Scalable molecular dynamics with NAMD

Author: Phillips, J.C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R.D.; Kale, L.; Schulten, K. Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts…

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Prediction of EF-hand calcium-binding proteins and analysis of bacterial EF-hand proteins

Author: Zhou, Y.; Yang, W.; Kirberger, M.; Lee, H.-W.; Ayalasomayajula, G.; Yang, J.J. Description: The EF-hand protein with a helix-loop-helix Ca(2+) binding motif constitutes one of the largest protein families and is involved in numerous biological processes. To facilitate the understanding of the role of Ca(2+) in biological systems using genomic information, we report, herein, our improvement on the pattern search method for the identification of EF-hand and EF-like Ca(2+)-binding proteins. The canonical EF-hand patterns are modified to cater to different flanking structural elements. In addition, on the basis of…

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FtsK is an essential cell division protein that is localized to the septum and induced as part of the SOS response

Author: Wang, L.; Lutkenhaus, J. Description: The role of ftsK in the growth of Escherichia coli was examined by turning off its expression. This resulted in smooth filaments without constrictions, indicating that FtsK was required at an early step in septation. Consistent with this, FtsK was found to localize to the septum in 70% of the cells, indicating that it was recruited relatively early in this process. FtsK localization required the function of FtsZ and FtsA but not FtsI and FtsQ. Consistent with this, Z rings were present in FtsK-depleted…

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SPCA1 pumps and Hailey-Hailey disease

Author: Missiaen, L.; Raeymaekers, L.; Dode, L.; Vanoevelen, J.; Van Baelen, K.; Parys, J.B.; Callewaert, G.; De Smedt, H.; Segaert, S.; Wuytack, F. Description: Both the endoplasmic reticulum and the Golgi apparatus are agonist-sensitive intracellular Ca2+ stores. The Golgi apparatus has Ca2+-release channels and a Ca2+-uptake mechanism consisting of sarco(endo)plasmic-reticulum Ca2+-ATPases (SERCA) and secretory-pathway Ca2+-ATPases (SPCA). SPCA1 has been shown to transport both Ca2+ and Mn2+ in the Golgi lumen and therefore plays an important role in the cytosolic and intra-Golgi Ca2+ and Mn2+ homeostasis. Human genetic studies have provided…

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Molecular call and response: the physiology of bacterial small RNAs

Author: Richards, G.R.; Vanderpool, C.K. Description: The vital role of bacterial small RNAs (sRNAs) in cellular regulation is now well-established. Although many diverse mechanisms by which sRNAs bring about changes in gene expression have been thoroughly described, comparatively less is known about their biological roles and effects on cell physiology. Nevertheless, for some sRNAs, insight has been gained into the intricate regulatory interplay that is required to sense external environmental and internal metabolic cues and turn them into physiological outcomes. Here, we review examples of regulation by selected sRNAs, emphasizing…

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An inducible DNA replication-cell division coupling mechanism in E. coli

Author: Huisman, O.; D’Ari, R. Description: Cell division is a tightly regulated periodic process. In steady-state cultures of Enterobacteriaceae, division takes place at a well defined cell mass and is strictly coordinated with DNA replication. In wild-type Escherichia coli the formation of cells lacking DNA is very rare, and interruptions of DNA replication arrest cell division. The molecular bases of this replication-division coupling have been elusive but several models have been proposed. It has been suggested, for example, that the termination of a round of DNA replication may trigger a…

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Integration of balance and strength training into daily life activity to reduce rate of falls in older people (the LiFE study): randomised parallel trial

Author: Clemson, L.; Fiatarone Singh, M.A.; Bundy, A.; Cumming, R.G.; Manollaras, K.; O’Loughlin, P.; Black, D. Description: OBJECTIVES: To determine whether a lifestyle integrated approach to balance and strength training is effective in reducing the rate of falls in older, high risk people living at home. DESIGN: Three arm, randomized parallel trial; assessments at baseline and after six and 12 months. Randomization done by computer generated random blocks, stratified by sex and fall history and concealed by an independent secure website. SETTING: Residents in metropolitan Sydney, Australia. PARTICIPANTS: Participants aged…

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Can patient-provider interaction increase the effectiveness of medical treatment or even substitute it? An exploration on why and how to study the specific effect of the provider

Author: Neumann, M.; Edelhauser, F.; Kreps, G.L.; Scheffer, C.; Lutz, G.; Tauschel, D.; Visser, A. Description: OBJECTIVE: Numerous studies demonstrate the impact of high-quality patient-provider interaction (PPI) on health outcomes. However, transformation of these findings into clinical practice is still a crucial problem. One reason might be that health communication research rarely investigated whether PPI can increase the effectiveness of medical treatment and/or even substitute it. Therefore, our objective was to provide empirical and methodological background of why and how to investigate the specific effect of the provider on patients’…

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Monitoring and mapping of hydrogen sulphide emissions across an active geothermal field: Rotorua, New Zealand

Author: Horwell, C. J.; Patterson, J. E.; Gamble, J. A.; Allen, A. G. Description: Hydrogen sulphide (H2S) is one of a number of gaseous species associated with geothermal activity in the Taupo Volcanic Zone (TVZ), New Zealand. The city of Rotorua is located within Rotorua Caldera in the TVZ and is one of the few urban areas in the world where a large population (>60,000 people) is frequently exposed to geothermal emissions. In order to evaluate the health hazard from long-term exposure to H2S being emitted from the Rotorua geothermal…

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Quantitative analysis of emergence of seedlings from buried weed seeds with increasing soil depth

Author: Benvenuti, Stefano; Macchia, Mario; Miele, Sergio Description: Trials were carried out to investigate the effects of seed burial depth on seedling emergence rate of 20 weed species. Marked depth-mediated variation in emergence ability of the different species was observed, together with a general pattern of decreasing emergence with increasing soil depth. At 10 cm, only johnsongrass, velvetleaf, catchweed bedstraw, and cutleaf geranium emerged, albeit only in limited numbers. Species most severely inhibited by burial depth were buckhorn plantain, large crabgrass, common purslane, chickweed, and corn spurry, none of which…

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