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At least 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Novel Insights Into the Spread of Enteric Pathogens Using Genomics

Diarrheal diseases continue to be a leading cause of mortality and morbidity across the globe. The use of next-generation sequencing data has provided major insights into understanding epidemiological spread, antimicrobial resistance, vaccine effects, and basic mechanisms of bacterial and viral evolution. Furthermore, we discuss how genomic data have informed investigations across enteric pathogens, such as Shigella, Vibrio cholerae, Salmonella Typhi, rotavirus, and norovirus.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Comparative genomics can provide new insights into the evolutionary mechanisms and gene function in CAM plants

Abstract Crassulacean acid metabolism (CAM) photosynthesis is an important biological innovation enabling plant adaptation to hot and dry environments. CAM plants feature high water-use efficiency, with potential for sustainable crop production under water-limited conditions. A deep understanding of CAM-related gene function and molecular evolution of CAM plants is critical for exploiting the potential of engineering CAM into C3 crops to enhance crop production on semi-arid or marginal agricultural lands. With the newly emerging genomics resources for multiple CAM species, progress has been made in comparative genomics studies on the molecular basis and subsequently on the evolution of CAM. Here, recent advances in CAM comparative genomics research in constitutive and facultative CAM plants are reviewed, with a focus on the analyses of DNA/protein sequences and gene expression to provide new insights into the path and driving force of CAM evolution and to identify candidate genes involved in CAM-related biological processes. Potential applications of new computational and experimental technologies (e.g. CRISPR/Cas-mediated genome-editing technology) to the comparative and evolutionary genomics research on CAM plants are offered.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Relaxing Direct Ptychography Sampling Requirements via Parallax Imaging Insights

Direct ptychography enables the retrieval of information encoded in the phase of an electron wave passing through a thin sample by deconvolving the interference effects of a converged probe with known aberrations. Under the weak phase object approximation, this permits the optimal transfer of information using noniterative techniques. However, the achievable resolution of the technique is traditionally limited by the probe step size—setting stringent Nyquist sampling requirements. At the same time, parallax imaging has emerged as a dose-efficient phase technique which relaxes sampling requirements and enables scan-upsampling. Here, we formulate parallax imaging as a quadratic approximation to part of the direct ptychography kernel and use this insight to enable upsampling in direct ptychography. We validate our analytical results numerically using simulated and experimental reconstructions.

direct ptychography, parallax imaging, scan Nyquis↗
DOE OSTI2020

The STRong lensing Insights into the Dark Energy Survey (STRIDES) 2017/2018 follow-up campaign: discovery of 10 lensed quasars and 10 quasar pairs

Here, we report the results of the STRong lensing Insights into the Dark Energy Survey (STRIDES) follow-up campaign of the late 2017/early 2018 season. We obtained spectra of 65 lensed quasar candidates with ESO Faint Object Spectrograph and Camera 2 on the NTT and Echellette Spectrograph and Imager on Keck, confirming 10 new lensed quasars and 10 quasar pairs. Eight lensed quasars are doubly imaged with source redshifts between 0.99 and 2.90, one is triply imaged (DESJ0345-2545, z = 1.68), and one is quadruply imaged (quad: DESJ0053-2012, z = 3.8). Singular isothermal ellipsoid models for the doubles, based on high-resolution imaging from SAMI on Southern Astrophysical Research Telescope or Near InfraRed Camera 2 on Keck, give total magnifications between 3.2 and 5.6, and Einstein radii between 0.49 and 1.97 arcsec. After spectroscopic follow-up, we extract multi-epoch grizY photometry of confirmed lensed quasars and contaminant quasar + star pairs from DES data using parametric multiband modelling, and compare variability in each system’s components. By measuring the reduced χ 2 associated with fitting all epochs to the same magnitude, we find a simple cut on the less variable component that retains all confirmed lensed quasars, while removing 94 per cent of contaminant systems. Based on our spectroscopic follow-up, this variability information improves selection of lensed quasars and quasar pairs from 34-45 per cent to 51–70 per cent, with most remaining contaminants being star-forming galaxies. Using mock lensed quasar light curves we demonstrate that selection based only on variability will over-represent the quad fraction by 10 per cent over a complete DES magnitude-limited sample, explained by the magnification bias and hence lower luminosity/more variable sources in quads.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

The STRong lensing Insights into the Dark Energy Survey (STRIDES) 2016 follow-up campaign – I. Overview and classification of candidates selected by two techniques

Here, the primary goals of the STRong lensing Insights into the Dark Energy Survey (STRIDES) collaboration are to measure the dark energy equation of state parameter and the free streaming length of dark matter. To this aim, STRIDES is discovering strongly lensed quasars in the imaging data of the Dark Energy Survey and following them up to measure time delays, high resolution imaging, and spectroscopy sufficient to construct accurate lens models. In this paper, we first present forecasts for STRIDES. Then, we describe the STRIDES classification scheme, and give an overview of the Fall 2016 follow-up campaign. We continue by detailing the results of two selection methods, the Outlier Selection Technique and a morphological algorithm, and presenting lens models of a system, which could possibly be a lensed quasar in an unusual configuration. We conclude with the summary statistics of the Fall 2016 campaign. Including searches presented in companion papers (Anguita et al.; Ostrovski et al.), STRIDES followed up 117 targets identifying 7 new strongly lensed systems, and 7 nearly identical quasars (NIQs), which could be confirmed as lenses by the detection of the lens galaxy. 76 candidates were rejected and 27 remain otherwise inconclusive, for a success rate in the range 6-35\%. This rate is comparable to that of previous searches like SQLS even though the parent dataset of STRIDES is purely photometric and our selection of candidates cannot rely on spectroscopic information.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Independent and parallel evolution of new genes by gene duplication in two origins of C4 photosynthesis provides new insight into the mechanism of phloem loading in C4 species

C4 photosynthesis is considered one of the most remarkable examples of evolutionary convergence in eukaryotes. However, it is unknown whether the evolution of C4 photosynthesis required the evolution of new genes. Genome-wide gene-tree species-tree reconciliation of seven monocot species that span two origins of C4 photosynthesis revealed that there was significant parallelism in the duplication and retention of genes coincident with the evolution of C4 photosynthesis in these lineages. Specifically, 21 orthologous genes were duplicated and retained independently in parallel at both C4 origins. Analysis of this gene cohort revealed that the set of parallel duplicated and retained genes is enriched for genes that are preferentially expressed in bundle sheath cells, the cell type in which photosynthesis was activated during C4 evolution. Moreover, functional analysis of the cohort of parallel duplicated genes identified SWEET-13 as a potential key transporter in the evolution of C4 photosynthesis in grasses, and provides new insight into the mechanism of phloem loading in these C4 species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mycobacterium tuberculosis Phe-tRNA synthetase: structural insights into tRNA recognition and aminoacylation

Abstract Tuberculosis, caused by Mycobacterium tuberculosis, responsible for ∼1.5 million fatalities in 2018, is the deadliest infectious disease. Global spread of multidrug resistant strains is a public health threat, requiring new treatments. Aminoacyl-tRNA synthetases are plausible candidates as potential drug targets, because they play an essential role in translating the DNA code into protein sequence by attaching a specific amino acid to their cognate tRNAs. We report structures of M. tuberculosis Phe-tRNA synthetase complexed with an unmodified tRNAPhe transcript and either L-Phe or a nonhydrolyzable phenylalanine adenylate analog. High-resolution models reveal details of two modes of tRNA interaction with the enzyme: an initial recognition via indirect readout of anticodon stem-loop and aminoacylation ready state involving interactions of the 3′ end of tRNAPhe with the adenylate site. For the first time, we observe the protein gate controlling access to the active site and detailed geometry of the acyl donor and tRNA acceptor consistent with accepted mechanism. We biochemically validated the inhibitory potency of the adenylate analog and provide the most complete view of the Phe-tRNA synthetase/tRNAPhe system to date. The presented topography of amino adenylate-binding and editing sites at different stages of tRNA binding to the enzyme provide insights for the rational design of anti-tuberculosis drugs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The crystal structure of bacteriophage λ RexA provides novel insights into the DNA binding properties of Rex-like phage exclusion proteins

Abstract RexA and RexB function as an exclusion system that prevents bacteriophage T4rII mutants from growing on Escherichia coli λ phage lysogens. Recent data established that RexA is a non-specific DNA binding protein that can act independently of RexB to bias the λ bistable switch toward the lytic state, preventing conversion back to lysogeny. The molecular interactions underlying these activities are unknown, owing in part to a dearth of structural information. Here, we present the 2.05-Å crystal structure of the λ RexA dimer, which reveals a two-domain architecture with unexpected structural homology to the recombination-associated protein RdgC. Modelling suggests that our structure adopts a closed conformation and would require significant domain rearrangements to facilitate DNA binding. Mutagenesis coupled with electromobility shift assays, limited proteolysis, and double electron–electron spin resonance spectroscopy support a DNA-dependent conformational change. In vivo phenotypes of RexA mutants suggest that DNA binding is not a strict requirement for phage exclusion but may directly contribute to modulation of the bistable switch. We further demonstrate that RexA homologs from other temperate phages also dimerize and bind DNA in vitro. Collectively, these findings advance our mechanistic understanding of Rex functions and provide new evolutionary insights into different aspects of phage biology.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Structural and functional insights into the interaction between the bacteriophage T4 DNA processing proteins gp32 and Dda

Abstract Bacteriophage T4 is a classic model system for studying the mechanisms of DNA processing. A key protein in T4 DNA processing is the gp32 single-stranded DNA-binding protein. gp32 has two key functions: it binds cooperatively to single-stranded DNA (ssDNA) to protect it from nucleases and remove regions of secondary structure, and it recruits proteins to initiate DNA processes including replication and repair. Dda is a T4 helicase recruited by gp32, and we purified and crystallized a gp32–Dda–ssDNA complex. The low-resolution structure revealed how the C-terminus of gp32 engages Dda. Analytical ultracentrifugation analyses were consistent with the crystal structure. An optimal Dda binding peptide from the gp32 C-terminus was identified using surface plasmon resonance. The crystal structure of the Dda–peptide complex was consistent with the corresponding interaction in the gp32–Dda–ssDNA structure. A Dda-dependent DNA unwinding assay supported the structural conclusions and confirmed that the bound gp32 sequesters the ssDNA generated by Dda. The structure of the gp32–Dda–ssDNA complex, together with the known structure of the gp32 body, reveals the entire ssDNA binding surface of gp32. gp32–Dda–ssDNA complexes in the crystal are connected by the N-terminal region of one gp32 binding to an adjacent gp32, and this provides key insights into this interaction.

Biochemistry & Molecular Biology↗
DOE OSTI2011

Structural insights to the metal specificity of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family

LigD 3'-phosphoesterase (PE) enzymes perform end-healing reactions at DNA breaks. Here we characterize the 3'-ribonucleoside-resecting activity of Candidatus Korarchaeum PE. CkoPE prefers a single-stranded substrate versus a primer– template. Activity is abolished by vanadate (10 mM), but is less sensitive to phosphate (IC 50 50 mM) or chloride (IC 50 150 mM). The metal requirement is satisfied by manganese, cobalt, copper or cadmium, but not magnesium, calcium, nickel or zinc. Insights to CkoPE metal specificity were gained by solving new 1.5 Å crystal structures of CkoPE in complexes with Co 2+ and Zn 2+ . His9, His15 and Asp17 coordinate cobalt in an octahedral complex that includes a phosphate anion, which is in turn coordinated by Arg19 and His51. The cobalt and phosphate positions and the atomic contacts in the active site are virtually identical to those in the CkoPE·Mn 2+ structure. By contrast, Zn 2+ binds in the active site in a tetrahedral complex, wherein the position, orientation and atomic contacts of the phosphate are shifted and its interaction with His51 is lost. We conclude that: (i) PE selectively binds to ‘soft’ metals in either productive or non-productive modes and (ii) PE catalysis depends acutely on proper metal and scissile phosphate geometry.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Crystal structure of tRNA m 1 G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate

Transfer RNA (tRNA) methylation is necessary for the proper biological function of tRNA. The N1 methylation of guanine at Position 9 (m1 G9) of tRNA, which is widely identified in eukaryotes and archaea, was found to be catalyzed by the Trm10 family of methyltransferases (MTases). Here, we report the first crystal structures of the tRNA MTase spTrm10 from Schizosaccharomyces pombe in the presence and absence of its methyl donor product S-adenosylhomocysteine (SAH) and its ortholog scTrm10 from Saccharomyces cerevisiae in complex with SAH. Our crystal structures indicated that the MTase domain (the catalytic domain) of the Trm10 family displays a typical SpoU-TrmD (SPOUT) fold. Furthermore, small angle X-ray scattering analysis reveals that Trm10 behaves as a monomer in solution, whereas other members of the SPOUT superfamily all function as homodimers. We also performed tRNA MTase assays and isothermal titration calorimetry experiments to investigate the catalytic mechanism of Trm10 in vitro. In combination with mutational analysis and electrophoretic mobility shift assays, our results provide insights into the substrate tRNA recognition mechanism of Trm10 family MTases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Structural insights into RNA duplexes with multiple 2'-5'-linkages

2 -5 -linked RNAs play important roles in many biological systems. In addition, the mixture of 2 -5 and 3 -5 phosphodiester bonds have emerged as a plausible structural element in prebiotic RNAs. Toward our mechanistic studies of RNA folding and structures with heterogeneous backbones, we recently reported two crystal structures of a decamer RNA duplex containing two and six 2 -5 -linkages, showing how RNA duplexes adjust the structures to accommodate these non-canonical linkages (Proc. Natl. Acad. Sci. USA, 2014, 111, 3050–3055). Herein, we present two additional high-resolution crystal structures of the same RNA duplex containing four and eight 2 -5 -linkages at different positions, providing new insights into the effects of these modifications and a dynamic view of RNA structure changes with increased numbers of 2 -5 -linkages in the same duplex. Our results show that the local structural perturbations caused by 2 -5 linkages can be distributed to nearly all the nucleotides with big ranges of changes in different geometry parameters. In addition, hydration pattern and solvation energy analysis indicate less favorable solvent interactions of 2 -5 -linkages comparing to the native 3 -5 -linkages. This study not only promotes our understanding of RNA backbone flexibility, but also provides a knowledge base for studying the biochemical and prebiotic significance of RNA 2 -5 -linkages.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Base pairing and structural insights into the 5-formylcytosine in RNA duplex

5-Formylcytidine (f 5 C), a previously discovered natural nucleotide in the mitochondrial tRNA of many species including human, has been recently detected as the oxidative product of 5-methylcytidine (m 5 C) through 5-hydroxymethylcytidine (hm 5 C) in total RNA of mammalian cells. The discovery indicated that these cytosine derivatives in RNA might also play important epigenetic roles similar as in DNA, which has been intensively investigated in the past few years. In this paper, we studied the base pairing specificity of f5C in different RNA duplex contexts. We found that the 5-formyl group could increase duplex thermal stability and enhance base pairing specificity. We present three high-resolution crystal structures of an octamer RNA duplex [5'-GUA(f 5 C)GUAC-3'] 2 that have been solved under three crystallization conditions with different buffers and pH values. Our results showed that the 5-formyl group is located in the same plane as the cytosine base and forms an intra-residue hydrogen bond with the amino group in the N4 position. In addition, this modification increases the base stacking between the f 5 C and the neighboring bases while not causing significant global and local structure perturbations. This work provides insights into the effects of 5-formylcytosine on RNA duplex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Insights into RNA binding by the anticancer drug cisplatin from the crystal structure of cisplatin-modified ribosome

Cisplatin is a widely prescribed anticancer drug, which triggers cell death by covalent binding to a broad range of biological molecules. Among cisplatin targets, cellular RNAs remain the most poorly characterized molecules. Although cisplatin was shown to inactivate essential RNAs, including ribosomal, spliceosomal and telomeric RNAs, cisplatin binding sites in most RNA molecules are unknown, and therefore it remains challenging to study how modifications of RNA by cisplatin contributes to its toxicity. Here we report a 2.6Å-resolution X-ray structure of cisplatin-modified 70S ribosome, which describes cisplatin binding to the ribosome and provides the first nearly atomic model of cisplatin–RNA complex. We observe nine cisplatin molecules bound to the ribosome and reveal consensus structural features of the cisplatin-binding sites. Two of the cisplatin molecules modify conserved functional centers of the ribosome—the mRNA-channel and the GTPase center. In the mRNA-channel, cisplatin intercalates between the ribosome and the messenger RNA, suggesting that the observed inhibition of protein synthesis by cisplatin is caused by impaired mRNA-translocation. Furthermore, our structure provides an insight into RNA targeting and inhibition by cisplatin, which can help predict cisplatin-binding sites in other cellular RNAs and design studies to elucidate a link between RNA modifications by cisplatin and cisplatin toxicity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structural and functional insight into the Mycobacterium tuberculosis protein PrpR reveals a novel type of transcription factor

The pathogenicity of Mycobacterium tuberculosis depends upon its ability to catabolize host cholesterol. Upregulation of the methylcitrate cycle (MCC) is required to assimilate and detoxify propionyl-CoA, a cholesterol degradation product. The transcription of key genes prpC and prpD in MCC is activated by MtPrpR, a member of a family of prokaryotic transcription factors whose structures and modes of action have not been clearly defined. We show that MtPrpR has a novel overall structure and directly binds to CoA or short-chain acyl-CoA derivatives to form a homotetramer that covers the binding cavity and locks CoA tightly inside the protein. The regulation of this process involves a [4Fe4S] cluster located close to the CoA-binding cavity on a neighboring chain. Mutations in the [4Fe4S] cluster binding residues rendered MtPrpR incapable of regulating MCC gene transcription. The structure of MtPrpR without the [4Fe4S] cluster-binding region shows a conformational change that prohibits CoA binding. The stability of this cluster means it is unlikely a redox sensor but may function by sensing ambient iron levels. These results provide mechanistic insights into this family of critical transcription factors who share similar structures and regulate gene transcription using a combination of acyl-CoAs and [4Fe4S] cluster.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Optimizing infrasound observations for sample return capsule re-entry: Insights from OSIRIS-REx and Hayabusa2

The atmospheric entry of meteoroids presents a rare and unpredictable phenomenon, posing challenges for systematic observation and detailed characterization. Such events are nonetheless critical for advancing understanding of acoustic wave propagation, atmospheric structure, and entry dynamics. In contrast, sample return capsules (SRCs) from space missions follow well constrained re-entry trajectories, enabling planned observations of shock wave generation and propagation under controlled conditions. This study compares two SRC atmospheric entries, Hayabusa2 in 2020 and OSIRIS-REx in 2023, to assess how different infrasound array configurations influence shock wave detection and trajectory validation. Hayabusa2’s re-entry was monitored using a distributed network of 28 portable infrasound sensors across seven arrays in Woomera, Australia, permitting three-dimensional reconstruction of the trajectory and analysis of wave characteristics. For OSIRIS-REx, a compact four-sensor array deployed near Eureka Airport provided trajectory confirmation through arrival-time differences and back-azimuth estimates. Spectral and waveform analyses revealed differences in signal properties associated with variations in entry angle and velocity. The results illustrate both the strengths and the limitations of the deployed array configurations. The dense and distributed arrays during Hayabusa2’s re-entry enabled detailed trajectory reconstruction, whereas the compact array at Eureka primarily provided confirmation of signal coherence and back-azimuth consistency. These case studies highlight that even relatively small arrays, if located close to the predicted ground track, can still capture useful information on arrival direction and timing. Such insights provide practical guidance for planning future observational campaigns of SRC returns and other controlled atmospheric entries, and may also inform approaches to opportunistic observations of meteoroid events and other atmospheric acoustic phenomena.

celestial mechanics: orbit determination↗
DOE OSTI2016

Conservation and Divergence of Mediator Structure and Function: Insights from Plants

The Mediator complex is a large, multisubunit, transcription co-regulator that is conserved across eukaryotes. Studies of the Arabidopsis Mediator complex and its subunits have shown that it functions in nearly every aspect of plant development and fitness. In addition to revealing mechanisms of regulation of plant-specific pathways, studies of plant Mediator complexes have the potential to shed light on the conservation and divergence of Mediator structure and function across Kingdoms and plant lineages. The majority of insights into plant Mediator function have come from Arabidopsis because it is the only plant from which Mediator has been purified and from which an array of Mediator mutants have been isolated by forward and reverse genetics. So far, these studies indicate that, despite low sequence similarity between many orthologous subunits, the overall structure and function of Mediator is well conserved between Kingdoms. Several studies have also expanded our knowledge of Mediator to other plant species, opening avenues of investigation into the role of Mediator in plant adaptation and fitness.

09 BIOMASS FUELS↗
DOE OSTI2025

Genomic insights into local adaptation and migration success in reintroduced Coho Salmon of the Wenatchee River basin

ABSTRACT Objective Reintroduction of salmonids into regions where they have been extirpated is a common conservation strategy that is often implemented through natural recolonization, translocation of natural populations, or hatchery-based programs. Locally adapting to specific environmental conditions is critical for long-term population viability, particularly for species like Coho Salmon Oncorhynchus kisutch, which face diverse selective pressures during their migration. This study focused on the mid-Columbia River Coho Salmon reintroduction program managed by Yakama Nation Fisheries, which has successfully reintroduced Coho Salmon into the Wenatchee and Methow River basins, Washington. Notably, these populations have adapted to the longer migration route than those in the founding stock, with selection favoring individuals with an earlier arrival time and that can navigate a 15-km, high-gradient canyon to reach optimal spawning grounds. The objectives of this study were to investigate whether specific genomic regions are under selection for traits associated with return location and timing in Coho Salmon. Methods Low-coverage whole-genome resequencing data were used to screen for genomic regions associated with the phenotypes of interest. Results A weak polygenic signal in female Coho Salmon was found to be associated with return group, with a subset of candidate adaptive regions occurring across eight chromosomes. Conclusions These findings provide insights into the genomic mechanisms underlying local adaptation in reintroduced salmon populations and inform broodstock selection strategies aimed at promoting natural production and long-term population sustainability.

Horn, Rebekah L.↗