id
stringlengths 9
16
| submitter
stringlengths 4
52
⌀ | authors
stringlengths 4
9.62k
| title
stringlengths 4
343
| comments
stringlengths 1
693
⌀ | journal-ref
stringlengths 4
330
⌀ | doi
stringlengths 12
138
⌀ | report-no
stringlengths 2
231
⌀ | categories
stringlengths 8
111
| license
stringclasses 9
values | abstract
stringlengths 7
3.87k
| update_date
stringlengths 10
10
|
|---|---|---|---|---|---|---|---|---|---|---|---|
0706.0349 | Nabanita Dasgupta-Schubert | N. Dasgupta-Schubert (UMSNH), S. Alexander (SWU), L. Sommer (SWU), T.
Whelan (UTPA), R. Alfaro Cuevas Villanueva (UMSNH), M. E. Mendez Lopez
(UMSNH), M. W. Persans (UTPA) | The Light Quanta Modulated Physiological Response of Brassica Juncea
Seedlings Subjected to Ni(II) Stress | 9 pages, 7 figures, PDF file only. Based on a lecture presented by N.
Dasgupta-Schubert at the ISEB/ESEB/JSEB International Symposium on
Environmental Biotechnology in Leipzig, Germany, July 9-13, 2006 | Engineering in the Life Sciences, 7(3), 259-267 (2007) | null | null | q-bio.OT | null | This work is a study of the inter-relationship between parameters that
principally affect metal up-take in the plant. The relationships between the
concentration of metal in the growth medium, Cs, the concentration of metal
absorbed by the plant, Cp, and the total biomass achieved, M, all of which are
factors relevant to the efficiency of phytoremediation of the plant, have been
investigated via the macro-physiological response of Brassica juncea seedlings
to Ni(II) stress. The factorial growth experiments treated the Ni(II)
concentration in the agar gel and the diurnal light quanta (DLQ) as
independently variable parameters. Observations included the evidence of light
enhancement of Ni toxicity at the root as well as at the whole plant level, the
shoot mass index as a possible indicator of shoot metal sequestration in B.
juncea, the logarithmic variation of Cp with Cs and the power-law dependence of
M on Cp. The sum total of these observations indicate that for the metal
accumulator B. juncea with regard to its capacity to accumulate Ni, the overall
metabolic nature of the plant is important; neither rapid biomass increase nor
a high metal concentration capability favor the removal of high metal mass from
the medium, but rather the plant with the moderate photosynthetically driven
biomass growth and moderate metal concentrations demonstrated the ability to
remove the maximum mass of metal from the medium. The implications of these
observations in the context of the perceived need in phytoremediation
engineering to maximize Cp and M simultaneously in the same plant, are
discussed.
| 2007-06-05 |
0706.0406 | Kavita Jain | Kavita Jain | Evolutionary dynamics of the most populated genotype on rugged fitness
landscapes | Minor changes. To appear in Phys Rev E | Phys. Rev. E 76, 031922 (2007) | 10.1103/PhysRevE.76.031922 | null | q-bio.PE cond-mat.stat-mech | null | We consider an asexual population evolving on rugged fitness landscapes which
are defined on the multi-dimensional genotypic space and have many local
optima. We track the most populated genotype as it changes when the population
jumps from a fitness peak to a better one during the process of adaptation.
This is done using the dynamics of the shell model which is a simplified
version of the quasispecies model for infinite populations and standard
Wright-Fisher dynamics for large finite populations. We show that the
population fraction of a genotype obtained within the quasispecies model and
the shell model match for fit genotypes and at short times, but the dynamics of
the two models are identical for questions related to the most populated
genotype. We calculate exactly several properties of the jumps in infinite
populations some of which were obtained numerically in previous works. We also
present our preliminary simulation results for finite populations. In
particular, we measure the jump distribution in time and find that it decays as
$t^{-2}$ as in the quasispecies problem.
| 2009-11-13 |
0706.0418 | Oscar Sotolongo | O. Sotolongo-Grau, D. Rodriguez-Perez, J. A. Santos-Miranda, O.
Sotolongo-Costa, J. C. Antoranz | Immune System -- Tumor Efficiency Rate as a new Oncological Index for
Radiotherapy Treatment Optimization | 10 pages, 3 figures | null | null | null | q-bio.PE | null | A dynamical system model for tumor -- immune system interaction together with
a method to mimic radiation therapy are proposed. A large population of virtual
patients is simulated following an ideal radiation treatment. A characteristic
parameter, the Immune System -- Tumor Efficiency Rate (ISTER), is introduced.
ISTER dependence of treatment success and other features is studied.
Statistical results allow us to give a patient classification scheme.
Radiotherapy treatment biological effective dose (BED) is thus optimized based
on the patient physical condition, following the ALARA (As Low As Reasonably
Achievable) criterion.
| 2007-06-28 |
0706.0643 | Dietrich Stauffer | Dietrich Stauffer, Christian Schulze, Dieter W. Heermann | Superdiffusion in a Model for Diffusion in a Molecularly Crowded
Environment | 8 pages including 4 figures | null | null | null | q-bio.SC | null | We present a model for diffusion in a molecularly crowded environment. The
model consists of random barriers in percolation network. Random walks in the
presence of slowly moving barriers show normal diffusion for long times, but
anomalous diffusion at intermediate times. The effective exponents for square
distance versus time usually are below one at these intermediate times, but can
be also larger than one for high barrier concentrations. Thus we observe sub-
as well as super-diffusion in a crowded environment.
| 2007-06-06 |
0706.0648 | Angel (Anxo) Sanchez | Raul Jimenez, Haydee Lugo, Jose A. Cuesta, Angel Sanchez | Emergence and resilience of cooperation in the spatial Prisoner's
Dilemma via a reward mechanism | null | null | null | null | q-bio.PE math.ST nlin.AO physics.soc-ph stat.TH | null | We study the problem of the emergence of cooperation in the spatial
Prisoner's Dilemma. The pioneering work by Nowak and May showed that large
initial populations of cooperators can survive and sustain cooperation in a
square lattice with imitate-the-best evolutionary dynamics. We revisit this
problem in a cost-benefit formulation suitable for a number of biological
applications. We show that if a fixed-amount reward is established for
cooperators to share, a single cooperator can invade a population of defectors
and form structures that are resilient to re-invasion even if the reward
mechanism is turned off. We discuss analytically the case of the invasion by a
single cooperator and present agent-based simulations for small initial
fractions of cooperators. Large cooperation levels, in the sustainability
range, are found. In the conclusions we discuss possible applications of this
model as well as its connections with other mechanisms proposed to promote the
emergence of cooperation.
| 2007-06-06 |
0706.0683 | Jacek Miekisz | Jan Gomulkiewicz, Jacek Miekisz, and Stanislaw Miekisz | Ion transport through cell membrane channels | review paper, 21 pages | null | null | null | q-bio.SC | null | We discuss various models of ion transport through cell membrane channels.
Recent experimental data shows that sizes of ion channels are compared to those
of ions and that only few ions may be simultaneously in any single channel.
Theoretical description of ion transport in such channels should therefore take
into account interactions between ions and between ions and channel proteins.
This is not satisfied by macroscopic continuum models based on
Poisson-Nernst-Planck equations. More realistic descriptions of ion transport
are offered by microscopic Brownian and molecular dynamics. One should also
take into account a dynamical character of the channel structure. This is not
yet addressed in the literature
| 2007-06-06 |
0706.0760 | Jing Qin | Emma Y. Jin, Jing Qin and Christian M. Reidys | Neutral Networks of Sequence to Shape Maps | 24 pages,4 figures | null | null | null | q-bio.QM math-ph math.CO math.MP q-bio.BM | null | In this paper we present a novel framework for sequence to shape maps. These
combinatorial maps realize exponentially many shapes, and have preimages which
contain extended connected subgraphs of diameter n (neutral networks). We prove
that all basic properties of RNA folding maps also hold for combinatorial maps.
Our construction is as follows: suppose we are given a graph $H$ over the $\{1
>...,n\}$ and an alphabet of nucleotides together with a symmetric relation
$\mathcal{R}$, implied by base pairing rules. Then the shape of a sequence of
length n is the maximal H subgraph in which all pairs of nucleotides incident
to H-edges satisfy $\mathcal{R}$. Our main result is to prove the existence of
at least $\sqrt{2}^{n-1}$ shapes with extended neutral networks, i.e. shapes
that have a preimage with diameter $n$ and a connected component of size at
least $(\frac{1+\sqrt{5}}{2})^n+(\frac{1-\sqrt{5}}{2})^n$. Furthermore, we show
that there exists a certain subset of shapes which carries a natural graph
structure. In this graph any two shapes are connected by a path of shapes with
respective neutral networks of distance one. We finally discuss our results and
provide a comparison with RNA folding maps.
| 2009-09-29 |
0706.1017 | Yves-Henri Sanejouand | Brice Juanico, Yves-Henri Sanejouand, Francesco Piazza, Paolo de los
Rios | Discrete breathers in nonlinear network models of proteins | 4 pages, 5 figures. Minor changes | Physical review letters vol. 99, 238104 (2007) | 10.1103/PhysRevLett.99.238104 | null | q-bio.BM | null | We introduce a topology-based nonlinear network model of protein dynamics
with the aim of investigating the interplay of spatial disorder and
nonlinearity. We show that spontaneous localization of energy occurs
generically and is a site-dependent process. Localized modes of nonlinear
origin form spontaneously in the stiffest parts of the structure and display
site-dependent activation energies. Our results provide a straightforward way
for understanding the recently discovered link between protein local stiffness
and enzymatic activity. They strongly suggest that nonlinear phenomena may play
an important role in enzyme function, allowing for energy storage during the
catalytic process.
| 2011-11-10 |
0706.1089 | Xuezhao Bao | Xuezhao Bao and Ali Zhang | Geochemistry of U and Th and its Influence on the Origin and Evolution
of the Crust of Earth and the Biological Evolution | 18 pages, 3 figures, 2 tables. Language correction | ActaPetrolog.Mineral.17:160-172,1998 | null | null | physics.geo-ph astro-ph q-bio.PE | null | We have investigated the migration behaviors of uranium (U) and thorium (Th)
in Earth and other terrestrial planets. Theoretical models of U and Th
migration have been proposed. These models suggest that the unique features of
Earth are closely connected with its unique U and Th migration models and
distribution patterns. In the Earth, U and Th can combine with oxidative
volatile components and water, migrate up to the asthenosphere position to form
an enrichment zone (EZ) of U and Th first, and then migrate up further to the
crusts through magmatism and metamorphism. We emphasize that the formation of
an EZ of U, Th and other heat-producing elements is a prerequisite for the
formation of a plate tectonic system. The heat-producing elements, currently
mainly U and Th, in the EZ are also the energy sources that drive the formation
and evolution of the crust of Earth and create special granitic continental
crusts. In other terrestrial planets, including Mercury, Venus, and Mars, an EZ
can not be formed because of a lack of oxidative volatile components and water.
For this reason, a plate tectonic system can not been developed in these
planets. We also emphasize the influence of U and Th in EZ on the development
and evolution of life on Earth. We propose that since the Earth and planets
were born in a united solar system, there should be some common mechanisms to
create the similarities and differences between them. We have tried to develop
an integrated view to explain some problems in the tectonics of Earth and
evolution, bio-evolution, and planetary dynamics through U and Th geochemistry.
We believe that a comprehensive exploration on energy sources and their
evolution is a good way to build bridges between different disciplines of
science in order to better understand the Earth and planets.
| 2008-11-26 |
0706.1102 | Piotr Szymczak | P. Szymczak and Marek Cieplak | Influence of Hydrodynamic Interactions on Mechanical Unfolding of
Proteins | to be published in Journal of Physics: Condensed Matter | null | 10.1088/0953-8984/19/28/285224 | null | q-bio.BM | null | We incorporate hydrodynamic interactions in a structure-based model of
ubiquitin and demonstrate that the hydrodynamic coupling may reduce the peak
force when stretching the protein at constant speed, especially at larger
speeds. Hydrodynamic interactions are also shown to facilitate unfolding at
constant force and inhibit stretching by fluid flows.
| 2015-05-13 |
0706.1198 | Anirban Banerjee | Anirban Banerjee and J\"urgen Jost | Spectral plots and the representation and interpretation of biological
data | 15 pages, 7 figures | Theory in Biosciences, 126(1), 15-21, (2007) | 10.1007/s12064-007-0005-9 | null | q-bio.QM | null | It is basic question in biology and other fields to identify the char-
acteristic properties that on one hand are shared by structures from a
particular realm, like gene regulation, protein-protein interaction or neu- ral
networks or foodwebs, and that on the other hand distinguish them from other
structures. We introduce and apply a general method, based on the spectrum of
the normalized graph Laplacian, that yields repre- sentations, the spectral
plots, that allow us to find and visualize such properties systematically. We
present such visualizations for a wide range of biological networks and compare
them with those for networks derived from theoretical schemes. The differences
that we find are quite striking and suggest that the search for universal
properties of biological networks should be complemented by an understanding of
more specific features of biological organization principles at different
scales.
| 2012-10-19 |
0706.1293 | Natalia Kudryavtseva | N.P. Bondar, I.L. Kovalenko, D.F. Avgustinovich, N.N. Kudryavtseva | Influence of experimental context on the development of anhedonia in
male mice imposed to chronic social stress | 9 pages, 3 figures, 1 table | null | null | null | q-bio.OT q-bio.QM | null | Anhedonia is one of the key symptoms of depression in humans. Consumption of
1% sucrose solution supplemented with 0.2% vanillin was studied in two
experimental contexts in male mice living under chronic social stress induced
by daily experience of defeats in agonistic interactions and leading to
development of depression. In the first experiment, vanillin sucrose solution
was made available as an option of water during 10 days to mice living in group
home cages. Then the mice were subjected to social defeat stress and during
stress exposure they were provided with both vanillin sucrose solution and
water using a free two bottles choice paradigm. In the other experiment,
vanillin sucrose solution were first offered to mice after 8 days of exposure
to social defeat stress. Males familiar with vanillin sucrose solution showed
vanillin sucrose preference while experiencing defeat stress: consumption of
vanillin sucrose solution was about 70% of total liquid consumption. However,
the consumption of vanillin sucrose solution per gram of body weight in mice
imposed to social stress during 20 days was significantly lower than in control
males. In the second experiment, males after 8 days of social defeat stress
were found to consume significantly less vanillin sucrose solution as compared
with control males. On average during two weeks of measurements, vanillin
sucrose solution intake was less than 20% of total liquid consumption in males
with symptoms of depression and anxiety. Consumption per gram of body weight
also appeared to be significantly lower than in control group. Influence of the
experimental context on the development of anhedonia, which was measured by the
reduction in sucrose solution intake by chronically stressed male mice, has
been discussed.
| 2008-05-10 |
0706.1306 | Alain Destexhe | Zuzanna Piwkowska, Martin Pospischil, Romain Brette, Julia Sliwa,
Michelle Rudolph-Lilith, Thierry Bal and Alain Destexhe | Characterizing synaptic conductance fluctuations in cortical neurons and
their influence on spike generation | 9 figures, Journal of Neuroscience Methods (in press, 2008) | Journal of Neuroscience Methods 169: 302-322, 2008. | null | null | q-bio.NC | null | Cortical neurons are subject to sustained and irregular synaptic activity
which causes important fluctuations of the membrane potential (Vm). We review
here different methods to characterize this activity and its impact on spike
generation. The simplified, fluctuating point-conductance model of synaptic
activity provides the starting point of a variety of methods for the analysis
of intracellular Vm recordings. In this model, the synaptic excitatory and
inhibitory conductances are described by Gaussian-distributed stochastic
variables, or colored conductance noise. The matching of experimentally
recorded Vm distributions to an invertible theoretical expression derived from
the model allows the extraction of parameters characterizing the synaptic
conductance distributions. This analysis can be complemented by the matching of
experimental Vm power spectral densities (PSDs) to a theoretical template, even
though the unexpected scaling properties of experimental PSDs limit the
precision of this latter approach. Building on this stochastic characterization
of synaptic activity, we also propose methods to qualitatively and
quantitatively evaluate spike-triggered averages of synaptic time-courses
preceding spikes. This analysis points to an essential role for synaptic
conductance variance in determining spike times. The presented methods are
evaluated using controlled conductance injection in cortical neurons in vitro
with the dynamic-clamp technique. We review their applications to the analysis
of in vivo intracellular recordings in cat association cortex, which suggest a
predominant role for inhibition in determining both sub- and supra-threshold
dynamics of cortical neurons embedded in active networks.
| 2009-04-29 |
0706.1330 | Mensur Omerbashich | M. Omerbashich | Note on: Considering the Case for Biodiversity Cycles: Reexamining the
Evidence for Periodicity in the Fossil Record, by Lieberman and Melott, arXiv
preprint 0704.2896 | A one-page note. For the supplementary information for this note,
including the cited Reply and Errata, see math-ph/0608014 | null | null | null | q-bio.PE astro-ph physics.geo-ph | null | Lieberman and Melott built their recent arXiv preprint 0704.2896 on my
published paper and (a preprint of) a subsequent comment by Liebermans
associate Cornette. But had this group waited for the Cornette comment to
actually appear in print together with the expected Reply, they would have
learned that his comment exposes Cornettes confusion that likely was due to
journal misprint of my figure. Thus 0704.2896 is baseless. Despite receiving
the extended Reply with Errata, these authors still fail to recognize that
detrending of paleontological records-which they erroneously promote as a
must-is an arbitrary rather than a universal operation.
| 2007-06-12 |
0706.1355 | Martin Chaplin | Martin Chaplin | Water's Hydrogen Bond Strength | 20 pages | null | null | null | cond-mat.soft physics.bio-ph | null | Water is necessary both for the evolution of life and its continuance. It
possesses particular properties that cannot be found in other materials and
that are required for life-giving processes. These properties are brought about
by the hydrogen bonded environment particularly evident in liquid water. Each
liquid water molecule is involved in about four hydrogen bonds with strengths
considerably less than covalent bonds but considerably greater than the natural
thermal energy. These hydrogen bonds are roughly tetrahedrally arranged such
that when strongly formed the local clustering expands, decreasing the density.
Such low density structuring naturally occurs at low and supercooled
temperatures and gives rise to many physical and chemical properties that
evidence the particular uniqueness of liquid water. If aqueous hydrogen bonds
were actually somewhat stronger then water would behave similar to a glass,
whereas if they were weaker then water would be a gas and only exist as a
liquid at sub-zero temperatures. The overall conclusion of this investigation
is that water's hydrogen bond strength is poised centrally within a narrow
window of its suitability for life.
| 2007-06-13 |
0706.1374 | Jeffrey Buboltz | Jeffrey T. Buboltz, Charles Bwalya, Krystle Williams, Matthew Schutzer | High Resolution Mapping of Phase Behavior in a Ternary Lipid Mixture: Do
Lipid-Raft Phase Boundaries Depend on Sample-Prep Procedure? | 4 pages, 4 figures; submitted to Langmuir as a Letter | null | null | null | physics.bio-ph | null | For some time now, we have been using a FRET-based strategy to make
high-resolution studies of phase behavior in ternary lipid-raft membrane
mixtures. Our FRET experiments can be carried out on ordinary, polydisperse
multilamellar vesicle suspensions, so we are able to prepare our samples
according to a procedure that was designed specifically to guard against
artifactual phase separation. In some respects (i.e., the number and nature of
two-phase regions observed), our phase diagrams are consistent with previously
published reports. However, in other respects (i.e., overall size of
miscibility gaps, phase boundary locations and their dependence on temperature)
there are clear differences. Here we present FRET data taken in
DOPC/DPPC/Cholesterol mixtures at 25.0, 35.0 and 45.0oC. Comparisons between
our results and previously reported phase boundaries suggest that lipid-raft
mixtures may be particularly susceptible to demixing effects during sample
preparation.
| 2007-08-14 |
0706.1437 | Ido Kanter | Michael Rosenbluh, Yaara Aviad, Elad Cohen, Lev Khaykovich, Wolfgang
Kinzel, Evi Kopelowitz, Pinhas Yoskovits and Ido Kanter | Spiking Optical Patterns and Synchronization | null | null | 10.1103/PhysRevE.76.046207 | null | physics.optics physics.bio-ph | null | We analyze the time resolved spike statistics of a solitary and two mutually
interacting chaotic semiconductor lasers whose chaos is characterized by
apparently random, short intensity spikes. Repulsion between two successive
spikes is observed, resulting in a refractory period which is largest at laser
threshold. For time intervals between spikes greater than the refractory
period, the distribution of the intervals follows a Poisson distribution. The
spiking pattern is highly periodic over time windows corresponding to the
optical length of the external cavity, with a slow change of the spiking
pattern as time increases. When zero-lag synchronization between the two lasers
is established, the statistics of the nearly perfectly matched spikes are not
altered. The similarity of these features to those found in complex interacting
neural networks, suggests the use of laser systems as simpler physical models
for neural networks.
| 2009-11-13 |
0706.1492 | Adrien Lerbret | A. Lerbret, P. Bordat, F. Affouard, A. Hedoux, Y. Guinet, M. Descamps | How do trehalose, maltose and sucrose influence some structural and
dynamical properties of lysozyme ? An insight from Molecular Dynamics
simulations | null | null | null | null | physics.chem-ph cond-mat.soft q-bio.BM | null | The influence of three well-known disaccharides, namely trehalose, maltose
and sucrose, on some structural and dynamical properties of lysozyme has been
investigated by means of molecular dynamics computer simulations in the 37-60
wt % concentration range. The effects of sugars on the protein conformation are
found relatively weak, in agreement with the preferential hydration of
lysozyme. Conversely, sugars seem to increase significantly the relaxation
times of the protein. These effects are shown to be correlated to the
fractional solvent accessibilities of lysozyme residues and further support the
slaving of protein dynamics. Moreover, a significant increase in the relaxation
times of lysozyme, sugars and water molecules is observed within the studied
concentration range and may result from the percolation of the hydrogen-bond
network of sugar molecules. This percolation appears to be of primary
importance to explain the influence of sugars on the dynamical properties of
lysozyme and water.
| 2007-06-12 |
0706.1504 | George Bass Ph.D. | George E. Bass, Bernd Meibohm, James T. Dalton and Robert Sayre | Free Energy of Activation for the Comorosan Effect | 21 pages, 3 figures, 2 tables | null | null | null | q-bio.SC q-bio.BM | null | Initial reaction rate data for lactic dehydrogenase / pyruvate, lactic
dehydrogenase / lactate and malic dehydrogenase / malate enzyme reactions were
analyzed to obtain activation free energy changes of -329, -195 and -221
cal/mole, respectively, for rate increases associated with time-specific
irradiation of the crystalline substrates prior to dissolution and
incorporation in the reaction solutions. These energies, presumably, correspond
to conformational or vibrational changes in the reactants or the activated
complex. For the lactic dehydrogenase / pyruvate reaction, it is estimated that
on the order of 10% of the irradiation energy (546 nm, 400 footcandles for 5
seconds) would be required to produce the observed reaction rate increase if a
presumed photoproduct is consumed stoichiometrically with the pyruvate
substrate. These findings are consistent with the proposition that the observed
reaction rate enhancement involves photoproducts derived from oscillatory
atmospheric gas reactions at the crystalline enzyme substrate surfaces rather
than photo-excitations of the substrate molecules, per se.
| 2007-06-12 |
0706.1568 | Zhihui Wang | Zhihui Wang, Le Zhang, Jonathan Sagotsky, and Thomas S. Deisboeck | Simulating non-small cell lung cancer with a multiscale agent-based
model | 37 pages, 7 figures | null | null | null | q-bio.CB | null | Background The epidermal growth factor receptor (EGFR) is frequently
overexpressed in many cancers, including non-small cell lung cancer (NSCLC). In
silcio modeling is considered to be an increasingly promising tool to add
useful insights into the dynamics of the EGFR signal transduction pathway.
However, most of the previous modeling work focused on the molecular or the
cellular level only, neglecting the crucial feedback between these scales as
well as the interaction with the heterogeneous biochemical microenvironment.
Results We developed a multiscale model for investigating expansion dynamics
of NSCLC within a two-dimensional in silico microenvironment. At the molecular
level, a specific EGFR-ERK intracellular signal transduction pathway was
implemented. Dynamical alterations of these molecules were used to trigger
phenotypic changes at the cellular level. Examining the relationship between
extrinsic ligand concentrations, intrinsic molecular profiles and microscopic
patterns, the results confirmed that increasing the amount of available growth
factor leads to a spatially more aggressive cancer system. Moreover, for the
cell closest to nutrient abundance, a phase-transition emerges where a minimal
increase in extrinsic ligand abolishes the proliferative phenotype altogether.
Conclusions Our in silico results indicate that, in NSCLC, in the presence of
a strong extrinsic chemotactic stimulus, and depending on the cell's location,
downstream EGFR-ERK signaling may be processed more efficiently, thereby
yielding a migration-dominant cell phenotype and overall, an accelerated
spatio-temporal expansion rate.
| 2007-06-13 |
0706.1611 | Vladislav Volman | Vladislav Volman, Richard Gerkin, Pak-Ming Lau, Eshel Ben-Jacob, and
Guo-Qiang Bi | Calcium and synaptic dynamics underlying reverberatory activity in
neuronal networks | null | Physical Biology, vol.4, pp.91-103, 2007 | 10.1088/1478-3975/4/2/003 | null | q-bio.NC q-bio.PE | null | Persistent activity is postulated to drive neural network plasticity and
learning. To investigate its underlying cellular mechanisms, we developed a
biophysically tractable model that explains the emergence, sustenance, and
eventual termination of short-term persistent activity. Using the model, we
reproduced the features of reverberating activity that were observed in small
(50-100 cells) networks of cultured hippocampal neurons, such as the appearance
of polysynaptic current clusters, the typical inter-cluster intervals, the
typical duration of reverberation, and the response to changes in
extra-cellular ionic composition. The model relies on action
potential-triggered residual presynaptic calcium, which we suggest plays an
important role in sustaining reverberations. We show that reverberatory
activity is maintained by enhanced asynchronous transmitter release from
pre-synaptic terminals, which in itself depends on the dynamics of residual
presynaptic calcium. Hence, asynchronous release, rather than being a "synaptic
noise", can play an important role in network dynamics. Additionally, we found
that a fast timescale synaptic depression is responsible for oscillatory
network activation during reverberations, whereas the onset of a slow timescale
depression leads to the termination of reverberation. The simplicity of our
model enabled a number of predictions that were confirmed by additional
analyses of experimental manipulations.
| 2009-11-13 |
0706.1683 | V. Thanh Ngo | D.L. Hien, N.T. Nhan, V. Thanh Ngo, and N.A. Viet | Simple Combined Model for Nonlinear Excitations in DNA | 6 pages, 10 figures, submitted to Phys. Rev. E | Phys. Rev. E 76, 021921 (2007) | 10.1103/PhysRevE.76.021921 | null | physics.bio-ph physics.atm-clus | null | We propose a new simple model for DNA denaturation bases on the pendulum
model of Englander\cite{A1} and the microscopic model of Peyrard {\it et
al.},\cite{A3} so called "combined model". The main parameters of our model
are: the coupling constant $k$ along each strand, the mean stretching $y^\ast$
of the hydrogen bonds, the ratio of the damping constant and driven force
$\gamma/F$. We show that both the length $L$ of unpaired bases and the velocity
$v$ of kinks depend on not only the coupling constant $k$ but also the
temperature $T$. Our results are in good agreement with previous works.
| 2007-08-23 |
0706.1685 | V. Thanh Ngo | T. T. Nhan, N. T. Nhan, V. Thanh Ngo, N. A. Viet | Theory on Plasmon Modes of the Cell Membranes | 4 pages, 4 figures, submitted to Phys. Lett. A | null | null | null | physics.bio-ph physics.gen-ph | null | Considering the plasmon oscillation of each layer of the cell membranes as a
quasi-particle, we introduce a simple model for the membrane collective charge
excitations, take into account the surface effective potential of the
plasmon-plasmon interaction between two layers. By using the useful Bogoliubov
transformation method, we easily obtained the expressions of the frequencies of
plasmon oscillations as a function of wave-number $k$ and membrane thickness
$d$, magnitude of these frequencies is in the order of $\sqrt{kd}$. Our results
are in good agreement with ones obtained by E. Manousakis.
| 2007-06-13 |
0706.1748 | George Bass Ph.D. | George E. Bass | Crystal Irradiation Stimulation of Enzyme Reactivity: An Explanation | 41 pages, 4 figures, 9 tables | null | null | null | q-bio.SC q-bio.BM | null | In 1968, Sorin Comorosan first reported a phenomenon wherein irradiation of
the substrate of an enzyme reaction, in the crystalline state, for a specific
number of seconds could lead to an enhanced aqueous solution reaction rate for
the enzyme(up to 30%). Dependence on crystal irradiation time was found to be
oscillatory with a fixed period. The basis for this unusual phenomenon has
remained a mystery. Previously unreported experimental results are presented
which demonstrate, for the LDH / pyruvate reaction, that the identity of the
crystalline material irradiated is, largely, inconsequential. It is proposed
here that the irradiation procedure drives oscillatory reactions involving
atmospheric gases adsorbed on the crystals and that these photoproducts, or
related dark-reaction species, when dissolved, function as enzyme cofactors.
| 2007-06-13 |
0706.1754 | Ivan Rankenburg Ph.D. | Ivan C. Rankenburg, Veit Elser | Protein structure prediction by an iterative search method | 20 pages, 7 figures | null | null | null | q-bio.BM | null | We demonstrate a new algorithm for finding protein conformations that
minimize a non-bonded energy function. The new algorithm, called the difference
map, seeks to find an atomic configuration that is simultaneously in two
constraint spaces. The first constraint space is the space of atomic
configurations that have a valid peptide geometry, while the second is the
space of configurations that have a non-bonded energy below a given target.
These two constraint spaces are used to define a deterministic dynamical
system, whose fixed points produce atomic configurations in the intersection of
the two constraint spaces. The rate at which the difference map produces low
energy protein conformations is compared with that of a contemporary search
algorithm, parallel tempering. The results indicate the difference map finds
low energy protein conformations at a significantly higher rate then parallel
tempering.
| 2007-06-13 |
0706.1852 | Erik Aurell | Maria Werner, LiZhe Zhu, Erik Aurell | Cooperative action in eukaryotic gene regulation: physical properties of
a viral example | 7 pages, 6 figures, 1 table | null | 10.1103/PhysRevE.76.061909 | null | q-bio.SC cond-mat.soft q-bio.MN | null | The Epstein-Barr virus (EBV) infects more than 90% of the human population,
and is the cause of several both serious and mild diseases. It is a
tumorivirus, and has been widely studied as a model system for gene
(de)regulation in human. A central feature of the EBV life cycle is its ability
to persist in human B cells in states denoted latency I, II and III. In latency
III the host cell is driven to cell proliferation and hence expansion of the
viral population, but does not enter the lytic pathway, and no new virions are
produced, while the latency I state is almost completely dormant. In this paper
we study a physico-chemical model of the switch between latency I and latency
III in EBV. We show that the unusually large number of binding sites of two
competing transcription factors, one viral and one from the host, serves to
make the switch sharper (higher Hill coefficient), either by cooperative
binding between molecules of the same species when they bind, or by competition
between the two species if there is sufficient steric hindrance.
| 2009-11-13 |
0706.1905 | Hiroshi Fujisaki | Hiroshi Fujisaki, Kiyoshi Yagi, Kimihiko Hirao, John E. Straub | Quantum dynamics of N-methylacetamide studied by the vibrational
configuration interaction method | 13 pages, 4 figures, 2 tables, to be published in Chem. Phys. Lett | null | 10.1016/j.cplett.2007.06.067 | null | q-bio.BM | null | Vibrational energy transfer of the amide I mode of N-methylacetamide (NMA) is
studied theoretically using the vibrational configuration interaction method. A
quartic force field of NMA is constructed at the B3LYP/6-31G+(d) level of
theory and its accuarcy is checked by comparing the resulting anharmonic
frequencies with available theoretical and experimental values. Quantum
dynamics calculations for the amide I mode excitation clarify the dominant
energy transfer pathways, which sensitively depend on the anharmonic couplings
among vibrational modes. A ratio of the anharmonic coupling to the frequency
mismatch is employed to predict and interpret the dominant energy flow
pathways.
| 2009-11-13 |
0706.1908 | Jason Locasale W | Jason W. Locasale | Computational investigations into the orgins of 'short term' biochemical
memory in T cell activation | 11 pages, published July 18th 2007 | Locasale JW (2007) Computational Investigations into the Origins
of Short-Term Biochemical Memory in T cell Activation. PLoS ONE 2(7): e627 | 10.1371/journal.pone.0000627 | null | q-bio.MN physics.bio-ph q-bio.CB q-bio.SC | null | Recent studies have reported that T cells can integrate signals between
interrupted encounters with Antigen Presenting Cells (APCs) in such a way that
the process of signal integration exhibits a form of memory. Here, we carry out
a computational study using a simple mathematical model of T cell activation to
investigate the ramifications of interrupted T cell-APC contacts on signal
integration. We consider several mechanisms of how signal integration at these
time scales may be achieved and conclude that feedback control of immediate
early gene products (IEGs) appears to be a highly plausible mechanism that
allows for effective signal integration and cytokine production from multiple
exposures to APCs. Analysis of these computer simulations provides an
experimental roadmap involving several testable predictions.
| 2007-07-18 |
0706.1991 | Razvan Radulescu M.D. | Razvan Tudor Radulescu and Kai Kehe | Antiproliferative MCR peptides block physical interaction of insulin
with retinoblastoma protein (RB) in human lung cancer cells | 12 pages, 3 figures | null | null | null | q-bio.SC q-bio.BM | null | Fifteen years ago, a structural analysis of the hormone insulin and the
retinoblastoma tumor suppressor protein (RB) revealed that they may physically
interact with one another. Subsequently, an RB peptide corresponding to the
proposed RB binding site for insulin was found to recognize full-length insulin
in vitro. As part of efforts aimed at developing this RB peptide into an
anti-cancer drug, this molecule was chemically coupled to a cellular
internalization signal and termed "MCR peptide". Meanwhile, several such MCR
peptide variants have been demonstrated to restrain the proliferation of
different human cancer cells in vitro and in vivo. Moreover, one of the MCR
peptides coined MCR-10 was shown to be capable of interfering with the complex
formation between insulin and RB in HepG2 human hepatoma cells, as monitored by
immunofluorescence. This latter result indicating an in vivo association
between insulin and RB was confirmed by a follow-up study combining the methods
of co-immunoprecipitation and immunoblotting. Here, we provide evidence for the
existence of the insulin-RB complex in A549 human non-small cell lung cancer
cells. Specifically, we demonstrate this heterodimer by means of a magnetic
beads-based immunoprecipitation approach and equally show that this dimer can
be disrupted by MCR-4 or MCR-10 each of which is known to possess
antiproliferative properties, yet to a much lesser extent by a control peptide.
Thus, this investigation has yielded another important proof for the occurrence
of the insulin-RB dimer and, furthermore, its validity as a target for
antineoplastic MCR peptides.
| 2007-06-15 |
0706.1996 | Razvan Radulescu M.D. | Razvan Tudor Radulescu | Planet RB: a personal contribution to a proteomic map of human
retinoblastoma protein | 4 pages, 1 table | null | null | null | q-bio.BM q-bio.SC | null | As I compress on the canvas of a few pages here major results of my research
on the retinoblastoma tumor suppressor protein (RB) spreading over the past 15
years, an exciting picture emerges on this unique host molecule which surpasses
in its complexity even that of the most capable viral proteins known to date.
Accordingly, RB has the potential to bind not only growth-promoting proteins
such as insulin, but also to attach itself to calcium and oxygen, as well as to
be secreted into the extracellular environment. Moreover, RB may exert
proteolytic, antimicrobial and anti-aging activities. These condensed
structure-based insights on RB are the substance of a scientific revolution I
have initiated a long time ago, yet likely to gain even further speed in the
years to come, thus expanding both our understanding of life at the molecular
level and the possibilities for pharmacological modulation of fundamental
biological phenomena, particularly in oncology and gerontology.
| 2007-06-15 |
0706.2007 | Ilya M. Nemenman | Ilya Nemenman, G. Sean Escola, William S. Hlavacek, Pat J. Unkefer,
Clifford J. Unkefer, Michael E. Wall | Reconstruction of metabolic networks from high-throughput metabolite
profiling data: in silico analysis of red blood cell metabolism | 14 pages, 3 figures. Presented at the DIMACS Workshop on Dialogue on
Reverse Engineering Assessment and Methods (DREAM), Sep 2006 | Ann. N.Y. Acad. Sci. 1115: 102\^a?"115 (2007) | 10.1196/annals.1407.013 | LANL LA-UR-07-3646 | q-bio.MN | null | We investigate the ability of algorithms developed for reverse engineering of
transcriptional regulatory networks to reconstruct metabolic networks from
high-throughput metabolite profiling data. For this, we generate synthetic
metabolic profiles for benchmarking purposes based on a well-established model
for red blood cell metabolism. A variety of data sets is generated, accounting
for different properties of real metabolic networks, such as experimental
noise, metabolite correlations, and temporal dynamics. These data sets are made
available online. We apply ARACNE, a mainstream transcriptional networks
reverse engineering algorithm, to these data sets and observe performance
comparable to that obtained in the transcriptional domain, for which the
algorithm was originally designed.
| 2007-11-19 |
0706.2024 | Eben Kenah | Eben Kenah, Marc Lipsitch, James M. Robins | Generation interval contraction and epidemic data analysis | 20 pages, 5 figures; to appear in Mathematical Biosciences | Mathematical Biosciences 213(1): 71-79, May 2008 | 10.1016/j.mbs.2008.02.007 | null | q-bio.QM math.PR stat.AP | null | The generation interval is the time between the infection time of an infected
person and the infection time of his or her infector. Probability density
functions for generation intervals have been an important input for epidemic
models and epidemic data analysis. In this paper, we specify a general
stochastic SIR epidemic model and prove that the mean generation interval
decreases when susceptible persons are at risk of infectious contact from
multiple sources. The intuition behind this is that when a susceptible person
has multiple potential infectors, there is a ``race'' to infect him or her in
which only the first infectious contact leads to infection. In an epidemic, the
mean generation interval contracts as the prevalence of infection increases. We
call this global competition among potential infectors. When there is rapid
transmission within clusters of contacts, generation interval contraction can
be caused by a high local prevalence of infection even when the global
prevalence is low. We call this local competition among potential infectors.
Using simulations, we illustrate both types of competition.
Finally, we show that hazards of infectious contact can be used instead of
generation intervals to estimate the time course of the effective reproductive
number in an epidemic. This approach leads naturally to partial likelihoods for
epidemic data that are very similar to those that arise in survival analysis,
opening a promising avenue of methodological research in infectious disease
epidemiology.
| 2023-10-24 |
0706.2040 | Edoardo Airoldi | Edoardo M Airoldi | Getting started in probabilistic graphical models | 12 pages, 1 figure | Airoldi EM (2007) Getting started in probabilistic graphical
models. PLoS Comput Biol 3(12): e252 | 10.1371/journal.pcbi.0030252 | null | q-bio.QM cs.LG physics.soc-ph stat.ME stat.ML | null | Probabilistic graphical models (PGMs) have become a popular tool for
computational analysis of biological data in a variety of domains. But, what
exactly are they and how do they work? How can we use PGMs to discover patterns
that are biologically relevant? And to what extent can PGMs help us formulate
new hypotheses that are testable at the bench? This note sketches out some
answers and illustrates the main ideas behind the statistical approach to
biological pattern discovery.
| 2010-02-22 |
0706.2053 | Michael Sadovsky | Michael G.Sadovsky, Maria Yu.Senashova, Kristina A.Kourshakova | Simple Model of Complex Reflection Behaviour in Two-Species Community | 10 pages, no figures | null | null | null | q-bio.PE | null | The model of smart migration for two-species community is developed, where
the individuals implement reflexive strategy of spatial redistribution.
Simulations have been used to figure out the situations where reflexy gives an
advantage over a non-reflexive spatial behaviour, and vice versa.
| 2007-06-15 |
0706.2077 | Michael Sadovsky | Michael G.Sadovsky, Julia A.Putintzeva | Codon Usage Bias Measured Through Entropy Approach | 15 pages, 1 figure | null | null | null | q-bio.GN | null | Codon usage bias measure is defined through the mutual entropy calculation of
real codon frequency distribution against the quasi-equilibrium one. This
latter is defined in three manners: (1) the frequency of synonymous codons is
supposed to be equal (i.e., the arithmetic mean of their frequencies); (2) it
coincides to the frequency distribution of triplets; and, finally, (3) the
quasi-equilibrium frequency distribution is defined as the expected frequency
of codons derived from the dinucleotide frequency distribution. The measure of
bias in codon usage is calculated for 125 bacterial genomes.
| 2007-06-15 |
0706.2115 | Debashish Chowdhury | Tripti Tripathi and Debashish Chowdhury | RNA polymerase motors on DNA track: effects of traffic congestion on RNA
synthesis | This paper is superseded by the more detailed version arXiv:0708.1067 | null | null | null | physics.bio-ph q-bio.GN | null | RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA)
strand which is complementary to a single-stranded DNA template. From the
perspective of physicists, an RNAP is a molecular motor that utilizes chemical
energy input to move along the track formed by a ssDNA. In some circumstances,
which are described in this paper, a large number of RNAPs move simultaneously
along the same track. We refer to such collective movements of the RNAPs as
RNAP traffic because of the similarities between the collective dynamics of the
RNAPs on ssDNA track and that of vehicles in highway traffic. In this paper we
develop a theoretical model for RNAP traffic by incorporating the steric
interactions between RNAPs as well as the mechano-chemical cycle of individual
RNAPs during the elongation of the mRNA. By a combination of analytical and
numerical techniques, we calculate the rates of mRNA synthesis and the average
density profile of the RNAPs on the ssDNA track. We also suggest novel
experiments for testing our theoretical predictions.
| 2007-08-08 |
0706.2126 | Thierry Cachat | Eugene Asarin (LIAFA), Thierry Cachat (LIAFA), Alexander Seliverstov
(IITP), Tayssir Touili (LIAFA), Vassily Lyubetsky (IITP) | Attenuation Regulation as a Term Rewriting System | to appear | Proceedings of the Second International Conference on Algebraic
Biology (06/07/2007) 12 | null | null | q-bio.QM | null | The classical attenuation regulation of gene expression in bacteria is
considered. We propose to represent the secondary RNA structure in the leader
region of a gene or an operon by a term, and we give a probabilistic term
rewriting system modeling the whole process of such a regulation.
| 2007-06-15 |
0706.2214 | Tatiana Kuriabova | Tatiana Kuriabova, Alex Levine | Nanorheology of viscoelastic shells: Applications to viral capsids | 17 pages | null | 10.1103/PhysRevE.77.031921 | null | cond-mat.soft q-bio.SC | null | We study the microrheology of nanoparticle shells [Dinsmore et al. Science
298, 1006 (2002)] and viral capsids [Ivanovska et al. PNAS 101, 7600 (2004)] by
computing the mechanical response function and thermal fluctuation spectrum of
a viscoelastic spherical shell that is permeable to the surrounding solvent. We
determine analytically the damped dynamics of the shear, bend, and compression
modes of the shell coupled to the solvent both inside and outside the sphere in
the zero Reynolds number limit. We identify fundamental length and time scales
in the system, and compute the thermal correlation function of displacements of
antipodal points on the sphere and the mechanical response to pinching forces
applied at these points. We describe how such a frequency-dependent antipodal
correlation and/or response function, which should be measurable in new
AFM-based microrheology experiments, can probe the viscoelasticity of these
synthetic and biological shells constructed of nanoparticles.
| 2009-11-13 |
0706.2285 | Michele Caselle | L. Martignetti and M. Caselle | Universal power law behaviors in genomic sequences and evolutionary
models | 15 pages, 3 figures | null | 10.1103/PhysRevE.76.021902 | null | q-bio.GN cond-mat.other physics.bio-ph q-bio.QM | null | We study the length distribution of a particular class of DNA sequences known
as 5'UTR exons. These exons belong to the messanger RNA of protein coding
genes, but they are not coding (they are located upstream of the coding portion
of the mRNA) and are thus less constrained from an evolutionary point of view.
We show that both in mouse and in human these exons show a very clean power law
decay in their length distribution and suggest a simple evolutionary model
which may explain this finding. We conjecture that this power law behaviour
could indeed be a general feature of higher eukaryotes.
| 2009-11-13 |
0706.2328 | Ophir Flomenbom | Ophir Flomenbom, Robert J. Silbey | Unique mechanisms from finite two-state trajectories | null | E. Barkai, F. L. H. Brown, M. Orrit & H. Yang Eds. THEORY AND
EVALUATION OF SINGLE-MOLECULE SIGNALS, (October, 2008) | null | null | q-bio.QM cond-mat.other q-bio.OT | null | Single molecule data made of on and off events are ubiquitous. Famous
examples include enzyme turnover, probed via fluorescence, and opening and
closing of ion-channel, probed via the flux of ions. The data reflects the
dynamics in the underlying multi-substate on-off kinetic scheme (KS) of the
process, but the determination of the underlying KS is difficult, and sometimes
even impossible, due to the loss of information in the mapping of the
mutli-dimensional KS onto two dimensions. A way to deal with this problem
considers canonical (unique) forms. (Unique canonical form is constructed from
an infinitely long trajectory, but many KSs.) Here we introduce canonical forms
of reduced dimensions that can handle any KS (i.e. also KSs with symmetry and
irreversible transitions). We give the mapping of KSs into reduced dimensions
forms, which is based on topology of KSs, and the tools for extracting the
reduced dimensions form from finite data. The canonical forms of reduced
dimensions constitute a powerful tool in discriminating between KSs.
| 2010-08-16 |
0706.2353 | Supratim Sengupta | Supratim Sengupta, Andrew D. Rutenberg | Modeling partitioning of Min proteins between daughter cells after
septation in Escherichia coli | 17 pages, including 6 figures. Typo in captions of fig.2,5 corrected.
Version which appears in Physical Biology | Phys. Biol. 4 (2007) 145-153. | 10.1088/1478-3975/4/3/001 | null | q-bio.SC | null | Ongoing sub-cellular oscillation of Min proteins is required to block
minicelling in E. coli. Experimentally, Min oscillations are seen in newly
divided cells and no minicells are produced. In model Min systems many daughter
cells do not oscillate following septation because of unequal partitioning of
Min proteins between the daughter cells. Using the 3D model of Huang et al., we
investigate the septation process in detail to determine the cause of the
asymmetric partitioning of Min proteins between daughter cells. We find that
this partitioning problem arises at certain phases of the MinD and MinE
oscillations with respect to septal closure and it persists independently of
parameter variation. At most 85% of the daughter cells exhibit Min oscillation
following septation. Enhanced MinD binding at the static polar and dynamic
septal regions, consistent with cardiolipin domains, does not substantially
increase this fraction of oscillating daughters. We believe that this problem
will be shared among all existing Min models and discuss possible biological
mechanisms that may minimize partitioning errors of Min proteins following
septation.
| 2009-11-13 |
0706.2380 | Piotr Su{\l}kowski | Joanna I. Su{\l}kowska, Piotr Su{\l}kowski, Piotr Szymczak and Marek
Cieplak | Tightening of knots in proteins | 4 pages, 5 figures | Phys. Rev. Lett. 100, 058106 (2008) | 10.1103/PhysRevLett.100.058106 | null | q-bio.BM cond-mat.soft | null | We perform theoretical studies of stretching of 20 proteins with knots within
a coarse grained model. The knot's ends are found to jump to well defined
sequential locations that are associated with sharp turns whereas in
homopolymers they diffuse around and eventually slide off. The waiting times of
the jumps are increasingly stochastic as the temperature is raised. Larger
knots do not return to their native locations when a protein is released after
stretching.
| 2008-04-01 |
0706.2383 | Jason Locasale W | Jason W. Locasale | Allovalency revisited: an analysis of multisite phosphorylation and
substrate rebinding | 44 pages, 5 figures; accepted Journal of Chemical Physics | null | 10.1063/1.2841124 | null | q-bio.SC q-bio.MN | null | The utilization of multiple phosphorylation sites in regulating a biological
response is ubiquitous in cell signaling. If each site contributes an
additional, equivalent binding site, then one consequence of an increase in the
number of phosphorylations may be to increase the probability that, upon
disassociation, a ligand immediately rebinds to its receptor. How such effects
may influence cell signaling systems has been less studied. Here, a
self-consistent integral equation formalism for ligand rebinding, in
conjunction with Monte Carlo simulations, is employed to further investigate
the effects of multiple, equivalent binding sites on shaping biological
responses. Multiple regimes that characterize qualitatively different physics
due to the differential prevalence of rebinding effects are predicted.
Calculations suggest that when ligand rebinding contributes significantly to
the dose response, a purely allovalent model can influence the binding curves
nonlinearly. The model also predicts that ligand rebinding in itself appears
insufficient to generative a highly cooperative biological response.
| 2009-11-13 |
0706.2458 | Nikos Theodorakopoulos | Jalal Errami, Michel Peyrard and Nikos Theodorakopoulos | Modeling DNA beacons at the mesoscopic scale | 15 pages, 17 figures, submitted to Eur. J. Phys. E | Eur. Phys. J. E 23, 397-411 (2007) | 10.1140/epje/i2007-10200-x | null | cond-mat.soft cond-mat.stat-mech physics.bio-ph | null | We report model calculations on DNA single strands which describe the
equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is
at the level of single bases. Strand rigidity is described in terms of simple
polymer models; alternative calculations performed using the freely rotating
chain and the discrete Kratky-Porod models are reported. Stem formation is
modeled according to the Peyrard-Bishop-Dauxois Hamiltonian. The kinetics of
opening and closing is described in terms of a diffusion-controlled motion in
an effective free energy landscape. Melting profiles, dependence of melting
temperature on loop length, and kinetic time scales are in semiquantitative
agreement with experimental data obtained from fluorescent DNA beacons forming
poly(T) loops. Variation in strand rigidity is not sufficient to account for
the large activation enthalpy of closing and the strong loop length dependence
observed in hairpins forming poly(A) loops. Implications for modeling single
strands of DNA or RNA are discussed.
| 2007-10-01 |
0706.2516 | Bhalchandra Thatte | Bhalchandra D. Thatte and Mike Steel | Reconstructing pedigrees: a stochastic perspective | 20 pages, 3 figures | null | null | null | q-bio.PE | null | A pedigree is a directed graph that describes how individuals are related
through ancestry in a sexually-reproducing population. In this paper we explore
the question of whether one can reconstruct a pedigree by just observing
sequence data for present day individuals. This is motivated by the increasing
availability of genomic sequences, but in this paper we take a more theoretical
approach and consider what models of sequence evolution might allow pedigree
reconstruction (given sufficiently long sequences). Our results complement
recent work that showed that pedigree reconstruction may be fundamentally
impossible if one uses just the degrees of relatedness between different extant
individuals. We find that for certain stochastic processes, pedigrees can be
recovered up to isomorphism from sufficiently long sequences.
| 2007-06-19 |
0706.2535 | Rostyslav Vlokh O | R. Vlokh, I.Vlokh, O. Moroz, Yu. Nastishin, K. Dudok, T. Dudok, N.
Grinchishin, I. Nechiporenko, A. Hul | Optical Marking of Alcohol Induced Hemoglobin Modification | 34 pages, 5 figures, 4 tables. submitted to the Journal of Biomedical
Optics | null | null | null | physics.bio-ph physics.med-ph | null | It has been shown that conformational modifications of Hb induced by ethanol
consumption can be visualized in optical spectra studying oxygenation kinetics
of hemoglobin or mixing hemoglobin with Cibacron blue dye. Better dye affinity
of blood proteins extracted from alcoholised rats with respect to those from
non-alcoholised ones confirms that ethanol and its metabolites induce
structural pathologies in blood protein molecules. The detected changes for the
case of the posterity of intoxicated animals may be explained as a
post-translation modification, as well as a disturbance of the structure and
function of tissue cellular gene mechanism for the blood creation. It is
established that alcohol intake during first four months leads to the decrease
of fractional weight of oxyhemoglobin and to the increase of methemoglobin
amount in blood. Further alcohol consumption is accompanied by recovering of
the normal level of hemoglobin derivatives in blood. Normalization of the
fractional weight of hemoglobin derivatives in blood after durable (longer than
5-6 months) ethanol intoxication is most probably due to the activation of the
enzyme (acetaldehyde dehydrogenase) system, lowering the level of acetaldehydes
in blood.
| 2007-06-19 |
0706.2549 | Massimo Pica Ciamarra | Massimo Pica Ciamarra, Gennaro Miele, Leopoldo Milano, Mario Nicodemi,
Giancarlo Raiconi | A statistical mechanics approach to reverse engineering: sparsity and
biological priors on gene regulatory networks | null | null | null | null | q-bio.MN q-bio.QM | null | The important task of determining the connectivity of gene networks, and at a
more detailed level even the kind of interaction existing between genes, can
nowadays be tackled by microarraylike technologies. Yet, there is still a large
amount of unknowns with respect to the amount of data provided by a single
microarray experiment, and therefore reliable gene network retrieval procedures
must integrate all of the available biological knowledge, even if coming from
different sources and of different nature. In this paper we present a reverse
engineering algorithm able to reveal the underlying gene network by using
time-series dataset on gene expressions considering the system response to
different perturbations. The approach is able to determine the sparsity of the
gene network, and to take into account possible {\it a priori} biological
knowledge on it. The validity of the reverse engineering approach is
highlighted through the deduction of the topology of several {\it simulated}
gene networks, where we also discuss how the performance of the algorithm
improves enlarging the amount of data or if any a priori knowledge is
considered. We also apply the algorithm to experimental data on a nine gene
network in {\it Escherichia coli
| 2007-06-19 |
0706.2602 | Hugues Berry | Benoit Siri (INRIA Futurs), Mathias Quoy (ETIS), Bruno Delord (ANIM),
Bruno Cessac (INLN, INRIA Sophia Antipolis), Hugues Berry (INRIA Futurs) | Effects of Hebbian learning on the dynamics and structure of random
networks with inhibitory and excitatory neurons | null | null | null | null | q-bio.NC | null | The aim of the present paper is to study the effects of Hebbian learning in
random recurrent neural networks with biological connectivity, i.e. sparse
connections and separate populations of excitatory and inhibitory neurons. We
furthermore consider that the neuron dynamics may occur at a (shorter) time
scale than synaptic plasticity and consider the possibility of learning rules
with passive forgetting. We show that the application of such Hebbian learning
leads to drastic changes in the network dynamics and structure. In particular,
the learning rule contracts the norm of the weight matrix and yields a rapid
decay of the dynamics complexity and entropy. In other words, the network is
rewired by Hebbian learning into a new synaptic structure that emerges with
learning on the basis of the correlations that progressively build up between
neurons. We also observe that, within this emerging structure, the strongest
synapses organize as a small-world network. The second effect of the decay of
the weight matrix spectral radius consists in a rapid contraction of the
spectral radius of the Jacobian matrix. This drives the system through the
``edge of chaos'' where sensitivity to the input pattern is maximal. Taken
together, this scenario is remarkably predicted by theoretical arguments
derived from dynamical systems and graph theory.
| 2007-06-19 |
0706.2770 | Yohan Payan | Nicolas Vuillerme (TIMC - IMAG), Nicolas Pinsault (TIMC - IMAG),
Matthieu Boisgontier (TIMC - IMAG), Olivier Chenu (TIMC - IMAG), Jacques
Demongeot (TIMC - IMAG), Yohan Payan (TIMC - IMAG) | Inter-individual variability in sensory weighting of a plantar
pressure-based, tongue-placed tactile biofeedback for controlling posture | null | Neuroscience Letters 431 (2007) 173 - 177 | 10.1016/j.neulet.2007.03.076 | null | physics.med-ph q-bio.NC | null | The purpose of the present experiment was to investigate whether the sensory
weighting of a plantar pressure-based, tongue-placed tactile biofeedback for
controlling posture could be subject to inter-individual variability. To
achieve this goal, 60 young healthy adults were asked to stand as immobile as
possible with their eyes closed in two conditions of No-biofeedback and
Biofeedback. Centre of foot pressure (CoP) displacements were recorded using a
force platform. Overall, results showed reduced CoP displacements in the
Biofeedback relative to the No-biofeedback condition, evidencing the ability of
the central nervous system to efficiently integrate an artificial
plantar-based, tongue-placed tactile biofeedback for controlling posture during
quiet standing. Results further showed a significant positive correlation
between the CoP displacements measured in the No-biofeedback condition and the
decrease in the CoP displacements induced by the use of the biofeedback. In
other words, the degree of postural stabilization appeared to depend on each
subject's balance control capabilities, the biofeedback yielding a greater
stabilizing effect in subjects exhibiting the largest CoP displacements when
standing in the No-biofeedback condition. On the whole, by evidencing a
significant inter-individual variability in sensory weighting of an additional
tactile information related to foot sole pressure distribution for controlling
posture, the present findings underscore the need and the necessity to address
the issue of inter-individual variability in the field of neuroscience.
| 2007-06-20 |
0706.2808 | Christina Goldschmidt | Anne-Laure Basdevant and Christina Goldschmidt | Asymptotics of the allele frequency spectrum associated with the
Bolthausen-Sznitman coalescent | 26 pages, 1 figure | null | null | null | math.PR math.CO q-bio.PE | null | We work in the context of the infinitely many alleles model. The allelic
partition associated with a coalescent process started from n individuals is
obtained by placing mutations along the skeleton of the coalescent tree; for
each individual, we trace back to the most recent mutation affecting it and
group together individuals whose most recent mutations are the same. The number
of blocks of each of the different possible sizes in this partition is the
allele frequency spectrum. The celebrated Ewens sampling formula gives precise
probabilities for the allele frequency spectrum associated with Kingman's
coalescent. This (and the degenerate star-shaped coalescent) are the only
Lambda coalescents for which explicit probabilities are known, although they
are known to satisfy a recursion due to Moehle. Recently, Berestycki,
Berestycki and Schweinsberg have proved asymptotic results for the allele
frequency spectra of the Beta(2-alpha,alpha) coalescents with alpha in (1,2).
In this paper, we prove full asymptotics for the case of the
Bolthausen-Sznitman coalescent.
| 2007-06-25 |
0706.2818 | Alberto Imparato | A. Imparato, A. Pelizzola, M. Zamparo | Protein mechanical unfolding: a model with binary variables | null | J. Chem. Phys. 127, 145105 (2007) | 10.1063/1.2776271 | null | cond-mat.soft q-bio.BM | null | A simple lattice model, recently introduced as a generalization of the
Wako--Sait\^o model of protein folding, is used to investigate the properties
of widely studied molecules under external forces. The equilibrium properties
of the model proteins, together with their energy landscape, are studied on the
basis of the exact solution of the model. Afterwards, the kinetic response of
the molecules to a force is considered, discussing both force clamp and dynamic
loading protocols and showing that theoretical expectations are verified. The
kinetic parameters characterizing the protein unfolding are evaluated by using
computer simulations and agree nicely with experimental results, when these are
available. Finally, the extended Jarzynski equality is exploited to investigate
the possibility of reconstructing the free energy landscape of proteins with
pulling experiments.
| 2007-10-16 |
0706.2867 | Kaushik Majumdar | Kaushik Majumdar | Outline of a novel architecture for cortical computation | 21 pages, four figures | null | 10.1007/s11571-007-9034-9 | null | q-bio.NC q-bio.QM | null | In this paper a novel architecture for cortical computation has been
proposed. This architecture is composed of computing paths consisting of
neurons and synapses only. These paths have been decomposed into lateral,
longitudinal and vertical components. Cortical computation has then been
decomposed into lateral computation (LaC), longitudinal computation (LoC) and
vertical computation (VeC). It has been shown that various loop structures in
the cortical circuit play important roles in cortical computation as well as in
memory storage and retrieval, keeping in conformity with the molecular basis of
short and long term memory. A new learning scheme for the brain has also been
proposed and how it is implemented within the proposed architecture has been
explained. A number of mathematical results about the architecture have been
proposed, many of which without proof.
| 2007-12-12 |
0706.2980 | Allon Klein | Allon M. Klein, David P. Doupe, Philip H. Jones, and Benjamin D.
Simons | Kinetics of cell division in epidermal maintenance | null | null | 10.1103/PhysRevE.76.021910 | null | physics.bio-ph cond-mat.stat-mech q-bio.CB | null | The rules governing cell division and differentiation are central to
understanding the mechanisms of development, aging and cancer. By utilising
inducible genetic labelling, recent studies have shown that the clonal
population in transgenic mouse epidermis can be tracked in vivo. Drawing on
these results, we explain how clonal fate data may be used to infer the rules
of cell division and differentiation underlying the maintenance of adult murine
tail-skin. We show that the rates of cell division and differentiation may be
evaluated by considering the long-time and short-time clone fate data, and that
the data is consistent with cells dividing independently rather than
synchronously. Motivated by these findings, we consider a mechanism for cancer
onset based closely on the model for normal adult skin. By analysing the
expected changes to clonal fate in cancer emerging from a simple two-stage
mutation, we propose that clonal fate data may provide a novel method for
studying the earliest stages of the disease.
| 2009-11-13 |
0706.3067 | Evgeni Gabev E | E. E. Gabev (1), Evgeni B. Gabev (2), E. E. Gabev Jr. (1), M. V.
Bogoeva (3) ((1) Institute of Experimental Pathology and Parasitology,
Bulgarian Academy of Sciences (2) Medical University, Sofia, Bulgaria, (3)
Institute of Zoology, Bulgarian Academy of Sciences, Sofia, Bulgaria) | Fitting analysis provides further evidence for eradication of hiv/aids
infection under combined liposome drug delivery treatment | 3 pages, 1 figure. Available at: http://www.geocities.com/hivaidsbg/ | Drug Delivery Systems and Sciences (UK). 2003, volume 3, No 2, pp.
49-51 | null | null | q-bio.TO | null | It is now evident that the commonly accepted strategy for treatment of
HIV/AIDS by highly active antiretroviral therapy (HAART) will not lead to
eradication of HIV in a reasonable time. This is straightforward from the
typical exponential viral load decay upon treatment revealing initial
considerable but incomplete reduction of plasma HIV RNA with subsequent low
level HIV persistence even in patients on effective antiretroviral therapy.
Here we show that the viral load follows a simple zero trend linear regression
line under different treatment approach recently proposed by us. This
unambiguously indicates a whole body HIV eradication in reasonable time.
| 2007-06-22 |
0706.3090 | Sergei Mukhin I | I.N. Krivonos and S.I. Mukhin | Flexible-to-semiflexible chain crossover on the pressure-area isotherm
of lipid bilayer | 31 pages; 7 figures; submitted to JETP | null | 10.1007/s11447-008-1011-6 | null | q-bio.QM q-bio.BM | null | We found theoretically that competition between ~Kq^4 and ~Qq^2 terms in the
Fourier transformed conformational energy of a single lipid chain, in
combination with inter-chain entropic repulsion in the hydrophobic part of the
lipid (bi)layer, may cause a crossover on the bilayer pressure-area isotherm
P(A)~(A-A_0)^{-n}. The crossover manifests itself in the transition from n=5/3
to n=3. Our microscopic model represents a single lipid molecule as a worm-like
chain with finite irreducible cross-section area A_0, flexural rigidity K and
stretching modulus Q in a parabolic potential with self-consistent curvature
B(A) formed by entropic interactions between hydrocarbon chains in the lipid
layer. The crossover area per lipid A* obeys relation Q^2/(KB(A*))~1 . We
predict a peculiar possibility to deduce effective elastic moduli K and Q of
the individual hydrocarbon chain from the analysis of the isotherm possessing
such crossover. Also calculated is crossover-related behavior of the area
compressibility modulus K_a, equilibrium area per lipid A_t, and chain order
parameter S.
| 2009-11-13 |
0706.3101 | Dietrich Stauffer | D. Stauffer | The Penna Model of Biological Aging | 16-page invited review submitted to Bioinformatics and Biology
Insights | null | null | null | q-bio.PE | null | This review deals with computer simulation of biological ageing, particularly
with the Penna model of 1995.
| 2007-06-22 |
0706.3137 | Emma Jin | Emma Y. Jin and Christian M. Reidys | Asymptotic Enumeration of RNA Structures with Pseudoknots | 22 pages, 7 figures | null | null | null | q-bio.BM math.CO | null | In this paper we present the asymptotic enumeration of RNA structures with
pseudoknots. We develop a general framework for the computation of exponential
growth rate and the sub exponential factors for $k$-noncrossing RNA structures.
Our results are based on the generating function for the number of
$k$-noncrossing RNA pseudoknot structures, ${\sf S}_k(n)$, derived in
\cite{Reidys:07pseu}, where $k-1$ denotes the maximal size of sets of mutually
intersecting bonds. We prove a functional equation for the generating function
$\sum_{n\ge 0}{\sf S}_k(n)z^n$ and obtain for $k=2$ and $k=3$ the analytic
continuation and singular expansions, respectively. It is implicit in our
results that for arbitrary $k$ singular expansions exist and via transfer
theorems of analytic combinatorics we obtain asymptotic expression for the
coefficients. We explicitly derive the asymptotic expressions for 2- and
3-noncrossing RNA structures. Our main result is the derivation of the formula
${\sf S}_3(n) \sim \frac{10.4724\cdot 4!}{n(n-1)...(n-4)}
(\frac{5+\sqrt{21}}{2})^n$.
| 2009-09-29 |
0706.3177 | Laurent Perrinet | Laurent Perrinet (INT, INCM) | Role of homeostasis in learning sparse representations | null | Neural Computation, Massachusetts Institute of Technology Press
(MIT Press), 2010, 22 (7), pp.1812-36 | 10.1162/neco.2010.05-08-795 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neurons in the input layer of primary visual cortex in primates develop
edge-like receptive fields. One approach to understanding the emergence of this
response is to state that neural activity has to efficiently represent sensory
data with respect to the statistics of natural scenes. Furthermore, it is
believed that such an efficient coding is achieved using a competition across
neurons so as to generate a sparse representation, that is, where a relatively
small number of neurons are simultaneously active. Indeed, different models of
sparse coding, coupled with Hebbian learning and homeostasis, have been
proposed that successfully match the observed emergent response. However, the
specific role of homeostasis in learning such sparse representations is still
largely unknown. By quantitatively assessing the efficiency of the neural
representation during learning, we derive a cooperative homeostasis mechanism
that optimally tunes the competition between neurons within the sparse coding
algorithm. We apply this homeostasis while learning small patches taken from
natural images and compare its efficiency with state-of-the-art algorithms.
Results show that while different sparse coding algorithms give similar coding
results, the homeostasis provides an optimal balance for the representation of
natural images within the population of neurons. Competition in sparse coding
is optimized when it is fair. By contributing to optimizing statistical
competition across neurons, homeostasis is crucial in providing a more
efficient solution to the emergence of independent components.
| 2016-12-09 |
0706.3195 | George Bass Ph.D. | George E. Bass | Genetic Transferability of Anomalous Irradiation Alterations of
Antibiotic Activity | 17 pages, 3 figures | null | null | null | q-bio.BM | null | It previously has been discovered that visible light irradiation of
crystalline substrates can lead to enhancement of subsequent enzymatic reaction
rates as sharply peaked oscillatory functions of irradiation time. The
particular activating irradiation times can vary with source of a given enzyme
and thus, presumably, its molecular structure. The experiments reported here
demonstrate that the potential for this anomalous enzyme reaction rate
enhancement can be transferred from one bacterial species to another coincident
with transfer of the genetic determinant for the relevant enzyme. In
particular, the effect of crystal-irradiated chloramphenicol on growth of
bacterial strains in which a transferable R-factor DNA plasmid coding for
chloramphenicol resistance was or was not present (S. panama R+, E. coli R+,
and E. coli R-) was determined. Chloramphenicol samples irradiated 10, 35 and
60 sec produced increased growth rates (diminished inhibition) for the
resistant S. panama and E. coli strains, while having no such effect on growth
rate of the sensitive E. coli strain. Consistent with past findings,
chloramphenicol samples irradiated 5, 30 and 55 sec produced decreased growth
rates (increased inhibition) for all three strains.
| 2007-06-22 |
0706.3211 | Ophir Flomenbom | O. Flomenbom and R. J. Silbey | Path probability density functions for semi-Markovian random walks | null | Phys. Rev. E 76, 041101 (2007) | 10.1103/PhysRevE.76.041101 | null | math-ph math.MP physics.bio-ph q-bio.OT | null | In random walks, the path representation of the Green's function is an
infinite sum over the length of path probability density functions (PDFs). Here
we derive and solve, in Laplace space, the recursion relation for the n order
path PDF for any arbitrarily inhomogeneous semi-Markovian random walk in a
one-dimensional (1D) chain of L states. The recursion relation relates the n
order path PDF to L/2 (round towards zero for an odd L) shorter path PDFs, and
has n independent coefficients that obey a universal formula. The z transform
of the recursion relation straightforwardly gives the generating function for
path PDFs, from which we obtain the Green's function of the random walk, and
derive an explicit expression for any path PDF of the random walk. These
expressions give the most detailed description of arbitrarily inhomogeneous
semi-Markovian random walks in 1D.
| 2019-08-19 |
0706.3234 | Edgar Delgado-Eckert MS | Edgar Delgado-Eckert | Reverse engineering time discrete finite dynamical systems: A feasible
undertaking? | Submitted to journal, currently under review | PLoS ONE, 4(3), 2009 | 10.1371/journal.pone.0004939. | null | q-bio.QM math.DS q-bio.MN | null | With the advent of high-throughput profiling methods, interest in reverse
engineering the structure and dynamics of biochemical networks is high.
Recently an algorithm for reverse engineering of biochemical networks was
developed by Laubenbacher and Stigler. It is a top-down approach using time
discrete dynamical systems. One of its key steps includes the choice of a term
order. The aim of this paper is to identify minimal requirements on data sets
to be used with this algorithm and to characterize optimal data sets. We found
minimal requirements on a data set based on how many terms the functions to be
reverse engineered display. Furthermore, we identified optimal data sets, which
we characterized using a geometric property called "general position".
Moreover, we developed a constructive method to generate optimal data sets,
provided a codimensional condition is fulfilled. In addition, we present a
generalization of their algorithm that does not depend on the choice of a term
order. For this method we derived a formula for the probability of finding the
correct model, provided the data set used is optimal. We analyzed the
asymptotic behavior of the probability formula for a growing number of
variables n (i.e. interacting chemicals). Unfortunately, this formula converges
to zero as fast as r^(q^n), where q is a natural number and 0<r<1. Therefore,
even if an optimal data set is used and the restrictions in using term orders
are overcome, the reverse engineering problem remains unfeasible, unless
prodigious amounts of data are available. Such large data sets are
experimentally impossible to generate with today's technologies.
| 2010-01-18 |
0706.3427 | Dmitri Starodub | D. Starodub (1), P. Rez (1), G. Hembree (1), M. Howells (2), D.
Shapiro (2), H. N. Chapman (3), P. Fromme (1), K. Schmidt (1), U. Weierstall
(1), R. B. Doak (1) and J. C. H. Spence (1) ((1) Arizona State University,
(2) Lawrence Berkeley National Laboratory, (3) Lawrence Livermore National
Laboratory) | Dose, exposure time, and resolution in Serial X-ray Crystallography | 19 pages, 7 figures, 1 table | null | null | null | physics.optics physics.bio-ph | null | The resolution of X-ray diffraction microscopy is limited by the maximum dose
that can be delivered prior to sample damage. In the proposed Serial
Crystallography method, the damage problem is addressed by distributing the
total dose over many identical hydrated macromolecules running continuously in
a single-file train across a continuous X-ray beam, and resolution is then
limited only by the available molecular and X-ray fluxes and molecular
alignment. Orientation of the diffracting molecules is achieved by laser
alignment. We evaluate the incident X-ray fluence (energy/area) required to
obtain a given resolution from (1) an analytical model, giving the count rate
at the maximum scattering angle for a model protein, (2) explicit simulation of
diffraction patterns for a GroEL-GroES protein complex, and (3) the frequency
cut off of the transfer function following iterative solution of the phase
problem, and reconstruction of an electron density map in the projection
approximation. These calculations include counting shot noise and multiple
starts of the phasing algorithm. The results indicate counting time and the
number of proteins needed within the beam at any instant for a given resolution
and X-ray flux. We confirm an inverse fourth power dependence of exposure time
on resolution, with important implications for all coherent X-ray imaging. We
find that multiple single-file protein beams will be needed for sub-nanometer
resolution on current third generation synchrotrons, but not on fourth
generation designs, where reconstruction of secondary protein structure at a
resolution of 0.7 nm should be possible with short exposures.
| 2007-06-26 |
0706.3477 | Robbe Wunschiers | Robbe Wunschiers and Martin Vellguth | OrfMapper: A Web-Based Application for Visualizing Gene Clusters on
Metabolic Pathway Maps | 5 pages, 1 figure | null | null | null | q-bio.GN | null | Computational analyses of, e.g., genomic, proteomic, or metabolomic data,
commonly result in one or more sets of candidate genes, proteins, or enzymes.
These sets are often the outcome of clustering algorithms. Subsequently, it has
to be tested if, e.g., the candidate gene-products are members of known
metabolic processes. With OrfMapper we provide a powerful but easy-to-use,
web-based database application, that supports such analyses. All services
provided by OrfMapper are freely available at http://www.orfmapper.com
| 2007-06-26 |
0706.3533 | Sunghwan Jung | Sunghwan Jung, Kathleen Mareck, Lisa Fauci, and Michael J. Shelley | Rotational dynamics of a superhelix towed in a Stokes fluid | null | null | 10.1063/1.2800287 | null | physics.flu-dyn physics.bio-ph | null | Motivated by the intriguing motility of spirochetes (helically-shaped
bacteria that screw through viscous fluids due to the action of internal
periplasmic flagella), we examine the fundamental fluid dynamics of
superhelices translating and rotating in a Stokes fluid. A superhelical
structure may be thought of as a helix whose axial centerline is not straight,
but also a helix. We examine the particular case where these two superimposed
helices have different handedness, and employ a combination of experimental,
analytic, and computational methods to determine the rotational velocity of
superhelical bodies being towed through a very viscous fluid. We find that the
direction and rate of the rotation of the body is a result of competition
between the two superimposed helices; for small axial helix amplitude, the body
dynamics is controlled by the short-pitched helix, while there is a cross-over
at larger amplitude to control by the axial helix. We find far better, and
excellent, agreement of our experimental results with numerical computations
based upon the method of Regularized Stokeslets than upon the predictions of
classical resistive force theory.
| 2009-11-13 |
0706.3589 | Janos Locsei | J. T. Locsei | Persistence of direction increases the drift velocity of run and tumble
chemotaxis | 17 pages, 5 figures | J. Math. Biol. 55, 2007, 41-60 | 10.1007/s00285-007-0080-z | null | q-bio.QM | null | Escherichia coli is a motile bacterium that moves up a chemoattractant
gradient by performing a biased random walk composed of alternating runs and
tumbles. Previous models of run and tumble chemotaxis neglect one or more
features of the motion, namely (i) a cell cannot directly detect a
chemoattractant gradient but rather makes temporal comparisons of
chemoattractant concentration, (ii) rather than being entirely random, tumbles
exhibit persistence of direction, meaning that the new direction after a tumble
is more likely to be in the forward hemisphere, and (iii) rotational Brownian
motion makes it impossible for an E. coli cell to swim in a straight line
during a run. This paper presents an analytic calculation of the chemotactic
drift velocity taking account of (i), (ii) and (iii), for weak chemotaxis. The
analytic results are verified by Monte Carlo simulation. The results reveal a
synergy between temporal comparisons and persistence that enhances the drift
velocity, while rotational Brownian motion reduces the drift velocity.
| 2007-06-26 |
0706.3603 | Pierre-Henri Chavanis | Pierre-Henri Chavanis | Critical mass of bacterial populations and critical temperature of
self-gravitating Brownian particles in two dimensions | In press | Physica A, 384, 392 (2007) | 10.1016/j.physa.2007.03.056 | null | physics.bio-ph q-bio.CB | null | We show that the critical mass M_c=8\pi of bacterial populations in two
dimensions in the chemotactic problem is the counterpart of the critical
temperature T_c=GMm/4k_B of self-gravitating Brownian particles in
two-dimensional gravity. We obtain these critical values by using the Virial
theorem or by considering stationary solutions of the Keller-Segel model and
Smoluchowski-Poisson system. We also consider the case of one dimensional
systems and develop the connection with the Burgers equation. Finally, we
discuss the evolution of the system as a function of M or T in bounded and
unbounded domains in dimensions d=1, 2 and 3 and show the specificities of each
dimension. This paper aims to point out the numerous analogies between
bacterial populations, self-gravitating Brownian particles and, occasionally,
two-dimensional vortices.
| 2009-11-13 |
0706.3647 | Vittoria Colizza | Vittoria Colizza, Alessandro Vespignani | Epidemic modeling in metapopulation systems with heterogeneous coupling
pattern: theory and simulations | 18 pages, 8 figures, minor corrections, inclusion of subleading terms | Journal of Theoretical Biology 251, 450-467 (2008) | null | null | q-bio.PE physics.soc-ph | null | The spatial structure of populations is a key element in the understanding of
the large scale spreading of epidemics. Motivated by the recent empirical
evidence on the heterogeneous properties of transportation and commuting
patterns among urban areas, we present a thorough analysis of the behavior of
infectious diseases in metapopulation models characterized by heterogeneous
connectivity and mobility patterns. We derive the basic reaction-diffusion
equation describing the metapopulation system at the mechanistic level and
derive an early stage dynamics approximation for the subpopulation invasion
dynamics. The analytical description uses degree block variables that allows us
to take into account arbitrary degree distribution of the metapopulation
network. We show that along with the usual single population epidemic threshold
the metapopulation network exhibits a global threshold for the subpopulation
invasion. We find an explicit analytic expression for the invasion threshold
that determines the minimum number of individuals traveling among
subpopulations in order to have the infection of a macroscopic number of
subpopulations. The invasion threshold is a function of factors such as the
basic reproductive number, the infectious period and the mobility process and
it is found to decrease for increasing network heterogeneity. We provide
extensive mechanistic numerical Monte Carlo simulations that recover the
analytical finding in a wide range of metapopulation network connectivity
patterns. The results can be useful in the understanding of recent data driven
computational approaches to disease spreading in large transportation networks
and the effect of containment measures such as travel restrictions.
| 2008-03-19 |
0706.3652 | Eric Lauga | Eric Lauga | Continuous breakdown of Purcell's scallop theorem with inertia | 6 pages, 1 figure | Phys. Fluids 19, 061703, 2007 | 10.1063/1.2738609 | null | cond-mat.soft physics.bio-ph physics.flu-dyn | null | Purcell's scallop theorem defines the type of motions of a solid body -
reciprocal motions - which cannot propel the body in a viscous fluid with zero
Reynolds number. For example, the flapping of a wing is reciprocal and, as was
recently shown, can lead to directed motion only if its frequency Reynolds
number, Re_f, is above a critical value of order one. Using elementary
examples, we show the existence of oscillatory reciprocal motions which are
effective for all arbitrarily small values of the frequency Reynolds number and
induce net velocities scaling as (Re_f)^\alpha (alpha > 0). This demonstrates a
continuous breakdown of the scallop theorem with inertia.
| 2008-10-02 |
0706.3676 | Marcin Molski | Marcin Molski and Jerzy Konarski | On the Gompertzian dynamics of growth and self-organization | null | null | null | null | q-bio.OT q-bio.QM | null | Comment on the Waliszewski's article "A principle of fractal-sto-chastic
dualism and Gompertzian dynamics of growth and self-organization" (BioSystems
82 (2005)61-73) is presented. It has been proved that the main idea of this
work that Gompertzian dynamics is governed by the Schr\"{o}dinger-like equation
including anharmonic Morse potential has been already introduced by Molski and
Konarski in 2003. Some inconsistencies and mathematical errors in the
Waliszewski's model are also pointed out.
| 2007-06-26 |
0706.3678 | Ioan Kosztin | Cyrille Norotte, Francoise Marga, Adrian Neagu, Ioan Kosztin and Gabor
Forgacs (University of Missouri - Columbia) | Experimental confirmation of tissue liquidity based on the exact
solution of the Laplace equation | 4 pages, 3 figures, submitted to Phys. Rev. Lett | null | 10.1209/0295-5075/81/46003 | null | physics.bio-ph physics.flu-dyn q-bio.TO | null | The notion of tissue surface tension has provided a physical understanding of
morphogenetic phenomena such as tissue spreading or cell sorting. The
measurement of tissue surface tension so far relied on strong approximations on
the geometric profile of a spherical droplet compressed between parallel
plates. We solved the Laplace equation for this geometry and tested its
solution on true liquids and embryonic tissue fragments as well as
multicellular aggregates. The analytic solution provides the surface tension in
terms of easily and accurately measurable geometric parameters. Experimental
results show that the various tissues and multicellular aggregates studied here
are incompressible and, similarly to true liquids, possess effective surface
tensions that are independent of the magnitude of the compressive force and the
volume of the droplet.
| 2009-11-13 |
0706.3681 | Marcin Molski | Marcin Molski | On the Classification Scheme for Phenomenological Universalities in
Growth Problems in Physics and Other Sciences | null | null | null | null | q-bio.OT q-bio.QM | null | Comment on "Classification Scheme for Phenomenological Universalities in
Growth Problems in Physics and Other Sciences" by P. Castorina, P. P. Delsanto
and C. Guiot, Phys. Rev. Lett. {\bf 96}, 188701 (2006) is presented. It has
been proved that the West-like function of growth derived by the authors is
incorrect and the approach does not take into account the growth of the
biological systems undergoing atrophy or demographic and economic systems
undergoing involution or regression. A simple extension of the model, which
permits derivation of the so far unknown involuted Gompertz function of growth
is proposed.
| 2007-06-26 |
0706.3684 | Pete Donnell | Pete Donnell, Murad Banaji and Stephen Baigent | Stability in generic mitochondrial models | 22 pages, 1 figure. Submitted to Mathematical Biosciences | null | null | null | q-bio.QM q-bio.SC | null | In this paper, we use a variety of mathematical techniques to explore
existence, local stability, and global stability of equilibria in abstract
models of mitochondrial metabolism. The class of models constructed is defined
by the biological description of the system, with minimal mathematical
assumptions. The key features are an electron transport chain coupled to a
process of charge translocation across a membrane. In the absence of charge
translocation these models have previously been shown to behave in a very
simple manner with a single, globally stable equilibrium. We show that with
charge translocation the conclusion about a unique equilibrium remains true,
but local and global stability do not necessarily follow. In sufficiently low
dimensions - i.e. for short electron transport chains - it is possible to make
claims about local and global stability of the equilibrium. On the other hand,
for longer chains, these general claims are no longer valid. Some particular
conditions which ensure stability of the equilibrium for chains of arbitrary
length are presented.
| 2007-06-26 |
0706.3693 | Ioan Kosztin | Elijah Flenner, Francoise Marga, Adrian Neagu, Ioan Kosztin and Gabor
Forgacs (University of Missouri - Columbia) | Relating Biophysical Properties Across Scales | 24 pages, 10 figures, To appear in Current Topics in Developmental
Biology | null | null | null | physics.bio-ph physics.comp-ph q-bio.CB q-bio.TO | null | A distinguishing feature of a multicellular living system is that it operates
at various scales, from the intracellular to organismal. Very little is known
at present on how tissue level properties are related to cell and subcellular
properties. Modern measurement techniques provide quantitative results at both
the intracellular and tissue level, but not on the connection between these. In
the present work we outline a framework to address this connection. We
specifically concentrate on the morphogenetic process of tissue fusion, by
following the coalescence of two contiguous multicellular aggregates. The time
evolution of this process can accurately be described by the theory of viscous
liquids. We also study fusion by Monte Carlo simulations and a novel Cellular
Particle Dynamics (CPD) model, which is similar to the earlier introduced
Subcellular Element Model (Newman, 2005). Using the combination of experiments,
theory and modeling we are able to relate the measured tissue level biophysical
quantities to subcellular parameters. Our approach has validity beyond the
particular morphogenetic process considered here and provides a general way to
relate biophysical properties across scales.
| 2007-06-26 |
0706.3735 | Jeremy Gunawardena | Matthew Thomson and Jeremy Gunawardena | Multi-bit information storage by multisite phosphorylation | 29 pages, 6 figures | null | null | null | q-bio.MN | null | Cells store information in DNA and in stable programs of gene expression,
which thereby implement forms of long-term cellular memory. Cells must also
possess short-term forms of information storage, implemented
post-translationally, to transduce and interpret external signals. CaMKII, for
instance, is thought to implement a one-bit (bistable) short-term memory
required for learning at post-synaptic densities. Here we show by mathematical
analysis that multisite protein phosphorylation, which is ubiquitous in all
eukaryotic signalling pathways, exhibits multistability for which the maximal
number of steady states increases with the number of sites. If there are n
sites, the maximal information storage capacity is at least log_2 (n+2)/2 bits
when n is even and log_2 (n+1)/2 bits when n is odd. Furthermore, when
substrate is in excess, enzyme saturation together with an alternating low/high
pattern in the site-specific relative catalytic efficiencies, enriches for
multistability. That is, within physiologically plausible ranges for
parameters, multistability becomes more likely than monostability. We discuss
the experimental challenges in pursuing these predictions and in determining
the biological role of short-term information storage.
| 2007-06-27 |
0706.3743 | Kilho Eom | Kilho Eom, Tae Yun Kwon, Dae Sung Yoon, Hong Lim Lee, Tae Song Kim | Dynamical Response of Nanomechanical Resonators to Biomolecular
Interactions | 17 page, 4 figures, accepted for publication at PRB. Physical Review
B, accepted | null | 10.1103/PhysRevB.76.113408 | null | cond-mat.soft q-bio.QM | null | We studied the dynamical response of a nanomechanical resonator to
biomolecular (e.g. DNA) adsorptions on a resonator's surface by using a
theoretical model, which considers the Hamiltonian H such that the potential
energy consists of elastic bending energy of a resonator and the potential
energy for biomolecular interactions. It was shown that the resonant frequency
shift of a resonator due to biomolecular adsorption depends on not only the
mass of adsorbed biomolecules but also the biomolecular interactions.
Specifically, for dsDNA adsorption on a resonator's surface, the resonant
frequency shift is also dependent on the ionic strength of a solvent, implying
the role of molecular interactions on the dynamic behavior of a resonator. This
indicates that nanomechanical resonators may enable one to quantify the
biomolecular mass, implying the enumeration of biomolecules, as well as gain
insight into intermolecular interactions between adsorbed biomolecules on the
surface.
| 2009-11-13 |
0706.3758 | Rajarshi Chakrabarti | Rajarshi Chakrabarti, Ananya Debnath and K. L. Sebastian | Diffusion of Macromolecules across the Nuclear Pore Complex | null | null | 10.1016/j.physa.2014.02.059 | null | cond-mat.soft cond-mat.stat-mech physics.bio-ph q-bio.CB | null | Nuclear pore complexes (NPCs) are very selective filters that monitor the
transport between the cytoplasm and the nucleoplasm. Two models have been
suggested for the plug of the NPC. They are (i) it is a reversible hydrogel or
(ii) it is a polymer brush. We propose a mesoscopic model for the transport of
a protein through the plug, that is general enough to cover both. The protein
stretches the plug and creates a local deformation. The bubble so created
(prtoein+deformation) executes random walk in the plug. We find that for faster
relaxation of the gel, the diffusion of the bubble is greater. Further, on
using parameters appropriate for the brush, we find that the diffusion
coefficient is much lower. Hence the gel model seems to be more likely
explanation for the workings of the plug.
| 2014-06-25 |
0706.3878 | Michael E. Wall | Dengming Ming (1), Marian Anghel (1), Michael E. Wall (1) ((1) Los
Alamos National Laboratory) | Hidden Structure in Protein Energy Landscapes | 11 pages, 4 figures; corrected citation of Ref. 10 | null | 10.1103/PhysRevE.77.021902 | LA-UR-07-1934 | q-bio.BM | null | Inherent structure theory is used to discover strong connections between
simple characteristics of protein structure and the energy landscape of a Go
model. The potential energies and vibrational free energies of inherent
structures are highly correlated, and both reflect simple measures of networks
of native contacts. These connections have important consequences for models of
protein dynamics and thermodynamics.
| 2009-11-13 |
0706.3883 | Pablo Fern\'andez | Pablo Fern\'andez and Albrecht Ott | Single cell mechanics: stress stiffening and kinematic hardening | 4 pages, 6 figures | null | 10.1103/PhysRevLett.100.238102 | null | physics.bio-ph | null | Cell mechanical properties are fundamental to the organism but remain poorly
understood. We report a comprehensive phenomenological framework for the
nonlinear rheology of single fibroblast cells: a superposition of elastic
stiffening and viscoplastic kinematic hardening. Our results show, that in
spite of cell complexity its mechanical properties can be cast into simple,
well-defined rules, which provide mechanical cell strength and robustness via
control of crosslink slippage.
| 2009-11-13 |
0706.3969 | Debabrata Panja | Debabrata Panja and Gerard T. Barkema | Passage Times for Polymer Translocation Pulled through a Narrow Pore | 7 pages, 4 figures, 6 eps figure files, minor expressions changed,
references updated; to appear in Biophys. J | Biophys. J. 94, 1630-1637 (2008) | 10.1529/biophysj.107.116434 | null | cond-mat.soft cond-mat.stat-mech physics.bio-ph q-bio.BM | null | We study the passage times of a translocating polymer of length $N$ in three
dimensions, while it is pulled through a narrow pore with a constant force $F$
applied to one end of the polymer. At small to moderate forces, satisfying the
condition $FN^{\nu}/k_BT\lesssim1$, where $\nu\approx0.588$ is the Flory
exponent for the polymer, we find that $\tau_N$, the mean time the polymer
takes to leave the pore, scales as $N^{2+\nu}$ independent of $F$, in agreement
with our earlier result for F=0. At strong forces, i.e., for
$FN^{\nu}/k_BT\gg1$, the behaviour of the passage time crosses over to
$\tau_N\sim N^2/F$. We show here that these behaviours stem from the polymer
dynamics at the immediate vicinity of the pore -- in particular, the memory
effects in the polymer chain tension imbalance across the pore.
| 2008-02-14 |
0706.3974 | Pierre-Henri Chavanis | Pierre-Henri Chavanis and Clement Sire | Kinetic and hydrodynamic models of chemotactic aggregation | In press | Physica A, 384, 199 (2007) | 10.1016/j.physa.2007.05.069 | null | physics.bio-ph | null | We derive general kinetic and hydrodynamic models of chemotactic aggregation
that describe certain features of the morphogenesis of biological colonies
(like bacteria, amoebae, endothelial cells or social insects). Starting from a
stochastic model defined in terms of N coupled Langevin equations, we derive a
nonlinear mean field Fokker-Planck equation governing the evolution of the
distribution function of the system in phase space. By taking the successive
moments of this kinetic equation and using a local thermodynamic equilibrium
condition, we derive a set of hydrodynamic equations involving a damping term.
In the limit of small frictions, we obtain a hyperbolic model describing the
formation of network patterns (filaments) and in the limit of strong frictions
we obtain a parabolic model which is a generalization of the standard
Keller-Segel model describing the formation of clusters (clumps). Our approach
connects and generalizes several models introduced in the chemotactic
literature. We discuss the analogy between bacterial colonies and
self-gravitating systems and between the chemotactic collapse and the
gravitational collapse (Jeans instability). We also show that the basic
equations of chemotaxis are similar to nonlinear mean field Fokker-Planck
equations so that a notion of effective generalized thermodynamics can be
developed.
| 2009-11-13 |
0706.4219 | Brigitte Gaillard | Audrey Bergouignan (DEPE-IPHC), Dale A Schoeller, Sylvie Normand,
Guillemette Gauquelin-Koch, Martine Laville, Timothy Shriver, Michel Desage,
Yvon Le Maho (DEPE-IPHC), Hiroshi Ohshima, Claude Gharib, St\'ephane Blanc
(DEPE-IPHC) | Effect of physical inactivity on the oxidation of saturated and
monounsaturated dietary Fatty acids: results of a randomized trial | null | PLoS Clin Trials 1, 5 (2006) e27 | 10.1371/journal.pctr.0010027 | null | q-bio.PE | null | OBJECTIVES: Changes in the way dietary fat is metabolized can be considered
causative in obesity. The role of sedentary behavior in this defect has not
been determined. We hypothesized that physical inactivity partitions dietary
fats toward storage and that a resistance exercise training program mitigates
storage.
| 2007-06-29 |
0706.4249 | Stefan Thurner | Rudolf Hanel and Stefan Thurner | Solution of the Unanimity Rule on exponential, uniform and scalefree
networks: A simple model for biodiversity collapse in foodwebs | 4 pages, 3 figs | null | 10.1140/epjb/e2008-00160-7 | null | physics.bio-ph q-bio.PE | null | We solve the Unanimity Rule on networks with exponential, uniform and
scalefree degree distributions. In particular we arrive at equations relating
the asymptotic number of nodes in one of two states to the initial fraction of
nodes in this state. The solutions for exponential and uniform networks are
exact, the approximation for the scalefree case is in perfect agreement with
simulation results. We use these solutions to provide a theoretical
understanding for experimental data on biodiversity loss in foodwebs, which is
available for the three network types discussed. The model allows in principle
to estimate the critical value of species that have to be removed from the
system to induce its complete collapse.
| 2009-11-13 |
0706.4291 | Michael Widom | M. Widom, J. Lidmar and D. R. Nelson | Soft modes near the buckling transition of icosahedral shells | 28 pages, 6 figures | null | 10.1103/PhysRevE.76.031911 | null | physics.bio-ph | null | Icosahedral shells undergo a buckling transition as the ratio of Young's
modulus to bending stiffness increases. Strong bending stiffness favors smooth,
nearly spherical shapes, while weak bending stiffness leads to a sharply
faceted icosahedral shape. Based on the phonon spectrum of a simplified
mass-and-spring model of the shell, we interpret the transition from smooth to
faceted as a soft-mode transition. In contrast to the case of a disclinated
planar network where the transition is sharply defined, the mean curvature of
the sphere smooths the transitition. We define elastic susceptibilities as the
response to forces applied at vertices, edges and faces of an icosahedron. At
the soft-mode transition the vertex susceptibility is the largest, but as the
shell becomes more faceted the edge and face susceptibilities greatly exceed
the vertex susceptibility. Limiting behaviors of the susceptibilities are
analyzed and related to the ridge-scaling behavior of elastic sheets. Our
results apply to virus capsids, liposomes with crystalline order and other
shell-like structures with icosahedral symmetry.
| 2009-11-13 |
0706.4396 | Thierry Rabilloud | Mireille Chevallet (BBSI), Sylvie Luche, Thierry Rabilloud (BBSI) | Silver staining of proteins in polyacrylamide gels | null | Nat Protoc 1, 4 (2006) 1852-8 | 10.1038/nprot.2006.288 | null | q-bio.GN | null | Silver staining is used to detect proteins after electrophoretic separation
on polyacrylamide gels. It combines excellent sensitivity (in the low nanogram
range) with the use of very simple and cheap equipment and chemicals. It is
compatible with downstream processing, such as mass spectrometry analysis after
protein digestion. The sequential phases of silver staining are protein
fixation, then sensitization, then silver impregnation and finally image
development. Several variants of silver staining are described here, which can
be completed in a time range from 2 h to 1 d after the end of the
electrophoretic separation. Once completed, the stain is stable for several
weeks.
| 2007-07-02 |
0707.0026 | Maria A. Avi\~no-Diaz | Maria A. Avino-Diaz | Introducing a Probabilistic Structure on Sequential Dynamical Systems,
Simulation and Reduction of Probabilistic Sequential Networks | 14 pages | null | null | null | q-bio.GN math.PR q-bio.MN | null | A probabilistic structure on sequential dynamical systems is introduced here,
the new model will be called Probabilistic Sequential Network, PSN. The
morphisms of Probabilistic Sequential Networks are defined using two algebraic
conditions. It is proved here that two homomorphic Probabilistic Sequential
Networks have the same equilibrium or steady state probabilities if the
morphism is either an epimorphism or a monomorphism. Additionally, the proof of
the set of PSN with its morphisms form the category PSN, having the category of
sequential dynamical systems SDS, as a full subcategory is given. Several
examples of morphisms, subsystems and simulations are given.
| 2008-04-30 |
0707.0114 | Nicholas Eriksson | Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin
Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel | Viral population estimation using pyrosequencing | 23 pages, 13 figures | null | 10.1371/journal.pcbi.1000074 | null | q-bio.PE | null | The diversity of virus populations within single infected hosts presents a
major difficulty for the natural immune response as well as for vaccine design
and antiviral drug therapy. Recently developed pyrophosphate based sequencing
technologies (pyrosequencing) can be used for quantifying this diversity by
ultra-deep sequencing of virus samples. We present computational methods for
the analysis of such sequence data and apply these techniques to pyrosequencing
data obtained from HIV populations within patients harboring drug resistant
virus strains. Our main result is the estimation of the population structure of
the sample from the pyrosequencing reads. This inference is based on a
statistical approach to error correction, followed by a combinatorial algorithm
for constructing a minimal set of haplotypes that explain the data. Using this
set of explaining haplotypes, we apply a statistical model to infer the
frequencies of the haplotypes in the population via an EM algorithm. We
demonstrate that pyrosequencing reads allow for effective population
reconstruction by extensive simulations and by comparison to 165 sequences
obtained directly from clonal sequencing of four independent, diverse HIV
populations. Thus, pyrosequencing can be used for cost-effective estimation of
the structure of virus populations, promising new insights into viral
evolutionary dynamics and disease control strategies.
| 2015-05-13 |
0707.0245 | Bard Ermentrout | G. Bard Ermentrout, Roberto F. Gal\'an Nathaniel N. Urban | Relating Neural Dynamics to Neural Coding | 10 pages, 3 figures | null | null | null | q-bio.NC | null | We demonstrate that two key theoretical objects used widely in Computational
Neuroscience, the phase-resetting curve (PRC) from dynamics and the spike
triggered average (STA) from statistical analysis, are closely related under a
wide range of stimulus conditions. We prove that the STA is proportional to the
derivative of the PRC. We compare these analytic results to numerical
calculations for the Hodgkin-Huxley neuron and we apply the method to neurons
in the olfactory bulb of mice. This observation allows us to relate the
stimulus-response properties of a neuron to its dynamics, bridging the gap
between dynamical and information theoretic approaches to understanding brain
computations and facilitating the interpretation of changes in channels and
other cellular properties as influencing the representation of stimuli.
| 2007-09-26 |
0707.0309 | Vladimir R. V. de Assis | Vladimir R. V. Assis and Mauro Copelli | Dynamic range of hypercubic stochastic excitable media | 7 pages, 4 figures | Phys. Rev. E 77, 011923 (2008) | 10.1103/PhysRevE.77.011923 | null | q-bio.NC cond-mat.dis-nn cond-mat.stat-mech nlin.CG physics.bio-ph | null | We study the response properties of d-dimensional hypercubic excitable
networks to a stochastic stimulus. Each site, modelled either by a three-state
stochastic susceptible-infected-recovered-susceptible system or by the
probabilistic Greenberg-Hastings cellular automaton, is continuously and
independently stimulated by an external Poisson rate h. The response function
(mean density of active sites rho versus h) is obtained via simulations (for
d=1, 2, 3, 4) and mean field approximations at the single-site and pair levels
(for all d). In any dimension, the dynamic range of the response function is
maximized precisely at the nonequilibrium phase transition to self-sustained
activity, in agreement with a reasoning recently proposed. Moreover, the
maximum dynamic range attained at a given dimension d is a decreasing function
of d.
| 2008-02-13 |
0707.0329 | Mareike Fischer | Mareike Fischer, Mike Steel | Expected Anomalies in the Fossil Record | null | Fischer, M. and Steel, M. (2008). Expected anomalies in the fossil
record. Evolutionary bioinformatics online 4: 61--67 | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The problem of intermediates in the fossil record has been frequently
discussed ever since Darwin. The extent of `gaps' (missing transitional stages)
has been used to argue against gradual evolution from a common ancestor.
Traditionally, gaps have often been explained by the improbability of
fossilization and the discontinuous selection of found fossils. Here we take an
analytical approach and demonstrate why, under certain sampling conditions, we
may not expect intermediates to be found. Using a simple null model, we show
mathematically that the question of whether a taxon sampled from some time in
the past is likely to be morphologically intermediate to other samples (dated
earlier and later) depends on the shape and dimensions of the underlying
phylogenetic tree that connects the taxa, and the times from which the fossils
are sampled.
| 2008-08-27 |
0707.0394 | Davide Cora | Davide Cora, Ferdinando Di Cunto, Michele Caselle, Paolo Provero | Identification of candidate regulatory sequences in mammalian 3' UTRs by
statistical analysis of oligonucleotide distributions | Added two references | BMC Bioinformatics. 2007 May 24;8:174. PMID: 17524134 | null | null | q-bio.GN | null | 3' untranslated regions (3' UTRs) contain binding sites for many regulatory
elements, and in particular for microRNAs (miRNAs). The importance of
miRNA-mediated post-transcriptional regulation has become increasingly clear in
the last few years.
We propose two complementary approaches to the statistical analysis of
oligonucleotide frequencies in mammalian 3' UTRs aimed at the identification of
candidate binding sites for regulatory elements. The first method is based on
the identification of sets of genes characterized by evolutionarily conserved
overrepresentation of an oligonucleotide. The second method is based on the
identification of oligonucleotides showing statistically significant strand
asymmetry in their distribution in 3' UTRs.
Both methods are able to identify many previously known binding sites located
in 3'UTRs, and in particular seed regions of known miRNAs. Many new candidates
are proposed for experimental verification.
| 2007-07-17 |
0707.0504 | Ching-Hwa Kiang | Nolan C. Harris, Yang Song, and Ching-Hwa Kiang | Experimental Free Energy Surface Reconstruction From Single-Molecule
Force Spectroscopy Using Jarzynski's Equality | 4 pages, 3 figures. Phys. Rev. Lett. (2007) accepted | null | 10.1103/PhysRevLett.99.068101 | null | physics.bio-ph physics.gen-ph | null | We used the atomic force microscope to manipulate and unfold individual
molecules of the titin I27 domain and reconstructed its free energy surface
using Jarzynski's equality. The free energy surface for both stretching and
unfolding was reconstructed using an exact formula that relates the
nonequilibrium work fluctuations to the molecular free energy. In addition, the
unfolding free energy barrier, i.e. the activation energy, was directly
obtained from experimental data for the first time. This work demonstrates that
Jarzynski's equality can be used to analyze nonequilibrium single-molecule
experiments, and to obtain the free energy surfaces for molecular systems,
including interactions for which only nonequilibrium work can be measured.
| 2009-11-13 |
0707.0567 | Nicolas Pollet | Ana C Fierro (DE), Rapha\"el Thuret (DE), Laurent Coen (ERE, LPGC),
Muriel Perron (DE), Barbara A Demeneix (ERE, LPGC), Maurice Wegnez (DE),
Gabor Gyapay (SEG), Jean Weissenbach (SEG), Patrick Wincker (SEG), Andr\'e
Mazabraud (DE), Nicolas Pollet (DE) | Exploring nervous system transcriptomes during embryogenesis and
metamorphosis in Xenopus tropicalis using EST analysis | null | BMC Genomics 8 (2007) 118 | 10.1186/1471-2164-8-118 | null | q-bio.GN q-bio.QM | null | Xenopus tropicalis is an anuran amphibian species used as model in vertebrate
comparative genomics. It provides the same advantages as Xenopus laevis but is
diploid and has a smaller genome of 1.7 Gbp. Therefore X. tropicalis is more
amenable to systematic transcriptome surveys. We initiated a large-scale
partial cDNA sequencing project to provide a functional genomics resource on
genes expressed in the nervous system during early embryogenesis and
metamorphosis in X. tropicalis. A gene index was defined and analysed after the
collection of over 48,785 high quality sequences. Partial cDNA sequences were
obtained from an embryonic head and retina library (30,272 sequences) and from
a metamorphic brain and spinal cord library (27,602 sequences). These ESTs are
estimated to represent 9,693 transcripts derived from an estimated 6,000 genes.
An estimated 46% of these cDNA sequences contain their start codon. Further
annotation included Gene Ontology functional classification, InterPro domain
analysis, alternative splicing and non-coding RNA identification. Gene
expression profiles were derived from EST counts and used to define transcripts
specific to metamorphic stages of development. Moreover, these ESTs allowed
identification of a set of 225 polymorphic microsatellites that can be used as
genetic markers. These cDNA sequences permit in silico cloning of numerous
genes and will facilitate studies aimed at deciphering the roles of cognate
genes expressed in the nervous system during neural development and
metamorphosis. The genomic resources developed to study X. tropicalis biology
will accelerate exploration of amphibian physiology and genetics.
| 2007-07-05 |
0707.0580 | Felix Ritort | J.-D. Wen, M. Manosas, P. T. X. Li, S. B. Smith, C. Bustamante, F.
Ritort, I. Tinoco Jr | Force unfolding kinetics of RNA using optical tweezers. I. Effects of
experimental variables on measured results | PDF file, 30 pages, 7 figures | Biophysical Journal, 92 (2007) 2996-3009 | 10.1529/biophysj.106.094052 | null | physics.bio-ph cond-mat.soft cond-mat.stat-mech q-bio.BM | null | Experimental variables of optical tweezers instrumentation that affect RNA
folding/unfolding kinetics were investigated. A model RNA hairpin, P5ab, was
attached to two micron-sized beads through hybrid RNA/DNA handles; one bead was
trapped by dual-beam lasers and the other was held by a micropipette. Several
experimental variables were changed while measuring the unfolding/refolding
kinetics, including handle lengths, trap stiffness, and modes of force applied
to the molecule. In constant-force mode where the tension applied to the RNA
was maintained through feedback control, the measured rate coefficients varied
within 40% when the handle lengths were changed by 10 fold (1.1 to 10.2 Kbp);
they increased by two- to three-fold when the trap stiffness was lowered to one
third (from 0.1 to 0.035 pN/nm). In the passive mode, without feedback control
and where the force applied to the RNA varied in response to the end-to-end
distance change of the tether, the RNA hopped between a high-force folded-state
and a low-force unfolded-state. In this mode, the rates increased up to
two-fold with longer handles or softer traps. Overall, the measured rates
remained with the same order-of-magnitude over the wide range of conditions
studied. In the companion paper (1), we analyze how the measured kinetics
parameters differ from the intrinsic molecular rates of the RNA, and thus how
to obtain the molecular rates.
| 2009-11-13 |
0707.0662 | Felix Ritort | M. Manosas, J.-D. Wen, P. T. X. Li, S. B. Smith, C. Bustamante, I.
Tinoco, Jr., F. Ritort | Force unfolding kinetics of RNA using optical tweezers. II. Modeling
experiments | PDF file, 32 pages including 9 figures plus supplementary material | Biophysical Journal, 92 (2007) 3010-3021 | 10.1529/biophysj.106.094243 | null | physics.bio-ph cond-mat.soft cond-mat.stat-mech q-bio.BM | null | By exerting mechanical force it is possible to unfold/refold RNA molecules
one at a time. In a small range of forces, an RNA molecule can hop between the
folded and the unfolded state with force-dependent kinetic rates. Here, we
introduce a mesoscopic model to analyze the hopping kinetics of RNA hairpins in
an optical tweezers setup. The model includes different elements of the
experimental setup (beads, handles and RNA sequence) and limitations of the
instrument (time lag of the force-feedback mechanism and finite bandwidth of
data acquisition). We investigated the influence of the instrument on the
measured hopping rates. Results from the model are in good agreement with the
experiments reported in the companion article (1). The comparison between
theory and experiments allowed us to infer the values of the intrinsic
molecular rates of the RNA hairpin alone and to search for the optimal
experimental conditions to do the measurements. We conclude that long handles
and soft laser traps represent the best conditions to extract rate estimates
that are closest to the intrinsic molecular rates. The methodology and
rationale presented here can be applied to other experimental setups and other
molecules.
| 2012-08-27 |
0707.0754 | Denis Semenov A. | Denis A. Semenov | The Symmetry of the Genetic Code and a Universal Trend of Amino Acid
Gain and Loss | 7 pages, 3 tables | null | null | null | q-bio.PE | null | Part 1 of the study intends to show that the universal trend of amino acid
gain and loss discovered by Jordan et al. (2005) can be accounted for by the
spontaneity of DNA typical damages. These damages lead to replacements of
guanine and cytosine by thymine. Part 2 proposes a hypothesis of the evolution
of the genetic code, the leading mechanism of which is the nucleotide
spontaneous damage. The hypothesis accounts for the universal trend of amino
acid gain and loss, stability of the genetic code towards point mutations, the
presence of code dialects, and the symmetry of the genetic code table.
| 2007-07-06 |
0707.0764 | Branko Dragovich | Branko Dragovich and Alexandra Dragovich | p-Adic Degeneracy of the Genetic Code | 11 pages, 1 table. Published in the Proceedings of '4th Summer School
in Modern Mathematcal Physics', September 2006, Belgrade (Serbia) | SFIN XX A1 (2007) 179-188 | null | null | q-bio.GN cs.IT math.IT physics.bio-ph | null | Degeneracy of the genetic code is a biological way to minimize effects of the
undesirable mutation changes. Degeneration has a natural description on the
5-adic space of 64 codons $\mathcal{C}_5 (64) = \{n_0 + n_1 5 + n_2 5^2
: n_i = 1, 2, 3, 4 \} ,$ where $n_i$ are digits related to nucleotides as
follows: C = 1, A = 2, T = U = 3, G = 4. The smallest 5-adic distance between
codons joins them into 16 quadruplets, which under 2-adic distance decay into
32 doublets. p-Adically close codons are assigned to one of 20 amino acids,
which are building blocks of proteins, or code termination of protein
synthesis. We shown that genetic code multiplets are made of the p-adic nearest
codons.
| 2007-07-16 |
0707.0804 | Brigitte Gaillard | M. Boos (DEPE-Iphc), C. Zimmer (DEPE-Iphc), A. Carriere (DEPE-Iphc),
J.P. Robin (DEPE-Iphc), O. Petit (DEPE-Iphc) | Post-hatching parental care behaviour and hormonal status in a precocial
bird | null | Behavioural Processes (18/05/2007) sous presse | 10.1016/j.beproc.2007.05.003 | null | q-bio.PE | null | In birds, the link between parental care behaviour and prolactin release
during incubation persists after hatching in altricial birds, but has never
been precisely studied during the whole rearing period in precocial species,
such as ducks. The present study aims to understand how changes in parental
care after hatching are related to circulating prolactin levels in mallard hens
rearing ducklings. Blood was sampled in hens over at least 13 post-hatching
weeks and the behaviour of the hens and the ducklings was recorded daily until
fledging. Contacts between hens and the ducklings, leadership of the ducklings
and gathering of them steadily decreased over post-hatching time. Conversely,
resting, preening and agonistic behaviour of hens towards ducklings increased.
Plasma prolactin concentrations remained at high levels after hatching and then
fell after week 6 when body mass and structural size of the young were close to
those of the hen. Parental care behaviour declined linearly with brood age,
showed a disruption of the hen-brood bond at week 6 post-hatching and was
related to prolactin concentration according to a sigmoid function. Our results
suggest that a definite threshold in circulating prolactin is necessary to
promote and/or to maintain post-hatching parental care in ducks.
| 2007-07-06 |
0707.0880 | Ching-Hwa Kiang | Nolan C. Harris and Ching-Hwa Kiang | Defects Can Increase the Melting Temperature of DNA-Nanoparticle
Assemblies | 12 pages, 3 figures | J. Phys. Chem. B, 110 (2006) 16393-16396 | 10.1021/jp062287d | null | physics.bio-ph | null | DNA-gold nanoparticle assemblies have shown promise as an alternative
technology to DNA microarrays for DNA detection and RNA profiling.
Understanding the effect of DNA sequences on the melting temperature of the
system is central to developing reliable detection technology. We studied the
effects of DNA base-pairing defects, such as mismatches and deletions, on the
melting temperature of DNA-nanoparticle assemblies. We found that, contrary to
the general assumption that defects lower the melting temperature of DNA, some
defects increase the melting temperature of DNA-linked nanoparticle assemblies.
The effects of mismatches and deletions were found to depend on the specific
base pair, the sequence, and the location of the defects. Our results
demonstrate that the surface-bound DNA exhibit hybridization behavior different
from that of free DNA. Such findings indicate that a detailed understanding of
DNA-nanoparticle assembly phase behavior is required for quantitative
interpretation of DNA-nanoparticle aggregation.
| 2007-07-09 |
0707.1078 | Vito Domenico Pietro Servedio | Paolo Butt\`a, Fiammetta Cerreti, Vito D. P. Servedio, Livio Triolo | Molecular Dynamics Simulation of Vascular Network Formation | 10 pages, 3 figures, 2 of which composite with 8 pictures each.
Accepted on J.Stat.Mech. (2009). Appeared at the poster session of
StatPhys23, Genoa, Italy, July 13 (2007) | Journal of Statistical Mechanics: Theory and Experiments (2009)
P05013, 10 pages | 10.1088/1742-5468/2009/05/P05013 | Roma01.Math.MP | cond-mat.soft q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Endothelial cells are responsible for the formation of the capillary blood
vessel network. We describe a system of endothelial cells by means of
two-dimensional molecular dynamics simulations of point-like particles. Cells'
motion is governed by the gradient of the concentration of a chemical substance
that they produce (chemotaxis). The typical time of degradation of the chemical
substance introduces a characteristic length in the system. We show that
point-like model cells form network resembling structures tuned by this
characteristic length, before collapsing altogether. Successively, we improve
the non-realistic point-like model cells by introducing an isotropic strong
repulsive force between them and a velocity dependent force mimicking the
observed peculiarity of endothelial cells to preserve the direction of their
motion (persistence). This more realistic model does not show a clear network
formation. We ascribe this partial fault in reproducing the experiments to the
static geometry of our model cells that, in reality, change their shapes by
elongating toward neighboring cells.
| 2022-12-22 |
0707.1093 | Lawrence R. Pratt | J. K. Shah, D. Asthagiri, L. R. Pratt, M. E. Paulaitis | Balancing Local Order and Long-Ranged Interactions in the Molecular
Theory of Liquid Water | 8 pages, 6 figures | null | 10.1063/1.2766940 | LA-UR-07-3494 | physics.chem-ph physics.bio-ph | null | A molecular theory of liquid water is identified and studied on the basis of
computer simulation of the TIP3P model of liquid water. This theory would be
exact for models of liquid water in which the intermolecular interactions
vanish outside a finite spatial range, and therefore provides a precise
analysis tool for investigating the effects of longer-ranged intermolecular
interactions. We show how local order can be introduced through quasi-chemical
theory. Long-ranged interactions are characterized generally by a conditional
distribution of binding energies, and this formulation is interpreted as a
regularization of the primitive statistical thermodynamic problem. These
binding-energy distributions for liquid water are observed to be unimodal. The
gaussian approximation proposed is remarkably successful in predicting the
Gibbs free energy and the molar entropy of liquid water, as judged by
comparison with numerically exact results. The remaining discrepancies are
subtle quantitative problems that do have significant consequences for the
thermodynamic properties that distinguish water from many other liquids. The
basic subtlety of liquid water is found then in the competition of several
effects which must be quantitatively balanced for realistic results.
| 2009-11-13 |
Subsets and Splits