255 research outputs found
Transverse fluctuations of grafted polymers
We study the statistical mechanics of grafted polymers of arbitrary stiffness
in a two-dimensional embedding space with Monte Carlo simulations. The
probability distribution function of the free end is found to be highly
anisotropic and non-Gaussian for typical semiflexible polymers. The reduced
distribution in the transverse direction, a Gaussian in the stiff and flexible
limits, shows a double peak structure at intermediate stiffnesses. We also
explore the response to a transverse force applied at the polymer free end. We
identify F-Actin as an ideal benchmark for the effects discussed.Comment: 10 pages, 4 figures, submitted to Physical Review
Self-organization and Mechanical Properties of Active Filament Bundles
A phenomenological description for active bundles of polar filaments is
presented. The activity of the bundle results from crosslinks, that induce
relative displacements between the aligned filaments. Our generic description
is based on momentum conservation within the bundle. By specifying the internal
forces, a simple minimal model for the bundle dynamics is obtained, capturing
generic dynamic behaviors. In particular, contracted states as well as solitary
and oscillatory waves appear through dynamic instabilities. The introduction of
filament adhesion leads to self-organized persistent filament transport.
Furthermore, calculating the tension, homogeneous bundles are shown to be able
to actively contract and to perform work against external forces. Our
description is motivated by dynamic phenomena in the cytoskeleton and could
apply to stress-fibers and self-organization phenomena during cell-locomotion.Comment: 19 pages, 10 figure
Structure formation in active networks
Structure formation and constant reorganization of the actin cytoskeleton are
key requirements for the function of living cells. Here we show that a minimal
reconstituted system consisting of actin filaments, crosslinking molecules and
molecular-motor filaments exhibits a generic mechanism of structure formation,
characterized by a broad distribution of cluster sizes. We demonstrate that the
growth of the structures depends on the intricate balance between
crosslinker-induced stabilization and simultaneous destabilization by molecular
motors, a mechanism analogous to nucleation and growth in passive systems. We
also show that the intricate interplay between force generation, coarsening and
connectivity is responsible for the highly dynamic process of structure
formation in this heterogeneous active gel, and that these competing mechanisms
result in anomalous transport, reminiscent of intracellular dynamics
Patterning of wound-induced intercellular Ca2+ flashes in a developing epithelium
Differential mechanical force distributions are increasingly recognized to provide important feedback into the control of an organ's final size and shape. As a second messenger that integrates and relays mechanical information to the cell, calcium ions (Ca2+) are a prime candidate for providing important information on both the overall mechanical state of the tissue and resulting behavior at the individual-cell level during development. Still, how the spatiotemporal properties of Ca2+ transients reflect the underlying mechanical characteristics of tissues is still poorly understood. Here we use an established model system of an epithelial tissue, the Drosophila wing imaginal disc, to investigate how tissue properties impact the propagation of Ca2+ transients induced by laser ablation. The resulting intercellular Ca2+ flash is found to be mediated by inositol 1,4,5-trisphosphate and depends on gap junction communication. Further, we find that intercellular Ca2+ transients show spatially non-uniform characteristics across the proximal–distal axis of the larval wing imaginal disc, which exhibit a gradient in cell size and anisotropy. A computational model of Ca2+ transients is employed to identify the principle factors explaining the spatiotemporal patterning dynamics of intercellular Ca2+ flashes. The relative Ca2+ flash anisotropy is principally explained by local cell shape anisotropy. Further, Ca2+ velocities are relatively uniform throughout the wing disc, irrespective of cell size or anisotropy. This can be explained by the opposing effects of cell diameter and cell elongation on intercellular Ca2+ propagation. Thus, intercellular Ca2+ transients follow lines of mechanical tension at velocities that are largely independent of tissue heterogeneity and reflect the mechanical state of the underlying tissue
Colloquium: Mechanical formalisms for tissue dynamics
The understanding of morphogenesis in living organisms has been renewed by
tremendous progressin experimental techniques that provide access to
cell-scale, quantitative information both on theshapes of cells within tissues
and on the genes being expressed. This information suggests that
ourunderstanding of the respective contributions of gene expression and
mechanics, and of their crucialentanglement, will soon leap forward.
Biomechanics increasingly benefits from models, which assistthe design and
interpretation of experiments, point out the main ingredients and assumptions,
andultimately lead to predictions. The newly accessible local information thus
calls for a reflectionon how to select suitable classes of mechanical models.
We review both mechanical ingredientssuggested by the current knowledge of
tissue behaviour, and modelling methods that can helpgenerate a rheological
diagram or a constitutive equation. We distinguish cell scale ("intra-cell")and
tissue scale ("inter-cell") contributions. We recall the mathematical framework
developpedfor continuum materials and explain how to transform a constitutive
equation into a set of partialdifferential equations amenable to numerical
resolution. We show that when plastic behaviour isrelevant, the dissipation
function formalism appears appropriate to generate constitutive equations;its
variational nature facilitates numerical implementation, and we discuss
adaptations needed in thecase of large deformations. The present article
gathers theoretical methods that can readily enhancethe significance of the
data to be extracted from recent or future high throughput
biomechanicalexperiments.Comment: 33 pages, 20 figures. This version (26 Sept. 2015) contains a few
corrections to the published version, all in Appendix D.2 devoted to large
deformation
Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics
Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons for viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we present a benchmark of metagenomics protocols used in clinical diagnostic laboratories initiated by the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS). A mock viral reference panel was designed to mimic low biomass clinical specimens. The panel was used to assess the performance of twelve metagenomic wet lab protocols currently in use in the diagnostic laboratories of participating ENNGS member institutions. Both Illumina and Nanopore, shotgun and targeted capture probe protocols were included. Performance metrics sensitivity, specificity, and quantitative potential were assessed using a central bioinformatics pipeline. Overall, viral pathogens with loads down to 104 copies/ml (corresponding to CT values of 31 in our PCR assays) were detected by all the evaluated metagenomic wet lab protocols. In contrast, lower abundant mixed viruses of CT values of 35 and higher were detected only by a minority of the protocols. Considering the reference panel as the gold standard, optimal thresholds to define a positive result were determined per protocol, based on the horizontal genome coverage. Implementing these thresholds, sensitivity and specificity of the protocols ranged from 67 to 100 % and 87 to 100 %, respectively. A variety of metagenomic protocols are currently in use in clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implying the need for standardization of metagenomic analysis for use in clinical settings.</p
Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics
Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons for viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we present a benchmark of metagenomics protocols used in clinical diagnostic laboratories initiated by the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS). A mock viral reference panel was designed to mimic low biomass clinical specimens. The panel was used to assess the performance of twelve metagenomic wet lab protocols currently in use in the diagnostic laboratories of participating ENNGS member institutions. Both Illumina and Nanopore, shotgun and targeted capture probe protocols were included. Performance metrics sensitivity, specificity, and quantitative potential were assessed using a central bioinformatics pipeline. Overall, viral pathogens with loads down to 104 copies/ml (corresponding to CT values of 31 in our PCR assays) were detected by all the evaluated metagenomic wet lab protocols. In contrast, lower abundant mixed viruses of CT values of 35 and higher were detected only by a minority of the protocols. Considering the reference panel as the gold standard, optimal thresholds to define a positive result were determined per protocol, based on the horizontal genome coverage. Implementing these thresholds, sensitivity and specificity of the protocols ranged from 67 to 100 % and 87 to 100 %, respectively. A variety of metagenomic protocols are currently in use in clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implying the need for standardization of metagenomic analysis for use in clinical settings.</p
Rapid semi-automated quantitative multiplex tandem PCR (MT-PCR) assays for the differential diagnosis of influenza-like illness
<p>Abstract</p> <p>Background</p> <p>Influenza A, including avian influenza, is a major public health threat in developed and developing countries. Rapid and accurate detection is a key component of strategies to contain spread of infection, and the efficient diagnosis of influenza-like-illness is essential to protect health infrastructure in the event of a major influenza outbreak.</p> <p>Methods</p> <p>We developed a multiplexed PCR (MT-PCR) assay for the simultaneous diagnosis of respiratory viruses causing influenza-like illness, including the specific recognition of influenza A haemagglutinin subtypes H1, H3, and H5. We tested several hundred clinical specimens in two diagnostic reference laboratories and compared the results with standard techniques.</p> <p>Results</p> <p>The sensitivity and specificity of these assays was higher than individual assays based on direct antigen detection and standard PCR against a range of control templates and in several hundred clinical specimens. The MT-PCR assays provided differential diagnoses as well as potentially useful quantitation of virus in clinical samples.</p> <p>Conclusions</p> <p>MT-PCR is a potentially powerful tool for the differential diagnosis of influenza-like illness in the clinical diagnostic laboratory.</p
Episodic Therapy for Genital Herpes in Sub-Saharan Africa: A Pooled Analysis from Three Randomized Controlled Trials
BACKGROUND: A randomized controlled trial in South Africa found a beneficial effect of acyclovir on genital ulcer healing, but no effect was seen in trials in Ghana, Central African Republic and Malawi. The aim of this paper is to assess whether the variation in impact of acyclovir on ulcer healing in these trials can be explained by differences in the characteristics of the study populations. METHODOLOGY/PRINCIPAL FINDINGS: Pooled data were analysed to estimate the impact of acyclovir on the proportion of ulcers healed seven days after randomisation by HIV/CD4 status, ulcer aetiology, size and duration before presentation; and impact on lesional HIV-1. Risk ratios (RR) were estimated using Poisson regression with robust standard errors. Of 1478 patients with genital ulcer, most (63%) had herpetic ulcers (16% first episode HSV-2 ulcers), and a further 3% chancroid, 2% syphilis, 0.7% lymphogranuloma venereum and 31% undetermined aetiology. Over half (58%) of patients were HIV-1 seropositive. The median duration of symptoms before presentation was 6 days. Patients on acyclovir were more likely to have a healed ulcer on day 7 (63% vs 57%, RR = 1.08, 95% CI 0.98-1.18), shorter time to healing (p = 0.04) and less lesional HIV-1 RNA (p = 0.03). Small ulcers (<50 mm(2)), HSV-2 ulcers, first episode HSV-2 ulcers, and ulcers in HIV-1 seropositive individuals responded best but the better effectiveness in South Africa was not explained by differences in these factors. CONCLUSIONS/SIGNIFICANCE: There may be slight benefit in adding acyclovir to syndromic management in settings where most ulcers are genital herpes. The stronger effect among HIV-1 infected individuals suggests that acyclovir may be beneficial for GUD/HIV-1 co-infected patients. The high prevalence in this population highlights that genital ulceration in patients with unknown HIV status provides a potential entry point for provider-initiated HIV testing
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