve the body's natural response to bleeding. This review examines the mechanisms of hemostasis, types of bleeding, and the in vitro or in vivo models and techniques used to study bleeding and hemostatic materials. It provides a detailed overview of the diverse hemostatic materials, including those that are highly absorbent, wet adhesives, and those that accelerate the biochemical cascade of blood clotting. These materials are currently marketed, under preclinical testing, or being researched. In exploring the latest advancements in hemostatic technologies, this paper highlights the potential of these materials to significantly improve bleeding control in clinical and emergency situations.

Leishmania tarentolae as a platform for the production of vaccines against viral pathogens

Infectious diseases remain a persistent public health problem and a leading cause of morbidity and mortality in both humans and animals. The most effective method of combating viral infections is the widespread use of prophylactic vaccinations, which are administered to both people at risk of disease and animals that may serve as significant sources of infection. Therefore, it is crucial to develop technologies for the production of vaccines that are highly effective, easy to transport and store, and cost-effective. The protein expression system based on the protozoan Leishmania tarentolae offers several advantages, validated by numerous studies, making it a good platform for producing vaccine antigens. This review provides a comprehensive overview into the potential applications of L. tarentolae for the safe production of effective viral antigens.

Virus nanotechnology for intratumoural immunotherapy

Viruses can be designed to be tools and carrier vehicles for intratumoural immunotherapy. Their nanometre-scale size and shape allow for functionalization with or encapsulation of medical cargoes and tissue-specific ligands. Importantly, immunotherapies may particularly benefit from the inherent immunomodulatory properties of viruses. For example, mammalian viruses have already been tested for oncolytic virotherapy, and bacteriophages and plant viruses can be engineered for immunotherapeutic treatment approaches. In this Review, we discuss how viruses - including oncolytic viruses, immunomodulatory plant viruses and bacteriophages - and virus-like particles can be designed for intratumoural immunotherapy to elicit anti-tumour immunity and induce systemic anti-tumour responses at distant non-injected sites. We further highlight the engineering of viruses and virus-like particles as drug-delivery systems, and outline key translational challenges and clinical opportunities.

Attachment promoting compounds significantly enhance cell proliferation and purity of bovine satellite cells grown on microcarriers in the absence of serum

Introduction

To bring cultivated beef to the market, a scalable system that can support growth of bovine satellite cells (bSCs) in a serum-free and preferably also animal-free medium is of utmost importance. The use of microcarriers (MCs) is, at the moment, one of the most promising technologies for scaling up. MCs offer a large surface to volume ratio, they can be used in scalable stirred tank bioreactors, where the culture conditions can be tightly controlled to meet the cells' requirements (temperature, pH, dissolved oxygen). The inherent capacity of the cells to migrate from one MC to another, also known as bead-to-bead transfer, facilitates a scale-up strategy involving MCs. Previous studies have shown growth of bSCs on three commercially available MCs in serum containing media. Unfortunately there is currently no information available regarding their growth on MCs in serum-free conditions.

Methods

In this study, we aimed to find suitable serum-free media, MCs and attachment promoting compounds (APCs) supporting the growth of bSCs. Initially, six commercial MCs and three serum-free media were evaluated. The effects of three APCs were compared (vitronectin, laminin and fibronectin). Subsequently, the effects of different concentrations and modes of addition of the best performing APC were investigated.

Results and Discussion

Our results showed that Cytodex 1, Synthemax II and CellBIND supported bSCs' growth in all serum-free media. Overall, better growth was observed with Cytodex 1 in serum-free proliferation media. We showed that the use of laminin or vitronectin with Cytodex 1 can significantly improve cell growth and purity. Laminin also allowed attachment and growth of bSCs on Plastic MCs which had been previously unsuccessful without APCs. Finally, we optimized the use of vitronectin from a sustainability and process perspective, and showed that it can be used solely as a coating for Cytodex 1 (16-100 ng/cm2) MCs, instead of as a medium supplement, enhancing cell attachment and proliferation.

High-Level Production of a Recombinant Protein in Nicotiana benthamiana Leaves Through Transient Expression Using a Double Terminator

Various bio-based recombinant proteins have been produced for industrial, medical, and research purposes. Plants are potential platforms for recombinant protein production because of several advantages. Therefore, establishing a system with high target gene expression to compensate for the low protein yield of plant systems is crucial. In particular, selecting and combining strong terminators is essential because the expression of target genes can be substantially enhanced. Here, we aimed to quantify the enhancement in the fluorescence intensity of the turbo green fluorescence protein (tGFP) caused by the best double-terminator combinations compared to that of the control vector using agroinfiltration in Nicotiana benthamiana leaves. tGFP fluorescence increased by 4.1-fold in leaf samples infiltrated with a vector containing a double terminator and markedly increased by a maximum of 23.7-fold when co-infiltrated with the geminiviral vector and P19 compared to that in constructs containing an octopine synthase terminator. Polyadenylation site analysis in leaf tissues expressing single or dual terminators showed that the first terminator influenced the polyadenylation site determination of the second terminator, resulting in different polyadenylation sites compared with when the terminator is located first. The combination of the high-expression terminators and geminiviral vectors can increase the production of target proteins.

Identification and analysis of the key genes for Escherichia coli heterologous protein expression by transcriptomic profiling

BACKGROUND

Escherichia coli is a frequently used host for heterologous protein expression, but its expression efficiency is hindered by several limitations, such as formation of inclusion bodies and proteolytic degradation.

METHODS AND RESULTS

In this study, we employed high-density fermentation of heterologous protein production in a 5-L bioreactor, resulting in a yield 2.25 times higher than that of the control group. Transcriptional analysis was conducted at three time points after induction for 0 h, 4 h, and 12 h, revealing 420, 301, and 570 upregulated differentially expressed genes, as well as 424, 202, and 525 downregulated genes, respectively. By conducting enrichment analysis, we constructed strains that relieved without iron limitation, exhibiting a 36% increase in biomass and a 32% increase in protein expression. Furthermore, no overflow metabolism of acetic acid was detected during the protein expression process when utilizing chemostat culture, which indicated that the utilization efficiency of glucose was significantly enhanced without iron limitation.

CONCLUSIONS

This study presents a novel approach to better comprehend the mechanism of high-yield production of heterologous proteins in Escherichia coli.

Modulation of the pharmacokinetics of soluble ACE2 decoy receptors through glycosylation

The Spike of SARS-CoV-2 recognizes a transmembrane protease, angiotensin-converting enzyme 2 (ACE2), on host cells to initiate infection. Soluble derivatives of ACE2, in which Spike affinity is enhanced and the protein is fused to Fc of an immunoglobulin, are potent decoy receptors that reduce disease in animal models of COVID-19. Mutations were introduced into an ACE2 decoy receptor, including adding custom N-glycosylation sites and a cavity-filling substitution together with Fc modifications, which increased the decoy's catalytic activity and provided small to moderate enhancements of pharmacokinetics following intravenous and subcutaneous administration in humanized FcRn mice. Most prominently, sialylation of native glycans increases exposures by orders of magnitude, and the optimized decoy is therapeutically efficacious in a mouse COVID-19 model. Ultimately, an engineered and highly sialylated decoy receptor produced using methods suitable for manufacture of representative drug substance has high exposure with a 5- to 9-day half-life. Finally, peptide epitopes at mutated sites in the decoys generally have low binding to common HLA class II alleles and the predicted immunogenicity risk is low. Overall, glycosylation is a critical molecular attribute of ACE2 decoy receptors and modifications that combine tighter blocking of Spike with enhanced pharmacokinetics elevate this class of molecules as viable drug candidates.

Next-Generation Therapeutic Antibodies for Cancer Treatment: Advancements, Applications, and Challenges

The field of cancer treatment has evolved significantly over the last decade with the emergence of next-generation therapeutic antibodies. Conventional treatments like chemotherapy pose significant challenges, including adverse side effects. Monoclonal antibodies have paved the way for more targeted and effective interventions. The evolution from chimeric to humanized and fully human antibodies has led to a reduction in immunogenicity and enhanced tolerance in vivo. The advent of next-generation antibodies, including bispecific antibodies, nanobodies, antibody-drug conjugates, glyco-engineered antibodies, and antibody fragments, represents a leap forward in cancer therapy. These innovations offer increased potency, adaptability, and reduced drug resistance. Challenges such as target validation, immunogenicity, and high production costs exist. However, technological advancements in antibody engineering techniques provide optimism for addressing these issues. The future promises a paradigm shift, where ongoing research will propel these powerful antibodies to the forefront, revolutionizing the fight against cancer and creating new preventive and curative treatments. This review provides an overview of three next-generation antibody-based molecules, namely bispecific antibodies, antibody-drug conjugates, and nanobodies that have shown promising results in cancer treatment. It discusses the evolution of antibodies from conventional forms to next-generation molecules, along with their applications in cancer treatment, production methods, and associated challenges. The review aims to offer researchers insights into the evolving landscape of next-generation antibody-based cancer therapeutics and their potential to revolutionize treatment strategies.

Model acetylcholinesterase-Fc fusion glycoprotein biotechnology system for the manufacture of an organophosphorus toxicant bioscavenging countermeasure

Organophosphate (OP) toxicants remain an active threat to public health and to warfighters in the military. Current countermeasures require near immediate administration following OP exposure and are reported to have controversial efficacies. Acetylcholinesterase (AChE) fused to the human immunoglobulin 1 (IgG1) Fc domain (AChE-Fc) is a potential bioscavenger for OP toxicants, but a reproducible AChE-Fc biomanufacturing strategy remains elusive. This report is the first to establish a comprehensive laboratory-scale bioprocessing strategy that can reproducibly produce AChE-Fc and AChE(W86A)-Fc which is a mutated AChE protein with reduced enzymatic activity. Characterization studies revealed that AChE-Fc and AChE(W86A)-Fc are N-glycosylated dimeric fusion glycoproteins but only AChE-Fc had the capability to bind to paraoxon (a model OP). This AChE-Fc fusion glycoprotein bioprocessing strategy can be leveraged during industrial biomanufacturing development, while the research-grade AChE-Fc proteins can be used to determine the potential clinical relevance of the countermeasure against OP toxicants.

Production of antigens expressed in Nicotiana benthamiana plant and Escherichia coli for the SARS-CoV-2 IgG antibody detection by ELISA

The recent COVID-19 pandemic disclosed a critical shortage of diagnostic kits worldwide, emphasizing the urgency of utilizing all resources available for the development and production of diagnostic tests. Different heterologous protein expression systems can be employed for antigen production. This study assessed novel SARS-CoV-2 proteins produced by a transient expression system in Nicotiana benthamiana utilizing an infectious clone vector based on pepper ringspot virus (PepRSV). These proteins included the truncated S1-N protein (spike protein N-terminus residues 12-316) and antigen N (nucleocapsid residues 37-402). Two other distinct SARS-CoV-2 antigens expressed in Escherichia coli were evaluated: QCoV9 chimeric antigen protein (spike protein residues 449-711 and nucleocapsid protein residues 160-406) and QCoV7 truncated antigen (nucleocapsid residues 37-402). ELISAs using the four antigens individually and the same panel of samples were performed for the detection of anti-SARS-CoV-2 IgG antibodies. Sensitivity was evaluated using 816 samples from 351 COVID-19 patients hospitalized between 5 and 65 days after symptoms onset; specificity was tested using 195 samples collected before 2018, from domiciliary contacts of leprosy patients. Our findings demonstrated consistent test sensitivity, ranging from 85 % to 88 % with specificity of 97.5 %, regardless of the SARS-CoV2 antigen and the expression system used for production. Our results highlight the potential of plant expression systems as useful alternative platforms to produce recombinant antigens and for the development of diagnostic tests, particularly in resource-constrained settings.

Development of a novel sandwich immunoassay based on targeting recombinant Francisella outer membrane protein A for the diagnosis of tularemia

Introduction

Tularemia, caused by the bacterium Francisella tularensis, poses health risks to humans and can spread through a variety of routes. It has also been classified as a Tier 1 Select agent by the CDC, highlighting its potential as a bioterrorism agent. Moreover, it is difficult to diagnose in a timely fashion, owing to the non-specific nature of tularemia infections. Rapid, sensitive, and accurate detection methods are required to reduce mortality rates. We aimed to develop antibodies directed against the outer membrane protein A of F. tularensis (FopA) for rapid and accurate diagnosis of tularemia.

Methods

We used a baculovirus insect cell expression vector system to produce the FopA antigen and generate anti-FopA antibodies through immunization of BALB/c mice. We then employed hybridoma and phage display technologies to screen for antibodies that could recognize unique epitopes on FopA.

Result

Two monoclonal antibodies, 6B12 and 3C1, identified through phage display screening specifically bound to recombinant FopA in a dose-dependent manner. The binding affinity of the anti-FopA 6B12 and 3C1 antibodies was observed to have an equilibrium dissociation constant of 1.76 × 10-10 M and 1.32 × 10-9 M, respectively. These antibodies were used to develop a sandwich ELISA system for the diagnosis of tularemia. This assay was found to be highly specific and sensitive, with detection limits ranging from 0.062 ng/mL in PBS to 0.064 ng/mL in skim milk matrices.

Discussion

Our findings demonstrate the feasibility of a novel diagnostic approach for detecting F. tularensis based on targeting FopA, as opposed to existing tests that target the bacterial lipopolysaccharide.

Recombinant fibrous protein biomaterials meet skin tissue engineering

Natural biomaterials, particularly fibrous proteins, are extensively utilized in skin tissue engineering. However, their application is impeded by batch-to-batch variance, limited chemical or physical versatility, and environmental concerns. Recent advancements in gene editing and fermentation technology have catalyzed the emergence of recombinant fibrous protein biomaterials, which are gaining traction in skin tissue engineering. The modular and highly customizable nature of recombinant synthesis enables precise control over biomaterial design, facilitating the incorporation of multiple functional motifs. Additionally, recombinant synthesis allows for a transition from animal-derived sources to microbial sources, thereby reducing endotoxin content and rendering recombinant fibrous protein biomaterials more amenable to scalable production and clinical use. In this review, we provide an overview of prevalent recombinant fibrous protein biomaterials (collagens, elastin, silk proteins and their chimeric derivatives) used in skin tissue engineering (STE) and compare them with their animal-derived counterparts. Furthermore, we discuss their applications in STE, along with the associated challenges and future prospects.

Development of a novel bacterial production system for recombinant bioactive proteins completely free from endotoxin contamination

Endotoxins, or lipopolysaccharides (LPS), are potent immunostimulatory molecules of critical concern in bacterial recombinant protein expression systems. The gram-negative bacterium Acinetobacter baumannii exhibits an interesting and unique phenotype characterized by the complete loss of LPS. In this study, we developed a novel system for producing recombinant proteins completely devoid of endotoxin contamination using LPS-deficient A. baumannii. We purified endotoxin-free functional green fluorescent protein, which reduced endotoxin contamination by approximately three orders of magnitude, and also purified the functional cytokine tumor necrosis factor (TNF)-α. Additionally, utilization of the Omp38 signal peptide of A. baumannii enabled the extracellular production of variable domain of heavy chain of heavy chain (VHH) antibodies. With these advantages, mNb6-tri-20aa, a multivalent VHH that specifically binds to the spike protein of severe acute respiratory syndrome coronavirus 2, was purified from the culture supernatant, and endotoxin contamination was reduced by a factor of approximately 2 × 105 compared with that in conventional expression systems. A virus neutralization assay demonstrated the functionality of the purified antibody in suppressing viral infections. Moreover, we applied our system to produce ozoralizumab, a multispecific VHH that binds to human TNF-α and albumin and are marketed as a rheumatoid arthritis drug. We successfully purified a functional antibody from endotoxin contamination. This system establishes a new, completely endotoxin-free platform for the expression of recombinant proteins, which distinguishes it from other bacterial expression systems, and holds promise for future applications.

PLM_Sol: predicting protein solubility by benchmarking multiple protein language models with the updated Escherichia coli protein solubility dataset

Protein solubility plays a crucial role in various biotechnological, industrial, and biomedical applications. With the reduction in sequencing and gene synthesis costs, the adoption of high-throughput experimental screening coupled with tailored bioinformatic prediction has witnessed a rapidly growing trend for the development of novel functional enzymes of interest (EOI). High protein solubility rates are essential in this process and accurate prediction of solubility is a challenging task. As deep learning technology continues to evolve, attention-based protein language models (PLMs) can extract intrinsic information from protein sequences to a greater extent. Leveraging these models along with the increasing availability of protein solubility data inferred from structural database like the Protein Data Bank holds great potential to enhance the prediction of protein solubility. In this study, we curated an Updated Escherichia coli protein Solubility DataSet (UESolDS) and employed a combination of multiple PLMs and classification layers to predict protein solubility. The resulting best-performing model, named Protein Language Model-based protein Solubility prediction model (PLM_Sol), demonstrated significant improvements over previous reported models, achieving a notable 6.4% increase in accuracy, 9.0% increase in F1_score, and 11.1% increase in Matthews correlation coefficient score on the independent test set. Moreover, additional evaluation utilizing our in-house synthesized protein resource as test data, encompassing diverse types of enzymes, also showcased the good performance of PLM_Sol. Overall, PLM_Sol exhibited consistent and promising performance across both independent test set and experimental set, thereby making it well suited for facilitating large-scale EOI studies. PLM_Sol is available as a standalone program and as an easy-to-use model at https://zenodo.org/doi/10.5281/zenodo.10675340.

Fermentation Analytical Technology (FAT): Monitoring industrial E. coli fermentations using absolute quantitative 1H NMR spectroscopy

BACKGROUND

To perform fast, reproducible, and absolute quantitative measurements in an automated manner has become of paramount importance when monitoring industrial processes, including fermentations. Due to its numerous advantages - including its inherent quantitative nature - Proton Nuclear Magnetic Resonance (1H NMR) spectroscopy provides an ideal tool for the time-resolved monitoring of fermentations. However, analytical conditions, including non-automated sample preparation and long relaxation times (T1) of some metabolites, can significantly lengthen the experimental time and make implementation in an industrial set up unfeasible.

RESULTS

We present a high throughput method based on Standard Operating Procedures (SOPs) and 1H NMR, which lays the foundation for what we call Fermentation Analytical Technology (FAT). Our method was developed for the accurate absolute quantification of metabolites produced during Escherichia coli industrial fermentations. The method includes: (1) a stopped flow system for non-invasive sample collection followed by sample quenching, (2) automatic robot-assisted sample preparation, (3) fast 1H NMR measurements, (4) metabolites quantification using multivariate curve resolution (MCR), and (5) metabolites absolute quantitation using a novel correction factor (k) to compensate for the short recycle delay (D1) employed in the 1H NMR measurements. The quantification performance was tested using two sample types: buffer solutions of chemical standards and real fermentation samples. Five metabolites - glucose, acetate, alanine, phenylalanine and betaine - were quantified. Absolute quantitation ranged between 0.64 and 3.40 mM in pure buffer, and 0.71-7.76 mM in real samples.

SIGNIFICANCE

The proposed method is generic and can be straight forward implemented to other types of fermentations, such as lactic acid, ethanol and acetic acid fermentations. It provides a high throughput automated solution for monitoring fermentation processes and for quality control through absolute quantification of key metabolites in fermentation broth. It can be easily implemented in an at-line industrial setting, facilitating the optimization of the manufacturing process towards higher yields and more efficient and sustainable use of resources.

Cloning and expression of recombinant arazyme with anti-inflammatory and anti-breast cancer potential

Arazyme is an extracellular metalloprotease which is secreted by a Gram-negative symbiotic bacterium called Serratia proteomaculans. There are limited studies on various biological activities of arazyme. This preliminary study was designed to investigate the anti-cancer and anti-inflammatory capacities of recombinant arazyme (rAra) in vitro and in vivo. Arazyme gene, araA was cloned and expressed in E. coli BL21 (DE3) using pET-28a as a vector. Nickel column purification was used to obtain pure rAra. SDS-PAGE and protein assay were used to identify the product and to measure protein content, respectively. Skimmed milk test and casein assay were carried out to assess protease activity. MCF7 cells as a breast cancer cell model were exposed to different concentrations of rAra to study anti-breast cancer potentials using MTT assay. The anti-inflammatory property of rAra was investigated using a murine air-pouch model. PCR and SDS-PAGE data showed that cloning and expression of rAra was successful and the enzyme of interest was observed at 52 KDa. Protein assay indicated that 1 mg/ml of rAra was obtained through purification. A clear zone around the enzyme on skimmed milk agar confirmed the proteolytic activity of rAra and the enzymatic activity was 320 U/mg protein in the casein assay. Cytotoxic effects of rAra reported as IC50 were 16.2 µg/ml and 13.2 mg/ml after 24 h and 48 h, respectively. In the air-pouch model, both the neutrophil count and myeloperoxidase activity, which are measures of inflammation, were significantly reduced. The results showed that rAra can be used in future mechanistic studies and R&D activities in the pharmaceutical industry to investigate the safety and efficacy of the recombinant arazyme.

Enantioselectivity regulation of antibody against chiral herbicide metolachlor based on interaction at chiral center

Enantioselective antibodies have emerged as great potential biomaterials in the fields of immunoassays and chiral separation. However, cross-reactivity of antibodies to the distomer may severely restrict the application. Comprehending the interaction mechanism between antibodies and enantiomers could be beneficial to produce superior enantioselective antibodies. In this study, a pair of recombinant antibodies (RAbs) against metolachlor enantiomers at chiral carbon (αSS-MET and αSR-MET) were generated and characterized. The αSS-MET-RAb and αSR-MET-RAb showed comparable sensitivity and specificity to the parental monoclonal antibodies by icELISA, with IC50 values of 3.45 and 223.77 ng/mL, respectively. Moreover, the complex structures of RAbs and corresponding eutomer were constructed and analyzed, and site-specific mutagenesis was utilized to verify the reliability of the enantioselective mechanism elucidated. It demonstrated that the strength of the interaction between the chiral center region of eutomer and the antibody was the key factor for the enantioselectivity of antibody. Increasing this interaction could limit the conformational adjustment of the distomer in a specific chiral recognition cavity, thus decreasing the affinity of the antibody to the distomer. This work provided the in-depth analysis of enantioselective mechanism for two RAbs and paved the way to regulate antibody enantioselective performance for immunoassays of chiral compounds.

Engineered coiled-coil HIF1α protein domain mimic

The development of targeted anti-cancer therapeutics offers the potential for increased efficacy of drugs and diagnostics. Utilizing modalities agnostic to tumor type, such as the hypoxic tumor microenvironment (TME), may assist in the development of universal tumor targeting agents. The hypoxia-inducible factor (HIF), in particular HIF1, plays a key role in tumor adaptation to hypoxia, and inhibiting its interaction with p300 has been shown to provide therapeutic potential. Using a multivalent assembled protein (MAP) approach based on the self-assembly of the cartilage oligomeric matrix protein coiled-coil (COMPcc) domain fused to the critical residues of the C-terminal transactivation domain (C-TAD) of the α subunit of HIF1 (HIF1α), we generate HIF1α-MAP (H-MAP). The resulting H-MAP demonstrates picomolar binding affinity to p300, the ability to downregulate hypoxia-inducible genes, and in vivo tumor targeting capability.

Practical deployment of automation to expedite aqueous two-phase extraction

The feasibility of bioprocess development relies heavily on the successful application of primary recovery and purification techniques. Aqueous two-phase extraction (ATPE) disrupts the definition of "unit operation" by serving as an integrative and intensive technique that combines different objectives such as the removal of biomass and integrated recovery and purification of the product of interest. The relative simplicity of processing large samples renders this technique an attractive alternative for industrial bioprocessing applications. However, process development is hindered by the lack of easily predictable partition behaviours, the elucidation of which necessitates a large number of experiments to be conducted. Liquid handling devices can assist to address this problem; however, they are configured to operate using low viscosity fluids such as water and water-based solutions as opposed to highly viscous polymeric solutions, which are typically required in ATPE. In this work, an automated high throughput ATPE process development framework is presented by constructing phase diagrams and identifying the binodal curves for PEG6000, PEG3000, and PEG2000. Models were built to determine viscosity- and volume-independent transfer parameters. The framework provided an appropriate strategy to develop a very precise and accurate operation by exploiting the relationship between different liquid transfer parameters and process error. Process accuracy, measured by mean absolute error, and device precision, evaluated by the coefficient of variation, were both shown to be affected by the mechanical properties, particularly viscosity, of the fluids employed. For PEG6000, the mean absolute error improved by six-fold (from 4.82% to 0.75%) and the coefficient of variation improved by three-fold (from 0.027 to 0.008) upon optimisation of the liquid transfer parameters accounting for the viscosity effect on the PEG-salt buffer utilising ATPE operations. As demonstrated here, automated liquid handling devices can serve to streamline process development for APTE enabling wide adoption of this technique in large scale bioprocess applications.

PhoCoil: An Injectable and Photodegradable Single-component Recombinant Protein Hydrogel for Localized Therapeutic Cell Delivery

Hydrogel biomaterials offer great promise for 3D cell culture and therapeutic delivery. Despite many successes, challenges persist in that gels formed from natural proteins are only marginally tunable while those derived from synthetic polymers lack intrinsic bioinstructivity. Towards the creation of biomaterials with both excellent biocompatibility and customizability, recombinant protein-based hydrogels have emerged as molecularly defined and user-programmable platforms that mimic the proteinaceous nature of the extracellular matrix. Here, we introduce PhoCoil, a dynamically tunable recombinant hydrogel formed from a single protein component with unique multi-stimuli responsiveness. Physical crosslinking through coiled-coil interactions promotes rapid shear-thinning and self-healing behavior, rendering the gel injectable, while an included photodegradable motif affords on-demand network dissolution via visible light. PhoCoil gel photodegradation can be spatiotemporally and lithographically controlled in a dose-dependent manner, through complex tissue, and without harm to encapsulated cells. We anticipate that PhoCoil will enable new applications in tissue engineering and regenerative medicine.

Genome-scale metabolic models in translational medicine: the current status and potential of machine learning in improving the effectiveness of the models

The genome-scale metabolic model (GEM) has emerged as one of the leading modeling approaches for systems-level metabolic studies and has been widely explored for a broad range of organisms and applications. Owing to the development of genome sequencing technologies and available biochemical data, it is possible to reconstruct GEMs for model and non-model microorganisms as well as for multicellular organisms such as humans and animal models. GEMs will evolve in parallel with the availability of biological data, new mathematical modeling techniques and the development of automated GEM reconstruction tools. The use of high-quality, context-specific GEMs, a subset of the original GEM in which inactive reactions are removed while maintaining metabolic functions in the extracted model, for model organisms along with machine learning (ML) techniques could increase their applications and effectiveness in translational research in the near future. Here, we briefly review the current state of GEMs, discuss the potential contributions of ML approaches for more efficient and frequent application of these models in translational research, and explore the extension of GEMs to integrative cellular models.

Generation of a highly specific recombinant full-length antibody for detecting ethirimol in fruit and environmental water

High-performance antibodies are core reagents for highly sensitive immunoassays. Herein, based on a novel hapten, a hybridoma secreting the high-affinity anti-ethirimol monoclonal antibody (mAb-14G5F6) was isolated with an IC50 value of 1.35 μg/L and cross-reactivity below 0.20% for 13 analogs. To further address the challenge of hybridoma preservation and antibody immortalization, a recombinant full-length antibody (rAb-14G5F6) was expressed using the HEK293(F) expression system based on the mAb-14G5F6 gene. The affinity, specificity, and tolerance of rAb-14G5F6, as characterized by indirect competitive enzyme-linked immunosorbent assay and noncompetitive surface plasmon resonance, exhibited high concordance with those of mAb-14G5F6. Further immunoassays based on rAb-14G5F6 were developed for irrigation water and strawberry fruit with limits of detection of 0.0066 and 0.036 mg/kg, respectively, recoveries of 80100%, and coefficients of variation below 10%. Furthermore, homology simulation and molecular docking revealed that GLU(L40), GLY(L107), GLY(H108), and ASP(H114) play important roles in forming hydrogen bonds and pi-anion ionic bonds between rAb-14G5F6 and ethirimol, resulting in the high specificity and affinity of rAb-14G5F6 for ethirimol, with a KD of 5.71 × 10-10 mol/L. Overall, a rAb specific for ethirimol was expressed successfully in this study, laying the groundwork for rAb-based immunoassays for monitoring fungicide residues in agricultural products and the environment.

Genetic algorithm-based semisupervised convolutional neural network for real-time monitoring of Escherichia coli fermentation of recombinant protein production using a Raman sensor

As a non-destructive sensing technique, Raman spectroscopy is often combined with regression models for real-time detection of key components in microbial cultivation processes. However, achieving accurate model predictions often requires a large amount of offline measurement data for training, which is both time-consuming and labor-intensive. In order to overcome the limitations of traditional models that rely on large datasets and complex spectral preprocessing, in addition to the difficulty of training models with limited samples, we have explored a genetic algorithm-based semi-supervised convolutional neural network (GA-SCNN). GA-SCNN integrates unsupervised process spectral labeling, feature extraction, regression prediction, and transfer learning. Using only an extremely small number of offline samples of the target protein, this framework can accurately predict protein concentration, which represents a significant challenge for other models. The effectiveness of the framework has been validated in a system of Escherichia coli expressing recombinant ProA5M protein. By utilizing the labeling technique of this framework, the available dataset for glucose, lactate, ammonium ions, and optical density at 600 nm (OD600) has been expanded from 52 samples to 1302 samples. Furthermore, by introducing a small component of offline detection data for recombinant proteins into the OD600 model through transfer learning, a model for target protein detection has been retrained, providing a new direction for the development of associated models. Comparative analysis with traditional algorithms demonstrates that the GA-SCNN framework exhibits good adaptability when there is no complex spectral preprocessing. Cross-validation results confirm the robustness and high accuracy of the framework, with the predicted values of the model highly consistent with the offline measurement results.

Improving the production of recombinant L-Asparaginase-II in Escherichia coli by co-expressing catabolite repressor activator (cra) gene

Identification of a single genetic target for microbial strain improvement is difficult due to the complexity of the genetic regulatory network. Hence, a more practical approach is to identify bottlenecks in the regulatory networks that control critical metabolic pathways. The present work focuses on enhancing cellular physiology by increasing the metabolic flux through the central carbon metabolic pathway. Global regulator cra (catabolite repressor activator), a DNA-binding transcriptional dual regulator was selected for the study as it controls the expression of a large number of operons that modulate central carbon metabolism. To upregulate the activity of central carbon metabolism, the cra gene was co-expressed using a plasmid-based system. Co-expression of cra led to a 17% increase in the production of model recombinant protein L-Asparaginase-II. A pulse addition of 0.36% of glycerol every two hours post-induction, further increased the production of L-Asparaginase-II by 35% as compared to the control strain expressing only recombinant protein. This work exemplifies that upregulating the activity of central carbon metabolism by tuning the expression of regulatory genes like cra can relieve the host from cellular stress and thereby promote the growth as well as expression of recombinant hosts.

Innovations and Challenges in the Development of COVID-19 Vaccines for a Safer Tomorrow

Vaccination, a historically effective public health intervention, has shielded millions from various diseases. Lessons from severe acute respiratory syndrome coronavirus (SARS-CoV) have improved COVID-19 vaccine development. Despite mRNA vaccines' efficacy, emerging variants pose challenges, exhibiting increased transmissibility, infectivity, and severity. Developing COVID-19 vaccines has faced hurdles due to urgency, limited virus understanding, and the need for safe solutions. Genetic variability necessitates continuous vaccine adjustments and production challenges demand scaling up manufacturing with stringent quality control. This review explores SARS-CoV-2's evolution, upcoming mutations that challenge vaccines, and strategies such as structure-based, T cell-based, respiratory mucosal-based, and nanotechnology approaches for vaccine development. This review insight provides a roadmap for navigating virus evolution and improving vaccine development.