Given the potential applications of gas vesicles (GVs) in multiple fields including antigen-displaying and imaging, heterologous reconstitution of synthetic GVs is an attractive and interesting study that has translational potential. Here, we attempted to express and assemble GV proteins (GVPs) into GVs using the model eukaryotic organism Saccharomyces cerevisiae. We first selected and expressed two core structural proteins, GvpA and GvpC from cyanobacteria Anabaena flos-aquae and Planktothrix rubescens, respectively. We then optimized the protein expression conditions and validated GV assembly in the context of cell flotation and GV shapes. We found that when two copies of AnaA were integrated into the genome, it resulted in cell floatation and GV production regardless of GvpC expression. Next, we co-expressed chaperone-RFP with the GFP-AnaA to aid the AnaA aggregation. The co-expression of individual chaperones (Hsp42, Sis1, Hsp104, and GvpN) with AnaA led to the formation of larger inclusions and enhanced the sequestration of AnaA into the perivacuolar site. To our knowledge, this represents the first study on reconstitution of GVs in S. cerevisiae. Our results could provide insights into optimizing conditions for heterologous protein expressions as well as the reconstitution of other synthetic microcompartments in yeast.

The occurrence of random mutations can increase the diversity of the genome and promote the evolutionary process of organisms. High efficiency mutagenesis techniques significantly accelerate the evolutionary process. In this work, we describe a targeted in vivo mutagenesis system to significantly increase mutation frequency and generate mutations across all four nucleotides. We constructed different DNA-modifying enzyme-PmCDA1-T7 RNA polymerase fusion proteins, achieved targeted mutagenesis by flanking the target gene with T7 promoters, and tuned the mutation spectra by introducing different DNA-modifying enzymes. With the mutagenesis fusion proteins, the mutation frequency of the target gene could reach 5.13x10-3, and the proportion of non-C→T mutations is 10~11-fold higher than the cytidine-based evolutionary tools. We also demonstrated that our mutagenesis tools could be used to evolve the essential enzyme in the β-carotene biosynthesis process and generate mutations with different types.

Nascent advanced therapies, including regenerative medicine and cell and gene therapies, rely on the production of cells in bioreactors that are highly heterogeneous in both space and time. Unfortunately, these promising therapies have failed to reach a wide patient population due to unreliable manufacturing processes that result in batch variability and cost prohibitive production. This can be attributed largely to a void in existing process analytical technologies (PATs) capable of characterizing the secreted critical quality attributes (CQAs) biomolecules that correlate with the final product quality. The Dynamic Sampling Platform (DSP) is a PAT for cell bioreactor monitoring that can be coupled to a suite of sensor techniques to provide real-time feedback on spatial and temporal CQA content in situ. In this study, DSP is coupled with electrospray ionization mass spectrometry (ESI-MS) and direct-from-culture sampling to obtain measures of CQA content in bulk media and the cell microenvironment throughout the entire cell culture process (~3 weeks). Post hoc analysis of this real-time data reveals that DSP output is heavily dependent on spatial context. Importantly, these results demonstrate that an effective PAT must incorporate both spatial and temporal resolution to serve as an effective input f or feedback control in advanced therapy production.

Because of their excellent therapeutic potential, mesenchymal stem cells (MSCs) have been used as cell therapeutics for various diseases. However, the survival rate and duration of MSCs after transplantation are extremely low and short, respectively. To solve these problems, in this study, we prepared multicellular spheroids of MSCs and investigated their survival and function after intravenous injection in mice. The murine adipose-derived MSC line m17.ASC was cultured in agarose-based microwell plates to obtain size-controlled m17.ASC spheroids of an average diameter and cell number of approximately 170 μm and 1100 cells/spheroid, respectively. The intravenously injected m17.ASC spheroids mainly accumulated in the lung and showed a higher survival rate than suspended m17.ASC cells during the experimental period of 7 days. m17.ASC spheroids efficiently reduced the lipopolysaccharide-induced increase in plasma concentrations of interleukin-6 and tumor necrosis factor-α. These results indicate that spheroid formation improved the pulmonary delivery and survival of MSCs, as well as their therapeutic potential against inflammatory pulmonary diseases.

Bioprocess development and optimization is a challenging, costly, and time-consuming effort. In this multidisciplinary task, upstream processing (USP) and downstream processing (DSP) are conventionally considered distinct disciplines. This consideration fosters “one-way” optimization without considering interdependencies between unit operations; thus, the full potential of the process chain cannot be achieved. Therefore, it is necessary to fully integrate USP and DSP process development to provide balanced biotechnological production processes. The aim of the present study was to investigate how different host/leader/antigen binding fragment (Fab) combinations in E. coli expression systems influence USP and primary recovery performance and the final product quality. We ran identical fed-batch cultivations with 16 different expression clones to study growth and product formation kinetics, as well as centrifugation efficiency, viscosity, extracellular DNA, and endotoxin content, which are important parameters in DSP. We observed a severe influence on cell growth, product titer, extracellular product, and cell lysis, accompanied by a significant impact on the analyzed parameters of DSP performance. Our results provide the basis for establishing integrated process development considering interdependencies between USP and DSP. These interdependencies need to be understood for rational decision-making and efficient process development.

We report a novel Cultured Neuronal Network on a chip as a viable alternative to current culture methods for the analysis of neuronal network formation and evolution of the structural properties of the network's graph . This innovative microfluidic chip fabricated from Polydimethylsiloxane, vinyl, and glass offers worthy features such as the posibility to develop and produce custom designs effortlessly, easy handling and monitoring, culture medium renewal, and reducing the exposure to contamination. Due to these benefits, longer survival of the neuronal networks are observed in comparison to conventional methods. In addition to the fast and cost-effective manufacturing of the chip, this technology provides a significant step forward in the studies of neuronal network development and many challening applications such as drug testing of in vitro cell culture models .

Tracheal resection and end-to-end anastomosis has been the standard clinical approach for the treatment of most airway diseases, especially invading the lower trachea or carina. However, when long-length (exceeding 2 cm in children or 5 cm in adults) tracheal circular resection is performed, tracheal replacement therapy is often required. In this study, we aimed to utilize autologous tracheal epithelia and bone marrow mesenchymal stem cells (BMSCs) as the seeding cells, utilize polycaprolactone (PCL) coated with Silk Fibroin Methacryloyl (SilMA) as the scaffold to carry the cells and Kartogenin (KGN). Firstly, SilMA with the concentration of 10%, 15% and 20% was made, and the experiment of swelling and degradation was performed. With the increase of the concentration, the swelling ratio decreased, the degradation progress slowed down. Upon the result of CCK-8 test and HE staining of 3D co-culture, the 20% SilMA was selected. Next, SilMA and the cells attached to SilMA were characterized by scanning electron microscopy (SEM). Furthermore, in vitro cytotoxicity test shows that 20% SilMA has good cytocompatibility. The hybrid scaffold was then made by PCL coated with 20% SilMA. The mechanical test shows this hybrid scaffold has better biomechanical properties. In vivo tracheal defect repair assays were done to evaluate the effect of the hybrid substitution. H&E staining, immunohistochemical (IHC) and immunofluorescence (IF) staining showed that this hybrid substitution ensured the viability, proliferation and migration of epithelium. This study is expected to provide new strategies for the fields of tracheal replacement therapy needing mechanical properties and epithelization.

The signaling molecular mechanisms in zebrafish response to electricity are unknown, so here we asked if changes to dopaminergic signaling pathways can affect their electrically-evoked locomotion. To answer this question, the effects of multiple selective and non-selective dopamine compounds on the electric response of zebrafish larvae is investigated. A microfluidic device with enhanced control of experimentation with multiple larvae is used, which features a novel design to immobilize four zebrafish larvae in parallel and expose them to electric current that induces tail locomotion. In 6 days post-fertilization zebrafish larvae, the electric induced locomotor response is quantified in terms of the tail movement duration and beating frequency to discern the effect of non-lethal concentrations of dopaminergic agonists (apomorphine, SKF-81297, and quinpirole), and antagonists (butaclamol, SCH-23390, and haloperidol). All dopamine antagonists decrease locomotor activity, while dopamine agonists do not induce similar behaviours in larvae. The D2- like selective dopamine agonist quinpirole enhances movement. However, exposure to non-selective and D1-selective dopamine agonists apomorphine and SKF-81297 cause no significant change in the electric response. Exposing larvae that were pre-treated with butaclamol and haloperidol to apomorphine and quinpirole, respectively, restores electric locomotion. The results demonstrate a correlation between electric response and the dopamine signalling pathway. We propose that the electrofluidic assay has profound application potential as a chemical screening method when investigating biological pathways, behaviors, and brain disorders.

Metabolic reprogramming has been coined as a hallmark of cancer, accompanied by which the alterations in metabolite levels have profound effects on gene expression, cellular differentiation and the tumor environment. Yet a systematic evaluation of quenching and extraction procedures for quantitative metabolome profiling of tumor cells is currently lacking. To achieve this, this study is aimed at establishing an unbiased and leakage-free metabolome preparation protocol for Hela carcinoma cell. We evaluated 12 combinations of quenching and extraction methods from three quenchers (liquid nitrogen, -40°C 50% methanol, 0.5°C normal saline) and four extractants (80% methanol, methanol: chloroform: water (1:1:1, v/v/v), 50% acetonitrile, 75°C 70% ethanol) for global metabolite profiling of adherent Hela carcinoma cells. Based on the isotope dilution mass spectrometry (IDMS) method, gas/liquid chromatography in tandem with mass spectrometry was used to quantitatively determine 43 metabolites including sugar phosphates, organic acids, amino acids, adenosine nucleotides and coenzymes involved in central carbon metabolism. Among 12 combinations, cells that washed twice with phosphate buffered saline (PBS), quenched with liquid nitrogen, and then extracted with 50% acetonitrile was found to be the most optimal method to acquire intracellular metabolites with minimal loss during sample preparation. Furthermore, a case study was carried out to evaluate the effect of doxorubicin (DOX) on both adherent cells and 3D tumor spheroids using quantitative metabolite profiling. Based on this, quantitative time-resolved metabolite data can serve to the generation of hypotheses on metabolic reprogramming to reveal its important role in tumor development and treatment.

There is a vast number of biomaterials ranging from drug-eluting stents, coated implants, drug delivery devices and artificial organs, among others, that have been developed in recent years. However, translation of many of these biomaterials to clinic is often plagued by biocompatibility challenges. This review focuses on strategies implemented in some of the recently developed biomaterials -- particularly for soft and hard tissue regeneration, organ manufacturing and disease remediation -- to overcome potential foreign body response to the incorporation of the biomaterials in the host.

As a rapidly developing cell engineering technique, cell electrofusion has been increasingly applied in the field of hybridoma preparation in recent years. However, electrofusion is a certain degree of difficulty to completely replace the polyethylene glycol-mediated cell fusion. The key elements limiting electrofusion in the field of hybridoma preparation are practical complicated. This review summarizes the state of art of cell electrofusion in hybridoma preparation based on recent published literatures, mainly focusing on electrofusion instruments and their components, process control, cell treatment, and process characterization. The review provides new information and insightful commentary, critically important to the promotion of further electrofusion development in the field of hybridoma preparation.

Microfluidic devices have been introduced for phenotypic screening of zebrafish larvae in both fundamental and pre-clinical research. One of the remaining challenges for the broad use of microfluidic devices is their limited throughput, especially in behavioural assays. Previously, we introduced the tail locomotion of a semi-mobile zebrafish larva evoked on-demand with electric signal in a microfluidic device. Here, we report the lessons learned for increasing the number of specimens from one to four larvae in this device. Multiple parameters including loading and testing time per fish and loading and orientation efficiencies were refined to optimize the performance of modified designs. Simulations of the flow and electric field within the final device provided insight into the flow behavior and functionality of traps when compared to previous single-larva devices. Outcomes led to a new design which decreased the testing time per larva by approximately 60%. Further, loading and orientation efficiencies increased by more than 80%. Critical behavioural parameters such as response duration and tail beat frequency were similar in both single and quadruple-fish devices. The optimized microfluidic device has significant advantages for greater throughput and efficiency when behavioral phenotyping is required in various applications, including chemical testing in toxicology and gene screening.

Statins as a lipid-lowering drug can selectively inhibit 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase and decrease cholesterol synthesis effectively. With the improvement of nutritional conditions, the demand for statins is increasing in global market. Due to the rapid development of modern biotechnologies, the biosynthesis of stains by microbial cell factory appears great advantages. It has the advantages of simple operation and easy separation of products. This review summarized the strategies on statins production via microbial cell factory, including both traditional fermentation culture and modern synthetic biology manufacture. Firstly, the complex fermentation parameters and process control technology on submerged fermentation (SmF) and solid-state fermentation (SSF) were introduced in detail. Especially, the possibility of recoverable agricultural wastes/(Biomass) as fermentation substrate on solid-state fermentation to produce statins was emphasized. Besides, metabolic engineering strategies to construct robust engineering strains and strains evolution were also discussed. The review highlights the potential and challenge of microbial cell factory to yield the statins. Thus, it will facilitate the production of statins in more green production mode.

In the attempt to bridge the widening gap from DNA sequence to biological function, we developed a novel methodology to assemble Long-Adapter Single-Strand Oligonucleotide (LASSO) probe libraries that enabled the massively multiplexed capture of kilobase-sized DNA fragments for downstream long read DNA sequencing or expression. This method uses short DNA oligonucleotides (pre-LASSO probes) and a plasmid vector that supplies the backbone for the mature LASSO probe through Cre-Loxp intramolecular recombination. This strategy generates high quality LASSO probes libraries (~46% of probes). We performed NGS analysis of the post-capture PCR amplification of DNA circles obtained from the LASSO capture of 3087 E.coli ORFs spanning from 400- to 4,000 bp. The median enrichment of all targeted ORFs versus untargeted ORFs was 30 times. For ORFs up to 1kb in size, targeted ORFs were enriched up to a median of 260-fold. Here, we show that LASSO probes obtained in this manner, are able to capture full-length open reading frames from total human cDNA. Furthermore, we show that the LASSO capture specificity and sensitivity is sufficient for target capture from total human genomic DNA template. This technology can be used for the preparation of long-read sequencing libraries and for massively multiplexed cloning of human sequences.

Microbial conversion of plant biomass into fuels and chemicals offers a practical solution to global concerns on limited natural resources, environmental pollution, and climate change. Pursuant to these goals, researchers have put tremendous efforts and resources towards engineering the yeast Saccharomyces cerevisiae to efficiently convert xylose, the second most abundant sugar in lignocellulosic biomass, into various fuels and chemicals. Although many challenges remain, these research investments have facilitated efficient and rapid fermentation of xylose, simultaneous co-consumption of xylose with carbon sources in lignocellulosic hydrolysates, and enhanced production of a wide range of valuable chemicals from xylose. In particular, understanding of xylose-induced metabolic rewiring in engineered yeast has stimulated the use of xylose as a preferred carbon source for the production of various non-ethanol bioproducts. Here, we summarize recent advances in metabolic engineering in yeast to address bottlenecks of xylose assimilation, and to enable simultaneous co-utilization of xylose and other cellulosic carbon sources. We also highlight distinct characteristics of xylose metabolism which can be harnessed for the production of advanced biofuels and chemicals.

In the development of personalized medicine, the ultrasensitive detection of point mutations that correlate with diseases is important to improve the efficacy of treatment and guide clinical medication. In this study, locked nucleic acid (LNA) was introduced as an amplification suppressor of a massive number of wild-type alleles in an amplification refractory mutation system (ARMS) to achieve the detection of low-abundance mutations with high specificity and sensitivity of at least 0.1%. By integrating the length of clamp, base type, number and position of LNA modifications, we have established a “shortest length with the fewest LNA bases” principle from which each LNA base would play a key role in the affinity and the ability of single base discrimination could be improve. Finally, based on this LNA design guideline, a series of the most important single point mutation sites of epidermal growth factor receptor (EGFR) was verified to achieve the optimal amplification state which as low as 0.1% mutation gene amplification was not affected under the wild gene amplification was completely inhibited, demonstrating that the proposed design principle has good applicability and versatility and is of great significance for the detection of circulating tumor DNA.

The production of recombinant proteins usually reduces cell fitness and the growth rate of producing cells. The growth disadvantage favors faster-growing non-producer mutants. Therefore, continuous bioprocessing is hardly feasible in Escherichia coli due to the high escape rate. We investigated the stability of E. coli expression systems under long-term production conditions and how metabolic load triggered by recombinant gene expression influences the characteristics of mutations. We conducted iterated fed-batch-like microbioreactor cultivations under production conditions. We used the easy-to-produce green fluorescent protein (GFP) and a challenging antigen-binding fragment (Fab) as model proteins, and BL21(DE3) and BL21Q strains as expression hosts. In comparative whole genome sequencing analyses, we identified mutations that allowed cells to grow unhindered despite recombinant protein production. A T7 RNA polymerase expression system is only conditionally suitable for long-term cultivation under production conditions. Mutations leading to non-producers occur in either the T7 RNA polymerase gene or the T7 promoter. The host RNA polymerase-based BL21Q expression system remained stable in the production of GFP in long-term cultivations. For the production of Fab, mutations in lacI of the BL21Q derivatives had positive effects on long-term stability. Our results indicate that adaptive evolution carried out with genome-integrated E. coli expression systems in microtiter cultivations under industrial relevant production conditions is an efficient strain development tool for production hosts.

We herein describe an ingenious centrifugal microfluidic system to accomplish a fully automated serial dilution. The liquid flow on the disc was automatically regulated by utilizing ferrowax microvalves systematically integrated into the channels within the specially designed metering structure. By opening the differently positioned microvalves through irradiation of IR laser to allow metering, the same amount of diluent was serially eluted to the dilution chamber from the same diluent chamber. After dilution, the diluted samples were automatically delivered to the respective final product chambers by appropriately opening or closing the microvalves in the connecting channels, followed by rotating the disc. Based on this unique design principle, six consecutive two-fold and ten-fold dilutions were successfully achieved, yielding excellent accuracy in a wide dynamic range up to six orders of magnitude. Very importantly, the overall serial dilution process, including the diluent addition, mixing, and product transfer steps, was completed very rapidly within five minutes, due to the minimized procedures enabled by the automated actuation of the ferrowax microvalves at the rationally designed positions. The centrifugal microfluidic system would serve as a powerful elemental tool to realize the fully automated diagnostic microsystem involving the serial dilution process.