Dealing with scarce data to understand how environmental gradients and propagule pressure shape fine‐scale alien distribution patterns on coastal dunes

Questions: On sandy coastal habitats, factors related to substrate and to wind action vary along the sea–inland ecotone, forming a marked directional disturbance and stress gradient. Further, input of propagules of alien plant species associated to touristic exploitation and development is intense. This has contributed to establishment and spread of aliens in coastal systems. Records of alien species in databases of such heterogeneous landscapes remain scarce, posing a challenge for statistical modelling. We address this issue and attempt to shed light on the role of environmental stress/disturbance gradients and propagule pressure on invasibility of plant communities in these typical model systems. Location: Sandy coasts of Lazio (Central Italy). Methods: We proposed an innovative methodology to deal with low prevalence of alien occurrence in a data set and high cost of field‐based sampling by taking advantage, through predictive modelling, of the strong interrelation between vegetation and abiotic features in coastal dunes. We fitted generalized additive models to analyse (1) overall patterns of alien occurrence and spread and (2) specific patterns of the most common alien species recorded. Conclusion: Even in the presence of strong propagule pressure, variation in local abiotic conditions can explain differences in invasibility within a local environment, and intermediate levels of natural disturbance and stress offer the best conditions for spread of alien species. However, in our model system, propagule pressure is actually the main determinant of alien species occurrence and spread. We demonstrated that extending the information of environmental features measured in a subsample of vegetation plots through predictive modelling allows complex questions in invasion biology to be addressed without requiring disproportionate funding and sampling effort.     

Scale specific determinants of tree diversity in an old growth temperate forest in China

The major processes generating pattern in plant community composition depend upon the spatial scale and resolution of observation, therefore understanding the role played by spatial scale on species patterns is of major concern. In this study, we investigate how well environmental (topography and soil variables) and spatial variables explain variation in species composition in a 25-ha temperate forest in northeastern China. We used new variation partitioning approaches to discover the spatial scale (using multi-scale spatial PCNM variables) at which environmental heterogeneity and other spatially structured processes influence tree community composition. We also test the effect of changing grain of the study (i.e. quadrat size) on the variation partitioning results. Our results indicate that (1) species composition in the Changbai mixed broadleaf-conifer forest was controlled mainly by spatially structured soil variation at broad scales, while at finer scales most of the explained variation was of a spatial nature, pointing to the importance of biotic processes. (2) These results held at all sampling grains. However, reducing quadrat size progressively reduced both spatially and environmentally explained variance. This probably partly reflects increasing stochasticity in species abundances, and the smaller proportion of quadrats occupied by each species, when quadrat size is reduced. The results suggest that environmental heterogeneity (i.e. niche processes) and other biotic processes such as dispersal work together, but at different spatial scales, to build up diversity patterns.     

Rat Mesentery Angiogenesis Assay

The adult rat mesentery window angiogenesis assay is biologically appropriate and is exceptionally well suited to the study of sprouting angiogenesis in vivo [see review papers], which is the dominating form of angiogenesis in human tumors and non-tumor tissues, as discussed in invited review papers^1,2. Angiogenesis induced in the membranous mesenteric parts by intraperitoneal (i.p.) injection of a pro-angiogenic factor can be modulated by subcutaneous (s.c.), intravenous (i.v.) or oral (p.o.) treatment with modifying agents of choice. Each membranous part of the mesentery is translucent and framed by fatty tissue, giving it a window-like appearance.The assay has the following advantageous features: (i) the test tissue is natively vascularized, albeit sparsely, and since it is extremely thin, the microvessel network is virtually two-dimensional, which allows the entire network to be assessed microscopically in situ; (ii) in adult rats the test tissue lacks significant physiologic angiogenesis, which characterizes most normal adult mammalian tissues; the degree of native vascularization is, however, correlated with age, as discussed in¹; (iii) the negligible level of trauma-induced angiogenesis ensures high sensitivity; (iv) the assay replicates the clinical situation, as the angiogenesis-modulating test drugs are administered systemically and the responses observed reflect the net effect of all the metabolic, cellular, and molecular alterations induced by the treatment; (v) the assay allows assessments of objective, quantitative, unbiased variables of microvascular spatial extension, density, and network pattern formation, as well as of capillary sprouting, thereby enabling robust statistical analyses of the dose-effect and molecular structure-activity relationships; and (vi) the assay reveals with high sensitivity the toxic or harmful effects of treatments in terms of decreased rate of physiologic body-weight gain, as adult rats grow robustly.Mast-cell-mediated angiogenesis was first demonstrated using this assay^3,4. The model demonstrates a high level of discrimination regarding dosage-effect relationships and the measured effects of systemically administered chemically or functionally closely related drugs and proteins, including: (i) low-dosage, metronomically administered standard chemotherapeutics that yield diverse, drug-specific effects (i.e., angiogenesis-suppressive, neutral or angiogenesis-stimulating activities⁵); (ii) natural iron-unsaturated human lactoferrin, which stimulates VEGF-A-mediated angiogenesis⁶, and natural iron-unsaturated bovine lactoferrin, which inhibits VEGF-A-mediated angiogenesis⁷; and (iii) low-molecular-weight heparin fractions produced by various means^8,9. Moreover, the assay is highly suited to studies of the combined effects on angiogenesis of agents that are administered systemically in a concurrent or sequential fashion.The idea of making this video originated from the late Dr. Judah Folkman when he visited our laboratory and witnessed the methodology being demonstrated.Review papers (invited) discussing and appraising the assayNorrby, K. In vivo models of angiogenesis. J. Cell. Mol. Med. 10, 588-612 (2006).Norrby, K. Drug testing with angiogenesis models. Expert Opin. Drug. Discov. 3, 533-549 (2008).     

Diel activity of adult pikeperch <Emphasis Type="Italic">Sander lucioperca</Emphasis> (L.) in a drainage canal in the Mediterranean basin during spring

Pikeperch (Sander lucioperca L.) is a broadly distributed fish species in Europe but little is known about its ecology in the southern part of its distribution area in warm climatic conditions. The aim of this study was to analyse pikeperch rate of movement and to assess whether it displayed a diel pattern related to temperature. Thus acoustic telemetry was used to track adult pikeperch in a drainage canal located in south of France. The survey was carried out in spring, during the spawning period. The results showed that females were more active than males. This is in accordance with previous data on the nest guardian behaviour of the males. For both genders, the activity rates increased during the study period as water temperature rose. Males and females displayed the same diel activity with a maximum at dusk, thereby confirming many indirect observations. Nevertheless, inter-individuals variations were observed. Thus, these results on diel activity are rather a general trend than a strict rule and suggest the involvement of other factors than light intensity in the control of diel activity. This diel rhythm is positively correlated to water temperature for females. Pikeperch activity may be the result of a trade-off between physiological requirements of temperature and light, satisfaction of energy needs and avoidance of predators.     

Rotifer community structure in three shallow lakes: seasonal fluctuations and explanatory factors

The present work aimed at studying the rotifer communities of three shallow eutrophic lakes in Portugal (lakes Mira, Vela and Linhos). At the time of the study, Mira and Vela faced large inputs of allochthonous nutrients, while Linhos was facing terrestrialisation, with cycles of dominance-senescence of macrophytes. The three lakes differed in terms of their abiotic features, with Linhos presenting very high nutrient levels and low pH, while Vela and Mira shared most of the characteristics. The rotifer communities of these two lakes were poorly diversified but highly abundant (max. > 2000 ind l⁻¹), with a clear dominance of eurytopic euplanktonic species (mainly Keratella cochlearis). On the other hand, Linhos presented lower abundances (<1000 ind l⁻¹) but higher species richness, mainly due to macrophyte-associated taxa, such as the littoral genera Lepadella, Testudinella and Squatinella. In all lakes, summertime represented a peak in terms of abundance and diversity. Canonical correspondence analysis (CCA) identified two main environmental gradients that shape up the rotifer assemblages: a temporal gradient, mainly related to temperature, and a eutrophy gradient, associated with nitrogenous nutrients. The latter gradient is clearly dependent on between-lake variation, due to the high nutrient levels observed in lake Linhos. Variance partitioning using CCA revealed that the largest portion (27.5%) of the total variation explained (52.1%) was attributed to the interaction between lake and environmental variables.     

Bayesian latent variable models for mixed discrete outcomes

In studies of complex health conditions, mixtures of discrete outcomes (event time, count, binary, ordered categorical) are commonly collected. For example, studies of skin tumorigenesis record latency time prior to the first tumor, increases in the number of tumors at each week, and the occurrence of internal tumors at the time of death. Motivated by this application, we propose a general underlying Poisson variable framework for mixed discrete outcomes, accommodating dependency through an additive gamma frailty model for the Poisson means. The model has log-linear, complementary log-log, and proportional hazards forms for count, binary and discrete event time outcomes, respectively. Simple closed form expressions can be derived for the marginal expectations, variances, and correlations. Following a Bayesian approach to inference, conditionally-conjugate prior distributions are chosen that facilitate posterior computation via an MCMC algorithm. The methods are illustrated using data from a Tg.AC mouse bioassay study.     

The stabilizability of a controlled system describing the dynamics of a fishery

This work presents two stock-effort dynamical models describing the evolution of a fish population growing and moving between two fishing zones, on which it is harvested by a fishing fleet, distributed on the two zones. The first model corresponds to the case of constant displacement rates of the fishing effort, and the second one to fish stock-dependent displacement rates. In equations of the fishing efforts, a control function is introduced as the proportion of the revenue to be invested, for each fleet. The stabilizability analysis of the aggregated model, in the neighborhood of the equilibrium point, enables the determination of a Lyapunov function, which ensures the existence of a stabilizing discontinuous feedback for this model. This enables us to control the system and to lead, in an uniform way, any solution of this system towards this desired equilibrium point.     

Genetically altered mice: phenotypes,no phenotypes,and Faux phenotypes

Phenotype means different things, but whatever the measure, phenotype can be profoundly influenced by genetic, environmental and infectious variables. The laboratory mouse is a complex multisystemic organism which, despite its genetically inbred nature, as highly variable pathophysiologic characteristics. Mouse strains have background characteristics that can influence genomics research. In addition to the mouse itself, different approaches toward creating mutant mice each create variables that influence phenotype. Different background strains of mice are utilized for these different approaches, and various strains are preferred among different laboratories. Background genotype significantly influences phenotype of gene mutations, as can insufficient genetic stabilization of a mutation. Research programs engaged in functional mouse genomics not only must use genetically well-defined mice, but also must incorporate environmental and infectious disease quality assurance/prevention programs. Laboratory mice are subject to over 60 different infectious disease agents, including a wide variety of viruses, bacteria, protozoa, and metazoa. Although these agents can be readily diagnosed and prevented, a number of forces are resulting in their rise in prevalence in mouse colonies. Infectious disease, including clinically silent infections, can and do influence phenotype, and can jeopardize research considerably through lost time, wasted effort, cost, and even loss of valuable strains.     

Different Patterns of Changes in the Dry Season Diameter at Breast Height of Dominant and Evergreen Tree Species in a Mature Subtropical Forest in South China

Information on changes in diameter at breast height （DBH） is important for net primary production （NPP） estimates, timing of forest inventory, and forest management. In the present study, patterns of DBH change were measured under field conditions during the dry season for three dominant and native tree species in a monsoon evergreen broad-leaved forest in the Dinghushan Biosphere Reserve. For each tree species, different patterns of DBH change were observed. In the case of the fast-growing tree species Castanopsis chinensis Hance, large diurnal fluctuations occur, with a peak DBH in the early morning （around 05：00 h） that decreases to a minimum by about 14：00 h. Both Schima superba Gardn. et Chemp and Cryptocarya chinensis （Hance） Hemsh exhibited less diurnal swelling and shrinkage. Diurnal fluctuations for these species were observed on a few occasions over the period of observation. Graphical comparisons and statistical analysis of changes in DBH with meteorological variables indicate that for different trees, the different changes in DBH observed responded to different meteorological variables. Large stem changes were found to occur for Ca. chinensis trees that were associated with variations in solar radiation. However, both S. superba and Cr. chinensis were found to be less sensitive to solar radiation. Changes in the DBH of these two species were found to be controlled mainly by soil temperature and soil moisture. During the later dry season, with a lower soil temperature and soil moisture, all three tree species stopped growing and only negligible shrinkage, expansion, or fluctuation occurred, suggesting that the optimum time to measure tree growth in the Dinghushan Biosphere Reserve is the later dry season.