Comparisons among model organisms make clear that, despite the fundamental importance of recombination in sexually-reproducing species, the mechanisms by which it is directed to the genome can vary markedly. Notably, in mice and humans, recombination almost exclusively occurs where the protein PRDM9 binds DNA. In such species, fine-scale recombination rates along the genome are rapidly evolving, as shifts in PRDM9 binding affinity remodel the landscape. In other species such as birds or canids, PRDM9 has been lost and recombination occurs preferentially at promoter-like features, leading to the conservation of recombination rates over large evolutionary distances. Increased recombination near promoters is also seen in human and mouse knockouts for PRDM9, indicating that this mechanism is normally out-competed by PRDM9 binding. The rapid evolution of complete orthologs of PRDM9 in non-mammalian vertebrates suggests that the protein may play a similar role in directing recombination outside of mammals. In chapter 2 of this work, we test this hypothesis by focusing on the corn snake Pantherophis guttatus, a representative vertebrate species with a single, complete PRDM9 ortholog that is rapidly evolving. We improved the assembly and annotation of the corn snake reference genome and resequenced 24 unrelated corn snake samples to high coverage in order to infer historical recombination rates across the genome from patterns of linkage disequilibrium. We find evidence for elevated recombination around computationally predicted PRDM9 binding sites but, surprisingly, also near promoter features. To verify these findings, we resequenced two pedigrees, identified the PRDM9 alleles segregating in the families and called crossover events that occurred in the parents. This analysis confirmed that crossover events overlap both PRDM9 binding sites and promoter features more than expected by chance. Thus, unlike in mammalian species that rely on PRDM9, in corn snakes there appears to be a mixed use of PRDM9 binding sites and promoter like features, and we find evidence that the relative importance of these features differs between macro- and microchomosomes. We hypothesize that the dual usage of these features reflects a tug of war between PRDM9 and promoter features, whose strength in snakes and possibly other vertebrates has been shifted by changes to a gene that reads the histone modifications made by PRDM9, and likely other genes. In chapter 3, I discuss how follow-up experiments based on these observations could help answer long-standing questions related to the conditions under which PRDM9-directed recombination localization is favorable. Beyond the specific results, this work illustrates how the study of non-model organisms can inform our understanding of basic genetic mechanisms.

No description available.

No description available.

No description available.

This dissertation addresses the question, how and why do 'flying' snakes (Chrysopelea) undulate through the air? Instead of deploying paired wings or wing-like surfaces, flying snakes jump, splay their ribs into a bluff-body airfoil, and undulate through the air. Aerial undulation is the dominant feature of snake flight, but its effects on locomotor performance and stability are unknown. Chapter 2 describes a new non-equilibrium framework to analyze gliding animals and how the pitch angle affects their translational motion. Chapter 3 combines flying snake glide experiments and detailed dynamic modeling to address what is aerial undulation and how each kinematic component affects rotational stability and translational performance. Chapter 4 combines the kinematic data of Chapter 3, with elements of the non-equilibrium framework of Chapter 2, to examine the kinematics of snake flight in greater detail. This chapter also tests if our current understanding of flying snake aerodynamics is sufficient to explain the observed center of mass motion. / Ph. D.

Understanding irrigator responses to previous changes in water availability is critical to building effective institutions that allow for efficient and resilient management of water resources in the face of potentially increasing scarcity due to climate change. Using remote sensing data, I examined irrigator responses to seasonal changes in water availability in Idaho's Snake River Plain over the past 33 years. Google Earth Engine's high performance cloud computing and big data processing capabilities were used to compare the performance of three spectral indices, three compositing algorithms and two sensors for 2002 and 2007 for distinguishing between irrigated and non-irrigated parcels. We demonstrate that, on average, the seasonal-maximum algorithm yields a 60% reduction in county scale root mean square error (RMSE) over the accepted single-date approach. We use the best performing classification method, a binary threshold of the seasonal maximum of the Normalized Difference Moisture Index (NDMI), to identify irrigated and non-irrigated lands in Idaho's Snake River Basin for 1984-2016 using Landsat 5-8 data. NDMI of irrigated lands was found to generally increase over time, likely as a result of changes in agricultural practices increasing crop productivity. Furthermore, we find that irrigators with rights to small areas, and those with only surface water rights are more likely to have a major reduction (>25%) in irrigated area and conversely those with a large, groundwater rights are more likely to have major increases (>25%) in the extent of their irrigation. / Master of Science

Due to shared coevolutionary history of snakes and primates with snakes acting as their main predators, snakes elicit fear in most of the primates, humans included. Humans are able to notice a stimulus that elicits fear, e.g., a snake, much faster. Such ability might have surely positively affected their survival in the past. In the nature, aposematic coloration acts as a warning of a dangerous prey to its predators not to devour it. The highly poisonous American coral snakes have this coloration pattern. The harmless king snakes of the Central and North Americas gain an anti-predatory advantage by becoming the coral snakes 'Batesian mimics, copying their bright pattern. Such pattern elicits an innate fear reaction in various species of wild birds who avoid a mere contact with patterned plastic dummies. The question arises whether other taxa, including primates and humans, generally recognize such pattern as dangerous. The aim of this study was to find whether humans fear coral snakes, although they have not long coevolutionary history with them. Further it was analyze, which visual factors of the snakes affect this fear reaction (i.e., a warning coloration, pattern or shape of snake). The atractiveness of these snakes was tested. Another question was whether humans are able to intuitively recognize...

In this thesis, we introduce our lasso-type grasping scheme. This 3-D lasso-type grasping scheme, different from the previously performed grasping schemes which are either planar or fixed base, is the novelty of our approach where the snake robot grasps an object with any of its body links which are at close proximity to the object while undergoing its serpentine motion with the remaining links and dragging the grasped object. Since our snake robot has the pitch motion for every link, we can ensure that the links do not run into each other as they wrap around the object. A lasso-type power grasp is then possible for our 15-link snake robot as seen in the simulation results of this thesis. Furthermore we develop the kinematic and control models for lasso-type grasping and for dragging the grasped object to a desired state. This control model includes an adaptively changing feedback gain which prevents excessively large inputs to corrupt the serpentine locomotion control. According to our lasso-type grasping model, while the snake robot can grasp the object beginning with the any body link at close proximity of the object, the contact points can be controlled to generate the curvilinear grasping curve by using our lasso-type grasping procedure. For dragging the grasped object, we define a scheme which can determine the appropriate desired state to drag the grasped object to a desired position. The stability of the grasped object is important to resist the disturbance forces as well as the force closure grasping is important to counteract the disturbance force. To analyze the stability of the lasso-type grasping, we introduce a stability model of lasso-type grasping based on contact stiffness matrices that faces the snake to regrasp when gone unstable.

Master’s thesis deals with design the link robot and motion simulation. It is divided into four parts. In first part are briefly explained basic information of industrial robots and manipulators, their design and structure. Further it is listed some examples of design industrial robots and manipulators and principle of computation of kinematic chain. On beginning of the second part is performed analysis of configuration link robots, description of their designs and structures, examples of design link robots and their applications. In third part is selected option of design, created mathematical and kinematic model. Then it is designed and described construction of robot. The last section is devoted to simulation of robot’s kinematics, description of simulation softwares and their use for required results.

Orientador: Aluir Porfírio Dal Poz / Resumo: Neste trabalho foi proposta uma metodologia para a extração de contornos de telhados de edifícios no espaço-objeto, a partir da integração de um estéreo par de imagens aéreas de alta resolução e modelos 3D aproximados de telhado obtidos a partir de dados de varredura a LASER. Um modelo matemático considerando as propriedades radiométricas e geométricas dos telhados foi formulado a fim de representar o contorno do telhado no espaçoimagem, tendo como base o modelo de contorno ativo Snake. Esse modelo foi então adaptado para descrever os contornos no espaço-objeto considerando um estéreo par de imagens aéreas. Finalmente, o polígono ótimo que representa um dado contorno do telhado foi determinado a partir da otimização, via Programação Dinâmica, da função de energia criada. A solução obtida é uma representação mais acurada para o correspondente contorno do modelo 3D do telhado. O método desenvolvido apresenta também mecanismos para realizar a compensação automática de três tipos de problemas comuns em ambientes urbanos e que podem prejudicar a extração automática de telhados: obstruções perspectivas causadas por edifícios elevados, obstruções diretas causadas por vegetação que se eleva acima do telhado e sombras adjacentes aos telhados, as quais podem ser confundidas com as bordas do telhado. Os experimentos foram realizados utilizando imagens aéreas com GSD ≈ 0,10 m e nuvem de pontos LASER com densidade média de 6 pontos/m2. Os resultados mostraram que o método funciona adequad... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: In this work a methodology was proposed for extracting building roof contours in the object-space, by integration of a high-resolution aerial images stereo pair and 3D roof models reconstructed from LASER scanning data. A mathematical model considering the radiometric and geometric properties of roofs was developed in order to represent the roof contour in the image-space, based on the Snake active contour model. Then, the model was adapted to represent the contours in the object space considering a stereo pair of aerial images. Finally, the optimal polygon representing a selected roof contour was obtained by optimizing the proposed energy function using Dynamic Programming algorithm. The solution obtained, i.e., a polygon representing each 3D roof contour, will be a higher accurate representation for the correspondent contour of the 3D roof model. The proposed method also presents mechanisms to perform the compensation of three types of common problems in urban environment and which can disturb the automatic roof extraction: perspective occlusions caused by high buildings, occlusions caused by vegetation that covers the roof and shadows that are adjacent to the roofs which can be misinterpreted as roof edges. The experiments were performed using aerial images with GSD ≈ 0,10 m and LASER point cloud with average density of 6 points/m2. The results showed that the proposed method works properly in contour extraction of roofs with occlusion and shadows areas, presenting complet... (Complete abstract click electronic access below) / Doutor