Molecular mechanisms underlying a cellular analog of operant reward learning.

Operant conditioning is a ubiquitous but mechanistically poorly understood form of associative learning in which an animal learns the consequences of its behavior. Using a single-cell analog of operant conditioning in neuron B51 of Aplysia, we examined second-messenger pathways engaged by activity and reward and how they may provide a biochemical association underlying operant learning. Conditioning was blocked by Rp-cAMP, a peptide inhibitor of PKA, a PKC inhibitor, and by expressing a dominant-negative isoform of Ca2+-dependent PKC (apl-I). Thus, both PKA and PKC were necessary for operant conditioning. Injection of cAMP into B51 mimicked the effects of operant conditioning. Activation of PKC also mimicked conditioning but was dependent on both cAMP and PKA, suggesting that PKC acted at some point upstream of PKA activation. Our results demonstrate how these molecules can interact to mediate operant conditioning in an individual neuron important for the expression of the conditioned behavior

ERβ Binds N-CoR in the Presence of Estrogens via an LXXLL-like Motif in the N-CoR C-terminus

Nuclear receptors (NRs) usually bind the corepressors N-CoR and SMRT in the absence of ligand or in the presence of antagonists. Agonist binding leads to corepressor release and recruitment of coactivators. Here, we report that estrogen receptor β (ERβ) binds N-CoR and SMRT in the presence of agonists, but not antagonists, in vitro and in vivo. This ligand preference differs from that of ERα interactions with corepressors, which are inhibited by estradiol, and resembles that of ERβ interactions with coactivators. ERβ /N-CoR interactions involve ERβ AF-2, which also mediates coactivator recognition. Moreover, ERβ recognizes a sequence (PLTIRML) in the N-CoR C-terminus that resembles coactivator LXXLL motifs. Inhibition of histone deacetylase activity specifically potentiates ERβ LBD activity, suggesting that corepressors restrict the activity of AF-2. We conclude that the ER isoforms show completely distinct modes of interaction with a physiologically important corepressor and discuss our results in terms of ER isoform specificity in vivo

Allosteric Conversation in the Androgen Receptor Ligand-Binding Domain Surfaces

Androgen receptor (AR) is a major therapeutic target that plays pivotal roles in prostate cancer (PCa) and androgen insensitivity syndromes. Wepreviously proposed that compounds recruited to ligand-binding domain (LBD) surfaces could regulate AR activity in hormone-refractory PCa and discovered several surface modulators of AR function. Surprisingly, the most effective compounds bound preferentially to a surface of unknown function [binding function 3 (BF-3)] instead of the coactivator-binding site [activation function 2 (AF-2)]. Different BF-3 mutations have been identified in PCa or androgen insensitivity syndrome patients, and they can strongly affect AR activity. Further, comparison of AR x-ray structures with and without bound ligands at BF-3 and AF-2 showed structural coupling between both pockets. Here, we combine experimental evidence and molecular dynamic simulations to investigate whether BF-3 mutations affect AR LBD function and dynamics possibly via allosteric conversation between surface sites. Our data indicate that AF-2 conformation is indeed closely coupled to BF-3 and provide mechanistic proof of their structural interconnection. BF-3 mutations may function as allosteric elicitors, probably shifting the AR LBD conformational ensemble toward conformations that alter AF-2 propensity to reorganize into subpockets that accommodate N-terminal domain and coactivator peptides. The induced conformation may result in either increased or decreased AR activity. Activating BF-3 mutations also favor the formation of another pocket (BF-4) in the vicinity of AF-2 and BF-3, which we also previously identified as a hot spot for a small compound. We discuss the possibility that BF-3 may be a protein-docking site that binds to the N-terminal domain and corepressors. AR surface sites are attractive pharmacological targets to develop allosteric modulators that might be alternative lead compounds for drug design. © 2012 by The Endocrie Society

Theoretical Studies of Electron Transfer in Metal Dimers: XY+→X+Y, Where X, Y=Be, Mg, Ca, Zn, Cd

The electronic matrix element responsible for electron exchange in a series of metal dimers was calculated using ab initio wave functions. The distance dependence is approximately exponential for a large range of internuclear separations. A localized description, where the two nonorthogonal structures characterizing the electron localized at the left and right sites are each obtained self‐consistently, is found to provide the best description of the electron exchange process. We find that Gaussian basis sets are capable of predicting the expected exponential decay of the electronic interactions even at quite large internuclear distances

Fast parallel skew and prefix‐doubling suffix array construction on the GPU

Suffix arrays are fundamental full-text index data structures of importance to a broad spectrum of applications in such fields as bioinformatics, Burrows-Wheeler Transform (BWT)-based lossless data compression, and information retrieval. In this work, we propose and implement two massively parallel approaches on the GPU based on two classes of suffix array construction algorithms. The first, parallel skew, makes algorithmic improvements to the previous work of Deo and Keely to achieve a speedup of 1.45x over their work. The second, a hybrid skew and prefix-doubling implementation, is the first of its kind on the GPU and achieves a speedup of 2.3–4.4x over Osipov’s prefix-doubling and 2.4–7.9x over our skew implementation on large datasets. Our implementations rely on two efficient parallel primitives, a merge and a segmented sort. We theoretically analyze the two formulations of suffix array construction algorithms and show performance comparisons on a large variety of practical inputs. We conclude that, with the novel use of our efficient segmented sort, prefix-doubling is more competitive than skew on the GPU. We also demonstrate the effectiveness of our methods in our implementations of the Burrows-Wheeler transform and in a parallel FM-index for pattern searching. This is the submitted version of the paper

An Unrecognized Source of PCB Contamination in Schools and Other Buildings

An investigation of 24 buildings in the Greater Boston Area revealed that one-third (8 of 24) contained caulking materials with polychlorinated biphenyl (PCB) content exceeding 50 ppm by weight, which is the U.S. Environmental Protection Agency (U.S. EPA) specified limit above which this material is considered to be PCB bulk product waste. These buildings included schools and other public buildings. In a university building where similar levels of PCB were found in caulking material, PCB levels in indoor air ranged from 111 to 393 ng/m(3); and in dust taken from the building ventilation system, < 1 ppm to 81 ppm. In this building, the U.S. EPA mandated requirements for the removal and disposal of the PCB bulk product waste as well as for confirmatory sampling to ensure that the interior and exterior of the building were decontaminated. Although U.S. EPA regulations under the Toxic Substances Control Act stipulate procedures by which PCB-contaminated materials must be handled and disposed, the regulations apparently do not require that materials such as caulking be tested to determine its PCB content. This limited investigation strongly suggests that were this testing done, many buildings would be found to contain high levels of PCBs in the building materials and potentially in the building environment. The presence of PCBs in schools is of particular concern given evidence suggesting that PCBs are developmental toxins

Learning the Words: Supervising Teachers and the Language of Impact in an Initial Teacher Education Programme

The language of “impact” has been foregrounded in the recent lexicon of Australian initial teacher education (ITE). How teacher education programmes and supervising teachers identify and assess the impact of pre-service teachers’ work with learners across a professional placement is a pressing issue for ITE providers. This paper reports on qualitative analysis of the language of supervising teachers’ summative assessments of pre-service teachers’ final-year professional experience placements in relation to impact. Analysis of written comments that addressed the Australian Professional Standards for Teachers Graduate Standards revealed that the language of impact is still emerging within the discourse of supervising teachers. This has professional learning implications for all ITE stakeholders