Spontaneous Emergence of Hierarchy in Biological Systems

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dc.contributor.advisorDeem, Michael W.en_US
dc.creatorHe, Jiankuien_US
dc.date.accessioned2013-03-08T00:34:17Zen_US
dc.date.available2013-03-08T00:34:17Zen_US
dc.date.issued2011en_US
dc.description.abstractHierarchy is widely observed in biological systems. In this thesis, evidence from nature is presented to show that protein interactions have became increasingly modular as evolution has proceeded over the last four billion years. The evolution of animal body plan development is considered. Results show the genes that determine the phylum and superphylum characters evolve slowly, while those genes that determine classes, families, and speciation evolve more rapidly. This result furnishes support to the hypothesis that the hierarchical structure of developmental regulatory networks provides an organizing structure that guides the evolution of aspects of the body plan. Next, the world trade network is treated as an evolving system. The theory of modularity predicts that the trade network is more sensitive to recessionary shocks and recovers more slowly from them now than it did 40 years ago, due to structural changes in the world trade network induced by globalization. Economic data show that recession-induced change to the world trade network leads to an increased hierarchical structure of the global trade network for a few years after the recession. In the study of influenza virus evolution, an approach for early detection of new dominant strains is presented. This method is shown to be able to identify a cluster around an incipient dominant strain before it becomes dominant. Recently, CRISPR has been suggested to provide adaptive immune response to bacteria. A population dynamics model is proposed that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is less diversifed. Finally, the creation of diversity of antibody repertoire is investigated. It is commonly believed that a heavy chain is generated by randomly combining V, D and J gene segments. However, using high throughput sequence data in this study, the naive VDJ repertoire is shown to be strongly correlated between individuals, which suggest VDJ recombination involves regulated mechanisms.en_US
dc.format.extent214 p.en_US
dc.format.mimetypeapplication/pdfen_US
dc.identifier.callnoTHESIS PHYS. 2011 HEen_US
dc.identifier.citationHe, Jiankui. "Spontaneous Emergence of Hierarchy in Biological Systems." (2011) Diss., Rice University. <a href="https://hdl.handle.net/1911/70257">https://hdl.handle.net/1911/70257</a>.en_US
dc.identifier.digitalHeJen_US
dc.identifier.urihttps://hdl.handle.net/1911/70257en_US
dc.language.isoengen_US
dc.rightsCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.subjectBiological sciencesen_US
dc.subjectInfluenzaen_US
dc.subjectAntibodiesen_US
dc.subjectVDJ recombinationen_US
dc.subjectEvolution & developmenten_US
dc.subjectBiophysicsen_US
dc.titleSpontaneous Emergence of Hierarchy in Biological Systemsen_US
dc.typeThesisen_US
dc.type.materialTexten_US
thesis.degree.departmentPhysicsen_US
thesis.degree.disciplineNatural Sciencesen_US
thesis.degree.grantorRice Universityen_US
thesis.degree.levelDoctoralen_US
thesis.degree.nameDoctor of Philosophyen_US
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