456 research outputs found
On the phylogenetic position of the hornless pecoran Amphimoschus – an example of arising challenges with the incorporation of fossils in extant combined frameworks
The mitochondrial genomes of sponges provide evidence for multiple invasions by Repetitive Hairpin-forming Elements (RHE)
Background: The mitochondrial (mt) genomes of sponges possess a variety of features, which appear to be intermediate between those of Eumetazoa and non-metazoan opisthokonts. Among these features is the presence of long intergenic regions, which are common in other eukaryotes, but generally absent in Eumetazoa. Here we analyse poriferan mitochondrial intergenic regions, paying particular attention to repetitive sequences within them. In this context we introduce the mitochondrial genome of Ircinia strobilina (Lamarck, 1816; Demospongiae: Dictyoceratida) and compare it with mtDNA of other sponges.
Results: Mt genomes of dictyoceratid sponges are identical in gene order and content but display major differences in size and organization of intergenic regions. An even higher degree of diversity in the structure of intergenic regions was found among different orders of demosponges. One interesting observation made from such comparisons was of what appears to be recurrent invasions of sponge mitochondrial genomes by repetitive hairpin-forming elements, which cause large genome size differences even among closely related taxa. These repetitive hairpin-forming elements are structurally and compositionally divergent and display a scattered distribution throughout various groups of demosponges.
Conclusion: Large intergenic regions of poriferan mt genomes are targets for insertions of repetitive hairpin- forming elements, similar to the ones found in non-metazoan opisthokonts. Such elements were likely present in some lineages early in animal mitochondrial genome evolution but were subsequently lost during the reduction of intergenic regions, which occurred in the Eumetazoa lineage after the split of Porifera. Porifera acquired their elements in several independent events. Patterns of their intra-genomic dispersal can be seen in the mt genome of Vaceletia sp
Mode-coupling theory of the stress-tensor autocorrelation function of a dense binary fluid mixture
We present a generalized mode-coupling theory for a dense binary fluid
mixture. The theory is used to calculate molecular-scale renormalizations to
the stress-tensor autocorrelation function (STAF) and to the long-wavelength
zero-frequency shear viscosity. As in the case of a dense simple fluid, we find
that the STAF appears to decay as over an intermediate range of
time. The coefficient of this long-time tail is more than two orders of
magnitude larger than that obtained from conventional mode-coupling theory. Our
study focuses on the effect of compositional disorder on the decay of the STAF
in a dense mixture.Comment: Published; withdrawn since ordering in the archive gives misleading
impression of new publicatio
Evolution of Group I Introns in Porifera: New Evidence for Intron Mobility and Implications for DNA Barcoding
BackgroundMitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarians, placozoans and one annelid species. Within demosponges, group I and group II introns are present in six families. Based on different insertion sites within the cox1 gene and secondary structures, four types of group I and two types of group II introns are known, which can harbor up to three encoding homing endonuclease genes (HEG) of the LAGLIDADG family (group I) and/or reverse transcriptase (group II). However, only little is known about sponge intron mobility, transmission, and origin due to the lack of a comprehensive dataset. We analyzed the largest dataset on sponge mitochondrial group I introns to date: 95 specimens, from 11 different sponge genera which provided novel insights into the evolution of group I introns.
ResultsFor the first time group I introns were detected in four genera of the sponge family Scleritodermidae (Scleritoderma, Microscleroderma, Aciculites, Setidium). We demonstrated that group I introns in sponges aggregate in the most conserved regions of cox1. We showed that co-occurrence of two introns in cox1 is unique among metazoans, but not uncommon in sponges. However, this combination always associates an active intron with a degenerating one. Earlier hypotheses of HGT were confirmed and for the first time VGT and secondary losses of introns conclusively demonstrated.
ConclusionThis study validates the subclass Spirophorina (Tetractinellida) as an intron hotspot in sponges. Our analyses confirm that most sponge group I introns probably originated from fungi. DNA barcoding is discussed and the application of alternative primers suggested
Hydrodynamic Detonation Instability in Electroweak and QCD Phase Transitions
The hydrodynamic stability of deflagration and detonation bubbles for a first
order electroweak and QCD phase transition has been discussed recently with the
suggestion that detonations are stable. We examine here the case of a
detonation more carefully. We find that in front of the bubble wall
perturbations do not grow with time, but behind the wall modes exist which grow
exponentially. We briefly discuss the possible meaning of this instability.Comment: 12 pages, 3 figures available on request, Latex,
FERMILAB--PUB--93/098--
Short-wavelength collective modes in a binary hard-sphere mixture
We use hard-sphere generalized hydrodynamic equations to discuss the extended
hydrodynamic modes of a binary mixture. The theory presented here is analytic
and it provides us with a simple description of the collective excitations of a
dense binary mixture at molecular length scales. The behavior we predict is in
qualitative agreement with molecular-dynamics results for soft-sphere mixtures.
This study provides some insight into the role of compositional disorder in
forming glassy configurations.Comment: Published; withdrawn since already published. Ordering in the archive
gives misleading impression of new publicatio
Transport coefficients for dense hard-disk systems
A study of the transport coefficients of a system of elastic hard disks,
based on the use of Helfand-Einstein expressions is reported. The
self-diffusion, the viscosity, and the heat conductivity are examined with
averaging techniques especially appropriate for the use in event-driven
molecular dynamics algorithms with periodic boundary conditions. The density
and size dependence of the results is analyzed, and comparison with the
predictions from Enskog's theory is carried out. In particular, the behavior of
the transport coefficients in the vicinity of the fluid-solid transition is
investigated and a striking power law divergence of the viscosity in this
region is obtained, while all other examined transport coefficients show a drop
in that density range.Comment: submitted to PR
A model for the atomic-scale structure of a dense, nonequilibrium fluid: the homogeneous cooling state of granular fluids
It is shown that the equilibrium Generalized Mean Spherical Model of fluid
structure may be extended to nonequilibrium states with equation of state
information used in equilibrium replaced by an exact condition on the two-body
distribution function. The model is applied to the homogeneous cooling state of
granular fluids and upon comparison to molecular dynamics simulations is found
to provide an accurate picture of the pair distribution function.Comment: 29 pages, 11 figures Revision corrects formatting of the figure
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Naturally drug-loaded chitin: Isolation and applications
Naturally occurring three-dimensional (3D) biopolymer-based matrices that can be used in different biomedical applications are sustainable alternatives to various artificial 3D materials. For this purpose, chitin-based structures from marine sponges are very promising substitutes. Marine sponges from the order Verongiida (class Demospongiae) are typical examples of demosponges with well-developed chitinous skeletons. In particular, species belonging to the family Ianthellidae possess chitinous, flat, fan-like fibrous skeletons with a unique, microporous 3D architecture that makes them particularly interesting for applications. In this work, we focus our attention on the demosponge Ianthella flabelliformis (Linnaeus, 1759) for simultaneous extraction of both naturally occurring (“ready-to-use”) chitin scaffolds, and biologically active bromotyrosines which are recognized as potential antibiotic, antitumor, and marine antifouling substances. We show that selected bromotyrosines are located within pigmental cells which, however, are localized within chitinous skeletal fibers of I. flabelliformis. A two-step reaction provides two products: treatment with methanol extracts the bromotyrosine compounds bastadin 25 and araplysillin-I N20 sulfamate, and a subsequent treatment with acetic acid and sodium hydroxide exposes the 3D chitinous scaffold. This scaffold is a mesh-like structure, which retains its capillary network, and its use as a potential drug delivery biomaterial was examined for the first time. The results demonstrate that sponge-derived chitin scaffolds, impregnated with decamethoxine, effectively inhibit growth of the human pathogen Staphylococcus aureus in an agar diffusion assa
Multi-Particle Collision Dynamics -- a Particle-Based Mesoscale Simulation Approach to the Hydrodynamics of Complex Fluids
In this review, we describe and analyze a mesoscale simulation method for
fluid flow, which was introduced by Malevanets and Kapral in 1999, and is now
called multi-particle collision dynamics (MPC) or stochastic rotation dynamics
(SRD). The method consists of alternating streaming and collision steps in an
ensemble of point particles. The multi-particle collisions are performed by
grouping particles in collision cells, and mass, momentum, and energy are
locally conserved. This simulation technique captures both full hydrodynamic
interactions and thermal fluctuations. The first part of the review begins with
a description of several widely used MPC algorithms and then discusses
important features of the original SRD algorithm and frequently used
variations. Two complementary approaches for deriving the hydrodynamic
equations and evaluating the transport coefficients are reviewed. It is then
shown how MPC algorithms can be generalized to model non-ideal fluids, and
binary mixtures with a consolute point. The importance of angular-momentum
conservation for systems like phase-separated liquids with different
viscosities is discussed. The second part of the review describes a number of
recent applications of MPC algorithms to study colloid and polymer dynamics,
the behavior of vesicles and cells in hydrodynamic flows, and the dynamics of
viscoelastic fluids
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