Substituted alkyl pyrazines - other than being extracted from various natural sources such as coffee beans, cocoa beans, nuts and vegetables - can be synthesized by the use of traditional chemical methods or by the help of certain microorganisms. The importance of pyrazines for food industry is expected to grow in the upcoming years due to the higher demand for ready meals, coffee and chocolate drinks; the roasty, nutty and earthy smell is reminiscent for coffee and cocoa depending on substitution and concentration of pyrazines. The growing awareness of people about the ingredients and the origin of their daily food has strongly influenced the market with labels like ’organic‘ and ’natural‘. Many flavor ingredients prepared by biotechnology methods have conquered the market in recent years and are destined to replace and optimize the ineffective (0.01% pyrazine/kg biomass) extraction from plants or animal sources. This overview focuses on the achievements and the upcoming challenges in pyrazine synthesis. Major parts deal with the extraction of natural products from sugar molasses, the chemical synthesis, fermentation by microorganisms and preparative methods by biocatalysis. The different types of production are decisive for the declaration and value of the final product and can span from 200-3500 $/kg for the synthetically produced or the naturally extracted 2,5-dimethylpyrazine, respectively.

Recent noteworthy advances in the development of high-performing microbial and mammalian strains have enabled the sustainable production of bio-economically valuable substances such as bio-compounds, biofuels, and biopharmaceuticals. However, to obtain an industrially viable mass-production scheme, much time and effort are required. The robust and rational design of fermentation processes requires analysis and optimization of different extracellular conditions and medium components, which have a massive effect on growth and productivity. In this regard, knowledge- and data-driven modeling methods have received much attention. Constraint-based modeling (CBM) is a knowledge-driven mathematical approach that has been widely used in fermentation analysis and optimization due to its capabilities of predicting the cellular phenotype from genotype through high-throughput means. On the other hand, machine learning (ML) is a data-driven statistical method that identifies the data patterns within sophisticated biological systems and processes, where there is inadequate knowledge to represent underlying mechanisms. Furthermore, ML models are becoming a viable complement to constraint-based models in a reciprocal manner when one is used as a pre-step of another. As a result, more predictable models are produced. This review highlights the applications of CBM and ML independently and the combination of these two approaches for analyzing and optimizing fermentation parameters.

Despite rapid progress in the field, scalable high-yield production of AAV is still one of the critical bottlenecks the manufacturing sector is facing. The insect cell-baculovirus expression vector system (IC-BEVS) has emerged as a mainstream platform for a scalable production of recombinant proteins with clinically approved products for human use. In this review, we provide a detailed overview on advancements in IC-BEVS for rAAV production. Since the first report of baculovirus induced production of rAAV in insect cells in 2002, this platform has undergone significant evolutions. The original three baculovirus system was improved to enhance expression stability and further streamlined to reduce the number of baculoviruses to two and eventually one. The one baculovirus system consisting of an inducible packaging insect cell line was further improved to enhance the AAV vector quality and potency. In parallel, implementation of advanced manufacturing approaches and control of critical processing parameters have demonstrated promising results with process validation in large scale bioreactor runs. Moreover, optimization of molecular design of vectors to enable higher cell-specific yield of functional AAV particles in combination with bioprocess intensification strategies may further contribute to addressing current and future manufacturing challenges.

The use of adeno-associated viruses (AAV) as vectors for gene and cell therapy has risen considerably in recent years. Consequently, the amount of AAV vectors required during the validation and clinical trials has also increased. AAV serotype 6 (AAV6) is well-documented for its efficiency in transducing different cell types and has been successfully used in gene and cell therapy protocols. However, the number of vectors required to effectively deliver the transgene to one single cell has been estimated at 106 viral genomes (VG). Overall, this means that large-scale production of AAV6 is needed. Suspension cell-based platforms are currently limited to low-cell-density productions, hindering the potential of this production process to increase yields. Here, we investigate the improvement of the production of AAV6 at higher cell densities. The production was performed by transient transfection of HEK293SF cells. When the plasmid DNA is provided on a cell basis, the production can be carried out at medium cell density without effects on cell-specific titer or particle functionality, resulting in titers above 1010 VG/mL. Medium supplementation alleviated the cell density effect, in terms of VG/cell, at high-cell-density productions. On the other hand, the cell-specific functional titer was not maintained, and further studies are necessary to understand the observed limitations. The medium-cell-density production method reported here lays the foundation for large-scale process operations, potentially solving the current vector shortage in AAV manufacturing.

Biomolecules are increasingly attractive templates for the synthesis of functional nanomaterials. Chief among them are the plant Tobacco mosaic virus (TMV) and Barley stripe mosaic virus (BSMV) due to their high aspect ratio, narrow size distribution, diverse biochemical functionalities presented on the surface, and compatibility with a number of chemical conjugations. These properties are also easily manipulated by genetic modification to enable the synthesis of a range of metallic and non-metallic nanomaterials for diverse applications. This article reviews the characteristics of TMV, BSMV, and their virus-like particle (VLP) derivatives and how these may be manipulated to extend their use and function. A focus of recent efforts has been on greater understanding and control of the self-assembly processes that drive biotemplate formation. We briefly outline how these features have been exploited in engineering applications such as sensing, catalysis, and energy storage, and discuss emerging advances that promise to accelerate the development of these biotemplates for widescale industrial use.

Food security is one of the main topics of today's agriculture especially facing challenging environmental conditions. As most humankind has a daily intake of cereal grains, current breeding programs focus on these crop plants. Within the breeders' toolbox, customised endonucleases became included after this universal application had been demonstrated. Due to technological restrictions, the main focus was on aboveground plant organs, while the essential belowground has been given only limited attention. In the present review, we summarise the knowledge on the root system architecture in cereals, the importance of phytohormones in this physiological process, and the molecular mechanisms involved. The review summarises how the use of the CRISPR methodology can improve the root system architecture to enhance crop production genetically. Finally, future research directions involving all this knowledge and technical advances are suggested.

Protein-based condensates have been proposed to accelerate biochemical reactions by enriching reactants and enzymes simultaneously. Here, we engineered those condensates into a Photo-Activated Switch in E. coli (PhASE) to regulate enzymatic reactions via tuning the spatial correlation of enzymes and substrates. In this system, scaffold proteins undergo liquid-liquid phase separation (LLPS) to form light-responsive compartments. Tethered with a light-responsive protein, enzymes of interest (EOIs) can be recruited by those compartments from cytosol within only a few seconds after a pulse of light induction and fully released in 15 minutes. Furthermore, we managed to enrich small molecular substrates simultaneously with enzymes in the compartments and achieved the acceleration of luciferin and catechol oxidation by 2.3 folds and 1.6 folds, respectively. We also developed a quantitative model to guide the further optimization of this de-mixed regulatory system. Our tool can thus be used to study the rapid redistribution of proteins, and reversibly regulate enzymatic reactions in E. coli.

Adeno-associated viral vectors (AAV) are one of the most efficient engineered tools for delivering genetic material into host cells. The commercialization of AAV-based drugs goes hand in hand with the need to increase manufacturing capacities and to develop appropriate quality controls. In particular, accurate methods to assess the level of residual DNA in AAV vector stocks are needed, considering the potential risk of co-transferring oncogenic or immunogenic sequences with the therapeutic vectors. Our laboratory has developed an assay based on high-throughput sequencing (HTS) to exhaustively identify and quantify DNA species in recombinant AAV batches. Compiled with a computational analysis of the single nucleotide variants (SNV), Single-Stranded Virus Sequencing (SSV-Seq) also provides information regarding rAAV genome identity. In this study, we show that the PCR amplification of regions with high GC content and including mononucleotide stretches can be biased during the DNA library preparation, leading to drops in the sequencing coverage along the AAV vector genome. To circumvent this problem, we have developed a PCR-free protocol, named SSV-Seq 2.0, that is optimized for the sequencing of rAAV genomes that contain sequences with a high percentage of GC and homopolymers, such as the CAG promoter. HTS-based assays are indispensable to provide accurate data to the regulatory agencies regarding nucleic acids content in AAV vector batches and to improve the safety and efficacy of these viral vectors.

In the past decade, recombinant adeno-associated virus (rAAV) has gained increased attention as a prominent gene therapy technology to treat monogenetic disease. One of the challenges in rAAV production is the enrichment of full-rAAV particles containing the gene of interested (GOI) payload. Herein, we demonstrated that by adjusting the mobile phase properties of anion-exchange chromatography (AEX), Empty and Full separation of rAAV was improved in monolith based preparative AEX chromatography. When compared to the baseline method using NaCl, the presence of tetraethylammonium acetate (TEA-Ac) in the AEX mobile phase resulted in enhanced resolution (from 0.75 to 1.23) between Empty and Full peaks by salt linear gradient elution, as well as increased the percentage of full-rAAV particles from 20% to 36% and GOI genome recovery (from 59% to 62%). Furthermore, a dual wash + step elution AEX method was developed to harness TEA-Ac contribution on Empty and Full separation in the first wash (wash1) step while removing TEA-Ac in the second wash (wash2) step to ensure product safety. The resulting optimized AEX purification method could be easily adapted in scaled-up manufacturing and could also be applied to purification processes involving other AAV serotypes facing similar Empty and Full rAAV separation challenges.

Genome editing and gene expression engineering using CRISPR-Cas systems in plants usually rely on labor-intensive tissue culture approaches to generate stably transformed plants that express the components of the reaction. Viral vectors have demonstrated to be a quick and effective alternative to express multiple guide RNAs, DNA templates for homologous recombination, and even Cas nucleases. Here we have developed an improved vector system based on tobacco rattle virus (TRV) to simplify logistics in genome editing and gene silencing approaches. The new system consists in a single Agrobacterium tumefaciens clone co-transformed with two compatible mini binary vectors from which TRV RNA1 and an engineered version of TRV RNA2 are expressed. Sequences of recombinant proteins, gene fragments for virus-induced gene silencing (VIGS) or guide RNAs can be easily inserted by one-step digestion-ligation and homology-based cloning methods in the RNA2 plasmid to produce vectors with a size substantially smaller than usual. Using this new one-Agrobacterium TRV mini vector system, we show robust VIGS of an endogenous host gene after infiltration of bacterial suspensions at low optical densities, and efficient production of recombinant proteins in Nicotiana benthamiana. Most importantly, we also show highly efficient heritable genome editing in more than half of the seedling originating from inoculated N. benthamiana plants that express Cas9.

The accelerating development of gene therapy from research towards clinical trials and beyond has elevated the demand for practical viral vector manufacturing solutions. The use of disposable upstream technology is gaining traction in clinical manufacturing. The world's first disposable, fully integrated, high-cell density fixed-bed bioreactor was launched approximately one decade ago. By now, the iCELLis fixed-bed technology has obtained the broadest customer base. This system is available in small scale but also provides the largest GMP compliant commercial system. However, there are several alternative technologies, which have been widely used for the manufacturing of different viral vectors, allowing for complementation within the market. This article will review virus production using the latest disposable fixed-bed bioreactors, present highlights of an interview with the inventor of these bioreactors, and share some user experience. It is predicted that single-use fixed-bed bioreactors will receive even more attention in the field of viral vector manufacturing and commercialization, especially with high virus yields.

The effects of climate change, soil depletion, a growing world population putting pressure on food safety and security are major challenges for agriculture in the 21st century. The breeding success of the green revolution has decelerated and current programs can only offset the yield affecting factors. New approaches are urgently needed and we propose, “Genome Editing accelerated Re-Domestication” (GEaReD) as a major new direction in plant breeding. By combining the upcoming technologies for phenotyping, omics and artificial intelligence with the promising new CRISPR-toolkits, this approach is closer than ever. Wild relatives of current crops are often adapted to harsh environments and have a high genetic diversity. Re-domestication of wild barley or teosinte could generate new cultivars adapted to environmental changes. De novo domestication of perennial relatives like Hordeum bulbosum could counter with soil depletion and increase soil carbon. Recent research already proved the principle of re-domestication in tomato and rice and therefore laid the foundation for GEaReD.

Interfaces between biomaterials and living system are critical in regulating their interactions. Poor biocontact properties always limited the performance of biomaterials in biological environment. Surface engineering aims to control the interface interaction to further enhance the desired behavior of biomaterials. Upon implantation of biomaterials into the biological environment, a series of host responses are initiated. Non-specific protein adsorption on biomaterials is the essential stage of all biological reactions that associated with implants failure, device-related infections and blood-coagulation. In this review, we first focused on surface modification techniques to eliminate protein adsorption by emphasizing PEGylation of both macroscopic surface and nanoparticle system. Next, recent developments in surface engineering of biomaterials to optimize interactions between biomaterials and specific host tissue and organs are discussed. Optimizing the biocontact property of blood-contact devices can improve their hemocompatibility and maintain vascular homeostasis. Surface modifications of orthopedic and dental implants confer improved osteointegration and tribology performance. Controlling the surface chemistry and topography, and immobilizing biomolecules can aid the expansion and direct the differentiation of stem cells.

Viral vectors have a great potential for gene delivery, but manufacturing at pharmaceutical scale is a big challenge for the industry. The baculovirus-insect cells system is one of the most scalable platforms to produce clinical grade recombinant Adeno-Associated Virus (rAAV) vectors, however, the standard procedure to generate recombinant baculovirus based on Tn7 transposition is time consuming and still suffers technical constraints. Indeed, we recently shown that baculoviral sequences adjacent to the AAV ITRs are preferentially encapsidated into the rAAV vector particles. This observation raised concern about safety for clinical applications due to the presence of bacterial and antibiotic resistance coding sequences with Tn7-mediated system for the construction of recombinant baculoviruses. Here, we investigated a faster and safer method to generate baculovirus reagents based on homologous recombination (HR) for its use in rAAV manufacturing compared to the Tn7-based system. First, we confirmed the functionality of inserted cassette and the absence of undesirable genes into HR-derived baculoviral genomes. Strikingly, we found that the exogenous cassette shown an increased stability over passages when using HR system. Finally, we tested these materials to produce rAAV vectors. The baculoviruses originated from either system lead to high rAAV vector genome yields, with the advantage for the HR method being that the rAAV lots are exempted of undesirable gentamycin and kanamycin genes derived sequences which provides an additional level of safety for the manufacturing of rAAV vectors. Overall, this study highlights the importance of the upstream process and starting biologic materials to generate safer rAAV biotherapeutic products.

The scale-up of bioprocesses is still one of the major obstacles in biotechnological industry. Scale-down bioreactors were identified as valuable tools to investigate the heterogeneities observed in large-scale tanks in laboratory-scale. Additionally, computational fluid dynamics (CFD) simulations can be used to gain information about fluid flow in tanks used for production. Here we present the rational design and comprehensive characterization of a scale-down setup, in which a flexible and modular plug-flow reactor is connected to a stirred tank bioreactor. With the help of CFD the mixing time difference between differently scaled bioreactors were evaluated and used as scale-down criterium. Additionally, it was used to characterize the setup at conditions were experiments could technically not be performed. This was the first time a scale-down setup was tested on high cell density Escherichia coli cultivations to produce industrial relevant antigen-binding fragments (Fab). Reduced biomass and product yields were observed during the scale-down cultivations. Additionally, the intracellular Fab fraction was increased by using the setup. The results show that including CFD in the design and characterization of a scale-down reactor can help to keep a connection to production scale and also gain intensive knowledge about the setup, which enhances usability.

Background: Epitope mapping is an increasingly important aspect of biotherapeutic and vaccine development. Recent advances in therapeutic antibody design and production has enabled candidate mAbs to be identified at a rapidly increasing rate resulting in a significant bottleneck in the characterization of ‘structural’ epitopes, that are challenging to determine using existing high throughput epitope mapping tools. Here, Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) epitope screening workflow was introduced that is well suited for accelerated characterization of epitopes with a common antigen. Main methods and major results: The method is demonstrated on set of 6 candidate mAbs targeting Pertactin (PRN). Using this approach, five of the six epitopes was unambiguously determined using two HDX mixing timepoints in 24 hours total run time, corresponding to substantial decrease in the instrument time required to map a single epitope using conventional HDX workflows. Conclusion: An accelerated HDX-MS epitope screening workflow was developed. The two-timepoint ‘screening’ workflow mapped all six mAbs and generated high confidence epitopes for five of the six mAbs assayed. The substantial improvement in the rate of data collection can advance HDX-MS for higher throughput investigations supporting the ability to evaluate a broader number of mAb candidates at an earlier stage of vaccine development.

Many transgenic animals have been produced using CRISPR–Cas9 technology to edit specific genes. However, there are few guidelines for the application of this technique in cattle. The goal of this study was to produce trait-improved cattle using the genome editing technology CRISPR–Cas9. Myostatin (MSTN) was selected as a target locus and synthetic mRNA of sgRNA and Cas9 was microinjected into bovine in vitro fertilized embryos. As a result, 17 healthy calves were born and 3 of these showed MSTN mutation rates of 10.5%, 45.4%, and 99.9%, respectively. Importantly, the offspring with the 99.9% MSTN mutation rate had biallelic mutation (-12bp) and a doubling muscle growth phenotype. In conclusion, we showed that the genome editing technology CRISPR–Cas9 can produce genetically modified calves with improved traits.

Today’s available therapies to treat patients infected with human immunodeficiency virus (HIV) aim at preventing viral replication and transmission but fail to eliminate the virus. Although transplantation of an allogeneic CCR5Δ32 homozygous stem cell grafts provided a cure for three patients, this approach is not considered a general therapeutic strategy because of potential severe side effects. Conversely, genome editing to disrupt the CCR5 locus that encodes the major HIV coreceptor was shown to confer resistance to R5-tropic HIV strains on the cellular level. Here, we present a clinically relevant and highly efficient approach to produce HIV-1 resistant CD4+ T cells. After transferring mRNA coding for CCR5-targeting TALEN into CD4+ T cells by electroporation, up to 89% of CCR5 alleles were disrupted. Genotyping confirmed genetic stability of the edited cell product and off-target analyses established absence of relevant mutagenic events. When challenging these edited T cells with R5-tropic HIV, we observed protection in a dose-dependent manner. Functional assessments revealed no significant differences between edited and control CD4+ T cells in terms of proliferation capacity and their ability to secrete cytokines upon exogenous stimuli. Overall, we successfully engineered HIV-resistant CD4+ T cells under clinically relevant conditions, paving the way for clinical translation.