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DOE OSTI2021

Evidence for Lignocellulose-Decomposing Enzymes in the Genome and Transcriptome of the Aquatic Hyphomycete Clavariopsis aquatica

Fungi are ecologically outstanding decomposers of lignocellulose. Fungal lignocellulose degradation is prominent in saprotrophic Ascomycota and Basidiomycota of the subkingdom Dikarya. Despite ascomycetes dominating the Dikarya inventory of aquatic environments, genome and transcriptome data relating to enzymes involved in lignocellulose decay remain limited to terrestrial representatives of these phyla. We sequenced the genome of an exclusively aquatic ascomycete (the aquatic hyphomycete Clavariopsis aquatica), documented the presence of genes for the modification of lignocellulose and its constituents, and compared differential gene expression between C. aquatica cultivated on lignocellulosic and sugar-rich substrates. We identified potential peroxidases, laccases, and cytochrome P450 monooxygenases, several of which were differentially expressed when experimentally grown on different substrates. Additionally, we found indications for the regulation of pathways for cellulose and hemicellulose degradation. Our results suggest that C. aquatica is able to modify lignin to some extent, detoxify aromatic lignin constituents, or both. Such characteristics would be expected to facilitate the use of carbohydrate components of lignocellulose as carbon and energy sources.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Analysis of 26S Proteasome Activity across Arabidopsis Tissues

Plants utilize the ubiquitin proteasome system (UPS) to orchestrate numerous essential cellular processes, including the rapid responses required to cope with abiotic and biotic stresses. The 26S proteasome serves as the central catalytic component of the UPS that allows for the proteolytic degradation of ubiquitin-conjugated proteins in a highly specific manner. Despite the increasing number of studies employing cell-free degradation assays to dissect the pathways and target substrates of the UPS, the precise extraction methods of highly potent tissues remain unexplored. Here, we utilize a fluorogenic reporting assay using two extraction methods to survey proteasomal activity in different Arabidopsis thaliana tissues. This study provides new insights into the enrichment of activity and varied presence of proteasomes in specific plant tissues.

26S proteasome↗

DOE OSTI2019

Impact of Water Ingress on Molybdenum Thin Films and Its Effect on Cu(In,Ga)Se 2 Solar Cells

Solar cell degradation can occur through many pathways and at the different stages of the fabrication process, notably because of the water condensation. In the case of Cu(In,Ga)Se 2 (CIGS) solar cells, the impact of water ingress on Mo back contact can be substantial for not only the film itself but also the device performance and reliability. Microstructural modification, change in film morphology, loss in reflectance, and increased resistivity because of the moisture ingress were observed via X-ray diffraction, transmission electron microscopy, spectroscopic ellipsometry, and four-point probe measurements, respectively. Secondary ion mass spectrometry measurements revealed drastic changes in the alkali (Na, K) profiles in both the CIGS and Mo layers, likely because of the modification of their diffusion coefficient through Mo. This, in turn, negatively impacts the solar cell efficiency by decreasing both fill factor and open-circuit voltage. Additional experiments, modifying the substrate and utilizing a NaF postdeposition treatment, highlight the mechanisms of degradation as being due to both a modification of the Mo/CIGS interface and the lack of alkali diffusion after water ingress.

14 SOLAR ENERGY↗

DOE OSTI2025

Surface Protected Organozirconium Catalyzes C─H Alumination of Saturated Hydrocarbons

Surface grafted organozirconium catalyzes C─H/Et─Al exchange reactions, involving saturated hydrocarbons and AlEt 3 , to afford organoaluminum compounds and ethane. The Zr(O t Bu) 3 @SiO 2 -Al 2 O 3 –700 (1) catalyst contains monopodal ≡SiO─Zr(O t Bu) 3 and only a few residual silanols (<5%). Nonetheless, these silanols are the Achille's heel of 1, providing a pathway for surface and catalyst degradation during catalysis, limiting the alkylaluminum yield and catalyst turnover. Support degradation, involving the cleavage of Si─O bonds by activated surface organometallics, is inhibited by capping silanols with ─SiMe 3 . Residual silanols in 1 react with allyltrimethylsilane, as determined by solid-state 13 C and 29 Si nuclear magnetic resonance (NMR) spectroscopy, infrared (IR) spectroscopy, and reaction stoichiometry, to form Zr(O t Bu) 3 /SiMe 3 @SiO 2 -Al 2 O 3–700 (2), which is resistant to degradation by AlEt 3 . C─H alumination of dodecane catalyzed by 2 produces higher yields of the 1-dodecylaluminum product in comparison to 1, and in >95% selectivity. Additionally, methane undergoes 2-catalyzed C─H alumination, providing a route to AlMe 3 .

Banerjee, Sayak [Iowa State Univ., Ames, IA (Unite↗

DOE OSTI2026

Pressure-Driven Helium Insertion for Structural Stability of CH 3 NH 3 PbBr 3 Hybrid Perovskites

Organic−inorganic metal halide perovskites (MHPs) have garnered significant attention due to their outstanding performance in optoelectronic devices, but they are prone to degradation through a variety of pathways. High-pressure studies are being used to understand the mechanical and structural stability of MHPs and investigate new methods for improving these. In this study, we map the high-pressure, low-temperature structural phase diagram of CH 3 NH 3 PbBr 3 (MAPbBr 3 ) between 15−300 K and up to 1.5 GPa. We first compare the temperature and pressure effects on the global and local structures of MAPbBr 3 using synchrotron X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS), respectively, and find evidence of PbBr 6 octahedral distortion. Our results also suggest that He inserts into the MAPbBr 3 structure. The thermodynamics of He insertion into MAPBHe x are calculated to be plausible at room temperature for x ≤ 1 and P = 1−3 GPa and shown to stabilize higher-symmetry phases. This phenomenon increases the fitted bulk modulus of MAPbBr 3 . Structural stabilization by inert atom insertion is proposed as a method to improve the mechanical robustness of MHPs and other soft hybrid materials.

Diffraction↗

DOE OSTI2021

Dynamic self-assembly of compartmentalized DNA nanotubes

Abstract Bottom-up synthetic biology aims to engineer artificial cells capable of responsive behaviors by using a minimal set of molecular components. An important challenge toward this goal is the development of programmable biomaterials that can provide active spatial organization in cell-sized compartments. Here, we demonstrate the dynamic self-assembly of nucleic acid (NA) nanotubes inside water-in-oil droplets. We develop methods to encapsulate and assemble different types of DNA nanotubes from programmable DNA monomers, and demonstrate temporal control of assembly via designed pathways of RNA production and degradation. We examine the dynamic response of encapsulated nanotube assembly and disassembly with the support of statistical analysis of droplet images. Our study provides a toolkit of methods and components to build increasingly complex and functional NA materials to mimic life-like functions in synthetic cells.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Multiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesis

Aquatic ecosystems are globally significant sources of the greenhouse gas methane to the atmosphere. Until recently, methane production was thought to be a strictly anaerobic process confined primarily to anoxic sediments. However, supersaturation of methane in oxygenated waters has been consistently observed in lakes and the ocean (termed the ‘methane paradox’), indicating that methane can be produced under oxic conditions through unclear mechanisms. Here we show aerobic methane production from multiple sources in freshwater incubation experiments under different treatments and based on biogeochemical, metagenomic, and metatranscriptomic data. We find that aerobic methane production appears to be associated with (bacterio)chlorophyll metabolism and photosynthesis, as well as with Proteobacterial degradation of methylphosphonate. Genes encoding pathways for putative photosynthetic- and methylphosphonate-based methane production also co-occur in Proteobacterial metagenome-assembled genomes. Our findings provide insight into known mechanisms of aerobic methane production, and suggest a potential co-occurring mechanism associated with bacterial photosynthesis in aquatic ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Sonic Wafering of III-V substrates for High Efficiency Cells: A path to <$0.50/W

This project developed and demonstrated Sonic Lift-off, a novel technology that enables the reuse of expensive semiconductor substrates used to manufacture high-efficiency solar cells. By using sound waves to precisely separate thin layers of material, the process significantly reduces manufacturing costs while maintaining the performance of advanced III–V solar cells. These solar cells are among the most efficient in the world and are used in space, aerospace, and emerging terrestrial applications. The results of this work show that substrate reuse can be achieved without degrading device performance, offering a pathway to more affordable, high-performance solar technologies. This advancement supports U.S. clean energy goals by enabling broader deployment of renewable energy systems and strengthening domestic manufacturing capabilities in advanced photovoltaics.

14 SOLAR ENERGY↗

DOE OSTI2022

Development of Surveillance Test Articles for Materials Degradation Management in MSR Environment

Information on materials degradations during advanced reactor operations is limited Effects of materials degradations during reactor operations are synergistic, involving: Irradiation, corrosion, elevated temperature exposure and stress (creep-fatigue loading) Establishment of surrogate materials surveillance program for the management of materials degradations would be an important pathway in support of the timely licensing of advanced reactors

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

Robust silane self-assembled monolayer coatings on plasma-engineered copper surfaces promoting dropwise condensation

Dropwise condensation is well known to result in better heat transfer performance owing to efficient condensate/droplet removal, which can be harnessed in various industrial heat/mass transfer applications such as power generation and conversion, water harvesting/desalination, and electronics thermal management. The key to enhancing condensation via the dropwise mode is thin low surface energy coatings (<100 nm) with low contact angle hysteresis. Ultrathin (<5 nm) silane self-assembled monolayers (or SAMs) have been widely studied to promote dropwise condensation due to their minimal thermal resistance and scalable integration processes. Such thin coatings typically degrade within an hour during condensation of water vapor. After coating failure, water vapor condensation transitions to the inefficient filmwise mode with poor heat transfer performance. We enhance silane SAM quality and durability during water vapor condensation on copper compared to state-of-the-art silane coatings on metal surfaces. We achieve this via (i) surface polishing to sub-10 nm levels, (ii) pure oxygen plasma surface treatment, and (iii) silane coating integration with the copper substrate in an anhydrous/moisture-free environment. The resulting silane SAM has low contact angle hysteresis (≈20°) and promotes efficient dropwise condensation of water for >360 hours without any visible sign of coating failure/degradation in the absence of non-condensable gases. We further demonstrate enhanced heat transfer performance (≈5-7× increase over filmwise condensation) over an extended period of time. Surface characterization data post-condensation leads us to propose that in the absence of non-condensable gases in the vapor environment, the silane SAM degrades due to reduction and subsequent dissolution of copper oxide at the oligomer-substrate interface. The experiments also indicate that the magnitude of surface subcooling (or condensation rate) affects the rate of coating degradation. Finally, this work identifies a pathway to durable dropwise promoter coatings that will enable efficient heat transfer in industrial applications.

42 ENGINEERING↗

DOE OSTI2023

Systems Engineering of Rhodococcus opacus to Enable Production of Drop-in Fuels from Lignocellulose

Production of drop-in fuels from lignocellulose using Rhodococcus opacus PD630 (hereafter R. opacus) is a challenging goal. During the grant period we have pushed the field forward significantly in several areas of research. Towards the end goal of accelerating the adoption of R. opacus in biofuel production, during the grant period we have expanded the phenotypic characterization of R. opacus grown in single aromatic (model lignocellulosic) compounds or their mixtures, modeling the growth conditions in lignocellulosic biomass. Harnessing the power of adaptive evolution, we produced evolved R. opacus isolates with superior lignin valorization capabilities and identified differentially expressed genes and pathways after adaptation. We used next generation multi-omic techniques such as genomic, transcriptomic, and metabolomic analyses, to identify the catabolic pathways used by R. opacus to degrade aromatic compounds and funnel these degradation products into central metabolism, as well as the aromatic transport genes required for increased tolerance and utilization. Taking this information one step further, we identified endogenous transcription factors and regulatory mechanisms important for degradation of five model aromatic compounds. To accurately estimate R. opacus growth and consumption on model lignin compounds we pioneered the use of novel extraction procedures prior to GC-MS analysis. Alongside 13 C-metabolic flux analysis, we have elucidated the metabolic routes preferred by Rhodococcus opacus during aromatic compound degradation. Finally, we used in tandem lipidomics and high-resolution mass spectrometry to identify the modulation of mycolic acids and phospholipid membrane composition modification as a strategy for aromatic tolerance in R. opacus. Being a non-model organism, R. opacus lacks the breadth of tools and technical foundation which drive biofuel research in more well-understood microbes such as Escherichia coli. To reduce this burden for use, we designed and produced new tools for genomic manipulation and engineering in R. opacus. These engineering breakthroughs support efficient genomic editing, enabling gene overexpression, repression, and genetic alteration. Using these tools, we have generated synthetically engineered strains with increased lipogenesis and growth, both positive traits required for increased lignin valorization. Optimizing engineered strains for biofuel production from lignocellulose requires extremely sophisticated synthetic rewiring of metabolism. To facilitate systems-level reorganization of metabolism in R. opacus, we created a genome-scale model that accurately predicts metabolic flux and growth rates on the aromatic compound phenol. Lignin requires extensive pre-treatment before biological degradation by R. opacus. Towards an eventual goal of degrading real-world lignin, we developed new depolymerization processes to generate lignin breakdown products (LBP). We optimized LBP storage and composition analysis techniques, enabling accurate prediction of specific LBP compound integration into cell wall components. Overall, through the work funded by this grant we generated 20 manuscripts (17 published, 3 in review/preparation), methods for increased accuracy in metabolomics of aromatic compounds, multiple genetic tools for altering the R. opacus genome, genome scale models for predicting flux through metabolic pathways, as well as multi-omic data for community use. The work funded by this grant has increased the knowledge of aromatic degradation in bacteria and advanced our efforts to optimize R. opacus for lignin valorization.

09 BIOMASS FUELS↗

DOE OSTI2025

Transcript profiling of plastid ferrochelatase two mutants reveals that chloroplast singlet oxygen signals lead to global changes in RNA profiles and are mediated by Plant U-Box 4

Abstract Background In response to environmental stresses, chloroplasts generate reactive oxygen species, including singlet oxygen ( 1 O 2 ), an excited state of oxygen that regulates chloroplast-to-nucleus (retrograde) signaling, chloroplast turnover, and programmed cell death (PCD). Yet, the central signaling mechanisms and downstream responses remain poorly understood. TheArabidopsis thaliana plastid ferrochelatase two(fc2) mutant conditionally accumulates 1 O 2 , and Plant U-Box 4 (PUB4), a cytoplasmic E3 ubiquitin ligase, is involved in propagating 1 O 2 signals for chloroplast turnover and cellular degradation. Thus, thefc2andfc2 pub4mutants are useful genetic tools to elucidate these signaling pathways. Previous studies have focused on the role of 1 O 2 in promoting cellular degradation infc2mutants, but its impact on retrograde signaling from mature chloroplasts (the major site of 1 O 2 production) is poorly understood. Results To gain mechanistic insights into 1 O 2 signaling pathways, we compared transcriptomes of adult wt,fc2, andfc2 pub4plants. The accumulation of 1 O 2 infc2plants broadly repressed genes involved in chloroplast function and photosynthesis, while inducing genes and transcription factors involved in abiotic and biotic stress, the biosynthesis of jasmonic acid (JA) and salicylic acid (SA), microautophagy, and senescence. Elevated JA and SA levels were observed in 1 O 2 -stressedfc2plants.pub4reversed most of this 1 O 2 -induced gene expression and reduced the JA content infc2plants. Thepub4mutation also blocked JA-induced senescence pathways in the dark. However, fc2 pub4 plantsmaintained constitutively elevated levels of SA even in the absence of bulk 1 O 2 accumulation. Conclusions Together, this work demonstrates that infc2plants, 1 O 2 leads to a robust retrograde signal that may protect cells by downregulating photosynthesis and ROS production while simultaneously mounting a stress response involving SA and JA. The induction of microautophagy and senescence pathways indicate that 1 O 2 -induced cellular degradation is a genetic response to this stress, and the bulk of this transcriptional response is modulated by the PUB4 protein. However, the effect ofpub4on hormone synthesis and signaling is complex and indicates that an intricate interplay of SA and JA are involved in promoting stress responses and programmed cell death during photo-oxidative damage.

Plant Sciences↗

DOE OSTI2024

Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation

Protein turnover is critical for proteostasis, but turnover quantification is challenging, and even in well-studied E. coli, proteome-wide measurements remain scarce. Here, we quantify the turnover rates of ~3200 E. coli proteins under 13 conditions by combining heavy isotope labeling with complement reporter ion quantification and find that cytoplasmic proteins are recycled when nitrogen is limited. We use knockout experiments to assign substrates to the known cytoplasmic ATP-dependent proteases. Surprisingly, none of these proteases are responsible for the observed cytoplasmic protein degradation in nitrogen limitation, suggesting that a major proteolysis pathway in E. coli remains to be discovered. Lastly, we show that protein degradation rates are generally independent of cell division rates. Thus, we present broadly applicable technology for protein turnover measurements and provide a rich resource for protein half-lives and protease substrates in E. coli, complementary to genomics data, that will allow researchers to study the control of proteostasis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

The lowdown on breakdown: Open questions in plant proteolysis

Abstract Proteolysis, including post-translational proteolytic processing as well as protein degradation and amino acid recycling, is an essential component of the growth and development of living organisms. In this article, experts in plant proteolysis pose and discuss compelling open questions in their areas of research. Topics covered include the role of proteolysis in the cell cycle, DNA damage response, mitochondrial function, the generation of N-terminal signals (degrons) that mark many proteins for degradation (N-terminal acetylation, the Arg/N-degron pathway, and the chloroplast N-degron pathway), developmental and metabolic signaling (photomorphogenesis, abscisic acid and strigolactone signaling, sugar metabolism, and postharvest regulation), plant responses to environmental signals (endoplasmic-reticulum-associated degradation, chloroplast-associated degradation, drought tolerance, and the growth-defense trade-off), and the functional diversification of peptidases. We hope these thought-provoking discussions help to stimulate further research.

Eckardt, Nancy A. (ORCID:0000000316581412)↗

DOE OSTI2022

Novel catalysts with multivalence copper for organic pollutants removal from wastewater with excellent selectivity and stability in Fenton‐like process under neutral pH conditions

Abstract Fenton‐like reaction has been widely used for organics degradation. However, most Fenton‐like reaction works at low pH range (pH < 4) with uncontrollable selectivity of hydroxyl radicals from H 2 O 2 activation, and unsatisfied catalyst stability, which is compromised advanced oxidation performance for water/wastewater treatments. In this work, to solve the drawbacks, novel copper catalysts were fabricated via hydrogen reduction/calcination of Cu 2+ ‐supported Al/MCM‐41 with precisely controllable copper valence state. Compared with catalysts with monovalence copper (i.e., CuO, Cu, and Cu 2+ ), the obtained catalysts with multivalence copper present higher selectivity, excellent stability towards •OH radical pathways, and outperformance in p CBA degradation efficiency at neutral state. In addition, the fabricated catalysts also exhibited excellent phenol removal efficiency (75.5%) and H 2 O 2 utilization efficiency (47.9%) within neutral environment. Moreover, the degradation efficiency of phenol approaches to 100% within only 2 h. The catalyst also shows good stability for organic pollutants removal, which shows good potential in catalytic oxidation for phenolic compounds‐containing wastewater in Fenton‐like reaction, especially under neutral pH conditions. Practitioner Points Multivalence copper presents great potentials for organic compounds removal at neutral condition. Multivalence copper shows higher selectivity toward •OH and good stability at neutral condition. Multivalence copper exhibiters outperformed phenol removal efficiency at neutral condition.

Li, Haitao↗

DOE OSTI2023

Designing High‐Donicity Anions for Rechargeable Potassium Superoxide/Peroxide Batteries

Abstract A battery cathode based on the superoxide/peroxide redox not only inherits the advantage of oxygen (O 2 ) batteries in high capacities and low costs but also overcomes the disadvantages in O 2 storage, electrolyte evaporation, and anode deactivation due to O 2 crossover. Herein, we report an enhanced potassium superoxide (KO 2 )/peroxide (K 2 O 2 ) conversion by adopting a high‐donicity anion additive in the ether‐based electrolyte. Such an anion was synthesized via a “Solvent‐in‐Anion” strategy and validated to enhance the electron donicity of the electrolyte. The use of high‐donicity anion could lead to enhanced KO 2 utilization (≈90.2 %) by retarding electrode passivation and allow the full charging back of K 2 O 2 through the solution‐mediated pathway without electrocatalysts. No apparent cell degradation is observed during the first 120 cycles by controlling the reversible depth‐of‐discharge capacity at 292 mAh g −1 within an O 2 ‐free region. The K−KO 2 cell delivers a high energy efficiency (>84.4 %) and a lifespan of over 1440 hours.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

TRIM16 overexpression inhibits the metastasis of colorectal cancer through mediating Snail degradation

Highlights: • TRIM16 does significantly inhibit CRC cell migration and metastasis. • TRIM16 negatively regulates CRC cells EMT. • TRIM16 directly interacts with Snail. • TRIM16 promotes degradation of Snail via ubiquition proteasome pathway. Tripartite motif containing 16 (TRIM16) is a member of the tripartite motif protein family and functions as a potential tumor suppressor in several cancers. However, the specific function and clinical significance of TRIM16 in colorectal cancer (CRC) remains unclear. In this study, we observed that low TRIM16 expression was detected frequently in primary colorectal cancer (CRC) tissues and was closely associated with a better prognosis. Functional studies demonstrate that TRIM16 overexpression notably inhibits the metastasis abilities of CRC in vivo and in vitro. Mechanistically, our results demonstrated that TRIM16 directly bound and ubiquitinated Snail family transcriptional repressor 1 (Snail), an important transcriptional factor of the epithelial-mesenchymal transition (EMT) process suppressing the EMT in CRC. Additionally, our data revealed that the inhibition effect of TRIM16 on cancer metastasis was dependent on Snail degradation. Collectively, our study is the first to report that TRIM16 plays a crucial anti-tumor role in CRC tumorigenesis. We also provided novel evidence that TRIM16 might act as a prognostic and therapeutic target to assess and inhibit CRC progression.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Designing High‐Donicity Anions for Rechargeable Potassium Superoxide/Peroxide Batteries

Qin, Lei↗