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  • Journal article
    Bonturi N, Pinheiro MJ, de Oliveira PM, Rusadze E, Eichinger T, Liudžiūtė G, De Biaggi JS, Brauer A, Remm M, Miranda EA, Ledesma-Amaro R, Lahtvee P-Jet al., 2022,

    Development of a dedicated Golden Gate Assembly Platform (RtGGA) for Rhodotorula toruloides.

    , Metabolic Engineering Communications, Vol: 15, Pages: 1-10, ISSN: 2214-0301

    Rhodotorula toruloides is a potential chassis for microbial cell factories as this yeast can metabolise different substrates into a diverse range of natural products, but the lack of efficient synthetic biology tools hinders its applicability. In this study, the modular, versatile and efficient Golden Gate DNA assembly system (RtGGA) was adapted to the first basidiomycete, an oleaginous yeast R. toruloides. R. toruloides CCT 0783 was sequenced, and used for the GGA design. The DNA fragments were assembled with predesigned 4-nt overhangs and a library of standardized parts was created containing promoters, genes, terminators, insertional regions, and resistance genes. The library was combined to create cassettes for the characterization of promoters strength and to overexpress the carotenoid production pathway. A variety of reagents, plasmids, and strategies were used and the RtGGA proved to be robust. The RtGGA was used to build three versions of the carotenoid overexpression cassette by using different promoter combinations. The cassettes were transformed into R. toruloides and the three new strains were characterized. Total carotenoid concentration increased by 41%. The dedicated GGA platform fills a gap in the advanced genome engineering toolkit for R. toruloides, enabling the efficient design of complex metabolic pathways.

  • Journal article
    Cao L, Yin M, Shi T-Q, Lin L, Ledesma-Amaro R, Ji X-Jet al., 2022,

    Engineering Yarrowia lipolytica to produce nutritional fatty acids: Current status and future perspectives.

    , Synthetic and Systems Biotechnology, Vol: 7, Pages: 1024-1033, ISSN: 2405-805X

    Due to their vital physiological functions, nutritional fatty acids have great potential as nutraceutical food supplements for preventing an array of diseases such as inflammation, depression, arthritis, osteoporosis, diabetes and cancer. Microbial biosynthesis of fatty acids follows the trend of sustainable development, as it enables green, environmentally friendly and efficient production. As a natural oleaginous yeast, Yarrowia lipolytica is especially well-suited for the production of fatty acids. Moreover, it has a variety of genetic engineering tools and novel metabolic engineering strategies that make it a robust workhorse for the production of an array of value-added products. In this review, we summarize recent advances in metabolic engineering strategies for accumulating nutritional fatty acids in Y. lipolytica, including conjugated fatty acids and polyunsaturated fatty acids. In addition, the future prospects of nutritional fatty acid production using the Y. lipolytica platform are discussed in light of the current progress, challenges, and trends in this field. Finally, guidelines for future studies are also emphasized.

  • Journal article
    Jones MP, Krexner T, Bismarck A, 2022,

    Repurposing Fischer-Tropsch and natural gas as bridging technologies for the energy revolution

    , Energy Conversion and Management, Vol: 267, ISSN: 0196-8904

    Immediate and widespread changes in energy generation and use are critical to safeguard our future on this planet. However, while the necessity of renewable electricity generation is clear, the aviation, transport and mobility, chemical and material sectors are challenging to fully electrify. The age-old Fischer-Tropsch process and natural gas industry could be the bridging solution needed to accelerate the energy revolution in these sectors – temporarily powering obsolete vehicles, acting as renewable energy's battery, supporting expansion of hydrogen fuel cell technologies and the agricultural and waste sectors as they struggle to keep up with a full switch to biofuels. Natural gas can be converted into hydrogen, synthetic natural gas, or heat during periods of low electricity demand and converted back to electricity again when needed. Moving methane through existing networks and converting it to hydrogen on-site at tanking stations also overcomes hydrogen distribution, storage problems and infrastructure deficiencies. Useful co-products include carbon nanotubes, a valuable engineering material, that offset emissions in the carbon nanotube and black industries. Finally, excess carbon can be converted back into syngas if desired. This flexibility and the compatibility of natural gas with both existing and future technologies provides a unique opportunity to rapidly decarbonise sectors struggling with complex requirements.

  • Journal article
    Lee CT, Feary J, Johannson KA, 2022,

    Environmental and occupational exposures in interstitial lung disease.

    , Curr Opin Pulm Med, Vol: 28, Pages: 414-420

    PURPOSE OF REVIEW: We highlight recent advances in the understanding of how environmental and occupational exposures increase the risk of developing interstitial lung disease (ILD), and how to evaluate a patient for potential exposures. RECENT FINDINGS: A review of emerging literature suggests that environmental and occupational exposures can be directly causal, as in the case of the pneumoconioses and smoking-related ILDs, or one of many contributors to disease, as in the case of idiopathic pulmonary fibrosis (IPF). Regardless of the level of association, exposures are clearly prevalent across all ILD subtypes studied. SUMMARY: Inhalational exposures are increasingly recognized as an important component in the development of ILDs, and novel exposure-disease associations continue to be discovered. These exposures represent potential opportunities for further understanding the pathobiology of disease and for the prevention of these often progressive and debilitating disorders. Prospective, comprehensive data collection regarding occupational and environmental exposures are needed in ILD patients to fully elucidate specific antigens and their relationships to disease incidence and outcomes. Systematically collected exposure information will also inform potential interventions to remediate exposures and thus mitigate the course of frequently progressive and fatal diseases.

  • Journal article
    Ledesma Amaro R, Ellis T, Shaw W, Studena L, Roy K, Mccarty N, Graham A, Hapeta Pet al., 2022,

    Inducible expression of large gRNA arrays for multiplexed CRISPRai applications

    , Nature Communications, ISSN: 2041-1723
  • Journal article
    Pugashetti JV, Adegunsoye A, Wu Z, Lee CT, Srikrishnan A, Ghodrati S, Vo V, Renzoni EA, Wells AU, Garcia CK, Chua F, Newton CA, Molyneaux PL, Oldham JMet al., 2022,

    Validation of proposed criteria for progressive pulmonary fibrosis.

    , American Journal of Respiratory and Critical Care Medicine, ISSN: 1073-449X

    RATIONALE: Criteria for progressive pulmonary fibrosis (PPF) have been proposed, but their prognostic value beyond categorical decline in forced vital capacity (FVC) remains unclear. OBJECTIVE: To determine whether proposed PPF criteria predict transplant-free survival (TFS) in patients with non-idiopathic pulmonary fibrosis (IPF) forms of interstitial lung disease (ILD). METHODS: A retrospective, multi-center cohort analysis was performed. Patients diagnosed with fibrotic connective tissue disease associated ILD, fibrotic hypersensitivity pneumonitis and non-IPF idiopathic interstitial pneumonia from three US centers and one UK center comprised test and validation cohorts, respectively. Cox proportional hazards regression was used to test the association between five-year TFS and 10% FVC decline, followed by thirteen additional PPF criteria satisfied in the absence of >=10% FVC decline. MAIN RESULTS: One thousand three hundred forty-one patients met inclusion criteria. A >=10% relative FVC decline was the strongest predictor of reduced TFS and showed consistent TFS association across cohorts, ILD subtypes and treatment groups, resulting in a phenotype that closely resembled IPF. Ten additional PPF criteria satisfied in the absence of >=10% relative FVC decline were also associated with reduced TFS in the US test cohort, with six maintaining TFS association in the UK validation cohort. Validated PPF criteria requiring a combination of physiologic, radiologic, and symptomatic worsening performed similarly to their stand-alone components but captured a smaller number of patients. CONCLUSIONS: An FVC decline of >=10% and six additional PPF criteria satisfied in the absence of such decline identify non-IPF ILD patients at increased risk of death or lung transplant.

  • Journal article
    Hewitt RJ, Bartlett EC, Ganatra R, Butt H, Kouranos V, Chua F, Kokosi M, Molyneaux PL, Desai SR, Wells AU, Jenkins RG, Renzoni EA, Kemp SV, Devaraj A, George PMet al., 2022,

    Lung cancer screening provides an opportunity for early diagnosis and treatment of interstitial lung disease.

    , Thorax

    Interstitial lung abnormalities (ILA) can be incidentally detected in patients undergoing low-dose CT screening for lung cancer. In this retrospective study, we explore the downstream impact of ILA detection on interstitial lung disease (ILD) diagnosis and treatment. Using a targeted approach in a lung cancer screening programme, the rate of de novo ILD diagnosis was 1.5%. The extent of abnormality on CT and severity of lung function impairment, but not symptoms were the most important factors in differentiating ILA from ILD. Disease modifying therapies were commenced in 39% of ILD cases, the majority being antifibrotic therapy for idiopathic pulmonary fibrosis.

  • Journal article
    Li W, Cui L, Mai J, Shi T-Q, Lin L, Zhang Z-G, Ledesma-Amaro R, Dong W, Ji X-Jet al., 2022,

    Advances in Metabolic Engineering Paving the Way for the Efficient Biosynthesis of Terpenes in Yeasts.

    , J Agric Food Chem, Vol: 70, Pages: 9246-9261

    Terpenes are a large class of secondary metabolites with diverse structures and functions that are commonly used as valuable raw materials in food, cosmetics, and medicine. With the development of metabolic engineering and emerging synthetic biology tools, these important terpene compounds can be sustainably produced using different microbial chassis. Currently, yeasts such as Saccharomyces cerevisiae and Yarrowia lipolytica have received extensive attention as potential hosts for the production of terpenes due to their clear genetic background and endogenous mevalonate pathway. In this review, we summarize the natural terpene biosynthesis pathways and various engineering strategies, including enzyme engineering, pathway engineering, and cellular engineering, to further improve the terpene productivity and strain stability in these two widely used yeasts. In addition, the future prospects of yeast-based terpene production are discussed in light of the current progress, challenges, and trends in this field. Finally, guidelines for future studies are also emphasized.

  • Journal article
    Wang J, Anthony DB, Fuentes CA, De Luca HG, Zhang D, Bismarck A, Van Vuure AW, Shaffer MSP, Seveno Det al., 2022,

    Wettability of carbon nanotube-grafted carbon fibers and their interfacial properties in polypropylene thermoplastic composite

    , Composites Part A: Applied Science and Manufacturing, Vol: 159, Pages: 1-10, ISSN: 1359-835X

    The interfacial properties of carbon fiber (CF) reinforced thermoplastic composites depend strongly on the wettability and surface characteristics of the reinforcing fibers, and their compatibility with a chosen matrix. The interface between conventional fibers and thermoplastic matrices is generally weak, due to a lack of specific chemical interaction, especially in the case of polyolefins. Carbon nanotube-grafted-carbon fibers (CNT-g-CF) are considered to be potential reinforcements as they provide additional mechanical interlocking. Commercial CFs were successfully grafted with nanotubes using a continuous, and hence scalable, CVD method. X-ray photoelectron spectroscopy, Wilhelmy wetting measurements, and scanning electron microscopy confirmed the successful grafting and resulting hydrophobic surface chemistry, dominated by van der Waals interactions. The grafted CNTs, with diameters and lengths around 10 nm and 140 nm respectively, were well suited to improve the overall wettability and interfacial shear strength (+53.4 %) of the CNT-g-CF in a polypropylene matrix when compared to as-received unsized CFs.

  • Journal article
    Lv X, Hueso-Gil A, Bi X, Wu Y, Liu Y, Liu L, Ledesma Amaro Ret al., 2022,

    New synthetic biology tools for metabolic control

    , Current Opinion in Biotechnology, Vol: 76, ISSN: 0958-1669

    In industrial bioprocesses, microbial metabolism dictates the product yields, and therefore, our capacity to control it has an enormous potential to help us move towards a bio-based economy. The rapid development of multiomics data has accelerated our systematic understanding of complex metabolic regulatory mechanisms, which allow us to develop tools to manipulate them. In the last few years, machine learning-based metabolic modeling, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) derived synthetic biology tools, and synthetic genetic circuits have been widely used to control the metabolism of microorganisms, manipulate gene expression, and build synthetic pathways for bioproduction. This review describes the latest developments for metabolic control, and focuses on the trends and challenges of metabolic engineering strategies.

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