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11.
Hervé?PhilippeEmail author Yan?Zhou Henner?Brinkmann Nicolas?Rodrigue Frédéric?Delsuc 《BMC evolutionary biology》2005,5(1):50
Background
Probabilistic methods have progressively supplanted the Maximum Parsimony (MP) method for inferring phylogenetic trees. One of the major reasons for this shift was that MP is much more sensitive to the Long Branch Attraction (LBA) artefact than is Maximum Likelihood (ML). However, recent work by Kolaczkowski and Thornton suggested, on the basis of simulations, that MP is less sensitive than ML to tree reconstruction artefacts generated by heterotachy, a phenomenon that corresponds to shifts in site-specific evolutionary rates over time. These results led these authors to recommend that the results of ML and MP analyses should be both reported and interpreted with the same caution. This specific conclusion revived the debate on the choice of the most accurate phylogenetic method for analysing real data in which various types of heterogeneities occur. However, variation of evolutionary rates across species was not explicitly incorporated in the original study of Kolaczkowski and Thornton, and in most of the subsequent heterotachous simulations published to date, where all terminal branch lengths were kept equal, an assumption that is biologically unrealistic. 相似文献12.
Macrophyte communities in unimpacted European streams: variability in assemblage patterns, abundance and diversity 总被引:5,自引:5,他引:0
Annette Baattrup-Pedersen Krzysztof Szoszkiewicz Rebi Nijboer Mattie O’Hare Teresa Ferreira 《Hydrobiologia》2006,566(1):179-196
Macrophytes are an important component of aquatic ecosystems and are used widely within the Water Framework Directive (WFD)
to establish ecological quality. In the present paper we investigated macrophyte community structure, i.e., composition, richness
and diversity measures in 60 unimpacted stream and river sites throughout Europe. The objectives were to describe assemblage
patterns in different types of streams and to assess the variability in various structural and ecological metrics within these
types to provide a basis for an evaluation of their suitability in ecological quality assessment. Macrophyte assemblage patterns
varied considerably among the main stream types. Moving from small-sized, shallow mountain streams to medium-sized, lowland
streams there was a clear transition in species richness, diversity and community structure. There was especially a shift
from a predominance of species-poor mosses and communities dominated by liverwort in the small-sized, shallow mountain streams
to more species-rich communities dominated by vascular plants in the medium-sized, lowland streams. The macrophyte communities
responded to most of the features underlying the typological framework defined in WFD. The present interpretation of the WFD
typology may not, however, be adequate for an evaluation of stream quality based on macrophytes. First and most important,
by using this typology we may overlook an important community type, which is characteristic of small-sized, relatively steep-gradient
streams that are an intermediate type between the small-sized, shallow mountain streams and the medium-sized, lowland streams.
Second, the variability in most of the calculated metrics was slightly higher when using the pre-defined typology. The consistency
of these results should be investigated by analysing a larger number of sites. Particularly the need of re-defining the typology
to improve the ability to detect impacts on streams and rivers from macrophyte assemblage patterns should be investigated.
Electronic supplementary material Electronic supplementary material is available for this article at
and accessible for authorised users. 相似文献
13.
Rocher C Taanman JW Pierron D Faustin B Benard G Rossignol R Malgat M Pedespan L Letellier T 《Journal of bioenergetics and biomembranes》2008,40(2):59-67
The total amount of cellular mitochondrial DNA (mtDNA) varies widely and seems to be related to the nature and metabolic state
of tissues and cells in culture. It is not known, however, whether this variation has any significance in vivo, and to which extent it regulates energy production. To better understand the importance of the cellular mtDNA level, we
studied the influence of a gradual reduction of mtDNA copy number on oxidative phosphorylation in two models: (a) a control
human cell line treated with different concentrations of 2′, 3′-dideoxycytidine, a nucleoside analogue that inhibits mtDNA
replication by interfering with mitochondrial DNA polymerase γ, and (b) a cell line derived from a patient presenting mtDNA
depletion. The two models were used to construct biochemical and phenotypic threshold curves. Our results show that oxidative
phosphorylation activities are under a tight control by the amount of mtDNA in the cell, and that the full complement of mtDNA
molecules are necessary to maintain a normal energy production level. 相似文献
14.
15.
Alice Malivert
zer Erguvan Antoine Chevallier Antoine Dehem Rodrigue Friaud Mengying Liu Marjolaine Martin Thophile Peyraud Olivier Hamant Stphane Verger 《PLoS biology》2021,19(11)
To survive, cells must constantly resist mechanical stress. In plants, this involves the reinforcement of cell walls, notably through microtubule-dependent cellulose deposition. How wall sensing might contribute to this response is unknown. Here, we tested whether the microtubule response to stress acts downstream of known wall sensors. Using a multistep screen with 11 mutant lines, we identify FERONIA (FER) as the primary candidate for the cell’s response to stress in the shoot. However, this does not imply that FER acts upstream of the microtubule response to stress. In fact, when performing mechanical perturbations, we instead show that the expected microtubule response to stress does not require FER. We reveal that the feronia phenotype can be partially rescued by reducing tensile stress levels. Conversely, in the absence of both microtubules and FER, cells appear to swell and burst. Altogether, this shows that the microtubule response to stress acts as an independent pathway to resist stress, in parallel to FER. We propose that both pathways are required to maintain the mechanical integrity of plant cells.In all living organisms, cells must resist mechanical stress to survive. This study of the model plant Arabidopsis reveals that the candidate cell wall mechanoreceptor FERONIA and microtubules independently contribute to this mechanical feedback. 相似文献
16.
Background
The evolutionary rate at a given homologous position varies across time. When sufficiently pronounced, this phenomenon – called heterotachy – may produce artefactual phylogenetic reconstructions under the commonly used models of sequence evolution. These observations have motivated the development of models that explicitly recognize heterotachy, with research directions proposed along two main axes: 1) the covarion approach, where sites switch from variable to invariable states; and 2) the mixture of branch lengths (MBL) approach, where alignment patterns are assumed to arise from one of several sets of branch lengths, under a given phylogeny. 相似文献17.
Mattie T. O’Hare Annette Baattrup-Pedersen Rebi Nijboer Krzysztof Szoszkiewicz Teresa Ferreira 《Hydrobiologia》2006,566(1):197-210
The impact of altering hydro-morphology on three macrophyte community types was investigated at 107 European stream sites.
Sites were surveyed using standard macrophyte and habitat survey techniques (Mean Trophic Rank Methodology and River Habitat
Survey respectively). Principal Components Analysis shows the macrophyte community of upland streams live in a more structurally
diverse physical habitat than lowland communities. Variables representing the homogeneity and diversity of the physical environment
were used to successfully separate un-impacted from impacted sites, e.g. homogeneity of depth and substrate increased with
decreasing quality class for lowland sites (ANOVA p < 0.05). Macrophyte attribute groups and structural metrics such as species richness were successfully linked to hydro-morphological
variables indicative of impact. Most links were specific to each macrophyte community type, e.g., the attribute group liverworts,
mosses and lichens decreased in abundance with increasing homogeneity of depth and decreasing substrate size at lowland sites
but not at upland sites. Elodea canadensis, Sparganium emersum and Potamogeton crispus were indicative of impacted lowland sites. Many of the indicator species are also known to be tolerant to other forms of
impact. The potential for a macrophyte tool indicative of hydro-morphological impact is discussed. It is concluded one could
be constructed by combining indicator species and metrics such as species richness and evenness. 相似文献
18.
Christine Talmard Rodrigue Leuma Yona Peter Faller 《Journal of biological inorganic chemistry》2009,14(3):449-455
The amyloidoses are a group of disorders characterized by aberrant protein folding and assembly, leading to the deposition
of insoluble protein fibrils (amyloid), which provokes cell dysfunction and later cell death. One of the physiologically relevant
environmental factors able to affect the conformation and hence the aggregation properties of amyloidogenic proteins/peptides
is metal ions. Zn(II) promotes aggregation of most amyloidogenic peptides/proteins in vitro, including amyloid β protein (Aβ),
but the underlying mechanism is not known. To better understand this mechanism the present study focused on the partially
α-helical conformer, supposed to be an intermediate in Aβ aggregation. This partially α-helical conformer is stabilized by
10–20% 2,2,2-trifluoroethanol (TFE): therefore, the influence of Zn binding on the aggregation of the amylidogenic model peptide
Aβ(1–28) (Aβ28) was investigated at different TFE concentrations. The results showed a synergistic effect of Zn(II) and 10%
TFE, i.e., that either Zn or 10% TFE accelerated Aβ28 aggregation on its own, but with them together an at least 10 times
promotion of Aβ28 aggregation was observed. Further studies by thioflavin T fluorescence spectroscopy, transmission electron
microscopy, and circular dichroism (CD) spectroscopy suggested that the aggregates of Zn-Aβ28 formed in 10%TFE contain a β-sheet
secondary structure and are more of the amyloid type. CD spectroscopy indicated that Zn binding disrupted partially the α-helical
structure of Aβ28 in TFE. Thus, we propose that the promotion of Aβ28 aggregation by Zn is based on the transformation of
the partially α-helical conformer (intermediate) towards the β-sheet amyloid structure by a destabilization of the α-helix
in the intermediate.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
相似文献
Peter FallerEmail: Email: |
19.
20.
Peyrin-Biroulet L Vignal C Dessein R Simonet M Desreumaux P Chamaillard M 《Trends in microbiology》2006,14(10):432-438
Defensins and cathelicidins are prevalent and essential gastrointestinal cationic antimicrobial peptides (CAPs). However, these defensive peptides are not infallible because certain enteropathogens can overcome their protective function. Furthermore, impaired defensin synthesis has been linked to the occurrence of Crohn's disease (CD), a chronic inflammatory bowel disease. Recently, defective bacterial sensing through NOD1 and NOD2 has been related to reduced defensin production, CD predisposition and susceptibility to enteric infection. Hence, we propose that microbial sensors at the gut interface monitor the levels of these effector peptides, which might function as "danger" signals to confer tolerance and alert immunocytes. Further work is required to clarify how gastrointestinal CAPs are regulated and to assess their role in maintaining epithelial homeostasis and triggering adaptive immunity. 相似文献