As the technology of robotics intelligence advances, and new application areas for mobile robots increase, the need for alternative fundamental locomotion mechanisms for robots that allow them to maneuver into complex unstructured terrain becomes critical. In this research we present a novel locomotion mechanism for mobile robots inspired by the motility mechanism of certain single celled organisms such as amoebae. Whole Skin Locomotion (WSL), as we call it, works by way of an elongated toroid which turns itself inside out in a single continuous motion, effectively generating the overall motion of the cytoplasmic streaming ectoplasmic tube in amoebae. This research presents the preliminary analytical study towards the design and development of the novel WSL mechanism. In this thesis we first investigate how amoebas move, then discuss how this motion can be replicated. By applying the biological theories of amoeboid motility mechanisms, different actuation models for WSL are developed including the Fluid Filled Toroid (FFT) and Concentric Solid Tube (CST) models. Then, a quasi-static force analysis is performed for the CST model and parametric studies for design, including power efficiency and force transition characteristics, are presented. / Master of Science

Dictyostelids (Amoebozoa) are a group of social amoebae consisting of approximately 150 species, which are found in terrestrial habitats worldwide. They are divided into eight major clades based on molecular phylogeny, and within these clades are many species complexes. Some species are seemingly cosmopolitan in distribution, while others are geographically restricted. In this thesis dictyostelids were recovered from high latitude habitats (soils in Sweden and Iceland) as well as from the soles of shoes. Morphological characters and DNA sequence analyses were used to identify isolates that were recovered and delimit new species, as well as to investigate the monophyly of Dictyostelium aureostipes. Nine species were reported from Northern Sweden and four from Iceland. Among the isolates recorded in Sweden were two new species, described as D. barbibulus and Polysphondylium fuscans. P. fuscans was among the four species recovered from footwear, contributing evidence for anthropogenic transport of dictyostelids. Ecological patterns were assessed using linear regression and generalized linear models. The ecological analyses of dictyostelids recovered from Iceland indicate that these organisms are most frequently found in soils of near-neutral pH, but also exhibit a species richness peak in moderately acidic soils. These analyses indicate that in Iceland dictyostelid species richness decreases with altitude, and in the northern hemisphere the species richness increases with decreasing latitude. A three-region analysis of the D. aureostipes species complex indicated that this species is in fact made up of at least five phylogenetically distinct clades, and in light of this the group is in need of taxonomic revision. These results indicate that the dictyostelid species richness is higher than previously known, especially in high-latitude regions, and that even seemingly well-defined species may harbour cryptic diversity. Presently, species ranges may be expanding via anthropogenic dispersal but despite this, the dictyostelids are found to exhibit biogeographic trends well known from macroorganisms, such as a latitudinal gradient of species richness.

The free-living amoeba and causative agent of Primary Amoebic Meningoencephalitis, Naegleria fowleri, has three life stages: the trophozoite, the flagellate, and the cyst. This study examined the ability of the cyst to attach to, excyst upon, and destroy cell cultures grown to confluent monolayers, and to cause Primary Amoebic Meningoencephalitis in a murine animal model. The co-culture of cysts with P388D.1, CHME3, Vero, human nasal epithelial, and rat primary mixed glial cells resulted in destruction of the monolayer of all cell types once the cysts attached and excysted. One day post exposure to cysts, the mixed glial cells exhibited a two-fold increase in lactate dehydrogenase (LDH) release compared to cells without cysts, and on day eight post exposure, showed a nearly four-fold increase in LDH. In this study, the cysts of N. fowleri were shown not to be infective in vivo in a murine model using B6C3F1 male mice. The mediation of the encystment process by the intracellular concentration of the secondary messenger cAMP, as described in other closely related genera and species of amoeba, was also investigated. Encystment of N. fowleri was shown to be mediated at least in part by the secondary messenger cAMP by treating cultures of the trophozoite with 100 uM dipyridamole, an inhibitor of cAMP-specific phosphodiesterases. Dipyridamole (100 μM) increased the rate of encystment by nearly two-fold compared to 0.1% DMSO by the end of a five day period of observation. This suggests that cAMP is an essential mediator of the encystment process within Naegleria fowleri.

The present thesis has three main topics: geometry of coamoebas, hypergeometric functions, and geometry of zeros. First, we study the coamoeba of a Laurent polynomial f in n complex variables. We define a simpler object, which we call the lopsided coamoeba, and associate to the lopsided coamoeba an order map. That is, we give a bijection between the set of connected components of the complement of the closed lopsided coamoeba and a finite set presented as the intersection of an affine lattice and a certain zonotope. Using the order map, we then study the topology of the coamoeba. In particular, we settle a conjecture of M. Passare concerning the number of connected components of the complement of the closed coamoeba in the case when the Newton polytope of f has at most n+2 vertices. In the second part we study hypergeometric functions in the sense of Gel'fand, Kapranov, and Zelevinsky. We define Euler-Mellin integrals, a family of Euler type hypergeometric integrals associated to a coamoeba. As opposed to previous studies of hypergeometric integrals, the explicit nature of Euler-Mellin integrals allows us to study in detail the dependence of A-hypergeometric functions on the homogeneity parameter of the A-hypergeometric system. Our main result is a complete description of this dependence in the case when A represents a toric projective curve. In the last chapter we turn to the theory of real univariate polynomials. The famous Descartes' rule of signs gives necessary conditions for a pair (p,n) of integers to represent the number of positive and negative roots of a real polynomial. We characterize which pairs fulfilling Descartes' conditions are realizable up to degree 7, and we provide restrictions valid in arbitrary degree.

The motivating question behind this body of research is Smale’s 17th problem: Can a zero of n complex polynomial equations in n unknowns be found approximately, on the average, in polynomial time with a uniform algorithm? While certain aspects and viewpoints of this problem have been solved, the analog over the real numbers largely remains open. This is an important question with applications in celestial mechanics, kinematics, polynomial optimization, and many others. Let A = {α_1, . . . , α_n+k } ⊂ Zn. The A-discriminant variety is, among other things, a tool that can be used to categorize polynomials based on the topology of their real solution set. This fact has made it useful in solving aspects and special cases of Smale’s 17th problem. In this thesis, we take a closer look at the structure of the A-discriminant with an eye toward furthering progress on analogs of Smale’s 17th problem. We examine a mostly ignored form called the Horn uniformization. This represents the discriminant in a compact form. We study properties of the Horn uniformization to find structural properties that can be used to better understand the A-discriminant variety. In particular, we use a little known theorem of Kapranov limiting the normals of the A-discriminant amoeba. We give new O(n^2) bounds on the number of components in the complement of the real A-discriminant when k = 3, where previous bounds had been O(n^6) or even exponential before that. We introduce new tools that can be used in discovering various types of extremal A-discriminants as well as examples found with these tools: a family of A-discriminant varieties with the maximal number of cusps and a family that appears to asymptotically admit the maximal number of chambers. Finally we give sage code that efficiently plots the A-discriminant amoeba for k = 3. Then we switch to a non-Archimedean point of view. Here we also give O(n^2) bounds for the number of connected components in the complement of the non- Archimedean A-discriminant amoeba when k = 3, but we also get a bound of O(n^(2(k−1)(k−2)) )when k > 3. As in the real case, we also give a family exhibiting O(n^2) connected components asymptotically. Finally we give code that efficiently plots the p-adic A-discriminant amoeba for all k ≥ 3. These results help us understand the structure of the A-discriminant to a degree, as yet, unknown. This can ultimately help in solving Smale’s 17th problem as it gives a better understanding of how complicated the solution set can be.

Heterolobosea is a group of mainly free-living amoebae, flagellates and amoeboflagellates closely related to Euglenozoa and Jakobida (supergroup Excavata). At least two heterolobosean lineages have reduced their mitochondria and live in low concentrations of oxygen (Psalteriomonadidae and extremely halophilic Pleurostomum). Moreover, some other presumably anaerobic species have been described in aerobic heteroloboseid genera, but their sequence data are still missing. The aim of this study is to recognize the diversity and phylogenetic position of both already described and novel non-hypersaline anaerobic heteroloboseans. We have isolated and cultivated 34 strains of free-living heterolobosean flagellates, amoebae and amoeboflagellates from freshwater, brackish and marine microoxic/anoxic habitats. 33 of these strains constitute a single clade (Psalteriomonadidae). We recognize 2 new genera and 3 new species. Phylogenetic analysis of SSU rDNA showed the genus Percolomonas is polyphyletic. The similar morphology of species formally placed within the genus Percolomonas is probably plesiomorphic. Finally, the marine strain PC4AM is morphologically unique and its morphology can not be compared with other heteroloboseans and eukaryotes. It is probably the most derived heterolobosean. Its cell structure...

Paratetramitus jugosus, a vahlkampfiid amoebomastigote, was isolated into monoprotist/monobacterial (Bacillus sp.), cultures from laminated microbial mats (Laguna Figueroa, Baja California Norte, Mexico) and muds (Eel Pond, Woods Hole, Massachusetts). Chromidia, roughly spherical (2-4 µm in diameter) were released from both walled spherical cysts (10-12 µm) and phagocytotic amoebic forms. Desiccation-resistant walled chromidia, at first spherical, resorb their walls and develop into small pleiomorphic phagocytotic amoeba. Small amoebae feed and mature into typical monopodial vahlkampfiid adults confirming previous work (Dobell, 1913, and especially the analysis of a larger encysting vahlkampfiid amoeba associated with Long Island oyster disease studied at Woods Hole by Mary Jane Hogue, 1914). I show here that P. jugosus reproduces and develops through its life history stages of chromidia, mature monopodial amoebae, and cysts as rapidly and abundantly under low oxygen levels as at ambient atmospheric oxygen concentrations. Anoxia was achieved in the laboratory by incubation of entirely desiccated inocula from old mat or mud samples in Brewer jars with or without gas packs to control atmospheric conditions. Three sets of experiments yielded the same results: vigorous growth on bacillus food occurred on manganese acetate media by two weeks on the surface of agar plates under ambient oxic or hypoxic to anoxic conditions. Preliminary investigations of similar amoeba from geographically distinct field sites in Europe, North America, and the Caribbean were made. From them, I suggest it is likely these coastal amoebomastigotes that propagate by small desiccation resistant, oxygen-independent, manganese tolerant chromidia are genuinely cosmopolitan in its distribution.

Amebas de vida livre (AVL) são protozoários amplamente distribuídos na natureza e em ambientes artificiais. Alguns gêneros são oportunistas ou patogênicos, com característica anfizóica, são esses: Acanthamoeba spp., Naegleria spp., Balamuthia spp., Sappinia spp., e recentemente Vermamoeba spp. AVL podem servirem de reservatórios de várias bactérias patogênicas, uma vez que se alimentam dessas no ambiente por fagocitose, algumas espécies de bactérias após internalizadas escapam da via de degradação sobrevivem e multiplicam-se no interior das amebas. Face ao exposto, o presente trabalho objetivou isolar e identificar AVL e as bactérias associadas presentes em águas de torres de resfriamento, cuja temperatura da água varia entre 25 a 30°C (ideal para o desenvolvimento de diversos microrganismos). Amebas foram isoladas em cultivo monoxênico com Escherichia coli inativadas pelo calor. Das amostras positivas, foram realizadas Reações em Cadeia de Polimerase (PCR), utilizando oligonucleotídeos específicos para cada gênero. Os produtos das PCR foram sequenciados e as sequências geradas foram comparadas com sequências parciais de cada gene alvo depositadas no GenBank. Das 36 amostras, 33 (91,66%) foram positivas para presença de AVL, destas 15 (45,4%) foram positivas para Acanthamoeba spp., 12 (36,3%) para Naegleria spp., 6 (18,2%) para Vermamoeba spp. Dos endossimbiontes pesquisados, somente Pseudomonas spp. foram identificadas em 13 (39,3%) isolados de AVL. Os resultados obtidos no presente estudo confirmam a presença de amebas de vida livre potencialmente patogênicas e carreadoras de bactérias patogênicas oportunistas que podem representar um risco à saúde humana. / Free-living amoebae (FLA) are protozoa widely distributed in natural and artificial environments. Some genus are opportunistic or pathogenic, with anfizoic feature : Acanthamoeba spp., Naegleria spp., Balamuthia spp., Sappinia spp., and recently Vermamoeba spp. AVL may serve as reservoirs for various pathogenic bacteria, since they feed by phagocytosis in the environment, some species of bacteria after internalized escape to the pathway of degradation surviving and multiplying within the amoebae. The aim of this study was to isolate and identify FLA and their associated bacteria present in water from cooling tower, whose temperature water varies between 25 to 30 °C (ideal for the development of different organisms). Amoebae were isolated in monoxenic cultivation with Escherichia coli inactivated by heat. Of the positive samples Polymerase Chain Reactions (PCR) were performed using specific primers for each genus. The PCR products were sequenced and the sequences were generated compared with partial sequences of each gene target deposited in GenBank. From the 36 samples, 33 (91.66%) were positive for the presence of FLA. Of these, 15 (45.4%) were positive for Acanthamoeba spp., 12 (36.3%) for Naegleria spp. and 6 (18.2 %) for Vermamoeba spp. Of the amoeba isolated, 13 (39.3%) were associated to bacteria wich belong to Pseudomonas genus (100%). Another bacteria investigated were absent. The results of this study confirm the presence of potentially pathogenic free-living amoebae as vehicles of opportunistic/pathogenic bacteria that can pose a risk to the human health.

Amebas de vida livre (AVL) são protozoários amplamente distribuídos na natureza e em ambientes artificiais. Alguns gêneros são oportunistas ou patogênicos, com característica anfizóica, são esses: Acanthamoeba spp., Naegleria spp., Balamuthia spp., Sappinia spp., e recentemente Vermamoeba spp. AVL podem servirem de reservatórios de várias bactérias patogênicas, uma vez que se alimentam dessas no ambiente por fagocitose, algumas espécies de bactérias após internalizadas escapam da via de degradação sobrevivem e multiplicam-se no interior das amebas. Face ao exposto, o presente trabalho objetivou isolar e identificar AVL e as bactérias associadas presentes em águas de torres de resfriamento, cuja temperatura da água varia entre 25 a 30°C (ideal para o desenvolvimento de diversos microrganismos). Amebas foram isoladas em cultivo monoxênico com Escherichia coli inativadas pelo calor. Das amostras positivas, foram realizadas Reações em Cadeia de Polimerase (PCR), utilizando oligonucleotídeos específicos para cada gênero. Os produtos das PCR foram sequenciados e as sequências geradas foram comparadas com sequências parciais de cada gene alvo depositadas no GenBank. Das 36 amostras, 33 (91,66%) foram positivas para presença de AVL, destas 15 (45,4%) foram positivas para Acanthamoeba spp., 12 (36,3%) para Naegleria spp., 6 (18,2%) para Vermamoeba spp. Dos endossimbiontes pesquisados, somente Pseudomonas spp. foram identificadas em 13 (39,3%) isolados de AVL. Os resultados obtidos no presente estudo confirmam a presença de amebas de vida livre potencialmente patogênicas e carreadoras de bactérias patogênicas oportunistas que podem representar um risco à saúde humana. / Free-living amoebae (FLA) are protozoa widely distributed in natural and artificial environments. Some genus are opportunistic or pathogenic, with anfizoic feature : Acanthamoeba spp., Naegleria spp., Balamuthia spp., Sappinia spp., and recently Vermamoeba spp. AVL may serve as reservoirs for various pathogenic bacteria, since they feed by phagocytosis in the environment, some species of bacteria after internalized escape to the pathway of degradation surviving and multiplying within the amoebae. The aim of this study was to isolate and identify FLA and their associated bacteria present in water from cooling tower, whose temperature water varies between 25 to 30 °C (ideal for the development of different organisms). Amoebae were isolated in monoxenic cultivation with Escherichia coli inactivated by heat. Of the positive samples Polymerase Chain Reactions (PCR) were performed using specific primers for each genus. The PCR products were sequenced and the sequences were generated compared with partial sequences of each gene target deposited in GenBank. From the 36 samples, 33 (91.66%) were positive for the presence of FLA. Of these, 15 (45.4%) were positive for Acanthamoeba spp., 12 (36.3%) for Naegleria spp. and 6 (18.2 %) for Vermamoeba spp. Of the amoeba isolated, 13 (39.3%) were associated to bacteria wich belong to Pseudomonas genus (100%). Another bacteria investigated were absent. The results of this study confirm the presence of potentially pathogenic free-living amoebae as vehicles of opportunistic/pathogenic bacteria that can pose a risk to the human health.

Amebas de vida livre (AVL) são protozoários amplamente distribuídos na natureza e em ambientes artificiais. Alguns gêneros são oportunistas ou patogênicos, com característica anfizóica, são esses: Acanthamoeba spp., Naegleria spp., Balamuthia spp., Sappinia spp., e recentemente Vermamoeba spp. AVL podem servirem de reservatórios de várias bactérias patogênicas, uma vez que se alimentam dessas no ambiente por fagocitose, algumas espécies de bactérias após internalizadas escapam da via de degradação sobrevivem e multiplicam-se no interior das amebas. Face ao exposto, o presente trabalho objetivou isolar e identificar AVL e as bactérias associadas presentes em águas de torres de resfriamento, cuja temperatura da água varia entre 25 a 30°C (ideal para o desenvolvimento de diversos microrganismos). Amebas foram isoladas em cultivo monoxênico com Escherichia coli inativadas pelo calor. Das amostras positivas, foram realizadas Reações em Cadeia de Polimerase (PCR), utilizando oligonucleotídeos específicos para cada gênero. Os produtos das PCR foram sequenciados e as sequências geradas foram comparadas com sequências parciais de cada gene alvo depositadas no GenBank. Das 36 amostras, 33 (91,66%) foram positivas para presença de AVL, destas 15 (45,4%) foram positivas para Acanthamoeba spp., 12 (36,3%) para Naegleria spp., 6 (18,2%) para Vermamoeba spp. Dos endossimbiontes pesquisados, somente Pseudomonas spp. foram identificadas em 13 (39,3%) isolados de AVL. Os resultados obtidos no presente estudo confirmam a presença de amebas de vida livre potencialmente patogênicas e carreadoras de bactérias patogênicas oportunistas que podem representar um risco à saúde humana. / Free-living amoebae (FLA) are protozoa widely distributed in natural and artificial environments. Some genus are opportunistic or pathogenic, with anfizoic feature : Acanthamoeba spp., Naegleria spp., Balamuthia spp., Sappinia spp., and recently Vermamoeba spp. AVL may serve as reservoirs for various pathogenic bacteria, since they feed by phagocytosis in the environment, some species of bacteria after internalized escape to the pathway of degradation surviving and multiplying within the amoebae. The aim of this study was to isolate and identify FLA and their associated bacteria present in water from cooling tower, whose temperature water varies between 25 to 30 °C (ideal for the development of different organisms). Amoebae were isolated in monoxenic cultivation with Escherichia coli inactivated by heat. Of the positive samples Polymerase Chain Reactions (PCR) were performed using specific primers for each genus. The PCR products were sequenced and the sequences were generated compared with partial sequences of each gene target deposited in GenBank. From the 36 samples, 33 (91.66%) were positive for the presence of FLA. Of these, 15 (45.4%) were positive for Acanthamoeba spp., 12 (36.3%) for Naegleria spp. and 6 (18.2 %) for Vermamoeba spp. Of the amoeba isolated, 13 (39.3%) were associated to bacteria wich belong to Pseudomonas genus (100%). Another bacteria investigated were absent. The results of this study confirm the presence of potentially pathogenic free-living amoebae as vehicles of opportunistic/pathogenic bacteria that can pose a risk to the human health.