Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering

<p>Abstract</p> <p>Background</p> <p>Mechanistic models are becoming more and more popular in Systems Biology; identification and control of models underlying biochemical pathways of interest in oncology is a primary goal in this field. Unfortunately the scarce availability of data still limits our understanding of the intrinsic characteristics of complex pathologies like cancer: acquiring information for a system understanding of complex reaction networks is time consuming and expensive. Stimulus response experiments (SRE) have been used to gain a deeper insight into the details of biochemical mechanisms underlying cell life and functioning. Optimisation of the input time-profile, however, still remains a major area of research due to the complexity of the problem and its relevance for the task of information retrieval in systems biology-related experiments.</p> <p>Results</p> <p>We have addressed the problem of quantifying the information associated to an experiment using the Fisher Information Matrix and we have proposed an optimal experimental design strategy based on evolutionary algorithm to cope with the problem of information gathering in Systems Biology. On the basis of the theoretical results obtained in the field of control systems theory, we have studied the dynamical properties of the signals to be used in cell stimulation. The results of this study have been used to develop a microfluidic device for the automation of the process of cell stimulation for system identification.</p> <p>Conclusion</p> <p>We have applied the proposed approach to the Epidermal Growth Factor Receptor pathway and we observed that it minimises the amount of parametric uncertainty associated to the identified model. A statistical framework based on Monte-Carlo estimations of the uncertainty ellipsoid confirmed the superiority of optimally designed experiments over canonical inputs. The proposed approach can be easily extended to multiobjective formulations that can also take advantage of identifiability analysis. Moreover, the availability of fully automated microfluidic platforms explicitly developed for the task of biochemical model identification will hopefully reduce the effects of the 'data rich-data poor' paradox in Systems Biology.</p

A bibliography of parasites and diseases of marine and freshwater fishes of India

With the increasing demand for fish as human food, aquaculture both in freshwater and salt water is rapidly developing over the world. In the developing countries, fishes are being raised as food. In many countries fish farming is a very important economic activity. The most recent branch, mariculture, has shown advances in raising fishes in brackish, estuarine and bay waters, in which marine, anadromous and catadromous fishes have successfully been grown and maintained

Karyotypes and DNA content in Bignoniaceae

Cytogenetic studies in 22 Bignoniaceae species were performed. Most taxa are from Argentina, one from Brazil, and two are cultivated (from South Africa and USA). All data are new, including first counts for Bignonia binata, Handroanthus ochraceus, Tabebuia aurea and the genus Podranea. Most taxa are diploid (2n= 40): members of tribes Bignonieae (Adenocalymma, Amphilophium, Bignonia, Cuspidaria, Dolichandra, Fridericia, and Tynanthus), Catalpeae (Catalpa) and the Tabebuia alliance (Handroanthus and Tabebuia). Dolichandra unguis-cati and Handroanthus chrysotrichus were polyploid (2n= 80). Tribes Jacarandeae (Jacaranda) and Tecomeae (Tecoma) were unusual (with 2n= 36), whereas Podranea ricasoliana(Tecomeae) had 2n=38. The basic numberx= 20 is proposed as the base number for the family. Chromosomes are small. The average length was 1.21 μm. Average haploid karyotype length was 28.13μm, ranging from 18.63 in Dolichandra cynanchoidesto 37.63 in D. unguis-cati. Type m chromosomes were the most common. One to five sm pairs were found in 16 species and one st pair inCuspidaria convolutaandPodranea ricasoliana. One to four microsatellites, in long or short arms, were detected in nine species. Karyotypes are symmetrical. Asymmetry indices ranges were: A1= 0.11?0.23, A2= 0.14?0.22. The karyotypes of P. ricasoliana and C. convoluta were the most asymmetrical. Most species were karyologically indistinguishable based on conventional staining, but some could be distinguished by a combination of traits. 1C nuclear DNA content for 12 species were within the range 0.64?2.02 pg. In Bignoniaceae there is a common karyotypical pattern of mostly small m chromosomes with few cryptic chromosomal rearrangements.Fil: Piazzano, Marianela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Instituto Multidisciplinario de Biología Vegetal (p); Argentina. Universidad Nacional de Córdoba; ArgentinaFil: Las Peñas, Maria Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Instituto Multidisciplinario de Biología Vegetal (p); Argentina. Universidad Nacional de Córdoba; ArgentinaFil: Chiarini, Franco Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Instituto Multidisciplinario de Biología Vegetal (p); Argentina. Universidad Nacional de Córdoba; ArgentinaFil: Bernardello, Gabriel Luis Mario. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Instituto Multidisciplinario de Biología Vegetal (p); Argentina. Universidad Nacional de Córdoba; Argentin