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Results for “Lilith”
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Lilith: An Enduring Plutonium Critical Assembly [Slides]
A design of an enduring Pu critical assembly has been produced. This is very important to DOE/NNSA missions. This assembly would result in advances/improvements in nuclear data validation, analytical methods validation, dosimetry, reactor kinetics, materials, and more.
Carbohydrate Deacetylase Unique to Gut Microbe Bacteroides Reveals Atypical Structure
Bacteroides are often the most abundant, commensal species in the gut microbiome of industrialized human populations. One of the most commonly detected species is Bacteroides ovatus. It has been linked to benefits like the suppression of intestinal inflammation but is also correlated with some autoimmune disorders, for example irritable bowel disorder (IBD). Bacterial cell surface carbohydrates, like capsular polysaccharides (CPS), may play a role in modulating these varied host interactions. Recent studies have begun to explore the diversity of CPS loci in Bacteroides; however, there is still much unknown. Here, we present structural and functional characterization of a putative polysaccharide deacetylase from Bacteroides ovatus (BoPDA) encoded in a CPS biosynthetic locus. We solved four high resolution crystal structures (1.36-1.56 Å) of the enzyme bound to divalent cations Co 2+ , Ni 2+ , Cu 2+ , or Zn 2+ and performed carbohydrate binding and deacetylase activity assays. Structural analysis of BoPDA revealed an atypical domain architecture that is unique to this enzyme, with a carbohydrate esterase 4 (CE4) superfamily catalytic domain inserted into a carbohydrate binding module (CBM). Additionally, BoPDA lacks the canonical CE4 His-His-Asp metal binding motif and our structures show it utilizes a noncanonical His-Asp dyad to bind metal ions. BoPDA is the first protein involved in CPS biosynthesis from B. ovatus to be characterized, furthering our understanding of significant biosynthetic processes in this medically relevant gut microbe.
Tre-DST: A Drug Susceptibility Test for Mycobacterium tuberculosis Using Solvatochromic Trehalose Probes
In 2024, an estimated 10 million people developed Tuberculosis (TB), nearly half a million of whom were infected with drug-resistant tuberculosis (DR-TB). Early detection of infection and drug resistance enables rapid engagement in effective care. Bacterial culture and nucleic acid testing remain the primary diagnostic methods, with smear microscopy being phased out. However, these methods present significant limitations for diagnosing drug resistance, such as lengthy time-to-result for phenotypic tests, as well as the need for prior knowledge of resistance mutations and prohibitive cost for molecular tests. To address this, we developed a rapid phenotypic TB drug susceptibility test, termed Tre-DST, based on novel metabolically incorporated trehalose probes, which specifically detect live mycobacteria. We used the nonpathogenic Mycobacterium smegmatis and the virulence-attenuated Mycobacterium tuberculosis (Mtb) H37Ra or auxotrophic Mtb to demonstrate a strong correlation between cost-effective plate reader results and flow cytometry data, suggesting that the plate reader is a suitable fluorescence detector for Tre-DST. We determined that adding a 1-week incubation step allowed Mtb samples originally seeded at 10 4 CFU/mL to become detectable, over 2 weeks earlier than colony-forming unit analysis. We found that Tre-DST reports on drug susceptibility in a drug-agnostic manner, demonstrating loss of fluorescence with frontline TB drugs as well as the newer drug bedaquiline. Tre-DST distinguished RIF- and INH-resistant auxotrophs from susceptible controls and accurately reported the resistance activity. Ultimately, because Tre-DST is agnostic to mechanisms of drug resistance, this assay is likely compatible with all WHO-recommended and future DR-TB drugs as a diagnostic in reference laboratories.
Systematics of the chemical freeze-out line in the high baryon density regime explored at SIS100
The systematic uncertainties of chemical freeze-out fits at SIS100 energies (Au+Au reactions at $\sqrt{s_{NN}}$ = 3 – 5 GeV) are studied using UrQMD simulations. Although hadron production in UrQMD does not occur on a sharp chemical freeze-out hyper-surface, the extracted fit quality is shown to be very good. The extracted chemical parameters depend on the selected hadron species as well as the underlying equation of state (EoS) of the matter. Including light nuclei and anti-protons in the fit increases the expected freeze-out temperature, while a stiffer EoS increases the obtained chemical potential. Similarly, the baryon densities extracted by the thermal fits depend on the choice of hadrons as well as the underlying equation of state. These results are important for the upcoming CBM@FAIR physics program and highlight that a degree of caution is advised when one relates the chemical freeze-out curve to features on the QCD phase diagram like the critical endpoint or a possible phase transition.