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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Supranutrition of microalgal docosahexaenoic acid and calcidiol improved growth performance, tissue lipid profiles, and tibia characteristics of broiler chickens

Abstract Background Docosahexaenoic acid (DHA) and calcidiol could be enriched in chicken for improving public nutrition and health. It remains unclear if supranutritional levels of DHA and calcidiol impair growth performance or metabolism of broiler chickens. This study was to determine singular and combined effects of high levels of supplemental DHA-rich microalgal biomass or oil and calcidiol on growth performance, concentrations of triglycerides, cholesterol, and nonesterfied fatty acids in plasma, liver, breast, and thigh, and biophysical properties of tibia. Methods In Exp. 1, 144 day-old Cornish chicks were divided into 4 groups (6 cages/treatment, 6 birds/cage), and were fed a corn-soybean meal basal diet (BD), BD + 10,000 IU calcidiol/kg (BD + Cal), BD + 1% DHA-rich Aurantiochytrium (1.2 g DHA/kg; BD + DHA), and BD + Cal + DHA for 6 weeks. In Exp. 2, 180 day-old chicks were divided into 5 groups, and were fed: BD, BD + DHA (0.33% to 0.66% oil, 1.5 to 3.0 g DHA/kg), BD + DHA + EPA (1.9% to 3.8% eicosapentaenoic acid-rich Nannochloropsis sp. CO18, 0.3 to 0.6 g EPA/kg), BD + DHA + calcidiol (6000 to 12,000 IU/kg diet), and BD + DHA + EPA + Cal for 6 weeks. Results Birds fed BD + Cal diet in Exp. 1 and BD + DHA + EPA diet in Exp. 2 had higher ( P < 0.05) body weight gain (10%–11%) and gain:feed ratio (7%), and lower ( P < 0.05) total cholesterol and triglyceride concentrations in plasma (18%–54%), liver (8%–26%), breast (19%–26%), and thigh (10%–19%), respectively, over the controls. The two diets also improved ( P < 0.05) tibial breaking strength (8%–24%), total bone volume (2%–13%), and (or) bone mineral density (3%–19%) of chickens. Conclusion Supranutrition of dietary calcidiol and DHA alone or together did not produce adverse effects, but led to moderate improvements of growth performance, lipid profiles of plasma and muscle, and bone properties of broiler chickens.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Quantitative differentiation of benign and misfolded glaucoma-causing myocilin variants on the basis of protein thermal stability

Accurate predictions of the pathogenicity of mutations associated with genetic diseases are key to the success of precision medicine. Inherited missense mutations in the myocilin (MYOC) gene, within its olfactomedin (OLF) domain, constitute the strongest genetic link to primary open-angle glaucoma via a toxic gain of function, and thus MYOC is an attractive precision-medicine target. However, not all mutations in MYOC cause glaucoma, and common variants are expected to be neutral polymorphisms. The Genome Aggregation Database (gnomAD) lists ~100 missense variants documented within OLF, all of which are relatively rare (allele frequency <0.001%) and nearly all are of unknown pathogenicity. To distinguish disease-causing OLF variants from benign OLF variants, we first characterized the most prevalent population-based variants using a suite of cellular and biophysical assays, and identified two variants with features of aggregation-prone familial disease variants. Next, we considered all available biochemical and clinical data to demonstrate that pathogenic and benign variants can be differentiated statistically based on a single metric: the thermal stability of OLF. Our results motivate genotyping MYOC in patients for clinical monitoring of this widespread, painless and irreversible ocular disease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Simulated Land Allocation, Nitrogen Use, and Nitrogen Loss in the Mississippi Atchafalaya River Basin for Various RFS2 (Renewable Fuel Standard) Policy Scenarios

Total nitrogen leaching rates were calculated over the Mississippi Atchafalaya River Basin (MARB) using an integrated economic-biophysical modeling approach. Land allocation for corn production and total nitrogen application rates were calculated for crop reporting districts using the Biofuel and Environmental Policy Analysis Model (BEPAM) for 5 RFS2 policy scenarios. These were used as input in the Integrated BIosphere Simulator-Agricultural Version (Agro-IBIS) and the Terrestrial Hydrologic Model with Biogeochemistry (THMB) to calculate the nitrogen loss. Land allocation and total nitrogen application simulations were simulated for the period 2016-2030 for 303 crop reporting districts (https://www.nass.usda.gov/Data_and_Statistics/County_Data_Files/Frequently_Asked_Questions/county_list.txt). The final 2030 values are reported here. Both are stored in csv files. Units for land allocation are million ha and nitrogen application are million kg. The nitrogen leaching rates were modeled with a spatial resolution of 5' x 5' using the North American Datum of 1983 projection and stored in NetCDF files. The 30-year average is calculated over the last 30 years of the 45 years being simulated. Leaching rates are calculated in kg-N/ha.

bioenergy crops↗
DOE OSTI2023

Data for Climate vs Energy Security: Quantifying the Trade-offs of BECCS Deployment and Overcoming Opportunity Costs on Set-Aside Land

Bioenergy with carbon capture and storage (BECCS) sits at the nexus of the climate and energy security. We evaluated trade-offs between scenarios that support climate stabilization (negative emissions and net climate benefit) or energy security (ethanol production). Our spatially explicit model indicates that the foregone climate benefit from abandoned cropland (opportunity cost) increased carbon emissions per unit of energy produced by 14–36%, making geologic carbon capture and storage necessary to achieve negative emissions from any given energy crop. The toll of opportunity costs on the climate benefit of BECCS from set-aside land was offset through the spatial allocation of crops based on their individual biophysical constraints. Dedicated energy crops consistently outperformed mixed grasslands. We estimate that BECCS allocation to land enrolled in the Conservation Reserve Program (CRP) could capture up to 9 Tg C year–1 from the atmosphere, deliver up to 16 Tg CE year–1 in emissions savings, and meet up to 10% of the US energy statutory targets, but contributions varied substantially as the priority shifted from climate stabilization to energy provision. Our results indicate a significant potential to integrate energy security targets into sustainable pathways to climate stabilization but underpin the trade-offs of divergent policy-driven agendas.

Field Data↗
DOE OSTI2021

Visualizing bleb mass dynamics in single cells using quantitative phase microscopy

Understanding biological responses to directed energy (DE) is critical to ensure the safety of personnel within the Department of Defense. At the Air Force Research Laboratory, we have developed or adapted advanced optical imaging systems that quantify biophysical responses to DE. One notable cellular response to DE exposure is the formation of blebs, or semi-spherical protrusions of the plasma membrane in living cells. In this work, we demonstrate the capacity of quantitative phase imaging (QPI) to both visualize and quantify the formation of membrane blebs following DE exposure. QPI is an interferometric imaging tool that uses optical path length as a label-free contrast mechanism and is sensitive to the non-aqueous mass density, or dry mass, of living cells. Blebs from both CHO-K1 and U937 cells were generated after exposure to a series of 600 ns, 21.2 kV/cm electric pulses. These blebs were visualized in real time, and their dry mass relative to the rest of the cell body was quantified as a function of time. It is our hope that this system will lead to an improved understanding of both DE-induced and apoptotic blebbing.

Steelman, Zachary A.↗
DOE OSTI2021

OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM’s Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM’s Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen’s early Nobel prize winning experiments by using OpenMM’s Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Characterizing inhibitors of human AP endonuclease 1

AP endonuclease 1 (APE1) processes DNA lesions including apurinic/apyrimidinic sites and 3´-blocking groups, mediating base excision repair and single strand break repair. Much effort has focused on developing specific inhibitors of APE1, which could have important applications in basic research and potentially lead to clinical anticancer agents. We used structural, biophysical, and biochemical methods to characterize several reported inhibitors, including 7-nitroindole-2-carboxylic acid (CRT0044876), given its small size, reported potency, and widespread use for studying APE1. Intriguingly, NMR chemical shift perturbation (CSP) experiments show that CRT0044876 and three similar indole-2-carboxylic acids bind a pocket distal from the APE1 active site. A crystal structure confirms these findings and defines the pose for 5-nitroindole-2-carboxylic acid. However, dynamic light scattering experiments show the indole compounds form colloidal aggregates that could bind (sequester) APE1, causing nonspecific inhibition. Endonuclease assays show the compounds lack significant APE1 inhibition under conditions (detergent) that disrupt aggregation. Thus, binding of the indole-2-carboxylic acids at the remote pocket does not inhibit APE1 repair activity. Myricetin also forms aggregates and lacks APE1 inhibition under aggregate-disrupting conditions. Two other reported compounds (MLS000552981, MLS000419194) inhibit APE1 in vitro with low micromolar IC50 and do not appear to aggregate in this concentration range. However, NMR CSP experiments indicate the compounds do not bind specifically to apo- or Mg 2+ -bound APE1, pointing to a non-specific mode of inhibition, possibly DNA binding. Our results highlight methods for rigorous interrogation of putative APE1 inhibitors and should facilitate future efforts to discover compounds that specifically inhibit this important repair enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Pressurized DNA state inside herpes capsids—A novel antiviral target

Drug resistance in viruses represents one of the major challenges of healthcare. As part of an effort to provide a treatment that avoids the possibility of drug resistance, we discovered a novel mechanism of action (MOA) and specific compounds to treat all nine human herpesviruses and animal herpesviruses. The novel MOA targets the pressurized genome state in a viral capsid, “turns off” capsid pressure, and blocks viral genome ejection into a cell nucleus, preventing viral replication. This work serves as a proof-of-concept to demonstrate the feasibility of a new antiviral target—suppressing pressure-driven viral genome ejection —that is likely impervious to developing drug resistance. This pivotal finding presents a platform for discovery of a new class of broad-spectrum treatments for herpesviruses and other viral infections with genome-pressure-dependent replication. A biophysical approach to antiviral treatment such as this is also a vital strategy to prevent the spread of emerging viruses where vaccine development is challenged by high mutation rates or other evasion mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Engineering well-expressed, V2-immunofocusing HIV-1 envelope glycoprotein membrane trimers for use in heterologous prime-boost vaccine regimens

HIV-1 vaccine immunofocusing strategies may be able to induce broadly-reactive neutralizing antibodies (NAbs). Here, we engineered a panel of diverse, membrane-resident native HIV-1 trimers vulnerable to two broad targets—the V2 apex and fusion peptide (FP). Selection criteria included i) high expression and ii) infectious function, so that trimer neutralization sensitivity can be profiled in pseudovirus (PV) assays. Initially, we boosted the expression of 17 candidate trimers by truncating gp41 and introducing a gp120-gp41 SOS disulfide to prevent gp120 shedding. "Repairs" were made to fill glycan holes and eliminate other strain-specific aberrations. A new neutralization assay allowed PV infection when our standard assay was insufficient. Trimers with exposed V3 loops, a target of non-NAbs, were discarded. To try to increase V2-sensitivity, we removed clashing glycans and modified the C-strand. Notably, a D167N mutation improved V2-sensitivity in several cases. Glycopeptide analysis of JR-FL trimers revealed near complete sequon occupation and that filling the N197 glycan hole was well-tolerated. In contrast, sequon optimization and inserting/removing glycans at other positions frequently had global "ripple" effects on glycan maturation and sequon occupation throughout the gp120 outer domain and gp41. V2 MAb CH01 selectively bound to trimers with small high mannose glycans near the base of the V1 loop, thereby avoiding clashes. Knocking in a rare N49 glycan was found to perturb gp41 glycans, increasing FP NAb sensitivity—and sometimes improving expression. Finally, a biophysical analysis of VLPs revealed that i) ~25% of particles bear Env spikes, ii) spontaneous particle budding is high and only increases 4-fold upon Gag transfection, and iii) Env+ particles express ~30–40 spikes. Taken together, we identified 7 diverse trimers with a range of sensitivities to two targets to allow rigorous testing of immunofocusing vaccine concepts.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

High-density binding to Plasmodium falciparum circumsporozoite protein repeats by inhibitory antibody elicited in mouse with human immunoglobulin repertoire

Antibodies targeting the human malaria parasite Plasmodium falciparum circumsporozoite protein (PfCSP) can prevent infection and disease. PfCSP contains multiple central repeating NANP motifs; some of the most potent anti-infective antibodies against malaria bind to these repeats. Multiple antibodies can bind the repeating epitopes concurrently by engaging into homotypic Fab-Fab interactions, which results in the ordering of the otherwise largely disordered central repeat into a spiral. Here, we characterize IGHV3-33/IGKV1-5-encoded monoclonal antibody (mAb) 850 elicited by immunization of transgenic mice with human immunoglobulin loci. mAb 850 binds repeating NANP motifs with picomolar affinity, potently inhibits Plasmodium falciparum (Pf) in vitro and, when passively administered in a mouse challenge model, reduces liver burden to a similar extent as some of the most potent anti-PfCSP mAbs yet described. Like other IGHV3-33/IGKV1-5-encoded anti-NANP antibodies, mAb 850 primarily utilizes its HCDR3 and germline-encoded aromatic residues to recognize its core NANP motif. Biophysical and cryo-electron microscopy analyses reveal that up to 19 copies of Fab 850 can bind the PfCSP repeat simultaneously, and extensive homotypic interactions are observed between densely-packed PfCSP-bound Fabs to indirectly improve affinity to the antigen. Together, our study expands on the molecular understanding of repeat-induced homotypic interactions in the B cell response against PfCSP for potently protective mAbs against Pf infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structures of SARS-CoV-2 N7-methyltransferase with DOT1L and PRMT7 inhibitors provide a platform for new antivirals

The RNA N7-methyltransferase (MTase) activity of SARS-CoV-2’s nsp14 protein is essential for viral replication and is a target for the development of new antivirals. Nsp14 uses S-adenosyl methionine (SAM) as the methyl donor to cap the 5’ end of the SARS-CoV-2 mRNA and generates S-adenosyl homocysteine (SAH) as the reaction byproduct. Due to the central role of histone MTases in cancer, many SAM/SAH analogs with properties of cell permeability have recently been developed for the inhibition of these MTases. We have succeeded in identifying two such compounds (SGC0946 and SGC8158) that display significant antiviral activity and bind to the SARS-CoV-2 nsp14 N7-MTase core. Unexpectedly, crystal structures of SGC0946 and SGC8158 with the SARS-CoV-2 nsp14 N7-MTase core identify them as bi-substrate inhibitors of the viral MTase, co-occupying both the SAM and RNA binding sites; positing novel features that can be derivatized for increased potency and selectivity for SARS-CoV-2 nsp14. Taken together, the high-resolution structures and the accompanying biophysical and viral replication data provide a new avenue for developing analogs of SGC0946 and SGC8158 as antivirals.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

The genotype-phenotype landscape of an allosteric protein

Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype-phenotype relationships remains elusive. Here, we report the large-scale measurement of the genotype-phenotype landscape for an allosteric protein: the lac repressor from Escherichia coli , LacI. Using a method that combines long-read and short-read DNA sequencing, we quantitatively measure the dose-response curves for nearly 10 5 variants of the LacI genetic sensor. The resulting data provide a quantitative map of the effect of amino acid substitutions on LacI allostery and reveal systematic sequence-structure-function relationships. We find that in many cases, allosteric phenotypes can be quantitatively predicted with additive or neural-network models, but unpredictable changes also occur. For example, we were surprised to discover a new band-stop phenotype that challenges conventional models of allostery and that emerges from combinations of nearly silent amino acid substitutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Data and scripts associated with the manuscript evaluating the hydrologic responses of the Pacific Northwest watersheds to wildfires (v2)

This data package is associated with the publication “Evaluating Post-fire Watershed Response to Varying Burn Severity and Precipitation Regimes Using Fully-distributed and Integrated Hydrologic Models” submitted to Journal of Hydrology (Li et al. 2025). In this study, we employed the Advanced Terrestrial Simulator (ATS), an integrated watershed model that couples surface flow, subsurface flow, and canopy biophysical processes, to investigate post-fire hydrologic responses in a few selected watersheds with varying burn severity.The data package contains the required input data (meteorological forcing, Leaf Area Index, wildfire burn severities, etc.) to run the model, configuration files, the Jupyter notebooks in Python to pre-process and post-process data, the figures in the manuscript, and the modeling output files. The variables include watershed-averaged evapotranspiration, watershed-averaged surface/subsurface/canopy water content, and river discharge at watershed outlet.The data package contains a file-level metadata that lists and describes all the files contained in the data package (ATS_flmd.csv), a data dictionary file that defines columns headers across all csv files contained in the data package (ATS_dd.csv), a data package level readme file (the current file), and four zipped folders.The ‘data’ folder provides data needed to run the model in .h5, .i2s, .xyz, .shp, and .exo formats. The sub-folders are for each data types. The ‘model’ folder provides input files (.xml format) and essential model outputs. Each sub-folder provides the files from each simulated watershed. The ‘notebooks’ folder provides the Jupyter notebooks (.ipynb format) for pre- and post- processing model files, and for producing the figures in the manuscript. The ‘figures’ folder provides the figures associated with manuscript in .pdf and .png formats.The ‘model’ folder and the ‘data’ folder have been split into 5GB-large pieces using the Linux command ‘split -b 5120m model.zip model.zip.’ and ‘split -b 5120m data.zip data.zip.’, respectively. They can be merged back using the Linux command ‘cat model.zip.* > model.zip’ and ‘cat data.zip.* > data.zip’, respectively.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Taking the Air Out of Respiratory Pandemics: An R&D Effort for Developing New, Far Less Disruptive and Frightening Protective Measures to Extinguish Airborne Pathogen Outbreaks

This short concept article discusses four specific ways to eradicate respiratory pandemics once and for all. These include: Protecting the nose, mouth, throat and lungs; New hygiene regimens; Clearing the air; and Biophysical interventions. Technical breakthoughs in all four of these areas would not only protect people from life-threatening pathogens, but also take the dread out of respiratory disease outbreaks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Reflectin: Protein Driver of Dynamically Tunable Biophotonics; New Paradigm for Tunably Reconfigurable Materials

We discovered that the reflectins, with architecture and sequences unlike those of any other proteins known, exhibit a novel interplay between signal-controlled nucleation and growth of dynamically arrested liquid-liquid phase-segregated assemblies that uniquely enables the continuous and precise fine-tuning of physical properties governing the color and brightness of light reflected from the membrane-enclosed nanostructures that contain them. Our research included high-resolution structural analyses conducted at the DOE-BES user facilities of the Stanford Synchrotron Light Source and LBL National Laboratory’s Molecular Foundry, leveraging their capabilities for time-resolved SAXS and cryo-TEM with our ongoing genetic engineering, biophysical and computational analyses to identify the structural determinants and mechanisms governing the dynamic behaviors of the reflectins. We augmented these methods with EPR analyses that revealed for the first time the existence of a specific pathway of reflectin assembly. Using dynamic light scattering and continuously monitored circular dichroism and Raman microscopy, we elucidated the progression of structural changes underlying the mechanisms of signal-induced condensation, folding, assembly, liquefaction, dynamic arrest, regulation and reversal.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Interdisciplinary Workshop on the Impacts of Land Use and Land Management on Earth System Evolution, Biogeochemical Cycles, Extremes, and Inter-Sectoral Dynamics (Final Report)

The Aspen Global Change Institute (AGCI) convened a week-long interdisciplinary science workshop from September 15-20, 2019 entitled, “Impacts of Land Use and Land Management on Earth System Evolution, Biogeochemical Cycles, Extremes, and Inter-Sectoral Dynamics.” The purpose of the workshop was to advance research on the impacts of land use and land management on climate, carbon emissions, and extremes, as well as the impact of land-use change on important societal issues such as food, water, and energy security. The workshop was co-chaired by Kate Calvin (PNNL), George Hurtt (University of Maryland), and Dave Lawrence (National Center for Atmospheric Research). Co-funders of the workshop included NASA, NOAA, and travel support for European colleagues through CRESCENDO. This workshop brought together 31 professionals with expertise across biogeochemistry, climate impacts, mitigation, land use datasets, and societal impacts to coordinate on upcoming research and publications on the role of biogeochemical and biophysical properties of the Earth surface and their implications for climate, as conducted through the Land Use model Intercomparison Project (LUMIP), which is part of Phase 6 of the Coupled Model Intercomparison Project (CMIP6). A primary outcome of the meeting was the definition and planning of a series of LUMIP papers that will rely on the LUMIP and CMIP6 simulations. By the end of the meeting more than twenty papers and paper lead authors had been identified and scoped out. Around ten of these papers were submitted by the December 31, 2019 IPCC deadline.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Semi-automated Design of Artificial Intelligence Earth Systems Models

Prediction and observation of water cycles at various scales involve not only patterns isolated in space and time, but also modeling of complex spatio-temporal relationships across multiple domains. For instance, evapotranspiration (ET) and leaf area indexes (LAI) are two parameters that are needed to accurately model and understand land-atmosphere processes. Accurate assessments of ET and LAI are critical for understanding hydrological processes, deforestation, crop yield, and irrigation impacts. However, ET estimates for global simulations are available at very coarse spatial resolution. They are usually derived from satellite data based on broad plant functional types (PFTs), which fail to capture fine-scale variations because of changes in vegetation type across the globe. Similarly LAI estimates have typically been derived from vegetation indices at global scales or estimated locally using physical models, both of which suffer from a range of uncertainties that impact model sensitivity. The new era of AI model development for Earth systems (ES) calls for data-driven methods that provide domain scientists with uncertainty-aware estimations of biophysical parameters such as ET and LAI in a generalizable, interpretable, and discoverable manner.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Light Energy Transduction in Green Sulfur Bacteria

Green sulfur bacteria (GSB) are exquisitely adapted for growth at extraordinarily low light intensities. They are important primary producers of biomass in many anoxic environments, and they contribute significantly to the biogeochemical cycling of carbon, nitrogen, and sulfur on Earth. Green bacteria more generally share the property of using chlorosomes for light-harvesting, and these unusual organelles have many unique features. These include the presence of a monolayer lipid-protein envelope, self-assembling bacteriochlorophylls (BChl) in which pigment-pigment interactions predominate, and the presence of redox components ([2Fe-2S] ferredoxins and quinones) that play a role in regulating excitation energy transfer to the type-1 homodimeric reaction centers. The reaction centers of GSB are related to Photosystem I of cyanobacteria and higher plants but also exhibit several unique structural and functional features. The long-term objectives of this research program are to understand the structure, functions, and biogenesis of the chlorosomes, reaction centers, and electron transport chains that carry out the photochemical transduction of light energy into chemical energy in the model green sulfur bacterium, Chlorobaculum (formerly Chlorobium) tepidum. Over a period of 26 years, we characterized chlorosomes in detail. We identified the proteins in the chlorosome envelopes of diverse organisms, identified the nearest neighbors of those proteins, and characterized the chlorosomes of mutant strains lacking one to five of these proteins. After the genome sequence of Cba. tepidum became available, we identified all genes encoding enzymes for BChl a , BChl c/d/e/ƒ , and Chl a biosynthesis Cba. tepidum . We additionally identified all genes encoding enzymes for carotenoid biosynthesis. By constructing a bchQRU mutant strain that produces [Et, Me]-BChl d , together with collaborators who are specialists in solid-state NMR and cryo-electron microscopy, we solved the structure of the BChls in chlorosomes. Using similar methods and chlorosomes containing [Et, Me]-BChl c , we then showed that alternative structures were possible using the same syn-anti BChl dimer. The structures were refined by introducing spectroscopic data from single-chlorosome measurements. Over the course of this project, we sequenced the genomes of approximately twenty GSB strains, which provided important information for comparative analyses. Through analyses of metagenomic data from Mushroom and Octopus Springs in Yellowstone National Park, we identified a novel chlorophototroph belonging to the phylum Acidobacteriota. We successfully isolated an axenic culture of this organism. We characterized the photosynthetic apparatus of this bacterium, named Chloracidobacterium thermophilum, in significant detail, in particular its type-1, homodimeric reaction centers. Surprisingly, these reaction centers contain three types of Chls, BChl a , Chl a , and Zn-BChl a' . We showed that a dimer of Zn-BChl a' is the primary donor and Chl a the primary acceptor of electrons in this reaction center by using advanced spectroscopic techniques. We isolated eight additional strains of Chloracidobacterium spp. from Mushroom Spring and Rupite hot springs in Bulgaria. Comparative genomes showed that these represent three species, Cab. thermophilum , Cab. aggregatum , and Cab. validum . By applying comparative genomics, genetic, biochemical biophysical and physiological approaches to study green bacteria, we produced a wealth of new information about the remarkable light-harvesting and energy transduction capabilities of these poorly characterized microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗