The Long-Rage Directional Behavior of the Nematode C. Elegans

Like any mobile organism, C. elegans relies on sensory cues to find food. In the absence of such cues, animals might display defined search patterns or other stereotyped behavior. The motion of C. elegans has previously been characterized as a sinusoid whose direction can be modulated by gradual steering or by sharp turns, reversals and omega bends. However, such a fine-grained behavioral description does not by itself predict the longrange features of the animals’ pattern of movement. Using large (24 cm x 24 cm) Petri dishes, we characterized the movement pattern of C. elegans in the absence of stimuli. To collect trajectories over such a large surface, we devised an imaging setup employing an array of consumer flatbed scanners. We have confirmed quantitatively the results obtained with the scanner-array setup with a camera imaging setup, in a more stringently homogeneous environment. Wild-type worms display striking behavior in the absence of food. The majority (~60%) of the animals’ paths displays persistence in the direction of motion over length scales that are 50-100 times the body-length of C. elegans. The overall direction of movement differs from animal to animal, suggesting that the directed motion we observe might not be interpreted as a taxis to an external cue in the experimental environment. Interestingly, animals appear to exhibit directionality at large scales despite nondirectional motion at smaller scales. We quantified the extent of local directional persistence by computing the autocorrelation function of the velocities. Unexpectedly, correlations in the direction of motion decay over time scales that are much faster than the scales over which directional persistence appears to be maintained. We sought to establish quantitatively that the worm motion is, in fact, biased. To determine whether a null, random walk-like model of locomotion could account for directional behavior, we generated synthetic trajectories drawing from the same angle and step distributions of individual trajectories, and quantified the probabilities of obtaining larger net displacements than the experimental. Such a model fails to reproduce the experimental results. Moreover, the mean square displacements computed for the data display non-diffusive behavior, further demonstrating that the observed directional persistence cannot be explained by a simple random-walk model. To corroborate the hypothesis of biased movement in a model-independent fashion, we employed a geometrical characterization of the trajectories. Isotropic, unbiased walks result in paths that display a random distribution of turning angles between consecutive segments. In contrast, parsing of the worm’s trajectories yields different results depending on the segmentation scale adopted. In fact, increasing the segment size results in increasingly narrow turning angle distributions, centered around the zero. This suggests the emergence of directional coherence at long time scales. In order to investigate whether directional persistence is attained by a sensory mechanism, we analyzed the paths displayed by animals with impaired sensory function. Animals mutant for che-2, which display disrupted ciliary morphology and pleiotropic behavioral defects, exhibited non-directional behavior. Surprisingly however, daf-19 mutants, which lack sensory cilia altogether, displayed residual directionality, albeit at a lower penetrance (~20%) than the wild-type. This result suggests that directionality might implicate sensory modalities that do not require ciliary function, such as AFD-mediated thermosensation or URX-mediated oxygen sensation. Alternatively, the behavior of daf-19 mutants might imply that neural activity, but not sensory inputs, are required to achieve directed motion. Mutations in osm-9, a TRPV channel implicated in several avoidance behaviors in the worm, did not result in an observable phenotype. In contrast, mutations in tax-2/tax-4, a cGMP-gated channel required to transduce a number of sensory stimuli, resulted in loss of directionality. However, specific mutations targeting the signal transduction pathways for thermotaxis, olfaction, phototaxis, and aerotaxis, upstream of TAX-4, did not disrupt directional behavior. To get further insight into the nature of the stimulus directing the animals’ behavior, if any, we performed rescue experiments of TAX-4 function in specific subsets of neurons. In agreement with the results obtained by genetic lesions in the signal transduction pathways for thermotaxis and odortaxis, no rescue of directional behavior was observed when expressing TAX-4 in the thermosensory neuron AFD, or in the olfactory neurons AWB and AWC. Partial rescue of wild-type behavior was obtained by expression of TAX-4 in a set of five cells, which comprised the oxygen-sensing AQR, PQR and URX neurons as well as the ASJ and ASK sensory neurons, which transduce chemical stimuli and responses to dauer pheromone. To address the concern that the animals’ motion might be directed to a chemosensory cue within the plate, we investigated the correlation between path directions displayed by animals that were assayed on a same plate. We did not observe a detectable correlation between path headings, indicating that the worm is not chemotaxing to a plate-specific cue. In conclusion, our results indicate that the motion of C. elegans cannot be assimilated to a random walk, and that directional persistence arises at long times despite local nondirectional behavior. In addition, although we have not conclusively ruled out a sensorybased explanation, the genetic and phenomenological evidence gathered foreshadows the intriguing possibility that C. elegans might be achieving directional motion by relying solely on self-based information

Washington University Senior Undergraduate Research Digest (WUURD), Spring 2018

From the Washington University Office of Undergraduate Research Digest (WUURD), Vol. 13, 05-01-2018. Published by the Office of Undergraduate Research. Joy Zalis Kiefer, Director of Undergraduate Research and Associate Dean in the College of Arts & Scien

Species Richness and Ecological Diversity of Myxomycetes and Myxomycete-Like Organisms in the Tropical Forests of Brazil

Tropical rain forests cover less than two percent of Earth\u27s surface, yet they sustain the greatest diversity of living organisms on the planet. Tropical rain forests cover nearly 73% of the Brazilian territory and besides harboring some of the most biodiverse ecosystems on the planet, this vast area also houses about 83% of the Brazilian population. Approximately 175 million people live in urban and rural areas with fragments of coverage of these biomes which contributes to the loss of biodiversity that rapidly increases over the years. Furthermore, the majority of the taxonomic and ecological efforts to describe and protect the Brazilian tropical biodiversity are usually focused on macroorganisms while the knowledge regarding the heterogeneity of microorganism species that compose the Brazilian microbiota increases slowly. Therefore, urgent efforts should be directed to the carrying out of inventories and studies on the species that make up the Brazilian microbiota, their biogeographical patterns, and their interactions with the environment in which they occupy. Aiming to contribute to the knowledge of the distribution and diversity of microorganism in the Neotropics, this dissertation includes (1) an overview of the biogeographical patterns of microorganisms; (2) a bibliographic revision of the myxomycetes species found in Brazil distributed among the different vegetation physiognomies throughout the country; (3) species listing and molecular identification of myxobacteria species; (4) the taxonomic and ecological studies of species of ceratiomyxomycetes and myxomycetes; (5) the taxonomic composition of dictyostelid cellular slime molds; and (6) species of protosteloid amoebae and related organisms present in tropical and subtropical moist broadleaf forests of Brazil

The role of cooperation in bacterial ecology and evolution

Bacteria can perform a range of cooperative behaviours, yet the significance of these cooperative behaviours in bacterial ecology and evolution is a burgeoning research area. In this thesis, I use a comparative genomics approach to elucidate the impact of cooperation on bacterial ecological and evolutionary processes. Specifically, I: (i) probe the effects of cooperation on the evolution of bacterial niche breadth; (ii) investigate the relationship between horizontal gene transfer and bacterial cooperation, with a specific emphasis on the interplay between gene connectivity and sociality in determining gene transfer potential. Additionally, I expand the scope by examining how ecological determinants and genomic characteristics shape the evolution of bacterial growth rates. In summary, this thesis offers novel perspectives on bacterial ecology and evolution through the lens of bacterial cooperation

An Approach Based on Particle Swarm Optimization for Inspection of Spacecraft Hulls by a Swarm of Miniaturized Robots

The remoteness and hazards that are inherent to the operating environments of space infrastructures promote their need for automated robotic inspection. In particular, micrometeoroid and orbital debris impact and structural fatigue are common sources of damage to spacecraft hulls. Vibration sensing has been used to detect structural damage in spacecraft hulls as well as in structural health monitoring practices in industry by deploying static sensors. In this paper, we propose using a swarm of miniaturized vibration-sensing mobile robots realizing a network of mobile sensors. We present a distributed inspection algorithm based on the bio-inspired particle swarm optimization and evolutionary algorithm niching techniques to deliver the task of enumeration and localization of an a priori unknown number of vibration sources on a simplified 2.5D spacecraft surface. Our algorithm is deployed on a swarm of simulated cm-scale wheeled robots. These are guided in their inspection task by sensing vibrations arising from failure points on the surface which are detected by on-board accelerometers. We study three performance metrics: (1) proximity of the localized sources to the ground truth locations, (2) time to localize each source, and (3) time to finish the inspection task given a 75% inspection coverage threshold. We find that our swarm is able to successfully localize the present so

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Simulator adaptation at runtime for component-based simulation software

Component-based simulation software can provide many opportunities to compose and configure simulators, resulting in an algorithm selection problem for the user of this software. This thesis aims to automate the selection and adaptation of simulators at runtime in an application-independent manner. Further, it explores the potential of tailored and approximate simulators - in this thesis concretely developed for the modeling language ML-Rules - supporting the effectiveness of the adaptation scheme.Komponenten-basierte Simulationssoftware kann viele Möglichkeiten zur Komposition und Konfiguration von Simulatoren bieten und damit zu einem Konfigurationsproblem für Nutzer dieser Software führen. Das Ziel dieser Arbeit ist die Entwicklung einer generischen und automatisierten Auswahl- und Adaptionsmethode für Simulatoren. Darüber hinaus wird das Potential von spezifischen und approximativen Simulatoren anhand der Modellierungssprache ML-Rules untersucht, welche die Effektivität des entwickelten Adaptionsmechanismus erhöhen können

2016 Oklahoma Research Day Full Program

This document contains all abstracts from the 2016 Oklahoma Research Day held at Northeastern State University

Use of microbiome data to explain the expression of productive traits in domestic species

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Veterinaria, leída el 11-03-2022El descubrimiento de comunidades microbianas asociadas simbióticamente a organismos eucariotas ha llevado a un cambio de paradigma en la definición de individuo biológico, que ahora se ve como una combinación codependiente del hospedador y su microbioma, u holobionte. Por tanto, el estudio de los microbiomas se ha convertido en algo fundamental para comprender la biología de los organismos vivos complejos. De hecho, se ha observado que las comunidades microbianas poseen un papel crucial en la salud, supervivencia, desarrollo y metabolismo del hospedador. Los recientes avances en secuenciación genética han supuesto un importante impulso para la investigación en microbiología, al permitir la obtención de bases de datos de secuenciación masiva que abarcan una gran parte de la diversidad presente dentro de los microbiomas. La era del next-generation sequencing ha aportado nuevos conocimientos sobre el efecto de las comunidades microbianas sobre el fenotipo del hospedador, con especial relevancia del microbioma intestinal. Para la industria ganadera este hecho ha dado lugar a importantes avances en la comprensión de los mecanismos biológicos que influyen en productividad, sostenibilidad y bienestar animal, lo que podría ser útil para afrontar los desafíos existentes en este sector...The discovery of microbial communities symbiotically associated with eukaryotic organisms has led to a paradigm shift in the definition of the biological individual, which is now seen as a co-dependent combination of the host and its microbiome, or holobiont. Thus, the study of microbiomes has become essential to understand the biology of complex living organisms. Indeed, current research points to a crucial role of microbial communities in host health, survivability, development and metabolism. Recent advances in DNA sequencing have entailed a significant boost to microbial research, allowing the generation of massive sequencing databases encompassing a large proportion of the diversity inside microbiomes. The era of next-generation sequencing has brought new knowledge about the role of microbial communities, with special significance for gut microbiomes, in host phenotype. For livestock industry, this has led to important advances in the understanding of biological mechanisms influencing animal welfare, productivity and sustainability, which could be useful to face existing challenges in animal production...Fac. de VeterinariaTRUEunpu