Critical speed estimated by statistically appropriate fitting procedures.

Intensity domains are recommended when prescribing exercise. The distinction between heavy and severe domains is made by the critical speed (CS), therefore requiring a mathematically accurate estimation of CS. The different model variants (distance versus time, running speed versus time, time versus running speed, and distance versus running speed) are mathematically equivalent. Nevertheless, error minimization along the correct axis is important to estimate CS and the distance that can be run above CS (d'). We hypothesized that comparing statistically appropriate fitting procedures, which minimize the error along the axis corresponding to the properly identified dependent variable, should provide similar estimations of CS and d' but that different estimations should be obtained when comparing statistically appropriate and inappropriate fitting procedure. Sixteen male runners performed a maximal incremental aerobic test and four exhaustive runs at 90, 100, 110, and 120% of their peak speed on a treadmill. Several fitting procedures (a combination of a two-parameter model variant and regression analysis: weighted least square) were used to estimate CS and d'. Systematic biases (P < 0.001) were observed between each pair of fitting procedures for CS and d', even when comparing two statistically appropriate fitting procedures, though negligible, thus corroborating the hypothesis. The differences suggest that a statistically appropriate fitting procedure should be chosen beforehand by the researcher. This is also important for coaches that need to prescribe training sessions to their athletes based on exercise intensity, and their choice should be maintained over the running seasons

Qualitative modelling and analysis of regulations in multi-cellular systems using Petri nets and topological collections

In this paper, we aim at modelling and analyzing the regulation processes in multi-cellular biological systems, in particular tissues. The modelling framework is based on interconnected logical regulatory networks a la Rene Thomas equipped with information about their spatial relationships. The semantics of such models is expressed through colored Petri nets to implement regulation rules, combined with topological collections to implement the spatial information. Some constraints are put on the the representation of spatial information in order to preserve the possibility of an enumerative and exhaustive state space exploration. This paper presents the modelling framework, its semantics, as well as a prototype implementation that allowed preliminary experimentation on some applications.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Differential regulation of lipopolysaccharide and Gram-positive bacteria induced cytokine and chemokine production in splenocytes by Gαi proteins

AbstractHeterotrimeric Gi proteins play a role in lipopolysaccharide (LPS) and Staphylococcus aureus (SA) activated signaling leading to inflammatory mediator production. We hypothesized that genetic deletion of Gi proteins would alter cytokine and chemokine production induced by LPS and SA. LPS- and heat killed SA-induced cytokine and chemokine production in splenocytes from wild type (WT), Gαi2 (−/−) or Gαi1/3 (−/−) mice were investigated. LPS- or SA-induced production of TNFα, IL-6, IFNγ, IL-12, IL-17, GM-CSF, MIP-1α, MCP-1, MIG and IP-10 were significantly increased (1.2 to 33 fold, p<0.05) in splenocytes harvested from Gαi2(−/−) mice compared with WT mice. The effect of Gαi protein depletion was remarkably isoform specific. In splenocytes from Gαi1/3 (−/−) mice relative to WT mice, SA-induced IL-6, IFNγ, GM-CSF, and IP-10 levels were decreased (59% to 86%, p<0.05), whereas other LPS- or SA-stimulated cytokines and chemokines were not different relative to WT mice. LPS- and SA-induced production of KC were unchanged in both groups of the genetic deficient mice. Splenocytes from both Gαi2 (−/−) and Gαi1/3 (−/−) mice did not exhibit changes in TLR2 and TLR4 expression. Also analysis of splenic cellular composition by flow cytometry demonstrated an increase in splenic macrophages and reduced CD4 T cells in both Gαi2 (−/−) and Gαi1/3 (−/−) mice relative to WT mice. The disparate response of splenocytes from the Gαi2 (−/−) relative to Gαi1/3 (−/−) mice therefore cannot be attributed to major differences in spleen cellular composition. These data demonstrate that Gi2 and Gi1/3 proteins are both involved and differentially regulate splenocyte inflammatory cytokine and chemokine production in a highly Gi isoform specific manner in response to LPS and Gram-positive microbial stimuli

Virus effects on plant quality and vector behavior are species specific and do not depend on host physiological phenotype

There is growing evidence that plant viruses manipulate host plants to increase transmission-conducive behaviors by vectors. Reports of this phenomenon frequently include only highly susceptible, domesticated annual plants as hosts, which constrains our ability to determine whether virus effects are a component of an adaptive strategy on the part of the pathogen or simply by-products of pathology. Here, we tested the hypothesis that transmission-conducive effects of a virus (Turnip yellows virus [TuYV]) on host palatability and vector behavior (Myzus persicae) are linked with host plant tolerance and physiological phenotype. Our study system consisted of a cultivated crop, false flax (Camelina sativa) (Brassicales: Brassicaceae), a wild congener (C. microcarpa), and a viable F1 hybrid of these two species. We found that the most tolerant host (C. microcarpa) exhibited the most transmission-conducive changes in phenotype relative to mock-inoculated healthy plants: Aphids preferred to settle and feed on TuYV-infected C. microcarpa and did not experience fitness changes due to infection—both of which will increase viruliferous aphid numbers. In contrast, TuYV induced transmission-limiting phenotypes in the least tolerant host (C. sativa) and to a greater degree in the F1 hybrid, which exhibited intermediate tolerance to infection. Our results provide no evidence that virus effects track with infection tolerance or physiological phenotype. Instead, vector preferences and performance are driven by host-specific changes in carbohydrates under TuYV infection. These results provide evidence that induction of transmission-enhancing phenotypes by plant viruses is not simply a by-product of general pathology, as has been proposed as an explanation for putative instances of parasite manipulation by viruses and many other taxa

Initial oak regeneration responses to experimental warming along microclimatic and macroclimatic gradients

Quercus spp. are one of the most important tree genera in temperate deciduous forests in terms of biodiversity, economic and cultural perspectives. However, natural regeneration of oaks, depending on specific environmental conditions, is still not sufficiently understood. Oak regeneration dynamics are impacted by climate change, but these climate impacts will depend on local forest management and light and temperature conditions. Here, we studied germination, survival and seedling performance (i.e. aboveground biomass, height, root collar diameter and specific leaf area) of four oak species (Q. cerris, Q. ilex, Q. robur and Q. petraea). Acorns were sown across a wide latitudinal gradient, from Italy to Sweden, and across several microclimatic gradients located within and beyond the species' natural ranges. Microclimatic gradients were applied in terms of forest structure, distance to the forest edge and experimental warming. We found strong interactions between species and latitude, as well as between microclimate and latitude or species. The species thus reacted differently to local and regional changes in light and temperature ; in southern regions the temperate Q. robur and Q. petraea performed best in plots with a complex structure, whereas the Mediterranean Q. ilex and Q. cerris performed better in simply structured forests with a reduced microclimatic buffering capacity. The experimental warming treatment only enhanced height and aboveground biomass of Mediterranean species. Our results show that local microclimatic gradients play a key role in the initial stages of oak regeneration; however, one needs to consider the species-specific responses to forest structure and the macroclimatic context

A guided tour of asynchronous cellular automata

Research on asynchronous cellular automata has received a great amount of attention these last years and has turned to a thriving field. We survey the recent research that has been carried out on this topic and present a wide state of the art where computing and modelling issues are both represented.Comment: To appear in the Journal of Cellular Automat

Functional response of soil microbial communities to tillage, cover crops and nitrogen fertilization

© 2016 Elsevier B.V.Agricultural practices such as tillage, cover crops, and nitrogen (N) fertilization affect physico-chemical and biological soil parameters. However, these factors were often studied separately and their combined effects remain unclear, especially with respect to soil microbial functional diversity and carbon (C) and N content. Thereafter, we aim to assess the links between cropping systems and functional response of microbial communities by using a large range of soil chemical and biological measurements. A 5-yr field experiment was conducted in Northern France using a combination of three factors: i) no-till (NT) vs. conventional tillage (CT); ii) with or without winter cover crops (bare fallow; cover crops with a low prevalence of legumes; cover crop with a high prevalence of legumes); and iii) with or without N fertilization. C and N inputs from cover crops and crop residues, C and N content, enzyme activities, and microbial functional diversity in the topsoil (0–10 cm) were measured over an industrial crop rotation: wheat, pea, corn, wheat, flax. No-till combined with any of the cover crops was characterized by increased total soil organic C and N contents by more than 20% between 2010 and 2015. Dehydrogenase and urease activities were significantly greatest under NT, irrespective of the presence of cover crops. Cover crops without N fertilization under no-till led to higher microbial functional activity (faster carbohydrate and phenolic compound degradation) and diversity. Bare fallow had lower soil microbial functional diversity and C and N contents compared with soil under NT and cover crops. On the other hand, NT associated with cover crops allowed to maintain the soil in both C and N, and to promote microbial activities without N fertilization. In conclusion, winter cover crops and/or NT are sustainable agricultural practices resulting in a greater soil quality index. These results demonstrate that NT and use of standard cover crops or cover crops with legumes for 5 years under a low biomass return in industrial crop production have a positive effect on: i) upper soil C content and microbial enzymes, irrespective of N fertilization regime; ii) soil microbial functional diversity in the absence of N fertilization

Comparative transcriptome sequencing of germline and somatic tissues of the Ascaris suum gonad

<p>Abstract</p> <p>Background</p> <p><it>Ascaris suum </it>(large roundworm of pigs) is a parasitic nematode that causes substantial losses to the meat industry. This nematode is suitable for biochemical studies because, unlike <it>C. elegans</it>, homogeneous tissue samples can be obtained by dissection. It has large sperm, produced in great numbers that permit biochemical studies of sperm motility. Widespread study of <it>A. suum </it>would be facilitated by more comprehensive genome resources and, to this end, we have produced a gonad transcriptome of <it>A. suum</it>.</p> <p>Results</p> <p>Two 454 pyrosequencing runs generated 572,982 and 588,651 reads for germline (TES) and somatic (VAS) tissues of the <it>A. suum </it>gonad, respectively. 86% of the high-quality (HQ) reads were assembled into 9,955 contigs and 69,791 HQ reads remained as singletons. 2.4 million bp of unique sequences were obtained with a coverage that reached 16.1-fold. 4,877 contigs and 14,339 singletons were annotated according to the <it>C. elegans </it>protein and the Kyoto Encyclopedia of Genes and Genomes (KEGG) protein databases. Comparison of TES and VAS transcriptomes demonstrated that genes participating in DNA replication, RNA transcription and ubiquitin-proteasome pathways are expressed at significantly higher levels in TES tissues than in VAS tissues. Comparison of the <it>A. suum </it>TES transcriptome with the <it>C. elegans </it>microarray dataset identified 165 <it>A. suum </it>germline-enriched genes (83% are spermatogenesis-enriched). Many of these genes encode serine/threonine kinases and phosphatases (KPs) as well as tyrosine KPs. Immunoblot analysis further suggested a critical role of phosphorylation in both testis development and spermatogenesis. A total of 2,681 <it>A. suum </it>genes were identified to have associated RNAi phenotypes in <it>C. elegans</it>, the majority of which display embryonic lethality, slow growth, larval arrest or sterility.</p> <p>Conclusions</p> <p>Using deep sequencing technology, this study has produced a gonad transcriptome of <it>A. suum</it>. By comparison with <it>C. elegans </it>datasets, we identified sets of genes associated with spermatogenesis and gonad development in <it>A. suum</it>. The newly identified genes encoding KPs may help determine signaling pathways that operate during spermatogenesis. A large portion of <it>A. suum </it>gonadal genes have related RNAi phenotypes in <it>C. elegans </it>and, thus, might be RNAi targets for parasite control.</p