The 2.1 angstrom crystal structure of copGFP, a representative member of the copepod clade within the green fluorescent protein superfamily

The green fluorescent protein (avGFP), its variants, and the closely related GFP-like proteins are characterized structurally by a cyclic tri-peptide chromophore located centrally within a conserved beta-can fold. Traditionally, these GFP family members have been isolated from the Cnidaria although recently, distantly related GFP-like proteins from the Bilateria, a sister group of the Cnidaria have been described, although no representative structure from this phylum has been reported to date. We have determined to 2.1 angstrom resolution the crystal structure of copGFP, a representative GFP-like protein from a copepod, a member of the Bilateria. The structure of copGFP revealed that, despite sharing only 19% sequence identity with GFP, the tri-peptide chromophore (Gly57-Tyr58-Gly59) of copGFP adopted a cis coplanar conformation within the conserved beta-can fold. However, the immediate environment surrounding the chromophore of copGFP was markedly atypical when compared to other members of the GFP-superfamily, with a large network of bulky residues observed to surround the chromophore. Arg87 and Glu222 (GFP numbering 96 and 222), the only two residues conserved between copGFP, GFP and GFP-like proteins are involved in autocatalytic genesis of the chromophore. Accordingly, the copGFP structure provides an alternative platform for the development of a new suite of fluorescent protein tools. Moreover, the structure suggests that the autocatalytic genesis of the chromophore is remarkably tolerant to a high degree of sequence and structural variation within the beta-can fold of the GFP superfamily. (c) 2006 Elsevier Ltd . All rights reserved.

Leximancer concept mapping of patient case studies

Quantitative databases are limited to information identified as important by their creators, while databases containing natural language are limited by our ability to analyze large unstructured bodies of text. Leximancer is a tool that uses semantic mapping to develop concept maps from natural language. We have applied Leximancer to educational based pathology case notes to demonstrate how real patient records or databases of case studies could be analyzed to identify unique relationships. We then discuss how such analysis could be used to conduct quantitative analysis from databases such as the Coronary Heart Disease Database.

Usability of a mobile, group communication prototype while rendezvousing

Mobile phones are increasingly being used collaboratively by social networks of users in spite of the fact that they are primarily designed to support single users and one-to-one communication. It is not well understood how services such as group SMS, SMS-based discussion lists and mobile instant messaging (IM) will be used by mobile groups in natural settings. Studying specific instances of common styles of in situ, group interaction may provide a way to see behavior patterns and typical interaction problems. We conducted a study of a mobile, group communication probe used during a rendezvousing activity in an urban environment. Usability problems relating to group usage, phone interface design and context were identified. Several major issues included: multitasking during message composition and reading; speed of text entry; excessive demand on visual attention; and ambiguity of intended recipients. We suggest that existing mobile device designs are overly-focused on individual users to the detriment of usability for mobile groups of users. We provide recommendations for the design of future mobile, group interfaces, used in similar situations to those explored here

From possessive pronoun to emphatic determiner: 'so' in Mauritian Creole

This paper argues that at a particular stage in the genesis of Mauritian Creole (MC), the 3sg possessive pronoun 'so', inherited from the French 'son' was used as a definite determiner as well as a possessive pronoun. It was used when there was a need to single out a unique element in the discourse, or to introduce a new referent which was to become the focus of attention. 'So' was mostly used with genitive constructions, where a phonologically null determiner was equally grammatical. This paper argues that, in the early creole, genitive constructions licensed the determinative use of this pronoun. The use of 'so' with genitive constructions is no longer grammatical in modern MC, but this particle continues to be used as an emphatic determiner, where it now modifies both singular and plural NPs.

Chromosomal gains and losses in ocular melanoma detected by comparative genomic hybridization in an Australian population-based study

To define the location of potential oncogenes and tumor suppressor genes in ocular melanoma we carried out comparative genomic hybridization (CGH) analysis on a population-based series of 25 formalin-fixed, paraffin-embedded primary tumors comprising 17 choroidal, 2 ciliary body, 4 iris, and 2 conjunctival melanomas. Twelve (48%) of the 25 melanomas showed no chromosomal changes and 13 (52%) had at least one chromosomal gain or loss. The mean number of CGH changes in all tumors was 3.3, with similar mean numbers of chromosomal gains (1.5) and losses (1.8). The highest number of chromosomal changes (i.e., nine) occurred in a conjunctival melanoma and included four changes not observed in tumors at any other ocular site (gains in 22q and 11p and losses in 6p and 17p). The most frequent gains in all primary ocular melanomas were on chromosome arm 8q (69%), 6p (31%) and 8p (23%) and the most frequent losses were on 6q (38%), 10q (23%), and 16q (23%). The most common pairing was gain in 8p and gain in 8q, implying a whole chromosome copy number increase; gains in 8p occurred only in conjunction with gains in 8q. The smallest regions of copy number alteration were mapped to gain of 8q21 and loss of 6q21, 10q21, and 16q22. Sublocalization of these chromosomal changes to single-band resolution should accelerate the identification of genes involved in the genesis of ocular melanoma.