Functional recycling of C2 domains throughout evolution: A comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches

The C2 domain is one of the most frequent and widely distributed calcium-binding motifs. Its structure comprises an eight-stranded beta-sandwich with two structural types as if the result of a circular permutation. Combining sequence, structural and modelling information, we have explored, at different levels of granularity, the functional characteristics of several families of C2 domains. At the coarsest level,the similarity correlates with key structural determinants of the C2 domain fold and, at the finest level, with the domain architecture of the proteins containing them, highlighting the functional diversity between the various subfamilies. The functional diversity appears as different conserved surface patches throughout this common fold. In some cases, these patches are related to substrate-binding sites whereas in others they correspond to interfaces of presumably permanent interaction between other domains within the same polypeptide chain. For those related to substrate-binding sites, the predictions overlap with biochemical data in addition to providing some novel observations. For those acting as protein-protein interfaces' our modelling analysis suggests that slight variations between families are a result of not only complementary adaptations in the interfaces involved but also different domain architecture. In the light of the sequence and structural genomic projects, the work presented here shows that modelling approaches along with careful sub-typing of protein families will be a powerful combination for a broader coverage in proteomics. (C) 2003 Elsevier Ltd. All rights reserved.

Importance of water for Archaean granitoid petrology: a comparative study of TTG and potassic granitoids from Barberton Mountain Land, South Africa

A new model for Archaean granitoid magmatism is presented which reconciles the most important geochemical similarities and differences between tonalite-trondhjemite-granodiorite (TTG) and potassic granitoids. Trace element abundances reveal a strong arc magmatism signature in all studied granitoids from Barberton Mountain Land. Characteristic features include HFSE depletion as well as distinct enrichment peaks of fluid-sensitive trace elements such as Pb in N-MORB normalisation, clearly indicating that all studied granitoids are derived from refertilised mantle above subduction zones. We envisage hydrous basaltic (s.l.) melts as parental liquids, which underwent extensive fractional crystallisation. Distinctive residual cumulates evolved depending on initial water content. High-H2O melts crystallised garnet/amphibole together with pyroxenes and minor plagioclase, but no olivine. This fractionation path ultimately led to TTG-like melts. Less hydrous basaltic melts also crystallised garnet/amphibole, but the lower compatible element content indicates that olivine was also a liquidus phase. Pronounced negative Eu-anomalies of the granitic melts, correlating with Na, Ca and Al, indicate plagioclase to be of major importance. In the context of our model, the post-Archaean disappearance of TTG and concomitant preponderance of granites (s.l.), therefore, is explained with secular decrease of aqueous fluid transport into subduction zones and/or efficiency of deep fluid release from slabs.

Physical activity cost in children following an acquired brain injury - a comparative study

Background: Alterations in energy expenditure during activity post head injury has not been investigated due primarily to the difficulty of measurement. Objective: The aim of this study was to compare energy expenditure during activity and body composition of children following acquired brain injury (ABI) with data from a group of normal. controls. Design: Energy expenditure was measured using the Cosmed K4b(2) in a group of 15 children with ABI and a group of 67 normal children during rest and when walking and running. Mean number of steps taken per 3 min run was also recorded and body composition was measured. Results: The energy expended during walking was not significantly different between both groups. A significant difference was found between the two groups in the energy expended during running and also for the number of steps taken as children with ABI took significantly less steps than the normal controls during a 3 min run. Conclusions: Children with ABI exert more energy per activity than healthy controls when controlled for velocity or distance. However, they expend less energy to walk and run when they are free to choose their own desirable, comfortable pace than normal controls. (C) 2003 Elsevier Ltd. All rights reserved.

Comparative study of hydrogen storage in Li- and K-doped carbon materials - theoretically revisited

Hydrogen adsorption in alkali-doped carbon materials is investigated theoretically. Our calculations show that hydrogen molecules can be physically adsorbed on alkali-doped graphite at 0 K but such an adsorption is thermodynamically unfavourable. The binding energy of hydrogen adsorption decreases significantly with the increase in temperature and becomes nearly zero at ambient temperature. We suggest that it may be unlikely to observe any hydrogen uptake in alkali-doped carbon materials at or above ambient temperature in the TGA (thermogravimetric) system, the previously reported hydrogen uptake in alkali-doped carbon materials was caused by either uncyclable chemisorbed hydrogen on the defects of carbon (defects were produced by repeated heat treatment) and/or moisture adsorption. (C) 2004 Elsevier Ltd. All rights reserved.

Comparative study of Li, Na, and K adsorptions on graphite by using ab initio method

A comprehensive study has been conducted to compare the adsorptions of alkali metals (including Li, Na, and K) on the basal plane of graphite by using molecular orbital theory calculations. All three metal atoms prefer to be adsorbed on the middle hollow site above a hexagonal aromatic ring. A novel phenomenon was observed, that is, Na, instead of Li or K, is the weakest among the three types of metal atoms in adsorption. The reason is that the SOMO (single occupied molecular orbital) of the Na atom is exactly at the middle point between the HOMO and the LUMO of the graphite layer in energy level. As a result, the SOMO of Na cannot form a stable interaction with either the HOMO or the LUMO of the graphite. On the other hand, the SOMO of Li and K can form a relatively stable interaction with either the HOMO or the LUMO of graphite. Why Li has a relatively stronger adsorption than K on graphite has also been interpreted on the basis of their molecular-orbital energy levels.

An in vivo comparative study of sonic, desert and Indian hedgehog reveals that hedgehog pathway activity regulates epidermal stem cell homeostasis

Despite the well-characterised role of sonic hedgehog (Shh) in promoting interfollicular basal cell proliferation and hair follicle downgrowth, the role of hedgehog signalling during epidermal stem cell fate remains largely uncharacterised. In order to determine whether the three vertebrate hedgehog molecules play a role in regulating epidermal renewal we overexpressed sonic (Shh), desert (Dhh) and Indian (Ihh) hedgehog in the basal cells of mouse skin under the control of the human keratin 14 promoter. We observed no overt epidermal morphogenesis phenotype in response to Ihh overexpression, however Dhh overexpression resulted in a range of embryonic and adult skin manifestations indistinguishable from Shh overexpression. Two distinct novel phenotypes were observed amongst Shh and Dhh transgenics, one exhibiting epidermal progenitor cell hyperplasia with the other displaying a complete loss of epidermal tissue renewal indicating deregulation of stem cell activity. These data suggest that correct temporal regulation of hedgehog activity is a key factor in ensuring epidermal stem cell maintenance. In addition, we observed Shh and Dhh transgenic skin from both phenotypes developed lesions reminiscent of human basal cell carcinoma (BCC), indicating that BCCs can be generated despite the loss of much of the proliferative (basal) compartment. These data suggest the intriguing possibility that BCC can arise outside the stem cell population. Thus the elucidation of Shh (and Dhh) target gene activation in the skin will likely identify those genes responsible for increasing the proliferative potential of epidermal basal cells and the mechanisms involved in regulating epidermal stem cell fate.

Managing ontologies: A comparative study of ontology servers

An ontology is increasingly becoming an essential tool for solving problems in many research areas. The ontology is a complex information object. It can contain millions of concepts in complex relationships. When we want to manage complex information objects, we generally turn to information systems technology. An information system intended to manage ontology is called an ontology server. The ontology server technology is at the time of writing quite immature. Therefore, this paper reviews and compares the main ontology servers that have been reported in the literatures. As a result, we point out several research questions related to server technology