Computational approaches for modelling intrinsic noise and delays in genetic regulatory networks

This chapter focuses on the interactions and roles between delays and intrinsic noise effects within cellular pathways and regulatory networks. We address these aspects by focusing on genetic regulatory networks that share a common network motif, namely the negative feedback loop, leading to oscillatory gene expression and protein levels. In this context, we discuss computational simulation algorithms for addressing the interplay of delays and noise within the signaling pathways based on biological data. We address implementational issues associated with efficiency and robustness. In a molecular biology setting we present two case studies of temporal models for the Hes1 gene (Monk, 2003; Hirata et al., 2002), known to act as a molecular clock, and the Her1/Her7 regulatory system controlling the periodic somite segmentation in vertebrate embryos (Giudicelli and Lewis, 2004; Horikawa et al., 2006).

Terra Preta : bioenergy, soil restoration, urban agriculture, art algorithm

The 2010 LAGI competition was held on three underutilized sites in the United Arab Emirates. By choosing Staten Island, New York in 2012 the competition organises have again brought into question new roles for public open space in the contemporary city. In the case of the UEA sites, the competition produced many entries which aimed to create a sculpture and by doing so, they attracted people to the selected empty spaces in an arid climate. In a way these proposals were the incubators and the new characters of these empty spaces. The competition was thus successful at advancing understandings of the expanded role of public open spaces in EAU and elsewhere. LAGI 2012 differs significantly to the UAE program because Fresh Kills Park has already been planned as a public open space for New Yorkers - with or without these clean energy sculptures. Furthermore, Fresh Kills Park is already an (gas) energy generating site in its own right. We believe Fresh Kills Park, as a site, presents a problem which somewhat transcends the aims of the competition brief. Advancing a sustainable urban design proposition for the site therefore requires a fundamental reconsideration of the established paradigms public open space. Hence our strategy is to not only create an energy generating, site specific art work, but to create synergy between the public and the site engagement while at the same time complement the idiosyncrasies of the pre-existing engineered landscape. Current PhD research about energy generation in public open spaces informs this work.

Detection of tissue plasminogen activator (t-PA) and plasminogen activator inhibitor 2(PAI-2) in gingival crevicular fluid from healthy, gingivitis and periodontitis patients

Background: The regulation of plasminogen activation is a key element in controlling proteolytic events in the extracellular matrix. Our previous studies had demonstrated that in inflamed gingival tissues, tissue-type plasminogen activator (t-PA) is significantly increased in the extracellular matrix of the connective tissue and that interleukin 1β (IL-1β) can up regulate the level of t-PA and plasminogen activator inhibitor-2 (PAI-2) synthesis by human gingival fibroblasts. Method: In the present study, the levels of t-PA and PAI-2 in gingival crevicular fluid (GCF) were measured from healthy, gingivitis and periodontitis sites and compared before and after periodontal treatment. Crevicular fluid from106 periodontal sites in 33 patients were collected. 24 sites from 11 periodontitis patients received periodontal treatment after the first sample collection and post-treatment samples were collected 14 days after treatment. All samples were analyzed by enzyme-linked immunosorbent assay (ELISA) for t-PA and PAI-2. Results: The results showed that significantly high levels of t-PA and PAI-2 in GCF were found in the gingivitis and periodontitis sites. Periodontal treatment led to significant decreases of PAI-2, but not t-PA, after 14 days. A significant positive linear correlation was found between t-PA and PAI-2 in GCF (r=0.80, p<0.01). In the healthy group, different sites from within the same subject showed little variation of t-PA and PAI-2 in GCF. However, the gingivitis and periodontitis sites showed large variation. These results suggest a good correlation between t-PA and PAI-2 with the severity of periodontal conditions. Conclusion: This study indicates that t-PA and PAI-2 may play a significant rôle in the periodontal tissue destruction and tissue remodeling and that t-PA and PAI-2 in GCF may be used as clinical markers to evaluate the periodontal diseases and assess treatment.

Lago Nicaraguense

Poem

Terra Preta (Agriculture+Art+Algorithm)

Terra Preta is a site-specific bio-energy project which aims to create a synergy between the public and the pre-existing engineered landscape of Freshkills Park on Staten Island, New York. The project challenges traditional paradigms of public space by proposing a dynamic and ever-changing landscape. The initiative allows the publuc to self-organise the landscape and to engage in 'algorithmic processes' of growth, harvest and space creation.