Browsing by Author "Keymer, Juan MI."

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    Diversity emerging: from competitive exclusion to neutral coexistence in ecosystems
    (2012) Keymer, Juan MI.; Marquet, P. A. (Pablo A.)
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    Expansion, Exploitation and Extinction : Niche Construction in Ephemeral Landscapes
    (2020) Wetherington, Miles T.; Keymer, Juan MI.
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    Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering
    (2017) Núñez Quijada, Isaac Natán; Matute Torres, Tamara Francisca; Herrera, Roberto; Keymer, Juan MI.; Marzullo, Timothy; Rudge, Timothy; Federici, Fernán
    The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential use in a high school environment to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for education, scientific research and bioengineering. All the resources developed here are available under open source licenses.
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    Pattern Formation in a Patch Occupancy Metapopulation Model: a Cellular Automata Approach
    (1998) Keymer, Juan MI.; Marquet, P. A. (Pablo A.)
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    The idiosyncrasy of spatial structure in bacterial competition
    (2015) Hol, F.; Keymer, Juan MI.