subject:(Origin of life)

McMaster University

1. Tupper, Andrew. Computational Modeling of RNA Replication in an RNA World.

Degree: PhD, 2020, McMaster University

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The biology of modern life predicts the existence of an ancient RNA world. A phase of evolution in which organisms utilized RNA as a genetic… (more)

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The biology of modern life predicts the existence of an ancient RNA world. A phase of evolution in which organisms utilized RNA as a genetic material and a catalyst. However, the existence of an RNA organism necessitates RNA’s ability to self-replicate, which has yet to be proven. In this thesis, we utilize computational modeling to address some of the problems facing RNA replication. In chapter 2, we consider a polymerase ribozyme replicating by the Qβ bacteriophage mechanism. When bound to a surface, limited diffusion allows for survival so long as the termination error rate is below an error threshold. In Chapter 3, we consider the replication of short oligomers through an abiotic mechanism proposed in prebiotic experiments. When limited by substrate availability, competition results in the emergence of uniform RNA polymers from a messy prebiotic soup containing nucleotides of different chirality and sugars. In chapter 4, we consider the possibility of an RNA world lacking cytosine. Without cytosine, the ability of RNA to fold to complex secondary structures is limited. Furthermore, G-U wobble base pairing hinders the transfer of information during replication. Nevertheless, we conclude that an RNA world lacking cytosine may be possible, but more difficult for the initial emergence of life. In chapter 5, we analyze abiotic and viral mechanisms of RNA replication using known kinetic and thermodynamic data. While most mechanisms fail under non-enzymatic conditions, rolling-circle replication appears possible. In chapter 6, we extend our analysis of the rolling-circle mechanism to consider the fidelity of replication. Due to the thermodynamic penalty of incorporating an error, rolling-circle replication appears to undergo error correction. This results in highly accurate replication and circumvents Eigen’s paradox. Rolling-circle replication therefore presents an appealing option for the emergence of RNA replication in an RNA world.

Thesis

Doctor of Philosophy (PhD)

Advisors/Committee Members: Higgs, Paul, Biochemistry.

Subjects/Keywords: RNA World; Origin of life

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APA (6^th Edition):

Tupper, A. (2020). Computational Modeling of RNA Replication in an RNA World. (Doctoral Dissertation). McMaster University. Retrieved from http://hdl.handle.net/11375/25836

Chicago Manual of Style (16^th Edition):

Tupper, Andrew. “Computational Modeling of RNA Replication in an RNA World.” 2020. Doctoral Dissertation, McMaster University. Accessed January 26, 2021. http://hdl.handle.net/11375/25836.

MLA Handbook (7^th Edition):

Tupper, Andrew. “Computational Modeling of RNA Replication in an RNA World.” 2020. Web. 26 Jan 2021.

Vancouver:

Tupper A. Computational Modeling of RNA Replication in an RNA World. [Internet] [Doctoral dissertation]. McMaster University; 2020. [cited 2021 Jan 26]. Available from: http://hdl.handle.net/11375/25836.

Council of Science Editors:

Tupper A. Computational Modeling of RNA Replication in an RNA World. [Doctoral Dissertation]. McMaster University; 2020. Available from: http://hdl.handle.net/11375/25836

University of Sydney

2. Ben-Barak, Idan. States of origin: influences on research into the origins of life .

Degree: 2012, University of Sydney

URL: http://hdl.handle.net/2123/12227

► The twentieth century has seen a continuous process of redefinition of scientific understanding of the process by which life appeared on planet earth, and the… (more)

Subjects/Keywords: Origin of life; NASA

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

APA (6^th Edition):

Ben-Barak, I. (2012). States of origin: influences on research into the origins of life . (Thesis). University of Sydney. Retrieved from http://hdl.handle.net/2123/12227

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):

Ben-Barak, Idan. “States of origin: influences on research into the origins of life .” 2012. Thesis, University of Sydney. Accessed January 26, 2021. http://hdl.handle.net/2123/12227.

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

MLA Handbook (7^th Edition):

Ben-Barak, Idan. “States of origin: influences on research into the origins of life .” 2012. Web. 26 Jan 2021.

Vancouver:

Ben-Barak I. States of origin: influences on research into the origins of life . [Internet] [Thesis]. University of Sydney; 2012. [cited 2021 Jan 26]. Available from: http://hdl.handle.net/2123/12227.

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

Council of Science Editors:

Ben-Barak I. States of origin: influences on research into the origins of life . [Thesis]. University of Sydney; 2012. Available from: http://hdl.handle.net/2123/12227

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

University of California – Berkeley

3. Mangiante, David Michael. Metal and mineral catalyzed organic photochemistry in modern and prebiotic environments.

Degree: Earth & Planetary Science, 2016, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/6jq7m95b

► Minerals and metals serve important roles in the organic geochemistry of natural environments. Mobility of organics, catalysis of degradation, and redox catalysis are among the… (more)

▼ Minerals and metals serve important roles in the organic geochemistry of natural environments. Mobility of organics, catalysis of degradation, and redox catalysis are among the processes affected by minerals. With the addition of ultraviolet light a new suite of photo-induced redox reactions is possible including reductive and oxidative ligand-to-metal/mineral charge transfer. Such reactions allow for novel chemistry that has relevance to the modern Earth as well as the pre-biotic origin of life. This thesis describes processes by which electrons transfer between minerals/metals and organic ligands relevant to natural systems as well as the origins of life. I present evidence of ultrafast electron transfer and the production of radical intermediates essential to deducing redox reaction mechanisms. I also present methods for communicating understanding of interfacial chemistry to the public that promote engagement in science. This thesis is broadly applicable to those interested in mineral organic photochemistry, electron transfer, the origin of life, and science teaching methods.I probed the chemistry between organic molecules and minerals/metals, using pump/probe transient absorption (TA) spectroscopy to observe the dynamics of electrons and vibrational modes at timescales ranging from picoseconds to nanoseconds. This technique can be conducted in solution and can be highly sensitive to intermediate reaction products. I examined the photolysis of the metal carboloto, ferric oxalate, under UV irradiation using mid-infrared TA spectroscopy in both D2O and H2O. Ferric oxalate is a model molecule for natural systems and is used to measure photo flux due to its well-characterized quantum efficiency. However, the mechanism of its photolysis is debated. This was the first time the intermediates of ferric oxalate photolysis were observed using techniques sensitive to the vibrational states of organic molecules. I observed the rapid intramolecular charge transfer and the production of CO2 and tentatively CO2•–. Additionally, we observed intermediate states that we interpret to be CO2 disassociating from ferrous iron, a signature never before reported. Investigations of photo-induced electron transfer were expanded to ZnS nanoparticles and fumarate. Fumarate is an intermediate metabolite in the tricarboxilic acid (TCA) cycle, which is a part of core metabolism in modern organisms. It undergoes a two-electron reduction to form succinate. Reductive versions of the TCA cycle may have been important for the origin of prebiotic metabolism. I measured the effect of adsorbed fumarate on the electronic states of photo-excited ZnS and observed electron transfer both at short (<1 ps) and long (>1 ns) timescales. Additionally, I observed an electronic signature tentatively attributed to fumarate radical, which persisted for at least 8 nanoseconds. The appearance of a long-lived radical intermediate product and the rapid initial electron transfer from the mineral to the organic suggests that ZnS could be a viable catalyst for prebiotic…

Subjects/Keywords: Geochemistry; Origin of life; Photochemistry; Transient Spectroscopy

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APA (6^th Edition):

Mangiante, D. M. (2016). Metal and mineral catalyzed organic photochemistry in modern and prebiotic environments. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/6jq7m95b

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):

Mangiante, David Michael. “Metal and mineral catalyzed organic photochemistry in modern and prebiotic environments.” 2016. Thesis, University of California – Berkeley. Accessed January 26, 2021. http://www.escholarship.org/uc/item/6jq7m95b.

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

MLA Handbook (7^th Edition):

Mangiante, David Michael. “Metal and mineral catalyzed organic photochemistry in modern and prebiotic environments.” 2016. Web. 26 Jan 2021.

Vancouver:

Mangiante DM. Metal and mineral catalyzed organic photochemistry in modern and prebiotic environments. [Internet] [Thesis]. University of California – Berkeley; 2016. [cited 2021 Jan 26]. Available from: http://www.escholarship.org/uc/item/6jq7m95b.

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

Council of Science Editors:

Mangiante DM. Metal and mineral catalyzed organic photochemistry in modern and prebiotic environments. [Thesis]. University of California – Berkeley; 2016. Available from: http://www.escholarship.org/uc/item/6jq7m95b

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

University of Bristol

4. Avila Castro, Alberto. Peptide Morse code : α/β-peptide β-sheets for information storage and transmission.

Degree: PhD, 2020, University of Bristol

URL: http://hdl.handle.net/1983/59019909-b6b2-4cc9-bef0-01223d3b9cfc

► The origin of life remains a most relevant scientific problem. It is clear that present-day life results from Darwinian evolution. However, in a prebiotic Earth,… (more)

Subjects/Keywords: Origin of life; peptide secondary structure

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APA (6^th Edition):

Avila Castro, A. (2020). Peptide Morse code : α/β-peptide β-sheets for information storage and transmission. (Doctoral Dissertation). University of Bristol. Retrieved from http://hdl.handle.net/1983/59019909-b6b2-4cc9-bef0-01223d3b9cfc

Chicago Manual of Style (16^th Edition):

Avila Castro, Alberto. “Peptide Morse code : α/β-peptide β-sheets for information storage and transmission.” 2020. Doctoral Dissertation, University of Bristol. Accessed January 26, 2021. http://hdl.handle.net/1983/59019909-b6b2-4cc9-bef0-01223d3b9cfc.

MLA Handbook (7^th Edition):

Avila Castro, Alberto. “Peptide Morse code : α/β-peptide β-sheets for information storage and transmission.” 2020. Web. 26 Jan 2021.

Vancouver:

Avila Castro A. Peptide Morse code : α/β-peptide β-sheets for information storage and transmission. [Internet] [Doctoral dissertation]. University of Bristol; 2020. [cited 2021 Jan 26]. Available from: http://hdl.handle.net/1983/59019909-b6b2-4cc9-bef0-01223d3b9cfc.

Council of Science Editors:

Avila Castro A. Peptide Morse code : α/β-peptide β-sheets for information storage and transmission. [Doctoral Dissertation]. University of Bristol; 2020. Available from: http://hdl.handle.net/1983/59019909-b6b2-4cc9-bef0-01223d3b9cfc

University of Bristol

5. Avila Castro, Alberto. Peptide Morse code : α/β-peptide β-sheets for information storage and transmission.

Degree: PhD, 2020, University of Bristol

URL: https://research-information.bris.ac.uk/en/studentTheses/59019909-b6b2-4cc9-bef0-01223d3b9cfc ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.809899

► The origin of life remains a most relevant scientific problem. It is clear that present-day life results from Darwinian evolution. However, in a prebiotic Earth,… (more)

Subjects/Keywords: Origin of life; peptide secondary structure

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

APA (6^th Edition):

Avila Castro, A. (2020). Peptide Morse code : α/β-peptide β-sheets for information storage and transmission. (Doctoral Dissertation). University of Bristol. Retrieved from https://research-information.bris.ac.uk/en/studentTheses/59019909-b6b2-4cc9-bef0-01223d3b9cfc ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.809899

Chicago Manual of Style (16^th Edition):

Avila Castro, Alberto. “Peptide Morse code : α/β-peptide β-sheets for information storage and transmission.” 2020. Doctoral Dissertation, University of Bristol. Accessed January 26, 2021. https://research-information.bris.ac.uk/en/studentTheses/59019909-b6b2-4cc9-bef0-01223d3b9cfc ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.809899.

MLA Handbook (7^th Edition):

Avila Castro, Alberto. “Peptide Morse code : α/β-peptide β-sheets for information storage and transmission.” 2020. Web. 26 Jan 2021.

Vancouver:

Avila Castro A. Peptide Morse code : α/β-peptide β-sheets for information storage and transmission. [Internet] [Doctoral dissertation]. University of Bristol; 2020. [cited 2021 Jan 26]. Available from: https://research-information.bris.ac.uk/en/studentTheses/59019909-b6b2-4cc9-bef0-01223d3b9cfc ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.809899.

Council of Science Editors:

Avila Castro A. Peptide Morse code : α/β-peptide β-sheets for information storage and transmission. [Doctoral Dissertation]. University of Bristol; 2020. Available from: https://research-information.bris.ac.uk/en/studentTheses/59019909-b6b2-4cc9-bef0-01223d3b9cfc ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.809899

McMaster University

6. Shah, Vismay. Comparing Protocell and Surface-Based Models of RNA Replicator Systems and Determining Favourable Conditions for Linkage of Functional Strands.

Degree: MSc, 2019, McMaster University

URL: http://hdl.handle.net/11375/24901

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In hypothesized RNA-World scenarios, replication of RNA strands is catalyzed by error-prone polymerase ribozymes. Incorrect replication leads to the creation of non-functional, parasitic strands which… (more)

▼

In hypothesized RNA-World scenarios, replication of RNA strands is catalyzed by error-prone polymerase ribozymes. Incorrect replication leads to the creation of non-functional, parasitic strands which can invade systems of replicators and lead to their death. Studies have shown two solutions to this problem: spatial clustering of polymerases in models featuring elements to limit diffusion, and group selection in models featuring protocells. Making a quantitative comparison of the methods using results from the literature has proven difficult due to differences in model design. Here we develop computational models of replication of a system of polymerases, polymerase complements and parasites in both spatial models and protocell models with near identical dynamics to make meaningful comparison viable. We compare the models in terms of the maximum mutation rate survivable by the system (the error threshold) as well as the minimum replication rate constant required. We find that protocell models are capable of sustaining much higher maximum mutation rates, and survive under much lower minimum replication rates than equivalent surface models. We then consider cases where parasites are favoured in replication, and show that the advantage of protocell models is increased. Given that a system of RNA strands undergoing catalytic replication by a polymerase is fairly survivable in protocell models, we attempt to determine whether isolated strands can develop into genomes. We extend our protocell model to include additional functional strands varying in length (and thus replication rate) and allow for the linkage of strands to form proto-chromosomes. We determine that linkage is possible over a broad range of lengths, and is stable when considering the joining of short functional strands to the polymerase (and the same for the complementary sequences). Moreover, linkage of short functional strands to the polymerase assures more cells remain viable post division by ensuing a good quantity of polymerase equivalents are present in the parent cell prior to splitting.

Thesis

Master of Science (MSc)

Collections of RNA polymers are good candidates for the origin of life. RNA is able to store genetic information and act as polymerase ribozymes allowing RNA to replicate RNA. Polymerases have been experimentally developed in labs, however none are sufficiently general to work well in an origins of life setting. These polymerases are vulnerable to mistakes during copying, making survival of RNA systems difficult. Such systems have been studied by computer simulations, showing that the strands need to be kept together for survival, either on surfaces or in primitive cells. Differences in the details of the models has made comparing the surfaces to cells difficult. This work creates a unified model base allowing for comparison of these two environments. We find that the existence of primitive cells is very beneficial to systems of RNA polymers and thus it is likely such cells existed at the origin of life.

Advisors/Committee Members: Higgs, Paul, Physics and Astronomy.

Subjects/Keywords: Origin of Life; RNA World; Protocells; Surface; Computational Models; RNA Polymerase

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

APA (6^th Edition):

Shah, V. (2019). Comparing Protocell and Surface-Based Models of RNA Replicator Systems and Determining Favourable Conditions for Linkage of Functional Strands. (Masters Thesis). McMaster University. Retrieved from http://hdl.handle.net/11375/24901

Chicago Manual of Style (16^th Edition):

Shah, Vismay. “Comparing Protocell and Surface-Based Models of RNA Replicator Systems and Determining Favourable Conditions for Linkage of Functional Strands.” 2019. Masters Thesis, McMaster University. Accessed January 26, 2021. http://hdl.handle.net/11375/24901.

MLA Handbook (7^th Edition):

Shah, Vismay. “Comparing Protocell and Surface-Based Models of RNA Replicator Systems and Determining Favourable Conditions for Linkage of Functional Strands.” 2019. Web. 26 Jan 2021.

Vancouver:

Shah V. Comparing Protocell and Surface-Based Models of RNA Replicator Systems and Determining Favourable Conditions for Linkage of Functional Strands. [Internet] [Masters thesis]. McMaster University; 2019. [cited 2021 Jan 26]. Available from: http://hdl.handle.net/11375/24901.

Council of Science Editors:

Shah V. Comparing Protocell and Surface-Based Models of RNA Replicator Systems and Determining Favourable Conditions for Linkage of Functional Strands. [Masters Thesis]. McMaster University; 2019. Available from: http://hdl.handle.net/11375/24901

University of Cambridge

7. Attwater, James. Ice as a medium for RNA-catalysed RNA synthesis and evolution.

Degree: PhD, 2011, University of Cambridge

URL: https://doi.org/10.17863/CAM.15946 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609847

► A critical event in the origin of life is thought to have been the emergence of a molecule capable of self-replication and evolution. According to… (more)

▼ A critical event in the origin of life is thought to have been the emergence of a molecule capable of self-replication and evolution. According to the RNA World hypothesis, this could have been an RNA polymerase ribozyme capable of generating copies of itself from simple nucleotide precursors. In vitro evolution experiments have provided modern examples of such ribozymes, such as the R18 RNA polymerase ribozyme, exhibiting basic levels of this crucial catalytic activity; R18’s activity, however, falls far short of that required of an RNA replicase, leaving unanswered the question of whether RNA can catalyse its self-replication. This thesis describes the development and use of a novel in vitro selection system, Compartmentalised Bead-Tagging (CBT), to isolate variants of the R18 ribozyme with improved sequence generality and extension capabilities. CBT evolution and engineering of polymerase ribozymes, together with RNA template evolution, allowed the synthesis of RNA molecules over 100 nucleotides long, as well as the RNA-catalysed transcription of a catalytic hammerhead ribozyme. This demonstrates the catalytic capabilities of ribozyme polymerases. The R18 ribozyme was also exploited as an analogue of a primordial replicase, to determine replicase behaviour in different reaction environments. Substantial ribozyme polymerisation occurred at −7˚C in the liquid eutectic phase of water-ice; increased ribozyme stability at these low temperatures allowed longer extension products to be generated than at ambient temperatures. The concentration effect of eutectic phase formation could also yield RNA synthesis from dilute solutions of substrates, and provide quasicellular compartmentalisation of ribozymes. These beneficial physicochemical features of ice make it a potential protocellular medium for the emergence of primordial replicases. Ice also could serve as a medium for CBT, allowing the isolation of a polymerase ribozyme adapted to the low temperatures in the ice phase, demonstrating the primordial potential and modern feasibility of ribozyme evolution in ice.

Subjects/Keywords: 610; RNA; Ribozyme; Origin of Life; RNA world; Ice

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

APA (6^th Edition):

Attwater, J. (2011). Ice as a medium for RNA-catalysed RNA synthesis and evolution. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.15946 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609847

Chicago Manual of Style (16^th Edition):

Attwater, James. “Ice as a medium for RNA-catalysed RNA synthesis and evolution.” 2011. Doctoral Dissertation, University of Cambridge. Accessed January 26, 2021. https://doi.org/10.17863/CAM.15946 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609847.

MLA Handbook (7^th Edition):

Attwater, James. “Ice as a medium for RNA-catalysed RNA synthesis and evolution.” 2011. Web. 26 Jan 2021.

Vancouver:

Attwater J. Ice as a medium for RNA-catalysed RNA synthesis and evolution. [Internet] [Doctoral dissertation]. University of Cambridge; 2011. [cited 2021 Jan 26]. Available from: https://doi.org/10.17863/CAM.15946 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609847.

Council of Science Editors:

Attwater J. Ice as a medium for RNA-catalysed RNA synthesis and evolution. [Doctoral Dissertation]. University of Cambridge; 2011. Available from: https://doi.org/10.17863/CAM.15946 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609847

University of Cambridge

8. Attwater, James. Ice as a medium for RNA-catalysed RNA synthesis and evolution.

Degree: PhD, 2011, University of Cambridge

URL: https://www.repository.cam.ac.uk/handle/1810/246525https://www.repository.cam.ac.uk/bitstream/1810/246525/2/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/246525/3/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/246525/6/James%20Attwater%20Thesis.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/246525/7/James%20Attwater%20Thesis.pdf.jpg

► A critical event in the origin of life is thought to have been the emergence of a molecule capable of self-replication and evolution. According to… (more)

▼ A critical event in the origin of life is thought to have been the emergence of a molecule capable of self-replication and evolution. According to the RNA World hypothesis, this could have been an RNA polymerase ribozyme capable of generating copies of itself from simple nucleotide precursors. In vitro evolution experiments have provided modern examples of such ribozymes, such as the R18 RNA polymerase ribozyme, exhibiting basic levels of this crucial catalytic activity; R18’s activity, however, falls far short of that required of an RNA replicase, leaving unanswered the question of whether RNA can catalyse its self-replication. This thesis describes the development and use of a novel in vitro selection system, Compartmentalised Bead-Tagging (CBT), to isolate variants of the R18 ribozyme with improved sequence generality and extension capabilities. CBT evolution and engineering of polymerase ribozymes, together with RNA template evolution, allowed the synthesis of RNA molecules over 100 nucleotides long, as well as the RNA-catalysed transcription of a catalytic hammerhead ribozyme. This demonstrates the catalytic capabilities of ribozyme polymerases. The R18 ribozyme was also exploited as an analogue of a primordial replicase, to determine replicase behaviour in different reaction environments. Substantial ribozyme polymerisation occurred at −7˚C in the liquid eutectic phase of water-ice; increased ribozyme stability at these low temperatures allowed longer extension products to be generated than at ambient temperatures. The concentration effect of eutectic phase formation could also yield RNA synthesis from dilute solutions of substrates, and provide quasicellular compartmentalisation of ribozymes. These beneficial physicochemical features of ice make it a potential protocellular medium for the emergence of primordial replicases. Ice also could serve as a medium for CBT, allowing the isolation of a polymerase ribozyme adapted to the low temperatures in the ice phase, demonstrating the primordial potential and modern feasibility of ribozyme evolution in ice.

Subjects/Keywords: RNA; Ribozyme; Origin of Life; RNA world; Ice

Record Details Similar Records Cite « Share

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

APA (6^th Edition):

Attwater, J. (2011). Ice as a medium for RNA-catalysed RNA synthesis and evolution. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/246525https://www.repository.cam.ac.uk/bitstream/1810/246525/2/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/246525/3/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/246525/6/James%20Attwater%20Thesis.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/246525/7/James%20Attwater%20Thesis.pdf.jpg

Chicago Manual of Style (16^th Edition):

Attwater, James. “Ice as a medium for RNA-catalysed RNA synthesis and evolution.” 2011. Doctoral Dissertation, University of Cambridge. Accessed January 26, 2021. https://www.repository.cam.ac.uk/handle/1810/246525https://www.repository.cam.ac.uk/bitstream/1810/246525/2/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/246525/3/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/246525/6/James%20Attwater%20Thesis.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/246525/7/James%20Attwater%20Thesis.pdf.jpg.

MLA Handbook (7^th Edition):

Attwater, James. “Ice as a medium for RNA-catalysed RNA synthesis and evolution.” 2011. Web. 26 Jan 2021.

Vancouver:

Attwater J. Ice as a medium for RNA-catalysed RNA synthesis and evolution. [Internet] [Doctoral dissertation]. University of Cambridge; 2011. [cited 2021 Jan 26]. Available from: https://www.repository.cam.ac.uk/handle/1810/246525https://www.repository.cam.ac.uk/bitstream/1810/246525/2/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/246525/3/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/246525/6/James%20Attwater%20Thesis.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/246525/7/James%20Attwater%20Thesis.pdf.jpg.

Council of Science Editors:

Attwater J. Ice as a medium for RNA-catalysed RNA synthesis and evolution. [Doctoral Dissertation]. University of Cambridge; 2011. Available from: https://www.repository.cam.ac.uk/handle/1810/246525https://www.repository.cam.ac.uk/bitstream/1810/246525/2/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/246525/3/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/246525/6/James%20Attwater%20Thesis.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/246525/7/James%20Attwater%20Thesis.pdf.jpg

Boston University

9. Goldford, Joshua Elliot. Multi-scale metabolism: from the origin of life to microbial ecology.

Degree: PhD, Bioinformatics GRS, 2018, Boston University

URL: http://hdl.handle.net/2144/33239

► Metabolism is a key attribute of life on Earth at multiple spatial and temporal scales, involved in processes ranging from cellular reproduction to biogeochemical cycles.… (more)

▼ Metabolism is a key attribute of life on Earth at multiple spatial and temporal scales, involved in processes ranging from cellular reproduction to biogeochemical cycles. While metabolic network modeling approaches have enabled significant progress at the cellular-scale, extending these techniques to address questions at both the ecosystem and planetary-scales remains highly unexplored. In this thesis, I integrate various multi-scale metabolic network modeling approaches to address key questions with regard to both the long-term evolution of metabolism in the biosphere and the metabolic processes that take place in complex microbial communities. The first portion of my thesis work, focused on the evolution of ancient metabolic networks, attempts to model the emergence of ecosystem-level metabolism from simple geochemical precursors. By integrating network-based algorithms, physiochemical constraints, and geochemical estimates of ancient Earth, I explored whether a complex metabolic network could have emerged without phosphate, a key molecular component in modern-day living systems, known to be poorly available at the onset of life. We found that phosphate may have not been essential in early living systems, and that thioesters may have been the primitive energy currency in ancient metabolic networks. By generalizing this approach to explore the scope of geochemical scenarios that could have given rise to living systems, I found that other key biomolecules, including fixed nitrogen, may have not been required at the earliest stages in biochemical evolution. The second portion of my thesis deals with a different aspect of ecosystem-level metabolism, namely the role of metabolism in shaping the structure of microbial communities. I studied the relationship between metabolism and microbial community assembly using microbial communities grown in synthetic laboratory environments. We found that a generalized statistical consumer-resource model recapitulates the emergent phenomena observed in these experiments. Future work could seek to better clarify the connection between the fundamental rules that led to life’s emergence over 4 billion years ago and the laws that shape microbial ecosystems today. An ecosystems-level metabolic perspective may aid in our understanding of both the emergence and maintenance of the biosphere. Advisors/Committee Members: Segre, Daniel (advisor).

Subjects/Keywords: Bioinformatics; Metabolic modeling; Metabolism; Microbial ecology; Origin of life; Thermodynamics

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APA (6^th Edition):

Goldford, J. E. (2018). Multi-scale metabolism: from the origin of life to microbial ecology. (Doctoral Dissertation). Boston University. Retrieved from http://hdl.handle.net/2144/33239

Chicago Manual of Style (16^th Edition):

Goldford, Joshua Elliot. “Multi-scale metabolism: from the origin of life to microbial ecology.” 2018. Doctoral Dissertation, Boston University. Accessed January 26, 2021. http://hdl.handle.net/2144/33239.

MLA Handbook (7^th Edition):

Goldford, Joshua Elliot. “Multi-scale metabolism: from the origin of life to microbial ecology.” 2018. Web. 26 Jan 2021.

Vancouver:

Goldford JE. Multi-scale metabolism: from the origin of life to microbial ecology. [Internet] [Doctoral dissertation]. Boston University; 2018. [cited 2021 Jan 26]. Available from: http://hdl.handle.net/2144/33239.

Council of Science Editors:

Goldford JE. Multi-scale metabolism: from the origin of life to microbial ecology. [Doctoral Dissertation]. Boston University; 2018. Available from: http://hdl.handle.net/2144/33239

University of Missouri – Columbia

10. Novy, Ronald, 1965-. Home aestheticus : species being and the struggle for existence.

Degree: PhD, 2007, University of Missouri – Columbia

URL: http://hdl.handle.net/10355/5946

► [ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] In this paper, I argue for the homo aestheticus thesis - the claim that… (more)

Subjects/Keywords: Life – Origin; Philosophy of nature

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APA (6^th Edition):

Novy, Ronald, 1. (2007). Home aestheticus : species being and the struggle for existence. (Doctoral Dissertation). University of Missouri – Columbia. Retrieved from http://hdl.handle.net/10355/5946

Chicago Manual of Style (16^th Edition):

Novy, Ronald, 1965-. “Home aestheticus : species being and the struggle for existence.” 2007. Doctoral Dissertation, University of Missouri – Columbia. Accessed January 26, 2021. http://hdl.handle.net/10355/5946.

MLA Handbook (7^th Edition):

Novy, Ronald, 1965-. “Home aestheticus : species being and the struggle for existence.” 2007. Web. 26 Jan 2021.

Vancouver:

Novy, Ronald 1. Home aestheticus : species being and the struggle for existence. [Internet] [Doctoral dissertation]. University of Missouri – Columbia; 2007. [cited 2021 Jan 26]. Available from: http://hdl.handle.net/10355/5946.

Council of Science Editors:

Novy, Ronald 1. Home aestheticus : species being and the struggle for existence. [Doctoral Dissertation]. University of Missouri – Columbia; 2007. Available from: http://hdl.handle.net/10355/5946

University of South Florida

11. Szenay, Brian Craig. Modeling Potential Chemical Environments: Implications for Astrobiology.

Degree: 2013, University of South Florida

URL: https://scholarcommons.usf.edu/etd/4847

► Modeling chemical environments is an important step to understanding the diversity of prebiotic systems that may have formed on the early earth or potentially can… (more)

Subjects/Keywords: early geochemistry; iron; origin of life; phosphorus; prebiotic evolution; Geochemistry

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APA (6^th Edition):

Szenay, B. C. (2013). Modeling Potential Chemical Environments: Implications for Astrobiology. (Thesis). University of South Florida. Retrieved from https://scholarcommons.usf.edu/etd/4847

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):

Szenay, Brian Craig. “Modeling Potential Chemical Environments: Implications for Astrobiology.” 2013. Thesis, University of South Florida. Accessed January 26, 2021. https://scholarcommons.usf.edu/etd/4847.

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

MLA Handbook (7^th Edition):

Szenay, Brian Craig. “Modeling Potential Chemical Environments: Implications for Astrobiology.” 2013. Web. 26 Jan 2021.

Vancouver:

Szenay BC. Modeling Potential Chemical Environments: Implications for Astrobiology. [Internet] [Thesis]. University of South Florida; 2013. [cited 2021 Jan 26]. Available from: https://scholarcommons.usf.edu/etd/4847.

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

Council of Science Editors:

Szenay BC. Modeling Potential Chemical Environments: Implications for Astrobiology. [Thesis]. University of South Florida; 2013. Available from: https://scholarcommons.usf.edu/etd/4847

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

University of Cambridge

12. Ding, Yang. Self-assembled Precipitation Membranes and the Implications for Natural Sciences.

Degree: PhD, 2020, University of Cambridge

URL: https://www.repository.cam.ac.uk/handle/1810/308261

► Far from thermodynamic equilibrium, many precipitation reactions can generate complex membrane structures. Such membranes are of great research interest in fields ranging from chemical engineering… (more)

▼ Far from thermodynamic equilibrium, many precipitation reactions can generate complex membrane structures. Such membranes are of great research interest in fields ranging from chemical engineering to geophysics, and even biology where they are thought to have played a vital role in the origin of life. Usually, the transport of chemicals by combined buoyancy, osmotic and diffusive mechanisms, support the precipitation reaction. In order to study these transport processes across a growing selective membrane, we use reactions forming chemical gardens. We focus on four studies: one in a micro-fluidic reactor where flow is forced by a pump and others in a Hele-Shaw cell where the flow is driven by the membrane itself. In the first, with externally forced flow, the growth of a wavy precipitate membrane is observed. We establish that its growth is controlled by transverse diffusion and dispersion of the ions in solution. We develop a precipitation model, taking into account diffusion of ions through the precipitate and through an adjacent gel layer. Results from our theory are in excellent agreement with the measurements and show that a wavy precipitate surface can enhance the transverse transport of ions by extracting energy from a longitudinal flow field. In the second study, the chemical gardens are formed in a horizontal Hele-Shaw cell. We examine the changes of the membrane morphology associated with the concentration of reactants. We also survey the growth rate of membrane, which is determined by the osmotic flow as well as by concentration effects. The motion of the fluid is visualized in order to understand the transport process. The pressure inside the membrane structure is measured and different patterns of pressure changes are identified. A pressure-concentration model is proposed to explain the harmonic pressure changes of this system. In our third study, we observe that a chemical garden confined to two dimensions is a clock reaction involving a phase change, so that after a reproducible and controllable induction period it explodes. The explosion of chemical garden is caused by the decreasing permeability of membrane, owing to the gradual blocking of its pores by the precipitate. A pressure-concentration-thickness model is developed to analyse the explosive system. In our final study, we return to a classic chemical garden where gravity force is of relevance. Oscillatory growth of tubes in the vertical direction is witnessed. The chemical gardens explode at a late phase of experiments, with longer life times than the corresponding horizontal cases. We also observe descending flow with a surrounding precipitation structure, which is controlled by gravity.

Subjects/Keywords: chemobrionics; chemical gardens; fluid dynamics; origin of life; clock reactions

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APA (6^th Edition):

Ding, Y. (2020). Self-assembled Precipitation Membranes and the Implications for Natural Sciences. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/308261

Chicago Manual of Style (16^th Edition):

Ding, Yang. “Self-assembled Precipitation Membranes and the Implications for Natural Sciences.” 2020. Doctoral Dissertation, University of Cambridge. Accessed January 26, 2021. https://www.repository.cam.ac.uk/handle/1810/308261.

MLA Handbook (7^th Edition):

Ding, Yang. “Self-assembled Precipitation Membranes and the Implications for Natural Sciences.” 2020. Web. 26 Jan 2021.

Vancouver:

Ding Y. Self-assembled Precipitation Membranes and the Implications for Natural Sciences. [Internet] [Doctoral dissertation]. University of Cambridge; 2020. [cited 2021 Jan 26]. Available from: https://www.repository.cam.ac.uk/handle/1810/308261.

Council of Science Editors:

Ding Y. Self-assembled Precipitation Membranes and the Implications for Natural Sciences. [Doctoral Dissertation]. University of Cambridge; 2020. Available from: https://www.repository.cam.ac.uk/handle/1810/308261

13. Roca, Flávio Oliveira. Contribuição de conceitos químicos ao estudo da origem da vida na disciplina de biologia.

Degree: Mestrado, Educação, 2012, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/48/48134/tde-04072012-101801/ ;

►

Esta pesquisa apresenta os resultados de um levantamento empírico de livros didáticos de Biologia e Química aprovados no PNLEM 2007, no sentido de investigar as… (more)

▼

Esta pesquisa apresenta os resultados de um levantamento empírico de livros didáticos de Biologia e Química aprovados no PNLEM 2007, no sentido de investigar as demandas de conceitos químicos no estudo de uma temática própria da disciplina de Biologia: a origem da vida. Adicionalmente, esta dissertação coteja essas demandas conceituais com os correspondentes saberes químicos sequenciados nos capítulos das coleções de Química e discute a potencial interlocução entre os conjuntos de saberes das duas disciplinas, visto que fazem parte da mesma área do conhecimento escolar. Considerando-se todas as obras divididas em três volumes um para cada ano do Ensino Médio e excetuando-se os volumes únicos, foram analisados os capítulos que tratam da origem da vida em quatro coleções de Biologia e todo o conteúdo programático de duas obras de Química. Reconhecendo a relevância do livro didático no cenário educacional brasileiro, o caráter notadamente disciplinar do currículo e as especificidades do ensino de Ciências, este trabalho reúne argumentos teóricos que fundamentam a necessidade de um olhar abrangente sobre a realidade, sempre complexa e multifacetada.

This research presents the results of an empirical survey from textbooks of Biology and Chemistry approved in PNLEM 2007, to investigate the demands of chemical concepts in the study of one the subjects in Biology: the origin of life. In addition to that, this dissertation collates these conceptual demands with the corresponding chemical knowledge sequenced in chapters of the chemical collections and discusses the potential dialogue between the sets of knowledge of those two disciplines, as part of the same area of school knowledge. Considering the works divided into three volumes one for each year of high school and except for the single volumes, were analyzed the chapters dealing with the origin of life in four collections of Biology and whole academic program in two works of Chemistry. Recognizing the relevance of the textbook in Brazilian educational scenario, the notably disciplinary character of the curriculum and the specificities of Natural Sciences who originated the school disciplines of Biology and Chemistry, this work gathers theoretical arguments that justify the need for a comprehensive look at the reality, always complex and multifaceted.

Advisors/Committee Members: Bizzo, Nelio Marco Vincenzo.

Subjects/Keywords: Ensino de ciências; Livro didático; Origem da vida; Origin of life; Science teaching; Textbook

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APA (6^th Edition):

Roca, F. O. (2012). Contribuição de conceitos químicos ao estudo da origem da vida na disciplina de biologia. (Masters Thesis). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/48/48134/tde-04072012-101801/ ;

Chicago Manual of Style (16^th Edition):

Roca, Flávio Oliveira. “Contribuição de conceitos químicos ao estudo da origem da vida na disciplina de biologia.” 2012. Masters Thesis, University of São Paulo. Accessed January 26, 2021. http://www.teses.usp.br/teses/disponiveis/48/48134/tde-04072012-101801/ ;.

MLA Handbook (7^th Edition):

Roca, Flávio Oliveira. “Contribuição de conceitos químicos ao estudo da origem da vida na disciplina de biologia.” 2012. Web. 26 Jan 2021.

Vancouver:

Roca FO. Contribuição de conceitos químicos ao estudo da origem da vida na disciplina de biologia. [Internet] [Masters thesis]. University of São Paulo; 2012. [cited 2021 Jan 26]. Available from: http://www.teses.usp.br/teses/disponiveis/48/48134/tde-04072012-101801/ ;.

Council of Science Editors:

Roca FO. Contribuição de conceitos químicos ao estudo da origem da vida na disciplina de biologia. [Masters Thesis]. University of São Paulo; 2012. Available from: http://www.teses.usp.br/teses/disponiveis/48/48134/tde-04072012-101801/ ;

Harvard University

14. Budin, Itay. Physical Models for the Early Evolution of Cell Membranes.

Degree: PhD, Biochemistry, 2012, Harvard University

URL: http://nrs.harvard.edu/urn-3:HUL.InstRepos:9904006

► Cells use lipid membranes to organize and define their chemical environments. All cell membranes are based on a common structure: bilayers composed of phospholipids with… (more)

▼ Cells use lipid membranes to organize and define their chemical environments. All cell membranes are based on a common structure: bilayers composed of phospholipids with two hydrocarbon chains. How did biology converge on this particular solution for cellular encapsulation? The first cell membranes are proposed to have assembled from simple, single-chain lipids, such as fatty acids and their derivatives, which would have been available in the prebiotic environment. Here we argue that the physical properties of fatty acid membranes would have made them well suited for a role as primitive cell membranes and predisposed their evolution to modern, phospholipid-based membranes. We first considered models for primitive membrane self-assembly, which faces significant concentration barriers due to the entropic cost of aggregation and the solubility of single-chain lipids. We therefore identified two physical mechanisms by which fatty acid membrane assembly can proceed from dilute solutions. Thermal diffusion columns, a proposed prebiotic concentration method, drive the formation of fatty acid vesicles by concentrating an initially isotropic solution past the critical concentration necessary for aggregation. Alternatively, mixtures of fatty acids with varying chain lengths, the expected products of abiotic lipid synthesis, intrinsically reduce the concentration barrier to aggregation through their polydispersity. These results motivated us to better understand the phase behavior of fatty acids in solutions. We found that the composition of fatty acid aggregates, whether vesicles or micelles, is also determined by concentration. Fatty acid vesicles feature significant amounts of coexisting micelles, whose abundance is enriched in low concentration solutions. We utilized this micelle-vesicle equilibrium to drive the growth of pre-existing fatty acid vesicles by changing amphiphile concentration. We next considered the evolution of phospholipid membranes, which was a critical and necessary step for the early evolution of cells. We found that the incorporation of even small amounts of phospholipids drives the growth of fatty acid vesicles by competition for monomers with neighboring vesicles lacking phospholipids. This competitive growth would have provided a strong selective advantage for primitive cells to evolve the catalytic machinery needed to synthesize phospholipids from their single-chain precursors. Growth is caused by any relative difference in phospholipid content, suggesting an evolutionary arms race among primitive cells for increasingly phospholipid membranes. What would have been the consequences for early cells of such a transition in membrane composition? We found that increasing phospholipid content inhibits the permeability of fatty acid membranes through changes in bilayer fluidity. For early heterotrophic cells, the emergence of increasingly phospholipid membranes would have therefore imposed new selective pressures for the evolution of membrane transport machinery and metabolism. Our model for early membrane… Advisors/Committee Members: Szostak, Jack William (advisor), Berg, Howard (committee member), Guidotti, Guido (committee member), Miller, Chris (committee member).

Subjects/Keywords: biophysics; biochemistry; early evolution; fatty acids; membranes; origin of life; phospholipids; protocell

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APA (6^th Edition):

Budin, I. (2012). Physical Models for the Early Evolution of Cell Membranes. (Doctoral Dissertation). Harvard University. Retrieved from http://nrs.harvard.edu/urn-3:HUL.InstRepos:9904006

Chicago Manual of Style (16^th Edition):

Budin, Itay. “Physical Models for the Early Evolution of Cell Membranes.” 2012. Doctoral Dissertation, Harvard University. Accessed January 26, 2021. http://nrs.harvard.edu/urn-3:HUL.InstRepos:9904006.

MLA Handbook (7^th Edition):

Budin, Itay. “Physical Models for the Early Evolution of Cell Membranes.” 2012. Web. 26 Jan 2021.

Vancouver:

Budin I. Physical Models for the Early Evolution of Cell Membranes. [Internet] [Doctoral dissertation]. Harvard University; 2012. [cited 2021 Jan 26]. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:9904006.

Council of Science Editors:

Budin I. Physical Models for the Early Evolution of Cell Membranes. [Doctoral Dissertation]. Harvard University; 2012. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:9904006

Harvard University

15. Blain, Jonathan Craig. Non-Enzymatic Copying of Nucleic Acid Templates.

Degree: PhD, Biology: Medical Sciences, Division of, 2013, Harvard University

URL: http://nrs.harvard.edu/urn-3:HUL.InstRepos:11744416

► All known living cells contain a complex set of molecular machinery to support their growth and replication. However, the earliest cells must have been much… (more)

Subjects/Keywords: Genetics; Biochemistry; Chemistry; Click chemistry; Origin of life; Protocell; Self replication; Synthetic biology

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APA (6^th Edition):

Blain, J. C. (2013). Non-Enzymatic Copying of Nucleic Acid Templates. (Doctoral Dissertation). Harvard University. Retrieved from http://nrs.harvard.edu/urn-3:HUL.InstRepos:11744416

Chicago Manual of Style (16^th Edition):

Blain, Jonathan Craig. “Non-Enzymatic Copying of Nucleic Acid Templates.” 2013. Doctoral Dissertation, Harvard University. Accessed January 26, 2021. http://nrs.harvard.edu/urn-3:HUL.InstRepos:11744416.

MLA Handbook (7^th Edition):

Blain, Jonathan Craig. “Non-Enzymatic Copying of Nucleic Acid Templates.” 2013. Web. 26 Jan 2021.

Vancouver:

Blain JC. Non-Enzymatic Copying of Nucleic Acid Templates. [Internet] [Doctoral dissertation]. Harvard University; 2013. [cited 2021 Jan 26]. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:11744416.

Council of Science Editors:

Blain JC. Non-Enzymatic Copying of Nucleic Acid Templates. [Doctoral Dissertation]. Harvard University; 2013. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:11744416

Harvard University

16. Ranjan, Sukrit. The UV Environment for Prebiotic Chemistry: Connecting Origin-of-Life Scenarios to Planetary Environments.

Degree: PhD, 2017, Harvard University

URL: http://nrs.harvard.edu/urn-3:HUL.InstRepos:41142052

► Recent laboratory studies of prebiotic chemistry (chemistry relevant to the origin of life) are revolutionizing our understanding of the origin of life (abiogenesis) on Earth… (more)

▼ Recent laboratory studies of prebiotic chemistry (chemistry relevant to the origin of life) are revolutionizing our understanding of the origin of life (abiogenesis) on Earth just as telescopes capable of searching for life elsewhere are coming online. This thesis sits at the intersection of these revolutions. I examine prebiotic chemical pathways postulated to be relevant to the origin of life and identify the environmental conditions they require to function. I compare these environmental requirements to what was available on Earth and other planets, and use the comparison to 1) improve studies of the origin of life on Earth and 2) explore the implications for the inhabitability of other worlds. Multiple lines of evidence suggest UV light may have played a critical role in the synthesis of molecules relevant to abiogenesis (prebiotic chemistry), such as RNA. I show that UV light interacts with prebiotic chemistry in ways that may be sensitive to the spectral shape and overall amplitude of irradiation. I use radiative transfer models to constrain the UV environment on early Earth (3.9 Ga). I find that the surface UV is insensitive to much of the considerable uncertainty in the atmospheric state, enabling me to constrain the UV environment for prebiotic chemistry on early Earth. Some authors have suggested Mars as a venue for prebiotic chemistry. Therefore, I explore plausible UV spectral fluences on Mars at 3.9 Ga. I find that the early Martian UV environment is comparable to Earth’s under conventional assumptions about the atmosphere. However, if the atmosphere was dusty or SO2 levels were high, UV fluence would have been strongly suppressed. Intriguingly, despite overall attenuation of UV fluence, SO2 preferentially attenuates destructive FUV radiation over prebiotically-useful NUV radiation, meaning high-SO2 epochs may have been more clement for the origin of life. Better measurements of the spectral dependence of prebiotic photoprocesses are required to constrain this hypothesis. Finally, I calculate the UV fluence on planets orbiting M-dwarfs. I find that UV irradiation on such planets is low compared to Earth. Laboratory studies are required to understand whether prebiotic processes that worked on Earth can function on low-UV M-dwarf planets. In addition to UV light, the most promising pathways for the prebiotic synthesis of RNA require reduced sulfidic anions. I show that prebiotically-relevant levels of such anions derived from volcanically-outgassed SO2 should be robustly available on early Earth, and that episodes of high volcanism may be especially clement for these prebiotic pathways. However, H2S-derived anions are much less common, and prebiotic chemistry which invokes them must rely on alternate, localized sources. My work 1) provides initial conditions for laboratory studies of prebiotic chemistry, 2) constrains the inhabitability of Mars and planets orbiting M-dwarfs, and 3) demonstrates the need for laboratory studies to characterize the sensitivity of putative prebiotic chemistry to environmental… Advisors/Committee Members: Sasselov, Dimitar S. (advisor), Catling, David C. (committee member), Elvis, Martin S. (committee member), Szostak, Jack W. (committee member).

Subjects/Keywords: Radiative Transfer; Origin of Life; Planetary Environments; UV Radiation; Prebiotic Chemistry; Astrobiology; M-dwarfs; Sulfur

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APA (6^th Edition):

Ranjan, S. (2017). The UV Environment for Prebiotic Chemistry: Connecting Origin-of-Life Scenarios to Planetary Environments. (Doctoral Dissertation). Harvard University. Retrieved from http://nrs.harvard.edu/urn-3:HUL.InstRepos:41142052

Chicago Manual of Style (16^th Edition):

Ranjan, Sukrit. “The UV Environment for Prebiotic Chemistry: Connecting Origin-of-Life Scenarios to Planetary Environments.” 2017. Doctoral Dissertation, Harvard University. Accessed January 26, 2021. http://nrs.harvard.edu/urn-3:HUL.InstRepos:41142052.

MLA Handbook (7^th Edition):

Ranjan, Sukrit. “The UV Environment for Prebiotic Chemistry: Connecting Origin-of-Life Scenarios to Planetary Environments.” 2017. Web. 26 Jan 2021.

Vancouver:

Ranjan S. The UV Environment for Prebiotic Chemistry: Connecting Origin-of-Life Scenarios to Planetary Environments. [Internet] [Doctoral dissertation]. Harvard University; 2017. [cited 2021 Jan 26]. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:41142052.

Council of Science Editors:

Ranjan S. The UV Environment for Prebiotic Chemistry: Connecting Origin-of-Life Scenarios to Planetary Environments. [Doctoral Dissertation]. Harvard University; 2017. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:41142052

Brigham Young University

17. Strait, James G. The Relationship Between Attachment Related Family-of-Origin Experiences and Sexual Satisfaction in Married Couples.

Degree: MS, 2010, Brigham Young University

URL: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3268&context=etd

► This study of married couples examined the relationship between perceptions of attachment related family-of-origin experiences and sexual satisfaction directly and when mediated by marital quality.… (more)

Subjects/Keywords: family-of-origin; marital quality; sexual satisfaction; attachment; Family, Life Course, and Society

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APA (6^th Edition):

Strait, J. G. (2010). The Relationship Between Attachment Related Family-of-Origin Experiences and Sexual Satisfaction in Married Couples. (Masters Thesis). Brigham Young University. Retrieved from https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3268&context=etd

Chicago Manual of Style (16^th Edition):

Strait, James G. “The Relationship Between Attachment Related Family-of-Origin Experiences and Sexual Satisfaction in Married Couples.” 2010. Masters Thesis, Brigham Young University. Accessed January 26, 2021. https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3268&context=etd.

MLA Handbook (7^th Edition):

Strait, James G. “The Relationship Between Attachment Related Family-of-Origin Experiences and Sexual Satisfaction in Married Couples.” 2010. Web. 26 Jan 2021.

Vancouver:

Strait JG. The Relationship Between Attachment Related Family-of-Origin Experiences and Sexual Satisfaction in Married Couples. [Internet] [Masters thesis]. Brigham Young University; 2010. [cited 2021 Jan 26]. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3268&context=etd.

Council of Science Editors:

Strait JG. The Relationship Between Attachment Related Family-of-Origin Experiences and Sexual Satisfaction in Married Couples. [Masters Thesis]. Brigham Young University; 2010. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3268&context=etd

Georgia Tech

18. McKee, Aaron D. Prebiotic chemistry on mineral surfaces: Proto-oligopeptide formation on silica and other substrates within depsipeptide forming systems.

Degree: PhD, Chemistry and Biochemistry, 2019, Georgia Tech

URL: http://hdl.handle.net/1853/62328

► The chemical origins of life on Earth and perhaps elsewhere in the universe is not utterly unknowable, though the subject is incredibly complex. To endeavor… (more)

▼ The chemical origins of life on Earth and perhaps elsewhere in the universe is not utterly unknowable, though the subject is incredibly complex. To endeavor to understand what events brought about life on early-Earth nearly 4 billion years ago, life itself must be broken down into its major processes, which themselves are constructed from increasingly simple and ordinary sub-units, and eventually, examined to describe the building blocks of life and how they might assemble. The presence of amino acids on extra-terrestrial bodies and in prebiotic simulation experiments suggests the plausibility of their existence on early Earth. In contrast to extant biological protein production, abiotic polypeptide formation presents several challenges, such as the thermodynamically disfavored condensation of non-activated amino acids in aqueous solution. Recent work has introduced α-hydroxy acids, a class of molecules found alongside amino acids in prebiotic contexts, into peptide forming systems. This has been shown as a robust route towards proto-polypeptides, producing long mixed-acid oligomers, referred to as depsipeptides. In pursuit of realistic model prebiotic environments, mineral-molecule interactions must be considered, and may facilitate new chemical pathways at interfacial regions. Presented in this thesis is a demonstration that the inclusion of silica and other minerals in hydroxy-acid/amino-acid and related reactions effects the composition of oligomers, resulting in amino acid enrichment relative to a substrate-absent controls. Evidence of surface ester formation suggests that the same ester aminolysis mechanism that proceeds in a homogeneous condition is also able to proceed on the substrate surface as silyl-ester aminolysis, indicating that silica is directly involved in the oligomer growth process and departs from previous studies of mineral catalyzed peptide formation on metal oxides. If depsipeptides are model proto-polypeptides, then surface functionalization of minerals with simple HAs might provide catalytic pathways useful for unraveling plausible routes to the production of complex molecules under early-Earth conditions or on extraterrestrial bodies. Advisors/Committee Members: Orlando, Thomas M. (advisor), Hud, Nicholas V. (advisor), Liotta, Charles L. (advisor), Fernández, Facundo M. (advisor), Wray, James J. (advisor).

Subjects/Keywords: Chemical origin of life; Prebiotic chemistry; Silica; Amino acids; Depsipeptides; Oligopeptides; Astrobiology; Surface science; Glycine

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APA (6^th Edition):

McKee, A. D. (2019). Prebiotic chemistry on mineral surfaces: Proto-oligopeptide formation on silica and other substrates within depsipeptide forming systems. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/62328

Chicago Manual of Style (16^th Edition):

McKee, Aaron D. “Prebiotic chemistry on mineral surfaces: Proto-oligopeptide formation on silica and other substrates within depsipeptide forming systems.” 2019. Doctoral Dissertation, Georgia Tech. Accessed January 26, 2021. http://hdl.handle.net/1853/62328.

MLA Handbook (7^th Edition):

McKee, Aaron D. “Prebiotic chemistry on mineral surfaces: Proto-oligopeptide formation on silica and other substrates within depsipeptide forming systems.” 2019. Web. 26 Jan 2021.

Vancouver:

McKee AD. Prebiotic chemistry on mineral surfaces: Proto-oligopeptide formation on silica and other substrates within depsipeptide forming systems. [Internet] [Doctoral dissertation]. Georgia Tech; 2019. [cited 2021 Jan 26]. Available from: http://hdl.handle.net/1853/62328.

Council of Science Editors:

McKee AD. Prebiotic chemistry on mineral surfaces: Proto-oligopeptide formation on silica and other substrates within depsipeptide forming systems. [Doctoral Dissertation]. Georgia Tech; 2019. Available from: http://hdl.handle.net/1853/62328

Arizona State University

19. Mathis, Nicholas. On the Origin of the Living State.

Degree: Physics, 2018, Arizona State University

URL: http://repository.asu.edu/items/50446

► The origin of Life on Earth is the greatest unsolved mystery in the history of science. In spite of progress in almost every scientific endeavor,… (more)

▼ The origin of Life on Earth is the greatest unsolved mystery in the history of science. In spite of progress in almost every scientific endeavor, we still have no clear theory, model, or framework to understand the processes that led to the emergence of life on Earth. Understanding such a processes would provide key insights into astrobiology, planetary science, geochemistry, evolutionary biology, physics, and philosophy. To date, most research on the origin of life has focused on characterizing and synthesizing the molecular building blocks of living systems. This bottom-up approach assumes that living systems are characterized by their component parts, however many of the essential features of life are system level properties which only manifest in the collective behavior of many components. In order to make progress towards solving the origin of life new modeling techniques are needed. In this dissertation I review historical approaches to modeling the origin of life. I proceed to elaborate on new approaches to understanding biology that are derived from statistical physics and prioritize the collective properties of living systems rather than the component parts. In order to study these collective properties of living systems, I develop computational models of chemical systems. Using these computational models I characterize several system level processes which have important implications for understanding the origin of life on Earth. First, I investigate a model of molecular replicators and demonstrate the existence of a phase transition which occurs dynamically in replicating systems. I characterize the properties of the phase transition and argue that living systems can be understood as a non-equilibrium state of matter with unique dynamical properties. Then I develop a model of molecular assembly based on a ribonucleic acid (RNA) system, which has been characterized in laboratory experiments. Using this model I demonstrate how the energetic properties of hydrogen bonding dictate the population level dynamics of that RNA system. Finally I return to a model of replication in which replicators are strongly coupled to their environment. I demonstrate that this dynamic coupling results in qualitatively different evolutionary dynamics than those expected in static environments. A key difference is that when environmental coupling is included, evolutionary processes do not select a single replicating species but rather a dynamically stable community which consists of many species. Finally, I conclude with a discussion of how these computational models can inform future research on the origins of life.

Subjects/Keywords: Physics; Computational physics; Biology; Astrobiology; Complex Systems; Origin Of Life; Prebiotic Chemistry; Systems Chemistry

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APA (6^th Edition):

Mathis, N. (2018). On the Origin of the Living State. (Doctoral Dissertation). Arizona State University. Retrieved from http://repository.asu.edu/items/50446

Chicago Manual of Style (16^th Edition):

Mathis, Nicholas. “On the Origin of the Living State.” 2018. Doctoral Dissertation, Arizona State University. Accessed January 26, 2021. http://repository.asu.edu/items/50446.

MLA Handbook (7^th Edition):

Mathis, Nicholas. “On the Origin of the Living State.” 2018. Web. 26 Jan 2021.

Vancouver:

Mathis N. On the Origin of the Living State. [Internet] [Doctoral dissertation]. Arizona State University; 2018. [cited 2021 Jan 26]. Available from: http://repository.asu.edu/items/50446.

Council of Science Editors:

Mathis N. On the Origin of the Living State. [Doctoral Dissertation]. Arizona State University; 2018. Available from: http://repository.asu.edu/items/50446

University of Kentucky

20. Shalash, Fatimah. SIBLING CONFLICT RESOLUTION STYLES AND MARITAL CONFLICT RESOLUTION STYLES.

Degree: 2011, University of Kentucky

URL: https://uknowledge.uky.edu/gradschool_theses/109

► This study used qualitative methods to examine if there was a connection between conflict resolution styles used with siblings in adolescence and conflict resolution styles… (more)

Subjects/Keywords: Conflict resolution; siblings; marriage; social learning theory; family of origin; Family, Life Course, and Society

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APA (6^th Edition):

Shalash, F. (2011). SIBLING CONFLICT RESOLUTION STYLES AND MARITAL CONFLICT RESOLUTION STYLES. (Masters Thesis). University of Kentucky. Retrieved from https://uknowledge.uky.edu/gradschool_theses/109

Chicago Manual of Style (16^th Edition):

Shalash, Fatimah. “SIBLING CONFLICT RESOLUTION STYLES AND MARITAL CONFLICT RESOLUTION STYLES.” 2011. Masters Thesis, University of Kentucky. Accessed January 26, 2021. https://uknowledge.uky.edu/gradschool_theses/109.

MLA Handbook (7^th Edition):

Shalash, Fatimah. “SIBLING CONFLICT RESOLUTION STYLES AND MARITAL CONFLICT RESOLUTION STYLES.” 2011. Web. 26 Jan 2021.

Vancouver:

Shalash F. SIBLING CONFLICT RESOLUTION STYLES AND MARITAL CONFLICT RESOLUTION STYLES. [Internet] [Masters thesis]. University of Kentucky; 2011. [cited 2021 Jan 26]. Available from: https://uknowledge.uky.edu/gradschool_theses/109.

Council of Science Editors:

Shalash F. SIBLING CONFLICT RESOLUTION STYLES AND MARITAL CONFLICT RESOLUTION STYLES. [Masters Thesis]. University of Kentucky; 2011. Available from: https://uknowledge.uky.edu/gradschool_theses/109

Brigham Young University

21. Urry, Shirene A. Gone But Not Forgetting: Examining the Differentiation of Flourishing and Floundering in Emerging Adulthood in the Context of Family Development.

Degree: MS, 2011, Brigham Young University

URL: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=4055&context=etd

► In emerging adulthood, distinctive groups have been found to exhibit "flourishing" (i.e., simultaneously experiencing positive, maturing relationships with parents, exploring identity in numerous positive areas,… (more)

Subjects/Keywords: emerging adulthood; family of origin; family of formation; flourishing; and floundering; Family, Life Course, and Society

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APA (6^th Edition):

Urry, S. A. (2011). Gone But Not Forgetting: Examining the Differentiation of Flourishing and Floundering in Emerging Adulthood in the Context of Family Development. (Masters Thesis). Brigham Young University. Retrieved from https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=4055&context=etd

Chicago Manual of Style (16^th Edition):

Urry, Shirene A. “Gone But Not Forgetting: Examining the Differentiation of Flourishing and Floundering in Emerging Adulthood in the Context of Family Development.” 2011. Masters Thesis, Brigham Young University. Accessed January 26, 2021. https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=4055&context=etd.

MLA Handbook (7^th Edition):

Urry, Shirene A. “Gone But Not Forgetting: Examining the Differentiation of Flourishing and Floundering in Emerging Adulthood in the Context of Family Development.” 2011. Web. 26 Jan 2021.

Vancouver:

Urry SA. Gone But Not Forgetting: Examining the Differentiation of Flourishing and Floundering in Emerging Adulthood in the Context of Family Development. [Internet] [Masters thesis]. Brigham Young University; 2011. [cited 2021 Jan 26]. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=4055&context=etd.

Council of Science Editors:

Urry SA. Gone But Not Forgetting: Examining the Differentiation of Flourishing and Floundering in Emerging Adulthood in the Context of Family Development. [Masters Thesis]. Brigham Young University; 2011. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=4055&context=etd

Brigham Young University

22. Johnson, Sabra Elyse. Factors Relating to Romantic Relationship Experiences for Emerging Adults.

Degree: MS, 2013, Brigham Young University

URL: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=4873&context=etd

► This study of 1,492 emerging adults focuses on the relationships among negative family of origin experiences, attitudes about marriage, positive communication and the influence of… (more)

Subjects/Keywords: negative family of origin experiences; influence of past relationships; attitudes about marriage; positive communication; emerging adults; Family, Life Course, and Society

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APA (6^th Edition):

Johnson, S. E. (2013). Factors Relating to Romantic Relationship Experiences for Emerging Adults. (Masters Thesis). Brigham Young University. Retrieved from https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=4873&context=etd

Chicago Manual of Style (16^th Edition):

Johnson, Sabra Elyse. “Factors Relating to Romantic Relationship Experiences for Emerging Adults.” 2013. Masters Thesis, Brigham Young University. Accessed January 26, 2021. https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=4873&context=etd.

MLA Handbook (7^th Edition):

Johnson, Sabra Elyse. “Factors Relating to Romantic Relationship Experiences for Emerging Adults.” 2013. Web. 26 Jan 2021.

Vancouver:

Johnson SE. Factors Relating to Romantic Relationship Experiences for Emerging Adults. [Internet] [Masters thesis]. Brigham Young University; 2013. [cited 2021 Jan 26]. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=4873&context=etd.

Council of Science Editors:

Johnson SE. Factors Relating to Romantic Relationship Experiences for Emerging Adults. [Masters Thesis]. Brigham Young University; 2013. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=4873&context=etd

McMaster University

23. Wu, Meng. The Origin of Life by Means of Autocatalytic Sets of Biopolymers.

Degree: PhD, 2012, McMaster University

URL: http://hdl.handle.net/11375/12403

►

A key problem in the origin of life is to understand how an autocatalytic, self-replicating biopolymer system may have originated from a non-living chemical… (more)

▼

A key problem in the origin of life is to understand how an autocatalytic, self-replicating biopolymer system may have originated from a non-living chemical system. This thesis presents mathematical and computational models that address this issue. We consider a reaction system in which monomers (nucleotides) and polymers (RNAs) can be formed by chemical reactions at a slow spontaneous rate, and can also be formed at a high rate by catalysis, if polymer catalysts (ribozymes) are present. The system has two steady states: a ‘dead’ state with a low concentration of ribozymes and a ‘living’ state with a high concentration of ribozymes. Using stochastic simulations, we show that if a small number of ribozymes is formed spontaneously, this can drive the system from the dead to the living state. In the well mixed limit, this transition occurs most easily in volumes of intermediate size. In a spatially-extended two-dimensional system with finite diffusion rate, there is an optimal diffusion rate at which the transition to life is very much faster than in the well-mixed case. We therefore argue that the origin of life is a spatially localized stochastic transition. Once life has arisen in one place by a rare stochastic event, the living state spreads deterministically through the rest of the system. We show that similar autocatalytic states can be controlled by nucleotide synthases as well as by polymerase ribozymes, and that the same mechanism can also work with recombinases, if the recombination reaction is not perfectly reversible. Chirality is introduced into the polymerization model by considering simultaneous synthesis and polymerization of left- and right-handed monomers. We show that there is a racemic non-living state and two chiral living states. In this model, the origin of life and the origin of homochirality may occur simultaneously due to the same stochastic transition.

Doctor of Philosophy (PhD)

Advisors/Committee Members: Higgs, Paul G., An-Chang Shi, Jonathan R. Stone, Jonathan Dushoff, Physics and Astronomy.

Subjects/Keywords: Origin of Life; RNA world; autocatalytic sets; ribozyme; stochastic simulation; Biological and Chemical Physics; Biology; Biological and Chemical Physics

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APA (6^th Edition):

Wu, M. (2012). The Origin of Life by Means of Autocatalytic Sets of Biopolymers. (Doctoral Dissertation). McMaster University. Retrieved from http://hdl.handle.net/11375/12403

Chicago Manual of Style (16^th Edition):

Wu, Meng. “The Origin of Life by Means of Autocatalytic Sets of Biopolymers.” 2012. Doctoral Dissertation, McMaster University. Accessed January 26, 2021. http://hdl.handle.net/11375/12403.

MLA Handbook (7^th Edition):

Wu, Meng. “The Origin of Life by Means of Autocatalytic Sets of Biopolymers.” 2012. Web. 26 Jan 2021.

Vancouver:

Wu M. The Origin of Life by Means of Autocatalytic Sets of Biopolymers. [Internet] [Doctoral dissertation]. McMaster University; 2012. [cited 2021 Jan 26]. Available from: http://hdl.handle.net/11375/12403.

Council of Science Editors:

Wu M. The Origin of Life by Means of Autocatalytic Sets of Biopolymers. [Doctoral Dissertation]. McMaster University; 2012. Available from: http://hdl.handle.net/11375/12403

Uppsala University

24. Hjerpe, Daniel. The destruction of life in a self replicating system.

Degree: Applied Mathematics and Statistics, 2018, Uppsala University

URL: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-355816

► This thesis explores the question of why life can not be revived when death occurs due to lack of resources. For example, why can't… (more)

Subjects/Keywords: Self replication; formose reaction; virus; death; necrosis; origin of life; Other Mathematics; Annan matematik; Other Biological Topics; Annan biologi

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APA (6^th Edition):

Hjerpe, D. (2018). The destruction of life in a self replicating system. (Thesis). Uppsala University. Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-355816

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):

Hjerpe, Daniel. “The destruction of life in a self replicating system.” 2018. Thesis, Uppsala University. Accessed January 26, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-355816.

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

MLA Handbook (7^th Edition):

Hjerpe, Daniel. “The destruction of life in a self replicating system.” 2018. Web. 26 Jan 2021.

Vancouver:

Hjerpe D. The destruction of life in a self replicating system. [Internet] [Thesis]. Uppsala University; 2018. [cited 2021 Jan 26]. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-355816.

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

Council of Science Editors:

Hjerpe D. The destruction of life in a self replicating system. [Thesis]. Uppsala University; 2018. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-355816

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

University of Washington

25. Blosser, Matthew C. Measuring how lipid membranes respond to physical perturbations: How charge alters lipid miscibility, how shear disrupts interleaflet coupling, and how prebiotic compounds affect membrane stability.

Degree: PhD, 2015, University of Washington

URL: http://hdl.handle.net/1773/27561

► The physical and chemical properties of lipid bilayers determine their biological function as the main structural component of cell membranes. The response of lipid membranes… (more)

▼ The physical and chemical properties of lipid bilayers determine their biological function as the main structural component of cell membranes. The response of lipid membranes to various perturbations is, in general, difficult to predict. This dissertation will discuss four sets of experiments to probe the behavior of lipid membranes in different conditions. In the first set of experiments, we show that the presence of charged lipids has a much smaller effect on the miscibility phase separation of lipid bilayers than predicted by simple theories. This conclusion is supported by the finding that the transition temperature of systems containing charged lipids are similar to the transition temperatures of systems without charged lipids, and by the finding that the addition of monovalent salt, which screens charge interactions, has a small effect on the transition temperatures of bilayers containing charged lipids. The second set of experiments examines the effect of high shear on phase-separated membranes. We find that an external shear is sufficient to move domains in each leaflet out of registration. By quantifying these results, we obtain a value for the free energetic cost per unit area of misregistration. In the third set of experiments, we show that it is possible to create bilayers containing high fractions of charge and in highly salty solutions. We achieve this using the method cDICE, where vesicles are created by centrifuging aqueous droplets through a layer of lipids dissolved in oil. We further show that in this scheme, no detectable amount of cholesterol is incorporated into bilayers. Finally, we examine interactions between bilayers of fatty acids and the building blocks of RNA, nucleobases and sugars. We show that the nucleobases and sugar that are found in RNA bind to fatty acid aggregates, and do so more strongly than chemically similar molecules. We also find that nucleobases and sugar stabilize fatty acid vesicles against flocculation in salty solutions. In contrast, under control conditions, salt induces the aggregation of vesicles into dense structures. These two effects suggest a role for fatty acid vesicles in the origin of life as a stable membrane in a salty ocean that could select and concentrate the components required to make RNA. Advisors/Committee Members: Keller, Sarah L (advisor).

Subjects/Keywords: fatty acid vesicle; fluorescence microscopy; lipid bilayer; Membrane; origin of life; phase separation; Biophysics; Condensed matter physics; Physical chemistry; physics

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APA (6^th Edition):

Blosser, M. C. (2015). Measuring how lipid membranes respond to physical perturbations: How charge alters lipid miscibility, how shear disrupts interleaflet coupling, and how prebiotic compounds affect membrane stability. (Doctoral Dissertation). University of Washington. Retrieved from http://hdl.handle.net/1773/27561

Chicago Manual of Style (16^th Edition):

Blosser, Matthew C. “Measuring how lipid membranes respond to physical perturbations: How charge alters lipid miscibility, how shear disrupts interleaflet coupling, and how prebiotic compounds affect membrane stability.” 2015. Doctoral Dissertation, University of Washington. Accessed January 26, 2021. http://hdl.handle.net/1773/27561.

MLA Handbook (7^th Edition):

Blosser, Matthew C. “Measuring how lipid membranes respond to physical perturbations: How charge alters lipid miscibility, how shear disrupts interleaflet coupling, and how prebiotic compounds affect membrane stability.” 2015. Web. 26 Jan 2021.

Vancouver:

Blosser MC. Measuring how lipid membranes respond to physical perturbations: How charge alters lipid miscibility, how shear disrupts interleaflet coupling, and how prebiotic compounds affect membrane stability. [Internet] [Doctoral dissertation]. University of Washington; 2015. [cited 2021 Jan 26]. Available from: http://hdl.handle.net/1773/27561.

Council of Science Editors:

Blosser MC. Measuring how lipid membranes respond to physical perturbations: How charge alters lipid miscibility, how shear disrupts interleaflet coupling, and how prebiotic compounds affect membrane stability. [Doctoral Dissertation]. University of Washington; 2015. Available from: http://hdl.handle.net/1773/27561

26. Myrgorodska, Iuliia. Rupture de symétrie chirale : asymétrie et origine des molécules chirales impliquées dans l’évolution prébiotique : Chiral symmetry breaking : asymmetry and origin of chiral molecules relevant in prebiotic evolution.

Degree: Docteur es, Chimie, 2016, Université Côte d'Azur (ComUE)

URL: http://www.theses.fr/2016AZUR4057

►

Depuis la découverte de la chiralité moléculaire par Pasteur il y a plus de 150 ans, l'origine de l'homochiralité de la vie reste un mystère… (more)

▼

Depuis la découverte de la chiralité moléculaire par Pasteur il y a plus de 150 ans, l'origine de l'homochiralité de la vie reste un mystère non résolu et troublant, qui remonte probablement à l'origine de la vie elle-même. Cette énigme a récemment été recensée dans Nature comme étant l’une des cinq plus grandes énigmes non résolues par la science.Aujourd'hui il existe deux façons d’aborder le problème de l'origine de l'asymétrie moléculaire impliquant des scénarios soit déterministes soit aléatoires. Ces derniers étant basés sur la résolution spontanée des énantiomères, et sont donc impossible à tester. En revanche, les théories déterministes peuvent être confrontées à l’expérience afin notamment de valider la reproductibilité de leur influence chirale.Le présent manuscrit est une synthèse bibliographique et expérimentale mettant en évidence les interactions de la LPC avec des molécules chirales dans le cadre de l’origine de l’homochiralité de la vie. Ces travaux ont pour but de mieux comprendre les propriétés chiroptiques de molécules chirales ainsi que de déterminer les espèces chirales susceptibles d'être présentes dans la glace cométaire

Since the Pasteur’s discovery of chirality more than 150 years ago, the origin of homochirality remains to be an unresolved mystery, which is probably linked to the origin of life-itself. This puzzle was named by the journal Nature as one of the five biggest unresolved puzzles in modern science.Today there exist two ways to address the question of the origin of molecular homochirality. It implies either deterministic or chance scenario. The latest is based on the spontaneous resolution of enantiomers by phase transition, and in consequence, it cannot be tested. On the other hand, deterministic theories can be subjected to experimental confirmation, since if there was, in fact, a chiral influence that imposed its chirality this should in principle be reproducible.The presented manuscript is a synthesis of bibliographic research and experimental studies that focus on the interaction of CPL with chiral molecules which are put in the context of the origin of homochirality of life. This work is aiming to advance our understanding of chiroptical properties of chiral molecules as well as to determine chiral species susceptible to be present in cometary ice

Advisors/Committee Members: Meierhenrich, Uwe (thesis director), Nahon, Laurent (thesis director).

Subjects/Keywords: Chiralité; Origine de la vie; Énantiomères; Dichroïsme circulaire; Comètes; Chirality; Origin of life; Enantiomers; Circular dichroism; Comets

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

APA (6^th Edition):

Myrgorodska, I. (2016). Rupture de symétrie chirale : asymétrie et origine des molécules chirales impliquées dans l’évolution prébiotique : Chiral symmetry breaking : asymmetry and origin of chiral molecules relevant in prebiotic evolution. (Doctoral Dissertation). Université Côte d'Azur (ComUE). Retrieved from http://www.theses.fr/2016AZUR4057

Chicago Manual of Style (16^th Edition):

Myrgorodska, Iuliia. “Rupture de symétrie chirale : asymétrie et origine des molécules chirales impliquées dans l’évolution prébiotique : Chiral symmetry breaking : asymmetry and origin of chiral molecules relevant in prebiotic evolution.” 2016. Doctoral Dissertation, Université Côte d'Azur (ComUE). Accessed January 26, 2021. http://www.theses.fr/2016AZUR4057.

MLA Handbook (7^th Edition):

Myrgorodska, Iuliia. “Rupture de symétrie chirale : asymétrie et origine des molécules chirales impliquées dans l’évolution prébiotique : Chiral symmetry breaking : asymmetry and origin of chiral molecules relevant in prebiotic evolution.” 2016. Web. 26 Jan 2021.

Vancouver:

Myrgorodska I. Rupture de symétrie chirale : asymétrie et origine des molécules chirales impliquées dans l’évolution prébiotique : Chiral symmetry breaking : asymmetry and origin of chiral molecules relevant in prebiotic evolution. [Internet] [Doctoral dissertation]. Université Côte d'Azur (ComUE); 2016. [cited 2021 Jan 26]. Available from: http://www.theses.fr/2016AZUR4057.

Council of Science Editors:

Myrgorodska I. Rupture de symétrie chirale : asymétrie et origine des molécules chirales impliquées dans l’évolution prébiotique : Chiral symmetry breaking : asymmetry and origin of chiral molecules relevant in prebiotic evolution. [Doctoral Dissertation]. Université Côte d'Azur (ComUE); 2016. Available from: http://www.theses.fr/2016AZUR4057

27. Bray, Marcus Salvatore. Iron as an integral constituent of ancient metabolism and biochemistry.

Degree: PhD, Biology, 2019, Georgia Tech

URL: http://hdl.handle.net/1853/61725

► Life on Earth evolved and proliferated for nearly 2 billion years in an environment devoid of molecular oxygen and replete with iron. Currently on Earth,… (more)

Subjects/Keywords: Microbiology; Biochemistry; Origin of life; Iron

…ribosome during the origin and early evolution of life. To test this hypothesis, I examined the… …of this work have expanded the potential role for Fe in the origin and propagation of life… …would have been especially true at the origin of life, where simple biopolymers, still unable… …present, and future of life on Earth 6.1 Expanding the role of Fe in biochemistry 6.2 Iron… …of the first metabolisms used by early life forms as both early biotic and abiotic…

10 more images…

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APA (6^th Edition):

Bray, M. S. (2019). Iron as an integral constituent of ancient metabolism and biochemistry. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/61725

Chicago Manual of Style (16^th Edition):

Bray, Marcus Salvatore. “Iron as an integral constituent of ancient metabolism and biochemistry.” 2019. Doctoral Dissertation, Georgia Tech. Accessed January 26, 2021. http://hdl.handle.net/1853/61725.

MLA Handbook (7^th Edition):

Bray, Marcus Salvatore. “Iron as an integral constituent of ancient metabolism and biochemistry.” 2019. Web. 26 Jan 2021.

Vancouver:

Bray MS. Iron as an integral constituent of ancient metabolism and biochemistry. [Internet] [Doctoral dissertation]. Georgia Tech; 2019. [cited 2021 Jan 26]. Available from: http://hdl.handle.net/1853/61725.

Council of Science Editors:

Bray MS. Iron as an integral constituent of ancient metabolism and biochemistry. [Doctoral Dissertation]. Georgia Tech; 2019. Available from: http://hdl.handle.net/1853/61725

Leiden University

28. Torrao, Pinto Martins Z.C. Chemical analysis of organic molecules in carbonaceous meteorites.

Degree: 2007, Leiden University

URL: http://hdl.handle.net/1887/9450

► Meteorites are extraterrestrial objects that survive the passage through the Earth's atmosphere and impact the Earth's surface. They can be divided into several classes, the… (more)

Subjects/Keywords: Extraterrestrial organic molecules; L-enantiomeric excess; Meteorites; Origin of life; Extraterrestrial organic molecules; L-enantiomeric excess; Meteorites; Origin of life

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

APA (6^th Edition):

Torrao, P. M. Z. C. (2007). Chemical analysis of organic molecules in carbonaceous meteorites. (Doctoral Dissertation). Leiden University. Retrieved from http://hdl.handle.net/1887/9450

Chicago Manual of Style (16^th Edition):

Torrao, Pinto Martins Z C. “Chemical analysis of organic molecules in carbonaceous meteorites.” 2007. Doctoral Dissertation, Leiden University. Accessed January 26, 2021. http://hdl.handle.net/1887/9450.

MLA Handbook (7^th Edition):

Torrao, Pinto Martins Z C. “Chemical analysis of organic molecules in carbonaceous meteorites.” 2007. Web. 26 Jan 2021.

Vancouver:

Torrao PMZC. Chemical analysis of organic molecules in carbonaceous meteorites. [Internet] [Doctoral dissertation]. Leiden University; 2007. [cited 2021 Jan 26]. Available from: http://hdl.handle.net/1887/9450.

Council of Science Editors:

Torrao PMZC. Chemical analysis of organic molecules in carbonaceous meteorites. [Doctoral Dissertation]. Leiden University; 2007. Available from: http://hdl.handle.net/1887/9450

University of North Texas

29. Brister, Brian. Layered Double Hydroxides and the Origins of Life on Earth.

Degree: 2001, University of North Texas

URL: https://digital.library.unt.edu/ark:/67531/metadc2766/

► A brief introduction to the current state of research in the Origins of Life field is given in Part I of this work. Part II… (more)

▼ A brief introduction to the current state of research in the Origins of Life field is given in Part I of this work. Part II covers original research performed by the author and co-workers. Layered Double Hydroxide (LDH) systems are anion-exchanging clays that have the general formula M(II)xM(III)(OH)(2x+2)Y, where M(II) and M(III) are any divalent and trivalent metals, respectively. Y can be nearly any anion, although modern naturally occuring LDH systems incorporate carbonate (CO32-), chloride (Cl-), or sulfate (SO42-) anions. Intercalated cobalticyanide anion shows a small yet observable deviation from local Oh symmetry causing small differences between its oriented and non-oriented infrared spectra. Nitroprusside is shown to intercalate into 2:1 Mg:Al LDH with decomposition to form intercalated ferrocyanide and nitrosyl groups of an unidentified nature. The [Ru(CN)6]4- anion is shown to intercalate into layered double hydroxides in the same manner as other hexacyano anions, such as ferrocyanide and cobalticyanide, with its three-fold rotational axis perpendicular to the hydroxide sheets. The square-planar tetracyano-nickelate(II), -palladate(II), and platinate(II) anions were intercalated into both 2:1 and 3:1 Mg:Al layered double hydroxides (LDH). The basal spacings in the 2:1 hosts are approximately 11 Å, indicating that the anions are inclined approximately 75 degrees relative to the hydroxide layers, while in the 3:1 hosts the square-planar anions have enough space to lie more nearly parallel to the LDH cation layers, giving basal spacings of approximately 8 Å. It has been found that the LDH Mg2Al(OH)6Cl catalyzes the self-addition of cyanide, to give in a one-pot reaction at low concentrations an increased yield of diaminomaleonitrile and in addition, at higher ($0.1M) concentrations, a purple-pink material that adheres to the LDH. We are investigating whether this reaction also occurs with hydrotalcite itself, what is the minimum effective concentration of cyanide, and what can be learned about the products and how they compare with those reported at high HCN concentrations in the absence of catalyst. Advisors/Committee Members: Braterman, Paul S., Acree, William E. (William Eugene), Thomas, Ruthanne D..

Subjects/Keywords: Layered double hydroxides.; Life – Origin.; Origins of life; layered double hydroxide systems

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APA (6^th Edition):

Brister, B. (2001). Layered Double Hydroxides and the Origins of Life on Earth. (Thesis). University of North Texas. Retrieved from https://digital.library.unt.edu/ark:/67531/metadc2766/

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):

Brister, Brian. “Layered Double Hydroxides and the Origins of Life on Earth.” 2001. Thesis, University of North Texas. Accessed January 26, 2021. https://digital.library.unt.edu/ark:/67531/metadc2766/.

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

MLA Handbook (7^th Edition):

Brister, Brian. “Layered Double Hydroxides and the Origins of Life on Earth.” 2001. Web. 26 Jan 2021.

Vancouver:

Brister B. Layered Double Hydroxides and the Origins of Life on Earth. [Internet] [Thesis]. University of North Texas; 2001. [cited 2021 Jan 26]. Available from: https://digital.library.unt.edu/ark:/67531/metadc2766/.

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

Council of Science Editors:

Brister B. Layered Double Hydroxides and the Origins of Life on Earth. [Thesis]. University of North Texas; 2001. Available from: https://digital.library.unt.edu/ark:/67531/metadc2766/

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

University of Texas – Austin

30. -1532-4097. Mineralogical controls on microbial community structure and biogeochemical processes in subsurface environments.

Degree: PhD, Geological sciences, 2015, University of Texas – Austin

URL: http://hdl.handle.net/2152/33498

► Nearly every ecological habitat in the microbiological world is predominately occupied by complex assemblages of multicellular, multifunctional communities attached to surfaces as biofilms. The motivating… (more)

▼ Nearly every ecological habitat in the microbiological world is predominately occupied by complex assemblages of multicellular, multifunctional communities attached to surfaces as biofilms. The motivating factors for this stationary community lifestyle appear to be as diverse as the organisms that occupy these habitats. However, there are also many commonalities primarily relating to nutritional requirements and environmental tolerances. Broadly, this dissertation focuses primarily on linking these motivating factors to specific microorganisms within diverse biofilm communities attached to mineral surfaces. To do this I used continuous-flow laboratory biofilm reactors (inoculated with a diverse subsurface biofilm community) to assess the roles of surface type, media pH, and carbon and phosphate availability on biofilm accumulation, community structure, function, and phylogenetic variability. I demonstrate that in nutrient-limited systems, taxonomy and growth of biofilm communities is highly dependent on surface chemistry to support their nutritional requirements and environmental tolerances. Moreover I present rigorous statistical evidence that, for a variety of environments, microbial communities attached to similar natural surfaces types (carbonates vs. silicates vs. aluminosilicates) are more phylogenetically similar. I find that surface type controls up to 90% of the variance in phylogenetic diversity of a system regardless of environmental pressures. This is strong evidence that mineral selection is genetically ingrained. We provide validated methodology for the use of continuous flow-bioreactors to expose the fundamentally dynamic nature of microbial structure within biofilms. I demonstrate that these shifts in community structure can occur rapidly, impacting geochemistry and carbonate mineral solubility. Specifically, carbonate dissolution is highly accelerated under autotrophic conditions dominated by sulfur-oxidizers. Immediately after adding acetate the community shifts to heterotrophic sulfur-reducers resulting in carbonate precipitation. Additionally, these functional shifts can be inferred by monitoring geochemical indicators (δ13CCO2, [CO2], Ca2+, and pH). I provide evidence that the responsiveness of carbonate system reactions to the metabolic products of sulfuric acid cave ecosystems are ideal model ecosystems for studying the effects of microbial community structure on stable carbon isotope fractionation. I submit that biogeochemical interactions with mineral surfaces have influenced development, evolution, and diversification of microbial life. Throughout geologic time, microorganisms have enhanced survival by colonizing mineral surfaces and developing complex biofilm communities genetically primed for specific mineral habitats. Advisors/Committee Members: Bennett, Philip C. (Philip Charles), 1959- (advisor), Breecker, Daniel O (committee member), Omelon, Christopher R (committee member), Bell, Christopher J (committee member), Hawkes, Christine V (committee member).

Subjects/Keywords: Geomicrobiology; Pyrosequencing; Origin of life; Microbe mineral interactions; Biofilm communities; Subsurface ecosystems; Dark life; Sulfur-metabolism; Speleogenesis; Carbonate dissolution; Carbon isotopes; Carbon fractionation; Biogeochemical interactions

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

APA (6^th Edition):

-1532-4097. (2015). Mineralogical controls on microbial community structure and biogeochemical processes in subsurface environments. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/33498

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Chicago Manual of Style (16^th Edition):

-1532-4097. “Mineralogical controls on microbial community structure and biogeochemical processes in subsurface environments.” 2015. Doctoral Dissertation, University of Texas – Austin. Accessed January 26, 2021. http://hdl.handle.net/2152/33498.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

MLA Handbook (7^th Edition):

-1532-4097. “Mineralogical controls on microbial community structure and biogeochemical processes in subsurface environments.” 2015. Web. 26 Jan 2021.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Vancouver:

-1532-4097. Mineralogical controls on microbial community structure and biogeochemical processes in subsurface environments. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2015. [cited 2021 Jan 26]. Available from: http://hdl.handle.net/2152/33498.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Council of Science Editors:

-1532-4097. Mineralogical controls on microbial community structure and biogeochemical processes in subsurface environments. [Doctoral Dissertation]. University of Texas – Austin; 2015. Available from: http://hdl.handle.net/2152/33498

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

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