Enhanced production of taxadiene in <i>Saccharomyces cerevisiae</i>

BackgroundCost-effective production of the highly effective anti-cancer drug, paclitaxel (Taxol®), remains limited despite growing global demands. Low yields of the critical taxadiene precursor remains a key bottleneck in microbial production. In this study, the key challenge of poor taxadiene synthase (TASY) solubility in S. cerevisiae was revealed, and the strains were strategically engineered to relieve this bottleneck.ResultsMulti-copy chromosomal integration of TASY harbouring a selection of fusion solubility tags improved taxadiene titres 22-fold, up to 57 ± 3 mg/L at 30 °C at microscale, compared to expressing a single episomal copy of TASY. The scalability of the process was highlighted through achieving similar titres during scale up to 25 mL and 250 mL in shake flask and bioreactor cultivations, respectively at 20 and 30 °C. Maximum taxadiene titres of 129 ± 15 mg/L and 127 mg/L were achieved through shake flask and bioreactor cultivations, respectively, of the optimal strain at a reduced temperature of 20 °C.ConclusionsThe results of this study highlight the benefit of employing a combination of molecular biology and bioprocess tools during synthetic pathway development, with which TASY activity was successfully improved by 6.5-fold compared to the highest literature titre in S. cerevisiae cell factories

Cellular Barcoding Identifies Clonal Substitution as a Hallmark of Local Recurrence in a Surgical Model of Head and Neck Squamous Cell Carcinoma

Local recurrence after surgery for head and neck squamous cell carcinoma (HNSCC) remains a common event associated with a dismal prognosis. Improving this outcome requires a better understanding of cancer cell populations that expand from postsurgical minimal residual disease (MRD). Therefore, we assessed clonal dynamics in a surgical model of barcoded HNSCC growing in the submental region of immunodeficient mice. Clonal substitution and massive reduction of clonal heterogeneity emerged as hallmarks of local recurrence, as the clones dominating in less heterogeneous recurrences were scarce in their matched primary tumors. These lineages were selected by their ability to persist after surgery and competitively expand from MRD. Clones enriched in recurrences exhibited both private and shared genetic features and likely originated from ancestors shared with clones dominating in primary tumors. They demonstrated high invasiveness and epithelial-to-mesenchymal transition, eventually providing an attractive target for obtaining better local control for these tumors

Lentivirus-meditated frataxin gene delivery reverses genome instability in Friedreich ataxia patient and mouse model fibroblasts

Friedreich ataxia (FRDA) is a progressive neurodegenerative disease caused by deficiency of frataxin protein, with the primary sites of pathology being the large sensory neurons of the dorsal root ganglia and the cerebellum. FRDA is also often accompanied by severe cardiomyopathy and diabetes mellitus. Frataxin is important in mitochondrial iron–sulfur cluster (ISC) biogenesis and low-frataxin expression is due to a GAA repeat expansion in intron 1 of the FXN gene. FRDA cells are genomically unstable, with increased levels of reactive oxygen species and sensitivity to oxidative stress. Here we report the identification of elevated levels of DNA double strand breaks (DSBs) in FRDA patient and YG8sR FRDA mouse model fibroblasts compared to normal fibroblasts. Using lentivirus FXN gene delivery to FRDA patient and YG8sR cells, we obtained long-term overexpression of FXN mRNA and frataxin protein levels with reduced DSB levels towards normal. Furthermore, γ-irradiation of FRDA patient and YG8sR cells revealed impaired DSB repair that was recovered on FXN gene transfer. This suggests that frataxin may be involved in DSB repair, either directly by an unknown mechanism, or indirectly via ISC biogenesis for DNA repair enzymes, which may be essential for the prevention of neurodegeneration.Ataxia UK, FARA Australasia and FARA US

Gene therapy for monogenic liver diseases: clinical successes, current challenges and future prospects

Over the last decade, pioneering liver-directed gene therapy trials for haemophilia B have achieved sustained clinical improvement after a single systemic injection of adeno-associated virus (AAV) derived vectors encoding the human factor IX cDNA. These trials demonstrate the potential of AAV technology to provide long-lasting clinical benefit in the treatment of monogenic liver disorders. Indeed, with more than ten ongoing or planned clinical trials for haemophilia A and B and dozens of trials planned for other inherited genetic/metabolic liver diseases, clinical translation is expanding rapidly. Gene therapy is likely to become an option for routine care of a subset of severe inherited genetic/metabolic liver diseases in the relatively near term. In this review, we aim to summarise the milestones in the development of gene therapy, present the different vector tools and their clinical applications for liver-directed gene therapy. AAV-derived vectors are emerging as the leading candidates for clinical translation of gene delivery to the liver. Therefore, we focus on clinical applications of AAV vectors in providing the most recent update on clinical outcomes of completed and ongoing gene therapy trials and comment on the current challenges that the field is facing for large-scale clinical translation. There is clearly an urgent need for more efficient therapies in many severe monogenic liver disorders, which will require careful risk-benefit analysis for each indication, especially in paediatrics

QubiC: An open source FPGA-based control and measurement system for superconducting quantum information processors

As quantum information processors grow in quantum bit (qubit) count and functionality, the control and measurement system becomes a limiting factor to large scale extensibility. To tackle this challenge and keep pace with rapidly evolving classical control requirements, full control stack access is essential to system level optimization. We design a modular FPGA (field-programmable gate array) based system called QubiC to control and measure a superconducting quantum processing unit. The system includes room temperature electronics hardware, FPGA gateware, and engineering software. A prototype hardware module is assembled from several commercial off-the-shelf evaluation boards and in-house developed circuit boards. Gateware and software are designed to implement basic qubit control and measurement protocols. System functionality and performance are demonstrated by performing qubit chip characterization, gate optimization, and randomized benchmarking sequences on a superconducting quantum processor operating at the Advanced Quantum Testbed at Lawrence Berkeley National Laboratory. The single-qubit and two-qubit process fidelities are measured to be 0.9980$\pm$0.0001 and 0.948$\pm$0.004 by randomized benchmarking. With fast circuit sequence loading capability, the QubiC performs randomized compiling experiments efficiently and improves the feasibility of executing more complex algorithms

QubiC: An open source FPGA-based control and measurement system for superconducting quantum information processors

As quantum information processors grow in quantum bit (qubit) count and functionality, the control and measurement system becomes a limiting factor to large scale extensibility. To tackle this challenge and keep pace with rapidly evolving classical control requirements, full control stack access is essential to system level optimization. We design a modular FPGA (field-programmable gate array) based system called QubiC to control and measure a superconducting quantum processing unit. The system includes room temperature electronics hardware, FPGA gateware, and engineering software. A prototype hardware module is assembled from several commercial off-the-shelf evaluation boards and in-house developed circuit boards. Gateware and software are designed to implement basic qubit control and measurement protocols. System functionality and performance are demonstrated by performing qubit chip characterization, gate optimization, and randomized benchmarking sequences on a superconducting quantum processor operating at the Advanced Quantum Testbed at Lawrence Berkeley National Laboratory. The single-qubit and two-qubit process fidelities are measured to be 0.9980$\pm$0.0001 and 0.948$\pm$0.004 by randomized benchmarking. With fast circuit sequence loading capability, the QubiC performs randomized compiling experiments efficiently and improves the feasibility of executing more complex algorithms

Automatic Qubit Characterization and Gate Optimization with QubiC

As the size and complexity of a quantum computer increases, quantum bit (qubit) characterization and gate optimization become complex and time-consuming tasks. Current calibration techniques require complicated and verbose measurements to tune up qubits and gates, which cannot easily expand to the large-scale quantum systems. We develop a concise and automatic calibration protocol to characterize qubits and optimize gates using QubiC, which is an open source FPGA (field-programmable gate array) based control and measurement system for superconducting quantum information processors. We propose mutli-dimensional loss-based optimization of single-qubit gates and full XY-plane measurement method for the two-qubit CNOT gate calibration. We demonstrate the QubiC automatic calibration protocols are capable of delivering high-fidelity gates on the state-of-the-art transmon-type processor operating at the Advanced Quantum Testbed at Lawrence Berkeley National Laboratory. The single-qubit and two-qubit Clifford gate infidelities measured by randomized benchmarking are of $4.9(1.1) \times 10^{-4}$ and $1.4(3) \times 10^{-2}$, respectively

Hardware-Efficient Microwave-Activated Tunable Coupling Between Superconducting Qubits

Generating high-fidelity, tunable entanglement between qubits is crucial for realizing gate-based quantum computation. In superconducting circuits, tunable interactions are often implemented using flux-tunable qubits or coupling elements, adding control complexity and noise sources. Here, we realize a tunable $ZZ$ interaction between two transmon qubits with fixed frequencies and fixed coupling, induced by driving both transmons off-resonantly. We show tunable coupling over one order of magnitude larger than the static coupling, and change the sign of the interaction, enabling cancellation of the idle coupling. Further, this interaction is amenable to large quantum processors: the drive frequency can be flexibly chosen to avoid spurious transitions, and because both transmons are driven, it is resilient to microwave crosstalk. We apply this interaction to implement a controlled phase (CZ) gate with a gate fidelity of $99.43(1)\%$ as measured by cycle benchmarking, and we find the fidelity is limited by incoherent errors