Stochastic protein folding simulation in the three-dimensional HP-model

We present results from three-dimensional protein folding simulations in the HP-model on ten benchmark problems. The simulations are executed by a simulated annealing-based algorithm with a time-dependent cooling schedule. The neighbourhood relation is determined by the pull-move set. The results provide experimental evidence that the maximum depth D of local minima of the underlying energy landscape can be upper bounded by D < n(2/3). The local search procedure employs the stopping criterion (In/delta)(D/gamma) where m is an estimation of the average number of neighbouring conformations, gamma relates to the mean of non-zero differences of the objective function for neighbouring conformations, and 1-delta is the confidence that a minimum conformation has been found. The bound complies with the results obtained for the ten benchmark problems. (c) 2008 Elsevier Ltd. All rights reserved.

Ionic Liquid-Based Routes to Conversion or Reuse of Recycled Ammonium Perchlorate

New, potentially green, and efficient synthetic routes for the remediation and/or re-use of perchlorate-based energetic materials have been developed. Four simple organic imidazolium- and phosphonium-based perchlorate salts/ionic liquids have been synthesized by simple, inexpensive, and nonhazardous methods, using ammonium perchlorate as the perchlorate source. By appropriate choice of the cation, perchlorate can be incorporated into an ionic liquid which serves as its own electrolyte for the electrochemical reduction of the perchlorate anion, allowing for the regeneration of the chloride-based parent ionic liquid. The electrochemical degradation of the hazardous perchlorate ion and its conversion to harmless chloride during electrolysis was studied using IR and Cl-35 NMR spectroscopies.

On the dissolution of non-metallic solid elements (sulfur, selenium, tellurium and phosphorus) in ionic liquids

Ionic liquids are shown to be good solvents for elemental sulfur, selenium, phosphorus and tellurium, and can be designed to maximise the solubility of these elements. The presence of the [S-3](center dot-) radical anion in diluted solutions of sulfur in some ionic liquids has been confirmed, and is the origin of their intense blue colour (cf. lapis lazuli).

Ranking of microRNA target prediction scores by Pareto front analysis

Over the past ten years, a variety of microRNA target prediction methods has been developed, and many of the methods are constantly improved and adapted to recent insights into miRNA-mRNA interactions. In a typical scenario, different methods return different rankings of putative targets, even if the ranking is reduced to selected mRNAs that are related to a specific disease or cell type. For the experimental validation it is then difficult to decide in which order to process the predicted miRNA-mRNA bindings, since each validation is a laborious task and therefore only a limited number of mRNAs can be analysed. We propose a new ranking scheme that combines ranked predictions from several methods and - unlike standard thresholding methods - utilises the concept of Pareto fronts as defined in multi-objective optimisation. In the present study, we attempt a proof of concept by applying the new ranking scheme to hsa-miR-21, hsa-miR-125b, and hsa-miR-373 and prediction scores supplied by PITA and RNAhybrid. The scores are interpreted as a two-objective optimisation problem, and the elements of the Pareto front are ranked by the STarMir score with a subsequent re-calculation of the Pareto front after removal of the top-ranked mRNA from the basic set of prediction scores. The method is evaluated on validated targets of the three miRNA, and the ranking is compared to scores from DIANA-microT and TargetScan. We observed that the new ranking method performs well and consistent, and the first validated targets are elements of Pareto fronts at a relatively early stage of the recurrent procedure. which encourages further research towards a higher-dimensional analysis of Pareto fronts. (C) 2010 Elsevier Ltd. All rights reserved.

Electron attachment to 2-nitro-m-xylene

Electron attachment to nitroaromatic compound 2-nitro-m-xylene in gas phase has been performed utilizing a double focusing two sector mass spectrometer with high mass resolution (m/Delta m approximate to 2500). At low energy (below 20 eV), electron interactions with the neutral 2-nitro-m-xylene molecule reveal a very rich fragmentation pattern. A total of 60 fragment anions have been detected and the ion yield for all observed negative ions has been recorded as a function of the incident electron energy, among them a long lived (metastable) non-dissociated parent anion which is formed at energies near zero eV, and some ions observed at the mass numbers 26,42 and 121. Comparison of calculated isotopic patterns with measured ion yields for these fragment anions and their successors in the mass spectrum, allows the assignment of the chemical composition of these fragments as CN- (26 Da), CNO- (42 Da) and C8H9O- (121 Da). Electron attachment to 2-nitro-m-xylene leads to anion formation at four energy ranges. Between 0 eV and 2 eV only few product ions are formed. Between 4.6 eV and 6.1 eV all fragment anions are formed and for most of them the anion yield reaches its maximum value in this range. NO2- which is the most abundant product [M-H](-) and O- are the only fragments that exhibit a feature at 7.4eV, 8.1 eV and 7.9eV, respectively. About half of the fragment anions exhibit a broad, mostly low-intensity resonance between 9 eV and 10 eV. (C) 2009 Elsevier B.V. All rights reserved.

Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target.

Transcription in eukaryotic genomes generates an extensive array of non-protein-coding RNA, the functional significance of which is mostly unknown. We are investigating the link between non-coding RNA and chromatin regulation through analysis of FLC - a regulator of flowering time in Arabidopsis and a target of several chromatin pathways. Here we use an unbiased strategy to characterize non-coding transcripts of FLC and show that sense/antisense transcript levels correlate in a range of mutants and treatments, but change independently in cold-treated plants. Prolonged cold epigenetically silences FLC in a Polycomb-mediated process called vernalization. Our data indicate that upregulation of long non-coding antisense transcripts covering the entire FLC locus may be part of the cold-sensing mechanism. Induction of these antisense transcripts occurs earlier than, and is independent of, other vernalization markers and coincides with a reduction in sense transcription. We show that addition of the FLC antisense promoter sequences to a reporter gene is sufficient to confer cold-induced silencing of the reporter. Our data indicate that cold-induced FLC antisense transcripts have an early role in the epigenetic silencing of FLC, acting to silence FLC transcription transiently. Recruitment of the Polycomb machinery then confers the epigenetic memory. Antisense transcription events originating from 3' ends of genes might be a general mechanism to regulate the corresponding sense transcription in a condition/stage-dependent manner.

Dinoflagellate cyst-based reconstructions of mid to late Holocene winter sea-surface temperature and productivity from an anoxic fjord in the NE Pacific Ocean

Published contemporary dinoflagellate distributional data from the NE Pacific margin and estuarine environments (n = 136) were re-analyzed using Canonical Correspondence Analysis (CCA) and partial Canonical Correspondence Analysis (pCCA). These analyses illustrated the dominant controls of winter temperature and productivity on the distribution of dinoflagellate cysts in this region. Dinoflagellate cyst-based predictive models for winter temperature and productivity were developed from the contemporary distributional data using the modern analogue technique and applied to subfossil data from two mid to late Holocene (~5500 calendar years before present–present) cores; TUL99B03 and TUL99B11, collected from Effingham Inlet, a 15 km long anoxic fjord located on the southwest coast of Vancouver Island that directly opens to the Pacific Ocean through Barkley Sound. Sedimentation within these basins largely comprises annually deposited laminated couplets, each made up of a winter deposited terrigenous layer and spring to fall deposited diatomaceous layer. The Effingham Inlet dinoflagellate cyst record provides evidence of a mid-Holocene gradual decline in winter SST, ending with the initiation of neoglacial advances in the region by ~3500 cal BP. A reconstructed Late Holocene increase in winter SST was initiated by a weakening of the California Current, which would have resulted in a warmer central gyre and more El Niño-like conditions.