Search NASA⌕ Search

SEARCH · Search NASA

Results for “CINDI”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 109 records · Page 6

Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism

In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S 1 , S 2 , S 3 , and S 0 , showing that a water molecule is inserted during the S 2 → S 3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O 2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S 2 → S 3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, Q A and Q B , are observed. At the donor site, tyrosine Y Z and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of O X (H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a “water wheel”-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S 2 → S 3 transition mirrors the appearance of O X electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.

59 BASIC BIOLOGICAL SCIENCES↗

Crystal structure engineering in multimetallic high-index facet nanocatalysts

Significance Crystal structure engineering in nanoparticles represents an important strategy in catalyst design, as catalytic performance is highly dependent on atomic arrangement. However, realizing crystal structure engineering in high-index facet nanocatalysts has been a synthetic challenge for decades. Here, we first employed density functional theory calculations to determine whether surface modifications can stabilize high-index facets during crystal structure transformations and then synthesized a library of multimetallic high-index facet tetrahexahedral (THH) nanoparticles with controllable crystal structures. Importantly, the crystal structural transition between the intermetallic and chemically disordered states is reversable, and the THH morphology of nanocatalysts is maintained during this transformation. This approach broadens the synthetic scope of nanocatalysts available for use in diverse chemical processes.

Shen, Bo↗

Prevention efficacy of the broadly neutralizing antibody VRC01 depends on HIV-1 envelope sequence features

In the Antibody Mediated Prevention (AMP) trials (HVTN 704/HPTN 085 and HVTN 703/HPTN 081), prevention efficacy (PE) of the monoclonal broadly neutralizing antibody (bnAb) VRC01 (vs. placebo) against HIV-1 acquisition diagnosis varied according to the HIV-1 Envelope (Env) neutralization sensitivity to VRC01, as measured by 80% inhibitory concentration (IC80). Here, we performed a genotypic sieve analysis, a complementary approach to gaining insight into correlates of protection that assesses how PE varies with HIV-1 sequence features. We analyzed HIV-1 Env amino acid (AA) sequences from the earliest available HIV-1 RNA-positive plasma samples from AMP participants diagnosed with HIV-1 and identified Env sequence features that associated with PE. The strongest Env AA sequence correlate in both trials was VRC01 epitope distance that quantifies the divergence of the VRC01 epitope in an acquired HIV-1 isolate from the VRC01 epitope of reference HIV-1 strains that were most sensitive to VRC01-mediated neutralization. In HVTN 704/HPTN 085, the Env sequence-based predicted probability that VRC01 IC80 against the acquired isolate exceeded 1 µg/mL also significantly associated with PE. In HVTN 703/HPTN 081, a physicochemical-weighted Hamming distance across 50 VRC01 binding-associated Env AA positions of the acquired isolate from the most VRC01-sensitive HIV-1 strain significantly associated with PE. These results suggest that incorporating mutation scoring by BLOSUM62 and weighting by the strength of interactions at AA positions in the epitope:VRC01 interface can optimize performance of an Env sequence-based biomarker of VRC01 prevention efficacy. Future work could determine whether these results extend to other bnAbs and bnAb combinations.

60 APPLIED LIFE SCIENCES↗

Early Oligocene kelp holdfasts and stepwise evolution of the kelp ecosystem in the North Pacific

Kelp forests are highly productive and economically important ecosystems worldwide, especially in the North Pacific Ocean. However, current hypotheses for their evolutionary origins are reliant on a scant fossil record. Here, in this work, we report fossil hapteral kelp holdfasts from western Washington State, USA, indicating that kelp has existed in the northeastern Pacific Ocean since the earliest Oligocene. This is consistent with the proposed North Pacific origin of kelp associated with global cooling around the Eocene–Oligocene transition. These fossils also support the hypotheses that a hapteral holdfast, rather than a discoid holdfast, is the ancestral state in complex kelps and suggest that early kelps likely had a flexible rather than a stiff stipe. Early kelps were possibly grazed upon by mammals like desmostylians, but fossil evidence of the complex ecological interactions known from extant kelp forests is lacking. The fossil record further indicates that the present-day, multi-story kelp forest had developed at latest after the mid-Miocene climate optimum. In summary, the fossils signify a stepwise evolution of the kelp ecosystem in the North Pacific, likely enabled by changes in the ocean-climate system.

54 ENVIRONMENTAL SCIENCES↗

Combatting melioidosis with chemical synthetic lethality

Burkholderia thailandensishas emerged as a nonpathogenic surrogate forBurkholderia pseudomallei, the causative agent of melioidosis, and an important Gram-negative model bacterium for studying the biosynthesis and regulation of secondary metabolism. We recently reported that subinhibitory concentrations of trimethoprim induce vast changes in both the primary and secondary metabolome ofB. thailandensis. In the current work, we show that the folate biosynthetic enzyme FolE2 is permissive under standard growth conditions but essential forB. thailandensisin the presence of subinhibitory doses of trimethoprim. Reasoning that FolE2 may serve as an attractive drug target, we screened for and identified ten inhibitors, including dehydrocostus lactone (DHL), parthenolide, and β-lapachone, all of which are innocuous individually but form a chemical-synthetic lethal combination with subinhibitory doses of trimethoprim. We show that DHL is a mechanism-based inhibitor of FolE2 and capture the structure of the covalently inhibited enzyme using X-ray crystallography. In vitro, the combination of subinhibitory trimethoprim and DHL is more potent than Bactrim, the current standard of care against melioidosis. Moreover, unlike Bactrim, this combination does not affect the growth of most commensal and beneficial gut bacteria tested, thereby providing a degree of specificity againstB. pseudomallei. Our work provides a path for identifying antimicrobial drug targets and for utilizing binary combinations of molecules that form a toxic cocktail based on metabolic idiosyncrasies of specific pathogens.

Science & Technology - Other Topics↗

The Q226L mutation can convert a highly pathogenic H5 2.3.4.4e virus to bind human-type receptors

H5Nx viruses continue to wreak havoc in avian and mammalian species worldwide. The virus distinguishes itself by the ability to replicate to high titers and transmit efficiently in a wide variety of hosts in diverse climatic environments. Fortunately, transmission to and between humans is scarce. Yet, if such an event were to occur, it could spark a pandemic as humans are immunologically naïve to H5 viruses. A significant determinant of transmission to and between humans is the ability of the influenza A virus hemagglutinin (HA) protein to shift from an avian-type to a human-type receptor specificity. Here, we demonstrate that a 2016 2.3.4.4e virus HA can convert to human-type receptor binding via a single Q226L mutation, in contrast to a cleavage-modified 2016 2.3.4.4b virus HA. Using glycan arrays, X-ray structural analyses, tissue- and direct glycan binding, we show that L133a Δ and 227Q are vital for this phenotype. Thus, whereas the 2.3.4.4e virus HA only needs a single amino acid mutation, the modified 2016 2.3.4.4b HA was not easily converted to human-type receptor specificity.

Science & Technology - Other Topics↗

Mechanical quantum sensing in the search for dark matter

Numerous astrophysical and cosmological observations are best explained by the existence of dark matter, a mass density which interacts only very weakly with visible, baryonic matter. Here, searching for the extremely weak signals produced by this dark matter strongly motivate the development of new, ultra-sensitive detector technologies. Paradigmatic advances in the control and readout of massive mechanical systems, in both the classical and quantum regimes, have enabled unprecedented levels of sensitivity. In this white paper, we outline recent ideas in the potential use of a range of solid-state mechanical sensing technologies to aid in the search for dark matter in a number of energy scales and with a variety of coupling mechanisms.

79 ASTRONOMY AND ASTROPHYSICS↗

Probing the role of CNTs in Pt nanoparticle/CNT/graphene nanohybrids H 2 sensors

Abstract In the carbon nanotubes film/graphene heterostructure decorated with catalytic Pt nanoparticles using atomic layer deposition (Pt-NPs/CNTs/Gr) H 2 sensors, the CNT film determines the effective sensing area and the signal transport to Gr channel. The former requires a large CNT aspect ratio for a higher sensing area while the latter demands high electric conductivity for efficient charge transport. Considering the CNT’s aspect ratio decreases, while its conductivity increases ( i.e. , bandgap decreases), with the CNT diameter, it is important to understand how quantitatively these effects impact the performance of the Pt-NPs/CNTs/Gr nanohybrids sensors. Motivated by this, this work presents a systematic study of the Pt-NPs/CNTs/Gr H 2 sensor performance with the CNT films made from different constituent CNTs of diameters ranging from 1 nm for single-wall CNTs, to 2 nm for double-wall CNTs, and to 10–30 nm for multi-wall CNTs (MWCNTs). By measuring the morphology and electric conductivity of SWCNT, DWCNT and MWCNT films, this work aims to reveal the quantitative correlation between the sensor performance and relevant CNT properties. Interestingly, the best performance is obtained on Pt-NPs/MWCNTs/Gr H 2 sensors, which can be attributed to the compromise of the effective sensing area and electric conductivity on MWCNT films and illustrates the importance of optimizing sensor design.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Standardized naming of microbiome samples in Genomes OnLine Database

The power of next-generation sequencing has resulted in an explosive growth in the number of projects aiming to understand the metagenomic diversity of complex microbial environments. The interdisciplinary nature of this microbiome research community, along with the absence of reporting standards for microbiome data and samples, poses a significant challenge for follow-up studies. Commonly used names of metagenomes and metatranscriptomes in public databases currently lack the essential information necessary to accurately describe and classify the underlying samples, which makes a comparative analysis difficult to conduct and often results in misclassified sequences in data repositories. The Genomes OnLine Database (GOLD) (https:// gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute has been at the forefront of addressing this challenge by developing a standardized nomenclature system for naming microbiome samples. GOLD, currently in its twenty-fifth anniversary, continues to enrich the research community with hundreds of thousands of metagenomes and metatranscriptomes with well-curated and easy-to-understand names. Through this manuscript, we describe the overall naming process that can be easily adopted by researchers worldwide. Additionally, we propose the use of this naming system as a best practice for the scientific community to facilitate better interoperability and reusability of microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗

Draft genome sequences of strains CBS6241 and CBS6242 of the basidiomycetous yeast Filobasidium floriforme

The Tremellomycetes are a species-rich group within the basidiomycete fungi; however, most analyses of this group to date have focused on pathogenic Cryptococcus species within the order Tremellales. Recent genome-assisted studies of other Tremellomycetes have identified interesting features with respect to biotechnological applications as well as the evolution of genes involved in mating and sexual development. Here, we report genome sequences of two strains of Filobasidium floriforme, a species from the order Filobasidiales, which branches basally to the Tremellales, Trichosporonales, and Holtermanniales. The assembled genomes of strains CBS6241 and CBS6242 are 27.4 Mb and 26.4 Mb in size, respectively, with 8314 and 7695 predicted protein-coding genes. Overall sequence identity at nucleic acid level between the strains is 97%. Among the predicted genes are pheromone precursor and pheromone receptor genes as well as two genes encoding homedomain (HD) transcription factors, which are predicted to be part of the mating type (MAT) locus. Sequence analysis indicates that CBS6241 and CBS6242 carry different alleles for both the pheromone/receptor genes as well as the HD transcription factors. Orthology inference identified 1482 orthogroups exclusively found in F. floriforme, some of which were involved in carbohydrate transport and metabolism. Subsequent CAZyme repertoire characterization identified 267 and 247 enzymes for CBS6241 and CBS6242, respectively, the second highest number of CAZymes among the analyzed Tremellomycete species. In addition, F. floriforme contains five CAZymes absent in other species and several plant-cell-wall degrading CAZymes with the highest copy number in Tremellomycota, indicating the biotechnological potential of this species.

59 BASIC BIOLOGICAL SCIENCES↗

CRISPR–Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells

DNA nanostructures are a promising tool to deliver molecular payloads to cells. DNA origami structures, where long single-stranded DNA is folded into a compact nanostructure, present an attractive approach to package genes; however, effective delivery of genetic material into cell nuclei has remained a critical challenge. Here, we describe the use of DNA nanostructures encoding an intact human gene and a fluorescent protein encoding gene as compact templates for gene integration by CRISPR-mediated homology-directed repair (HDR). Our design includes CRISPR–Cas9 ribonucleoprotein binding sites on DNA nanostructures to increase shuttling into the nucleus. We demonstrate efficient shuttling and genomic integration of DNA nanostructures using transfection and electroporation. These nanostructured templates display lower toxicity and higher insertion efficiency compared to unstructured double-stranded DNA templates in human primary cells. Furthermore, our study validates virus-like particles as an efficient method of DNA nanostructure delivery, opening the possibility of delivering nanostructures in vivo to specific cell types. Together, these results provide new approaches to gene delivery with DNA nanostructures and establish their use as HDR templates, exploiting both their design features and their ability to encode genetic information. This work also opens a door to translate other DNA nanodevice functions, such as biosensing, into cell nuclei.

59 BASIC BIOLOGICAL SCIENCES↗

Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9

We report the Genomes OnLine Database (GOLD) (https://gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute (DOE-JGI) continues to maintain its role as one of the flagship genomic metadata repositories of the world. The ever-increasing number of projects and metadata are freely available to the user community world-wide. GOLD’s metadata is consumed by scientists and remains an important source for large-scale comparative genomics analysis initiatives. Encouraged by this active user engagement and growth, GOLD has continued to add new components and capabilities. The new features such as a public Application Programming Interface (API) and Ecosystem landing page as well as the growth of different entities in this current GOLD v.9 edition are described in detail in this manuscript.

59 BASIC BIOLOGICAL SCIENCES↗

Genomes OnLine Database (GOLD) v.10: new features and updates

The Genomes OnLine Database (GOLD; https://gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute is a comprehensive online metadata repository designed to catalog and manage information related to (meta)genomic sequence projects. GOLD provides a centralized platform where researchers can access a wide array of metadata from its four organization levels namely Study, Organism/Biosample, Sequencing Project and Analysis Project. GOLD continues to serve as a valuable resource and has seen significant growth and expansion since its inception in 1997. With its expanded role as a collaborative platform, it not only actively imports data from other primary repositories like National Center for Biotechnology Information but also supports contributions from researchers worldwide. This collaborative approach has enriched the database with diverse datasets, creating a more integrated resource to enhance scientific insights. As genomic research becomes increasingly integral to various scientific disciplines, more researchers and institutions are turning to GOLD for their metadata needs. To meet this growing demand, GOLD has expanded by adding diverse metadata fields, intuitive features, advanced search capabilities and enhanced data visualization tools, making it easier for users to find and interpret relevant information. This manuscript provides an update and highlights the new features introduced over the last 2 years.

59 BASIC BIOLOGICAL SCIENCES↗

Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii

The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass (Panicum hallii, P. hallii) is a wild perennial grass that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the 2 major ecotypes in P. hallii, the upland ecotype (P. hallii var hallii, HAL2 genotype) with compact inflorescence and large seed and the lowland ecotype (P. hallii var filipes, FIL2 genotype) with an open inflorescence and small seed. Here we conducted a comparative analysis of the transcriptome and DNA methylome, an epigenetic mark that influences gene expression regulation, across different stages of inflorescence development using genomic references for each ecotype. Global transcriptome analysis of differentially expressed genes (DEGs) and co-expression modules underlying the inflorescence divergence revealed the potential role of cytokinin signaling in heterochronic changes. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of P. hallii inflorescence. We found that a large proportion of differentially methylated regions (DMRs) were located in the flanking regulatory regions of genes. Intriguingly, we observed a substantial bias of CHH hypermethylation in the promoters of FIL2 genes. The integration of DEGs, DMRs, and $K_a$/$K_s$ ratio results characterized the evolutionary features of DMR-associated DEGs that contribute to the divergence of the P. hallii inflorescence. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a genomic resource for perennial grass biology.

59 BASIC BIOLOGICAL SCIENCES↗

Giving Research Software Engineers a Larger Stage Through the Better Scientific Software Fellowship

The Better Scientific Software Fellowship (BSSwF) was launched in 2018 to foster and promote practices, processes, and tools to improve developer productivity and software sustainability of scientific codes. The BSSwF’s vision is to grow the community with practitioners, leaders, mentors, and consultants to increase the visibility of scientific software. Over the last five years, many fellowship recipients and honorable mentions have identified as research software engineers (RSEs). Furthermore, case studies from several of the program’s participants illustrate the diverse ways the BSSwF has benefited both the RSE and scientific communities. In an environment where the contributions of RSEs are too often undervalued, we believe that programs such as the BSSwF can help recognize and encourage community members to step outside of their regular commitments and expand on their work, collaborations, and ideas for a larger audience.

97 MATHEMATICS AND COMPUTING↗

The Algae Foundation® and Algae Technology Educational Consortium

Abstract The Algae Foundation established in February 2013 has developed a diverse portfolio of algal‐based education and workforce development programs covering education levels from kindergarten through college, aquaculture extension, and free online courses. The Algae Foundation created the Algae Technology Educational Consortium (ATEC) with five major foci including community college certificate program in algae cultivation; community college curriculum adopted for algal biotechnology degree programs; Algal Massive Open Online Courses (Algal MOOCs); Algae Academy, a kindergarten to 12th grade STEM curriculum initiative; and aquaculture extension education through the Algae Cultivation Extension Short courses (ACES). The results include the education and training of over 102,000 students, aquaculturists, entrepreneurs, and bioeconomy‐based professionals aged 8–75 years in all 50 U.S. states and 66 countries. ATEC has completed agreements with 21 community colleges and universities located in Arizona, California, Connecticut, Hawaii, Louisiana, Maine, New Mexico, North Carolina, Oregon, Texas, and Washington. The first ATEC‐sponsored certificate degree program graduation was in May 2018. The Algae MOOC #1 has had over 15,752 students enrolled. ATEC initiated the Algae Academy in spring 2016 in Carlsbad, CA, and expanded to serving over 34,000 students in 46 states during the academic year 2019–2020. ACES has enrolled over 1,550 students from 66 countries.

59 BASIC BIOLOGICAL SCIENCES↗

Visualization of shocked material instabilities using a fast-framing camera and XFEL four-pulse train

Many questions regarding dynamic materials could be answered by using time-resolved ultra-fast imaging techniques to characterize the physical and chemical behavior of materials in extreme conditions and their evolution on the nanosecond scale. In this work, we perform multi-frame phase-contrast imaging (PCI) of micro-voids in low density polymers under laser-driven shock compression. At the Matter in Extreme Conditions (MEC) Instrument at the Linac Coherent Light Source (LCLS), we used a train of four x-ray free electron laser (XFEL) pulses to probe the evolution of the samples. To visualize the void and shock wave interaction, here, we deployed the Icarus V2 detector to record up to four XFEL pulses, separated by 1-3 nanoseconds. In this work, we image elastic waves interacting with the micro-voids at a pressure of several GPa. Monitoring how the material’s heterogeneities, like micro-voids, dictate its response to a compressive wave is important for benchmarking the performances of inertial confinement fusion energy materials. For the first time in a single sample, we have combined an ultrafast x-ray framing camera and four XFEL pulse train to create an ultrafast movie of micro-void evolution under laser-driven shock compression. Eventually, we hope this technique will resolve the material density as it evolves dynamically under laser shock compression.

fusion↗