Building the Games Students Want to Play: BiblioBouts Project Interim Report #3

The University of Michigan's School of Information and its partner, the Center for History and New Media at George Mason University, are undertaking the 3-year BiblioBouts Project (October 1, 2008 to September 30, 2011) to support the design, development, testing, and evaluation of the web-based BiblioBouts game to teach incoming undergraduate students information literacy skills and concepts. This third interim report describes the BiblioBouts Project team’s 6-month progress achieving the project's 4 objectives: designing, developing, deploying, and evaluating the BiblioBouts game and recommending best practices for future information literacy games. This latest 6-month period was marked by extensive progress in the deployment and evaluation of the alpha version of BiblioBouts. Major tasks that will occupy the team for the next 6 months are applying evaluation findings to game redesign and enhancement. For general information about game design, pedagogical goals, scoring, game play, project participants, and playing BiblioBouts in your course, consult the BiblioBouts Project web site.Institute of Museum and Library Serviceshttp://deepblue.lib.umich.edu/bitstream/2027.42/69157/1/bbInterimReportToIMLS03.pd

Nucleotide excision repair-initiating proteins bind to oxidative DNA lesions in vivo

Base excision repair (BER) is the main repair pathway to eliminate abundant oxidative DNA lesions such as 8-oxo-7,8-dihydroguanine. Recent data suggest that the key transcription-coupled nucleotide excision repair factor (TC-NER) Cockayne syndrome group B (CSB) and the global genome NER-initiating factor XPC are implicated in the protection of cells against oxidative DNA damages. Our novel live-cell imaging approach revealed a strong and very rapid recruitment of XPC an CSB to sites of oxidative DNA lesions in living cells. The absence of detectable accumulation of downstrea NER factors at the site of local oxidative DNA damage provide the first in vivo indication of the involvement of CSB and XPC in the repair of oxidative DNA lesions independent of the remainder of the NER reaction. Interestingly, CSB exhibited different and transcription-dependent kinetics in the two compartments studied (nucleolus and nucleoplasm), suggesting a direct transcription-dependent involvement of CSB in the repair of oxidative lesions associated with different RNA polymerases but not involving other NER proteins

The effect of size and composition on structural transitions in monometallic nanoparticles

Predicting the morphological stability of nanoparticles is an essential step towards the accurate modelling of their chemophysical properties. Here we investigate solid–solid transitions in monometallic clusters of 0.5–2.0 nm diameter at finite temperatures and we report the complex dependence of the rearrangement mechanism on the nanoparticle’s composition and size. The concerted Lipscomb’s Diamond-Square-Diamond mechanisms which connects the decahedral or the cuboctahedral to the icosahedral basins, take place only below a material dependent critical size above which surface diffusion prevails and leads to low-symmetry and defected shapes still belonging to the initial basin

Natural selection of more designable folds: A mechanism for thermophilic adaptation

An open question of great interest in biophysics is whether variations in structure cause protein folds to differ in the number of amino acid sequences that can fold to them stably, i.e., in their designability. Recently, we have shown that a novel quantitative measure of a fold's tertiary topology, called its contact trace, strongly correlates with the fold's designability. Here, we investigate the relationship between a fold's contact trace and its relative frequency of usage in mesophilic vs. thermophilic eubacteria. We observe that thermophilic organisms exhibit a bias toward using folds of higher contact trace when compared with mesophiles. We establish this difference both for the distributions of folds at the whole-proteome level and also through more focused structural comparisons of orthologous proteins. Our findings suggest that thermophilic adaptation in bacterial genomes occurs in part through natural selection of more designable folds, pointing to designability as a key component of protein fitness