arXiv
(422,153 recursos)
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Mostrando recursos 141 - 160 de 4,680
141.
Graph theoretic analysis of protein interaction networks of eukaryotes - Goh, K. -I.; Kahng, B.; Kim, D.
Thanks to recent progress in high-throughput experimental techniques, the
datasets of large-scale protein interactions of prototypical multicellular
species, the nematode worm Caenorhabditis elegans and the fruit fly Drosophila
melanogaster, have been assayed. The datasets are obtained mainly by using the
yeast hybrid method, which contains false-positive and false-negative
simultaneously. Accordingly, while it is desirable to test such datasets
through further wet experiments, here we invoke recent developed network theory
to test such high throughput datasets in a simple way. Based on the fact that
the key biological processes indispensable to maintaining life are universal
across eukaryotic species, and the comparison of structural properties of the
protein interaction networks (PINs) of...
142.
Mechanical unfolding of RNA hairpins - Hyeon, Changbong; Thirumalai, D.
Mechanical unfolding trajectories, generated by applying constant force in
optical tweezer experiments, show that RNA hairpins and the P5abc subdomain of
the group I intron unfold reversibly. We use coarse-grained Go-like models for
RNA hairpins to explore forced-unfolding over a broad range of temperatures. A
number of predictions that are amenable to experimental tests are made. At the
critical force the hairpin jumps between folded and unfolded conformations
without populating any discernible intermediates. The phase diagram in the
force-temperature (f,T) plane shows that the hairpin unfolds by an all-or-none
process. The cooperativity of the unfolding transition increases dramatically
at low temperatures. Free energy of stability, obtained from time averages...
143.
Gene Algebra from a Genetic Code Algebraic Structure - Sanchez, Robersy; Morgado, Eberto; Grau, Ricardo
The biological distinction between the base positions in the codon, the
chemical types of bases (purine and pyrimidine) and their hydrogen bond number
have been the most relevant codon properties used in the genetic code analysis.
Now, these properties have allowed us to build a Genetic Code ring isomorphic
to the ring (Z64, +,*) of the integer module 64. On the Z64-algebra of the set
of 64^N codon sequences of length N, gene mutations are described by means of
endomorphisms F: (Z64)^N->(Z64)^N. Endomorphisms and automorphisms helped us
describe the gene mutation pathways. For instance, 77.7% mutations in 749 HIV
protease gene sequences correspond to unique diagonal endomorphisms of...
144.
Uni-directional polymerization leading to homochirality in the RNA world - Nilsson, M.; Brandenburg, A.; Andersen, A. C.; Hoefner, S.
The differences between uni-directional and bi-directional polymerization are
considered. The uni-directional case is discussed in the framework of the RNA
world. Similar to earlier models of this type, where polymerization was assumed
to proceed in a bi-directional fashion (presumed to be relevant to peptide
nucleic acids), left-handed and right-handed monomers are produced via an
autocatalysis from an achiral substrate. The details of the bifurcation from a
racemic solution to a homochiral state of either handedness is shown to be
remarkably independent of whether the polymerization in uni-directional or
bi-directional. Slightly larger differences are seen when dissociation is
allowed and the dissociation fragments are being recycled into the achiral
substrate.
145.
Functional modes of proteins are among the most robust ones - Nicolay, Samuel; Sanejouand, Yves-Henri
It is shown that a small subset of modes which are likely to be involved in
protein functional motions of large amplitude can be determined by retaining
the most robust normal modes obtained using different protein models. This
result should prove helpful in the context of several applications proposed
recently, like for solving difficult molecular replacement problems or for
fitting atomic structures into low-resolution electron density maps. Moreover,
it may also pave the way for the development of methods allowing to predict
such motions accurately.
146.
Density-Dependence as a Size-Independent Regulatory Mechanism - de Vladar, Harold P.
The growth function of populations is central in biomathematics. The main
dogma is the existence of density dependence mechanisms, which can be modelled
with distinct functional forms that depend on the size of the population. One
important class of regulatory functions is the $\theta$-logistic, which
generalises the logistic equation. Using this model as a motivation, this paper
introduces a simple dynamical reformulation that generalises many growth
functions. The reformulation consists of two equations, one for population
size, and one for the growth rate. Furthermore, the model shows that although
population is density-dependent, the dynamics of the growth rate does not
depend either on population size, nor on the carrying...
147.
Implications of Aging in Bacteria - Johnson, Leah R.; Mangel, Marc
Motivated by recent research of aging in E. coli, we explore the effects of
aging on bacterial fitness. The disposable soma theory of aging was developed
to explain how differences in lifespans and aging rates could be linked to life
history trade-offs. Although generally applied for multicellular organisms, it
is also useful for exploring life history strategies of single celled organisms
such as bacteria. Starting from the Euler-Lotka equation, we propose a
mathematical model to explore how a finite lifespan effects fitness of
bacteria. We find that that there is surprisingly little loss of fitness when
the bacterium has limited opportunities to reproduce. Instead, the fitness
gained each time...
148.
Model evaluation for glycolytic oscillations in yeast biotransformations
of xenobiotics - Brusch, Lutz; Cuniberti, Gianaurelio; Bertau, Martin
Anaerobic glycolysis in yeast perturbed by the reduction of xenobiotic
ketones is studied numerically in two models which possess the same topology
but different levels of complexity. By comparing both models' predictions for
concentrations and fluxes as well as steady or oscillatory temporal behavior we
answer the question what phenomena require what kind of minimum model
abstraction. While mean concentrations and fluxes are predicted in agreement by
both models we observe different domains of oscillatory behavior in parameter
space. Generic properties of the glycolytic response to ketones are discussed.
149.
Prediction of site-specific amino acid distributions and limits of
divergent evolutionary changes in protein sequences - Porto, Markus; Roman, H. Eduardo; Vendruscolo, Michele; Bastolla, Ugo
We derive an analytic expression for site-specific stationary distributions
of amino acids from the Structurally Constrained Neutral (SCN) model of protein
evolution with conservation of folding stability. The stationary distributions
that we obtain have a Boltzmann-like shape, and their effective temperature
parameter, measuring the limit of divergent evolutionary changes at a given
site, can be predicted from a site-specific topological property, the principal
eigenvector of the contact matrix of the native conformation of the protein.
These analytic results, obtained without free parameters, are compared with
simulations of the SCN model and with the site-specific amino acid
distributions obtained from the Protein Data Bank. These results also provide
new insights into...
150.
An Unusual 500,000 Bases Long Oscillation of Guanine and Cytosine
Content in Human Chromosome 21 - Li, Wentian; Holste, Dirk
An oscillation with a period of around 500 kb in guanine and cytosine content
(GC%) is observed in the DNA sequence of human chromosome 21. This oscillation
is localized in the rightmost one-eighth region of the chromosome, from 43.5 Mb
to 46.5 Mb. Five cycles of oscillation are observed in this region with six
GC-rich peaks and five GC-poor valleys. The GC-poor valleys comprise regions
with low density of CpG islands and, alternating between the two DNA strands,
low gene density regions. Consequently, the long-range oscillation of GC%
result in spacing patterns of both CpG island density, and to a lesser extent,
gene densities.
151.
Universal 1/f noise, cross-overs of scaling exponents, and chromosome
specific patterns of GC content in DNA sequences of the human genome - Li, Wentian; Holste, Dirk
Spatial fluctuations of guanine and cytosine base content (GC%) are studied
by spectral analysis for the complete set of human genomic DNA sequences. We
find that (i) the 1/f^alpha decay is universally observed in the power spectra
of all twenty-four chromosomes, and that (ii) the exponent alpha \approx 1
extends to about 10^7 bases, one order of magnitude longer than what has
previously been observed. We further find that (iii) almost all human
chromosomes exhibit a cross-over from alpha_1 \approx 1 (1/f^alpha_1) at lower
frequency to alpha_2 < 1 (1/f^alpha_2) at higher frequency, typically occurring
at around 30,000--100,000 bases, while (iv) the cross-over in this frequency
range is virtually...
152.
Spectral Analysis of Guanine and Cytosine Fluctuations of Mouse Genomic
DNA - Li, Wentian; Holste, Dirk
We study global fluctuations of the guanine and cytosine base content (GC%)
in mouse genomic DNA using spectral analyses. Power spectra S(f) of GC%
fluctuations in all nineteen autosomal and two sex chromosomes are observed to
have the universal functional form S(f) \sim 1/f^alpha (alpha \approx 1) over
several orders of magnitude in the frequency range 10^-7< f < 10^-5 cycle/base,
corresponding to long-ranging GC% correlations at distances between 100 kb and
10 Mb. S(f) for higher frequencies (f > 10^-5 cycle/base) shows a flattened
power-law function with alpha < 1 across all twenty-one chromosomes. The
substitution of about 38% interspersed repeats does not affect the functional
form of...
153.
Model for the robust establishment of precise proportions in the early
Drosophila embryo - Aegerter-Wilmsen, Tinri; Aegerter, Christof M.; Bisseling, Ton
During embryonic development, a spatial pattern is formed in which
proportions are established precisely. As an early pattern formation step in
Drosophila embryos, an anterior-posterior gradient of Bicoid (Bcd) induces
hunchback (hb) expression (Driever et al. 1989; Tautz et al. 1988). In contrast
to the Bcd gradient, the Hb profile includes information about the scale of the
embryo. Furthermore, the resulting hb expression pattern shows a much lower
embryo-to-embryo variability than the Bcd gradient (Houchmandzadeh et al.
2002). An additional graded posterior repressing activity could theoretically
account for the observed scaling. However, we show that such a model cannot
produce the observed precision in the Hb boundary, such that...
154.
Combinatorial complexity and dynamical restriction of network flows in
signal transduction - Faeder, James R.; Blinov, Michael L.; Goldstein, Byron; Hlavacek, William S.
The activities and interactions of proteins that govern the cellular response
to a signal generate a multitude of protein phosphorylation states and
heterogeneous protein complexes. Here, using a computational model that
accounts for 307 molecular species implied by specified interactions of four
proteins involved in signalling by the immunoreceptor Fc$\epsilon$RI, we
determine the relative importance of molecular species that can be generated
during signalling, chemical transitions among these species, and reaction paths
that lead to activation of the protein tyrosine kinase (PTK) Syk. By all of
these measures and over 2- and 10-fold ranges of model parameters--rate
constants and initial concentrations--only a small portion of the biochemical
network is active....
155.
A Phenomenological model of Myosin II dynamics in the presence of
external loads - Buonocore, A.; Caputo, L.; Ishii, Y.; Pirozzi, E.; Yanagida, T.; Ricciardi, L. M.
We address the controversial hot question concerning the validity of the
loose coupling versus the lever-arm theories in the actomyosin dynamics by
re-interpreting and extending the phenomenological washboard potential model
proposed by some of us in a previous paper. In this new model a Brownian motion
harnessing thermal energy is assumed to co-exist with the deterministic swing
of the lever-arm, to yield an excellent fit of the set of data obtained by some
of us on the sliding of Myosin II heads on immobilized actin filaments under
various load conditions. Our theoretical arguments are complemented by accurate
numerical simulations, and the robustness of the model is tested via...
156.
Predicting Genetic Regulatory Response Using Classification - Middendorf, Manuel; Kundaje, Anshul; Wiggins, Chris; Freund, Yoav; Leslie, Christina
We present a novel classification-based method for learning to predict gene
regulatory response. Our approach is motivated by the hypothesis that in simple
organisms such as Saccharomyces cerevisiae, we can learn a decision rule for
predicting whether a gene is up- or down-regulated in a particular experiment
based on (1) the presence of binding site subsequences (``motifs'') in the
gene's regulatory region and (2) the expression levels of regulators such as
transcription factors in the experiment (``parents''). Thus our learning task
integrates two qualitatively different data sources: genome-wide cDNA
microarray data across multiple perturbation and mutant experiments along with
motif profile data from regulatory sequences. We convert the regression...
157.
Neurokinematic Modeling of Complex Swimming Patterns of the Larval
Zebrafish - Hill, Scott A.; Liu, Xiao-Ping; Borla, Melissa A.; Jose, Jorge V.; O'Malley, Donald M.
Larval zebrafish exhibit a variety of complex undulatory swimming patterns.
This repertoire is controlled by the 300 neurons projecting from brain into
spinal cord. Understanding how descending control signals shape the output of
spinal circuits, however, is nontrivial. We have therefore developed a
segmental oscillator model (using NEURON) to investigate this system. We found
that adjusting the strength of NMDA and glycinergic synapses enabled the
generation of oscillation (tail-beat) frequencies over the range exhibited in
different larval swim patterns. In addition, we developed a kinematic model to
visualize the more complex axial bending patterns used during prey capture.
158.
Signal processing of acoustic signals in the time domain with an active
nonlinear nonlocal cochlear model - Lamar, M. D.; Xin, J.; Qi, Y.
A two space dimensional active nonlinear nonlocal cochlear model is
formulated in the time domain to capture nonlinear hearing effects such as
compression, multi-tone suppression and difference tones. The micromechanics of
the basilar membrane (BM) are incorporated to model active cochlear properties.
An active gain parameter is constructed in the form of a nonlinear nonlocal
functional of BM displacement. The model is discretized with a boundary
integral method and numerically solved using an iterative second order accurate
finite difference scheme. A block matrix structure of the discrete system is
exploited to simplify the numerics with no loss of accuracy. Model responses to
multiple frequency stimuli are shown in agreement...
159.
An Information-Theoretic Approach to Network Modularity - Ziv, Etay; Middendorf, Manuel; Wiggins, Chris
Exploiting recent developments in information theory, we propose, illustrate,
and validate a principled information-theoretic algorithm for module discovery
and resulting measure of network modularity. This measure is an order parameter
(a dimensionless number between 0 and 1). Comparison is made to other
approaches to module-discovery and to quantifying network modularity using
Monte Carlo generated Erdos-like modular networks. Finally, the Network
Information Bottleneck (NIB) algorithm is applied to a number of real world
networks, including the "social" network of coauthors at the APS March Meeting
2004.
160.
MultiNeuron - Neural Networks Simulator For Medical, Physiological, and
Psychological Applications - Gorban, A. N.; Rossiyev, D. A.; Dorrer, M. G.
This work describes neural software applied in medicine and physiology to:
investigate and diagnose immune deficiencies; diagnose and study allergic and
pseudoallergic reactions; forecast emergence or aggravation of stagnant cardiac
insufficiency in patients with cardiac rhythm disorders; forecast development
of cardiac arrhythmia after myocardial infarction; reveal relationships between
the accumulated radiation dose and a set of immunological, hormonal, and
bio-chemical parameters of human blood and find a method to be able to judge by
these parameters the dose value; propose a technique for early diagnosis of
chor-oid melanomas; Neural networks also help to predict human relations within
a group.
141.
