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981.
Poplar and shrub willow energy crops in the United States: field trial results from the multiyear regional feedstock partnership and yield potential maps based on the PRISM‐ELM model
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Timothy A. Volk Bill Berguson Christopher Daly Michael D. Halbleib Raymond Miller Timothy G. Rials Lawrence P. Abrahamson Dan Buchman Marylin Buford Michael W. Cunningham Mark Eisenbies Eric S. Fabio Karl Hallen Justin Heavey Gregg A Johnson Yulia A Kuzovkina Bo Liu Bernie Mcmahon Randy Rousseau Shun Shi Richard Shuren Lawrence B. Smart Glen Stanosz Brain Stanton Bryce Stokes Jeff Wright 《Global Change Biology Bioenergy》2018,10(10):735-751
To increase the understanding of poplar and willow perennial woody crops and facilitate their deployment for the production of biofuels, bioproducts, and bioenergy, there is a need for broadscale yield maps. For national analysis of woody and herbaceous crops production potential, biomass feedstock yield maps should be developed using a common framework. This study developed willow and poplar potential yield maps by combining data from a network of willow and poplar field trials and the modeling power of PRISM‐ELM. Yields of the top three willow cultivars across 17 sites ranged from 3.60 to 14.6 Mg ha?1 yr?1 dry weight, while the yields from 17 poplar trials ranged from 7.5 to 15.2 Mg ha?1 yr?1. Relationships between the environmental suitability estimates from the PRISM‐ELM model and results from field trials had an R2 of 0.60 for poplar and 0.81 for willow. The resulting potential yield maps reflected the range of poplar and willow yields that have been reported in the literature. Poplar covered a larger geographic range than willow, which likely reflects the poplar breeding efforts that have occurred for many more decades using genotypes from a broader range of environments than willow. While the field trial data sets used to develop these models represent the most complete information at the time, there is a need to expand and improve the model by monitoring trials over multiple cutting cycles and across a broader range of environmental gradients. Despite some limitations, the results of these models represent a dramatic improvement in projections of potential yield of poplar and willow crops across the United States. 相似文献
982.
Chaperone-mediated reduction of RepA dimerization is associated with RepA conformational change 总被引:2,自引:1,他引:1
RepA, the initiator protein of plasmid P1, binds to multiple sites (iterons) in the origin. The binding normally requires participation of chaperones, DnaJ, DnaK and GrpE. When purified, RepA appears dimeric and is inactive in iteron binding. On reaction with chaperones, a species active in iteron binding is formed and found to be monomeric. To test whether the chaperones can reduce dimerization, RepA was used to replace the dimerization domain of the λ repressor. The hybrid protein repressed the λ operator efficiently, indicating that RepA can dimerize in vivo . A further increase in repressor activity was seen in dnaJ mutant cells. These results are consistent with a chaperone-mediated reduction of RepA dimerization. We also found that RepA mutants defective in dimerization still depend on DnaJ for iteron binding. Conversely, RepA mutants that no longer require chaperones for iteron binding remain dimerization proficient. These results indicate that the chaperone dependence of RepA activity is not solely owing to RepA dimerization. Our results are most simply explained by a chaperone-mediated conformational change in RepA protomer that activates iteron binding. This conformational change also results in reduced RepA dimerization. 相似文献
983.
A trait‐based approach for predicting species responses to environmental change from sparse data: how well might terrestrial mammals track climate change?
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Luca Santini Thomas Cornulier James M. Bullock Stephen C. F. Palmer Steven M. White Jenny A. Hodgson Greta Bocedi Justin M. J. Travis 《Global Change Biology》2016,22(7):2415-2424
Estimating population spread rates across multiple species is vital for projecting biodiversity responses to climate change. A major challenge is to parameterise spread models for many species. We introduce an approach that addresses this challenge, coupling a trait‐based analysis with spatial population modelling to project spread rates for 15 000 virtual mammals with life histories that reflect those seen in the real world. Covariances among life‐history traits are estimated from an extensive terrestrial mammal data set using Bayesian inference. We elucidate the relative roles of different life‐history traits in driving modelled spread rates, demonstrating that any one alone will be a poor predictor. We also estimate that around 30% of mammal species have potential spread rates slower than the global mean velocity of climate change. This novel trait‐space‐demographic modelling approach has broad applicability for tackling many key ecological questions for which we have the models but are hindered by data availability. 相似文献
984.
985.
Justin Warne Gareth Pryce Julia M. Hill Xiao Shi Felicia Lenner?s Fabiola Puentes Maarten Kip Laura Hilditch Paul Walker Michela I. Simone A. W. Edith Chan Greg J. Towers Alun R. Coker Michael R. Duchen Gyorgy Szabadkai David Baker David L. Selwood 《The Journal of biological chemistry》2016,291(9):4356-4373
The mitochondrial permeability transition pore is a recognized drug target for neurodegenerative conditions such as multiple sclerosis and for ischemia-reperfusion injury in the brain and heart. The peptidylprolyl isomerase, cyclophilin D (CypD, PPIF), is a positive regulator of the pore, and genetic down-regulation or knock-out improves outcomes in disease models. Current inhibitors of peptidylprolyl isomerases show no selectivity between the tightly conserved cyclophilin paralogs and exhibit significant off-target effects, immunosuppression, and toxicity. We therefore designed and synthesized a new mitochondrially targeted CypD inhibitor, JW47, using a quinolinium cation tethered to cyclosporine. X-ray analysis was used to validate the design concept, and biological evaluation revealed selective cellular inhibition of CypD and the permeability transition pore with reduced cellular toxicity compared with cyclosporine. In an experimental autoimmune encephalomyelitis disease model of neurodegeneration in multiple sclerosis, JW47 demonstrated significant protection of axons and improved motor assessments with minimal immunosuppression. These findings suggest that selective CypD inhibition may represent a viable therapeutic strategy for MS and identify quinolinium as a mitochondrial targeting group for in vivo use. 相似文献
986.
macroeco is a Python package that supports the analysis of empirical macroecological patterns and the comparison of these patterns to theoretical predictions. Here we describe the use of macroeco and the various functions that it contains. We also highlight a unique high‐level interface included with the package, MacroecoDesktop, that allows non‐programmers to access the functionality of macroeco. MacroecoDesktop takes simple text‐based metadata and parameter files as inputs and generates both tabular and graphical outputs, supporting users in creating reproducible workflows that follow the principles of simplicity, provenance, and automation. Both macroeco and MacroecoDesktop provide case studies for developers of analytically‐focused scientific software packages who wish to better support the reproducible use of their tools. 相似文献
987.
Justin M. Roberts Sreya Tarafdar Raji E. Joseph Amy H. Andreotti Thomas E. Smithgall John R. Engen Thomas E. Wales 《Protein science : a publication of the Protein Society》2016,25(4):852-864
The Src Homology 3 (SH3) domain is an important regulatory domain found in many signaling proteins. X‐ray crystallography and NMR structures of SH3 domains are generally conserved but other studies indicate that protein flexibility and dynamics are not. We previously reported that based on hydrogen exchange mass spectrometry (HX MS) studies, there is variable flexibility and dynamics among the SH3 domains of the Src‐family tyrosine kinases and related proteins. Here we have extended our studies to the SH3 domains of the Tec family tyrosine kinases (Itk, Btk, Tec, Txk, Bmx). The SH3 domains of members of this family augment the variety in dynamics observed in previous SH3 domains. Txk and Bmx SH3 were found to be highly dynamic in solution by HX MS and Bmx was unstructured by NMR. Itk and Btk SH3 underwent a clear EX1 cooperative unfolding event, which was localized using pepsin digestion and mass spectrometry after hydrogen exchange labeling. The unfolding was localized to peptide regions that had been previously identified in the Src‐family and related protein SH3 domains, yet the kinetics of unfolding were not. Sequence alignment does not provide an easy explanation for the observed dynamics behavior, yet the similarity of location of EX1 unfolding suggests that higher‐order structural properties may play a role. While the exact reason for such dynamics is not clear, such motions can be exploited in intra‐ and intermolecular binding assays of proteins containing the domains. 相似文献
988.
Sara M. Stieb Karen L. Carleton Fabio Cortesi N. Justin Marshall Walter Salzburger 《Molecular ecology》2016,25(15):3645-3661
Phenotypic plasticity plays an important role in adapting the visual capability of many animal species to changing sensory requirements. Such variability may be driven by developmental change or may result from environmental changes in light habitat, thereby improving performance in different photic environments. In this study, we examined inter‐ and intraspecific plasticity of visual sensitivities in seven damselfish species, part of the species‐rich and colourful fish fauna of the Great Barrier Reef in Australia. Our goal was to test whether the visual systems of damselfish were tuned to the prevailing light environment in different habitats and/or other aspects of their lifestyle. More specifically, we compared the opsin gene expression levels from individuals living in different photic habitats. We found that all species expressed rod opsin (RH1) used for dim‐light vision, and primarily three cone opsins (SWS1, RH2B and RH2A) used for colour vision. While RH1 levels changed exclusively following a diurnal cycle, cone opsin expression varied with depth in four of the seven species. Estimates of visual pigment performance imply that changes in opsin expression adjust visual sensitivities to the dominant photic regime. However, we also discovered that some species show a more stable opsin expression profile. Further, we found indication that seasonal changes, possibly linked to changes in the photic environment, might also trigger opsin expression. These findings suggest that plasticity in opsin gene expression of damselfish is highly species‐specific, possibly due to ecological differences in visual tasks or, alternatively, under phylogenetic constraints. 相似文献
989.
The genes that encode the gonococcal transferrin binding proteins,TbpB and TbpA,are differentially regulated by MisR under iron‐replete and iron‐depleted conditions
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Justin L. Kandler Rosuany Vélez Acevedo Mary Kathryne Dickinson Devin R. Cash William M. Shafer Cynthia Nau Cornelissen 《Molecular microbiology》2016,102(1):137-151
Neisseria gonorrhoeae produces two transferrin binding proteins, TbpA and TbpB, which together enable efficient iron transport from human transferrin. We demonstrate that expression of the tbp genes is controlled by MisR, a response regulator in the two‐component regulatory system that also includes the sensor kinase MisS. The tbp genes were up‐regulated in the misR mutant under iron‐replete conditions but were conversely down‐regulated in the misR mutant under iron‐depleted conditions. The misR mutant was capable of transferrin‐iron uptake at only 50% of wild‐type levels, consistent with decreased tbp expression. We demonstrate that phosphorylated MisR specifically binds to the tbpBA promoter and that MisR interacts with five regions upstream of the tbpB start codon. These analyses confirm that MisR directly regulates tbpBA expression. The MisR binding sites in the gonococcus are only partially conserved in Neisseria meningitidis, which may explain why tbpBA was not MisR‐regulated in previous studies using this related pathogen. This is the first report of a trans‐acting protein factor other than Fur that can directly contribute to gonococcal tbpBA regulation. 相似文献
990.
Tshimangadzo Ramakuwela Justin Hatting Mark D. Laing Selcuk Hazir Nicolene Thiebaut 《Biocontrol Science and Technology》2016,26(6):792-808
Low-cost mass production of entomopathogenic nematodes (EPNs) is an important prerequisite towards their successful commercialisation. This study evaluated six low-cost solid substrate media for in vitro mass production of Steinernema innovationi. Cost analysis was undertaken and an estimated retail price was calculated. This was then compared to the costs of commercial EPN products currently on the market. The highest yield of infective juveniles (IJs) was obtained from a medium containing a puree of house fly, Musca domestica, larvae?+?0.15?g canola oil, (781,678?±?221 IJs/5?g medium). This medium also had the lowest number of adults remaining in the medium and dead IJs (<10%) at the time of harvest (Day 28). The estimated retail price (R243.27 per 50 million IJs) for S. innovationi produced with our solid culture system was considerably lower than the market price for other Steinernema species products sold by E~nema, BASF corporation, Koppert, BioBest and Natural Insect Control. The production system developed in this study offers a competitive technology to produce EPN products without having to invest in large-scale liquid fermentation equipment, by using a relatively cheap production medium and simple solid culture growing conditions using Erlenmeyer flasks. 相似文献