Search for: All records

DNA methylation occurs predominantly on cytosine-phosphate-guanine (CpG) dinucleotides in the mammalian genome, and the methylation landscape is maintained over mitotic cell division. It has been posited that coupling of maintenance methylation activity among neighbouring CpGs is critical to stability over cellular generations; however, the mechanism is unclear. We used mathematical models and stochastic simulation to analyse data from experiments that probe genome-wide methylation of nascent DNA post-replication in cells. We find that DNA methylation maintenance rates on individual CpGs are locally correlated, and the degree of this correlation varies by genomic regional context. By using theory of protein diffusion along DNA, we show that exponential decay of methylation rate correlation with genomic distance is consistent with enzyme processivity. Our results provide quantitative evidence of genome-wide methyltransferase processivity in vivo . We further developed a method to disentangle different mechanistic sources of kinetic correlations. From the experimental data, we estimate that an individual methyltransferase methylates neighbour CpGs processively if they are 36 basepairs apart, on average. But other mechanisms of coupling dominate for longer inter-CpG distances. Our study demonstrates that quantitative insights into enzymatic mechanisms can be obtained from replication-associated, cell-based genome-wide measurements, by combining data-driven statistical analyses with hypothesis-driven mathematical modelling. 

Narrative and collaboration are two core features of rich interactive learning. Narrative-centered learning environments offer significant potential for supporting student learning. By contextualizing learning within interactive narratives, these environments leverage students’ innate facilities for developing understandings through stories. Computer-supported collaborative learning environments offer students rich, collaborative learning experiences in which small groups of students engage in constructing artifacts, addressing disciplinary challenges, and solving problems. Narrative and collaboration have distinct affordances for learning, but combining them poses significant challenges. In this paper, we present initial work on solving this problem by introducing collaborative narrative-centered learning environments. These environments will enable small groups of students to collaboratively solve problems in rich multi-participant storyworlds. We propose a novel framework for designing and developing these environments, which we are using to create a collaborative narrative-centered learning environment for middle school ecosystems education. In the learning environment, students work on problem-solving scenarios centered on how to support optimal fish health in aquatic environments. Results from pilot testing the learning environment with 45 students suggest it supports the creation of engaging and effective collaborative narrative-centered learning experiences. 

Seedling emergence, survival, morphological and physiological traits, and oxidative stress resistance of southwestern white pine (Pinus strobiformisEngelm.) were studied in response to warming treatments applied during embryogenesis, germination, and early seedling growth. Daytime air temperature surrounding cones in tree canopies was warmed by +2.1°C during embryo development. Resulting seeds and seedlings were assigned to three thermal regimes in growth chambers, with each regime separated by 4°C to encompass the wide range of temperatures observed over space and time across the species’ range, plus the effect of heat waves coupled with a high carbon emissions scenario of climate warming. The embryo warming treatment reduced percent seedling emergence in all germination and growth environments and reduced mortality of seedlings grown in the warmest environment. Warm thermal regimes during early seedling growth increased subsequent seedling resistance to oxidative stress and transpirational water use. Experimental warming during seed development, germination, and seedling growth affected seedling emergence and survival. Oxidative stress resistance, morphology, and water relations were affected only by warming imposed during germination and seedling growth. This work explores potential outcomes of climate warming on multiple dimensions of seedling performance and uniquely illustrates that plant responses to heat vary with plant developmental stage in addition to the magnitude of temperature change.

 

This article addresses the sustainable design of organic Rankine cycle‐based geothermal binary power systems under economic and environmental criteria. A novel superstructure with multiple heat source temperatures, working fluids, and heat rejection systems is proposed. Based on the superstructure, a life cycle optimization model is formulated as a mixed‐integer nonlinear fractional program (MINFP) to determine the optimal design. The nonconvex MINFP is efficiently solved by a tailored global optimization algorithm. Two case studies are considered to demonstrate the proposed modeling framework and solution algorithm. One case is based on a geothermal energy system located in California, and the other one is in New York (NY) State. The results show that the geothermal energy system in California is much more economically competitive than that in NY State. The difference in life cycle environmental impacts is less pronounced because the environmental impacts are less sensitive to geological conditions than the capital investments.

 

The Savannah River Basin (SRB), a highly stressed southeastern river in United States is a conservation priority for State, Federal government, and nongovernment organizations. A four‐stage sustainable development tool was developed in this study using meta‐analysis and the drivers–pressures–state–impacts–responses (DPSIR) framework. Through the synthesis of ~150 references in the SRB this study addressed three research questions: (1) What were the drivers, pressures, state, impacts, and responses (components of DRSIR framework) in SRB (2) Can these components be grouped together from various studies in SRB (3) Can causal chain/loops be developed, and will they be useful for policy and decision making? First in the Stage 1, the state of the SRB was represented (S component of DPSIR), in Stage 2, the drivers–pressures–impacts–responses (DPIR components of DPSIR) were represented, in the third stage (Stage 3) the common units characterizing each DPSIR component were identified. Finally, in Stage 4, the causal chains/loops were developed and organized into scientific research at a level appropriate for building better understanding about SRB and helping stakeholders and policy makers in managing basin sustainability challenges. Although the tool was applied to SRB, the methodology is applicable to other river basins and ecosystems.