Modelling the unfolding pathway of biomolecules: theoretical approach and experimental prospect

We analyse the unfolding pathway of biomolecules comprising several independent modules in pulling experiments. In a recently proposed model, a critical velocity $v_{c}$ has been predicted, such that for pulling speeds $v>v_{c}$ it is the module at the pulled end that opens first, whereas for $v<v_{c}$ it is the weakest. Here, we introduce a variant of the model that is closer to the experimental setup, and discuss the robustness of the emergence of the critical velocity and of its dependence on the model parameters. We also propose a possible experiment to test the theoretical predictions of the model, which seems feasible with state-of-art molecular engineering techniques.Comment: Accepted contribution for the Springer Book "Coupled Mathematical Models for Physical and Biological Nanoscale Systems and Their Applications" (proceedings of the BIRS CMM16 Workshop held in Banff, Canada, August 2016), 16 pages, 6 figure

Randomized Comparison of Two Techniques for Titrating Power During Radiofrequency Ablation of Accessory Pathways

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75733/1/j.1540-8167.1996.tb00592.x.pd

Generality of shear thickening in suspensions

Suspensions are of wide interest and form the basis for many smart fluids. For most suspensions, the viscosity decreases with increasing shear rate, i.e. they shear thin. Few are reported to do the opposite, i.e. shear thicken, despite the longstanding expectation that shear thickening is a generic type of suspension behavior. Here we resolve this apparent contradiction. We demonstrate that shear thickening can be masked by a yield stress and can be recovered when the yield stress is decreased below a threshold. We show the generality of this argument and quantify the threshold in rheology experiments where we control yield stresses arising from a variety of sources, such as attractions from particle surface interactions, induced dipoles from applied electric and magnetic fields, as well as confinement of hard particles at high packing fractions. These findings open up possibilities for the design of smart suspensions that combine shear thickening with electro- or magnetorheological response.Comment: 11 pages, 9 figures, accepted for publication in Nature Material

Towards an understanding of hole superconductivity

From the very beginning K. Alex M\"uller emphasized that the materials he and George Bednorz discovered in 1986 were $hole$ superconductors. Here I would like to share with him and others what I believe to be $the$ key reason for why high $T_c$ cuprates as well as all other superconductors are hole superconductors, which I only came to understand a few months ago. This paper is dedicated to Alex M\"uller on the occasion of his 90th birthday.Comment: Dedicated to Alex M\"uller on the Occasion of his 90th Birthday. arXiv admin note: text overlap with arXiv:1703.0977

Feasibility of the porous zone approach to modelling vegetation in CFD

Vegetation within stormwater ponds varies seasonly and its presence affects the flow field, which in turn affects the pond’s Residence Time Distribution and its effectiveness at pollutant removal. Vegetated flows are complex and, as a result, few suitable tools exist for evaluating realistic stormwater pond designs. Recent research has suggested using a porous zone to represent vegetation within a CFD model, and this paper investigates the feasibility of this approach using ANSYS Fluent. One of the main benefits of using a porous zone is the ability to derive the relevant parameters from the known physical characteristics of stem diameter and porosity using the Ergun equation. A sensitivity analysis on the viscous resistance factor 1/α1/α and the inertial resistance factor C2C2 has been undertaken by comparing model results to data collected from an experimental vegetated channel. Best fit values of C2C2 were obtained for a range of flow conditions including emergent and submerged vegetation. Results show the CFD model to be insensitive to 1/α1/α but very sensitive to values of C2C2. For submerged vegetation, values of C2C2 derived from the Ergun equation are under-predictions of best-fit C2C2 values as only the turbulence due to the shear layer is represented. The porous zone approach does not take into account turbulence generated from stem wakes such that no meaningful predictions for emergent vegetation were obtained. C2C2 values calculated using a force balance show better agreement with best-fit C2C2 values than those derived from the Ergun equation. Manually fixing values of kk and εε within the porous zone of the model shows initial promise as a means of taking stem wakes into account

Parental transfer of the antimicrobial protein LBP/BPI protects Biomphalaria glabrata eggs against oomycete infections

Copyright: © 2013 Baron et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was funded by ANR (ANR-07-BLAN-0214 and ANR-12-EMMA-00O7-01), CNRS and INRA. PvW was financially supported by the BBSRC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Candidate Genes Detected in Transcriptome Studies Are Strongly Dependent on Genetic Background

Whole genome transcriptomic studies can point to potential candidate genes for organismal traits. However, the importance of potential candidates is rarely followed up through functional studies and/or by comparing results across independent studies. We have analysed the overlap of candidate genes identified from studies of gene expression in Drosophila melanogaster using similar technical platforms. We found little overlap across studies between putative candidate genes for the same traits in the same sex. Instead there was a high degree of overlap between different traits and sexes within the same genetic backgrounds. Putative candidates found using transcriptomics therefore appear very sensitive to genetic background and this can mask or override effects of treatments. The functional importance of putative candidate genes emerging from transcriptome studies needs to be validated through additional experiments and in future studies we suggest a focus on the genes, networks and pathways affecting traits in a consistent manner across backgrounds

NCF1 gene and pseudogene pattern: association with parasitic infection and autoimmunity

<p>Abstract</p> <p>Background</p> <p>Neutrophil cytosolic factor 1, p47^phox(NCF1) is a component of the leukocyte NADPH oxidase complex mediating formation of reactive oxygen intermediates (ROI) which play an important role in host defense and autoimmunity. An individual genomic pattern of <it>ncf1 </it>and its two types of pseudogenes (reflected by the ΔGT/GTGT ratio) may influence the individual capacity to produce ROI.</p> <p>Methods</p> <p>NCF1ΔGT/GTGT ratios were correlated with clinical parameters and ROI production during <it>Plasmodium falciparum </it>malaria and with susceptibility to the autoimmune disease multiple sclerosis (MS).</p> <p>Results</p> <p>Among Gabonese children with severe malaria, ROI production from peripheral blood tended to be higher in individuals with a ΔGT/GTGT ratio ≤ 1:1. ΔGT/GTGT ratios were not associated with susceptibility to MS, but to age-of-onset among MS patients.</p> <p>Conclusion</p> <p>The genomic pattern of <it>NCF1 </it>and its pseudogenes might influence ROI production but only marginally influence susceptibility to and outcome of malaria and MS.</p

Ploidy elicits a whole-genome dosage effect: growth of triploid Atlantic salmon is linked to the genetic origin of the second maternal chromosome set

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