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Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes.

ABSTRACT: A-tracts are A:T rich DNA sequences that exhibit unique structural and mechanical properties associated with several functions in vivo. The crystallographic structure of A-tracts has been well characterized. However, the mechanical properties of these sequences is controversial and their response to force remains unexplored. Here, we rationalize the mechanical properties of in-phase A-tracts present in the Caenorhabditis elegans genome over a wide range of external forces, using single-molecule experiments and theoretical polymer models. Atomic Force Microscopy imaging shows that A-tracts induce long-range (?200 nm) bending, which originates from an intrinsically bent structure rather than from larger bending flexibility. These data are well described with a theoretical model based on the worm-like chain model that includes intrinsic bending. Magnetic tweezers experiments show that the mechanical response of A-tracts and arbitrary DNA sequences have a similar dependence with monovalent salt supporting that the observed A-tract bend is intrinsic to the sequence. Optical tweezers experiments reveal a high stretch modulus of the A-tract sequences in the enthalpic regime. Our work rationalizes the complex multiscale flexibility of A-tracts, providing a physical basis for the versatile character of these sequences inside the cell.

SUBMITTER: Marin-Gonzalez A

PROVIDER: S-EPMC7229863 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes.

Marin-Gonzalez Alberto A Pastrana Cesar L CL Bocanegra Rebeca R Martín-González Alejandro A Vilhena J G JG Pérez Rubén R Ibarra Borja B Aicart-Ramos Clara C Moreno-Herrero Fernando F

Nucleic acids research 20200501 9

A-tracts are A:T rich DNA sequences that exhibit unique structural and mechanical properties associated with several functions in vivo. The crystallographic structure of A-tracts has been well characterized. However, the mechanical properties of these sequences is controversial and their response to force remains unexplored. Here, we rationalize the mechanical properties of in-phase A-tracts present in the Caenorhabditis elegans genome over a wide range of external forces, using single-molecule ...[more]

PMID: 32282908

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Project description:The synchronization of different γ-rhythms arising in different brain areas has been implicated in various cognitive functions. Here, we focus on the effect of the ubiquitous neuronal heterogeneity on the synchronization of ING (interneuronal network gamma) and PING (pyramidal-interneuronal network gamma) rhythms. The synchronization properties of rhythms depends on the response of their collective phase to external input. We therefore determine the macroscopic phase-response curve for finite-amplitude perturbations (fmPRC) of ING- and PING-rhythms in all-to-all coupled networks comprised of linear (IF) or quadratic (QIF) integrate-and-fire neurons. For the QIF networks we complement the direct simulations with the adjoint method to determine the infinitesimal macroscopic PRC (imPRC) within the exact mean-field theory. We show that the intrinsic neuronal heterogeneity can qualitatively modify the fmPRC and the imPRC. Both PRCs can be biphasic and change sign (type II), even though the phase-response curve for the individual neurons is strictly non-negative (type I). Thus, for ING rhythms, say, external inhibition to the inhibitory cells can, in fact, advance the collective oscillation of the network, even though the same inhibition would lead to a delay when applied to uncoupled neurons. This paradoxical advance arises when the external inhibition modifies the internal dynamics of the network by reducing the number of spikes of inhibitory neurons; the advance resulting from this disinhibition outweighs the immediate delay caused by the external inhibition. These results explain how intrinsic heterogeneity allows ING- and PING-rhythms to become synchronized with a periodic forcing or another rhythm for a wider range in the mismatch of their frequencies. Our results identify a potential function of neuronal heterogeneity in the synchronization of coupled γ-rhythms, which may play a role in neural information transfer via communication through coherence.

Project description:BackgroundChest wall loading has been shown to paradoxically improve respiratory system compliance (CRS) in patients with moderate to severe acute respiratory distress syndrome (ARDS). The most likely, albeit unconfirmed, mechanism is relief of end-tidal overdistension in 'baby lungs' of low-capacity. The purpose of this study was to define how small changes of tidal volume (VT) and positive end-expiratory pressure (PEEP) affect CRS (and its associated airway pressures) in patients with ARDS who demonstrate a paradoxical response to chest wall loading. We hypothesized that small reductions of VT or PEEP would alleviate overdistension and favorably affect CRS and conversely, that small increases of VT or PEEP would worsen CRS.MethodsProspective, multi-center physiologic study of seventeen patients with moderate to severe ARDS who demonstrated paradoxical responses to chest wall loading. All patients received mechanical ventilation in volume control mode and were passively ventilated. Airway pressures were measured before and after decreasing/increasing VT by 1 ml/kg predicted body weight and decreasing/increasing PEEP by 2.5 cmH2O.ResultsDecreasing either VT or PEEP improved CRS in all patients. Driving pressure (DP) decreased by a mean of 4.9 cmH2O (supine) and by 4.3 cmH2O (prone) after decreasing VT, and by a mean of 2.9 cmH2O (supine) and 2.2 cmH2O (prone) after decreasing PEEP. CRS increased by a mean of 3.1 ml/cmH2O (supine) and by 2.5 ml/cmH2O (prone) after decreasing VT. CRS increased by a mean of 5.2 ml/cmH2O (supine) and 3.6 ml/cmH2O (prone) after decreasing PEEP (P < 0.01 for all). Small increments of either VT or PEEP worsened CRS in the majority of patients.ConclusionPatients with a paradoxical response to chest wall loading demonstrate uniform improvement in both DP and CRS following a reduction in either VT or PEEP, findings in keeping with prior evidence suggesting its presence is a sign of end-tidal overdistension. The presence of 'paradox' should prompt re-evaluation of modifiable determinants of end-tidal overdistension, including VT, PEEP, and body position.

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Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes.

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Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes.

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