arXiv
(422,153 recursos)
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Mostrando recursos 21 - 40 de 4,680
21.
A protein structural alphabet and its substitution matrix CLESUM - Zheng, Wei-Mou; Liu, Xin
By using a mixture model for the density distribution of the three pseudobond
angles formed by $C_\alpha$ atoms of four consecutive residues, the local
structural states are discretized as 17 conformational letters of a protein
structural alphabet. This coarse-graining procedure converts a 3D structure to
a 1D code sequence. A substitution matrix between these letters is constructed
based on the structural alignments of the FSSP database.
22.
Modeling Genetic Networks from Clonal Analysis - Nagarajan, Radhakrishnan; Aubin, Jane E.; Peterson, Charlotte A.
In this report a systematic approach is used to determine the approximate
genetic network and robust dependencies underlying differentiation. The data
considered is in the form of a binary matrix and represent the expression of
the nine genes across the ninety-nine colonies. The report is divided into two
parts: the first part identifies significant pair-wise dependencies from the
given binary matrix using linear correlation and mutual information. A new
method is proposed to determine statistically significant dependencies
estimated using the mutual information measure. In the second, a Bayesian
approach is used to obtain an approximate description (equivalence class) of
network structures. The robustness of linear correlation, mutual information
and the...
23.
Vibrational energy relaxation in proteins - Fujisaki, Hiroshi; Straub, John E.
An overview of theories related to vibrational energy relaxation (VER) in
proteins is presented. VER of a selected mode in cytochrome c is studied using
two theoretical approaches. One is the equilibrium simulation approach with
quantum correction factors, and the other is the reduced model approach which
describes the protein as an ensemble of normal modes interacting through
nonlinear coupling elements. Both methods result in estimates of the VER time
(sub ps) for a CD stretching mode in the protein at room temperature. The
theoretical predictions are in accord with the experimental data of Romesberg's
group. A perspective on future directions for the detailed study of time scales
and...
24.
Nonlinear Protein Degradation and the Function of Genetic Circuits - Buchler, Nicolas E.; Gerland, Ulrich; Hwa, Terence
The functions of most genetic circuits require sufficient degrees of
cooperativity in the circuit components. While mechanisms of cooperativity have
been studied most extensively in the context of transcriptional initiation
control, cooperativity from other processes involved in the operation of the
circuits can also play important roles. In this study, we examine a simple
kinetic source of cooperativity stemming from the nonlinear degradation of
multimeric proteins. Ample experimental evidence suggests that protein subunits
can degrade less rapidly when associated in multimeric complexes, an effect we
refer to as cooperative stability. For dimeric transcription factors, this
effect leads to a concentration-dependence in the degradation rate because
monomers, which are predominant at...
25.
The posterior-Viterbi: a new decoding algorithm for hidden Markov models - Fariselli, Piero; Martelli, Pier Luigi; Casadio, Rita
Background: Hidden Markov models (HMM) are powerful machine learning tools
successfully applied to problems of computational Molecular Biology. In a
predictive task, the HMM is endowed with a decoding algorithm in order to
assign the most probable state path, and in turn the class labeling, to an
unknown sequence. The Viterbi and the posterior decoding algorithms are the
most common. The former is very efficient when one path dominates, while the
latter, even though does not guarantee to preserve the automaton grammar, is
more effective when several concurring paths have similar probabilities. A
third good alternative is 1-best, which was shown to perform equal or better
than Viterbi. Results:...
26.
Information Capacity of Biological Macromoleculae Reloaded - Sadovsky, Michael G.
Information capacity of a symbol sequence is a measure of the unexpectedness
of a continuation of given string of symbols. Continuation of a string is
determined through the maximum entropy of the reconstructed frequency
dictionary; the capacity, in turn, is determined through the calculation of
mutual entropy of a real frequency dictionary of a sequence with respect to the
reconstructed one. The capacity does not depend on the length of strings in a
dictionary. The capacity calculated for various genomes exhibits a multi-minima
pattern reflecting an order observed within a sequence.
27.
Stochastic models in population biology and their deterministic analogs - McKane, A. J.; Newman, T. J.
In this paper we introduce a class of stochastic population models based on
"patch dynamics". The size of the patch may be varied, and this allows one to
quantify the departures of these stochastic models from various mean field
theories, which are generally valid as the patch size becomes very large. These
models may be used to formulate a broad range of biological processes in both
spatial and non-spatial contexts. Here, we concentrate on two-species
competition. We present both a mathematical analysis of the patch model, in
which we derive the precise form of the competition mean field equations (and
their first order corrections in the non-spatial case),...
28.
Synaptic Plasticity with Discrete state synapses - Abarbanel, H. D.; Talathi, S. S.; Gibb, L.; Rabinovich, M.
Experimental observations on synaptic plasticity at individual glutamatergic
synapses from the CA3 Shaffer collateral pathway onto CA1 pyramidal cells in
the hippocampus suggest that the transitions in synaptic strength occur among
discrete levels at individual synapses (~\cite{Peter} and S. S.-H. Wang,
unpublished data used with the authors' permission). This happens for both long
term potentiation (LTP) and long term depression (LTD) induction protocols.
O'Connor, Wittenberg, and Wang have argued that three states would account for
their observations on individual synapses in the CA3-CA1 pathway. We develop a
quantitative model of this three state system with transitions among the states
determined by a competition between kinases and phosphatases shown by...
29.
Are scale-free regulatory networks larger than random ones? - Fortuna, Miguel A.; Melian, Carlos J.
Network of packages with regulatory interactions (dependences and conflicts)
from Debian GNU/Linux operating system is compiled and used as analogy of a
gene regulatory network. Using a trace-back algorithm we assembly networks from
the potential pool of packages for both scale-free and exponential topology
from real and a null model data, respectively. We calculate the maximum number
of packages that can be functionally installed in the system (i.e., the active
network size). We show that scale-free regulatory networks allow a larger
active network size than random ones. Small genomes with scale-free regulatory
topology could allow much more functionality than large genomes with an
exponential one, with implications on its...
30.
Filament depolymerization by motor molecules - Klein, Gernot A.; Kruse, Karsten; Cuniberti, Gianaurelio; Juelicher, Frank
Motor proteins that specifically interact with the ends of cytoskeletal
filaments can induce filament depolymerization. A phenomenological description
of this process is presented. We show that under certain conditions motors
dynamically accumulate at the filament ends. We compare simulations of two
microscopic models to the phenomenological description. The depolymerization
rate can exhibit maxima and dynamic instabilities as a function of the bulk
motor density for processive depolymerization. We discuss our results in
relation to experimental studies of Kin-13 family motor proteins.
31.
The Effects of EGF-Receptor Density on Multiscale Tumor Growth Patterns - Athale, Chaitanya A.; Deisboeck, Thomas S.
We studied the effects of epidermal growth factor receptor (EGFR) density on
tumor growth dynamics, both on the sub- and the multi-cellular level using our
previously developed model. This algorithm simulates the growth of a brain
tumor using a multi-scale two-dimensional agent-based approach with an
integrated transforming growth factor alpha (TGFalpha) induced
EGFR-gene-protein interaction network. The results confirm that increasing cell
receptor density correlates with an acceleration of the tumor system's
spatio-temporal expansion dynamics. This multicellular behavior cannot be
explained solely on the basis of spatial sub-cellular dynamics, which remain
qualitatively similar amongst the three glioma cell lines investigated here in
silico. Rather, we find that cells with higher EGFR...
32.
Telomere loss limits the rate of human epithelial tumor formation - Frieboes, Hermann B.; Brody, James P.
Most human carcinomas exhibit telomere abnormalities early in the
carcinogenesis process suggesting that crisis caused by telomere shortening may
be a necessary event leading to human carcinomas. Epidemiological records of
the age at which each patient in a population develops carcinoma are known as
age-incidence data; these provide a quantitative measure of human tumor
initiation and dynamics. If crisis brought on by telomere shortening is
necessary for most human carcinomas, it may also be the rate limiting step. To
test this, we compared a mathematical model in which telomere loss is the rate
limiting step during carcinogenesis with age-incidence data compiled by the
Surveillance, Epidemiology and End Results (SEER)...
33.
What can one learn from two-state single molecule trajectories? - Flomenbom, Ophir; Klafter, Joseph; Szabo, Attila
A time trajectory of an observable that fluctuates between two values (say,
on and off), stemming from some unknown multi-substate kinetic scheme, is the
output of many single molecule experiments. Here we show that when all
successive waiting times along the trajectory are uncorrelated the on and the
off waiting time probability density functions (PDFs) contain all the
information. By relating the lack of correlation in the trajectory to the
topology of kinetic schemes, we can immediately specify those kinetic schemes
that are equally consistent with experiment, which means that it is impossible
to differentiate between them by any sophisticated analyses of the trajectory.
Correlated trajectories, however, contain additional...
34.
Statistical analysis of simple repeats in the human genome - Piazza, Francesco; Lio, Pietro
The human genome contains repetitive DNA at different level of sequence
length, number and dispersion. Highly repetitive DNA is particularly rich in
homo-- and di--nucleotide repeats, while middle repetitive DNA is rich of
families of interspersed, mobile elements hundreds of base pairs (bp) long,
among which the Alu families. A link between homo- and di-polymeric tracts and
mobile elements has been recently highlighted. In particular, the mobility of
Alu repeats, which form 10% of the human genome, has been correlated with the
length of poly(A) tracts located at one end of the Alu. These tracts have a
rigid and non-bendable structure and have an inhibitory effect on nucleosomes,
which...
35.
Accelerating, hyper-accelerating, and decelerating probabilistic networks - Gagen, M. J.; Mattick, J. S.
Many growing networks possess accelerating statistics where the number of
links added with each new node is an increasing function of network size so the
total number of links increases faster than linearly with network size. In
particular, biological networks can display a quadratic growth in regulator
number with genome size even while remaining sparsely connected. These features
are mutually incompatible in standard treatments of network theory which
typically require that every new network node possesses at least one
connection. To model sparsely connected networks, we generalize existing
approaches and add each new node with a probabilistic number of links to
generate either accelerating, hyper-accelerating, or even decelerating network
statistics...
36.
A stochastic approach to multi-gene expression dynamics - Ochiai, T.; Nacher, J. C.; Akutsu, T.
In the last years, tens of thousands gene expression profiles for cells of
several organisms have been monitored. Gene expression is a complex
transcriptional process where mRNA molecules are translated into proteins,
which control most of the cell functions. In this process, the correlation
among genes is crucial to determine the specific functions of genes. Here, we
propose a novel multi-dimensional stochastic approach to deal with the gene
correlation phenomena. Interestingly, our stochastic framework suggests that
the study of the gene correlation requires only one theoretical assumption
-Markov property- and the experimental transition probability, which
characterizes the gene correlation system. Finally, a gene expression
experiment is proposed for future applications...
37.
Pairwise alignment incorporating dipeptide covariation - Crooks, Gavin E.; Green, Richard E.; Brenner, Steven E.
Motivation: Standard algorithms for pairwise protein sequence alignment make
the simplifying assumption that amino acid substitutions at neighboring sites
are uncorrelated. This assumption allows implementation of fast algorithms for
pairwise sequence alignment, but it ignores information that could conceivably
increase the power of remote homolog detection. We examine the validity of this
assumption by constructing extended substitution matrixes that encapsulate the
observed correlations between neighboring sites, by developing an efficient and
rigorous algorithm for pairwise protein sequence alignment that incorporates
these local substitution correlations, and by assessing the ability of this
algorithm to detect remote homologies. Results: Our analysis indicates that
local correlations between substitutions are not strong on the...
38.
Stochastic gene expression in switching environments - Gander, Martin; Mazza, Christian; Rummler, Hansklaus
We study a stochastic model proposed recently in the genetic literature to
explain the heterogeneity of cell populations or of gene products. Cells are
located in two colonies, whose sizes fluctuate as birth and migration processes
in switching environments. We prove that there is a range of parameters where
heterogeneity induces a larger mean fitness
39.
The Species Abundances Distribution in a new perspective - Ravasz, M.; Balog, A.; Marko, V.; Neda, Z.
Studies on distribution, abundance and diversity of species revealed
fascinating universalities in macroecology. Many of these patterns, like the
species-area and range-abundance relationship or the year-to-year fluctuations
in population sizes are expressed as power-law distributions, and indicate thus
scale-invariance. The species abundance distribution (SAD) apparently shows
this scale-free nature only for rare species, and its mathematical form is much
debated. In the present work we propose a new mathematical expression for SAD
which describes reasonable well most of the presently available large-scale
experimental data and the results of the neutral models. This distribution
function leads to an interesting relation between the total number of
individuals, total number of species and...
40.
Modelling butterfly wing eyespot patterns - Dilao, Rui; Sainhas, Joaquim
Eyespots are concentric motifs with contrasting colours on butterfly wings.
Eyespots have intra- and inter-specific visual signalling functions with
adaptive and selective roles. We propose a reaction-diffusion model that
accounts for eyespot development. The model considers two diffusive morphogens
and three non-diffusive pigment precursors. The first morphogen is produced in
the focus and determines the differentiation of the first eyespot ring. A
second morphogen is then produced, modifying the chromatic properties of the
wing background pigment precursor, inducing the differentiation of a second
ring. The model simulates the general structural organisation of eyespots,
their phenotypic plasticity and seasonal variability, and predicts effects from
microsurgical manipulations on pupal wings as reported...
21.
