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Charles R. Watts Mihaly Mezei Richard F. Murphy Sándor Lovas 《Journal of biomolecular structure & dynamics》2013,31(5):733-748
Abstract The conformational space available to GnRH and 1GnRH-III was compared using 5.2 ns constant temperature and pressure molecular dynamics simulations with explicit TIP3P solvation and the AMBER v. 5.0 force field. Cluster analysis of both trajectories resulted in two groups of conformations. Results of free energy calculations, in agreement with previous experimental data, indicate that a conformation with a turn from residues 5 through 8 is preferred for GnRH in an aqueous environment. By contrast, a conformation with a helix from residues 2 through 7 with a bend from residues 6 through 10 is preferred for 1GnRH-III in an aqueous environment. The side chains of His2 and Trp3 in 1GnRH-III occupy different regions of phase space and participate in weakly polar interactions different from those in GnRH. The unique conformational properties of 1GnRH-III may account for its specific anti cancer activity. 相似文献
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Hugh F. Davies Willie Rioli Jos Puruntatameri Willie Roberts Colin Kerinaiua Vivian Kerinauia Kim Brooks Womatakimi Graeme R. Gillespie Brett P. Murphy 《Austral ecology》2019,44(5):868-879
Since European settlement, many granivorous birds of northern Australia's savanna landscapes have declined. One such example, the partridge pigeon (Geophaps smithii), has suffered a significant range contraction, disappearing from at least half of its pre‐European range. Multiple factors have been implicated in this decline, including the loss of traditional Aboriginal burning practices, grazing by large exotic herbivores and predation by feral cats (Felis catus). While populations of partridge pigeon on the Tiwi Islands may be particularly important for the long‐term persistence of this species, they too may be at risk of decline. However, as a reliable method to detect this species has not yet been developed and tested, we lack the ability to identify, at an early stage, the species' decline in a given location or region. This severely limits our capacity to make informed management decisions. Here, we demonstrate that the standard camera trapping approach for native mammal monitoring in northern Australia attained an overall probability of detecting partridge pigeon greater than 0.98. We thus provide a robust estimate of partridge pigeon site occupancy (0.30) on Melville Island, the larger of the two main Tiwi Islands. The information presented here for the partridge pigeon represents a critical first step towards the development of optimal monitoring programmes with which to gauge population trajectories, as well as the response to remedial management actions. In the face of ongoing biodiversity loss, such baseline information is vital for management agencies to make informed decisions and should therefore be sought for as many species as possible. 相似文献
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Hugh A. L. Henry Stephen D. Murphy Mhairi L. McFarlane Heather Barna Katelyn Dunning Alexandra Hood Jill C. Crosthwaite 《Restoration Ecology》2019,27(2):457-465
While best practices for evaluating restoration ecology projects are emerging rapidly, budget constraints often limit postrestoration monitoring, which emphasizes the need for practical and efficient monitoring strategies. We examined the postrestoration outcome for an ENGO (Nature Conservancy of Canada) project, to assess retroactively how variation in intensity and frequency of sampling would have affected estimates of plant species composition, diversity, and richness over time. The project restored four habitat types (mesic forest, oak woodland, wet meadow, and sand barren) using sculptured seeding of tallgrass prairie and woody species. Species‐level plant cover was monitored annually for 10 years in 168 2 × 2–m quadrats. We performed randomization tests to examine estimates of species diversity and richness as a function of the number of quadrats sampled, and assessed the necessity of annual sampling for describing changes in species composition and successional trajectories. The randomization tests revealed that sampling 10–17 quadrats, depending on habitat type, was sufficient to obtain estimates of species diversity that were at least 95% of values obtained from the whole dataset. Species richness as a function of number of quadrats sampled did not plateau, which suggests that rather than increasing the number of sampling quadrats, richness could be estimated more efficiently using nonquadrat based sampling techniques. Nonmetric multidimensional scaling analysis revealed that plant species composition largely stabilized by 3–5 years postrestoration depending on habitat type. By that time, native, seeded species dominated the restoration, and the benefits of annual sampling for tracking changes in species composition diminished. 相似文献
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Andrew R. J. Murphy David J. Scanlan Yin Chen Gary D. Bending John P. Hammond Elizabeth M. H. Wellington Ian D. E. A. Lidbury 《Environmental microbiology》2022,24(4):1902-1917
Bacteria possess various regulatory mechanisms to detect and coordinate a response to elemental nutrient limitation. In pseudomonads, the two-component system regulators CbrAB, NtrBC and PhoBR, are responsible for regulating cellular response to carbon (C), nitrogen (N) and phosphorus (P) respectively. Phosphonates are reduced organophosphorus compounds produced by a broad range of biota and typified by a direct C-P bond. Numerous pseudomonads can use the environmentally abundant phosphonate species 2-aminoethylphosphonate (2AEP) as a source of C, N, or P, but only PhoBR has been shown to play a role in 2AEP utilization. On the other hand, utilization of 2AEP as a C and N source is considered substrate inducible. Here, using the plant-growth-promoting rhizobacterium Pseudomonas putida BIRD-1 we present evidence that 2AEP utilization is under dual regulation and only occurs upon depletion of C, N, or P, controlled by CbrAB, NtrBC, or PhoBR respectively. However, the presence of 2AEP was necessary for full gene expression, i.e. expression was substrate inducible. Mutation of a LysR-type regulator, termed AepR, upstream of the 2AEP transaminase-phosphonatase system (PhnWX), confirmed this dual regulatory mechanism. To our knowledge, this is the first study identifying coordination between global stress response and substrate-specific regulators in phosphonate metabolism. 相似文献
100.
DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals 总被引:1,自引:0,他引:1 下载免费PDF全文
Min‐Sheng Peng Long Fan Ni‐Ni Shi Tiao Ning Yong‐Gang Yao Robert W. Murphy Wen‐Zhi Wang Ya‐Ping Zhang 《Molecular ecology resources》2015,15(5):1238-1242
Mitochondrial DNA (mtDNA) is widely used in various genetic studies of domesticated animals. Many applications require comprehensive knowledge about the phylogeny of mtDNA variants. Herein, we provide the most up‐to‐date mtDNA phylogeny (i.e. haplogroup tree or matrilineal genealogy) and a standardized hierarchical haplogroup nomenclature system for domesticated cattle, dogs, goats, horses, pigs, sheep, yaks and chickens. These high‐resolution mtDNA haplogroup trees based on 1240 complete or near‐complete mtDNA genome sequences are available in open resource DomeTree ( http://www.dometree.org ). In addition, we offer the software MitoToolPy ( http://www.mitotool.org/mp.html ) to facilitate the mtDNA data analyses. We will continuously and regularly update DomeTree and MitoToolPy. 相似文献