Dynamical complexity of discrete time regulatory networks

Genetic regulatory networks are usually modeled by systems of coupled differential equations and by finite state models, better known as logical networks, are also used. In this paper we consider a class of models of regulatory networks which present both discrete and continuous aspects. Our models consist of a network of units, whose states are quantified by a continuous real variable. The state of each unit in the network evolves according to a contractive transformation chosen from a finite collection of possible transformations, according to a rule which depends on the state of the neighboring units. As a first approximation to the complete description of the dynamics of this networks we focus on a global characteristic, the dynamical complexity, related to the proliferation of distinguishable temporal behaviors. In this work we give explicit conditions under which explicit relations between the topological structure of the regulatory network, and the growth rate of the dynamical complexity can be established. We illustrate our results by means of some biologically motivated examples.Comment: 28 pages, 4 figure

Complete factorization of equations of motion for generalized scalar field theories

We demonstrate that the complete factorization of equations of motion into first-order differential equations can be obtained for real and complex scalar field theories with non-canonical dynamics.Comment: 5 pages; version published in EP

Cell Therapy for Type 1 Diabetes

Acknowledgements The work described in this review was supported by a grant from the MRC. K.R.M. is supported by a fellowship from the Scottish Translational Medicines and Therapeutics Initiative through the Wellcome Trust.Peer reviewedPublisher PD

Mutagens require to be considered when isolating and preserving fungi

Microorganisms are preserved in collections to ensure they represent wild type strains from Nature. Others may be preserved for specific properties not associated with wild types. To protect these from mutagens is a priority seldom considered. Some fungi produce mutagenic secondary metabolites in culture and it is unknown whether the metabolites affect the DNA/RNA of microorganisms to be isolated and preserved. For example, aflatoxins are the most carcinogenic, naturally-occurring compounds. The producing fungi are obtained from the environment quite frequently and so may be isolated with other microorganisms during isolation: Other compounds from the same or different fungi may be mutagenic. Furthermore, mutagenic secondary metabolites may be produced at high concentrations when pure fungal cultures are grown from preservation or for maintenance, which may affect the DNA/RNA of the producing fungi. Fungi producing “self-affecting” metabolites and spontaneous mutants in pure culture are well-known. Preserved fungi are required to be grown to minimise secondary metabolite production if representative wild types, or strains with specific properties, are to be obtained with absolute confidence – it is a matter of the adequate design of culture collection protocols

Ergosterol as a rapid measurement of Ganoderma rot of oil palm

Palm oil (PO) is a very important commodity for many countries and especially Indonesia and Malaysia who are the predominant producers. PO is used in ca. 30% of supermarket foods, cosmetics, cooking and as biodiesel. The growth of oil palms in plantations is controversial as the production methods contribute to climate change and cause environmental damage [1]. The plant is subjected to a devastating disease in these two countries caused by the white rot fungus Ganoderma. There are no satisfactory methods to diagnose the disease in the plant as they are too slow and/or inaccurate. The lipid compound ergosterol is unique to fungi and is used to measure growth especially in solid substrates. We report here on the use of ergosterol to measure the growth of Ganoderma in oil palms using HPLC and TLC methods [2]. The method is rapid and correlates well with other methods and is capable of being used on-site, hence improving the speed of analysis and allowing remedial action. Climate change will affect the health of OP [1] and rapid detection methods will be increasingly required to control the disease. [1] Paterson, RRM, Kumar, L, Taylor, S, Lima N. Future climate effects on suitability for growth of oil palms in Malaysia and Indonesia. Scientific Reports, 5, 2015, 14457. [2] Muniroh, MS, Sariah M, Zainal Abidin, MA, Lima, N, Paterson, RRM. Rapid detection of Ganoderma-infected oil palms by microwave ergosterol extraction with HPLC and TLC. Journal of Microbiological Methods, 100, 2014, 143–147

How will climate change affect mycotoxins in food?

This invited review and opinion piece, assesses the impact of climate change on mycotoxins in food: only one paper and an abstract referred directly from a substantial literature search and then only in relation to Europe. Climate change is an accepted probability by most scientists. Favourable temperature and water activity are crucial for mycotoxigenic fungi and mycotoxin production. Fungal diseases of crops provide relevant information for pre-harvest mycotoxin contamination. However, the mycotoxin issue also involves post-harvest scenarios. There are no data on how mycotoxins affect competing organisms in crop ecosystems. In general, if the temperature increases in cool or temperate climates, the relevant countries may become more liable to aflatoxins. Tropical countries may become too inhospitable for conventional fungal growth and mycotoxin production. Could this lead to the extinction of thermotolerant Aspergillus flavus? Currently cold regions may become liable to temperate problems concerning ochratoxin A, patulin and Fusarium toxins (e.g. deoxynivalenol). Regions which can afford to control the environment of storage facilities may be able to avoid post-harvest problems but at high additional cost. There appears to be a lack of awareness of the issue in some non-European countries. The era will provide numerous challenges for mycotoxicologists.Fundação para a Ciência e a Tecnologia (FCT) - bolsa SFRH/BPD/34879/2007, Commitment to Science ref. C2008-UMINHO-CEB-2

Microbial nucleic acids employed in diagnostics, sequencing and phylogenetics are subject to detrimental inhibitors and mutagens

Sequencing the genomes of microbial species has increased tremendously. Nucleic acids (NA) are used also for diagnostic and phylogenetic analyses of microbes. It is essential that protocols ensure representative NA. The effect of the "spent" growth medium on NA has not been considered. Surprisingly, fungi are grown on media that support inhibitors and mutagens when producing NA for these purposes1,2,3. This situation is illogical as these secondary metabolites may affect the structure of NA2 and/or inhibit PCR polymerases used in PCR3. The objective of the work was to highlight how NA analyses could be affected by self produced mutagens and inhibitors. Hence, (a) PCR of the idh gene of patulin production in fungi (e.g. Penicillium expansum) and (b) interpretation of the scientific literature were employed to determine the seriousness of the situation. Analysis of idh was successful for culture dependant PCR (CDP) and culture independent PCR (CIP). A reversible inhibition was observed in CDP presumably from inhibitors in cultures. Inhibition was observed in CIP. In some cases, taxa which were predicted to be positive for idh were not, and vice versa. A logical interpretation of this was that the gene was mutated by cultural components. In addition, the PCR reaction may have been inhibited and internal amplification controls (IAC) are required. The conclusions were that it is illogical to grow microbes for NA analysis in a milieu of mutagens and inhibitors. Reports on diagnostic methods and phylogenetic schemes are undermined consequently. Work on Aspergillus flavus ismost vulnerable to this criticism, as they produce aflatoxins which are the most carcinogenic natural compounds. Numerous fungi produce inhibitors and mutagens and so the problem is widespread. There may be an equivalent situation for bacteria2,3. It is essential to grow microbes in a manner to avoid mutagens and inhibitors. Some recommended procedures would be to grow the cultures for a shorter period, although the ratio of mutagen to NA is important. Analysing cultures immediately upon isolation is preferred. Continuous culture could be used to avoid secondary metabolism. Finally, IAC are required for PCR in general