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At least 343 records · Page 19

Identification of recG genetic interactions in Escherichia coli by transposon sequencing

ABSTRACT Maintaining the integrity of the genome is of utmost importance for cell division and propagation. In Escherichia coli , the RecG protein has been implicated in processing branched recombination intermediates during DNA repair processes, but the primary cellular role(s) of RecG and the repair pathways in which it acts have been difficult to define. To gain additional insight into RecG function, we employed transposon sequencing to identify recG genetic interactions and reveal complementary or redundant functions. The strongest hits from the screen were the dam , uvrD , rnhA , radA , and rep genes. The conditional importance of these five genes in cells lacking recG was confirmed using a plasmid-based assay, revealing synthetic lethal interactions for most double deletion strains. Several of the synthetic lethal gene combinations (with uvrD, rep, and radA , but not rnhA or dam ) were suppressed by deletion of recF or recO , indicating that their genetic relationships involved roles in post-replication gap repair. Additionally, loss of the RecG/SSB interaction phenocopied a recG deletion when combined with dam , uvrD , radA , or rnhA deletions but not with rep . The results reinforce the idea of RecG as a general genome guardian. RecG has at least two functions. It plays an important role in the resolution of joint molecules behind the fork, formed during post-replication gap repair. RecG is also required to suppress genome over-replication caused by unscheduled replication initiation at R-loops, at double-strand breaks caused by dam inactivation, and during replication termination. IMPORTANCE DNA damage and subsequent DNA repair processes are mutagenic in nature and an important driver of evolution in prokaryotes, including antibiotic resistance development. Genetic screening approaches, such as transposon sequencing (Tn-seq), have provided important new insights into gene function and genetic relationships. Here, we employed Tn-seq to gain insight into the function of the recG gene, which renders Escherichia coli cells moderately sensitive to a variety of DNA-damaging agents when they are absent. The reported recG genetic interactions can be used in combination with future screens to aid in a more complete reconstruction of DNA repair pathways in bacteria.

59 BASIC BIOLOGICAL SCIENCES↗

Multiscale simulations of novel lithium electrolytes for improved processability and performance of solid-state batteries

In FY23, we performed atomic-scale simulations and developed analysis tools to understand the dynamic behaviors of Li ions and cation/anion components and predict mechanical properties in a new class of Li-ion solid electrolytes (SEs) developed by TRINA. Specifically, we revealed the transport characteristics of Li ions in anion sublattice, rotational dynamics of anion and cation components, and the effect of cation and anion on Li transport as well as interactions between cation and anions. The results imply that the transport characteristics in these soft materials may be affected by processing conditions significantly, which will offer the necessary insights to optimize these future SEs and accelerate the deployment of practical and easily processable Solid-state batteries (SSBs).

25 ENERGY STORAGE↗

Testing Protocol Development for the Fracture Toughness of Parts Built with Big Area Additive Manufacturing

The mechanical testing of additively manufactured parts has largely relied on the existing standards developed for traditional manufacturing. While this approach leverages the investment made in current standards development, it inaccurately assumes that the mechanical response of additive manufacturing (AM) parts is identical to that of parts manufactured through traditional processes. When considering thermoplastic, material extrusion AM, the differences in response can be attributed to an AM part’s inherent inhomogeneity caused by porosity, interlayer zones, and surface texture. Additionally, the interlayer bonding of parts printed with large-scale AM is difficult to adequately assess, as much testing is performed such that stress is distributed across many layer interfaces; therefore, the lack of AM-specific standards to assess interlayer bonding is a significant research gap. To quantify interlayer bonding via fracture toughness, double cantilever beam (DCB) testing has been used for some AM materials, and DCB has been generally used for a variety of materials including metal, wood, and laminates. Mode I DCB testing was performed on thermoplastic matrix composites printed with Big Area Additive Manufacturing (BAAM). Of particular interest was the notch shape and deflection speed during testing. The results examine the differences when using two notch types and three deflection speeds. The testing method introduced by the following paper differentiates itself from the ones described in the standards used by modernizing the methodology. This was conducted with the introduction of Digital Image Correlation (DIC) to gather displacement and load data simultaneously without human intervention.

Polymer Science↗

Earlier Ecological Drought Detection by Involving the Interaction of Phenology and Eco-Physiological Function

Meteorological drought indices like the Standardized Precipitation Evaporation Index (SPEI) are frequently used to diagnose “ecological drought,” despite the fact that they were not explicitly designed for this purpose. More recently developed indices like the Evaporative Stress Index (ESI), which is based on the degree of coupling between actual to potential evapotranspiration, may better capture dynamic plant response to moisture limitations. However, the skill of these indices at describing plant water stress is rarely evaluated at sub-seasonal timescales over which drought evolves. Moreover, it remains unclear how variability in phenological timing impacts and complicates early drought detection. Here, we compared the ability of ESI and SPEI to reflect the dynamics of ecological drought in forests and grasslands, based on anomalies of Gross Primary Productivity (GPP), surface conductance (G s , a proxy for stomatal conductance), soil moisture, and vapor pressure deficit. ESI performed better than SPEI in capturing the dynamics of GPP and G s , but still missed early ecological drought signals due to biases linked to earlier onset of spring leaf development. Thus, we developed a modified variant of the ESI (ESI LAI ) that accounts for the complicating effects of phenological shifts in leaf area index (LAI). The ESI LAI detected drought onset up to 7–10 weeks earlier than SPEI and ESI. Additionally, drought onset dates determined from ESI LAI are close to (±2 weeks) the dates determined from LAI-corrected anomalies of G s , and GPP, as well as the onset dates of soil water deficit and atmospheric aridity.

54 ENVIRONMENTAL SCIENCES↗

Transformation and gene editing in the bioenergy grass Miscanthus

Miscanthus, a C4 member of Poaceae, is a promising perennial crop for bioenergy, renewable bioproducts, and carbon sequestration. Species of interest include nothospecies M. x giganteus and its parental species M. sacchariflorus and M. sinensis. Use of biotechnology-based procedures to genetically improve Miscanthus, to date, have only included plant transformation procedures for introduction of exogenous genes into the host genome at random, non-targeted sites. We developed gene editing procedures for Miscanthus using CRISPR/Cas9 that enabled the mutation of a specific (targeted) endogenous gene to knock out its function. Classified as paleo-allopolyploids (duplicated ancient Sorghum-like DNA plus chromosome fusion event), design of guide RNAs (gRNAs) for Miscanthus needed to target both homeologs and their alleles to account for functional redundancy. Prior research in Zea mays demonstrated that editing the lemon white1 (lw1) gene, involved in chlorophyll and carotenoid biosynthesis, via CRISPR/Cas9 yielded pale green/yellow, striped or white leaf phenotypes making lw1 a promising target for visual confirmation of editing in other species. Using sequence information from both Miscanthus and sorghum, orthologs of maize lw1 were identified; a multi-step screening approach was used to select three gRNAs that could target homeologs of lw1. Embryogenic calli of M. sacchariflorus, M. sinensis and M. x giganteus were transformed via particle bombardment (biolistics) or Agrobacterium tumefaciens introducing the Cas9 gene and three gRNAs to edit lw1. Leaves on edited Miscanthus plants displayed the same phenotypes noted in maize. Sanger sequencing confirmed editing; deletions in lw1 ranged from 1 to 26 bp in length, and one deletion (433 bp) encompassed two target sites. Confocal microscopy verified lack of autofluorescence (chlorophyll) in edited leaves/sectors. We developed procedures for gene editing via CRISPR/Cas9 in Miscanthus and, to the best of our knowledge, are the first to do so. This included five genotypes representing three Miscanthus species. Designed gRNAs targeted all copies of lw1 (homeologous copies and their alleles); results also confirmed lw1 made a good editing target in species other than Z. mays. The ability to target specific loci to enable endogenous gene editing presents a new avenue for genetic improvement of this important biomass crop.

09 BIOMASS FUELS↗

Neotropical termite microbiomes as sources of novel plant cell wall degrading enzymes

In this study, we used shotgun metagenomic sequencing to characterise the microbial metabolic potential for lignocellulose transformation in the gut of two colonies of Argentine higher termite species with different feeding habits, Cortaritermes fulviceps and Nasutitermes aquilinus. Our goal was to assess the microbial community compositions and metabolic capacity, and to identify genes involved in lignocellulose degradation. Individuals from both termite species contained the same five dominant bacterial phyla (Spirochaetes, Firmicutes, Proteobacteria, Fibrobacteres and Bacteroidetes) although with different relative abundances. However, detected functional capacity varied, with C. fulviceps (a grass-wood-feeder) gut microbiome samples containing more genes related to amino acid metabolism, whereas N. aquilinus (a wood-feeder) gut microbiome samples were enriched in genes involved in carbohydrate metabolism and cellulose degradation. The C. fulviceps gut microbiome was enriched specifically in genes coding for debranching- and oligosaccharide-degrading enzymes. These findings suggest an association between the primary food source and the predicted categories of the enzymes present in the gut microbiomes of each species. To further investigate the termite microbiomes as sources of biotechnologically relevant glycosyl hydrolases, a putative GH10 endo-β-1,4-xylanase, Xyl10E, was cloned and expressed in Escherichia coli. Functional analysis of the recombinant metagenome-derived enzyme showed high specificity towards beechwood xylan (288.1 IU/mg), with the optimum activity at 50 °C and a pH-activity range from 5 to 10. These characteristics suggest that Xy110E may be a promising candidate for further development in lignocellulose deconstruction applications.

59 BASIC BIOLOGICAL SCIENCES↗

Research and development of hydrogen carrier based solutions for hydrogen compression and storage

Industrial and public interest in hydrogen technologies has risen strongly recently, as hydrogen is the ideal means for medium to long term energy storage, transport and usage in combination with renewable and green energy supply. In a future energy system, the production, storage and usage of green hydrogen is a key technology. Hydrogen is and will in future be even more used for industrial production processes as a reduction agent or for the production of synthetic hydrocarbons, especially in the chemical industry and in refineries. Under certain conditions material based systems for hydrogen storage and compression offer advantages over the classical systems based on gaseous or liquid hydrogen. This includes in particular lower maintenance costs, higher reliability and safety. Hydrogen storage is possible at pressures and temperatures much closer to ambient conditions. Hydrogen compression is possible without any moving parts and only by using waste heat. In this paper, we summarize the newest developments of hydrogen carriers for storage and compression and in addition, give an overview of the different research activities in this field.

08 HYDROGEN↗

Forecasting Marine Sediment Properties with Geospatial Machine Learning

Using a combination of geospatial machine learning prediction and sediment thermodynamic/physical modeling, we have developed a novel software workflow to create probabilistic maps of geoacoustic and geomechanical sediment properties of the global seabed. This new technique for producing reliable estimates of seafloor properties can better support Naval operations relying on sonar performance and seabed strength, can constrain models of shallow tomographic structure important for nuclear treaty compliance monitoring/detection, and can provide constraints on the distribution and inventory of shallow methane gas and gas hydrate accumulations on the continental shelves.

58 GEOSCIENCES↗

The Austin Chalk/Eagle Ford Field Laboratory (ACEFFL)

This project, led by Texas A&M University, developed a science-based field laboratory in the Austin Chalk/Eagle Ford Shale Formation to determine the stimulated reservoir volume created by the fracturing of multiple wells. Utilizing newly developed monitoring solutions, the team delivered comprehensive high-quality field data on the extent and morphologies of productive fractures created from these wells. Advanced field monitoring was complemented by laboratory testing on cores and drill cuttings, and coupled modeling for design, prediction, calibration, and code validation. The Austin Chalk/Eagle Ford Field Laboratory (ACEFFL) was hosted by SM Energy, which provided access to the wells of opportunity.

02 PETROLEUM↗

Enhancing the EVI-X National Framework to Address Emerging Questions on Charging Infrastructure Deployment

As national investments in EV charging infrastructure accelerate, this project advances the state-of-the-art in infrastructure analysis to better inform deployment strategies. It enhances NLR's EVI-X Suite, a set of tools supporting national network planning, local site design, and financial evaluation. These capabilities will position VTO to provide timely analysis to the DOT/DOE Joint Office, and to guide the strategic buildout of the national charging network. EVI-X development is closely coordinated with other VTO-funded efforts to ensure consistent, integrated use of key inputs and outputs, including EV adoption scenarios from TEMPO and infrastructure designs developed through EVs@Scale.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Growth and biochemical composition of the carrageenophyte Eucheumatopsis isiformis (Solieriaceae, Rhodophyta) under cultivation at different irradiance levels

Long-term production of a few species of Eucheuma and Kappaphycus from the Indo-Pacific Ocean supports the global carrageenan industry. The widespread use of vegetative propagation has resulted in low genetic diversity among farmed populations, making these crops increasingly vulnerable to diseases and environmental stressors, and resulting in declining yields and reduced biomass production over time. Insufficient efforts to develop and select new native cultivars, combined with the ecological risks posed by introducing nonindigenous species, underscore the urgent need to enhance cultivar diversification in eucheumatoid farming. Eucheumatopsis isiformis , a native carrageenophyte to the Atlantic Ocean, has potential for its cultivation in the Yucatán peninsula, Mexico. This study evaluated the growth and biochemical composition (pigments, elemental C and N, kappa/iota carrageenan ratio) of E. isiformis under different irradiance conditions in an indoor cultivation system. Specimens were collected in a subtidal population in Yucatán, Mexico, characterized, acclimatized to laboratory conditions, and exposed to five irradiance levels (71 ± 10.59 –1014 ± 65.85 µmol quanta m −2 s −1 ; 23.4 °C, salinity 33–34). Growth was measured weekly for six weeks, and elemental C and N content, pigment composition, and the kappa/iota-carrageenan ratio were evaluated. Growth and chromatic photoacclimation to light conditions were observed in all treatments. Highest growth rates (3.1–3.2% day −1 ) were registered between 238 ± 28.3 – 518 ± 44.3 µmol quanta m −2 s −1 , with a predominant iota-type carrageenan (0.97 ± 0.02) observed in all treatments. This study aims to provide guidelines for the successful development of the aquaculture of this carrageenophyte.

FTIR↗

Resilient, untethered soft robot

A pneumatically powered, fully untethered mobile soft robot is described. Composites consisting of silicone elastomer, polyaramid fabric, and hollow glass microspheres were used to fabricate a sufficiently large soft robot to carry the miniature air compressors, battery, valves, and controller needed for autonomous operation. Fabrication techniques were developed to mold a 0.65 meter long soft body with modified Pneumatic network actuators capable of operating at the elevated pressures (up to 138 kPa) required to actuate the legs of the robot and hold payloads of up to 8 kg. The soft robot is safe to handle, and its silicone body is innately resilient to a variety of adverse environmental conditions including snow, puddles of water, direct (albeit limited) exposure to flames, and the crushing force of being run over by an automobile.

42 ENGINEERING↗

Storage-Induced Collapse of Lignin Macromolecular Structure and Its Impacts on the Biorefinery

Lignin plays a vital role in the economics of biorefineries, serving as a source of process energy and a feedstock for sustainable fuels and chemical production. While understanding lignin’s chemical composition is crucial, emerging evidence suggests that a more comprehensive understanding of its macromolecular structure is critical to explaining its complex behavior in the biorefinery. This study investigated the partial collapse of the lignin network in corn stover feedstock after harvest and storage as a result of the microbial digestion of hemicellulose. Fluorescence microscopy was used to detect the collapse of lignin in terms of lignin’s inter-molecular interaction and the re-orientation of lignin’s chromophores, by the changes in lignin’s fluorescence lifetime, anisotropy, and the number of effective emitters. With minimal sample perturbation, our in-situ microscopic results revealed lignin's coil-globule transition phenomena, which was only previously predicted by molecular dynamics modeling extracted lignin in solvent. This collapse of lignin macromolecular structure was confirmed by results from NMR, IR, Raman, and powder X-ray diffraction. We also investigated the impact of this storage-induced collapse on the downstream biorefinery processes. Our study revealed that the two major approaches for lignin valorization in the lignin-first biorefinery model, namely monomer extraction and milled wood lignin extraction, were negatively impacted by the lignin collapse. As changes during storage are a source of feedstock variability, our study highlights the importance of understanding the effect of feedstock handling on biorefinery operations and economics.

09 BIOMASS FUELS↗

The Gene Ontology knowledgebase in 2026

Abstract The Gene Ontology (GO) knowledgebase (https://geneontology.org) is a comprehensive resource describing the functions of genes. The GO knowledgebase is regularly updated and improved. We describe here the major updates that have been made in the past 3 years. The ontology and annotations have been expanded and revised, particularly in several areas of biology: cellular metabolism, multi-organism interactions (e.g. host-pathogen), extracellular matrix proteins, chromatin remodeling (e.g. the “histone code”), and noncoding RNA functions. We have released version 2 of a comprehensive set of integrated, reviewed annotations for human genes, which we call the “functionome.” We have also dramatically increased the number of GO-CAM models, with over 1500 models of metabolic and signaling pathways, primarily in human, mouse, budding and fission yeast, and fruit fly. Finally, we discuss our current recommendations and future prospects of AI in the use and development of GO.

Aleksander, Suzi A (ORCID:0000000167872901)↗

Source-Resolved Inversion of Elemental Carbon Emissions in California Using Log-Space Bayesian Inference

Elemental carbon (EC), operationally quantified by thermal-optical analysis, is widely used as a proxy for black carbon (BC) relevant to short-term climate forcing and public health. Current EC emission inventories remain highly uncertain, with persistent discrepancies between bottom-up and top-down estimates. In this study, we develop a source-resolved, log-space Bayesian inversion framework applied to estimate California’s statewide EC emissions in 2019. By integrating surface EC measurements from the EPA’s Air Quality System network with high-resolution source contributions simulated by a chemical transport model, we identify a one-third underestimation in the existing statewide EC inventory, requiring an increase of the total from a prior of 8.58 [5.49–13.75] Gg year–1 to a posterior estimate of 12.78 [10.71–15.37] Gg year–1. This discrepancy is primarily driven by substantial underestimations in the power and industrial and off-road mobile sectors. Furthermore, population-weighted exposure analysis reveals a marked sectoral divergence between emission mass and health burden: off-road mobile sources dominate both emissions and exposure, accounting for 31% of statewide exposure, while residential wood combustion contributes 26% of total exposure despite comprising only 19% of total emissions, due to its source proximity to population. These findings underscore the need to update sector-specific EC speciation profiles and demonstrate that mitigation strategies targeting off-road mobile sources and residential wood combustion are critical for reducing EC-related health impacts in California.

Zhang, Jie↗

From minimum-viable-products to full models: a step-wise development of diagnostic forward models in support of design, analysis and modelling on the ST40 tokamak

Like most magnetic confined fusion experiments, the ST40 tokamak started off with a small subset of diagnostics and gradually increased the diagnostic set to include more complex and comprehensive systems. To make the most of each operational phase, forward models of various diagnostics are used and developed to aid design, provide consistency-checks during commissioning, test analysis methods, and build workflows to constrain high-level parameters to inform interpretation, theory and modelling. For new models and new analysis workflows, minimum-viable-products are released early, and their complexity is increased in a step-wise manner, facilitating the support of all programme phases on multiple parallel applications, while enabling learning opportunities and feedback loops. In this contribution we review the philosophy, scope and architecture of the framework under development. We discuss the details of some forward models, with examples on how they are used to aid diagnostic design, to investigate analysis methodologies through synthetic data, and how they are embedded in experimental analysis workflows. We compare previously published experimental results with new, more advanced analysis workflows employing more recent, detailed models and new diagnostic data, providing confirmation of the published material from the 2021–22 experimental campaign.

integrated data analysis↗

The Circular Home: Development and Demonstration of a Net Negative Carbon, Reusable Residence

This project started the development of an innovative modular building system intended for residential construction. The project was centered around single-family homes that were carbon-negative cradle-to-grave over a 100 year time frame, which is approximately double the current standard for operational life. The project sought to accomplish this objective by designing the modular home in a manner that ensures circularity, where the main house components can be used over several consecutive 50-year lifespans. To accomplish these objectives, this project utilized integrated design with the inclusion of life-cycle assessment to design the single-family house for architectural, structural, energy, mechanical, thermal, and moisture demands, while ensuring carbon negativity and annual net-zero energy use. The core technology of this project was the use of cross-laminated timber and biogenic materials, such as wood-fiber insulation, in the construction of the modular building units. The robustness and factory manufacturing ability of cross-laminated timber allow for factory construction of most of the home, which minimizes on-site time, saving money and reducing construction waste. During this project, initial milestones were met that delivered the architectural plans for the circular home and an initial structural testing matrix. Compared to current code-built homes, which average 13 kg CO2eq. / ft2 and are demolished at their end of life, the circular home has an estimated -30 kg CO2eq. / ft2 of embodied carbon emissions during its first build iteration. It is estimated that approximately 60%-70% of the total building mass could be reused and/or recycled during subsequent rebuilds. This project was concluded at approximately the 1/3 point and a separate project was established to conclude the remaining milestones. This project promises to benefit the public by delivering another option for single-family, and eventually multi-family, housing using a novel building construction system. The system of reusable modular construction facilitates not only lower emissions during the first building iteration, but also lower emissions during subsequent iterations that drastically reduce waste and help society meet its climate goals. Many other industries, such as clothing and technology sectors, are starting to focus on circularity and this project adds the residential building construction industry to that list.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Coastal Acoustic Buoy for Offshore Wind: Project Synthesis

The population of North Atlantic right whales is critically endangered and their habitat overlaps with offshore windfarm leases. It is therefore imperative that effective mitigation strategies be used to avoid impacts on right whales during the construction of offshore windfarms. The Department of Energy issued FOA Number DE-FOA-0001924 to encourage the development of technology that could monitor large exclusion zones for right whales in order to mitigate potential impact of construction noise on right whales. This report summarizes the past two years of the development and evaluation of the Coastal Acoustic Buoy for Offshore Wind (CABOW) project which aimed to develop technology to monitor large exclusion zones for North Atlantic right whales. Over the course of the project SMRU Consulting have implemented a rigorous design process including comparison of different approaches (e.g., single sensor vs multiple sensors), as well as consideration of placement and timing of acoustic monitoring. We have evaluated critical components of the CABOW system including, reliability, detection range, and bearing accuracy in areas adjacent to offshore windfarm leases in Maryland by conducting 3,536 playbacks of simulated right whale upcalls. The maximum call detection range was 7.5 km when noise was 99 dB re 1µPa rms (50-225 Hz), but this reduced to < 1 km when ambient noise levels were high. Our detection probability in the field was measured as a function of range as well as the source-to-noise level ratio allowing us to build a model to predict the probability of detection under various scenarios (sample size: 3,536 calls x 5 buoys = 17,680). The median bearing error was -0.25° but this is likely an underestimate of error due to experimental design. Using the published recall and precision of the two detectors we implemented in the CABOW system, we estimate that at a recall of 80%, our precision was > 80%, within the range of what we were aiming for in this project. To estimate our exclusion zone false negative and false positive rates, we built a simulation model using the empirical data from our field trial. We modelled three to nine CABOW units placed on the 10 km exclusion zone and estimated our false negative rate to be 1% or less (which was our project goal) and our false positive rate to be between seven and nine percent, slightly above our goal of 5%. However, we also modelled an equivalent PAM system that does not have bearing capabilities and found the false positive rates for that system to be six to eight times higher than the CABOW rate. This higher false positive rate of PAM systems with low spatial information could have significant cost repercussions for offshore wind developers by adding work shutdowns or delays without providing additional protection for right whales. The model we built allows us to explore the placement of PAM systems under various scenarios and will thus help facilitate planning of PAM mitigation systems to meet NOAA Incidental Harassment Authorizations for specific windfarms. We achieved an average system uptime of 98.3%, just below our goal of 99%. The issues that caused these short losses of data have been identified and fixed. Right whale detections and audio clips were typically transferred via radio from the buoys to the base station in two to four seconds. We therefore believe we have developed a highly robust real-time PAM system. Based on the above, we feel we have achieved the stated funding goal of developing a cost-effective and robust real-time PAM system that enables the monitoring of large exclusion zones for right whales during the constructions of offshore windfarms. This should lead to decreased costs and risks for the offshore wind sector while providing robust mitigation for right whales. It is important to state that PAM mitigation will need to be implemented with other mitigation strategies (e.g., visual observers) to provide a complete mitigation strategy to ensure that any effects on right whales from offshore windfarm construction is minimized.

17 WIND ENERGY↗