A new species abundance distribution model based on model combination

Species abundance distribution (SAD) is one of the important measures of biodiversity and one of the most significant concepts in ecology communities. Using this concept, the biologists can infer a lot of information from their collected data. In this article, we proposed a new method for predicting SAD. This method is based on the combination of several measures parameterized by machine learning techniques and decomposition of the model in sub-ranges having their proper combination. The goal is to use the combination of several individual models to design a better and more informative model. We show in this article by using many datasets representing different ecological situations that our new method is more robust and outperforms the predictive capacity of the other existing models.

Speciation with gene flow in a heterogeneous virtual world: can physical obstacles accelerate speciation?

The origin of species remains one of the most controversial and least understood topics in evolution. While it is being widely accepted that complete cessation of gene-flow between populations owing to long-lasting geographical barriers results in a steady, irreversible increase of divergence and eventually speciation, the extent to which various degrees of habitat heterogeneity influences speciation rates is less well understood. Here, we investigate how small, randomly distributed physical obstacles influence the distribution of populations and species, the level of population connectivity (e.g. gene flow), as well as the mode and tempo of speciation in a virtual ecosystem composed of prey and predator species. We adapted an existing individual-based platform, EcoSim, to allow fine tuning of the gene flow's level between populations by adding various numbers of obstacles in the world. The platform implements a simple food chain consisting of primary producers, herbivores (prey) and predators. It allows complex intra- and inter-specific interactions, based on individual evolving behavioural models, as well as complex predator-prey dynamics and coevolution in spatially homogenous and heterogeneous worlds. We observed a direct and continuous increase in the speed of evolution (e.g. the rate of speciation) with the increasing number of obstacles in the world. The spatial distribution of species was also more compact in the world with obstacles than in the world without obstacles. Our results suggest that environmental heterogeneity and other factors affecting demographic stochasticity can directly influence speciation and extinction rates.

The composition of house dust mite is critical for mucosal barrier dysfunction and allergic sensitisation

BACKGROUND

House dust mite (HDM) allergens have been reported to increase airway epithelial permeability, thereby facilitating access of allergens and allergic sensitisation.

OBJECTIVES

The authors aimed to understand which biochemical properties of HDM are critical for epithelial immune and barrier responses as well as T helper 2-driven experimental asthma in vivo.

METHODS

Three commercially available HDM extracts were analysed for endotoxin levels, protease and chitinase activities and effects on transepithelial resistance, junctional proteins and pro-inflammatory cytokine release in the bronchial epithelial cell line 16HBE and normal human bronchial cells. Furthermore, the effects on epithelial remodelling and airway inflammation were investigated in a mouse model.

RESULTS

The different HDM extracts varied extensively in their biochemical properties and induced divergent responses in vitro and in vivo. Importantly, the Greer extract, with the lowest serine protease activity, induced the most pronounced effects on epithelial barrier function and CCL20 release in vitro. In vivo, this extract induced the most profound epithelial E-cadherin delocalisation and increase in CCL20, CCL17 and interleukin 5 levels, accompanied by the most pronounced induction of HDM-specific IgE, goblet cell hyperplasia, eosinophilic inflammation and airway hyper-reactivity.

CONCLUSIONS

This study shows the ability of HDM extracts to alter epithelial immune and barrier responses is related to allergic sensitisation but independent of serine/cysteine protease activity.

43 genes support the lungfish-coelacanth grouping related to the closest living relative of tetrapods with the Bayesian method under the coalescence model

BACKGROUND

Since the discovery of the "living fossil" in 1938, the coelacanth (Latimeria chalumnae) has generally been considered to be the closest living relative of the land vertebrates, and this is still the prevailing opinion in most general biology textbooks. However, the origin of tetrapods has not been resolved for decades. Three principal hypotheses (lungfish-tetrapod, coelacanth-tetrapod, or lungfish-coelacanth sister group) have been proposed.

FINDINGS

We used the Bayesian method under the coalescence model with the latest published program (Bayesian Estimation of Species Trees, or BEST) to perform a phylogenetic analysis for seven relevant taxa and 43 nuclear protein-coding genes with the jackknife method for taxon sub-sampling. The lungfish-coelacanth sister group was consistently reconstructed with the Bayesian method under the coalescence model in 17 out of 21 taxon sets with a Bayesian posterior probability as high as 99%. Lungfish-tetrapod was only inferred from BCLS and BACLS. Neither coelacanth-tetrapod nor lungfish-coelacanth-tetrapod was recovered out of all 21 taxon sets.

CONCLUSIONS

Our results provide strong evidence in favor of accepting the hypothesis that lungfishes and coelacanths form a monophyletic sister-group that is the closest living relative of tetrapods. This clade was supported by high Bayesian posterior probabilities of the branch (a lungfish-coelacanth clade) and high taxon jackknife supports.

Regularity analysis of an individual-based ecosystem simulation

We analyze the results of a large simulation of an evolving ecosystem to evaluate its complexity. In particular, we are interested to know how close to a stochastic or a deterministic behavior our simulation is. Four methods have been used for this analysis: Higuchi fractal dimension, correlation dimension, largest Lyapunov exponent, and P&H method. Besides, we use a surrogate data test to reach a final decision about analysis. As we expect, our results show that there is a deterministic and chaotic behavior in ecosystem simulation.

Management of cervical lymph node recurrence of melanoma of the head and neck

OBJECTIVES

To compare the diagnostic accuracy between Positron emission tomography using 2-[fluorine-18] fluoro-2-deoxy-D-glucose (FDG-PET scan) and conventional work-up such as ultrasound (US) and/or Computed tomography (CT) in the detection of cervical lymph node recurrences of melanoma of the head and neck after initial cervical lymph node surgery.

METHODS

A retrospective review was performed on patients who presented with clinical and/or radiological suspicion of isolated cervical lymph node recurrence after lymph node surgery from April 2004 to January 2007. All patients underwent CT and/or US of the neck, and FDG-PET scan before salvage neck dissection. None of included patients had clinical or radiological detectable distant metastases at the time of the lymph node dissection. Performances of conventional imaging and FDG-PET scan in detection of lymph node recurrence were calculated and compared by using the histopathological results of lymphadenectomy as gold standard with Fischer's exact test.

RESULTS

Of the twelve cases in included in the study (9 patients, 3 of them had 2 consecutive lymph node redissection for a second lymph node recurrence), melanoma recurrence was found in 10 cases (83%). Sensitivity, specificity, positive predictive value and negative predictive values were 78.6%, 40%, 78.6%, and 40% respectively for conventional imaging and 85.7%, 40%, 80% and 50% for FDG-PET scan. No statistically significant difference was found between the 2 methods.

CONCLUSION

This is the first study that compares the diagnostic accuracy between FDG-PET scan and conventional imaging in the detection of cervical lymph node recurrence of melanoma of the head and neck. Our results showed that FDG-PET scan is actually not better than conventional imaging to detect these cervical lymphatic recurrences.

An individual-based evolving predator-prey ecosystem simulation using a fuzzy cognitive map as the behavior model

We present an individual-based predator-prey model with, for the first time, each agent behavior being modeled by a fuzzy cognitive map (FCM), allowing the evolution of the agent behavior through the epochs of the simulation. The FCM enables the agent to evaluate its environment (e.g., distance to predator or prey, distance to potential breeding partner, distance to food, energy level) and its internal states (e.g., fear, hunger, curiosity), and to choose several possible actions such as evasion, eating, or breeding. The FCM of each individual is unique and is the result of the evolutionary process. The notion of species is also implemented in such a way that species emerge from the evolving population of agents. To our knowledge, our system is the only one that allows the modeling of links between behavior patterns and speciation. The simulation produces a lot of data, including number of individuals, level of energy by individual, choice of action, age of the individuals, and average FCM associated with each species. This study investigates patterns of macroevolutionary processes, such as the emergence of species in a simulated ecosystem, and proposes a general framework for the study of specific ecological problems such as invasive species and species diversity patterns. We present promising results showing coherent behaviors of the whole simulation with the emergence of strong correlation patterns also observed in existing ecosystems.

Analysis of proteomes using the molecular scanner

INTRODUCTIONThe molecular scanner offers a flexible and powerful visualization tool that can create a fully annotated 2D gel electrophoresis map. Proteins separated by 2D gel electrophoresis are simultaneously digested while undergoing electrotransfer from the gel to a membrane. The peptides are subjected to peptide mass fingerprint (PMF) analysis to identify proteins directly from the PVDF membranes by MALDI-TOF-MS scanning. An ensemble of dedicated tools is then used to create, analyze, and visualize a proteome as a multidimensional image. The molecular scanner method reduces to a minimum the sample handling prior to mass analysis and decreases the sample size to a few tens of micrometers, that is, the size of the MALDI-TOF-MS laser beam impact. The process can be divided into four parts: separation and digestion of proteins, acquisition of PMF data, processing of the MS data and protein identification, and creation of multidimensional proteome maps.