6,982 research outputs found

### INITIAL CHARACTERIZATION OF MAJOR HISTOCOMPATIBILITY COMPLEX (MHC) CLASS IIB EXON 2 IN AN ENDANGERED RATTLESNAKE, THE EASTERN MASSASAUGA (SISTRURUS CATENATUS)

Genes of the major histocompatibility complex (MHC) play an important role in the vertebrate immune system and exhibit remarkably high levels of polymorphism, maintained by strong balancing selection. While the conservation implications of MHC variation have been explored in a variety of vertebrates, non-avian reptiles (most notably snakes) have received less attention. To address this gap and take the first steps toward more extensive population-level analyses, we cloned and sequenced MHC IIB exon 2 in an endangered rattlesnake, the Eastern Massasauga (Sistrurus catenatus). Based on three individuals, we found evidence of at least four putatively functional loci. These sequences exhibited relatively high levels of variation and significantly higher rates of nonsynonymous to synonymous substitutions, especially within the antigen-binding sites, indicating strong positive selection. Phylogenetic analysis revealed a pattern of trans-species polymorphism, also suggesting positive selection. These results contribute to our understanding of MHC variation in non-avian reptiles and form a basis for more studies of MHC variation in snakes of conservation concern

### Large phenotype jumps in biomolecular evolution

By defining the phenotype of a biopolymer by its active three-dimensional
shape, and its genotype by its primary sequence, we propose a model that
predicts and characterizes the statistical distribution of a population of
biopolymers with a specific phenotype, that originated from a given genotypic
sequence by a single mutational event. Depending on the ratio g0 that
characterizes the spread of potential energies of the mutated population with
respect to temperature, three different statistical regimes have been
identified. We suggest that biopolymers found in nature are in a critical
regime with g0 in the range 1-6, corresponding to a broad, but not too broad,
phenotypic distribution resembling a truncated Levy flight. Thus the biopolymer
phenotype can be considerably modified in just a few mutations. The proposed
model is in good agreement with the experimental distribution of activities
determined for a population of single mutants of a group I ribozyme.Comment: to appear in Phys. Rev. E; 7 pages, 6 figures; longer discussion in
VII, new fig.

### Phase transition in inelastic disks

This letter investigates the molecular dynamics of inelastic disks without
external forcing. By introducing a new observation frame with a rescaled time,
we observe the virtual steady states converted from asymptotic energy
dissipation processes. System behavior in the thermodynamic limit is carefully
investigated. It is found that a phase transition with symmetry breaking occurs
when the magnitude of dissipation is greater than a critical value.Comment: 9 pages, 6 figure

### A Model for Force Fluctuations in Bead Packs

We study theoretically the complex network of forces that is responsible for
the static structure and properties of granular materials. We present detailed
calculations for a model in which the fluctuations in the force distribution
arise because of variations in the contact angles and the constraints imposed
by the force balance on each bead of the pile. We compare our results for force
distribution function for this model, including exact results for certain
contact angle probability distributions, with numerical simulations of force
distributions in random sphere packings. This model reproduces many aspects of
the force distribution observed both in experiment and in numerical simulations
of sphere packings

### Uncertainty reconciles complementarity with joint measurability

The fundamental principles of complementarity and uncertainty are shown to be
related to the possibility of joint unsharp measurements of pairs of
noncommuting quantum observables. A new joint measurement scheme for
complementary observables is proposed. The measured observables are represented
as positive operator valued measures (POVMs), whose intrinsic fuzziness
parameters are found to satisfy an intriguing pay-off relation reflecting the
complementarity. At the same time, this relation represents an instance of a
Heisenberg uncertainty relation for measurement imprecisions. A
model-independent consideration show that this uncertainty relation is
logically connected with the joint measurability of the POVMs in question.Comment: 4 pages, RevTeX. Title of previous version: "Complementarity and
uncertainty - entangled in joint path-interference measurements". This new
version focuses on the "measurement uncertainty relation" and its role,
disentangling this issue from the special context of path interference
duality. See also http://www.vjquantuminfo.org (October 2003

### Suppression of mitochondrial respiration through recruitment of p160 myb binding protein to PGC-1Î± : modulation by p38 MAPK

The transcriptional coactivator PPAR gamma coactivator 1 Î± (PGC-1Î±) is a key regulator of metabolic processes such as mitochondrial biogenesis and respiration in muscle and gluconeogenesis in liver. Reduced levels of PGC-1Î± in humans have been associated with type II diabetes. PGC-1Î± contains a negative regulatory domain that attenuates its transcriptional activity. This negative regulation is removed by phosphorylation of PGC-1Î± by p38 MAPK, an important kinase downstream of cytokine signaling in muscle and Î²-adrenergic signaling in brown fat. We describe here the identification of p160 myb binding protein (p160MBP) as a repressor of PGC-1Î±. The binding and repression of PGC-1Î± by p160MBP is disrupted by p38 MAPK phosphorylation of PGC-1Î±. Adenoviral expression of p160MBP in myoblasts strongly reduces PGC-1Î±'s ability to stimulate mitochondrial respiration and the expression of the genes of the electron transport system. This repression does not require removal of PGC-1Î± from chromatin, suggesting that p160MBP is or recruits a direct transcriptional suppressor. Overall, these data indicate that p160MBP is a powerful negative regulator of PGC-1Î± function and provide a molecular mechanism for the activation of PGC-1Î± by p38 MAPK. The discovery of p160MBP as a PGC-1Î± regulator has important implications for the understanding of energy balance and diabetes

### Breakdown of self-organized criticality

We introduce two sandpile models which show the same behavior of real
sandpiles, that is, an almost self-organized critical behavior for small
systems and the dominance of large avalanches as the system size increases. The
systems become fully self-organized critical, with the critical exponents of
the Bak, Tang and Wiesenfeld model, as the system parameters are changed,
showing that these systems can make a bridge between the well known theoretical
and numerical results and what is observed in real experiments. We find that a
simple mechanism determines the boundary where self-organized can or cannot
exist, which is the presence of local chaos.Comment: 3 pages, 4 figure

### Slowly driven sandpile formation with granular mixtures

We introduce a one-dimensional sandpile model with $N$ different particle types and an infinitesimal driving rate. The parameters for the model are the N^2 critical slopes for one type of particle on top of another. The model is trivial when N=1, but for N=2 we observe four broad classes of sandpile structure in different regions of the parameter space. We describe and explain the behaviour of each of these classes, giving quantitative analysis wherever possible. The behaviour of sandpiles with N>2 essentially consists of combinations of these four classes. We investigate the model's robustness and highlight the key areas that any experiment designed to reproduce these results should focus on

### Inelastic Collapse of Three Particles

A system of three particles undergoing inelastic collisions in arbitrary
spatial dimensions is studied with the aim of establishing the domain of
``inelastic collapse''---an infinite number of collisions which take place in a
finite time. Analytic and simulation results show that for a sufficiently small
restitution coefficient, $0\leq r<7-4\sqrt{3}\approx 0.072$, collapse can
occur. In one dimension, such a collapse is stable against small perturbations
within this entire range. In higher dimensions, the collapse can be stable
against small variations of initial conditions, within a smaller $r$ range,
$0\leq r<9-4\sqrt{5}\approx 0.056$.Comment: 6 pages, figures on request, accepted by PR

### Demonstration of the Complementarity of One- and Two-Photon Interference

The visibilities of second-order (single-photon) and fourth-order
(two-photon) interference have been observed in a Young's double-slit
experiment using light generated by spontaneous parametric down-conversion and
a photon-counting intensified CCD camera. Coherence and entanglement underlie
one-and two-photon interference, respectively. As the effective source size is
increased, coherence is diminished while entanglement is enhanced, so that the
visibility of single-photon interference decreases while that of two-photon
interference increases. This is the first experimental demonstration of the
complementarity between single- and two-photon interference (coherence and
entanglement) in the spatial domain.Comment: 21 pages, 7 figure

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