Identification of neurotoxic compounds in cyanobacteria exudate mixtures

Release of toxic cyanobacterial secondary metabolites threatens biosecurity, foodwebs and public health. Microcystis aeruginosa (Ma), the dominant species in global freshwater cyanobacterial blooms, produces exudates (MaE) that cause adverse outcomes including nerve damage. Previously, we identified > 300 chemicals in MaE. It is critical to investigate neurotoxicity mechanisms of active substances among this suite of Ma compounds. Here, we screened 103 neurotoxicity assays from the ToxCast database to reveal targets of action of MaE using machine learning. We then built a potential Adverse Outcome Pathway (AOP) to identify neurotoxicity mechanisms of MaE as well as key targets. Finally, we selected potential neurotoxins matched with those targets using molecular docking. We found 38 targets that were inhibited and eight targets that were activated, collectively mainly related to neurotransmission (i.e. cholinergic, dopaminergic and serotonergic neurotransmitter systems). The potential AOP of MaE neurotoxicity could be caused by blocking calcium voltage-gated channel (CACNA1A), because of antagonizing neurotransmitter receptors, or because of inhibiting solute carrier transporters. We identified nine neurotoxic MaE compounds with high affinity to those targets, including LysoPC(16:0), 2-acetyl-1-alkyl-sn-glycero-3-phosphocholine, egonol glucoside, polyoxyethylene (600) monoricinoleate, and phytosphingosine. Our study enhances understanding of neurotoxicity mechanisms and identifies neurotoxins in cyanobacterial bloom exudates, which may help identify priority compounds for cyanobacteria management.

A comparison of stable and fluctuating resources with respect to evolutionary adaptation and life-history traits using individual-based modeling and machine learning

There are three non-mutually-exclusive key strategies evolved by gene pools to cope with fluctuating food resource availability, including evolutionary adaptation, phenotypic plasticity, and migration. We focus primarily on evolutionary adaptation and behavioral plasticity, which is a type of phenotypic plasticity, resulting in life-history changes as ways of dealing with fluctuations in food resource availability. Using EcoSim, a predator-prey individual-based model, we compare individuals with stable food resources with those in environments where there are fluctuating food resources in terms of adaptation through behavioral plasticity and evolution. The purpose of our study is to determine whether evolution and behavioral plasticity truly play a role in adapting to an environment with fluctuating food resources, as well as to determine whether there are specific gene divergences between gene pools in fluctuating food resource environments versus gene pools where food resources are relatively stable. An important result of our study is that individuals in environments that are unstable with respect to food resource availability exhibited significant differences in behaviors versus those in environments with stable food resources. Although behavioral plasticity facilitates a rapid response to unstable food conditions, our study revealed the evolution of perceptual traits such as vision range in reaction to fluctuating food resources, indicating the importance of evolution in adapting to unstable resource environments in the long run. Moreover, using decision trees, we found that there were significant behavioral gene divergences between individuals in environments with fluctuating food resources as opposed to individuals in environments with stable food resources.

[Cutaneous foreign body granulomas following cervico-facial arterial embolization: Three cases]

BACKGROUND

Foreign body granuloma is an inflammatory tissue reaction to exogenous material. Classically it appears on the face after aesthetic procedures. Herein we report for the first time three cases of facial granulomatous reactions to microbeads after arterial cervico-facial embolization.

PATIENTS AND METHODS

Three patients underwent embolization of the facial arteries using Embogold^® microbeads in a setting of epistaxis or tumoral hemostasis. Within 10 to 45 days painful, inflammatory, subcutaneous nodules appeared on the homolateral side of the face. Histological samples showed an inflammatory response with giant cells as well as the presence of microbeads in the skin. A favorable outcome was achieved with colchicine in one patient and with surgery in another; the third patient was lost to follow-up.

DISCUSSION

The embolizing microspheres produced a local inflammatory reaction, with destruction of the vascular wall and bead migration to facial tissue leading to a granulomatous reaction. The occurrence of three cases within a period of few weeks, with several different operators and batches of products, is surprising considering the long-standing use of the product. There was no common comorbidity in the patients and no suggestion of trauma. Retrospective analysis of the product batches was normal. Gold staining could play a role in severe inflammatory response to Embogold^® particles.

CONCLUSION

These three cases illustrate the value of discussing potential foreign body granulomatous reaction in cases of facial nodules following cervico-facial embolization. Colchicine may offer a valuable therapeutic alternative.

Optimization and performance testing of a sequence processing pipeline applied to detection of nonindigenous species

Genetic taxonomic assignment can be more sensitive than morphological taxonomic assignment, particularly for small, cryptic or rare species. Sequence processing is essential to taxonomic assignment, but can also produce errors because optimal parameters are not known a priori. Here, we explored how sequence processing parameters influence taxonomic assignment of 18S sequences from bulk zooplankton samples produced by 454 pyrosequencing. We optimized a sequence processing pipeline for two common research goals, estimation of species richness and early detection of aquatic invasive species (AIS), and then tested most optimal models' performances through simulations. We tested 1,050 parameter sets on 18S sequences from 20 AIS to determine optimal parameters for each research goal. We tested optimized pipelines' performances (detectability and sensitivity) by computationally inoculating sequences of 20 AIS into ten bulk zooplankton samples from ports across Canada. We found that optimal parameter selection generally depends on the research goal. However, regardless of research goal, we found that metazoan 18S sequences produced by 454 pyrosequencing should be trimmed to 375-400 bp and sequence quality filtering should be relaxed (1.5 ≤ maximum expected error ≤ 3.0, Phred score = 10). Clustering and denoising were only viable for estimating species richness, because these processing steps made some species undetectable at low sequence abundances which would not be useful for early detection of AIS. With parameter sets optimized for early detection of AIS, 90% of AIS were detected with fewer than 11 target sequences, regardless of whether clustering or denoising was used. Despite developments in next-generation sequencing, sequence processing remains an important issue owing to difficulties in balancing false-positive and false-negative errors in metabarcoding data.

Subcutaneous immunotherapy suppresses Th2 inflammation and induces neutralizing antibodies, but sublingual immunotherapy suppresses airway hyperresponsiveness in grass pollen mouse models for allergic asthma

BACKGROUND

Both subcutaneous and sublingual allergen immunotherapy (SCIT and SLIT) have been shown to effectively suppress allergic manifestations upon allergen exposure, providing long-term relief from symptoms in allergic disorders including allergic asthma. Clinical studies directly comparing SCIT and SLIT report a different kinetics and magnitude of immunological changes induced during treatment. Comparative studies into the mechanisms underlying immune suppression in SCIT and SLIT are lacking.

OBJECTIVE

We aimed to establish an experimental model for grass pollen (GP) SCIT and SLIT that would allow a head-to-head comparison of the two treatments.

METHODS

BALB/c mice were sensitized with GP extract, followed by SCIT and SLIT treatments with various GP dosages. Subsequently, we challenged mice with GP and measured airway responsiveness (AHR), GP-specific immunoglobulins, ear swelling tests (EST), eosinophilic inflammation in bronchoalveolar lavage fluid (BALF), and T cell cytokine release after restimulation of lung cells (IL-5, IL-10, and IL-13).

RESULTS

We find that SLIT treatment was able to suppress allergen-induced AHR, while allergic inflammation was not effectively suppressed even at the highest GP dose in this model. In contrast, SCIT treatment induced higher levels of GP-specific IgG1, while SLIT was superior in inducing a GP-specific IgG2a response, which was associated with increased Th1 activity in lung tissue after SLIT, but not SCIT treatment. Interestingly, SCIT was able to suppress Th2-type cytokine production in lung cell suspensions, while SLIT failed to do so.

CONCLUSIONS AND CLINICAL RELEVANCE

In conclusion, GP-SCIT suppresses Th2 inflammation and induced neutralizing antibodies, while GP-SLIT suppresses the clinically relevant lung function parameters in an asthma mouse model, indicating that the two application routes depend on partially divergent mechanisms of tolerance induction. Interestingly, these data mirror observations in clinical studies, underscoring the translational value of these mouse models.

Piston-cylinder based micro liquid–liquid extraction with GC–qMS for trace analysis of targeted chlorinated organic compounds in water

A fast and reliable approach for the measurement of sub parts-per-billion levels of targeted chlorinated compounds like tetrachloroethane, hexachloroethane, hexachlorobutadiene, pentachlorobenzene, and hexachlorobenzene in various water matrices such as waste water is described. The method employed a novel piston-cylinder-based micro liquid–liquid extraction technique using hexane as an extraction solvent. The device, known commercially as the MIXXOR, substantially accelerates extraction time by a factor of more than 100 times and reduces solvent consumption by a factor of 25 times when compared with the solvent extraction technique using wrist-action mechanical agitation. A recently introduced 6% cyanopropylphenyl –94% dimethylpolysiloxane capillary column offering a high degree of inertness was used for the separation of the analytes. A quadrupole mass spectrometer equipped with a triple-axis detector was also employed to enhance the instrument detection limit. With this technique, a complete separation for the analytes in water can be conducted in less than 10 min using a three-port SilFlow planar microfluidic device for back-flushing. Repeatability of retention times for all compounds were found to be less than 0.04% (n = 10). The compounds cited can be analyzed from 1 ng/mL to 10 μg/mL, with a detection limit and correlation coefficient of at least 0.5 ng/mL and 0.999, respectively. A relative precision of less than 1.2% relative standard deviation (RSD) (n = 20) at the 50 ng/mL level, with analyte recovery of greater than 99% (n = 3) from 10 ng/mL to 10 μg/mL, was obtained.

Speciation without Pre-Defined Fitness Functions

The forces promoting and constraining speciation are often studied in theoretical models because the process is hard to observe, replicate, and manipulate in real organisms. Most models analyzed to date include pre-defined functions influencing fitness, leaving open the question of how speciation might proceed without these built-in determinants. To consider the process of speciation without pre-defined functions, we employ the individual-based ecosystem simulation platform EcoSim. The environment is initially uniform across space, and an evolving behavioural model then determines how prey consume resources and how predators consume prey. Simulations including natural selection (i.e., an evolving behavioural model that influences survival and reproduction) frequently led to strong and distinct phenotypic/genotypic clusters between which hybridization was low. This speciation was the result of divergence between spatially-localized clusters in the behavioural model, an emergent property of evolving ecological interactions. By contrast, simulations without natural selection (i.e., behavioural model turned off) but with spatial isolation (i.e., limited dispersal) produced weaker and overlapping clusters. Simulations without natural selection or spatial isolation (i.e., behaviour model turned off and high dispersal) did not generate clusters. These results confirm the role of natural selection in speciation by showing its importance even in the absence of pre-defined fitness functions.

Pim1 kinase protects airway epithelial cells from cigarette smoke-induced damage and airway inflammation

Exposure to cigarette smoke (CS) is the main risk factor for developing chronic obstructive pulmonary disease and can induce airway epithelial cell damage, innate immune responses, and airway inflammation. We hypothesized that cell survival factors might decrease the sensitivity of airway epithelial cells to CS-induced damage, thereby protecting the airways against inflammation upon CS exposure. Here, we tested whether Pim survival kinases could protect from CS-induced inflammation. We determined expression of Pim kinases in lung tissue, airway inflammation, and levels of keratinocyte-derived cytokine (KC) and several damage-associated molecular patterns in bronchoalveolar lavage in mice exposed to CS or air. Human bronchial epithelial BEAS-2B cells were treated with CS extract (CSE) in the presence or absence of Pim1 inhibitor and assessed for loss of mitochondrial membrane potential, induction of cell death, and release of heat shock protein 70 (HSP70). We observed increased expression of Pim1, but not of Pim2 and Pim3, in lung tissue after exposure to CS. Pim1-deficient mice displayed a strongly enhanced neutrophilic airway inflammation upon CS exposure compared with wild-type controls. Inhibition of Pim1 activity in BEAS-2B cells increased the loss of mitochondrial membrane potential and reduced cell viability upon CSE treatment, whereas release of HSP70 was enhanced. Interestingly, we observed release of S100A8 but not of double-strand DNA or HSP70 in Pim1-deficient mice compared with wild-type controls upon CS exposure. In conclusion, we show that expression of Pim1 protects against CS-induced cell death in vitro and neutrophilic airway inflammation in vivo. Our data suggest that the underlying mechanism involves CS-induced release of S100A8 and KC.

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.