Dominant gain-of-function mutations in Hsp104p reveal crucial roles for the middle region

Heat-shock protein 104 (Hsp104p) is a protein-remodeling factor that promotes survival after extreme stress by disassembling aggregated proteins and can either promote or prevent the propagation of prions (protein-based genetic elements). Hsp104p can be greatly overexpressed without slowing growth, suggesting tight control of its powerful protein-remodeling activities. We isolated point mutations in Hsp104p that interfere with this control and block cell growth. Each mutant contained alterations in the middle region (MR). Each of the three MR point mutations analyzed in detail had distinct phenotypes. In combination with nucleotide binding site mutations, Hsp104p(T499I) altered bud morphology and caused septin mislocalization, colocalizing with the misplaced septins. Point mutations in the septin Cdc12p suppressed this phenotype, suggesting that it is due to direct Hsp104p–septin interactions. Hsp104p(A503V) did not perturb morphology but stopped cell growth. Remarkably, when expressed transiently, the mutant protein promoted survival after extreme stress as effectively as did wild-type Hsp104p. Hsp104p(A509D) had no deleterious effects on growth or morphology but had a greatly reduced ability to promote thermotolerance. That mutations in an 11-amino acid stretch of the MR have such profound and diverse effects suggests the MR plays a central role in regulating Hsp104p function

Quantum System Identification by Bayesian Analysis of Noisy Data: Beyond Hamiltonian Tomography

We consider how to characterize the dynamics of a quantum system from a restricted set of initial states and measurements using Bayesian analysis. Previous work has shown that Hamiltonian systems can be well estimated from analysis of noisy data. Here we show how to generalize this approach to systems with moderate dephasing in the eigenbasis of the Hamiltonian. We illustrate the process for a range of three-level quantum systems. The results suggest that the Bayesian estimation of the frequencies and dephasing rates is generally highly accurate and the main source of errors are errors in the reconstructed Hamiltonian basis.Comment: 6 pages, 3 figure

Mesoscopic Effects in Quantum Phases of Ultracold Quantum Gases in Optical Lattices

We present a wide array of quantum measures on numerical solutions of 1D Bose- and Fermi-Hubbard Hamiltonians for finite-size systems with open boundary conditions. Finite size effects are highly relevant to ultracold quantum gases in optical lattices, where an external trap creates smaller effective regions in the form of the celebrated "wedding cake" structure and the local density approximation is often not applicable. Specifically, for the Bose-Hubbard Hamiltonian we calculate number, quantum depletion, local von-Neumann entropy, generalized entanglement or Q-measure, fidelity, and fidelity susceptibility; for the Fermi-Hubbard Hamiltonian we also calculate the pairing correlations, magnetization, charge-density correlations, and antiferromagnetic structure factor. Our numerical method is imaginary time propagation via time-evolving block decimation. As part of our study we provide a careful comparison of canonical vs. grand canonical ensembles and Gutzwiller vs. entangled simulations. The most striking effect of finite size occurs for bosons: we observe a strong blurring of the tips of the Mott lobes accompanied by higher depletion, and show how the location of the first Mott lobe tip approaches the thermodynamic value as a function of system size.Comment: 13 pages, 10 figure

Efficient Algorithms for Optimal Control of Quantum Dynamics: The "Krotov'' Method unencumbered

Efficient algorithms for the discovery of optimal control designs for coherent control of quantum processes are of fundamental importance. One important class of algorithms are sequential update algorithms generally attributed to Krotov. Although widely and often successfully used, the associated theory is often involved and leaves many crucial questions unanswered, from the monotonicity and convergence of the algorithm to discretization effects, leading to the introduction of ad-hoc penalty terms and suboptimal update schemes detrimental to the performance of the algorithm. We present a general framework for sequential update algorithms including specific prescriptions for efficient update rules with inexpensive dynamic search length control, taking into account discretization effects and eliminating the need for ad-hoc penalty terms. The latter, while necessary to regularize the problem in the limit of infinite time resolution, i.e., the continuum limit, are shown to be undesirable and unnecessary in the practically relevant case of finite time resolution. Numerical examples show that the ideas underlying many of these results extend even beyond what can be rigorously proved.Comment: 19 pages, many figure

Leaf Fragment Identification of Subtropical Native Grass Species

The present study was carried out to characterise leaf fragments of important plant species of a subtropical native sward in the southernmost state of Brazil. Thirteen important grass species were collected from April to May 1999. Both sides of the leaves were observed using a stereomicroscope. In addition, two approaches were tested to provide a clearer characterisation of the leaves of each species: the leaves were either dried or frozen. The kind and number of veins, the kind and number of hair, and the arrangements and number of stomates on both sides of each leaf are the most useful characteristics to differentiate fragments of native grass species’ leaves. These characteristics can be more easily observed when the plant material is dried

Analysis of RNA-Seq datasets reveals enrichment of tissue-specific splice variants for nuclear envelope proteins

<p>Laminopathies yield tissue-specific pathologies, yet arise from mutation of ubiquitously-expressed genes. A little investigated hypothesis to explain this is that the mutated proteins or their partners have tissue-specific splice variants. To test this, we analyzed RNA-Seq datasets, finding novel isoforms or isoform tissue-specificity for: Lap2, linked to cardiomyopathy; Nesprin 2, linked to Emery-Dreifuss muscular dystrophy and Lmo7, that regulates the Emery-Dreifuss muscular dystrophy linked emerin gene. Interestingly, the muscle-specific Lmo7 exon is rich in serine phosphorylation motifs, suggesting regulatory function. Muscle-specific splice variants in non-nuclear envelope proteins linked to other muscular dystrophies were also found. Nucleoporins tissue-specific variants were found for Nup54, Nup133, Nup153 and Nup358/RanBP2. RT-PCR confirmed novel Lmo7 and RanBP2 variants and specific knockdown of the Lmo7 variantreduced myogenic index. Nuclear envelope proteins were enriched for tissue-specific splice variants compared to the rest of the genome, suggesting that splice variants contribute to its tissue-specific functions.</p

Constraints on relaxation rates for N-level quantum systems

We study the constraints imposed on the population and phase relaxation rates by the physical requirement of completely positive evolution for open N-level systems. The Lindblad operators that govern the evolution of the system are expressed in terms of observable relaxation rates, explicit formulas for the decoherence rates due to population relaxation are derived, and it is shown that there are additional, non-trivial constraints on the pure dephasing rates for N>2. Explicit experimentally testable inequality constraints for the decoherence rates are derived for three and four-level systems, and the implications of the results are discussed for generic ladder-, Lambda- and V-systems, and transitions between degenerate energy levels.Comment: 10 pages, RevTeX, 4 figures (eps/pdf