arXiv
(422,153 recursos)
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Mostrando recursos 101 - 120 de 4,680
101.
Reading Sequences of Interspike Intervals in Biological Neural Circuits - Abarbanel, Henry D. I.; Talathi, Sachin
Sensory systems pass information about an animal's environment to higher
nervous system units through sequences of action potentials. When these action
potentials have essentially equivalent waveforms, all information is contained
in the interspike intervals (ISIs) of the spike sequence. We address the
question: How do neural circuits recognize and read these ISI sequences?
Our answer is given in terms of a biologically inspired neural circuit that
we construct using biologically realistic neurons. The essential ingredients of
the ISI Reading Unit (IRU) are (i) a tunable time delay circuit modelled after
one found in the anterior forebrain pathway of the birdsong system and (ii) a
recently observed rule for...
102.
Shock waves in virus fitness evolution - Carvalhaes, Fernando G.; Goldman, Carla
We consider a nonlinear partial differential equation of conservation type to
describe the dynamics of vesicular stomatitis virus observed in aliquots of
fixed particle number taken from an evolving clone at periodic intervals of
time \cite{novella 95}. The changes in time behavior of fitness function
noticed in experimental data are related to a crossover exhibited by the
solutions to this equation in the transient regime for pulse-like initial
conditions. As a consequence, the average replication rate of the population is
predicted to reach a plateau as a power t^{-(1/2)}.
103.
Master equation approach to the assembly of viral capsids - Keef, T.; Micheletti, C.; Twarock, R.
The distribution of inequivalent geometries occurring during self-assembly of
the major capsid protein in thermodynamic equilibrium is determined based on a
master equation approach. These results are implemented to characterize the
assembly of SV40 virus and to obtain information on the putative pathways
controlling the progressive build-up of the SV40 capsid. The experimental
testability of the predictions is assessed and an analysis of the geometries of
the assembly intermediates on the dominant pathways is used to identify targets
for antiviral drug design.
104.
Assembly Models for Papovaviridae based on Tiling Theory - Keef, T.; Taormina, A.; Twarock, R.
A vital constituent of a virus is its protein shell, called the viral capsid,
that encapsulates and hence provides protection for the viral genome. Assembly
models are developed for viral capsids built from protein building blocks that
can assume different local bonding structures in the capsid. This situation
occurs, for example, for viruses in the family of Papovaviridae, which are
linked to cancer and are hence of particular interest for the health sector.
More specifically, the viral capsids of the (pseudo-) T=7 particles in this
family consist of pentamers that exhibit two different types of bonding
structures. While this scenario cannot be described mathematically in terms of
Caspar-Klug Theory...
105.
A Modified Iterative IOM Approach for Optimization of Biochemical Systems - Xu, Gongxian; Shao, Cheng; Xiu, Zhilong
The presented previously indirect optimization method (IOM) developed within
biochemical systems theory (BST) provides a versatile and mathematically
tractable optimization strategy for biochemical systems. However, due to the
local approximations nature of the BST formalism, the iterative version of this
technique possibly does not yield the truth optimum solution. In this work, an
algorithm is proposed to obtain the correct and consistent optimum steady-state
operating point of biochemical systems. The existing linear optimization
problem of the direct IOM approach is modified by adding an equality constraint
of describing the consistency of solutions between the S-system and the
original model. Lagrangian analysis is employed to derive the first order
necessary optimality...
106.
Should you believe that this coin is fair? - Bialek, William
Faced with a sequence of N binary events, such as coin flips (or Ising
spins), it is natural to ask whether these events reflect some underlying
dynamic signals or are just random. Plausible models for the dynamics of hidden
biases lead to surprisingly high probabilities of misidentifying random
sequences as biased. In particular, this probability decays as N^(-1/4), so
that no reasonable amount of data would be sufficient to induce the concept of
a fair coin with high probability. I suggest that these theoretical results may
be relevant to understanding experiments on the apparent misperception of
random sequences by human observers.
107.
Quasispecies can exist under neutral drift at finite population sizes - Forster, Robert; Adami, Christoph; Wilke, Claus O.
We investigate the evolutionary dynamics of a finite population of RNA
sequences adapting to a neutral fitness landscape. Despite the lack of
differential fitness between viable sequences, we observe typical properties of
adaptive evolution, such as increase of mean fitness over time and punctuated
equilibrium transitions. We discuss the implications of these results for
understanding evolution at high mutation rates, and extend the relevance of the
quasispecies concept to finite populations and time scales. Our results imply
that the quasispecies concept and neutral drift are not complementary concepts,
and that the relative importance of each is determined by a combination of
population size and mutation rate.
108.
Equation of state of looped DNA - Kulic, I. M.; Mohrbach, H.; Thaokar, R.; Schiessel, H.
We calculate the equation of state of DNA under tension for the case that the
DNA features loops. Such loops occur transiently during DNA condensation in the
presence of multivalent ions or sliding cationic protein linkers. The
force-extension relation of such looped DNA modelled as a wormlike chain is
calculated via path integration in the semiclassical limit. This allows us to
determine rigorously the high stretching asymptotics. Notably the functional
form of the force-extension curve resembles that of straight DNA, yet with a
strongly renormalized apparent persistence length. That means that the
experimentally extracted single molecule elasticity does not necessarily
reflect the bare DNA stiffness only, but can also...
109.
Networks of Mobile Elements for Biological Systems - Thadani, Kanchan; Ashutosh
In this paper we present a network model to study the impact of spatial
distribution of constituents, coupling between them and diffusive processes in
the context of biological situations. The model is in terms of network of
mobile elements whose internal dynamics is given by differential equations
exhibiting switching and/or oscillatory behaviour. To make the model more
consistent with the underlying biological phenomena we incorporate properties
like growth and decay into the network.
We characterise this network by calculating the usual network measures like
network efficiency, entropy growth, vertex degree distribution, geodesic
lengths, centrality as well as fractal dimensions and generalised entropy. It
is seen that the model can...
110.
High resolution protein folding with a transferable potential - Hubner, Isaac A.; Deeds, Eric J.; Shakhnovich, Eugene I.
A generalized computational method for folding proteins with a fully
transferable potential and geometrically realistic all-atom model is presented
and tested on seven different helix bundle proteins. The protocol, which
includes graph-theoretical analysis of the ensemble of resulting folded
conformations, was systematically applied and consistently produced structure
predictions of approximately 3 Angstroms without any knowledge of the native
state. To measure and understand the significance of the results, extensive
control simulations were conducted. Graph theoretic analysis provides a means
for systematically identifying the native fold and provides physical insight,
conceptually linking the results to modern theoretical views of protein
folding. In addition to presenting a method for prediction of structure...
111.
Mathematical modeling of evolution of horizontally transferred genes - Novozhilov, Artem S.; Karev, Georgy P.; Koonin, Eugene V.
We describe a stochastic birth-and-death model of evolution of horizontally
transferred genes in microbial populations. The model is a generalization of
the stochastic model described by Berg and Kurland and includes five
parameters: the rate of mutational inactivation, selection coefficient,
immigration rate (i.e., rate of arrival of a novel sequence from outside of the
recipient population), within-population horizontal transmission rate, and
population size. The model of Berg and Kurland included four parameters,
namely, mutational inactivation, selection coefficient, population size, and
transmission rate. However, the effect of transmission was disregarded in the
interpretation of the results, and the overall conclusion was that horizontally
acquired sequences can be fixed in a population...
112.
In silicio stretching of chromatin - Aumann, Frank; Lankas, Filip; Caudron, Maiwen; Langowski, Jörg
We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm
chromatin fiber. The model approximates the DNA by a flexible polymer chain
with Debye-H\"uckel electrostatics and uses a two-angle zig-zag model for the
geometry of the linker DNA connecting the nucleosomes. The latter are
represented by flat disks interacting via an attractive Gay-Berne potential.
Our results show that the stiffness of the chromatin fiber strongly depends on
the linker DNA length. Furthermore, changing the twisting angle between
nucleosomes from 90 deg to 130 deg increases the stiffness significantly. An
increase in the opening angle from 22 deg to 34 deg leads to softer fibers for
small...
113.
Weighted and unweighted network of amino acids within protein - Aftabuddin, Md.; Kundu, Sudip
The information regarding the structure of a single protein is encoded in the
network of interacting amino acids. Considering each protein as a weighted and
unweighted network of amino acids we have analyzed a total of forty nine
protein structures that covers the three branches of life on earth. Our results
show that the probability degree distribution of network connectivity follows
Poisson's distribution; whereas the probability strength distribution does not
follow any known distribution. However, the average strength of amino acid node
depends on its degree (k). For some of the proteins, the strength of a node
increases linearly with k. On the other hand, for a set...
114.
Embedded transfer RNA Genes - Ghosh, Zhumur; Das, Smarajit; Chakrabarti, Jayprokas; Mallick, Bibekanand; Sahoo, Satyabrata
In euryarchaeal methanogen M.kandleri and in Nanoarchaea N. equitans some of
the missing tRNA genes are embedded in others. We argue from bioinformatic
evidence that position specific intron splicing is the key behind co-location
of these tRNA genes.
115.
Universality of Long-Range Correlations in Expansion-Randomization
Systems - Messer, Philipp W.; Lassig, Michael; Arndt, Peter F.
We study the stochastic dynamics of sequences evolving by single site
mutations, segmental duplications, deletions, and random insertions. These
processes are relevant for the evolution of genomic DNA. They define a
universality class of non-equilibrium 1D expansion-randomization systems with
generic stationary long-range correlations in a regime of growing sequence
length. We obtain explicitly the two-point correlation function of the sequence
composition and the distribution function of the composition bias in sequences
of finite length. The characteristic exponent $\chi$ of these quantities is
determined by the ratio of two effective rates, which are explicitly calculated
for several specific sequence evolution dynamics of the universality class.
Depending on the value of $\chi$,...
116.
Stimulus - response curves of a neuronal model for noisy subthreshold
oscillations and related spike generation - Braun, Martin Tobias Huber And Hans Albert
We investigate the stimulus-dependent tuning properties of a noisy ionic
conductance model for intrinsic subthreshold oscillations in membrane potential
and associated spike generation. On depolarization by an applied current, the
model exhibits subthreshold oscillatory activity with occasional spike
generation when oscillations reach the spike threshold. We consider how the
amount of applied current, the noise intensity, variation of maximum
conductance values and scaling to different temperature ranges alter the
responses of the model with respect to voltage traces, interspike intervals and
their statistics and the mean spike frequency curves. We demonstrate that
subthreshold oscillatory neurons in the presence of noise can sensitively and
also selectively be tuned by stimulus-dependent variation...
117.
Some protein interaction data do not exhibit power law statistics - Tanaka, Reiko; Yi, Tau-Mu; Doyle, John
It has been claimed that protein-protein interaction (PPI) networks are
scale-free based on the observation that the node degree sequence follows a
power law. Here we argue that these claims are likely to be based on erroneous
statistical analysis. Typically, the supporting data are presented using
frequency-degree plots. We show that such plots can be misleading, and should
correctly be replaced by rank-degree plots. We provide two PPI network examples
in which the frequency-degree plots appear linear on a log-log scale, but the
rank-degree plots demonstrate that the node degree sequence is far from a power
law. We conclude that at least these PPI networks are not scale-free.
118.
Domesticated P elements in the Drosophila montium species subgroup have
a new function related to a DNA binding property - Reiss, Daphné; Nouaud, Danielle; Ronsseray, Stéphane; Anxolabéhère, Dominique
Molecular domestication of a transposable element is defined as its
functional recruitment by the host genome. To date, two independent events of
molecular domestication of the P transposable element have been described: in
the Drosophila obscura species group and in the Drosophila montium species
subgroup. These P neogenes consist to stationary, non repeated sequences,
potentially encoding 66 kDa repressor-like proteins (RLs). Here we investigate
the function of the montium P neogenes. We provide evidence for the presence of
RLs proteins in two montium species (D. tsacasi and D. bocqueti) specifically
expressed in adult and larval brain and gonads. We tested the hypothesis that
the montium P neogenes function is...
119.
Speciational view of macroevolution: are micro and macroevolution
decoupled? - Schwammle, V.; Brigatti, E.
We introduce a simple computational model that, with a microscopic dynamics
driven by natural selection and mutation alone, allows the description of true
speciation events. A statistical analysis of the so generated evolutionary tree
captures realistic features showing power laws for frequency distributions in
time and size. Albeit these successful predictions, the difficulty in obtaining
punctuated dynamics with mass extinctions suggests the necessity of decoupling
micro and macro-evolutionary mechanisms in agreement with some ideas of Gould's
and Eldredge's theory of punctuated equilibrium.
120.
Age-Associated Disorders As A Proxy Measure Of Biological Age: Findings
From the NLTCS Data - Kulminski, A.; Yashin, A.; Ukraintseva, S.; Akushevich, I.; Arbeev, K.; Land, K.; Manton, K.
Background: The relative contribution of different aging-associated processes
to the age phenotype may differ among individuals, creating variability in
aging manifestations among age-peers. Capturing this variability can
significantly advance understanding the aging and mortality. An index of
age-associated health disorders (deficits), called a "frailty index" (FI),
appears to be a promising characteristic of such processes. In this study we
address the connections of the FI with age focusing on disabled individuals who
might be at excessive risk of frailty. Methods: The National Long Term Care
Survey (NLTCS) assessed health and functioning of the U.S. elderly in 1982,
1984, 1989, 1994, and 1999. Detailed information for our sample was assessed
from...
101.
