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See detailSimulation of Left Atrial Function Using a Multi-Scale Model of the Cardiovascular System
Pironet, Antoine ULg; Dauby, Pierre ULg; Paeme, Sabine ULg et al

in PLoS ONE (2013), 8(6), 65146

During a full cardiac cycle, the left atrium successively behaves as a reservoir, a conduit and a pump. This complex behavior makes it unrealistic to apply the time-varying elastance theory to ... [more ▼]

During a full cardiac cycle, the left atrium successively behaves as a reservoir, a conduit and a pump. This complex behavior makes it unrealistic to apply the time-varying elastance theory to characterize the left atrium, first, because this theory has known limitations, and second, because it is still uncertain whether the load independence hypothesis holds. In this study, we aim to bypass this uncertainty by relying on another kind of mathematical model of the cardiac chambers. In the present work, we describe both the left atrium and the left ventricle with a multi-scale model. The multi-scale property of this model comes from the fact that pressure inside a cardiac chamber is derived from a model of the sarcomere behavior. Macroscopic model parameters are identified from reference dog hemodynamic data. The multi-scale model of the cardiovascular system including the left atrium is then simulated to show that the physiological roles of the left atrium are correctly reproduced. This include a biphasic pressure wave and an eight-shaped pressure-volume loop. We also test the validity of our model in non basal conditions by reproducing a preload reduction experiment by inferior vena cava occlusion with the model. We compute the variation of eight indices before and after this experiment and obtain the same variation as experimentally observed for seven out of the eight indices. In summary, the multi-scale mathematical model presented in this work is able to correctly account for the three roles of the left atrium and also exhibits a realistic left atrial pressure-volume loop. Furthermore, the model has been previously presented and validated for the left ventricle. This makes it a proper alternative to the time-varying elastance theory if the focus is set on precisely representing the left atrial and left ventricular behaviors. [less ▲]

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See detailSubstrate Marking by an Invasive Ladybeetle: Seasonal Changes in Hydrocarbon Composition and Behavioral Responses
Durieux, Delphine ULg; Fassotte, Bérénice ULg; Vanderplanck et al

in PLoS ONE (2013), 8(4),

The multicolored Asian ladybeetle, Harmonia axyridis (Pallas), aggregates inside dwellings during the winter to survive the cold. Recent published reports have highlighted that overwintering individuals ... [more ▼]

The multicolored Asian ladybeetle, Harmonia axyridis (Pallas), aggregates inside dwellings during the winter to survive the cold. Recent published reports have highlighted that overwintering individuals use hydrocarbon markings deposited on surfaces by conspecifics to orient toward aggregation sites. In the current study, monthly GC-MS analyses revealed seasonal modifications in the chemical profile of substrate markings deposited by moving individuals. The markings of overwintering ladybeetles contained larger proportions of heptacosadiene, nonacosadiene, hentriacontadienes, and methyl-nonacosanes, along with a lower proportion of heptacosene and nonacosene. This finding suggests the importance of the unsaturated and/or branched hydrocarbons in the H. axyridis aggregation process. Subsequently, we conducted behavioral assays to test whether (1) there is seasonal variation in the behavioral response of H. axyridis individuals toward substrate markings deposited by conspecifics in the same physiological state and (2) the observed behavioral modification is due to a change in ladybeetle sensitivity and/or a change in the chemical composition of the substrate marking. The results indicate that overwintering individuals exhibit a stronger ‘‘following’’ response toward conspecific substrate markings. This behavior is linked to both the physiological state of ladybeetles and the specific chemical profile of the marking biomolecules deposited under overwintering conditions. [less ▲]

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See detailCharacteristics of Near-Death Experiences Memories as Compared to Real and Imagined Events Memories
Thonnard, Marie ULg; Charland-Verville, Vanessa ULg; Brédart, Serge ULg et al

in PLoS ONE (2013), 8(3),

Since the dawn of time, Near-Death Experiences (NDEs) have intrigued and, nowadays, are still not fully explained. Since reports of NDEs are proposed to be imagined events, and since memories of imagined ... [more ▼]

Since the dawn of time, Near-Death Experiences (NDEs) have intrigued and, nowadays, are still not fully explained. Since reports of NDEs are proposed to be imagined events, and since memories of imagined event have, on average, fewer phenomenological characteristics than real events memories, we here compared phenomenological characteristics of NDEs reports with memories of imagined and real events. We included three groups of coma survivors (8 patients with NDE as defined by the Greyson NDE scale, 6 patients without NDE but with memory of their coma, 7 patients without memories of their coma) and a group of 18 age-matched healthy volunteers. Five types of memories were assessed using Memory Characteristics Questionnaire (MCQ – Johnson et al., 1988): target memory (NDE for NDE memory group, coma memory for coma memory group, and first childhood memory for no memory and control groups), old and recent real event memories and old and recent imagined event memories. Since NDEs are known to have high emotional content, participants were requested to choose the most emotionally salient memories for both real and imagined recent and old event memories. Results showed that, in NDE memories group, NDE memories have more characteristics than memories of imagined and real events (p<0.02). NDE memories contain more self-referential and emotional information and have better clarity than memories of coma (all p<0.02). The present study showed that NDE memories contain more characteristics than real event memories and coma memories. Thus, this suggests that they cannot be considered as imagined event memories. On the contrary, their physiological origins could lead them to be really perceived although not lived in the reality. Further work is needed to better understand this phenomenon. [less ▲]

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See detailA triad of highly divergent polymeric immunoglobulin receptor (PIGR) haplotypes with major effect on IgA concentration in bovine milk.
Berry, Sarah; Coppieters, Wouter ULg; Davis, Stephen et al

in PloS one (2013), 8(3), 57219

The aim of this study was to determine a genetic basis for IgA concentration in milk of Bos taurus. We used a Holstein-Friesian x Jersey F2 crossbred pedigree to undertake a genome-wide search for QTL ... [more ▼]

The aim of this study was to determine a genetic basis for IgA concentration in milk of Bos taurus. We used a Holstein-Friesian x Jersey F2 crossbred pedigree to undertake a genome-wide search for QTL influencing IgA concentration and yield in colostrum and milk. We identified a single genome-wide significant QTL on chromosome 16, maximising at 4.8 Mbp. The polymeric immunoglobulin receptor gene (PIGR) was within the confidence interval of the QTL. In addition, mRNA expression analysis revealed a liver PIGR expression QTL mapping to the same locus as the IgA quantitative trait locus. Sequencing and subsequent genotyping of the PIGR gene revealed three divergent haplotypes that explained the variance of both the IgA QTL and the PIGR expression QTL. Genetic selection based on these markers will facilitate the production of bovine herds producing milk with higher concentrations of IgA. [less ▲]

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See detailOn the Relevance of Sophisticated Structural Annotations for Disulfide Connectivity Pattern Prediction
Becker, Julien ULg; Maes, Francis; Wehenkel, Louis ULg

in PLoS ONE (2013), 8(2), 56621

Disulfide bridges strongly constrain the native structure of many proteins and predicting their formation is therefore a key sub-problem of protein structure and function inference. Most recently proposed ... [more ▼]

Disulfide bridges strongly constrain the native structure of many proteins and predicting their formation is therefore a key sub-problem of protein structure and function inference. Most recently proposed approaches for this prediction problem adopt the following pipeline: first they enrich the primary sequence with structural annotations, second they apply a binary classifier to each candidate pair of cysteines to predict disulfide bonding probabilities and finally, they use a maximum weight graph matching algorithm to derive the predicted disulfide connectivity pattern of a protein. In this paper, we adopt this three step pipeline and propose an extensive study of the relevance of various structural annotations and feature encodings. In particular, we consider five kinds of structural annotations, among which three are novel in the context of disulfide bridge prediction. So as to be usable by machine learning algorithms, these annotations must be encoded into features. For this purpose, we propose four different feature encodings based on local windows and on different kinds of histograms. The combination of structural annotations with these possible encodings leads to a large number of possible feature functions. In order to identify a minimal subset of relevant feature functions among those, we propose an efficient and interpretable feature function selection scheme, designed so as to avoid any form of overfitting. We apply this scheme on top of three supervised learning algorithms: k-nearest neighbors, support vector machines and extremely randomized trees. Our results indicate that the use of only the PSSM (position-specific scoring matrix) together with the CSP (cysteine separation profile) are sufficient to construct a high performance disulfide pattern predictor and that extremely randomized trees reach a disulfide pattern prediction accuracy of on the benchmark dataset SPX+, which corresponds to +3.2% improvement over the state of the art. A web-application is available at http://m24.giga.ulg.ac.be:81/x3CysBridge​s. [less ▲]

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See detailUnmanned aerial survey of elephants
Vermeulen, Cédric ULg; Lejeune, Philippe ULg; Lisein, Jonathan ULg et al

in PLoS ONE (2013), 8(2),

The use of a UAS (Unmanned Aircraft System) was tested to survey large mammals in the Nazinga Game Ranch in the south of Burkina Faso. The Gatewing ×100™ equipped with a Ricoh GR III camera was used to ... [more ▼]

The use of a UAS (Unmanned Aircraft System) was tested to survey large mammals in the Nazinga Game Ranch in the south of Burkina Faso. The Gatewing ×100™ equipped with a Ricoh GR III camera was used to test animal reaction as the UAS passed, and visibility on the images. No reaction was recorded as the UAS passed at a height of 100 m. Observations, made on a set of more than 7000 images, revealed that only elephants (Loxodonta africana) were easily visible while medium and small sized mammals were not. The easy observation of elephants allows experts to enumerate them on images acquired at a height of 100 m. We, therefore, implemented an aerial strip sample count along transects used for the annual wildlife foot count. A total of 34 elephants were recorded on 4 transects, each overflown twice. The elephant density was estimated at 2.47 elephants/km2 with a coefficient of variation (CV%) of 36.10%. The main drawback of our UAS was its low autonomy (45 min). Increased endurance of small UAS is required to replace manned aircraft survey of large areas (about 1000 km of transect per day vs 40 km for our UAS). The monitoring strategy should be adapted according to the sampling plan. Also, the UAS is as expensive as a second-hand light aircraft. However the logistic and flight implementation are easier, the running costs are lower and its use is safer. Technological evolution will make civil UAS more efficient, allowing them to compete with light aircraft for aerial wildlife surveys. [less ▲]

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See detailInteraction between hippocampal and striatal systems predicts subsequent consolidation of motor sequence memory.
Albouy, Geneviève; Sterpenich, Virginie; Vandewalle, Gilles ULg et al

in PLoS ONE (2013), 8(3), 59490

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See detailSimilar local and landscape processes affect both a common and a rare newt species
Denoël, Mathieu ULg; Perez, Amélie; Cornet, Yves ULg et al

in PLoS ONE (2013), 8(5), 62727

Although rare species are often the focus of conservation measures, more common species may experience similar decline and suffer from the same threatening processes. We tested this hypothesis by ... [more ▼]

Although rare species are often the focus of conservation measures, more common species may experience similar decline and suffer from the same threatening processes. We tested this hypothesis by examining, through an information-theoretic approach, the importance of ecological processes at multiple scales in the great crested newt Triturus cristatus, regionally endangered and protected in Europe, and the more common smooth newt, Lissotriton vulgaris. Both species were similarly affected by the same processes, i.e. suitability of aquatic and terrestrial components of their habitat at different scales, connectivity among breeding sites, and the presence of introduced fish. T. cristatus depended more on water depth and aquatic vegetation than L. vulgaris. The results show that environmental pressures threaten both common and rare species, and therefore the more widespread species should not be neglected in conservation programs. Because environmental trends are leading to a deterioration of aquatic and terrestrial habitat features required by newt populations, populations of the common species may follow the fate of the rarest species. This could have substantial conservation implications because of the numerical importance of common species in ecosystems and because commonness could be a transient state moving towards rarity. On the other hand, in agreement with the umbrella species concept, targeting conservation efforts on the most demanding species would also protect part of the populations of the most common species. [less ▲]

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See detailThe homeodomain transcription factor Hoxa2 interacts with and promotes the proteasomal degradation of the E3 ubiquitin protein ligase RCHY1.
Bergiers, Isabelle; Bridoux, Laure; Nguyen, Nathan et al

in PloS one (2013), 8(11), 80387

Hox proteins are conserved homeodomain transcription factors known to be crucial regulators of animal development. As transcription factors, the functions and modes of action (co-factors, target genes) of ... [more ▼]

Hox proteins are conserved homeodomain transcription factors known to be crucial regulators of animal development. As transcription factors, the functions and modes of action (co-factors, target genes) of Hox proteins have been very well studied in a multitude of animal models. However, a handful of reports established that Hox proteins may display molecular activities distinct from gene transcription regulation. Here, we reveal that Hoxa2 interacts with 20S proteasome subunits and RCHY1 (also known as PIRH2), an E3 ubiquitin ligase that targets p53 for degradation. We further show that Hoxa2 promotes proteasome-dependent degradation of RCHY1 in an ubiquitin-independent manner. Correlatively, Hoxa2 alters the RCHY1-mediated ubiquitination of p53 and promotes p53 stabilization. Together, our data establish that Hoxa2 can regulate the proteasomal degradation of RCHY1 and stabilization of p53. [less ▲]

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See detailLocal Mechanical Stimuli Regulate Bone Formation and Resorption in Mice at the Tissue Level
Schulte, Friederike A.; Ruffoni, Davide ULg; Lambers, Floor M. et al

in PLOS ONE (2013), 8(4), 62172-12

Bone is able to react to changing mechanical demands by adapting its internal microstructure through bone forming and resorbing cells. This process is called bone modeling and remodeling. It is evident ... [more ▼]

Bone is able to react to changing mechanical demands by adapting its internal microstructure through bone forming and resorbing cells. This process is called bone modeling and remodeling. It is evident that changes in mechanical demands at the organ level must be interpreted at the tissue level where bone (re) modeling takes place. Although assumed for a long time, the relationship between the locations of bone formation and resorption and the local mechanical environment is still under debate. The lack of suitable imaging modalities for measuring bone formation and resorption in vivo has made it difficult to assess the mechanoregulation of bone three-dimensionally by experiment. Using in vivo micro-computed tomography and high resolution finite element analysis in living mice, we show that bone formation most likely occurs at sites of high local mechanical strain (p<0.0001) and resorption at sites of low local mechanical strain (p<0.0001). Furthermore, the probability of bone resorption decreases exponentially with increasing mechanical stimulus (R-2 = 0.99) whereas the probability of bone formation follows an exponential growth function to a maximum value (R-2 = 0.99). Moreover, resorption is more strictly controlled than formation in loaded animals, and ovariectomy increases the amount of non-targeted resorption. Our experimental assessment of mechanoregulation at the tissue level does not show any evidence of a lazy zone and suggests that around 80% of all (re) modeling can be linked to the mechanical microenvironment. These findings disclose how mechanical stimuli at the tissue level contribute to the regulation of bone adaptation at the organ level. [less ▲]

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See detailBehaviours Associated with Acoustic Communication in Nile Tilapia (Oreochromis niloticus)
Longrie, Nicolas; Poncin, Pascal ULg; Denoël, Mathieu ULg et al

in PLoS ONE (2013), 8(4), 61467

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See detailMithramycin Exerts an Anti-Myeloma Effect and Displays Anti-Angiogenic Effects through Up-Regulation of Anti-Angiogenic Factors.
Otjacques, Eléonore ULg; Binsfeld, Marilène ULg; Rocks, Natacha ULg et al

in PLoS ONE (2013), 8(5), 62818

Mithramycin (MTM), a cytotoxic compound, is currently being investigated for its anti-angiogenic activity that seems to be mediated through an inhibition of the transcription factor SP1. In this study we ... [more ▼]

Mithramycin (MTM), a cytotoxic compound, is currently being investigated for its anti-angiogenic activity that seems to be mediated through an inhibition of the transcription factor SP1. In this study we evaluated its anti-myeloma effects in the syngenic 5TGM1 model in vitro as well as in vivo. In vitro, MTM inhibited DNA synthesis of 5TGM1 cells with an IC50 of 400 nM and induced an arrest in cell cycle progression at the G1/S transition point. Western-blot revealed an up-regulation of p53, p21 and p27 and an inhibition of c-Myc, while SP1 remained unaffected. In rat aortic ring assays, a strong anti-angiogenic effect was seen, which could be explained by a decrease of VEGF production and an up-regulation of anti-angiogenic proteins such as IP10 after MTM treatment. The administration of MTM to mice injected with 5TGM1 decreased 5TGM1 cell invasion into bone marrow and myeloma neovascularisation. These data suggest that MTM displays anti-myeloma and anti-angiogenic effects that are not mediated by an inhibition of SP1 but rather through c-Myc inhibition and p53 activation. [less ▲]

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See detailThe Importance of Encoding-Related Neural Dynamics in the Prediction of Inter-Individual Differences in Verbal Working Memory Performance
Majerus, Steve ULg; Salmon, Eric ULg; Attout, Lucie ULg

in PLoS ONE (2013), 8(7),

Studies of brain-behaviour interactions in the field of working memory (WM) have associated WM success with activation of a fronto-parietal network during the maintenance stage, and this mainly for visuo ... [more ▼]

Studies of brain-behaviour interactions in the field of working memory (WM) have associated WM success with activation of a fronto-parietal network during the maintenance stage, and this mainly for visuo-spatial WM. Using an inter-individual differences approach, we demonstrate here the equal importance of neural dynamics during the encoding stage, and this in the context of verbal WM tasks which are characterized by encoding phases of long duration and sustained attentional demands. Participants encoded and maintained 5-word lists, half of them containing an unexpected word intended to disturb WM encoding and associated task-related attention processes. We observed that inter-individual differences in WM performance for lists containing disturbing stimuli were related to activation levels in a region previously associated with task-related attentional processing, the left intraparietal sulcus (IPS), and this during stimulus encoding but not maintenance; functional connectivity strength between the left IPS and lateral prefrontal cortex (PFC) further predicted WM performance. This study highlights the critical role, during WM encoding, of neural substrates involved in task-related attentional processes for predicting inter-individual differences in verbal WM performance, and, more generally, provides support for attention-based models of WM. © 2013 Majerus et al. [less ▲]

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See detailSputum IgE and Cytokines in Asthma: Relationship with Sputum Cellular Profile.
Manise, Maïté ULg; Holtappels, Gabriele; Van Crombruggen, Koen et al

in PLoS ONE (2013), 8(3), 58388

BACKGROUND: Local IgE production may play a role in asthma pathogenesis. The aim of the study was to assess sputum total IgE and cytokines in asthmatics according to sputum cellular phenotype. METHODS: We ... [more ▼]

BACKGROUND: Local IgE production may play a role in asthma pathogenesis. The aim of the study was to assess sputum total IgE and cytokines in asthmatics according to sputum cellular phenotype. METHODS: We studied 122 subjects including 22 non atopic healthy subjects, 41 eosinophilic (sputum eosinophils >/=3%), 16 neutrophilic (sputum neutrophils >76%) and 43 pauci-granulocytic asthmatics (sputum eosinophils <3% and sputum neutrophils </=76%) recruited from the asthma clinic at CHU Liege. Sputum supernatant total IgE (tIgE) was measured by ImmunoCAP and sputum supernatant cytokines (IL-4, IL-5, IL-6, IL-10, IL-13, IL-17, IFN-gamma and TNF-alpha) were measured with the Luminex xMAP Technology by using commercially available Fluorokine MAP kits. RESULTS: After concentrating sputum samples, total IgE was detectable in the majority of subjects. Sputum IgE was raised in asthmatics when compared to healthy subjects. Overall, asthmatics did not significantly differ from healthy subjects with respect to cytokine levels. The eosinophilic asthma phenotype, however, was characterised by raised sputum tIgE, IL-5 and IL-13 compared to healthy subjects (p<0.001, p<0.001 and p<0.05 respectively) and pauci-granulocytic asthma (p<0.01, p<0.001 and p<0.05 respectively) and raised IL-5 compared to neutrophilic asthma (p<0.01). When patients were classified according to sputum IgE levels, it appeared that IL-5, IL-6, IL-17 and TNF-alpha sputum supernatant levels were raised in the "IgE high" asthmatics (IgE >/=0.1 kU/l) when compared to "IgE low" asthmatics (IgE<0.1 kU/l). CONCLUSION: The eosinophilic asthma phenotype was associated with raised sputum IgE and a Th2 cytokine profile. Raised sputum IgE was associated with a heterogeneous cytokine overproduction. [less ▲]

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See detailDevastating Decline of Forest Elephants in Central Africa.
Maisels, Fiona; Strindberg, Samantha; Blake, Stephen et al

in PLoS ONE (2013), 8(3),

African forest elephants– taxonomically and functionally unique–are being poached at accelerating rates, but we lack range-wide information on the repercussions. Analysis of the largest survey dataset ... [more ▼]

African forest elephants– taxonomically and functionally unique–are being poached at accelerating rates, but we lack range-wide information on the repercussions. Analysis of the largest survey dataset ever assembled for forest elephants (80 foot-surveys; covering 13,000 km; 91,600 person-days of fieldwork) revealed that population size declined by ca. 62% between 2002–2011, and the taxon lost 30% of its geographical range. The population is now less than 10% of its potential size, occupying less than 25% of its potential range. High human population density, hunting intensity, absence of law enforcement, poor governance, and proximity to expanding infrastructure are the strongest predictors of decline. To save the remaining African forest elephants, illegal poaching for ivory and encroachment into core elephant habitat must be stopped. In addition, the international demand for ivory, which fuels illegal trade, must be dramatically reduced. [less ▲]

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See detailMolecular reclassification of Crohn's disease: a cautionary note on population stratification.
Maus, Barbel; Jung, Camille; Mahachie John, Jestinah ULg et al

in PloS one (2013), 8(10), 77720

Complex human diseases commonly differ in their phenotypic characteristics, e.g., Crohn's disease (CD) patients are heterogeneous with regard to disease location and disease extent. The genetic ... [more ▼]

Complex human diseases commonly differ in their phenotypic characteristics, e.g., Crohn's disease (CD) patients are heterogeneous with regard to disease location and disease extent. The genetic susceptibility to Crohn's disease is widely acknowledged and has been demonstrated by identification of over 100 CD associated genetic loci. However, relating CD subphenotypes to disease susceptible loci has proven to be a difficult task. In this paper we discuss the use of cluster analysis on genetic markers to identify genetic-based subgroups while taking into account possible confounding by population stratification. We show that it is highly relevant to consider the confounding nature of population stratification in order to avoid that detected clusters are strongly related to population groups instead of disease-specific groups. Therefore, we explain the use of principal components to correct for population stratification while clustering affected individuals into genetic-based subgroups. The principal components are obtained using 30 ancestry informative markers (AIM), and the first two PCs are determined to discriminate between continental origins of the affected individuals. Genotypes on 51 CD associated single nucleotide polymorphisms (SNPs) are used to perform latent class analysis, hierarchical and Partitioning Around Medoids (PAM) cluster analysis within a sample of affected individuals with and without the use of principal components to adjust for population stratification. It is seen that without correction for population stratification clusters seem to be influenced by population stratification while with correction clusters are unrelated to continental origin of individuals. [less ▲]

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See detailRapid Plant Invasion in Distinct Climates Involves Different Sources of Phenotypic Variation
Monty, Arnaud ULg; Bizoux, Jean-Philippe ULg; Escarré, José et al

in PLoS ONE (2013), 8(1), 55627

When exotic species spread over novel environments, their phenotype will depend on a combination of different processes, including phenotypic plasticity (PP), local adaptation (LA), environmental maternal ... [more ▼]

When exotic species spread over novel environments, their phenotype will depend on a combination of different processes, including phenotypic plasticity (PP), local adaptation (LA), environmental maternal effects (EME) and genetic drift (GD). Few attempts have been made to simultaneously address the importance of those processes in plant invasion. The present study uses the well-documented invasion history of Senecio inaequidens (Asteraceae) in southern France, where it was introduced at a single wool-processing site. It gradually invaded the Mediterranean coast and the Pyrenean Mountains, which have noticeably different climates. We used seeds from Pyrenean and Mediterranean populations, as well as populations from the first introduction area, to explore the phenotypic variation related to climatic variation. A reciprocal sowing experiment was performed with gardens under Mediterranean and Pyrenean climates. We analyzed climatic phenotypic variation in germination, growth, reproduction, leaf physiology and survival. Genetic structure in the studied invasion area was characterized using AFLP. We found consistent genetic differentiation in growth traits but no home-site advantage, so weak support for LA to climate. In contrast, genetic differentiation showed a relationship with colonization history. PP in response to climate was observed for most traits, and it played an important role in leaf trait variation. EME mediated by seed mass influenced all but leaf traits in a Pyrenean climate. Heavier, earlier-germinating seeds produced larger individuals that produced more flower heads throughout the growing season. However, in the Mediterranean garden, seed mass only influenced the germination rate. The results show that phenotypic variation in response to climate depends on various ecological and evolutionary processes associated with geographical zone and life history traits. Seeing the relative importance of EME and GD, we argue that a “local adaptation vs. phenotypic plasticity” approach is therefore not sufficient to fully understand what shapes phenotypic variation and genetic architecture of invasive populations. [less ▲]

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See detailOctarellin VI: using rosetta to design a putative artificial (beta/alpha)8 protein.
Figueroa Yévenes, Maximiliano ULg; Oliveira, Nicolas; Lejeune, Annabelle et al

in PloS one (2013), 8(8), 71858

The computational protein design protocol Rosetta has been applied successfully to a wide variety of protein engineering problems. Here the aim was to test its ability to design de novo a protein adopting ... [more ▼]

The computational protein design protocol Rosetta has been applied successfully to a wide variety of protein engineering problems. Here the aim was to test its ability to design de novo a protein adopting the TIM-barrel fold, whose formation requires about twice as many residues as in the largest proteins successfully designed de novo to date. The designed protein, Octarellin VI, contains 216 residues. Its amino acid composition is similar to that of natural TIM-barrel proteins. When produced and purified, it showed a far-UV circular dichroism spectrum characteristic of folded proteins, with alpha-helical and beta-sheet secondary structure. Its stable tertiary structure was confirmed by both tryptophan fluorescence and circular dichroism in the near UV. It proved heat stable up to 70 degrees C. Dynamic light scattering experiments revealed a unique population of particles averaging 4 nm in diameter, in good agreement with our model. Although these data suggest the successful creation of an artificial alpha/beta protein of more than 200 amino acids, Octarellin VI shows an apparent noncooperative chemical unfolding and low solubility. [less ▲]

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See detailIndividual – to – resource landscape interaction strength can explain different collective feeding behaviours
Bode, Nikolai WF; Delcourt, Johann ULg

in PLoS ONE (2013), 8(10), 75879

Taking in sufficient quantities of nutrients is vital for all living beings and in doing so, individuals interact with the local resource environment. Here, we focus explicitly on the interactions between ... [more ▼]

Taking in sufficient quantities of nutrients is vital for all living beings and in doing so, individuals interact with the local resource environment. Here, we focus explicitly on the interactions between feeding individuals and the resource landscape. In particular, we are interested in the emergent movement dynamics resulting from these interactions. We present an individual-based simulation model for the movement of populations in a resource landscape that allows us to vary the strength of the interactions mentioned above. The key assumption and novelty of our model is that individuals can cause the release of additional nutrients, as well as consuming them. Our model produces clear predictions. For example, we expect more tortuous individual movement paths and higher levels of aggregation in populations occupying homogeneous environments where individual movement makes more nutrients available. We also show how observed movement dynamics could change when local nutrient sources are depleted or when the population density increases. Our predictions are testable and qualitatively reproduce the different feeding behaviours observed in filter-feeding ducks, for example. We suggest that considering two-way interactions between feeding individuals and resource landscapes could help to explain fine-scale movement dynamics. [less ▲]

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See detailConditioned Medium from Bone marrow-derived Mesenchymal Stem Cells improves recovery after Spinal Cord Injury in rats: an original strategy to avoid cell transplantation.
CANTINIEAUX, Dorothée ULg; QUERTAINMONT, Renaud; BLACHER, Silvia ULg et al

in PLoS ONE (2013), 8(8), 69515

Spinal cord injury triggers irreversible loss of motor and sensory functions. Numerous strategies aiming at repairing the injured spinal cord have been studied. Among them, the use of bone marrow-derived ... [more ▼]

Spinal cord injury triggers irreversible loss of motor and sensory functions. Numerous strategies aiming at repairing the injured spinal cord have been studied. Among them, the use of bone marrow-derived mesenchymal stem cells (BMSCs) is promising. Indeed, these cells possess interesting properties to modulate CNS environment and allow axon regeneration and functional recovery. Unfortunately, BMSC survival and differentiation within the host spinal cord remain poor, and these cells have been found to have various adverse effects when grafted in other pathological contexts. Moreover, paracrine-mediated actions have been proposed to explain the beneficial effects of BMSC transplantation after spinal cord injury. We thus decided to deliver BMSC-released factors to spinal cord injured rats and to study, in parallel, their properties in vitro. We show that, in vitro, BMSC-conditioned medium (BMSC-CM) protects neurons from apoptosis, activates macrophages and is pro-angiogenic. In vivo, BMSC-CM administered after spinal cord contusion improves motor recovery. Histological analysis confirms the pro-angiogenic action of BMSC-CM, as well as a tissue protection effect. Finally, the characterization of BMSC-CM by cytokine array and ELISA identified trophic factors as well as cytokines likely involved in the beneficial observed effects. In conclusion, our results support the paracrine-mediated mode of action of BMSCs and raise the possibility to develop a cell-free therapeutic approach. [less ▲]

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