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0704.0021 | Yuichi Togashi | Vanessa Casagrande, Yuichi Togashi, Alexander S. Mikhailov | Molecular Synchronization Waves in Arrays of Allosterically Regulated
Enzymes | 5 pages, 4 figures | Phys. Rev. Lett. 99, 048301 (2007) | 10.1103/PhysRevLett.99.048301 | null | nlin.PS physics.chem-ph q-bio.MN | null | Spatiotemporal pattern formation in a product-activated enzymic reaction at
high enzyme concentrations is investigated. Stochastic simulations show that
catalytic turnover cycles of individual enzymes can become coherent and that
complex wave patterns of molecular synchronization can develop. The analysis
based on the mean-field approximation indicates that the observed patterns
result from the presence of Hopf and wave bifurcations in the considered
system.
| 2007-07-24 |
0704.0034 | Vasily Ogryzko V | Vasily Ogryzko | Origin of adaptive mutants: a quantum measurement? | 5 pages | null | null | null | q-bio.PE q-bio.CB quant-ph | null | This is a supplement to the paper arXiv:q-bio/0701050, containing the text of
correspondence sent to Nature in 1990.
| 2007-05-23 |
0704.0036 | Eduardo D. Sontag | Liming Wang and Eduardo D. Sontag | A remark on the number of steady states in a multiple futile cycle | Resubmit with new results on the upper bound of the number of steady
states. 20 pages, 2 figures, See
http://www.math.rutgers.edu/~sontag/PUBDIR/index.html for online preprints
and reprints of related work | null | null | null | q-bio.QM q-bio.MN | null | The multisite phosphorylation-dephosphorylation cycle is a motif repeatedly
used in cell signaling. This motif itself can generate a variety of dynamic
behaviors like bistability and ultrasensitivity without direct positive
feedbacks. In this paper, we study the number of positive steady states of a
general multisite phosphorylation-dephosphorylation cycle, and how the number
of positive steady states varies by changing the biological parameters. We show
analytically that (1) for some parameter ranges, there are at least n+1 (if n
is even) or n (if n is odd) steady states; (2) there never are more than 2n-1
steady states (in particular, this implies that for n=2, including single
levels of MAPK cascades, there are at most three steady states); (3) for
parameters near the standard Michaelis-Menten quasi-steady state conditions,
there are at most n+1 steady states; and (4) for parameters far from the
standard Michaelis-Menten quasi-steady state conditions, there is at most one
steady state.
| 2011-11-09 |
0704.0158 | Huijie Yang | Fangcui Zhao, Huijie Yang, and Binghong Wang | Complexities of Human Promoter Sequences | 5 pages, 3 figures, To appear in Journal of Theoretical Biology | Journal of Theoretical Biology 247 (2007) 645?C649 | 10.1016/j.jtbi.2007.03.035 | null | q-bio.OT | null | By means of the diffusion entropy approach, we detect the scale-invariance
characteristics embedded in the 4737 human promoter sequences. The exponent for
the scale-invariance is in a wide range of $[ {0.3,0.9} ]$, which centered at
$\delta_c = 0.66$. The distribution of the exponent can be separated into left
and right branches with respect to the maximum. The left and right branches are
asymmetric and can be fitted exactly with Gaussian form with different widths,
respectively.
| 2011-11-09 |
0704.0191 | Peter Virnau | Peter Virnau (1), Leonid A. Mirny (1,2), Mehran Kardar (1) ((1)
Massachusetts Institute of Technology, Department of Physics, Cambridge, MA,
United States of America, (2) Massachusetts Institute of Technology,
Harvard-MIT Division of Health Science and Technology, Cambridge, MA, United
States of America) | Intricate Knots in Proteins: Function and Evolution | 6 pages, 2 figures, 1 table | P. Virnau, L. A. Mirny, M. Kardar, PLoS Comp Biol 2, 1074-1079
(2006) | null | null | physics.bio-ph physics.data-an q-bio.BM | null | A number of recently discovered protein structures incorporate a rather
unexpected structural feature: a knot in the polypeptide backbone. These knots
are extremely rare, but their occurrence is likely connected to protein
function in as yet unexplored fashion. Our analysis of the complete Protein
Data Bank reveals several new knots which, along with previously discovered
ones, can shed light on such connections. In particular, we identify the most
complex knot discovered to date in human ubiquitin hydrolase, and suggest that
its entangled topology protects it against unfolding and degradation by the
proteasome. Knots in proteins are typically preserved across species and
sometimes even across kingdoms. However, we also identify a knot which only
appears in some transcarbamylases while being absent in homologous proteins of
similar structure. The emergence of the knot is accompanied by a shift in the
enzymatic function of the protein. We suggest that the simple insertion of a
short DNA fragment into the gene may suffice to turn an unknotted into a
knotted structure in this protein.
| 2007-05-23 |
0704.0271 | Edgardo Brigatti | E. Brigatti, V. Schwammle and Minos A. Neto | An individual based model with global competition interaction:
fluctuations effects in pattern formation | 9 pages, 9 figures, minor changes | Physical Review E 77, 021914 (2008) | 10.1103/PhysRevE.77.021914 | null | cond-mat.stat-mech q-bio.PE | null | We present some numerical results obtained from a simple individual based
model that describes clustering of organisms caused by competition. Our aim is
to show how, even when a deterministic description developed for continuum
models predicts no pattern formation, an individual based model displays well
defined patterns, as a consequence of fluctuations effects caused by the
discrete nature of the interacting agents.
| 2009-11-13 |
0704.0304 | Carlos Gershenson | Carlos Gershenson | The World as Evolving Information | 16 pages. Extended version, three more laws of information, two
classifications, and discussion added. To be published (soon) in
International Conference on Complex Systems 2007 Proceedings | Minai, A., Braha, D., and Bar-Yam, Y., eds. Unifying Themes in
Complex Systems VII, pp. 100-115. Springer, Berlin Heidelberg, 2012 | 10.1007/978-3-642-18003-3_10 | null | cs.IT cs.AI math.IT q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper discusses the benefits of describing the world as information,
especially in the study of the evolution of life and cognition. Traditional
studies encounter problems because it is difficult to describe life and
cognition in terms of matter and energy, since their laws are valid only at the
physical scale. However, if matter and energy, as well as life and cognition,
are described in terms of information, evolution can be described consistently
as information becoming more complex.
The paper presents eight tentative laws of information, valid at multiple
scales, which are generalizations of Darwinian, cybernetic, thermodynamic,
psychological, philosophical, and complexity principles. These are further used
to discuss the notions of life, cognition and their evolution.
| 2013-04-05 |
0704.0305 | Yongxing Guo | Yongxing Guo, Yifeng Liu, Jay X. Tang, and James M. Valles Jr | Polymerization Force Driven Buckling of Microtubule Bundles Determines
the Wavelength of Patterns Formed in Tubulin Solutions | 4 pages, 4 figures | Phys. Rev. Lett. 98, 198103 (2007) | 10.1103/PhysRevLett.98.198103 | null | physics.bio-ph | null | We present a model for the spontaneous formation of a striated pattern in
polymerizing microtubule solutions. It describes the buckling of a single
microtubule (MT) bundle within an elastic network formed by other similarly
aligned and buckling bundles and unaligned MTs. Phase contrast and polarization
microscopy studies of the temporal evolution of the pattern imply that the
polymerization of MTs within the bundles creates the driving compressional
force. Using the measured rate of buckling, the established MT force-velocity
curve and the pattern wavelength, we obtain reasonable estimates for the MT
bundle bending rigidity and the elastic constant of the network. The analysis
implies that the bundles buckle as solid rods.
| 2007-06-13 |
0704.0322 | Liu Quanxing | Quan-Xing Liu, Gui-Quan Sun, Bai-Lian Li and Zhen Jin | Emergence of spatiotemporal chaos driven by far-field breakup of spiral
waves in the plankton ecological systems | 9 Figures and 11 pages, REVTeX 4 | 2009 Chinese Phys. B 18 506-515 | 10.1088/1674-1056/18/2/021 | null | nlin.PS nlin.CD q-bio.PE | null | Alexander B. Medvinsky \emph{et al} [A. B. Medvinsky, I. A. Tikhonova, R. R.
Aliev, B.-L. Li, Z.-S. Lin, and H. Malchow, Phys. Rev. E \textbf{64}, 021915
(2001)] and Marcus R. Garvie \emph{et al} [M. R. Garvie and C. Trenchea, SIAM
J. Control. Optim. \textbf{46}, 775-791 (2007)] shown that the minimal
spatially extended reaction-diffusion model of phytoplankton-zooplankton can
exhibit both regular, chaotic behavior, and spatiotemporal patterns in a patchy
environment. Based on that, the spatial plankton model is furtherly
investigated by means of computer simulations and theoretical analysis in the
present paper when its parameters would be expected in the case of mixed
Turing-Hopf bifurcation region. Our results show that the spiral waves exist in
that region and the spatiotemporal chaos emerge, which arise from the far-field
breakup of the spiral waves over large ranges of diffusion coefficients of
phytoplankton and zooplankton. Moreover, the spatiotemporal chaos arising from
the far-field breakup of spiral waves does not gradually involve the whole
space within that region. Our results are confirmed by means of computation
spectra and nonlinear bifurcation of wave trains. Finally, we give some
explanations about the spatially structured patterns from the community level.
| 2009-05-29 |
0704.0331 | C. Soule | J.-L. Jestin, C. Soule (IHES) | Symmetries by base substitutions in the genetic code predict 2' or 3'
aminoacylation of tRNAs | Accepted for publication in the Journal of Theoretical Biology | null | null | null | q-bio.OT | null | This letter reports complete sets of two-fold symmetries between partitions
of the universal genetic code. By substituting bases at each position of the
codons according to a fixed rule, it happens that properties of the degeneracy
pattern or of tRNA aminoacylation specificity are exchanged.
| 2007-05-23 |
0704.0357 | Gergely J Sz\"oll\H{o}si | Gergely J Szollosi and Imre Derenyi | Evolutionary games on minimally structured populations | Supporting information available as EPAPS Document No.
E-PLEEE8-78-144809 at http://ftp.aip.org/epaps/phys_rev_e/E-PLEEE8-78-144809/ | PHYSICAL REVIEW E 78, 031919 (2008) | 10.1103/PhysRevE.78.031919 | null | q-bio.PE q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Population structure induced by both spatial embedding and more general
networks of interaction, such as model social networks, have been shown to have
a fundamental effect on the dynamics and outcome of evolutionary games. These
effects have, however, proved to be sensitive to the details of the underlying
topology and dynamics. Here we introduce a minimal population structure that is
described by two distinct hierarchical levels of interaction. We believe this
model is able to identify effects of spatial structure that do not depend on
the details of the topology. We derive the dynamics governing the evolution of
a system starting from fundamental individual level stochastic processes
through two successive meanfield approximations. In our model of population
structure the topology of interactions is described by only two parameters: the
effective population size at the local scale and the relative strength of local
dynamics to global mixing. We demonstrate, for example, the existence of a
continuous transition leading to the dominance of cooperation in populations
with hierarchical levels of unstructured mixing as the benefit to cost ratio
becomes smaller then the local population size. Applying our model of spatial
structure to the repeated prisoner's dilemma we uncover a novel and
counterintuitive mechanism by which the constant influx of defectors sustains
cooperation. Further exploring the phase space of the repeated prisoner's
dilemma and also of the "rock-paper-scissor" game we find indications of rich
structure and are able to reproduce several effects observed in other models
with explicit spatial embedding, such as the maintenance of biodiversity and
the emergence of global oscillations.
| 2009-11-13 |
0704.0392 | Marcus Kaiser | Marcus Kaiser, Robert Martin, Peter Andras and Malcolm P. Young | Simulation of Robustness against Lesions of Cortical Networks | submitted to European Journal of Neuroscience (under review) | European Journal of Neuroscience, 25:3185--3192, 2007 | 10.1111/j.1460-9568.2007.05574.x | null | q-bio.NC cond-mat.dis-nn physics.soc-ph | null | Structure entails function and thus a structural description of the brain
will help to understand its function and may provide insights into many
properties of brain systems, from their robustness and recovery from damage, to
their dynamics and even their evolution. Advances in the analysis of complex
networks provide useful new approaches to understanding structural and
functional properties of brain networks. Structural properties of networks
recently described allow their characterization as small-world, random
(exponential) and scale-free. They complement the set of other properties that
have been explored in the context of brain connectivity, such as topology,
hodology, clustering, and hierarchical organization. Here we apply new network
analysis methods to cortical inter-areal connectivity networks for the cat and
macaque brains. We compare these corticocortical fibre networks to benchmark
rewired, small-world, scale-free and random networks, using two analysis
strategies, in which we measure the effects of the removal of nodes and
connections on the structural properties of the cortical networks. The brain
networks' structural decay is in most respects similar to that of scale-free
networks. The results implicate highly connected hub-nodes and bottleneck
connections as structural basis for some of the conditional robustness of brain
systems. This informs the understanding of the development of brain networks'
connectivity.
| 2008-08-27 |
0704.0429 | Ping Ao | P. Ao | Quantitative Resolution to some "Absolute Discrepancies" in Cancer
Theories: a View from Phage lambda Genetic Switch | latex, 7 pages | CellularOncology29:67-69,2007 | null | null | q-bio.SC q-bio.CB | null | Is it possible to understand cancer? Or more specifically, is it possible to
understand cancer from genetic side? There already many answers in literature.
The most optimistic one has claimed that it is mission-possible. Duesberg and
his colleagues reviewed the impressive amount of research results on cancer
accumulated over 100 years. It confirms the a general opinion that considering
all available experimental results and clinical observations there is no cancer
theory without major difficulties, including the prevailing gene-based cancer
theories. They have then listed 9 "absolute discrepancies" for such cancer
theory. In this letter the quantitative evidence against one of their major
reasons for dismissing mutation cancer theory, by both in vivo experiment and a
first principle computation, is explicitly pointed out.
| 2008-11-26 |
0704.0464 | Edward Lyman Ph.D. | Edward Lyman and Daniel M. Zuckerman | Annealed importance sampling of dileucine peptide | null | null | 10.1063/1.2754267 | null | q-bio.BM | null | Annealed importance sampling is a means to assign equilibrium weights to a
nonequilibrium sample that was generated by a simulated annealing protocol. The
weights may then be used to calculate equilibrium averages, and also serve as
an ``adiabatic signature'' of the chosen cooling schedule. In this paper we
demonstrate the method on the 50-atom dileucine peptide, showing that
equilibrium distributions are attained for manageable cooling schedules. For
this system, as naively implemented here, the method is modestly more efficient
than constant temperature simulation. However, the method is worth considering
whenever any simulated heating or cooling is performed (as is often done at the
beginning of a simulation project, or during an NMR structure calculation), as
it is simple to implement and requires minimal additional CPU expense.
Furthermore, the naive implementation presented here can be improved.
| 2009-11-13 |
0704.0598 | Ignazio Licata | Ignazio Licata, Luigi Lella | Evolutionary Neural Gas (ENG): A Model of Self Organizing Network from
Input Categorization | 16 pages, 8 figures | EJTP,vol.4,, No.14 (2007),31-50 | null | null | physics.gen-ph q-bio.PE | null | Despite their claimed biological plausibility, most self organizing networks
have strict topological constraints and consequently they cannot take into
account a wide range of external stimuli. Furthermore their evolution is
conditioned by deterministic laws which often are not correlated with the
structural parameters and the global status of the network, as it should happen
in a real biological system. In nature the environmental inputs are noise
affected and fuzzy. Which thing sets the problem to investigate the possibility
of emergent behaviour in a not strictly constrained net and subjected to
different inputs. It is here presented a new model of Evolutionary Neural Gas
(ENG) with any topological constraints, trained by probabilistic laws depending
on the local distortion errors and the network dimension. The network is
considered as a population of nodes that coexist in an ecosystem sharing local
and global resources. Those particular features allow the network to quickly
adapt to the environment, according to its dimensions. The ENG model analysis
shows that the net evolves as a scale-free graph, and justifies in a deeply
physical sense- the term gas here used.
| 2010-04-26 |
0704.0615 | Trevor Bruen TB | Trevor Bruen, David Bryant | Parsimony via concensus | Final published version of article | Systematic Biology (2008), 57(2): 251-56 | 10.1080/10635150802040597 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The parsimony score of a character on a tree equals the number of state
changes required to fit that character onto the tree. We show that for
unordered, reversible characters this score equals the number of tree
rearrangements required to fit the tree onto the character. We discuss
implications of this connection for the debate over the use of consensus trees
or total evidence, and show how it provides a link between incongruence of
characters and recombination.
| 2013-10-02 |
0704.0634 | Mark Bathe | Mark Bathe | A Finite Element framework for computation of protein normal modes and
mechanical response | null | null | null | null | q-bio.BM q-bio.QM | null | A coarse-grained computational procedure based on the Finite Element Method
is proposed to calculate the normal modes and mechanical response of proteins
and their supramolecular assemblies. Motivated by the elastic network model,
proteins are modeled as homogeneous isotropic elastic solids with volume
defined by their solvent-excluded surface. The discretized Finite Element
representation is obtained using a surface simplification algorithm that
facilitates the generation of models of arbitrary prescribed spatial
resolution. The procedure is applied to compute the normal modes of a mutant of
T4 phage lysozyme and of filamentous actin, as well as the critical Euler
buckling load of the latter when subject to axial compression. Results compare
favorably with all-atom normal mode analysis, the Rotation Translation Blocks
procedure, and experiment. The proposed methodology establishes a computational
framework for the calculation of protein mechanical response that facilitates
the incorporation of specific atomic-level interactions into the model,
including aqueous-electrolyte-mediated electrostatic effects. The procedure is
equally applicable to proteins with known atomic coordinates as it is to
electron density maps of proteins, protein complexes, and supramolecular
assemblies of unknown atomic structure.
| 2007-05-23 |
0704.0648 | Kaushik Majumdar | Kaushik Majumdar | Behavioral response to strong aversive stimuli: A neurodynamical model | Submitted to journal | null | null | null | q-bio.NC | null | In this paper a theoretical model of functioning of a neural circuit during a
behavioral response has been proposed. A neural circuit can be thought of as a
directed multigraph whose each vertex is a neuron and each edge is a synapse.
It has been assumed in this paper that the behavior of such circuits is
manifested through the collective behavior of neurons belonging to that
circuit. Behavioral information of each neuron is contained in the coefficients
of the fast Fourier transform (FFT) over the output spike train. Those
coefficients form a vector in a multidimensional vector space. Behavioral
dynamics of a neuronal network in response to strong aversive stimuli has been
studied in a vector space in which a suitable pseudometric has been defined.
The neurodynamical model of network behavior has been formulated in terms of
existing memory, synaptic plasticity and feelings. The model has an analogy in
classical electrostatics, by which the notion of force and potential energy has
been introduced. Since the model takes input from each neuron in a network and
produces a behavior as the output, it would be extremely difficult or may even
be impossible to implement. But with the help of the model a possible
explanation for an hitherto unexplained neurological observation in human brain
has been offered. The model is compatible with a recent model of sequential
behavioral dynamics. The model is based on electrophysiology, but its relevance
to hemodynamics has been outlined.
| 2007-05-23 |
0704.0673 | Mark McDonnell | Mark D. McDonnell, Nigel G. Stocks and Derek Abbott | Optimal stimulus and noise distributions for information transmission
via suprathreshold stochastic resonance | Accepted for publication by Physical Review E, 28 pages of text and
references, 5 figures, 2 tables | Phys. Rev. E 75, 061105 (2007) | 10.1103/PhysRevE.75.061105 | null | cond-mat.stat-mech q-bio.NC | null | Suprathreshold stochastic resonance (SSR) is a form of noise enhanced signal
transmission that occurs in a parallel array of independently noisy identical
threshold nonlinearities, including model neurons. Unlike most forms of
stochastic resonance, the output response to suprathreshold random input
signals of arbitrary magnitude is improved by the presence of even small
amounts of noise. In this paper the information transmission performance of SSR
in the limit of a large array size is considered. Using a relationship between
Shannon's mutual information and Fisher information, a sufficient condition for
optimality, i.e. channel capacity, is derived. It is shown that capacity is
achieved when the signal distribution is Jeffrey's prior, as formed from the
noise distribution, or when the noise distribution depends on the signal
distribution via a cosine relationship. These results provide theoretical
verification and justification for previous work in both computational
neuroscience and electronics.
| 2007-07-02 |
0704.1147 | Giulio Ruffini | Giulio Ruffini | Information, complexity, brains and reality (Kolmogorov Manifesto) | This is a live essay, kind of a mental log book on a series of topics
under the theme of information and compression | null | null | Starlab TN00054 | physics.gen-ph physics.bio-ph | null | I discuss several aspects of information theory and its relationship to
physics and neuroscience. The unifying thread of this somewhat chaotic essay is
the concept of Kolmogorov or algorithmic complexity (Kolmogorov Complexity, for
short). I argue that it is natural to interpret cognition as the art of finding
algorithms that apprach the Solomonoff-Kolmogorov-Chaitin (algorithmic)
Complexity limit with appropriate tradeoffs. In addition, I claim that what we
call the universe is an interpreted abstraction--a mental construct--based on
the observed coherence between multiple sensory input streams and our own
interactions. Hence, the notion of Universe is itself a model.
| 2007-05-23 |
0704.1169 | Dirson Jian Li | Dirson Jian Li, Shengli Zhang | Holographic bound and protein linguistics | 4 pages, 4 figures. A trial application of holographic bound in life
science | null | null | null | q-bio.GN hep-th q-bio.QM | null | The holographic bound in physics constrains the complexity of life. The
finite storage capability of information in the observable universe requires
the protein linguistics in the evolution of life. We find that the evolution of
genetic code determines the variance of amino acid frequencies and genomic GC
content among species. The elegant linguistic mechanism is confirmed by the
experimental observations based on all known entire proteomes.
| 2007-05-23 |
0704.1362 | J.H. van Hateren | J. H. van Hateren | Fast recursive filters for simulating nonlinear dynamic systems | 20 pages, 8 figures, 1 table. A comparison with 4th-order Runge-Kutta
integration shows that the new algorithm is 1-2 orders of magnitude faster.
The paper is in press now at Neural Computation | Neural Computation 20:1821-1846 (2008) | null | null | q-bio.QM q-bio.NC | null | A fast and accurate computational scheme for simulating nonlinear dynamic
systems is presented. The scheme assumes that the system can be represented by
a combination of components of only two different types: first-order low-pass
filters and static nonlinearities. The parameters of these filters and
nonlinearities may depend on system variables, and the topology of the system
may be complex, including feedback. Several examples taken from neuroscience
are given: phototransduction, photopigment bleaching, and spike generation
according to the Hodgkin-Huxley equations. The scheme uses two slightly
different forms of autoregressive filters, with an implicit delay of zero for
feedforward control and an implicit delay of half a sample distance for
feedback control. On a fairly complex model of the macaque retinal horizontal
cell it computes, for a given level of accuracy, 1-2 orders of magnitude faster
than 4th-order Runge-Kutta. The computational scheme has minimal memory
requirements, and is also suited for computation on a stream processor, such as
a GPU (Graphical Processing Unit).
| 2008-06-20 |
0704.1390 | Azam Gholami | Azam Gholami, Martin Falcke, Erwin Frey | Velocity oscillations in actin-based motility | 5 pages, 6 figures | null | 10.1088/1367-2630/10/3/033022 | HMI 18779, LMU-ASC 18/07 | q-bio.CB | null | We present a simple and generic theoretical description of actin-based
motility, where polymerization of filaments maintains propulsion. The dynamics
is driven by polymerization kinetics at the filaments' free ends, crosslinking
of the actin network, attachment and detachment of filaments to the obstacle
interfaces and entropic forces. We show that spontaneous oscillations in the
velocity emerge in a broad range of parameter values, and compare our findings
with experiments.
| 2015-05-13 |
0704.1546 | Richard A Neher | Richard A. Neher, Wolfram Mobius, Erwin Frey, Ulrich Gerland | Optimal flexibility for conformational transitions in macromolecules | 4 pages, 4 figures | null | 10.1103/PhysRevLett.99.178101 | LMU-ASC 22/07 | q-bio.BM | null | Conformational transitions in macromolecular complexes often involve the
reorientation of lever-like structures. Using a simple theoretical model, we
show that the rate of such transitions is drastically enhanced if the lever is
bendable, e.g. at a localized "hinge''. Surprisingly, the transition is fastest
with an intermediate flexibility of the hinge. In this intermediate regime, the
transition rate is also least sensitive to the amount of "cargo'' attached to
the lever arm, which could be exploited by molecular motors. To explain this
effect, we generalize the Kramers-Langer theory for multi-dimensional barrier
crossing to configuration dependent mobility matrices.
| 2009-11-13 |
0704.1547 | Martin Castelnovo | Fabien Montel, Emeline Fontaine, Philippe St-Jean, Martin Castelnovo,
Cendrine Moskalenko-Faivre | AFM Imaging of SWI/SNF action: mapping the nucleosome remodeling and
sliding | 25 pages,5 figures, to appear in Biophysical Journal | null | 10.1529/biophysj.107.105569 | null | physics.bio-ph cond-mat.soft q-bio.BM | null | We propose a combined experimental (Atomic Force Microscopy) and theoretical
study of the structural and dynamical properties of nucleosomes. In contrast to
biochemical approaches, this method allows to determine simultaneously the DNA
complexed length distribution and nucleosome position in various contexts.
First, we show that differences in the nucleo-proteic structure observed
between conventional H2A and H2A.Bbd variant nucleosomes induce quantitative
changes in the in the length distribution of DNA complexed with histones. Then,
the sliding action of remodeling complex SWI/SNF is characterized through the
evolution of the nucleosome position and wrapped DNA length mapping. Using a
linear energetic model for the distribution of DNA complexed length, we extract
the net wrapping energy of DNA onto the histone octamer, and compare it to
previous studies.
| 2009-11-13 |
0704.1571 | Philippe Gambette | Philippe Gambette (LIAFA), St\'ephane Vialette (LRI) | On restrictions of balanced 2-interval graphs | null | Dans Lecture Notes In Computer Science - 33rd International
Workshop on Graph-Theoretic Concepts in Computer Science (WG'07), Dornburg :
Allemagne (2007) | 10.1007/978-3-540-74839-7_6 | null | cs.DM q-bio.QM | null | The class of 2-interval graphs has been introduced for modelling scheduling
and allocation problems, and more recently for specific bioinformatic problems.
Some of those applications imply restrictions on the 2-interval graphs, and
justify the introduction of a hierarchy of subclasses of 2-interval graphs that
generalize line graphs: balanced 2-interval graphs, unit 2-interval graphs, and
(x,x)-interval graphs. We provide instances that show that all the inclusions
are strict. We extend the NP-completeness proof of recognizing 2-interval
graphs to the recognition of balanced 2-interval graphs. Finally we give hints
on the complexity of unit 2-interval graphs recognition, by studying
relationships with other graph classes: proper circular-arc, quasi-line graphs,
K_{1,5}-free graphs, ...
| 2008-02-04 |
0704.1667 | Erel Levine | Erel Levine and Terence Hwa | Stochastic fluctuations in metabolic pathways | null | PNAS 2007 | 10.1073/pnas.0610987104 | null | q-bio.MN cond-mat.stat-mech | null | Fluctuations in the abundance of molecules in the living cell may affect its
growth and well being. For regulatory molecules (e.g., signaling proteins or
transcription factors), fluctuations in their expression can affect the levels
of downstream targets in a network. Here, we develop an analytic framework to
investigate the phenomenon of noise correlation in molecular networks.
Specifically, we focus on the metabolic network, which is highly inter-linked,
and noise properties may constrain its structure and function. Motivated by the
analogy between the dynamics of a linear metabolic pathway and that of the
exactly soluable linear queueing network or, alternatively, a mass transfer
system, we derive a plethora of results concerning fluctuations in the
abundance of intermediate metabolites in various common motifs of the metabolic
network. For all but one case examined, we find the steady-state fluctuation in
different nodes of the pathways to be effectively uncorrelated. Consequently,
fluctuations in enzyme levels only affect local properties and do not propagate
elsewhere into metabolic networks, and intermediate metabolites can be freely
shared by different reactions. Our approach may be applicable to study
metabolic networks with more complex topologies, or protein signaling networks
which are governed by similar biochemical reactions. Possible implications for
bioinformatic analysis of metabolimic data are discussed.
| 2009-11-13 |
0704.1672 | Ilia Solov'yov | Ilia A. Solov'yov, Alexander V. Yakubovich, Andrey V. Solov'yov and
Walter Greiner | Two center multipole expansion method: application to macromolecular
systems | 23 pages, 7 figures, 1 table | null | 10.1103/PhysRevE.75.051912 | null | physics.bio-ph physics.comp-ph | null | We propose a new theoretical method for the calculation of the interaction
energy between macromolecular systems at large distances. The method provides a
linear scaling of the computing time with the system size and is considered as
an alternative to the well known fast multipole method. Its efficiency,
accuracy and applicability to macromolecular systems is analyzed and discussed
in detail.
| 2009-11-13 |
0704.1763 | Ilia Solov'yov | Ilia A. Solov'yov, Walter Greiner | Towards understanding of birds magnetoreceptor mechanism | 10 pages, 4 figures | null | null | null | physics.bio-ph | null | In the present letter we suggest a new theoretical model for a quantitative
description of the magnetoreception mechanism in birds. The considered
mechanism involves two types of iron minerals (magnetite and maghemite) which
were found in subcellular compartments within sensory dendrites of the upper
beak of several bird species. The analysis of forces acting between the iron
particles shows that the orientation of the external geomagnetic field can
significantly change the probability of the mechanosensitive ion channels
opening and closing. The performed theoretical analysis shows that the
suggested magnetoreceptor system might be a sensitive biological magnetometer
providing an essential part of the magnetic map for navigation.
| 2007-05-23 |
0704.1811 | Samarth Swarup | Samarth Swarup and Les Gasser | Unifying Evolutionary and Network Dynamics | 11 pages, 12 figures, Accepted for publication in Physical Review E | null | 10.1103/PhysRevE.75.066114 | null | q-bio.QM q-bio.PE | null | Many important real-world networks manifest "small-world" properties such as
scale-free degree distributions, small diameters, and clustering. The most
common model of growth for these networks is "preferential attachment", where
nodes acquire new links with probability proportional to the number of links
they already have. We show that preferential attachment is a special case of
the process of molecular evolution. We present a new single-parameter model of
network growth that unifies varieties of preferential attachment with the
quasispecies equation (which models molecular evolution), and also with the
Erdos-Renyi random graph model. We suggest some properties of evolutionary
models that might be applied to the study of networks. We also derive the form
of the degree distribution resulting from our algorithm, and we show through
simulations that the process also models aspects of network growth. The
unification allows mathematical machinery developed for evolutionary dynamics
to be applied in the study of network dynamics, and vice versa.
| 2009-11-13 |
0704.1885 | Jesse Bloom | Jesse D. Bloom, Zhongyi Lu, David Chen, Alpan Raval, Ophelia S.
Venturelli, and Frances H. Arnold | Evolution favors protein mutational robustness in sufficiently large
populations | null | BMC Biology 5:29 (2007) | 10.1186/1741-7007-5-29 | null | q-bio.PE q-bio.BM | null | BACKGROUND: An important question is whether evolution favors properties such
as mutational robustness or evolvability that do not directly benefit any
individual, but can influence the course of future evolution. Functionally
similar proteins can differ substantially in their robustness to mutations and
capacity to evolve new functions, but it has remained unclear whether any of
these differences might be due to evolutionary selection for these properties.
RESULTS: Here we use laboratory experiments to demonstrate that evolution
favors protein mutational robustness if the evolving population is sufficiently
large. We neutrally evolve cytochrome P450 proteins under identical selection
pressures and mutation rates in populations of different sizes, and show that
proteins from the larger and thus more polymorphic population tend towards
higher mutational robustness. Proteins from the larger population also evolve
greater stability, a biophysical property that is known to enhance both
mutational robustness and evolvability. The excess mutational robustness and
stability is well described by existing mathematical theories, and can be
quantitatively related to the way that the proteins occupy their neutral
network.
CONCLUSIONS: Our work is the first experimental demonstration of the general
tendency of evolution to favor mutational robustness and protein stability in
highly polymorphic populations. We suggest that this phenomenon may contribute
to the mutational robustness and evolvability of viruses and bacteria that
exist in large populations.
| 2009-04-16 |
0704.1908 | Radek Erban | Radek Erban, Jonathan Chapman and Philip Maini | A practical guide to stochastic simulations of reaction-diffusion
processes | 35 pages | null | null | null | q-bio.SC physics.ed-ph q-bio.QM | null | A practical introduction to stochastic modelling of reaction-diffusion
processes is presented. No prior knowledge of stochastic simulations is
assumed. The methods are explained using illustrative examples. The article
starts with the classical Gillespie algorithm for the stochastic modelling of
chemical reactions. Then stochastic algorithms for modelling molecular
diffusion are given. Finally, basic stochastic reaction-diffusion methods are
presented. The connections between stochastic simulations and deterministic
models are explained and basic mathematical tools (e.g. chemical master
equation) are presented. The article concludes with an overview of more
advanced methods and problems.
| 2007-11-19 |
0704.1912 | Adrian Melott | L.C. Natarajan, A.L. Melott, B.M. Rothschild, and L.D. Martin
(University of Kansas) | Bone Cancer Rates in Dinosaurs Compared with Modern Vertebrates | As published in Transactions of the Kansas Academy of Science | TKAS 110, 155-158 (2007) | null | null | q-bio.PE astro-ph physics.geo-ph | null | Data on the prevalence of bone cancer in dinosaurs is available from past
radiological examination of preserved bones. We statistically test this data
for consistency with rates extrapolated from information on bone cancer in
modern vertebrates, and find that there is no evidence of a different rate.
Thus, this test provides no support for a possible role of ionizing radiation
in the K-T extinction event.
| 2007-10-16 |
0704.2114 | A. Mary Selvam | A. M. Selvam | Universal spectrum for DNA base CG frequency distribution in Takifugu
rubripes (Puffer fish) genome | 32 pages, 8 figures | null | null | null | physics.gen-ph physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The frequency distribution of DNA bases A, C, G, T exhibit fractal
fluctuations ubiquitous to dynamical systems in nature. The power spectra of
fractal fluctuations exhibit inverse power law form signifying long-range
correlations between local (small-scale) and global (large-scale)
perturbations. The author has developed a general systems theory based on
classical statistical physics for fractal fluctuations which predicts that the
probability distribution of eddy amplitudes and the variance (square of eddy
amplitude)spectrum of fractal fluctuations follow the universal Boltzmann
inverse power law expressed as a function of the golden mean. The model
predicted distribution is very close to statistical normal distribution for
fluctuations within two standard deviations from the mean and exhibits a fat
long tail. In this paper it is shown that DNA base CG frequency distribution in
Takifugu rubripes (Puffer fish) Genome Release 4 exhibit universal inverse
power law form consistent with model prediction. The observed long-range
correlations in the DNA bases implies that the non-coding 'junk' or 'selfish'
DNA which appear to be redundant, may also contribute to the efficient
functioning of the protein coding DNA, a result supported by recent studies.
| 2011-03-07 |
0704.2132 | Roberto Chignola | C. Tomelleri, E. Milotti, C. Dalla Pellegrina, O. Perbellini, A. Del
Fabbro, M. T. Scupoli and R. Chignola | A quantitative study on the growth variability of tumour cell clones in
vitro | 31 pages, 5 figures | null | null | null | q-bio.CB q-bio.QM | null | Objectives: In this study, we quantify the growth variability of tumour cell
clones from a human leukemia cell line. Materials and methods: We have used
microplate spectrophotometry to measure the growth kinetics of hundreds of
individual cell clones from the Molt3 cell line. The growth rate of each clonal
population has been estimated by fitting experimental data with the logistic
equation. Results: The growth rates were observed to vary among different
clones. Up to six clones with a growth rate above or below the mean growth rate
of the parent population were further cloned and the growth rates of their
offsprings were measured. The distribution of the growth rates of the subclones
did not significantly differ from that of the parent population thus suggesting
that growth variability has an epigenetic origin. To explain the observed
distributions of clonal growth rates we have developed a probabilistic model
assuming that the fluctuations in the number of mitochondria through successive
cell cycles are the leading cause of growth variability. For fitting purposes,
we have estimated experimentally by flow cytometry the maximum average number
of mitochondria in Molt3 cells. The model fits nicely the observed
distributions of growth rates, however, cells in which the mitochondria were
rendered non functional (rho-0 cells) showed only a 30% reduction in the clonal
growth variability with respect to normal cells. Conclusions: A tumor cell
population is a dynamic ensemble of clones with highly variable growth rate. At
least part of this variability is due to fluctuations in the number of
mitochondria.
| 2007-05-23 |
0704.2191 | Bo Deng | Bo Deng | Mismatch Repair Error Implies Chargaff's Second Parity Rule | null | null | null | null | q-bio.GN | null | Chargaff's second parity rule holds empirically for most types of DNA that
along single strands of DNA the base contents are equal for complimentary
bases, A = T, G = C. A Markov chain model is constructed to track the evolution
of any single base position along single strands of genomes whose organisms are
equipped with replication mismatch repair. Under the key assumptions that
mismatch error rates primarily depend the number of hydrogen bonds of
nucleotides and that the mismatch repairing process itself makes strand
recognition error, the model shows that the steady state probabilities for any
base position to take on one of the 4 nucleotide bases are equal for
complimentary bases. As a result, Chargaff's second parity rule is the
manifestation of the Law of Large Number acting on the steady state
probabilities. More importantly, because the model pinpoints mismatch repair as
a basis of the rule, it is suitable for experimental verification.
| 2007-09-20 |
0704.2200 | Stefan Bornholdt | Maria I. Davidich, Stefan Bornholdt | Boolean network model predicts cell cycle sequence of fission yeast | 10 pages, 3 figures | null | 10.1371/journal.pone.0001672 | null | q-bio.MN | null | A Boolean network model of the cell-cycle regulatory network of fission yeast
(Schizosaccharomyces Pombe) is constructed solely on the basis of the known
biochemical interaction topology. Simulating the model in the computer,
faithfully reproduces the known sequence of regulatory activity patterns along
the cell cycle of the living cell. Contrary to existing differential equation
models, no parameters enter the model except the structure of the regulatory
circuitry. The dynamical properties of the model indicate that the biological
dynamical sequence is robustly implemented in the regulatory network, with the
biological stationary state G1 corresponding to the dominant attractor in state
space, and with the biological regulatory sequence being a strongly attractive
trajectory. Comparing the fission yeast cell-cycle model to a similar model of
the corresponding network in S. cerevisiae, a remarkable difference in
circuitry, as well as dynamics is observed. While the latter operates in a
strongly damped mode, driven by external excitation, the S. pombe network
represents an auto-excited system with external damping.
| 2015-05-13 |
0704.2260 | Frederick Matsen IV | Frederick A. Matsen and Mike Steel | Phylogenetic mixtures on a single tree can mimic a tree of another
topology | null | null | null | null | q-bio.PE | null | Phylogenetic mixtures model the inhomogeneous molecular evolution commonly
observed in data. The performance of phylogenetic reconstruction methods where
the underlying data is generated by a mixture model has stimulated considerable
recent debate. Much of the controversy stems from simulations of mixture model
data on a given tree topology for which reconstruction algorithms output a tree
of a different topology; these findings were held up to show the shortcomings
of particular tree reconstruction methods. In so doing, the underlying
assumption was that mixture model data on one topology can be distinguished
from data evolved on an unmixed tree of another topology given enough data and
the ``correct'' method. Here we show that this assumption can be false. For
biologists our results imply that, for example, the combined data from two
genes whose phylogenetic trees differ only in terms of branch lengths can
perfectly fit a tree of a different topology.
| 2007-06-30 |
0704.2346 | Marcio Rocha | M. S. Rocha, M. C. Ferreira, and O. N. Mesquita | Transition on the entropic elasticity of DNA induced by intercalating
molecules | This experimental article shows and discuss a transition observed in
the persistence length of DNA molecules when studied as a function of some
intercalating drug concentrations, like daunomycin and ethidium bromide. It
has 15 pages and 4 figures. The article presented here is in preprint format | null | 10.1063/1.2768945 | null | physics.bio-ph physics.chem-ph | null | We use optical tweezers to perform stretching experiments on DNA molecules
when interacting with the drugs daunomycin and ethidium bromide, which
intercalate the DNA molecule. These experiments are performed in the low-force
regime from zero up to 2 pN. Our results show that the persistence length of
the DNA-drug complexes increases strongly as the drug concentration increases
up to some critical value. Above this critical value, the persistence length
decreases abruptly and remains practically constant for larger drug
concentrations. The contour length of the molecules increases monotonically and
saturates as drugs concentration increases. Measured in- tercalants critical
concentrations for the persistence length transition coincide with reported
values for the helix-coil transition of DNA-drug complexes, obtained from
sedimentation experiments.
| 2009-11-13 |
0704.2409 | Jose Vilar | Leonor Saiz and Jose M.G. Vilar | Multilevel Deconstruction of the In Vivo Behavior of Looped DNA-Protein
Complexes | Open Access article available at
http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0000355 | PLoS ONE 2(4): e355 (2007) | 10.1371/journal.pone.0000355 | null | q-bio.BM q-bio.SC | null | Protein-DNA complexes with loops play a fundamental role in a wide variety of
cellular processes, ranging from the regulation of DNA transcription to
telomere maintenance. As ubiquitous as they are, their precise in vivo
properties and their integration into the cellular function still remain
largely unexplored. Here, we present a multilevel approach that efficiently
connects in both directions molecular properties with cell physiology and use
it to characterize the molecular properties of the looped DNA-lac repressor
complex while functioning in vivo. The properties we uncover include the
presence of two representative conformations of the complex, the stabilization
of one conformation by DNA architectural proteins, and precise values of the
underlying twisting elastic constants and bending free energies. Incorporation
of all this molecular information into gene-regulation models reveals an
unprecedented versatility of looped DNA-protein complexes at shaping the
properties of gene expression.
| 2007-05-23 |
0704.2454 | Vahid Rezania | Vahid Rezania, Jack Tuszynski, Michael Hendzel | Modeling transcription factor binding events to DNA using a random
walker/jumper representation on a 1D/2D lattice with different affinity sites | 24 pages, 9 figures | Physical Biology, 4, 256-267 (2007) | 10.1088/1478-3975/4/4/003 | null | q-bio.QM q-bio.BM | null | Surviving in a diverse environment requires corresponding organism responses.
At the cellular level, such adjustment relies on the transcription factors
(TFs) which must rapidly find their target sequences amidst a vast amount of
non-relevant sequences on DNA molecules. Whether these transcription factors
locate their target sites through a 1D or 3D pathway is still a matter of
speculation. It has been suggested that the optimum search time is when the
protein equally shares its search time between 1D and 3D diffusions. In this
paper, we study the above problem using a Monte Carlo simulation by considering
a very simple physical model. A 1D strip, representing a DNA, with a number of
low affinity sites, corresponding to non-target sites, and high affinity sites,
corresponding to target sites, is considered and later extended to a 2D strip.
We study the 1D and 3D exploration pathways, and combinations of the two modes
by considering three different types of molecules: a walker that randomly walks
along the strip with no dissociation; a jumper that represents dissociation and
then re-association of a TF with the strip at later time at a distant site; and
a hopper that is similar to the jumper but it dissociates and then
re-associates at a faster rate than the jumper. We analyze the final
probability distribution of molecules for each case and find that TFs can
locate their targets fast enough even if they spend 15% of their search time
diffusing freely in the solution. This indeed agrees with recent experimental
results obtained by Elf et al. 2007 and is in contrast with theoretical
expectation.
| 2009-11-13 |
0704.2474 | Yi Xiao | Changjun Chen and Yi Xiao | Observation of Multiple folding Pathways of beta-hairpin Trpzip2 from
Independent Continuous Folding Trajectories | 13 pages, 8 figures | null | null | null | q-bio.BM | null | We report 10 successfully folding events of trpzip2 by molecular dynamics
simulation. It is found that the trizip2 can fold into its native state through
different zipper pathways, depending on the ways of forming hydrophobic core.
We also find a very fast non-zipper pathway. This indicates that there may be
no inconsistencies in the current pictures of beta-hairpin folding mechanisms.
These pathways occur with different probabilities. zip-out is the most probable
one. This may explain the recent experiment that the turn formation is the
rate-limiting step for beta-hairpin folding.
| 2007-05-23 |
0704.2533 | Frank Schweitzer | Frank Schweitzer | Multi-Agent Approach to the Self-Organization of Networks | 20 papges, to appear in: F. Reed-Tsochas, N. F. Johnson, J.
Efstathiou: Understanding and Managing Complex Agent-Based Dynamical
Networks, Singapore: World Scientific (2007) | null | null | null | nlin.AO physics.bio-ph q-bio.QM | null | Is it possible to link a set of nodes without using preexisting positional
information or any kind of long-range attraction of the nodes? Can the process
of generating positional information, i.e. the detection of ``unknown'' nodes
and the estabishment of chemical gradients, \emph{and} the process of network
formation, i.e. the establishment of links between nodes, occur in parallel, on
a comparable time scale, as a process of co-evolution?
The paper discusses a model where the generation of relevant information for
establishing the links between nodes results from the interaction of many
\emph{agents}, i.e. subunits of the system that are capable of performing some
activities. Their collective interaction is based on (indirect) communication,
which also includes memory effects and the dissemination of information in the
system. The relevant (``pragmatic'') information that leads to the
establishment of the links then emerges from an evolutionary interplay of
selection and reamplification.
| 2007-05-23 |
0704.2547 | Remi Monasson | Valentina Baldazzi (LPS), Serena Bradde (LPS), Simona Cocco (LPS),
Enzo Marinari, Remi Monasson (LPTENS) | Inferring DNA sequences from mechanical unzipping data: the
large-bandwidth case | null | Phys. Rev. E 75 (2007) 011904 | 10.1103/PhysRevE.75.011904 | null | q-bio.BM cond-mat.stat-mech | null | The complementary strands of DNA molecules can be separated when stretched
apart by a force; the unzipping signal is correlated to the base content of the
sequence but is affected by thermal and instrumental noise. We consider here
the ideal case where opening events are known to a very good time resolution
(very large bandwidth), and study how the sequence can be reconstructed from
the unzipping data. Our approach relies on the use of statistical Bayesian
inference and of Viterbi decoding algorithm. Performances are studied
numerically on Monte Carlo generated data, and analytically. We show how
multiple unzippings of the same molecule may be exploited to improve the
quality of the prediction, and calculate analytically the number of required
unzippings as a function of the bandwidth, the sequence content, the elasticity
parameters of the unzipped strands.
| 2015-05-13 |
0704.2551 | Sophie Lebre | Sophie L\`ebre (SG) | Inferring dynamic genetic networks with low order independencies | null | null | null | null | math.ST q-bio.QM stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we propose a novel inference method for dynamic genetic
networks which makes it possible to face with a number of time measurements n
much smaller than the number of genes p. The approach is based on the concept
of low order conditional dependence graph that we extend here in the case of
Dynamic Bayesian Networks. Most of our results are based on the theory of
graphical models associated with the Directed Acyclic Graphs (DAGs). In this
way, we define a minimal DAG G which describes exactly the full order
conditional dependencies given the past of the process. Then, to face with the
large p and small n estimation case, we propose to approximate DAG G by
considering low order conditional independencies. We introduce partial qth
order conditional dependence DAGs G(q) and analyze their probabilistic
properties. In general, DAGs G(q) differ from DAG G but still reflect relevant
dependence facts for sparse networks such as genetic networks. By using this
approximation, we set out a non-bayesian inference method and demonstrate the
effectiveness of this approach on both simulated and real data analysis. The
inference procedure is implemented in the R package 'G1DBN' freely available
from the CRAN archive.
| 2009-05-29 |
0704.2554 | Yannick Brohard | Brigitte Meyer-Berthaud (AMAP), Anne-Laure Decombeix (AMAP) | A tree without leaves | null | Nature 446, 7138 (2006) 861-862 | 10.1038/446861a | A-07-09 | q-bio.PE | null | The puzzle presented by the famous stumps of Gilboa, New York, finds a
solution in the discovery of two fossil specimens that allow the entire
structure of these early trees to be reconstructed.
| 2007-05-23 |
0704.2649 | Mike Steel Prof. | Mike Steel, Aki Mimoto, Arne O. Mooers | Hedging our bets: the expected contribution of species to future
phylogenetic diversity | 19 pages, 2 figures | null | null | null | q-bio.PE | null | If predictions for species extinctions hold, then the `tree of life' today
may be quite different to that in (say) 100 years. We describe a technique to
quantify how much each species is likely to contribute to future biodiversity,
as measured by its expected contribution to phylogenetic diversity. Our
approach considers all possible scenarios for the set of species that will be
extant at some future time, and weights them according to their likelihood
under an independent (but not identical) distribution on species extinctions.
Although the number of extinction scenarios can typically be very large, we
show that there is a simple algorithm that will quickly compute this index. The
method is implemented and applied to the prosimian primates as a test case, and
the associated species ranking is compared to a related measure (the `Shapley
index'). We describe indices for rooted and unrooted trees, and a modification
that also includes the focal taxon's probability of extinction, making it
directly comparable to some new conservation metrics.
| 2007-05-23 |
0704.2700 | Ivan Degtyarenko Mr. | Ivan Degtyarenko, Karl J. Jalkanen, Andrey A. Gurtovenko and Risto M.
Nieminen | The aqueous and crystalline forms of L-alanine zwitterion | preprint of 22 pages, 7 figures, and 2 tables | null | null | null | physics.bio-ph physics.chem-ph physics.comp-ph | null | The structural properties of L-alanine amino acid in aqueous solution and in
crystalline phase have been studied by means of density-functional
electronic-structure and molecular dynamics simulations. The solvated
zwitterionic structure of L-alanine (+NH3-C2H4-COO-) was systematically
compared to the structure of its zwitterionic crystalline analogue acquired
from both computer simulations and experiments. It turns out that the
structural properties of an alanine molecule in aqueous solution can differ
significantly from those in crystalline phase, these differences being mainly
attributed to hydrogen bonding interactions. In particular, we found that the
largest difference between the two alanine forms can be seen for the
orientation and bond lengths of the carboxylate (COO-) group: in aqueous
solution the C-O bond lengths appear to strongly correlate with the number of
water molecules which form hydrogen bonds with the COO- group. Furthermore, the
hydrogen bond lengths are shorter and the hydrogen bond angles are larger for
L-alanine in water as compared to crystal. Overall, our findings strongly
suggest that the generally accepted approach of extending the structural
information acquired from crystallographic data to a L-alanine molecule in
aqueous solution should be used with caution.
| 2007-05-23 |
0704.2750 | Nikolai Lebovka I | Nikolai Lebovka, Eugene Vorobiev | The kinetics of inactivation of spheroidal microbial cells by pulsed
electric fields | 12 pages, 10 figures | null | null | null | physics.bio-ph | null | The nature of non-exponential kinetics in microbial cells inactivation by
pulsed electric fields (PEF) is discussed. It was demonstrated that possible
mechanism of non-exponential kinetics can be related to orientational disorder
in suspension of microbial cells of anisotropic form. A numerical studies of
spheroidal cell suspensions was carried out. The most pronounced deviations
from the exponential kinetics were observed for disordered suspensions of
prolate spheroids at small electric field strength $E$ or at large aspect ratio
$a$. For partially oriented suspensions, efficiency of inactivation enhances
with increasing of order parameter and field strength. A possibility of the
PEF-induced orientational ordering in microbial suspensions is discussed.
| 2007-05-23 |
0704.2793 | Matthew Scott | Matthew Scott, Terence Hwa and Brian Ingalls | Deterministic characterization of stochastic genetic circuits | 6 pages (Supplementary Information is appended) | Proceedings of the National Academy of Sciences USA (2007), vol.
104(18): 7402-7407 | 10.1073/pnas.0610468104 | null | q-bio.MN q-bio.QM | null | For cellular biochemical reaction systems where the numbers of molecules is
small, significant noise is associated with chemical reaction events. This
molecular noise can give rise to behavior that is very different from the
predictions of deterministic rate equation models. Unfortunately, there are few
analytic methods for examining the qualitative behavior of stochastic systems.
Here we describe such a method that extends deterministic analysis to include
leading-order corrections due to the molecular noise. The method allows the
steady-state behavior of the stochastic model to be easily computed,
facilitates the mapping of stability phase diagrams that include stochastic
effects and reveals how model parameters affect noise susceptibility, in a
manner not accessible to numerical simulation. By way of illustration we
consider two genetic circuits: a bistable positive-feedback loop and a
negative-feedback oscillator. We find in the positive feedback circuit that
translational activation leads to a far more stable system than transcriptional
control. Conversely, in a negative-feedback loop triggered by a
positive-feedback switch, the stochasticity of transcriptional control is
harnessed to generate reproducible oscillations.
| 2009-11-13 |
0704.2794 | Rafael Quintero-Torres | R. Quintero-Torres and J.L. Aragon, M. Torres, M. Estrada and L. Cros | Strong far field coherent scattering of ultraviolet radiation by
holococcolithophores | 4 pages and 4 figures | Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Sep;74:2006 Sep 12 | null | null | physics.bio-ph | null | By considering the structure of holococcoliths (calcite plates that cover
holococcolithophores, a haploid phase of the coccolithophore life cycle) as a
photonic structure, we apply a discrete dipolar approximation to study the
light backscattering properties of these algae. We show that some holococcolith
structures have the ability to scatter the ultraviolet (UV) radiation. This
property may represent an advantage for holococcolithophores possessing it, by
allowing them to live higher in the water column than other coccolithophores.
| 2007-05-23 |
0704.2896 | Adrian Melott | Bruce S.Lieberman and Adrian L. Melott (University of Kansas) | Considering the Case for Biodiversity Cycles: Reexamining the Evidence
for Periodicity in the Fossil Record | Minor modifications to reflect final published version | PLoS ONE 2(8): e759 (2007) | 10.1371/journal.pone.0000759 | null | q-bio.PE astro-ph physics.geo-ph | null | Medvedev and Melott (2007) have suggested that periodicity in fossil
biodiversity may be induced by cosmic rays which vary as the Solar System
oscillates normal to the galactic disk. We re-examine the evidence for a 62
million year (Myr) periodicity in biodiversity throughout the Phanerozoic
history of animal life reported by Rohde & Mueller (2005), as well as related
questions of periodicity in origination and extinction. We find that the signal
is robust against variations in methods of analysis, and is based on
fluctuations in the Paleozoic and a substantial part of the Mesozoic.
Examination of origination and extinction is somewhat ambiguous, with results
depending upon procedure. Origination and extinction intensity as defined by RM
may be affected by an artifact at 27 Myr in the duration of stratigraphic
intervals. Nevertheless, when a procedure free of this artifact is implemented,
the 27 Myr periodicity appears in origination, suggesting that the artifact may
ultimately be based on a signal in the data. A 62 Myr feature appears in
extinction, when this same procedure is used. We conclude that evidence for a
periodicity at 62 Myr is robust, and evidence for periodicity at approximately
27 Myr is also present, albeit more ambiguous.
| 2007-08-22 |
0704.2964 | Ashok Palaniappan | Ashok Palaniappan | Fourier Analysis of Biological Evolution: Concept of Selection Moment | null | null | null | null | q-bio.BM q-bio.QM | null | Secondary structure elements of many protein families exhibit differential
conservation on their opposing faces. Amphipathic helices and beta-sheets by
definition possess this property, and play crucial functional roles. This type
of evolutionary trajectory of a protein family is usually critical to the
functions of the protein family, as well as in creating functions within
subfamilies. That is, differential conservation maintains properties of a
protein structure related to its orientation, and that are important in
packing, recognition, and catalysis. Here I define and formulate a new concept,
called the selection moment, that detects this evolutionary process in protein
sequences. A treatment of its various applications is detailed.
| 2007-05-23 |
0704.3005 | Yasser Roudi | Yasser Roudi, Peter E. Latham | A balanced memory network | Accepted for publications in PLoS Comp. Biol | null | 10.1371/journal.pcbi.0030141 | null | q-bio.NC cond-mat.dis-nn | null | A fundamental problem in neuroscience is understanding how working memory --
the ability to store information at intermediate timescales, like 10s of
seconds -- is implemented in realistic neuronal networks. The most likely
candidate mechanism is the attractor network, and a great deal of effort has
gone toward investigating it theoretically. Yet, despite almost a quarter
century of intense work, attractor networks are not fully understood. In
particular, there are still two unanswered questions. First, how is it that
attractor networks exhibit irregular firing, as is observed experimentally
during working memory tasks? And second, how many memories can be stored under
biologically realistic conditions? Here we answer both questions by studying an
attractor neural network in which inhibition and excitation balance each other.
Using mean field analysis, we derive a three-variable description of attractor
networks. From this description it follows that irregular firing can exist only
if the number of neurons involved in a memory is large. The same mean field
analysis also shows that the number of memories that can be stored in a network
scales with the number of excitatory connections, a result that has been
suggested for simple models but never shown for realistic ones. Both of these
predictions are verified using simulations with large networks of spiking
neurons.
| 2015-05-13 |
0704.3049 | Ryan Gutenkunst | Ryan N. Gutenkunst, Fergal P. Casey, Joshua J. Waterfall, Christopher
R. Myers, James P. Sethna | Extracting falsifiable predictions from sloppy models | 4 pages, 2 figures. Submitted to the Annals of the New York Academy
of Sciences for publication in "Reverse Engineering Biological Networks:
Opportunities and Challenges in Computational Methods for Pathway Inference" | Annals of the New York Academy of Sciences 1115:203-211 (2007) | 10.1196/annals.1407.003 | null | q-bio.QM | null | Successful predictions are among the most compelling validations of any
model. Extracting falsifiable predictions from nonlinear multiparameter models
is complicated by the fact that such models are commonly sloppy, possessing
sensitivities to different parameter combinations that range over many decades.
Here we discuss how sloppiness affects the sorts of data that best constrain
model predictions, makes linear uncertainty approximations dangerous, and
introduces computational difficulties in Monte-Carlo uncertainty analysis. We
also present a useful test problem and suggest refinements to the standards by
which models are communicated.
| 2007-11-24 |
0704.3071 | Karina Mazzitello | K. I. Mazzitello, C. M. Arizmendi, and H. G. E. Hentschel | Converting genetic network oscillations into somite spatial pattern | 7 pages, 7 figures | null | 10.1103/PhysRevE.78.021906 | null | q-bio.QM | null | In most vertebrate species, the body axis is generated by the formation of
repeated transient structures called somites. This spatial periodicity in
somitogenesis has been related to the temporally sustained oscillations in
certain mRNAs and their associated gene products in the cells forming the
presomatic mesoderm. The mechanism underlying these oscillations have been
identified as due to the delays involved in the synthesis of mRNA and
translation into protein molecules [J. Lewis, Current Biol. {\bf 13}, 1398
(2003)]. In addition, in the zebrafish embryo intercellular Notch signalling
couples these oscillators and a longitudinal positional information signal in
the form of an Fgf8 gradient exists that could be used to transform these
coupled temporal oscillations into the observed spatial periodicity of somites.
Here we consider a simple model based on this known biology and study its
consequences for somitogenesis. Comparison is made with the known properties of
somite formation in the zebrafish embryo . We also study the effects of
localized Fgf8 perturbations on somite patterning.
| 2009-11-13 |
0704.3079 | Ilia Solov'yov | Alexander V. Yakubovich, Ilia A. Solov'yov, Andrey V. Solov'yov and
Walter Greiner | Ab initio theory of helix-coil phase transition | 24 pages, 3 figures | null | 10.1140/epjd/e2007-00328-9 | null | physics.bio-ph physics.chem-ph | null | In this paper we suggest a theoretical method based on the statistical
mechanics for treating the alpha-helix-random coil transition in alanine
polypeptides. We consider this process as a first-order phase transition and
develop a theory which is free of model parameters and is based solely on
fundamental physical principles. It describes essential thermodynamical
properties of the system such as heat capacity, the phase transition
temperature and others from the analysis of the polypeptide potential energy
surface calculated as a function of two dihedral angles, responsible for the
polypeptide twisting. The suggested theory is general and with some
modification can be applied for the description of phase transitions in other
complex molecular systems (e.g. proteins, DNA, nanotubes, atomic clusters,
fullerenes).
| 2009-11-13 |
0704.3085 | Ilia Solov'yov | Ilia A. Solov'yov, Alexander V. Yakubovich, Andrey V. Solov'yov and
Walter Greiner | Alpha helix-coil phase transition: analysis of ab initio theory
predictions | 34 pages, 12 figures | null | 10.1140/epjd/e2007-00327-x | null | physics.bio-ph physics.chem-ph | null | In the present paper we present results of calculations obtained with the use
of the theoretical method described in our preceding paper [1] and perform
detail analysis of alpha helix-random coil transition in alanine polypeptides
of different length. We have calculated the potential energy surfaces of
polypeptides with respect to their twisting degrees of freedom and construct a
parameter-free partition function of the polypeptide using the suggested method
[1]. From the build up partition function we derive various thermodynamical
characteristics for alanine polypeptides of different length as a function of
temperature. Thus, we analyze the temperature dependence of the heat capacity,
latent heat and helicity for alanine polypeptides consisting of 21, 30, 40, 50
and 100 amino acids. Alternatively, we have obtained same thermodynamical
characteristics from the use of molecular dynamics simulations and compared
them with the results of the new statistical mechanics approach. The comparison
proves the validity of the statistical mechanic approach and establishes its
accuracy.
| 2009-11-13 |
0704.3138 | Branislav Brutovsky | Branislav Brutovsky, Denis Horvath and Vladimir Lisy | Inverse Geometric Approach to the Simulation of the Circular Growth. The
Case of Multicellular Tumor Spheroids | null | null | 10.1016/j.physa.2007.10.036 | null | q-bio.CB | null | We demonstrate the power of the genetic algorithms to construct the cellular
automata model simulating the growth of 2-dimensional close-to-circular
clusters revealing the desired properties, such as the growth rate and, at the
same time, the fractal behavior of their contours. The possible application of
the approach in the field of tumor modeling is outlined.
| 2009-11-13 |
0704.3172 | Debaprasad Giri | Sanjay Kumar and Debaprasad Giri | Force induced conformational transition in a system of interacting stiff
polymer: Application to unfolding | RevTeX v4, 9 pages with 6 eps figures | Phys. Rev. E 72, 052901 (2005) | 10.1103/PhysRevE.72.052901 | BHU-PHY/CMPT/05-01 | cond-mat.soft cond-mat.stat-mech physics.bio-ph | null | We consider a stiff polymer chain in poor solvent and apply a force at one
end of the chain. We find that by varying the stiffness parameter, polymer
undergoes a transition from the globule state to the folded like state. The
conformation of folded state mimics the $\beta$-sheet as seen in titin
molecule. Using exact enumeration technique, we study the extension-force and
force-temperature diagrams of such a system. Force-temperature diagram shows
the re-entrance behaviour for flexible chain. However, for stiff chain this
re-entrance behaviour is absent and there is an enhancement in
$\theta$-temperature with the rise of stiffness. We further propose that the
internal information about the frozen structure of polymer can be read from the
distribution of end-to-end distance which shows saw-tooth like behaviour.
| 2015-05-13 |
0704.3174 | Ma\'ira Aguiar | Ma\'ira Aguiar, Nico Stollenwerk | A new chaotic attractor in a basic multi-strain epidemiological model
with temporary cross-immunity | 16 pages, 15 figures | null | null | null | nlin.CD q-bio.PE | null | An epidemic multi-strain model with temporary cross-immunity shows chaos,
even in a previously unexpected parameter region. Especially dengue fever
models with strong enhanced infectivity on secondary infection have previously
shown deterministic chaos motivated by experimental findings of
antibody-dependent-enhancement (ADE). Including temporary cross-immunity in
such models, which is common knowledge among field researchers in dengue, we
find a deterministically chaotic attractor in the more realistic parameter
region of reduced infectivity on secondary infection (''inverse ADE'' parameter
region). This is realistic for dengue fever since on second infection people
are more likely to be hospitalized, hence do not contribute to the force of
infection as much as people with first infection.
Our finding has wider implications beyond dengue in any multi-strain
epidemiological systems with altered infectivity upon secondary infection,
since we can relax the condition of rather high infectivity on secondary
infection previously required for deterministic chaos. For dengue the finding
of wide ranges of chaotic attractors open new ways to analysis of existing data
sets.
| 2007-06-25 |
0704.3175 | Debaprasad Giri | Debaprasad Giri and Sanjay Kumar | Effects of Eye-phase in DNA unzipping | RevTeX v4, 9 pages with 7 eps figures | Phys. Rev. E 73, 050903(R) (2006) | 10.1103/PhysRevE.73.050903 | BHU-PHY/CMPT/05-03 | cond-mat.soft cond-mat.stat-mech physics.bio-ph | null | The onset of an "eye-phase" and its role during the DNA unzipping is studied
when a force is applied to the interior of the chain. The directionality of the
hydrogen bond introduced here shows oscillations in force-extension curve
similar to a "saw-tooth" kind of oscillations seen in the protein unfolding
experiments. The effects of intermediates (hairpins) and stacking energies on
the melting profile have also been discussed.
| 2015-05-13 |
0704.3193 | Elsa Henriques S | Elsa S. Henriques, Andrey V. Solov'yov | A Rational Method for Probing Macromolecules Dissociation: The
Antibody-Hapten System | 22 pages, 10 figures | null | 10.1140/epjd/e2008-00009-3 | null | physics.bio-ph physics.chem-ph | null | The unbinding process of a protein-ligand complex of major biological
interest was investigated by means of a computational approach at atomistic
classical mechanical level. An energy minimisation-based technique was used to
determine the dissociation paths of the system by probing only a relevant set
of generalized coordinates. The complex problem was reduced to a
low-dimensional scanning along a selected distance between the protein and the
ligand. Orientational coordinates of the escaping fragment (the ligand) were
also assessed in order to further characterise the unbinding. Solvent effects
were accounted for by means of the Poisson--Boltzmann continuum model. The
corresponding dissociation time was derived from the calculated barrier height,
in compliance with the experimentally reported Arrhenius-like behaviour. The
computed results are in good agreement with the available experimental data.
| 2009-11-13 |
0704.3221 | Manuel Lladser | Manuel Lladser, M. D. Betterton, Rob Knight | Multiple pattern matching: A Markov chain approach | Final version to appear in the Journal of Mathematical Biology | null | null | null | math.PR math.CO math.ST q-bio.GN q-bio.QM stat.TH | null | RNA motifs typically consist of short, modular patterns that include base
pairs formed within and between modules. Estimating the abundance of these
patterns is of fundamental importance for assessing the statistical
significance of matches in genomewide searches, and for predicting whether a
given function has evolved many times in different species or arose from a
single common ancestor. In this manuscript, we review in an integrated and
self-contained manner some basic concepts of automata theory, generating
functions and transfer matrix methods that are relevant to pattern analysis in
biological sequences. We formalize, in a general framework, the concept of
Markov chain embedding to analyze patterns in random strings produced by a
memoryless source. This conceptualization, together with the capability of
automata to recognize complicated patterns, allows a systematic analysis of
problems related to the occurrence and frequency of patterns in random strings.
The applications we present focus on the concept of synchronization of
automata, as well as automata used to search for a finite number of keywords
(including sets of patterns generated according to base pairing rules) in a
general text.
| 2007-05-23 |
0704.3223 | Benedikt Obermayer | Benedikt Obermayer and Oskar Hallatschek | Coupling of transverse and longitudinal response in stiff polymers | 4 pages, 3 figures, 1 table; final version | Phys. Rev. Lett. 99 (2007) 098302 | 10.1103/PhysRevLett.99.098302 | LMU-ASC 25/07 | cond-mat.soft q-bio.BM | null | The time-dependent transverse response of stiff polymers, represented as
weakly-bending wormlike chains (WLCs), is well-understood on the linear level,
where transverse degrees of freedom evolve independently from the longitudinal
ones. We show that, beyond a characteristic time scale, the nonlinear coupling
of transverse and longitudinal motion in an inextensible WLC significantly
weakens the polymer response compared to the widely used linear response
predictions. The corresponding feedback mechanism is rationalized by scaling
arguments and quantified by a multiple scale approach that exploits an inherent
separation of transverse and longitudinal correlation length scales. Crossover
scaling laws and exact analytical and numerical solutions for characteristic
response quantities are derived for different experimentally relevant setups.
Our findings are applicable to cytoskeletal filaments as well as DNA under
tension.
| 2007-09-03 |
0704.3226 | Radhakrishnan Nagarajan | Radhakrishnan Nagarajan | Delay estimation in a two-node acyclic network | 33 Pages, 6 Figures | Physica A: Volume 376, 15 March 2007, Pages 725-737 | 10.1016/j.physa.2006.10.067 | null | q-bio.QM q-bio.MN | null | Linear measures such as cross-correlation have been used successfully to
determine time delays from the given processes. Such an analysis often precedes
identifying possible causal relationships between the observed processes. The
present study investigates the impact of a positively correlated driver whose
correlation function decreases monotonically with lag on the delay estimation
in a two-node acyclic network with one and two-delays. It is shown that
cross-correlation analysis of the given processes can result in spurious
identification of multiple delays between the driver and the dependent
processes. Subsequently, delay estimation of increment process as opposed to
the original process under certain implicit constraints is explored.
Short-range and long-range correlated driver processes along with those of
their coarse-grained counterparts are considered.
| 2015-05-13 |
0704.3259 | James P. Sethna | Christopher R. Myers, Ryan N. Gutenkunst, and James. P. Sethna | Python Unleashed on Systems Biology | Submitted to special issue of CiSE | null | null | null | q-bio.QM q-bio.MN | null | We have built an open-source software system for the modeling of biomolecular
reaction networks, SloppyCell, which is written in Python and makes substantial
use of third-party libraries for numerics, visualization, and parallel
programming. We highlight here some of the powerful features that Python
provides that enable SloppyCell to do dynamic code synthesis, symbolic
manipulation, and parallel exploration of complex parameter spaces.
| 2007-05-23 |
0704.3263 | Dominique Jean-Marie Mornet | Karim Hnia, G\'erald Hugon, Ahmed Masmoudi, Jacques Mercier,
Fran\c{c}ois Rivier, Dominique Jean-Marie Mornet | Effect of beta-Dystroglycan Processing on Utrophin / DP116 Anchorage in
Normal and MDX Mouse Schwann Cell Membrane | null | Neuroscience 141 (18/04/2006) 607-620 | 10.1016/J.neuroscience.2006.04.043 | null | q-bio.NC | null | In the peripheral nervous system, utrophin and the short dystrophin isoform
(Dp116) are co-localized at the outermost layer of the myelin sheath of nerve
fibers; together with the dystroglycan complex. In peripheral nerve, matrix
metalloproteinase (MMP) creates a 30 kDa fragment of beta-dystroglycan, leading
to a disruption of the link between the extracellular matrix and the cell
membrane. Here we asked if the processing of the beta-dystroglycan could
influence the anchorage of Dp116 or/and utrophin in normal and mdx Schwann cell
membrane. We showed that MMP-9 was more activated in mdx nerve than in
wild-type one. This activation leads to an accumulation of the 30 kDa
beta-dystroglycan isoform and have an impact on the anchorage of Dp116 and
utrophin isoforms in mdx Schwann cells membrane. Our results showed that Dp116
had greater affinity to the full length form of beta-dystroglycan than the 30
kDa form. Moreover, we showed for the first time that the short isoform of
utrophin (Up71) was over-expressed in mdx Schwann cells compared to wild-type.
In addition, this utrophin isoform (Up71) seems to have greater affinity to the
30 kDa beta-dystroglycan which could explain a more stabilization of this 30
kDa at the membrane compartment. Our results highlight the potential
participation of the short utrophin isoform and the cleaved form of
beta-dystroglycan in mdx Schwann cell membrane architecture.
| 2007-05-23 |
0704.3264 | Jose Vilar | Leonor Saiz and Jose M. G. Vilar | Efficiency and versatility of distal multisite transcription regulation | null | null | null | null | q-bio.SC q-bio.MN | null | Transcription regulation typically involves the binding of proteins over long
distances on multiple DNA sites that are brought close to each other by the
formation of DNA loops. The inherent complexity of the assembly of regulatory
complexes on looped DNA challenges the understanding of even the simplest
genetic systems, including the prototypical lac operon. Here we implement a
scalable quantitative computational approach to analyze systems regulated
through multiple DNA sites with looping. Our approach applied to the lac operon
accurately predicts the transcription rate over five orders of magnitude for
wild type and seven mutants accounting for all the combinations of deletions of
the three operators. A quantitative analysis of the model reveals that the
presence of three operators provides a mechanism to combine robust repression
with sensitive induction, two seemingly mutually exclusive properties that are
required for optimal functioning of metabolic switches.
| 2007-05-23 |
0704.3312 | Yohan Payan | Nicolas Vuillerme (TIMC - IMAG), Olivier Chenu (TIMC - IMAG),
Alexandre Moreau-Gaudry (TIMC - IMAG), Jacques Demongeot (TIMC - IMAG), Yohan
Payan (TIMC - IMAG) | Artificial Tongue-Placed Tactile Biofeedback for perceptual
supplementation: application to human disability and biomedical engineering | null | Human Machine iNteraction Conference Human'07 (2007) 105-112 | null | null | physics.med-ph q-bio.NC | null | The present paper aims at introducing the innovative technologies, based on
the concept of "sensory substitution" or "perceptual supplementation", we are
developing in the fields of human disability and biomedical engineering.
Precisely, our goal is to design, develop and validate practical assistive
biomedical and/technical devices and/or rehabilitating procedures for persons
with disabilities, using artificial tongue-placed tactile biofeedback systems.
Proposed applications are dealing with: (1) pressure sores prevention in case
of spinal cord injuries (persons with paraplegia, or tetraplegia); (2) ankle
proprioceptive acuity improvement for driving assistance in older and/or
disabled adults; and (3) balance control improvement to prevent fall in older
and/or disabled adults. This paper presents results of three feasibility
studies performed on young healthy adults.
| 2007-05-23 |
0704.3321 | Chikara Furusawa | Chikara Furusawa and Kunihiko Kaneko | A generic mechanism for adaptive growth rate regulation | 14 pages, 5 figures, submitted to PLoS Computational Biology | null | 10.1371/journal.pcbi.0040003 | null | q-bio.MN | null | How can a microorganism adapt to a variety of environmental conditions
despite there exists a limited number of signal transduction machineries? We
show that for any growing cells whose gene expression is under stochastic
fluctuations, adaptive cellular state is inevitably selected by noise, even
without specific signal transduction network for it. In general, changes in
protein concentration in a cell are given by its synthesis minus dilution and
degradation, both of which are proportional to the rate of cell growth. In an
adaptive state with a higher growth speed, both terms are large and balanced.
Under the presence of noise in gene expression, the adaptive state is less
affected by stochasticity since both the synthesis and dilution terms are
large, while for a non-adaptive state both the terms are smaller so that cells
are easily kicked out of the original state by noise. Hence, escape time from a
cellular state and the cellular growth rate are negatively correlated. This
leads to a selection of adaptive states with higher growth rates, and model
simulations confirm this selection to take place in general. The results
suggest a general form of adaptation that has never been brought to light - a
process that requires no specific machineries for sensory adaptation. The
present scheme may help explain a wide range of cellular adaptive responses
including the metabolic flux optimization for maximal cell growth.
| 2015-05-13 |
0704.3356 | Yohan Payan | Alexandre Moreau-Gaudry (TIMC - IMAG), Anne Prince (CMUDD), Jacques
Demongeot (TIMC - IMAG), Yohan Payan (TIMC - IMAG) | Pr\'evention des escarres chez les parapl\'egiques : une nouvelle
approche par \'electrostimulation linguale | null | Actes de la 4\`eme Conf\'erence Handicap 2006 "Nouvelles
Technologies au service de l'homme" (2006) 216-220 | null | null | physics.med-ph q-bio.NC | null | Pressure ulcers are recognized as a major health issue in individuals with
spinal cord injuries and new approaches to prevent this pathology are
necessary. An innovative health strategy is being developed through the use of
computer and sensory substitution via the tongue in order to compensate for the
sensory loss in the buttock area for individuals with paraplegia. This sensory
compensation will enable individuals with spinal cord injuries to be aware of a
localized excess of pressure at the skin/seat interface and, consequently, will
enable them to prevent the formation of pressure ulcers by relieving the
cutaneous area of suffering. This work reports an initial evaluation of this
approach and the feasibility of creating an adapted behavior, with a change in
pressure as a response to electro-stimulated information on the tongue.
Obtained during a clinical study in 10 healthy seated subjects, the first
results are encouraging, with 92% success in 100 performed tests. These
results, which have to be completed and validated in the paraplegic population,
may lead to a new approach to education in health to prevent the formation of
pressure ulcers within this population. Keywords: Spinal Cord Injuries,
Pressure Ulcer, Sensory Substitution, Health Education, Biomedical Informatics.
| 2007-05-23 |
0704.3365 | Takehiro Nagasima | Takehiro Nagasima, Akira R. Kinjo, Takashi Mitsui, Ken Nishikawa | Wang-Landau molecular dynamics technique to search for low-energy
conformational space of proteins | 8 pages, 7 figures, accepted for publication in Physical Review E | Phys. Rev. E 75, 066706 (2007) | 10.1103/PhysRevE.75.066706 | null | physics.comp-ph physics.bio-ph | null | Multicanonical molecular dynamics (MD) is a powerful technique for sampling
conformations on rugged potential surfaces such as protein. However, it is
notoriously difficult to estimate the multicanonical temperature effectively.
Wang and Landau developed a convenient method for estimating the density of
states based on a multicanonical Monte Carlo method. In their method, the
density of states is calculated autonomously during a simulation. In this paper
we develop a set of techniques to effectively apply the Wang-Landau method to
MD simulations. In the multicanonical MD, the estimation of the derivative of
the density of states is critical. In order to estimate it accurately, we
devise two original improvements. First, the correction for the density of
states is made smooth by using the Gaussian distribution obtained by a short
canonical simulation. Second, an approximation is applied to the derivative,
which is based on the Gaussian distribution and the multiple weighted histogram
technique. A test of this method was performed with small polypeptides,
Met-enkephalin and Trp-cage, and it is demonstrated that Wang-Landau MD is
consistent with replica exchange MD but can sample much larger conformational
space.
| 2007-11-01 |
0704.3406 | Martin Weigt | Hamed Mahmoudi, Andrea Pagnani, Martin Weigt, Riccardo Zecchina | Propagation of external regulation and asynchronous dynamics in random
Boolean networks | 19 pages, 14 figures, to appear in Chaos | Chaos 17, 026109 (2007) | 10.1063/1.2742931 | null | cond-mat.stat-mech cond-mat.dis-nn q-bio.MN | null | Boolean Networks and their dynamics are of great interest as abstract
modeling schemes in various disciplines, ranging from biology to computer
science. Whereas parallel update schemes have been studied extensively in past
years, the level of understanding of asynchronous updates schemes is still very
poor. In this paper we study the propagation of external information given by
regulatory input variables into a random Boolean network. We compute both
analytically and numerically the time evolution and the asymptotic behavior of
this propagation of external regulation (PER). In particular, this allows us to
identify variables which are completely determined by this external
information. All those variables in the network which are not directly fixed by
PER form a core which contains in particular all non-trivial feedback loops. We
design a message-passing approach allowing to characterize the statistical
properties of these cores in dependence of the Boolean network and the external
condition. At the end we establish a link between PER dynamics and the full
random asynchronous dynamics of a Boolean network.
| 2007-07-19 |
0704.3453 | Tshilidzi Marwala | S. Mohamed, D. Rubin, and T. Marwala | An Adaptive Strategy for the Classification of G-Protein Coupled
Receptors | 9 pages, 5 tables, 3 figures | null | null | null | cs.AI q-bio.QM | null | One of the major problems in computational biology is the inability of
existing classification models to incorporate expanding and new domain
knowledge. This problem of static classification models is addressed in this
paper by the introduction of incremental learning for problems in
bioinformatics. Many machine learning tools have been applied to this problem
using static machine learning structures such as neural networks or support
vector machines that are unable to accommodate new information into their
existing models. We utilize the fuzzy ARTMAP as an alternate machine learning
system that has the ability of incrementally learning new data as it becomes
available. The fuzzy ARTMAP is found to be comparable to many of the widespread
machine learning systems. The use of an evolutionary strategy in the selection
and combination of individual classifiers into an ensemble system, coupled with
the incremental learning ability of the fuzzy ARTMAP is proven to be suitable
as a pattern classifier. The algorithm presented is tested using data from the
G-Coupled Protein Receptors Database and shows good accuracy of 83%. The system
presented is also generally applicable, and can be used in problems in genomics
and proteomics.
| 2007-06-25 |
0704.3551 | J\"org Langowski | Annika Wedemeier, Holger Merlitz, Chen-Xu Wu, and J\"org Langowski | Modelling diffusional transport in the interphase cell nucleus | 9 pages, 8 figures | null | 10.1063/1.2753158 | null | physics.bio-ph physics.comp-ph | null | In this paper a lattice model for diffusional transport of particles in the
interphase cell nucleus is proposed. Dense networks of chromatin fibers are
created by three different methods: randomly distributed, non-interconnected
obstacles, a random walk chain model, and a self avoiding random walk chain
model with persistence length. By comparing a discrete and a continuous version
of the random walk chain model, we demonstrate that lattice discretization does
not alter particle diffusion. The influence of the 3D geometry of the fiber
network on the particle diffusion is investigated in detail, while varying
occupation volume, chain length, persistence length and walker size. It is
shown that adjacency of the monomers, the excluded volume effect incorporated
in the self avoiding random walk model, and, to a lesser extent, the
persistence length, affect particle diffusion. It is demonstrated how the
introduction of the effective chain occupancy, which is a convolution of the
geometric chain volume with the walker size, eliminates the conformational
effects of the network on the diffusion, i.e., when plotting the diffusion
coefficient as a function of the effective chain volume, the data fall onto a
master curve.
| 2009-11-13 |
0704.3560 | Christian Blum | Christian Blum, Willem L. Vos, and Vinod Subramaniam | Tuning Spontaneous Emission versus Forster Energy Transfer in Biological
Systems by Manipulating the Density of Photonic States | 12 pages, 3 figures, pdf | null | null | null | physics.chem-ph physics.bio-ph | null | We theoretically discuss how to tune the competition between Forster transfer
and spontaneous emission in a continuous and nondestructive fashion. The
proposed approach is especially suitable for delicate biological systems like
light harvesting complexes and fluorescent protein oligomers. We demonstrate
that the manipulation of the density of photonic states at the emission
frequency of the energy donor results in a change of the quantum efficiencies
of the competing energy transfer and spontaneous emission processes. This
change will be manifested in a modification of the donor and acceptor emission
intensities. Thus, by controlling the local density of photonic states Forster
coupled systems can be manipulated and analyzed without the need to physically
separate donor and acceptor chromophores for individual analysis, which is of
interest, for example, for oligomeric reef coral fluorescent proteins.
| 2007-06-19 |
0704.3619 | Marcus Kaiser | Luciano da F Costa, Marcus Kaiser, Claus C Hilgetag | Predicting the connectivity of primate cortical networks from
topological and spatial node properties | null | BMC Systems Biology 2007, 1:16 | 10.1186/1752-0509-1-16 | null | q-bio.NC physics.soc-ph | null | The organization of the connectivity between mammalian cortical areas has
become a major subject of study, because of its important role in scaffolding
the macroscopic aspects of animal behavior and intelligence. In this study we
present a computational reconstruction approach to the problem of network
organization, by considering the topological and spatial features of each area
in the primate cerebral cortex as subsidy for the reconstruction of the global
cortical network connectivity. Starting with all areas being disconnected,
pairs of areas with similar sets of features are linked together, in an attempt
to recover the original network structure. Inferring primate cortical
connectivity from the properties of the nodes, remarkably good reconstructions
of the global network organization could be obtained, with the topological
features allowing slightly superior accuracy to the spatial ones. Analogous
reconstruction attempts for the C. elegans neuronal network resulted in
substantially poorer recovery, indicating that cortical area interconnections
are relatively stronger related to the considered topological and spatial
properties than neuronal projections in the nematode. The close relationship
between area-based features and global connectivity may hint on developmental
rules and constraints for cortical networks. Particularly, differences between
the predictions from topological and spatial properties, together with the
poorer recovery resulting from spatial properties, indicate that the
organization of cortical networks is not entirely determined by spatial
constraints.
| 2007-05-23 |
0704.3639 | Filipe Tostevin | Filipe Tostevin, Pieter Rein ten Wolde, Martin Howard | Fundamental Limits to Position Determination by Concentration Gradients | 24 pages, 2 figures | PLoS Computational Biology 3 e78 (2007) | 10.1371/journal.pcbi.0030078 | null | q-bio.SC cond-mat.stat-mech | null | Position determination in biological systems is often achieved through
protein concentration gradients. Measuring the local concentration of such a
protein with a spatially-varying distribution allows the measurement of
position within the system. In order for these systems to work effectively,
position determination must be robust to noise. Here, we calculate fundamental
limits to the precision of position determination by concentration gradients
due to unavoidable biochemical noise perturbing the gradients. We focus on
gradient proteins with first order reaction kinetics. Systems of this type have
been experimentally characterised in both developmental and cell biology
settings. For a single gradient we show that, through time-averaging, great
precision can potentially be achieved even with very low protein copy numbers.
As a second example, we investigate the ability of a system with oppositely
directed gradients to find its centre. With this mechanism, positional
precision close to the centre improves more slowly with increasing averaging
time, and so longer averaging times or higher copy numbers are required for
high precision. For both single and double gradients, we demonstrate the
existence of optimal length scales for the gradients, where precision is
maximized, as well as analyzing how precision depends on the size of the
concentration measuring apparatus. Our results provide fundamental constraints
on the positional precision supplied by concentration gradients in various
contexts, including both in developmental biology and also within a single
cell.
| 2007-05-23 |
0704.3640 | Dennis Wylie | Dennis Cates Wylie | Linked by Loops: Network Structure and Switch Integration in Complex
Dynamical Systems | 21 pages, 5 figures. Paper simplified and shortened. Quantities
presented in table 1 are different, though related, to quantities previously
presented in table 1 | null | null | null | q-bio.QM cond-mat.dis-nn math.DS nlin.CD | null | Simple nonlinear dynamical systems with multiple stable stationary states are
often taken as models for switchlike biological systems. This paper considers
the interaction of multiple such simple multistable systems when they are
embedded together into a larger dynamical "supersystem." Attention is focused
on the network structure of the resulting set of coupled differential
equations, and the consequences of this structure on the propensity of the
embedded switches to act independently versus cooperatively. Specifically, it
is argued that both larger average and larger variance of the node degree
distribution lead to increased switch independence. Given the frequency of
empirical observations of high variance degree distributions (e.g., power-law)
in biological networks, it is suggested that the results presented here may aid
in identifying switch-integrating subnetworks as comparatively homogenous,
low-degree, substructures. Potential applications to ecological problems such
as the relationship of stability and complexity are also briefly discussed.
| 2008-04-10 |
0704.3715 | Pablo Echenique | Pablo Echenique, J. L. Alonso | Efficient model chemistries for peptides. I. Split-valence Gaussian
basis sets and the heterolevel approximation in RHF and MP2 | 54 pages, 16 figures, LaTeX, AMSTeX, Submitted to J. Comp. Chem | J. Comp. Chem. (2008) 1408-1422 | 10.1002/jcc.20900 | null | q-bio.QM cond-mat.soft q-bio.BM | null | We present an exhaustive study of more than 250 ab initio potential energy
surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The model chemistries
(MCs) used are constructed as homo- and heterolevels involving possibly
different RHF and MP2 calculations for the geometry and the energy. The basis
sets used belong to a sample of 39 selected representants from Pople's
split-valence families, ranging from the small 3-21G to the large
6-311++G(2df,2pd). The reference PES to which the rest are compared is the
MP2/6-311++G(2df,2pd) homolevel, which, as far as we are aware, is the more
accurate PES of a dipeptide in the literature. The aim of the study presented
is twofold: On the one hand, the evaluation of the influence of polarization
and diffuse functions in the basis set, distinguishing between those placed at
1st-row atoms and those placed at hydrogens, as well as the effect of different
contraction and valence splitting schemes. On the other hand, the investigation
of the heterolevel assumption, which is defined here to be that which states
that heterolevel MCs are more efficient than homolevel MCs. The heterolevel
approximation is very commonly used in the literature, but it is seldom
checked. As far as we know, the only tests for peptides or related systems,
have been performed using a small number of conformers, and this is the first
time that this potentially very economical approximation is tested in full
PESs. In order to achieve these goals, all data sets have been compared and
analyzed in a way which captures the nearness concept in the space of MCs.
| 2013-06-21 |
0704.3724 | Paul Smolen | Paul Smolen | A Model of Late Long-Term Potentiation Simulates Aspects of Memory
Maintenance | Accepted to PLoS One. 8 figures at end | null | 10.1371/journal.pone.0000445 | null | q-bio.NC q-bio.MN | null | Late long-term potentiation (L-LTP) appears essential for the formation of
long-term memory, with memories at least partly encoded by patterns of
strengthened synapses. How memories are preserved for months or years, despite
molecular turnover, is not well understood. Ongoing recurrent neuronal
activity, during memory recall or during sleep, has been hypothesized to
preferentially potentiate strong synapses, preserving memories. This hypothesis
has not been evaluated in the context of a mathematical model representing
biochemical pathways important for L-LTP. I incorporated ongoing activity into
two such models: a reduced model that represents some of the essential
biochemical processes, and a more detailed published model. The reduced model
represents synaptic tagging and gene induction intuitively, and the detailed
model adds activation of essential kinases by Ca. Ongoing activity was modeled
as continual brief elevations of [Ca]. In each model, two stable states of
synaptic weight resulted. Positive feedback between synaptic weight and the
amplitude of ongoing Ca transients underlies this bistability. A tetanic or
theta-burst stimulus switches a model synapse from a low weight to a high
weight stabilized by ongoing activity. Bistability was robust to parameter
variations. Simulations illustrated that prolonged decreased activity reset
synapses to low weights, suggesting a plausible forgetting mechanism. However,
episodic activity with shorter inactive intervals maintained strong synapses.
Both models support experimental predictions. Tests of these predictions are
expected to further understanding of how neuronal activity is coupled to
maintenance of synaptic strength.
| 2015-05-13 |
0704.3730 | Volkan Sevim | Volkan Sevim, Per Arne Rikvold | Network Growth with Preferential Attachment for High Indegree and Low
Outdegree | null | Physica A, Volume 387, Issue 11, 2631-2636 (2008) | 10.1016/j.physa.2008.01.034 | null | cond-mat.stat-mech q-bio.PE | null | We study the growth of a directed transportation network, such as a food web,
in which links carry resources. We propose a growth process in which new nodes
(or species) preferentially attach to existing nodes with high indegree (in
food-web language, number of prey) and low outdegree (or number of predators).
This scheme, which we call inverse preferential attachment, is intended to
maximize the amount of resources available to each new node. We show that the
outdegree (predator) distribution decays at least exponentially fast for large
outdegree and is continuously tunable between an exponential distribution and a
delta function. The indegree (prey) distribution is poissonian in the
large-network limit.
| 2008-03-17 |
0704.3748 | Gerald A. Miller | Gerald A. Miller, Yi Y. Shi, Hong Qian, and Karol Bomsztyk | Clustering Coefficients of Protein-Protein Interaction Networks | 16 pages, 3 figures, in Press PRE uses pdflatex | Phys. Rev. E 75, 051910 (2007) | 10.1103/PhysRevE.75.051910 | null | q-bio.QM cond-mat.stat-mech physics.bio-ph q-bio.MN | null | The properties of certain networks are determined by hidden variables that
are not explicitly measured. The conditional probability (propagator) that a
vertex with a given value of the hidden variable is connected to k of other
vertices determines all measurable properties. We study hidden variable models
and find an averaging approximation that enables us to obtain a general
analytical result for the propagator. Analytic results showing the validity of
the approximation are obtained. We apply hidden variable models to
protein-protein interaction networks (PINs) in which the hidden variable is the
association free-energy, determined by distributions that depend on
biochemistry and evolution. We compute degree distributions as well as
clustering coefficients of several PINs of different species; good agreement
with measured data is obtained. For the human interactome two different
parameter sets give the same degree distributions, but the computed clustering
coefficients differ by a factor of about two. This shows that degree
distributions are not sufficient to determine the properties of PINs.
| 2009-11-13 |
0704.3771 | James P. Crutchfield | Olof Gornerup and James P. Crutchfield | Primordial Evolution in the Finitary Process Soup | 7 pages, 10 figures;
http://cse.ucdavis.edu/~cmg/compmech/pubs/pefps.htm | null | 10.1142/9789812779953_0012 | null | q-bio.PE q-bio.MN | null | A general and basic model of primordial evolution--a soup of reacting
finitary and discrete processes--is employed to identify and analyze
fundamental mechanisms that generate and maintain complex structures in
prebiotic systems. The processes--$\epsilon$-machines as defined in
computational mechanics--and their interaction networks both provide well
defined notions of structure. This enables us to quantitatively demonstrate
hierarchical self-organization in the soup in terms of complexity. We found
that replicating processes evolve the strategy of successively building higher
levels of organization by autocatalysis. Moreover, this is facilitated by local
components that have low structural complexity, but high generality. In effect,
the finitary process soup spontaneously evolves a selection pressure that
favors such components. In light of the finitary process soup's generality,
these results suggest a fundamental law of hierarchical systems: global
complexity requires local simplicity.
| 2016-11-23 |
0704.3808 | Jakob Enemark | Jakob Enemark and Kim Sneppen | On Gene Duplication Models for Evolving Regulatory Networks | 14 pages, 7 figures | null | 10.1088/1742-5468/2007/11/P11007 | null | q-bio.PE q-bio.OT | null | Background: Duplication of genes is important for evolution of molecular
networks. Many authors have therefore considered gene duplication as a driving
force in shaping the topology of molecular networks. In particular it has been
noted that growth via duplication would act as an implicit way of preferential
attachment, and thereby provide the observed broad degree distributions of
molecular networks.
Results: We extend current models of gene duplication and rewiring by
including directions and the fact that molecular networks are not a result of
unidirectional growth. We introduce upstream sites and downstream shapes to
quantify potential links during duplication and rewiring. We find that this in
itself generates the observed scaling of transcription factors for genome sites
in procaryotes. The dynamical model can generate a scale-free degree
distribution, p(k)∝ 1/k^γ, with exponent γ=1 in the
non-growing case, and with γ>1 when the network is growing.
Conclusions: We find that duplication of genes followed by substantial
recombination of upstream regions could generate main features of genetic
regulatory networks. Our steady state degree distribution is however to broad
to be consistent with data, thereby suggesting that selective pruning acts as a
main additional constraint on duplicated genes. Our analysis shows that gene
duplication can only be a main cause for the observed broad degree
distributions, if there is also substantial recombinations between upstream
regions of genes.
| 2009-11-13 |
0704.3809 | Laurent Cognet | David Lasne (CPMOH), Gerhard A. Blab (CPMOH), St\'ephane Berciaud
(CPMOH), Martin Heine (PCS), Laurent Groc (PCS), Daniel Choquet (PCS),
Laurent Cognet (CPMOH), Brahim Lounis (CPMOH) | Single NanoParticle Photothermal Tracking (SNaPT) of 5 nm gold beads in
live cells | null | Biophysical Journal 91, 12 (15/12/2006) 4598 | 10.1529/biophysj.106.089771 | null | physics.bio-ph physics.optics | null | Tracking individual nano-objets in live cells during arbitrary long times is
an ubiquitous need in modern biology. We present here a method for tracking
individual 5 nm gold nanoparticles on live cells. It relies on the photothermal
effect and the detection of the Laser Induced Scattering around a NanoAbsorber
(LISNA). The key point for recording trajectories at video rate is the use of a
triangulation procedure. The effectiveness of the method is tested against
Single fluorescent Molecule Tracking in live COS7 cells on subsecond time
scales. We further demonstrate recordings for several minutes of AMPA receptors
trajectories on the plasma membrane of live neurons. SNaPT has the unique
potential to record arbitrary long trajectory of membrane proteins using
non-fluorescent nanometer sized labels.
| 2007-05-23 |
0704.3816 | Laurent Cognet | Laurent Cognet (CPMOH), Catherine Tardin (CPMOH), David Boyer (CPMOH),
Daniel Choquet (PCS), Philippe Tamarat (CPMOH), Brahim Lounis (CPMOH) | Single metallic nanoparticle imaging for protein detection in cells | null | Proceeding of the national academy of sciences 100, 20
(30/09/2003) 11350 | 10.1073/pnas.1534635100 | null | physics.optics physics.bio-ph | null | We performed a visualization of membrane proteins labeled with 10-nm gold
nanoparticles in cells, using an all-optical method based on photothermal
interference contrast. The high sensitivity of the method and the stability of
the signals allows 3D imaging of individual nanoparticles without the drawbacks
of photobleaching and blinking inherent to fluorescent markers. A simple
analytical model is derived to account for the measurements of the signal
amplitude and the spatial resolution. The photothermal interference contrast
method provides an efficient, reproducible, and promising way to visualize low
amounts of proteins in cells by optical means.
| 2007-05-23 |
0704.3826 | Mark Ya. Azbel' | Mark Ya. Azbel | Non-coding DNA programs express adaptation and its universal law | Refined version 19 pages, 10 figs | null | null | null | q-bio.GN cond-mat.other nlin.AO q-bio.OT q-bio.PE q-bio.QM | null | Significant fraction (98.5% in humans) of most animal genomes is non- coding
dark matter. Its largely unknown function (1-5) is related to programming
(rather than to spontaneous mutations) of accurate adaptation to rapidly
changing environment. Programmed adaptation to the same universal law for
non-competing animals from anaerobic yeast to human is revealed in the study of
their extensively quantified mortality (6-21). Adaptation of animals with
removed non-coding DNA fractions may specify their contribution to genomic
programming. Emergence of new adaptation programs and their (non-Mendelian)
heredity may be studied in antibiotic mini-extinctions (22-24). On a large
evolutionary scale rapid universal adaptation was vital for survival, and
evolved, in otherwise lethal for diverse species major mass extinctions
(25-28). Evolutionary and experimental data corroborate these conclusions
(6-21, 29-32). Universal law implies certain biological universality of diverse
species, thus quantifies applicability of animal models to humans). Genomic
adaptation programming calls for unusual approach to its study and implies
unanticipated perspectives, in particular, directed biological changes.
| 2007-08-02 |
0704.3853 | Laurent Cognet | Laurent Cognet (CPMOH), Fran\c{c}oise Coussen (PCS), Daniel Choquet
(PCS), Brahim Lounis (CPMOH) | Fluorescence microscopy of single autofluorescent proteins for cellular
biology | null | Comptes Rendus de l Acad\'emie des Sciences - Series IV - Physics
3 (15/08/2002) 645 | null | null | physics.optics physics.bio-ph | null | In this paper we review the applicability of autofluorescent proteins for
single-molecule imaging in biology. The photophysical characteristics of
several mutants of the Green Fluorescent Protein (GFP) and those of DsRed are
compared and critically discussed for their use in cellular biology. The
alternative use of two-photon excitation at the single-molecule level or
Fluorescence Correlation Spectroscopy is envisaged for the study of individual
autofluorescent proteins. Single-molecule experiments performed in live cells
using eGFP and preferably eYFP fusion proteins are reviewed. Finally, the first
use at the single-molecule level of citrine, a more photostable variant of the
eYFP is reported when fused to a receptor for neurotransmitter in live cells.
| 2007-05-23 |
0704.3854 | Laurent Cognet | Laurent Cognet (CPMOH), Laurent Groc (PCS), Brahim Lounis (CPMOH),
Daniel Choquet (PCS) | Multiple Routes for Glutamate Receptor Trafficking: Surface Diffusion
and Membrane Traffic Cooperate to Bring Receptors to Synapses | null | Science's STKE (electronic resource) : signal transduction
knowledge environment 327 (21/03/2006) 13 | null | null | physics.optics physics.bio-ph | null | Trafficking of glutamate receptors into and out of synapses is critically
involved in the plasticity of excitatory synaptic transmission. Endocytosis and
exocytosis of receptors have initially been thought to account alone for this
trafficking. However, membrane proteins also traffic through surface lateral
diffusion in the plasma membrane. We describe developments in
electrophysiological and optical approaches that have allowed for the real time
measurement of glutamate receptor surface trafficking in live neurons. These
include (i) specific imaging of surface receptors using a pH sensitive
fluorescent protein, (ii) design of a photoactivable drug to inactivate locally
surface receptors and monitor electrophysiologically their recovery, and
(iii)application of single molecule fluorescence microscopy to directly track
the movement of individual surface receptors with nanometer resolution inside
and outside synapses. Altogether, these approaches have demonstrated that
glutamate receptors diffuse at high rates in the neuronal membrane and suggest
a key role for surface diffusion in the regulation of receptor numbers at
synapses.
| 2007-05-23 |
0704.3855 | Laurent Cognet | Piet H M Lommerse, Gerhard A Blab, Laurent Cognet, Gregory S Harms, B
Ewa Snaar-Jagalska, Herman P Spaink, Thomas Schmidt | Single-molecule imaging of the H-ras membrane-anchor reveals domains in
the cytoplasmic leaflet of the cell membrane | null | Biophys J 86, 1 Pt 1 (01/2004) 609-16 | null | null | physics.optics physics.bio-ph | null | In the last decade evidence has accumulated that small domains of 50-700 nm
in diameter are located in the exoplasmic leaflet of the plasma membrane. Most
of these domains supposedly consist of specific sets of lipids and proteins,
and are believed to coordinate signal transduction cascades. Whether similar
domains are also present in the cytoplasmic leaflet of the plasma membrane is
unclear so far. To investigate the presence of cytoplasmic leaflet domains, the
H-Ras membrane-targeting sequence was fused to the C-terminus of the enhanced
yellow fluorescent protein. Using single-molecule fluorescence microscopy,
trajectories of individual molecules diffusing in the cytoplasmic leaflet of
the plasma membrane were recorded. From these trajectories, the diffusion of
individual membrane-anchored enhanced yellow fluorescent protein molecules was
studied in live cells on timescales from 5 to 200 ms. The results show that the
diffusion of 30-40% of the molecules is constrained in domains with a typical
size of 200 nm. Neither breakdown of actin nor cholesterol extraction changed
the domain characteristics significantly, indicating that the observed domains
may not be related to the membrane domains identified so far.
| 2007-05-23 |
0704.3858 | Laurent Cognet | Catherine Tardin (CPMOH), Laurent Cognet (CPMOH), C\'ecile Bats (PCS),
Brahim Lounis (CPMOH), Daniel Choquet (PCS) | Direct imaging of lateral movements of AMPA receptors inside synapses | null | EMBO J 22, 18 (15/09/2003) 4656-65 | 10.1093/emboj/cdg463 | null | physics.optics physics.bio-ph | null | Trafficking of AMPA receptors in and out of synapses is crucial for synaptic
plasticity. Previous studies have focused on the role of endo/exocytosis
processes or that of lateral diffusion of extra-synaptic receptors. We have now
directly imaged AMPAR movements inside and outside synapses of live neurons
using single-molecule fluorescence microscopy. Inside individual synapses, we
found immobile and mobile receptors, which display restricted diffusion.
Extra-synaptic receptors display free diffusion. Receptors could also exchange
between these membrane compartments through lateral diffusion. Glutamate
application increased both receptor mobility inside synapses and the fraction
of mobile receptors present in a juxtasynaptic region. Block of inhibitory
transmission to favor excitatory synaptic activity induced a transient increase
in the fraction of mobile receptors and a decrease in the proportion of
juxtasynaptic receptors. Altogether, our data show that rapid exchange of
receptors between a synaptic and extra-synaptic localization occurs through
regulation of receptor diffusion inside synapses.
| 2007-05-23 |
0704.3948 | Alexey Mazur K | Alexey K. Mazur | The Worm-Like Chain Theory And Bending Of Short DNA | 4 pages, 3 figures, to appear in PRL | Phys. Rev. Lett. 98, 218102, 2007. | 10.1103/PhysRevLett.98.218102 | null | q-bio.BM cond-mat.soft physics.bio-ph | null | The probability distributions for bending angles in double helical DNA
obtained in all-atom molecular dynamics simulations are compared with
theoretical predictions. The computed distributions remarkably agree with the
worm-like chain theory for double helices of one helical turn and longer, and
qualitatively differ from predictions of the semi-elastic chain model. The
computed data exhibit only small anomalies in the apparent flexibility of short
DNA and cannot account for the recently reported AFM data (Wiggins et al,
Nature nanotechnology 1, 137 (2006)). It is possible that the current atomistic
DNA models miss some essential mechanisms of DNA bending on intermediate length
scales. Analysis of bent DNA structures reveals, however, that the bending
motion is structurally heterogeneous and directionally anisotropic on the
intermediate length scales where the experimental anomalies were detected.
These effects are essential for interpretation of the experimental data and
they also can be responsible for the apparent discrepancy.
| 2009-11-13 |
0704.3957 | Vasily Ogryzko V | Vasily Ogryzko | Erwin Schroedinger, Francis Crick and epigenetic stability | New and improved version of the essay, now published in the online
journal 'Biology Direct'. Contains more expanded discussion on entanglement.
18 pages, 2 figures. The file includes open reviews by E.Koonin, V.Vedral and
E.Karsenti | Biol Direct. 2008 Apr 17;3(1):15 | null | null | physics.gen-ph q-bio.MN | null | Schroedinger's book 'What is Life?' is widely credited for having played a
crucial role in development of molecular and cellular biology. My essay
revisits the issues raised by this book from the modern perspective of
epigenetics and systems biology. I contrast two classes of potential mechanisms
of epigenetic stability: 'epigenetic templating' and 'systems biology'
approaches, and consider them from the point of view expressed by Schroedinger.
I also discuss how quantum entanglement, a nonclassical feature of quantum
mechanics, can help to address the 'problem of small numbers' that lead
Schroedinger to promote the idea of molecular code-script for explanation of
stability of biological order.
| 2008-05-30 |
0705.0078 | Claudius Gros | Claudius Gros | Neural networks with transient state dynamics | null | New J.Phys.9:109,2007 | 10.1088/1367-2630/9/4/109 | null | cond-mat.dis-nn astro-ph cond-mat.other nlin.AO q-bio.NC | null | We investigate dynamical systems characterized by a time series of distinct
semi-stable activity patterns, as they are observed in cortical neural activity
patterns. We propose and discuss a general mechanism allowing for an adiabatic
continuation between attractor networks and a specific adjoined transient-state
network, which is strictly dissipative. Dynamical systems with transient states
retain functionality when their working point is autoregulated; avoiding
prolonged periods of stasis or drifting into a regime of rapid fluctuations. We
show, within a continuous-time neural network model, that a single local
updating rule for online learning allows simultaneously (i) for information
storage via unsupervised Hebbian-type learning, (ii) for adaptive regulation of
the working point and (iii) for the suppression of runaway synaptic growth.
Simulation results are presented; the spontaneous breaking of time-reversal
symmetry and link symmetry are discussed.
| 2010-02-11 |
0705.0201 | Jesse Bloom | Jesse D Bloom, Philip A Romero, Zhongyi Lu, and Frances H Arnold | Neutral genetic drift can aid functional protein evolution | null | Biology Direct 2:17 (2007) | 10.1186/1745-6150-2-17 | null | q-bio.PE q-bio.BM | null | BACKGROUND: Many of the mutations accumulated by naturally evolving proteins
are neutral in the sense that they do not significantly alter a protein's
ability to perform its primary biological function. However, new protein
functions evolve when selection begins to favor other, "promiscuous" functions
that are incidental to a protein's biological role. If mutations that are
neutral with respect to a protein's primary biological function cause
substantial changes in promiscuous functions, these mutations could enable
future functional evolution.
RESULTS: Here we investigate this possibility experimentally by examining how
cytochrome P450 enzymes that have evolved neutrally with respect to activity on
a single substrate have changed in their abilities to catalyze reactions on
five other substrates. We find that the enzymes have sometimes changed as much
as four-fold in the promiscuous activities. The changes in promiscuous
activities tend to increase with the number of mutations, and can be largely
rationalized in terms of the chemical structures of the substrates. The
activities on chemically similar substrates tend to change in a coordinated
fashion, potentially providing a route for systematically predicting the change
in one function based on the measurement of several others.
CONCLUSIONS: Our work suggests that initially neutral genetic drift can lead
to substantial changes in protein functions that are not currently under
selection, in effect poising the proteins to more readily undergo functional
evolution should selection "ask new questions" in the future.
| 2007-07-18 |
0705.0227 | Graeme J. Ackland | Graeme J. Ackland, Richard D.L.Hanes, Morrel H. Cohen | Self assembly of a model multicellular organism resembling the
Dictyostelium slime molds | null | null | null | null | q-bio.CB q-bio.PE | null | The evolution of multicellular organisms from monocellular ancestors
represents one of the greatest advances of the history of life. The assembly of
such multicellular organisms requires signalling and response between cells:
over millions of years these signalling processes have become extremely
sophisticated and refined by evolution, such that study of modern organisms may
not be able to shed much light on the original ancient processes . Here we are
interested in determining how simple a signalling method can be, while still
achieving self-assembly. In 2D a coupled cellular automaton/differential
equation approach models organisms and chemotaxic chemicals, producing
spiralling aggregation. In 3D Lennard-Jones-like particles are used to
represent single cells, and their evolution in response to signalling is
followed by molecular dynamics. It is found that if a single cell is able to
emit a signal which induces others to move towards it, then a colony of
single-cell organisms can assemble into shapes as complex as a tower, a ball
atop a stalk, or a fast-moving slug. The similarity with the behaviour of
modern Dictyostelium slime molds signalling with cyclic adenosine monophosphate
(cAMP) is striking.
| 2007-05-23 |
0705.0313 | Gasper Tkacik | Gasper Tkacik, Curtis G Callan Jr, William Bialek | Information flow and optimization in transcriptional control | 5 pages, 4 figures | Proc Natl Acad Sci USA 105 (2008): 12265-12270 | 10.1073/pnas.0806077105 | null | q-bio.MN | null | In the simplest view of transcriptional regulation, the expression of a gene
is turned on or off by changes in the concentration of a transcription factor
(TF). We use recent data on noise levels in gene expression to show that it
should be possible to transmit much more than just one regulatory bit.
Realizing this optimal information capacity would require that the dynamic
range of TF concentrations used by the cell, the input/output relation of the
regulatory module, and the noise levels of binding and transcription satisfy
certain matching relations. This parameter-free prediction is in good agreement
with recent experiments on the Bicoid/Hunchback system in the early Drosophila
embryo, and this system achieves ~90% of its theoretical maximum information
transmission.
| 2013-08-01 |
0705.0374 | Razvan Radulescu M.D. | Razvan T. Radulescu, Angelika Jahn, Daniela Hellmann and Gregor
Weirich | Immunohistochemical pitfalls in the demonstration of insulin-degrading
enzyme in normal and neoplastic human tissues | 17 pages, 6 figures | null | null | null | q-bio.TO q-bio.QM | null | Previously, we have identified the cytoplasmic zinc metalloprotease
insulin-degrading enzyme(IDE) in human tissues by an immunohistochemical method
involving no antigen retrieval (AR) by pressure cooking to avoid artifacts by
endogenous biotin exposure and a detection kit based on the labeled
streptavidin biotin (LSAB) method. Thereby, we also employed 3% hydrogen
peroxide(H2O2) for the inhibition of endogenous peroxidase activity and
incubated the tissue sections with the biotinylated secondary antibody at room
temperature (RT). We now add the immunohistochemical details that had led us to
this optimized procedure as they also bear a more general relevance when
demonstrating intracellular tissue antigens. Our most important result is that
endogenous peroxidase inhibition by 0.3% H2O2 coincided with an apparently
positive IDE staining in an investigated breast cancer specimen whereas
combining a block by 3% H2O2 with an incubation of the biotinylated secondary
antibody at RT, yet not at 37 degrees Celsius, revealed this specimen as almost
entirely IDE-negative. Our present data caution against three different
immunohistochemical pitfalls that might cause falsely positive results and
artifacts when using an LSAB- and peroxidase-based detection method: pressure
cooking for AR, insufficient quenching of endogenous peroxidases and heating of
tissue sections while incubating with biotinylated secondary antibodies.
| 2007-05-23 |
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