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51.
Recognizing the forest for the trees: testing temporal patterns of cladogenesis using a null model of stochastic diversification 总被引:2,自引:1,他引:1
Computer simulations are developed and employed to examine the expected
temporal distributions of nodes under a null model of stochastic lineage
bifurcation and extinction. These Markovian models of phylogenetic process
were constructed so as to permit direct comparisons against empirical
phylogenetic trees generated from molecular or other information available
solely from extant species. For replicate simulated phylads with n extant
species, cumulative distribution functions (cdf's) of branching times were
calculated, and compared (using the Kolmogorov-Smirnov test statistic D) to
those from three published empirical trees. Molecular phylogenies for
columbine plants and avian cranes showed statistically significant
departures from the null expectations, in directions indicating recent and
ancient species' radiations, respectively, whereas a molecular phylogeny
for the Drosophila virilis species group showed no apparent historical
clustering of branching events. Effects of outgroup choice and phylogenetic
frame of reference were investigated for the columbines and found to have a
predictable influence on the types of conclusions to be drawn from such
analyses. To enable other investigators to statistically test for
nonrandomness in temporal cladogenetic pattern in empirical trees generated
from data on extant species, we present tables of mean cdf's and associated
probabilities under the null model for expected branching times in phylads
of varying size. The approaches developed in this report complement and
extend those of other recent methods for employing null models to assess
the statistical significance of pattern in evolutionary trees.
相似文献
52.
Prioritizing targets for structural biology through the lens of proteomics: The archaeal protein TGAM_1934 from Thermococcus gammatolerans 下载免费PDF全文
Yin‐Shan Yang Bernard Fernandez Arnaud Lagorce Valérie Aloin Karine Montet De Guillen Jean‐Baptiste Boyer Alain Dedieu Fabrice Confalonieri Jean Armengaud Christian Roumestand 《Proteomics》2015,15(1):114-123
ORFans are hypothetical proteins lacking any significant sequence similarity with other proteins. Here, we highlighted by quantitative proteomics the TGAM_1934 ORFan from the hyperradioresistant Thermococcus gammatolerans archaeon as one of the most abundant hypothetical proteins. This protein has been selected as a priority target for structure determination on the basis of its abundance in three cellular conditions. Its solution structure has been determined using multidimensional heteronuclear NMR spectroscopy. TGAM_1934 displays an original fold, although sharing some similarities with the 3D structure of the bacterial ortholog of frataxin, CyaY, a protein conserved in bacteria and eukaryotes and involved in iron–sulfur cluster biogenesis. These results highlight the potential of structural proteomics in prioritizing ORFan targets for structure determination based on quantitative proteomics data. The proteomic data and structure coordinates have been deposited to the ProteomeXchange with identifier PXD000402 ( http://proteomecentral.proteomexchange.org/dataset/PXD000402 ) and Protein Data Bank under the accession number 2mcf, respectively. 相似文献
53.
M. Gouasmi P. Mordelet V. Demarez J. -P. Gastellu-Etchegorry V. Le Dantec G. Dedieu J. -C. Menaut J. -C. Calvet T. Lamaze 《Photosynthetica》2009,47(3):331-339
The objectives of the study were to characterize photosynthesis of temperate fallow C3herbaceous species and examine the performance of a simple photosynthesis model (based on the Farquhar’s equations) to simulate
carbon fluxes at the leaf and canopy levels. The maximum rate of carboxylation at 25°C (V
m0) was estimated for sunlit leaves using in situ gas exchange data under saturating irradiance. Throughout the seasons, leaf measurements indicate that values of V
m0 were similar for the four major species of the fallow. The rate declined from March (100 μmol m−2 s−1) to July (50 μmol m−2 s−1) and remained almost constant until November. The maximum quantum yield estimated for Potentilla reptans L. (dominant species) was 0.082 mol(CO2) mol−1(photon absorbed), similar to values already published for C3 species. Leaf area index (LAI) increased from winter (less than 0.2 m2 m−2) to spring (up to 4 m2 m−2). Rates of canopy photosynthesis (measured with a canopy chamber) strongly depended on LAI and temperature, in addition to
irradiance. They reached a maximum of 25 μmol m−2 s−1 and were intermediate between those published for C4 grassland or cultivated species, and on woody species. At leaf level, simulations gave realistic predictions. At canopy level,
the model had the ability to reproduce the effects of environmental and seasonal conditions. However, simulations underestimated
the photosynthetic activity of the fallow canopy. 相似文献
54.
Benoit Langlois Gwenn Perrot Christophe Schneider Patrick Henriet Hervé Emonard Laurent Martiny Stéphane Dedieu 《PloS one》2010,5(7)
Background
The low-density lipoprotein receptor-related protein-1 (LRP-1) is an endocytic receptor mediating the clearance of various extracellular molecules involved in the dissemination of cancer cells. LRP-1 thus appeared as an attractive receptor for targeting the invasive behavior of malignant cells. However, recent results suggest that LRP-1 may facilitate the development and growth of cancer metastases in vivo, but the precise contribution of the receptor during cancer progression remains to be elucidated. The lack of mechanistic insights into the intracellular signaling networks downstream of LRP-1 has prevented the understanding of its contribution towards cancer.Methodology/Principal Findings
Through a short-hairpin RNA-mediated silencing approach, we identified LRP-1 as a main regulator of ERK and JNK signaling in a tumor cell context. Co-immunoprecipitation experiments revealed that LRP-1 constitutes an intracellular docking site for MAPK containing complexes. By using pharmacological agents, constitutively active and dominant-negative kinases, we demonstrated that LRP-1 maintains malignant cells in an adhesive state that is favorable for invasion by activating ERK and inhibiting JNK. We further demonstrated that the LRP-1-dependent regulation of MAPK signaling organizes the cytoskeletal architecture and mediates adhesive complex turnover in cancer cells. Moreover, we found that LRP-1 is tethered to the actin network and to focal adhesion sites and controls ERK and JNK targeting to talin-rich structures.Conclusions
We identified ERK and JNK as the main molecular relays by which LRP-1 regulates focal adhesion disassembly of malignant cells to support invasion. 相似文献55.
JC Biro 《Theoretical biology & medical modelling》2006,3(1):15-12
Background
Prediction of protein folding and specific interactions from only the sequence (ab initio) is a major challenge in bioinformatics. It is believed that such prediction will prove possible if Anfinsen's thermodynamic principle is correct for all kinds of proteins, and all the information necessary to form a concrete 3D structure is indeed present in the sequence. 相似文献56.
Dargelos E Dedieu S Moyen C Poussard S Veschambre P Brustis JJ Cottin P 《Molecular and cellular biochemistry》2002,231(1-2):147-154
Many studies have demonstrated that the calcium-dependent proteolytic system (calpains and calpastatin) is involved in myoblast differentiation. It is also known that myogenic differentiation can be studied in vitro. In the present experiments, using a mouse muscle cell line (C2C12) we have analyzed both the sequences of appearance and the expression profiles of calpains 1, 2, 3 and calpastatin during the course of myoblast differentiation. Our results mainly show that the expression of ubiquitous calpains (calpain 1 and 2) and muscle-specific calpain (calpain 3) at the mRNAs level as well as at the protein level do not change significantly all along this biological process. In the same time, the specific inhibitor of ubiquitous calpains, calpastatin, presents a stable expression at mRNAs level as well as protein level, all along myoblast to myotube transition. A comparison with other myogenic cells is presented. 相似文献
57.
58.
The demonstration that interleukin 2 (IL-2) is a lectin specific for
oligomannosides allows to understand a new function for this cytokine: as a
bifunctional molecule when bound to its receptor ss, IL-2 associates the
latter which the CD3/TCR complex, interacting with oligosaccharides of CD3
through its carbohydrate-recognition domain (Zanetta et al. , 1996,
Biochem. J., 318, 49-53). This induces the tyrosine phosphorylation of the
IL-2R beta by ++p56(lck) , the first step of the IL-2-dependent signaling.
Since this specific association is disrupted in vitro by oligomannosides
with five and six mannose residues, we made the hypothesis that pathogenic
cells or microorganisms could bind IL-2, consequently disturbing the IL-2-
dependent response. This study shows that the pathogenic yeast Candida
albicans (in contrast with nonpathogenic yeasts) binds high amounts of IL-2
as did cancer cells. In contrast with cancer cells, yeasts do not bind the
Man6GlcNAc2-specific lectin CSL, an endogenous "amplifier of activation
signals" (Zanetta et al. , 1995, Biochem. J., 311, 629-636).
相似文献
59.
60.
Effect of insulin on ultrastructure and glycogenesis in primary cultures of adult rat hepatocytes 下载免费PDF全文
Insulin in the presence of high concentrations of glucose has a beneficial trophic effect on the development of primary cultures of hepatocytes. Compared to the situation observed in hormone-free control cultures, the flattening of the reaggregated hepatocytes is enhanced, and the reconstituted cell trabeculae are enlarged and tend to form a confluent monolayer after 3 days; the survival time is prolonged from 3 to 5 or 6 days. Ultrastructural modifications are also initiated by insulin; numerous glycogen particles appear after 24 h, in between the cisternae of the proliferated smooth endoplasmic reticulum. After 48 h, large amounts of glycogen are stored, and numerous polysomes are present. A small number of cells showed an increased synthesis of lipid droplets in the lumen of the smooth endoplasmic reticulum and form liposomes at the same time. After 72 h, cytolysomes filled with glycogen develop, simulating glycogenosis type II. Simultaneously, microtubules and microfilaments, closely related to numerous polysomes, appear in cytoplasmic extensions constituting undulating membranes. The biochemical data demonstrate that, in the absence of insulin, a high concentration of glucose stimulates glycogenesis and hinders glycogenolysis. This effect of glucose on polysaccharide synthesis is progressively lost. The addition of insulin to the culture induces after 48 and 72 h, a three- to fivefold increase of the glucose incorporation into glycogen, as compared to the controls. The presence of insulin is required to maintain the hepatocyte's capacity to store glycogen. Glycogen synthetase is converted into its active form under the influence of glucose. Insulin increases the rate of activation. 相似文献