1,142 research outputs found
Effect of shear force on the separation of double stranded DNA
Using the Langevin Dynamics simulation, we have studied the effects of the
shear force on the rupture of short double stranded DNA at different
temperatures. We show that the rupture force increases linearly with the chain
length and approaches to the asymptotic value in accordance with the
experiment. The qualitative nature of these curves almost remains same for
different temperatures but with a shift in the force. We observe three
different regimes in the extension of covalent bonds (back bone) under the
shear force.Comment: 4 pages, 4 figure
Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules
Understanding the melting of short DNA sequences probes DNA at the scale of
the genetic code and raises questions which are very different from those posed
by very long sequences, which have been extensively studied. We investigate
this problem by combining experiments and theory. A new experimental method
allows us to make a mapping of the opening of the guanines along the sequence
as a function of temperature. The results indicate that non-local effects may
be important in DNA because an AT-rich region is able to influence the opening
of a base pair which is about 10 base pairs away. An earlier mesoscopic model
of DNA is modified to correctly describe the time scales associated to the
opening of individual base pairs well below melting, and to properly take into
account the sequence. Using this model to analyze some characteristic sequences
for which detailed experimental data on the melting is available [Montrichok et
al. 2003 Europhys. Lett. {\bf 62} 452], we show that we have to introduce
non-local effects of AT-rich regions to get acceptable results. This brings a
second indication that the influence of these highly fluctuating regions of DNA
on their neighborhood can extend to some distance.Comment: To be published in J. Phys. Condensed Matte
Numerical Calculations of the B1g Raman Spectrum of the Two-Dimensional Heisenberg Model
The B1g Raman spectrum of the two-dimensional S=1/2 Heisenberg model is
discussed within Loudon-Fleury theory at both zero and finite temperature. The
exact T=0 spectrum for lattices with up to 6*6 sites is computed using Lanczos
exact diagonalization. A quantum Monte Carlo (QMC) method is used to calculate
the corresponding imaginary-time correlation function and its first two
derivatives for lattices with up to 16*16 spins. The imaginary-time data is
continued to real frequency using the maximum-entropy method, as well as a fit
based on spinwave theory. The numerical results are compared with spinwave
calculations for finite lattices. There is a surprisingly large change in the
exact spectrum going from 4*4 to 6*6 sites. In the former case there is a
single dominant two-magnon peak at frequency w/J appr. 3.0, whereas in the
latter case there are two approximately equal-sized peaks at w/J appr. 2.7 and
3.9. This is in good qualitative agreement with the spinwave calculations
including two-magnon processes on the same lattices. Both the Lanczos and the
QMC results indicate that the actual infinite-size two-magnon profile is
broader than the narrow peak obtained in spinwave theory, but the positions of
the maxima agree to within a few percent. The higher-order contributions
present in the numerical results are merged with the two-magnon profile and
extend up to frequencies w/J appr. 7. The first three frequency cumulants of
the spectrum are in excellent agreement with results previously obtained from a
series expansion around the Ising limit. Typical experimental B1g$ spectra for
La2CuO4 are only slightly broader than what we obtain here. The exchange
constant extracted from the peak position is J appr. 1400K, in good agreement
with values obtained from neutron scattering and NMR experiments.Comment: 15 pages, Revtex, 13 PostScript figure
Recommended from our members
Multicenter assessment of a hemoglobin A1c point-of-care device for diagnosis of diabetes mellitus.
ObjectiveA multisite investigation compared the analytical performance of a point-of-care (POC) HbA1c device with multiple commonly used HbA1c laboratory methods and an NGSP (National Glycohemoglobin Standardization Program) reference method.Research design and methodsThe Afinion AS100 POC device analyzed HbA1c using 618 EDTA whole blood excess patient specimens with clinically indicated HbA1c testing. Results were compared to measurements across five clinical laboratories and the NGSP reference method. Precision was evaluated over 8-10 consecutive days for low-, mid-, and high-range HbA1c specimens at all five sites.ResultsOver a wide range of HbA1c values (4.0%-15% HbA1c), 97.1% of the POC results and 94.5% of routine laboratory results fell within the target value of ±6% of the NGSP reference method results. The POC HbA1c results at 6.5% exhibited a total relative bias of -0.6% (-0.04% HbA1c) compared to the reference method while the aggregate of laboratory methods displayed a relative bias of -0.9% (-0.06% HbA1c). The total imprecision of the POC results ranged from 0.74-2.13% CV across the analytic measurement range compared to 0.81-3.23% CV for the routine laboratory methods.ConclusionsThe accuracy and precision of the Afinion POC HbA1c method was comparable to the laboratory HbA1c methods supporting the FDA's recent approval of the Afinion HbA1c Dx device for use in the diagnosis of diabetes
Transgenic Expression of the Anti-parasitic Factor TEP1 in the Malaria Mosquito Anopheles gambiae
Mosquitoes genetically engineered to be resistant to Plasmodium parasites represent a promising novel approach in the fight against malaria. The insect immune system itself is a source of anti-parasitic genes potentially exploitable for transgenic designs. The Anopheles gambiae thioester containing protein 1 (TEP1) is a potent anti-parasitic protein. TEP1 is secreted and circulates in the mosquito hemolymph, where its activated cleaved form binds and eliminates malaria parasites. Here we investigated whether TEP1 can be used to create malaria resistant mosquitoes. Using a GFP reporter transgene, we determined that the fat body is the main site of TEP1 expression. We generated transgenic mosquitoes that express TEP1r, a potent refractory allele of TEP1, in the fat body and examined the activity of the transgenic protein in wild-type or TEP1 mutant genetic backgrounds. Transgenic TEP1r rescued loss-of-function mutations, but did not increase parasite resistance in the presence of a wild-type susceptible allele. Consistent with previous reports, TEP1 protein expressed from the transgene in the fat body was taken up by hemocytes upon a challenge with injected bacteria. Furthermore, although maturation of transgenic TEP1 into the cleaved form was impaired in one of the TEP1 mutant lines, it was still sufficient to reduce parasite numbers and induce parasite melanization. We also report here the first use of Transcription Activator Like Effectors (TALEs) in Anopheles gambiae to stimulate expression of endogenous TEP1. We found that artificial elevation of TEP1 expression remains moderate in vivo and that enhancement of endogenous TEP1 expression did not result in increased resistance to Plasmodium. Taken together, our results reveal the difficulty of artificially influencing TEP1-mediated Plasmodium resistance, and contribute to further our understanding of the molecular mechanisms underlying mosquito resistance to Plasmodium parasites
Chromatin: a tunable spring at work inside chromosomes
This paper focuses on mechanical aspects of chromatin biological functioning.
Within a basic geometric modeling of the chromatin assembly, we give for the
first time the complete set of elastic constants (twist and bend persistence
lengths, stretch modulus and twist-stretch coupling constant) of the so-called
30-nm chromatin fiber, in terms of DNA elastic properties and geometric
properties of the fiber assembly. The computation naturally embeds the fiber
within a current analytical model known as the ``extensible worm-like rope'',
allowing a straightforward prediction of the force-extension curves. We show
that these elastic constants are strongly sensitive to the linker length, up to
1 bp, or equivalently to its twist, and might locally reach very low values,
yielding a highly flexible and extensible domain in the fiber. In particular,
the twist-stretch coupling constant, reflecting the chirality of the chromatin
fiber, exhibits steep variations and sign changes when the linker length is
varied.
We argue that this tunable elasticity might be a key feature for chromatin
function, for instance in the initiation and regulation of transcription.Comment: 38 pages 15 figure
Attraction between DNA molecules mediated by multivalent ions
The effective force between two parallel DNA molecules is calculated as a
function of their mutual separation for different valencies of counter- and
salt ions and different salt concentrations. Computer simulations of the
primitive model are used and the shape of the DNA molecules is accurately
modelled using different geometrical shapes. We find that multivalent ions
induce a significant attraction between the DNA molecules whose strength can be
tuned by the averaged valency of the ions. The physical origin of the
attraction is traced back either to electrostatics or to entropic
contributions. For multivalent counter- and monovalent salt ions, we find a
salt-induced stabilization effect: the force is first attractive but gets
repulsive for increasing salt concentration. Furthermore, we show that the
multivalent-ion-induced attraction does not necessarily correlate with DNA
overcharging.Comment: 51 pages and 13 figure
Hydrodynamic properties of cyclodextrin molecules in dilute solutions
Three well-known representatives of the cyclodextrin family were completely characterized by molecular hydrodynamics methods in three different solvents. For the first time the possibility of an estimation of velocity sedimentation coefficients s between 0.15 and 0.5 S by the numerical solution of the Lamm equation is shown. Comparison of the experimental hydrodynamic characteristics of the cyclodextrins with theoretical calculations for toroidal molecules allows an estimation of the thickness of the solvent layers on the surface of cyclodextrin molecules
The Context of Current Content Analysis of Gender Roles: An Introduction to a Special Issue
The aim of this paper is to provide context for the quantitative content analyses of gender roles that are to be included in both parts of this special issue. First, a timeline of historical uses of the content analysis methodology is presented. Second, research objectives that frequently drive content analysis of gender roles are described; these include: to support feminist claims, to compare media with real life, to predict effects on audiences, and to detect effects of media producers on content. Third, previous content analyses published in Sex Roles and other gender-focused journals are reviewed and categorized in terms of medium, genre, time span, gender, and nationality. Finally, contributions of each of the articles in this special issue are outlined
The Intrinsic Resolution Limit in the Atomic Force Microscope: Implications for Heights of Nano-Scale Features
Background; Accurate mechanical characterization by the atomic force microscope at the highest spatial resolution requires that topography is deconvoluted from indentation. The measured height of nanoscale features in the atomic force microscope (AFM) is almost always smaller than the true value, which is often explained away as sample deformation, the formation of salt deposits and/or dehydration. We show that the real height of nano-objects cannot be obtained directly: a result arising as a consequence of the local probe-sample geometry.
Methods and Findings; We have modeled the tip-surface-sample interaction as the sum of the interaction between the tip and the surface and the tip and the sample. We find that the dynamics of the AFM cannot differentiate between differences in force resulting from 1) the chemical and/or mechanical characteristics of the surface or 2) a step in topography due to the size of the sample; once the size of a feature becomes smaller than the effective area of interaction between the AFM tip and sample, the measured height is compromised. This general result is a major contributor to loss of height and can amount to up to ∼90% for nanoscale features. In particular, these very large values in height loss may occur even when there is no sample deformation, and, more generally, height loss does not correlate with sample deformation. DNA and IgG antibodies have been used as model samples where experimental height measurements are shown to closely match the predicted phenomena.
Conclusions; Being able to measure the true height of single nanoscale features is paramount in many nanotechnology applications since phenomena and properties in the nanoscale critically depend on dimensions. Our approach allows accurate predictions for the true height of nanoscale objects and will lead to reliable mechanical characterization at the highest spatial resolution
- …