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Virology By The Numbers: A Quantitative Exploration of Viral Energetics, Genomics, and Ecology

Citation

Mahmoudabadi, Gita (2018) Virology By The Numbers: A Quantitative Exploration of Viral Energetics, Genomics, and Ecology. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9Q81B91. https://resolver.caltech.edu/CaltechTHESIS:04172018-174233725

Abstract

Over the past couple of decades, technological advancements in sequencing and imaging have unequivocally proven that the world of viruses is far bigger and more consequential than previously imagined. There are 1031 viruses estimated to inhabit our planet, outnumbering even bacteria. Despite their astronomical numbers and staggering sequence diversity, environmental viruses are poorly characterized. In this thesis we will demonstrate our three-pronged exploration of viruses through the lenses of energetics (Chapters 2 and 3), genomics (Chapter 4) and ecology (Chapter 5). We will first focus on one of the defining features of viruses, namely their reliance on their host for energy, and demonstrate the energetic cost of building a virus and mounting an infection. In our second study, we present one of the largest surveys of complete viral genomes, providing a comprehensive and quantitative snapshot of viral genomic trends for thousands of viruses. In our third study, we shift our focus towards ecological questions surrounding the large number of commensal phages inhabiting the human body. We discovered that phage community composition could serve as a fingerprint, or a "phageprint" – highly personal and stable over time. To our knowledge, this study is one of the largest studies of human phages and the first to demonstrate the feasibility of human identification based on phage sequences.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Virus; Phage; Bacteriophage; Viral Genomics; Viral Energetics; Viral Ecology; Human Virome; Oral Virome; Oral Phageome
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Bioengineering
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Phillips, Robert B.
Thesis Committee:
  • Phillips, Robert B. (chair)
  • Leadbetter, Jared R.
  • Goentoro, Lea A.
  • Orphan, Victoria J.
  • Gelbart, William
Defense Date:20 November 2017
Funders:
Funding AgencyGrant Number
John Templeton Foundation51250
National Institutes of Health (NIH)RFA-GM-17-002
National Science Foundation Graduate Research FellowshipDGE‐1144469
National Institutes of Health (NIH)R01- GM098465
National Science FoundationNSF PHY11-25915
Record Number:CaltechTHESIS:04172018-174233725
Persistent URL:https://resolver.caltech.edu/CaltechTHESIS:04172018-174233725
DOI:10.7907/Z9Q81B91
Related URLs:
URLURL TypeDescription
https://doi.org/10.1073/pnas.1701670114DOIChapters 2 and 3
https://doi.org/10.7554/eLife.31955DOIChapter 4
ORCID:
AuthorORCID
Mahmoudabadi, Gita0000-0002-8812-7246
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:10812
Collection:CaltechTHESIS
Deposited By: Gita Mahmoudabadi
Deposited On:26 Apr 2018 15:54
Last Modified:04 Oct 2019 00:20

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