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At least 145 records · Page 8

From clutter to clarity: Emergent neural operators via questionnaire metrics

Real-world datasets in chemical engineering and bioengineering processes—such as those from catalytic reactors, multiphase flows, polymerization reactors, bioreactors, and clinical trials—can often be unlabeled or disorganized, rendering the training of existing supervised learning models ineffective at learning the underlying dynamics. To salvage these datasets for decision-making, we first seek to obtain clarity from the cluttered data. Here, we present a framework for developing “structural” generative models, discovering emergent equations, and constructing efficient emulators from scrambled datasets by integrating unsupervised organizational learning techniques (Questionnaires) with advanced deep learning architectures (Deep Hidden Physics Models and Deep Operator Networks). Our approach is demonstrated on two illustrative model systems: (a) a 1D advection–diffusion partial differential equation representing a winding underground pipe and (b) an ensemble of Stuart–Landau oscillators, an agent-based system of coupled ordinary differential equations. In both cases, we successfully reconstruct meaningful spatial, temporal, and parameter embeddings from scrambled data, enabling good predictions of system dynamics. As a result, we highlight the framework’s potential for broader applications, enabling data-driven system identification in fields with inherently disorganized or hidden parameter spaces.

42 ENGINEERING↗

Optogenetics and biosensors set the stage for metabolic cybergenetics

We report cybergenetic systems use computer interfaces to enable feed-back controls over biological processes in real time. The complex and dynamic nature of cellular metabolism makes cybergenetics attractive for controlling engineered metabolic pathways in microbial fermentations. Cybergenetics would not only create new avenues of research into cellular metabolism, it would also enable unprecedented strategies for pathway optimization and bioreactor operation and automation. Implementation of metabolic cybergenetics, however, will require new capabilities from actuators, biosensors, and control algorithms. The recent application of optogenetics in metabolic engineering, the expanding role of genetically encoded biosensors in strain development, and continued progress in control algorithms for biological processes suggest that this technology will become available in the not so distant future.

59 BASIC BIOLOGICAL SCIENCES↗

Graphene oxide exposure alters gut microbial community composition and metabolism in an in vitro human model

Graphene oxide (GO) nanomaterials have unique physicochemical properties that make them highly promising for biomedical, environmental, and agricultural applications. Despite the increasing interest and the use of GO, assessments of its nanotoxicity have largely not interrogated its potential impact on the gut microbiome. This study addresses an important knowledge gap by investigating the impact of GO exposure- both at low (25 ppm) and high (250ppm) doses and fed (nutrient rich) and fasted (nutrient deplete) conditions- on the gut microbial community structure and function, using an in vitro human colon bioreactor model. 16S rRNA amplicon sequencing revealed that GO exposure resulted in a restructuring of community composition. 25 ppm GO induced a marked decrease in the Bacteroidota phylum and increased the ratio of Firmicutes to Bacteroidota (F/B). Untargeted metabolomics on the supernatants indicated that 25 ppm GO impaired microbial utilization and metabolism of substrates (amino acids, carbohydrate metabolites) and reduced production of beneficial microbial metabolites such as 5-hydroxyindole-3-acetic acid and GABA. Exposure to 250 ppm GO resulted in community composition and metabolome profiles that were very similar to the controls that lacked both GO and digestive enzymes, suggesting that high concentrations of GO may interact with digestive enzymes to form protein coronas, causing their depletion in the gut environment. Differential abundance analyses revealed that 3 genera from the phylum Bacteroidota (Bacteroides, Dysgonomonas, and Parabacteroides) were more abundant after 250 ppm GO exposure, irrespective of feed state. Integrative correlation network analysis indicated that the phylum Bacteroidota showed strong positive correlations to multiple microbial metabolites including GABA and 3-indoleacetic acid, are much larger number of correlations compared to other phyla. These results show that GO exposure has a significant impact on gut microbial community composition and metabolism and different mechanisms are at play for low and high GO concentrations.

59 BASIC BIOLOGICAL SCIENCES↗

SynMADE: synthetic microbiota across diverse ecosystems

The last two decades have witnessed rapid advances in engineering individual microbial strains to produce biochemicals and biomaterials. Furthermore, engineering microbial consortia has been relatively slow. Using systems and synthetic biology approaches, researchers have been developing tools for engineering complex microbiota. In this article, I discuss future directions and visions regarding developing microbiota as a biomanufacturing host. Specifically, I propose that we can develop the soil microbial community itself as a huge bioreactor. Ultimately, researchers will provide a generalizable system that enables us to understand microbial consortium’s interaction and metabolism at diverse temporal and spatial scales to address global problems, including the climate crisis, food inequality, waste issue, and sustainable bioproduction.

59 BASIC BIOLOGICAL SCIENCES↗

Environmental life cycle assessment of treatment and management strategies for food waste and sewage sludge

A consequential life cycle assessment (LCA) was utilized to compare the environmental impacts of food waste and sewage sludge management strategies. The strategies included a novel two-phase anaerobic digestion (AD) system and alternatives including landfill, waste-to-energy, composting, anaerobic membrane bioreactor, and conventional AD (wet continuous stirred-tank reactor [CSTR]). The co-management of food waste with sewage sludge was also considered for the two-phase AD system and for a conventional AD reactor. Further, a multidimensional LCA approach was taken, considering the five-midpoint impact categories of global warming, smog, human health particulate, acidification, and eutrophication estimated using the U.S. EPA Tool for the Reduction and Assessment of Chemical and Other Environmental Impacts. Co-management of food waste and sewage sludge using the novel two-phase AD system was shown to maximize energy recovery and had a net global warming benefit while reducing other environmental impacts compared with the alternative management strategies. It had similar relative environmental advantages across all categories as conventional AD, with the advantage of a smaller physical footprint. However, both approaches featured net environmental burdens when the background electric grid intensity fell below 0.25 kg CO 2 -eq kWh -1 , as could be expected in a decarbonized electric future. Upgrading the biogas produced from AD to renewable natural gas can displace the use of fossil natural gas for other non-electricity energy requirements that are difficult to decarbonize and may extend the time period of significant environmental benefits of utilizing AD for organic waste management. Treatment of the nutrient-rich supernatant generated by the novel two-phase AD system could be an obstacle for utilities with stringent nutrient discharge limits. Future research and full-scale implementation are needed to demonstrate the benefits of the two-phase AD system predicted through this analysis.

54 ENVIRONMENTAL SCIENCES↗

Dynamic control over feedback regulatory mechanisms improves NADPH flux and xylitol biosynthesis in engineered E. coli

We report improved NADPH flux and xylitol biosynthesis in engineered E. coli. Xylitol is produced from xylose via an NADPH dependent reductase. We utilize 2-stage dynamic metabolic control to compare two approaches to optimize xylitol biosynthesis, a stoichiometric approach, wherein competitive fluxes are decreased, and a regulatory approach wherein the levels of key regulatory metabolites are reduced. The stoichiometric and regulatory approaches lead to a 20-fold and 90-fold improvement in xylitol production, respectively. Strains with reduced levels of enoyl-ACP reductase and glucose-6-phosphate dehydrogenase, led to altered metabolite pools resulting in the activation of the membrane bound transhydrogenase and an NADPH generation pathway, consisting of pyruvate ferredoxin oxidoreductase coupled with NADPH dependent ferredoxin reductase, leading to increased NADPH fluxes, despite a reduction in NADPH pools. Furthermore, these strains produced titers of 200 g/L of xylitol from xylose at 86% of theoretical yield in instrumented bioreactors. We expect dynamic control over the regulation of the membrane bound transhydrogenase as well as NADPH production through pyruvate ferredoxin oxidoreductase to broadly enable improved NADPH dependent bioconversions or production via NADPH dependent metabolic pathways.

59 BASIC BIOLOGICAL SCIENCES↗

Debottlenecking 4-hydroxybenzoate hydroxylation in Pseudomonas putida KT2440 improves muconate productivity from p -coumarate

The transformation of 4-hydroxybenzoate (4-HBA) to protocatechuate (PCA) is catalyzed by flavoprotein oxygenases known as para-hydroxybenzoate-3-hydroxylases (PHBHs). In Pseudomonas putida KT2440 (P. putida) strains engineered to convert lignin-related aromatic compounds to muconic acid (MA), PHBH activity is rate-limiting, as indicated by the accumulation of 4-HBA, which ultimately limits MA productivity. Here, we hypothesized that replacement of PobA, the native P. putida PHBH, with PraI, a PHBH from Paenibacillus sp. JJ-1b with a broader nicotinamide cofactor preference, could alleviate this bottleneck. Biochemical assays confirmed the strict preference of NADPH for PobA, while PraI can utilize either NADH or NADPH. Kinetic assays demonstrated that both PobA and PraI can utilize NADPH with comparable catalytic efficiency and that PraI also efficiently utilizes NADH at roughly half the catalytic efficiency. The X-ray crystal structure of PraI was solved and revealed absolute conservation of the active site architecture to other PHBH structures despite their differing cofactor preferences. To understand the effect in vivo, we compared three P. putida strains engineered to produce MA from p-coumarate (pCA), showing that expression of praI leads to lower 4-HBA accumulation and decreased NADP+/NADPH ratios relative to strains harboring pobA, indicative of a relieved 4-HBA bottleneck due to increased NADPH availability. In bioreactor cultivations, a strain exclusively expressing praI achieved a titer of 40 g/L MA at 100% molar yield and a productivity of 0.5 g/L/h. Altogether, this study demonstrates the benefit of sampling readily available natural enzyme diversity for debottlenecking metabolic flux in an engineered strain for microbial conversion of lignin-derived compounds to value-added products.

09 BIOMASS FUELS↗

Engineering Escherichia coli for selective 1-decanol production using the reverse β-oxidation (rBOX) pathway

1-Decanol has great value in the pharmaceutical and fragrance industries and plays an important role in the chemical industry. Here, in this study, we engineered Escherichia coli to selectively synthesize 1-decanol by using enzymes of the core reverse β-oxidation (rBOX) pathway and termination module with overlapping chain-length specificity. Through screening for acyl-CoA reductase termination enzymes and proper regulation of rBOX pathway expression, a 1-decanol titer of 1.4 g/L was achieved. Further improvements were realized by engineering pyruvate dissimilation to ensure the generation of NADH through pyruvate dehydrogenase (PDH) and reducing byproduct synthesis via a tailored YigI thioesterase knockout, increasing 1-decanol titer to 1.9 g/L. The engineered strain produced about 4.4 g/L 1-decanol with a yield of 0.21 g/g in 36 hours in a bi-phasic fermentation that used a dodecane overlay to increase 1-decanol transport and reduce its toxicity. Adjustment of pathway expression (varying inducer concentration) and cell growth (oxygen availability) enabled 1-decanol production at 6.1 g/L (0.26 g/g yield) and 10.05 g/L (0.2 g/g yield) using rich in shake flasks and bioreactor, respectively. Remarkably, the use of minimal medium resulted in 1-decanol production at 100% specificity at 2.8 g/L (0.14 g/g yield) and a per cell mass yield higher than rich medium. These 1-decanol titers, yields and purity are at least 10-fold higher than others reported to date and the engineered strain shows great potential for industrial production. Taken together, our findings suggest that using rBOX pathway and termination enzymes of proper chain-length specificity in combination with optimal chassis engineering should be an effective approach for the selective production of alcohols.

1-decanol↗

Comparison of wild-type KT2440 and genome-reduced EM42 Pseudomonas putida strains for muconate production from aromatic compounds and glucose

Pseudomonas putida KT2440 is a robust, aromatic catabolic bacterium that has been widely engineered to convert bio-based and waste-based feedstocks to target products. Towards industrial domestication of P. putida KT2440, rational genome reduction has been previously conducted, resulting in P. putida strain EM42, which exhibited characteristics that could be advantageous for production strains. Here, we compared P. putida KT2440-and EM42-derived strains for cis,cis-muconic acid production from an aromatic compound, p-coumarate, and in separate strains, from glucose. To our surprise, the EM42-derived strains did not outperform the KT2440-derived strains in muconate production from either substrate. In bioreactor cultivations, KT2440-and EM42-derived strains produced muconate from p-coumarate at titers of 45 g/L and 37 g/L, respectively, and from glucose at 20 g/L and 13 g/L, respectively. To provide additional insights about the differences in the parent strains, we analyzed growth profiles of KT2440 and EM42 on aromatic compounds as the sole carbon and energy sources. In general, the EM42 strain exhibited reduced growth rates but shorter growth lags than KT2440. We also observed that EM42-derived strains resulted in higher growth rates on glucose compared to KT2440-derived strains, but only at the lowest glucose concentrations tested. Transcriptomics revealed that genome reduction in EM42 had global effects on transcript levels and showed that the EM42-derived strains that produce muconate from glucose exhibit reduced modulation of gene expression in response to changes in glucose concentrations. Overall, our results highlight that additional studies are warranted to understand the effects of genome reduction on microbial metabolism and physiology, especially when intended for use in production strains.

09 BIOMASS FUELS↗

The oleaginous yeast Rhodosporidium toruloides engineered for biomass hydrolysate-derived (E)-α-bisabolene production

The oleaginous yeast Rhodosporidium toruloides has been exploited for many bioproducts, including several terpenes, owing to its oleaginous nature and biomass inhibitor tolerance. Here, we built upon previous (E)-a-bisabolene work by iteratively stacking the complete mevalonate pathway from Saccharomyces cerevisiae onto a multicopy bisabolene synthase parent strain. Metabolomics and proteomics verified heterologous pathway expression and identified metabolic bottlenecks at three intermediate steps, with candidate feedback-resistant mevalonate kinases screening improving titers 15%. Subtle differences in codon optimization, and preliminary attenuation of competing flux toward lipids resulted in 6-fold, 7-fold higher titers relative to controls, respectively. Media optimization led to modest improvements, with zinc identified as the most promising at 10% titer improvement. Ultimately, high-performance strains were cultivated with corn-stover biomass hydrolysate in microtiter plates at 300g/L total sugar, achieving 20.8g/L bisabolene, the highest reported titer in the literature. A 2L glucose minimal medium bioreactor achieved 19.3 g/L bisabolene and a literature-high productivity of 0.11 g/L/h.

60 APPLIED LIFE SCIENCES↗

Engineering quorum-sensing circuits in Synechococcus elongatus PCC 7942 towards self-inducible systems

Despite significant potential for cyanobacteria as sustainable bioproduction chases, there are limited examples of scaled cyanobacterial bioproduction. In part, this is because most cyanobacterial species are poorly adapted to bioreactor cultivation conditions and lack features that facilitate biomass growth and harvesting at scale. We explored quorum sensing (QS) pathways derived from heterotrophic microbes as a method for autoinduction of gene expression circuits coordinated to population density in cyanobacteria. Here, we integrated genetic modules designed to produce and detect the diffusible QS signal, acyl-homoserine lactones (AHLs), in the cyanobacterial model, Synechococcus elongatus PCC 7942 (S. elongatus). We demonstrate that S. elongatus heterologously produces sufficient AHL signals to activate gene expression in a dose-dependent and population density-responsive manner. A hybrid combination of AHL synthesis enzyme from Vibrio fischeri (Lux system) with the transcription factor receiver from Pseudomonas aeruginosa (Las system) provides an ideal activation ratio and mitigates toxicity observed with some AHL systems. As a proof of concept, we coupled the QS pathway to the expression of a cell division inhibitory gene, cdv3, facilitating late-phase cell elongation, cell sedimentation, and improved biomass recovery. Our findings provide a foundation for the development of auto-induction systems leverageable to improve cyanobacterial biotechnology applications.

Acyl homoserine lactones (AHL)↗

Demonstration and technoeconomic analysis of dodecanol production from acetate using metabolically engineered Escherichia coli

In a circular bioeconomy, the one-way conversion of petroleum to chemicals and CO 2 is replaced with processes that reduce CO 2 to energy carriers and useful materials that are returned to CO 2 upon combustion. A circular bioeconomy that relies on photosynthesis to generate sugars as the chief energy carrier and precursor to chemical building blocks has yet to overcome many recalcitrant aspects of plant-based photosynthesis, namely, high feedstock costs, arable land scarcity, food competition, and fertilizer overuse. Acetate is a potential sustainable energy carrier because it can be produced from CO 2 either electrocatalytically or by acetogens via the Wood-Ljungdahl pathway. Here, in this work, we conducted a metabolic engineering study of Escherichia coli 's ability to convert acetate into dodecanol as a model oleochemical product. We performed techno-economic and life cycle analyses to determine break-even points with alternative fossil fuel-based strategies and identified critical process performance parameters for supporting an industrial acetate-based bioprocess. These analyses showed that oleochemical yield is the primary driver of minimum oleochemical selling price and carbon intensity. Therefore, to increase yield on acetate, we deleted the aceBAK operon, which facilitates funneling of acetate into biomass instead of product. We performed additional strain engineering to increase flux towards dodecanol and increase acetate uptake. Finally, we demonstrated increased yield in controlled bioreactors, improving from 13% of the maximum theoretical yield to 37%. Rigorous uncertainty analyses assuming a range of market conditions and future technological performances resulted in 88% and 37% of simulated scenarios having lower carbon intensities than fossil fuel-based routes and lower minimum selling prices than the market price.

Acetate↗

Three-Dimensional Bubble Fluidics in Architected Porous Media

Gas bubble flows in porous media often exhibit complex and seemingly unpredictable behaviors that are difficult to control. This lack of control limits the ability to design effective devices which manage multiphase flows. Here, we show how the design of 3D printed pores can deterministically control the flow path of an injected gas stream. Open cell structures can be designed to shape the gas/liquid interface with fidelity to control how the two phases are distributed throughout a porous material. The distributed gas volume is free to interact physically and chemically with the surrounding liquid phase, an effect we exploit to create a logical control gate to redirect flows within a lattice. This also allows us to design architectures for reactive capture and aerating bioreactors, resulting in patterned boundaries which can make more effective use of the liquid and gas reagents.

3D microfluidics↗

Postanaerobic Digestion Manure Fibers as a Renewable Source of Lignin-Derived Aromatic Compounds for Microbial Upgrading

Abstract Postanaerobic digestion manure fibers are an abundant solid residue that remains underutilized. The substantial lignocellulosic content of digested manure opens the possibility of using it as a renewable resource for producing valuable products. In this study, we performed compositional and nuclear magnetic resonance analyses to determine lignin content and aromatic composition of these fibers. Additionally, alkaline-based treatment and reductive catalytic fractionation were evaluated as two different processes to produce aromatic-rich streams. The liquor from the alkaline treatment was subsequently utilized for microbial upgrading to produce 2-pyrone-4,6-dicarboxylic acid (PDC). The results showed that lignin in manure fibers represents 30% of the biomass (dry weight basis), with a ∼26% abundance of β-ether-linked aromatics and ∼13% p-coumarate moieties, indicating that the amount of lignin in the postanaerobic biomass is comparable to a moderately pretreated plant biomass. The alkaline treatment released 5.6 g aromatics/kg fibers, while reductive catalytic fractionation produced 14.0 g aromatics/kg fibers. A bioreactor operated in fed-batch mode produced a yield of ∼1 mol of PDC/mol measured aromatics at a rate of 0.2 g PDC/L·h and a titer of 2.6 g PDC/L. This study demonstrates how postanaerobic digestion manure fibers could be used in a circular bioeconomy by harnessing their lignocellulosic content to extract aromatic compounds and use them for obtaining valuable chemicals via microbial upgrading.

Riascos, Brayan D. [University of Wisconsin-Madiso↗

Quorum-driven microbial consortium for Bioplastic production from agro-waste

Microbial consortia have high relevance in natural environments. Here we present the production of polyhydroxyalkanoates (PHA) from agro-industrial residues by a synthetic interkingdom consortium formed by the saprotrophic fungus Ophiostoma piceae CECT 20146, which encodes a wide range of lignocellulolytic enzymes, and a natural PHA producer, Pseudomonas putida KT2440. Two agro-industrial residues were utilized: Brewer's Spent Grain (BSG) as a carbon/nitrogen source and biofilm scaffold and waste cooking oil (WCO) as a carbon source for PHA synthesis. Through biochemistry, microscopy, and omics analyses, it is shown that P. putida accumulates up to 40.2% of intracellular PHA when the quorum sensing molecule, farnesol (naturally produced by O. piceae) is added, thanks to the increased proliferation of P. putida cells. An interactive Shiny application has also been developed for an easy visualization and comprehension of all the transcriptomics and metabolomics data: https://jgf-bioinformatics.shinyapps.io/Visualization_app/. These results support the increased PHA production of the consortium by an induction of gene phaG, which redirects intermediaries of the fatty acid biosynthesis to PHA precursors, and the repression of the PHA depolymerase phaZ in P. putida. The trophic interaction between microorganisms seems to rely on the citric acid produced by O. piceae and the glycerol liberated from WCO, which can both be consumed by P. putida. Bioreactor scale-up experiments allowed a 3.3-fold increase in the PHA concentration in the consortium (6.7 g·L-1) without pretreatment or sterilization of the substrates, laying the groundwork for the implementation of an industrial consolidated bioprocess (CBP).

Bacteria↗

Engineering and Application of a Thermostable MHETase for PET Depolymerization

Enzymatic hydrolysis of poly(ethylene terephthalate) (PET) releases mono(2-hydroxyethyl) terephthalate (MHET) as a major product, the accumulation of which can prolong reactor residence times and complicate downstream monomer separations. The use of a MHETase enzyme can enable MHET hydrolysis to the monomers, terephthalic acid and ethylene glycol, but industrial PETases typically operate at thermophilic temperatures and the well-known MHETase from Ideonella sakaiensis is a mesophilic enzyme, thus warranting the development of thermophilic MHETases. Here, we characterize thermostable MHET-active enzymes from a natural diversity screen by applying a hidden Markov model based on the previously reported, archaeal ferulic acid esterase, PET46. We identified enzymes with higher thermostability than PET46 and quantified their MHETase activity in reactions at 70 °C. The crystal structure of MHT077, the homologue with the highest MHETase activity and an apparent melting temperature (T m,app ) of 94.6 °C, informed site saturation mutagenesis in the active site and lid-domain interface. MHT077 exhibited a ∼100-fold slower unfolding rate at 65 °C than PET46, indicating substantially greater kinetic stability. In parallel, we applied evolution-informed design, a probabilistic model that leverages coevolutionary patterns in large multiple sequence alignments, to improve the activity and thermostability of five ferulic acid esterases. One design, EV-MHT043–5 was identified with a comparable thermostability (T m,app = 96.1 °C) and a 3-fold improvement in its MHETase activity relative to the wildtype enzyme, MHT043. Combination variants of beneficial mutations were screened and afforded a variant, MHT077 LFK , which reduced MHET accumulation in bioreactor experiments with postconsumer PET waste. Overall, this study expands the known MHET-hydrolyzing protein scaffolds available for enzymatic PET recycling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Media Robustness and Scalability of Phosphate Regulated Promoters Useful for Two-Stage Autoinduction in E. coli

A key challenge in synthetic biology is the successful utilization of characterized parts, such as promoters, in different biological contexts. We report the evaluation of the media robustness of a small library of E. coli PhoB regulated promoters that enable heterologous protein production in two-stage cultures. Expression levels were measured both in a rich Autoinduction Broth as well as a minimal mineral salts media. Expression was both media and promoter dependent. Of the 16 promoters tested, 4 were identified to have tightly controlled expression, which was also robust to media formulation. Improved promoter robustness led to more predictable scale up and consistent expression in instrumented bioreactors. Furthermore, this subset of PhoB activated promoters, useful for two-stage autoinduction, highlights the impact of the environment on the performance of biological parts and the importance of robustness testing in synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗

Genetically engineered oleaginous yeast Lipomyces starkeyi for sesquiterpene a-zingiberene production

In this study we demonstrate that transgenic Lipomyces starkeyi strains expressing a ?-zingiberene synthase gene from Lemon basil or Hall’s panicgrass can produce up to 17 mg/l of ?-zingiberene in yeast extract peptone dextrose (YPD) medium containing 4% glucose. Following these findings, the transgenic strain was examined in 8% glucose media with C/N ratios of 20 or 80, and YPD. YPD medium resulted in 59.2 mg/l??-zingiberene accumulation. We further improved ?-zingiberene production by over-expression of selected genes from mevalonate pathway and achieved 145% improvement in ?-zingiberene synthesis. The growth medium was optimized for ?-zingiberene production, which resulted in 14.9% higher titer than YPD medium. The final transgenic strain produced 700 mg/l ?-zingiberene in fed-batch bioreactor culture. This study opens a new synthetic route to produce ?-zingiberene or other terpenoids in the oleaginous yeast L. starkeyi and establishes this yeast as a platform for jet fuel biosynthesis.

Dai, Ziyu↗