Directed evolution of Vibrio fischeri LuxR for improved response to butanoyl-homoserine lactone

LuxR is the 3-oxohexanoyl-homoserine lactone (3OC6HSL) dependent transcriptional activator of the prototypical acyl-homoserine lactone (AHL) quorum sensing system of Vibrio fischeri. Wild-type LuxR exhibits no response to butanoyl-HSL (C4HSL) in quantitative bioassays at concentrations of up to 1 µM; a previously described LuxR variant (LuxR-G2E) exhibits a broadened response to diverse AHLs, including pentanoyl-HSL (C5HSL), but not to C4HSL. Here, two rounds of directed evolution of LuxR-G2E generated variants of LuxR that responded to C4HSL at concentrations as low as 10 nM. One variant, LuxR-G4E, had only one change, I45F, relative to the parent LuxR-G2E, which itself differs from wild-type at three residues. Dissection of the four mutations within LuxR-G4E demonstrated that at least three of these changes were simultaneously required to achieve any measurable C4HSL response. The four changes improved both sensitivity and specificity towards C4HSL relative to any of the other 14 possible combinations of those residues. These data confirm that LuxR is evolutionarily pliable and suggest that LuxR is not intrinsically asymmetric in its response to quorum sensing signals with different acyl-side chain lengths

Novel cell adhesion/migration pathways are predictive markers of HDAC inhibitor resistance in cutaneous T cell lymphoma

BACKGROUND: Treatment for Cutaneous T Cell Lymphoma (CTCL) is generally not curative. Therefore, selecting therapy that is effective and tolerable is critical to clinical decision-making. Histone deacetylase inhibitors (HDACi), epigenetic modifier drugs, are commonly used but effective in only ~30% of patients. There are no predictive markers of HDACi response and the CTCL histone acetylation landscape remains unmapped. We sought to identify pre-treatment molecular markers of resistance in CTCL that progressed on HDACi therapy. METHODS: Purified T cells from 39 pre/post-treatment peripheral blood samples and skin biopsies from 20 patients were subjected to RNA-seq and ChIP-seq for histone acetylation marks (H3K14/9 ac, H3K27ac). We correlated significant differences in histone acetylation with gene expression in HDACi-resistant/sensitive CTCL. We extended these findings in additional CTCL patient cohorts (RNA-seq, microarray) and using ELISA in matched CTCL patient plasma. FINDINGS: Resistant CTCL exhibited high levels of histone acetylation, which correlated with increased expression of 338 genes (FDR \u3c 0·05), including some novel to CTCL: BIRC5 (anti-apoptotic); RRM2 (cell cycle); TXNDC5, GSTM1 (redox); and CXCR4, LAIR2 (cell adhesion/migration). Several of these, including LAIR2, were elevated pre-treatment in HDACi-resistant CTCL. In CTCL patient plasma (n = 6), LAIR2 protein was also elevated (p \u3c 0·01) compared to controls. INTERPRETATION: This study is the first to connect genome-wide differences in chromatin acetylation and gene expression to HDACi-resistance in primary CTCL. Our results identify novel markers with high pre-treatment expression, such as LAIR2, as potential prognostic and/or predictors of HDACi-resistance in CTCL. FUNDING: NIH:CA156690, CA188286; NCATS: WU-ICTS UL1 TR000448; Siteman Cancer Center: CA091842

Understanding the decision to marry versus cohabit: the role of interpersonal dedication and constraints and the impact on life satisfaction

The current study explored men's and women's reasons for choosing to marry rather than to cohabit using a national data set (n = 786) of adults who were currently married or had been married previously. Using commitment theory participant's open-ended reasons for choosing to marry were coded into categories of either interpersonal dedication or constraint commitment. A variety of demographic, attitudinal, and relationship history variables were then used to predict commitment type. The influence of commitment type during the decision to marry on life satisfaction was also explored. Results indicate that current marital status (being married vs. being divorced or separated) and cohabiting before marriage were the strongest predictors of interpersonal dedication reasons for marriage for both men and women. Level of conventionality and parents' marital status also emerged as significant predictors of constraint commitment. Finally, marrying for reasons related to interpersonal dedication significantly predicted higher life satisfaction for men but not for women

Coherent electronic transfer in quantum dot systems using adiabatic passage

We describe a scheme for using an all-electrical, rapid, adiabatic population transfer between two spatially separated dots in a triple-quantum dot system. The electron spends no time in the middle dot and does not change its energy during the transfer process. Although a coherent population transfer method, this scheme may well prove useful in incoherent electronic computation (for example quantum-dot cellular automata) where it may provide a coherent advantage to an otherwise incoherent device. It can also be thought of as a limiting case of type II quantum computing, where sufficient coherence exists for a single gate operation, but not for the preservation of superpositions after the operation. We extend our analysis to the case of many intervening dots and address the issue of transporting quantum information through a multi-dot system.Comment: Replaced with (approximately) the published versio

High precision quantum control of single donor spins in silicon

The Stark shift of the hyperfine coupling constant is investigated for a P donor in Si far below the ionization regime in the presence of interfaces using Tight-binding and Band Minima Basis approaches and compared to the recent precision measurements. The TB electronic structure calculations included over 3 million atoms. In contrast to previous effective mass based results, the quadratic Stark coefficient obtained from both theories agrees closely with the experiments. This work represents the most sensitive and precise comparison between theory and experiment for single donor spin control. It is also shown that there is a significant linear Stark effect for an impurity near the interface, whereas, far from the interface, the quadratic Stark effect dominates. Such precise control of single donor spin states is required particularly in quantum computing applications of single donor electronics, which forms the driving motivation of this work.Comment: 5 pages, 2 figure

Uncertainty estimates and L_2 bounds for the Kuramoto-Sivashinsky equation

We consider the Kuramoto-Sivashinsky (KS) equation in one spatial dimension with periodic boundary conditions. We apply a Lyapunov function argument similar to the one first introduced by Nicolaenko, Scheurer, and Temam, and later improved by Collet, Eckmann, Epstein and Stubbe, and Goodman, to prove that ||u||_2 < C L^1.5. This result is slightly weaker than that recently announced by Giacomelli and Otto, but applies in the presence of an additional linear destabilizing term. We further show that for a large class of Lyapunov functions \phi the exponent 1.5 is the best possible from this line of argument. Further, this result together with a result of Molinet gives an improved estimate for L_2 boundedness of the Kuramoto-Sivashinsky equation in thin rectangular domains in two spatial dimensions.Comment: 17 pages, 1 figure; typos corrected, references added; figure modifie