Getting off on the right foot: Integration of spatial distribution of genetic variability for aquaculture development and regulations, the European perch case

International audienceKnowledge of spatial genetic variability patterns allows improving conservation actions, translocation regulations, and farming productivity. However, these genetic variability patterns are often considered after issues are observed, long after the beginning of production. By taking into account lessons from other species, we investigate the genetic variability of Perca fluviatilis, a species at a nascent stage of production. The genetic variability has been previously studied but, due to discrepancies between conclusions and methodological limits, the spatial distribution of genetic variability in P. fluviatilis has not been demonstrated conclusively. Here, we characterise the genetic variability across 84 West-Palaearctic sampling sites using mitochondrial and microsatellite markers. We aim to provide (i) a genetically-based population structure that could act as an impetus for further production improvement and (ii) guidelines for translocation regulations. Our analyses show an uneven distribution of genetic variability. Based on inter-populational genetic differentiation, we identify five large geographic scale clusters which are further divided into several subgroups. Local genetic diversity mapping highlights a spatial pattern with several hotspots, which has serious implications in the development of appropriate regulations of translocations. Moreover, we here report an association between genetic differentiations and previously reported zootechnical performances. We ultimately propose guidelines for further investigations of population-specific performances in aquaculture and potentially efficient regulations for policy-makers

Testing of quantum phase in matter wave optics

Various phase concepts may be treated as special cases of the maximum likelihood estimation. For example the discrete Fourier estimation that actually coincides with the operational phase of Noh, Fouge`res and Mandel is obtained for continuous Gaussian signals with phase modulated mean.Since signals in quantum theory are discrete, a prediction different from that given by the Gaussian hypothesis should be obtained as the best fit assuming a discrete Poissonian statistics of the signal. Although the Gaussian estimation gives a satisfactory approximation for fitting the phase distribution of almost any state the optimal phase estimation offers in certain cases a measurable better performance. This has been demonstrated in neutron--optical experiment.Comment: 8 pages, 4 figure

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

<p>Abstract</p> <p>Background</p> <p>In the post-genomic era, the rapid increase in high-throughput data calls for computational tools capable of integrating data of diverse types and facilitating recognition of biologically meaningful patterns within them. For example, protein-protein interaction data sets have been clustered to identify stable complexes, but scientists lack easily accessible tools to facilitate combined analyses of multiple data sets from different types of experiments. Here we present <it>clusterMaker</it>, a Cytoscape plugin that implements several clustering algorithms and provides network, dendrogram, and heat map views of the results. The Cytoscape network is linked to all of the other views, so that a selection in one is immediately reflected in the others. <it>clusterMaker </it>is the first Cytoscape plugin to implement such a wide variety of clustering algorithms and visualizations, including the only implementations of hierarchical clustering, dendrogram plus heat map visualization (tree view), k-means, k-medoid, SCPS, AutoSOME, and native (Java) MCL.</p> <p>Results</p> <p>Results are presented in the form of three scenarios of use: analysis of protein expression data using a recently published mouse interactome and a mouse microarray data set of nearly one hundred diverse cell/tissue types; the identification of protein complexes in the yeast <it>Saccharomyces cerevisiae</it>; and the cluster analysis of the vicinal oxygen chelate (VOC) enzyme superfamily. For scenario one, we explore functionally enriched mouse interactomes specific to particular cellular phenotypes and apply fuzzy clustering. For scenario two, we explore the prefoldin complex in detail using both physical and genetic interaction clusters. For scenario three, we explore the possible annotation of a protein as a methylmalonyl-CoA epimerase within the VOC superfamily. Cytoscape session files for all three scenarios are provided in the Additional Files section.</p> <p>Conclusions</p> <p>The Cytoscape plugin <it>clusterMaker </it>provides a number of clustering algorithms and visualizations that can be used independently or in combination for analysis and visualization of biological data sets, and for confirming or generating hypotheses about biological function. Several of these visualizations and algorithms are only available to Cytoscape users through the <it>clusterMaker </it>plugin. <it>clusterMaker </it>is available via the Cytoscape plugin manager.</p

Go hard or go home : primary motivations for engagement at the elite level in one of the fastest extreme sports

Organisers of extreme sports need to better understand the motivations of participants who are prepared to face significant injury and maybe even death on a regular basis. For example, being flipped from your motorcycle at speeds in excess of 300 km/h or sliding over a hard bitumen surface with no control, often resulting in broken bones, comprise simply one aspect of competition in an activity accepted as an extreme sport (Lewis, 2004). One might wonder do competitors simply suffer from a death-wish or, in fact, just the opposite. That is, they seek to live life to the very fullest and, in so doing, want to enjoy every possible minute. The intent of the study therefore, was to explore the phenomena more closely by determining the primary motivations for engagement of individuals in motorcycle road racing at an Australian Championship. This exploratory study was undertaken using grounded theory with one-on-one phone interviews the primary means of data collection. Advocates of motivational theory (Martens & Webber, 2002) posit that there are three primary types of internal and external motivation, as well as a form of amotivation. Study results indicated that all three intrinsic forms of motivation were experienced but only one extrinsic form was highlighted as significant by study participants. The three instrinsic motivators are the intrinsic motivation to know, to accomplish and to experience stimulation. Intrinsic motivation to know was demonstrated through learning how to ride their bike faster and smoother, resulting in faster lap times. Intrinsic motivation to accomplish occurred when riders derived satisfaction and pleasure from the experience which resulted in personal satisfaction and mastery. Intrinsic motivation to experience stimulation resulted from the respondents’ perception of pleasure, fun and excitement from participation. On the other hand, tangible extrinsic rewards were generally limited to riders who had access to a factory-backed motorcycle with the majority of riders considering they suffered financially as a consequence of their participation. Intangible extrinsic rewards revealed themselves in the form of deep, personal identification with the attainment of personal goals which, in turn, lead to personal growth and development. Interestingly, all four motivators were found to result in positive outcomes for the riders which they indicated kept them engaged in the high risk sport. Such results suggest that organisers of such competitive meets need be aware that prize money is not the major attractant for participants. Rather, the personal benefits derived by participants when motorcycle racing was the primary determinant of enduring engagement in this extreme sport

Identifying the satisfactions derived from leisure gardening by older adults

gardening is a popular leisure activity among older adults in most Western countries. however, few systematic academic studies have focused on the benefits of gardening engaged in by this cohort. The purpose of this study was to identify the contribution of gardening to the leisure and life satisfaction of older adults. Self-administered questionnaire surveys were completed by 433 older adults who were recruited at a 'gardening Australia Expo' held in Brisbane, Queensland in April 2009. findings of this study indicated that older adults obtained high levels of leisure satisfaction specifically from the relaxation, psychological and physiological aspects of gardening. Those whose engagement in gardening was at the level of serious leisure received the greatest satisfaction. Most participants reported that gardening contributed to their overall life satisfaction. Implications for future studies and leisure providers are discussed

DFMO/eflornithine inhibits migration and invasion downstream of MYCN and involves p27Kip1 activity in neuroblastoma

Neuroblastoma (NB) is the most common extracranial pediatric tumor. NB patients over 18 months of age at the time of diagnosis are often in the later stages of the disease, present with widespread dissemination, and often possess MYCN tumor gene amplification. MYCN is a transcription factor that regulates the expression of a number of genes including ornithine decarboxylase (ODC), a rate-limiting enzyme in the biosynthesis of polyamines. Inhibiting ODC in NB cells produces many deleterious effects including G(1) cell cycle arrest, inhibition of cell proliferation, and decreased tumor growth, making ODC a promising target for drug interference. DFMO treatment leads to the accumulation of the cyclin-dependent kinase inhibitor p27(Kip1) protein and causes p27(Kip1)/Rb-coupled G(1) cell cycle arrest in MYCN-amplified NB tumor cells through a process that involves p27(Kip1) phosphorylation at residues Ser10 and Thr198. While p27(Kip1) is well known for its role as a cyclin-dependent kinase inhibitor, recent studies have revealed a novel function of p27(Kip1) as a regulator of cell migration and invasion. In the present study we found that p27(Kip1) regulates the migration and invasion in NB and that these events are dependent on the state of phosphorylation of p27(Kip1). DFMO treatments induced MYCN protein downregulation and phosphorylation of Akt/PKB (Ser473) and GSK3-β (Ser9), and polyamine supplementation alleviated the DFMO-induced effects. Importantly, we provide strong evidence that p27(Kip1) mRNA correlates with clinical features and the survival probability of NB patient

Getting off on the right foot: Integration of spatial distribution of genetic variability for aquaculture development and regulations, the European perch case

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The polyamine metabolism genes ornithine decarboxylase and antizyme 2 predict aggressive behavior in neuroblastomas with and without MYCN amplification

High polyamine (PA) levels and ornithine decarboxylase (ODC) overexpression are well-known phenomena in many aggressive cancer types. We analyzed the expression of ODC and ODC-activity regulating genes antizymes 1-3 (OAZ1-3) and antizyme inhibitors 1-2 (AZ-IN1-2) in human neuroblastoma (NB) tumors and correlated these with genetic and clinical features of NB. Since ODC is a known target gene of MYCN, the correlation between ODC and MYCN was of special interest. Data were obtained from Affymetrix micro-array analysis of 88 NB tumor samples. In addition, mRNA expression levels of ODC, OAZ2 and MYCN in a MYCN-inducible NB cell line were determined by quantitative real-time reverse-transcriptase polymerase chain reaction (RT-PCR). ODC mRNA expression in NB tumors was significantly predictive of decreased overall survival probability and correlated with several unfavorable clinical NB characteristics (all p <0.005). Interestingly, high ODC mRNA expression also showed significant correlation with poor survival prognosis in Kaplan-Meier analyses stratified for patients without MYCN amplification, suggesting an additional rote for ODC independent of MYCN. Conversely, high OAZ2 mRNA expression correlated with increased survival and with several favorable clinical NB characteristics (all p <0.003). In addition, we provide first evidence of a role for MYCN-associated transcription factors MAD2 and MAD7 in ODC regulation. In NB cell cultures, ectopic overexpression of MYCN altered ODC but not OAZ2 mRNA levels. In conclusion, these data suggest that elevated ODC and low OAZ2 mRNA expression levels correlate with several unfavorable genetic and clinical features in NB, offering new insights into PA pathways and PA metabolism-targeting therapy in N