Structural and mutagenic analysis of the RM controller protein C.Esp1396I

Bacterial restriction-modification (RM) systems are comprised of two complementary enzymatic activities that prevent the establishment of foreign DNA in a bacterial cell: DNA methylation and DNA restriction. These two activities are tightly regulated to prevent over-methylation or auto-restriction. Many Type II RM systems employ a controller (C) protein as a transcriptional regulator for the endonuclease gene (and in some cases, the methyltransferase gene also). All high-resolution structures of C-protein/DNA-protein complexes solved to date relate to C.Esp1396I, from which the interactions of specific amino acid residues with DNA bases and/or the phosphate backbone could be observed. Here we present both structural and DNA binding data for a series of mutations to the key DNA binding residues of C.Esp1396I. Our results indicate that mutations to the backbone binding residues (Y37, S52) had a lesser affect on DNA binding affinity than mutations to those residues that bind directly to the bases (T36, R46), and the contributions of each side chain to the binding energies are compared. High-resolution X-ray crystal structures of the mutant and native proteins showed that the fold of the proteins was unaffected by the mutations, but also revealed variation in the flexible loop conformations associated with DNA sequence recognition. Since the tyrosine residue Y37 contributes to DNA bending in the native complex, we have solved the structure of the Y37F mutant protein/DNA complex by X-ray crystallography to allow us to directly compare the structure of the DNA in the mutant and native complexes

Thermohaline mixing in low-mass giants: RGB and beyond

Thermohaline mixing has recently been proposed to occur in low mass red giants, with large consequence for the chemical yields of low mass stars. We investigate the role of thermohaline mixing during the evolution of stars between 1 Msun and 3 Msun. We use a stellar evolution code which includes rotational mixing and internal magnetic fields. We confirm that thermohaline mixing has the potential to destroy most of the helium 3 which is produced earlier on the main sequence during the red giant stage, in stars below 1.5Msun. We find this process to continue during core helium burning and beyond. We find rotational and magnetic mixing to be negligible compared to the thermohaline mixing in the relevant layers, even if the interaction of thermohaline motions with the differential rotation may be essential to establish the time scale of thermohaline mixing in red giants.Comment: Proceedings of the Conference "Unsolved problems in stellar physics" - Cambridge, July 200

Long GRBs from binary stars: runaway, Wolf-Rayet progenitors

The collapsar model for long gamma-ray bursts requires a rapidly rotating Wolf-Rayet star as progenitor. We test the idea of producing rapidly rotating Wolf-Rayet stars in massive close binaries through mass accretion and consecutive quasi-chemically homogeneous evolution; the latter had previously been shown to provide collapsars below a certain metallicity threshold for single stars. The binary channel presented here may provide a means for massive stars to obtain the high rotation rates required to evolve quasi-chemically homogeneous and fulfill the collapsar scenario. Moreover, it suggests that a possibly large fraction of long gamma-ray bursts occurs in runaway stars.Comment: To appear in the proceedings of the conference "Unsolved problems in stellar physics" - Cambridge, July 200

Some Remarks on Effective Range Formula in Potential Scattering

In this paper, we present different proofs of very recent results on the necessary as well as sufficient conditions on the decrease of the potential at infinity for the validity of effective range formulas in 3-D in low energy potential scattering (Andr\'e Martin, private communication, to appear. See Theorem 1 below). Our proofs are based on compact formulas for the phase-shifts. The sufficiency conditions are well-known since long. But the necessity of the same conditions for potentials keeping a constant sign at large distances are new. All these conditions are established here for dimension 3 and for all angular momenta $\ell \geq 0$

Electron-Phonon Interactions in C28_{28}-derived Molecular Solids

We present {\it ab initio} density-functional calculations of molecular solids formed from C$_{28}$-derived closed-shell fullerenes. Solid C$_{28}$H$_4$ is found to bind weakly and exhibits many of the electronic structure features of solid C$_{60}$ with an enhanced electron-phonon interaction potential. We show that chemical doping of this structure is feasible, albeit more restrictive than its C$_{60}$ counterpart, with an estimated superconducting transition temperature exceeding those of the alkali-doped C$_{60}$ solids.Comment: Lower quality postscript file for Figure 1 is used in the manuscript in order to meet submission quota for pre-print server. Higher quality postscript file available from author: [email protected] This article has been updated to reflect changes incorporated during the peer review process. It is published in PRB 70, 140504(R) 200

The cost of stochastic resetting

Resetting a stochastic process has been shown to expedite the completion time of some complex task, such as finding a target for the first time. Here we consider the cost of resetting by associating a cost to each reset, which is a function of the distance travelled during the reset event. We compute the Laplace transform of the joint probability of first passage time $t_f$, number of resets $N$ and resetting cost $C$, and use this to study the statistics of the total cost. We show that in the limit of zero resetting rate the mean cost is finite for a linear cost function, vanishes for a sub-linear cost function and diverges for a super-linear cost function. This result contrasts with the case of no resetting where the cost is always zero. For the case of an exponentially increasing cost function we show that the mean cost diverges at a finite resetting rate. We explain this by showing that the distribution of the cost has a power-law tail with continuously varying exponent that depends on the resetting rate.Comment: 22 pages, 7 figure

Mott-Hubbard insulators for systems with orbital degeneracy

We study how the electron hopping reduces the Mott-Hubbard band gap in the limit of a large Coulomb interaction U and as a function of the orbital degeneracy N. The results support the conclusion that the hopping contribution grows as roughly \sqrt{N}W, where W is the one-particle band width, but in certain models a crossover to a \sim NW behavior is found for a sufficiently large N.Comment: 7 pages, revtex, 6 figures more information at http://www.mpi-stuttgart.mpg.de/dokumente/andersen/fullerene

A consistent derivation of the quark--antiquark and three quark potentials in a Wilson loop context

In this paper we give a new derivation of the quark-antiquark potential in the Wilson loop context. This makes more explicit the approximations involved and enables an immediate extension to the three-quark case. In the $q\overline{q}$ case we find the same semirelativistic potential obtained in preceding papers but for a question of ordering. In the $3q$ case we find a spin dependent potential identical to that already derived in the literature from the ad hoc and non correct assumption of scalar confinement. Furthermore we obtain the correct form of the spin independent potential up to the $1/m^2$ order.Comment: 30 pages, Revtex (3 figures available as hard copies only), IFUM 452/F

Effect of Pre-breeding Weight and MGA Supplementation on Heifer Performance

Developing heifers to reach a target weight of 50% of mature body weight at the beginning of the breeding season is an effective method for reducing heifer development cost. Net costs to produce a bred yearling heifer and 2-year-old cow were lower when heifers were developed to 50% rather than 55% of mature body weight, regardless of breeding season length. Administration of oral progestin to heifers developed to 50% mature body weight prior to breeding did not affect reproductive performance during the first breeding season when heifers were exposed to bulls 13 days after the end of progestin treatment