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At least 865 records · Page 48

All sources NASA NTRS DOE OSTI

DOE OSTI2012

Reevaluation of the Coding Potential and Proteomic Analysis of the BAC Derived Rhesus Cytomegalovirus Strain 68-1

Cytomegaloviruses are highly host restricted resulting in co-speciation with their hosts. As a natural pathogen of rhesus macaques (RM), Rhesus Cytomegalovirus (RhCMV) has therefore emerged as a highly relevant experimental model for pathogenesis and vaccine development due to its close evolutionary relationship to human CMV (HCMV). To date, most in vivo experiments performed with RhCMV employed strain 68-1 cloned as bacterial artificial chromosome (BAC). However, the complete genome sequence of the 68-1 BAC has not been determined. Furthermore, the gene content of the RhCMV genome is unknown and previous open reading frame (ORF) predictions relied solely on uninterrupted ORFs with an arbitrary cutoff of 300bp. To obtain a more precise picture of the actual proteins encoded by the most commonly used molecular clone of RhCMV we re-evaluated the RhCMV 68-1 BAC-genome by whole genome shotgun sequencing and determined the protein content of the resulting RhCMV virions by proteomics. By additionally comparing the RhCMV genome to that of several closely related Old World Monkey (OWM) CMVs we were able to filter out many unlikely ORFs and obtain a simplified map of the RhCMV genome. This comparative genomics analysis eliminated many genes previously characterized as RhCMV-specific while consolidating a high conservation of ORFs among OWM-CMVs and between RhCMV and HCMV. Moreover, virion proteomics independently validated the revised ORF predictions since only proteins encoded by predicted ORFs could be detected. Taken together these data suggest a much higher conservation of genome and virion structure between CMVs of humans, apes and OWMs than previously assumed. Remarkably, BAC-derived RhCMV is able to establish and maintain persistent infection despite the lack of multiple genes homologous to HCMV genes involved in tissue tropism.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2012

Structural Controls of the Emerson Pass Geothermal System, Washoe County, Nevada

We have conducted a detailed geologic study to better characterize a blind geothermal system in Emerson Pass on the Pyramid Lake Paiute Tribe Reservation, western Nevada. A thermal anomaly was discovered in Emerson Pass by use of 2 m temperature surveys deployed within a structurally favorable setting and proximal to surface features indicative of geothermal activity. The anomaly lies at the western edge of a broad left step at the northeast end of Pyramid Lake between the north- to north-northeast-striking, west-dipping, Fox and Lake Range normal faults. The 2-m temperature surveys have defined a N-S elongate thermal anomaly that has a maximum recorded temperature of ~60°C and resides on a north- to north-northeaststriking fault. Travertine mounds, chalcedonic silica veins, and silica cemented Pleistocene lacustrine gravels in Emerson Pass indicate a robust geothermal system active at the surface in the recent past. Structural complexity and spatial heterogeneities of the strain and stress field have developed in the step-over region, but kinematic data suggest a WNW-trending (~280° azimuth) extension direction. The geothermal system is likely hosted in Emerson Pass as a result of enhanced permeability generated by the intersection of two oppositely dipping, southward terminating north- to north-northwest-striking (Fox Range fault) and northnortheast- striking faults.

15 GEOTHERMAL ENERGY↗

DOE OSTI2017

A STUDY OF CHANGES IN DEFORMATION AND METABOLISM IN LEFT VENTRICLE AS A FUNCTION OF HYPERTROPHY IN SPONTANEOUS HYPERTENSIVE RATS USING MICROPET TECHNOLOGY

Problem: In the case of hypertrophy caused by pressure overload (hypertension) there is an increase in cardiac mass and modification cardiac metabolism. Aim: This study was designed to study the changes in glucose metabolism, ejection fraction, and deformation in the left ventricle with the progression of hypertrophy in spontaneous hypertensive rats (SHR). Methods: Dynamic PET data were acquired using the microPET II at UC Davis. Two rats were imaged at 10-week intervals for 18 months. Each time a dose of approximately 1- 1.5 mCi of F-18-FDG was injected into a normotensive Wistar Kyoto (WKY) rat and the same dose was injected into a SHR rat. Each rat was imaged using a gated dynamic acquisition for 80 minutes acquiring list mode data with cardiac gating of approximately 600-900 million total counts. For the analysis of glucose of metabolism, the list mode data were histogrammed into a dynamic sequence (42 frames over 80 mins). For each time frame, projection data of 1203 140x210 sinograms of 0.582 mm bins were formed by summing the last three gates before and one after the R-wave trigger to correspond to the diastolic phase of the cardiac cycle. Dynamic sequences of 128x128x83 matrices of 0.4x0.4x0.582 mm3 voxels in x, y, and z were reconstructed using an iterative MAP reconstruction which used a prior that penalized the high frequency components of the reconstruction using appropriate weighting between 26 nearest neighboring voxels. Time activity curves were generated from the dynamic reconstructed sequence for the blood and left ventricular tissue regions of interest which were fit to a 2-compartment model to obtain a least squares fit for the kinetic parameters. For the analysis of deformation, the list mode data were histogrammed into 8 gates of the cardiac cycle, each gate was the total sum of the later 60 mins of the 80 min acquisition. Images of 128x128x83 matrices for each gate were reconstructed using the same iterative MAP reconstruction used to reconstruct the dynamic sequence. The in-plane image dimensions were doubled to 256x256x83 in order to increase the resolution for the Warping analyses. These image data sets were then cropped to 128x128x83. The end-systolic image data sets were designated as the template images and the end-diastole image data sets were designated as the target images, thus providing an analysis of the diastolic relaxation and filling phases of the cardiac cycle. The template images were manually segmented to create surface definitions representing the epi- and endocardial surfaces. Finite element models of the left ventricles were created using the segmented surfaces and defining a transversely isotropic material with fiber angles varying from the epicardial surface to the endocardial surface. A Warping analyses was performed to obtain the LV strain tensor and fiber stretch distributions. Results: In one study, the average first principal Green-Lagrange strain, fiber stretch, ejection fraction, and metabolic rate of F-18-FDG was 0.22, 1.08, 80%, 0.1 for the WKY rat and 0.16, 1.06, 50%, 0.25 for the SHR rat, respectively. These same rats studied a year later presented with a metabolic rate of F-18-FDG of 0.11 and 0.25 for the WKY and SHR, respectively. A follow-up study the average strain (n=10) and ejection fraction (n=18) was 0.21, 72.7% for WKY and 0.17, 69.8% for the SHR, respectively. Conclusion: In the case of pressure overload there is an increased reliance on carbohydrate oxidation in an attempt to maintain contractile function.

Sitek, Arkadiusz↗

DOE OSTI2018

Electrometry by optical charge conversion of deep defects in 4H-SiC

Optically active point defects in various host materials, such as diamond and silicon carbide (SiC), have shown significant promise as local sensors of magnetic fields, electric fields, strain, and temperature. Modern sensing techniques take advantage of the relaxation and coherence times of the spin state within these defects. Here we show that the defect charge state can also be used to sense the environment, in particular high-frequency (megahertz to gigahertz) electric fields, complementing established spin-based techniques. This is enabled by optical charge conversion of the defects between their photoluminescent and dark charge states, with conversion rate dependent on the electric field (energy density). The technique provides an all-optical high-frequency electrometer which is tested in 4H-SiC for both ensembles of divacancies and silicon vacancies, from cryogenic to room temperature, and with a measured sensitivity of 41±8(V/cm) 2 /√Hz. In conclusion, due to the piezoelectric character of SiC, we obtain spatial 3D maps of surface acoustic wave modes in a mechanical resonator.

36 MATERIALS SCIENCE↗

DOE OSTI2018

A Review of Classical Swine Fever Virus and Routes of Introduction into the United States and the Potential for Virus Establishment

Classical swine fever (CSF) is caused by CSF virus (CSFV) which can be the source of substantial morbidity and mortality events in affected swine. The disease can take one of several forms (acute, chronic, or prenatal) and depending on the virulence of the inoculating strain may result in a lethal infection irrespective of the form acquired. Because of the disease-free status of the United States and the high cost of a viral incursion, a summary of US vulnerabilities for viral introduction and persistence is provided. The legal importation of live animals as well as animal products, byproducts, and animal feed serve as a potential route of viral introduction. Current import regulations are described as are mitigation strategies that are commonly utilized to prevent pathogens, including CSFV, from entering the US. The illegal movement of suids and their products as well as an event of bioterrorism are both feasible routes of viral introduction but are difficult to restrict or regulate. Ultimately, recommendations are made for data that would be useful in the event of a viral incursion. Population and density mapping for feral swine across the United States would be valuable in the event of a viral introduction or spillover; density data could further contribute to understanding the risk of infection in domestic swine. Additionally, ecological and behavioral studies, including those that evaluate the effects of anthropogenic food sources that support feral swine densities far above the carrying capacity would provide invaluable insight to our understanding of how human interventions affect feral swine populations. Further analyses to determine the sampling strategies necessary to detect low levels of antibody prevalence in feral swine would also be valuable.

Veterinary Sciences↗

DOE OSTI2019

Toward high-throughput defect density quantification: A comparison of techniques for irradiated samples

Transmission electron microscopy (TEM) is an established tool used for the investigation of defects in materials. Traditionally, diffraction contrast techniques—two-beam bright-field and weak-beam dark-field—have been used to image defects due to contrast sensitivity from weak lattice strains. Use of these methods entail an intricate tilt series of imaging using different diffracting vectors, g, to verify the g•b invisibility criterion relative to the different defect types and habit planes inherent to the material. Recently, the addition of down-zone imaging and STEM imaging has also proven to be effective imaging techniques for defect density analysis. Interest in nanocrystalline (NC) materials, spurred by their conjectured superior properties compared to their coarse-grain counterparts, has been thriving and the investigation of their defect morphologies is essential. Maneuvering within NC samples in the TEM adds another layer of difficulty making the aforementioned techniques not practical for application to specimens with complex microstructures. For this reason, we have devised a protocol for identifying NC grains optimally oriented for quantitative analysis using NanoMegas ASTAR automated crystal orientation mapping (ACOM) in the TEM. In this work, we conduct a series of experiments assessing the effectiveness of conventional two-beam bright-field, weak-beam dark-field, and down-zone STEM imaging. Here, we also evaluate an ACOM-assisted multibeam imaging method and compare defect density results obtained using each technique in an irradiated nanocrystalline Au sample.

36 MATERIALS SCIENCE↗

NASA NTRS1980

The geology and morphology of Ina

The lunar feature Ina, an unusual D-shaped depression, is located in Lacus Felicitatis north of Mare Vaporum. Attention was drawn to the feature because of its strange 'blistered' appearance. Using detailed topographic data available from the Lunar Topographic Orthophotomap (LTO) series, it is now possible to depict the morphology and structure of Ina and the surrounding region more accurately than was previously feasible. The maps employed in the study are 41C3 and 41C4 at 1:250,000 scale, and 41C3S1 (Ina) at 1:10,000 scale. Attention is given to the regional setting, and the morphologic characteristics and origins of features. It is concluded that Ina is an apparently unique volcanic feature. It rests on a dome displaying evidence of episodic extrusive activity. Its odd D-shape is probably related to a local fracture pattern, since the straight edge is aligned with other small lineaments in the area. Ina's floor exhibits several volcanic units.

Strain, P. L.↗

DOE OSTI2024

Exploring Geothermal Potential of Great Basin Sub-Regions: Preprint

The INnovative Geothermal Exploration through Novel Investigations Of Undiscovered Systems (INGENIOUS) project aims to discover new, economically viable hidden geothermal systems in the Great Basin region by building on previous work in play fairway analysis and machine learning. A key objective of this project is to develop an exploration workflow to reduce geothermal exploration risks for hidden geothermal systems. A single preliminary play fairway workflow was developed from the assessment of the regional INGENIOUS geological, geophysical, and geochemical datasets. This workflow provided new preliminary predictive geothermal fairway maps for the INGENIOUS study area, which encompasses most of Nevada, western Utah, southern Idaho, southeastern Oregon, and easternmost California. However, a recent study (incorporating machine learning techniques) of a portion of Nevada identified four geologic domains and determined that the relative importance of individual datasets or features as indicators of geothermal potential may differ across these domains. The INGENIOUS study area includes a much larger and more geologically diverse region; therefore, additional geologic domains or sub-regions are expected. To assess the sub-regions in the INGENIOUS study area, principal component analysis and k-means clustering were applied. Preliminary results indicate that the INGENIOUS regional data cluster into groups that relate to different geologic domains in the Great Basin region. These include domains such as the Walker Lane, extensional western Great Basin region, broad lower strain region in the eastern Great Basin of western Utah and eastern Nevada, Quaternary volcanic fields, and the area adjacent to the Snake River Plain. These clusters are assessed to determine the key geologic drivers of the identified clusters. Understanding this variability can provide key insights for the exploration and characterization of hidden geothermal systems in the Great Basin region and could indicate the need to develop multiple geothermal conceptual models and play fairway workflows for the INGENIOUS study area.

GEOTHERMAL ENERGY↗

DOE OSTI2025

Exploring Geothermal Potential of Great Basin Sub-Regions

exploration↗

NASA NTRS2000

Cloning and characterization of ftsZ and pyrF from the archaeon Thermoplasma acidophilum

To characterize cytoskeletal components of archaea, the ftsZ gene from Thermoplasma acidophilum was cloned and sequenced. In T. acidophilum ftsZ, which is involved in cell division, was found to be in an operon with the pyrF gene, which encodes orotidine-5'-monophosphate decarboxylase (ODC), an essential enzyme in pyrimidine biosynthesis. Both ftsZ and pyrF from T. acidophilum were expressed in Escherichia coli and formed functional proteins. FtsZ expression in wild-type E. coli resulted in the filamentous phenotype characteristic of ftsZ mutants. T. acidophilum pyrF expression in an E. coli mutant lacking pyrF complemented the mutation and rescued the strain. Sequence alignments of ODCs from archaea, bacteria, and eukarya reveal five conserved regions, two of which have homology to 3-hexulose-6-phosphate synthase (HPS), suggesting a common substrate recognition and binding motif. Copyright 2000 Academic Press.

Bacterial Proteins/chemistry/genetics/metabolism↗

DOE OSTI2016

Scanning thermo-ionic microscopy for probing local electrochemistry at the nanoscale

Conventional electrochemical characterization techniques based on voltage and current measurements only probe faradaic and capacitive rates in aggregate. In this work we develop a scanning thermo-ionic microscopy (STIM) to probe local electrochemistry at the nanoscale, based on imaging of Vegard strain induced by thermal oscillation. It is demonstrated from both theoretical analysis and experimental validation that the second harmonic response of thermally induced cantilever vibration, associated with thermal expansion, is present in all solids, whereas the fourth harmonic response, caused by local transport of mobile species, is only present in ionic materials. The origin of STIM response is further confirmed by its reduced amplitude with respect to increased contact force, due to the coupling of stress to concentration of ionic species and/or electronic defects. The technique has been applied to probe Sm-doped Ceria and LiFePO{sub 4}, both of which exhibit higher concentrations of mobile species near grain boundaries. The STIM gives us a powerful method to study local electrochemistry with high sensitivity and spatial resolution for a wide range of ionic systems, as well as ability to map local thermomechanical response.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2013

Beyond hard x-ray photoelectron spectroscopy: Simultaneous combination with x-ray diffraction

Hard x-ray photoelectron spectroscopy (HAXPES) is a powerful and novel emerging technique for the nondestructive determination of electronic properties and chemical composition of bulk, buried interfaces and surfaces. It benefits from the exceptionally large escape depth of high kinetic energy photoelectrons, increasing the information depth up to several tens of nanometers. Complementing HAXPES with an atomic structure sensitive technique (such as x-ray diffraction) opens a new research field with major applications for materials science. At SpLine, the Spanish CRG beamline at the European Synchrotron Radiation Facility, we have developed a novel experimental set-up that combines HAXPES and x-ray diffraction (x-ray reflectivity, surface x-ray diffraction, grazing incidence x-ray diffraction, and reciprocal space maps). Both techniques can be operated simultaneously on the same sample and using the same excitation source. The set-up includes a robust 2S + 3D diffractometer hosting a ultrahigh vacuum chamber equipped with a unique photoelectron spectrometer (few eV < electron kinetic energy < 15 keV), x-ray tube (Mg/Ti), 15 keV electron gun, and auxiliary standard surface facilities (molecular beam epitaxy evaporator, ion gun, low energy electron diffraction, sample heating/cooling system, leak valves, load-lock sample transfer, etc.). This end-station offers the unique possibility of performing simultaneous HAXPES + x-ray diffraction studies. In the present work, we describe the experimental set-up together with two experimental examples that emphasize its outstanding capabilities: (i) nondestructive characterization of the Si/Ge and HfO{sub 2}/SiO{sub 2} interfaces on Ge-based CMOS devices, and (ii) strain study on La{sub 0.7}Ca{sub 0.3}MnO{sub 3} ultrathin films grown on SrTiO{sub 3}(001) substrate.

36 MATERIALS SCIENCE↗

DOE OSTI2021

A method for achieving complete microbial genomes and improving bins from metagenomics data

Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. However, less than 100 circularized bacterial and archaeal genomes have been assembled and published from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a semi-automated method called Jorg to help circularize small bacterial, archaeal, and viral genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. In addition to 34 circular CPR genomes, we present one circular Margulisbacteria genome, one circular Chloroflexi genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg and is available on the DOE Systems Biology KnowledgeBase as a beta app.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2013

STRUCTURAL CONTROLS OF THE EMERSON PASS GEOTHERMAL SYSTEM, NORTHWESTERN NEVADA: CHARACTERIZATION OF A "BLIND" SYSTEM

The Pyramid Lake area is favorable for geothermal development due to the tectonic setting of the region. The Walker Lane belt, a dextral shear zone that accommodates ~20% relative motion between the Pacific and North American plates, terminates northwestward in northeast California. NW-directed dextral shear is transferred to WNW extension accommodated by N-to -NNE striking normal faults of the Basin and Range. As a consequence, enhanced dilation occurs on favorably oriented faults generating high geothermal potential in the northwestern Great Basin. The NW-striking right-lateral Pyramid Lake fault, a major structure of the northern Walker Lane, terminates at the southern end of Pyramid Lake and transfers strain to the NNE-striking down to the west Lake Range fault, resulting in high geothermal potential. Known geothermal systems in the area have not been developed due to cultural considerations of the Pyramid Lake Paiute Tribe. Therefore, exploration has been focused on discovering blind geothermal systems elsewhere on the reservation by identifying structurally favorable settings and indicators of past geothermal activity. One promising area is the northeast end of Pyramid Lake, where a broad left step between the west-dipping range-bounding faults of the Lake and Fox Ranges has led to the formation of a broad, faulted relay ramp. Furthermore, tufa mounds, mineralized veins, and altered Miocene rocks occur proximal to a thermal anomaly discovered by a 2-m shallow temperature survey at the north end of the step-over in Emerson Pass. Detailed geologic mapping has revealed a system of mainly NNE-striking down to the west normal faults. However, there are three notable exceptions to this generality, including 1) a prominent NW-striking apparent right-lateral fault, 2) a NW-striking down to the south fault which juxtaposes the base of the mid-Miocene Pyramid sequence against younger late Tertiary sedimentary rocks, and 3) a NNE-striking down to the east normal fault, which accommodates motion such that the Mesozoic Nightingale sequence is juxtaposed with late Tertiary sedimentary rocks. The NW dextral fault, the NNE-down to east fault, and several NNE-down to the west faults intersect roughly at the thermal anomaly in Emerson Pass. This suggests that fault intersections locally control upwelling of geothermal fluids within the step-over. Based on this assumption, it is proposed that the area near Buckbrush Springs be investigated further for geothermal potential. At this location, a NNE-down to the west normal fault, with >1 km of offset, intersects a NW-striking down to the south fault at a small left step in the NNE fault. Further studies will include collection of available kinematic indicators near the shallow thermal anomaly in Emerson Pass, geothermometry on Buckbrush Spring, and possibly drilling of temperature gradient wells in Emerson Pass and at Buckbrush Spring.

15 GEOTHERMAL ENERGY↗

DOE OSTI2020

Quantitative nanoscale tracking of oxygen vacancy diffusion inside single ceria grains by in situ transmission electron microscopy

Oxygen vacancy formation and migration in ceria is critical to its electrochemical and catalytic properties in systems for chemical and energy transformation, but its quantification is rather challenging especially at atomic-scale because of disordered distribution. Here we report a rational approach to track oxygen vacancy diffusion in single grains of pure and Sm-doped ceria at -20 °C to 160 °C using in situ (scanning) transmission electron microscopy ((S)TEM). To create a gradient in oxygen vacancy concentration, a small region (~30 nm in diameter) inside a ceria grain is reduced to the C-type CeO 1.68 phase by the ionization or radiolysis effect of a high-energy electron beam. The evolution in oxygen vacancy concentration is then mapped through lattice expansion measurement using scanning nano-beam diffraction or 4D STEM at a spatial resolution better than 2 nm; this allows direct determination of local oxygen vacancy diffusion coefficients in a very small domain inside pure and Sm-doped ceria at different temperatures. Further, the activation energies for oxygen transport are determined to be 0.59, 0.66, 1.12, and 1.27 eV for pure CeO 2 , Ce 0.94 Sm 0.06 O 1.97 , Ce 0.89 Sm 0.11 O 1.945 , and Ce 0.8 Sm 0.2 O 1.9 , respectively, implying that activation energy increases due to impurity scattering. The results are qualitatively supported by density functional theory (DFT) calculations. In addition, our in situ TEM investigation reveals that dislocations impede oxygen vacancy diffusion by absorbing oxygen vacancies from the surrounding areas and pinning them locally. With more oxygen vacancies absorbed, dislocations show extended strain fields with local tensile zone sandwiched between the compressed ones. Therefore, dislocation density should be reduced in order to minimize the resistance to oxygen vacancy diffusion at low temperatures.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Reliability metrics and their management implications for open pond algae cultivation

The prevalence of contaminating organisms in outdoor algae cultivation, with the often-associated dramatic crop failures, necessitates the need for metrics describing production system reliability. Standard metrics for algae cultivation reliability are critically needed to be able to map improvements in operational parameters, but do not currently exist. In this work, we present a set of standard metrics including mean time to failure (MTTF) and mean time between failures (MTBF) as the basis for the calculation of pond failure rate (FR) and reliability coefficient (RC). Metrics associated with the numbers of contaminating organisms such as abundance ratio (AR), prevalence of infection (PI), and mean intensity of infection (MII) are also relevant. These metrics, based on measured experimental values of outdoor pond performance during the Algae Testbed Public-Private Partnership (ATP3) Unified Field Studies (UFS), provide a basis for quantifying pond failure and provide insight into potential pond management and contaminant mitigation strategies. From these reliability metrics applied to this dataset, we are able to link operational parameters, such as harvest frequency and inoculum source, to pond reliability for different algae strains and seasons, and from an assessment of AR, provide contamination thresholds beyond which a culture may be unrecoverable. Ultimately, the implementation of widely-practiced and simple-to-calculate algae pond reliability metrics calculated from rapid and easy to collect data or observations will reduce risk and uncertainty in large-scale algae deployment and aid in the development of integrated pest management (IPM) strategies.

09 BIOMASS FUELS↗

DOE OSTI2024

A novel conjugative transposon carrying an autonomously amplified plasmid

Tetracyclines serve as broad-spectrum antibiotics to treat bacterial infections. The discovery of new tetracycline resistance genes has led to new questions about the underlying mechanisms of resistance, gene transfer, and their relevance to human health. We tracked changes in the abundance of a 55-kbp conjugative transposon (CTn214) carrying tetQ, a tetracycline resistance gene, within a Bacteroides fragilis metagenome-assembled genome derived from shotgun sequencing of microbial DNA extracted from the ileal pouch of a patient with ulcerative colitis. The mapping of metagenomic reads to CTn214 revealed the multi-copy nature of a 17,044-nt region containing tetQ in samples collected during inflammation and uninflamed visits. B. fragilis cultivars isolated from the same patient during periods of inflammation harbored CTn214 integrated into the chromosome or both a circular, multi-copy, extrachromosomal region of the CTn214 containing tetQ and the corresponding integrated form. The tetracycline-dependent mechanism for the transmission of CTn214 is nearly identical to a common conjugative transposon found in the genome of B. fragilis (CTnDOT), but the autonomously amplified nature of a circular 17,044-nt region of CTn214 that codes for tetQ and the integration of the same sequence in the linear chromosome within the same cell is a novel observation. Genome and transcriptome sequencing of B. fragilis cultivars grown under different concentrations of tetracycline and ciprofloxacin indicates that tetQ in strains containing the circular form remains actively expressed regardless of treatment, while the expression of tetQ in strains containing the linear form increases only in the presence of tetracycline.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Molecular Design of Al(II) Intermediates for Small Molecule Activation

Promoting societally important small molecule activation processes with earth-abundant metals is foundational for a sustainable chemistry future. In this context, mapping new reaction pathways that would enable abundant main-group elements to mimic the behaviors of d- and f-block elements is facilitated by exploring unusual oxidation states. The most abundant metal on earth, aluminum, has been well studied in the Lewis acidic +III and Lewis basic +I oxidation states but rarely in the potentially biphilic +II oxidation state until recently, when a renaissance of Al(II) chemistry emerged from a range of research groups. In this Perspective, we review the chemistry of mononuclear Al radicals, including both Al-centered radicals (i.e., Al(II) compounds) and redox non-innocent systems (i.e., formally Al(II) species that are physically Al(III) with ligand-centered radicals), with an emphasis on small molecule reactivity. We also provide a meta-analysis of the Al(II) literature to summarize how different design strategies (e.g., redox non-innocence, strained coordination geometries) have been shown to impart biphilic character to Al radicals and tune their behavior, thus allowing Al radicals to mimic the chemistry of certain d- and f-block metal ions such as Ti(III) and Sm(II). We expect these molecular design concepts to inform future Al(II) studies as the chemistry of this unusual oxidation state of Al continues to grow.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗