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Over the past decade, numerous approaches have been taken to replace unsustainable chemical syntheses with green biosynthetic alternatives. In a landmark paper, Yim et al. utilised an in silico-to-in vivo workflow to enable the high-level bioproduction of the unnatural small molecule 1,4-butanediol in the bacterium Escherichia coli.

Transition-metal nanoparticles produced by living bacteria are emerging as novel catalysts for sustainable synthesis. However, the scope of their catalytic activity and their ability to be integrated within metabolic pathways for the bioproduction of non-natural small molecules has been underexplored. Herein we report that Pd nanoparticles synthesized by the sulfate-reducing bacterium Desulfovibrio alaskensis G20 (DaPdNPs) catalyze the Sonogashira coupling of phenyl acetylenes and aryl iodides, and the subsequent one-pot hydrogenation to bibenzyl derivatives using hydrogen gas generated from d-glucose by engineered Escherichia coli DD-2. The formal hydroarylation reaction is biocompatible, occurs in aqueous media at ambient temperature, and affords products in 70–99% overall yield. This is the first reported microbial nanoparticle to catalyze the Sonogashira reaction and the first demonstration that these biogenic catalysts can be interfaced with the products of engineered metabolism for small molecule synthesis.

The fundamental biology and application of bacterial exopolysaccharides is gaining increasing attention. However, current synthetic biology efforts to produce the major component of Escherichia sp. slime, colanic acid, and functional derivatives thereof have been limited. Herein, we report the overproduction of colanic acid (up to 1.32 g/L) from d-glucose in an engineered strain of Escherichia coli JM109. Furthermore, we report that chemically synthesized l-fucose analogues containing an azide motif can be metabolically incorporated into the slime layer via a heterologous fucose salvage pathway from Bacteroides sp. and used in a click reaction to attach an organic cargo to the cell surface. This molecular-engineered biopolymer has potential as a new tool for use in chemical, biological, and materials research.

The discovery and engineering of new plastic degrading enzymes is an important challenge in chemical biotechnology to enable transition to a more sustainable and circular plastics economy. This field has so far yielded a range of enzymes and microbial pathways for the recycling and valorization of plastic waste. New research from Uttamapinant et al. reports the discovery of a novel polyethylene terephthalate (PET) hydrolase from the human saliva metagenome that displays improved properties and catalytic performance over previously characterized PET hydrolases (PETases). The authors also demonstrate the site-specific incorporation of a photocaged unnatural amino acid, 2,3-diaminopropionic acid (DAP), which upon photodecaging enables covalent binding of DAP to the PET surface. Thus, this work highlights metagenomic datasets as an untapped source of new PET degrading enzymes and the chemical modification of PETases via genetic code expansion, enabling new biotechnologies for the circular plastics economy.

OBJECTIVES To determine if the relative distance between the acetabular teardrops on unstressed and lateral compressive stress examination under anesthesia (EUA) pelvic fluoroscopic images is reproducible between independent reviewers. DESIGN Retrospective database review. SETTING Level 1 trauma center. PATIENTS/INTERVENTION Fifty-eight patients with a lateral compression type 1 pelvic ring injury who underwent EUA. MAIN OUTCOME MEASURE Validation of EUA objective measurements between blinded, independent reviewers using interclass and intraclass correlation coefficients. RESULTS There was excellent interobserver and intraobserver reliability between all reviewers. Values for each intraclass correlation coefficients (including 95% confidence intervals) were between 0.96 (0.95-0.098) and 0.99 (0.99-0.99) for all measurements. P values were

The fundamental biology and application of bacterial exopolysaccharides is gaining increasing attention. However, current synthetic biology efforts to produce the major component ofEscherichia sp. slime, colanic acid, and functional derivatives thereof have been limited. Herein, we report the overproduction of colanic acid (up to 1.32 g/L) from D-glucose in an engineered strain ofE. coliJM109. Furthermore, we report that chemically-synthesized L-fucose analogues containing an azide motif can be metabolically incorporated into the slime layer via a heterologous fucose salvage pathway fromBacteroides sp. and used in a click reaction to attach an organic cargo to the cell surface. This molecular engineered bio-polymer possesses enormous potential as a new tool for use in chemical, biological and materials research.

The management of staggering volume of food waste generated (∼1.3 billion tons) is a serious challenge. The readily available untapped food waste can be promising feedstock for setting up biorefineries and one good example is bread waste (BW). The current review emphasis on capability of BW as feedstock for sustainable production of platform and commercially important chemicals. It describes the availability of BW (>100 million tons) to serve as a feedstock for sustainable biorefineries followed by examples of platform chemicals which have been produced using BW including ethanol, lactic acid, succinic acid and 2,3-butanediol through biological route. The BW-based production of these metabolites is compared against 1G and 2G (lignocellulosic biomass) feedstocks. The review also discusses logistic and supply chain challenges associated with use of BW as feedstock. Towards the end, it is concluded with a discussion on life cycle analysis of BW-based production and comparison with other feedstocks.

Biogenic amine organocatalysts have transformed the field of synthetic organic chemistry. Yet despite their use in synthesis and to label biomolecules in vitro , amine organocatalysis in vivo has received comparatively little attention – despite the potential of such reactions to be interfaced with living cells and to modify cellular metabolites. Herein we report that biogenic amines derived from L-tyrosine catalyze the self-aldol condensation of butanal to 2-ethylhexenal – a key intermediate in the production of the bulk chemical 2-ethylhexanol – in the presence of living Escherichia coli and outperform many amine organocatalysts currently used in synthetic organic chemistry. Furthermore, we demonstrate that cell lysate from E. coli and the prolific amine overproducer Corynebacterium glutamicum ATCC 13032 catalyze this reaction in vitro , demonstrating the potential for microbial metabolism to be used as a source of organocatalysts for biocompatible reactions in cells.

Transition-metal nanoparticles produced by living bacteria are emerging as novel catalysts for sustainable synthesis. However, the scope of their catalytic activity and their ability to be integrated within metabolic pathways for the bioproduction of non-natural small molecules has been underexplored. Herein we report that Pd nanoparticles synthesized by the sulfate-reducing bacterium

Interfacing non-enzymatic catalysis with cellular metabolism is emerging as a powerful approach to produce a range of high value small molecules and polymers. In this review, we highlight recent examples from this promising young field. Specifically, we discuss demonstrations of living cells mediating redox processes for biopolymer production, interfacing solar-light driven chemistry with microbial metabolism, and intra- and extracellular non-enzymatic catalysis to generate high value molecules. This review highlights the vast potential of this nascent field to bridge the two disciplines of synthetic chemistry and synthetic biology for a sustainable chemical industry., This review highlights recent advances in the field of biocompatible chemistry. It focusses on the combined use of non-enzymatic catalysis and microbial metabolism to support cellular function and to synthesise high value chemicals.

Adipic acid is one of the most important small molecules in the modern chemical industry. However, the damaging environmental impact of the current industrial synthesis of adipic acid has necessitated the development of greener, biobased approaches to its manufacture. Herein we report the first one-pot synthesis of adipic acid from guaiacol, a lignin-derived feedstock, using genetically engineered whole-cells of Escherichia coli. The reaction is mild, efficient, requires no additional additives or reagents, and produces no byproducts. This study demonstrates how modern synthetic biology can be used to valorize abundant feedstocks into industrially relevant small molecules in living cells.

Rattling around on a cold, damp Edinburgh street, a plastic water bottle is a stark reminder of one of the greatest environmental crises facing our planet. In little under 100 years a growing tsunami of plastic waste has contaminated not just our streets but nearly every corner of the natural world – from Mount Everest to the deepest oceans. But this plastic bottle provided the inspiration that could yet turn the tide. Diverted from landfill to the laboratory the bottle soon grabbed the attention of the world’s media by undergoing a remarkable transformation from plastic into vanillin – the main component of vanilla and one of the most in-demand spices in the world. This seemingly impossible act of alchemy was made possible by harnessing the metabolic power of bacteria. Its success has enormous implications. Not only could it meet our insatiable appetite for this rare flavouring, but it could radically change the way we tackle another addiction – the endless stream of single-use and disposable plastics that have become part of everyday life. Yet this only scratches the surface of the potential of this approach. By coaxing microbes to behave as eco-friendly factories that produce useful materials, we could tackle many other global challenges.

Model explainability is essential for the creation of trustworthy Machine Learning models in healthcare. An ideal explanation resembles the decision-making process of a domain expert and is expressed using concepts or terminology that is meaningful to the clinicians. To provide such explanation, we first associate the hidden units of the classifier to clinically relevant concepts. We take advantage of radiology reports accompanying the chest X-ray images to define concepts. We discover sparse associations between concepts and hidden units using a linear sparse logistic regression. To ensure that the identified units truly influence the classifier’s outcome, we adopt tools from Causal Inference literature and, more specifically, mediation analysis through counterfactual interventions. Finally, we construct a low-depth decision tree to translate all the discovered concepts into a straightforward decision rule, expressed to the radiologist. We evaluated our approach on a large chest x-ray dataset, where our model produces a global explanation consistent with clinical knowledge.

PURPOSE: To reconstruct virtual MR elastography (MRE) images based on traditional MRI inputs with a machine learning algorithm. MATERIALS AND METHODS: In this single-institution, retrospective study, 149 patients (mean age, 58 years ± 12 [standard deviation]; 71 men) with nonalcoholic fatty liver disease who underwent MRI and MRE between January 2016 and January 2019 were evaluated. Nine conventional MRI sequences and clinical data were used to train a convolutional neural network to reconstruct MRE images at the per-voxel level. The architecture was further modified to accept multichannel three-dimensional inputs and to allow inclusion of clinical and demographic information. Liver stiffness and fibrosis category (F0 [no fibrosis] to F4 [significant fibrosis]) of reconstructed images were assessed by using voxel- and patient-level agreement by correlation, sensitivity, and specificity calculations; in addition, classification by receiver operator characteristic analyses was performed, and Dice score was used to evaluate hepatic stiffness locality. RESULTS: The model for predicting liver stiffness incorporated four image sequences (precontrast T1-weighted liver acquisition with volume acquisition [LAVA] water and LAVA fat, 120-second–delay T1-weighted LAVA water, and single-shot fast spin-echo T2 weighted) and clinical data. The model had a patient-level and voxel-level correlation of 0.50 ± 0.05 and 0.34 ± 0.03, respectively. By using a stiffness threshold of 3.54 kPa to make a binary classification into no fibrosis or mild fibrosis (F0–F1) versus clinically significant fibrosis (F2–F4), the model had sensitivity of 80% ± 4, specificity of 75% ± 5, accuracy of 78% ± 3, area under the receiver operating characteristic curve of 84 ± 0.04, and a Dice score of 0.74. CONCLUSION: The generation of virtual elastography images is feasible by using conventional MRI and clinical data with a machine learning algorithm. Keywords: MR Imaging, Abdomen/GI, Liver, Cirrhosis, Computer Applications/Virtual Imaging, Experimental Investigations, Feature Detection, Classification, Reconstruction Algorithms, Supervised Learning, Convolutional Neural Network (CNN) Supplemental material is available for this article. © RSNA, 2021

Microorganisms produce metal nanoparticles (MNPs) upon exposure to toxic metal ions. However, the catalytic activity of biosynthesised MNPs remains underexplored, despite the potential of these biological processes to be used for the sustainable recovery of critical metals, including palladium. Herein we report that biogenic palladium nanoparticles generated by the sulfate-reducing bacterium Desulfovibrio alaskensis G20 catalyse the ligand-free Suzuki Miyaura reaction of abiotic substrates. The reaction is highly efficient (>99% yield, 0.5 mol% Pd), occurs under mild conditions (37 °C, aqueous media) and can be accelerated within biocompatible micelles at the cell membrane to yield products containing challenging biaryl bonds. This work highlights how native metabolic processes in anaerobic bacteria can be combined with green chemical technologies to produce highly efficient catalytic reactions for use in sustainable organic synthesis.

Breadfruit from Samoa potentially host the Pacific fruit fly (Bactrocera xanthodes) and so their export to New Zealand requires a disinfestation treatment. Heat treatments by air (HAT) or water (HWT) are common fruit-fly disinfestation treatments for tropical crops. Two breadfruit cultivars – Puou and Ma’afala – were subjected to three heat treatments, HAT-1 (minimum 47.2oC for 20 min at core), HAT-2 (49.0oC for 100 min at core) and HWT (47.2oC for 20 min at core), and an untreated control was also included. Fruit were stored for one week at 15oC followed by three days at 25oC. Disorders observed were heat damage to the skin (blackening) and increased decay on the body and stem-end. Heat damage was at an acceptably low level following HAT-1 but was unacceptable following HAT-2 or HWT. Initial results suggest that a HAT can be tolerated, but the effect of ramp rate and the potential of using a two-step HWT system should be examined.

Poly(ethylene terephthalate) (PET) is an abundant and extremely useful material, with widespread applications across society. However, there is an urgent need to develop technologies to valorise post-consumer PET waste to tackle plastic pollution and move towards a circular economy. Whilst PET degradation and recycling technologies have been reported, examples focus on repurposing the resultant monomers to produce more PET or other second-generation materials. Herein, we report a novel pathway in engineered Escherichia coli for the direct upcycling of PET derived monomer terephthalic acid into the value-added small molecule vanillin, a flavour compound ubiquitous in the food and cosmetic industries, and an important bulk chemical. After process optimisation, 79% conversion to vanillin from TA was achieved, a 157-fold improvement over our initial conditions. Parameters such as temperature, cell permeabilisation and in situ product removal were key to maximising vanillin titres. Finally, we demonstrate the conversion of post-consumer PET from a plastic bottle into vanillin by coupling the pathway with enzyme-catalysed PET hydrolysis. This work demonstrates the first biological upcycling of post-consumer plastic waste into vanillin using an engineered microorganism., An engineered biosynthetic pathway in Escherichia coli enables the one-pot upcycling of post-consumer plastic waste into vanillin.

Microorganisms produce metal nanoparticles (MNPs) upon exposure to toxic metal ions. However, the catalytic activity of biosynthesised MNPs remains underexplored, despite the potential of these biological processes to be used for the sustainable recovery of critical metals, including palladium. Herein we report that biogenic palladium nanoparticles generated by the sulfate-reducing bacterium Desulfovibrio alaskensis G20 catalyse the ligand-free Suzuki Miyaura reaction of abiotic substrates. The reaction is highly efficient (>99% yield, 0.5 mol% Pd), occurs under mild conditions (37 °C, aqueous media) and can be accelerated within biocompatible micelles at the cell membrane to yield products containing challenging biaryl bonds. This work highlights how native metabolic processes in anaerobic bacteria can be combined with green chemical technologies to produce highly efficient catalytic reactions for use in sustainable organic synthesis., Nano-micelles meet biogenic Pd nanoparticles at the cell membrane promoting Suzuki Miyaura coupling reactions under mild conditions.

We propose a BlackBox Counterfactual Explainer that is explicitly developed for medical imaging applications. Classical approaches (e.g., saliency maps) assessing feature importance do not explain how and why variations in a particular anatomical region are relevant to the outcome, which is crucial for transparent decision making in healthcare application. Our framework explains the outcome by gradually exaggerating the semantic effect of the given outcome label. Given a query input to a classifier, Generative Adversarial Networks produce a progressive set of perturbations to the query image that gradually changes the posterior probability from its original class to its negation. We design the loss function to ensure that essential and potentially relevant details, such as support devices, are preserved in the counterfactually generated images. We provide an extensive evaluation of different classification tasks on the chest X-Ray images. Our experiments show that a counterfactually generated visual explanation is consistent with the disease's clinical relevant measurements, both quantitatively and qualitatively.

Taxadien-5α-hydroxylase and taxadien-5α-ol O-acetyltransferase catalyse the oxidation of taxadiene to taxadien-5α-ol and subsequent acetylation to taxadien-5α-yl-acetate in the biosynthesis of the blockbuster anti-cancer drug, paclitaxel (Taxol®). Despite decades of research, the promiscuous and multispecific CYP725A4 enzyme remains a major bottleneck in microbial biosynthetic pathway development. In this study, an interdisciplinary approach was applied for the construction and optimisation of the early pathway in Saccharomyces cerevisiae, across a range of bioreactor scales. High-throughput microscale optimisation enhanced total oxygenated taxane titre to 39.0±5.7 mg/L and total taxane product titres were comparable at micro and mini-bioreactor scale at 95.4±18.0 and 98.9 mg/L, respectively. The introduction of pH control successfully mitigated a reduction of oxygenated taxane production, enhancing the potential taxadien-5α-ol isomer titre to 19.2 mg/L, comparable to the 23.8±3.7 mg/L achieved at microscale. A combination of bioprocess optimisation and increased GC-MS resolution at 1L bioreactor scale facilitated taxadien-5α-yl-acetate detection with a final titre of 3.7 mg/L. Total oxygenated taxane titres were improved 2.7-fold at this scale to 78 mg/L, the highest reported titre in yeast. Critical parameters affecting the productivity of the engineered strain were identified across a range of scales, providing a foundation for the development of robust integrated bioprocess control systems. This article is protected by copyright. All rights reserved.

Background All-terrain vehicle (ATV)-related injuries remain a large public health problem in the United States and disproportionately affect American youth. Although children account for only 14–18% of ATV riders, they comprise 37–57% of those injured in ATV-related accidents. Since the U.S. Consumer Product Safety Commission began collecting data in 1982, 23% of ATV-related deaths have occurred in children. Objective With this review, we outline the major risk factors for injuries among young ATV riders in the United States and suggest research-based interventions to successfully modify such risk factors. Discussion We reviewed data from 16 published reviews regarding epidemiology and risk factors among ATV-related injuries in American children. All data pointed to young driver age and lack of appropriate safety equipment as major risk factors for such injuries. Although these risk factors are modifiable, legislation and programs designed to mitigate such risks have been unsuccessful. Among adults, the brief intervention model has become widely used among trauma patients exhibiting risky behaviors. Additionally, peer-to-peer interventions have demonstrated success with respect to drug and alcohol use in school-aged children. Both the brief and peer-to-peer interventions are promising avenues for decreasing risky ATV-related behavior in youths but have not been studied in this field. Conclusions ATV-related injuries disproportionately affect American youths. Although risk factors for such injuries are modifiable, current methods for intervention (mainly legislation) have not been successfully implemented. The brief intervention and peer-to-peer interventions have shown promise in other fields and should be studied with respect to pediatric ATV use.

Microorganisms can be programmed to perform chemical synthesis via metabolic engineering. However, despite an increasing interest in the use of de novo metabolic pathways and designer whole-cells for small molecule synthesis, the inherent synthetic capabilities of native microorganisms remain underexplored. Herein, we report the use of unmodified E. coli BL21(DE3) cells for the reduction of keto-acrylic compounds and apply this whole-cell biotransformation to the synthesis of aminolevulinic acid from a lignin-derived feedstock. The reduction reaction is rapid, chemo-, and enantioselective, occurs under mild conditions (37 °C, aqueous media), and requires no toxic transition metals or external reductants. This study demonstrates the remarkable promiscuity of central metabolism in bacterial cells and how these processes can be leveraged for synthetic chemistry without the need for genetic manipulation.

The city of Syracuse in New York announced an ambitious smart city plan which, when fully implemented, promises to make it the most connected city in the northeastern US. Thanks to a strategic investment by the State of New York, the city is home to what is billed as the world’s first Drone Corridor for RD. We outline a decision framework (The Syracuse Wheel) for public private partnership to help city leaders and private investors navigate the exciting implications stemming from these two strategic developments and the city’s environment to augment the priority areas of Autonomous Mobility and Connectivity. The Wheel positions Syracuse as a prime market for visionary Public Private Partnership (PPP) proposals given its infrastructure and assets specific to Unmanned Aerial Systems (UASs) and Autonomous Vehicle Testing. The research also suggests ways to mitigate the problems associated with data governance and IP governance that various large-scale PPPs have faced in the past. We conclude with a decision-making framework which facilitates a fast-track approval mechanism for investment proposals from private entities as Syracuse prepares for its future as leading-edge Smart City and UAS RD hub.

Synthetic biology has enabled the production of many value-added chemicals via microbial fermentation. However, the problem of low product titers from recombinant pathways has limited the utility of this approach. Methods to increase metabolic flux are therefore critical to the success of metabolic engineering. Here we demonstrate that vitamin E-derived designer micelles, originally developed for use in synthetic chemistry, are biocompatible and accelerate flux through a styrene production pathway in Escherichia coli. We show that these micelles associate non-covalently with the bacterial outer-membrane and that this interaction increases membrane permeability. In addition, these micelles also accommodate both heterogeneous and organic-soluble transition metal catalysts and accelerate biocompatible cyclopropanation in vivo. Overall, this work demonstrates that these surfactants hold great promise for further application in the field of synthetic biotechnology, and for expanding the types of molecules that can be readily accessed from renewable resources via the combination of microbial fermentation and biocompatible chemistry.

The introduction of new reactivity into living organisms is a major challenge in synthetic biology. Despite an increasing interest in both the development of small-molecule catalysts that are compatible with aqueous media and the engineering of enzymes to perform new chemistry in vitro, the integration of non-native reactivity into metabolic pathways for small-molecule production has been underexplored. Herein we report a biocompatible iron(III) phthalocyanine catalyst capable of efficient olefin cyclopropanation in the presence of a living microorganism. By interfacing this catalyst with E. coli engineered to produce styrene, we synthesized non-natural phenyl cyclopropanes directly from D-glucose in single-vessel fermentations. This process is the first example of the combination of nonbiological carbene-transfer reactivity with cellular metabolism for small-molecule production.

The use of organic chemistry principles and prediction techniques has enabled the development of new bioorthogonal reactions. As this "toolbox" expands to include new reaction manifolds and orthogonal reaction pairings, the continued development of existing reactions remains an important objective. This is particularly important in cellular imaging, where non-specific background fluorescence has been linked to the hydrophobicity of the bioorthogonal moiety. Here we report that trans-5-oxocene (oxoTCO) displays enhanced reactivity and hydrophilicity compared to trans-cyclooctene (TCO) in the tetrazine ligation reaction. Aided by ab initio calculations we show that the insertion of a single oxygen atom into the trans-cyclooctene (TCO) ring system is sufficient to impart aqueous solubility and also results in significant rate acceleration by increasing angle strain. We demonstrate the rapid and quantitative cycloaddition of oxoTCO using a water-soluble tetrazine derivative and a protein substrate containing a site-specific genetically encoded tetrazine moiety both in vitro and in vivo. We anticipate that oxoTCO will find use in studies where hydrophilicity and fast bioconjugation kinetics are paramount.

Biocompatible chemistry represents a new way of merging chemical and biological synthesis by interfacing nonenzymatic reactions with metabolic pathways. This approach can enable the production of nonnatural molecules directly from renewable starting materials via microbial fermentation. When developing a new biocompatible reaction certain criteria must be satisfied, i.e., the reaction must be (1) functional in aqueous growth media at ambient temperature and pH, (2) nontoxic to the producing microorganism, and (3) have negligible effects on the targeted metabolic pathway. This chapter provides a detailed outline of two biocompatible reaction procedures (hydrogenation and cyclopropanation), and describes some of the chemical and microbiological experiments and considerations required during biocompatible reaction development.

Transition metal catalysis has emerged as a powerful strategy to expand synthetic flexibility of protein modification. Herein, we report a cationic Ru(II) system that enables the first example of alkyne hydrosilylation between dimethylarylsilanes and $\textit{O}$-propargyl-functionalized proteins using a substoichiometric amount or low-loading of Ru(II) catalyst to achieve the first C–Si bond formation on full-length substrates. The reaction proceeds under physiological conditions at a rate comparable to other widely used bioorthogonal reactions. Moreover, the resultant $\textit{gem}$-disubstituted vinylsilane linkage can be further elaborated through thiol–ene coupling or fluoride-induced protodesilylation, demonstrating its utility in further rounds of targeted modifications.

A concise and efficient synthesis of (-)-gephyrotoxin from L-pyroglutaminol has been realized. The key step in this approach is a diastereoselective intramolecular enamine/Michael cascade reaction that forms two rings and two stereocenters and generates a stable tricyclic iminium cation. A hydroxy-directed reduction of this intermediate plays a key role in establishing the required cis-decahydroquinoline ring system, enabling the total synthesis of (-)-gephyrotoxin in nine steps and 14% overall yield. The absolute configuration of the synthetic material was confirmed by single-crystal X-ray diffraction and is consistent with the structure originally proposed for material isolated from the natural source.