831 research outputs found
Localization of Denaturation Bubbles in Random DNA Sequences
We study the thermodynamic and dynamic behaviors of twist-induced
denaturation bubbles in a long, stretched random sequence of DNA. The small
bubbles associated with weak twist are delocalized. Above a threshold torque,
the bubbles of several tens of bases or larger become preferentially localized
to \AT-rich segments. In the localized regime, the bubbles exhibit ``aging''
and move around sub-diffusively with continuously varying dynamic exponents.
These properties are derived using results of large-deviation theory together
with scaling arguments, and are verified by Monte-Carlo simulations.Comment: TeX file with postscript figure
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Nutritional composition of browse and diets fed to ungulates at the Breeding Centre for Endangered Arabian Wildlife
Captive browsing ruminants are particularly susceptible to gastrointestinal disorders, and inappropriate diets are an underlying factor. This study investigated the nutritional composition of browse and pelleted feedstuffs used in an Arabian facility and compared nutrient intake against current recommendations for exotic ungulates. Additionally, retrospective evaluation of post-mortem findings with regard to gastrointestinal pathologies was conducted (n = 497). Samples of browse from seven species of locally cultivated plants, as well as three brands of pelleted feeds, were submitted for laboratory analysis. Following a five-day feed intake study, nutrient intake was calculated. Only moderate variation was seen among browse species’ composition compared to previous reports. However, significant variation occurred between plant fractions (stem, leaves and seed pods) for neutral detergent fibre and several minerals. Browse comprised over half of the metabolisable energy (ME) intake of Arabian tahr (rabitragus jayakari), but only 11% of ME for Arabian gazelle (Gazella gazella cora) and Dorcas gazelle (G. gazella dorcas). However, no relationship could be detected between gastrointestinal disease and browse provision in these species. No nutrient deficiencies were identified, but the Arabian tahr diet exceeded the recommended amount of crude protein, and both gazelle diets provided excess iron, manganese, copper and zinc. These mineral excesses are the subject of on-going investigations in order to better balance the diets offered. Moreover, the high starch content of pelleted diets evaluated in the current study (22-29%, on a dry matter basis) indicates that a reduction in the proportional provision of pellets would improve the diet suitability, particularly for the gazelles. This study highlights a number of areas for potential improvement, although further research is required to fully understand the implications of these findings
Stretching Instability of Helical Spring
We show that when a gradually increasing tensile force is applied to the ends
of a helical spring with sufficiently large ratios of radius to pitch and twist
to bending rigidity, the end-to-end distance undergoes a sequence of
discontinuous stretching transitions. Subsequent decrease of the force leads to
step-like contraction and hysteresis is observed. For finite helices, the
number of these transitions increases with the number of helical turns but only
one stretching and one contraction instability survive in the limit of an
infinite helix. We calculate the critical line that separates the region of
parameters in which the deformation is continuous from that in which stretching
instabilities occur, and propose experimental tests of our predictions.Comment: 5 pages, 4 figure
Cation–chromatin binding as shown by ion microscopy is essential for the structural integrity of chromosomes
Mammalian interphase and mitotic cells were analyzed for their cation composition using a three-dimensional high resolution scanning ion microprobe. This instrument maps the distribution of bound and unbound cations by secondary ion mass spectrometry (SIMS). SIMS analysis of cryofractured interphase and mitotic cells revealed a cell cycle dynamics of Ca2+, Mg2+, Na+, and K+. Direct analytical images showed that all four, but no other cations, were detected on mitotic chromosomes. SIMS measurements of the total cation content for diploid chromosomes imply that one Ca2+ binds to every 12.5–20 nucleotides and one Mg2+ to every 20–30 nucleotides. Only Ca2+ was enriched at the chromosomal DNA axis and colocalized with topoisomerase IIα (Topo II) and scaffold protein II (ScII). Cells depleted of Ca2+ and Mg2+ showed partially decondensed chromosomes and a loss of Topo II and ScII, but not hCAP-C and histones. The Ca2+-induced inhibition of Topo II catalytic activity and direct binding of Ca2+ to Topo II by a fluorescent filter-binding assay supports a regulatory role of Ca2+ during mitosis in promoting solely the structural function of Topo II. Our study directly implicates Ca2+, Mg2+, Na+, and K+ in higher order chromosome structure through electrostatic neutralization and a functional interaction with nonhistone proteins
Layering transitions for adsorbing polymers in poor solvents
An infinite hierarchy of layering transitions exists for model polymers in
solution under poor solvent or low temperatures and near an attractive surface.
A flat histogram stochastic growth algorithm known as FlatPERM has been used on
a self- and surface interacting self-avoiding walk model for lengths up to 256.
The associated phases exist as stable equilibria for large though not infinite
length polymers and break the conjectured Surface Attached Globule phase into a
series of phases where a polymer exists in specified layer close to a surface.
We provide a scaling theory for these phases and the first-order transitions
between them.Comment: 4 pages, 4 figure
Pulling a polymer out of a potential well and the mechanical unzipping of DNA
Motivated by the experiments on DNA under torsion, we consider the problem of
pulling a polymer out of a potential well by a force applied to one of its
ends. If the force is less than a critical value, then the process is activated
and has an activation energy proportinal to the length of the chain. Above this
critical value, the process is barrierless and will occur spontaneously. We use
the Rouse model for the description of the dynamics of the peeling out and
study the average behaviour of the chain, by replacing the random noise by its
mean. The resultant mean-field equation is a nonlinear diffusion equation and
hence rather difficult to analyze. We use physical arguments to convert this in
to a moving boundary value problem, which can then be solved exactly. The
result is that the time required to pull out a polymer of segments
scales like . For models other than the Rouse, we argue that Comment: 11 pages, 6 figures. To appear in PhysicalReview
The antiparallel loops in gal DNA
Interactions between proteins bound to distant sites along a DNA molecule require bending and twisting deformations in the intervening DNA. In certain systems, the sterically allowed protein–DNA and protein–protein interactions are hypothesized to produce loops with distinct geometries that may also be thermodynamically and biologically distinct. For example, theoretical models of Gal repressor/HU-mediated DNA-looping suggest that the antiparallel DNA loops, A1 and A2, are thermodynamically quite different. They are also biologically different, since in experiments using DNA molecules engineered to form only one of the two loops, the A2 loop failed to repress in vitro transcription. Surprisingly, single molecule measurements show that both loop trajectories form and that they appear to be quite similar energetically and kinetically
Pulling self-interacting polymers in two-dimensions
We investigate a two-dimensional problem of an isolated self-interacting
end-grafted polymer, pulled by one end. In the thermodynamic limit, we find
that the model has only two different phases, namely a collapsed phase and a
stretched phase. We show that the phase diagram obtained by Kumar {\it at al.\}
[Phys. Rev. Lett. {\bf 98}, 128101 (2007)] for small systems, where differences
between various statistical ensembles play an important role, differ from the
phase diagram obtained here in the thermodynamic limit.Comment: 20 pages, 22 figure
The Development of the Basal Ganglia in Capuchin Monkeys (\u3cem\u3eCebus apella\u3c/em\u3e)
The basal ganglia are subcortical structures involved in the planning, initiation and regulation of movement as well as a variety of non-motor, cognitive and affective functions. Capuchin monkeys share several important characteristics of development with humans, including a prolonged infancy and juvenile period, a long lifespan, and complex manipulative abilities. This makes capuchins important comparative models for understanding age-related neuroanatomical changes in these structures. Here we report developmental volumetric data on the three subdivisions of the basal ganglia, the caudate, putamen and globus pallidus in brown capuchin monkeys (Cebus apella). Based on a cross-sectional sample, we describe brain development in 28 brown capuchin monkeys (male n = 17, female n = 11; age range = 2 months-20 years) using high-resolution structural MRI. We found that the raw volumes of the putamen and caudate varied significantly with age, decreasing in volume from birth through early adulthood. Notably, developmental changes did not differ between sexes. Because these observed developmental patterns are similar to humans, our results suggest that capuchin monkeys may be useful animal models for investigating neurodevelopmental disorders of the basal ganglia
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