Partial automation of database processing of simulation outputs from L-systems models of plant morphogenesis

Models of plant architecture allow us to explore how genotype environment interactions effect the development of plant phenotypes. Such models generate masses of data organised in complex hierarchies. This paper presents a generic system for creating and automatically populating a relational database from data generated by the widely used L-system approach to modelling plant morphogenesis. Techniques from compiler technology are applied to generate attributes (new fields) in the database, to simplify query development for the recursively-structured branching relationship. Use of biological terminology in an interactive query builder contributes towards making the system biologist-friendly.     

Signaling and Adhesion Activities of Mammalian β-Catenin and Plakoglobin in Drosophila

The armadillo protein of Drosophila and its vertebrate homologues, β-catenin and plakoglobin, are implicated in cell adhesion and wnt signaling. Here, we examine the conservation of these two functions by assaying the activities of mammalian β-catenin and plakoglobin in Drosophila. We show that, in the female germ line, both mammalian β-catenin and plakoglobin complement an armadillo mutation. We also show that shotgun mutant germ cells (which lack Drosophila E-cadherin) have a phenotype identical to that of armadillo mutant germ cells. It therefore appears that armadillo's role in the germ line is solely in a complex with Drosophila E-cadherin (possibly an adhesion complex), and both β-catenin and plakoglobin can function in Drosophila cadherin complexes. In embryonic signaling assays, we find that plakoglobin has no detectable activity whereas β-catenin's activity is weak. Surprisingly, when overexpressed, either in embryos or in wing imaginal disks, both β-catenin and plakoglobin have dominant negative activity on signaling, an effect also obtained with COOH-terminally truncated armadillo. We suggest that the signaling complex, which has been shown by others to comprise armadillo and a member of the lymphocyte enhancer binding factor-1/T cell factor–family, may contain an additional factor that normally binds to the COOH-terminal region of armadillo.     

Extending the Namibian protected area network to safeguard hotspots of endemism and diversity

Namibia's state protected area network (PAN) covers 13.8% of the country's land area, but is seriously inadequate as a basis for effective biodiversity conservation. The early parks system was not designed with biological diversity in mind, and reflects instead a history of ideological, economic and veterinary considerations. Currently, parks in the Namib Desert biome make up 69% of the PAN, while savanna and woodland biomes are somewhat underrepresented (7.5 and 8.4% of their respective land areas), and the Karoo biome is badly underrepresented (1.6%). Four of 14 desert vegetation types are comprehensively protected, with 67 to 94% representation in the PAN, yet six savanna types have 0 to 2% representation by area. Mountain Savanna, a vegetation type unique to Namibia, is wholly unprotected. The status of two marine reserves, which in theory protect only 0.01% of Namibia's marine environment, needs clarification and augmentation with new reserves. Nearly 85% of Namibia's land is zoned for agriculture, so effective biodiversity protection means working outside the PAN to improve the sustainability and diversity of farming practices. Wildlife conservancies on commercial and communal farmlands show excellent potential to mitigate the ecological skew in the state PAN, with the ecological management of large areas being decentralized to rural communities in habitats otherwise neglected for conservation. Two important endemism zones, the Kaoko escarpment and coastal plain and the Sperrgebiet succulent steppe, plus the species-rich Caprivi area, offer three valuable opportunities for regional consolidation of protected areas into transboundary 'peace parks' or biosphere reserves.     

Implication of C-Terminal Deletion on the Structure and Stability of Bovine β-casein

Bovine β-casein (β-CN) with its C-terminal truncated by chymosin digestion, β-CN-(f1-192), was examined and characterized using circular dichroism (CD) under various temperature conditions. CONTIN/LL analysis of the CD data revealed significant secondary structure disruption in β-CN-(f1-192) relative to its parent protein,β-CN, in the temperature range (5° to 70°C) studied. Near-UV CD spectra indicated significant temperature dependent structural changes. Analytical ultracentrifugation results showed significant reduction but not complete abolishment of self-association in β-CN-(f1-192) compared to whole β-casein at 2°–37°C. Furthermore, binding experiments with the common hydrophobic probe – 8-anilino-1- naphthalene sulfonic acid (ANS) illustrated that β-CN-(f1-192) is nearly incapable of binding to ANS relative to whole β-CN, suggesting a nearly complete open overall tertiary structure brought about by the C-terminal truncation. It has been demonstrated clearly that the tail peptide β-CN-(f193-209) is important in maintaining the hydrophobic core of β-CN but the residual association observed argues for a minor role for other sites as well.     

IHF and HU: flexible architects of bent DNA

The energetic cost of bending short segments of DNA is very high. This bending is critical for the packaging of DNA and is exploited to regulate many cellular processes. In prokaryotes, IHF and HU are key architectural proteins present at high concentrations. New protein-DNA co-crystal structures, and the adaptation of advanced biophysical and biochemical techniques have led to an improved understanding of how these proteins interact with DNA. These techniques include time-resolved synchrotron X-ray footprinting, differential scanning calorimetry, isothermal titration calorimetry and single-molecule experiments.     

Reporting Thyroid Function Tests in Pregnancy

While there is agreement that overt maternal hypothyroidism (serum thyroid stimulating hormone (TSH) >10 mIU/L) should be treated immediately, the evidence is mixed regarding the harm associated with subclinical hypothyroidism and the benefits of thyroxine replacement. The diagnosis of subclinical hypothyroidism rests on the recognition of an increased serum concentration of TSH which may be affected by many factors including gestational age, analytical method, the antibody status of the mother, ethnicity, iodine nutrition and even the time of day when the blood is collected. The 97.5^th percentile of TSH at the end of the first trimester is commonly used as the upper boundary of normal in early pregnancy with a default value of 2.5 mIU/L specified in a number of recent clinical guidelines. There have now been numerous papers showing that a more realistic figure is between 3.0 and 4.0 mIU/L depending on the analytical method that is used. There are suggestions that ethnicity may also have a significant effect on TSH and FT4 reference limits in pregnancy.