826 research outputs found
Genetic Correlations in Mutation Processes
We study the role of phylogenetic trees on correlations in mutation
processes. Generally, correlations decay exponentially with the generation
number. We find that two distinct regimes of behavior exist. For mutation rates
smaller than a critical rate, the underlying tree morphology is almost
irrelevant, while mutation rates higher than this critical rate lead to strong
tree-dependent correlations. We show analytically that identical critical
behavior underlies all multiple point correlations. This behavior generally
characterizes branching processes undergoing mutation.Comment: revtex, 8 pages, 2 fig
Mechanical activation of vinculin binding to talin locks talin in an unfolded conformation
The force-dependent interaction between talin and vinculin plays a crucial role in the initiation and growth of focal adhesions. Here we use magnetic tweezers to characterise the mechano-sensitive compact N-terminal region of the talin rod, and show that the three helical bundles R1-R3 in this region unfold in three distinct steps consistent with the domains unfolding independently. Mechanical stretching of talin R1-R3 enhances its binding to vinculin and vinculin binding inhibits talin refolding after force is released. Mutations that stabilize R3 identify it as the initial mechano-sensing domain in talin, unfolding at ~5 pN, suggesting that 5 pN is the force threshold for vinculin binding and adhesion progression
Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria)
Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef
building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary
relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders,
families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the
stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous
data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various
outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ßtubulin,
ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be
polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly
divergent "robust" and "complex" clades. However, the recent suggestion that corallimorpharians are true corals that have
lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also
often by morphological characters which had been ignored or never noted previously. The concordance of molecular
characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as
the potential to trace the evolutionary history of this ecologically important group using fossils
The anisotropy of granular materials
The effect of the anisotropy on the elastoplastic response of two dimensional
packed samples of polygons is investigated here, using molecular dynamics
simulation. We show a correlation between fabric coefficients, characterizing
the anisotropy of the granular skeleton, and the anisotropy of the elastic
response. We also study the anisotropy induced by shearing on the subnetwork of
the sliding contacts. This anisotropy provides an explanation to some features
of the plastic deformation of granular media.Comment: Submitted to PR
On the accuracy of language trees
Historical linguistics aims at inferring the most likely language
phylogenetic tree starting from information concerning the evolutionary
relatedness of languages. The available information are typically lists of
homologous (lexical, phonological, syntactic) features or characters for many
different languages.
From this perspective the reconstruction of language trees is an example of
inverse problems: starting from present, incomplete and often noisy,
information, one aims at inferring the most likely past evolutionary history. A
fundamental issue in inverse problems is the evaluation of the inference made.
A standard way of dealing with this question is to generate data with
artificial models in order to have full access to the evolutionary process one
is going to infer. This procedure presents an intrinsic limitation: when
dealing with real data sets, one typically does not know which model of
evolution is the most suitable for them. A possible way out is to compare
algorithmic inference with expert classifications. This is the point of view we
take here by conducting a thorough survey of the accuracy of reconstruction
methods as compared with the Ethnologue expert classifications. We focus in
particular on state-of-the-art distance-based methods for phylogeny
reconstruction using worldwide linguistic databases.
In order to assess the accuracy of the inferred trees we introduce and
characterize two generalizations of standard definitions of distances between
trees. Based on these scores we quantify the relative performances of the
distance-based algorithms considered. Further we quantify how the completeness
and the coverage of the available databases affect the accuracy of the
reconstruction. Finally we draw some conclusions about where the accuracy of
the reconstructions in historical linguistics stands and about the leading
directions to improve it.Comment: 36 pages, 14 figure
Fast computation of distance estimators
BACKGROUND: Some distance methods are among the most commonly used methods for reconstructing phylogenetic trees from sequence data. The input to a distance method is a distance matrix, containing estimated pairwise distances between all pairs of taxa. Distance methods themselves are often fast, e.g., the famous and popular Neighbor Joining (NJ) algorithm reconstructs a phylogeny of n taxa in time O(n(3)). Unfortunately, the fastest practical algorithms known for Computing the distance matrix, from n sequences of length l, takes time proportional to l·n(2). Since the sequence length typically is much larger than the number of taxa, the distance estimation is the bottleneck in phylogeny reconstruction. This bottleneck is especially apparent in reconstruction of large phylogenies or in applications where many trees have to be reconstructed, e.g., bootstrapping and genome wide applications. RESULTS: We give an advanced algorithm for Computing the number of mutational events between DNA sequences which is significantly faster than both Phylip and Paup. Moreover, we give a new method for estimating pairwise distances between sequences which contain ambiguity Symbols. This new method is shown to be more accurate as well as faster than earlier methods. CONCLUSION: Our novel algorithm for Computing distance estimators provides a valuable tool in phylogeny reconstruction. Since the running time of our distance estimation algorithm is comparable to that of most distance methods, the previous bottleneck is removed. All distance methods, such as NJ, require a distance matrix as input and, hence, our novel algorithm significantly improves the overall running time of all distance methods. In particular, we show for real world biological applications how the running time of phylogeny reconstruction using NJ is improved from a matter of hours to a matter of seconds
High-Tc Superconductivity and Antiferromagnetism in Multilayered Copper Oxides - A New Paradigm of Superconducting Mechanism -
High-temperature superconductivity (HTSC) in copper oxides emerges on a
layered CuO2 plane when an antiferromagnetic Mott insulator is doped with
mobile hole carriers. We review extensive studies of multilayered copper oxides
by site-selective nuclear magnetic resonance (NMR), which have uncovered the
intrinsic phase diagram of antiferromagnetism (AFM) and HTSC for a
disorder-free CuO2 plane with hole carriers. We present our experimental
findings such as the existence of the AFM metallic state in doped Mott
insulators, the uniformly mixed phase of AFM and HTSC, and the emergence of
d-wave SC with a maximum Tc just outside a critical carrier density, at which
the AFM moment on a CuO2 plane disappears. These results can be accounted for
by the Mott physics based on the t-J model. The superexchange interaction J_in
among spins plays a vital role as a glue for Cooper pairs or mobile
spin-singlet pairs, in contrast to the phonon-mediated attractive interaction
among electrons established in the Bardeen-Cooper-Schrieffer (BCS) theory. We
remark that the attractive interaction for raising the of HTSC up to
temperatures as high as 160 K is the large J_in (~0.12 eV), which binds
electrons of opposite spins to be on neighboring sites, and that there are no
bosonic glues. It is the Coulomb repulsive interaction U(> 6 eV) among Cu-3d
electrons that plays a central role in the physics behind high-Tc phenomena. A
new paradigm of the SC mechanism opens to strongly correlated electron matter.Comment: 20 pages, 25 figures, Special topics "Recent Developments in
Superconductivity" in J. Phys. Soc. Jpn., Published December 26, 201
Dating Phylogenies with Hybrid Local Molecular Clocks
BACKGROUND: Because rates of evolution and species divergence times cannot be estimated directly from molecular data, all current dating methods require that specific assumptions be made before inferring any divergence time. These assumptions typically bear either on rates of molecular evolution (molecular clock hypothesis, local clocks models) or on both rates and times (penalized likelihood, Bayesian methods). However, most of these assumptions can affect estimated dates, oftentimes because they underestimate large amounts of rate change. PRINCIPAL FINDINGS: A significant modification to a recently proposed ad hoc rate-smoothing algorithm is described, in which local molecular clocks are automatically placed on a phylogeny. This modification makes use of hybrid approaches that borrow from recent theoretical developments in microarray data analysis. An ad hoc integration of phylogenetic uncertainty under these local clock models is also described. The performance and accuracy of the new methods are evaluated by reanalyzing three published data sets. CONCLUSIONS: It is shown that the new maximum likelihood hybrid methods can perform better than penalized likelihood and almost as well as uncorrelated Bayesian models. However, the new methods still tend to underestimate the actual amount of rate change. This work demonstrates the difficulty of estimating divergence times using local molecular clocks
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