subject:(Compartmentalization)

Penn State University

1. Frankel, Erica Ann. Towards Investigation of RNA Catalysis and Compartmentalization.

Degree: 2017, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/14674eaf203

► The assembly of molecules and their subsequent reactions that led to the origins of life on Earth nearly four billion years ago remains one of… (more)

▼ The assembly of molecules and their subsequent reactions that led to the origins of life on Earth nearly four billion years ago remains one of the most elusive mysteries in modern science. One of the first steps scientists look along this timeline is how potentially important molecules, such as early forms of peptides, lipids, and nucleic acids, could have formed. In some cases, it seems plausible that these molecules could have been created on Earth through a sequence of reactions with simple precursors, including methane and cyanide, catalyzed by an electric shock. In other cases, it is proposed that meteors that hit the Earth’s surface brought a menagerie of early molecules that could have acted as precursors for the biomolecules that are pertinent in modern biology today. A second step along this timeline that scientists are particularly interested in is how these newly formed molecules could have been concentrated to form some of the first protocells. Environmental conditions such as warm little ponds, which circuitously evaporate and refill, and porous rock, which would attract various charged molecules to their surface, are examples where potentially important molecules could concentrate, interact, and form the first non-membranous compartments. These highly concentrated environments could have facilitated some of the first autocatalyzed reactions, such as ligation, polymerization, and cleavage. RNA was thought to play a key role in some of these initial pertinent reactions, for its dual functionality to autocatalyze self-cleavage/self-ligation reactions and store genetic information. A third step represents a progression from the second, through the cultivation of more advanced self-catalytic systems. One of the biggest challenges in the origins of life is the ability for a system to self-replicate. Under most RNA systems, RNA replication uses a template strand to build a complementary strand off of, one nucleotide at a time. One limitation for early replication methods is strand dissociation of the product-template complex in order to promote turnover of the template. Again, the earliest primordial systems could have used environmental changes such as temperature and pH to denature template-product complexed to allow for turnover to occur. It is important to note that these steps are relatively arbitrary and most likely did not happen sequentially. It is more than possible that many of these events could have occurred at the same time. Moreover, there are many other steps not included herein, and it is almost certainly the case that the number of steps to reach the earliest organisms may be countless. This thesis, however, lies right at the cusp of steps two and three, as it focuses on the compartmentalization and catalysis of RNA molecules. One key obstacle to forming longer polymers of progenitor molecules would be to concentrate precursor molecules into compartments. In Chapter Two, I characterize the compartmentalization of nucleotides in the presence of a long polyamine. The combination of these two… Advisors/Committee Members: Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor, Philip C. Bevilacqua, Committee Chair/Co-Chair, Scott A Showalter, Committee Member, Amie Kathleen Boal, Committee Member, James Kasting, Outside Member, Christine Dolan Keating, Dissertation Advisor/Co-Advisor, Christine Dolan Keating, Committee Chair/Co-Chair.

Subjects/Keywords: RNA; Catalysis; Compartmentalization; Cooperativity; Origins of Life

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APA (6^th Edition):

Frankel, E. A. (2017). Towards Investigation of RNA Catalysis and Compartmentalization. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/14674eaf203

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):

Frankel, Erica Ann. “Towards Investigation of RNA Catalysis and Compartmentalization.” 2017. Thesis, Penn State University. Accessed April 11, 2021. https://submit-etda.libraries.psu.edu/catalog/14674eaf203.

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

MLA Handbook (7^th Edition):

Frankel, Erica Ann. “Towards Investigation of RNA Catalysis and Compartmentalization.” 2017. Web. 11 Apr 2021.

Vancouver:

Frankel EA. Towards Investigation of RNA Catalysis and Compartmentalization. [Internet] [Thesis]. Penn State University; 2017. [cited 2021 Apr 11]. Available from: https://submit-etda.libraries.psu.edu/catalog/14674eaf203.

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

Council of Science Editors:

Frankel EA. Towards Investigation of RNA Catalysis and Compartmentalization. [Thesis]. Penn State University; 2017. Available from: https://submit-etda.libraries.psu.edu/catalog/14674eaf203

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

2. Schott, Micah. Gravin Regulates Crosstalk Between Calcium And PkA Dependent Signaling Pathways In Cultured Cells.

Degree: PhD, Biology, 2014, University of North Dakota

URL: https://commons.und.edu/theses/1709

► A-Kinase Anchoring Proteins (AKAPs) comprise a family of roughly 70 scaffolds that anchor PKA and other enzymes to a variety of subcellular compartments. Although… (more)

▼ A-Kinase Anchoring Proteins (AKAPs) comprise a family of roughly 70 scaffolds that anchor PKA and other enzymes to a variety of subcellular compartments. Although characterized as "anchoring proteins", some AKAPs are not spatially and temporally static but can undergo dynamic subcellular trafficking, thus repositioning anchored enzyme complexes within the cell. Gravin (also called SSeCKS or AKAP12) anchors PKA and other enzymes to the plasma membrane but redistributes to the cytosol upon intracellular calcium ([Ca2+]i) elevation. However, the impact of gravin redistribution on PKA-dependent signaling pathways is poorly understood. We hypothesize that through Ca2+-mediated redistribution, gravin facilitates cross-talk between Ca2+-dependent and PKA-dependent pathways. First, we tested this by characterizing the impact of [Ca2+]i elevation on the distribution of gravin and PKA. In cells expressing gravin-EGFP, [Ca2+]i elevation with ionomycin or thapsigargin caused gravin redistribution from the cell periphery to the cytosol in as little as 60 seconds. ATP treatment also triggered gravin redistribution through receptor-mediated pathways involving both [Ca2+]i and PKC. Gravin redistribution in response to ionomycin, thapsigargin, and ATP each triggered the gravin-dependent loss of PKA localization at the cell periphery. In addition, we also found that a fourth putative calmodulin binding domain, which we call CB4 (a.a. 669-693), is essential for localization of gravin to the cell periphery. Either deletion of the CB4 domain or mutation of a calmodulin-binding consensus sequence within the CB4 domain disrupted the membrane localization of gravin. Next, we measured the impact of exogenous gravin-V5/His expression on compartmentalized PKA activity using the PKA FRET biosensor AKAR3. Expression of gravin-V5/His in AN3 CA cells, which lack endogenous gravin, caused an increase in forskolin-stimulated PKA activity at the plasma membrane when compared to control cells lacking gravin. Under these conditions, gravin also decreased PKA activity in the cytosol. Gravin's impact on subcellular PKA activity required both interaction with PKA and localization at the cell periphery. Pre-treatment with the [Ca2+]i elevating agent thapsigargin caused gravin redistribution and inhibited gravin-mediated elevation of PKA activity the plasma membrane. These results support the hypothesis that gravin mediates crosstalk between Ca2+-dependent and PKA-dependent signaling pathways. Advisors/Committee Members: Bryon D. Grove.

Subjects/Keywords: Cell signaling; Compartmentalization; Kinase; Microscopy; Scaffold

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APA (6^th Edition):

Schott, M. (2014). Gravin Regulates Crosstalk Between Calcium And PkA Dependent Signaling Pathways In Cultured Cells. (Doctoral Dissertation). University of North Dakota. Retrieved from https://commons.und.edu/theses/1709

Chicago Manual of Style (16^th Edition):

Schott, Micah. “Gravin Regulates Crosstalk Between Calcium And PkA Dependent Signaling Pathways In Cultured Cells.” 2014. Doctoral Dissertation, University of North Dakota. Accessed April 11, 2021. https://commons.und.edu/theses/1709.

MLA Handbook (7^th Edition):

Schott, Micah. “Gravin Regulates Crosstalk Between Calcium And PkA Dependent Signaling Pathways In Cultured Cells.” 2014. Web. 11 Apr 2021.

Vancouver:

Schott M. Gravin Regulates Crosstalk Between Calcium And PkA Dependent Signaling Pathways In Cultured Cells. [Internet] [Doctoral dissertation]. University of North Dakota; 2014. [cited 2021 Apr 11]. Available from: https://commons.und.edu/theses/1709.

Council of Science Editors:

Schott M. Gravin Regulates Crosstalk Between Calcium And PkA Dependent Signaling Pathways In Cultured Cells. [Doctoral Dissertation]. University of North Dakota; 2014. Available from: https://commons.und.edu/theses/1709

University of Manchester

3. Qu, Peng. Metabolic Flux Balance Analysis with Plant Cell Compartmentallization.

Degree: 2018, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:315139

► The aim of this research was the development of both a homogeneous and a heterogeneous metabolic model for Nicotiana tabacum cell suspension cultures using computational… (more)

Subjects/Keywords: Metabolism; MFBA; Heterogeneous; Homogeneous; Model; Compartmentalization

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

APA (6^th Edition):

Qu, P. (2018). Metabolic Flux Balance Analysis with Plant Cell Compartmentallization. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:315139

Chicago Manual of Style (16^th Edition):

Qu, Peng. “Metabolic Flux Balance Analysis with Plant Cell Compartmentallization.” 2018. Doctoral Dissertation, University of Manchester. Accessed April 11, 2021. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:315139.

MLA Handbook (7^th Edition):

Qu, Peng. “Metabolic Flux Balance Analysis with Plant Cell Compartmentallization.” 2018. Web. 11 Apr 2021.

Vancouver:

Qu P. Metabolic Flux Balance Analysis with Plant Cell Compartmentallization. [Internet] [Doctoral dissertation]. University of Manchester; 2018. [cited 2021 Apr 11]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:315139.

Council of Science Editors:

Qu P. Metabolic Flux Balance Analysis with Plant Cell Compartmentallization. [Doctoral Dissertation]. University of Manchester; 2018. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:315139

University of Manchester

4. Qu, Peng. Metabolic flux balance analysis with plant cell compartmentalization.

Degree: PhD, 2018, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/metabolic-flux-balance-analysis-with-plant-cell-compartmentallization(24cd599a-b4e8-4e28-b863-0e286bcba806).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.823002

► The aim of this research was the development of both a homogeneous and a heterogeneous metabolic model for Nicotiana tabacum cell suspension cultures using computational… (more)

Subjects/Keywords: Model; Metabolism; MFBA; Heterogeneous; Homogeneous; Compartmentalization

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

APA (6^th Edition):

Qu, P. (2018). Metabolic flux balance analysis with plant cell compartmentalization. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/metabolic-flux-balance-analysis-with-plant-cell-compartmentallization(24cd599a-b4e8-4e28-b863-0e286bcba806).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.823002

Chicago Manual of Style (16^th Edition):

Qu, Peng. “Metabolic flux balance analysis with plant cell compartmentalization.” 2018. Doctoral Dissertation, University of Manchester. Accessed April 11, 2021. https://www.research.manchester.ac.uk/portal/en/theses/metabolic-flux-balance-analysis-with-plant-cell-compartmentallization(24cd599a-b4e8-4e28-b863-0e286bcba806).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.823002.

MLA Handbook (7^th Edition):

Qu, Peng. “Metabolic flux balance analysis with plant cell compartmentalization.” 2018. Web. 11 Apr 2021.

Vancouver:

Qu P. Metabolic flux balance analysis with plant cell compartmentalization. [Internet] [Doctoral dissertation]. University of Manchester; 2018. [cited 2021 Apr 11]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/metabolic-flux-balance-analysis-with-plant-cell-compartmentallization(24cd599a-b4e8-4e28-b863-0e286bcba806).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.823002.

Council of Science Editors:

Qu P. Metabolic flux balance analysis with plant cell compartmentalization. [Doctoral Dissertation]. University of Manchester; 2018. Available from: https://www.research.manchester.ac.uk/portal/en/theses/metabolic-flux-balance-analysis-with-plant-cell-compartmentallization(24cd599a-b4e8-4e28-b863-0e286bcba806).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.823002

UCLA

5. Shin, KWANG SUP. Biomechanics of Compartmentalized Mechanical Properties of Extraocular Muscle and Tendon.

Degree: Mechanical Engineering, 2014, UCLA

URL: http://www.escholarship.org/uc/item/0fx3w530

► A controversial issue in the eye movement field involves the compartmentalization of extraocular muscle (EOM). Conventionally, it has been believed that each individual EOM is… (more)

▼ A controversial issue in the eye movement field involves the compartmentalization of extraocular muscle (EOM). Conventionally, it has been believed that each individual EOM is innervated uniformly by its motor nerve, and behaves uniformly. However, recent studies have revealed that motor nerves innervating horizontal rectus EOMs are bifurcated into two divisions that control, respectively, the superior and inferior zones of muscle fibers. This finding has motivated the proposition that each of the two compartments of these EOMs might be controlled independently, so that each EOM could behave as it were two parallel but independent actuators. The compartmental independence postulate requires a mechanically low degree of transverse force coupling among parallel EOM and extraocular tendon (EOT) fibers. This project aimed to employ biomechanical characterization to EOM and EOT to test the plausibility of this hypothesis.The first study described the biomechanical characterization of EOT, in both at the level of individual fibers and whole tendon. Nano indentation of EOT fiber bundles analyzed within the Hertzian framework effectively characterized the transverse Young's modulus for bovine EOT fiber bundles using atomic force microscopy (AFM). A precise estimate of the Poisson ratio (PR) of bovine EOTs was calculated using optical coherence tomography (OCT) during tensile loading. The second study investigated mechanical potential for independent compartmental behavior in EOM and EOT. Extensive experimental study was performed to examine the passive mechanical interaction between sets compartments using a custom fabricated dual channel micro-tensile load cell. Independent active contractile behavior of EOM compartments was also examined using calcium-induced EOM contraction. Both passive loading and active contraction findings indicate that EOM and tendon have a high degree of biomechanical independence, sufficient to support the proposed functional diversity of actions in distinct neuromuscular compartments of the horizontal rectus EOMs.Finally, biomechanical effects of Z-tenotomy and Z-myotomy, surgical techniques employing transverse incisions for EOT or EOM weakening to correct strabismus (misalignment of the eyes), were characterized using tensile loading. Both Z-tenotomy and Z-myotomy demonstrated minimal shear force coupling, which confirms and extends the findings of independent compartmental behavior in second study, and explains the surgical effects of the procedure. Additional viscoelastic characterization was performed using EOM specimens.

Subjects/Keywords: Mechanical engineering; Biomechanics; Biomedical engineering; Biomechanics; Compartmentalization; Extraocular Muscle; Extraocular Tendon

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

APA (6^th Edition):

Shin, K. S. (2014). Biomechanics of Compartmentalized Mechanical Properties of Extraocular Muscle and Tendon. (Thesis). UCLA. Retrieved from http://www.escholarship.org/uc/item/0fx3w530

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):

Shin, KWANG SUP. “Biomechanics of Compartmentalized Mechanical Properties of Extraocular Muscle and Tendon.” 2014. Thesis, UCLA. Accessed April 11, 2021. http://www.escholarship.org/uc/item/0fx3w530.

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

MLA Handbook (7^th Edition):

Shin, KWANG SUP. “Biomechanics of Compartmentalized Mechanical Properties of Extraocular Muscle and Tendon.” 2014. Web. 11 Apr 2021.

Vancouver:

Shin KS. Biomechanics of Compartmentalized Mechanical Properties of Extraocular Muscle and Tendon. [Internet] [Thesis]. UCLA; 2014. [cited 2021 Apr 11]. Available from: http://www.escholarship.org/uc/item/0fx3w530.

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

Council of Science Editors:

Shin KS. Biomechanics of Compartmentalized Mechanical Properties of Extraocular Muscle and Tendon. [Thesis]. UCLA; 2014. Available from: http://www.escholarship.org/uc/item/0fx3w530

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

Cornell University

6. Forster, Brian. Regulation Of The Metalloprotease Of Listeria Monocytogenes During Intracellular Infection.

Degree: PhD, Microbiology, 2011, Cornell University

URL: http://hdl.handle.net/1813/30617

► Listeria monocytogenes is a Gram-positive, facultative intracellular bacterial pathogen that multiplies in the cytosol of host cells and relies on an actin-based mechanism of motility… (more)

▼ Listeria monocytogenes is a Gram-positive, facultative intracellular bacterial pathogen that multiplies in the cytosol of host cells and relies on an actin-based mechanism of motility to spread from cell-to-cell without exiting the intracellular milieu. Virulence of L. monocytogenes is related to its ability to escape from vacuoles formed upon initial entry into a host cell and during cell-to-cell spread. One factor contributing to escape from vacuoles is a broad-range phospholipase C (PC-PLC). PC-PLC is translocated across the bacterial membrane as an inactive proenzyme and accumulates in the periplasmic space. PC-PLC maturation is dependent upon a decrease in pH and on the metalloprotease of L. monocytogenes (Mpl). Mpl, a thermolysin-like protease, is produced as a zymogen and matures via intramolecular autocatalysis. In this study, we wished to investigate the regulation of Mpl during intracellular infection. Our results show that at physiological pH, the zymogen remains bacterium-associated, presumably in the periplasm. Mpl produced in absence of its propeptide is aberrantly secreted suggesting that the propeptide regulates compartmentalization. Upon a decrease in pH, the bacterium-associated zymogen undergoes autocatalysis and mediates the proteolytic activation of PC-PLC. Mature Mpl and PC-PLC are then rapidly secreted across the cell wall. Two amino acids in the catalytic domain of Mpl, H226 and H241, influence mature Mpl secretion and its ability to process PC-PLC. The compartmentalization of the zymogen is also influenced by PrsA2, a peptidyl prolyl cis-trans isomerase that is anchored by an acyl chain to the trans side of the membrane. In absence of PrsA2, the proforms of Mpl and PC-PLC are aberrantly secreted across the cell wall and no longer undergo maturation upon a decrease in pH. Taken together, these results indicate that PrsA2 and the propeptide of Mpl serve to maintain the association of Mpl with bacteria and that this compartmentalization is required for Mpl to undergo autocatalysis at acidic pH and to mediate the proteolytic activation of PC-PLC. Advisors/Committee Members: Marquis, Helene (chair), Scidmore, Marci (committee member), Wilson, David B (committee member).

Subjects/Keywords: Listeria monocytogenes; metalloprotease; proproteins; compartmentalization; pH; peptidyl-prolyl cis/trans isomerase

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

APA (6^th Edition):

Forster, B. (2011). Regulation Of The Metalloprotease Of Listeria Monocytogenes During Intracellular Infection. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/30617

Chicago Manual of Style (16^th Edition):

Forster, Brian. “Regulation Of The Metalloprotease Of Listeria Monocytogenes During Intracellular Infection.” 2011. Doctoral Dissertation, Cornell University. Accessed April 11, 2021. http://hdl.handle.net/1813/30617.

MLA Handbook (7^th Edition):

Forster, Brian. “Regulation Of The Metalloprotease Of Listeria Monocytogenes During Intracellular Infection.” 2011. Web. 11 Apr 2021.

Vancouver:

Forster B. Regulation Of The Metalloprotease Of Listeria Monocytogenes During Intracellular Infection. [Internet] [Doctoral dissertation]. Cornell University; 2011. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/1813/30617.

Council of Science Editors:

Forster B. Regulation Of The Metalloprotease Of Listeria Monocytogenes During Intracellular Infection. [Doctoral Dissertation]. Cornell University; 2011. Available from: http://hdl.handle.net/1813/30617

Texas A&M University

7. Alfaleh, Abdulhamed A. Use of Topological Data Analysis in Reservoir Engineering: Application to Inverted 4D Seismic Data.

Degree: MS, Petroleum Engineering, 2014, Texas A&M University

URL: http://hdl.handle.net/1969.1/154176

► Data analysis is one of the most important topics in any industry. In petroleum engineering, the complexity of reservoir data presents a challenge for engineers… (more)

Subjects/Keywords: Topological Data Analysis; Inverted 4D Seismic; Reservoirs connectivity; compartmentalization

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

APA (6^th Edition):

Alfaleh, A. A. (2014). Use of Topological Data Analysis in Reservoir Engineering: Application to Inverted 4D Seismic Data. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/154176

Chicago Manual of Style (16^th Edition):

Alfaleh, Abdulhamed A. “Use of Topological Data Analysis in Reservoir Engineering: Application to Inverted 4D Seismic Data.” 2014. Masters Thesis, Texas A&M University. Accessed April 11, 2021. http://hdl.handle.net/1969.1/154176.

MLA Handbook (7^th Edition):

Alfaleh, Abdulhamed A. “Use of Topological Data Analysis in Reservoir Engineering: Application to Inverted 4D Seismic Data.” 2014. Web. 11 Apr 2021.

Vancouver:

Alfaleh AA. Use of Topological Data Analysis in Reservoir Engineering: Application to Inverted 4D Seismic Data. [Internet] [Masters thesis]. Texas A&M University; 2014. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/1969.1/154176.

Council of Science Editors:

Alfaleh AA. Use of Topological Data Analysis in Reservoir Engineering: Application to Inverted 4D Seismic Data. [Masters Thesis]. Texas A&M University; 2014. Available from: http://hdl.handle.net/1969.1/154176

Penn State University

8. Aumiller, William Michael. Understanding Intracellular Organization Using Aqueous Phase Model Systems.

Degree: 2015, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/26407

► The intracellular milieu is a heterogeneous environment composed of many different organelles and compartments that perform specific functions simultaneously in spatially confined areas. This environment… (more)

▼ The intracellular milieu is a heterogeneous environment composed of many different organelles and compartments that perform specific functions simultaneously in spatially confined areas. This environment is incredibly complex, which can make studying enzyme reactions inside cells challenging. The aqueous phase model systems described here aim to provide insight as to the mechanisms used by cells to control enzyme activity, compartment formation, and compartmentalization of biomolecules. Chapter 1 provides a general background of intracellular organization in biological cells, followed by a discussion of fundamental principles governing biomolecule activity within a nonideal solution. The types of aqueous phase separation that appear in later chapters are discussed, as well as a review of related aqueous phase-separated model systems. Chapter 2 describes complex coacervation of a long poly(uridylic acid) RNA (poly U, a polyanion) and short cationic peptide (RRASLRRASL) that undergo reversible phase separation in response to the phosphorylation state (and therefore charge state) of the peptide. Phosphorylation was controlled enzymatically by a kinase and phosphatase pair. This demonstrates that phosphorylation could be a viable means to control compartment formation and dissolution in vivo. Additionally, the poly U/RRASLRRASL coacervates were capable of concentrating solutes up to 1150×. In Chapter 3, sequential enzyme activity is studied in a polyethylene glycol (PEG)/sodium citrate biphasic system. The enzymes glucose oxidase (GOX) and horseradish peroxidase (HRP) and substrate Amplex Red partitioned to opposite phases and required mass transport across an interface for product formation. A mathematical model was developed to describe the complex kinetics in the system, and the model was validated when it accurately described other experimental conditions. Chapter 4 looks at the reaction of HRP with two different substrates that differed in their relative hydrophobicity. Catalysis by HRP was highly dependent on solution composition because attractive interactions between the more hydrophobic substrate and more hydrophobic crowders and cosolutes (different molecular weights of PEG) caused a larger decrease in enzyme activity. This was confirmed by diffusion nuclear magnetic resonance (NMR) measurements. This is significant because it is the first systematic study of substrate-crowder interactions within the macromolecular crowding community. In Chapter 5, enzymes and substrates of the purine biosynthesis pathway were partitioned to the dextran-rich phase of a PEG/dextran biphasic system. The mathematical model developed in Chapter 3 was used in this phase system to describe the kinetics and mass transport under conditions that were difficult to study experimentally. The results suggest that significant advantages of enzyme colocalization may only be observed if essentially all of the enzyme is restricted to compartments, rather than only being weakly partitioned. Finally, Chapter 6 offers some general conclusions from… Advisors/Committee Members: Christine Dolan Keating, Dissertation Advisor/Co-Advisor, Christine Dolan Keating, Committee Chair/Co-Chair, Carsten Krebs, Committee Member, Scott A Showalter, Committee Member, Antonios Armaou, Committee Member.

Subjects/Keywords: aqueous phase separation; macromolecular crowding; phosphorylation; coacervate; sequential enzymes; compartmentalization

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

APA (6^th Edition):

Aumiller, W. M. (2015). Understanding Intracellular Organization Using Aqueous Phase Model Systems. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/26407

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):

Aumiller, William Michael. “Understanding Intracellular Organization Using Aqueous Phase Model Systems.” 2015. Thesis, Penn State University. Accessed April 11, 2021. https://submit-etda.libraries.psu.edu/catalog/26407.

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

MLA Handbook (7^th Edition):

Aumiller, William Michael. “Understanding Intracellular Organization Using Aqueous Phase Model Systems.” 2015. Web. 11 Apr 2021.

Vancouver:

Aumiller WM. Understanding Intracellular Organization Using Aqueous Phase Model Systems. [Internet] [Thesis]. Penn State University; 2015. [cited 2021 Apr 11]. Available from: https://submit-etda.libraries.psu.edu/catalog/26407.

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

Council of Science Editors:

Aumiller WM. Understanding Intracellular Organization Using Aqueous Phase Model Systems. [Thesis]. Penn State University; 2015. Available from: https://submit-etda.libraries.psu.edu/catalog/26407

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

Penn State University

9. Strulson, Christopher A. toward understanding RNA structure, folding, and function in cells.

Degree: 2014, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/20143

► Ever since the discovery of RNA as an integral biomolecule in cellular function, the principles governing RNA folding and function have been studied. These studies… (more)

▼ Ever since the discovery of RNA as an integral biomolecule in cellular function, the principles governing RNA folding and function have been studied. These studies have primarily focused on the thermodynamics and kinetics of RNA folding in conditions that are folding-favorable and non-physiological including dilute solution with relatively high ionic strength and Mg2+ ion concentrations. While these studies have imparted invaluable knowledge towards the understanding of RNA biophysics, there is still a great need to characterize RNA folding and function in conditions that are much closer to those of a cell; however, because of the intricacies of the cellular environment, elucidating meaningful biophysical properties from experiments directly in living cells remains difficult. In an effort to capture the effects of this complex environment on RNA folding, in vitro experiments focusing on distinct features of the cellular environment are performed in attempt to learn how these specific properties of the cellular matrix impact RNA. In this thesis, RNA structure, folding, and function are assessed from both a thermodynamic and kinetic prospective under conditions that mimic those of cells. In particular, effects of compartmentalization, macromolecular crowding, and low molecular cosolutes are examined in terms of RNA catalysis and RNA folding using an array of techniques including RNA partitioning, ribozyme kinetics, small angle X-ray scattering (SAXS), structure mapping methods, and RNA folding thermodynamics. One key aspect of cells is their ability to compartmentalize biomolecules; thus, allowing them to control local concentrations of these molecules. In Chapter Two and Three of this thesis, it is revealed that local concentrations of RNA can be controlled using an aqueous two-phase system composed of two high molecular weight polymers. Additionally, increasing the local concentration of an enzyme strand of a two-piece ribozyme within one of the aqueous phase compartments, leads to a significant enhancement in catalysis under single-turnover conditions. This work indicates that compartmentalization could be very important for RNA function in modern cells as well as in RNA regulation and activation in early-earth protocells. Another key factor of the cellular environment is the concentration of free Mg2+, which is only ~0.5 mM and ~2 mM in eukaryotic and prokaryotic cells, respectively. These values are considerably lower than the free Mg2+ (~10 mM) typically used in RNA structure and folding studies in the literature. Additionally, there are high concentrations of molecules (both high- and low-molecular weight) inside cells that can interact with RNA, exclude volume, and alter solvent conditions. These molecules can have large impacts on RNA structure, folding, and function especially when Mg2+ concentrations are physiological. It is revealed in Chapter Four of this thesis that the self-cleavage of a small catalytic RNA, the cytoplasmic polyadenylation element–binding protein 3 HDV-like ribozyme (CPEB3),… Advisors/Committee Members: Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor, Christine Dolan Keating, Dissertation Advisor/Co-Advisor, Squire J Booker, Committee Member, Tae Hee Lee, Committee Member, Kenneth Charles Keiler, Committee Member.

Subjects/Keywords: RNA; ribozyme; molecular crowding; macromolecular crowding; catalysis; compartmentalization; folding cooperativity

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

APA (6^th Edition):

Strulson, C. A. (2014). toward understanding RNA structure, folding, and function in cells. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/20143

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):

Strulson, Christopher A. “toward understanding RNA structure, folding, and function in cells.” 2014. Thesis, Penn State University. Accessed April 11, 2021. https://submit-etda.libraries.psu.edu/catalog/20143.

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

MLA Handbook (7^th Edition):

Strulson, Christopher A. “toward understanding RNA structure, folding, and function in cells.” 2014. Web. 11 Apr 2021.

Vancouver:

Strulson CA. toward understanding RNA structure, folding, and function in cells. [Internet] [Thesis]. Penn State University; 2014. [cited 2021 Apr 11]. Available from: https://submit-etda.libraries.psu.edu/catalog/20143.

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

Council of Science Editors:

Strulson CA. toward understanding RNA structure, folding, and function in cells. [Thesis]. Penn State University; 2014. Available from: https://submit-etda.libraries.psu.edu/catalog/20143

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

UCLA

10. Yaeger, Courtney. A transient microcircuit underlying critical period plasticity in the visual cortex.

Degree: Neuroscience, 2018, UCLA

URL: http://www.escholarship.org/uc/item/0sw060pz

► During so-called critical periods of early postnatal life, sensory experience profoundly and permanently sculpts cortical neural circuitry. After critical period closure, experience-dependent plasticity is dramatically… (more)

Subjects/Keywords: Neurosciences; binocular matching; critical period; dendritic compartmentalization; disinhibition; inhibition; neuromodulation

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APA (6^th Edition):

Yaeger, C. (2018). A transient microcircuit underlying critical period plasticity in the visual cortex. (Thesis). UCLA. Retrieved from http://www.escholarship.org/uc/item/0sw060pz

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):

Yaeger, Courtney. “A transient microcircuit underlying critical period plasticity in the visual cortex.” 2018. Thesis, UCLA. Accessed April 11, 2021. http://www.escholarship.org/uc/item/0sw060pz.

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

MLA Handbook (7^th Edition):

Yaeger, Courtney. “A transient microcircuit underlying critical period plasticity in the visual cortex.” 2018. Web. 11 Apr 2021.

Vancouver:

Yaeger C. A transient microcircuit underlying critical period plasticity in the visual cortex. [Internet] [Thesis]. UCLA; 2018. [cited 2021 Apr 11]. Available from: http://www.escholarship.org/uc/item/0sw060pz.

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

Council of Science Editors:

Yaeger C. A transient microcircuit underlying critical period plasticity in the visual cortex. [Thesis]. UCLA; 2018. Available from: http://www.escholarship.org/uc/item/0sw060pz

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

University of Toronto

11. Li, Junting. Using Compartmentalization to Mitigate the Impacts of Stack Effect in Tall Residential Buildings.

Degree: 2018, University of Toronto

URL: http://hdl.handle.net/1807/89635

►

Natural stack action affects all types of buildings, but it becomes a significant driving force and imposes adverse impacts on tall buildings. Traditional approaches such… (more)

Subjects/Keywords: Compartmentalization; Computer Simulation; Stack Effect; Tall Residential Buildings; 0543

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APA (6^th Edition):

Li, J. (2018). Using Compartmentalization to Mitigate the Impacts of Stack Effect in Tall Residential Buildings. (Masters Thesis). University of Toronto. Retrieved from http://hdl.handle.net/1807/89635

Chicago Manual of Style (16^th Edition):

Li, Junting. “Using Compartmentalization to Mitigate the Impacts of Stack Effect in Tall Residential Buildings.” 2018. Masters Thesis, University of Toronto. Accessed April 11, 2021. http://hdl.handle.net/1807/89635.

MLA Handbook (7^th Edition):

Li, Junting. “Using Compartmentalization to Mitigate the Impacts of Stack Effect in Tall Residential Buildings.” 2018. Web. 11 Apr 2021.

Vancouver:

Li J. Using Compartmentalization to Mitigate the Impacts of Stack Effect in Tall Residential Buildings. [Internet] [Masters thesis]. University of Toronto; 2018. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/1807/89635.

Council of Science Editors:

Li J. Using Compartmentalization to Mitigate the Impacts of Stack Effect in Tall Residential Buildings. [Masters Thesis]. University of Toronto; 2018. Available from: http://hdl.handle.net/1807/89635

Colorado State University

12. Higgins, Jenny. Compartmentalization of membrane proteins by the actin cytoskeleton.

Degree: MS(M.S.), Biomedical Engineering, 2013, Colorado State University

URL: http://hdl.handle.net/10217/81011

► Acting as the point of contact for the outside world, the plasma membrane is crucial for cellular signaling events. Proper organization of membrane components is… (more)

Subjects/Keywords: membrane protein; superresolution; plasma membrane compartmentalization; actin; cytoskeleton; PALM

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APA (6^th Edition):

Higgins, J. (2013). Compartmentalization of membrane proteins by the actin cytoskeleton. (Masters Thesis). Colorado State University. Retrieved from http://hdl.handle.net/10217/81011

Chicago Manual of Style (16^th Edition):

Higgins, Jenny. “Compartmentalization of membrane proteins by the actin cytoskeleton.” 2013. Masters Thesis, Colorado State University. Accessed April 11, 2021. http://hdl.handle.net/10217/81011.

MLA Handbook (7^th Edition):

Higgins, Jenny. “Compartmentalization of membrane proteins by the actin cytoskeleton.” 2013. Web. 11 Apr 2021.

Vancouver:

Higgins J. Compartmentalization of membrane proteins by the actin cytoskeleton. [Internet] [Masters thesis]. Colorado State University; 2013. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/10217/81011.

Council of Science Editors:

Higgins J. Compartmentalization of membrane proteins by the actin cytoskeleton. [Masters Thesis]. Colorado State University; 2013. Available from: http://hdl.handle.net/10217/81011

Université Paris-Sud – Paris XI

13. Le bars, Romain. Morphogenèse de compartiments membranaires : formation de l'autophagosome chez les plantes : Morphogenesis of membranar compartments : autophagosome formation in plants.

Degree: Docteur es, Biologie, 2013, Université Paris-Sud – Paris XI

URL: http://www.theses.fr/2013PA112349

►

L'autophagie est un processus permettant la dégradation de constituants cytosoliques dans un compartiment lytique, par leur séquestration au sein d'une vésicule à double membrane :… (more)

▼

L'autophagie est un processus permettant la dégradation de constituants cytosoliques dans un compartiment lytique, par leur séquestration au sein d'une vésicule à double membrane : l'autophagosome. L'autophagie est, avec la voie ubiquitine-protéasome, l'une des deux grandes voies de dégradation présente de manière fortement conservée chez les cellules eucaryotes. Présente à un niveau basal, elle peut être stimulée afin de permettre la remobilisation de ressources cellulaires, ou d'assurer des fonctions cytoprotectrices et de détoxification. La formation d'autophagosomes traduit alors la capacité du système endomembranaire à s'adapter aux besoins cellulaires. Cependant, la mécanique membranaire et moléculaire de ce phénomène reste mal comprise. L'objectif de ce travail de thèse était de mieux comprendre la formation de ce compartiment dans la cellule végétale. Pour cela, nous avons tout d'abord mis au point les conditions propices à l'étude de l'autophagie dans la racine d’Arabidopsis thaliana, puis nous avons entrepris l'identification de marqueurs des étapes de formation de l'autophagosome. L'étude par imagerie en temps réel et 3D de la protéine ATG5, impliquée dans l’expansion membranaire, nous a permis de mettre en évidence son recrutement transitoire sur un domaine particulier de l'autophagosome en formation, son ouverture. De plus, l'étude de différents acteurs du système endomembranaire, nous a permis de mettre en évidence et de caractériser l'implication du réticulum endoplasmique et de ATG9, pour aboutir à un modèle de la formation de l'autophagosome chez les plantes.

Autophagy is a catabolic process targeting cytosolic compounds to the lytic compartment after sequestration within a double membrane bound vesicle: the autophagosome. Along with the ubiquitin-proteasome pathway, autophagy is one of the main catabolic processes conserved among eukaryotic cells. Present at a basal level, it can be stimulated to allow: remobilization of cell resources, cytoprotective functions, and detoxification. Autophagosome formation demonstrates the capacity of the endomembrane system to adapt dynamically to the cell's environment. However, the membrane and molecular processes involved are still poorly understood. This work aimed to advance understanding of autophagosome formation in plant cells. First of all, we set up suitable conditions for the study of autophagy in the Arabidopsis root, then we identified markers of the autophagosome formation steps. Live and 3D imaging of the ATG5 protein, involved in membrane expansion, demonstrated its transient recruitment to a specific domain of the forming autophagosome, its aperture. Furthermore, studying different actors of the endomembrane system has allowed us to implicate the endoplasmic reticulum and ATG9, and to establish a model for autophagosome formation in plants.

Advisors/Committee Members: Satiat-Jeunemaître, Béatrice (thesis director).

Subjects/Keywords: Autophagosome; Autophagie; Compartimentation cellulaire; Autophagosome; Autophagy; Cell compartmentalization

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

APA (6^th Edition):

Le bars, R. (2013). Morphogenèse de compartiments membranaires : formation de l'autophagosome chez les plantes : Morphogenesis of membranar compartments : autophagosome formation in plants. (Doctoral Dissertation). Université Paris-Sud – Paris XI. Retrieved from http://www.theses.fr/2013PA112349

Chicago Manual of Style (16^th Edition):

Le bars, Romain. “Morphogenèse de compartiments membranaires : formation de l'autophagosome chez les plantes : Morphogenesis of membranar compartments : autophagosome formation in plants.” 2013. Doctoral Dissertation, Université Paris-Sud – Paris XI. Accessed April 11, 2021. http://www.theses.fr/2013PA112349.

MLA Handbook (7^th Edition):

Le bars, Romain. “Morphogenèse de compartiments membranaires : formation de l'autophagosome chez les plantes : Morphogenesis of membranar compartments : autophagosome formation in plants.” 2013. Web. 11 Apr 2021.

Vancouver:

Le bars R. Morphogenèse de compartiments membranaires : formation de l'autophagosome chez les plantes : Morphogenesis of membranar compartments : autophagosome formation in plants. [Internet] [Doctoral dissertation]. Université Paris-Sud – Paris XI; 2013. [cited 2021 Apr 11]. Available from: http://www.theses.fr/2013PA112349.

Council of Science Editors:

Le bars R. Morphogenèse de compartiments membranaires : formation de l'autophagosome chez les plantes : Morphogenesis of membranar compartments : autophagosome formation in plants. [Doctoral Dissertation]. Université Paris-Sud – Paris XI; 2013. Available from: http://www.theses.fr/2013PA112349

Université Catholique de Louvain

14. Woronoff, Gabrielle. Development of methods for the directed evolution of penicillin G acylase by in vitro compartmentalization.

Degree: 2012, Université Catholique de Louvain

URL: http://hdl.handle.net/2078.1/110274

►

Enzymatic catalysts have been finely tuned for their specific function though natural evolution, by iterative mutations and selections cycles. Directed evolution mimics natural evolution at… (more)

▼

Enzymatic catalysts have been finely tuned for their specific function though natural evolution, by iterative mutations and selections cycles. Directed evolution mimics natural evolution at the laboratory scale and allows the selection, in large collections of variants, of enzymes bearing new properties. In vitro compartmentalization (IVC) is the directed evolution technique used in this work, and consists of aqueous microdroplets dispersed in oil acting as artificial cells. Single genes can be encapsulated in droplets together with the proteins encoded by this gene and substrates to test its enzymatic activity. These compartments can be easily manipulated using microfluidic techniques. Two fluorogenic enzymatic tests applied to the detection of the penicillin G acylase in droplets were developed. The retention of coumarin compounds in microdroplets was evaluated and a collection of substrates with a sulfonated coumarin as leaving group was synthesized. Libraries of mutants of penicillin acylase were created and screened for variants that would have acquired broader substrate specificity compared to the wild type enzyme. The second enzymatic test called AFET (for Activity Fed Enzyme Translation) is based on the in vitro translation of proteins. It consists of the linkage between the enzymatic activity of the enzyme of interest with its own in vitro translation together with the translation of a reporter gene, in our case the GFP. The presented work lays a solid foundation for future work in the directed evolution of penicillin acylase and other enzymes of interest.

Des catalyseurs enzymatiques aux paramètres finement ajustés pour leur fonction spécifique ont été développés au cours de l’évolution par cycles itératifs de mutations et sélections. L’évolution dirigée mime l’évolution naturelle à l’échelle du laboratoire afin de trouver au sein de larges collections de variants, des enzymes présentant des propriétés nouvelles. La compartimentalisation in vitro (IVC), technique d’évolution dirigée utilisée dans ce travail, consiste à utiliser des gouttes aqueuses dispersées dans une phase huileuse comme cellules artificielles. Il est possible d’encapsuler au sein d’une même goutte un gène, la protéine qu’il encode et d’éventuels substrats permettant de tester son activité. Ces compartiments peuvent ensuite être facilement manipulés par techniques microfluidiques. Deux tests enzymatiques fluorogéniques applicables à la détection de l’activité de la pénicilline G acylase en gouttes ont été développés. La rétention de composés coumarinés au sein des microcompartiments d’émulsion a été évaluée et une collection de substrats possédant une coumarine sulfonate comme groupe partant a été synthétisée. Des banques de mutants de la pénicilline acylase ont été créées et criblées en IVC afin de trouver des variants de l’enzyme possédant une spécificité de substrat plus large que l’enzyme sauvage. Le second test enzymatique appelé « AFET » (pour Activity Fed Enzyme Translation), et basé sur la traduction protéique in vitro, a…

Advisors/Committee Members: UCL - SST/ISV/ISV - Institut des sciences de la vie, Soumillion, Patrice, Remacle, Claude, Fastrez, Jacques, Elias, Benjamin, Janssen, Dick B., Griffiths, Andrew.

Subjects/Keywords: Directed evolution; Penicillin G acylase; Dropletb-based microfluidics; In vitro compartmentalization

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APA (6^th Edition):

Woronoff, G. (2012). Development of methods for the directed evolution of penicillin G acylase by in vitro compartmentalization. (Thesis). Université Catholique de Louvain. Retrieved from http://hdl.handle.net/2078.1/110274

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):

Woronoff, Gabrielle. “Development of methods for the directed evolution of penicillin G acylase by in vitro compartmentalization.” 2012. Thesis, Université Catholique de Louvain. Accessed April 11, 2021. http://hdl.handle.net/2078.1/110274.

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

MLA Handbook (7^th Edition):

Woronoff, Gabrielle. “Development of methods for the directed evolution of penicillin G acylase by in vitro compartmentalization.” 2012. Web. 11 Apr 2021.

Vancouver:

Woronoff G. Development of methods for the directed evolution of penicillin G acylase by in vitro compartmentalization. [Internet] [Thesis]. Université Catholique de Louvain; 2012. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/2078.1/110274.

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

Council of Science Editors:

Woronoff G. Development of methods for the directed evolution of penicillin G acylase by in vitro compartmentalization. [Thesis]. Université Catholique de Louvain; 2012. Available from: http://hdl.handle.net/2078.1/110274

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

Princeton University

15. Hammer, Sarah Katherine. Metabolic engineering of Saccharomyces cerevisiae for enhanced production of branched-chain higher alcohols .

Degree: PhD, 2020, Princeton University

URL: http://arks.princeton.edu/ark:/88435/dsp01gm80hz258

► Branched-chain higher alcohols (BCHAs) are promising advanced biofuels with properties that enable their use as complete gasoline substitutes in spark-ignition engines or as precursors to… (more)

▼ Branched-chain higher alcohols (BCHAs) are promising advanced biofuels with properties that enable their use as complete gasoline substitutes in spark-ignition engines or as precursors to jet fuel. Of particular interest are isobutanol, isopentanol, and 2-methyl-1-butanol, which are naturally produced by the ethanol workhorse Saccharomyces cerevisiae as products of amino acid degradation. Using a combination of metabolic engineering, synthetic biology, systems biology, and protein engineering, this dissertation describes the engineering of S. cerevisiae for the production of isobutanol and isopentanol at high yields and titers. In order to optimize S. cerevisiae for isobutanol production, we elucidated the roles of the mitochondrial and cytosolic branched-chain amino acid transaminases involved in isobutanol biosynthesis from glucose. Our results demonstrate that deletion of the gene encoding the mitochondrial branched-chain amino acid transaminase increases isobutanol production by 14.2-fold in the absence of externally supplied valine. We next sought to enhance tolerance of yeast to isobutanol, as product toxicity remains a major barrier to achieving high titers. Screening the haploid S. cerevisiae gene deletion library revealed that deletion of GLN3, a gene involved in nitrogen utilization, increases yeast tolerance to isobutanol and boosts isobutanol production in engineered strains as much as 4.9-fold. Transcriptomic analyses suggest a mechanism by which isobutanol induces a nitrogen starvation response dependent on GLN3. In order to expand the diversity of BCHA products we can efficiently produce in S. cerevisiae, we harnessed mitochondria to enhance isopentanol production at the expense of isobutanol. Mitochondrial localization of the three enzymes that comprise the recursive 2-ketoacid carbon-elongation pathway enabled us to achieve the highest isopentanol titer and isopentanol to isobutanol product ratio as of yet reported in S. cerevisiae. Lastly, we develop genetically encoded biosensors to enable rapid phenotyping of S. cerevisiae strains for isobutanol or isopentanol production, and describe future work applying these biosensors to select high producers from diverse strain libraries. Overall, this work has led to the improvement of BCHA production in S. cerevisiae by developing novel tools, strategies, and strains to enable the economically viable production of isobutanol and isopentanol. Advisors/Committee Members: Avalos, José L (advisor).

Subjects/Keywords: Biofuels; Isobutanol; Isopentanol; Metabolic engineering; Mitochondrial compartmentalization; Saccharomyces cerevisiae

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

APA (6^th Edition):

Hammer, S. K. (2020). Metabolic engineering of Saccharomyces cerevisiae for enhanced production of branched-chain higher alcohols . (Doctoral Dissertation). Princeton University. Retrieved from http://arks.princeton.edu/ark:/88435/dsp01gm80hz258

Chicago Manual of Style (16^th Edition):

Hammer, Sarah Katherine. “Metabolic engineering of Saccharomyces cerevisiae for enhanced production of branched-chain higher alcohols .” 2020. Doctoral Dissertation, Princeton University. Accessed April 11, 2021. http://arks.princeton.edu/ark:/88435/dsp01gm80hz258.

MLA Handbook (7^th Edition):

Hammer, Sarah Katherine. “Metabolic engineering of Saccharomyces cerevisiae for enhanced production of branched-chain higher alcohols .” 2020. Web. 11 Apr 2021.

Vancouver:

Hammer SK. Metabolic engineering of Saccharomyces cerevisiae for enhanced production of branched-chain higher alcohols . [Internet] [Doctoral dissertation]. Princeton University; 2020. [cited 2021 Apr 11]. Available from: http://arks.princeton.edu/ark:/88435/dsp01gm80hz258.

Council of Science Editors:

Hammer SK. Metabolic engineering of Saccharomyces cerevisiae for enhanced production of branched-chain higher alcohols . [Doctoral Dissertation]. Princeton University; 2020. Available from: http://arks.princeton.edu/ark:/88435/dsp01gm80hz258

University of Toronto

16. Radford, Devon Richard. Understanding the Encapsulins:Prediction and Characterization of Phage Capsid-like Nanocompartments in Prokaryotes.

Degree: PhD, 2014, University of Toronto

URL: http://hdl.handle.net/1807/69450

► Encapsulins are a distinct family of prokaryotic compartments, comprised of an icosahedral shell encapsulating a variety of enzymes. The encapsulin shell protein is similar in… (more)

▼ Encapsulins are a distinct family of prokaryotic compartments, comprised of an icosahedral shell encapsulating a variety of enzymes. The encapsulin shell protein is similar in sequence and structure to the capsid protein of dsDNA tailed bacteriophages. Although found across diverse phyla of Bacteria and Archaea, few encapsulins were previously characterized. My thesis work utilized a bioinformatic approach to identify and investigate the functions of all encapsulins found in bacteria and Archaea. I found 590 encapsulins showing definite sequence similarity to the previously described encapsulins, which I refer to as "classical encapsulins". I identified four new enzyme families strongly predicted to be classical encapsulin cargo enzymes: ferredoxins, rubrerythrin-like, Dps-bacterioferritin-like, and hemerythrin-like proteins. While most species encode encapsulin cargo proteins adjacent to the encapsulin gene, I discovered 113 species encoding cargo proteins in genomic regions far removed from the encapsulin gene. I also found 118 genomes encoding two or three different enzymes strongly predicted to be targeted to the same encapsulin. Genes encoding three protein families, radical SAM oxidoreductases, CutA1-like proteins and metalloproteases, are highly enriched near encapsulin genes, but without targeting motifs for direct encapsulation. In addition to classical encapsulins, I discovered 1060 novel putative encapsulins related to diverse families of phage capsids. The largest family of these novel encapsulins, with 986 proteins is larger than the classical encapsulin family, and conserves a sulphur metabolism operon encoding cysteine desulfurases, acetyltransferases, and rhodaneses. These activities are predicted to relieve sulphur restriction, and toxicity of cyanide and other oxidants. Overall, novel and classical encapsulins and their encapsulated enzymes are predicted to contribute to polyvalent cation dependent catalytic activities, and relieve heavy metal and cyanide toxicity. Phylogenies predicted capsids and encapsulins share intermingled ancestry. My work shows that encapsulins perform more diverse functions and are much more widely distributed than any other prokaryotic compartment. Advisors/Committee Members: Davidson, Alan R, Parkinson, John, Molecular and Medical Genetics.

Subjects/Keywords: bacterial physiology; bacteriophage; compartmentalization; computational biology; encapsulin; 0307

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APA (6^th Edition):

Radford, D. R. (2014). Understanding the Encapsulins:Prediction and Characterization of Phage Capsid-like Nanocompartments in Prokaryotes. (Doctoral Dissertation). University of Toronto. Retrieved from http://hdl.handle.net/1807/69450

Chicago Manual of Style (16^th Edition):

Radford, Devon Richard. “Understanding the Encapsulins:Prediction and Characterization of Phage Capsid-like Nanocompartments in Prokaryotes.” 2014. Doctoral Dissertation, University of Toronto. Accessed April 11, 2021. http://hdl.handle.net/1807/69450.

MLA Handbook (7^th Edition):

Radford, Devon Richard. “Understanding the Encapsulins:Prediction and Characterization of Phage Capsid-like Nanocompartments in Prokaryotes.” 2014. Web. 11 Apr 2021.

Vancouver:

Radford DR. Understanding the Encapsulins:Prediction and Characterization of Phage Capsid-like Nanocompartments in Prokaryotes. [Internet] [Doctoral dissertation]. University of Toronto; 2014. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/1807/69450.

Council of Science Editors:

Radford DR. Understanding the Encapsulins:Prediction and Characterization of Phage Capsid-like Nanocompartments in Prokaryotes. [Doctoral Dissertation]. University of Toronto; 2014. Available from: http://hdl.handle.net/1807/69450

Queens University

17. Truong, Tammy. Compartmentalized phosphodiesterase 4D isoforms expression, targeting and localization in vascular myocytes .

Degree: Pathology and Molecular Medicine, 2014, Queens University

URL: http://hdl.handle.net/1974/8658

► During the development of atherosclerosis, contractile vascular smooth muscle cells (VSMCs) change to cells capable of migrating and proliferating to mediate repair, where the responses… (more)

▼ During the development of atherosclerosis, contractile vascular smooth muscle cells (VSMCs) change to cells capable of migrating and proliferating to mediate repair, where the responses may be adaptive or mal-adaptive in effect. Cyclic adenosine monophosphate (cAMP)-elevating agents have been shown to inhibit migration of VSMC. cAMP activity within the cell is known to be ubiquitous and dynamic, requiring control through signal termination mechanisms for cellular homeostasis. Phosphodiesterase (PDE) enzymes are central to this critical regulatory process catalyzing the hydrolysis of cAMP. A great deal of insight into the role of PDEs in defining compartmentalization of cAMP signaling has arisen predominately from recent studies on the cAMP-specific PDE4 family. Compartmentalization of PDE4 is mediated by their unique N-terminal domains, which have been proposed to provide the “postcodes/zipcodes” for cellular localization. PDE4D isoforms vary widely, yet their conservation over evolutionary time suggests important non-redundant roles in distinct cellular processes. To study the potential role of individual PDE4D isoforms we seek to utilize the unique N-terminal targeting domains that are proposed to be responsible for their protein-protein interactions and site-directed localization. Herein, we report on the expression, targeting and localization of five “long” PDE4D isoforms and the impact on cell morphology of certain amino-terminal domains of individual PDE4D constructs expressing green fluorescent protein (NT-PDE4D/GFP) in human aortic smooth muscle cells (HASMCs). Through the development of engineered NT-PDE4D/GFP expression plasmids, we were able to study the cell biological impacts associated with the overexpression of individual PDE4D amino-terminal variants in HASMCs. We show that NT-PDE4D5/GFP and NT-PDE4D7/GFP expressing cells exhibited an elongated cell morphology, where this effect was much more marked in NT-PDE4D7/GFP expressing cells, exhibiting multiple leading edge structures and highly elongated “tails”. We identify a potential role for PDE4D7 targeting in the regulation of cell polarity and migration. Our results suggest the novel idea that PDE4D7, rather than the four other long PDE4D isoforms (PDE4D3, PDE4D5, PDE4D8, or PDE4D9), represents the dominant PDE4D variant involved in controlling cAMP-mediated effects on cell tail retraction dynamics.

Subjects/Keywords: cell migration ; vascular smooth muscle cell ; cAMP ; compartmentalization ; phosphodiesterase 4D

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APA (6^th Edition):

Truong, T. (2014). Compartmentalized phosphodiesterase 4D isoforms expression, targeting and localization in vascular myocytes . (Thesis). Queens University. Retrieved from http://hdl.handle.net/1974/8658

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):

Truong, Tammy. “Compartmentalized phosphodiesterase 4D isoforms expression, targeting and localization in vascular myocytes .” 2014. Thesis, Queens University. Accessed April 11, 2021. http://hdl.handle.net/1974/8658.

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

MLA Handbook (7^th Edition):

Truong, Tammy. “Compartmentalized phosphodiesterase 4D isoforms expression, targeting and localization in vascular myocytes .” 2014. Web. 11 Apr 2021.

Vancouver:

Truong T. Compartmentalized phosphodiesterase 4D isoforms expression, targeting and localization in vascular myocytes . [Internet] [Thesis]. Queens University; 2014. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/1974/8658.

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

Council of Science Editors:

Truong T. Compartmentalized phosphodiesterase 4D isoforms expression, targeting and localization in vascular myocytes . [Thesis]. Queens University; 2014. Available from: http://hdl.handle.net/1974/8658

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

Kansas State University

18. Evans, Drew W. The compartmentalization and biomarker analysis of the spivey-grabs-basil field, south-central Kansas.

Degree: MS, Department of Geology, 2011, Kansas State University

URL: http://hdl.handle.net/2097/8785

► The Spivey-Grabs-Basil oil field is a highly developed field in south-central Kansas, having large variability in its production and in the Pineville Tripolite facies. The… (more)

▼ The Spivey-Grabs-Basil oil field is a highly developed field in south-central Kansas, having large variability in its production and in the Pineville Tripolite facies. The Pineville Tripolite is the primary producing formation of this field having major isopach variations, possibly influencing production. The hypothesis that the field is highly compartmentalized is from the varied production, isopach and structure of the field. This study investigated the Pineville Tripolite facies in the Spivey-Grabs-Basil Oil Field, with the Basil area the predominant focus, and its possible compartmentalization by looking at the gas chromatograms and their biomarker signatures. This field has had several studies investigating the geophysical attributes, depositional setting and large-scale compartmentalization. Post depositional sea-level changes and possibly syntectonics exposed the Reeds Spring to a sub-aerial environment where meteoric alteration created immense porosity and the Pineville Tripolite facies. Geochemical data shows evidence that this section of the field is sourced from both a marine shale and carbonate source at peak oil maturity, deposited in an anoxic environment. Biodegradation appears very slight, with most alterations transpiring in the alkane ranges only, leaving all other susceptible hydrocarbons unaltered. Compartments within the field are harder to identify when comparing geological data to oil data. Isopach data shows altered thickness of the Pineville Tripolite from well to well, as do Pineville structure values. The isopach and structural data point to possible areas for compartments, but it is from oil geochemical data that compartments become more visible. API gravities and GOR show motley values, but do indicate two significant areas of segregation. The deepest, most southern end of the study showed lighter gravity oils than the middle, suggesting possible fill and spill between the two. However, biomarker abundance indicates three possible compartments. The southern compartment has many more biomarker volumes than do the middle compartment, both divided by a reservoir pinch-out. The third most northeastern well has high biomarker abundance, but shows no geological separators from the other wells. Production from this field may be improved by investigating the biomarkers to allocate these compartments and possible barriers close to wells. Advisors/Committee Members: Matthew W. Totten.

Subjects/Keywords: Compartmentalization; Biomarkers; Geology; Geochemistry; Geochemistry (0996); Geology (0372)

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APA (6^th Edition):

Evans, D. W. (2011). The compartmentalization and biomarker analysis of the spivey-grabs-basil field, south-central Kansas. (Masters Thesis). Kansas State University. Retrieved from http://hdl.handle.net/2097/8785

Chicago Manual of Style (16^th Edition):

Evans, Drew W. “The compartmentalization and biomarker analysis of the spivey-grabs-basil field, south-central Kansas.” 2011. Masters Thesis, Kansas State University. Accessed April 11, 2021. http://hdl.handle.net/2097/8785.

MLA Handbook (7^th Edition):

Evans, Drew W. “The compartmentalization and biomarker analysis of the spivey-grabs-basil field, south-central Kansas.” 2011. Web. 11 Apr 2021.

Vancouver:

Evans DW. The compartmentalization and biomarker analysis of the spivey-grabs-basil field, south-central Kansas. [Internet] [Masters thesis]. Kansas State University; 2011. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/2097/8785.

Council of Science Editors:

Evans DW. The compartmentalization and biomarker analysis of the spivey-grabs-basil field, south-central Kansas. [Masters Thesis]. Kansas State University; 2011. Available from: http://hdl.handle.net/2097/8785

Universiteit Utrecht

19. Pepermans, R.A. Cytoskeleton induced partitioning of the plasma membrane: The picket-fence model and the compartmentalized plasma membrane theory.

Degree: 2012, Universiteit Utrecht

URL: http://dspace.library.uu.nl:8080/handle/1874/256468

► The development of single-particle tracking has allowed membrane researchers to observe individual movements of membrane molecules, thereby gaining new insights into the dynamics of the… (more)

Subjects/Keywords: single-particle tracking; membrane-skeleton fence model; anchored-protein picket model; hop diffusion; compartmentalization.

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APA (6^th Edition):

Pepermans, R. A. (2012). Cytoskeleton induced partitioning of the plasma membrane: The picket-fence model and the compartmentalized plasma membrane theory. (Masters Thesis). Universiteit Utrecht. Retrieved from http://dspace.library.uu.nl:8080/handle/1874/256468

Chicago Manual of Style (16^th Edition):

Pepermans, R A. “Cytoskeleton induced partitioning of the plasma membrane: The picket-fence model and the compartmentalized plasma membrane theory.” 2012. Masters Thesis, Universiteit Utrecht. Accessed April 11, 2021. http://dspace.library.uu.nl:8080/handle/1874/256468.

MLA Handbook (7^th Edition):

Pepermans, R A. “Cytoskeleton induced partitioning of the plasma membrane: The picket-fence model and the compartmentalized plasma membrane theory.” 2012. Web. 11 Apr 2021.

Vancouver:

Pepermans RA. Cytoskeleton induced partitioning of the plasma membrane: The picket-fence model and the compartmentalized plasma membrane theory. [Internet] [Masters thesis]. Universiteit Utrecht; 2012. [cited 2021 Apr 11]. Available from: http://dspace.library.uu.nl:8080/handle/1874/256468.

Council of Science Editors:

Pepermans RA. Cytoskeleton induced partitioning of the plasma membrane: The picket-fence model and the compartmentalized plasma membrane theory. [Masters Thesis]. Universiteit Utrecht; 2012. Available from: http://dspace.library.uu.nl:8080/handle/1874/256468

20. Rasid, Orhan. NK cells and systemic inflammation : compartmentalization and memory responses : Cellules NK et inflammation systémique : compartimentalisation et réponse mémoire.

Degree: Docteur es, Immunologie, 2016, Sorbonne Paris Cité

URL: http://www.theses.fr/2016USPCB078

►

L'inflammation systémique est une réaction qui implique l’ensemble de l’organisme suite une agression sévère, potentiellement mortelle, illustrée par le syndrome de réponse inflammatoire systémique (SIRS).… (more)

▼

L'inflammation systémique est une réaction qui implique l’ensemble de l’organisme suite une agression sévère, potentiellement mortelle, illustrée par le syndrome de réponse inflammatoire systémique (SIRS). De nombreux acteurs cellulaires et moléculaires contribuent au développement de cette cascade inflammatoire parmi lesquels les cellules NK jouent un rôle clé. Malgré l'accumulation de preuves sur l’existence de propriétés spécifiques à chaque organe en réponse à l'inflammation systémique, en termes de cellules NK, on sait peu de choses sur la dynamique compartimentalisée de l’activation des cellules NK pendant un SIRS. En outre, le statut immunitaire des cellules NK après la résolution d’un SIRS est également mal connu. Dans le présent travail, nous avons étudié les réponses des cellules NK provenant de différents organes en utilisant un modèle d’endotoxinémie murine. Nous avons caractérisé la réponse des cellules NK au sein de la rate, du poumon, de la moelle osseuse, de la cavité péritonéale, et dans la circulation. Nous avons trouvé que, malgré une dynamique similaire de la réponse dans les différents organes, les réponses des cellules NK sont compartimentalisées avec des seuils différent et spécifiques. A l’aide de transferts adoptifs, nous avons constaté que la réactivité des cellules NK spécifiques d'organes peut refléter le compartiment d’origine lors des phases initiales de l'inflammation. Cependant, les cellules NK ont la capacité de s’adapter rapidement à leur nouvel environnement et d'ajuster leurs niveaux de réponse à ceux des cellules NK résidentes. Ainsi, cette étude fournit une preuve de concept qui confirme la compartimentalisation de la réponse des cellules NK lors de l'inflammation systémique. Dans une deuxième partie, nous avons analysé le statut des cellules NK à différents moments après une endotoxinémie. Les réponses des cellules NK au sein d’une préparation de cellules de la rate sont fortement supprimées en réponse à une restimulation in vitro, 14 jours après l'endotoxinémie. Cependant, nous avons montré que la réactivité intrinsèque des cellules NK est en fait augmentée après l'injection d’endotoxine, aboutissant à des cellules NK présentant des caractéristiques de cellules NK mémoires. Des expériences de transfert adoptif ont confirmé les propriétés de mémoire des cellules NK après endotoxinémie. Nos résultats accroissent la connaissance concernant le rôle des cellules NK dans un contexte d'inflammation systémique, révélant des réponses compartimentalisés et l’induction d’une mémoire suite à l’endotoxinémie. L'observation selon laquelle les cellules NK développent des propriétés de mémoire après une inflammation systémique dans le contexte d'un environnement suppressif est d’une grande nouveauté et ce phénomène est rapporté pour la première fois.

Systemic inflammation is whole-body reaction to a triggering insult that often results in life threatening illness like systemic inflammatory response syndrome (SIRS). Contributing to the development of this inflammatory cascade are numerous…

Advisors/Committee Members: Cavaillon, Jean-Marc (thesis director).

Subjects/Keywords: Cellules NK; Compartimentalisation; Inflammation systémique; Mémoire innée; NK cells; Compartmentalization; Systemic inflammation; Innate memory; 571.6

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APA (6^th Edition):

Rasid, O. (2016). NK cells and systemic inflammation : compartmentalization and memory responses : Cellules NK et inflammation systémique : compartimentalisation et réponse mémoire. (Doctoral Dissertation). Sorbonne Paris Cité. Retrieved from http://www.theses.fr/2016USPCB078

Chicago Manual of Style (16^th Edition):

Rasid, Orhan. “NK cells and systemic inflammation : compartmentalization and memory responses : Cellules NK et inflammation systémique : compartimentalisation et réponse mémoire.” 2016. Doctoral Dissertation, Sorbonne Paris Cité. Accessed April 11, 2021. http://www.theses.fr/2016USPCB078.

MLA Handbook (7^th Edition):

Rasid, Orhan. “NK cells and systemic inflammation : compartmentalization and memory responses : Cellules NK et inflammation systémique : compartimentalisation et réponse mémoire.” 2016. Web. 11 Apr 2021.

Vancouver:

Rasid O. NK cells and systemic inflammation : compartmentalization and memory responses : Cellules NK et inflammation systémique : compartimentalisation et réponse mémoire. [Internet] [Doctoral dissertation]. Sorbonne Paris Cité; 2016. [cited 2021 Apr 11]. Available from: http://www.theses.fr/2016USPCB078.

Council of Science Editors:

Rasid O. NK cells and systemic inflammation : compartmentalization and memory responses : Cellules NK et inflammation systémique : compartimentalisation et réponse mémoire. [Doctoral Dissertation]. Sorbonne Paris Cité; 2016. Available from: http://www.theses.fr/2016USPCB078

University of Western Ontario

21. Kazemi Movahed, Leily. Soybean root exudates increase the physiological diversity of bacteria in cadmium-treated soil.

Degree: 2020, University of Western Ontario

URL: https://ir.lib.uwo.ca/etd/6908

► Three soybean cultivars with contrasting retention of cadmium (Cd) in the root were grown in Cd-spiked nutrient solution and used to determine that symplastic compartmentalization… (more)

Subjects/Keywords: Bacterial community diversity; Cadmium; Compartmentalization; Organic acids; Root exudates; Soybean; Plant Biology

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APA (6^th Edition):

Kazemi Movahed, L. (2020). Soybean root exudates increase the physiological diversity of bacteria in cadmium-treated soil. (Thesis). University of Western Ontario. Retrieved from https://ir.lib.uwo.ca/etd/6908

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):

Kazemi Movahed, Leily. “Soybean root exudates increase the physiological diversity of bacteria in cadmium-treated soil.” 2020. Thesis, University of Western Ontario. Accessed April 11, 2021. https://ir.lib.uwo.ca/etd/6908.

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

MLA Handbook (7^th Edition):

Kazemi Movahed, Leily. “Soybean root exudates increase the physiological diversity of bacteria in cadmium-treated soil.” 2020. Web. 11 Apr 2021.

Vancouver:

Kazemi Movahed L. Soybean root exudates increase the physiological diversity of bacteria in cadmium-treated soil. [Internet] [Thesis]. University of Western Ontario; 2020. [cited 2021 Apr 11]. Available from: https://ir.lib.uwo.ca/etd/6908.

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

Council of Science Editors:

Kazemi Movahed L. Soybean root exudates increase the physiological diversity of bacteria in cadmium-treated soil. [Thesis]. University of Western Ontario; 2020. Available from: https://ir.lib.uwo.ca/etd/6908

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

22. Harris, Garrett R. Evaluation of Groundwater Quality in Paleozoic Aquifers Using GIS Techniques, Central Texas.

Degree: MS- Geology, Geology, 2016, Stephen F. Austin State University

URL: https://scholarworks.sfasu.edu/etds/45

► Lab analyses of groundwater chemistry from monitoring wells completed in the Paleozoic Aquifers surrounding the Llano Uplift of Central Texas has been recorded and… (more)

Subjects/Keywords: Hydraulic Connectivity; Nested Pairs; Piper Diagrams; Compartmentalization; Groundwater; Aquifer; Earth Sciences; Geochemistry; Geology; Hydrology

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APA (6^th Edition):

Harris, G. R. (2016). Evaluation of Groundwater Quality in Paleozoic Aquifers Using GIS Techniques, Central Texas. (Masters Thesis). Stephen F. Austin State University. Retrieved from https://scholarworks.sfasu.edu/etds/45

Chicago Manual of Style (16^th Edition):

Harris, Garrett R. “Evaluation of Groundwater Quality in Paleozoic Aquifers Using GIS Techniques, Central Texas.” 2016. Masters Thesis, Stephen F. Austin State University. Accessed April 11, 2021. https://scholarworks.sfasu.edu/etds/45.

MLA Handbook (7^th Edition):

Harris, Garrett R. “Evaluation of Groundwater Quality in Paleozoic Aquifers Using GIS Techniques, Central Texas.” 2016. Web. 11 Apr 2021.

Vancouver:

Harris GR. Evaluation of Groundwater Quality in Paleozoic Aquifers Using GIS Techniques, Central Texas. [Internet] [Masters thesis]. Stephen F. Austin State University; 2016. [cited 2021 Apr 11]. Available from: https://scholarworks.sfasu.edu/etds/45.

Council of Science Editors:

Harris GR. Evaluation of Groundwater Quality in Paleozoic Aquifers Using GIS Techniques, Central Texas. [Masters Thesis]. Stephen F. Austin State University; 2016. Available from: https://scholarworks.sfasu.edu/etds/45

University of Oklahoma

23. Ban, Yue. Biophysical mechanisms for the generation of electrosensory and communication signal in the weakly electric fish Eigenmannia virescens.

Degree: PhD, 2018, University of Oklahoma

URL: http://hdl.handle.net/11244/299778

► The weakly electric fish Eigenmannia virescens generates electric organ discharges (EODs) to navigate and communicate. The EODs are brief monophasic voltage pulses with brief inter-pulse… (more)

▼ The weakly electric fish Eigenmannia virescens generates electric organ discharges (EODs) to navigate and communicate. The EODs are brief monophasic voltage pulses with brief inter-pulse intervals, resulting in a sinusoidal waveform. EODs are produced by the simultaneous action potentials (APs) of ~1000 electric organ (EO) cells (electrocytes). Electrocytes generate APs at steady frequencies of 200-600 Hz with Na+ currents that exceed 10 microamperes during each AP, creating large energetic demands. The aim of this study was to investigate the biophysical mechanisms that allow fast spiking and manage the large ionic currents in electroctyes. E.virescens elecrocytes initiate the AP using voltage-gated Na+ (Nav) channels and terminate the AP using Na+-activated K+ (KNa) channels, rather than voltage-gated K+ (Kv) channels, as is the case in other electric fish where electrophysiological data are available. The characteristics of K+ channels are key determinants of an excitable cell’s firing pattern. Using degenerate PCR and RACE-PCR, I identified the presence of three types of KNa channel subunit in electrocytes, eSlack1 and eSlick, closely related to KNa channel subunits in other vertebrates, and a shorter isoform, eSlack2. Whole-cell currents recorded from Xenopus laevis oocytes expressing these KNa channels revealed that eSlack1 and eSlick can form functional homomeric K+ channels and eSlick currents activated much more rapidly than eSlack1 currents. eSlack2 could not form functional homomeric ion channels, even though the subunits could be successfully trafficked to the plasma membrane. To investigate how ion channels coordinate to generate high-frequency APs, I studied the expression pattern of ion channels and Na+/K+ ATPases using immunohistochemistry and by expressing fluorescent protein-tagged ion channels in electrocytes. Cholinergic receptors and Nav channels are only localized on the posterior side, while all K+ channels including the three KNa channel subunits and the ATP sensitive Kir6.2 are expressed on the anterior side. Na+/K+ ATPases are widely distributed on both the posterior and anterior membranes. Two-photon 3D imaging of electrocytes showed the cell’s posterior membrane is densely occupied by narrow invaginations providing extensive surface area for the expression of Na+ channels and Na+/K+ ATPases to manage the large ionic currents. Abundant vesicles were present underneath the posterior membrane, which may be associated with the trafficking of Na+ channels and Na+/K+ ATPases to the plasma membrane when the amplitude of AP is under modulation. Finally, I investigated the ionic mechanisms associated with variations in AP frequency in the fast-spiking electrocytes by measuring the transcription levels of ion channels and ion transporters in EO from fish with different EOD frequencies. EOD frequency is correlated with the transcription levels of Nav1.4a, the fast-activating Slick KNa channel subunits, Kir6.2 and Na+/K+ ATPases but not Nav1.4b, eSlack1 and eSlack2. … Advisors/Committee Members: Markham, Michael (advisor), Berkowitz, Ari (committee member), Masly, John (committee member), Lemon, Christian (committee member), Bartley, Laura (committee member).

Subjects/Keywords: weakly electric fish; three-dimensional electrocyte morphology; ion channel compartmentalization; sodium-activated potassium channels

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

APA (6^th Edition):

Ban, Y. (2018). Biophysical mechanisms for the generation of electrosensory and communication signal in the weakly electric fish Eigenmannia virescens. (Doctoral Dissertation). University of Oklahoma. Retrieved from http://hdl.handle.net/11244/299778

Chicago Manual of Style (16^th Edition):

Ban, Yue. “Biophysical mechanisms for the generation of electrosensory and communication signal in the weakly electric fish Eigenmannia virescens.” 2018. Doctoral Dissertation, University of Oklahoma. Accessed April 11, 2021. http://hdl.handle.net/11244/299778.

MLA Handbook (7^th Edition):

Ban, Yue. “Biophysical mechanisms for the generation of electrosensory and communication signal in the weakly electric fish Eigenmannia virescens.” 2018. Web. 11 Apr 2021.

Vancouver:

Ban Y. Biophysical mechanisms for the generation of electrosensory and communication signal in the weakly electric fish Eigenmannia virescens. [Internet] [Doctoral dissertation]. University of Oklahoma; 2018. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/11244/299778.

Council of Science Editors:

Ban Y. Biophysical mechanisms for the generation of electrosensory and communication signal in the weakly electric fish Eigenmannia virescens. [Doctoral Dissertation]. University of Oklahoma; 2018. Available from: http://hdl.handle.net/11244/299778

24. Marcos Alexandre Milanesi. Identificação de unidades climáticas na Ilha de São Sebastião.

Degree: 2017, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/8/8135/tde-09062017-114749/

► Unidades climáticas são determinadas áreas da superfície terrestre que apresentam características climáticas relativamente homogêneas ao longo do tempo e do espaço. Sua existência, a priori,… (more)

▼ Unidades climáticas são determinadas áreas da superfície terrestre que apresentam características climáticas relativamente homogêneas ao longo do tempo e do espaço. Sua existência, a priori, depende da relação única entre a superfície terrestre e a dinâmica atmosférica, quando a primeira exerce controle sobre a segunda, influenciando tais características. Essas características climáticas, sob a forma da variação temporal da temperatura, umidade, chuvas, entre outros, são espacialmente melhor percebidas de acordo com a escala de trabalho da pesquisa adotada e podem realçar a existência de ambientes diferenciados (daqueles conhecidos em escalas mais generalistas) - os climas locais e os topoclimas, que são a base climatológica mais complexa dos planos de ordenação territorial. O município de Ilhabela reflete as transformações socioeconômicas e ambientais que vem ocorrendo na região do Litoral Norte do estado de São Paulo, essencialmente no período posterior a 1970, com a inauguração da Rodovia Rio-Santos (BR101/SP55), que pressupõem, por conta do aporte migratório, transformações nas paisagens locais e regionais. Entretanto, a Ilha de São Sebastião (a maior e sede do município) resguarda 75% de seu território sob a forma de unidade de conservação Parque Estadual de Ilhabela (PEIb). Desta forma, a essência do estudo aqui proposto é a identificação das unidades climáticas naturais da ilha, por meio da análise da variação de temperatura, umidade relativa e precipitações identificadas em diferentes localidades deste ambiente ilhéu e avaliar possíveis influências da urbanização sobre este processo. O método utilizado nesta pesquisa está assentado na instalação de equipamentos sensores da temperatura do ar, umidade relativa e da precipitação líquida como os termo-higrômetros (eletrônicos) e os pluviômetros (totalizadores e registradores, manuais e eletrônicos, respectivamente), dentro do período de um ano. A análise dos dados considerou aspectos geográficos e climatológicos de ordem local, assim como aqueles de ordem regional (meteorológicos sinóticos) resultando em informações quantitativas e qualitativas, que sob a luz da análise rítmica e da heurística possibilitaram sua análise crítica. Os resultados, quando observados individualmente, representam a situação geoclimática dos sítios de instalação da instrumentação meteorológica; por outro lado, a variabilidade espacial dos atributos em sua relação com os sistemas atmosféricos atuantes, considerados então como representativos dos meso e topoclimas, permite a identificação, individualização e definição de unidades climáticas da ilha no período da coleta de dados. Foram então definidos 12 ambientes topoclimaticamente diferenciados com a clara percepção de heterogeneidade entre si, organizados sob 5 mesoclimas conforme a insolação, os fluxos de ar predominantes, a orientação geral das vertentes e das bacias hidrográficas e a variação dos atributos do clima. O setor norte: quente e pouco chuvoso. A vertente leste: mais ensolarada e úmida. O sul sudoeste: barlavento dos… Advisors/Committee Members: Emerson Galvani, Raul Reis Amorim, Gustavo Armani, Jose Bueno Conti, Marisa de Souto Matos Fierz.

Subjects/Keywords: Climatologia geográfica; Compartimentação; Ilhabela; Orografia; Topoclima; Compartmentalization; Geographical climatology; Ilhabela; Orography; Topoclimatic

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

APA (6^th Edition):

Milanesi, M. A. (2017). Identificação de unidades climáticas na Ilha de São Sebastião. (Doctoral Dissertation). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/8/8135/tde-09062017-114749/

Chicago Manual of Style (16^th Edition):

Milanesi, Marcos Alexandre. “Identificação de unidades climáticas na Ilha de São Sebastião.” 2017. Doctoral Dissertation, University of São Paulo. Accessed April 11, 2021. http://www.teses.usp.br/teses/disponiveis/8/8135/tde-09062017-114749/.

MLA Handbook (7^th Edition):

Milanesi, Marcos Alexandre. “Identificação de unidades climáticas na Ilha de São Sebastião.” 2017. Web. 11 Apr 2021.

Vancouver:

Milanesi MA. Identificação de unidades climáticas na Ilha de São Sebastião. [Internet] [Doctoral dissertation]. University of São Paulo; 2017. [cited 2021 Apr 11]. Available from: http://www.teses.usp.br/teses/disponiveis/8/8135/tde-09062017-114749/.

Council of Science Editors:

Milanesi MA. Identificação de unidades climáticas na Ilha de São Sebastião. [Doctoral Dissertation]. University of São Paulo; 2017. Available from: http://www.teses.usp.br/teses/disponiveis/8/8135/tde-09062017-114749/

25. Ferreira, Mayara Nicolau [UNESP]. Sensibilidade ambiental a hidrocarbonetos para rodovias: estudo de caso em trecho da Rodovia Anhanguera (SP-330).

Degree: 2017, Universidade Estadual Paulista (UNESP)

URL: http://hdl.handle.net/11449/152309

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Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Considerando o crescente número de acidentes com produtos perigosos em rodovias e que este é o modal mais utilizado para o transporte de cargas no Brasil, principalmente hidrocarbonetos e derivados de petróleo. Bem como, os insipientes estudos de índices de sensibilidade ambiental para ambientes terrestres. E que os mapas de sensibilidade são importantes ferramentas técnico-gerenciais utilizadas na tomada de decisões emergenciais em caso de combate a derrames de óleo. Além de fornecer informações para o planejamento de contenção e limpeza para mitigar os impactos ambientais, auxiliar a identificação de locais sensíveis antes que ocorra o acidente, de modo que as estratégias de proteção e contenção possam ser organizadas antecipadamente, objetiva-se a confecção de um índice de sensibilidade ambiental aos hidrocarbonetos para rodovias, utilizando como área de estudo um trecho da Rodovia Anhanguera (SP-330), segunda maior em números de acidentes com produtos perigosos no estado de São Paulo, e sua respectiva carta de sensibilidade ambiental. Para tanto, procede-se fazendo uso de geotecnologias para confecção de mapas básicos necessários a pesquisa; da compartimentação fisiográfica para dividir a área de estudo em zonas homólogas; do trabalho de campo para corroborar a compartimentação; da escolha dos cinco parâmetros e seus respectivos pesos, que compõem o índice de sensibilidade ambiental aos hidrocarbonetos para rodovias; e consequentemente, a confecção da carta de sensibilidade ambiental. Desse modo, observa-se que no trecho foram encontrados os índices 5, 7 e 8, sendo que o índice 7 é predominante em seis das oito Unidade Básicas de Compartimentação, o que permite concluir que a área estudada tem média-alta sensibilidade ambiental, levando em consideração que o índice vai de 1 a 10 A. Além de colaborar com o desenvolvimento de uma adaptação do método das cartas SAO utilizadas em…

Advisors/Committee Members: Universidade Estadual Paulista (UNESP), Riedel, Paulina Setti [UNESP].

Subjects/Keywords: Sensibilidade ambiental; Compartimentação fisiográfica; Geotecnologias; Hidrocarbonetos; Environmental sensitivity; Physiographic compartmentalization; Geotechnology; Hydrocarbons

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

APA (6^th Edition):

Ferreira, M. N. [. (2017). Sensibilidade ambiental a hidrocarbonetos para rodovias: estudo de caso em trecho da Rodovia Anhanguera (SP-330). (Masters Thesis). Universidade Estadual Paulista (UNESP). Retrieved from http://hdl.handle.net/11449/152309

Chicago Manual of Style (16^th Edition):

Ferreira, Mayara Nicolau [UNESP]. “Sensibilidade ambiental a hidrocarbonetos para rodovias: estudo de caso em trecho da Rodovia Anhanguera (SP-330).” 2017. Masters Thesis, Universidade Estadual Paulista (UNESP). Accessed April 11, 2021. http://hdl.handle.net/11449/152309.

MLA Handbook (7^th Edition):

Ferreira, Mayara Nicolau [UNESP]. “Sensibilidade ambiental a hidrocarbonetos para rodovias: estudo de caso em trecho da Rodovia Anhanguera (SP-330).” 2017. Web. 11 Apr 2021.

Vancouver:

Ferreira MN[. Sensibilidade ambiental a hidrocarbonetos para rodovias: estudo de caso em trecho da Rodovia Anhanguera (SP-330). [Internet] [Masters thesis]. Universidade Estadual Paulista (UNESP); 2017. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/11449/152309.

Council of Science Editors:

Ferreira MN[. Sensibilidade ambiental a hidrocarbonetos para rodovias: estudo de caso em trecho da Rodovia Anhanguera (SP-330). [Masters Thesis]. Universidade Estadual Paulista (UNESP); 2017. Available from: http://hdl.handle.net/11449/152309

26. Cabral, Alessandro Expedito. O sistema geomorfológico de Campos Gerais: aspectos dinâmicos e estruturais na evolução do relevo regional.

Degree: 2019, Universidade Federal de Juiz de Fora (UFJF); Programa de Pós-graduação em Geografia; UFJF; Brasil; ICH – Instituto de Ciências Humanas

URL: https://repositorio.ufjf.br/jspui/handle/123456789/10161

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O modelado terrestre passa por diversas transformações decorrentes de fatores endógenos e exógenos ocorrentes ao longo dos anos, muitos desses processos ainda estão longe de… (more)

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O modelado terrestre passa por diversas transformações decorrentes de fatores endógenos e exógenos ocorrentes ao longo dos anos, muitos desses processos ainda estão longe de ser desvendados pelo homem, porém, outros estão cada vez mais presentes em análises, propostas e conclusões desenvolvidas ao longo de decorrentes pesquisas sobre os processos atuantes no sistema Terra. O presente trabalho se propõe a realizar uma análise geomorfológica do município de Campos Gerais a fim de desvelar os processos atuantes sobre a paisagem, entendendo a configuração do sistema geomorfológico da área de estudo, e como esses influenciam sobre os processos dinâmicos e evolutivos do relevo regional. O município localiza-se no sul de Minas Gerais na microrregião de Varginha, tendo como cidades limítrofes Boa Esperança e Campo do Meio ao norte, Santana da Vargem e Três Pontas a leste, Paraguaçu e Fama a sul e Alfenas a oeste. Integra juntamente com estas cidades o Circuito das Águas, que compreende todo o complexo da Represa de Furnas. O relevo da área é composto por cristas estruturais escarpadas alinhadas no sentido E-W, patamares reafeiçoados, morros, morrotes, colinas, terraços e planícies. A cobertura vegetal e o uso da terra destacam-se pela ocorrência de Floresta Estacional Semidecidual, pastagens, culturas temporárias e predomínio de lavouras de café. O embasamento do trabalho se apóia na abordagem sistêmica oriunda da Teoria Geral dos Sistemas, proposta pelo biólogo Ludwig von Bertalanffy e aplicada na Geomorfologia a partir das concepções de Chorley. A metodologia aplicada fundamenta-se na óptica da fisiologia da paisagem preconizada pelo geógrafo Aziz Nacib Ab'Saber, propagando os três níveis de abordagem por ele proposto, a compartimentação do relevo, a estrutura superficial da paisagem e a fisiologia da paisagem, dando maior ênfase no primeiro nível. No decorrer do trabalho foram elaborados mapas de compartimentação morfológica e morfoestruturais, os quais subsidiaram a elaboração do mapa geomorfológico, de suma importância no auxílio às interpretações sobre os processos atuantes na superfície. Os resultados obtidos darão suporte teórico para futuros planejamentos socioambientais para o município.

The terrestrial modeling undergoes several transformations due to endogenous and exogenous factors occurring over the years, many of these processes are still far from being unveiled by man, but others are increasingly present in analyzes, proposals and conclusions developed along the ensuing research on the processes in the Earth system. The present research proposes to perform a geomorphological analysis of the municipality of Campos Gerais in order to reveal the processes involved in the landscape, understanding the configuration of the geomorphological system of the study area, and how this influence in the dynamic and evolutionary processes of the regional relief. The municipality is located in the south of Minas Gerais in the microregion of Varginha, having as neighboring cities, Boa…

Advisors/Committee Members: Marques Neto, Roberto, Felippi, Miguel Fernandes, Ferreira, Marta Felicia Marujo.

Subjects/Keywords: CNPQ::CIENCIAS HUMANAS::GEOGRAFIA; Compartimentação geomorfológica; Morfoestrutura; Lineamentos; Geomorphological compartmentalization; Morphostructure; Lineaments

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

APA (6^th Edition):

Cabral, A. E. (2019). O sistema geomorfológico de Campos Gerais: aspectos dinâmicos e estruturais na evolução do relevo regional. (Masters Thesis). Universidade Federal de Juiz de Fora (UFJF); Programa de Pós-graduação em Geografia; UFJF; Brasil; ICH – Instituto de Ciências Humanas. Retrieved from https://repositorio.ufjf.br/jspui/handle/123456789/10161

Chicago Manual of Style (16^th Edition):

Cabral, Alessandro Expedito. “O sistema geomorfológico de Campos Gerais: aspectos dinâmicos e estruturais na evolução do relevo regional.” 2019. Masters Thesis, Universidade Federal de Juiz de Fora (UFJF); Programa de Pós-graduação em Geografia; UFJF; Brasil; ICH – Instituto de Ciências Humanas. Accessed April 11, 2021. https://repositorio.ufjf.br/jspui/handle/123456789/10161.

MLA Handbook (7^th Edition):

Cabral, Alessandro Expedito. “O sistema geomorfológico de Campos Gerais: aspectos dinâmicos e estruturais na evolução do relevo regional.” 2019. Web. 11 Apr 2021.

Vancouver:

Cabral AE. O sistema geomorfológico de Campos Gerais: aspectos dinâmicos e estruturais na evolução do relevo regional. [Internet] [Masters thesis]. Universidade Federal de Juiz de Fora (UFJF); Programa de Pós-graduação em Geografia; UFJF; Brasil; ICH – Instituto de Ciências Humanas; 2019. [cited 2021 Apr 11]. Available from: https://repositorio.ufjf.br/jspui/handle/123456789/10161.

Council of Science Editors:

Cabral AE. O sistema geomorfológico de Campos Gerais: aspectos dinâmicos e estruturais na evolução do relevo regional. [Masters Thesis]. Universidade Federal de Juiz de Fora (UFJF); Programa de Pós-graduação em Geografia; UFJF; Brasil; ICH – Instituto de Ciências Humanas; 2019. Available from: https://repositorio.ufjf.br/jspui/handle/123456789/10161

27. Gabelini, Beatriz Marques [UNESP]. Suscetibilidade a escorregamentos na região entre Caraguatatuba e São Sebastião (SP): análise fisiográfica e quantitativa.

Degree: 2017, Universidade Estadual Paulista (UNESP)

URL: http://hdl.handle.net/11449/151503

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Os escorregamentos são movimentos de massa recorrentes na Serra do Mar. Quando ocorrem de forma generalizada podem causar prejuízos e perdas de vidas, como no acidente ocorrido no município de Caraguatatuba (SP) em 1967. Com o intuito de evitar estes danos, na literatura, são propostos vários métodos para analisar e prever a ocorrência destes processos. Diante do exposto, o objetivo principal desta pesquisa consiste em analisar a suscetibilidade a escorregamentos na região entre Caraguatatuba e São Sebastião (SP), utilizando a compartimentação fisiográfica e a análise quantitativa. Para alcançar estes objetivos foi realizada a análise e compartimentação do terreno e a análise quantitativa dos fatores condicionantes (declividade, hipsometria e geologia) e da compartimentação fisiográfica. Foram testados, em ambiente SIG, diversos cenários a partir de dois métodos distintos. No Método 1, os fatores condicionantes foram analisados através de pesos de influência. No Método 2, os fatores condicionantes mantiveram os mesmos pesos do Método 1 e foram somados pesos para as classes de cada fator. A compartimentação fisiográfica definiu 16 unidades. Os resultados demonstraram que a maioria dos escorregamentos se concentraram na unidade fisiográfica IV e que há um controle topográfico na distribuição dos escorregamentos entre 100 e 400 m de altitude, em encostas com declividade entre 15º e 30º, compostas por gnaisse migmatítico e granito-gnaisse. Os mapas elaborados a partir do Método 2 apresentaram expressiva concordância com o mapeamento de cicatrizes de Fúlfaro et al. (1976). O cenário escolhido como mais coerente foi o Cenário O, em que houve 60% de influência da declividade, 30% de hipsometria e 10% de geologia. Portanto, a partir do estudo da suscetibilidade, por meio da análise fisiográfica e quantitativa, é possível afirmar que o fator que tem mais influência na ocorrência de escorregamentos, na área de estudo, é a declividade, seguida da hipsometria e geologia.

Landslides are recurrent mass movements in the Serra do Mar. When they occur in a generalized way, as in the event occurred in Caraguatatuba city (SP) in 1967, they can cause a lot of environmental damage and deaths. In order to avoid this damage, several methods were proposed to analyze and predict the occurrence of this process. Considering the above, the main…

Advisors/Committee Members: Universidade Estadual Paulista (UNESP), Reis, Fábio Augusto Gomes Vieira [UNESP].

Subjects/Keywords: Escorregamentos; Suscetibilidade; Compartimentação fisiográfica; Análise quantitativa; SIG; Landslides; Susceptibility analysis; Quantitative analysis; Physiographic compartmentalization; GIS

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

APA (6^th Edition):

Gabelini, B. M. [. (2017). Suscetibilidade a escorregamentos na região entre Caraguatatuba e São Sebastião (SP): análise fisiográfica e quantitativa. (Masters Thesis). Universidade Estadual Paulista (UNESP). Retrieved from http://hdl.handle.net/11449/151503

Chicago Manual of Style (16^th Edition):

Gabelini, Beatriz Marques [UNESP]. “Suscetibilidade a escorregamentos na região entre Caraguatatuba e São Sebastião (SP): análise fisiográfica e quantitativa.” 2017. Masters Thesis, Universidade Estadual Paulista (UNESP). Accessed April 11, 2021. http://hdl.handle.net/11449/151503.

MLA Handbook (7^th Edition):

Gabelini, Beatriz Marques [UNESP]. “Suscetibilidade a escorregamentos na região entre Caraguatatuba e São Sebastião (SP): análise fisiográfica e quantitativa.” 2017. Web. 11 Apr 2021.

Vancouver:

Gabelini BM[. Suscetibilidade a escorregamentos na região entre Caraguatatuba e São Sebastião (SP): análise fisiográfica e quantitativa. [Internet] [Masters thesis]. Universidade Estadual Paulista (UNESP); 2017. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/11449/151503.

Council of Science Editors:

Gabelini BM[. Suscetibilidade a escorregamentos na região entre Caraguatatuba e São Sebastião (SP): análise fisiográfica e quantitativa. [Masters Thesis]. Universidade Estadual Paulista (UNESP); 2017. Available from: http://hdl.handle.net/11449/151503

University of Michigan

28. Kojima, Taisuke. Development Of Microcompartmentalization Using Macromolecules And Liquid-Liquid Interfaces.

Degree: PhD, Macromolecular Science and Engineering, 2016, University of Michigan

URL: http://hdl.handle.net/2027.42/120885

► Compartmentalization combined with regulated exchange and release of biomaterials is the key biological function. At the subcellular level, organelles sequester enzymes and substrates for storage… (more)

▼ Compartmentalization combined with regulated exchange and release of biomaterials is the key biological function. At the subcellular level, organelles sequester enzymes and substrates for storage while processing and releasing on demand. At the organism level, appropriate cellular compartmentalization gives rise to tissue organization and higher order function. Man-made bioreaction compartmentalization typically relies on micro-reactors constructed with glass, silicon, hard plastic, or amiphiphilic molecular walls. Reactors with such physical barriers, in return for excellent compartmentalization, lack amenability to molecular and cellular release and exchange as seen in the body. This thesis describes the engineering of multi-compartment bioreactors that utilize stable reagent partitioning within immiscible aqueous solutions. The all aqueous compartmentalization scheme, when combined with a micropatterned surface that pins the liquid-liquid interfaces, enable versatile direct printing of arbitrary multi-compartment bioreactor networks. Additionally, the lack of physical barriers at the liquid-liquid interface between the different aqueous compartments allows use of phase-altering chemicals to trigger rapid and selective mixing of materials between compartments in ways not possible with conventional miroreactors. Specific examples demonstrated include a compartmentalized cascade reaction that utilizes glucose and oxygen as nutrients to catalzye the production of different colored dyes within microcompartments and the localization-enhanced degradation of the microcompartments with a polysaccharide-degrading enzyme. In a separate strategy, a shrinking microreactor platform was created using oil dehydration. These shrinking bioreactors were utilized for micro-scale ATPS phase diagram determination and also adopted for micro-scale self-assembly of CdTe nanoparticles. Finally, surface-templated hydrogel micropatterning was used to compartmentalize cancer cells as well as limit diffusion of chemoattractants. This platform revealed the importance of extracellular matrix-mediated capture and localization of chemoattractants in triggering cancer cell migration that lead to a breakdown of cellular compartmentalization, tissue dis-organization and cancer metastasis. In addition to the specific demonstrations and biological insights obtained, the described macromolecular phase-separation microreactor platforms are versatile in configuration possibilities, particularly when combined with microfabrication technologies, and amenable to further explore materials science and biomedical engineering applications. Advisors/Committee Members: Takayama, Shuichi (committee member), Kotov, Nicholas (committee member), Lahann, Joerg (committee member), Robertson, Richard E (committee member), Tuteja, Anish (committee member).

Subjects/Keywords: Compartmentalization; Microreactor; Macromolecule; Liquid-liquid Interface; Biomedical Engineering; Engineering (General); Materials Science and Engineering; Chemistry; Science (General); Engineering; Science

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

APA (6^th Edition):

Kojima, T. (2016). Development Of Microcompartmentalization Using Macromolecules And Liquid-Liquid Interfaces. (Doctoral Dissertation). University of Michigan. Retrieved from http://hdl.handle.net/2027.42/120885

Chicago Manual of Style (16^th Edition):

Kojima, Taisuke. “Development Of Microcompartmentalization Using Macromolecules And Liquid-Liquid Interfaces.” 2016. Doctoral Dissertation, University of Michigan. Accessed April 11, 2021. http://hdl.handle.net/2027.42/120885.

MLA Handbook (7^th Edition):

Kojima, Taisuke. “Development Of Microcompartmentalization Using Macromolecules And Liquid-Liquid Interfaces.” 2016. Web. 11 Apr 2021.

Vancouver:

Kojima T. Development Of Microcompartmentalization Using Macromolecules And Liquid-Liquid Interfaces. [Internet] [Doctoral dissertation]. University of Michigan; 2016. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/2027.42/120885.

Council of Science Editors:

Kojima T. Development Of Microcompartmentalization Using Macromolecules And Liquid-Liquid Interfaces. [Doctoral Dissertation]. University of Michigan; 2016. Available from: http://hdl.handle.net/2027.42/120885

29. Foureau, Emilien. Elucidation de la voie de biosynthèse des alcaloïdes de Catharanthus roseus et ingénierie métabolique dans la levure : Elucidation of the Catharanthus roseus alkaloid pathway and metabolic engineering in yeast.

Degree: Docteur es, Sciences de la Vie et de la Santé, 2016, Université François-Rabelais de Tours

URL: http://www.theses.fr/2016TOUR3805

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Catharanthus roseus est une plante médicinale produisant divers types d’alcaloïdes indoliques monoterpéniques (AIM) d’intérêt en santé humaine. Ainsi, les AIM dimères comme la vinblastine et… (more)

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Catharanthus roseus est une plante médicinale produisant divers types d’alcaloïdes indoliques monoterpéniques (AIM) d’intérêt en santé humaine. Ainsi, les AIM dimères comme la vinblastine et la vincristine sont utilisés en chimiothérapie anticancéreuse et les alcaloïdes monomères de type hétéroyohimbine présentent diverses activités pharmacologiques. La fabrication de ces molécules dans la plante est fort complexe. Elle requiert un haut niveau de compartimentation tissulaire et subcellulaire et met en jeu plus d’une trentaine d’étapes enzymatiques, dont certaines sont encore très mal connues. Dans ce contexte, l’objectif de la thèse a consisté à élucider plusieurs étapes enzymatiques de la voie de biosynthèse des AIM. Nos travaux ont permis de caractériser de nouvelles isoformes enzymatiques de la famille des cytochromes P450 ainsi que les réductases qui leur sont associées. Ils ont abouti à l’identification de nouvelles déshydrogénases et mis en évidence, in planta, leurs interactions avec la strictosidine synthase suggérant une biosynthèse orientée vers les divers alcaloïdes de type hétéroyohimbine. Enfin, en ayant recours à l’ingénierie métabolique, un segment de la voie de biosynthèse a été transféré dans la levure Saccharomyces cerevisiae, lui conférant la capacité de bio-transformer la tabersonine en vindoline, l’un des deux précurseurs finaux des alcaloïdes dimères.

Catharanthus roseus is a medicinal plant producing various types of monoterpene indole alkaloids (MIA) with a great interest in human health. Dimeric alkaloids such as vinblastine and vincristine are used in cancer chemotherapy and monomeric heteroyohimbine alkaloids exhibit various pharmacological activities. The production of these molecules in the plant is very complex. It requires a high level of tissular and subcellular compartmentalization and involves more than thirty enzymatic steps, some of which are largely unknown. In this context, the aim of this thesis was to elucidate several enzymatic steps of the MIA biosynthetic pathway. Our work allowed us to characterize new enzyme isoforms of cytochrome P450 and their associated reductases. They also resulted in the identification of new dehydrogenases and highlighted their interactions with the strictosidine synthase suggesting a directed biosynthesis towards various heteroyohimbine type of alkaloids. Finally, engineered yeast containing a segment of the MIA biosynthetic pathway was able to convert tabersonine into vindoline, one of the two final precursors of the dimeric alkaloids.

Advisors/Committee Members: Clastre, Marc (thesis director), Courdavault, Vincent (thesis director).

Subjects/Keywords: Catharanthus roseus; Alcaloïdes indoliques monoterpéniques; Biosynthèse; Compartimentation subcellulaire; Ingénierie métabolique; Catharanthus roseus; Monoterpene indole alkaloid; Biosynthesis; Subcellular compartmentalization; Metabolic engineering

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

APA (6^th Edition):

Foureau, E. (2016). Elucidation de la voie de biosynthèse des alcaloïdes de Catharanthus roseus et ingénierie métabolique dans la levure : Elucidation of the Catharanthus roseus alkaloid pathway and metabolic engineering in yeast. (Doctoral Dissertation). Université François-Rabelais de Tours. Retrieved from http://www.theses.fr/2016TOUR3805

Chicago Manual of Style (16^th Edition):

Foureau, Emilien. “Elucidation de la voie de biosynthèse des alcaloïdes de Catharanthus roseus et ingénierie métabolique dans la levure : Elucidation of the Catharanthus roseus alkaloid pathway and metabolic engineering in yeast.” 2016. Doctoral Dissertation, Université François-Rabelais de Tours. Accessed April 11, 2021. http://www.theses.fr/2016TOUR3805.

MLA Handbook (7^th Edition):

Foureau, Emilien. “Elucidation de la voie de biosynthèse des alcaloïdes de Catharanthus roseus et ingénierie métabolique dans la levure : Elucidation of the Catharanthus roseus alkaloid pathway and metabolic engineering in yeast.” 2016. Web. 11 Apr 2021.

Vancouver:

Foureau E. Elucidation de la voie de biosynthèse des alcaloïdes de Catharanthus roseus et ingénierie métabolique dans la levure : Elucidation of the Catharanthus roseus alkaloid pathway and metabolic engineering in yeast. [Internet] [Doctoral dissertation]. Université François-Rabelais de Tours; 2016. [cited 2021 Apr 11]. Available from: http://www.theses.fr/2016TOUR3805.

Council of Science Editors:

Foureau E. Elucidation de la voie de biosynthèse des alcaloïdes de Catharanthus roseus et ingénierie métabolique dans la levure : Elucidation of the Catharanthus roseus alkaloid pathway and metabolic engineering in yeast. [Doctoral Dissertation]. Université François-Rabelais de Tours; 2016. Available from: http://www.theses.fr/2016TOUR3805

30. Matochko, Wadim L. In vitro compartmentalization and deep sequencing enable discovery of functional cell-binding ligands by phage display.

Degree: PhD, Department of Chemistry, 2015, University of Alberta

URL: https://era.library.ualberta.ca/files/cb5644r57s

► Phage display is a technique that accelerated the discovery of peptide and protein-based ligands to numerous targets in academia and industry. Many FDA-approved antibodies and… (more)

▼ Phage display is a technique that accelerated the discovery of peptide and protein-based ligands to numerous targets in academia and industry. Many FDA-approved antibodies and peptides on the market have originated from phage display experiments. However, one of the main drawbacks to this technique is that there are two independent steps in the selection process, an enrichment step for ligands with binding affinity towards a target and an amplification step to amplify the enriched phage clones. The amplification step introduces a bias towards enriching phage clones with a different phenotype based on growth rate. The implication of this bias is that target-binding ligands are enriched from a small subset, with low diversity, of the phage library that contains fast growing phage clones. Furthermore, selection from the fast growing phage population gives rise to a large number of target unrelated ligands. This undesired amplification bias is especially detrimental when selecting for ligands against multi-site binding target, such as cell or tissues. In this thesis, we examine whether the collapse of diversity can be prevented in phage libraries by amplifying these libraries in emulsions. We show that preventing the diversity collapse, we can identify more ligands than the standard selection method and speed up the discovery of ligands to targets with multiple binding sites. This thesis first describes the development of the emulsion amplification technique. We describe the manufacturing of the microfluidic devices and synthesis of the perfluoro-surfactant needed to maintain stable emulsions throughout the amplification process. To analyze the amplification process, we develop a method for deep-sequencing of phage display libraries using Illumina and Ion Torrent platforms, as well as MATLAB scripts, to analyze deep-sequencing data. We applied deep sequencing to examine how diversity of peptides in phage display libraries changes as a result of amplification of libraries in bacteria. Using a Ph.D.-12 library as our model library, we observed that amplification enriches ~150 clones, which dominate ~20% of the library. Deep sequencing, for the first time, characterized the collapse of diversity in phage libraries. We extend the use of next-generation sequencing to characterize the Ph.D. 7 library. Using Illumina and Ion Torrent sequencing and multiple biological replicates of amplification of the Ph.D.-7 library, we identified a focused population of 770 sequences that grow quickly, we term these sequences ‘parasites’. In all, 197 sequences from this population have been identified in literature reports that used Ph.D.-7 library. Many of these enriched sequences have confirmed function (e.g., target binding capacity). The bias in the literature, thus, can be viewed as a selection with two different selection pressures: i) target-binding selection, and ii) amplification-induced selection. Enrichment of parasitic sequences could be minimized if amplification bias is removed. Here, we demonstrate that emulsion amplification…

Subjects/Keywords: Phage display; Deep-sequencing; In vitro compartmentalization

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APA (6^th Edition):

Matochko, W. L. (2015). In vitro compartmentalization and deep sequencing enable discovery of functional cell-binding ligands by phage display. (Doctoral Dissertation). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/cb5644r57s

Chicago Manual of Style (16^th Edition):

Matochko, Wadim L. “In vitro compartmentalization and deep sequencing enable discovery of functional cell-binding ligands by phage display.” 2015. Doctoral Dissertation, University of Alberta. Accessed April 11, 2021. https://era.library.ualberta.ca/files/cb5644r57s.

MLA Handbook (7^th Edition):

Matochko, Wadim L. “In vitro compartmentalization and deep sequencing enable discovery of functional cell-binding ligands by phage display.” 2015. Web. 11 Apr 2021.

Vancouver:

Matochko WL. In vitro compartmentalization and deep sequencing enable discovery of functional cell-binding ligands by phage display. [Internet] [Doctoral dissertation]. University of Alberta; 2015. [cited 2021 Apr 11]. Available from: https://era.library.ualberta.ca/files/cb5644r57s.

Council of Science Editors:

Matochko WL. In vitro compartmentalization and deep sequencing enable discovery of functional cell-binding ligands by phage display. [Doctoral Dissertation]. University of Alberta; 2015. Available from: https://era.library.ualberta.ca/files/cb5644r57s

Open Access Theses and Dissertations