Prion proteins: evolution and preservation of secondary structure

AbstractPrions cause a variety of neurodegenerative disorders that seem to result from a conformational change in the prion protein (PrP). Thirty-two PrP sequences have been subjected to phylogenetic analysis followed by reconstruction of the most probable evolutionary spectrum of amino acid replacements. The replacement rates suggest that the protein does not seem to be very conservative, but in the course of evolution amino acids have only been substituted within the elements of the secondary structure by those with very similar physico-chemical properties. Analysis of the full spectrum of single-step amino acid substitutions in human PrP using secondary structure prediction algorithms shows an over-representation of substitutions that tend to destabilize α-helices

A "saddle-node" bifurcation scenario for birth or destruction of a Smale-Williams solenoid

Formation or destruction of hyperbolic chaotic attractor under parameter variation is considered with an example represented by Smale--Williams solenoid in stroboscopic Poincar\'{e} map of two alternately excited non-autonomous van der Pol oscillators. The transition occupies a narrow but finite parameter interval and progresses in such way that periodic orbits constituting a "skeleton" of the attractor undergo saddle-node bifurcation events involving partner orbits from the attractor and from a non-attracting invariant set, which forms together with its stable manifold a basin boundary of the attractor.Comment: 7 pages, 7 figures, 1 tabl

Chemostratigraphy of Neoproterozoic carbonates: implications for 'blind dating'

The delta C-13(carb) and Sr-87/Sr-86 secular variations in Neoproteozoic seawater have been used for the purpose of 'isotope stratigraphy' but there are a number of problems that can preclude its routine use. In particular, it cannot be used with confidence for 'blind dating'. The compilation of isotopic data on carbonate rocks reveals a high level of inconsistency between various carbon isotope age curves constructed for Neoproteozoic seawater, caused by a relatively high frequency of both global and local delta C-13(carb) fluctuations combined with few reliable age determinations. Further complication is caused by the unresolved problem as to whether two or four glaciations, and associated negative delta C-13(carb) excursions, can be reliably documented. Carbon isotope stratigraphy cannot be used alone for geological correlation and 'blind dating'. Strontium isotope stratigraphy is a more reliable and precise tool for stratigraphic correlations and indirect age determinations. Combining strontium and carbon isotope stratigraphy, several discrete ages within the 590-544 Myr interval, and two age-groups at 660-610 and 740-690 Myr can be resolved

Demonstration of the temporal matter-wave Talbot effect for trapped matter waves

We demonstrate the temporal Talbot effect for trapped matter waves using ultracold atoms in an optical lattice. We investigate the phase evolution of an array of essentially non-interacting matter waves and observe matter-wave collapse and revival in the form of a Talbot interference pattern. By using long expansion times, we image momentum space with sub-recoil resolution, allowing us to observe fractional Talbot fringes up to 10th order.Comment: 17 pages, 7 figure

Azimuthal anisotropy at RHIC: the first and fourth harmonics

We report the first observations of the first harmonic (directed flow, v_1), and the fourth harmonic (v_4), in the azimuthal distribution of particles with respect to the reaction plane in Au+Au collisions at the Relativistic Heavy Ion Collider (RHIC). Both measurements were done taking advantage of the large elliptic flow (v_2) generated at RHIC. From the correlation of v_2 with v_1 it is determined that v_2 is positive, or {\it in-plane}. The integrated v_4 is about a factor of 10 smaller than v_2. For the sixth (v_6) and eighth (v_8) harmonics upper limits on the magnitudes are reported.Comment: 6 pages with 3 figures, as accepted for Phys. Rev. Letters The data tables are at http://www.star.bnl.gov/central/publications/pubDetail.php?id=3

Pion, kaon, proton and anti-proton transverse momentum distributions from p+p and d+Au collisions at sNN=200\sqrt{s_{NN}} = 200 GeV

Identified mid-rapidity particle spectra of $\pi^{\pm}$, $K^{\pm}$, and $p(\bar{p})$ from 200 GeV p+p and d+Au collisions are reported. A time-of-flight detector based on multi-gap resistive plate chamber technology is used for particle identification. The particle-species dependence of the Cronin effect is observed to be significantly smaller than that at lower energies. The ratio of the nuclear modification factor ($R_{dAu}$) between protons $(p+\bar{p})$ and charged hadrons ($h$) in the transverse momentum range $1.2<{p_{T}}<3.0$ GeV/c is measured to be $1.19\pm0.05$(stat)$\pm0.03$(syst) in minimum-bias collisions and shows little centrality dependence. The yield ratio of $(p+\bar{p})/h$ in minimum-bias d+Au collisions is found to be a factor of 2 lower than that in Au+Au collisions, indicating that the Cronin effect alone is not enough to account for the relative baryon enhancement observed in heavy ion collisions at RHIC.Comment: 6 pages, 4 figures, 1 table. We extended the pion spectra from transverse momentum 1.8 GeV/c to 3. GeV/

Rapid selection of BRCA1-proficient tumor cells during neoadjuvant therapy for ovarian cancer in BRCA1 mutation carriers

Ovarian carcinomas (OC) often demonstrate rapid tumor shrinkage upon neoadjuvant chemotherapy (NACT). However, complete pathologic responses are very rare and the mechanisms underlying the emergence of residual tumor disease remain elusive. We hypothesized that the change of somatic BRCA1 status may contribute to this process. The loss-of-heterozygosity (LOH) at the BRCA1 locus was determined for 23 paired tumor samples obtained from BRCA1 germ-line mutation carriers before and after NACT. We observed a somatic loss of the wild-type BRCAI allele in 74% (17/23) of OCs before NACT. However, a retention of the wild-type BRCA1 copy resulting in a reversion of LOH status was detected in 65% (11/17) of those patients after NACT. Furthermore, we tested 3 of these reversion samples for LOH at intragenic BRCA1single nucleotide polymorphisms (SNPs) and confirmed a complete restoration of the SNP heterozygosity in all instances. The neoadjuvant chemotherapy for BRCA1-associated OC is accompanied by a rapid expansion of pre-existing BRCA1-proficient tumor clones suggesting that continuation of the same therapy after NACT and surgery may not be justified even in patients initially experiencing a rapid tumor regression. (C) 2017 Elsevier B.V. All rights reserved.Peer reviewe