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91.
Jane Elith Catherine H. Graham Robert P. Anderson Miroslav Dudík Simon Ferrier Antoine Guisan Robert J. Hijmans Falk Huettmann John R. Leathwick Anthony Lehmann Jin Li Lucia G. Lohmann Bette A. Loiselle Glenn Manion Craig Moritz Miguel Nakamura Yoshinori Nakazawa Jacob McC. M. Overton A. Townsend Peterson Steven J. Phillips Karen Richardson Ricardo Scachetti-Pereira Robert E. Schapire Jorge Soberón Stephen Williams Mary S. Wisz Niklaus E. Zimmermann 《Ecography》2006,29(2):129-151
Prediction of species' distributions is central to diverse applications in ecology, evolution and conservation science. There is increasing electronic access to vast sets of occurrence records in museums and herbaria, yet little effective guidance on how best to use this information in the context of numerous approaches for modelling distributions. To meet this need, we compared 16 modelling methods over 226 species from 6 regions of the world, creating the most comprehensive set of model comparisons to date. We used presence-only data to fit models, and independent presence-absence data to evaluate the predictions. Along with well-established modelling methods such as generalised additive models and GARP and BIOCLIM, we explored methods that either have been developed recently or have rarely been applied to modelling species' distributions. These include machine-learning methods and community models, both of which have features that may make them particularly well suited to noisy or sparse information, as is typical of species' occurrence data. Presence-only data were effective for modelling species' distributions for many species and regions. The novel methods consistently outperformed more established methods. The results of our analysis are promising for the use of data from museums and herbaria, especially as methods suited to the noise inherent in such data improve. 相似文献
92.
Yuki F. Kita Kazuyoshi Hosomichi Sakae Kohara Yasushi Itoh Kazumasa Ogasawara Hideaki Tsuchiya Ryuzo Torii Hidetoshi Inoko Antoine Blancher Jerzy K. Kulski Takashi Shiina 《Immunogenetics》2009,61(9):635-648
Cynomolgus macaques (Macaca fascicularis, Mafa) have emerged as important animal models for biomedical research, necessitating a more extensive characterization of their major histocompatibility complex polymorphic regions. The current information on the polymorphism or diversity of the polygenetic Mafa class I A loci is limited in comparison to the more commonly studied rhesus macaque Mafa class I A loci. Therefore, in this paper, to better elucidate the degree and types of polymorphisms and genetic differences of Mafa-A1 among three native Southeast Asian populations (Indonesian, Vietnamese, and Filipino) and to investigate how the allele differences between macaques and humans might have evolved to affect their respective immune responses, we identified 83 Mafa-A loci-derived alleles by DNA sequencing of which 66 are newly described. Most alleles are unique to each population, but seven of the most frequent alleles were identical in sequence to some alleles in other macaque species. We also revealed (1) the large and dynamic genetic and structural differences and similarities in allelic variation by analyzing the population allele frequencies, Hardy-Weinberg’s equilibrium, heterozygosity, nucleotide diversity profiles, and phylogeny, (2) the difference in genetic structure of populations by Wright’s FST statistic and hierarchical analysis of molecular variance, and (3) the different demographic and selection pressures on the three populations by performing Tajima’s D test of neutrality. The large level of diversity and polymorphism at the Mafa-A1 was less evident in the Filipino than in the Vietnam or the Indonesian populations, which may have important implications in animal capture, selection, and breeding for medical research. 相似文献
93.
An analysis of determinants of amino acids substitution rates in bacterial proteins 总被引:14,自引:0,他引:14
The variation of amino acid substitution rates in proteins depends on several variables. Among these, the protein's expression level, functional category, essentiality, or metabolic costs of its amino acid residues may play an important role. However, the relative importance of each variable has not yet been evaluated in comparative analyses. To this aim, we made regression analyses combining data available on these variables and on evolutionary rates, in two well-documented model bacteria, Escherichia coli and Bacillus subtilis. In both bacteria, the level of expression of the protein in the cell was by far the most important driving force constraining the amino acids substitution rate. Subsequent inclusion in the analysis of the other variables added little further information. Furthermore, when the rates of synonymous substitutions were included in the analysis of the E. coli data, only the variable expression levels remained statistically significant. The rate of nonsynonymous substitution was shown to correlate with expression levels independently of the rate of synonymous substitution. These results suggest an important direct influence of expression levels, or at least codon usage bias for translation optimization, on the rates of nonsynonymous substitutions in bacteria. They also indicate that when a control for this variable is included, essentiality plays no significant role in the rate of protein evolution in bacteria, as is the case in eukaryotes. 相似文献
94.
Wildfire–vegetation dynamics affect predictions of climate change impact on bird communities 下载免费PDF全文
Adrián Regos Miguel Clavero Manuela D'Amen Antoine Guisan Lluís Brotons 《Ecography》2018,41(6):982-995
Community‐level climate change indicators have been proposed to appraise the impact of global warming on community composition. However, non‐climate factors may also critically influence species distribution and biological community assembly. The aim of this paper was to study how fire–vegetation dynamics can modify our ability to predict the impact of climate change on bird communities, as described through a widely‐used climate change indicator: the community thermal index (CTI). Potential changes in bird species assemblage were predicted using the spatially‐explicit species assemblage modelling framework – SESAM – that applies successive filters to constrained predictions of richness and composition obtained by stacking species distribution models that hierarchically integrate climate change and wildfire–vegetation dynamics. We forecasted future values of CTI between current conditions and 2050, across a wide range of fire–vegetation and climate change scenarios. Fire–vegetation dynamics were simulated for Catalonia (Mediterranean basin) using a process‐based model that reproduces the spatial interaction between wildfire, vegetation dynamics and wildfire management under two IPCC climate scenarios. Net increases in CTI caused by the concomitant impact of climate warming and an increasingly severe wildfire regime were predicted. However, the overall increase in the CTI could be partially counterbalanced by forest expansion via land abandonment and efficient wildfire suppression policies. CTI is thus strongly dependent on complex interactions between climate change and fire–vegetation dynamics. The potential impacts on bird communities may be underestimated if an overestimation of richness is predicted but not constrained. Our findings highlight the need to explicitly incorporate these interactions when using indicators to interpret and forecast climate change impact in dynamic ecosystems. In fire‐prone systems, wildfire management and land‐use policies can potentially offset or heighten the effects of climate change on biological communities, offering an opportunity to address the impact of global climate change proactively. 相似文献
95.
96.
Anja T. Rovio Josef Abel Arja L. Ahola Aida M. Andres Jaume Bertranpetit Antoine Blancher Ronald E. Bontrop Leona G. Chemnick Howard J. Cooke James M. Cummins Heidi A. Davis David J. Elliott Ellen Fritsche Timothy B. Hargreave Susan M. G. Hoffman Anne M. Jequier Shu-Huei Kao Heui-Soo Kim David R. Marchington Denise Mehmet Nel Otting Joanna Poulton Oliver A. Ryder Hans-Christian Schuppe Osamu Takenaka Yau-Huei Wei Lars Wichmann Howard T. Jacobs 《Mammalian genome》2004,15(6):492-502
The human nuclear gene for the catalytic subunit of mitochondrial DNA polymerase (POLG) contains within its coding region a CAG microsatellite encoding a polyglutamine repeat. Previous studies demonstrated an association between length variation at this repeat and male infertility, suggesting a mechanism whereby the prevalent (CAG)10 allele, which occurs at a frequency of >80% in different populations, could be maintained by selection. Sequence analysis of the POLG CAG microsatellite region of more than 1000 human chromosomes reveals that virtually all allelic variation at the locus is accounted for by length variation of the CAG repeat. Analysis of POLG from African great apes shows that a prevalent length allele is present in each species, although its exact length is species-specific. In common chimpanzee (Pan troglodytes) a number of different sequence variants contribute to the prevalent length allele, strongly supporting the idea that the length of the POLG microsatellite region, rather than its exact nucleotide or amino acid sequence, is what is maintained. Analysis of POLG in other primates indicates that the repeat has expanded from a shorter, glutamine-rich sequence, present in the common ancestor of Old and New World monkeys. 相似文献
97.
An approach to automatic prediction of the amino acid type from NMR chemical shift values of its nuclei is presented here, in the frame of a model to calculate the probability of an amino acid type given the set of chemical shifts. The method relies on systematic use of all chemical shift values contained in the BioMagResBank (BMRB). Two programs were designed, one (BMRB stats) for extracting statistical chemical shift parameters from the BMRB and another one (RESCUE2) for computing the probabilities of each amino acid type, given a set of chemical shifts. The Bayesian prediction scheme presented here is compared to other methods already proposed: PROTYP RESCUE and PLATON and is found to be more sensitive and more specific. Using this scheme, we tested various sets of nuclei. The two nuclei carrying the most information are C(beta) and H(beta), in agreement with observations made in Grzesiek and Bax, 1993. Based on four nuclei: H(beta), C(beta), C(alpha) and C', it is possible to increase correct predictions to a rate of more than 75%. Taking into account the correlations between the nuclei chemical shifts has only a slight impact on the percentage of correct predictions: indeed, the largest correlation coefficients display similar features on all amino acids. 相似文献
98.
Géraldine?Verquin Ga?lle?Fontaine Marc?Bria Elena?Zhilinskaya Edmond?Abi-Aad Antoine?Abouka?s Brigitte?Baldeyrou Christian?Bailly Jean-Luc?BernierEmail author 《Journal of biological inorganic chemistry》2004,9(3):345-353
Oxovanadium(IV) complexes of hydroxysalen derivatives have been prepared and tested as DNA reactive agents. The nuclease activity has been investigated under oxidative or reducing conditions, on the basis of the various oxidation states of vanadium: VIII, VIV and VV. In the absence of an activating agent, none of the compounds tested was able to induce cleavage of DNA, whereas in the presence of mercaptopropionic acid (MPA) or Oxone the four complexes induced DNA modifications. Under both conditions, the para-hydroxy complex was found to be the most active compound. Reaction of these salen complexes with DNA occurs essentially at guanine residues and is more efficient in the presence of Oxone than under reducing conditions. The extent of Oxone-mediated DNA oxidation by the four vanadyl complexes was clearly superior to VOSO4
and was observed without piperidine treatment. EPR studies provided information on the reactive metal-oxo species involved under each conditions and a mechanism of reaction with DNA is discussed.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00775-004-0529-0Abbreviations BPE buffer
bis-phosphate EDTA buffer
- DMPO
5,5-dimethylpyrroline
N-oxide
- DMS
dimethyl sulfate
- HFS
hyperfine structure
- Lin
linear
- MPA
3-mercaptopropionic acid
- Nck
nicked
- salen
(salicylidene)ethylenediamine
- Sc
supercoiled
- TBE buffer
tris-borate EDTA buffer
- Tris
tris(hydroxymethyl)aminomethane 相似文献
99.
Bily AC Burt AJ Ramputh AI Livesey J Regnault-Roger C Philogène BR Arnason JT 《Phytochemical analysis : PCA》2004,15(1):9-15
A new, rapid HPLC-PAD-APCI/MS assay has been developed in order to measure accurately the amount of p-coumaric, E- and Z-ferulic acid and the dehydrodimers of ferulic acid in cereal grain. In the positive ionisation mode, MS patterns gave additional information for the identification of the dimers. The time required and the quantities of solvents employed in the developed analytical method are much lower than those involved in previously available assays of these compounds, thus making the method suitable for the screening of cereal genotypes. Application of the method to accessions of maize, wheat and sorghum showed that E-ferulic was the most abundant phenylpropanoid, whilst the major dimer was 8-O-4' dehydrodimer of ferulic acid followed by the 5-5' and then the 8-5' forms. Maize grains, especially of the Mexican landraces, contained the highest levels of these dimers. 相似文献
100.
Ehrlich M Boll W Van Oijen A Hariharan R Chandran K Nibert ML Kirchhausen T 《Cell》2004,118(5):591-605
Clathrin-coated vesicles carry traffic from the plasma membrane to endosomes. We report here the real-time visualization of cargo sorting and endocytosis by clathrin-coated pits in living cells. We have detected the formation of coats by monitoring incorporation of fluorescently tagged clathrin or its adaptor AP-2; we have also followed clathrin-mediated uptake of transferrin and of single LDL or reovirus particles. The intensity of a cargo-loaded clathrin cluster grows steadily during its lifetime, and the time required to complete assembly is proportional to the size of the cargo particle. These results are consistent with a nucleation-growth mechanism and an approximately constant growth rate. There are no strongly preferred nucleation sites. A proportion of the nucleation events are weak and short lived. Cargo incorporation occurs primarily or exclusively in a newly formed coated pit. Our data lead to a model in which coated pits initiate randomly but collapse unless stabilized, perhaps by cargo capture. 相似文献