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At least 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Molecular Epidemiology of Foot-and-Mouth Disease Virus in the Context of Transboundary Animal Movement in the Far North Region of Cameroon

Transboundary movement of animals is an important mechanism for foot-and-mouth disease virus (FMDV) spread in endemic regions, such as Cameroon. Several transboundary animal trade routes cross the Far North Region of Cameroon, and cattle moved on foot along these routes often come in contact with native (sedentary and transhumant) herds. The purpose of this study was to investigate the role of transboundary trade cattle in the epidemiology of FMDV in the Far North Region of Cameroon. A total of 582 oropharyngeal fluid (OPF) samples were collected from asymptomatic transboundary trade cattle at official border check points and 57 vesicle epithelial tissues were collected from clinically affected native cattle in the Far North Region of Cameroon during 2010–2014. Viral protein 1 (VP1) coding sequences were obtained from 6 OPF samples from transboundary cattle (4 serotype O, 2 serotype SAT2) and 19 epithelial tissue samples from native cattle (7 serotype O, 3 serotype SAT2, 9 serotype A). FMDV serotype O viruses belonged to two topotypes (East Africa-3 and West Africa), and phylogenetic analyses suggested a pattern of continuous transmission in the region. Serotype SAT2 viruses belonged to a single topotype (VII), and phylogenetic analysis suggested a pattern of repeated introductions of different SAT2 lineages in the region. Serotype A viruses belonged to topotype AFRICA/G-IV, and the pattern of transmission was unclear. Spearman rank correlation analysis of VP1 coding sequences obtained in this study from transboundary and native cattle showed a positive correlation between genetic distance and time for serotype O ( ρ = 0.71, p = 0.003) and between genetic distance and geographic distance for serotype SAT2 ( ρ = 0.54, p = 0.1). These data suggest that transboundary trade cattle participate in the transmission of FMDV in the Far North Region of Cameroon, however the dynamics and direction of transmission could not be determined in this study. Results of this study contribute to the understanding of transboundary FMDV epidemiology in Central Africa and will help to inform control programs in Cameroon and in the region.

Veterinary Sciences↗
DOE OSTI2012

Time-dependent 2-D modeling of edge plasma transport with high intermittency due to blobs

The results on time-dependent 2-D fluid modeling of edge plasmas with non-diffusive intermittent transport across the magnetic field (termed cross-field) based on the novel macro-blob approach are presented. The capability of this approach to simulate the long temporal evolution ({approx}0.1 s) of the background plasma and simultaneously the fast spatiotemporal dynamics of blobs ({approx}10{sup -4} s) is demonstrated. An analysis of a periodic sequence of many macro-blobs (PSMB) is given showing that the resulting plasma attains a dynamic equilibrium. Plasma properties in the dynamic equilibrium are discussed. In PSMB modeling, the effect of macro-blob generation frequency on edge plasma parameters is studied. Comparison between PSMB modeling and experimental profile data is given. The calculations are performed for the same plasma discharge using two different models for anomalous cross-field transport: time-average convection and PSMB. Parametric analysis of edge plasma variation with transport coefficients in these models is presented. The capability of the models to accurately simulate enhanced transport due to blobs is compared. Impurity dynamics in edge plasma with macro-blobs is also studied showing strong impact of macro-blob on profiles of impurity charge states caused by enhanced outward transport of high-charge states and simultaneous inward transport of low-charge states towards the core. Macro-blobs cause enhancement of sputtering rates, increase radiation and impurity concentration in plasma, and change erosion/deposition patterns.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

A multi-level anomaly detection algorithm for time-varying graph data with interactive visualization

This work presents a novel modeling and analysis framework for graph sequences which addresses the challenge of detecting and contextualizing anomalies in labelled, streaming graph data. We introduce a generalization of the BTER model of Seshadhri et al. by adding flexibility to community structure, and use this model to perform multi-scale graph anomaly detection. Specifically, probability models describing coarse subgraphs are built by aggregating node probabilities, and these related hierarchical models simultaneously detect deviations from expectation. This technique provides insight into a graph's structure and internal context that may shed light on a detected event. Additionally, this multi-scale analysis facilitates intuitive visualizations by allowing users to narrow focus from an anomalous graph to particular subgraphs or nodes causing the anomaly. For evaluation, two hierarchical anomaly detectors are tested against a baseline Gaussian method on a series of sampled graphs. We demonstrate that our graph statistics-based approach outperforms both a distribution-based detector and the baseline in a labeled setting with community structure, and it accurately detects anomalies in synthetic and real-world datasets at the node, subgraph, and graph levels. Furthermore, to illustrate the accessibility of information made possible via this technique, the anomaly detector and an associated interactive visualization tool are tested on NCAA football data, where teams and conferences that moved within the league are identified with perfect recall, and precision greater than 0.786.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Multi-Level Anomaly Detection on Time-Varying Graph Data

This work presents a novel modeling and analysis framework for graph sequences which addresses the challenge of detecting and contextualizing anomalies in labelled, streaming graph data. We introduce a generalization of the BTER model of Seshadhri et al. by adding flexibility to community structure, and use this model to perform multi-scale graph anomaly detection. Specifically, probability models describing coarse subgraphs are built by aggregating probabilities at finer levels, and these closely related hierarchical models simultaneously detect deviations from expectation. This technique provides insight into a graph's structure and internal context that may shed light on a detected event. Additionally, this multi-scale analysis facilitates intuitive visualizations by allowing users to narrow focus from an anomalous graph to particular subgraphs or nodes causing the anomaly. For evaluation, two hierarchical anomaly detectors are tested against a baseline Gaussian method on a series of sampled graphs. We demonstrate that our graph statistics-based approach outperforms both a distribution-based detector and the baseline in a labeled setting with community structure, and it accurately detects anomalies in synthetic and real-world datasets at the node, subgraph, and graph levels. To illustrate the accessibility of information made possible via this technique, the anomaly detector and an associated interactive visualization tool are tested on NCAA football data, where teams and conferences that moved within the league are identified with perfect recall, and precision greater than 0.786.

anomaly detection↗
DOE OSTI2016

Coordinate action of distinct sequence elements localizes checkpoint kinase Hsl1 to the septin collar at the bud neck in Saccharomyces cerevisiae

Passage through the eukaryotic cell cycle requires processes that are tightly regulated both spatially and temporally. Surveillance mechanisms (checkpoints) exert quality control and impose order on the timing and organization of downstream events by impeding cell cycle progression until the necessary components are available and undamaged and have acted in the proper sequence. In budding yeast, a checkpoint exists that does not allow timely execution of the G2/M transition unless and until a collar of septin filaments has properly assembled at the bud neck, which is the site where subsequent cytokinesis will occur. An essential component of this checkpoint is the large (1518-residue) protein kinase Hsl1, which localizes to the bud neck only if the septin collar has been correctly formed. Hsl1 reportedly interacts with particular septins; however, the precise molecular determinants in Hsl1 responsible for its recruitment to this cellular location during G2 have not been elucidated. We performed a comprehensive mutational dissection and accompanying image analysis to identify the sequence elements within Hsl1 responsible for its localization to the septins at the bud neck. Unexpectedly, we found that this targeting is multipartite. A segment of the central region of Hsl1 (residues 611–950), composed of two tandem, semiredundant but distinct septin-associating elements, is necessary and sufficient for binding to septin filaments both in vitro and in vivo. However, in addition to 611–950, efficient localization of Hsl1 to the septin collar in the cell obligatorily requires generalized targeting to the cytosolic face of the plasma membrane, a function normally provided by the C-terminal phosphatidylserine-binding KA1 domain (residues 1379–1518) in Hsl1 but that can be replaced by other, heterologous phosphatidylserine-binding sequences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

The main sequences of star-forming galaxies and active galactic nuclei at high redshift

We provide a novel, unifying physical interpretation on the origin, average shape, scatter, and cosmic evolution for the main sequences of star-forming galaxies and active galactic nuclei (AGNs) at high redshift z≳1. We achieve this goal in a model-independent way by exploiting: (i) the redshift-dependent star formation rate functions based on the latest UV/far-IR data from HST/Herschel, and related statistics of strong gravitationally lensed sources; (ii) deterministic evolutionary tracks for the history of star formation and black hole accretion, gauged on a wealth of multiwavelength observations including the observed Eddington ratio distribution. We further validate these ingredients by showing their consistency with the observed galaxy stellar mass functions and AGN bolometric luminosity functions at different redshifts via the continuity equation approach. Our analysis of the main sequence for high-redshift galaxies and AGNs highlights that the present data are consistently interpreted in terms of an in situ coevolution scenario for star formation and black hole accretion, envisaging these as local, time-coordinated processes.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Comparative genomics of the genus Desulfitobacterium

The Desulfitobacterium genus comprises anaerobic Gram-positive bacteria, of which the majority are facultative organohalide respirers. We here present the genomes of eight strains of Desulfitobacterium spp., including five strains of Desulfitobacterium hafniense, one strain each from D. dichloroeliminans and D. metallireducens, and one strain that had not been assigned to any species prior to this study. The newly sequenced genomes were compared with four previously published desulfitobacterial genomes. The average genome sizes are 5.5, 4.3 and 3.4 Mbp for D. hafniense, D. dehalogenans and D. dichloroeliminans/metallireducens, respectively. The genomes encode up to seven reductive dehalogenases, the genomes of both D. hafniense DP7 and D. metallireducens 853–15A T did not encode any reductive dehalogenase. The latter result was a surprise as D. metallireducens 853–15A T has been reported to carry out organohalide respiration. Unlike reported for the pce ABCT gene cluster, the other reductive dehalogenase gene clusters do not show any signs of being genetically mobile. All analyzed desulfitobacterial genomes encode a complete cobalamin synthesis pathway. A menaquinone synthesis pathway was found in all strains except D. dichloroeliminans DCA1T. The detailed analysis of the genome sequence of 12 desulfitobacteria from four different species confirmed that this genus has an extremely large metabolic repertoire.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

A High Diversity of Eurasian Lineage Low Pathogenicity Avian Influenza A Viruses Circulate among Wild Birds Sampled in Egypt

Surveillance for influenza A viruses in wild birds has increased substantially as part of efforts to control the global movement of highly pathogenic avian influenza A (H5N1) virus. Studies conducted in Egypt from 2003 to 2007 to monitor birds for H5N1 identified multiple subtypes of low pathogenicity avian influenza A viruses isolated primarily from migratory waterfowl collected in the Nile Delta. Phylogenetic analysis of 28 viral genomes was performed to estimate their nearest ancestors and identify possible reassortants. Migratory flyway patterns were included in the analysis to assess gene flow between overlapping flyways. Overall, the viruses were most closely related to Eurasian, African and/or Central Asian lineage low pathogenicity viruses and belonged to 15 different subtypes. A subset of the internal genes seemed to originate from specific flyways (Black Sea-Mediterranean, East African-West Asian). The remaining genes were derived from a mixture of viruses broadly distributed across as many as 4 different flyways suggesting the importance of the Nile Delta for virus dispersal. Molecular clock date estimates suggested that the time to the nearest common ancestor of all viruses analyzed ranged from 5 to 10 years, indicating frequent genetic exchange with viruses sampled elsewhere. The intersection of multiple migratory bird flyways and the resulting diversity of influenza virus gene lineages in the Nile Delta create conditions favoring reassortment, as evident from the gene constellations identified by this study. In conclusion, we present for the first time a comprehensive phylogenetic analysis of full genome sequences from low pathogenic avian influenza viruses circulating in Egypt, underscoring the significance of the region for viral reassortment and the potential emergence of novel avian influenza A viruses, as well as representing a highly diverse influenza A virus gene pool that merits continued monitoring.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Structural and Functional Studies of H. seropedicae RecA Protein – Insights into the Polymerization of RecA Protein as Nucleoprotein Filament

The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. In conclusion, our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Genomewide and Enzymatic Analysis Reveals Efficient D-Galacturonic Acid Metabolism in the Basidiomycete Yeast Rhodosporidium toruloides

Biorefining of renewable feedstocks is one of the most promising routes to replace fossil-based products. Since many common fermentation hosts, such as Saccharomyces cerevisiae , are naturally unable to convert many component plant cell wall polysaccharides, the identification of organisms with broad catabolism capabilities represents an opportunity to expand the range of substrates used in fermentation biorefinery approaches. The red basidiomycete yeast Rhodosporidium toruloides is a promising and robust host for lipid- and terpene-derived chemicals. Previous studies demonstrated assimilation of a range of substrates, from C 5 /C 6 sugars to aromatic molecules similar to lignin monomers. In the current study, we analyzed the potential of R. toruloides to assimilate d -galacturonic acid, a major sugar in many pectin-rich agricultural waste streams, including sugar beet pulp and citrus peels. d -Galacturonic acid is not a preferred substrate for many fungi, but its metabolism was found to be on par with those of d -glucose and d -xylose in R. toruloides . A genomewide analysis by combined transcriptome sequencing (RNA-seq) and RB-TDNA-seq revealed those genes with high relevance for fitness on d -galacturonic acid. While R. toruloides was found to utilize the nonphosphorylative catabolic pathway known from ascomycetes, the maximal velocities of several enzymes exceeded those previously reported. In addition, an efficient downstream glycerol catabolism and a novel transcription factor were found to be important for d -galacturonic acid utilization. These results set the basis for use of R. toruloides as a potential host for pectin-rich waste conversions and demonstrate its suitability as a model for metabolic studies with basidiomycetes. The switch from the traditional fossil-based industry to a green and sustainable bioeconomy demands the complete utilization of renewable feedstocks. Many currently used bioconversion hosts are unable to utilize major components of plant biomass, warranting the identification of microorganisms with broader catabolic capacity and characterization of their unique biochemical pathways. d -Galacturonic acid is a plant component of bioconversion interest and is the major backbone sugar of pectin, a plant cell wall polysaccharide abundant in soft and young plant tissues. The red basidiomycete and oleaginous yeast Rhodosporidium toruloides has been previously shown to utilize a range of sugars and aromatic molecules. Using state-of-the-art functional genomic methods and physiological and biochemical assays, we elucidated the molecular basis underlying the efficient metabolism of d -galacturonic acid. This study identified an efficient pathway for uronic acid conversion to guide future engineering efforts and represents the first detailed metabolic analysis of pectin metabolism in a basidiomycete fungus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Whole Genome Sequencing Links Mycobacterium bovis From Cattle, Cheese and Humans in Baja California, Mexico

Mycobacterium bovis causes tuberculosis (TB) in cattle, which in turn can transmit the pathogen to humans. Tuberculosis in dairy cattle is of particular concern where the consumption of raw milk and dairy products is customary. Baja California (BCA), Mexico, presents high prevalence of TB in both cattle and humans, making it important to investigate the molecular epidemiology of the disease in the region. A long-term study was undertaken to fully characterize the diversity of M. bovis genotypes circulating in dairy cattle, cheese and humans in BCA by whole-genome sequencing (WGS). During a 2-year period, 412 granulomatous tissue samples were collected from local abattoirs and 314 cheese samples were purchased from local stores and vendors in BCA and sent to the laboratory for mycobacterial culture, histology, direct PCR and WGS. For tissue samples M. bovis was recovered from 86.8%, direct PCR detected 90% and histology confirmed 85.9% as mycobacteriosis-compatible. For cheese, M. bovis was recovered from 2.5% and direct PCR detected 6% of the samples. There was good agreement between diagnostic tests. Subsequently, a total of 345 whole-genome SNP sequences were obtained. Phylogenetic analysis grouped these isolates into 10 major clades. SNP analysis revealed putative transmission clusters where the pairwise SNP distance between isolates from different dairies was ≤3 SNP. Also, human and/or cheese isolates were within 8.45 (range 0–17) and 5.8 SNP (range 0–15), respectively, from cattle isolates. Finally, a comparison between the genotypes obtained in this study and those reported previously suggests that the genetic diversity of M. bovis in BCA is well-characterized, and can be used to determine if BCA is the likely source of M. bovis in humans and cattle in routine epidemiologic investigations and future studies. In conclusion, WGS provided evidence of ongoing local transmission of M. bovis among the dairies in this high-TB burden region of BCA, as well as show close relationships between isolates recovered from humans, cheese, and cattle. This confirms the need for a coordinated One Health approach in addressing the elimination of TB in animals and humans. Overall, the study contributes to the knowledge of the molecular epidemiology of M. bovis in BCA, providing insight into the pathogen's dynamics in a high prevalence setting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes

Transcriptional regulation of protein-coding genes is increasingly well-understood on a global scale, yet no comparable information exists for long non-coding RNA (lncRNA) genes, which were recently recognized to be as numerous as protein-coding genes in mammalian genomes. We performed a genome-wide comparative analysis of the promoters of human lncRNA and protein-coding genes, finding global differences in specific genetic and epigenetic features relevant to transcriptional regulation. These two groups of genes are hence subject to separate transcriptional regulatory programs, including distinct transcription factor (TF) proteins that significantly favor lncRNA, rather than coding-gene, promoters. We report a specific signature of promoter-proximal transcriptional regulation of lncRNA genes, including several distinct transcription factor binding sites (TFBS). Experimental DNase I hypersensitive site profiles are consistent with active configurations of these lncRNA TFBS sets in diverse human cell types. TFBS ChIP-seq datasets confirm the binding events that we predicted using computational approaches for a subset of factors. For several TFs known to be directly regulated by lncRNAs, we find that their putative TFBSs are enriched at lncRNA promoters, suggesting that the TFs and the lncRNAs may participate in a bidirectional feedback loop regulatory network. Accordingly, cells may be able to modulate lncRNA expression levels independently of mRNA levels via distinct regulatory pathways. Our results also raise the possibility that, given the historical reliance on protein-coding gene catalogs to define the chromatin states of active promoters, a revision of these chromatin signature profiles to incorporate expressed lncRNA genes is warranted in the future.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

High-Power Clock Laser Spectrally Tailored for High-Fidelity Quantum State Engineering

Highly frequency-stable lasers are ubiquitous tools for optical-frequency metrology, precision interferometry, and quantum information science. While making a universally applicable laser is unrealistic, spectral noise can be tailored for specific applications. Here we report a high-power 698-nm clock laser with a maximum output of 4W and minimized frequency noise up to a few kHz Fourier frequency, together with long-term instability of 3.5 × 10 −17 at one to thousands of seconds. The laser-frequency noise is precisely characterized with atom-based spectral analysis that employs a pulse sequence designed to suppress sensitivity to intensity noise. This method provides universally applicable tunability of the spectral response and analysis of quantum sensors over a wide frequency range. With the optimized laser system characterized by this technique, we achieve an average single-qubit Clifford gate fidelity of up to 𝐹$^2_1$ = 0.999⁢64⁢(3) when simultaneously driving 3000 optical qubits with a homogeneous Rabi frequency ranging from 10 Hz to 1 kHz. This result represents the highest single optical-qubit-gate fidelity for a large number of atoms.

atomic gases↗
DOE OSTI2023

Neutralization profiles of HIV-1 viruses from the VRC01 Antibody Mediated Prevention (AMP) trials

The VRC01 Antibody Mediated Prevention (AMP) efficacy trials conducted between 2016 and 2020 showed for the first time that passively administered broadly neutralizing antibodies (bnAbs) could prevent HIV-1 acquisition against bnAb-sensitive viruses. HIV-1 viruses isolated from AMP participants who acquired infection during the study in the sub-Saharan African (HVTN 703/HPTN 081) and the Americas/European (HVTN 704/HPTN 085) trials represent a panel of currently circulating strains of HIV-1 and offer a unique opportunity to investigate the sensitivity of the virus to broadly neutralizing antibodies (bnAbs) being considered for clinical development. Pseudoviruses were constructed using envelope sequences from 218 individuals. The majority of viruses identified were clade B and C; with clades A, D, F and G and recombinants AC and BF detected at lower frequencies. We tested eight bnAbs in clinical development (VRC01, VRC07-523LS, 3BNC117, CAP256.25, PGDM1400, PGT121, 10–1074 and 10E8v4) for neutralization against all AMP placebo viruses (n = 76). Compared to older clade C viruses (1998–2010), the HVTN703/HPTN081 clade C viruses showed increased resistance to VRC07-523LS and CAP256.25. At a concentration of 1μg/ml (IC80), predictive modeling identified the triple combination of V3/V2-glycan/CD4bs-targeting bnAbs (10-1074/PGDM1400/VRC07-523LS) as the best against clade C viruses and a combination of MPER/V3/CD4bs-targeting bnAbs (10E8v4/10-1074/VRC07-523LS) as the best against clade B viruses, due to low coverage of V2-glycan directed bnAbs against clade B viruses. Overall, the AMP placebo viruses represent a valuable resource for defining the sensitivity of contemporaneous circulating viral strains to bnAbs and highlight the need to update reference panels regularly. Our data also suggests that combining bnAbs in passive immunization trials would improve coverage of global viruses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

PWR ENDF/B-VII cross-section libraries for ORIGEN-ARP

New pressurized water reactor (PWR) cross-section libraries were generated for use with the ORIGEN-ARP depletion sequence in the SCALE nuclear analysis code system. These libraries are based on ENDF/B-VII nuclear data and were generated using the two-dimensional depletion sequence, TRITON/NEWT, in SCALE 6.1. The libraries contain multiple burnup-dependent cross-sections for seven PWR fuel designs, with enrichments ranging from 1.5 to 6 wt% {sup 235}U. The burnup range has been extended from the 72 GWd/MTU used in previous versions of the libraries to 90 GWd/MTU. Validation of the libraries using radiochemical assay measurements and decay heat measurements for PWR spent fuel showed good agreement between calculated and experimental data. Verification against detailed TRITON simulations for the considered assembly designs showed that depletion calculations performed in ORIGEN-ARP with the pre-generated libraries provide similar results as obtained with direct TRITON depletion, while greatly reducing the computation time. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2019

Structural and functional characterization of three Type B and C chloramphenicol acetyltransferases from Vibrio species

Chloramphenicol acetyltransferases (CATs) were among the first antibiotic resistance enzymes identified and have long been studied as model enzymes for examining plasmid-mediated antibiotic resistance. These enzymes acetylate the antibiotic chloramphenicol, which renders it incapable of inhibiting bacterial protein synthesis. CATs can be classified into different types: Type A CATs are known to be important for antibiotic resistance to chloramphenicol and fusidic acid. Type B CATs are often called xenobiotic acetyltransferases and adopt a similar structural fold to streptogramin acetyltransferases, which are known to be critical for streptogramin antibiotic resistance. Type C CATs have recently been identified and can also acetylate chloramphenicol, but their roles in antibiotic resistance are largely unknown. In this work, we structurally and kinetically characterized three Vibrio CAT proteins from a nonpathogenic species ( Aliivibrio fisheri ) and two important human pathogens ( Vibrio cholerae and Vibrio vulnificus ). We found all three proteins, including one in a superintegron ( V. cholerae ), acetylated chloramphenicol, but did not acetylate aminoglycosides or dalfopristin. We also determined the 3D crystal structures of these CATs alone and in complex with crystal violet and taurocholate. These compounds are known inhibitors of Type A CATs, but have not been explored in Type B and Type C CATs. Based on sequence, structure, and kinetic analysis, we concluded that the V. cholerae and V. vulnificus CATs belong to the Type B class and the A. fisheri CAT belongs to the Type C class. Ultimately, our results provide a framework for studying the evolution of antibiotic resistance gene acquisition and chloramphenicol acetylation in Vibrio and other species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Investigating the role of the transcriptional regulator Ure2 on the metabolism of Saccharomyces cerevisiae: a multi-omics approach

Ure2 regulates nitrogen catabolite repression in Saccharomyces cerevisiae. Deletion of URE2 induces a physiological state mimicking the nitrogen starvation and autophagic responses. Previous work has shown that deletion of URE2 increases the fermentation rate of some wine-producing strains of S. cerevisiae. In this work, we investigated the effect of URE2 deletion (ΔURE2) on the metabolism of S. cerevisiae. During growth on glucose, the ΔURE2 mutant grew less well than the wild type; however, it produced ethanol at higher rates. To better under the behavior of this mutant, we performed transcriptomics and metabolomics. Analysis of the RNA sequencing results and metabolite levels indicate that the mutant strain exhibited characteristics of both nitrogen starvation and autophagy. In addition, many pyruvate decarboxylase and alcohol dehydrogenase isoforms were expressed at higher rates than the wild type. The mutant also accumulated less trehalose and glycogen, and produced more lipids. These results suggest that URE2 may be a promising target for metabolic engineering in S. cerevisiae and potentially other strains of yeast as well for the production of lipid-based fuels and chemicals.

59 BASIC BIOLOGICAL SCIENCES↗