Untangling the Mechanics and Topology in the Frictional Response of Long Overhand Elastic Knots

Article / Letter to editorLeids Instituut Onderzoek Natuurkund

Improved Quantitative Plant Proteomics via the Combination of Targeted and Untargeted Data Acquisition.

Quantitative proteomics strategies - which are playing important roles in the expanding field of plant molecular systems biology - are traditionally designated as either hypothesis driven or non-hypothesis driven. Many of these strategies aim to select individual peptide ions for tandem mass spectrometry (MS/MS), and to do this mixed hypothesis driven and non-hypothesis driven approaches are theoretically simple to implement. In-depth investigations into the efficacies of such approaches have, however, yet to be described. In this study, using combined samples of unlabeled and metabolically (15)N-labeled Arabidopsis thaliana proteins, we investigate the mixed use of targeted data acquisition (TDA) and data dependent acquisition (DDA) - referred to as TDA/DDA - to facilitate both hypothesis driven and non-hypothesis driven quantitative data collection in individual LC-MS/MS experiments. To investigate TDA/DDA for hypothesis driven data collection, 7 miRNA target proteins of differing size and abundance were targeted using inclusion lists comprised of 1558 m/z values, using 3 different TDA/DDA experimental designs. In samples in which targeted peptide ions were of particularly low abundance (i.e., predominantly only marginally above mass analyser detection limits), TDA/DDA produced statistically significant increases in the number of targeted peptides identified (230 ± 8 versus 80 ± 3 for DDA; p = 1.1 × 10(-3)) and quantified (35 ± 3 versus 21 ± 2 for DDA; p = 0.038) per experiment relative to the use of DDA only. These expected improvements in hypothesis driven data collection were observed alongside unexpected improvements in non-hypothesis driven data collection. Untargeted peptide ions with m/z values matching those in inclusion lists were repeatedly identified and quantified across technical replicate TDA/DDA experiments, resulting in significant increases in the percentages of proteins repeatedly quantified in TDA/DDA experiments only relative to DDA experiments only (33.0 ± 2.6% versus 8.0 ± 2.7%, respectively; p = 0.011). These results were observed together with uncompromised broad-scale MS/MS data collection in TDA/DDA experiments relative to DDA experiments. Using our observations we provide guidelines for TDA/DDA method design for quantitative plant proteomics studies, and suggest that TDA/DDA is a broadly underutilized proteomics data acquisition strategy

A conditional silencing suppression system for transient expression.

RNA silencing is a powerful tool deployed by plants against viral infection and abnormal gene expression. Plant viruses have evolved a suite of silencing suppressors for counter-defense, which are also widely used to boost transcript and protein accumulation in transient assays. However, only wild type silencing suppressor proteins have been reported to date. Here we demonstrate that P0 of Potato leafroll virus (PLRV), PLP0, can be split into two proteins that only show silencing suppression activity upon co-expression. We cloned each of these proteins in two different constructs and transiently co-infiltrated them in N. benthamiana leaves. We expressed a fluorescent protein from one of the vectors and observed that cells expressing both halves of PLP0 suppressed gene silencing. Further, we showed that Q system of Neurospora crassa, based on co-expression of a transcription activator and inhibitor, is functional in agroinfiltrated leaves of N. benthamiana. Q system combined with the split PLP0 system showed very tight co-expression of Q system's transcriptional activator and inhibitor. Altogether, our experiments demonstrate a functioning conditional silencing suppressor system and its potential as a powerful tool for transient expression in N. benthamiana leaves, as well as the application of the Q system in plants

Sex and Exercise Intensity Do Not Influence Oxygen Uptake Kinetics in Submaximal Swimming.

The aim of this study was to compare the oxygen uptake ([Formula: see text]) kinetics in front crawl between male and female swimmers at moderate and heavy intensity. We hypothesized that the time constant for the primary phase [Formula: see text] kinetics was faster in men than in women, for both intensities. Nineteen well trained swimmers (8 females mean ± SD; age 17.9 ± 3.5 years; mass 55.2 ± 3.6 kg; height 1.66 ± 0.05 m and 11 male 21.9 ± 2.8 years; 78.2 ± 11.1 kg; 1.81 ± 0.08 m) performed a discontinuous maximal incremental test and two 600-m square wave transitions for both moderate and heavy intensities to determine the [Formula: see text] kinetics parameters using mono- and bi-exponential models, respectively. All the tests involved breath-by-breath analysis of front crawl swimming using a swimming snorkel. The maximal oxygen uptake [Formula: see text] was higher in men than in women [4,492 ± 585 ml·min(-1) and 57.7 ± 4.4 ml·kg(-1)·min(-1) vs. 2,752.4 ± 187.9 ml·min(-1) (p ≤ 0.001) and 50.0 ± 5.7 ml·kg(-1)·min(-1)(p = 0.007), respectively]. Similarly, the absolute amplitude of the primary component was higher in men for both intensities (moderate: 1,736 ± 164 vs. 1,121 ± 149 ml·min(-1); heavy: 2,948 ± 227 vs. 1,927 ± 243 ml·min(-1), p ≤ 0.001, for males and females, respectively). However, the time constant of the primary component (τp) was not influenced by sex (p = 0.527) or swimming intensity (p = 0.804) (moderate: 15.1 ± 5.6 vs. 14.4 ± 5.1 s; heavy: 13.5 ± 3.3 vs. 16.0 ± 4.5 s, for females and males, respectively). The slow component in the heavy domain was not significantly different between female and male swimmers (3.2 ± 2.4 vs. 3.8 ± 1.0 ml·kg(-1)·min(-1), p = 0.476). Overall, only the absolute amplitude of the primary component was higher in men, while the other [Formula: see text] kinetics parameters were similar between female and male swimmers at both moderate and heavy intensities. The mechanisms underlying these similarities remain unclear

Oscillatory fracture path in thin elastic sheet

We report a novel mode of oscillatory crack propagation when a cutting tip is driven through a thin brittle polymer film. The phenomenon is so robust that it can easily be reproduced at hand (using CD packaging material for example). Careful experiments show that the amplitude and wavelength of the oscillatory crack path scale lineraly with the width of the cutting tip over a wide range of lenghtscales but are independant of the width of thje sheet and the cutting speed. A simple geometric model is presented, which provides a simple but thorough interpretation of the oscillations.Comment: 6 pages, submitted to Comptes Rendus Academie des Sciences. Movies available at http://www.lmm.jussieu.fr/platefractur

Untangling the Mechanics and Topology in the Frictional Response of Long Overhand Elastic Knots

Biological and Soft Matter Physic

Structural Properties of Self-Attracting Walks

Self-attracting walks (SATW) with attractive interaction u > 0 display a swelling-collapse transition at a critical u_{\mathrm{c}} for dimensions d >= 2, analogous to the \Theta transition of polymers. We are interested in the structure of the clusters generated by SATW below u_{\mathrm{c}} (swollen walk), above u_{\mathrm{c}} (collapsed walk), and at u_{\mathrm{c}}, which can be characterized by the fractal dimensions of the clusters d_{\mathrm{f}} and their interface d_{\mathrm{I}}. Using scaling arguments and Monte Carlo simulations, we find that for u<u_{\mathrm{c}}, the structures are in the universality class of clusters generated by simple random walks. For u>u_{\mathrm{c}}, the clusters are compact, i.e. d_{\mathrm{f}}=d and d_{\mathrm{I}}=d-1. At u_{\mathrm{c}}, the SATW is in a new universality class. The clusters are compact in both d=2 and d=3, but their interface is fractal: d_{\mathrm{I}}=1.50\pm0.01 and 2.73\pm0.03 in d=2 and d=3, respectively. In d=1, where the walk is collapsed for all u and no swelling-collapse transition exists, we derive analytical expressions for the average number of visited sites and the mean time to visit S sites.Comment: 15 pages, 8 postscript figures, submitted to Phys. Rev.

Selective stimulatory action of olfactory ensheathing glia-conditioned medium on oligodendroglial differentiation, with additional reference to signaling mechanisms

AbstractWe examined the effects of conditioned medium from olfactory ensheathing glia (OEGCM) on the differentiation of oligodendrocytes in mixed cultures of early postnatal hippocampi. Differentiation was judged from the numerical density (ND) of cells immunoreactive to 2′3′ cyclic nucleotide 3′phosphodiesterase (CNPase) and O4 antibodies. NDs increased according to inverted-U dose–response curves, particularly for CNPase+ cells (9-fold at optimal dilution) and these changes were blocked by inhibitors of ERK1, p38-MAPK, and PI3K. Our results raise the possibility that OEG secreted factor(s) may counteract demyelination induced by trauma, neurodegenerative diseases, and advanced age, and should stimulate novel methods to deliver these factors and/or potentiating chemicals

CONGELABILIDADE DO SÊMEN SUÍNO DE ACORDO COM O PERÍODO DE EQUILÍBRIO PRÉ-CONGELAMENTO E DA SENSIBILIDADE AO RESFRIAMENTO

O objetivo deste estudo foi avaliar a influência do período de equilíbrio pré-congelamento e da sensibilidade ao resfriamento sobre a qualidade do sêmen suíno congelado. Foram utilizados dez ejaculados de cada um dos 8 machos doadores. A motilidade de doses de sêmen preparadas a partir dos mesmos ejaculados utilizados no congelamento, foi avaliada simultaneamente, durante o resfriamento a 15ºC, a cada 24h. A porção de cada ejaculado destinada ao congelamento foi separada em duas partes que foram submetidas a equilíbrio prévio, a 20ºC, curto (1,5h) ou longo (20h). As palhetas foram descongeladas a 37ºC por 20 segundos e seu conteúdo (0,5mL) foi diluído (1:6) em Beltsville Thawing Solution (BTS). Foram avaliados a motilidade (MOT), acrossomos normais após o descongelamento (NARPD) e após o teste de termoresistência (NARTTR), e membranas íntegras (MI). Para a análise estatística, os ejaculados foram separados, de acordo com sua sensibilidade ao resfriamento, em dois grupos: motilidade 0,05). O equilíbrio por 20h não apresentou diferenças na MOT e MI (P>0,05), mas o NARPD e NARTTR foram superiores (

A mathematical analysis of the evolution of perturbations in a modified Chaplygin gas model

One approach in modern cosmology consists in supposing that dark matter and dark energy are different manifestations of a single `quartessential' fluid. Following such idea, this work presents a study of the evolution of perturbations of density in a flat cosmological model with a modified Chaplygin gas acting as a single component. Our goal is to obtain properties of the model which can be used to distinguish it from another cosmological models which have the same solutions for the general evolution of the scale factor of the universe, without the construction of the power spectrum. Our analytical results, which alone can be used to uniquely characterize the specific model studied in our work, show that the evolution of the density contrast can be seen, at least in one particular case, as composed by a spheroidal wave function. We also present a numerical analysis which clearly indicates as one interesting feature of the model the appearence of peaks in the evolution of the density constrast.Comment: 21 pages, accepted for publication in General Relativity and Gravitatio