arXiv
(422,153 recursos)
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Mostrando recursos 121 - 140 de 4,680
121.
Analytic approach to the evolutionary effects of genetic exchange - Cohen, Elisheva; Kessler, David A.; Levine, Herbert
We present an approximate analytic study of our previously introduced model
of evolution including the effects of genetic exchange. This model is motivated
by the process of bacterial transformation. We solve for the velocity, the rate
of increase of fitness, as a function of the fixed population size, $N$. We
find the velocity increases with $\ln N$, eventually saturated at an $N$ which
depends on the strength of the recombination process. The analytical treatment
is seen to agree well with direct numerical simulations of our model equations.
122.
Frailty Index as a Major Indicator of Aging Processes and Mortality in
Elderly: Results From Analyses of the National Long Term Care Survey Data - Kulminski, A.; Yashin, A.; Akushevich, I.; Ukraintseva, S.; Land, K.; Arbeev, K.; Manton, K.
To better understand mortality change with age capturing the variability in
individuals' rates of aging, we performed comprehensive analysis of statistical
properties of a cumulative index of age-associated disorders (deficits), called
a "frailty index" (FI). This index is calculated as the proportion of the
health deficits in an individual. It is found, first, that frequency,
time-to-death, mortality-rate, and relative-risk-of-death exhibit remarkably
similar FI- and age- patterns. Second, the FI, on the one hand, and mortality
rate and relative risk, on the other hand, also exhibit similar age patterns
with accelerated increase up to oldest-old ages and with subsequent
deceleration and even decline. Third, distribution of the FI with time-to-death
is...
123.
The response of amino acid frequencies to directional mutation pressure
in mitochondrial genome sequences is related to the physical properties of the
amino acids and to the structure of the genetic code - Urbina, Daniel; Tang, Bin; Higgs, Paul G.
The frequencies of A, C, G and T in mitochondrial DNA vary among species due
to unequal rates of mutation between the bases. The frequencies of bases at
four-fold degenerate sites respond directly to mutation pressure. At 1st and
2nd positions, selection reduces the degree of frequency variation. Using a
simple evolutionary model, we show that 1st position sites are less constrained
by selection than 2nd position sites, and therefore that the frequencies of
bases at 1st position are more responsive to mutation pressure than those at
2nd position. We define a similarity measure between amino acids that is a
function of 8 measured physical properties. We define...
124.
Algorithmic and Complexity Results for Decompositions of Biological
Networks into Monotone Subsystems - DasGupta, Bhaskar; Enciso, German Andres; Sontag, Eduardo; Zhang, Yi
A useful approach to the mathematical analysis of large-scale biological
networks is based upon their decompositions into monotone dynamical systems.
This paper deals with two computational problems associated to finding
decompositions which are optimal in an appropriate sense. In graph-theoretic
language, the problems can be recast in terms of maximal sign-consistent
subgraphs. The theoretical results include polynomial-time approximation
algorithms as well as constant-ratio inapproximability results. One of the
algorithms, which has a worst-case guarantee of 87.9 percent from optimality,
is based on the semidefinite programming relaxation approach of
Goemans-Williamson. The algorithm was implemented and tested on a Drosophila
segmentation network and an Epidermal Growth Factor Receptor pathway model, and
it was...
125.
Sexual replication in the quasispecies model - Tannenbaum, Emmanuel
This paper develops a simplified model for sexual replication within the
quasispecies formalism. We assume that the genomes of the replicating organisms
are two-chromosomed and diploid, and that the fitness is determined by the
number of chromosomes that are identical to a given master sequence. We also
assume that there is a cost to sexual replication, given by a characteristic
time $ \tau_{seek} $ during which haploid cells seek out a mate with which to
recombine. If the mating strategy is such that only viable haploids can mate,
then when $ \tau_{seek} = 0 $, it is possible to show that sexual replication
will always outcompete asexual replication....
126.
Comparative analysis of some models of mixed-substrate microbial growth - Narang, Atul
Mixed-substrate microbial growth is among the most intensely studied systems
in molecular microbiology. Several mathematical models have been developed to
account for the genetic regulation of such systems, especially those resulting
in diauxic growth. In this work, we compare the dynamics of three such models
(Narang, Biotech. Bioeng., 59, 116, 1998; Thattai & Shraiman, Biophys. J, 85,
744, 2003; Brandt et al, Water Research, 38, 1004, 2004). We show that these
models are dynamically similar - the initial motion of the inducible enzymes in
all the models is described by Lotka-Volterra equations for competing species.
The dynamic similarity occurs because in all the models, the inducible enzymes
possess properties...
127.
Statistical Indicators of Collective Behavior and Functional Clusters
in Gene Networks of Yeast - Zivkovic, Jelena; Tadic, Bosiljka; Wick, Nikolaus; Thurner, Stefan
We analyze gene expression time-series data of yeast S. cerevisiae measured
along two full cell-cycles. We quantify these data by using q-exponentials,
gene expression ranking and a temporal mean-variance analysis. We construct
gene interaction networks based on correlation coefficients and study the
formation of the corresponding giant components and minimum spanning trees. By
coloring genes according to their cell function we find functional clusters in
the correlation networks and functional branches in the associated trees. Our
results suggest that a percolation point of functional clusters can be
identified on these gene expression correlation networks.
128.
Physical origins of protein superfamilies - Zeldovich, Konstantin B.; Berezovsky, Igor N.; Sha, Eugene I.
In this work, we discovered a fundamental connection between selection for
protein stability and emergence of preferred structures of proteins. Using
standard exact 3-dimensional lattice model we evolve sequences starting from
random ones and determining exact native structure after each mutation.
Acceptance of mutations is biased to select for stable proteins. We found that
certain structures, wonderfold, are independently discovered numerous times as
native states of stable proteins in many unrelated runs of selection. Diversity
of sequences that fold into wonderfold structures gives rise to superfamilies,
i.e. sets of dissimilar sequences that fold into the same or very similar
structures. Wonderfolds appear to be the most designable structures out...
129.
A p53 Oscillator Model of DNA Break Repair Control - Chickarmane, Vijay; Nadim, Ali; Ray, Animesh; Sauro, Herbert M.
The transcription factor p53 is an important regulator of cell fate.
Mutations in p53 gene are associated with many cancers. In response to signals
such as DNA damage, p53 controls the transcription of a series of genes that
cause cell cycle arrest during which DNA damage is repaired, or triggers
programmed cell death that eliminates possibly cancerous cells wherein DNA
damage might have remained unrepaired. Previous experiments showed oscillations
in p53 level in response to DNA damage, but the mechanism of oscillation
remained unclear. Here we examine a model where the concentrations of p53
isoforms are regulated by Mdm22, Arf, Siah, and beta-catenin. The extent of DNA
damage is...
130.
Control of neural chaos by synaptic noise - Cortes, J. M.; Marro, J.; Torres, J. J.
We studied neural automata -or neurobiologically inspired cellular automata-
which exhibits chaotic itinerancy among the different stored patterns or
memories. This is a consequence of activity-dependent synaptic fluctuations,
which continuously destabilize the attractor and induce irregular hopping to
other possible attractors. The nature of the resulting irregularity depends on
the dynamic details, namely, on the intensity of the synaptic noise and on the
number of sites of the network that are synchronously updated at each time
step. Varying these details, different regimes occur from regular to chaotic.
In the absence of external agents, the chaotic behavior may turn regular after
tuning the noise intensity. It is argued that a...
131.
The simplest model of spatially distributed population with
reasonable migration of organisms - Sadovsky, Michael
The simplest model of a smart spatial redistribution of individuals is
proposed. A single-species population is considered, to be composed of two
discrete subpopulations inhabiting two stations; migration is a transfer
between them. The migration is not random and yields the maximization of net
reproduction, with respect to the transaction costs. The organisms are supposed
to be globally informed. Discrete time model is studied, since it shows all the
features of a smart migrations, while the continuous time case brings no new
knowledge but the technical problems. Some properties of the model are studied
and discussed.
132.
The Tangled nature model with inheritance and constraint:
Evolutionary ecology restricted by a conserved resource - Laird, Simon; Jensen, Henrik Jeldtoft
We study a version of the Tangled Nature model of evolutionary ecology
redefined in a phenotype space where mutants have properties correlated to
their parents. The model has individual-based dynamics whilst incorporating
species scale competitive constraints and a system scale resource constraint.
Multiple species arise that coexist in a species interaction network with
evolving global properties. Both the mean interaction strength and the network
connectance increase relative to the null system as mutualism becomes more
extensive. From a study of the dependence of average degree on the resource
level we extract the diversity-connectance relationship which conforms to the
hyperbolic form seen in field data. This is adjudged to arise...
133.
A Novel Lie Algebra of the Genetic Code over the Galois Field of Four
DNA Bases - Sanchez, Robersy; Grau, Ricardo
By starting from the four DNA bases order in the Boolean lattice, a novel Lie
Algebra of the genetic code is proposed. Here, the principal partitions of the
genetic code table were obtained as equivalent classes of quotient subspaces of
the genetic code vector space over the Galois field of the four DNA bases. The
new algebraic structure shows strong connections among algebraic relationships,
codon assignment and physicochemical properties of amino acids. Moreover, a
distance function defined between codons in the Lie algebra was demonstrated to
have a linear behavior respect to physical variables such as the mean of amino
acids energy in proteins. It was also noticed...
134.
A new formalism for calculation of the partition function of single
stranded nucleic acids - Dimitrov, Roumen A.
A new formalism for calculation of the partition function of single stranded
nucleic acids is presented. Secondary structures and the topology of structure
elements are the level of resolution that is used. The folding model deals with
matches, mismatches, symmetric and asymmetric interior loops, stacked pairs in
loop and dangling end regions, multi-branched loops, bulges and single base
stacking that might exist at duplex ends or at the ends of helices.
Calculations on short and long sequences show, that for short oligonucleotides,
a duplex formation often displays a two-state transition. However, for longer
oligonucleotides, the thermodynamic properties of the single self-folding
transition affects the transition nature of the duplex...
135.
The protein map of Synechococcus sp. PCC 7942 - the first overlook - Koksharova, Olga A.; Klint, Johan; Rasmussen, Ulla
The unicellular cyanobacterium Synechococcus PCC 7942 has been used as a
model organism for studies of prokaryotic circadian rhythms,
carbon-concentrating mechanisms, response to a variety of nutrient and
environmental stresses, and cell division. This paper presents the results of
the first proteomic exploratory study of Synechococcus PCC 7942. The proteome
was analyzed using two-dimensional gel electrophoresis followed by MALDI-TOF
mass spectroscopy, and database searching. Of 140 analyzed protein spots, 110
were successfully identified as 62 different proteins, many of which occurred
as multiple spots on the gel. The identified proteins were organized into 18
different functional categories reflecting the major metabolic and cellular
processes occurring in the cyanobacterial cells in...
136.
Predictive Models for Characterization of Ecological Data - Tan, Can Ozan; Ozesmi, Uygar; Kurt, Bahtiyar
Although ARTMAP and ART-based models were introduced in early 70's they were
not used in characterizing and classifying ecological observations. ART-based
models have been extensively used for classification models based on satellite
imagery. This report, to our knowledge, is the first application of ART-based
methods and specifically ARTMAP for predicting habitat selection and spatial
distribution of species. We compare the performance of ARTMAP to assess the
breeding success of three bird species (Lanius senator, Hippolais pallida, and
Calandrella brachydactyla) based on multi-spectral satellite imagery and
environmental variables. ARTMAP is superior both in terms of performance
(percent correctly classified - pcc = 1.00) and generalizability (pcc >0.96) to
those of feedforward...
137.
Statistical modeling of primary Ewing tumours of the bone - Malakar, Sreepurna; Smarandache, Florentin; Bhattacharya, Sukanto
This short technical paper advocates a bootstrapping algorithm from which we
can form a statistically reliable opinion based on limited clinically observed
data, regarding whether an osteo-hyperplasia could actually be a case of
Ewing's osteosarcoma. The basic premise underlying our methodology is that a
primary bone tumour, if it is indeed Erwing's osteosarcoma, cannot increase in
volume beyond some critical limit without showing metastasis. We propose a
statistical method to extrapolate such critical limit to primary tumour volume.
Our model does not involve any physiological variables but rather is entirely
based on time series observations of increase in primary tumour volume from the
point of initial detection to the...
138.
Gene Copy Number and Cell Cycle Arrest - Ghosh, Bhaswar; Bose, Indrani
The cell cycle is an orderly sequence of events which ultimately lead to the
division of a single cell into two daughter cells. In the case of DNA damage by
radiation or chemicals, the damage checkpoints in the $G_{1}$ and $G_{2}$
phases of the cell cycle are activated. This results in an arrest of the cell
cycle so that the DNA damage can be repaired. Once this is done, the cell
continues with its usual cycle of activity. We study a mathematical model of
the DNA damage checkpoint in the $G_{2}$ phase which arrests the transition
from the $G_{2}$ to the $M$ (mitotic) phase of the cell...
139.
The prion-like folding behavior in aggregated proteins - Ji, Yong-Yun; Li, You-Quan; Mao, Jun-Wen; Tang, Xiao-Wei
We investigate the folding behavior of protein sequences by numerically
studying all sequences with maximally compact lattice model through exhaustive
enumeration. We get the prion-like behavior of protein folding. Individual
proteins remaining stable in the isolated native state may change their
conformations when they aggregate. We observe the folding properties as the
interfacial interaction strength changes, and find that the strength must be
strong enough before the propagation of the most stable structures happens.
140.
Probability Models for Degree Distributions of Protein Interaction
Networks - Stumpf, Michael P. H.; Ingram, Piers J.
The degree distribution of many biological and technological networks has
been described as a power-law distribution. While the degree distribution does
not capture all aspects of a network, it has often been suggested that its
functional form contains important clues as to underlying evolutionary
processes that have shaped the network. Generally, the functional form for the
degree distribution has been determined in an ad-hoc fashion, with clear
power-law like behaviour often only extending over a limited range of
connectivities. Here we apply formal model selection techniques to decide which
probability distribution best describes the degree distributions of protein
interaction networks. Contrary to previous studies this well defined approach
suggests that...
121.
