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Chapter 1: Functional Specialization and Arm Length in Octopus bimaculoides<br/>Although studies are limited, there is some evidence that octopuses use their arms for specialized functions. For example, in Octopus maya and O. vulgaris, the anterior arms are utilized more frequently for grasping and exploring (Lee, 1992; Byrne et al., 2006a),

Chapter 1: Functional Specialization and Arm Length in Octopus bimaculoides<br/>Although studies are limited, there is some evidence that octopuses use their arms for specialized functions. For example, in Octopus maya and O. vulgaris, the anterior arms are utilized more frequently for grasping and exploring (Lee, 1992; Byrne et al., 2006a), while posterior arms are more frequently utilized for crawling in O. vulgaris (Levy et al., 2015). In addition, O. vulgaris uses favored arms when retrieving food and making contact with a T-maze as dictated by their lateralized vision (Byrne, 2006b). O. vulgaris also demonstrates a preference for anterior arms when retrieving food from a Y-maze (Gutnick et. al. 2020). In Octopus bimaculoides bending and elongation were more frequent in anterior arms than posterior arms during reaching and grasping tasks, and right arms displayed deformation more frequently than left arms, with the exception of the hectocotylus (R3) in males (Kennedy et. al. 2020). Given these observed functional differences, the goal of this study was to determine if morphological differences exist between different octopus arm identities, coded as L1-L4 and R1-R4. In particular, the relationship between arm length and arm identity was analyzed statistically. The dataset included 111 intact arms from 22 wild-caught specimens of O. bimaculoides (11 male and 11 female). Simple linear regressions and an analysis of covariance were performed to test the relationship between arm length and a number of factors, including body mass, sex, anterior versus posterior location, and left versus the right side. Mass had a significant linear relationship with arm length and a one-way ANOVA demonstrated that arm identity is significantly correlated with arm length. Moreover, an analysis of covariance demonstrated that independent of mass, arm identity has a significant linear relationship with arm length. Despite an overall appearance of bilateral symmetry, arms of different identities do not have statistically equivalent lengths in O. bimaculoides. Furthermore, differences in arm length do not appear to be related to sex, anterior versus posterior location, or left or right side. These results call into question the existing practice of treating all arms as equivalent by either using a single-arm measurement as representative of all eight or calculating an average length and suggest that morphological analyses of specific arm identities may be more informative.<br/><br/>Chapter 2: Predicting and Analyzing Octopus bimaculoides Sensitivity to Global Anesthetic<br/>Although global anesthetic is widely used in human and veterinary medicine the mechanism and impact of global anesthetic is relatively poorly comprehended, even in well-studied mammalian models. Invertebrate anesthetic is even less understood. In order to evaluate factors that impact anesthetic effectiveness analyses were conducted on 22 wild-caught specimens of Octopus bimaculoides during 72 anesthetic events.Three machine learning models: regression tree, random forest, and generalized additive model were utilized to make predictions of the concentration of anesthetic (percent ethanol by volume) from 11 features and to determine feature importance in making those predictions. The fit of each model was analyzed on three criteria: correlation coefficient, mean squared error, and relative error. Feature importance was determined in a model-specific manner. Predictions from the best performing model, random forest, have a .82 correlation coefficient with experimental values. Feature importance suggests that temperature on arrival and cohabitation factors strongly influence predictions for anesthesia concentration. This likely indicates the transportation process was incurring stress on the animals and that cohabitation was also stressful for the typically solitary O. bimaculoides. This long-term stress could lead to a decline in the animal’s well-being and a lower necessary ethanol concentration (Horvath et al., 2013). This analysis provides information to improve the care of octopus in laboratory settings and furthers the understanding of the effects of global anesthetic in invertebrates, particularly one with a distributed nervous system.

ContributorsSorge, Marieke Alexandria (Author) / Fisher, Rebecca (Thesis director) / Zhao, Yunpeng (Committee member) / Marvi, Hamid (Committee member) / School of Life Sciences (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Octopus arms employ a complex three dimensional array of musculature, called a
muscular hydrostat, which allows for nearly infinite degrees of freedom of movement without
the structure of a skeletal system. This study employed Magnetic Resonance Imaging with a
Gadoteridol-based contrast agent to image the octopus arm and view the internal tissues. Muscle
layering

Octopus arms employ a complex three dimensional array of musculature, called a
muscular hydrostat, which allows for nearly infinite degrees of freedom of movement without
the structure of a skeletal system. This study employed Magnetic Resonance Imaging with a
Gadoteridol-based contrast agent to image the octopus arm and view the internal tissues. Muscle
layering was mapped and area was measured using AMIRA image processing and the trends in
these layers at the proximal, middle, and distal portions of the arms were analyzed. A total of 39
arms from 6 specimens were scanned to give 112 total imaged sections (38 proximal, 37 middle,
37 distal), from which to ascertain and study the possible differences in musculature. The
images revealed significant increases in the internal longitudinal muscle layer percentages
between the proximal and middle, proximal and distal, and middle and distal sections of the
arms. These structural differences are hypothesized to be used for rapid retraction of the distal
segment when encountering predators or noxious stimuli. In contrast, a significant decrease in
the transverse muscle layer was found when comparing the same sections. These structural
differences are hypothesized to be a result of bending behaviors during retraction. Additionally,
the internal longitudinal layer was separately studied orally, toward the sucker, and aborally,
away from the sucker. The significant differences in oral and aboral internal longitudinal
musculature in proximal, middle, and distal sections is hypothesized to support the pseudo-joint
functionality displayed in octopus fetching behaviors. The results indicate that individual
octopus arm morphology is more unique than previously thought and supports that internal
structural differences exist to support behavioral functionality.
ContributorsCummings, Sheldon Daniel (Author) / Fisher, Rebecca (Thesis director) / Marvi, Hamidreza (Committee member) / Cherry, Brian (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
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The morphological characteristics of organisms are intricately linked to their ecological features. As a result, species with similar ecological niches may exhibit shared morphological traits due to convergent evolution. Some genomic features could be relevant to influencing the occurrence of convergence evolution. Anoles, with over 400 species, are an excellent

The morphological characteristics of organisms are intricately linked to their ecological features. As a result, species with similar ecological niches may exhibit shared morphological traits due to convergent evolution. Some genomic features could be relevant to influencing the occurrence of convergence evolution. Anoles, with over 400 species, are an excellent model for studying this process. Within Anolis, groups of species that have evolved similar morphological traits and ecological adaptations in response to specific environmental niches are described as ecomorphs. One ecomorph, the crown-giant anoles, has independently evolved large body sizes and adapted to arboreal habitats, predominantly occupying the upper canopy layer of forests. The objective of this study was to explore the convergent evolution of morphological traits in crown giant anoles, by comparing the osteological traits of two crown giants, Anolis frenatus, and A. equestris, to four non-crown giant species from different ecomorphs, A. auratus, A. carolinensis, A. biporcatus, and A. sagrei. The analysis indicated an absence of convergence in most morphological traits except for body size (SVL). Additionally, this study explored the potential role of transposable elements (TEs) as a genomic feature shaping the morphological diversity of crown giant anoles. The genes located within TE-rich regions on the genome were identified across selected Anolis species. An enrichment of genes associated with regulation and developmental processes was detected in regions with high TE abundance for all analyzed species, but not exclusive to crown giants. The results suggest that crown giants seem to only converge in their substantial body size and that the variability in other morphological characteristics could be attributed to some other ecological features or the phylogenetic relationships of each species. Moreover, TEs may play a role in facilitating morphological evolution and adaptability in all Anolis species, as they could influence gene expression and regulatory pathways. This highlights the need for further investigation into the genomic mechanisms determining convergent evolution.
ContributorsJohnson, Jaime (Author) / Kusumi, Kenro (Thesis director) / Araya-Donoso, Raúl (Committee member) / Dolby, Greer (Committee member) / Fisher, Rebecca (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2024-05
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The exceptional mechanical properties of polymers with heterogeneous structure, such as the high toughness of polyethylene and the excellent blast-protection capability of polyurea, are strongly related to their morphology and nanoscale structure. Different polymer microstructures, such as semicrystalline morphology and segregated nanophases, lead to coordinated molecular motions during deformation

The exceptional mechanical properties of polymers with heterogeneous structure, such as the high toughness of polyethylene and the excellent blast-protection capability of polyurea, are strongly related to their morphology and nanoscale structure. Different polymer microstructures, such as semicrystalline morphology and segregated nanophases, lead to coordinated molecular motions during deformation in order to preserve compatibility between the different material phases. To study molecular relaxation in polyethylene, a coarse-grained model of polyethylene was calibrated to match the local structural variable distributions sampled from supercooled atomistic melts. The coarse-grained model accurately reproduces structural properties, e.g., the local structure of both the amorphous and crystalline phases, and thermal properties, e.g., glass transition and melt temperatures, and dynamic properties: including the vastly different relaxation time scales of the amorphous and crystalline phases. A hybrid Monte Carlo routine was developed to generate realistic semicrystalline configurations of polyethylene. The generated systems accurately predict the activation energy of the alpha relaxation process within the crystalline phase. Furthermore, the models show that connectivity to long chain segments in the amorphous phase increases the energy barrier for chain slip within crystalline phase. This prediction can guide the development of tougher semicrystalline polymers by providing a fundamental understanding of how nanoscale morphology contributes to chain mobility. In a different study, the macroscopic shock response of polyurea, a phase segregated copolymer, was analyzed using density functional theory (DFT) molecular dynamics (MD) simulations and classical MD simulations. The two models predict the shock response consistently up to shock pressures of 15 GPa, beyond which the DFT-based simulations predict a softer response. From the DFT simulations, an analysis of bond scission was performed as a first step in developing a more fundamental understanding of how shock induced material transformations effect the shock response and pressure dependent strength of polyurea subjected to extreme shocks.
ContributorsLi, Yiyang (Author) / Oswald, Jay (Thesis advisor) / Rajan, Subramaniam D. (Committee member) / Solanki, Kiran (Committee member) / Chamberlin, Ralph (Committee member) / Rajagopalan, Jagannathan (Committee member) / Arizona State University (Publisher)
Created2017
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Physical vapor deposition (PVD) of phase-separating multicomponent alloy films generates a rich variety of unique self-organized nanoscale morphologies. However, an understanding of how the different material and process parameters influence the formation of these nanostructures is limited. My dissertation aims to bridge this gap by developing phase-field models that can

Physical vapor deposition (PVD) of phase-separating multicomponent alloy films generates a rich variety of unique self-organized nanoscale morphologies. However, an understanding of how the different material and process parameters influence the formation of these nanostructures is limited. My dissertation aims to bridge this gap by developing phase-field models that can predict an entire spectrum of nanostructures as a function of processing conditions and composition in multicomponent alloys under a set of material-specific constraints. Firstly, I developed a numerical model to simulate nanoscale phase separation in codeposited immiscible binary alloy films. An investigation on the influence of deposition rates, phase-fraction, and temperature, on the evolution of self-assembled nanostructures yielded many characteristic patterns, including well-known morphologies such as the lateral and vertical concentration modulations, as well as some previously undocumented variants. I also simulated phase-separation in ternary alloyed PVD films, and studied the influence of deposition rate and composition on the evolution of self-assembled nanostructures, and recorded many novel nanoscale morphologies. I then sought to understand the role of material properties such as elastic misfit due to lattice mismatch between phases, grain boundaries formed in polycrystalline films, and the interplay of interphase and surface boundaries at the film surface. To this end, I developed phase-field models of binary PVD film deposition that incorporated these constraints and studied their role in altering the temporal and spatial characteristics of the evolving morphologies. I also investigated the formation of surface hillocks and the role of surface and interfacial energies in their evolution. By studying the change in total free energy across the different deposition models, I established that, in addition to influencing the temporal and spatial characteristics of nanoscale structures in the films, this quantity is also responsible for driving morphological transitions as the rate of deposition is increased. Insights gained from this computational study will demonstrate the viability of these models in predicting experimentally observed morphologies and form a basis for understanding the various factors involved in driving phase-separation and morphological transitions. In addition, morphology maps will serve as templates for developing new pathways for morphology control in the manufacturing of PVD alloy films.
ContributorsRaghavan, Rahul (Author) / Ankit, Kumar (Thesis advisor) / Rajagopalan, Jagannathan (Committee member) / Mushongera, Leslie T (Committee member) / Arizona State University (Publisher)
Created2021