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Journal articleJones MP, Weiland K, Mitterer C, et al., 2023,
Journal articlePeng H, Chen R, Shaw WM, et al., 2023,
Modular metabolic engineering and synthetic coculture strategies for the production of aromatic compounds in yeast, ACS Synthetic Biology, Vol: 12, Pages: 1739-1749, ISSN: 2161-5063
Microbial-derived aromatics provide a sustainable and renewable alternative to petroleum-derived chemicals. In this study, we used the model yeast Saccharomyces cerevisiae to produce aromatic molecules by exploiting the concept of modularity in synthetic biology. Three different modular approaches were investigated for the production of the valuable fragrance raspberry ketone (RK), found in raspberry fruits and mostly produced from petrochemicals. The first strategy used was modular cloning, which enabled the generation of combinatorial libraries of promoters to optimize the expression level of the genes involved in the synthesis pathway of RK. The second strategy was modular pathway engineering and involved the creation of four modules, one for product formation: RK synthesis module (Mod. RK); and three for precursor synthesis: aromatic amino acid synthesis module (Mod. Aro), p-coumaric acid synthesis module (Mod. p-CA), and malonyl-CoA synthesis module (Mod. M-CoA). The production of RK by combinations of the expression of these modules was studied, and the best engineered strain produced 63.5 mg/L RK from glucose, which is the highest production described in yeast, and 2.1 mg RK/g glucose, which is the highest yield reported in any organism without p-coumaric acid supplementation. The third strategy was the use of modular cocultures to explore the effects of division of labor on RK production. Two two-member communities and one three-member community were created, and their production capacity was highly dependent on the structure of the synthetic community, the inoculation ratio, and the culture media. In certain conditions, the cocultures outperformed their monoculture controls for RK production, although this was not the norm. Interestingly, the cocultures showed up to 7.5-fold increase and 308.4 mg/L of 4-hydroxy benzalacetone, the direct precursor of RK, which can be used for the semi-synthesis of RK. This study illustrates the utility of modularity in synth
Journal articleLiu P, Gong Y, Yang C, et al., 2023,
Biorefining of rapeseed meal: a new and sustainable strategy for improving Cr(VI) biosorption on residual wastes from agricultural byproducts after phenolic extraction, Waste Management, Vol: 165, Pages: 70-81, ISSN: 0956-053X
Phenolic recovery from agricultural byproducts has been highlighted due to their health-promoting bioactivities. However, uncontrolled discard of residues after extraction process would induce environmental pollution and bioresource waste. In this study, biorefining of phenolic-rich rapeseed meal (RSM) and its defatted sample (dRSM) was attempted by holistic utilization of phenolic extract and residue separately. Phenolic removal could significantly improve residues' Cr(VI) adsorption capacities by about 21%, which presented extended physical surface and more released functional groups. Moreover, simulating raw material by remixing 3% separated phenolic extracts or main component sinapic acid therein with corresponding residues further improved about 12% adsorption efficiencies. These indicated that the different present forms of phenolics had opposite effects on Cr(VI) removal. While natural conjugational form inhibited hosts' biosorption, free form had enhanced functions for either extract or residue. Four optimal adsorption parameters (pH, adsorbent dosage, contact time and initial Cr(VI) concentration), three kinetic (pseudo-first order, pseudo-second order and intra-particle diffusion) models and two isotherms (Langmuir and Freundlich) were used to reveal the adsorption process. The maximum Cr(VI) adsorption capacity on residues could reach about 100 mg/g, which was superior to that of most biosorbents derived from agricultural byproducts, even some biochar. Together with the residues' advantages with everlasting capacity after 3 adsorption-desorption cycles and excellent abilities for adsorbing multiple co-existed metal ions (Cr(VI), Cd(II), Cu(II), Pb(II), Ni(II) and Zn(II)), phenolic recovery was first proved to be a new and sustainable strategy for modifying biosorbents from agricultural byproducts with zero waste.
Journal articleOldham JM, Allen RJ, Lorenzo-Salazar JM, et al., 2023,
RATIONALE: Idiopathic pulmonary fibrosis (IPF) is a devastating disease characterized by limited treatment options and high mortality. A better understanding of the molecular drivers of IPF progression is needed. OBJECTIVE: To identify and validate molecular determinants of IPF survival. METHODS: A staged genome-wide association study (GWAS) was performed using paired genomic and survival data. Stage I cases were drawn from centers across the US and Europe and stage II cases from Vanderbilt University. Cox proportional hazards regression was used to identify gene variants associated with differential transplant-free survival (TFS). Stage I variants with nominal significance (p<5x10-5) were advanced for stage II testing and meta-analyzed to identify those reaching genome-wide significance (p<5x10-8). Downstream analyses were performed for genes and proteins associated with variants reaching genome-wide significance. MAIN RESULTS: After quality controls, 1481 stage I cases and 397 stage II cases were included in the analysis. After filtering, 9,075,629 variants were tested in stage I, with 158 meeting advancement criteria. Four variants associated with TFS with consistent effect direction were identified in stage II, including one in an intron of proprotein convertase subtilisin/kexin type 6 (PCSK6) reaching genome-wide significance (HR 4.11; 95%CI 2.54-6.67; p=9.45x10-9). PCSK6 protein was highly expressed in IPF lung parenchyma. PCSK6 lung staining intensity, peripheral blood gene expression and plasma concentration were associated with reduced transplant-free survival. CONCLUSIONS: We identified four novel variants associated with IPF survival, including one in PCSK6 that reached genome-wide significance. Downstream analyses suggested that PCSK6 protein plays a potentially important role in IPF progression. This article is open access and distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/lic
Journal articleFeary J, Lindstrom I, Huntley CC, et al., 2023,
Journal articleRusakov D, Menner A, Bismarck A, 2023,
Journal articlede Hoog S, Tintelnot K, Fisher MC, et al., 2023,
Journal articleWang K, Lin L, Wei P, et al., 2023,
Journal articleChua F, Low S, Chai GT, et al., 2023,
Journal articleDavies J, Dobra R, Wilson G, et al., 2023,
A systematic review to identify and collate factors influencing patient journeys through clinical trials, JRSM Open, Vol: 14, Pages: 1-11, ISSN: 2054-2704
Patient-centred trial design and delivery; improves recruitment and retention; increases participant satisfaction; encourages participation by a more representative cohort; and allows researchers to better meet participants’ needs. Research in this area mostly focusses on narrow facets of trial participation. We aimed to systematically identify the breadth of patient-centred factors influencing participation and engagement in trials, and collate them into a framework. Through this we hoped to assist researchers to identify factors that could improve patient-centred trial design and delivery. Robust qualitative and mixed methods systematic reviews are becoming increasingly common in health research. The protocol for this review was prospectively registered on PROSPERO, CRD42020184886. We used the SPIDER (Sample, Phenomenon of Interest, Design, Evaluation, Research Type) framework as a standardised systematic search strategy tool. 3 databases were searched as well as references checking, and thematic synthesis was conducted. Screening agreement was performed and code and theme checking were conducted by 2 independent researchers. Data were drawn from 285 peer-reviewed articles. 300 discrete factors were identified, and sorted into 13 themes and subthemes. The full catalogue of factors is included in the Supplementary Material. A summary framework is included in the body of the article. This paper focusses on outlining common ground that themes share, highlighting critical features, and exploring interesting points from the data. Through this, we hope researchers from multiple specialities may be better able to meet patients’ needs, protect patients’ psychosocial wellbeing, and optimise trial recruitment and retention, with direct positive impact on research time and cost efficiency.
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