Dynamic removal of replication protein A by Dna2 facilitates primer cleavage during Okazaki fragment processing in Saccharomyces cerevisiae

Eukaryotic Okazaki fragments are initiated by an RNA/DNA primer, which is removed before the fragments are joined. Polymerase d displaces the primer into a flap for processing. Dna2 nuclease/helicase and flap endonuclease 1 (FEN1) are proposed to cleave the flap. The single-stranded DNA binding protein, replication protein A (RPA), governs cleavage activity. Flap-bound RPA inhibits FEN1. This necessitates cleavage by Dna2, which is stimulated by RPA. FEN1 then cuts the remaining RPA-free flap to create a nick for ligation. Cleavage by Dna2 requires that it enter the 5'-end and track down the flap. Since Dna2 cleaves the RPA-bound flap, we investigated the mechanism by which Dna2 accesses the protein-coated flap for cleavage. Using a nuclease-defective Dna2 mutant, we showed that just binding of Dna2 dissociates the flap-bound RPA. Facile dissociation is specific to substrates with a genuine flap, and will not occur with an RPA-coated single strand. We also compared the cleavage patterns of Dna2 with and without RPA to better define RPA stimulation of Dna2. Stimulation derived from removal of DNA folding in the flap. Apparently, coordinated with its dissociation, RPA relinquishes the flap to Dna2 for tracking in a way that does not allow flap structure to reform. We also found that RPA strand melting activity promotes excessive flap elongation, but it is suppressed by Dna2-promoted RPA dissociation. Overall, results indicate that Dna2 and RPA coordinate their functions for efficient flap cleavage and preparation for FEN1

Meteorology of Jupiter's Equatorial Hot Spots and Plumes from Cassini

We present an updated analysis of Jupiter's equatorial meteorology from Cassini observations. For two months preceding the spacecraft's closest approach, the Imaging Science Subsystem (ISS) onboard regularly imaged the atmosphere. We created time-lapse movies from this period in order to analyze the dynamics of equatorial hot spots and their interactions with adjacent latitudes. Hot spots are quasi-stable, rectangular dark areas on visible-wavelength images, with defined eastern edges that sharply contrast with surrounding clouds, but diffuse western edges serving as nebulous boundaries with adjacent equatorial plumes. Hot spots exhibit significant variations in size and shape over timescales of days and weeks. Some of these changes correspond with passing vortex systems from adjacent latitudes interacting with hot spots. Strong anticyclonic gyres present to the south and southeast of the dark areas appear to circulate into hot spots. Impressive, bright white plumes occupy spaces in between hot spots. Compact cirrus-like 'scooter' clouds flow rapidly through the plumes before disappearing within the dark areas. These clouds travel at 150-200 m/s, much faster than the 100 m/s hot spot and plume drift speed. This raises the possibility that the scooter clouds may be more illustrative of the actual jet stream speed at these latitudes. Most previously published zonal wind profiles represent the drift speed of the hot spots at their latitude from pattern matching of the entire longitudinal image strip. If a downward branch of an equatorially-trapped Rossby waves controls the overall appearance of hot spots, however, the westward phase velocity of the wave leads to underestimates of the true jet stream speed.Comment: 33 pages, 11 figures; accepted for publication in Icarus; for supplementary movies, please contact autho

Light front synchronization and rest frame densities of the proton: Electromagnetic densities

We clarify the physical origin and meaning of the two-dimensional relativistic densities of the light front formalism. The densities are shown to originate entirely from the use of light front time instead of instant form time, which physically corresponds to using an alternative synchronization convention. This is shown by using tilted light front coordinates, which consist of light front time and ordinary spatial coordinates, and which are also used to show that the obtained densities describe a system at rest rather than at infinite momentum. These coordinates allow all four components of the electromagnetic current density to be given clear physical meanings. We explicate the formalism for spin-half targets, obtaining charge and current densities of the proton and neutron using empirical form factor parametrizations, as well as up and down quark densities and currents. Angular modulations in the densities of transversely-polarized states are explained as originating from redshifts and blueshifts due to quarks moving in different longitudinal directions.Comment: 26 pages, 7 figures, version accepted for publicatio

On the true meaning of spatial densities of hadrons

We clarify the meaning of spatial densities of hadrons. A physical density is given by the expectation value of a local operator for a physical state, and depends on both internal structure and the hadron's wave packet. In some particular cases, the physical density can be written as a convolution between a density function that depends on internal structure but not wave packet, and a smearing function that depends on wave packet but not internal structure. In these cases, the former constitutes a true internal density of the hadron. We show that the light front densities often encountered in the literature qualify as true densities in this respect, but that instant form densities obtained through wave packet localization do not. We additionally clarify that Breit frame densities constitute apparent internal densities of hadrons prepared in broad wave packets, but do not provide a complete description of hadron spatial structure.Comment: 19 pages, 4 figure

Synchronization effects on rest frame energy and momentum densities in the proton

We obtain two-dimensional relativistic densities and currents of energy and momentum in a proton at rest. These densities are obtained at surfaces of fixed light front time, which physically corresponds to using an alternative synchronization convention. Mathematically, this is done using tilted light front coordinates, which consist of light front time and ordinary spatial coordinates. In this coordinate system, all sixteen components of the energy-momentum tensor (when written in the mixed representation) obtain clear physical interpretations, and the nine Galilean components reproduce results from standard light front coordinates (several of which we report for the first time). We find several optical synchronization effects that are absent in instant form densities, indicating motion within the target. Spin-zero and spin-half targets both exhibit an internal longitudinal energy flux related to the $D(t)$ form factor, and transversely-polarized spin-half targets exhibit an energy dipole moment -- which evaluates to $-1/4$ for all targets if the Belinfante EMT is used, but which is target dependent and vanishes for pointlike fermions if the asymmetric EMT is instead used.Comment: 29 pages, 8 figure

Mass decomposition of the pion in the 't Hooft model

We obtain the energy-momentum tensor (EMT) in the 't Hooft model of two-dimensional quantum chromodynamics. The EMT is decomposed into contributions from quark and gluon fields, with all of the (plus component of) the light front momentum being carried by the quark field. The energy is split between quark and gluon fields, with the gluon field carrying the self-energy of the dressed quarks. We consider the pion in the limit of small but non-zero quark masses -- which has previously withstood numerical treatment -- as as a concrete example. We solve for the pion wave function using a variational method and obtain numerical results for its energy breakdown into quark and gluon contributions.Comment: 10 pages, 4 figure

Probing the distance and morphology of the Large Magellanic Cloud with RR Lyrae stars

We present a Bayesian analysis of the distances to 15,040 Large Magellanic Cloud (LMC) RR Lyrae stars using $V$- and $I$-band light curves from the Optical Gravitational Lensing Experiment, in combination with new $z$-band observations from the Dark Energy Camera. Our median individual RR Lyrae distance statistical error is 1.89 kpc (fractional distance error of 3.76 per cent). We present three-dimensional contour plots of the number density of LMC RR Lyrae stars and measure a distance to the core LMC RR Lyrae centre of ${50.2482\pm0.0546 {\rm(statistical)} \pm0.4628 {\rm(systematic)} {\rm kpc}}$, equivalently ${\mu_{\rm LMC}=18.5056\pm0.0024 {\rm(statistical)} \pm0.02 {\rm(systematic)}}$. This finding is statistically consistent with and four times more precise than the canonical value determined by a recent meta-analysis of 233 separate LMC distance determinations. We also measure a maximum tilt angle of $11.84^{\circ}\pm0.80^{\circ}$ at a position angle of $62^\circ$, and report highly precise constraints on the $V$, $I$, and $z$ RR Lyrae period--magnitude relations. The full dataset of observed mean-flux magnitudes, derived colour excess ${E(V-I)}$ values, and fitted distances for the 15,040 RR Lyrae stars produced through this work is made available through the publication's associated online data.Comment: 7 pages, 8 figure

Multiplex stress resistance in cells from long‐lived dwarf mice

Mutations that extend nematode longevity by interference with IGF‐I/insulin sensing pathways also lead to resistance to multiple forms of stress. Here, we report that skin‐derived fibroblasts from Snell dwarf mice, already known to show increased longevity and delayed aspects of aging, are resistant to multiple forms of cellular stress, including UV light, heat, paraquat, H2O2, and the toxic metal cadmium. The findings suggest that increases in cellular resistance to stress may mediate extended longevity in mammals.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154324/1/fsb2fj021092fje-sup-0001-S1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154324/2/fsb2fj021092fje.pd