1,584 research outputs found

    Dimensionality and dynamics in the behavior of C. elegans

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    A major challenge in analyzing animal behavior is to discover some underlying simplicity in complex motor actions. Here we show that the space of shapes adopted by the nematode C. elegans is surprisingly low dimensional, with just four dimensions accounting for 95% of the shape variance, and we partially reconstruct "equations of motion" for the dynamics in this space. These dynamics have multiple attractors, and we find that the worm visits these in a rapid and almost completely deterministic response to weak thermal stimuli. Stimulus-dependent correlations among the different modes suggest that one can generate more reliable behaviors by synchronizing stimuli to the state of the worm in shape space. We confirm this prediction, effectively "steering" the worm in real time.Comment: 9 pages, 6 figures, minor correction

    Robot-Assisted Full Automation Interface: Touch-Response On Zebrafish Larvae

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    Expressivity in Natural and Artificial Systems

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    Roboticists are trying to replicate animal behavior in artificial systems. Yet, quantitative bounds on capacity of a moving platform (natural or artificial) to express information in the environment are not known. This paper presents a measure for the capacity of motion complexity -- the expressivity -- of articulated platforms (both natural and artificial) and shows that this measure is stagnant and unexpectedly limited in extant robotic systems. This analysis indicates trends in increasing capacity in both internal and external complexity for natural systems while artificial, robotic systems have increased significantly in the capacity of computational (internal) states but remained more or less constant in mechanical (external) state capacity. This work presents a way to analyze trends in animal behavior and shows that robots are not capable of the same multi-faceted behavior in rich, dynamic environments as natural systems.Comment: Rejected from Nature, after review and appeal, July 4, 2018 (submitted May 11, 2018

    Reducing Results Variance in Lifespan Machines: An Analysis of the Influence of Vibrotaxis on Wild-Type Caenorhabditis elegans for the Death Criterion

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    [EN] Nowadays, various artificial vision-based machines automate the lifespan assays of C. elegans. These automated machines present wider variability in results than manual assays because in the latter worms can be poked one by one to determine whether they are alive or not. Lifespan machines normally use a "dead or alive criterion" based on nematode position or pose changes, without poking worms. However, worms barely move on their last days of life, even though they are still alive. Therefore, a long monitoring period is necessary to observe motility in order to guarantee worms are actually dead, or a stimulus to prompt worm movement is required to reduce the lifespan variability measure. Here, a new automated vibrotaxis-based method for lifespan machines is proposed as a solution to prompt a motion response in all worms cultured on standard Petri plates in order to better distinguish between live and dead individuals. This simple automated method allows the stimulation of all animals through the whole plate at the same time and intensity, increasing the experiment throughput. The experimental results exhibited improved live-worm detection using this method, and most live nematodes (>93%) reacted to the vibration stimulus. This method increased machine sensitivity by decreasing results variance by approximately one half (from +/- 1 individual error per plate to +/- 0.6) and error in lifespan curve was reduced as well (from 2.6% to 1.2%).This study was also supported by the Universitat Politecnica de Valencia with Project 20170020-UPV, Plan Nacional de I+D with Project RTI2018-094312-B-I00 and by European FEDER funds. ADM Nutrition, Biopolis SL and Archer Daniels Midland provided support in the supply of C. elegans.Puchalt-Rodríguez, JC.; Layana-Castro, PE.; Sánchez Salmerón, AJ. (2020). Reducing Results Variance in Lifespan Machines: An Analysis of the Influence of Vibrotaxis on Wild-Type Caenorhabditis elegans for the Death Criterion. Sensors. 20(21):1-17. https://doi.org/10.3390/s20215981S117202

    Micro-electro-opto-fluidic systems for biomedical drug screening and electromagnetic filtering and cloaking applications

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    Microfluidic is a multidisciplinary field that deals with the flow of liquid inside micro-meter size channels. In order to be considered as microfluidics, at least one dimension of the channel should be in the range of one micrometer or sub-millimeter. Microfluidic technology includes designing, manufacturing, formulating devices and processing the liquid. As numerous bio-science and engineering techniques have utilized microfluidics and highly integrated with this remarkable technology, the microfluidic platform technology has extended to several sub-techs: micro-scale analysis, soft-lithography fabrication, polymer science and processing, on-chip sensing and micro-scale fluid manipulation. Those sub-techs have been developed rapidly along with the booming microfluidics. The advance of those techniques has promoted microfluidic system diverse and widespread applications. Some examples that employ this technology include on-chip drug screening, micro-scale analysis, flexible electronics, biochemical assays. Many engineering field, such as optics, electronics, chemicals and electromagnetics, have been integrated with the microfluidic system to form a completed system for sensing, analyzing or realizing some specific applications. Through the fusion of those technologies with microfluidics, many emerging technologies are well initiated, such as optofluidics and electrofluidics. Despite of rapid advancement of each parent technology field, those intersected technologies are still in their infancy and many technological elements and even some fundamental concepts are just now being developed. Thus, it provides great opportunity to explore more about those emerging technologies. Some particular areas that mainly interest researchers including cost deduction, effective fabrication, highly integration, portability and applicability. Due to the wide and diversity nature of the microfluidic technology and numerous combinations from the integration with other fields, it is very difficult to choose a single aspect or particular subject to research. Hence, we would like to focus on the application orientated microfluidic techniques that integrated with other engineering areas, in particular optics and electronics. Correspondingly, I will present four microfluidic platforms that integrated with optics, electronics for different application purpose. First of all, fiber-optics was integrated into a microfluidic device to detect muscular force generation of microscopic nematodes. The integrated opto-fluidic device is capable of measuring the muscular force of nematode worms normal to the translational movement direction with high sensitivity, high data reliability, and simple device structure. The ability to quantify the muscular forces of small nematode worms will provide a new approach for screening mutants at single animal resolution. Secondly, electronic grids were integrated into a microfluidic chip to realize on-chip tracking of nematode locomotion. The micro-electro-fluidic approach is capable of real-time lens-less and image-sensor-less monitoring of the locomotion of microscopic nematodes. The technology showed promise for overcoming the constraint of the limited field of view of conventional optical microscopy, with relatively low cost, good spatial resolution, and high portability. Thirdly, electromagnetic spit ring resonator (SRR) structure was adopted as microfluidic channel filled with liquid metal to fabricate a tunable microfluidic microwave electronics called meta-atom. The presented meta-atom is capable of tuning its electromagnetic (EM) response characteristics over a broad frequency range via simple mechanical stretching. The meta-atom in this study presents a simple but effective building block for realizing mechanically tunable metamaterials. Finally, based on the meta-atom we previously developed, an array of electromagnetic SRR shaped microfluidic channels filled with liquid metal to form a flexible metamaterial-based microwave electronic “skin” or meta-skin. When stretched, the meta-skin performs as a tunable frequency selective surface with a wide resonance frequency tuning range. When wrapped around a curved dielectric material, the meta-skin functions as a flexible “cloaking” surface to significantly suppress scattering from the surface of the dielectric material along different directions. The microfluidic platform will find great applications when it integrates with other technologies. The development of such integration will greatly intersect different research areas and benefit all of the intersected technologies and fields, thus broadening the future applications

    Development and Evaluation of New Methods for Automating Experiments with C. Elegans Based on Active Vision

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    Tesis por compendio[ES] Esta tesis se centra en el desarrollo de nuevas técnicas automatizadas que permiten inspeccionar nematodos Caenorhabidits elegans (C. elegans) en placas de Petri estándar, para el análisis de sus comportamientos. C. elegans es un nemátodo de 1mm de longitud, con el cual se pueden realizar distintos experimentos para analizar los efectos de fármacos, compuestos o alteraciones genéticas en su longevidad, su salud física o su cognición. El campo principal metodológico del presente trabajo para el análisis de esos efectos es la visión por computador; y con ello, el desarrollo completo del sistema de visión activo: sistema de iluminación inteligente, sistema de captura óptimo, procesamiento de las imágenes para detección y clasificación de nematodos. Los campos secundarios en esta investigación son el control y robotización. Los C. elegans son animales sensibles a la luz y por ello el primero de los métodos está en la rama de la iluminación inteligente, con el cual se permite regular la intensidad y las longitudes de onda de la luz que reciben los nematodos. El siguiente método es el procesado para la detección y clasificación de movimiento a partir de las imágenes obtenidas con esa iluminación controlada. Tener el ambiente controlado es fundamental, los nematodos son muy sensibles a las condiciones ambientales por lo que puede alterarse su actividad biológica, y con ello los resultados, así que el tercer método es la integración de las técnicas en un nuevo dispositivo que permite automatizar ensayos de lifespan y validar los resultados automáticos comparándolos con los manuales. El movimiento del animal es clave para poder realizar inferencias estadísticas que puedan mostrar tendencias en sus comportamientos, por ello la estimulación automatizada que provoque una reacción de su movilidad es el cuarto de los métodos. Por último, el aumento de la resolución en las imágenes muestra mayor detalle, mejorando el procesamiento y extracción de características. El quinto método es un robot multivista que posibilita tomar imágenes a distintas resoluciones, lo que permite mantener el seguimiento global de los gusanos, al mismo tiempo que se toman imágenes con un encuadre de mayor detalle del nematodo objetivo.[CA] Esta tesi doctoral se centra en el desentrollament de noves tècniques automatitzades que permeten inspeccionar nemàtodes Caenorhabidits elegans (C. elegans) en plaques de Petri estàndar, per a l'anàlisi dels seus comportaments. C. elegans és un nemàtode d'1mm de llargària, ab el qual se poden realitzar distints experiments per a analitzar els efectes de fàrmacs, composts o alteracions genètiques en sa longevitat, la seua salut física o la seua cognició. El camp principal metodològic del present treball per a l'anàlisi d'eixos efectes és la visió per computador; i ab açò, el desentrollament complet del sistema de visió actiu: sistema d'il.luminació inteligent, sistema de captura òptim, processament de les imàtgens per a detecció i classificació de nematode. Els camps secundaris en esta investigació són el control i robotització. Els C. elegans són animals sensibles a la llum i por ello el primer dels mètodes està en la branca de la il.luminació intel.ligent, ab el qual es permet regular la intensitat i les longituds d'ona de la llum que reben els nematodes. El següent mètode és el processat per a la detecció i classificació de moviment a partir de les imàtgens obtinguda ab eixa il.luminació controlada. Tindre l'ambient controlat és fonamental, els nemàtodes són molt sensibles a les condicions ambientals per lo que pot alterar-se la seua activitat biològica, i ab aço els resultats, aixina que el tercer mètode és la integració de les tècniques en un nou dispositiu que permet automatitzar ensajos de lifespan i validar els resultats automàtics comparant-los ab els manuals. El moviment de l'animal és clau per a poder realitzar inferencies estadístiques que puguen mostrar tendències en el seus comportaments, per això la estimulació automatitzada que provoque una reacció de la seua mobilitat és el quart dels mètodes. Per últim, l'augment de la resolució en les imàtgens mostra major detall, millorant el processament i extracció de característiques. El quint mètode és un robot multivista que possibilita prendre imàtgens a distintes resolucions, lo que permet mantindre el seguiment global dels cucs, al mateix temps que se prenguen imàtgens ab un enquadrament de major detall del nematode objectiu.[EN] This thesis focuses on the development of new automated techniques that allow the inspection of Caenorhabidits elegans nematodes (C. elegans) in Petri dishes, for the analysis of their behavior. This nematode is a 1mm long worm, with which different experiments can be carried out to analyze the effects of drugs, compounds or genetic alterations on its longevity, physical health or cognition. The main methodological field of the present work for the analysis of these effects is computer vision; and with it, the complete development of the active vision system: intelligent lighting system, optimal capture system, image processing for detection and classification of nematodes. The secondary fields in this research are control and robotization. C. elegans are light-sensitive animals and therefore the first method is in the field of intelligent lighting, with which it is possible to regulate the intensity and wavelength of the light that nematodes receive. The next method is the processing for the detection and classification of movement from the images obtained with that controlled lighting. Having a controlled environment is essential, worms are very sensitive to environmental conditions so it can alter biological activity, and with it the results, so the third method is the integration of techniques in a new device that allows automating tests of lifespan and validate the automatic results comparing them with the manual ones. The movement of the animal is key to be able to carry out statistical conferences that can show trends in its behaviors, therefore the automated stimulation that causes a reaction of its mobility is the fourth of the methods. Finally, increasing the resolution in the images shows greater detail, improving the processing and extraction of features. The fifth method is a multiview robot that enables images to be taken at different resolutions, allowing global tracking of worms to be maintained, while at the same time taking images with a more detailed frame of the target worm.Puchalt Rodríguez, JC. (2022). Development and Evaluation of New Methods for Automating Experiments with C. Elegans Based on Active Vision [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/181359Compendi

    Running Worms: C. elegans Self-Sorting by Electrotaxis

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    The nematode C. elegans displays complex dynamical behaviors that are commonly used to identify relevant phenotypes. Although its maintenance is straightforward, sorting large populations of worms when looking for a behavioral phenotype is difficult, time consuming and hardly quantitative when done manually. Interestingly, when submitted to a moderate electric field, worms move steadily along straight trajectories. Here, we report an inexpensive method to measure worms crawling velocities and sort them within a few minutes by taking advantage of their electrotactic skills. This method allows to quantitatively measure the effect of mutations and aging on worm's crawling velocity. We also show that worms with different locomotory phenotypes can be spatially sorted, fast worms traveling away from slow ones. Group of nematodes with comparable locomotory fitness could then be isolated for further analysis. C. elegans is a growing model for neurodegenerative diseases and using electrotaxis for self-sorting can improve the high-throughput search of therapeutic bio-molecules

    Time-Resolved Quantification of Centrosomes by Automated Image Analysis Suggests Limiting Component to Set Centrosome Size in C. Elegans Embryos

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    The centrosome is a dynamic organelle found in all animal cells that serves as a microtubule organizing center during cell division. Most of the centrosome components have been identified by genetic screens over the last decade, but little is known about how these components interact with each other to form a functional centrosome. Towards a better understanding of the molecular organization of the centrosome, we investigated the mechanism that regulates the size of the centrosome in the early C. elegans embryo. For this, we monitored fluorescently labeled centrosomes in living embryos and developed a suite of image analysis algorithms to quantify the centrosomes in the resulting 3D time-lapse images. In particular, we developed a novel algorithm involving a two-stage linking process for tracking entrosomes, which is a multi-object tracking task. This fully automated analysis pipeline enabled us to acquire time-resolved data of centrosome growth in a large number of embryos and could detect subtle phenotypes that were missed by previous assays based on manual image analysis. In a first set of experiments, we quantified centrosome size over development in wild-type embryos and made three essential observations. First, centrosome volume scales proportionately with cell volume. Second, beginning at the 4-cell stage, when cells are small, centrosome size plateaus during the cell cycle. Third, the total centrosome volume the embryo gives rise to in any one cell stage is approximately constant. Based on our observations, we propose a ‘limiting component’ model in which centrosome size is limited by the amounts of maternally derived centrosome components. In a second set of experiments, we tested our hypothesis by varying cell size, centrosome number and microtubule-mediated pulling forces. We then manipulated the amounts of several centrosomal proteins and found that the conserved centriolar and pericentriolar material protein SPD-2 is one such component that determines centrosome size

    Microswimmers and Microfluidics: Understanding and Manipulating the Locomotion of Undulatory Microswimmers

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    Undulatory microswimmers, such as nematodes, are of great importance to agriculture, animal and human health, and fundamental biological research. The nematode Caenorhabditis (C.) elegans is widely used as a model organism for medical studies. My work focuses on studying the locomotion of nematodes; their interactions with surfaces, fluid flow, and each other; and developing new tools to manipulate their motion for diverse applications. In the first half (chapters 2-4) of this dissertation, I investigate experimentally and theoretically the effects of flat solid surfaces, external channel flow, and other swimmers on the swimming dynamics of undulatory microswimmers. I discovered that 1) when swimming in close proximity, undulatory microswimmers synchronize their swimming gait. This synchronization is facilitated by direct collisions among the swimmers, rather than by long-range hydrodynamic interactions or deliberate actions of the swimmers; 2) undulatory micro-swimmers have a tendency to accumulate near and swim along surfaces. This behavior does not require touch sensation ability of the swimmers, and can be explained by a short-range hydrodynamic interaction between the swimmers and adjacent surface; 3) undulatory microswimmers exhibit positive rheotaxis (upstream swimming behavior) near solid surfaces. This behavior is induced by the combination of a hydrodynamic surface attraction effect and the velocity gradient of external flow near solid surfaces. These findings help explain certain intriguing behaviors of undulatory microswimmers, highlight the diverse roles of hydrodynamic forces in microswimmers\u27 life cycles, and lay the foundations for novel microswimmer manipulation methods for fundamental biological research and clinical applications. In the second half (chapters 5-7) of this dissertation, I present the design, fabrication, characterization, and applications of a few engineering devices/methods for dynamic trapping, motility measurement, motility-based sorting, and directing the motion of microswimmers. These new devices/methods enabled many studies that would be impossible or impractical with conventional methods

    A practical review on the measurement tools for cellular adhesion force

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    Cell cell and cell matrix adhesions are fundamental in all multicellular organisms. They play a key role in cellular growth, differentiation, pattern formation and migration. Cell-cell adhesion is substantial in the immune response, pathogen host interactions, and tumor development. The success of tissue engineering and stem cell implantations strongly depends on the fine control of live cell adhesion on the surface of natural or biomimetic scaffolds. Therefore, the quantitative and precise measurement of the adhesion strength of living cells is critical, not only in basic research but in modern technologies, too. Several techniques have been developed or are under development to quantify cell adhesion. All of them have their pros and cons, which has to be carefully considered before the experiments and interpretation of the recorded data. Current review provides a guide to choose the appropriate technique to answer a specific biological question or to complete a biomedical test by measuring cell adhesion
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