Modelling fungal colonies and communities:challenges and opportunities

This contribution, based on a Special Interest Group session held during IMC9, focuses on physiological based models of filamentous fungal colony growth and interactions. Fungi are known to be an important component of ecosystems, in terms of colony dynamics and interactions within and between trophic levels. We outline some of the essential components necessary to develop a fungal ecology: a mechanistic model of fungal colony growth and interactions, where observed behaviour can be linked to underlying function; a model of how fungi can cooperate at larger scales; and novel techniques for both exploring quantitatively the scales at which fungi operate; and addressing the computational challenges arising from this highly detailed quantification. We also propose a novel application area for fungi which may provide alternate routes for supporting scientific study of colony behaviour. This synthesis offers new potential to explore fungal community dynamics and the impact on ecosystem functioning

Prominent effect of soil network heterogeneity on microbial invasion

Using a network representation for real soil samples and mathematical models for microbial spread, we show that the structural heterogeneity of the soil habitat may have a very significant influence on the size of microbial invasions of the soil pore space. In particular, neglecting the soil structural heterogeneity may lead to a substantial underestimation of microbial invasion. Such effects are explained in terms of a crucial interplay between heterogeneity in microbial spread and heterogeneity in the topology of soil networks. The main influence of network topology on invasion is linked to the existence of long channels in soil networks that may act as bridges for transmission of microorganisms between distant parts of soil

Parkin-deficient mice are not more sensitive to 6-hydroxydopamine or methamphetamine neurotoxicity

BACKGROUND: Autosomal recessive juvenile parkinsonism (AR-JP) is caused by mutations in the parkin gene which encodes an E3 ubiquitin-protein ligase. Parkin is thought to be critical for protecting dopaminergic neurons from toxic insults by targeting misfolded or oxidatively damaged proteins for proteasomal degradation. Surprisingly, mice with targeted deletions of parkin do not recapitulate robust behavioral or pathological signs of parkinsonism. Since Parkin is thought to protect against neurotoxic insults, we hypothesized that the reason Parkin-deficient mice do not develop parkinsonism is because they are not exposed to appropriate environmental triggers. To test this possibility, we challenged Parkin-deficient mice with neurotoxic regimens of either methamphetamine (METH) or 6-hydroxydopamine (6-OHDA). Because Parkin function has been linked to many of the pathways involved in METH and 6-OHDA toxicity, we predicted that Parkin-deficient mice would be more sensitive to the neurotoxic effects of these agents. RESULTS: We found no signs consistent with oxidative stress, ubiquitin dysfunction, or degeneration of striatal dopamine neuron terminals in aged Parkin-deficient mice. Moreover, results from behavioral, neurochemical, and immunoblot analyses indicate that Parkin-deficient mice are not more sensitive to dopaminergic neurotoxicity following treatment with METH or 6-OHDA. CONCLUSION: Our results suggest that the absence of a robust parkinsonian phenotype in Parkin-deficient mice is not due to the lack of exposure to environmental triggers with mechanisms of action similar to METH or 6-OHDA. Nevertheless, Parkin-deficient mice could be more sensitive to other neurotoxins, such as rotenone or MPTP, which have different mechanisms of action; therefore, identifying conditions that precipitate parkinsonism specifically in Parkin-deficient mice would increase the utility of this model and could provide insight into the mechanism of AR-JP. Alternatively, it remains possible that the absence of parkinsonism in Parkin-deficient mice could reflect fundamental differences between the function of human and mouse Parkin, or the existence of a redundant E3 ubiquitin-protein ligase in mouse that is not found in humans. Therefore, additional studies are necessary to understand why Parkin-deficient mice do not display robust signs of parkinsonism

Manipulating the Attractiveness and Suitability of Hosts for Diamondback Moth (Lepidoptera: Plutellidae)

Ovipositional preference and larval survival of the diamondback moth, Plutella xylostella (L.), were compared among cabbage, Brassica oleracea L. variety capitata; glossy collards, Brassica oleracea L. variety acephala; and yellow rocket, Barbarea vulgaris (R. Br.) variety arcuata in different treatments of planting density, host plant age, intercropping, and water stress in 2003 and 2004. P. xylostella laid nearly twice as many eggs per plant in the high planting densities of glossy collards and yellow rocket than in the standard planting densities. Ovipositional preference was positively correlated with plant age in cabbage, glossy collards, and yellow rocket. Larval survival on cabbage was 1.9 times higher on 6-wk than on 12-wk-old plants, whereas larval survival on collards was 12.1 times higher on the younger plants. No larvae survived on either 6- or 12-wk-old yellow rocket plants. Intercropping cabbage with either tomato, Lycopersicon esculentum Mill., or fava bean, Vicia fava L., did not reduce the number of eggs laid on cabbage. No significant differences in oviposition were found between water-stressed and well-irrigated host plants treatments. Yet, P. xylostella larval survival on water-stressed cabbage was 2.1 times lower than on well-irrigated cabbage plants. Based on our findings, the effectiveness of trap crops of glossy collards and yellow rocket could be enhanced by integrating the use of higher planting densities in the trap crop than in the main crop and seeding of the trap crop earlier than the main cro

Using Yellow Rocket as a Trap Crop for Diamondback Moth (Lepidoptera: Plutellidae)

Yellow rocket, Barbarea vulgaris (R. Br.) variety arcuata, was evaluated as a trap crop for diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae), in cabbage, Brassica oleracea L. variety capitata, in 2003 and 2004. In 2003, the numbers of P. xylostella larvae found in field plots of cabbage alone were 5.2-11.3 times higher than those on cabbage plants in plots that included cabbage and several rows of yellow rocket. In an outdoor experiment in screenhouses, P. xylostella oviposition on cabbage was compared among six treatments that varied in the percentage of yellow rocket in relation to cabbage (0, 4, 8, 16, 24, and 32% of the plants were yellow rocket). Results indicated that the percentage of eggs laid on cabbage decreased as the percentage of yellow rocket in the treatment increased, but this decrease was not significant beyond 20% of the plants being yellow rocket. In 2004, the numbers of P. xylostella larvae in field plots of cabbage alone were 1.6-2.4 and 1.7-2.8 times higher than numbers in treatments with 10 and 20% trap crop, respectively. Sticky trap and sweep net captures of P. xylostella adults indicated that within-field dispersal was reduced by the presence of yellow rocket and aggregation occurred around yellow rocket plants. Our study suggests that using yellow rocket as a trap crop may reduce P. xylostella infestations in cabbage fields, and this possibility is discussed in the context of general crop and insect pest management practices in crucifer

Cardiovascular disease versus periodontal disease: chronic systemic infection as a link

Objective : Analysis of the alleged connection between the periodontal and cardiovascular disease, with reference to periodontal pathogens as a risk factor for heart disease. Researching method : A research was carried out at Medline/Pubmed. Included criteria and researching strategy. The articles selection has been made taking into account key-terms appearing either in the title or in the summary. Experimental studies in animals, clinical prospective studies performed with a minimum sample size (>30) and studies written in English have been included. The rejected criteria were the following: clinical retrospective studies and/or studies carried out with a low sample size (n<30). Results : Within systemic diseases related to periodontal ones, the alleged link between periodontal and heart and circulatory disease has been one of the most investigated in recent times. Different authors consider the existence of a link between the diseases as such, inappropriate and implausible since both the diseases have risk factors in common (age, gender, smoking, diet, oral hygiene and diabetes). However, speculations about the origin of the diseases were raised when it was demonstrated that some bacteria species, bacteria proteins and lipopolysaccharide are present at the plaques of atherosclerosis that obstruct the coronary arteries. The mechanisms of this connection have been analyzed following an actualized review. Conclusion : Most of the experimental and clinical studies ensure that a positive association between periodontal disease and heart disease has been found, once the con-founder factors have been eliminate

Soil health -- a new challenge for microbiologists and chemists.

The original publication is available on LINK at http://revistes.iec.cat/index.php/IM/article/view/4c457c718d531.002 This work, including photographs and other illustrations, unless the contrary is indicated, is subject to an Attributions–Non-Commercial–ShareAlike 3.0 Creative Commons License, the full text of which can be consulted at http://creativecommons.org/licenses/by-nc-sa/3.0/. You are free to share, copy, distribute and transmit the work provided that the author is credited and reuse of the material is restricted to non-commercial purposes only and that if you alter, transform, or build upon this work, you may distribute the resulting work only under the same or similar license to this on

Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data

BACKGROUND: Use of alternative gene promoters that drive widespread cell-type, tissue-type or developmental gene regulation in mammalian genomes is a common phenomenon. Chromatin immunoprecipitation methods coupled with DNA microarray (ChIP-chip) or massive parallel sequencing (ChIP-seq) are enabling genome-wide identification of active promoters in different cellular conditions using antibodies against Pol-II. However, these methods produce enrichment not only near the gene promoters but also inside the genes and other genomic regions due to the non-specificity of the antibodies used in ChIP. Further, the use of these methods is limited by their high cost and strong dependence on cellular type and context. METHODS: We trained and tested different state-of-art ensemble and meta classification methods for identification of Pol-II enriched promoter and Pol-II enriched non-promoter sequences, each of length 500 bp. The classification models were trained and tested on a bench-mark dataset, using a set of 39 different feature variables that are based on chromatin modification signatures and various DNA sequence features. The best performing model was applied on seven published ChIP-seq Pol-II datasets to provide genome wide annotation of mouse gene promoters. RESULTS: We present a novel algorithm based on supervised learning methods to discriminate promoter associated Pol-II enrichment from enrichment elsewhere in the genome in ChIP-chip/seq profiles. We accumulated a dataset of 11,773 promoter and 46,167 non-promoter sequences, each of length 500 bp, generated from RNA Pol-II ChIP-seq data of five tissues (Brain, Kidney, Liver, Lung and Spleen). We evaluated the classification models in building the best predictor and found that Bagging and Random Forest based approaches give the best accuracy. We implemented the algorithm on seven different published ChIP-seq datasets to provide a comprehensive set of promoter annotations for both protein-coding and non-coding genes in the mouse genome. The resulting annotations contain 13,413 (4,747) protein-coding (non-coding) genes with single promoters and 9,929 (1,858) protein-coding (non-coding) genes with two or more alternative promoters, and a significant number of unassigned novel promoters. CONCLUSION: Our new algorithm can successfully predict the promoters from the genome wide profile of Pol-II bound regions. In addition, our algorithm performs significantly better than existing promoter prediction methods and can be applied for genome-wide predictions of Pol-II promoters