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Green solvent-processable poly(3-hexylthiophene) derivative maintains high hole mobility in diodes
The development of environmentally sustainable fabrication methods for organic solar cells (OSCs) is critical to enable their large-scale adoption. Conventional solution-processed OSCs often rely on halogenated, toxic solvents that pose health and environmental risks, limiting their scalability. This is because π-conjugated polymers tend to have a low solubility in non-halogenated solvents. A common strategy to enhance solubility in alternative solvents is through the incorporation of polar solubilizing groups, often on every repeat unit of at least one monomer. However, too many polar side chains tend to disrupt favorable morphology and decrease charge transport properties. In this study, we demonstrate that a minimal degree of side chain functionalization can improve green solvent processability while preserving electrical performance. We tested this hypothesis using our previously reported random copolymer derivative of poly(3-hexylthiophene) (P3HT) where ∼10 mol% of the side chains are 6-pentanoatehexyl side chains. We find that this low-level functionalization significantly broadens the solvents that can be used to process P3HT to less toxic solvents such as o-xylene and anisole. Furthermore, the copolymer processed from greener solvents showed high hole mobilities (∼10⁻ 3 cm 2 /Vs by the Space-Charge Limiting Current method in diodes), comparable to P3HT films cast from toxic chloroform. These findings suggest that minimal side-chain modification is a viable strategy for expanding green solvent compatibility while preserving electrical performance, paving the way toward more sustainable organic semiconductor designs.
Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model
Although implicated as deleterious in many organisms, aneuploidy can underlie rapid phenotypic evolution. However, aneuploidy will be maintained only if the benefit outweighs the cost, which remains incompletely understood. To quantify this cost and the molecular determinants behind it, we generated a panel of chromosome duplications in Saccharomyces cerevisiae and applied comparative modeling and molecular validation to understand aneuploidy toxicity. We show that 74%–94% of the variance in aneuploid strains’ growth rates is explained by the cumulative cost of genes on each chromosome, measured for single-gene duplications using a genomic library, along with the deleterious contribution of small nucleolar RNAs (snoRNAs) and beneficial effects of tRNAs. Machine learning to identify properties of detrimental gene duplicates provided no support for the balance hypothesis of aneuploidy toxicity and instead identified gene length as the best predictor of toxicity. Our results present a generalized framework for the cost of aneuploidy with implications for disease biology and evolution.
Biological upgrading of pyrolysis-derived wastewater: Engineering Pseudomonas putida for alkylphenol, furfural, and acetone catabolism and (methyl)muconic acid production
While biomass-derived carbohydrates have been predominant substrates for biological production of renewable fuels, chemicals, and materials, organic waste streams are growing in prominence as potential alternative feedstocks to improve the sustainability of manufacturing processes. Catalytic fast pyrolysis (CFP) is a promising approach to generate biofuels from lignocellulosic biomass, but it generates a complex, carbon-rich, and toxic wastewater stream that is challenging to process catalytically but could be biologically upgraded to valuable co-products. Here, we implemented modular, heterologous catabolic pathways in the Pseudomonas putida KT2440-derived EM42 strain along with the overexpression of native toxicity tolerance machinery to enable utilization of 89% (w/w) of carbon in CFP wastewater. The dmp monooxygenase and meta-cleavage pathway from Pseudomonas putida CF600 were constitutively expressed to enable utilization of phenol, cresols, 2- and 3-ethyl phenol, and methyl catechols, and the native chaperones clpB, groES, and groEL were overexpressed to improve toxicity tolerance to diverse aromatic substrates. Next, heterologous furfural and acetone utilization pathways were incorporated, and a native alcohol dehydrogenase was overexpressed to improve methanol utilization, generating reducing equivalents. All pathways (encoded by genes totaling ~30 kilobases of DNA) were combined into a single strain that can catabolize a mock CFP wastewater stream as a sole carbon source. Further engineering enabled conversion of all aromatic compounds in the mock wastewater stream to (methyl)muconates with a ~90% (mol/mol) yield. Biological upgrading of CFP wastewater as outlined in this work provides a roadmap for future applications in valorizing other heterogeneous waste streams.
Chemical-damage MINE: A database of curated and predicted spontaneous metabolic reactions
Spontaneous reactions between metabolites are often neglected in favor of emphasizing enzyme-catalyzed chemistry because spontaneous reaction rates are assumed to be insignificant under physiological conditions. However, synthetic biology and engineering efforts can raise natural metabolites' levels or introduce unnatural ones, so that previously innocuous or nonexistent spontaneous reactions become an issue. Problems arise when spontaneous reaction rates exceed the capacity of a platform organism to dispose of toxic or chemically active reaction products. While various reliable sources list competing or toxic enzymatic pathways' side-reactions, no corresponding compilation of spontaneous side-reactions exists, nor is it possible to predict their occurrence. We addressed this deficiency by creating the Chemical Damage (CD)-MINE resource. First, we used literature data to construct a comprehensive database of metabolite reactions that occur spontaneously in physiological conditions. We then leveraged this data to construct 148 reaction rules describing the known spontaneous chemistry in a substrate-generic way. We applied these rules to all compounds in the ModelSEED database, predicting 180,891 spontaneous reactions. The resulting (CD)-MINE is available at https://minedatabase.mcs.anl. gov/cdmine/#/home and through developer tools. We also demonstrate how damage-prone intermediates and end products are widely distributed among metabolic pathways, and how predicting spontaneous chemical damage helps rationalize toxicity and carbon loss using examples from published pathways to commercial products. We explain how analyzing damage-prone areas in metabolism helps design effective engineering strategies. Finally, we use the CD-MINE toolset to predict the formation of the novel damage product N-carbamoyl proline, and present mass spectrometric evidence for its presence in Escherichia coli.
Bioactivity Profiling of Chemical Mixtures for Hazard Characterization
Abstract The assessment and regulation of chemical toxicity to protect human health and the environment are done one chemical at a time and seldom at environmentally relevant concentrations. However, chemicals are found in the environment as mixtures, and their toxicity is largely unknown. Understanding the hazard posed by chemicals within the mixture is critical to enforce protective measures. Here, we demonstrate the application of bioactivity profiling of environmental water samples using the sentinel and ecotoxicology model species Daphnia to reveal the biomolecular response induced by exposure to real-world mixtures. We exposed a Daphnia strain to 30 sampled waters of the Chaobai River and measured the gene expression response profiles. Using a multiblock correlation analysis, we establish correlations between chemical mixtures identified in 30 water samples with gene expression patterns induced by these chemical mixtures. We identified 80 metabolic pathways putatively activated by mixtures of inorganic ions, heavy metals, polycyclic aromatic hydrocarbons, industrial chemicals, and a set of biocides, pesticides, and pharmacologically active substances. Our data-driven approach discovered both known bioactivity signatures with previously described modes of action and new pathways linked to undiscovered potential hazards. This study demonstrates the feasibility of reducing the complexity of real-world mixture toxicity to characterize the biomolecular effects of a defined number of chemical components based on gene expression monitoring of the sentinel species Daphnia.
Exceptional NH 3 Detection by Cu(cyhdc) MOF Sensor Due to H 2 O Coadsorption
Metal–organic framework (MOF)-based electrical impedance sensors are a growing class of sensors that show utility in the detection of environmentally toxic gases. Detection of trace NH 3 has been particularly difficult to design due to the low electrical response of NH 3 . However, this has been circumvented by judiciously selecting a MOF that has enhanced electrical response to NH 3 due to coadsorption with predominant atmospheric gases such as water. Herein, an MOF Cu(cyhdc) based sensor has been successfully demonstrated for the enhanced detection of environmentally toxic NH 3 gas. The sensor shows a change in impedance when it is exposed to 5 ppm of NH 3 . At 20 °C, >30% relative humidity (RH) is necessary to elicit a change, with the response increasing with RH and reaching 3170× at 92% RH, producing the largest published response to NH 3 for a MOF direct electrical sensor. In the absence of water, no change is observed toward 5 ppm of NH 3 over 20–50 °C. Here, this electrical response is largely driven by huge decreases in the imaginary component of the impedance, attributed to increased capacitance at the surface of the MOF crystallites upon NH 3 and H 2 O coadsorption. Complementary structural and microstructural characterization proves that the Cu(cyhdc) crystalline structure and morphology remain intact under trace NH 3 and/or H 2 O adsorption. Despite extremely low NH 3 , loadings seen in TGA, XPS, and FT-IR confirm NH 3 and H 2 O adsorption, and changes to the metal-carboxylate IR peak positions are observed upon NH 3 adsorption. Concentrated primarily at the outer surfaces of the MOF crystallites, this NH 3 and H 2 O coadsorption effectively increases the surface capacitance across the Cu(cyhdc) powder and enables direct electrical detection of trace NH 3 . Together, these results demonstrate how coadsorption of specific molecules (H 2 O) can be used to enable the electrical detection of trace toxic gases that would otherwise not have produced a MOF sensor response.
Rheinheimera sp . T2C2 Bacterial Biofilm for Bioremediation of Cobalt(II)
Toxic metals, including cobalt, are often the cause of the contamination of rivers and lakes in mining regions. Heavy metal water pollution has been linked to numerous human health problems, prompting the need for environmental remediation. Existing techniques for removing heavy metals from water, such as chemical precipitation and filtration, produce toxic waste, are costly, or require high power consumption for pumping. Biosorption is a potential alternative strategy that is cost-effective and uses readily available and naturally produced biomass and living material to absorb pollutants. Engineering living materials, such as biofilms, which consist of living cells and a secreted polymer matrix, offer the potential to integrate toxin sensing, sequestration, and metabolism capabilities of cells to improve pollution remediation strategies. Alternative biofilm producing candidates need to be explored to implement these material capabilities. Previous biosorption studies have primarily used bacterial biofilms from known pathogens and/or generated toxic waste in the form of the absorbent material combined with the heavy metal. Here, we describe a recently isolated bacterium called Rheinheimera sp. T2C2 that forms biofilms with promising biosorption characteristics. T2C2 is an aquatic bacterium with low nutrient requirements and high biofilm production that is not known to be pathogenic. We demonstrate (1) the efficacy of Rheinheimera sp. T2C2 as a biosorbent for cobalt bioremediation; (2) how biosorption is altered by water conditions to establish the efficacy of this strategy in different environments; and (3) how the metal can be released from the biofilm for metal recycling. Our findings will provide a living materials strategy that overcomes the existing barriers for bioremediation and improves the health of ecosystems and humans through heavy metal removal and recycling.
Serial femtosecond crystallography on in vivo-grown crystals drives elucidation of mosquitocidal Cyt1Aa bioactivation cascade
Cyt1Aa is the one of four crystalline protoxins produced by mosquitocidal bacterium Bacillus thuringiensis israelensis (Bti) that has been shown to delay the evolution of insect resistance in the field. Limiting our understanding of Bti efficacy and the path to improved toxicity and spectrum has been ignorance of how Cyt1Aa crystallizes in vivo and of its mechanism of toxicity. Here, we use serial femtosecond crystallography to determine the Cyt1Aa protoxin structure from sub-micron-sized crystals produced in Bti. Structures determined under various pH/redox conditions illuminate the role played by previously uncharacterized disulfide-bridge and domain-swapped interfaces from crystal formation in Bti to dissolution in the larval mosquito midgut. Biochemical, toxicological and biophysical methods enable the deconvolution of key steps in the Cyt1Aa bioactivation cascade. We additionally show that the size, shape, production yield, pH sensitivity and toxicity of Cyt1Aa crystals grown in Bti can be controlled by single atom substitution.
Bioorthogonal catalytic patch
The toxicity and complicated administration procedures of transition metal catalysts have hampered the applications of bioorthogonal catalysis in vivo. Here the authors fill the needles of a microneedle array patch with palladium nanoparticles deposited on titanium nanosheets and show that the device, applied locally on the skin of mouse models bearing melanoma, promotes intratumoural conversion of systemically injected caged doxorubicin into the active drug, reducing its toxicity and side effects. Bioorthogonal catalysis mediated by transition metals has inspired a new subfield of artificial chemistry complementary to enzymatic reactions, enabling the selective labelling of biomolecules or in situ synthesis of bioactive agents via non-natural processes. However, the effective deployment of bioorthogonal catalysis in vivo remains challenging, mired by the safety concerns of metal toxicity or complicated procedures to administer catalysts. Here, we describe a bioorthogonal catalytic device comprising a microneedle array patch integrated with Pd nanoparticles deposited on TiO 2 nanosheets. This device is robust and removable, and can mediate the local conversion of caged substrates into their active states in high-level living systems. In particular, we show that such a patch can promote the activation of a prodrug at subcutaneous tumour sites, restoring its parent drug's therapeutic anticancer properties. Finally, this in situ applied device potentiates local treatment efficacy and eliminates off-target prodrug activation and dose-dependent side effects in healthy organs or distant tissues.
Molecular speciation controls arsenic and lead bioaccessibility in fugitive dusts from sulfidic mine tailings
Communities nearby mine wastes in arid and semi-arid regions are potentially exposed to high concentrations of toxic metal(loid)s from fugitive dusts deriving from impoundments. To assess the relation between potentially lofted particles and human health risk, we studied the relationship between pharmacokinetic bioaccessibility and metal(loid) molecular speciation for mine tailings dust particulate matter (PM), with elevated levels of arsenic and lead (up to 59 and 34 mmol kg -1 , respectively), by coupling in vitro bioassay (IVBA) with X-ray absorption spectroscopy (XAS). Mine tailing efflorescent salts (PM ES ) and PM from the surface crust (0–1 cm, PM SC ) and near surface (0–25 cm) were isolated to <10 μm and <150 μm effective spherical diameter (PM 10 and PM 150 ) and reacted with synthetic gastric and lung fluid for 30 s to 100 h to investigate toxic metal(loid) release kinetics. Bioaccessible (BAc) fractions of arsenic and lead were about 10 and 100 times greater in gastric than in lung fluid simulant, respectively, and 10–100% of the maximum gastric BAc from PM 10 and PM 150 occurred within 30 s, with parabolic dissolution of fine, highly-reactive particles followed by slower release from less soluble sources. Evaporite salts were almost completely solubilized in gastric-fluid simulants. Arsenate within jarosite and sorbed to ferrihydrite, and lead from anglesite, were identified by XAS as the principal contaminant sources in the near surface tailings. In the synthetic lung fluid, arsenic was released continuously to 100 h, suggesting that residence time in vivo must be considered for risk determination. Analysis of pre- and post-IVBA PM indicated the release of arsenic in lung fluid was principally from arsenic-substituted jarosite, whereas in synthetic gastric fluid arsenic complexed on ferrihydrite surfaces was preferentially released and subsequently repartitioned to jarosite-like coordination at extended exposures. Lead dissolved at 30 s was subsequently repartitioned back to the solid phase as pyromorphite in phosphate rich lung fluid. The bioaccessibility of lead in surface tailings PM was limited due to robust sequestration in plumbojarosite. Kinetic release of toxic elements in both synthetic biofluids indicated that a single IVBA interval may not adequately describe release dynamics.
Dry electrodes with a printed cellulose–graphene ink for low-profile strain sensors in electromyography
Dihydrolevoglucosenone, commonly known as Cyrene, is a renewable and fully biodegradable cellulose-waste derived, environmentally friendly solvent, presenting a non-toxic alternative to N-methyl-2-pyrrolidone (NMP). Currently, solution-based processing of graphene and other similar van der Waals solids favor toxic solvents such as NMP, limiting their use for biosensing. However, with the use of Cyrene, bio-compatible printable devices are possible, and studies have already demonstrated its use in temperature and other biosensing methods through screen-printing. Screen-printing unfortunately often requires masks that constrain the minimum acquirable feature size to be above hundreds of centimeters and wastes material, adding to process complexity and cost. Conversely, inkjet-printing is an attractive alternative for the maskless patterning of hierarchically assembled structures, with micron length scales attainable. Graphene's high conductivity positions it ideally for long-wear sensors such as dry electrodes or respiration monitors. Here, we demonstrate the potential of Cyrene-based graphene inks through few-layer inkjet printing on flexible substrates for the first time, to produce non-toxic conductors toward a strain-mediated mechanism for biosensing, used to detect bodily motion for wearable electronics. The challenges overcome in this study include engineering ink chemistry and printing parameters such that Cyrene's relatively high viscosity compared to typical inkjet solvents, still allows for droplet ejection in a conventional material printer, yielding well-resolved clean line-edges in contrast to other solvents that exhibit diffuse line-edges possibly from stray droplets and ink-splashing. Temperature-dependent transport measurements on the inkjet-printed Cyrene-based graphene films showed the conductivity to be largely temperature-invariant but at lower temperatures below 100 K, conductivity decreased, likely as a result of increased inter-membrane separation arising from thermal contraction. Additionally, temperature-dependent Raman spectroscopy showed the red-shift in the G-band, 2D-band and D-band peaks, as temperature increased. As a result, by validating flexion motion detection of the proximal interphalangeal joint demonstrated in this study, our work is the first of its kind to successfully additively manufacture inkjet-printed Cyrene-based graphene strain sensors on flexible substrates for bio-sensing and wearables.
Engineering a tumor-selective prodrug T-cell engager bispecific antibody for safer immunotherapy
T-cell engaging (TCE) bispecific antibodies are potent drugs that trigger the immune system to eliminate cancer cells, but administration can be accompanied by toxic side effects that limit dosing. TCEs function by binding to cell surface receptors on T cells, frequently CD3, with one arm of the bispecific antibody while the other arm binds to cell surface antigens on cancer cells. On-target, off-tumor toxicity can arise when the target antigen is also present on healthy cells. The toxicity of TCEs may be ameliorated through the use of pro-drug forms of the TCE, which are not fully functional until recruited to the tumor microenvironment. This can be accomplished by masking the anti-CD3 arm of the TCE with an autoinhibitory motif that is released by tumor-enriched proteases. Here, we solve the crystal structure of the antigen-binding fragment of a novel anti-CD3 antibody, E10, in complex with its epitope from CD3 and use this information to engineer a masked form of the antibody that can activate by the tumor-enriched protease matrix metalloproteinase 2 (MMP-2). We demonstrate with binding experiments and in vitro T-cell activation and killing assays that our designed prodrug TCE is capable of tumor-selective T-cell activity that is dependent upon MMP-2. Furthermore, we demonstrate that a similar masking strategy can be used to create a pro-drug form of the frequently used anti-CD3 antibody SP34. This study showcases an approach to developing immune-modulating therapeutics that prioritizes safety and has the potential to advance cancer immunotherapy treatment strategies.
Adaptive responses of Trichlorobacter lovleyi to nitrite detoxification reveal overlooked contributions of Geobacterales to nitrate ammonification
Abstract Poorly understood microorganisms “short-circuit” the nitrogen cycle via the dissimilatory nitrate reduction to ammonium to retain the element in agricultural lands and stimulate crop productivity. The prevalence of Geobacterales closely related to Trichlorobacter lovleyi in nitrate ammonification hotspots motivated us to investigate adaptive responses contributing to ammonification rates in the laboratory type strain T. lovleyi SZ. Here, we describe the identification of tightly regulated pathways for efficient nitrate foraging and respiration with acetate, an important intermediate of organic matter degradation that Geobacterales efficiently assimilate and oxidize. Challenging the established dogma that high carbon/nitrate ratios stimulate the reduction of nitrate to ammonium, T. lovleyi doubled rapidly across a wide range of ratios provided nitrate concentrations were low enough to prevent the accumulation of the toxic nitrite intermediate. Yet, excess electrons during hydrogenotrophic growth alleviated nitrite toxicity and stimulated the reduction of nitrate to ammonium even under conditions of severe acetate limitation. These findings underscore the importance of nitrite toxicity in the ammonification of nitrate by Geobacterales and provide much needed mechanistic understanding of microbial adaptations contributing to soil nitrogen conservation. This information is critical to enhance the predictive value of genomic-based traits in environmental surveys and to guide strategies for sustainable management of nitrogen fertilization as well as mitigation of green-house emissions and agrochemical leaching from agricultural lands.
Screening the complex biological behavior of late lanthanides through genome-wide interactions
Abstract Despite their similar physicochemical properties, recent studies have demonstrated that lanthanides can display different biological behaviors. Hence, the lanthanide series can be divided into three parts, namely early, mid, and late lanthanides, based on their interactions with biological systems. In particular, the late lanthanides demonstrate distinct, but poorly understood biological activity. In the current study, we employed genome-wide functional screening to help understand biological effects of exposure to Yb(III) and Lu(III), which were selected as representatives of the late lanthanides. As a model organism, we used Saccharomyces cerevisiae, since it shares many biological functions with humans. Analysis of the functional screening results indicated toxicity of late lanthanides is consistent with disruption of vesicle-mediated transport, and further supported a role for calcium transport processes and mitophagy in mitigating toxicity. Unexpectedly, our analysis suggested that late lanthanides target proteins with SH3 domains, which may underlie the observed toxicity. This study provides fundamental insights into the unique biological chemistry of late lanthanides, which may help devise new avenues toward the development of decorporation strategies and bio-inspired separation processes.
4'-Deoxypyridoxine disrupts vitamin B 6 homeostasis in Escherichia coli K12 through combined inhibition of cumulative B 6 uptake and PLP-dependent enzyme activity
Pyridoxal 5'-phosphate (PLP) is the active form of vitamin B 6 and a cofactor for many essential metabolic processes such as amino acid biosynthesis and one carbon metabolism. 4’-deoxypyridoxine (4dPN) is a long known B 6 antimetabolite but its mechanism of action was not totally clear. By exploring different conditions in which PLP metabolism is affected in the model organism Escherichia coli K12, we showed that 4dPN cannot be used as a source of vitamin B 6 as previously claimed and that it is toxic in several conditions where vitamin B 6 homeostasis is affected, such as in a B 6 auxotroph or in a mutant lacking the recently discovered PLP homeostasis gene, yggS . In addition, we found that 4dPN sensitivity is likely the result of multiple modes of toxicity, including inhibition of PLP-dependent enzyme activity by 4’-deoxypyridoxine phosphate (4dPNP) and inhibition of cumulative pyridoxine (PN) uptake. These toxicities are largely dependent on the phosphorylation of 4dPN by pyridoxal kinase (PdxK).
Utilization of formic acid by extremely thermoacidophilic archaea species
The exploration of novel hosts with the ability to assimilate formic acid, a C1 substrate that can be produced from renewable electrons and CO 2 , is of great relevance for developing novel and sustainable biomanufacturing platforms. Formatotrophs can use formic acid or formate as a carbon and/or reducing power source. Formatotrophy has typically been studied in neutrophilic microorganisms because formic acid toxicity increases in acidic environments below the pKa of 3.75 (25°C). Because of this toxicity challenge, utilization of formic acid as either a carbon or energy source has been largely unexplored in thermoacidophiles, species that possess the ability to produce a variety of metabolites and enzymes of high biotechnological relevance. Here we investigate the capacity of several thermoacidophilic archaea species from the Sulfolobales order to tolerate and metabolize formic acid. Metallosphaera prunae, Sulfolobus metallicus and Sulfolobus acidocaldarium were found to metabolize and grow with 1–2 mM of formic acid in batch cultivations. Formic acid was co-utilized by this species alongside physiological electron donors, including ferrous iron. To enhance formic acid utilization while maintaining aqueous concentrations below the toxicity threshold, we developed a bioreactor culturing method based on a sequential formic acid feeding strategy. By dosing small amounts of formic acid sequentially and feeding H 2 as co-substrate, M. prunae could utilize a total of 16.3 mM of formic acid and grow to higher cell densities than when H 2 was supplied as a sole electron donor. These results demonstrate the viability of culturing thermoacidophilic species with formic acid as an auxiliary substrate in bioreactors to obtain higher cell densities than those yielded by conventional autotrophic conditions. Our work underscores the significance of formic acid metabolism in extreme habitats and holds promise for biotechnological applications in the realm of sustainable energy production and environmental remediation.