81 research outputs found
An effective all-atom potential for proteins
We describe and test an implicit solvent all-atom potential for simulations
of protein folding and aggregation. The potential is developed through studies
of structural and thermodynamic properties of 17 peptides with diverse
secondary structure. Results obtained using the final form of the potential are
presented for all these peptides. The same model, with unchanged parameters, is
furthermore applied to a heterodimeric coiled-coil system, a mixed alpha/beta
protein and a three-helix-bundle protein, with very good results. The
computational efficiency of the potential makes it possible to investigate the
free-energy landscape of these 49--67-residue systems with high statistical
accuracy, using only modest computational resources by today's standards
Synthesis and structure of polymorph B of zeolite Beta
[EN] It was found that either polymorph B or polymorph C of zeolite beta can be obtained from the same structure directing agent: 4,4-dimethyl-4-azonia-tricyclo[5.2.2.0(2,6)] undec-8-ene hydroxide. The synthesis occurs through a consecutive process where polymorph B is first formed and then transformed into polymorph C. It is possible to produce a zeolite highly enriched in polymorph B, provided that the transformation of this phase into polymorph C is slowed down up to the point where polymorph C is only detected at trace levels. The structure of polymorph B was determined for the first time by electron crystallography with SAED and HRTEM from areas of unfaulted polymorph B crystals.Financial support from the Spanish Government (Project MAT2006-14274-C02â01) and the EU Commission (TOPCOMBI Project) is gratefully acknowledged. M.M. thanks CSIC for an I3P grant. J.S. is supported by a postdoctoral grant from the Carl Trygger Foundation. The Berzelii Centre EXSELENT is supported by the Swedish Research Council (VR) and the Swedish Governmental Agency for Innovation Systems (VINNOVA).Corma CanĂłs, A.; Moliner Marin, M.; Cantin Sanz, A.; DĂaz Cabañas, MJ.; Jorda Moret, JL.; Zhang, D.; Sun, J.... (2008). Synthesis and structure of polymorph B of zeolite Beta. Chemistry of Materials. 20(9):3218-3223. doi:10.1021/cm8002244S3218322320
Idebenone reduces respiratory complications in patients with Duchenne muscular dystrophy
In Duchenne muscular dystrophy (DMD), progressive loss of respiratory function leads to restrictive pulmonary disease and places patients at significant risk for severe respiratory complications. Of particular concern are ineffective cough, secretion retention and recurrent respiratory tract infections. In a Phase 3 randomized controlled study (DMD Long-term Idebenone Study, DELOS) in DMD patients 10â18 years of age and not taking concomitant glucocorticoid steroids, idebenone (900âmg/day) reduced significantly the loss of respiratory function over a 1-year study period. In a post-hoc analysis of DELOS we found that more patients in the placebo group compared to the idebenone group experienced bronchopulmonary adverse events (BAEs): placebo: 17 of 33 patients, 28 events; idebenone: 6 of 31 patients, 7 events. The hazard ratios (HR) calculated âby patientâ (HR 0.33, pâ=â0.0187) and for âall BAEsâ (HR 0.28, pâ=â0.0026) indicated a clear idebenone treatment effect. The overall duration of BAEs was 222 days (placebo) vs. 82 days (idebenone). In addition, there was also a difference in the use of systemic antibiotics utilized for the treatment of BAEs. In the placebo group, 13 patients (39.4%) reported 17 episodes of antibiotic use compared to 7 patients (22.6%) reporting 8 episodes of antibiotic use in the idebenone group. Furthermore, patients in the placebo group used systemic antibiotics for longer (105 days) compared to patients in the idebenone group (65 days). This post-hoc analysis of DELOS indicates that the protective effect of idebenone on respiratory function is associated with a reduced risk of bronchopulmonary complications and a reduced need for systemic antibiotics
Mechanics and thermodynamics of a new minimal model of the atmosphere
The understanding of the fundamental properties of the climate system has long benefitted from the use of simple numerical models able to parsimoniously represent the essential ingredients of its processes. Here, we introduce a new model for the atmosphere that is constructed by supplementing the now-classic Lorenz â96 one-dimensional lattice model with temperature-like variables. The model features an energy cycle that allows for energy to be converted between the kinetic form and the potential form and for introducing a notion of efficiency. The modelâs evolution is controlled by two contributionsâa quasi-symplectic and a gradient one, which resemble (yet not conforming to) a metriplectic structure. After investigating the linear stability of the symmetric fixed point, we perform a systematic parametric investigation that allows us to define regions in the parameters space where at steady-state stationary, quasi-periodic, and chaotic motions are realised, and study how the terms responsible for defining the energy budget of the system depend on the external forcing injecting energy in the kinetic and in the potential energy reservoirs. Finally, we find preliminary evidence that the model features extensive chaos. We also introduce a more complex version of the model that is able to accommodate for multiscale dynamics and that features an energy cycle that more closely mimics the one of the Earthâs atmosphere
Phylogeographic Analysis Elucidates the Influence of the Ice Ages on the Disjunct Distribution of Relict Dragonflies in Asia
Unusual biogeographic patterns of closely related groups reflect events in the past, and molecular analyses can help to elucidate these events. While ample research on the origin of disjunct distributions of different organism groups in the Western Paleartic has been conducted, such studies are rare for Eastern Palearctic organisms. In this paper we present a phylogeographic analysis of the disjunct distribution pattern of the extant species of the strongly cool-adapted Epiophlebia dragonflies from Asia. We investigated sequences of the usually more conserved 18 S rDNA and 28 S rDNA genes and the more variable sequences of ITS1, ITS2 and CO2 of all three currently recognised Epiophlebia species and of a sample of other odonatan species. In all genes investigated the degrees of similarity between species of Epiophlebia are very high and resemble those otherwise found between different populations of the same species in Odonata. This indicates that substantial gene transfer between these populations occurred in the comparatively recent past. Our analyses imply a wide distribution of the ancestor of extant Epiophlebia in Southeast Asia during the last ice age, when suitable habitats were more common. During the following warming phase, its range contracted, resulting in the current disjunct distribution. Given the strong sensitivity of these species to climatic parameters, the current trend to increasing global temperatures will further reduce acceptable habitats and seriously threaten the existences of these last representatives of an ancient group of Odonata
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