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1. Activity Monitoring for Analysis of Sleep in Drosophila melanogaster

   https://doi.org/10.1101/pdb.top108095  

   Sitaraman, Divya; Vecsey, Christopher G; Koochagian, Casey (February 2024, Cold Spring Harbor Protocols)

   Sleep is important for survival, and the need for sleep is conserved across species. In the past two decades, the fruit flyDrosophila melanogasterhas emerged as a promising system in which to study the genetic, neural, and physiological bases of sleep. Through significant advances in our understanding of the regulation of sleep in flies, the field is poised to address several open questions about sleep, such as how the need for sleep is encoded, how molecular regulators of sleep are situated within brain networks, and what the functions of sleep are. Here, we describe key findings, open questions, and commonly used methods that have been used to inform existing theories and develop new ways of thinking about the function, regulation, and adaptability of sleep behavior. 

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2. Quantitative Analysis of the Trade-Offs of Colony Formation for Trichodesmium

   https://doi.org/10.1128/spectrum.02025-22  

   Agarwal, Vitul; Inomura, Keisuke; Mouw, Colleen B. (December 2022, Microbiology Spectrum)

   Veach, Allison (Ed.)

   ABSTRACT There is considerable debate about the benefits and trade-offs for colony formation in a major marine nitrogen fixer, Trichodesmium . To quantitatively analyze the trade-offs, we developed a metabolic model based on carbon fluxes to compare the performance of Trichodesmium colonies and free trichomes under different scenarios. Despite reported reductions in carbon fixation and nitrogen fixation rates for colonies relative to free trichomes, we found that model colonies can outperform individual cells in several cases. The formation of colonies can be advantageous when respiration rates account for a high proportion of the carbon fixation rate. Negative external influence on vital rates, such as mortality due to predation or micronutrient limitations, can also create a net benefit for colony formation relative to individual cells. In contrast, free trichomes also outcompete colonies in many scenarios, such as when respiration rates are equal for both colonies and individual cells or when there is a net positive external influence on rate processes (i.e., optimal environmental conditions regarding light and temperature or high nutrient availability). For both colonies and free trichomes, an increase in carbon fixation relative to nitrogen fixation rates would increase their relative competitiveness. These findings suggest that the formation of colonies in Trichodesmium might be linked to specific environmental and ecological circumstances. Our results provide a road map for empirical studies and models to evaluate the conditions under which colony formation in marine phytoplankton can be sustained in the natural environment. IMPORTANCE Trichodesmium is a marine filamentous cyanobacterium that fixes nitrogen and is an important contributor to the global nitrogen cycle. In the natural environment, Trichodesmium can exist as individual cells (trichomes) or as colonies (puffs and tufts). In this paper, we try to answer a longstanding question in marine microbial ecology: how does colony formation benefit the survival of Trichodesmium ? To answer this question, we developed a carbon flux model that utilizes existing published rates to evaluate whether and when colony formation can be sustained. Enhanced respiration rates, influential external factors such as environmental conditions and ecological interactions, and variable carbon and nitrogen fixation rates can all create scenarios for colony formation to be a viable strategy. Our results show that colony formation is an ecologically beneficial strategy under specific conditions, enabling Trichodesmium to be a globally significant organism. 

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3. PhenoImage : An open‐source graphical user interface for plant image analysis

   https://doi.org/10.1002/ppj2.20015  

   Zhu, Feiyu; Saluja, Manny; Dharni, Jaspinder Singh; Paul, Puneet; Sattler, Scott E.; Staswick, Paul; Walia, Harkamal; Yu, Hongfeng (January 2021, The Plant Phenome Journal)
4. Ab Initio Thermochemistry of Highly Flexible Molecules for Thermal Decomposition Analysis

   https://doi.org/10.1021/acs.jctc.3c00265  

   Kwon, Hyunguk; Mpourmpakis, Giannis (June 2023, Journal of Chemical Theory and Computation)
5. learnPopGen : An R package for population genetic simulation and numerical analysis

   https://doi.org/10.1002/ece3.5412  

   Revell, Liam J. (July 2019, Ecology and Evolution)

   Abstract Here, I briefly present a new R package calledlearnPopGenthat has been designed primarily for the purposes of teaching evolutionary biology, population genetics, and evolutionary theory. Functions of the package can be used to conduct simulations and numerical analyses of a wide range of evolutionary phenomena that would typically be covered in advanced undergraduate through graduate‐level curricula in population genetics or evolution. For instance,learnPopGenfunctions can be used to visualize gene frequency changes through time under multiple deterministic and stochastic processes, to compute and animate the changes in phenotypic trait values or distributions under natural selection, to numerically analyze and graph the outcome of simple game theory models, and to plot coalescence within a population experiencing genetic drift, along with a number of other things. Functions have been designed to be maximally didactic and frequently employ compelling animated visualizations. Furthermore, it is straightforward to export plots and animations from R in the form of flat or animated graphics, or as videos. For maximum flexibility, students working with the package can run functions directly in R; however, instructors may choose to guide students less adept in the R environment to one of various web interfaces that I have built for a number of the functions of the package and that are already available online. 

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