191 research outputs found
Nanomechanics of membrane tubulation and DNA assembly
We report an interesting regime of tubule formation in multilamellar membrane vesicles. An optically trapped bead is used to apply a localized subpicoNewton force on a cationic vesicle to form a membrane tubule. The force extension curves reveal a saturation phase, with the tubule length extending up to tens of microns, beyond a threshold force 0.6±0.2 pN. We then use the tubule as a sensor for monitoring the dynamics of charge induced DNA integration on cationic membrane vesicles. Our results may also have applications in the development of nanowires and nanofluidic devices
Possible observation of coulomb blockade at room temperature
We have studied the (I-V) characteristics of the tunnel junction formed between the tip and the substrate in an STM at room temperature. We find that in such an arrangement it may be possible to get a junction capacitance ⋍10−19 F and junction conductance < 1 μs. When the junction conductance is < 1 μs strong nonlinearity is observed in the (I-V) characteristics. We explain this nonlinearity as onset of coulomb blockade of tunneling electrons
Maximal fluctuations of confined actomyosin gels: dynamics of the cell nucleus
We investigate the effect of stress fluctuations on the stochastic dynamics
of an inclusion embedded in a viscous gel. We show that, in non-equilibrium
systems, stress fluctuations give rise to an effective attraction towards the
boundaries of the confining domain, which is reminiscent of an active Casimir
effect. We apply this generic result to the dynamics of deformations of the
cell nucleus and we demonstrate the appearance of a fluctuation maximum at a
critical level of activity, in agreement with recent experiments [E. Makhija,
D. S. Jokhun, and G. V. Shivashankar, Proc. Natl. Acad. Sci. U.S.A. 113, E32
(2016)].Comment: 12 pages, 5 figure
Role of actin dependent nuclear deformation in regulating early gene expression
The nucleus of a living cell is constantly undergoing changes in shape and size as a result of various mechanical forces in physiology. These changes correlate with alterations in gene expression, however it is unclear whether nuclear deformation alone is sufficient to elicit these alterations. We used T-cell activation as a model system to test the coupling between nuclear deformation (elongation) and gene expression. Naïve T-cell activation with surrogate antigens resulted in actin dependent nuclear elongation. This was accompanied with Erk and NF-κB signaling to the nucleus to induce CD69 expression. Importantly, inhibiting actin polymerization abolished both nuclear elongation and CD69 expression, while inhibiting Erk, NF-κB or microtubule depolymerization only abolished expression but not elongation. Immobilization of antigen-coated beads, under conditions where actin polymerization was inhibited, rescued both nuclear elongation and CD69 expression. In addition, fibroblast cells plated on fibronectin micropatterns of different sizes showed correlation between nuclear shape index and tenascin C expression. Upon inhibiting the signaling intermediate Erk, tenascin C expression was down regulated although the nuclear shape index remained unaltered. Our results highlight the importance of specific signaling intermediates accompanied with nuclear deformation in the modulation of cellular genomic programs
Kinetic measurement of ribosome motor stalling force
We measure the ribosome motor stalling forces to unzip mRNA polymers during gene expression. An approach of using the changes in the reaction rate constants to determine the molecular motor forces is presented. Specific antisense DNA oligomers complementary to mRNA templates are used as kinetic barriers for estimating the ribosome forces using real time bioluminescence detection of luciferase gene expression. The rate constants are determined by comparing the experimental data with numerical simulation of gene expression to deduce the ribosome force (26.5±1 pN) required to unzip mRNA polymers. Understanding the forces generated by the ribosome may also enable the construction of information-based artificial nanoscale machines
Distinct levels in the nanoscale organization of DNA-histone complex revealed by its mechanical unfolding
Mechanical unfolding of nanoscale DNA-histone complex, using an atomic force microscope, shows a stepwise disassembly of histones from the nucleosome. A quantitative analysis of the rupture jump statistics and the length released per jump reveals insights into the possible histone contacts within the octamer complex. The measured ruptures correlate with the breakage of multiple contacts that stabilize the histone octamer. These results provide a mechanistic basis by which stepwise disassembly of histone proteins may result from an external force exerted by the adenosinetriphosphate (ATP) dependent chromatin remodeling machines to access regulatory sites on DNA
Transient-linking activity enhances subnuclear dynamics by affecting chromatin remodeling
Spatiotemporal coordination of chromatin and subnuclear compartments is
crucial for cells. A plethora of enzymes act inside nucleus, and some of those
transiently link two chromatin segments. Here, we theoretically study how such
transient-linking activities affect fluctuating dynamics of an inclusion in the
chromatic medium. Numerical simulations and a coarse-grained model analysis
categorize inclusion dynamics into three distinct modes. The transient-linking
activity speeds up the inclusion dynamics by affecting a slow mode associated
with chromatin remodeling, viz., size and shape of the chromatin meshes
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