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NASA NTRS2014

Cofactors in the RNA World

RNA world theories figure prominently in many scenarios for the origin and early evolution of life. These theories posit that RNA molecules played a much larger role in ancient biology than they do now, acting both as the dominant biocatalysts and as the repository of genetic information. Many features of modern RNA biology are potential examples of molecular fossils from an RNA world, such as the pervasive involvement of nucleotides in coenzymes, the existence of natural aptamers that bind these coenzymes, the existence of natural ribozymes, a biosynthetic pathway in which deoxynucleotides are produced from ribonucleotides, and the central role of ribosomal RNA in protein synthesis in the peptidyl transferase center of the ribosome. Here, we uses both a top-down approach that evaluates RNA function in modern biology and a bottom-up approach that examines the capacities of RNA independent of modern biology. These complementary approaches exploit multiple in vitro evolution techniques coupled with high-throughput sequencing and bioinformatics analysis. Together these complementary approaches advance our understanding of the most primitive organisms, their early evolution, and their eventual transition to modern biochemistry.

RNA↗
NASA NTRS2002

Amphioxus and lamprey AP-2 genes: implications for neural crest evolution and migration patterns

The neural crest is a uniquely vertebrate cell type present in the most basal vertebrates, but not in cephalochordates. We have studied differences in regulation of the neural crest marker AP-2 across two evolutionary transitions: invertebrate to vertebrate, and agnathan to gnathostome. Isolation and comparison of amphioxus, lamprey and axolotl AP-2 reveals its extensive expansion in the vertebrate dorsal neural tube and pharyngeal arches, implying co-option of AP-2 genes by neural crest cells early in vertebrate evolution. Expression in non-neural ectoderm is a conserved feature in amphioxus and vertebrates, suggesting an ancient role for AP-2 genes in this tissue. There is also common expression in subsets of ventrolateral neurons in the anterior neural tube, consistent with a primitive role in brain development. Comparison of AP-2 expression in axolotl and lamprey suggests an elaboration of cranial neural crest patterning in gnathostomes. However, migration of AP-2-expressing neural crest cells medial to the pharyngeal arch mesoderm appears to be a primitive feature retained in all vertebrates. Because AP-2 has essential roles in cranial neural crest differentiation and proliferation, the co-option of AP-2 by neural crest cells in the vertebrate lineage was a potentially crucial event in vertebrate evolution.

NASA Discipline Evolutionary Biology↗
DOE OSTI2024

Cacao pod transcriptome profiling of seven genotypes identifies features associated with post-penetration resistance to Phytophthora palmivora

Abstract The oomycete Phytophthora palmivora infects the fruit of cacao trees ( Theobroma cacao ) causing black pod rot and reducing yields. Cacao genotypes vary in their resistance levels to P. palmivora , yet our understanding of how cacao fruit respond to the pathogen at the molecular level during disease establishment is limited. To address this issue, disease development and RNA-Seq studies were conducted on pods of seven cacao genotypes (ICS1, WFT, Gu133, Spa9, CCN51, Sca6 and Pound7) to better understand their reactions to the post-penetration stage of P. palmivora infection. The pod tissue- P. palmivora pathogen assay resulted in the genotypes being classified as susceptible (ICS1, WFT, Gu133 and Spa9) or resistant (CCN51, Sca6 and Pound7). The number of differentially expressed genes (DEGs) ranged from 1625 to 6957 depending on genotype. A custom gene correlation approach identified 34 correlation groups. De novo motif analysis was conducted on upstream promoter sequences of differentially expressed genes, identifying 76 novel motifs, 31 of which were over-represented in the upstream sequences of correlation groups and associated with gene ontology terms related to oxidative stress response, defense against fungal pathogens, general metabolism and cell function. Genes in one correlation group (Group 6) were strongly induced in all genotypes and enriched in genes annotated with defense-responsive terms. Expression pattern profiling revealed that genes in Group 6 were induced to higher levels in the resistant genotypes. An additional analysis allowed the identification of 17 candidate cis -regulatory modules likely to be involved in cacao defense against P. palmivora . This study is a comprehensive exploration of the cacao pod transcriptional response to P. palmivora spread after infection. We identified cacao genes, promoter motifs, and promoter motif combinations associated with post-penetration resistance to P. palmivora in cacao pods and provide this information as a resource to support future and ongoing efforts to breed P. palmivora -resistant cacao.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1988

On the relation between photospheric flow fields and the magnetic field distribution on the solar surface

Using the technique of local correlation tracking on a 28 minute time sequence of white-light images of solar granulation, the horizontal flow field on the solar surface is measured. The time series was obtained by the Solar Optical Universal Polarimeter (SOUP) on Spacelab 2 (Space Shuttle flight 51-F) and is free from atmospheric blurring and distortion. The SOUP flow fields have been compared with carefully aligned magnetograms taken over a nine hour period at the Big Bear Solar Observatory before, during, and after the SOUP images. The flow field and the magnetic field agree in considerable detail: vectors which define the flow of the white-light intensity pattern (granulation) point toward magnetic field regions, magnetic fields surround flow cells, and magnetic features move along the flow arrows. The projected locations of free particles ('corks') in the measured flow field congregate at the same locations where the magnetic field is observed.

Simon, George W.↗
NASA NTRS2016

A Human-in-the Loop Evaluation of a Coordinated Arrival Departure Scheduling Operations for Managing Departure Delays at LaGuardia Airport

LaGuardia (LGA) departure delay was identified by the stakeholders and subject matter experts as a significant bottleneck in the New York metropolitan area. Departure delay at LGA is primarily due to dependency between LGA's arrival and departure runways: LGA departures cannot begin takeoff until arrivals have cleared the runway intersection. If one-in one-out operations are not maintained and a significant arrival-to-departure imbalance occurs, the departure backup can persist through the rest of the day. At NASA Ames Research Center, a solution called "Departure-sensitive Arrival Spacing" (DSAS) was developed to maximize the departure throughput without creating significant delays in the arrival traffic. The concept leverages a Terminal Sequencing and Spacing (TSS) operations that create and manage the arrival schedule to the runway threshold and added an interface enhancement to the traffic manager's timeline to provide the ability to manually adjust inter-arrival spacing to build precise gaps for multiple departures between arrivals. A more complete solution would include a TSS algorithm enhancement that could automatically build these multi-departure gaps. With this set of capabilities, inter-arrival spacing could be controlled for optimal departure throughput. The concept was prototyped in a human-in-the- loop (HITL) simulation environment so that operational requirements such as coordination procedures, timing and magnitude of TSS schedule adjustments, and display features for Tower, TRACON and Traffic Management Unit could be determined. A HITL simulation was conducted in August 2014 to evaluate the concept in terms of feasibility, controller workload impact, and potential benefits. Three conditions were tested, namely a Baseline condition without scheduling, TSS condition that schedules the arrivals to the runway threshold, and TSS+DSAS condition that adjusts the arrival schedule to maximize the departure throughput. The results showed that during high arrival demand period, departure throughput could be incrementally increased under TSS and TSS+DSAS conditions without compromising the arrival throughput. The concept, operational procedures, and summary results were originally published in ATM20151 but detailed results were omitted. This paper expands on the earlier paper to provide the detailed results on throughput, conformance, safety, flight time/distance, etc. that provide extra insights into the feasibility and the potential benefits on the concept.

trajectory-based operations↗
DOE OSTI2023

Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae

It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae . A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S . cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects. Most S . cerevisiae partitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite genome encoding an RNA-dependent RNA polymerase (RdRP) and a coat protein (CP). Phylogenetic analysis of ScPVs identified three species of ScPV, which are most closely related to viruses of the genus Cryspovirus from the mammalian pathogenic protozoan Cryptosporidium parvum . Molecular modeling of the ScPV RdRP revealed a conserved tertiary structure and catalytic site organization when compared to the RdRPs of the Picornaviridae . The ScPV CP is the smallest so far identified in the Partitiviridae and has structural homology with the CP of other partitiviruses but likely lacks a protrusion domain that is a conspicuous feature of other partitivirus particles. ScPVs were stably maintained during laboratory growth and were successfully transferred to haploid progeny after sporulation, which provides future opportunities to study partitivirus-host interactions using the powerful genetic tools available for the model organism S . cerevisiae .

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1988

The 2.5-12 micrometers spectrum of comet Halley from the IKS-VEGA experiment

The infrared instrument IKS flown on board the VEGA space probes was designed for the detection of emission bands of parent molecules, and for a measurement of the size and temperature of the thermal emitting nuclear region. The instrument had three channels with cooled detectors: an "imaging channel" designed to modulate the signal of the nucleus and two spectroscopic channels operating at 2.5-5 and 6-12 micrometers, respectively, equipped with circular variable filters of resolving power approximately 50. This paper presents and discusses the results from the spectral channels. On VEGA 1, usable spectra were obtained at distances D from the comet nucleus ranging from 250,000 to 40,000 km corresponding to fields of view 4000 and 700 km in diameter, respectively. The important internal background signal caused by the instrument itself, which could not be cooled, had to be eliminated. Since no sky chopping was performed, we obtain difference spectra between the current spectrum and a reference spectrum with little or no cometary signal taken at the beginning of the observing sequence (D approximately 200,000 km). Final discrimination between cometary signal and instrumental background is achieved using their different time evolution, since the instrumental background is proportional to the slow temperature drift of the instrument, and the cometary signal due to parent molecules or dust grains is expected to vary in first order as D-1. The 2.5-5 micrometers IKS spectra definitely show strong narrow signals at 2.7 and 4.25 micrometers, attributed to the nu 3 vibrational bands of H2O and CO2, respectively, and a broader signal in the region 3.2-3.5 micrometers, which may be attributed to CH-bearing molecules. All these signals present the expected D-1 intensity variation. Weaker emission features at 3.6 and 4.7 micrometers could correspond to the nu 1 and nu 5 bands of H2CO and the (1 - 0) band of CO, respectively. Molecular production rates are derived from the observed emissions, assuming that they are due to resonance fluorescence excited by the Sun's infrared radiation. For the strong bands of H2O and CO2, the rovibrational lines are optically thick, and radiative transfer is taken into account. We derive production rates, at the moment of the VEGA 1 flyby, of approximately 10(30) sec-1 for H2O, approximately 2.7 x 10(28) sec-1 for CO2, approximately 5 x 10(28) sec-1 for CO, and 4 x 10(28) sec-1 for H2CO, if attributions to CO and H2CO are correct. The production rate of carbon atoms in CH-bearing molecules is approximately 9 x 10(29) sec-1 assuming fluorescence of molecules in the gas phase, but could be much less if the 3.2-3.5 micrometers emission is attributed to C-H stretch in polycyclic aromatic hydrocarbons or small organic grains. In addition, marginal features are present at 4.85 and 4.45 micrometers, tentatively attributed to OCS and molecules with the CN group, respectively. Broad absorption at 2.8-3.0 micrometers, as well as a narrow emission at 3.15 micrometers, which follow well the D-1 intensity variation, might be due to water ice. Emission at 2.8 micrometers is also possibly present, and might be due to OH created in vibrationally excited states after water photodissociation. The 6-12 micrometers spectrum does not show any molecular emission, nor emission in the 7.5-micrometers region. The spectrum is dominated by silicate emission showing a double structure with maxima at 9.0 and 11.2 micrometers, which suggests the presence of olivine.

NASA Discipline Number 52-10↗
DOE OSTI2018

Genetic background effects in quantitative genetics: gene-by-system interactions

Proper cell function depends on networks of proteins that interact physically and functionally to carry out physiological processes. Thus, it seems logical that the impact of sequence variation in one protein could be significantly influenced by genetic variants at other loci in a genome. Nonetheless, the importance of such genetic interactions, known as epistasis, in explaining phenotypic variation remains a matter of debate in genetics. Recent work from our lab revealed that genes implicated from an association study of toxin tolerance in Saccharomyces cerevisiae show extensive interactions with the genetic background: most implicated genes, regardless of allele, are important for toxin tolerance in only one of two tested strains. The prevalence of background effects in our study adds to other reports of widespread genetic-background interactions in model organisms. We suggest that these effects represent many-way interactions with myriad features of the cellular system that vary across classes of individuals. Such gene-by-system interactions may influence diverse traits and require new modeling approaches to accurately represent genotype–phenotype relationships across individuals.

09 BIOMASS FUELS↗
NASA NTRS1972

An interdisciplinary analysis of ERTS data for Colorado mountain environments using ADP Techniques

Author identified significant preliminary results from the Ouachita portion of the Texoma frame of data indicate many potentials in the analysis and interpretation of ERTS data. It is believed that one of the more significant aspects of this analysis sequence has been the investigation of a technique to relate ERTS analysis and surface observation analysis. At present a sequence involving (1) preliminary analysis based solely upon the spectral characteristics of the data, followed by (2) a surface observation mission to obtain visual information and oblique photography to particular points of interest in the test site area, appears to provide an extremely efficient technique for obtaining particularly meaningful surface observation data. Following such a procedure permits concentration on particular points of interest in the entire ERTS frame and thereby makes the surface observation data obtained to be particularly significant and meaningful. The analysis of the Texoma frame has also been significant from the standpoint of demonstrating a fast turn around analysis capability. Additionally, the analysis has shown the potential accuracy and degree of complexity of features that can be identified and mapped using ERTS data.

Hoffer, R. M.↗
DOE OSTI2022

Unconventional isoquinoline-based SERMs elicit fulvestrant-like transcriptional programs in ER+ breast cancer cells

Estrogen receptor alpha (ERα) is a ligand-dependent master transcriptional regulator and key driver of breast cancer pathology. Small molecule hormones and competitive antagonists favor unique ERα conformational ensembles that elicit ligand-specific transcriptional programs in breast cancer and other hormone-responsive tissues. By affecting disparate ligand binding domain structural features, unconventional ligand scaffolds can redirect ERα genomic binding patterns to engage novel therapeutic transcriptional programs. To improve our understanding of these ERα structure-transcriptional relationships, we develop a series of chemically unconventional antagonists based on the antiestrogens elacestrant and lasofoxifene. High-resolution x-ray co-crystal structures show that these molecules affect both classical and unique structural motifs within the ERα ligand binding pocket. They show moderately reduced antagonistic potencies on ERα genomic activities but are effective anti-proliferative agents in luminal breast cancer cells. Interestingly, they favor a 4-hydroxytamoxifen-like accumulation of ERα in breast cancer cells but lack uterotrophic activities in an endometrial cell line. Importantly, RNA sequencing shows that the lead molecules engage transcriptional pathways similar to the selective estrogen receptor degrader fulvestrant. This advance shows that fulvestrant-like genomic activities can be achieved without affecting ERα accumulation in breast cancer cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Genomic Features of Antimicrobial Resistance in Staphylococcus pseudintermedius Isolated from Dogs with Pyoderma in Argentina and the United States: A Comparative Study

Staphylococcus pseudintermedius is the most common opportunistic pathogen in dogs and methicillin resistance (MRSP) has been identified as an emerging problem in canine pyoderma. Here, we evaluated the antimicrobial resistance (AMR) features and phylogeny of S. pseudintermedius isolated from canine pyoderma cases in Argentina (n = 29) and the United States (n = 29). 62% of isolates showed multi-drug resistance. The AMR genes found: mecA, blaZ, ermB, dfrG, catA, tetM, aac(6')-aph(2"), in addition to tetK and lnuA (only found in U.S. isolates). Two point mutations were detected: grlA(S80I)-gyrA(S84L), and grlA(D84N)-gyrA(S84L) in one U.S. isolate. A mutation in rpoB (H481N) was found in two isolates from Argentina. SCCmec type III, SCCmec type V, ΨSCCmec 57395 were identified in the Argentinian isolates; and SCCmec type III, SCCmec type IVg, SCCmec type V, and SCCmec type VII variant in the U.S. cohort. Sequence type (ST) ST71 belonging to a dominant clone was found in isolates from both countries, and ST45 only in Argentinian isolates. This is the first study to comparatively analyze the population structure of canine pyoderma-associated S. pseudintermedius isolates in Argentina and in the U.S. It is important to maintain surveillance on S. pseudintermedius populations to monitor AMR and gain further understanding of its evolution and dissemination.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1972

A study of the utilization of ERTS-A data from the Wabash River Basin

The author has identified the following significant results. Preliminary results from the Texoma frame of data indicate many potentials in the analysis and interpretation of ERTS-1 data. It is believed that one of the more significant aspects of this analysis sequence has been the investigation of a technique to relate ERTS analysis and surface observation analysis. At present a sequence involving (1) preliminary analysis based solely upon the spectral characteristics of the data, followed by (2) a surface observation mission to obtain visual information and oblique color photography of particular points of interest in the test site area, appears to provide an extremely efficient technique for obtaining particularly meaningful surface observation data. Following such a procedure allows concentration on particular points of interest in the entire ERTS frame and thereby making the surface observation data obtained to be particularly significant and meaningful. The analysis of the Texoma frame has also been significant from the standpoint of demonstrating a fast turn around analysis capability. Additionally, the analysis has shown the potential accuracy and degree of complexity of features that can be identified and mapped using ERTS-1 data.

Landgrebe, D. A.↗
DOE OSTI2024

PCET‐Driven Reactivity of Neptunyl(VI) Yields Oxo‐Bridged Np(V) and Np(IV) Species

Two unconventional polynuclear complexes of neptunium (Np) featuring mono-mathematical equation -oxo motifs have been accessed by proton-coupled electron transfer (PCET) reactivity involving the dissolution of neptunyl(VI) diacetate dihydrate (NpO 2 (OAc) 2 (H 2 O) 2 ∙ HOAc) in methanol followed by addition of a pentadentate Schiff-base ligand. One complex is a mixed-valent [Np V ,Np IV , Np V ] trimer with two bridging mathematical equation μ 2 -oxos and the other is a [Np V , Np V ] dimer featuring a single mathematical equation μ 2 -oxo. In both complexes the outer Np centers are capped with terminal oxo ligands. Spectroscopic and spectrokinetic studies aimed at elucidating mechanistic details of complex formation in this system show that intermediate multinuclear [Np V O 2 (OAc)] n species form prior to metal chelation by the ligand; electrolysis experiments demonstrate that production of Np(V) gives rise to asynchronous proton transfer that does not occur otherwise (in the Np(VI) state) as well as condensation with loss of H 2 O and formation of the polynuclear complexes. We attribute the oxo-deficient nature of these products, with respect to conventional actinyl ([AnO 2 ] m+ ) species, to the reduction/condensation reaction sequence of PCET.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Structure and Thermal Stability of (H 2 O) 4 Tetrahedron and (H 2 O) 6 Hexagon Adsorbed on NaY Zeolite Studied by Synchrotron-Based Time-Resolved X-ray Diffraction

Water adsorption and desorption features play an important role in determining the adsorptive and catalytic properties of zeolites. In this study, the extraframework structure (water and cations) in NaY faujasite zeolite was studied by synchrotron-based in situ time-resolved X-ray diffraction (TR-XRD) in combination with the Rietveld refinement method. It was observed that Na cations locating at different sites migrated between each other during the dehydration process. Water molecules at three separate sites showed interesting geometries: (H 2 O) 4 tetrahedron W1, (H 2 O) 6 ice-like hexagonal W2, and disordered triangle W3. Interactions between each form of water and Na cations were deeply investigated. Here, the stability of the waters followed the sequence of W1 > W3 > W2. This work provides insights into both framework structure and cation positions of model zeolite under actual working conditions, which helps fully understand the properties of zeolites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Mid-Atlantic U.S. Offshore Carbon Storage Resource Assessment Project (Final Technical Report)

The greatest potential for carbon storage in the northeastern United States lies in the offshore geologic formations comprising the outer continental shelf (Monteverde et al., 2011). Offshore storage can be linked to large point-sources of carbon dioxide (CO 2 ) while avoiding many of the logistical difficulties and potential risks encountered when siting onshore projects, especially in densely populated areas of the East Coast. Offshore CO 2 storage assessment and research in the United States is underway to address uncertainty in potential storage resources, particularly in the mid- and north-Atlantic offshore area. Given the current knowledge base and access to publicly available data, the objectives of the Mid-Atlantic U.S. Offshore Carbon Storage Resource Assessment Project (MAOCSRAP) were fourfold: (1) complete a systematic carbon storage resource assessment of the mid-Atlantic offshore coastal region from the Georges Bank Basin (GBB) through the Long Island Platform (LIP) to the southern Baltimore Canyon Trough (BCT); (2) define key input parameters to reduce uncertainty for offshore storage resource and efficiency estimates; (3) perform a preliminary assessment of risk factors, uncertainties, and data gaps; and (4) engage industry and regulatory stakeholders through development of a Road Map to assist future project planning and implementation. The MAOCSRAP project has compiled, inventoried, and assimilated various publicly available data sets to provide a strong technical basis on which future carbon storage studies and applications can be built. The knowledge infrastructure necessary to support the development of full-scale offshore carbon storage include: Defining the geologic characteristics of candidate storage sites (Chapter 2). Using existing seismic data to better define the continuity of the storage zones and seals (Chapter 3). Cataloguing the hydrogeologic properties of mid-Atlantic offshore storage sites (Chapter 4). Calculating prospective CO 2 storage resources using net effective pore volumes and fluid displacement properties specific to offshore lithologies (Chapter 5). Examining risk factors related to offshore storage (Chapter 6). Communicating with industry and other stakeholders about the future prospects for offshore storage (Chapter 7). Ensuring technology transfer to industry and other stakeholders (Chapter 8). Led by Battelle, this project was conducted by public and private entities with expertise in offshore geology and resources for the study region, including state geological surveys of Delaware, Maryland, and Pennsylvania; United States Geological Survey-Woods Hole Coastal and Marine Science Center and Haifa University; Rutgers University; Harvard University; and Lamont-Doherty Earth Observatory (LDEO) at Columbia University. The storage resource assessment was completed for a broad region offshore of the U.S. East Coast, from Massachusetts to Virginia. The results include high-level storage resource estimates for areas not previously characterized and improved storage resource estimates for geographically expansive portions of offshore geologic units. Results of the project provide a foundation for developing CO 2 storage along offshore areas of the mid-Atlantic United States. A combination of information was used to provide confidence in project results. Key findings of the major project tasks are summarized as follows. Subsurface Data Analysis: Legacy seismic, well-log, core, and biostratigraphic data were digitized, reprocessed, and analyzed using modern techniques, augmenting previous characterization efforts. The sequence stratigraphic framework for the Cretaceous and Jurassic strata was developed by correlating well-log depositional sequences to seismic reflectors identified in the BCT, LIP, and GBB. The integration of well-log stratigraphy with seismic stratigraphy and petrophysical analysis helped to identify and map potential storage zones within sequences of the Logan Canyon (LC), Missisauga, and Mohawk formations, as well as the regionally extensive caprock comprised of the Dawson Canyon shale. Approximately 4,000 kilometers (km) of seismic data was reprocessed to create a structural framework that was used to tie together all available well data, constrain sequence stratigraphic interpretations, and make regional assessments of offshore carbon storage resources. Prospective storage resource estimates were 150 to 1136 megatons (Mt) for the combined storage zones. This suggests mid-Atlantic U.S. offshore formations can store decades of CO 2 from industrial sources in the region. Preliminary local reservoir simulations suggest that injection rates of 1 Mt CO 2 /year may be sustained for 30 years in single injection wells in the BCT. Advanced geologic modeling and new data acquisition are needed to address data gaps and advance carbon capture and storage (CCS) in key offshore areas selected for further investigation. Offshore Risk Factors: Offshore geologic risk factors include soft sediment deformation, unit continuity, sedimentological and structural features, seismicity and hydrates. CO 2 storage risks include inadequate seals, migration/leakage, and chemical interactions leading to decreased storage. Sensitive habitats, environmental impacts, disturbance to seafloor, and other risks need to be identified in advance of project activities and integrated into detailed mitigation plans for all project phases. Stakeholder Engagement: Input and participation from government, industry, and environmental groups provided input into the Road Map and address next steps needed for project deployment. Early engagement and ongoing communication, as well as policy framework development, is key to large-scale deployment of CCS. Next Steps: This project represents an important first step by completing a high-level CO 2 storage resource assessment and building the knowledge infrastructure necessary to improve quantitative storage resource estimates. The data sets that have been curated under this project provide an opportunity to conduct research and development (R&D) needed to address data gaps and reduce risk and uncertainty. Offshore characterization and validation strategies that are systematically designed to provide data and infrastructure that can be upscaled to meet commercial requirements could be developed off of this foundation.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
NASA NTRS2000

Models of the Protocellular Structures, Functions and Evolution

In the absence of extinct or extant record of protocells, the most direct way to test our understanding of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids: First, a very large population of candidate molecules is generated using a random synthetic approach. Next, the small numbers of molecules that can accomplish the desired task are selected. These molecules are next vastly multiplied using the polymerase chain reaction. A mutagenic approach, in which the sequences of selected molecules are randomly altered, can yield further improvements in performance or alterations of specificities. Unfortunately, the catalytic potential of nucleic acids is rather limited. Proteins are more catalytically capable but cannot be directly amplified. In the new technique, this problem is circumvented by covalently linking each protein of the initial, diverse, pool to the RNA sequence that codes for it. Then, selection is performed on the proteins, but the nucleic acids are replicated. To date, we have obtained "a proof of concept" by evolving simple, novel proteins capable of selectively binding adenosine tri-phosphate (ATP). Our next goal is to create an enzyme that can phosphorylate amino acids and another to catalyze the formation of peptide bonds in the absence of nucleic acid templates. This latter reaction does not take place in contemporary cells. once developed, these enzymes will be encapsulated in liposomes so that they will function in a simulated cellular environment. To provide a continuous energy supply, usually needed to activate the substrates, an energy transduction complex which generates ATP from adenosine diphosphate, inorganic phosphate and light will be used. This system, consisting of two modern proteins, ATP synthase and bacteriorhodopsin, has already been built and shown to work efficiently. By coupling chemical synthesis to such a system, it will be possible to drive chemical reactions by light if only the substrates for these reactions are supplied.

Pohorille, Andrew↗
DOE OSTI2019

Insights into an unusual Auxiliary Activity 9 family member lacking the histidine brace motif of lytic polysaccharide monooxygenases

Lytic polysaccharide monooxygenases (LPMOs) are redox-enzymes involved in biomass degradation. All characterized LPMOs possess an active site of two highly conserved histidine residues coordinating a copper ion (the histidine brace), which are essential for LPMO activity. However, some protein sequences that belong to the AA9 LPMO family display a natural N-terminal His to Arg substitution (Arg-AA9). These are found almost entirely in the phylogenetic fungal class Agaricomycetes, associated with wood decay, but no function has been demonstrated for any Arg-AA9. Through bioinformatics, transcriptomic, and proteomic analyses we present data, which suggest that Arg-AA9 proteins could have a hitherto unidentified role in fungal degradation of lignocellulosic biomass in conjunction with other secreted fungal enzymes. We present the first structure of an Arg-AA9, LsAA9B, a naturally occurring protein from Lentinus similis The LsAA9B structure reveals gross changes in the region equivalent to the canonical LPMO copper-binding site, whereas features implicated in carbohydrate binding in AA9 LPMOs have been maintained. We obtained a structure of LsAA9B with xylotetraose bound on the surface of the protein although with a considerably different binding mode compared with other AA9 complex structures. In addition, we have found indications of protein phosphorylation near the N-terminal Arg and the carbohydrate-binding site, for which the potential function is currently unknown. Finally, our results are strong evidence that Arg-AA9s function markedly different from canonical AA9 LPMO, but nonetheless, may play a role in fungal conversion of lignocellulosic biomass.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes

The Integrated Microbial Genomes & Microbiomes system v.5.0 (IMG/M: https://img.jgi.doe.gov/m/) contains annotated datasets categorized into: archaea, bacteria, eukarya, plasmids, viruses, genome fragments, metagenomes, cell enrichments, single particle sorts, and metatranscriptomes. Source datasets include those generated by the DOE's Joint Genome Institute (JGI), submitted by external scientists, or collected from public sequence data archives such as NCBI. All submissions are typically processed through the IMG annotation pipeline and then loaded into the IMG data warehouse. IMG's web user interface provides a variety of analytical and visualization tools for comparative analysis of isolate genomes and metagenomes in IMG. IMG/M allows open access to all public genomes in the IMG data warehouse, while its expert review (ER) system (IMG/MER: https://img.jgi.doe.gov/mer/) enabled registered users to access their private genomes and to store their private datasets in workspace for sharing and for further analysis. IMG/M data content has increased by 60% since the last report published in the 2017 NAR Database Issue. IMG/M v.5.0 has a new and more powerful genome search feature, new statistical tools, and supports metagenome binning.

59 BASIC BIOLOGICAL SCIENCES↗