18,588 research outputs found
Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea)
Complete mitochondrial genomes have been shown to be reliable markers for phylogeny reconstruction among diverse animal groups. However, the relative difficulty and high cost associated with obtaining de novo full mitogenomes have frequently led to conspicuously low taxon sampling in ensuing studies. Here, we report the successful use of an economical and accessible method for assembling complete or near-complete mitogenomes through shot-gun next-generation sequencing of a single library made from pooled total DNA extracts of numerous target species. To avoid the use of separate indexed libraries for each specimen, and an associated increase in cost, we incorporate standard polymerase chain reaction-based “bait” sequences to identify the assembled mitogenomes. The method was applied to study the higher level phylogenetic relationships in the weevils (Coleoptera: Curculionoidea), producing 92 newly assembled mitogenomes obtained in a single Illumina MiSeq run. The analysis supported a separate origin of wood-boring behavior by the subfamilies Scolytinae, Platypodinae, and Cossoninae. This finding contradicts morphological hypotheses proposing a close relationship between the first two of these but is congruent with previous molecular studies, reinforcing the utility of mitogenomes in phylogeny reconstruction. Our methodology provides a technically simple procedure for generating densely sampled trees from whole mitogenomes and is widely applicable to groups of animals for which bait sequences are the only required prior genome knowledge
emgr - The Empirical Gramian Framework
System Gramian matrices are a well-known encoding for properties of
input-output systems such as controllability, observability or minimality.
These so-called system Gramians were developed in linear system theory for
applications such as model order reduction of control systems. Empirical
Gramian are an extension to the system Gramians for parametric and nonlinear
systems as well as a data-driven method of computation. The empirical Gramian
framework - emgr - implements the empirical Gramians in a uniform and
configurable manner, with applications such as Gramian-based (nonlinear) model
reduction, decentralized control, sensitivity analysis, parameter
identification and combined state and parameter reduction
The LifeV library: engineering mathematics beyond the proof of concept
LifeV is a library for the finite element (FE) solution of partial
differential equations in one, two, and three dimensions. It is written in C++
and designed to run on diverse parallel architectures, including cloud and high
performance computing facilities. In spite of its academic research nature,
meaning a library for the development and testing of new methods, one
distinguishing feature of LifeV is its use on real world problems and it is
intended to provide a tool for many engineering applications. It has been
actually used in computational hemodynamics, including cardiac mechanics and
fluid-structure interaction problems, in porous media, ice sheets dynamics for
both forward and inverse problems. In this paper we give a short overview of
the features of LifeV and its coding paradigms on simple problems. The main
focus is on the parallel environment which is mainly driven by domain
decomposition methods and based on external libraries such as MPI, the Trilinos
project, HDF5 and ParMetis.
Dedicated to the memory of Fausto Saleri.Comment: Review of the LifeV Finite Element librar
Simple biophysics underpins collective conformations of the intrinsically disordered proteins of the Nuclear Pore Complex
Nuclear Pore Complexes (NPCs) are key cellular transporter that control nucleocytoplasmic transport in eukaryotic cells, but its transport mechanism is still not understood. The centerpiece of NPC transport is the assembly of intrinsically disordered polypeptides, known as FG nucleoporins, lining its passageway. Their conformations and collective dynamics during transport are difficult to assess in vivo. In vitro investigations provide partially conflicting results, lending support to different models of transport, which invoke various conformational transitions of the FG nucleoporins induced by the cargo-carrying transport proteins. We show that the spatial organization of FG nucleoporin assemblies with the transport proteins can be understood within a first principles biophysical model with a minimal number of key physical variables, such as the average protein interaction strengths and spatial densities. These results address some of the outstanding controversies and suggest how molecularly divergent NPCs in different species can perform essentially the same function
Nonlinear multigrid based on local spectral coarsening for heterogeneous diffusion problems
This work develops a nonlinear multigrid method for diffusion problems
discretized by cell-centered finite volume methods on general unstructured
grids. The multigrid hierarchy is constructed algebraically using aggregation
of degrees of freedom and spectral decomposition of reference linear operators
associated with the aggregates. For rapid convergence, it is important that the
resulting coarse spaces have good approximation properties. In our approach,
the approximation quality can be directly improved by including more spectral
degrees of freedom in the coarsening process. Further, by exploiting local
coarsening and a piecewise-constant approximation when evaluating the nonlinear
component, the coarse level problems are assembled and solved without ever
re-visiting the fine level, an essential element for multigrid algorithms to
achieve optimal scalability. Numerical examples comparing relative performance
of the proposed nonlinear multigrid solvers with standard single-level
approaches -- Picard's and Newton's methods -- are presented. Results show that
the proposed solver consistently outperforms the single-level methods, both in
efficiency and robustness
De Novo Assembly of Nucleotide Sequences in a Compressed Feature Space
Sequencing technologies allow for an in-depth analysis
of biological species but the size of the generated datasets
introduce a number of analytical challenges. Recently, we
demonstrated the application of numerical sequence representations
and data transformations for the alignment of short
reads to a reference genome. Here, we expand out approach
for de novo assembly of short reads. Our results demonstrate
that highly compressed data can encapsulate the signal suffi-
ciently to accurately assemble reads to big contigs or complete
genomes
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