arXiv
(422,153 recursos)
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Mostrando recursos 81 - 100 de 4,680
81.
A single determinant for the rate of yeast protein evolution - Drummond, D. Allan; Raval, Alpan; Wilke, Claus O.
A gene's rate of sequence evolution is among the most fundamental
evolutionary quantities in common use, but what determines evolutionary rates
has remained unclear. Here, we show that the two most commonly used methods to
disentangle the determinants of evolutionary rate, partial correlation analysis
and ordinary multivariate regression, produce misleading or spurious results
when applied to noisy biological data. To overcome these difficulties, we
employ an alternative method, principal component regression, which is a
multivariate regression of evolutionary rate against the principal components
of the predictor variables. We carry out the first combined analysis of seven
predictors (gene expression level, dispensability, protein abundance, codon
adaptation index, gene length, number of...
82.
Statistical model selection methods applied to biological networks - Stumpf, M. P. H.; Ingram, P. J.; Nouvel, I.; Wiuf, C.
Many biological networks have been labelled scale-free as their degree
distribution can be approximately described by a powerlaw distribution. While
the degree distribution does not summarize 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
determining the appropriate functional form for the degree distribution has
been fitted in an ad-hoc fashion.
Here we apply formal statistical model selection methods to determine which
functional form best describes degree distributions of protein interaction and
metabolic networks. We interpret the degree distribution as belonging to a
class of probability models and determine which...
83.
Living Transistors: a Physicist's View of Ion Channels - Eisenberg, Bob
Ion channels are proteins with a hole down the middle embedded in cell
membranes. Membranes form insulating structures and the channels through them
allow and control the movement of charged particles, spherical ions, mostly
Na+, K+, Ca++, and Cl-. Membranes contain hundreds or thousands of types of
channels, most of which are closed at any time. Channels control an enormous
range of biological channel by opening and closing in response to specific
stimuli by mechanisms that are not yet understood in physical language. Open
channels conduct current of charged particles following laws of
electrodiffusion rather like the laws of electrodiffusion of quasiparticles in
semiconductors. Open channels select between similar...
84.
Built to evolve - Hoeneisen, B.; Trueba, G.
We study the probabilities of evolution based on random mutations and natural
selection. We conclude that evolution to multicellular eukaryots, or even
prokaryots, is unlikely to be the result of only random mutations. Complex
organisms have evolved through several mechanisms besides random mutations,
namely DNA recombination, adaptive mutations, and acquisition of foreign DNA.
We conclude that all living organisms, in addition to being self-organizing and
reproducing (autopoyetic), have built-in mechanisms of evolution, some of which
respond in very specific ways to environmental stress.
85.
Turing Pattern with Proportion Preservation - Ishihara, Shuji; Kaneko, Kunihiko
Although Turing pattern is one of the most universal mechanisms for pattern
formation, in its standard model the number of stripes changes with the system
size, since the wavelength of the pattern is invariant: It fails to preserve
the proportionality of the pattern, i.e., the ratio of the wavelength to the
size, that is often required in biological morphogeneis. To get over this
problem, we show that the Turing pattern can preserve proportionality by
introducing a catalytic chemical whose concentration depends on the system
size. Several plausible mechanisms for such size dependence of the
concentration are discussed. Following this general discussion, two models are
studied in which arising Turing...
86.
Microbial origin of excess greenhouse gases in glacial ice - Tung, H. C.; Bramall, N. E.; Price, P. B.
We report the discovery of methanogenic archaea that account for abrupt
factor 10 increases in methane concentration found by E. Brook at depths of
2954 and 3036 m in the GISP2 (Greenland Ice Sheet Project 2) ice core. The
total microbial concentration we measured with direct cell counts tracks the
excesses of methanogens that we identified by their F420 fluorescence. The
highly localized (<1 m thick) layers of methanogens suggest flow induced mixing
of layers of microbe laden anaerobic basal ice with glacial ice. The metabolic
rate we found for microbes at 2954 and 3036 m lies roughly on the Arrhenius
line for microbes imprisoned in rock, sediment,...
87.
Towards a Quantitative, Metabolic Theory for Mammalian Sleep - Savage, Van M.; West, Geoffrey B.
Sleep is one of the most noticeable and widespread phenomena occurring in
multicellular animals. Nevertheless, no consensus for a theory of its origins
has emerged. In particular, no explicit, quantitative theory exists that
elucidates or distinguishes between the myriad hypotheses proposed for sleep.
Here, we develop a general, quantitative theory for mammalian sleep that
relates many of its fundamental parameters to metabolic rate and body size.
Most mechanisms suggested for the function of sleep can be placed in this
framework, e.g., cellular repair of damage caused by metabolic processes and
cortical reorganization to process sensory input. Our theory leads to
predictions for sleep time, sleep cycle time, and REM...
88.
Quantitative Measure of Stability in Gene Regulatory Networks - Ao, P.
A quantitative measure of stability in stochastic dynamics starts to emerge
in recent experiments on bioswitches. This quantity, similar to the potential
function in mathematics, is deeply rooted in biology, dated back at the
beginning of quantitative description of biological processes: the adaptive
landscape of Wright (1932) and the development landscape of Waddington (1940).
Nevertheless, its quantitative implication has been frequently challenged by
biologists. Recent progresses in quantitative biology begin to meet those
outstanding challenges.
89.
Power laws of complex systems from Extreme physical information - Frieden, B. Roy; Gatenby, Robert A.
Many complex systems obey allometric, or power, laws y=Yx^{a}. Here y is the
measured value of some system attribute a, Y is a constant, and x is a
stochastic variable. Remarkably, for many living systems the exponent a is
limited to values +or- n/4, n=0,1,2... Here x is the mass of a randomly
selected creature in the population. These quarter-power laws hold for many
attributes, such as pulse rate (n=-1). Allometry has, in the past, been
theoretically justified on a case-by-case basis. An ultimate goal is to find a
common cause for allometry of all types and for both living and nonliving
systems. The principle I - J...
90.
Differential gene expression in Bacillus subtilis - Iber, Dagmar; Clarkson, Joanna; Yudkin, Michael D; Campbell, Iain D
Sporulation in Bacillus subtilis serves as a paradigm for the development of
two different cell types (mother cell and prespore) from a single cell. The
mechanism by which the two different developmental programs are initiated has
been much studied but is not well understood. With the help of existing and new
experimental results, a mathematical model has been developed that reproduces
all published in vitro experiments and makes new predictions about the
properties of the system in vivo.
91.
Dynamics of DNA Ejection From Bacteriophage - Inamdar, Mandar M.; Gelbart, William M.; Phillips, Rob
The ejection of DNA from a bacterial virus (``phage'') into its host cell is
a biologically important example of the translocation of a macromolecular chain
along its length through a membrane. The simplest mechanism for this motion is
diffusion, but in the case of phage ejection a significant driving force
derives from the high degree of stress to which the DNA is subjected in the
viral capsid. The translocation is further sped up by the ratcheting and
entropic forces associated with proteins that bind to the viral DNA in the host
cell cytoplasm. We formulate a generalized diffusion equation that includes
these various pushing and pulling effects and...
92.
Modeling Human Erythrocyte Shape and Size Abnormalities - Munoz, S.; Sebastian, J. L.; Sancho, M.; Alvarez, G.
We present simple parametric equations in terms of Jacobi elliptic functions
that provide a realistic model of the shape of human normal erythrocytes as
well as of variations in size (anisocytosis) and shape (poikilocytosis)
thereof. We illustrate our results with parameterizations of microcytes,
macrocytes and stomatocytes, and show the applicability of these
parameterizations to the numerical calculation of the induced transmembrane
voltage in microcytes, macrocytes and stomatocytes exposed to an external RF
field of 1800 MHz.
93.
Biological applications of the theory of birth-and-death processes - Novozhilov, Artem S.; Karev, Georgy P.; Koonin, Eugene V.
In this review, we discuss the applications of the theory of birth-and-death
processes to problems in biology, primarily, those of evolutionary genomics.
The mathematical principles of the theory of these processes are briefly
described. Birth-and-death processes, with some straightforward additions such
as innovation, are a simple, natural formal framework for modeling a vast
variety of biological processes such as population dynamics, speciation, genome
evolution, including growth of paralogous gene families and horizontal gene
transfer, and somatic evolution of cancers. We further describe how empirical
data, e.g., distributions of paralogous gene family size, can be used to choose
the model that best reflects the actual course of evolution among different
versions...
94.
Simulation of Rapoport's rule for latitudinal species spread - Stauffer, Dietrich; Rohde, Klaus
Rapoport's rule claims that latitudinal ranges of plant and animal species
are generally smaller at low than at high latitudes. However, doubts as to the
generality of the rule have been expressed, because studies providing evidence
against the rule are more numerous than those in support of it. In groups for
which support has been provided, the trend of increasing latitudinal ranges
with latitude is restricted to or at least most distinct at high latitudes,
suggesting that the effect may be a local phenomenon, for example the result of
glaciations. Here we test the rule using two models, a simple one-dimensional
one with a fixed number of animals...
95.
Dynamics and pattern formation in invasive tumor growth - Khain, Evgeniy; Sander, Leonard M.
In this work, we study the in-vitro dynamics of the most malignant form of
the primary brain tumor: Glioblastoma Multiforme. Typically, the growing tumor
consists of the inner dense proliferating zone and the outer less dense
invasive region. Experiments with different types of cells show qualitatively
different behavior. Wild-type cells invade a spherically symmetric manner, but
mutant cells are organized in tenuous branches. We formulate a model for this
sort of growth using two coupled reaction-diffusion equations for the cell and
nutrient concentrations. When the ratio of the nutrient and cell diffusion
coefficients exceeds some critical value, the plane propagating front becomes
unstable with respect to transversal perturbations. The...
96.
A stochastic model for wound healing - Callaghan, Thomas; Khain, Evgeniy; Sander, Leonard M.; Ziff, Robert M.
We present a discrete stochastic model which represents many of the salient
features of the biological process of wound healing. The model describes fronts
of cells invading a wound. We have numerical results in one and two dimensions.
In one dimension we can give analytic results for the front speed as a power
series expansion in a parameter, p, that gives the relative size of
proliferation and diffusion processes for the invading cells. In two dimensions
the model becomes the Eden model for p near 1. In both one and two dimensions
for small p, front propagation for this model should approach that of the
Fisher-Kolmogorov equation. However,...
97.
A core genetic module : the Mixed Feedback Loop - Francois, Paul; Hakim, Vincent
The so-called Mixed Feedback Loop (MFL) is a small two-gene network where
protein A regulates the transcription of protein B and the two proteins form a
heterodimer. It has been found to be statistically over-represented in
statistical analyses of gene and protein interaction databases and to lie at
the core of several computer-generated genetic networks. Here, we propose and
mathematically study a model of the MFL and show that, by itself, it can serve
both as a bistable switch and as a clock (an oscillator) depending on kinetic
parameters. The MFL phase diagram as well as a detailed description of the
nonlinear oscillation regime are presented and some...
98.
Computational Fluid Dynamic Approach for Biological System Modeling - Xiao, Weidong Huang; Chundu Wu; Bingjia; Xia, Weidong
Various biological system models have been proposed in systems biology, which
are based on the complex biological reactions kinetic of various components.
These models are not practical because we lack of kinetic information. In this
paper, it is found that the enzymatic reaction and multi-order reaction rate is
often controlled by the transport of the reactants in biological systems. A
Computational Fluid Dynamic (CFD) approach, which is based on transport of the
components and kinetics of biological reactions, is introduced for biological
system modeling. We apply this approach to a biological wastewater treatment
system for the study of metabolism of organic carbon substrates and the
population of microbial. The...
99.
Effects of fast presynaptic noise in attractor neural networks - Cortes, J. M.; Torres, J. J.; Marro, J.; Garrido, P. L.; Kappen, H. J.
We study both analytically and numerically the effect of presynaptic noise on
the transmission of information in attractor neural networks. The noise occurs
on a very short-time scale compared to that for the neuron dynamics and it
produces short-time synaptic depression. This is inspired in recent
neurobiological findings that show that synaptic strength may either increase
or decrease on a short-time scale depending on presynaptic activity. We thus
describe a mechanism by which fast presynaptic noise enhances the neural
network sensitivity to an external stimulus. The reason for this is that, in
general, the presynaptic noise induces nonequilibrium behavior and,
consequently, the space of fixed points is qualitatively modified...
100.
Monte carlo simulations of parapatric speciation - Schwammle, V.; Sousa, A. O.; de Oliveira, S. M.
Parapatric speciation is studied using an individual--based model with sexual
reproduction. We combine the theory of mutation accumulation for biological
ageing with an environmental selection pressure that varies according to the
individuals geographical positions and phenotypic traits. Fluctuations and
genetic diversity of large populations are crucial ingredients to model the
features of evolutionary branching and are intrinsic properties of the model.
Its implementation on a spatial lattice gives interesting insights into the
population dynamics of speciation on a geographical landscape and the
disruptive selection that leads to the divergence of phenotypes. Our results
suggest that assortative mating is not an obligatory ingredient to obtain
speciation in large populations at low...
81.
