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991.
Lineage sorting and introgression can lead to incongruence among gene phylogenies, complicating the inference of species trees for large groups of taxa that have recently and rapidly radiated. In addition, it can be difficult to determine which of these processes is responsible for this incongruence. We explore these issues with the radiation of New Zealand alpine cicadas of the genus Maoricicada Dugdale. Gene trees were estimated from four putative independent loci: mitochondrial DNA (2274 nucleotides), elongation factor 1-alpha (1275 nucleotides), period (1709 nucleotides), and calmodulin (678 nucleotides). We reconstructed phylogenies using maximum likelihood and Bayesian methods from 44 individuals representing the 19 species and subspecies of Maoricicada and two outgroups. Species-level relationships were reconstructed using a novel extension of gene tree parsimony, whereby gene trees were weighted by their Bayesian posterior probabilities. The inferred gene trees show marked incongruence in the placement of some taxa, especially the enigmatic forest and scrub dwelling species, M. iolanthe. Using the species tree estimated by gene tree parsimony, we simulated coalescent gene trees in order to test the null hypothesis that the nonrandom placement of M. iolanthe among gene trees has arisen by chance. Under the assumptions of constant population size, known generation time, and panmixia, we were able to reject this null hypothesis. Furthermore, because the two alternative placements of M. iolanthe are in each case with species that share a similar song structure, we conclude that it is more likely that an ancient introgression event rather than lineage sorting has caused this incongruence. 相似文献
992.
Saunders PU Telford RD Pyne DB Peltola EM Cunningham RB Gore CJ Hawley JA 《Journal of strength and conditioning research / National Strength & Conditioning Association》2006,20(4):947-954
Fifteen highly trained distance runners VO(2)max 71.1 +/- 6.0 ml.min(-1).kg(-1), mean +/- SD) were randomly assigned to a plyometric training (PLY; n = 7) or control (CON; n = 8) group. In addition to their normal training, the PLY group undertook 3 x 30 minutes PLY sessions per week for 9 weeks. Running economy (RE) was assessed during 3 x 4 minute treadmill runs (14, 16, and 18 km.h(-1)), followed by an incremental test to measure VO(2)max. Muscle power characteristics were assessed on a portable, unidirectional ground reaction force plate. Compared with CON, PLY improved RE at 18 km.h(-1) (4.1%, p = 0.02), but not at 14 or 16 km.h(-1). This was accompanied by trends for increased average power during a 5-jump plyometric test (15%, p = 0.11), a shorter time to reach maximal dynamic strength during a strength quality assessment test (14%, p = 0.09), and a lower VO(2)-speed slope (14%, p = 0.12) after 9 weeks of PLY. There were no significant differences in cardiorespiratory measures or VO(2)max as a result of PLY. In a group of highly-trained distance runners, 9 weeks of PLY improved RE, with likely mechanisms residing in the muscle, or alternatively by improving running mechanics. 相似文献
993.
A hidden-state Markov model for cell population deconvolution. 总被引:1,自引:0,他引:1
Sushmita Roy Terran Lane Chris Allen Anthony D Aragon Margaret Werner-Washburne 《Journal of computational biology》2006,13(10):1749-1774
Microarrays measure gene expression typically from a mixture of cell populations during different stages of a biological process. However, the specific effects of the distinct or pure populations on measured gene expression are difficult or impossible to determine. The ability to deconvolve measured gene expression into the contributions from pure populations is critical to maximizing the potential of microarray analysis for investigating complex biological processes. In this paper, we describe a novel approach called the multinomial hidden Markov model (MHMM) that produces: (i) a maximum a posteriori estimate of the fraction represented by each pure population and (ii) gene expression values for each pure population. Our method uses an unsupervised, probabilistic approach for handling missing data points and clusters genes based on expression in pure populations. MHMM, used with several yeast datasets, identified statistically significant temporal dynamics. This method, unlike the linear decomposition models used previously for deconvolution, can extract information from different types of data, does not require a priori identification of pure gene expression, exploits the temporal nature of time series data, and is less affected by missing data. 相似文献
994.
Landing mats that can undergo a large amount of area deformation are now essential for the safe completion of landings in gymnastics. The objective of this study was to develop an analytical model of a landing mat that reproduces the key characteristics of the mat-ground force during impact with minimal simulation run time. A force plate and two high-speed video cameras were used to record the mat deformation during vertical drop testing of a 24-kg impactor. Four increasingly complex point mass spring-damper models, from a single mass spring-damper system, Model 1, to a 3-layer mass spring-damper system, Model 4, were constructed using Matlab to model the mat's behavior during impact. A fifth model composed of a 3-layer mass spring-damper system was developed using visual Nastran 4D. The results showed that Models 4 and 5 were able to match the loading phase of the impact with simulation times of less than 1 second for Model 4 and 28 seconds for Model 5. Both Models 4 and 5 successfully reproduced the key force-time characteristics of the mat-ground interface, such as peak forces, time of peak forces, interpeak minima and initial rates of loading, and could be incorporated into a gymnast-mat model. 相似文献
995.
Bunney TD Harris R Gandarillas NL Josephs MB Roe SM Sorli SC Paterson HF Rodrigues-Lima F Esposito D Ponting CP Gierschik P Pearl LH Driscoll PC Katan M 《Molecular cell》2006,21(4):495-507
Ras proteins signal to a number of distinct pathways by interacting with diverse effectors. Studies of ras/effector interactions have focused on three classes, Raf kinases, ral guanylnucleotide-exchange factors, and phosphatidylinositol-3-kinases. Here we describe ras interactions with another effector, the recently identified phospholipase C epsilon (PLCepsilon). We solved structures of PLCepsilon RA domains (RA1 and RA2) by NMR and the structure of the RA2/ras complex by X-ray crystallography. Although the similarity between ubiquitin-like folds of RA1 and RA2 proves that they are homologs, only RA2 can bind ras. Some of the features of the RA2/ras interface are unique to PLCepsilon, while the ability to make contacts with both switch I and II regions of ras is shared only with phosphatidylinositol-3-kinase. Studies of PLCepsilon regulation suggest that, in a cellular context, the RA2 domain, in a mode specific to PLCepsilon, has a role in membrane targeting with further regulatory impact on PLC activity. 相似文献
996.
A conserved GTPase-containing complex is required for intracellular sorting of the general amino-acid permease in yeast 总被引:1,自引:0,他引:1
The Saccharomyces cerevisiae general amino-acid permease, Gap1p, is a model for membrane proteins that are regulated by intracellular sorting according to physiological cues set by the availability of amino acids. Here, we report the identification of a conserved sorting complex for Gap1p, named the GTPase-containing complex for Gap1p sorting in the endosomes (GSE complex), which is required for proper sorting of Gap1p from the late endosome for eventual delivery to the plasma membrane. The complex contains two small GTPases (Gtr1p and Gtr2p) and three other proteins (Ybr077c, Ykr007w and Ltv1p) that are located in the late endosomal membrane. Importantly, Gtr2p interacts with the carboxy (C)-terminal cytosolic domain of Gap1p and a tyrosine-containing motif in this domain is necessary both to bind Gtr2p and to direct sorting of Gap1p to the plasma membrane. Together, these studies provide evidence that the GSE complex has a key role in trafficking Gap1p out of the endosome and may serve as coat proteins in this process. 相似文献
997.
Asymmetric cell division generates cell diversity during development and regulates stem-cell self-renewal in Drosophila and mammals. In Drosophila, neuroblasts align their spindle with a cortical Partner of Inscuteable (Pins)-G alpha i crescent to divide asymmetrically, but the link between cortical polarity and the mitotic spindle is poorly understood. Here, we show that Pins directly binds, and coimmunoprecipitates with, the NuMA-related Mushroom body defect (Mud) protein. Pins recruits Mud to the neuroblast apical cortex, and Mud is also strongly localized to centrosome/spindle poles, in a similar way to NuMA. In mud mutants, cortical polarity is normal, but the metaphase spindle frequently fails to align with the cortical polarity axis. When spindle orientation is orthogonal to cell polarity, symmetric division occurs. We propose that Mud is a functional orthologue of mammalian NuMA and Caenorhabditis elegans Lin-5, and that Mud coordinates spindle orientation with cortical polarity to promote asymmetric cell division. 相似文献
998.
Fusaro AF Matthew L Smith NA Curtin SJ Dedic-Hagan J Ellacott GA Watson JM Wang MB Brosnan C Carroll BJ Waterhouse PM 《EMBO reports》2006,7(11):1168-1175
RNA interference (RNAi) is widely used to silence genes in plants and animals. It operates through the degradation of target mRNA by endonuclease complexes guided by approximately 21 nucleotide (nt) short interfering RNAs (siRNAs). A similar process regulates the expression of some developmental genes through approximately 21 nt microRNAs. Plants have four types of Dicer-like (DCL) enzyme, each producing small RNAs with different functions. Here, we show that DCL2, DCL3 and DCL4 in Arabidopsis process both replicating viral RNAs and RNAi-inducing hairpin RNAs (hpRNAs) into 22-, 24- and 21 nt siRNAs, respectively, and that loss of both DCL2 and DCL4 activities is required to negate RNAi and to release the plant's repression of viral replication. We also show that hpRNAs, similar to viral infection, can engender long-distance silencing signals and that hpRNA-induced silencing is suppressed by the expression of a virus-derived suppressor protein. These findings indicate that hpRNA-mediated RNAi in plants operates through the viral defence pathway. 相似文献
999.
Angers S Thorpe CJ Biechele TL Goldenberg SJ Zheng N MacCoss MJ Moon RT 《Nature cell biology》2006,8(4):348-357
Dishevelled is a conserved protein that interprets signals received by Frizzled receptors. Using a tandem-affinity purification strategy and mass spectrometry we have identified proteins associated with Dishevelled, including a Cullin-3 ubiquitin ligase complex containing the Broad Complex, Tramtrack and Bric à Brac (BTB) protein Kelch-like 12 (KLHL12). This E3 ubiquitin ligase complex is recruited to Dishevelled in a Wnt-dependent manner that promotes its poly-ubiquitination and degradation. Functional analyses demonstrate that regulation of Dishevelled by this ubiquitin ligase antagonizes the Wnt-beta-catenin pathway in cultured cells, as well as in Xenopus and zebrafish embryos. Considered with evidence that the distinct Cullin-1 based SCF(beta-TrCP)complex regulates beta-catenin stability, our data on the stability of Dishevelled demonstrates that two distinct ubiquitin ligase complexes regulate the Wnt-beta-catenin pathway. 相似文献
1000.