A model-driven discovery process, Computing Life, is used to identify an ensemble of genetic networks that describe the biological clock. A clock mechanism involving the genes white-collar-1 and white-collar-2 (wc-1 and wc-2) that encode a transcriptional activator (as well as a blue-light receptor) and an oscillator frequency (frq) that encodes a cyclin that deactivates the activator is used to guide this discovery process through three cycles of microarray experiments. Central to this discovery process is a new methodology for the rational design of a Maximally Informative Next Experiment (MINE), based on the genetic network ensemble. In each experimentation cycle, the MINE approach is used to select the most informative new experiment in order to mine for clock-controlled genes, the outputs of the clock. As much as 25% of the N. crassa transcriptome appears to be under clock-control. Clock outputs include genes with products in DNA metabolism, ribosome biogenesis in RNA metabolism, cell cycle, protein metabolism, transport, carbon metabolism, isoprenoid (including carotenoid) biosynthesis, development, and varied signaling processes. Genes under the transcription factor complex WCC ( = WC-1/WC-2) control were resolved into four classes, circadian only (612 genes), light-responsive only (396), both circadian and light-responsive (328), and neither circadian nor light-responsive (987). In each of three cycles of microarray experiments data support that wc-1 and wc-2 are auto-regulated by WCC. Among 11,000 N. crassa genes a total of 295 genes, including a large fraction of phosphatases/kinases, appear to be under the immediate control of the FRQ oscillator as validated by 4 independent microarray experiments. Ribosomal RNA processing and assembly rather than its transcription appears to be under clock control, suggesting a new mechanism for the post-transcriptional control of clock-controlled genes.

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Abstract:This paper reports a theory-driven experimental study for designing and evaluating two different forms of attention-guidance functionalities integrated into an anchored-discussion system. Using social constructivism as a motivating theory, we constructed a theoretical framework that emphasizes the importance of students' attention allocation in online learning conversations and its influence on message quality and interaction patterns. The development of the functionalities, named faded instructor-led and peer-oriented attention guidance, aimed to direct students' attention toward instructional materials' central domain principles while offering them an open learning environment in which they could choose their own topics and express their own ideas. We evaluated the functionalities with heat map analysis, repeated measures general linear model analysis, and sequence analysis to assess the utility of the developed functionalities. Results show that attention guidance helped students more properly allocate their attention in online learning conversations. Furthermore, we found that the improved attention allocation led to better quality of students' online learning conversations. We discuss implications for researchers and practitioners who wish to promote more fruitful online discussions.

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