Matching Items (339)
Description
Rhodoferax antarcticus strain ANT.BR, a purple nonsulfur bacterium isolated from a microbial mat in Ross Island, Antarctica, is the first described anoxygenic phototrophic bacterium that is adapted to cold habitats and is the first beta-proteobacterium to undergo complete genome sequencing. R. antarcticus has unique absorption spectra and there are no obvious intracytoplasmic membranes in cells grown phototrophically, even under low light intensity. Analysis of the finished genome sequence reveals a single chromosome (3,809,266 bp) and a large plasmid (198,615 bp) that together harbor 4,262 putative genes. The genome contains two types of Rubiscos, Form IAq and Form II, which are known to exhibit quite different kinetic properties in other bacteria. The presence of multiple Rubisco forms could give R. antarcticus high metabolic flexibility in diverse environments. Annotation of the complete genome sequence along with previous experimental results predict the presence of structural genes for three types of light-harvesting (LH) complexes, LH I (B875), LH II (B800/850), and LH III (B800/820). There is evidence that expression of genes for the LH II complex might be inhibited when R. antarcticus is under low temperature and/or low light intensity. These interesting condition-dependent light-harvesting apparatuses and the control of their expression are very valuable for the further understanding of photosynthesis in cold environments. Finally, R. antarcticus exhibits a highly motile lifestyle. The genome content and organization of all putative polar flagella genes are characterized and discussed.
ContributorsZhao, Tingting, M.S (Author) / Touchman, Jeffrey (Thesis advisor) / Rosenberg, Michael (Committee member) / Redding, Kevin (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2011
Description
In this thesis I introduce a new direction to computing using nonlinear chaotic dynamics. The main idea is rich dynamics of a chaotic system enables us to (1) build better computers that have a flexible instruction set, and (2) carry out computation that conventional computers are not good at it. Here I start from the theory, explaining how one can build a computing logic block using a chaotic system, and then I introduce a new theoretical analysis for chaos computing. Specifically, I demonstrate how unstable periodic orbits and a model based on them explains and predicts how and how well a chaotic system can do computation. Furthermore, since unstable periodic orbits and their stability measures in terms of eigenvalues are extractable from experimental times series, I develop a time series technique for modeling and predicting chaos computing from a given time series of a chaotic system. After building a theoretical framework for chaos computing I proceed to architecture of these chaos-computing blocks to build a sophisticated computing system out of them. I describe how one can arrange and organize these chaos-based blocks to build a computer. I propose a brand new computer architecture using chaos computing, which shifts the limits of conventional computers by introducing flexible instruction set. Our new chaos based computer has a flexible instruction set, meaning that the user can load its desired instruction set to the computer to reconfigure the computer to be an implementation for the desired instruction set. Apart from direct application of chaos theory in generic computation, the application of chaos theory to speech processing is explained and a novel application for chaos theory in speech coding and synthesizing is introduced. More specifically it is demonstrated how a chaotic system can model the natural turbulent flow of the air in the human speech production system and how chaotic orbits can be used to excite a vocal tract model. Also as another approach to build computing system based on nonlinear system, the idea of Logical Stochastic Resonance is studied and adapted to an autoregulatory gene network in the bacteriophage λ.
ContributorsKia, Behnam (Author) / Ditto, William (Thesis advisor) / Huang, Liang (Committee member) / Lai, Ying-Cheng (Committee member) / Helms Tillery, Stephen (Committee member) / Arizona State University (Publisher)
Created2011
Description
As an evolutionary force, hybridization outcomes include introgression, admixture, speciation, and reproductive isolation. While hybridization has been studied in several primates, the marmoset genus Callithrix is an important, but little studied example of Neotropical hybridization. Varying degrees of reproductive isolation exist between Callithrix species, and hybridization occurs at species borders or regions containing introduced and native species. Interbreeding between Callithrix species carries important implications for biodiversity and genetic integrity within the genus. However, species origins and levels of genetic admixture in marmoset hybrid zones are generally unknown, and few population genetic studies of individual Callithrix species exist. Using the mitochondrial control region and 44 microsatellite markers, this work explored the genetic diversity and species origins of two C. penicillata and C. jacchus hybrid zones, as well as genetic diversity and divergence in the parental species. Both marker types showed that C. penicillata is more genetically diverse than C. jacchus. Based on mtDNA, C. jacchus seems to have experienced a past population expansion and C. penicillata evolved under constant population size. The data revealed the existence of a previously undocumented natural hybrid zone along the São Francisco River in NE Brazil and confirmed species origins of an anthropogenic zone in Rio de Janeiro state. The data also showed much lower levels of admixture and genetic diversity within the natural hybrid zone than in the anthropogenic zone. Further, the data suggested that the São Francisco River is an important geographic barrier to gene flow in the natural hybrid zone. On the other hand, admixture patterns within the anthropogenic hybrid zone suggested collapse of reproductive barriers, and the formation of a hybrid marmoset swarm. Thus, this work suggested different evolutionary dynamics in anthropogenic vs. natural animal hybrid zones. Restriction Associated DNA sequencing (RADseq) identified a large number of single nucleotide polymorphisms within C. jacchus and C. penicillata genomes. These preliminary data were used to measure intraspecific genomic diversity and interspecific divergence. In the future, RADseq will be used to study genus-wide diversity of Callithrix species, examine past and present marmoset demographic history, and applied to the evolutionary study of marmoset hybridization.
ContributorsMalukiewicz, Joanna (Author) / Stone, Anne C. (Thesis advisor) / Nash, Leanne (Committee member) / Rosenberg, Michael (Committee member) / Hedrick, Phil (Committee member) / Ruiz-Miranda, Carlo (Committee member) / Arizona State University (Publisher)
Created2013
Description
The Cape Floral Region (CFR) in southwestern South Africa is one of the most diverse in the world, with >9,000 plant species, 70% of which are endemic, in an area of only ~90,000 km2. Many have suggested that the CFR's heterogeneous environment, with respect to landscape gradients, vegetation, rainfall, elevation, and soil fertility, is responsible for the origin and maintenance of this biodiversity. While studies have struggled to link species diversity with these features, no study has attempted to associate patterns of gene flow with environmental data to determine how CFR biodiversity evolves on different scales. Here, a molecular population genetic data is presented for a widespread CFR plant, Leucadendron salignum, across 51 locations with 5-kb of chloroplast (cpDNA) and 6-kb of unlinked nuclear (nuDNA) DNA sequences in a dataset of 305 individuals. In the cpDNA dataset, significant genetic structure was found to vary on temporal and spatial scales, separating Western and Eastern Capes - the latter of which appears to be recently derived from the former - with the highest diversity in the heart of the CFR in a central region. A second study applied a statistical model using vegetation and soil composition and found fine-scale genetic divergence is better explained by this landscape resistance model than a geographic distance model. Finally, a third analysis contrasted cpDNA and nuDNA datasets, and revealed very little geographic structure in the latter, suggesting that seed and pollen dispersal can have different evolutionary genetic histories of gene flow on even small CFR scales. These three studies together caution that different genomic markers need to be considered when modeling the geographic and temporal origin of CFR groups. From a greater perspective, the results here are consistent with the hypothesis that landscape heterogeneity is one driving influence in limiting gene flow across the CFR that can lead to species diversity on fine-scales. Nonetheless, while this pattern may be true of the widespread L. salignum, the extension of this approach is now warranted for other CFR species with varying ranges and dispersal mechanisms to determine how universal these patterns of landscape genetic diversity are.
ContributorsTassone, Erica (Author) / Verrelli, Brian C (Thesis advisor) / Dowling, Thomas (Committee member) / Cartwright, Reed (Committee member) / Rosenberg, Michael S. (Committee member) / Wojciechowski, Martin (Committee member) / Arizona State University (Publisher)
Created2013
Description
Collaborative learning is a common teaching strategy in classrooms across age groups and content areas. It is important to measure and understand the cognitive process involved during collaboration to improve teaching methods involving interactive activities. This research attempted to answer the question: why do students learn more in collaborative settings? Using three measurement tools, 142 participants from seven different biology courses at a community college and at a university were tested before and after collaborating about the biological process of natural selection. Three factors were analyzed to measure their effect on learning at the individual level and the group level. The three factors were: difference in prior knowledge, sex and religious beliefs. Gender and religious beliefs both had a significant effect on post-test scores.
ContributorsTouchman, Stephanie (Author) / Baker, Dale (Thesis advisor) / Rosenberg, Michael (Committee member) / Ganesh, Tirupalavanam G. (Committee member) / Arizona State University (Publisher)
Created2012
Description
Complex dynamical systems consisting interacting dynamical units are ubiquitous in nature and society. Predicting and reconstructing nonlinear dynamics of units and the complex interacting networks among them serves the base for the understanding of a variety of collective dynamical phenomena. I present a general method to address the two outstanding problems as a whole based solely on time-series measurements. The method is implemented by incorporating compressive sensing approach that enables an accurate reconstruction of complex dynamical systems in terms of both nodal equations that determines the self-dynamics of units and detailed coupling patterns among units. The representative advantages of the approach are (i) the sparse data requirement which allows for a successful reconstruction from limited measurements, and (ii) general applicability to identical and nonidentical nodal dynamics, and to networks with arbitrary interacting structure, strength and sizes. Another two challenging problem of significant interest in nonlinear dynamics: (i) predicting catastrophes in nonlinear dynamical systems in advance of their occurrences and (ii) predicting the future state for time-varying nonlinear dynamical systems, can be formulated and solved in the framework of compressive sensing using only limited measurements. Once the network structure can be inferred, the dynamics behavior on them can be investigated, for example optimize information spreading dynamics, suppress cascading dynamics and traffic congestion, enhance synchronization, game dynamics, etc. The results can yield insights to control strategies design in the real-world social and natural systems. Since 2004, there has been a tremendous amount of interest in graphene. The most amazing feature of graphene is that there exists linear energy-momentum relationship when energy is low. The quasi-particles inside the system can be treated as chiral, massless Dirac fermions obeying relativistic quantum mechanics. Therefore, the graphene provides one perfect test bed to investigate relativistic quantum phenomena, such as relativistic quantum chaotic scattering and abnormal electron paths induced by klein tunneling. This phenomenon has profound implications to the development of graphene based devices that require stable electronic properties.
ContributorsYang, Rui (Author) / Lai, Ying-Cheng (Thesis advisor) / Duman, Tolga M. (Committee member) / Akis, Richard (Committee member) / Huang, Liang (Committee member) / Arizona State University (Publisher)
Created2012
Description
What can classical chaos do to quantum systems is a fundamental issue highly relevant to a number of branches in physics. The field of quantum chaos has been active for three decades, where the focus was on non-relativistic quantumsystems described by the Schr¨odinger equation. By developing an efficient method to solve the Dirac equation in the setting where relativistic particles can tunnel between two symmetric cavities through a potential barrier, chaotic cavities are found to suppress the spread in the tunneling rate. Tunneling rate for any given energy assumes a wide range that increases with the energy for integrable classical dynamics. However, for chaotic underlying dynamics, the spread is greatly reduced. A remarkable feature, which is a consequence of Klein tunneling, arise only in relativistc quantum systems that substantial tunneling exists even for particle energy approaching zero. Similar results are found in graphene tunneling devices, implying high relevance of relativistic quantum chaos to the development of such devices. Wave propagation through random media occurs in many physical systems, where interesting phenomena such as branched, fracal-like wave patterns can arise. The generic origin of these wave structures is currently a matter of active debate. It is of fundamental interest to develop a minimal, paradigmaticmodel that can generate robust branched wave structures. In so doing, a general observation in all situations where branched structures emerge is non-Gaussian statistics of wave intensity with an algebraic tail in the probability density function. Thus, a universal algebraic wave-intensity distribution becomes the criterion for the validity of any minimal model of branched wave patterns. Coexistence of competing species in spatially extended ecosystems is key to biodiversity in nature. Understanding the dynamical mechanisms of coexistence is a fundamental problem of continuous interest not only in evolutionary biology but also in nonlinear science. A continuous model is proposed for cyclically competing species and the effect of the interplay between the interaction range and mobility on coexistence is investigated. A transition from coexistence to extinction is uncovered with a non-monotonic behavior in the coexistence probability and switches between spiral and plane-wave patterns arise. Strong mobility can either promote or hamper coexistence, while absent in lattice-based models, can be explained in terms of nonlinear partial differential equations.
ContributorsNi, Xuan (Author) / Lai, Ying-Cheng (Thesis advisor) / Huang, Liang (Committee member) / Yu, Hongbin (Committee member) / Akis, Richard (Committee member) / Arizona State University (Publisher)
Created2012
Description
Plasmodium falciparum and Plasmodium vivax are two of the main propagators of human malaria. Both species contain the protein, Apical Membrane Antigen 1 (AMA-1), which is involved in the process of host cell invasion. However, the high degree of polymorphisms and antigenic diversity in this protein has prevented consistent single-vaccine success. Furthermore, the three main domains within AMA-1 (Domains I, II, and III), possess variable polymorphic features and levels of diversity. Overcoming this issue may require an understanding of the type of selection acting on AMA-1 in P. falciparum and P. vivax. Therefore, this investigation aimed to determine the type of selection acting on the whole AMA-1 coding sequence and in each domain for P. falciparum and P. vivax. Population structure was investigated on a global scale and among individual countries. AMA-1 sequences were obtained from the National Center for Biotechnology. For P. falciparum, 649 complete and 382 partial sequences were obtained. For P. vivax, 395 sequences were obtained (370 partial). The AMA-1 gene in P. falciparum was found to possess high nonsynonymous polymorphisms and disproportionately low synonymous polymorphisms. Domain I was found to have the most diverse region with consistently high nonsynonymous substitutions across all countries. Large, positive, and significant Z-test scores indicated the presence of positive selection while FST and NST values showed low genetic differentiation across populations. Data trends for all analyses were relatively consistent for the global and country-based analyses. The only country to deviate was Venezuela, which was the only South American country analyzed. Network analyses did not show distinguishable groupings. For P. falciparum, it was concluded that positive diversifying selection was acting on the AMA-1 gene, particularly in Domain I. In AMA-1 of P. vivax, nonsynonymous and synonymous polymorphisms were relatively equal across all analyses. FST and NST values were high, indicating that countries were genetically distinct populations. Network analyses did not show distinguishable grouping; however, the data was limited to small sample sizes. From the data, it was concluded that AMA-1 in P. vivax was evolving neutrally, where selective pressures did not strongly encourage positive or purifying selection specifically. In addition, different AMA-1 P. vivax strains were genetically distinct and this genetic identity correlated with geographic region. Therefore, AMA-1 strains in P. falciparum and P. vivax not only evolve differently and undergo different form of selection, but they also require different vaccine development strategies. A combination of strain-specific vaccines along with preventative measures on an environmental level will likely be more effective than trying to achieve a single, comprehensive vaccine.
ContributorsEspinas, Jaye Frances Palma (Author) / Escalante, Ananias (Thesis director) / Taylor, Jay (Committee member) / Rosenberg, Michael (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Triops (Branchiopoda: Notostraca) and Streptocephalus (Branchiopoda: Anostraca) are two crustaceans which cohabitate in ephemeral freshwater pools. They both lay desiccation resistant eggs that disperse passively to new hydrologically isolated environments. The extent of genetic distance among regions and populations is of perennial interest in animals that live in such isolated habitats. Populations in six natural ephemeral pool habitats located in two different regions of the Sonoran Desert and a transition area between the Sonoran and Chihuahuan Deserts were sampled. Sequences from Genbank were used for reference points in the determination of species as well as to further identify regional genetic distance within species. This study estimated the amount of within and between genetic distance of individuals from each region and population through the use of a neutral marker, cytochrome oxidase I (COI). We concluded that, although the method of passive dispersal may differ between the two genera, the differences do not results in different patterns of genetic distances between regions and populations. Furthermore, we only found the putative species, Triops longicaudatus "short", with enough distinct speciation. Although Triops longicaudatus "long" and Triops newberryi may be in the early stages of speciation, this study does not find enough support to conclude that they have separated.
ContributorsMurphy Jr., Patrick Joseph (Author) / Rutowski, Ronald (Thesis director) / Cartwright, Reed (Committee member) / Lessios, Nikos (Committee member) / School of Life Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
The evolution of blindness in cave animals has been heavily studied; however, little research has been done on the interaction of migration and drift on the development of blindness in these populations. In this study, a model is used to compare the effect that genetic drift has on the fixation of a blindness allele for varying amounts of migration and selection. For populations where the initial frequency is quite low, genetic drift plays a much larger role in the fixation of blindness than populations where the initial frequency is high. In populations where the initial frequency is high, genetic drift plays almost no role in fixation. Our results suggest that migration plays a greater role in the fate of the blindness allele than selection.
ContributorsMerry, Alexandra Leigh (Author) / Cartwright, Reed (Thesis director) / Rosenberg, Michael (Committee member) / Schwartz, Rachel (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05