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At least 433 records · Page 24

Balancing Trade-Offs Imposed by Growth Media and Mass Spectrometry for Bacterial Exometabolomics

The bacterial exometabolome consists of a vast array of specialized metabolites, many of which are only produced in response to specific environmental stimuli. For this reason, it is desirable to control the extracellular environment with a defined growth medium composed of pure ingredients. However, complex (undefined) media are expected to support the robust growth of a greater variety of microorganisms than defined media. Here, we investigate the trade-offs inherent to a range of complex and defined solid media for the growth of soil microorganisms, production of specialized metabolites, and detection of these compounds using direct infusion mass spectrometry. We find that complex media support growth of more soil microorganisms, as well as allowing for the detection of more previously discovered natural products as a fraction of total m/z features detected in each sample. However, the use of complex media often caused mass spectrometer injection failures and poor-quality mass spectra, which in some cases resulted in over a quarter of samples being removed from analysis. Defined media, while more limiting in growth, generated higher quality spectra and yielded more m/z features after background subtraction. These results inform future exometabolomic experiments requiring a medium that supports the robust growth of many soil microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗

Data for Bioprocessing, Recovery, and Mass Balance of Vegetative Lipids from Metabolically Engineered ‘Oilcane’ Demonstrates Its Potential as an Alternative Feedstock for Drop-In Fuel Production

Plant oils are increasingly in demand as renewable feedstocks for biodiesel and biochemicals. Currently, oilseeds are the primary source of plant oils. Although the vegetative tissues of plants express lipid metabolism pathways, they do not hyper-accumulate lipids. Elevated synthesis, storage, and accumulation of lipids in vegetative tissues have been achieved by metabolic engineering of sugarcane to produce “oilcane.” This study evaluates the potential of oilcane as a renewable feedstock for the co-production of lipids and fermentable sugars. Oilcane was grown under favorable climatic and field conditions in Florida (FLOC) as well as during an abbreviated growing season, outside its typical growing region, in Illinois (ILOC). The potential lipid yield of 0.35 tons/ha was projected from the hyperaccumulation of fatty acids in the stored vegetative biomass of FLOC, which is approaching the lipid yield of soybean (0.44 tons/ha). Processing of the vegetative tissues of oilcane recovered 0.20 tons/ha, which represents the recovery of 55% of the total lipids from FLOC. Chemical-free hydrothermal bioprocessing of ILOC and FLOC bagasse and leaves at 180 °C for 10 min prevented the degeneration of in situ plant lipids. This allowed the recovery of lipids at the end of the bioprocess with a major fraction of lipids remaining in the biomass residues after pretreatment and saccharification. Improvements through refined biomass processing, crop management, and metabolic engineering are expected to boost lipid yields and make oilcane a prime feedstock for the production of biodiesel.

Conversion↗

Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds

The ammonia-oxidizing bacterium Nitrosomonas europaea has been widely recognized as an important player in the nitrogen cycle as well as one of the most abundant members in microbial communities for the treatment of industrial or sewage wastewater. Its natural metabolic versatility and extraordinary ability to degrade environmental pollutants (e.g., aromatic hydrocarbons such as benzene and toluene) enable it to thrive under various harsh environmental conditions. Constraint-based metabolic models constructed from genome sequences enable quantitative insight into the central and specialized metabolism within a target organism. These genome-scale models have been utilized to understand, optimize, and design new strategies for improved bioprocesses. Reduced modeling approaches have been used to elucidate Nitrosomonas europaea metabolism at a pathway level. However, genome-scale knowledge about the simultaneous oxidation of ammonia and pollutant metabolism of N . europaea remains limited. Here, we describe the reconstruction, manual curation, and validation of the genome-scale metabolic model for N . europaea , i GC535. This reconstruction is the most accurate metabolic model for a nitrifying organism to date, reaching an average prediction accuracy of over 90% under several growth conditions. The manually curated model can predict phenotypes under chemolithotrophic and chemolithoorganotrophic conditions while oxidating methane and wastewater pollutants. Calculated flux distributions under different trophic conditions show that several key pathways are affected by the type of carbon source available, including central carbon metabolism and energy production.

59 BASIC BIOLOGICAL SCIENCES↗

SARS-CoV-2 evolution balances conflicting roles of N protein phosphorylation

All lineages of SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic, contain mutations between amino acids 199 and 205 in the nucleocapsid (N) protein that are associated with increased infectivity. The effects of these mutations have been difficult to determine because N protein contributes to both viral replication and viral particle assembly during infection. Here, we used single-cycle infection and virus-like particle assays to show that N protein phosphorylation has opposing effects on viral assembly and genome replication. Ancestral SARS-CoV-2 N protein is densely phosphorylated, leading to higher levels of genome replication but 10-fold lower particle assembly compared to evolved variants with low N protein phosphorylation, such as Delta (N:R203M), Iota (N:S202R), and B.1.2 (N:P199L). A new open reading frame encoding a truncated N protein called N*, which occurs in the B.1.1 lineage and subsequent lineages of the Alpha, Gamma, and Omicron variants, supports high levels of both assembly and replication. Our findings help explain the enhanced fitness of viral variants of concern and a potential avenue for continued viral selection.

Microbiology↗

Diagonally implicit Runge–Kutta schemes: Discrete energy-balance laws and compactness properties

Abstract We study diagonally implicit Runge–Kutta (DIRK) schemes when applied to abstract evolution problems that fit into the Gelfand-triple framework. We introduce novel stability notions that are well-suited to this setting and provide simple, necessary and sufficient, conditions to verify that a DIRK scheme is stable in our sense and in Bochner-type norms. We use several popular DIRK schemes in order to illustrate cases that satisfy the required structural stability properties and cases that do not. In addition, under some mild structural conditions on the problem we can guarantee compactness of families of discrete solutions with respect to time discretization.

Mathematics↗

Dryland feedbacks to future climate change: how species mortality and replacement will affect coupled biogeochemical cycles and energy balance (Final Technical Report)

The overall goal of the dryland climate manipulation experiment is to improve our understanding and ability to forecast dryland responses to increasing temperatures and altered precipitation regimes. Drylands cover over 40% of Earth’s terrestrial surface and are predicted to increase in size 11-23% by 2100. Yet our understanding of this vast biome, which exchanges enormous amounts of CO 2 and energy with the atmosphere, is exceedingly poor. This project aims to transform and improve that understanding in order to reduce uncertainty and increase the confidence with which we can make global predictions of future climate. We focus on both above- and belowground processes, and explore temperature controls over critical aspects of carbon and nutrient cycling for dryland plants, soil, and microbes. We have 60 climate manipulation plots where plants (from above the canopy) and soils are warmed using infrared lamps and where precipitation has been altered using targeted watering regimes. We have measured myriad aspects of plant physiology, morphology, carbon exchange, energy exchange, and phenology, as well as analogous climate-induced changes to biological soil crusts and soil microbial communities. Our goals are to investigate temperature responses and acclimation potential of dryland plant and soil processes. Concurrent soil incubation experiments complement the in-situ soil warming component and enable more controlled mechanistic investigations of temperature response on microbial function. Automated soil CO 2 efflux chambers within the plots provide phenomenal opportunity to improve our understanding of dryland CO 2 exchange with the atmosphere and are coupled with plant CO 2 exchange measurements. The project has been exceptionally successful, with 35 peer-reviewed publications (and more in review), including in high-profile journals such as Nature Climate Change and PNAS. We have given over fifty presentations on the work and it has been featured in many high-profile media outlets, such as Discover Magazine and on NPR.

54 ENVIRONMENTAL SCIENCES↗

Europe’s energy policy based on large-scale use of renewables most likely will require supplemental power supplies to balance their electrical power systems

Political decisions toward an increased role for renewable energy sources (wind & solar) in Europe will have an impact on the functioning of the electrical power systems that will have to be offset due to the inherent intermittent nature of renewable sources. The offset can be accomplished either through increasing non-renewable energy supply and production from other means, including purchasing Russian piped natural gas and LNG, or decreasing demand by curtailing power consumption. Europe likely will also need increased energy supplies to cover reduced gas production in the North Sea and Netherlands. Also, expected disconnection of Baltic states from the BRELL (Belarus-Russia-EstoniaLatvia-Lithuania) grid will force these countries to acquire electricity from Europe, resulting in increased demands on the European power grid that will require additional capacity to offset.

24 POWER TRANSMISSION AND DISTRIBUTION↗

A Technical and Economic Assessment of LWR Flexible Operation for Generation and Demand Balancing to Optimize Plant Revenue

With increased penetration of subsidized variable renewable energy (VRE) resources and competition from low natural gas prices, existing light water reactor (LWR) nuclear power plants (NPPs) are struggling to remain economically competitive. This work examines the potential economic competitiveness of various thermal energy storage (TES) technologies when coupled directly or indirectly with a NPP. To highlight their relative economic competitiveness, we contrast several energy storage solutions in stochastic dispatch optimization. We leverage data from recent work analyzing a range of TES technologies with varying capital costs, performance, and technology readiness level (TRL) to establish our case. We explore inserting these technologies into an electricity market with existing nuclear generation and large projected variable renewable energy (VRE) penetration. Although these technologies' projected capital costs may make them unlikely candidates in their current state, this analysis demonstrates a high-fidelity techno-economic analysis of energy storage. Furthermore, as the projected cost of energy storage technologies evolves, this analysis sets a precedent for similar future investigations. One region with projected trends that may be unfavorable for existing nuclear capacity is the New York Independent System Operator (NYISO) market. New York state’s baseload generation has been historically provided by fossil-fired and nuclear assets. However, amid economic pressures from subsidized VREs and low natural gas prices, the state has recently deactivated Indian Point nuclear power plant units 2 and 3. Furthermore, the state plans to meet its zero-emission generation target by 2040 by replacing fossil-fired capacity with significant investments in VRE resources like wind and solar photovoltaic (PV) and battery storage. Increased intermittent resource penetration lowers the baseload power requirement, adding further economic pressure to the state’s three remaining NPPs still in operation. With three NPPs still in operation in New York, this work analyzes potential economic benefits to NPPs on the New York grid when directly or indirectly coupled with various TES technologies. This work requires two modeling steps to analyze the potential economic benefits of various system configurations of the TES directly or indirectly coupled with nuclear. First, this analysis leverages capacity expansion modeling by experts at the Electric Power Research Institute (EPRI). Using their deterministic capacity expansion model, U.S. Regional Economy, Greenhouse Gas, and Energy (US-REGEN), EPRI analysts evaluated the capacity and generation evolution of the New York state energy market under four projection scenarios. These four projection scenarios were developed to represent the potential evolution of the capacity and generation in NYISO from 2015 to 2050 under various economic, technology, and policy constraints. The results from these capacity expansion models are then used as boundary conditions in the second modeling step. The second modeling step uses the Holistic Energy Resource Optimization Network (HERON) for a set of stochastic techno-economic analyses (STEAs) to investigate the potential increase in the economic viability of various configurations of the TES. With no current capacity expansion capabilities, HERON takes the data generated from US-REGEN for 2050 to generate synthetic load, solar, and wind data. Then HERON economically optimizes the capacity and dispatch of the various TES configurations. The potential economic benefit is the differential net present value (NPV) of the TES configurations from the no-TES baseline. As a stochastic techno-economic analysis package, HERON introduces uncertainty into the economic metrics, while US-REGEN trades resolution for reduced computational complexity. Using HERON also allows the modeling of direct thermal coupling, a feature not common in capacity and dispatch models. As expected, with high capital costs, the costs of introducing energy storage for all the technologies considered outweighed the potential economic benefit of this strategy for flexible plant operation. The benefit of this analysis is primarily in demonstrating a workflow that examines innovative solutions to increase NPP revenue via TES coupling. HERON’s stochastic capacity and dispatch optimization process used in this work has proven an effective tool in observing and evaluating the impact of introducing storage technologies in a grid energy system.

25 ENERGY STORAGE↗