Control of template positioning during de novo initiation of RNA synthesis by the bovine viral diarrhea virus NS5B polymerase

The RNA-dependent RNA polymerase of the hepatitis C virus and the bovine viral diarrhea virus (BVDV) is able to initiate RNA synthesis de novo in the absence of a primer. Previous crystallographic datahave pointed to the existence of a GTP-specific binding site (G-site) that is located in the vicinity of the active site of the BVDV enzyme. Here we have studied the functional role of the G-site and present evidence to show that specific GTP binding affects the positioning of the template during de novo initiation. Following the formation of the first phosphodiester bond, the polymerase translocates relative to the newly synthesized dinucleotide, which brings the 5′-end of the primer into the G-site, releasing the previously bound GTP. At this stage, the 3′-end of the template can remain opposite to the 5′-end of the primer or be repositioned to its original location before RNA synthesis proceeds. We show that the template can freely move between the two locations, and both complexes can isomerize to equilibrium. These data suggest that the bound GTP can stabilize the interaction between the 3′-end of the template and the priming nucleotide, preventing the template to overshoot and extend beyond the active site during de novo initiation. The hepatitis C virus enzyme utilizes a dinucleotide primer exclusively from the blunt end; the existence of a functionally equivalent G-site is therefore uncertain. For the BVDV polymerase we showed that de novo initiation is severely compromised by the T320A mutant that likely affects hydrogen bonding between the G-site and the guanine base. Dinucleotide-primed reactions are not influenced by this mutation, which supports the notion that the G-site is located in close proximity but not at the active site of the enzyme. © 2006 by The American Society for Biochemistry and Molecular Biology, Inc

2022 report from the Auger-TA working group on UHECR arrival directions

After over 60 years, the powerful engines that accelerate ultra-high-energy cosmic rays (UHECRs) to the formidable energies at which we observe them from Earth remain mysterious. Assuming standard physics, we expect UHECR sources to lie within the local Universe (up to a few hundred~Mpc). The distribution of matter in the local Universe is anisotropic, and we expect this anisotropy to be imprinted on the distribution of UHECR arrival directions. Even though intervening intergalactic and Galactic magnetic fields deflect charged UHECRs and can distort these anisotropies, some amount of information on the distribution of the sources is preserved. In this proceedings contribution, we present the results of the joint Pierre Auger Observatory and Telescope Array searches for (a) the largest-scale anisotropies (the harmonic dipole and quadrupole) and (b) correlations with a sample of nearby starburst galaxies and the 2MRS catalogue tracing stellar mass within~250~Mpc. This analysis updates our previous results with the most recent available data, notably with the addition of 3~years of new Telescope Array data. The main finding is a correlation between the arrival directions of $12.1\%_{-3.1\%}^{+4.5\%}$~of UHECRs detected with $E \geq 38$~EeV by~Auger or with~$E \gtrsim 49$~EeV by~TA and the positions of nearby starburst galaxies on a ${15.1\text{deg}}_{-3.0\text{deg}}^{+4.6\text{deg}}$~angular scale, with a $4.7\sigma$~post-trial significance, up from $4.2\sigma$ obtained in our previous study.Comment: proceedings of the 6th International Symposium on Ultra High Energy Cosmic Rays (UHECR2022), 3-7 October 2022, L'Aquila, Ital

Specific shifts in the endocannabinoid system in hibernating brown bears

In small hibernators, global downregulation of the endocannabinoid system (ECS), which is involved in modulating neuronal signaling, feeding behavior, energy metabolism, and circannual rhythms, has been reported to possibly drive physiological adaptation to the hibernating state. In hibernating brown bears (Ursus arctos), we hypothesized that beyond an overall suppression of the ECS, seasonal shift in endocannabinoids compounds could be linked to bear's peculiar features that include hibernation without arousal episodes and capacity to react to external disturbance. We explored circulating lipids in serum and the ECS in plasma and metabolically active tissues in free-ranging subadult Scandinavian brown bears when both active and hibernating. In winter bear serum, in addition to a 2-fold increase in total fatty acid concentration, we found significant changes in relative proportions of circulating fatty acids, such as a 2-fold increase in docosahexaenoic acid C22:6 n-3 and a decrease in arachidonic acid C20:4 n-6. In adipose and muscle tissues of hibernating bears, we found significant lower concentrations of 2-arachidonoylglycerol (2-AG), a major ligand of cannabinoid receptors 1 (CB1) and 2 (CB2). Lower mRNA level for genes encoding CB1 and CB2 were also found in winter muscle and adipose tissue, respectively. The observed reduction in ECS tone may promote fatty acid mobilization from body fat stores, and favor carbohydrate metabolism in skeletal muscle of hibernating bears. Additionally, high circulating level of the endocannabinoid-like compound N-oleoylethanolamide (OEA) in winter could favor lipolysis and fatty acid oxidation in peripheral tissues. We also speculated on a role of OEA in the conservation of an anorexigenic signal and in the maintenance of torpor during hibernation, while sustaining the capacity of bears to sense stimuli from the environment

Direct measurement of the pion valence quark momentum distribution, the pion light-cone wave function squared

We present the first direct measurements of the pion valence quark momentum distribution which is related to the square of the pion light-cone wave function. The measurements were carried out using data on diffractive dissociation of 500 GeV/c $\pi^-$ into di-jets from a platinum target at Fermilab experiment E791. The results show that the $|q\bar {q}>$ light-cone asymptotic wave function, which was developed using perturbative QCD methods, describes the data well for $Q^2 \sim 10 ~{\rm (GeV/c)^2}$ or more. We also measured the transverse momentum distribution of the diffractive di-jets.Comment: 13 pages, 4 figure

UHECR results of combined analyses of TA and Auger experiments

The origin of ultra-high-energy cosmic rays (UHECRs) is still unknown. Their sources are believed to be within the local universe (a few hundred megaparsecs), but deflections by intergalactic and Galactic magnetic fields prevent us from straightforwardly associating UHECRs to their sources based on their arrival directions, making their angular distribution mostly isotropic. At higher energies, the number of potential source candidates and the magnetic deflections are both expected to be smaller, but so is the available amount of statistics. Hence, it is interesting to perform searches for anisotropies using several different energy thresholds. With a threshold of 8 EeV a dipole modulation has been discovered, and with higher thresholds evidence is mounting for correlations with certain nearby galaxies. Neither of the two main UHECR detectors, the Pierre Auger Observatory and the Telescope Array project, has full-sky coverage. Full-sky searches require combining the datasets of both, and a working group with members of both collaborations has been tasked with this. We present an overview of the challenges encountered in such analyses, recent results from the working group, possible ways of interpreting them, and an outlook for the near future

Sn-Beta zeolites with borate salts catalyse the epimerization of carbohydrates via an intramolecular carbon shift

Carbohydrate epimerization is an essential technology for the widespread production of rare sugars. In contrast to other enzymes, most epimerases are only active on sugars substituted with phosphate or nucleotide groups, thus drastically restricting their use. Here we show that Sn-Beta zeolite in the presence of sodium tetraborate catalyses the selective epimerization of aldoses in aqueous media. Specifically, a 5 wt% aldose (for example, glucose, xylose or arabinose) solution with a 4:1 aldose:sodium tetraborate molar ratio reacted with catalytic amounts of Sn-Beta yields near-equilibrium epimerization product distributions. The reaction proceeds by way of a 1,2 carbon shift wherein the bond between C-2 and C-3 is cleaved and a new bond between C-1 and C-3 is formed, with C-1 moving to the C-2 position with an inverted configuration. This work provides a general method of performing carbohydrate epimerizations that surmounts the main disadvantages of current enzymatic and inorganic processes.National Science Foundation (U.S.). Materials Research Science and Engineering Centers (Program) (Award DMR-0819762)DuPont MIT Alliance (Graduate Research Fellowship)National Institutes of Health (U.S.) (Grant EB-001960)National Institutes of Health (U.S.) (Grant EB-002026)National Science Foundation (U.S.). Graduate Research Fellowship Program (Grant 1122374