Computational and Mathematical Modelling of the EGF Receptor System

This chapter gives an overview of computational and mathematical modelling of the EGF receptor system. It begins with a survey of motivations for producing such models, then describes the main approaches that are taken to carrying out such modelling, viz. differential equations and individual-based modelling. Finally, a number of projects that applying modelling and simulation techniques to various aspects of the EGF receptor system are described

Comparison of the protein-coding genomes of three deep-sea, sulfur-oxidising bacteria: “Candidatus Ruthia magnifica”, “Candidatus Vesicomyosocius okutanii” and Thiomicrospira crunogena

Abstract Objective “ Candidatus Ruthia magnifica”, “Candidatus Vesicomyosocius okutanii” and Thiomicrospira crunogena are all sulfur-oxidising bacteria found in deep-sea vent environments. Recent research suggests that the two symbiotic organisms, “Candidatus R. magnifica” and “Candidatus V. okutanii”, may share common ancestry with the autonomously living species T. crunogena. We used comparative genomics to examine the genome-wide protein-coding content of all three species to explore their similarities. In particular, we used the OrthoMCL algorithm to sort proteins into groups of putative orthologs on the basis of sequence similarity. Results The OrthoMCL inflation parameter was tuned using biological criteria. Using the tuned value, OrthoMCL delimited 1070 protein groups. 63.5% of these groups contained one protein from each species. Two groups contained duplicate protein copies from all three species. 123 groups were unique to T. crunogena and ten groups included multiple copies of T. crunogena proteins but only single copies from the other species. “Candidatus R. magnifica” had one unique group, and had multiple copies in one group where the other species had a single copy. There were no groups unique to “Candidatus V. okutanii”, and no groups in which there were multiple “Candidatus V. okutanii” proteins but only single proteins from the other species. Results align with previous suggestions that all three species share a common ancestor. However this is not definitive evidence to make taxonomic conclusions and the possibility of horizontal gene transfer was not investigated. Methodologically, the tuning of the OrthoMCL inflation parameter using biological criteria provides further methods to refine the OrthoMCL procedure

Temporal variation of biomass and nutrient status of azolla filiculoides lam: (sal viniaceae) in a small shallow dystrophic lake

This study determined the temporal variation of the biomass and the concentrations of carbon, nitrogen and phosphorus in Azolla filiculoides Lam. in a small (0.5 ha) shallow dystrophic lake located in the city of Rio Grande (Rio Grande do Sul State, Brazil). Method: Sampling was conducted monthly between November 2000 and October 2001. The macrophytes were collected randomly in three replicates with a circular collector 0.3 m in diameter and subsequently washed with tap water and oven-dried at 60 °C for determination of the dry weight and the nutrient status (i.e., carbon, nitrogen and phosphorus). Primary productivity was estimated by the variation in biomass among successive samples. Results: A. filiculoides was present in the lake throughout the year and occupied between 50 and 80% of the surface area. The biomass values ranged from 34.2 g DW.m–2, recorded in May (autumn), to 170.9 g DW.m–2 in January (summer). The highest rate of primary productivity was 3.3 g DW.m–2.d–1, observed in June. The concentrations of carbon, nitrogen and phosphorus in the plant ranged between 403 and 551 g.kg–1, 13.4 and 25.7 g.kg–1 and 0.5 and 1.9 g.kg–1, respectively. The water N:P ratio ranged between 19:1 and 368:1. Conclusion: The coverage of the surface of the lake by A. filiculoides throughout the study period and the nutritional status of the plant demonstrate the importance of the cycling of nutrients by macrophytes in this aquatic environment. The higher N:P ratio in the water column, compared with other neighboring environments without macrophytes, shows that the enrichment of the lake may result from the biological N-fixation activity produced by A. filiculoides.Este estudo determinou a variação temporal da biomassa e as concentrações de carbono, nitrogênio e fósforo de Azolla filiculoides Lam., em um pequeno lago raso distrófico situado no município do Rio Grande (Rio Grande do Sul, Brasil). Método: As amostragens foram realizadas mensalmente no período entre novembro de 2000 e outubro de 2001. As macrófitas foram coletadas aleatoriamente em três repetições, utilizando-se coletor circular de 0,3 m de diâmetro e posteriormente lavadas com água corrente e secas em estufa 60 °C para determinação do peso seco e dos nutrientes: carbono, nitrogênio e fósforo. A produção primária foi estimada pela variação de biomassa entre coletas sucessivas. Resultados: A. filiculoides esteve presente no lago durante todo o ano, ocupando sempre entre 50 e 80% da superfície do lago. Os valores de biomassa variaram entre 34,2 g PS.m–2, registrado em maio (outono) e 170,9 g PS.m–2 em janeiro (verão). A maior taxa de produtividade primária foi 3,3 g PS.m–2.d–1 foi registrada em Junho. As concentrações de carbono, nitrogênio e fósforo na planta variaram entre: 403 e 551 g. kg–1, 13,4 e 25,7 g.kg–1 e 0,5 e 1,9 g.kg–1, respectivamente. Os valores da relação N:P na coluna de água variou entre 19:1 e 368:1. Conclusão: A cobertura da superfície do lago por A. filiculoides durante todo o período do estudo e o seu estado nutricional demonstram sua importância na ciclagem dos nutrientes neste ambiente aquático. A maior relação N:P na coluna de água quando comparada a outro ambiente próximo sem a presença desta macrófita, apoia a ideia de que A. filiculoides pode ser a responsável pelo enriquecimento do lago por meio da atividade de fixação biológica de nitrogênio