Jeesoo Lee

Gas/liquid sensing via chemotaxis of Euglena cells confined in an isolated micro-aquarium

We demonstrate on-chip gas/liquid sensing by using the chemotaxis of live bacteria (Euglena gracilis) confined in an isolated micro-aquarium, and gas/liquid permeation through porous polydimethylsiloxane (PDMS). The sensing chip consisted of one closed micro-aquarium and two separated bypass microchannels along the perimeter of the micro-aquarium. Test gas/liquid and reference samples were introduced into the two individual microchannels separately, and the gas/liquid permeated through the PDMS walls and dissolved in the micro-aquarium water, resulting in a chemical concentration gradient in the micro-aquarium. By employing the closed micro-aquarium isolated from sample flows, we succeeded in measuring the chemotaxis of Euglena for a gas substance quantitatively, which cannot be achieved with the conventional flow-type or hydro-gel-type microfluidic devices. We found positive (negative) chemotaxis for CO2 concentrations below (above) 15%, with 64 ppm as the minimum concentration affecting the cells. We also observed chemotaxis for ethanol and H2O2. By supplying culture medium via the microchannels, the Euglena culture remained alive for more than 2 months. The sensing chip is thus useful for culturing cells and using them for environmental toxicity/nutrition studies by monitoring their motion.

Two-dimensional optical feedback control of Euglena confined in closed-type microfluidic channels

We examined two-dimensional (2D) optical feedback control of phototaxis flagellate Euglena cells confined in closed-type microfluidic channels (microaquariums), and demonstrated that the 2D optical feedback enables the control of the density and position of Euglena cells in microaquariums externally, flexibly, and dynamically. Using three types of feedback algorithms, the density of Euglena cells in a specified area can be controlled arbitrarily and dynamically, and more than 70% of the cells can be concentrated into a specified area. Separation of photo-sensitive/insensitive Euglena cells was also demonstrated. Moreover, Euglena-based neuro-computing has been achieved, where 16 imaginary neurons were defined as Euglena-activity levels in 16 individual areas in microaquariums. The study proves that 2D optical feedback control of photoreactive flagellate microbes is promising for microbial biology studies as well as applications such as microbe-based particle transportation in microfluidic channels or separation of photo-sensitive/insensitive microbes.

Euglena-based neurocomputing with two-dimensional optical feedback on swimming cells in micro-aquariums

We report on neurocomputing performed with real Euglena cells confined in micro-aquariums, on which two-dimensional optical feedback is applied using the Hopfield-Tank algorithm. Trace momentum, an index of swimming activity of Euglena cells, is used as the input/output signal for neurons in the neurocomputation. Feedback as blue-light illumination results in temporal changes in trace momentum according to the photophobic reactions of Euglena. Combinatorial optimization for a four-city traveling salesman problem is achieved with a high occupation ratio of the best solutions. Two characteristics of Euglena-based neurocomputing desirable for combinatorial optimization are elucidated: (1) attaining one of the best solutions to the problem, and (2) searching for a number of solutions via dynamic transition between the best solutions. Mechanisms responsible for the two characteristics are analyzed in terms of network energy, photoreaction ratio, and dynamics/statistics of Euglena movements. The spontaneous fluctuation in input/output signals and reduction in photoreaction ratio were found to be key factors in producing characteristic (1), while the photo-insensitive Euglena cells or the accidental evacuation of cells from non-illuminated areas causes characteristic (2). Furthermore, we show that the photophobic reactions of Euglena involves various survival strategies such as adaptation to blue-light or awakening from dormancy, which can extend the performance of Euglena-based neurocomputing toward deadlock avoidance or program-less adaptation. Finally, two approaches for achieving a high-speed Euglena-inspired Si-based computation are described.

Analog feedback in Euglena-based neural network computing – Enhancing solution-search capability through reaction threshold diversity among cells

Abstract Microbe-based neural network computing, where the reaction of microbial cells to external stimuli is incorporated in the function of virtual neurons, has high potential for developing soft computing based on the survival strategies of the microbe. To utilize reaction-threshold diversity among the cells, we examined analog feedback in Euglena -based neurocomputing by solving a simple combinatorial optimization problem. The analog feedback was performed by blue light illumination to Euglena cells, where the intensity of the blue light was controlled using the Hopfield-Tank algorithm with a sigmoid function. The solution patterns obtained with analog feedback had greater variations than those with digital feedback, implying that the solution-search capability of Euglena -based neurocomputing is enhanced by analog feedback. Moreover, the solutions obtained with analog feedback comprised one stable core-motive selection and additional flexible selections, which are associated with hesitation shown by humans when faced with a frustrated task. The study shows that using analog feedback in Euglena -based neurocomputing is promising in terms of incorporating the diversity of photoreactions of Euglena cells to enhance the solution-search capability for combinatorial optimization problems and to utilize the adaptive reaction of Euglena cells.

Autonomous pattern formation of micro-organic cell density with optical interlink between two isolated culture dishes

Artificial linking of two isolated culture dishes is a fascinating means of investigating interactions among multiple groups of microbes or fungi. We examined artificial interaction between two isolated dishes containing Euglena cells, which are photophobic to strong blue light. The spatial distribution of swimming Euglena cells in two micro-aquariums in the dishes was evaluated as a set of new measures: the trace momentums (TMs). The blue light patterns next irradiated onto each dish were deduced from the set of TMs using digital or analogue feedback algorithms. In the digital feedback experiment, one of two different pattern-formation rules was imposed on each feedback system. The resultant cell distribution patterns satisfied the two rules with an and operation, showing that cooperative interaction was realized in the interlink feedback. In the analogue experiment, two dishes A and B were interlinked by a feedback algorithm that illuminated dish A (B) with blue light of intensity proportional to the cell distribution in dish B (A). In this case, a distribution pattern and its reverse were autonomously formed in the two dishes. The autonomous formation of a pair of reversal patterns reflects a type of habitat separation realized by competitive interaction through the interlink feedback. According to this study, interlink feedback between two or more separate culture dishes enables artificial interactions between isolated microbial groups, and autonomous cellular distribution patterns will be achieved by correlating various microbial species, despite environmental and spatial scale incompatibilities. The optical interlink feedback is also useful for enhancing the performance of Euglena-based soft biocomputing.

Optical analog feedback in euglena -based neural network computing

Using living microbial cells in computational processing is a fascinating challenge to incorporate their autonomous adaptation and exploration abilities into a physical computing algorithm [1]. When the stimulus to the cells is given as analog values, more flexible solutions would be expected in microbe-based neurocomputing [1] owing to the diversity of reaction threshold among the cells. We have investigated the optical analog feedback in Euglena-based neurocomputing, for a task to select some from 16 compartments with avoiding the first and second nearest compartments [2].

Development of Polydiacetylene-Embedded Microfibers Using 3-D Hydrodynamic Focusing Technique

Polydiacetylene (PDA), conjugated polymer, is an attractive sensor material that has a unique optical property to transform its color from visible blue to fluorescent red upon environmental perturbations like heat, pH, specific metal ions, and etc. In this study, we propose a novel method to detect metal ions by using polydiacetylene (PDA)-embedded sensor microfibers fabricated with a 3-D hydrodynamic focusing technique using alginate and calcium solutions. Moreover, by changing the head groups of PDA, we successfully detected Al3+ and Zn2+ ions up to 1mM using PDA micro fibers.Copyright