subject:(Structure Evolution)

University of Guelph

1. Landy, Christian Peter. An Examination of the Effects of Age-Structure on Mutation Rate Evolution in a Changing Environment by Computer Simulation.

Degree: MS, Department of Integrative Biology, 2015, University of Guelph

URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8863

► A life-history involves the scheduling of events in an individual’s life, such as growth, reproduction, and survivorship. This thesis seeks to focus on the possibility… (more)

Subjects/Keywords: age-structure; mutation rate; evolution

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APA (6^th Edition):

Landy, C. P. (2015). An Examination of the Effects of Age-Structure on Mutation Rate Evolution in a Changing Environment by Computer Simulation. (Masters Thesis). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8863

Chicago Manual of Style (16^th Edition):

Landy, Christian Peter. “An Examination of the Effects of Age-Structure on Mutation Rate Evolution in a Changing Environment by Computer Simulation.” 2015. Masters Thesis, University of Guelph. Accessed April 14, 2021. https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8863.

MLA Handbook (7^th Edition):

Landy, Christian Peter. “An Examination of the Effects of Age-Structure on Mutation Rate Evolution in a Changing Environment by Computer Simulation.” 2015. Web. 14 Apr 2021.

Vancouver:

Landy CP. An Examination of the Effects of Age-Structure on Mutation Rate Evolution in a Changing Environment by Computer Simulation. [Internet] [Masters thesis]. University of Guelph; 2015. [cited 2021 Apr 14]. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8863.

Council of Science Editors:

Landy CP. An Examination of the Effects of Age-Structure on Mutation Rate Evolution in a Changing Environment by Computer Simulation. [Masters Thesis]. University of Guelph; 2015. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8863

University of California – Santa Cruz

2. Fang, Jerome Joseph. The Link between Galaxy Structure and Star Formation across Cosmic Time.

Degree: Astronomy & Astrophysics, 2015, University of California – Santa Cruz

URL: http://www.escholarship.org/uc/item/6xj9x3jx

► The processes that fuel and quench star formation in galaxies are expected to leave imprints on their structure. Moreover, these imprints can serve as signposts… (more)

▼ The processes that fuel and quench star formation in galaxies are expected to leave imprints on their structure. Moreover, these imprints can serve as signposts to identify galaxies at various stages of their evolution. In this dissertation, we describe our efforts to characterize changes in galaxy structure (1) as star formation is going out, (2) after star formation has ostensibly quenched, and (3) during active star formation, with the goal of elucidating the relevant processes that regulate star formation in each case.In Chapter 2, we use a local (z~0) sample of galaxies drawn from the Sloan Digital Sky Survey (SDSS) to investigate the first two cases. We find that, as galaxies quench, their outer stellar mass density profiles remain essentially constant. However, their inner stellar mass density (within 1 kpc) increases, even while galaxies are still star-forming, until it reaches a mass-dependent threshold, at which point quenching can occur. The existence of this threshold indicates that quenching is connected with processes that grow bulges. In Chapter 3, we then study the morphologies and color profiles of 19 z~0 early-type galaxies located in the green valley. Combining high-resolution Hubble ultraviolet images with SDSS optical photometry, we find that these objects harbor low-level star formation that is clearly detectable in the ultraviolet. Moreover, the recently formed stars are distributed in symmetric rings that often span the entire optical extent of the galaxy. The presence of an old underlying population in their outer parts suggests that star formation in these galaxies is either gradually fading out or possibly rejuvenated by smooth accretion from the intergalactic medium. Such galaxies comprise ~13% of green valley galaxies of similar mass and color, and they may linger in the green valley for several Gyr. Finally, in Chapter 4, we focus on the evolution of star-forming galaxies since z=2.5, leveraging the rich multi-wavelength datasets produced by the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey (CANDELS). By finely dissecting our sample into narrow mass and redshift slices, we are able to uncover several striking trends, including evidence for mass-dependent evolution in terms of disk formation and the buildup of metals and dust, i.e., massive galaxies are more evolved at all epochs. However, at fixed mass, no correlation between structure and specific star-formation rate is seen for galaxies on the star-forming "main sequence." This behavior persists at all redshifts, despite the considerable diversity in size and shape among star-forming galaxies. This suggests that, on the main sequence, star formation is regulated primarily by external factors, e.g., halo accretion rate, rather than the internal structure of the galaxy.

Subjects/Keywords: Astrophysics; Astronomy; Galaxies; Galaxy evolution; Galaxy structure

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Fang, J. J. (2015). The Link between Galaxy Structure and Star Formation across Cosmic Time. (Thesis). University of California – Santa Cruz. Retrieved from http://www.escholarship.org/uc/item/6xj9x3jx

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Fang, Jerome Joseph. “The Link between Galaxy Structure and Star Formation across Cosmic Time.” 2015. Thesis, University of California – Santa Cruz. Accessed April 14, 2021. http://www.escholarship.org/uc/item/6xj9x3jx.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Fang, Jerome Joseph. “The Link between Galaxy Structure and Star Formation across Cosmic Time.” 2015. Web. 14 Apr 2021.

Vancouver:

Fang JJ. The Link between Galaxy Structure and Star Formation across Cosmic Time. [Internet] [Thesis]. University of California – Santa Cruz; 2015. [cited 2021 Apr 14]. Available from: http://www.escholarship.org/uc/item/6xj9x3jx.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Fang JJ. The Link between Galaxy Structure and Star Formation across Cosmic Time. [Thesis]. University of California – Santa Cruz; 2015. Available from: http://www.escholarship.org/uc/item/6xj9x3jx

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Oulu

3. Herrera Endoqui, M. (Martín). Study of the morphological features in the Spitzer Survey of Stellar Structure in Galaxies (S⁴G).

Degree: 2016, University of Oulu

URL: http://urn.fi/urn:isbn:9789526213231

► Abstract Conspicuous morphological features such as rings, ringlenses, lenses, barlenses, and spiral arms are observed in many nearby disk galaxies. These features are believed to… (more)

▼ Abstract Conspicuous morphological features such as rings, ringlenses, lenses, barlenses, and spiral arms are observed in many nearby disk galaxies. These features are believed to form due to the so-called secular evolution after the galaxies were formed, which means that their disks evolve in a more passive fashion and in longer timescales, compared to their formation processes. This slow evolution of disks is due to the effect of non-axisymmetric potentials, among which, a bar potential is perhaps the most effective of all. Strong rotating bars redistribute angular momentum and material through the disks of galaxies very effciently, and produce resonances. At these resonances the material is trapped and starts forming stars, creating beautiful rings. However, rings are not the only structure observed in disk galaxies. There are also spiral arms that, might or might not be created by bars. Other type of structures are lenses, which in images appear as flat light distributions with sharp edges, and ringlenses, whose appearance is intermediate between those of rings and lenses. Also, there are barlenses, which are conspicuous lens-like structures embedded in bars, and have been suggested to be the more face-on counterparts of Boxy/Peanut/X-shaped bulges. The study of the physical properties of all these structures provides a tool to investigate the mechanisms that create them and hence, to determine which are the processes that drive the slow evolution of galaxies. In this thesis I study the morphological structures using mainly data from the Spitzer Survey of Stellar Structure in Galaxies (S⁴G), by means of their sizes, orientations, shapes and colors. The S⁴G contains images of ~ 2500 nearby galaxies of all Hubble types at 3.6 and 4.5 μm, allowing a dust free view of the old stellar population which is subject of the secular evolution. Among the results presented in this thesis and the respective companion papers are the following. A catalog that contains the sizes, ellipticities and position angles of the morphological features in the S⁴G was created. This catalog also includes the measurements of the pitch angles of spiral arms. There is a corroboration of previous results showing that different types of morphological features appear in galaxies with different Hubble stages and bar families, and a confirmation of the resonant nature of rings but also of a high fraction of lenses and ringlenses. There is also an observation indicating that low mass galaxies lack nuclear structures such as nuclear rings due to the lack of inner Lindblad resonances caused by their low central mass concentrations. Observational evidence is presented indicating that a fraction of inner lenses in unbarred galaxies might be former barlenses of which the "thin bar" has probably dissolved or it is too faint to be detected. The sizes of barlenses show a tight linear correlation with those of bars, being the size of the barlens typically half the size of the bar. The study of the optical colors of barlenses reveals their similarity with… Advisors/Committee Members: Laurikainen, E. (Eija), Salo, H. (Heikki).

Subjects/Keywords: galaxies: morphology; galaxies: secular evolution; galaxies: structure

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Herrera Endoqui, M. (. (2016). Study of the morphological features in the Spitzer Survey of Stellar Structure in Galaxies (S⁴G). (Doctoral Dissertation). University of Oulu. Retrieved from http://urn.fi/urn:isbn:9789526213231

Chicago Manual of Style (16^th Edition):

Herrera Endoqui, M (Martín). “Study of the morphological features in the Spitzer Survey of Stellar Structure in Galaxies (S⁴G).” 2016. Doctoral Dissertation, University of Oulu. Accessed April 14, 2021. http://urn.fi/urn:isbn:9789526213231.

MLA Handbook (7^th Edition):

Herrera Endoqui, M (Martín). “Study of the morphological features in the Spitzer Survey of Stellar Structure in Galaxies (S⁴G).” 2016. Web. 14 Apr 2021.

Vancouver:

Herrera Endoqui M(. Study of the morphological features in the Spitzer Survey of Stellar Structure in Galaxies (S⁴G). [Internet] [Doctoral dissertation]. University of Oulu; 2016. [cited 2021 Apr 14]. Available from: http://urn.fi/urn:isbn:9789526213231.

Council of Science Editors:

Herrera Endoqui M(. Study of the morphological features in the Spitzer Survey of Stellar Structure in Galaxies (S⁴G). [Doctoral Dissertation]. University of Oulu; 2016. Available from: http://urn.fi/urn:isbn:9789526213231

University of Edinburgh

4. Doney, Tom. The Proximate-Ultimate Distinction and its Relation to the Emergence of Linguistic Structure.

Degree: 2014, University of Edinburgh

URL: http://hdl.handle.net/1842/8601

► Ernst Mayr's Proximate-Ultimate distinction has come under scrutiny in recent years for its supposed failure to account for reciprocal evolutionary processes such as niche-construction and… (more)

Subjects/Keywords: Proximate-Ultimate; Iterated Learning; Linguistic Structure; Evolution

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APA (6^th Edition):

Doney, T. (2014). The Proximate-Ultimate Distinction and its Relation to the Emergence of Linguistic Structure. (Thesis). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/8601

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Doney, Tom. “The Proximate-Ultimate Distinction and its Relation to the Emergence of Linguistic Structure.” 2014. Thesis, University of Edinburgh. Accessed April 14, 2021. http://hdl.handle.net/1842/8601.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Doney, Tom. “The Proximate-Ultimate Distinction and its Relation to the Emergence of Linguistic Structure.” 2014. Web. 14 Apr 2021.

Vancouver:

Doney T. The Proximate-Ultimate Distinction and its Relation to the Emergence of Linguistic Structure. [Internet] [Thesis]. University of Edinburgh; 2014. [cited 2021 Apr 14]. Available from: http://hdl.handle.net/1842/8601.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Doney T. The Proximate-Ultimate Distinction and its Relation to the Emergence of Linguistic Structure. [Thesis]. University of Edinburgh; 2014. Available from: http://hdl.handle.net/1842/8601

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

5. Roy, Sunando. IDENTIFYING STRUCTURAL CHANGES IN EVOLVING VIRAL PROTEINS.

Degree: 2011, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/12277

► Proteins are macromolecules that facilitate the basic biochemical functions of a cell. Proteins help organisms adapt to their new environment by changing their function, which… (more)

Subjects/Keywords: Protein; Structure; Evolution; Adaptation; Viruses; Multivariate Statistics

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APA (6^th Edition):

Roy, S. (2011). IDENTIFYING STRUCTURAL CHANGES IN EVOLVING VIRAL PROTEINS. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/12277

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Roy, Sunando. “IDENTIFYING STRUCTURAL CHANGES IN EVOLVING VIRAL PROTEINS.” 2011. Thesis, Penn State University. Accessed April 14, 2021. https://submit-etda.libraries.psu.edu/catalog/12277.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Roy, Sunando. “IDENTIFYING STRUCTURAL CHANGES IN EVOLVING VIRAL PROTEINS.” 2011. Web. 14 Apr 2021.

Vancouver:

Roy S. IDENTIFYING STRUCTURAL CHANGES IN EVOLVING VIRAL PROTEINS. [Internet] [Thesis]. Penn State University; 2011. [cited 2021 Apr 14]. Available from: https://submit-etda.libraries.psu.edu/catalog/12277.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Roy S. IDENTIFYING STRUCTURAL CHANGES IN EVOLVING VIRAL PROTEINS. [Thesis]. Penn State University; 2011. Available from: https://submit-etda.libraries.psu.edu/catalog/12277

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Boston College

6. Bayegan, Amir Hossein. Novel algorithms to analyze RNA secondary structure evolution and folding kinetics.

Degree: PhD, Biology, 2018, Boston College

URL: http://dlib.bc.edu/islandora/object/bc-ir:108256

► RNA molecules play important roles in living organisms, such as protein translation, gene regulation, and RNA processing. It is known that RNA secondary structure is… (more)

Subjects/Keywords: alignment; evolution; folding kinetics; RNA; secondary structure

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APA (6^th Edition):

Bayegan, A. H. (2018). Novel algorithms to analyze RNA secondary structure evolution and folding kinetics. (Doctoral Dissertation). Boston College. Retrieved from http://dlib.bc.edu/islandora/object/bc-ir:108256

Chicago Manual of Style (16^th Edition):

Bayegan, Amir Hossein. “Novel algorithms to analyze RNA secondary structure evolution and folding kinetics.” 2018. Doctoral Dissertation, Boston College. Accessed April 14, 2021. http://dlib.bc.edu/islandora/object/bc-ir:108256.

MLA Handbook (7^th Edition):

Bayegan, Amir Hossein. “Novel algorithms to analyze RNA secondary structure evolution and folding kinetics.” 2018. Web. 14 Apr 2021.

Vancouver:

Bayegan AH. Novel algorithms to analyze RNA secondary structure evolution and folding kinetics. [Internet] [Doctoral dissertation]. Boston College; 2018. [cited 2021 Apr 14]. Available from: http://dlib.bc.edu/islandora/object/bc-ir:108256.

Council of Science Editors:

Bayegan AH. Novel algorithms to analyze RNA secondary structure evolution and folding kinetics. [Doctoral Dissertation]. Boston College; 2018. Available from: http://dlib.bc.edu/islandora/object/bc-ir:108256

Clemson University

7. Tannous, Jaad Antoun. The Effect of Rotation on Stellar Structure and Evolution.

Degree: MS, Physics and Astronomy, 2020, Clemson University

URL: https://tigerprints.clemson.edu/all_theses/3267

► In this thesis, we investigate the eects of rotation on the evolution of stars in the mass range of 2-15 M assuming solar-like initial… (more)

Subjects/Keywords: Rotation; s-process; Stellar Evolution; Stellar Structure

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Tannous, J. A. (2020). The Effect of Rotation on Stellar Structure and Evolution. (Masters Thesis). Clemson University. Retrieved from https://tigerprints.clemson.edu/all_theses/3267

Chicago Manual of Style (16^th Edition):

Tannous, Jaad Antoun. “The Effect of Rotation on Stellar Structure and Evolution.” 2020. Masters Thesis, Clemson University. Accessed April 14, 2021. https://tigerprints.clemson.edu/all_theses/3267.

MLA Handbook (7^th Edition):

Tannous, Jaad Antoun. “The Effect of Rotation on Stellar Structure and Evolution.” 2020. Web. 14 Apr 2021.

Vancouver:

Tannous JA. The Effect of Rotation on Stellar Structure and Evolution. [Internet] [Masters thesis]. Clemson University; 2020. [cited 2021 Apr 14]. Available from: https://tigerprints.clemson.edu/all_theses/3267.

Council of Science Editors:

Tannous JA. The Effect of Rotation on Stellar Structure and Evolution. [Masters Thesis]. Clemson University; 2020. Available from: https://tigerprints.clemson.edu/all_theses/3267

University of Illinois – Urbana-Champaign

8. Nasir, Arshan. Origin of viruses revealed by the genomic study of protein domain structures.

Degree: MS, 4026, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/34445

► The discovery of giant viruses with complex proteomes, remnants of translation machinery and virus-specific parasites have raised important questions about their origin. Evidence advocates for… (more)

Subjects/Keywords: Mimivurs; phylogenomics, protein domain, structure, evolution

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Nasir, A. (2012). Origin of viruses revealed by the genomic study of protein domain structures. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/34445

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Nasir, Arshan. “Origin of viruses revealed by the genomic study of protein domain structures.” 2012. Thesis, University of Illinois – Urbana-Champaign. Accessed April 14, 2021. http://hdl.handle.net/2142/34445.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Nasir, Arshan. “Origin of viruses revealed by the genomic study of protein domain structures.” 2012. Web. 14 Apr 2021.

Vancouver:

Nasir A. Origin of viruses revealed by the genomic study of protein domain structures. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Apr 14]. Available from: http://hdl.handle.net/2142/34445.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Nasir A. Origin of viruses revealed by the genomic study of protein domain structures. [Thesis]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/34445

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Waterloo

9. Adams, Jeremy Bruce. Structure-aided detection of functional innovation in protein phylogenies.

Degree: 2016, University of Waterloo

URL: http://hdl.handle.net/10012/10155

► Detection of positive selection in proteins is both a common and powerful approach for investigating the molecular basis of adaptation. In this thesis, I explore… (more)

▼ Detection of positive selection in proteins is both a common and powerful approach for investigating the molecular basis of adaptation. In this thesis, I explore the use of protein three- dimensional (3D) structure to assist in prediction of historical adaptations in proteins. Building on a method first introduced by Wagner (Genetics, 2007, 176: 2451–2463), I present a novel framework called Adaptation3D for detecting positive selection by integrating sequence, structural, and phylogenetic information for protein families. Adaptation3D identifies possible instances of positive selection by reconstructing historical substitutions along a phylogenetic tree and detecting branch-specific cases of spatially clustered substitution. The Adaptation3D method was capable of identifying previously characterized cases of positive selection in proteins, as demonstrated through an analysis of the pathogenesis-related protein 5 (PR-5) phylogeny. It was then applied on a phylogenomic scale in an analysis of thousands of vertebrate protein phylogenetic trees from the Selectome database. Adaptation3D’s reconstruction of historical mutations in vertebrate protein families revealed several evolutionary phenomena. First, clustered mutation is widespread and occurs significantly more often than that expected by chance. Second, numerous top-scoring cases of predicted positive selection are consistent with existing literature on vertebrate protein adaptation. Third, in the vertebrate lineage, clustered mutation has occurred disproportionately in proteins from certain families and functional categories such as zinc-finger transcription factors (TFs). Finally, by separating paralogous and orthologous lineages, it was found that TF paralogs display significantly elevated levels of clustered mutation in their DNA-binding sites compared to orthologs, consistent with historical DNA-binding specificity divergence in newly duplicated TFs. Ultimately, Adaptation3D is a powerful framework for reconstructing structural patterns of historical mutation, and provides important insights into the nature of protein adaptation.

Subjects/Keywords: bioinformatics; molecular evolution; protein structure; phylogenetics

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APA (6^th Edition):

Adams, J. B. (2016). Structure-aided detection of functional innovation in protein phylogenies. (Thesis). University of Waterloo. Retrieved from http://hdl.handle.net/10012/10155

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Adams, Jeremy Bruce. “Structure-aided detection of functional innovation in protein phylogenies.” 2016. Thesis, University of Waterloo. Accessed April 14, 2021. http://hdl.handle.net/10012/10155.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Adams, Jeremy Bruce. “Structure-aided detection of functional innovation in protein phylogenies.” 2016. Web. 14 Apr 2021.

Vancouver:

Adams JB. Structure-aided detection of functional innovation in protein phylogenies. [Internet] [Thesis]. University of Waterloo; 2016. [cited 2021 Apr 14]. Available from: http://hdl.handle.net/10012/10155.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Adams JB. Structure-aided detection of functional innovation in protein phylogenies. [Thesis]. University of Waterloo; 2016. Available from: http://hdl.handle.net/10012/10155

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Massey University

10. Saraswat, Mayank. In search of novel folds : protein evolution via non-homologous recombination.

Degree: PhD, Biochemistry, 2014, Massey University

URL: http://hdl.handle.net/10179/5979

► The emergence of proteins from short peptides or subdomains, facilitated by the duplication and fusion of the minigenes encoding them, is believed to have played… (more)

▼ The emergence of proteins from short peptides or subdomains, facilitated by the duplication and fusion of the minigenes encoding them, is believed to have played a role in the origin of life. In this study it was hypothesised that new domains or basic elements of protein structure, may result from nonhomologous recombination of the genes coding for smaller subdomains. The hypothesis was tested by randomly recombining two distantly related (βα)8-barrel proteins: Escherichia coli phosphoribosylanthranilate isomerase (PRAI), and β subunit of voltage dependent K+ channels (Kvβ2) from Rattus norvegicus. The aim was to identify new, folded structures, which may or may not be (βα)8-barrels. Incremental truncation (ITCHY), a method for fragmenting and randomly recombining genes, was used to mimic in vivo non-homologous recombination and to create a library of chimeric variants. Clones from the library were selected for right reading frame and solubility (foldability) of the recombined chimeras, using the pSALect selection system. Out of the six clones identified as soluble by pSALect, only one (P25K86) was found to be actually soluble. The protein, P25K86, was found to form oligomers and on treatment with a reducing agent, β-mercaptoethanol the multimeric state disappeared. The protein has three cysteines and one of the cysteines (Cys56) was found to mediate in the bond formation, thus giving a dimeric state. An engineered version of P25K86 that has the Cys56 replaced by serine was expressed as a monomer and additionally it was found to be ! iv! more stable. As the pSALect folding selection system reported false positives, i.e. only one of the six chimeras was actually soluble, it was concluded that the in vivo solubility selection system was leaky. A series of experiments were conducted so as to improve pSALect that led to the creation of pFoldM – a more stringent selection system, discussed in chapter 4. Comparing the newer improved version with the old, two more interesting chimeras were discovered. A total of 240,000 non-homologous recombination events were created in vitro and three soluble chimeras (evolutionary solutions) were found. Data from circular dichroism spectroscopy (CD) combined with heteronuclear single quantum coherence (HSQC) spectra suggest that the proteins, P24K89 and P25K86, are present in a molten globule state. ITCHY, as a means of mimicking the subdomain assembly model, was applied in vitro. The discovery of two interesting chimeras (P25K86 and P24K89) using highthroughput engineering experiments widens the possibilities of exploring the protein structure space, and perhaps offers close encounters with these never born proteins that may be trapped in an ensemble of fluctuating (structured and unstructured) states.

Subjects/Keywords: Protein evolution; Protein structure; Genetic recombination

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Saraswat, M. (2014). In search of novel folds : protein evolution via non-homologous recombination. (Doctoral Dissertation). Massey University. Retrieved from http://hdl.handle.net/10179/5979

Chicago Manual of Style (16^th Edition):

Saraswat, Mayank. “In search of novel folds : protein evolution via non-homologous recombination.” 2014. Doctoral Dissertation, Massey University. Accessed April 14, 2021. http://hdl.handle.net/10179/5979.

MLA Handbook (7^th Edition):

Saraswat, Mayank. “In search of novel folds : protein evolution via non-homologous recombination.” 2014. Web. 14 Apr 2021.

Vancouver:

Saraswat M. In search of novel folds : protein evolution via non-homologous recombination. [Internet] [Doctoral dissertation]. Massey University; 2014. [cited 2021 Apr 14]. Available from: http://hdl.handle.net/10179/5979.

Council of Science Editors:

Saraswat M. In search of novel folds : protein evolution via non-homologous recombination. [Doctoral Dissertation]. Massey University; 2014. Available from: http://hdl.handle.net/10179/5979

University of Cambridge

11. Perron, Umberto. The influence of structural constraints on protein evolution.

Degree: PhD, 2020, University of Cambridge

URL: https://doi.org/10.17863/CAM.58154 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.818131

► Few mathematical models of sequence evolution incorporate parameters describing protein structure, despite its high conservation, essential functional role and the increasing availability of structural data.… (more)

▼ Few mathematical models of sequence evolution incorporate parameters describing protein structure, despite its high conservation, essential functional role and the increasing availability of structural data. The primary goal of my PhD project was to create a structurally aware amino acid substitution model in which proteins are represented using an expanded alphabet that relays both amino acid identity and structural information. Each character in this alphabet specifies an amino acid as well as information about the rotamer configuration of its side chain: the discrete geometric pattern of permitted side chain atomic positions, as defined by the dihedral angles between covalently linked atoms. I generated a 55-state “Dayhoff-like” substitution model (RAM55) by assigning rotamer states in 79,558 structures (∼50%of all PDBe entries) and identifying substitutions between closely related sequences. RAM55’s rotamer state exchange patterns clearly show that the evolutionary properties of amino acids depend strongly upon side chain geometry. Exploiting knowledge of these patterns assists in phylogenetic analyses: I show that RAM55 performs as well as, or better than, traditional 20-state models on simulated and empirical data for divergence time estimation, tree inference, side chain configuration prediction and ancestral sequence reconstruction. Further, encoding observed characters in an alignment as ambiguous representations of characters in a larger state-space allows the application of RAM55 to 20-state amino acid data for which structures are not known. Adding structural information to as few as 12.5% of the sequences in an amino acid alignment results in excellent ancestral reconstruction performance compared to a benchmark that considers the full rotamer state information. This strategy significantly expands the applicability of RAM55 to real-world scenarios where structure might only be available for some of the sequences of interest. Thus, not only is rotamer configuration a valuable source of information for phylo-genetic studies, but modelling the concomitant evolution of sequence and structure may have important implications for understanding protein folding and function.

Subjects/Keywords: protein; evolution; protein structure; phylogenetics; modelling

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Perron, U. (2020). The influence of structural constraints on protein evolution. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.58154 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.818131

Chicago Manual of Style (16^th Edition):

Perron, Umberto. “The influence of structural constraints on protein evolution.” 2020. Doctoral Dissertation, University of Cambridge. Accessed April 14, 2021. https://doi.org/10.17863/CAM.58154 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.818131.

MLA Handbook (7^th Edition):

Perron, Umberto. “The influence of structural constraints on protein evolution.” 2020. Web. 14 Apr 2021.

Vancouver:

Perron U. The influence of structural constraints on protein evolution. [Internet] [Doctoral dissertation]. University of Cambridge; 2020. [cited 2021 Apr 14]. Available from: https://doi.org/10.17863/CAM.58154 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.818131.

Council of Science Editors:

Perron U. The influence of structural constraints on protein evolution. [Doctoral Dissertation]. University of Cambridge; 2020. Available from: https://doi.org/10.17863/CAM.58154 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.818131

University of Cambridge

12. Perron, Umberto. The Influence of Structural Constraints on Protein Evolution.

Degree: PhD, 2020, University of Cambridge

URL: https://www.repository.cam.ac.uk/handle/1810/311064

► Few mathematical models of sequence evolution incorporate parameters describingprotein structure, despite its high conservation, essential functional role and the increasingavailability of structural data. The primary… (more)

▼ Few mathematical models of sequence evolution incorporate parameters describingprotein structure, despite its high conservation, essential functional role and the increasingavailability of structural data. The primary goal of my PhD project was to create astructurally aware amino acid substitution model in which proteins are represented usingan expanded alphabet that relays both amino acid identity and structural information.Each character in this alphabet specifies an amino acid as well as information aboutthe rotamer configuration of its side chain: the discrete geometric pattern of permittedside chain atomic positions, as defined by the dihedral angles between covalently linkedatoms. I generated a 55-state “Dayhoff-like” substitution model (RAM55) by assigningrotamer states in 79,558 structures (∼50%of all PDBe entries) and identifying substitu-tions between closely related sequences. RAM55’s rotamer state exchange patterns clearlyshow that the evolutionary properties of amino acids depend strongly upon side chain ge-ometry. Exploiting knowledge of these patterns assists in phylogenetic analyses: I showthat RAM55 performs as well as or better than traditional 20-state models on simulatedand empirical data for divergence time estimation, tree inference, side chain configurationprediction and ancestral sequence reconstruction.Further, encoding observed characters in an alignment as ambiguous representations ofcharacters in a larger state-space allows the application of RAM55 to 20-state amino aciddata for which structures are not known. Adding structural information to as few as12.5%of the sequences in an amino acid alignment results in excellent ancestral reconstructionperformance compared to a benchmark that considers the full rotamer state information.This strategy significantly expands the applicability of RAM55 to real-world scenarioswhere structure might only be available for some of the sequences of interest.Thus, not only is rotamer configuration a valuable source of information for phylo-genetic studies, but modelling the concomitant evolution of sequence and structure mayhave important implications for understanding protein folding and function.

Subjects/Keywords: protein; evolution; protein structure; phylogenetics; modelling

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Perron, U. (2020). The Influence of Structural Constraints on Protein Evolution. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/311064

Chicago Manual of Style (16^th Edition):

Perron, Umberto. “The Influence of Structural Constraints on Protein Evolution.” 2020. Doctoral Dissertation, University of Cambridge. Accessed April 14, 2021. https://www.repository.cam.ac.uk/handle/1810/311064.

MLA Handbook (7^th Edition):

Perron, Umberto. “The Influence of Structural Constraints on Protein Evolution.” 2020. Web. 14 Apr 2021.

Vancouver:

Perron U. The Influence of Structural Constraints on Protein Evolution. [Internet] [Doctoral dissertation]. University of Cambridge; 2020. [cited 2021 Apr 14]. Available from: https://www.repository.cam.ac.uk/handle/1810/311064.

Council of Science Editors:

Perron U. The Influence of Structural Constraints on Protein Evolution. [Doctoral Dissertation]. University of Cambridge; 2020. Available from: https://www.repository.cam.ac.uk/handle/1810/311064

University of California – Riverside

13. Dunn, Matthew Bjorn. Reviving the Organismic Analogy in Sociology: Human Society as an Organism.

Degree: Sociology, 2016, University of California – Riverside

URL: http://www.escholarship.org/uc/item/1179k78v

► Comparing the operation of human societies to the operation of organisms was a common theme in the theories of sociology’s classical era. Despite this early… (more)

▼ Comparing the operation of human societies to the operation of organisms was a common theme in the theories of sociology’s classical era. Despite this early prominence, the organismic analogy has received little attention from sociologists during the late 20th and early 21st centuries. The present dissertation is an attempt to revive the organismic analogy in sociological theory. In so doing, the present dissertation will first outline the organismic analogy as it appeared in the sociological theories of Auguste Comte, Herbert Spencer and Émile Durkheim. After providing that historical foundation, this dissertation will then use contemporary evolutionary theory to define an organism as a collective entity featuring a high level of cooperation and a low level of conflict among its component parts. Featuring a high level of cooperation and a low level of conflict among its component parts allows an organism to adaptively modify flows of energy in its environment, which in turn, enables its persistence. Also, organisms emerge through a three-part evolutionary process involving social group formation, social group maintenance, and social group transformation. After providing that background, this dissertation will then argue that a human society is a collective entity that exhibits a high level of cooperation and a low level of conflict among the individuals that compose the society. This arrangement allows the society to adaptively modify flows of energy in its environment, which in turn, enables the society’s persistence. Furthermore, human societies emerged through a three-part evolutionary process involving social group formation, social group maintenance, and social group transformation. Following from these arguments, human societies can be considered organisms. After arguing that human societies can be considered organisms, this dissertation will then argue that the organismic character of human societies has, in general, increased over time as societal evolution has unfolded.

Subjects/Keywords: Sociology; Social structure; Evolution & development; Evolution; Macrohistory; Organism; Societal Evolution; Superorganism; Theory

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Dunn, M. B. (2016). Reviving the Organismic Analogy in Sociology: Human Society as an Organism. (Thesis). University of California – Riverside. Retrieved from http://www.escholarship.org/uc/item/1179k78v

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Dunn, Matthew Bjorn. “Reviving the Organismic Analogy in Sociology: Human Society as an Organism.” 2016. Thesis, University of California – Riverside. Accessed April 14, 2021. http://www.escholarship.org/uc/item/1179k78v.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Dunn, Matthew Bjorn. “Reviving the Organismic Analogy in Sociology: Human Society as an Organism.” 2016. Web. 14 Apr 2021.

Vancouver:

Dunn MB. Reviving the Organismic Analogy in Sociology: Human Society as an Organism. [Internet] [Thesis]. University of California – Riverside; 2016. [cited 2021 Apr 14]. Available from: http://www.escholarship.org/uc/item/1179k78v.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Dunn MB. Reviving the Organismic Analogy in Sociology: Human Society as an Organism. [Thesis]. University of California – Riverside; 2016. Available from: http://www.escholarship.org/uc/item/1179k78v

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Illinois – Urbana-Champaign

14. Nasir, Arshan. Structural and functional advances in the evolutionary studies of cells and viruses.

Degree: PhD, Informatics, 2015, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/78703

► Phylogenomics aims to describe evolutionary relatedness between organisms by analyzing genomic data. The common practice is to produce phylogenomic trees from molecular information in the… (more)

▼ Phylogenomics aims to describe evolutionary relatedness between organisms by analyzing genomic data. The common practice is to produce phylogenomic trees from molecular information in the sequence, order and content of genes in genomes. These phylogenies describe the evolution of life and have become valuable tools for taxonomy. The recent availability of structural and functional data for hundreds of genomes now offer the opportunity to study evolution using more conserved sets of molecular features. Here we report a phylogenomic (i.e. historical) and comparative (ahistorical) analysis that yields novel insights into the origin of cells (Chapters 1-3) and viruses (Chapters 4-6). We utilized conserved protein domain structure information (fold families [FFs] and fold superfamilies [FSFs]) and ontological definitions of gene products (Gene Ontology [GO]) to reconstruct rooted trees of life (ToL), taking advantage of a genomic census of molecular structure and function in the genomes of sampled organisms and viruses. The analysis revealed a global tendency in the proteomic repertories of cellular organisms to increase domain abundance. ToLs built directly from the census of molecular functions confirmed an early origin of Archaea relative to Bacteria and Eukarya, a conclusion further supported by comparative analysis. The analysis further revealed an ancient history of viruses and their evolution by gene loss. Despite the very high levels of variability seen in the replication strategies, morphologies, and host preferences of extant viruses, we recovered a conserved and ancient structural core of protein domains that was shared between cellular organisms and distantly related viruses. This core together with an analysis of the evolution of virion morphotypes strongly suggests an ancient origin for the viral supergroup. Moreover, a large number of viral proteins lacked cellular homologs and strongly negated the idea that viruses merely evolve by acquiring cellular genes. These virus-specific proteins confer pathogenic abilities to viruses and appeared late in evolution suggesting that the shift to parasitic mode of life happened later in viral evolution. The strong evolutionary association between viruses and cells is likely reminiscent of their ancient co-existence inside primordial cells. Moreover, the crucial dependency of viruses to replicate in an intracellular environment creates fertile grounds for genetic innovation. Interestingly, protein domains shared with viruses were widespread in the proteomes of all three cellular superkingdoms suggesting that viruses mediate gene transfer and crucially enhance biodiversity. The phylogenomic trees identify viruses as a ‘fourth supergroup’ along with cellular superkingdoms, Archaea, Bacteria, and Eukarya. The new model for the origin and evolution of viruses and cells is backed by strong molecular data and is compatible with the existing models of viral evolution. Our experiments indicate that structure and functionomic data represent a useful addition to the set of… Advisors/Committee Members: Caetano-Anolles, Gustavo (advisor), Caetano-Anolles, Gustavo (Committee Chair), Mittenthal, Jay (committee member), Hudson, Matthew E. (committee member), Ma, Jian (committee member).

Subjects/Keywords: Gene ontology; Protein structure; Viral evolution; Phylogenomics; Comparative genomics; Evolution

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Nasir, A. (2015). Structural and functional advances in the evolutionary studies of cells and viruses. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/78703

Chicago Manual of Style (16^th Edition):

Nasir, Arshan. “Structural and functional advances in the evolutionary studies of cells and viruses.” 2015. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed April 14, 2021. http://hdl.handle.net/2142/78703.

MLA Handbook (7^th Edition):

Nasir, Arshan. “Structural and functional advances in the evolutionary studies of cells and viruses.” 2015. Web. 14 Apr 2021.

Vancouver:

Nasir A. Structural and functional advances in the evolutionary studies of cells and viruses. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2015. [cited 2021 Apr 14]. Available from: http://hdl.handle.net/2142/78703.

Council of Science Editors:

Nasir A. Structural and functional advances in the evolutionary studies of cells and viruses. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2015. Available from: http://hdl.handle.net/2142/78703

Duke University

15. Challis, Christopher. Bayesian Structural Phylogenetics .

Degree: 2013, Duke University

URL: http://hdl.handle.net/10161/8262

► This thesis concerns the use of protein structure to improve phylogenetic inference. There has been growing interest in phylogenetics as the number of available… (more)

▼ This thesis concerns the use of protein structure to improve phylogenetic inference. There has been growing interest in phylogenetics as the number of available DNA and protein sequences continues to grow rapidly and demand from other scientific fields increases. It is now well understood that phylogenies should be inferred jointly with alignment through use of stochastic evolutionary models. It has not been possible, however, to incorporate protein structure in this framework. Protein structure is more strongly conserved than sequence over long distances, so an important source of information, particularly for alignment, has been left out of analyses. I present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. Indels arise from a classic Links model and mutations follow a standard substitution matrix, while backbone atoms diffuse in three-dimensional space according to an Ornstein-Uhlenbeck process. The model allows for simultaneous estimation of evolutionary distances, indel rates, structural drift rates, and alignments, while fully accounting for uncertainty. The inclusion of structural information enables pairwise evolutionary distance estimation on time scales not previously attainable with sequence evolution models. Ideally inference should not be performed in a pairwise fashion between proteins, but in a fully Bayesian setting simultaneously estimating the phylogenetic tree, alignment, and model parameters. I extend the initial pairwise model to this framework and explore model variants which improve agreement between sequence and structure information. The model also allows for estimation of heterogeneous rates of structural evolution throughout the tree, identifying groups of proteins structurally evolving at different speeds. In order to explore the posterior over topologies by Markov chain Monte Carlo sampling, I also introduce novel topology + alignment proposals which greatly improve mixing of the underlying Markov chain. I show that the inclusion of structural information reduces both alignment and topology uncertainty. The software is available as plugin to the package StatAlign. Finally, I also examine limits on statistical inference of phylogeny through sequence information models. These limits arise due to the `cutoff phenomenon,' a term from probability which describes processes which remain far from their equilibrium distribution for some period of time before swiftly transitioning to stationarity. Evolutionary sequence models all exhibit a cutoff; I show how to find the cutoff for specific models and sequences and relate the cutoff explicitly to increased uncertainty in inference of evolutionary distances. I give theoretical results for symmetric models, and demonstrate with simulations that these results apply to more realistic and widespread models as well. This analysis also highlights several drawbacks to common default priors for phylogenetic analysis, I and… Advisors/Committee Members: Schmidler, Scott C (advisor).

Subjects/Keywords: Statistics; Biology; Evolution & development; Bayesian; evolution; phylogenetics; prior; protein; structure

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Challis, C. (2013). Bayesian Structural Phylogenetics . (Thesis). Duke University. Retrieved from http://hdl.handle.net/10161/8262

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Challis, Christopher. “Bayesian Structural Phylogenetics .” 2013. Thesis, Duke University. Accessed April 14, 2021. http://hdl.handle.net/10161/8262.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Challis, Christopher. “Bayesian Structural Phylogenetics .” 2013. Web. 14 Apr 2021.

Vancouver:

Challis C. Bayesian Structural Phylogenetics . [Internet] [Thesis]. Duke University; 2013. [cited 2021 Apr 14]. Available from: http://hdl.handle.net/10161/8262.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Challis C. Bayesian Structural Phylogenetics . [Thesis]. Duke University; 2013. Available from: http://hdl.handle.net/10161/8262

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Georgia

16. Huang, Zhibin. Computational search of RNA pseudoknots and structural variations in genomes.

Degree: 2014, University of Georgia

URL: http://hdl.handle.net/10724/27167

► Non-coding RNA (ncRNA) secondary structural homologs can be detected effectively in genomes based on a covariance model (CM) and associated dynamic programming algorithms. However, the… (more)

Subjects/Keywords: ncRNA structure search; Sequence structure alignment; pseudoknot; ncRNA structure variation; RNA structure evolution; Graph tree decomposition; Dynamic Programming

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Huang, Z. (2014). Computational search of RNA pseudoknots and structural variations in genomes. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/27167

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Huang, Zhibin. “Computational search of RNA pseudoknots and structural variations in genomes.” 2014. Thesis, University of Georgia. Accessed April 14, 2021. http://hdl.handle.net/10724/27167.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Huang, Zhibin. “Computational search of RNA pseudoknots and structural variations in genomes.” 2014. Web. 14 Apr 2021.

Vancouver:

Huang Z. Computational search of RNA pseudoknots and structural variations in genomes. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Apr 14]. Available from: http://hdl.handle.net/10724/27167.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Huang Z. Computational search of RNA pseudoknots and structural variations in genomes. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/27167

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

17. O'Dowd, Conor Lee. Petrology and Geochemistry of the Bearwallow Mountain Andesite, Mogollon-Datil Volcanic Field, New Mexico.

Degree: MSin Geospatial Sciences, Geography, Geology, and Planning, 2019, Missouri State University

URL: https://bearworks.missouristate.edu/theses/3341

► The Mogollon-Datil volcanic field (MDVF), located in southern New Mexico, is the result of episodic volcanism and the transition between arc and rift magmatism.… (more)

Subjects/Keywords: Andesite; Arc Magmatism; MDVF; New Mexico; Crustal Evolution; Magma Evolution; Geochemistry; Tectonics and Structure; Volcanology

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APA (6^th Edition):

O'Dowd, C. L. (2019). Petrology and Geochemistry of the Bearwallow Mountain Andesite, Mogollon-Datil Volcanic Field, New Mexico. (Masters Thesis). Missouri State University. Retrieved from https://bearworks.missouristate.edu/theses/3341

Chicago Manual of Style (16^th Edition):

O'Dowd, Conor Lee. “Petrology and Geochemistry of the Bearwallow Mountain Andesite, Mogollon-Datil Volcanic Field, New Mexico.” 2019. Masters Thesis, Missouri State University. Accessed April 14, 2021. https://bearworks.missouristate.edu/theses/3341.

MLA Handbook (7^th Edition):

O'Dowd, Conor Lee. “Petrology and Geochemistry of the Bearwallow Mountain Andesite, Mogollon-Datil Volcanic Field, New Mexico.” 2019. Web. 14 Apr 2021.

Vancouver:

O'Dowd CL. Petrology and Geochemistry of the Bearwallow Mountain Andesite, Mogollon-Datil Volcanic Field, New Mexico. [Internet] [Masters thesis]. Missouri State University; 2019. [cited 2021 Apr 14]. Available from: https://bearworks.missouristate.edu/theses/3341.

Council of Science Editors:

O'Dowd CL. Petrology and Geochemistry of the Bearwallow Mountain Andesite, Mogollon-Datil Volcanic Field, New Mexico. [Masters Thesis]. Missouri State University; 2019. Available from: https://bearworks.missouristate.edu/theses/3341

18. Durkalec, Anna. Properties and evolution of galaxy clustering at 2<z<5 based on the VIMOS Ultra Deep Survey : Hydrometallurgical process for the valorization of nickel contained in hyperaccumulating plants.

Degree: Docteur es, Astrophysique et Cosmologie, 2014, Aix Marseille Université

URL: http://www.theses.fr/2014AIXM4758

►

Cette thèse porte sur l'étude des propriétés et l'évolution de regroupement de galaxies pour les galaxies de la gamme de 2<z<5 de VUDS Sondage, qui… (more)

▼

Cette thèse porte sur l'étude des propriétés et l'évolution de regroupement de galaxies pour les galaxies de la gamme de 2<z<5 de VUDS Sondage, qui est la plus grande enquête de galaxie spectroscopique à z>2. Je ai pu mesurer la distribution spatiale d'une population générale de galaxie à redshift z~3 pour la première fois avec une grande précision. Je ai quantifié le regroupement de galaxie en estimation et la modélisation de la fonction de corrélation projetée (espace réel) à deux points, pour une population générale de 3022 galaxies. Je ai prolongé les mesures de regroupement à la luminosité et des sous-échantillons de masse sélectionné stellaires. Mes résultats montrent que la force de regroupement de la population générale de la galaxie ne change pas de redshift z~3,5 à z~2,5, mais dans les deux redshift va plus lumineux et des galaxies plus massives sont plus regroupées que les moins lumineux (massives). En utilisant la distribution d'occupation de halo (HOD) formalisme je mesuré une masse moyenne de halo hôte au redshift z~3 significativement plus faible que les masses halo moyens observés à faible redshift. Je ai conclu que la population de formation d'étoiles observé des galaxies à z~3 aurait évolué dans le massif et lumineux la population de galaxies au z=0. Aussi, je interpréter les mesures de regroupement en termes de biais de galaxies à grande échelle linéaire. Je trouve que ce est nettement plus élevé que le biais des galaxies redshift intermédiaire et faible. Enfin, je ai calculé le ratio-stellaire Halo masse (SHMR) et l'efficacité intégrée de formation d'étoiles (ISFE) pour étudier l'efficacité de la formation des étoiles et l'assemblage masse stellaire.

This thesis focuses on the study of the properties and evolution of galaxy clustering for galaxies in the redshift range 2<z<5 from the VIMOS Ultra Deep Survey (VUDS), which is the largest spectroscopic galaxy survey at z>2. I was able to measure the spatial distribution of a general galaxy population at redshift z~3 for the first time with a high accuracy. I quantified the galaxy clustering by estimating and modelling the projected (real-space) two-point correlation function, for a general population of 3022 galaxies. I extended the clustering measurements to the luminosity and stellar mass-selected sub-samples. My results show that the clustering strength of the general galaxy population does not change significantly from redshift z~3.5 to z~2.5, but in both redshift ranges more luminous and more massive galaxies are more clustered than less luminous (massive) ones. Using the halo occupation distribution (HOD) formalism I measured an average host halo mass at redshift z~3 significantly lower than the observed average halo masses at low redshift. I concluded that the observed star-forming population of galaxies at z~3 might have evolved into the massive and bright (Mr<-21.5) galaxy population at redshift z=0. Also, I interpret clustering measurements in terms of a linear large-scale galaxy bias. I find it to be significantly higher than the bias…

Advisors/Committee Members: Le Fèvre, Olivier (thesis director).

Subjects/Keywords: Large scale structure; Galaxy clustering; Hod; Correlation function; Galaxy evolution; Large scale structure; Galaxy clustering; Hod; Correlation function; Galaxy evolution

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APA (6^th Edition):

Durkalec, A. (2014). Properties and evolution of galaxy clustering at 2<z<5 based on the VIMOS Ultra Deep Survey : Hydrometallurgical process for the valorization of nickel contained in hyperaccumulating plants. (Doctoral Dissertation). Aix Marseille Université. Retrieved from http://www.theses.fr/2014AIXM4758

Chicago Manual of Style (16^th Edition):

Durkalec, Anna. “Properties and evolution of galaxy clustering at 2<z<5 based on the VIMOS Ultra Deep Survey : Hydrometallurgical process for the valorization of nickel contained in hyperaccumulating plants.” 2014. Doctoral Dissertation, Aix Marseille Université. Accessed April 14, 2021. http://www.theses.fr/2014AIXM4758.

MLA Handbook (7^th Edition):

Durkalec, Anna. “Properties and evolution of galaxy clustering at 2<z<5 based on the VIMOS Ultra Deep Survey : Hydrometallurgical process for the valorization of nickel contained in hyperaccumulating plants.” 2014. Web. 14 Apr 2021.

Vancouver:

Durkalec A. Properties and evolution of galaxy clustering at 2<z<5 based on the VIMOS Ultra Deep Survey : Hydrometallurgical process for the valorization of nickel contained in hyperaccumulating plants. [Internet] [Doctoral dissertation]. Aix Marseille Université 2014. [cited 2021 Apr 14]. Available from: http://www.theses.fr/2014AIXM4758.

Council of Science Editors:

Durkalec A. Properties and evolution of galaxy clustering at 2<z<5 based on the VIMOS Ultra Deep Survey : Hydrometallurgical process for the valorization of nickel contained in hyperaccumulating plants. [Doctoral Dissertation]. Aix Marseille Université 2014. Available from: http://www.theses.fr/2014AIXM4758

19. Pan, Lei. The earliest members of the genus Homo in South Africa : evidence from inner structure of lower postcanine dentition : Les premiers membres du genre Homo en Afrique du sud : preuve de la structure interne de faible dentition postcanine.

Degree: Docteur es, Anthropobiologie, 2016, Université Toulouse III – Paul Sabatier

URL: http://www.theses.fr/2016TOU30087

►

Cette thèse se compose de deux projets individuels et six chapitres, qui sont basées sur l'examen de la structure interne dentaire inférieure dentition postcanine dans… (more)

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Cette thèse se compose de deux projets individuels et six chapitres, qui sont basées sur l'examen de la structure interne dentaire inférieure dentition postcanine dans un certain nombre de fossiles et modernes spécimens, à travers lesquels une étude approfondie a été effectuée à l'aide de micro-tomodensitométrie et ordinateur-outils de paleonanthropology assistée. Nous avons d'abord recensé et évalué la valeur taxinomique de l'épaisseur de l'émail et des modèles de distribution de l'épaisseur de l'émail 3D entier couronne dans un certain nombre des premiers membres du genre Homo en Afrique du Sud, et examiné dans le relavence taxonomique de EDJ morphologie long postcanine dentition, et discuté de la facteurs d'adaptation possibles / développement qui tiennent compte de la variation de la morphologie EDJ nous avons observé ici. Les trois premiers chapitres (Introduction, Matériel et méthodes) donnent un aperçu des objectifs de cette thèse, et d'examiner les études précédentes. En outre, ils fournissent une introduction détaillée des matières fossiles, les sites et un arrière-plan de la méthode assistée par ordinateur (micro-XCT) pour analyser la structure interne dentaire. Le chapitre des résultats comprend deux documents de recherche indépendants, dans les différentes étapes de soumission et de publication. Les résultats et les chapitres de discussion offrent un résumé détaillé de l'épaisseur de l'émail, EDJ morphométrie géométrique et 3D-EDJ variation métamérique entre les espèces, et de comparer les résultats avec un certain nombre d'études morphologiques et de développement, et de fournir une perspective d'étude future. Le dernier chapitre atteint des points décisifs de cette thèse, il met en évidence la valeur taxinomique des prémolaires EDJ, et met l'accent sur les caractéristiques de la mosaïque de la dentition des premiers membres du genre Homo sud-africaine.

This thesis consists of two individual projects and six chapters, which are based on the examination of dental inner structure of lower postcanine dentition in a number of fossil and modern specimens, through which a comprehensive study has been done using micro-computed tomography and computer-assisted paleonanthropology tools. We first documented and assessed the taxonomical value of enamel thickness and 3D whole-crown enamel thickness distribution patterns in a number of earliest members of the genus Homo in South Africa, and looked into the taxonomic relavence of EDJ morphology along postcanine dentition, and discussed the possible adaptive/developmental factors that account for the variation of EDJ morphology we observed here. The first three chapters (Introduction, Materials and Methods) provide an overview of the objectives of this thesis, and review previous studies. Also, they provide a detailed introduction of fossil materials, sites and a background of computer-aided method (micro-XCT) to analyze the dental inner structure. The Results chapter comprises of two independent research papers, in different stages of submission and publication.…

Advisors/Committee Members: Braga, José (thesis director).

Subjects/Keywords: Evolution humaine; Anatomie comparée; Structure interne dentaire; Micro-CT; Human evolution; Comparative anatomy; Dental inner structure; Micro-CT

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Pan, L. (2016). The earliest members of the genus Homo in South Africa : evidence from inner structure of lower postcanine dentition : Les premiers membres du genre Homo en Afrique du sud : preuve de la structure interne de faible dentition postcanine. (Doctoral Dissertation). Université Toulouse III – Paul Sabatier. Retrieved from http://www.theses.fr/2016TOU30087

Chicago Manual of Style (16^th Edition):

Pan, Lei. “The earliest members of the genus Homo in South Africa : evidence from inner structure of lower postcanine dentition : Les premiers membres du genre Homo en Afrique du sud : preuve de la structure interne de faible dentition postcanine.” 2016. Doctoral Dissertation, Université Toulouse III – Paul Sabatier. Accessed April 14, 2021. http://www.theses.fr/2016TOU30087.

MLA Handbook (7^th Edition):

Pan, Lei. “The earliest members of the genus Homo in South Africa : evidence from inner structure of lower postcanine dentition : Les premiers membres du genre Homo en Afrique du sud : preuve de la structure interne de faible dentition postcanine.” 2016. Web. 14 Apr 2021.

Vancouver:

Pan L. The earliest members of the genus Homo in South Africa : evidence from inner structure of lower postcanine dentition : Les premiers membres du genre Homo en Afrique du sud : preuve de la structure interne de faible dentition postcanine. [Internet] [Doctoral dissertation]. Université Toulouse III – Paul Sabatier; 2016. [cited 2021 Apr 14]. Available from: http://www.theses.fr/2016TOU30087.

Council of Science Editors:

Pan L. The earliest members of the genus Homo in South Africa : evidence from inner structure of lower postcanine dentition : Les premiers membres du genre Homo en Afrique du sud : preuve de la structure interne de faible dentition postcanine. [Doctoral Dissertation]. Université Toulouse III – Paul Sabatier; 2016. Available from: http://www.theses.fr/2016TOU30087

Université Montpellier II

20. Débarre, Florence. Persistance, compétition et évolution dans un environnement hétérogène : Living, competing and evolving in a heterogeneous environment.

Degree: Docteur es, Biologie des populations et écologie, 2010, Université Montpellier II

URL: http://www.theses.fr/2010MON20067

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Tout observateur peut constater la diversité des milieux sur Terre. La compréhension des liens entre cette diversité des habitats et la biodiversité est l'un des… (more)

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Tout observateur peut constater la diversité des milieux sur Terre. La compréhension des liens entre cette diversité des habitats et la biodiversité est l'un des thèmes centraux en Écologie, en Évolution et en Biologie de la conservation. Je m'intéresse dans cette thèse aux conséquences écologiques (à court terme) et évolutives (à plus long terme) de la structuration spatiale et de l'hétérogénéité de l'environnement. Je développe et analyse plusieurs modèles mathématiques, combinant différents formalismes théoriques (dynamiques adaptatives, génétique des populations, génétique quantitative). Ces modèles permettent d'explorer les conséquences de l'hétérogénéité spatiale de l'environnement sur (1) les conditions de persistance des populations ; (2) la coexistence entre différents phénotypes et (3) la dynamique évolutive des populations. Je montre ainsi l'importance (i) de l'intensité et de la place de la migration dans le cycle de vie ; (ii) du type de structure spatiale (explicite ou implicite, continu ou discret) ; (iii) de la forme du compromis évolutif, et donc des coûts d'adaptation à une autre ressource ; et enfin (iv) des éventuels rétrocontrôles démographiques. J'illustre à l'aide des interactions entre hôtes et parasites l'importance des hétérogénéités spatiales. Un premier exemple concerne leur utilisation dans la gestion des pharmacorésistances ou des résistances aux insecticides : une répartition hétérogène du traitement permet d'éviter la propagation de parasites ou de nuisibles résistants. Un second exemple, enfin, illustre comment les hétérogénéités dues à l'auto-structuration spatiale influencent l'évolution de stratégies de défense des hôtes, et permettent l'évolution de défenses altruistes.

Any observer can notice the diversity of habitats on Earth. Understanding the links betweenthis diversity of habitats and biodiversity is a core topic in Ecology, Evolution andConservation Biology.In this thesis, I study the ecological (short-term) and evolutionary (long-term) consequencesof spatial structuring and environmental heterogeneities. I develop and analyzeseveral mathematical models, which combine different theoretical frameworks (adaptivedynamics, population genetics, and quantitative genetics). I explore the consequences ofspatial heterogeneities on (1) the conditions for population persistence; (2) the coexistenceof different phenotypes, and (3) evolutionary dynamics of populations. I show that theresults depend on (i) the life-cycle, and in particular whether migration influences local regulation;(ii) the choice of the spatial structure (explicit or implicit, continuous or discrete);(iii) the shape of the trade-off, and hence the costs of adaptation to another resource, andfinally (iv) the potential demographical feedbacks.I use the specific case of hosts and parasites interactions to illustrate the importanceof spatial heterogeneities. As a first example, I show that a heterogeneous application oftreatments can help prevent the spread of resistant parasites or pests. Secondly, I show howspatial…

Advisors/Committee Members: Gandon, Sylvain (thesis director).

Subjects/Keywords: Structure spatiale; Evolution; Spécialisation; Cline; Résistance; Adaptation locale; Spatial structure; Evolution; Specialization; Cline; Resistance; Local adaptation

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Débarre, F. (2010). Persistance, compétition et évolution dans un environnement hétérogène : Living, competing and evolving in a heterogeneous environment. (Doctoral Dissertation). Université Montpellier II. Retrieved from http://www.theses.fr/2010MON20067

Chicago Manual of Style (16^th Edition):

Débarre, Florence. “Persistance, compétition et évolution dans un environnement hétérogène : Living, competing and evolving in a heterogeneous environment.” 2010. Doctoral Dissertation, Université Montpellier II. Accessed April 14, 2021. http://www.theses.fr/2010MON20067.

MLA Handbook (7^th Edition):

Débarre, Florence. “Persistance, compétition et évolution dans un environnement hétérogène : Living, competing and evolving in a heterogeneous environment.” 2010. Web. 14 Apr 2021.

Vancouver:

Débarre F. Persistance, compétition et évolution dans un environnement hétérogène : Living, competing and evolving in a heterogeneous environment. [Internet] [Doctoral dissertation]. Université Montpellier II; 2010. [cited 2021 Apr 14]. Available from: http://www.theses.fr/2010MON20067.

Council of Science Editors:

Débarre F. Persistance, compétition et évolution dans un environnement hétérogène : Living, competing and evolving in a heterogeneous environment. [Doctoral Dissertation]. Université Montpellier II; 2010. Available from: http://www.theses.fr/2010MON20067

21. Deal, Morgan. Importance de la diffusion atomique et de ses conséquences hydrodynamiques sur la structure interne et les paramètres observationnels des étoiles : Importance of atomic diffusion and of its hydrodynamic consequences on internal structure and observational parameters of stars.

Degree: Docteur es, Physique, 2016, Montpellier

URL: http://www.theses.fr/2016MONTT318

► La diffusion atomique doit être prise en compte dans les modèles d'évolution stellaire car il s'agit d'une conséquence directe du fait que les étoiles sont… (more)

▼ La diffusion atomique doit être prise en compte dans les modèles d'évolution stellaire car il s'agit d'une conséquence directe du fait que les étoiles sont des sphères auto-gravitantes composées d'un mélange de différents gaz (les éléments chimiques). L'équilibre des étoiles conduit à des gradients internes de pression, de densité et de température ainsi qu'à un transfert radiatif, l'ensemble produisant un effet sélectif sur les éléments (dans la plupart des cas dominé par la compétition entre le triage gravitationnel et les accélérations radiatives).Les interactions entre la diffusion atomique et les processus hydrodynamiques tels que la convection dynamique et la perte de masse sont étudiées depuis longtemps. Un processus important a cependant été oublié dans les modèles. Il s'agit de la convection double diffusive (ou thermohaline) induite par un gradient de μ instable, qui peut être produite par une accumulation locale d'éléments lourds à l'intérieur des étoiles due aux accélérations radiatives. Contrairement aux autres processus de mélange, il s'agit d'une conséquence directe de la diffusion atomique. Un effet similaire se produit à la base de la zone convective de surface en cas d'accrétion d’éléments lourds à la surface de l'étoile.Nous avons étudié la convection thermohaline induite par l'accrétion dans le cas du système 16 Cygni et les propriétés de ces deux étoiles avec le code TGEC. Nous avons inclus la prescription de Brown et al. 2013 pour la convection thermohaline. Nous avons ensuite calculé les fréquences d'oscillations de ces modèles à l'aide du code PULSE pour les comparer aux fréquences observées par Kepler. A partir de ces modèles, nous avons pu montrer qu'en accrétant 2/3 de la masse terrestre au début de la séquence principale (sur le modèle 16 Cyg B), la convection thermohaline induite par l'accrétion mélangeait l'étoile suffisamment profondément pour atteindre la zone de destruction du lithium et ainsi obtenir des abondances de lithium cohérentes avec les observations de 16 Cyg A et B.Nous avons étudié l'accumulation d’éléments lourds et l'effet de la convection thermohaline dans le cas des étoiles de type A. Dans ces étoiles, des abondances "particulières" (par rapport au soleil) ont été observées. Ceci est dû aux effets de la diffusion atomique qui sont très importants dans ces étoiles. Cependant, la diffusion atomique seule produit des variations d'abondances trop importantes et un moyen de reproduire les observations est de mélanger l'étoile assez profondément. Nous avons ensuite calculé des modèles incluant la diffusion atomique et la convection thermohaline en utilisant le code TGEC. Nous avons montré que ce processus pouvait modifier la structure interne de ces étoiles, et aussi les abondances de surface. Nous avons aussi inclus la convection thermohaline et l'accrétion dans le code de Montréal/Montpellier. Nous avons modifié plusieurs parties de ce code afin de pouvoir faire des comparaisons avec le TGEC pour comparer les résultats. Les résultats obtenus sont très similaires.Nous avons… Advisors/Committee Members: Richard, Olivier (thesis director).

Subjects/Keywords: Abondances; Diffusion; Evolution stellaire; Processus de transport; Structure interne; Abundances; Diffusion; Stellar evolution; Transport processes; Stellar structure

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Deal, M. (2016). Importance de la diffusion atomique et de ses conséquences hydrodynamiques sur la structure interne et les paramètres observationnels des étoiles : Importance of atomic diffusion and of its hydrodynamic consequences on internal structure and observational parameters of stars. (Doctoral Dissertation). Montpellier. Retrieved from http://www.theses.fr/2016MONTT318

Chicago Manual of Style (16^th Edition):

Deal, Morgan. “Importance de la diffusion atomique et de ses conséquences hydrodynamiques sur la structure interne et les paramètres observationnels des étoiles : Importance of atomic diffusion and of its hydrodynamic consequences on internal structure and observational parameters of stars.” 2016. Doctoral Dissertation, Montpellier. Accessed April 14, 2021. http://www.theses.fr/2016MONTT318.

MLA Handbook (7^th Edition):

Deal, Morgan. “Importance de la diffusion atomique et de ses conséquences hydrodynamiques sur la structure interne et les paramètres observationnels des étoiles : Importance of atomic diffusion and of its hydrodynamic consequences on internal structure and observational parameters of stars.” 2016. Web. 14 Apr 2021.

Vancouver:

Deal M. Importance de la diffusion atomique et de ses conséquences hydrodynamiques sur la structure interne et les paramètres observationnels des étoiles : Importance of atomic diffusion and of its hydrodynamic consequences on internal structure and observational parameters of stars. [Internet] [Doctoral dissertation]. Montpellier; 2016. [cited 2021 Apr 14]. Available from: http://www.theses.fr/2016MONTT318.

Council of Science Editors:

Deal M. Importance de la diffusion atomique et de ses conséquences hydrodynamiques sur la structure interne et les paramètres observationnels des étoiles : Importance of atomic diffusion and of its hydrodynamic consequences on internal structure and observational parameters of stars. [Doctoral Dissertation]. Montpellier; 2016. Available from: http://www.theses.fr/2016MONTT318

University of California – San Diego

22. Bliven, Spencer Edward. Structure-Preserving Rearrangements: Algorithms for Structural Comparison and Protein Analysis.

Degree: Bioinformatics, 2015, University of California – San Diego

URL: http://www.escholarship.org/uc/item/0t54p4gj

► Protein structure is fundamental to a deep understanding of how proteins function. Since structure is highly conserved, structural comparison can provide deep information about the… (more)

▼ Protein structure is fundamental to a deep understanding of how proteins function. Since structure is highly conserved, structural comparison can provide deep information about the evolution and function of protein families. The Protein Data Bank (PDB) continues to grow rapidly, providing copious opportunities for advancing our understanding of proteins through large-scale searches and structural comparisons. In this work I present several novel structural comparison methods for specific applications, as well as apply structure comparison tools systematically to better understand global properties of protein fold space.Circular permutation describes a relationship between two proteins where the N-terminal portion of one protein is related to the C-terminal portion of the other. Proteins that are related by a circular permutation generally share the same structure despite the rearrangement of their primary sequence. This non-sequential relationship makes them difficult for many structure alignment tools to detect. Combinatorial Extension for Circular Permutations (CE-CP) was developed to align proteins that may be related by a circular permutation. It is widely available due to its incorporation into the RCSB PDB website.Symmetry and structural repeats are common in protein structures at many levels. The CE-Symm tool was developed in order to detect internal pseudosymmetry within individual polypeptide chains. Such internal symmetry can arise from duplication events, so aligning the individual symmetry units provides insights about conservation and evolution. In many cases, internal symmetry can be shown to be important for a number of functions, including ligand binding, allostery, folding, stability, and evolution.Structural comparison tools were applied comprehensively across all PDB structures for systematic analysis. Pairwise structural comparisons of all proteins in the PDB have been computed using the Open Science Grid computing infrastructure, and are kept continually up-to-date with the release of new structures. These provide a network-based view of protein fold space. CE-Symm was also applied to systematically survey the PDB for internally symmetric proteins. It is able to detect symmetry in ~20% of all protein families. Such PDB-wide analyses give insights into the complex evolution of protein folds.

Subjects/Keywords: Bioinformatics; Molecular biology; Computer science; circular permutation; evolution; fold space; protein structure; structure comparison; symmetry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Bliven, S. E. (2015). Structure-Preserving Rearrangements: Algorithms for Structural Comparison and Protein Analysis. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/0t54p4gj

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Bliven, Spencer Edward. “Structure-Preserving Rearrangements: Algorithms for Structural Comparison and Protein Analysis.” 2015. Thesis, University of California – San Diego. Accessed April 14, 2021. http://www.escholarship.org/uc/item/0t54p4gj.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Bliven, Spencer Edward. “Structure-Preserving Rearrangements: Algorithms for Structural Comparison and Protein Analysis.” 2015. Web. 14 Apr 2021.

Vancouver:

Bliven SE. Structure-Preserving Rearrangements: Algorithms for Structural Comparison and Protein Analysis. [Internet] [Thesis]. University of California – San Diego; 2015. [cited 2021 Apr 14]. Available from: http://www.escholarship.org/uc/item/0t54p4gj.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Bliven SE. Structure-Preserving Rearrangements: Algorithms for Structural Comparison and Protein Analysis. [Thesis]. University of California – San Diego; 2015. Available from: http://www.escholarship.org/uc/item/0t54p4gj

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

23. Dridi, Kaouther. Evolution moléculaire et structurale des membres de la famille génique des lipases pancréatique : Structural and functional evolution within the pancreatic lipases gene family.

Degree: Docteur es, Immunologie, 2013, Aix Marseille Université

URL: http://www.theses.fr/2013AIXM4019

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Helicoverpa armigera et Epiphyas postvittana, deux insectes nuisibles pour l'agriculture, ont développé des résistances contre la plupart des insecticides connus. Les lipides étant les constituants… (more)

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Helicoverpa armigera et Epiphyas postvittana, deux insectes nuisibles pour l'agriculture, ont développé des résistances contre la plupart des insecticides connus. Les lipides étant les constituants majeurs de leur régime alimentaire, les fonctions digestives des lipases deviennent alors une cible privilégiée pour l'élaboration de nouveaux insecticides. L'identification récente de gènes codant pour l'expression de protéines potentiellement actives et inactives apparentées aux lipases pancréatiques (PLRP) dans le tractus digestif de ces deux insectes et dont le niveau de transcription varie en fonction de leur régime alimentaire a ouvert un nouveau champ de recherche. Dans le but de contribuer à cette thématique, nous avons construit cinq lipases recombinantes d'E. postvittana (EpLIPs) et testé leur expression dans trois systèmes différents (E.coli, P.pastoris et bacculovirus). Le tractus digestif de Helicoverpa armigera a été étudié par chromatographie échangeuse d'ions et les différentes protéines séparées ont été testées en spectrométrie de masse et sur pHstat pour l'activité. Les résultats obtenus ont permis de mettre en évidence, pour la première fois, la présence à la fois d'une lipase active et d'une lipase inactive dans le tractus digestif d'un lépidoptère. Par ailleurs, la caractérisation biochimique d'un mutant GPLRP2-Δ β9 a été faite dans le but de comprendre l'effet de cette boucle, partiellement délétée dans les lipases d'insectes, dans la spécificité du substrat. Nous avons pu montrer que cette boucle β9 est essentielle pour la stabilisation de la chaîne acyle durant la réaction de lipolyse.

Helicoverpa armigera and Epiphyas postvittana, two major pest crops, have developed resistances against most of the known insecticides. Lipids being a major component of insect diet, digestive function of lipase are a target of choice for new insecticide design. The recent identification of active and inactive pancreatic lipase related protein (PLRP) genes in those two insects midgut, with a level of transcription depending on the diet, opened the field of insect digestive lipase study. In order to contribute to this thematic, we built five recombinants lipase from E. postvittana (EpLIPs) and tested their expression in three different systems (E.coli, P.pastoris and bacculovirus). Protein structure prediction of EpLIPs allowed us to develop some functional hypothesis enlightening the role of inactive lipase in lipid transport. H. armigera midgut contents were separated through a one step purification chromatography and the different fractions were tested for activity and mass spectrometry. The results obtained gave the first evidence of the presence of both an active and an inactive lipase in lepidopteran midgut. In addition to this work, a biochemical characterisation of a β9 GPLRP2 mutant was carried out to understand the effect of this loop, partially deleted in insect lipase, in substrate specificity. The result shows that β9 loop is essential for stabilizing the leaving acyl chain during the lipolysis…

Advisors/Committee Members: Carrière, Frédéric (thesis director).

Subjects/Keywords: Lipase; Epiphyas postvittana; Évolution; Pancréatique lipase; Structure; Lipase; Epiphyas postvittana; Evolution; Pancreatic lipase; Structure; 571

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Dridi, K. (2013). Evolution moléculaire et structurale des membres de la famille génique des lipases pancréatique : Structural and functional evolution within the pancreatic lipases gene family. (Doctoral Dissertation). Aix Marseille Université. Retrieved from http://www.theses.fr/2013AIXM4019

Chicago Manual of Style (16^th Edition):

Dridi, Kaouther. “Evolution moléculaire et structurale des membres de la famille génique des lipases pancréatique : Structural and functional evolution within the pancreatic lipases gene family.” 2013. Doctoral Dissertation, Aix Marseille Université. Accessed April 14, 2021. http://www.theses.fr/2013AIXM4019.

MLA Handbook (7^th Edition):

Dridi, Kaouther. “Evolution moléculaire et structurale des membres de la famille génique des lipases pancréatique : Structural and functional evolution within the pancreatic lipases gene family.” 2013. Web. 14 Apr 2021.

Vancouver:

Dridi K. Evolution moléculaire et structurale des membres de la famille génique des lipases pancréatique : Structural and functional evolution within the pancreatic lipases gene family. [Internet] [Doctoral dissertation]. Aix Marseille Université 2013. [cited 2021 Apr 14]. Available from: http://www.theses.fr/2013AIXM4019.

Council of Science Editors:

Dridi K. Evolution moléculaire et structurale des membres de la famille génique des lipases pancréatique : Structural and functional evolution within the pancreatic lipases gene family. [Doctoral Dissertation]. Aix Marseille Université 2013. Available from: http://www.theses.fr/2013AIXM4019

Universiteit Utrecht

24. Janssen, B.J.C. conformational complexity of complement component C3.

Degree: 2007, Universiteit Utrecht

URL: http://dspace.library.uu.nl:8080/handle/1874/23001

► The complement system is an important part of the immune system and critical for the elimination of pathogens. In mammals the complement system consists of… (more)

▼ The complement system is an important part of the immune system and critical for the elimination of pathogens. In mammals the complement system consists of an intricate set of about 35 soluble and cell-surface plasma proteins. Central to complement is component C3, a large protein of 1,641 residues. Activation of C3 into C3b leads to several molecular and cellular responses, and to stimulation of the adaptive immune system. Chapter 1 gives an overview of the complement system, the central complement component C3 and its activation products. We solved the crystal structures of human, native C3 and its final main proteolytic fragment C3c which are described in chapter 2. These structures show in detail the composition of C3. C3 consists of thirteen domains of which nine were not recognised by previous sequence analysis. The structures indicate that the proteins of the C3/alpha2-macroglobulin family may have evolved from a core of eight homologous domains. The highly reactive thioester, essential for covalent attachment to target surfaces, is protected within C3 from reaction with water by a double mechanism. The changes that take place upon activation of C3 into C3b are revealed by the crystal structure of human C3b and are described in chapter 3. The thioester is activated and fully exposed for covalent attachment over 85 Å away from its buried position in C3. Large conformational changes in the alpha-chain present a changed molecular surface exposing and forming cryptic binding sites for many ligands which are essential for the biological activity and regulation of C3b. Undue complement activation is a major cause of tissue injury and associated with many inflammatory diseases. The activation of C3 into C3b is a key step of the complement response. The thirteen residue peptide, compstatin, inhibits the activation of C3. In chapter 4 we describe the crystal structure of C3c in complex with compstatin. The structure shows that compstatin binds to domains MG4 and MG5 of the stable MG-ring. Compstatin does not induce a structural change in C3c; however, compstatin itself undergoes a large conformational change upon binding. Possibly compstatin binds to an exosite on C3 for substrate binding to the convertase and thereby sterically hinders C3 activation. This structure, together with the structures of C3, C3b and C3c, may lead to enhanced compstatin analogues and create new opportunities for drug design to target a wide variety of immune complex diseases. In the past two years long-awaited advances in structural biology of the central steps of complement activity have provided a wealth of information. In chapter 5 we discuss the recently solved crystal structure of factor B and the crystal and electron-microscopy structures of C3 and all of its activation products. We relate the structural insights of these molecules to their biological function in the complement response. In summary, the crystal structures of the central complement component C3, its activation products C3b and C3c, and C3c in complex with an inhibitor…

Subjects/Keywords: Scheikunde; immune system; complement; C3; C3b; crystal structure; inhibitor design; evolution

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Janssen, B. J. C. (2007). conformational complexity of complement component C3. (Doctoral Dissertation). Universiteit Utrecht. Retrieved from http://dspace.library.uu.nl:8080/handle/1874/23001

Chicago Manual of Style (16^th Edition):

Janssen, B J C. “conformational complexity of complement component C3.” 2007. Doctoral Dissertation, Universiteit Utrecht. Accessed April 14, 2021. http://dspace.library.uu.nl:8080/handle/1874/23001.

MLA Handbook (7^th Edition):

Janssen, B J C. “conformational complexity of complement component C3.” 2007. Web. 14 Apr 2021.

Vancouver:

Janssen BJC. conformational complexity of complement component C3. [Internet] [Doctoral dissertation]. Universiteit Utrecht; 2007. [cited 2021 Apr 14]. Available from: http://dspace.library.uu.nl:8080/handle/1874/23001.

Council of Science Editors:

Janssen BJC. conformational complexity of complement component C3. [Doctoral Dissertation]. Universiteit Utrecht; 2007. Available from: http://dspace.library.uu.nl:8080/handle/1874/23001

University of California – Santa Cruz

25. Cheung, Edmond. Shaping Galaxy Evolution with Galaxy Structure.

Degree: Astronomy & Astrophysics, 2014, University of California – Santa Cruz

URL: http://www.escholarship.org/uc/item/9sq624hk

► A fundamental pursuit of astronomy is to understand galaxy evolution. The enormous scales and complex physics involved in this endeavor guarantees a never-ending journey that… (more)

Subjects/Keywords: Astronomy; Astrophysics; Galaxy Bars; Galaxy Bulges; Galaxy Evolution; Galaxy Structure

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Cheung, E. (2014). Shaping Galaxy Evolution with Galaxy Structure. (Thesis). University of California – Santa Cruz. Retrieved from http://www.escholarship.org/uc/item/9sq624hk

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Cheung, Edmond. “Shaping Galaxy Evolution with Galaxy Structure.” 2014. Thesis, University of California – Santa Cruz. Accessed April 14, 2021. http://www.escholarship.org/uc/item/9sq624hk.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Cheung, Edmond. “Shaping Galaxy Evolution with Galaxy Structure.” 2014. Web. 14 Apr 2021.

Vancouver:

Cheung E. Shaping Galaxy Evolution with Galaxy Structure. [Internet] [Thesis]. University of California – Santa Cruz; 2014. [cited 2021 Apr 14]. Available from: http://www.escholarship.org/uc/item/9sq624hk.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Cheung E. Shaping Galaxy Evolution with Galaxy Structure. [Thesis]. University of California – Santa Cruz; 2014. Available from: http://www.escholarship.org/uc/item/9sq624hk

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of California – Riverside

26. Darvish Sarvestani, Behnam. Evolution of Galaxies in the Cosmic Web.

Degree: Physics, 2015, University of California – Riverside

URL: http://www.escholarship.org/uc/item/679334zr

► We study the effects of environment on the evolution of galaxies, with an emphasis on two different approaches towards the definition of environment: (1) environment… (more)

▼ We study the effects of environment on the evolution of galaxies, with an emphasis on two different approaches towards the definition of environment: (1) environment defined based on the local surface density of galaxies and (2) environment defined based on the major components of the cosmic web; i.e., filaments, clusters and the field. In the first approach, surface density field is estimated using a variety of estimators and tested with simulations. Using the estimated surface densities assigned to galaxies, we observe a strong environmental dependence on the properties of galaxies (e.g., SFR, sSFR and the quiescent fraction) at z ≤ sssim1. We explore the fractional role of stellar mass and environment in quenching the star-formation. In the second approach, we use the Multi-scale Morphology Filter algorithm to disentangle the density field into its component. We apply this method to a sample of star-forming galaxies for a large-scale structure at z∼0.84 in the HiZELS-COSMOS field. We show that the observed median SFR, stellar mass, sSFR, the mean SFR-mass relation and its scatter for star-forming galaxies do not strongly depend on the cosmic web. However, the fraction of Hα star-forming galaxies varies with environment and is enhanced in filaments. Furthermore, we study the physical properties of a spectroscopic sample of star-forming galaxies in a large filament in the COSMOS field at z∼0.53, with spectroscopic data taken with the Keck/DEIMOS spectrograph, and compare them with a control sample of field galaxies. We spectroscopically confirm the presence of a large galaxy filament (∼ 8 Mpc). We show that within the uncertainties, the ionization parameter, EW, EW versus sSFR relation, EW versus stellar mass relation, line-of-sight velocity dispersion, dynamical mass, and stellar-to-dynamical mass ratio are similar for filament and field star-forming galaxies. However, we show that on average, filament star-forming galaxies are more metal-enriched (∼ 0.1-0.15 dex) and the electron densities are significantly lower (a factor of ∼17) in filament star-forming systems compared to those in the field. Our results highlight the potential role of galaxy filaments and intermediate-density environments on the evolution of galaxies, which has been poorly investigated.

Subjects/Keywords: Astronomy; Astrophysics; Galaxy Evolution; Large-Scale Structure of the Universe

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Darvish Sarvestani, B. (2015). Evolution of Galaxies in the Cosmic Web. (Thesis). University of California – Riverside. Retrieved from http://www.escholarship.org/uc/item/679334zr

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Darvish Sarvestani, Behnam. “Evolution of Galaxies in the Cosmic Web.” 2015. Thesis, University of California – Riverside. Accessed April 14, 2021. http://www.escholarship.org/uc/item/679334zr.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Darvish Sarvestani, Behnam. “Evolution of Galaxies in the Cosmic Web.” 2015. Web. 14 Apr 2021.

Vancouver:

Darvish Sarvestani B. Evolution of Galaxies in the Cosmic Web. [Internet] [Thesis]. University of California – Riverside; 2015. [cited 2021 Apr 14]. Available from: http://www.escholarship.org/uc/item/679334zr.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Darvish Sarvestani B. Evolution of Galaxies in the Cosmic Web. [Thesis]. University of California – Riverside; 2015. Available from: http://www.escholarship.org/uc/item/679334zr

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Oulu

27. Díaz García, S. (Simón). Signatures of secular evolution in disk galaxies.

Degree: 2016, University of Oulu

URL: http://urn.fi/urn:isbn:9789526213187

► Abstract In this thesis we shed light on the formation and evolution of disk galaxies, which often host a stellar bar (about 2/3 of cases).… (more)

▼ Abstract In this thesis we shed light on the formation and evolution of disk galaxies, which often host a stellar bar (about 2/3 of cases). In particular, we address the bar-driven secular evolution, that is, the steady redistribution of stellar and gaseous material through the disk induced by the bar torques and resonances. We characterize the mass distribution of the disks in the Spitzer Survey of Stellar Structure in Galaxies (S4G, Sheth et al. 2010) and study the properties of the different stellar structure components and the interplay between them. We use 3.6µm photometry for ~ 1300 face-on and moderately inclined disk galaxies to analyze the frequency, dimensions, orientations and shapes of stellar bars, spiral arms, rings, (ring)lenses, and barlenses (i.e. lens-like structures embedded in the bars). We calculate the strength of the bars in the S4G via ellipse ﬁtting, Fourier decomposition of the galaxy images, and from the gravitational tangential-to-radial forces. We also estimate the stellar contribution to the circular velocity, allowing us to analyze the coupling between non-baryonic and stellar matter within the optical disk. We average stellar density proﬁles (1D), the disk(+bulge) component of the rotation curve, and stellar bars (2D) as a function of fundamental galaxy parameters. We complement the study with integral-ﬁeld unit kinematic data from Seidel et al. (2015b) for a subsample of 16 S4G barred galaxies. We quantify the bar-induced perturbation strengths in the stellar and gaseous disk from the kinematics, and show that they agree with the estimates obtained from the images. We also use Hα Fabry-Perot observations from Erroz-Ferrer et al. (2015) for 29 S4G disk galaxies to study the inner slope of the rotation curves. We provide possible observational evidence for the growth of bars in a Hubble time. We demonstrate the role of bars causing the spreading of the disk and the enhancement of the central stellar concentration. Our observations support the idea that Boxy/Peanut bulges in face-on perspective manifest as barlenses, that are often identfied in early-type galaxies hosting strong bars, and some of them also as inner lenses. We ﬁnd that the amount of dark matter within the optical disk scales with the total stellar mass, as expected in the ΛCDM models. We also conﬁrm that the observed inner velocity gradient is correlated with the central surface brightness, showing a strong connection between the inner shape of the potential well and the central stellar density. We show that disks and bars in early-type (T < 5 ≡ Sc) and late-type (T ≥ 5) disk galaxies, or alternatively in galaxies having total stellar masses greater or smaller than 1010M☉, are characterized by very distinct properties. Late-type disks are less centrally concentrated (many galaxies are bulge-less) and present a larger halo-to-stellar mass ratio, what probably affects the disk stability properties. The detection of bars in late-type galaxies is strongly dependent on the identification criteria. On average, bars in… Advisors/Committee Members: Salo, H. (Heikki), Laurikainen, E. (Eija).

Subjects/Keywords: galaxies: barred; galaxies: dark matter; galaxies: evolution; galaxies: statistics; galaxies: structure

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Díaz García, S. (. (2016). Signatures of secular evolution in disk galaxies. (Doctoral Dissertation). University of Oulu. Retrieved from http://urn.fi/urn:isbn:9789526213187

Chicago Manual of Style (16^th Edition):

Díaz García, S (Simón). “Signatures of secular evolution in disk galaxies.” 2016. Doctoral Dissertation, University of Oulu. Accessed April 14, 2021. http://urn.fi/urn:isbn:9789526213187.

MLA Handbook (7^th Edition):

Díaz García, S (Simón). “Signatures of secular evolution in disk galaxies.” 2016. Web. 14 Apr 2021.

Vancouver:

Díaz García S(. Signatures of secular evolution in disk galaxies. [Internet] [Doctoral dissertation]. University of Oulu; 2016. [cited 2021 Apr 14]. Available from: http://urn.fi/urn:isbn:9789526213187.

Council of Science Editors:

Díaz García S(. Signatures of secular evolution in disk galaxies. [Doctoral Dissertation]. University of Oulu; 2016. Available from: http://urn.fi/urn:isbn:9789526213187

University of Saskatchewan

28. Raveendran Thampy, Prasobh 1987-. Ecological genetics aspects of anthropogenic host-shifts in soapberry bugs (Rhopalidae).

Degree: 2016, University of Saskatchewan

URL: http://hdl.handle.net/10388/7297

► Host range expansion, or adaptation of insects to new hosts, is a worldwide phenomenon that has been observed repeatedly and extensively; still, the genetic mechanisms… (more)

▼ Host range expansion, or adaptation of insects to new hosts, is a worldwide phenomenon that has been observed repeatedly and extensively; still, the genetic mechanisms behind host-shifts are not well known. In this thesis I focus on the morphological and genetic variation associated with two recent anthropogenic host shifts in two species of soapberry bug, Leptocoris tagalicus and Jadera haematoloma.. First, I investigated the host-associated genetic differentiation in Australian Leptocoris soapberry bugs, as determined by genome-wide variation patterns. My results show that specimens feeding on two naturalized Neotropical balloon vines, (Cardiospermum halicacabum and C. grandiflorum) have longer “beaks” that those living on the native trees Atalaya hemiglauca and Alectryon tomentosus. Genetic analyses of mitochondrial haplotypes and amplified fragment length polymorphic (AFLP) markers indicate that the lineage of bugs on the annual vine C. halicacabum, is intermediate between two subspecies of L. tagalicus found on the native hosts. Moreover, where this annual vine and whitewood tree (A. hemiglauca) co-occur, the morphology and genomic composition of the bugs are similar to those occurring in allopatry. These results show that hybridization provided the genetic elements underlying the strongly differentiated ‘halicacabum bugs’. In contrast, the bugs feeding on the recently introduced perennial balloon vine (C. grandiflorum) showed no evidence of admixture, and are genetically indistinguishable from the nearby populations on a native host. Second I used a candidate gene approach to investigate the molecular genetic basis of host-adaptation in Floridian populations of the red-shouldered soapberry bug, J. haematoloma. While in Southern Florida soapberry bugs have long beaks to penetrate the large fruits of the native balloon vine (C. corindum), in northern and central Florida, bugs have evolved to feed on an introduced, flat-podded host, the Taiwanese Golden rain tree (Koelreuteria elegans). Specifically I focused on five genes because of their potential role in host preference (orco), “beak” length (Dll, dac, hth) and the adaptation to the toxic compounds of host-plants (Na+/K+-ATPase). My results suggest these genes are highly conserved in this system, and that genetic variation at these loci is not associated with the different host-plants. Advisors/Committee Members: Andres, Jose, Chilton, Neil, Gillott, Cedric, Plante, Yves.

Subjects/Keywords: Host-shifts; Molecular Evolution; Phylogenetics; Population Genetics; Population Structure

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APA (6^th Edition):

Raveendran Thampy, P. 1. (2016). Ecological genetics aspects of anthropogenic host-shifts in soapberry bugs (Rhopalidae). (Thesis). University of Saskatchewan. Retrieved from http://hdl.handle.net/10388/7297

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Raveendran Thampy, Prasobh 1987-. “Ecological genetics aspects of anthropogenic host-shifts in soapberry bugs (Rhopalidae).” 2016. Thesis, University of Saskatchewan. Accessed April 14, 2021. http://hdl.handle.net/10388/7297.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Raveendran Thampy, Prasobh 1987-. “Ecological genetics aspects of anthropogenic host-shifts in soapberry bugs (Rhopalidae).” 2016. Web. 14 Apr 2021.

Vancouver:

Raveendran Thampy P1. Ecological genetics aspects of anthropogenic host-shifts in soapberry bugs (Rhopalidae). [Internet] [Thesis]. University of Saskatchewan; 2016. [cited 2021 Apr 14]. Available from: http://hdl.handle.net/10388/7297.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Raveendran Thampy P1. Ecological genetics aspects of anthropogenic host-shifts in soapberry bugs (Rhopalidae). [Thesis]. University of Saskatchewan; 2016. Available from: http://hdl.handle.net/10388/7297

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

McMaster University

29. Ghenu, Ana-Hermina. Multicopy gene family evolution on primate Y chromosomes.

Degree: MSc, 2015, McMaster University

URL: http://hdl.handle.net/11375/18277

►

Unlike the autosomes, the Y chromosome in humans and other primates has few protein coding genes, with only a few dozen single-copy genes and several… (more)

Subjects/Keywords: Y chromosome; gene copy number evolution; Old World Primates; genome structure

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APA (6^th Edition):

Ghenu, A. (2015). Multicopy gene family evolution on primate Y chromosomes. (Masters Thesis). McMaster University. Retrieved from http://hdl.handle.net/11375/18277

Chicago Manual of Style (16^th Edition):

Ghenu, Ana-Hermina. “Multicopy gene family evolution on primate Y chromosomes.” 2015. Masters Thesis, McMaster University. Accessed April 14, 2021. http://hdl.handle.net/11375/18277.

MLA Handbook (7^th Edition):

Ghenu, Ana-Hermina. “Multicopy gene family evolution on primate Y chromosomes.” 2015. Web. 14 Apr 2021.

Vancouver:

Ghenu A. Multicopy gene family evolution on primate Y chromosomes. [Internet] [Masters thesis]. McMaster University; 2015. [cited 2021 Apr 14]. Available from: http://hdl.handle.net/11375/18277.

Council of Science Editors:

Ghenu A. Multicopy gene family evolution on primate Y chromosomes. [Masters Thesis]. McMaster University; 2015. Available from: http://hdl.handle.net/11375/18277

Penn State University

30. Schwartz, Brandon. THE ROLE OF PORE STRUCTURE IN PERMEABILITY EVOLUTION OBSERVED IN LABORATORY STUDIES OF MARCELLUS AND WOLFCAMP SHALE.

Degree: 2018, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/15889bos5313

► We explored the role of pore geometry and stiffness on the distribution of strain around pores for Marcellus and Wolfcamp shales. Relationships exist to model… (more)

▼ We explored the role of pore geometry and stiffness on the distribution of strain around pores for Marcellus and Wolfcamp shales. Relationships exist to model permeability evolution as well as bulk stiffness evolution—here we find a relationship relating these two variables to each other. Whereas bulk stiffness is determined by bulk mineralogy and initial pore structure, evolving bulk stiffness is determined by the evolution of the pore structure alone. Permeability evolution is also determined by the evolution of the pore structure. We cast the permeability evolution in terms of evolving material properties including the Poisson ratio, the crack density parameter, and the bulk modulus—all of which can be measured via acoustic waves. The end result is a method to measure permeability evolution via acoustic waves alone. We modeled the effects of fracture spacing, aspect ratio, and pore stiffness on the permeability evolution of an ellipsoid crack under uniaxial stress and varying pore pressure. We found that rocks undergoing identical compressional strain and pore pressure can undergo significantly different magnitudes of fracture closure or dilation based on these three variables. This is especially important is gas shales, where nano-porosity is challenging to characterize and heterogeneity between basins has led to disparate permeability responses in the field and in the laboratory. We found that the aspect ratio is the most sensitive parameter influencing pore compressibility. The fracture spacing becomes important when external stress is applied, but it has no significant effect when pore pressure is varied is the absence of external stress. To capture effects of mineral distribution around pores, we simulated mismatches between a pore’s skeletal stiffness and the surrounding matrix and determined that for a given strain soft pores relative to the bulk material experience greater permeability evolution than pores that are stiff relative to the surrounding matrix. While soft pores experience greater closure than stiff pores for a given applied stress, they also experience a greater amount of dilation when pore pressure increases. This highlights that while some shale basins such as the Marcellus can experience large permeability drops relative to other basins given the same production conditions, pressure maintenance may be the most important tool to preserve permeability. We compare the permeability response of Marcellus shale to Wolfcamp shale under changing strain to explore differences in pore structure between them. This work highlights that while magnitude of strain for a given stress is determined predominantly through a shale’s mineral composition, the response of transport properties to a given strain are dependent on fracture spacing, fracture geometry, and mineral distribution around pores. We dynamically stress samples of Marcellus and Wolfcamp shales and observed levels of compaction, creep, and permeability evolution. We characterize the differences between the two shales using bulk… Advisors/Committee Members: Derek Elsworth, Dissertation Advisor/Co-Advisor, Derek Elsworth, Committee Chair/Co-Chair, Hamid Emami-Meybodi, Committee Member, Shimin Liu, Committee Member, Chris J Marone, Outside Member.

Subjects/Keywords: permeability evolution; shale; pore structure; pore geometry; material stiffness; permeability enhancement

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Schwartz, B. (2018). THE ROLE OF PORE STRUCTURE IN PERMEABILITY EVOLUTION OBSERVED IN LABORATORY STUDIES OF MARCELLUS AND WOLFCAMP SHALE. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/15889bos5313

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Schwartz, Brandon. “THE ROLE OF PORE STRUCTURE IN PERMEABILITY EVOLUTION OBSERVED IN LABORATORY STUDIES OF MARCELLUS AND WOLFCAMP SHALE.” 2018. Thesis, Penn State University. Accessed April 14, 2021. https://submit-etda.libraries.psu.edu/catalog/15889bos5313.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Schwartz, Brandon. “THE ROLE OF PORE STRUCTURE IN PERMEABILITY EVOLUTION OBSERVED IN LABORATORY STUDIES OF MARCELLUS AND WOLFCAMP SHALE.” 2018. Web. 14 Apr 2021.

Vancouver:

Schwartz B. THE ROLE OF PORE STRUCTURE IN PERMEABILITY EVOLUTION OBSERVED IN LABORATORY STUDIES OF MARCELLUS AND WOLFCAMP SHALE. [Internet] [Thesis]. Penn State University; 2018. [cited 2021 Apr 14]. Available from: https://submit-etda.libraries.psu.edu/catalog/15889bos5313.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Schwartz B. THE ROLE OF PORE STRUCTURE IN PERMEABILITY EVOLUTION OBSERVED IN LABORATORY STUDIES OF MARCELLUS AND WOLFCAMP SHALE. [Thesis]. Penn State University; 2018. Available from: https://submit-etda.libraries.psu.edu/catalog/15889bos5313

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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Open Access Theses and Dissertations