Changes in students’ mental models from computational modeling of gene regulatory networks

Background: Computational modeling is an increasingly common practice for disciplinary experts and therefore necessitates integration into science curricula. Computational models afford an opportunity for students to investigate the dynamics of biological systems, but there is significant gap in our knowledge of how these activities impact student knowledge of the structures, relationships, and dynamics of the system. We investigated how a computational modeling activity affected introductory biology students’ mental models of a prokaryotic gene regulatory system (lac operon) by analyzing conceptual models created before and after the activity. Results: Students’ pre-lesson conceptual models consisted of provided, system-general structures (e.g., activator, repressor) connected with predominantly incorrect relationships, representing an incomplete mental model of gene regulation. Students’ post-lesson conceptual models included more context-specific structures (e.g., cAMP, lac repressor) and increased in total number of structures and relationships. Student conceptual models also included higher quality relationships among structures, indicating they learned about these context-specific structures through integration with their expanding mental model rather than in isolation. Conclusions: Student mental models meshed structures in a manner indicative of knowledge accretion while they were productively re-constructing their understanding of gene regulation. Conceptual models can inform instructors about how students are relating system structures and whether students are developing more sophisticated models of system-general and system-specific dynamics

Simvastatin suppresses experimental aortic aneurysm expansion

ObjectiveAbdominal aortic aneurysm (AAA) formation is a result of inflammation and extracellular matrix (ECM) remodeling mediated by matrix metalloproteinases (MMPs). Hydroxymethylglutaryl-coenzyme A inhibitors (statins), although clinically used as lipid-lowering agents, have also been demonstrated to have anti-inflammatory effects. This study was designed to determine whether the hydroxymethylglutaryl-coenzyme A inhibitor simvastatin suppresses aneurysm formation in an elastase-induced rat AAA model.MethodsAneurysms were created in adult male Wistar rats by infusion of elastase into isolated infrarenal aortic segments. The rats were randomized to receive either simvastatin (n = 17) or placebo (n = 17) by gastric lavage daily starting the day before surgery. The rats were euthanized and the infrarenal aortas harvested on postoperative day 7. Aortic diameters were measured before infusion, immediately after infusion, and at the time of harvesting. Protein expression was measured by immunoblot analysis. Gene expression profiling using Affymetrix U34A rat genome chips was performed to identify changes in gene expression caused by simvastatin treatment.ResultsMean aneurysm diameter was significantly less in the simvastatin treatment group compared with controls (3.4 ± 0.08 mm vs 4.3 ± 0.19 mm; P = .0001). MMP-9 and nuclear factor-κB protein levels were decreased in the aortas of simvastatin-treated animals. Gene microarray analysis revealed 315 genes with statistically significant changes in expression (P < .05) in the simvastatin group. Genes related to inflammation, ECM remodeling, and oxidative stress function were downregulated. These included genes for interleukin 1, interleukin 4, inducible nitric oxide synthase, P-selectin, platelet-derived growth factor α, tumor necrosis factor, and several chemokines.ConclusionsSimvastatin significantly suppresses experimental aneurysm expansion and reduces protein levels of MMP-9 and nuclear factor-κB. Gene array analysis provides evidence that several mediators of inflammation, matrix remodeling, and oxidative stress are downregulated by simvastatin treatment. This suggests that simvastatin inhibits AAA formation by blocking the expression of certain proinflammatory genes. Simvastatin may be useful as an adjuvant therapy to suppress the growth of small aneurysms.Clinical RelevanceHuman aortic aneurysms are characterized histologically by an inflammatory infiltrate with severe proteolytic destruction. Statins, although used clinically as lipid-lowering agents, have been shown to have anti-inflammatory effects. Simvastatin reduced experimental aneurysm size in this study. It seems that this reduction is mediated by interfering with multiple pathways, including oxidative stress, inflammation, and ECM and matrix remodeling. Further study into the effect of statins in reducing the growth of AAAs in patients is warranted

Detecting sterile dark matter in space

Space-based instruments provide new and, in some cases, unique opportunities to search for dark matter. In particular, if dark matter comprises sterile neutrinos, the x ray detection of their decay line is the most promising strategy for discovery. Sterile neutrinos with masses in the keV range could solve several long-standing astrophysical puzzles, from supernova asymmetries and the pulsar kicks to star formation, reionization, and baryogenesis. The best current limits on sterile neutrinos come from Chandra and XMM-Newton. Future advances can be achieved with a high-resolution x-ray spectrometry in space.Comment: 11 pages, 1 figure, to appear in proceedings "From Quantum to Cosmos: fundametal physics research in space", Washington, DC, May 22-24, 200

Dynamics of a ferromagnetic domain wall and the Barkhausen effect

We derive an equation of motion for the the dynamics of a ferromagnetic domain wall driven by an external magnetic field through a disordered medium and we study the associated depinning transition. The long-range dipolar interactions set the upper critical dimension to be $d_c=3$, so we suggest that mean-field exponents describe the Barkhausen effect for three-dimensional soft ferromagnetic materials. We analyze the scaling of the Barkhausen jumps as a function of the field driving rate and the intensity of the demagnetizing field, and find results in quantitative agreement with experiments on crystalline and amorphous soft ferromagnetic alloys.Comment: 4 RevTex pages, 3 ps figures embedde

Modern Electronic Techniques Applied to Physics and Engineering

Contains reports on two research projects

Dynamics of a ferromagnetic domain wall: avalanches, depinning transition and the Barkhausen effect

We study the dynamics of a ferromagnetic domain wall driven by an external magnetic field through a disordered medium. The avalanche-like motion of the domain walls between pinned configurations produces a noise known as the Barkhausen effect. We discuss experimental results on soft ferromagnetic materials, with reference to the domain structure and the sample geometry, and report Barkhausen noise measurements on Fe$_{21}$Co$_{64}$B$_{15}$ amorphous alloy. We construct an equation of motion for a flexible domain wall, which displays a depinning transition as the field is increased. The long-range dipolar interactions are shown to set the upper critical dimension to $d_c=3$, which implies that mean-field exponents (with possible logarithmic correction) are expected to describe the Barkhausen effect. We introduce a mean-field infinite-range model and show that it is equivalent to a previously introduced single-degree-of-freedom model, known to reproduce several experimental results. We numerically simulate the equation in $d=3$, confirming the theoretical predictions. We compute the avalanche distributions as a function of the field driving rate and the intensity of the demagnetizing field. The scaling exponents change linearly with the driving rate, while the cutoff of the distribution is determined by the demagnetizing field, in remarkable agreement with experiments.Comment: 17 RevTeX pages, 19 embedded ps figures + 1 extra figure, submitted to Phys. Rev.

The ENCODE Project at UC Santa Cruz

The goal of the Encyclopedia Of DNA Elements (ENCODE) Project is to identify all functional elements in the human genome. The pilot phase is for comparison of existing methods and for the development of new methods to rigorously analyze a defined 1% of the human genome sequence. Experimental datasets are focused on the origin of replication, DNase I hypersensitivity, chromatin immunoprecipitation, promoter function, gene structure, pseudogenes, non-protein-coding RNAs, transcribed RNAs, multiple sequence alignment and evolutionarily constrained elements. The ENCODE project at UCSC website () is the primary portal for the sequence-based data produced as part of the ENCODE project. In the pilot phase of the project, over 30 labs provided experimental results for a total of 56 browser tracks supported by 385 database tables. The site provides researchers with a number of tools that allow them to visualize and analyze the data as well as download data for local analyses. This paper describes the portal to the data, highlights the data that has been made available, and presents the tools that have been developed within the ENCODE project. Access to the data and types of interactive analysis that are possible are illustrated through supplemental examples

Visualizing the Anthropocene dialectically: Jessica Woodworth and Peter Brosens’ eco-crisis trilogy

The ambition of this article is to propose a way of visualizing the Anthropocene dialectically. As suggested by the Dutch atmospheric chemist Paul Crutzen and the professor of biology Eugene F. Stoermer, the term Anthropocene refers to a historical period in which humankind has turned into a geological force that transforms the natural environment in such a way that it is hard to distinguish between the human and the natural world. Crutzen and Stoermer explain that the Anthropocene has begun after the Holocene, the geological epoch that followed the last ice age and lasted until the industrial revolution. Drawing on a number of figures such as the “tenfold” increase in urbanisation, the extreme transformation of land surface by human action, the use of more than 50% of all accessible fresh water by humans, and the massive increase in greenhouse emissions, Crutzen and Stoermer conclude that the term Anthropocene describes aptly mankind's influence on ecological and geological cycles (Crutzen & Stoermer, 2000, p.17). The wager of this article is that we need to identify ways to visualize the Anthropocene dialectically and I proceed to do so using as a case study Jessica Woodworth's and Peter Brosen's trilogy on the conflict between humans and nature, which consists of Khadak (2006), Altiplano (2009), and The Fifth Season (La Cinquième Saison, 2012)

Microparticles from apoptotic platelets promote resident macrophage differentiation

Platelets shed microparticles not only upon activation, but also upon ageing by an apoptosis-like process (apoptosis-induced platelet microparticles, PMap). While the activation-induced microparticles have widely been studied, not much is known about the (patho)physiological consequences of PMap formation. Flow cytometry and scanning electron microscopy demonstrated that PMap display activated integrins and interact to form microparticle aggregates. PMap were chemotactic for monocytic cells, bound to these cells, an furthermore stimulated cell adhesion and spreading on a fibronectin surface. After prolonged incubation, PMap promoted cell differentiation, but inhibited proliferation. Monocyte membrane receptor analysis revealed increased expression levels of CD11b (integrin αMβ2), CD14 and CD31 (platelet endothelial cell adhesion molecule-1), and the chemokine receptors CCR5 and CXCR4, but not of CCR2. This indicated that PMap polarized the cells into resident M2 monocytes. Cells treated with PMap actively consumed oxidized low-density lipoprotein (oxLDL), and released matrix metalloproteinases and hydrogen peroxide. Further confirmation for the differentiation towards resident professional phagocytes came from the finding that PMap stimulated the expression of the (ox)LDL receptors, CD36 and CD68, and the production of proinflammatory and immunomodulating cytokines by monocytes. In conclusion, interaction of PMap with monocytic cells has an immunomodulating potential. The apoptotic microparticles polarize the cells into a resident M2 subset, and induce differentiation to resident professional phagocytes