subject:(biophysics)

University of California, Irvine

1. Plett, Timothy Stephen. Ion Transport Phenomena at the Nanoscale in Different Model Battery Systems.

Degree: 2017, University of California, Irvine

URL: http://pqdtopen.proquest.com/#viewpdf?dispub=10287815

► Lithium ion battery technology has flourished since its introduction into the consumer market. Not only has it helped revolutionize consumer electronics, it also compliments… (more)

▼ Lithium ion battery technology has flourished since its introduction into the consumer market. Not only has it helped revolutionize consumer electronics, it also compliments R&D into clean forms of energy harvest e.g. solar, wind, and hydro-electric. As demand for the technology grows, innovative approaches have been taken to improve capacity, output, and lifetime in Li-ion batteries. The approach studied in this research involves the inclusion of nanostructures, which have the potential to significantly increase capacity. While several techniques to fabricate nanostructures are understood, underlying phenomena governing ion transport in and around these nanostructures is only partially understood, which could directly impact design principles for such devices. This thesis examines a variety of model systems which could serve to simulate environments found in proposed devices and answer questions regarding ion transport phenomena. The main components we studied from such battery systems were electrolyte and cathode materials. The electrolyte experiences different ion transport phenomena arising from the nanoconfinement of the cathode structures both around and inside the electrode material. Thus, having model systems to examine electrolyte and cathode material separately and in tandem is useful for elucidating phenomena without the challenge of deconvolution resulting from other current-carrying mechanisms. Our main tools for carrying out our research were synthetic nanopores. The nanopore structures afforded means to access nanoscale, control environment, and even fabricate components for study. By studying the current-voltage curves in these systems, we were able to draw meaningful conclusions about mechanisms of ion transport in these model systems. The main findings of this research include the inducement of positive surface charge on nanopore structures by organic solvent-based electrolytes by means of dipole and/or ion adsorption, positive evidence of gel electrolyte fitting current models of ion current rectification, and the impact of oxidation state and cycling in cathode material on ion transport through its porous media. Each of these findings is directly related to the thrust of the research and potentially provide insights for future battery design.

Subjects/Keywords: Biophysics

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APA (6^th Edition):

Plett, T. S. (2017). Ion Transport Phenomena at the Nanoscale in Different Model Battery Systems. (Thesis). University of California, Irvine. Retrieved from http://pqdtopen.proquest.com/#viewpdf?dispub=10287815

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):

Plett, Timothy Stephen. “Ion Transport Phenomena at the Nanoscale in Different Model Battery Systems.” 2017. Thesis, University of California, Irvine. Accessed January 17, 2021. http://pqdtopen.proquest.com/#viewpdf?dispub=10287815.

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

MLA Handbook (7^th Edition):

Plett, Timothy Stephen. “Ion Transport Phenomena at the Nanoscale in Different Model Battery Systems.” 2017. Web. 17 Jan 2021.

Vancouver:

Plett TS. Ion Transport Phenomena at the Nanoscale in Different Model Battery Systems. [Internet] [Thesis]. University of California, Irvine; 2017. [cited 2021 Jan 17]. Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=10287815.

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

Council of Science Editors:

Plett TS. Ion Transport Phenomena at the Nanoscale in Different Model Battery Systems. [Thesis]. University of California, Irvine; 2017. Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=10287815

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

University of California – Berkeley

2. Baer, Christina Elizabeth. Mechanisms of Mycobacterium tuberculosis Serine/Threonine Protein Kinase Activation.

Degree: Biophysics, 2010, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/45v1h1bf

► Mycobacterium tuberculosis (Mtb) coordinates a wide variety of metabolic and cellular responses to changing external environments throughout the multiple stages of infection. Signaling kinases are… (more)

▼ Mycobacterium tuberculosis (Mtb) coordinates a wide variety of metabolic and cellular responses to changing external environments throughout the multiple stages of infection. Signaling kinases are critical for these responses. The Mtb genome encodes 11 Serine/Threonine Protein Kinases (STPKs) that function as important nodes of this sensing and response network, but the chemical and structural changes that mediate kinase activation have not been elucidated. Autophosphorylation activates several of the Mtb STPKs, and kinase dimerization can activate receptor kinases for autophosphorylation through an allosteric dimer interface. Inter-kinase phosphorylation has been reported, but the function and specificity of these interactions remain unknown. In this study, a biochemical approach was used to comprehensively map the cross-kinase trans-phosphorylation activity of the Mtb STPKs. The results reveal a pattern of kinase interactions that suggests each protein plays a distinct regulatory role in controlling cellular processes by phosphorylating other kinases. The PknB and PknH STPKs act in vitro as master regulators that are activated only through autophosphorylation and also phosphorylate other STPKs. In contrast, the signal-transduction kinases PknE, PknJ and PknL are phosphorylated by the master regulatory STPKs and phosphorylate other kinases. The substrate STPKs PknA, PknD, PknF and PknK are phosphorylated by upstream STPKs, but do not phosphorylate other kinases. The delineation of the Mtb STPK signaling networks reveals for the first time the specific network of STPK phosphorylation that may mediate the intracellular signaling circuitry. STPKS are activated and inhibited by phosphorylation at different residues. The regulatory role of the extensive Mtb STPK trans-phosphorylation network is unknown. Through mass spectrophotometry and mutagenesis, the amino acids targeted by each phosphorylation were identified. I find that key activation loop residues are the targets of both autophosphorylation and trans-phosphorylation. Mutation of the two conserved threonines in the activation loops of nine Mtb STPKs renders the kinases inactive. These results demonstrate that activation loop phosphorylation is a common mechanism of Mtb STPK activation. To explore the structural implications of activation loop phosphorylation, I determined the crystal structures of the phosphorylated and unphosphorylated Mtb PknH kinase domain. The PknH kinase domain forms a back-to-back dimer observed previously in the structures of Mtb PknB and PknE. Amino-acid substitutions in the dimer interface fail to block kinase dimerization or autophosphorylation. Unexpectedly, the PknH activation loop is folded in the unphosphorylated form and disordered in the active, phosphorylated enzyme. These structures revealed that the back-to-back kinase dimer is a surprisingly stable structure that does not undergo global conformational changes with phosphorylation or nucleotide binding. Unlike the well-established, conformational regulatory…

Subjects/Keywords: Biophysics

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

APA (6^th Edition):

Baer, C. E. (2010). Mechanisms of Mycobacterium tuberculosis Serine/Threonine Protein Kinase Activation. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/45v1h1bf

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):

Baer, Christina Elizabeth. “Mechanisms of Mycobacterium tuberculosis Serine/Threonine Protein Kinase Activation.” 2010. Thesis, University of California – Berkeley. Accessed January 17, 2021. http://www.escholarship.org/uc/item/45v1h1bf.

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

MLA Handbook (7^th Edition):

Baer, Christina Elizabeth. “Mechanisms of Mycobacterium tuberculosis Serine/Threonine Protein Kinase Activation.” 2010. Web. 17 Jan 2021.

Vancouver:

Baer CE. Mechanisms of Mycobacterium tuberculosis Serine/Threonine Protein Kinase Activation. [Internet] [Thesis]. University of California – Berkeley; 2010. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/45v1h1bf.

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

Council of Science Editors:

Baer CE. Mechanisms of Mycobacterium tuberculosis Serine/Threonine Protein Kinase Activation. [Thesis]. University of California – Berkeley; 2010. Available from: http://www.escholarship.org/uc/item/45v1h1bf

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

UCLA

3. Roongthumskul, Yuttana. Mechanical entrainment of saccular hair cell bundles.

Degree: Physics, 2014, UCLA

URL: http://www.escholarship.org/uc/item/9399s6bn

► Mechanical detection of auditory and vestibular system displays exquisite sensitivity, with sub-nanometer detection threshold. The system is also highly nonlinear, exhibiting sharply tuned frequency selectivity… (more)

▼ Mechanical detection of auditory and vestibular system displays exquisite sensitivity, with sub-nanometer detection threshold. The system is also highly nonlinear, exhibiting sharply tuned frequency selectivity and compression of dynamic range. Detection of sounds and vibrations is mediated by the sensory hair cells, which transduce mechanical inputs into electrical signals via hair bundles' deflections. Experiments have consistently shown that hair bundles are not just passive detectors, as they spontaneously oscillate and respond to mechanical stimulus in an active manner. A number of theories based on nonlinear dynamics have described the active hair bundle as a nonlinear system poised near a Hopf bifurcation. Prior studies of mechanical response of hair bundles were done in spontaneously oscillating hair bundles, with mechanical stimulus fluctuating around bundles' resting positions. These conditions, however, might not be true under in vivo conditions. In fact, hair bundles from the bullfrog sacculus are coupled to an overlying membrane, which imposes a steady state offset to the bundle position, and suppresses bundles' spontaneous activity. In this dissertation, we study entrainment of hair bundles from the bullfrog sacculus by sinusoidal stimuli under different mechanical manipulations: offsets and couplings. First, multimode oscillations are more frequently observed upon application of a small negative offset onto spontaneous oscillating hair bundles. Using a numerical model based on detailed physiology of hair bundle, this complex temporal profile requires an additional element - a variable gating spring - with a stiffness that varies with calcium concentration. The dynamics of the process are slow compared to other timescales in the bundle, i.e. gating of transduction channels and slow adaptation process. Second, oscillating hair bundles subject to weak mechanical stimuli are extremely sensitive, with response in the phase histogram already observed at 0.4-pN stimulus. Time-dependent phase-locking behavior at slightly higher signal amplitudes exhibits phase slips, indicating that the system undergoes phase-locking via a SNIC bifurcation. Study of hair bundle dynamics under mechanical offsets reveals a spiking regime, which is even more sensitive to stimulus compared to the oscillatory regime. Larger mechanical offset yields suppression of spontaneous activity, during which spikes can be evoked by stimulus. Evoked spikes occur at a preferred phase of the stimulus cycle, and exhibit a constant amplitude, regardless of signal amplitude and frequency, and leading to an amplifying movement. Finally, we study how coupling between hair bundles affects their mechanical response. Synchronization of bundles' spontaneous movements is always observed, regardless of the original characteristic frequencies of hair bundles prior to coupling. While some coupled bundles show an enhancement, we find that, in general, coupling only two bundles does not significantly improve the sensitivity and frequency tuning.

Subjects/Keywords: Biophysics

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

APA (6^th Edition):

Roongthumskul, Y. (2014). Mechanical entrainment of saccular hair cell bundles. (Thesis). UCLA. Retrieved from http://www.escholarship.org/uc/item/9399s6bn

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):

Roongthumskul, Yuttana. “Mechanical entrainment of saccular hair cell bundles.” 2014. Thesis, UCLA. Accessed January 17, 2021. http://www.escholarship.org/uc/item/9399s6bn.

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

MLA Handbook (7^th Edition):

Roongthumskul, Yuttana. “Mechanical entrainment of saccular hair cell bundles.” 2014. Web. 17 Jan 2021.

Vancouver:

Roongthumskul Y. Mechanical entrainment of saccular hair cell bundles. [Internet] [Thesis]. UCLA; 2014. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/9399s6bn.

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

Council of Science Editors:

Roongthumskul Y. Mechanical entrainment of saccular hair cell bundles. [Thesis]. UCLA; 2014. Available from: http://www.escholarship.org/uc/item/9399s6bn

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

University of California – Berkeley

4. Sen, Maya. Dissecting the molecular mechanisms of the ClpXP protease, one molecule at a time.

Degree: Chemistry, 2014, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/9m9149j4

► The cell is a fundamental unit of life, and in order for survival, maintaining a stable intracellular enviroment is crucial. ATP-dependent protease complexes regulate protein… (more)

▼ The cell is a fundamental unit of life, and in order for survival, maintaining a stable intracellular enviroment is crucial. ATP-dependent protease complexes regulate protein quality and abundance to ensure homeostasis in the cell. They use chemical energy to power processes necessary for regulating the intracellular environment including protein unfolding, polypeptide translocation, and targeted degradation of abnormal and short-lived regulatory proteins. ClpXP, a well-studied ATP-dependent protease complex from Escherichia coli, is an assembly of homohexameric ClpX coaxially stacked onto a barrel-shaped protease ClpP. ClpX utilizes the energy from ATP hydrolysis to bind the appropriately tagged polypeptide substrates, denature and translocate them into the degradation cavity of ClpP. There have been long-standing questions in the field, specifically whether ClpX can generate force to unfold proteins, how do the six ClpX subunits communicate, and coordinate their ATPases cycles to generate force. Optical tweezers are used as a powerful single-molecule technique to characterize the mechanochemical properties of biomolecules in the nanometer and piconewton range. After a decade of research, we have developed a novel optical tweezers assay to monitor ClpX as it binds, unfolds and translocates various green fluorescent protein (GFP) fusion substrates in real time under a range of ATP concentrations. We characterized the general properties of the motor, which are described in chapter 2. From the analysis of these single-molecule trajectories, we have determined several unique properties of the motor previously undetectable in bulk. First, ClpX can generate up to 20 pN of force to translocate and unfold proteins, eventually being stalled in movement as the opposing force approaches 20 pN. We subsequently explored the communication within the hexameric ring of wild-type ClpX at various ATP, ADP, and Pi concentrations. Our results, described in chapter 3, provided the first direct evidence of a force-generation mechanism and that the phosphate release is coupled to the force-generating step of ClpX. We demonstrated that two to four subunits of the ClpX hexamer actively participates in bursts of translocation and that between the translocation bursts, the motor has a mean constant dwell duration independent of ATP concentration. Our analysis revealed defined a new archetype of motor coordination, which is critical as a fail-safe mechanism to prevent the motor disengagement from its substrate.

Subjects/Keywords: Biophysics

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

APA (6^th Edition):

Sen, M. (2014). Dissecting the molecular mechanisms of the ClpXP protease, one molecule at a time. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/9m9149j4

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):

Sen, Maya. “Dissecting the molecular mechanisms of the ClpXP protease, one molecule at a time.” 2014. Thesis, University of California – Berkeley. Accessed January 17, 2021. http://www.escholarship.org/uc/item/9m9149j4.

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

MLA Handbook (7^th Edition):

Sen, Maya. “Dissecting the molecular mechanisms of the ClpXP protease, one molecule at a time.” 2014. Web. 17 Jan 2021.

Vancouver:

Sen M. Dissecting the molecular mechanisms of the ClpXP protease, one molecule at a time. [Internet] [Thesis]. University of California – Berkeley; 2014. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/9m9149j4.

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

Council of Science Editors:

Sen M. Dissecting the molecular mechanisms of the ClpXP protease, one molecule at a time. [Thesis]. University of California – Berkeley; 2014. Available from: http://www.escholarship.org/uc/item/9m9149j4

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

University of California – Santa Cruz

5. Long, Xi. Single Molecule Studies of Telomere DNA.

Degree: Chemistry, 2014, University of California – Santa Cruz

URL: http://www.escholarship.org/uc/item/7934241b

► Since the discovery by Blackburn in 1978, telomere has been the subject of intense research focus due to its close relationship with aging and cancer.… (more)

▼ Since the discovery by Blackburn in 1978, telomere has been the subject of intense research focus due to its close relationship with aging and cancer. Despite extensive research efforts more than three decades, the structural properties of telomere remain elusive. In this dissertation, I used single molecule techniques to examine the physical properties of telomere. These studies have identified the kinetically favorable telomere G-quadruplex (GQ) structure, revealed the mechanical unfolding pathway of telomere GQ, and characterized the mechanical properties of duplex telomere DNA and the formation of the telomere D-loop. Since the discovery by Blackburn in 1978, the telomere has been the subject of intense research focus due to its close relationship with aging and cancer. Despite extensive research efforts for more than three decades, the structural properties of telomere remain elusive. In this dissertation, I used single molecule techniques to examine the physical properties of telomere. These studies have identified the kinetically favorable telomere G- quadruplex (GQ) structure, revealed the mechanical unfolding pathway of telomere GQ, and characterized the mechanical properties of duplex telomere DNA and the formation of the telomere D-loop. Telomeres are specialize DNA sequence that prevent degradation and aberrant fusion of chromosome ends. The foundation of human telomeres consists of 5-10 kb of duplex TTAGGG repeats follow by a 50 to 200 nucleotides of 3' single stranded overhang. The G-rich single stranded telomere has a propensity to fold into a secondary structure known as GQ. In Chapter 2, single-molecule Förster resonance energy transfer (smFRET) was used for constructing the distribution of telomere DNA GQ conformations under physiological salt conditions. With circular dichroism, the kinetic trapped GQ conformation was discovered. In Chapter 3, smFRET and magnetic tweezers (MT) was used to dissect the folding property telomere GQ. Under stretching force, the unfolding pathway of telomere GQ was characterized by a distance less than 1nm. In Chapter 4, the magnetic tweezers assay revealed that telomere is more resistant to torque-induced denaturation. The direct observation of telomere strand invasion suggested that the stretching force can influence the rate of the invasion and the formation of the telomere displacement loop. The subsequent chapters detail the setup and experimental protocol for the MT-FRET, and describe how to use MT to manipulate DNA. These single molecule assays setup a foundation for investigating the interaction between the telomere and its associated proteins and serve as an experimental platform for telomere drug assessment. Ultimately, with these single molecule assays we will enhance our knowledge on how telomere regulates telomerase activity.

Subjects/Keywords: Biophysics

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

APA (6^th Edition):

Long, X. (2014). Single Molecule Studies of Telomere DNA. (Thesis). University of California – Santa Cruz. Retrieved from http://www.escholarship.org/uc/item/7934241b

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):

Long, Xi. “Single Molecule Studies of Telomere DNA.” 2014. Thesis, University of California – Santa Cruz. Accessed January 17, 2021. http://www.escholarship.org/uc/item/7934241b.

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

MLA Handbook (7^th Edition):

Long, Xi. “Single Molecule Studies of Telomere DNA.” 2014. Web. 17 Jan 2021.

Vancouver:

Long X. Single Molecule Studies of Telomere DNA. [Internet] [Thesis]. University of California – Santa Cruz; 2014. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/7934241b.

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

Council of Science Editors:

Long X. Single Molecule Studies of Telomere DNA. [Thesis]. University of California – Santa Cruz; 2014. Available from: http://www.escholarship.org/uc/item/7934241b

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

University of California – Berkeley

6. Katira, Shachi. Physical Considerations of the Organization of Inclusions in Lipid Bilayer Systems.

Degree: Bioengineering, 2015, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/7jz0t3nh

► Lipid bilayers, along with embedded inclusions such as cholesterol and proteins, constitute a biological membrane—the interface between a cell or organelle and its environment. Understanding… (more)

▼ Lipid bilayers, along with embedded inclusions such as cholesterol and proteins, constitute a biological membrane—the interface between a cell or organelle and its environment. Understanding the structure of a biological membrane and the physical principles responsible for the organization of membrane inclusions is crucial to understanding the processes that occur on the surface of a cell or organelle such as inter-cellular signaling, immune synapse processes, exo- and endocytosis, and membrane fusion. In this work, we study the organization and effect of inclusions in a lipid bilayer using statistical mechanics principles and large-scale molecular simulations.In the first part of this work, we propose a generic physical force for the assembly of inclusions in lipid bilayers—the orderphobic effect. Inspired by modern theories of the hydrophobic effect, this force is governed by the physics of the first-order phase transition between the ordered (i.e., solid-like) and disordered (i.e., fluid) phases of lipid bilayers. We show the existence and nature of this force using coarse-grained molecular dynamics simulations, and demonstrate the lateral assembly of two model proteins, or ‘orderphobes’, within a lipid bilayer. The effect is powerful and operates at nano- to mesoscopic scales, and could be a potential explanation for the clustering of proteins in a biological membrane.In the second part of this work, we focus on hydrophobic inclusions within the lipid bilayer that give rise to organelles known as lipid droplets. These droplets, earlier thought to be passive stores of hydrophobic material in an otherwise aqueous cytosol, have now been implicated in various metabolic diseases. Since the growth and behavior of nascent droplets is sub-microscopic, little is known about the details of this process. We construct a computational framework that allows for a lipid reservoir to study asymmetric inclusions in a lipid bilayer such as the lipid droplet. Further, we identify key stages in the growth and budding of this organelle.

Subjects/Keywords: Biophysics

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APA (6^th Edition):

Katira, S. (2015). Physical Considerations of the Organization of Inclusions in Lipid Bilayer Systems. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/7jz0t3nh

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):

Katira, Shachi. “Physical Considerations of the Organization of Inclusions in Lipid Bilayer Systems.” 2015. Thesis, University of California – Berkeley. Accessed January 17, 2021. http://www.escholarship.org/uc/item/7jz0t3nh.

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

MLA Handbook (7^th Edition):

Katira, Shachi. “Physical Considerations of the Organization of Inclusions in Lipid Bilayer Systems.” 2015. Web. 17 Jan 2021.

Vancouver:

Katira S. Physical Considerations of the Organization of Inclusions in Lipid Bilayer Systems. [Internet] [Thesis]. University of California – Berkeley; 2015. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/7jz0t3nh.

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

Council of Science Editors:

Katira S. Physical Considerations of the Organization of Inclusions in Lipid Bilayer Systems. [Thesis]. University of California – Berkeley; 2015. Available from: http://www.escholarship.org/uc/item/7jz0t3nh

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

University of California – Riverside

7. Erdemci Tandogan, Gonca. Physics of Viruses: The Role of Genome and Membrane.

Degree: Physics, 2016, University of California – Riverside

URL: http://www.escholarship.org/uc/item/6md8x6zp

► We study the physics of virus assembly. The dissertation can be separated into two parts. The first part focuses on spherical single stranded (ss) RNA… (more)

▼ We study the physics of virus assembly. The dissertation can be separated into two parts. The first part focuses on spherical single stranded (ss) RNA viruses or virus like particles. Using mean-field theory, we explore the role of the secondary structure of RNA on the viral assembly by modeling the RNA as an annealed branched polymer. Our results verify that RNA branchedness maximizes the amount of encapsulated genome into a relatively small capsid and makes assembly more efficient. We furthermore offer an explanation for the phenomena of overcharging observed in viral particles. Chapter 5 demonstrates an application of our theory to satellite tobacco mosaic virus (STMV). Our theory explains, energetically, why a truncated RNA is encapsidated by STMV capsid proteins more favorably.In the second part, we explore the role of genome on the structure of human immunodeficiency virus (HIV) shells (Chapter 6). Our analytical results show that the free energy of confinement of genome into a conical capsid is less than that for a cylindrical one when the genome does not interact with the capsid as in in vivo experiments. This may explain why the conical structures favor over the cylindrical ones in in vivo. In Chapter 7, we carry out coarse-grained simulations to examine the HIV maturation pathways and the role of genome and membrane on the formation of conical shells. We show that the membrane restricts the growth of the otherwise extended incomplete shell and induces local stresses causing formation of the pentamers necessary for the assembly of closed conical or tubular shells. More interestingly, we find that any asymmetry developed in the growing lattice due to interaction with the membrane or genome, or due to the shape of initial immature lattice creates conical capsids, as opposed to cylindrical shells. Furthermore, our work confirms that viruses employ all the accessible pathways to maturation, explaining many aspects of the previous HIV pathway experiments.

Subjects/Keywords: Biophysics

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APA (6^th Edition):

Erdemci Tandogan, G. (2016). Physics of Viruses: The Role of Genome and Membrane. (Thesis). University of California – Riverside. Retrieved from http://www.escholarship.org/uc/item/6md8x6zp

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):

Erdemci Tandogan, Gonca. “Physics of Viruses: The Role of Genome and Membrane.” 2016. Thesis, University of California – Riverside. Accessed January 17, 2021. http://www.escholarship.org/uc/item/6md8x6zp.

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

MLA Handbook (7^th Edition):

Erdemci Tandogan, Gonca. “Physics of Viruses: The Role of Genome and Membrane.” 2016. Web. 17 Jan 2021.

Vancouver:

Erdemci Tandogan G. Physics of Viruses: The Role of Genome and Membrane. [Internet] [Thesis]. University of California – Riverside; 2016. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/6md8x6zp.

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

Council of Science Editors:

Erdemci Tandogan G. Physics of Viruses: The Role of Genome and Membrane. [Thesis]. University of California – Riverside; 2016. Available from: http://www.escholarship.org/uc/item/6md8x6zp

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

UCLA

8. Zhang, Tracy-Ying. The Nonlinear Dynamics of Coupled Hair Bundles.

Degree: Physics, 2017, UCLA

URL: http://www.escholarship.org/uc/item/81t714rm

► The sensitivity of the auditory system depends in part on the active response of hair cells in the inner ear. Individual hair bundles display frequency… (more)

Subjects/Keywords: Biophysics

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APA (6^th Edition):

Zhang, T. (2017). The Nonlinear Dynamics of Coupled Hair Bundles. (Thesis). UCLA. Retrieved from http://www.escholarship.org/uc/item/81t714rm

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):

Zhang, Tracy-Ying. “The Nonlinear Dynamics of Coupled Hair Bundles.” 2017. Thesis, UCLA. Accessed January 17, 2021. http://www.escholarship.org/uc/item/81t714rm.

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

MLA Handbook (7^th Edition):

Zhang, Tracy-Ying. “The Nonlinear Dynamics of Coupled Hair Bundles.” 2017. Web. 17 Jan 2021.

Vancouver:

Zhang T. The Nonlinear Dynamics of Coupled Hair Bundles. [Internet] [Thesis]. UCLA; 2017. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/81t714rm.

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

Council of Science Editors:

Zhang T. The Nonlinear Dynamics of Coupled Hair Bundles. [Thesis]. UCLA; 2017. Available from: http://www.escholarship.org/uc/item/81t714rm

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

University of California – Berkeley

9. Dong, Meimei. Spatial and Mechanical Regulation of EphB Receptor in Neural Stem Cell Function.

Degree: Biophysics, 2015, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/2c43v41h

► EphB4 receptor tyrosine kinases bind and cluster with membrane bound ephrinB2 ligands on apposing cells to signal juxtacrine. While this signal activation plays a regulatory… (more)

Subjects/Keywords: Biophysics

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APA (6^th Edition):

Dong, M. (2015). Spatial and Mechanical Regulation of EphB Receptor in Neural Stem Cell Function. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/2c43v41h

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):

Dong, Meimei. “Spatial and Mechanical Regulation of EphB Receptor in Neural Stem Cell Function.” 2015. Thesis, University of California – Berkeley. Accessed January 17, 2021. http://www.escholarship.org/uc/item/2c43v41h.

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

MLA Handbook (7^th Edition):

Dong, Meimei. “Spatial and Mechanical Regulation of EphB Receptor in Neural Stem Cell Function.” 2015. Web. 17 Jan 2021.

Vancouver:

Dong M. Spatial and Mechanical Regulation of EphB Receptor in Neural Stem Cell Function. [Internet] [Thesis]. University of California – Berkeley; 2015. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/2c43v41h.

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

Council of Science Editors:

Dong M. Spatial and Mechanical Regulation of EphB Receptor in Neural Stem Cell Function. [Thesis]. University of California – Berkeley; 2015. Available from: http://www.escholarship.org/uc/item/2c43v41h

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

University of California – Berkeley

10. DeWitt, Mark Alan. Studies of Inter-and Intra-Molecular Coordination in Cytoplasmic Dynein.

Degree: Biophysics, 2014, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/2hb6m146

► Cytoplasmic dynein is one of the principle motors in eukaryotic cells, responsible for most microtubule (MT) minus end-directed motility and force generation processes, including vesicular… (more)

▼ Cytoplasmic dynein is one of the principle motors in eukaryotic cells, responsible for most microtubule (MT) minus end-directed motility and force generation processes, including vesicular and organelle transport, and mitotic spindle MT organization. Despite being essential to the maintanence of cellular structure in higher eukaryotes, many aspects of dynein's stepping mechanism have remained enigmatic. In this Dissertation, I directly observe several fundamental aspects of dynein's mechanism, and build a strong framework for future studies. I outline in detail the methods for the fluorescent tracking of motor proteins, including advanced two-color and super-resolution techniques. To study cytoplasmic dynein, I developed a two-color fluorescent tracking assay to simultaneously measure the positions of both heads of the motor while it walks along the MT. The results of this experiment clearly show that dynein steps through a unique mechanism: the heads remain widely separated, and do not appear to coordinate with each other to a significant extent. However, the leading head is less likely to take a step at large inter-head separations, indicating some degree of residual coordination remains. I hypothesized that tension along the linker connecting the two heads is the source of this coordination. Using a high-speed two-color assay, I examined the motility of a homodimeric dynein with a flexible linker between the two heads that decreases inter-molecular tension. Despite this alteration, this homodimer has identical stepping and overall motility properties to wild-type dynein, but has reduced coordination, indicating that coordination is dispensable to motility. Coordination could be achieved by gating one of the heads. I investigated gating using a heterodimeric dynein with a wild-type head and an inactive, tightly-bound head. In this heterodimer, we find that the WT head is gated when widely separated from its inactive partner, but becomes un-gated when immediately behind it, indicating that the gating is caused by extension-dependent changes in linker tension as predicted. I next I turned from inter- to intra-molecular communication. Dynein has six distinct AAA subdomains on its motor head, of which only two AAA1 and AAA3, are essential to robust motility. By reducing MT affinity with added salt, I found that AAA3 is required for robust MT release, and that MT release in turn promotes hydrolysis at AAA1. To investigate coordination between AAA1 and AAA3, I analyzed motility in the presence of a slowly-hydrolyzable ATP analog, ATPγS. I found that ATPγS selectively inhibits the AAA3 site. In the presence of saturating analog, the motor can still take long runs of fast motility, indicating that the hydrolysis cycle of AAA3 is much shorter than AAA1. These results show that AAA1 and AAA3 do not coordinate. Instead, AAA3 acts as a "switch" that controls AAA1-directed release from the MT.

Subjects/Keywords: Biophysics

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

APA (6^th Edition):

DeWitt, M. A. (2014). Studies of Inter-and Intra-Molecular Coordination in Cytoplasmic Dynein. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/2hb6m146

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):

DeWitt, Mark Alan. “Studies of Inter-and Intra-Molecular Coordination in Cytoplasmic Dynein.” 2014. Thesis, University of California – Berkeley. Accessed January 17, 2021. http://www.escholarship.org/uc/item/2hb6m146.

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

MLA Handbook (7^th Edition):

DeWitt, Mark Alan. “Studies of Inter-and Intra-Molecular Coordination in Cytoplasmic Dynein.” 2014. Web. 17 Jan 2021.

Vancouver:

DeWitt MA. Studies of Inter-and Intra-Molecular Coordination in Cytoplasmic Dynein. [Internet] [Thesis]. University of California – Berkeley; 2014. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/2hb6m146.

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

Council of Science Editors:

DeWitt MA. Studies of Inter-and Intra-Molecular Coordination in Cytoplasmic Dynein. [Thesis]. University of California – Berkeley; 2014. Available from: http://www.escholarship.org/uc/item/2hb6m146

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

University of California – Berkeley

11. Crow, Alexis Kohnstamm. The Cellular Mechanoresponse: Single-Cell Studies by Atomic Force Microscopy.

Degree: Biophysics, 2011, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/0dd370j1

► Cells in their native environment are bombarded by mechanical signals ranging from strains within a developing embryo to stiffening of diseased tissue. How these extracellular… (more)

▼ Cells in their native environment are bombarded by mechanical signals ranging from strains within a developing embryo to stiffening of diseased tissue. How these extracellular mechanical signals are converted to biological activity on the cellular scale is a complex and unresolved problem in biology with implications in development and disease. This dissertation focuses on development and implementation of Atomic Force Microscopy (AFM)-based techniques to probe the interactions of cells with the mechanical microenvironment and use of these techniques towards characterizing and explaining the cellular mechanoresponse.We began by integrating a DNA-based adhesion technology with AFM that enables the manipulation of cells by a cantilever without influencing cell viability or signaling. This technique surpasses existing approaches both in the tunability and magnitude of adhesion strength to allow single-cell de-adhesion experiments that measure cell-ligand bonds without cell-surface rupture. The first step in the cellular mechanoresponse is the translation of an extracellular mechanical signal to an intracellular mechanical signal. We used high-resolution three-dimensional multi-particle tracking to measure how local stress applied by an AFM cantilever is propagated through an adherent cell. We observe a distance-dependent propagation on the timescale of seconds and that required an intact cytoskeletal network. This slow stress propagation is consistent with a poroelastic description of the cell that controls the timescales and lengthscales over which external stresses can be transmitted through cells.Recent studies have demonstrated that cells exhibit stiffness-dependent behaviors over long timescales, but the mechanism of how cells sense stiffness over short timescales remains particularly elusive. To study early events in stiffness sensing, we developed a feedback algorithm that enables dynamic and reversible control of the stiffness exposed to a single cell. We employ this stiffness clamp technique to study the contractile response of cells to sudden changes in extracellular stiffness, as defined by the cantilever. We find that the cell contraction rate adapts by accelerating upon a step decrease in stiffness or decelerating upon a step increase, both on a timescale of seconds. This seconds-timescale adaptation is independent of focal adhesion signaling, but it depends strongly on cell contractility suggesting that extracellular stiffness signals are filtered by the viscoelastic cytoskeleton.Together, the techniques described here provide novel and tunable control of the mechanical signals presented to and measured from a single cell with AFM precision. The results obtained using these techniques describe important timescales and considerations towards understanding the cellular mechanoresponse.

Subjects/Keywords: Biophysics

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

APA (6^th Edition):

Crow, A. K. (2011). The Cellular Mechanoresponse: Single-Cell Studies by Atomic Force Microscopy. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/0dd370j1

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):

Crow, Alexis Kohnstamm. “The Cellular Mechanoresponse: Single-Cell Studies by Atomic Force Microscopy.” 2011. Thesis, University of California – Berkeley. Accessed January 17, 2021. http://www.escholarship.org/uc/item/0dd370j1.

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

MLA Handbook (7^th Edition):

Crow, Alexis Kohnstamm. “The Cellular Mechanoresponse: Single-Cell Studies by Atomic Force Microscopy.” 2011. Web. 17 Jan 2021.

Vancouver:

Crow AK. The Cellular Mechanoresponse: Single-Cell Studies by Atomic Force Microscopy. [Internet] [Thesis]. University of California – Berkeley; 2011. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/0dd370j1.

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

Council of Science Editors:

Crow AK. The Cellular Mechanoresponse: Single-Cell Studies by Atomic Force Microscopy. [Thesis]. University of California – Berkeley; 2011. Available from: http://www.escholarship.org/uc/item/0dd370j1

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

University of California – Berkeley

12. Weinberger, Ariel. Multi-Strain Virus-Host Dynamics from HIV to Phage.

Degree: Biophysics, 2011, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/4fm794hm

► This dissertation uses mathematical modeling to probe the causes and consequences of multi-strain virus-host coexistence from the applied public health realm in which a second… (more)

▼ This dissertation uses mathematical modeling to probe the causes and consequences of multi-strain virus-host coexistence from the applied public health realm in which a second strain of HIV accelerates human mortality to the basic science realm in which persisting, previously dominant viruses drive the evolution of immunological memory in single-celled Bacteria and Archaea. In both applications, population-scale models are built from the ground up, utilizing experimentally measured parameters of virus and host molecules interacting within a cell to predict how virus and host populations coevolve across time. Model predictions are shown to match time-series data of virus-host dynamics in human hosts in the case of HIV and in prokaryotic hosts in the case of phage. Further, both sets of models generate experimentally testable hypotheses, suggesting therapeutic interventions against two major drivers of human mortality: HIV and pathogenic, antibiotic-resistant bacteria. The first area of application, and the focus of Chapters 2 and 3, is HIV. No one understands why, in about 50% of HIV infections in the West, a more deadly HIV strain emerges late in infection. The new strain, known as X4, differs from its predecessor, known as R5, because X4 only infects CD4+ T cells displaying the receptor CXCR4, while R5 only infects CD4+ T cells displaying the receptor CCR5. Due to the apparent health and anti-HIV immunity of the approximately 10% of Europeans lacking a functional CCR5 receptor, some researchers have touted anti-R5 therapy as an alternative to current anti-HIV drug cocktails. Chapter 2 uses simulations of a novel mathematical model to show how anti-R5 treatment alone may accelerate X4 emergence and resultant immunodeficiency. As an alternative, I show that CCR5 blockers may be more successful in combination with effective HAART therapy or, should they become available, CXCR4 blockers. Chapter 3 probes why X4 only emerges during late-stage HIV infection, showing how X4 persists for many years at low levels, avoiding competitive exclusion to the initially fitter R5 Virus, through X4's unique, low-level infection of naïve CD4+ T cells. In this chapter, I derive a minimal target-cell based model for dual R5, X4 HIV infection in which late-stage switches (bifurcations) to X4 autonomously occur. In this simplified model, an analytic switch condition is probed, allowing us to theoretically predict how different interventions modulate the time to X4 emergence, and providing a compelling explanation for why 50% of Western HIV patients never actually switch to X4 Virus. In Chapter 4, the focus turns to understanding the evolution of adaptive antiviral immunity – such as the T cell immunity targeted by HIV – in its most elemental setting: single-celled prokaryotes possessing the CRISPR immune system. A novel mathematical model of virus-microbe coevolution is derived to understand why prokaryotes with CRISPR-encoded specific immunity conserve old immune sequences for thousands of microbial generations despite compact…

Subjects/Keywords: Biophysics

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

APA (6^th Edition):

Weinberger, A. (2011). Multi-Strain Virus-Host Dynamics from HIV to Phage. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/4fm794hm

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):

Weinberger, Ariel. “Multi-Strain Virus-Host Dynamics from HIV to Phage.” 2011. Thesis, University of California – Berkeley. Accessed January 17, 2021. http://www.escholarship.org/uc/item/4fm794hm.

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

MLA Handbook (7^th Edition):

Weinberger, Ariel. “Multi-Strain Virus-Host Dynamics from HIV to Phage.” 2011. Web. 17 Jan 2021.

Vancouver:

Weinberger A. Multi-Strain Virus-Host Dynamics from HIV to Phage. [Internet] [Thesis]. University of California – Berkeley; 2011. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/4fm794hm.

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

Council of Science Editors:

Weinberger A. Multi-Strain Virus-Host Dynamics from HIV to Phage. [Thesis]. University of California – Berkeley; 2011. Available from: http://www.escholarship.org/uc/item/4fm794hm

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

University of California – Berkeley

13. Koulechova, Diana. The Role of Conformational Energetics in Ligand Binding and Thermal Sensation.

Degree: Molecular & Cell Biology, 2014, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/2z65j8wf

► A major outstanding question in protein science is how different regions of a protein communicate with one another. Although we can identify action-at-a-distance phenomena when… (more)

▼ A major outstanding question in protein science is how different regions of a protein communicate with one another. Although we can identify action-at-a-distance phenomena when they occur, a generalized mechanism and an understanding sufficiently thorough as to allow for de novo design remain works in progress. This is particularly true for natively disordered proteins and channel proteins, both of which have traditionally been more technically difficult to characterize biophysically. In this work, I explore the functional relevance of their unique energetics and dynamics.The first project investigates the functional relevance of the hydrophobic core of disordered transcription factor MarA. We randomized the MarA hydrophobic core and selected for variants able to bind the consensus sequence. We find that MarA is highly intolerant of core mutation; this is in contrast to what is seen for the well-folded transcription factor λ-repressor. Furthermore, core variants that do retain the ability to bind consensus sequence have differentially altered affinities for different binding partners. We propose that this can be explained by taking into account the varying energetic impact of these mutations on different MarA conformations and posit that residues distant from the active site can alter both binding affinity and specificity in natively disordered proteins.The second project aims to shed light on the mechanisms of thermosensation. Protein channel TRPA is a heat sensor in rattlesnakes but exhibits no heat-dependent activation in mammals. This discrepancy was mapped to select ankyrin repeats within the protein's cytoplasmic N-terminal domain. We hypothesized that temperature-dependent conformational changes within these repeats propagated to the pore region may be the thermosensing mechanism employed by TRPA1. The isolated repeats were purified and analyzed biophysically. Rattlesnake ankyrin repeats 3-8 are unique in that they do not appear to unfold with temperature on the timescale tested. The mechanism of this remarkable thermotolerance and its physiological relevance are currently under investigation.

Subjects/Keywords: Biophysics

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

APA (6^th Edition):

Koulechova, D. (2014). The Role of Conformational Energetics in Ligand Binding and Thermal Sensation. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/2z65j8wf

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):

Koulechova, Diana. “The Role of Conformational Energetics in Ligand Binding and Thermal Sensation.” 2014. Thesis, University of California – Berkeley. Accessed January 17, 2021. http://www.escholarship.org/uc/item/2z65j8wf.

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

MLA Handbook (7^th Edition):

Koulechova, Diana. “The Role of Conformational Energetics in Ligand Binding and Thermal Sensation.” 2014. Web. 17 Jan 2021.

Vancouver:

Koulechova D. The Role of Conformational Energetics in Ligand Binding and Thermal Sensation. [Internet] [Thesis]. University of California – Berkeley; 2014. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/2z65j8wf.

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

Council of Science Editors:

Koulechova D. The Role of Conformational Energetics in Ligand Binding and Thermal Sensation. [Thesis]. University of California – Berkeley; 2014. Available from: http://www.escholarship.org/uc/item/2z65j8wf

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

University of California – Berkeley

14. Rosen, Laura. Detailed characterization of the earliest events in protein folding.

Degree: Biophysics, 2014, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/5rm0r75g

► A major goal in biology is to understand how the amino acid sequence encodes all aspects of a protein's structure and dynamics. A protein spends… (more)

Subjects/Keywords: Biophysics

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

APA (6^th Edition):

Rosen, L. (2014). Detailed characterization of the earliest events in protein folding. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/5rm0r75g

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):

Rosen, Laura. “Detailed characterization of the earliest events in protein folding.” 2014. Thesis, University of California – Berkeley. Accessed January 17, 2021. http://www.escholarship.org/uc/item/5rm0r75g.

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

MLA Handbook (7^th Edition):

Rosen, Laura. “Detailed characterization of the earliest events in protein folding.” 2014. Web. 17 Jan 2021.

Vancouver:

Rosen L. Detailed characterization of the earliest events in protein folding. [Internet] [Thesis]. University of California – Berkeley; 2014. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/5rm0r75g.

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

Council of Science Editors:

Rosen L. Detailed characterization of the earliest events in protein folding. [Thesis]. University of California – Berkeley; 2014. Available from: http://www.escholarship.org/uc/item/5rm0r75g

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

University of California – Berkeley

15. Bothma, Jacques. Mechanisms of Transcriptional Precision in the Drosophila Embryo.

Degree: Biophysics, 2013, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/84x1d0pz

► Contemplating how a single cell can turn into the trillions of specialized cells that make a human being staggers the imagination. We still do not… (more)

▼ Contemplating how a single cell can turn into the trillions of specialized cells that make a human being staggers the imagination. We still do not fully understand how the information in a genome is interpreted by a cell to orchestrate this incredible process. One thing that we do know is that much of the complexity we see in the natural world comes down to how essentially the same set of proteins are differentially deployed. One of the key places where this is controlled is at the level of transcription which is the first step in protein production. In this thesis we attempt to shed light on this process by looking at how transcription is regulated in the early Drosophila embryo with a focus on mechanisms of transcriptional precision. We developed imaging and segmentation techniques that allowed for the quantitative visualization of the transcriptional state of thousands of nuclei in the embryo. Using this approach we discovered the phenomenon of repression lag, whereby genes containing large introns are not only slow to be switched on (intron delay), but are also slow to be repressed. Many sequence-specific repressors have been implicated in early development, but the mechanisms by which they silence gene expression have remained elusive. We found that elongating Pol II complexes complete transcription after the onset of repression. As a result, moderately sized genes are fully silenced only after tens of minutes of repression. We propose that this "repression lag" imposes a severe constraint on the regulatory dynamics of embryonic patterning.Having laid the foundations for using quantitative imaging in the early Drosophila embryo we next sought to understand the mechanisms underlying developmental timing, the temporal control of gene expression. Previous studies have provided considerable information about the spatial regulation of gene expression, but there is very little information regarding the temporal coordination of expression. Paused RNA Polymerase (pausd Pol II) is a pervasive feature of Drosophila embryos and mammalian stem cells, but its role in development is uncertain. We demonstrate that there is a spectrum of paused Pol II, which determines the "time to synchrony" the time required to achieve coordinate gene expression across the different cells of a tissue. To determine whether synchronous patterns of gene activation are significant in development, we manipulated the timing of snail expression, which controls the coordinated invagination of 1000 mesoderm cells during gastrulation. Replacement of the strongly paused snail promoter with moderately paused or nonpaused promoters resulted in stochastic activation of snail expression and the progressive loss of mesoderm invagination. Computational modeling of the dorsal-ventral patterning network recapitulated these variable and bistable gastrulation profiles, and emphasized the importance of timing of gene activation in development. We concluded that paused Pol II and transcriptional synchrony are essential for coordinating cell behavior during…

Subjects/Keywords: Biophysics

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

APA (6^th Edition):

Bothma, J. (2013). Mechanisms of Transcriptional Precision in the Drosophila Embryo. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/84x1d0pz

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):

Bothma, Jacques. “Mechanisms of Transcriptional Precision in the Drosophila Embryo.” 2013. Thesis, University of California – Berkeley. Accessed January 17, 2021. http://www.escholarship.org/uc/item/84x1d0pz.

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

MLA Handbook (7^th Edition):

Bothma, Jacques. “Mechanisms of Transcriptional Precision in the Drosophila Embryo.” 2013. Web. 17 Jan 2021.

Vancouver:

Bothma J. Mechanisms of Transcriptional Precision in the Drosophila Embryo. [Internet] [Thesis]. University of California – Berkeley; 2013. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/84x1d0pz.

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

Council of Science Editors:

Bothma J. Mechanisms of Transcriptional Precision in the Drosophila Embryo. [Thesis]. University of California – Berkeley; 2013. Available from: http://www.escholarship.org/uc/item/84x1d0pz

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

16. Dill, Jesse. Struts, springs and crumple zones: protein structures under force.

Degree: Biophysics, 2012, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/69r5s9s3

► In this dissertation, I describe studies on the folding and unfolding of several proteins using a combination of bulk solution spectroscopy and force denaturation experiments… (more)

Subjects/Keywords: Biophysics

10 more images…

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

APA (6^th Edition):

Dill, J. (2012). Struts, springs and crumple zones: protein structures under force. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/69r5s9s3

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):

Dill, Jesse. “Struts, springs and crumple zones: protein structures under force.” 2012. Thesis, University of California – Berkeley. Accessed January 17, 2021. http://www.escholarship.org/uc/item/69r5s9s3.

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

MLA Handbook (7^th Edition):

Dill, Jesse. “Struts, springs and crumple zones: protein structures under force.” 2012. Web. 17 Jan 2021.

Vancouver:

Dill J. Struts, springs and crumple zones: protein structures under force. [Internet] [Thesis]. University of California – Berkeley; 2012. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/69r5s9s3.

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

Council of Science Editors:

Dill J. Struts, springs and crumple zones: protein structures under force. [Thesis]. University of California – Berkeley; 2012. Available from: http://www.escholarship.org/uc/item/69r5s9s3

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

University of California – San Diego

17. Kim, Young Hun. Biophysical Study of Membrane Forming Biomaterials and Development of Novel Small Molecule Responsive Ion Channel Sensors.

Degree: Materials Sci and Engineering, 2017, University of California – San Diego

URL: http://www.escholarship.org/uc/item/02c2g9zp

► Lipids are amphiphilic molecules that naturally form membrane assemblies inaqueous conditions. Along with proteins, they are a major component in all biologicalmembranes found in archaeal,… (more)

▼ Lipids are amphiphilic molecules that naturally form membrane assemblies inaqueous conditions. Along with proteins, they are a major component in all biologicalmembranes found in archaeal, prokaryotic, and eukaryotic cells. Lipid molecules playcritical roles in controlling specific protein functions such as cell signaling and gating inthe membrane. The molecular composition of the lipids, with a hydrophilic headgroupand hydrophobic acyl tail, allow membranes to continuously and responsively change itsconfiguration to maintain these functions. In particular, the intermolecular forces andelectrostatic forces among the headgroup and tail regulate the biophysical properties of the membrane such as fluidity, compression, curvature, deformation energy, membrane packing. Studying the biophysical properties of lipid membranes is not only critical forunderstanding their fundamental biological functions in nature but also for developingpromising biomaterials. The first two chapters of this dissertation present the study ofsynthetic lipids and natural extracted lipids to understand the molecular and biophysicalfactors that influence membrane properties. Synthetic nature-inspired lipids based onarchaea membranes, with a tethered acyl chain in their hydrophobic tail part connectingtwo headgroups, were evaluated using a temperature-dependent leakage assay to understandthe effect of tethering the tail groups of two individual lipid molecules on improvingmembrane stability. The effect of the tethered chain on the membrane stability according totemperature change was analyzed by calculating the entropy of activation in transition statetheory. Next, the biophysical properties of lipid membranes were studied to understand theeffect of headgroup and tail structure on the membrane, both with synthetic phospholipidsand with natural lipid extracts. Specifically, three biophysical characteristics, i.e. lateraldiffusion of membranes, ion channel lifetimes on membranes, and effective elastic modulusof the membranes, were measured by fluorescence recovery after photobleaching, black lipidmembrane (BLM), and atomic force microscopy (AFM). In the chapter 4, the pore formationand function of the Alzheimers disease (AD) associated channel-forming protein, beta-amyloid(Abeta), was examined in Brain total lipid extract (BTLE) membranes and model membranesThe structure and ion conducting properties of Abeta were studied using BLM and AFM Theincrease in anionic lipid content in a membrane alters the formation and ion conductingbehavior of Abeta pores. The last chapter of this dissertation describes a semi-synthetic ionchannel platform capable of detecting small molecule analytes using a gramicidin A (gA).The sensor system utilizes a monoclonal antibody and its fab fragments to sequester the channel activity of a C-terminal modified gA derivative initially. By introducing a small molecule into the system, the channel activity of gA derivative was restored by competitivebinding to the antibody. The sensitivity of the system was examined by two methods:…

Subjects/Keywords: Biophysics

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APA (6^th Edition):

Kim, Y. H. (2017). Biophysical Study of Membrane Forming Biomaterials and Development of Novel Small Molecule Responsive Ion Channel Sensors. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/02c2g9zp

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):

Kim, Young Hun. “Biophysical Study of Membrane Forming Biomaterials and Development of Novel Small Molecule Responsive Ion Channel Sensors.” 2017. Thesis, University of California – San Diego. Accessed January 17, 2021. http://www.escholarship.org/uc/item/02c2g9zp.

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

MLA Handbook (7^th Edition):

Kim, Young Hun. “Biophysical Study of Membrane Forming Biomaterials and Development of Novel Small Molecule Responsive Ion Channel Sensors.” 2017. Web. 17 Jan 2021.

Vancouver:

Kim YH. Biophysical Study of Membrane Forming Biomaterials and Development of Novel Small Molecule Responsive Ion Channel Sensors. [Internet] [Thesis]. University of California – San Diego; 2017. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/02c2g9zp.

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

Council of Science Editors:

Kim YH. Biophysical Study of Membrane Forming Biomaterials and Development of Novel Small Molecule Responsive Ion Channel Sensors. [Thesis]. University of California – San Diego; 2017. Available from: http://www.escholarship.org/uc/item/02c2g9zp

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

University of California, San Francisco

18. Greenberg, Charles Harold. Inferring Optimally Precise and Maximally Accurate Models from Electron Microscopy Data.

Degree: 2016, University of California, San Francisco

URL: http://pqdtopen.proquest.com/#viewpdf?dispub=10165386

► Advances in electron microscopy (EM) allow for structure determination of large macromolecular machines at increasingly high resolutions. A key step in this process is… (more)

▼ Advances in electron microscopy (EM) allow for structure determination of large macromolecular machines at increasingly high resolutions. A key step in this process is interpreting the EM density map with structural models of maximal accuracy and optimal precision. Model precision should be determined by the uncertainty in the experimental data; however, current methods only set uncertainty in an ad hoc manner with arbitrary weight terms. Thus, there is a need for more objective methods. In Chapter 2, I present a novel Bayesian approach to modeling macromolecular structures based on EM density maps. The key advancement is the development of a scoring function that uses the local uncertainty of the density map to set the data weight and allows for correlation between neighboring density values. Unlike traditional approaches, the score does not require an expert user to set arbitrary parameters. I assessed the accuracy of models generated by this approach with a set of experimentally-derived, previously-published EM data of macromolecular complexes at varying resolutions from 3 to 6Å. I found that this approach leads to higher fluctuations in the model ensemble in locations with higher local uncertainty, and obtained accurate ensembles for a 3.2Å resolution map of Trpvl and 3.4Å and 5.4Å resolution maps of γ-secretase. In Chapter 3, I present models of the γ-tubulin small complex in two functional states based on a challenging data set consisting of low-resolution EM density maps and a remotely related structure. Here, I used a traditional scoring techniques, but extensively sampled alignments and conformations in order to ensure that the model ensemble reflected the uncertainty in the data. The resulting models form a tight cluster for each state and were consistent with a set of newly reported chemical cross-links. Comparing the two states, I found significant structural differences and predict stabilizing interactions of the two states. The work in this chapter shows the difficulties of traditional modeling and serves as motivation for the methods developed in Chapter 2. Both approaches are incorporated into the open source Integrative Modeling Platform (IMP) package, enabling integration with multiple other data types and usage of myriad sampling and analysis tools.

Subjects/Keywords: Biophysics

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APA (6^th Edition):

Greenberg, C. H. (2016). Inferring Optimally Precise and Maximally Accurate Models from Electron Microscopy Data. (Thesis). University of California, San Francisco. Retrieved from http://pqdtopen.proquest.com/#viewpdf?dispub=10165386

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):

Greenberg, Charles Harold. “Inferring Optimally Precise and Maximally Accurate Models from Electron Microscopy Data.” 2016. Thesis, University of California, San Francisco. Accessed January 17, 2021. http://pqdtopen.proquest.com/#viewpdf?dispub=10165386.

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

MLA Handbook (7^th Edition):

Greenberg, Charles Harold. “Inferring Optimally Precise and Maximally Accurate Models from Electron Microscopy Data.” 2016. Web. 17 Jan 2021.

Vancouver:

Greenberg CH. Inferring Optimally Precise and Maximally Accurate Models from Electron Microscopy Data. [Internet] [Thesis]. University of California, San Francisco; 2016. [cited 2021 Jan 17]. Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=10165386.

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

Council of Science Editors:

Greenberg CH. Inferring Optimally Precise and Maximally Accurate Models from Electron Microscopy Data. [Thesis]. University of California, San Francisco; 2016. Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=10165386

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

Temple University

19. Ayesa, Umme. CHARACTERIZATION OF THERMOSENSITIVE HYBRID ARCHAEOSOMES AND DPA-CY3[22,22]/POPC LIPOSOMES AND IN VITRO EVALUATION OF THEIR POTENTIAL USEFULNESS IN TARGETED DELIVERY AND CONTROLLED RELEASE.

Degree: PhD, 2016, Temple University

URL: http://digital.library.temple.edu/u?/p245801coll10,368614

►

Biochemistry

One of earlier challenges in treating cancer was utilizing drugs that are powerful yet do not cause severe toxicity to patients. Although the use… (more)

▼

Biochemistry

One of earlier challenges in treating cancer was utilizing drugs that are powerful yet do not cause severe toxicity to patients. Although the use of liposomal drugs has somewhat met that challenge, our objective now is to create liposomal drugs with an even better drug efficacy and further reduced toxicity. Doxorubicin hydrochloride (DXO), for example, is an anticancer drug used to treat many types of cancers, but it is toxic to the gastrointestinal tract and the heart. Encapsulating DXO into liposomes as done in the first FDA-approved liposomal DXO, Doxil, minimizes toxicity and improves the half-life, allowing more opportunities for the drug to reach the tumor. While liposomal DXO is in the market with an annual sale of approximately 450 million dollars, the addition of cholesterol and lipids with polyethylene glycol (PEG) in the formulation increase liposome stability and circulation time, but can give rise to other concerns such as potential harm to the patient and reduction in drug loading/release. In addition, in hopes of increasing drug accumulation at the diseased tissue, the use of active or targeted nanoparticles has been explored for selective drug delivery. However, despite ongoing efforts to design and test targeted nanocarriers for drug delivery, there is no known targeted liposome commercially available at this time. This illustrates that there is still room to improve the formulation of the liposomal carriers in the areas of stability, specificity to the cancer sites, and maximum drug at diseased sites. The main focus of our research is to develop novel liposomal carriers that have a higher therapeutic index and lower cytotoxicity than currently used liposomal drugs. In this research, we were able to construct two stable liposomal systems. First, we constructed a liposomal system having the ability to specifically target phosphatidylserine (PS) exposed tissues. This liposomal system contains 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and hydrophobic PS-targeting molecule bis-dipicolylamine-Zn-Cy3[C22,22] (abbreviated DPA-Cy3[22,22]). We have tested stability and PS binding ability of DPA-Cy3[22,22]/POPC liposomal carriers using light scattering and ion-exchange chromatography, respectively. In addition, with confocal microscopy and flow cytometry, we have tested DPA-Cy3[22,22]/POPC liposomes’ affinity to cancer cells. Furthermore, cell viability assay was used to determine the cytotoxic effect of DPA-Cy3[22,22]/POPC liposomes on cancer cells and non-cancer cells. In short, we found that DPA-Cy3[22,22]/POPC liposomes were stable, displayed binding to PS-exposed cells, and were taken up by PS-exposed cells inducing considerable cytoxicity. Second, we have developed and characterized the physical properties of thermosensitive liposomes made of archaeal bipolar tetraether lipids (BTL) and “conventional” monopolar diester lipids. These liposomes are also termed hybrid archaeosomes. Specifically, we used the polar lipid fraction E (PLFE) isolated from the thermoacidophilic…

Advisors/Committee Members: Chong, Parkson Lee-Gau;, Rothberg, Brad S., Gamero, Ana, Grubmeyer, Charles, Ramirez, Servio;.

Subjects/Keywords: Biophysics

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

APA (6^th Edition):

Ayesa, U. (2016). CHARACTERIZATION OF THERMOSENSITIVE HYBRID ARCHAEOSOMES AND DPA-CY3[22,22]/POPC LIPOSOMES AND IN VITRO EVALUATION OF THEIR POTENTIAL USEFULNESS IN TARGETED DELIVERY AND CONTROLLED RELEASE. (Doctoral Dissertation). Temple University. Retrieved from http://digital.library.temple.edu/u?/p245801coll10,368614

Chicago Manual of Style (16^th Edition):

Ayesa, Umme. “CHARACTERIZATION OF THERMOSENSITIVE HYBRID ARCHAEOSOMES AND DPA-CY3[22,22]/POPC LIPOSOMES AND IN VITRO EVALUATION OF THEIR POTENTIAL USEFULNESS IN TARGETED DELIVERY AND CONTROLLED RELEASE.” 2016. Doctoral Dissertation, Temple University. Accessed January 17, 2021. http://digital.library.temple.edu/u?/p245801coll10,368614.

MLA Handbook (7^th Edition):

Ayesa, Umme. “CHARACTERIZATION OF THERMOSENSITIVE HYBRID ARCHAEOSOMES AND DPA-CY3[22,22]/POPC LIPOSOMES AND IN VITRO EVALUATION OF THEIR POTENTIAL USEFULNESS IN TARGETED DELIVERY AND CONTROLLED RELEASE.” 2016. Web. 17 Jan 2021.

Vancouver:

Ayesa U. CHARACTERIZATION OF THERMOSENSITIVE HYBRID ARCHAEOSOMES AND DPA-CY3[22,22]/POPC LIPOSOMES AND IN VITRO EVALUATION OF THEIR POTENTIAL USEFULNESS IN TARGETED DELIVERY AND CONTROLLED RELEASE. [Internet] [Doctoral dissertation]. Temple University; 2016. [cited 2021 Jan 17]. Available from: http://digital.library.temple.edu/u?/p245801coll10,368614.

Council of Science Editors:

Ayesa U. CHARACTERIZATION OF THERMOSENSITIVE HYBRID ARCHAEOSOMES AND DPA-CY3[22,22]/POPC LIPOSOMES AND IN VITRO EVALUATION OF THEIR POTENTIAL USEFULNESS IN TARGETED DELIVERY AND CONTROLLED RELEASE. [Doctoral Dissertation]. Temple University; 2016. Available from: http://digital.library.temple.edu/u?/p245801coll10,368614

University of California – San Diego

20. Tiee, Nicholas Shaofeng. On the Structure and Dynamics of IL-36Ra, a Key Player in Psoriatic and Inflammatory Diseases.

Degree: Chemistry, 2018, University of California – San Diego

URL: http://www.escholarship.org/uc/item/6h4666vq

► Interleukin-36 receptor antagonist is a cytokine that recently has been implicated in psoriatic diseases. Genome wide association studies observed single point mutations in the IL36RN… (more)

▼ Interleukin-36 receptor antagonist is a cytokine that recently has been implicated in psoriatic diseases. Genome wide association studies observed single point mutations in the IL36RN gene which were associated with psoriasis patients. Characterizing how IL-36Ra works at a molecular level is critical in determining how diseases states may arise. Two observations regarding IL-36Ra were studied in detail in this work. Firstly, IL-36Ra was observed to be highly sensitive to N-terminal cleavage, in that the removal of the initiator methionine can activate the cytokine to its full activity. Secondly, IL-36Ra contains a unique disulfide bond that is not found in any related family member. Chapter 3 details the NMR (Nuclear Magnetic Resonance) assignments of IL-36Ra necessary to solve the solution structure and probe phenomena at a residue resolution. Chapter 4 details our observations of the structural changes and dynamics changes in IL-36Ra when comparing full length IL-36Ra to the N-terminal methionine cleaved IL-36Ra. Using a combination of NMR and hydrogen/deuterium we observed subtle differences in the two isoforms. The structural studies implicated the barrel structure in allowing allosteric transmission from N-terminal face to the opposite side of the molecule. Additionally, our dynamics studies revealed changes in the motions of the loops in the cap of the protein that are responsible for receptor binding. The changes were likely mediated via the residues at the cap-barrel interface which allowed changes in the barrel architecture to affect the loops in the cap subdomain.Chapter 5 details our observations of the structural changes as well as dynamics changes in IL-36Ra when comparing oxidized IL-36Ra to the reduced IL-36Ra. Our data shows that the reduced form is highly destabilized overall, and specifically in the strands local to the disulfide bond. However, H/D exchange revealed that the residue diametrically opposed to the disulfide increased in protection from exchange, whereas most other residues decreased after the removal of the disulfide bond. These observations allowed us to construct a model in which the barrel expands without the presence of a disulfideLastly, Chapter 6 details the changes in H/D protection when IL-36Ra interacts with its receptor IL-36R. Different exchange profiles were observed for the two N-terminal isoforms when interacting with IL-36R. Using the observations, we were able to build a model in which the fully active IL-36Ra likely tunes the receptor off rate through the N-terminal/2nd trefoil interface that does not exist in the less active isoform.

Subjects/Keywords: Biophysics

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

APA (6^th Edition):

Tiee, N. S. (2018). On the Structure and Dynamics of IL-36Ra, a Key Player in Psoriatic and Inflammatory Diseases. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/6h4666vq

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):

Tiee, Nicholas Shaofeng. “On the Structure and Dynamics of IL-36Ra, a Key Player in Psoriatic and Inflammatory Diseases.” 2018. Thesis, University of California – San Diego. Accessed January 17, 2021. http://www.escholarship.org/uc/item/6h4666vq.

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

MLA Handbook (7^th Edition):

Tiee, Nicholas Shaofeng. “On the Structure and Dynamics of IL-36Ra, a Key Player in Psoriatic and Inflammatory Diseases.” 2018. Web. 17 Jan 2021.

Vancouver:

Tiee NS. On the Structure and Dynamics of IL-36Ra, a Key Player in Psoriatic and Inflammatory Diseases. [Internet] [Thesis]. University of California – San Diego; 2018. [cited 2021 Jan 17]. Available from: http://www.escholarship.org/uc/item/6h4666vq.

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

Council of Science Editors:

Tiee NS. On the Structure and Dynamics of IL-36Ra, a Key Player in Psoriatic and Inflammatory Diseases. [Thesis]. University of California – San Diego; 2018. Available from: http://www.escholarship.org/uc/item/6h4666vq

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

Drexel University

21. Voelker, Matthew J. Porelike Morphologies in Amyloidogenic Proteins.

Degree: 2017, Drexel University

URL: http://hdl.handle.net/1860/idea:7570

► Intrinsically disordered proteins (IDPs) have been linked to a variety of human diseases. The roles that IDPs play in physiological functions and disease pathology are… (more)

▼ Intrinsically disordered proteins (IDPs) have been linked to a variety of human diseases. The roles that IDPs play in physiological functions and disease pathology are frequently an enigma. Their disordered nature and structural complexity presents significant experimental and computational challenges, and makes IDPs difficult to study and characterize effectively. Soluble, low molecular weight (LMW) oligomers of the IDPs amyloid beta-protein (Abeta) and alpha-synuclein (alphaS) have been hypothesized to be the primary neurotoxic agents in Alzheimer's Disease (AD) and Parkinson's Disease (PD) respectively, however their structure remains elusive. In this thesis, we take a varied computational approach in studies of Abeta and alphaS oligomers in order to probe and elucidate their structure. Aβ oligomers have been observed to impair cognition in live rats and to negatively affect memory by hindering long-term potentiation in the hippocampus. Of the two predominant Aβ alloforms, Abeta40 and Abeta42, the latter is more strongly associated with AD. Here, we structurally characterize Abeta40 and Abeta42 monomers through pentamers via a multi-scale computational approach, wherein conformations derived by discrete molecular dynamics combined with an implicit – solvent intermediate – resolution protein model and amino acid-specific interactions (DMD4B-HYDRA) were converted into all-atom conformations and subjected to explicit-solvent MD. Unlike the initial DMD4B-HYDRA conformations, fully atomistic Abeta40 and Abeta42 trimers, tetramers, and pentamers form water-permeable pores, whereby the tendency for pore formation sharply increases with oligomer order and is the highest for Abeta42 pentamers. Our findings reveal an extraordinary ability of Abeta oligomers to form pores in pure water prior to their insertion into a membrane. PD is characterized in part by the cerebral accumulation of alpha-synuclein, a 140 amino acids – long protein produced naturally in the body, into abnormal intracellular protein deposits in the brain. Soluble alphaS oligomers in particular have been shown to be toxic to neuronal cell cultures in vitro. We here characterize the structure of alphaS oligomers computationally using the DMD4B-HYDRA approach. We vary the implicit-solvent parameter corresponding to the strength of electrostatic interactions (E_CH) to fine tune the solvent conditions in order to obtain an alphaS oligomer distribution consistent with experimental data. The population of alphaS oligomers is characterized by a monotonically decreasing propensity of monomers through septamers followed by an increase in octamers. We observe that alphaS forms water-permeable pores in all assembly states, with a propensity for pore formation that increases with oligomer order. Previous studies have reported that both Abeta and alphaS oligomers form ion channels when embedded into a cellular membrane, which causes an abnormal ion flux and eventually leads to cell death. These observations form a leading theory for the mechanism behind the… Advisors/Committee Members: Urbanc, Brigita, College of Arts and Sciences.

Subjects/Keywords: Biophysics

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

APA (6^th Edition):

Voelker, M. J. (2017). Porelike Morphologies in Amyloidogenic Proteins. (Thesis). Drexel University. Retrieved from http://hdl.handle.net/1860/idea:7570

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):

Voelker, Matthew J. “Porelike Morphologies in Amyloidogenic Proteins.” 2017. Thesis, Drexel University. Accessed January 17, 2021. http://hdl.handle.net/1860/idea:7570.

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

MLA Handbook (7^th Edition):

Voelker, Matthew J. “Porelike Morphologies in Amyloidogenic Proteins.” 2017. Web. 17 Jan 2021.

Vancouver:

Voelker MJ. Porelike Morphologies in Amyloidogenic Proteins. [Internet] [Thesis]. Drexel University; 2017. [cited 2021 Jan 17]. Available from: http://hdl.handle.net/1860/idea:7570.

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

Council of Science Editors:

Voelker MJ. Porelike Morphologies in Amyloidogenic Proteins. [Thesis]. Drexel University; 2017. Available from: http://hdl.handle.net/1860/idea:7570

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

University of Oxford

22. Schneider, Falk. Plasma membrane dynamics in immune signalling.

Degree: PhD, 2020, University of Oxford

URL: http://ora.ox.ac.uk/objects/uuid:ed986cb9-5849-4bfd-88f5-e45ae95f0176 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.800182

► The cellular plasma membrane encloses all mammalian cells and is a heterogeneous structure organised on small length- and short timescales. Separation from the exterior milieu… (more)

▼ The cellular plasma membrane encloses all mammalian cells and is a heterogeneous structure organised on small length- and short timescales. Separation from the exterior milieu allows non-equilibrium processes and renders the membrane the first point of contact in cell-cell interactions or the first line of defence in cell-pathogen encounters. Unravelling the mechanisms contributing to the dynamic membrane architecture offers the opportunity to shed light on one of the biggest mysteries of cell biology: How do structure and organisation emerge from a seemingly chaotic and fluid plasma membrane? This thesis describes the development and application of new fluorescence microscopy-based methods to understand the nature of membrane heterogeneity, such as compartmentalisation to facilitate receptor engagement. Taking snapshots of cellular processes using imaging techniques yields detailed insights into the static structure of the cells, yet overlooks fast and transient interactions, which are increasingly recognised as drivers of molecular organisation. In this work, imaging and spectroscopy approaches are used together to show that molecular diffusion dynamics can serve as a readout for membrane heterogeneity. A combination of super-resolution stimulated emission depletion (STED) microscopy and fluorescence correlation spectroscopy (FCS) is employed to obtain dynamic information at the nano-scale and developed further to measure the diffusion behaviour of lipids and proteins in living cells and model membrane systems across space at sub-diffraction resolution. Special emphasis is given to the evaluation of new detection equipment allowing flexible, robust, and easy-to-perform measurements. Additionally, a novel analysis pipeline based on confocal FCS is introduced to enable advanced diffusion measurements in live cell membranes with conventional equipment. Finally, the developed approaches are exploited to elucidate the organisation of a crucial T-cell signalling protein, the Src-kinase Lck, in model membrane systems as well as in live resting T cells and during their activation.

Subjects/Keywords: Biophysics

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APA (6^th Edition):

Schneider, F. (2020). Plasma membrane dynamics in immune signalling. (Doctoral Dissertation). University of Oxford. Retrieved from http://ora.ox.ac.uk/objects/uuid:ed986cb9-5849-4bfd-88f5-e45ae95f0176 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.800182

Chicago Manual of Style (16^th Edition):

Schneider, Falk. “Plasma membrane dynamics in immune signalling.” 2020. Doctoral Dissertation, University of Oxford. Accessed January 17, 2021. http://ora.ox.ac.uk/objects/uuid:ed986cb9-5849-4bfd-88f5-e45ae95f0176 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.800182.

MLA Handbook (7^th Edition):

Schneider, Falk. “Plasma membrane dynamics in immune signalling.” 2020. Web. 17 Jan 2021.

Vancouver:

Schneider F. Plasma membrane dynamics in immune signalling. [Internet] [Doctoral dissertation]. University of Oxford; 2020. [cited 2021 Jan 17]. Available from: http://ora.ox.ac.uk/objects/uuid:ed986cb9-5849-4bfd-88f5-e45ae95f0176 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.800182.

Council of Science Editors:

Schneider F. Plasma membrane dynamics in immune signalling. [Doctoral Dissertation]. University of Oxford; 2020. Available from: http://ora.ox.ac.uk/objects/uuid:ed986cb9-5849-4bfd-88f5-e45ae95f0176 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.800182

23. Maulbetsch, William. Nanopore Mass Spectrometry.

Degree: Department of Physics, 2018, Brown University

URL: https://repository.library.brown.edu/studio/item/bdr:792908/

► My research is motivated by an idea for a new method of sequencing individual biopolymers, including proteins and nucleic acids, that combines mass spectrometry with… (more)

▼ My research is motivated by an idea for a new method of sequencing individual biopolymers, including proteins and nucleic acids, that combines mass spectrometry with nanopores. The basic idea is to take advantage of a mass spectrometer’s ability to identify monomers by their mass, paired with a nanopore’s ability to force biopolymers into a linear configuration so that their monomers are delivered into the mass spectrometer in sequence. I address two major challenges for such a method to succeed. First, monomers must be ionized and transferred to the gas phase, necessary for mass analysis. Second, before monomers are transferred into vacuum, but after they are cleaved in solution from their parent polymer, they undergo random thermal motion which tends to randomize their sequential order. This order between neighboring monomers must be preserved between when they are cleaved and when they exit into this charged gas phase. If a strong electric field is applied to the liquid surface at the tip of a solution filled needle-like capillary, it will emit a spray of ions through a process known as electrospray. Ions emitted in this spray can leave the liquid surface in two main ways. They can leave inside large multiply charged liquid drops usually on the order of 100's nm in diameter, or they can leave the surface individually as partially solvated ions, called ion clusters. Since monomer ions trapped in drops would prevent us from obtaining sequence information, I conducted experiments on a version of electrospray known as ion evaporation in which ion clusters in solution are emitted directly from the electrospray capillary’s liquid surface. I have helped to build and test a machine capable of investigating this mechanism of ion production from electrospray using capillaries with nanoscale tip openings. I present measurements of the voltages necessary to produce electrospray for capillaries in this nanoscale regime. Generally, the electrospray is composed of both ion clusters and charged droplets, and the latter must be suppressed for the success of this sequencing strategy. I compare the number of ion clusters that reach our mass spectrometer with the total number of ions leaving our nanocapillaries to explore the conditions under which ion cluster production is favored over drop formation. Finally, I present a simplified one dimensional model of the dynamics of Brownian particles in the electric fields at the tips of these electrospraying capillaries to estimate the conditions under which sequential information is preserved. Advisors/Committee Members: Stein, Derek (Advisor), Ying, See-Chen (Reader), Mandre, Shreyas (Reader).

Subjects/Keywords: Biophysics

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

APA (6^th Edition):

Maulbetsch, W. (2018). Nanopore Mass Spectrometry. (Thesis). Brown University. Retrieved from https://repository.library.brown.edu/studio/item/bdr:792908/

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):

Maulbetsch, William. “Nanopore Mass Spectrometry.” 2018. Thesis, Brown University. Accessed January 17, 2021. https://repository.library.brown.edu/studio/item/bdr:792908/.

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

MLA Handbook (7^th Edition):

Maulbetsch, William. “Nanopore Mass Spectrometry.” 2018. Web. 17 Jan 2021.

Vancouver:

Maulbetsch W. Nanopore Mass Spectrometry. [Internet] [Thesis]. Brown University; 2018. [cited 2021 Jan 17]. Available from: https://repository.library.brown.edu/studio/item/bdr:792908/.

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

Council of Science Editors:

Maulbetsch W. Nanopore Mass Spectrometry. [Thesis]. Brown University; 2018. Available from: https://repository.library.brown.edu/studio/item/bdr:792908/

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

24. Fan, Yi. Three-dimensional measurements of dynamics and structure in kinesin-driven active fluids.

Degree: School of Engineering, 2018, Brown University

URL: https://repository.library.brown.edu/studio/item/bdr:792895/

► Active matter systems remain in a far-from-equilibrium state due to the motion generated at small scales by their self-driven constituents. These systems can exhibit complex… (more)

▼ Active matter systems remain in a far-from-equilibrium state due to the motion generated at small scales by their self-driven constituents. These systems can exhibit complex behavior, such as collective motion and pattern formation, and understanding the governing principles of active matter systems is tremendously challenging. The active fluids studied here are artificial systems assembled from kinesin-driven bundled microtubule networks. We focus on characterizing the three-dimensional dynamical behavior and structure of the active fluids, subject to different confining geometries. The systems are measured using an epi-fluorescence microscope equipped with two-color fluorescent imaging and synchronized z-scanning. The fluorescently-labeled microtubules (red) and the dispersed passive fluorescent tracer particles (blue) are simultaneously observed at multiple z-positions. A three-dimensional tracking method, using the Airy disks of diffracted particles, extends the measurement to the entire observation volume. The active systems exhibit transitions between two dynamical states — a chaotic turbulent state and a coherent state — depending on the confining geometry. The turbulent flows have no net transport while, in contrast, the coherent flows exhibit long-term self-pumping motion. We find that the self-pumping motion correlates with a three-dimensional flow structure, which is affected by the dimension and the surface treatment of the confinement. Besides, the coherent flows can be scaled across different dimensions and surface conditions. The influence of boundaries is further studied in the chaotic turbulent state of bulk active systems. Far from confining boundaries, the active systems exhibit small-scale isotropy, however, we obtain evidence of large-scale collective motion that extends beyond the scale of our measurement. As the confinement increases, the active systems preserve the small-scale isotropy, but demonstrate increasing large-scale anisotropy, a decrease in the temporal correlation (flow "memory") and a reduction in the characteristic size of the structure. Lastly, our results show that the large-scale dynamics in the active systems, either in the turbulent state or in the coherent state, hardly affect the micrometer-scale interaction between an active microtubule bundle and the motion of its nearby passive tracer particles. Advisors/Committee Members: Breuer, Kenneth S. (Advisor), Powers, Thomas R. (Reader), Tang, Jay X. (Reader).

Subjects/Keywords: Biophysics

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APA (6^th Edition):

Fan, Y. (2018). Three-dimensional measurements of dynamics and structure in kinesin-driven active fluids. (Thesis). Brown University. Retrieved from https://repository.library.brown.edu/studio/item/bdr:792895/

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):

Fan, Yi. “Three-dimensional measurements of dynamics and structure in kinesin-driven active fluids.” 2018. Thesis, Brown University. Accessed January 17, 2021. https://repository.library.brown.edu/studio/item/bdr:792895/.

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

MLA Handbook (7^th Edition):

Fan, Yi. “Three-dimensional measurements of dynamics and structure in kinesin-driven active fluids.” 2018. Web. 17 Jan 2021.

Vancouver:

Fan Y. Three-dimensional measurements of dynamics and structure in kinesin-driven active fluids. [Internet] [Thesis]. Brown University; 2018. [cited 2021 Jan 17]. Available from: https://repository.library.brown.edu/studio/item/bdr:792895/.

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

Council of Science Editors:

Fan Y. Three-dimensional measurements of dynamics and structure in kinesin-driven active fluids. [Thesis]. Brown University; 2018. Available from: https://repository.library.brown.edu/studio/item/bdr:792895/

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

25. Qu, Zijie. Flagellated bacteria swimming in polymer solutions.

Degree: Fluids and Thermal Sciences, 2018, Brown University

URL: https://repository.library.brown.edu/studio/item/bdr:792806/

► The research is motivated by some previously-reported conflicting observations and explanations regarding the motility of flagellated bacteria swimming in polymer solutions. Three-dimensional real-time tracking microscopy… (more)

Subjects/Keywords: Biophysics

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APA (6^th Edition):

Qu, Z. (2018). Flagellated bacteria swimming in polymer solutions. (Thesis). Brown University. Retrieved from https://repository.library.brown.edu/studio/item/bdr:792806/

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):

Qu, Zijie. “Flagellated bacteria swimming in polymer solutions.” 2018. Thesis, Brown University. Accessed January 17, 2021. https://repository.library.brown.edu/studio/item/bdr:792806/.

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

MLA Handbook (7^th Edition):

Qu, Zijie. “Flagellated bacteria swimming in polymer solutions.” 2018. Web. 17 Jan 2021.

Vancouver:

Qu Z. Flagellated bacteria swimming in polymer solutions. [Internet] [Thesis]. Brown University; 2018. [cited 2021 Jan 17]. Available from: https://repository.library.brown.edu/studio/item/bdr:792806/.

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

Council of Science Editors:

Qu Z. Flagellated bacteria swimming in polymer solutions. [Thesis]. Brown University; 2018. Available from: https://repository.library.brown.edu/studio/item/bdr:792806/

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

Purdue University

26. Lin, David Yin-wei. Biochemical and Structural Studies of a HECT-Like Ubiquitin Ligase from E. Coli O157|H7.

Degree: 2016, Purdue University

URL: http://pqdtopen.proquest.com/#viewpdf?dispub=10160100

► Many microbial pathogens deliver effector proteins, via type III secretion system, into infected host cells. Elucidating the function of these effectors is essential for… (more)

▼ Many microbial pathogens deliver effector proteins, via type III secretion system, into infected host cells. Elucidating the function of these effectors is essential for our understanding of pathogenesis. Here I describe biochemical and structural characterization of an effector protein (NleL) from E. coli O157:H7, a widespread pathogen causing severe food borne diseases. NleL functionally and structurally mimics eukaryotic HECT E3 ligases and catalyzes formation of unanchored polyubiquitin chains using K6 and K48 linkage. The catalytic cysteine residue forms a thioester intermediate with ubiquitin. The structure of NleL contains two domains, a β-helix domain formed by pentapeptide repeats and a bilobed catalytic domain reminiscent of the N- and C-lobe architecture of HECT E3sstructures of NleL observed in two crystal forms revealed a large range of different positions of the C-lobe relative to the N-lobe, indicating that the helix linking the two lobes is extremely flexible. Comparing the structure of NleL with that of the Salmonella homolog SopA showed that the orientation of the C-lobes differ by as much as 108?, suggesting that large movements of the C-lobe may be required to facilitate the transfer of ubiquitin from E2 to the substrate. In the structure of NleL/UbcH7 complex, UbcH7 binds at the end of the N-lobe that is closer to the C-lobe as observed in the structure of SopA/UbcH7 complex. The conserved phenylalanine of E2s (Phe63 of UbcH7) is involved heavily in the binding. The C-lobe of NleL in the complex rotates as much as ~168? towards UbcH7 compared with the structures of the isolated NleLs and the catalytic cysteines of E2 and E3 are within 7? of each other. In the structure of SopA/UbcH7 complex, the C-lobe bends towards the putative substrate binding domain (β-helix domain). The orientation of the C-lobes in the NleL and SopA complexes differs by ~180?, demonstrating that large movements of the C-lobes are possible, and the two complexes could represent two different stages of the transfer of ubiquitin from E2 to the substrate. These results provide critical knowledge towards understanding the molecular mechanism by which pathogens utilize the host ubiquitination system during infection.

Subjects/Keywords: Biophysics

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

APA (6^th Edition):

Lin, D. Y. (2016). Biochemical and Structural Studies of a HECT-Like Ubiquitin Ligase from E. Coli O157|H7. (Thesis). Purdue University. Retrieved from http://pqdtopen.proquest.com/#viewpdf?dispub=10160100

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):

Lin, David Yin-wei. “Biochemical and Structural Studies of a HECT-Like Ubiquitin Ligase from E. Coli O157|H7.” 2016. Thesis, Purdue University. Accessed January 17, 2021. http://pqdtopen.proquest.com/#viewpdf?dispub=10160100.

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

MLA Handbook (7^th Edition):

Lin, David Yin-wei. “Biochemical and Structural Studies of a HECT-Like Ubiquitin Ligase from E. Coli O157|H7.” 2016. Web. 17 Jan 2021.

Vancouver:

Lin DY. Biochemical and Structural Studies of a HECT-Like Ubiquitin Ligase from E. Coli O157|H7. [Internet] [Thesis]. Purdue University; 2016. [cited 2021 Jan 17]. Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=10160100.

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

Council of Science Editors:

Lin DY. Biochemical and Structural Studies of a HECT-Like Ubiquitin Ligase from E. Coli O157|H7. [Thesis]. Purdue University; 2016. Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=10160100

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

27. Doktorova, Milka N. Biophysics of Asymmetric Membranes| Protocols and Revelations.

Degree: 2018, Weill Medical College of Cornell University

URL: http://pqdtopen.proquest.com/#viewpdf?dispub=10844615

► Lipid membranes enclose cells and organelles, and actively participate in cellular processes. Their many functional roles require tight regulation of properties including structure and… (more)

▼ Lipid membranes enclose cells and organelles, and actively participate in cellular processes. Their many functional roles require tight regulation of properties including structure and dynamics. Cells achieve this by producing and dynamically tuning the concentration and organization of hundreds of structurally different types of lipid molecules in the various cellular membranes. The cell-bounding plasma membranes of eukaryotes in particular, exhibit an actively maintained asymmetric lipid distribution across their two leaflets. In addition to exposing certain types of lipids to the extracellular space or intracellular milieu, this specialized transbilayer lipid arrangement also affects the properties of the membrane itself and its interactions with proteins, in ways that are difficult to explore and thus not understood. To address this problem and enable further advancements in the field, we have developed both in vitro and in silico protocols for building asymmetric model membranes with finely controlled lipid compositions. These protocols allowed us to investigate the dynamics, energetics and structural consequences of interleaflet communication: with small-angle scattering we uncovered asymmetry-mediated changes in the lipid packing of individual leaflets in free-floating liposomes; with electron spin resonance we revealed the ensuing trends in lipid order; and nuclear magnetic resonance helped us bring new appreciation of the interplay between asymmetric bilayers and transmembrane protein inclusions. To interpret and better understand the experimental observations, we developed a new in silico protocol for constructing atomistic models of tension-free asymmetric bilayers and used it to simulate the experimentally measured membranes and validate the simulation conditions. By devising a novel computational framework for calculating the compressibility of individual bilayer leaflets, we analyzed the energetics of protein interaction with the asymmetric membranes and obtained an estimate of the elastic energy of mixing the two leaflets. Together with additional experimental and computational studies of symmetric membrane systems, the results revealed fascinating ways in which cells can mediate the functional diversity of their membranes. The new methods and protocols leading to these insights generate previously unattainable opportunities for dissecting and exploring membrane-mediated cellular processes.

Subjects/Keywords: Biophysics

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APA (6^th Edition):

Doktorova, M. N. (2018). Biophysics of Asymmetric Membranes| Protocols and Revelations. (Thesis). Weill Medical College of Cornell University. Retrieved from http://pqdtopen.proquest.com/#viewpdf?dispub=10844615

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):

Doktorova, Milka N. “Biophysics of Asymmetric Membranes| Protocols and Revelations.” 2018. Thesis, Weill Medical College of Cornell University. Accessed January 17, 2021. http://pqdtopen.proquest.com/#viewpdf?dispub=10844615.

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

MLA Handbook (7^th Edition):

Doktorova, Milka N. “Biophysics of Asymmetric Membranes| Protocols and Revelations.” 2018. Web. 17 Jan 2021.

Vancouver:

Doktorova MN. Biophysics of Asymmetric Membranes| Protocols and Revelations. [Internet] [Thesis]. Weill Medical College of Cornell University; 2018. [cited 2021 Jan 17]. Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=10844615.

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

Council of Science Editors:

Doktorova MN. Biophysics of Asymmetric Membranes| Protocols and Revelations. [Thesis]. Weill Medical College of Cornell University; 2018. Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=10844615

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

Harvard University

28. Xu, Jiabin. Computer Simulations of Protein Folding and Evolution.

Degree: PhD, Chemical Physics, 2013, Harvard University

URL: http://nrs.harvard.edu/urn-3:HUL.InstRepos:11169764

► Computer simulations for investigating protein folding and evolution are presented. In chapter 1, an all-atom model with a knowledge-based potential is used to study the… (more)

Subjects/Keywords: Biophysics

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APA (6^th Edition):

Xu, J. (2013). Computer Simulations of Protein Folding and Evolution. (Doctoral Dissertation). Harvard University. Retrieved from http://nrs.harvard.edu/urn-3:HUL.InstRepos:11169764

Chicago Manual of Style (16^th Edition):

Xu, Jiabin. “Computer Simulations of Protein Folding and Evolution.” 2013. Doctoral Dissertation, Harvard University. Accessed January 17, 2021. http://nrs.harvard.edu/urn-3:HUL.InstRepos:11169764.

MLA Handbook (7^th Edition):

Xu, Jiabin. “Computer Simulations of Protein Folding and Evolution.” 2013. Web. 17 Jan 2021.

Vancouver:

Xu J. Computer Simulations of Protein Folding and Evolution. [Internet] [Doctoral dissertation]. Harvard University; 2013. [cited 2021 Jan 17]. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:11169764.

Council of Science Editors:

Xu J. Computer Simulations of Protein Folding and Evolution. [Doctoral Dissertation]. Harvard University; 2013. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:11169764

Harvard University

29. Liu, Julia Chang. DNA-damage-induced apoptosis in stem and cancer cells.

Degree: PhD, Biophysics, 2014, Harvard University

URL: http://nrs.harvard.edu/urn-3:HUL.InstRepos:12274582

► This work comprises analyses of cell fate decision-making in response to DNA damage. DNA damage is a ubiquitous threat to genomic stability, and depending on… (more)

Subjects/Keywords: Biophysics

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APA (6^th Edition):

Liu, J. C. (2014). DNA-damage-induced apoptosis in stem and cancer cells. (Doctoral Dissertation). Harvard University. Retrieved from http://nrs.harvard.edu/urn-3:HUL.InstRepos:12274582

Chicago Manual of Style (16^th Edition):

Liu, Julia Chang. “DNA-damage-induced apoptosis in stem and cancer cells.” 2014. Doctoral Dissertation, Harvard University. Accessed January 17, 2021. http://nrs.harvard.edu/urn-3:HUL.InstRepos:12274582.

MLA Handbook (7^th Edition):

Liu, Julia Chang. “DNA-damage-induced apoptosis in stem and cancer cells.” 2014. Web. 17 Jan 2021.

Vancouver:

Liu JC. DNA-damage-induced apoptosis in stem and cancer cells. [Internet] [Doctoral dissertation]. Harvard University; 2014. [cited 2021 Jan 17]. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:12274582.

Council of Science Editors:

Liu JC. DNA-damage-induced apoptosis in stem and cancer cells. [Doctoral Dissertation]. Harvard University; 2014. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:12274582

Wayne State University

30. Gunther, Laura. The Effects Of The N-Terminal Extensions Of Cardiac Troponins On The Ca2+ Regulation Of Myosin Atpase Kinetics In Cardiac Myofibrils.

Degree: PhD, Physics and Astronomy, 2016, Wayne State University

URL: https://digitalcommons.wayne.edu/oa_dissertations/1539

► Contraction of cardiac muscle is the basis of heart function. Heart failure, i.e., weakened contraction of cardiac muscle is the most common cause of… (more)

▼ Contraction of cardiac muscle is the basis of heart function. Heart failure, i.e., weakened contraction of cardiac muscle is the most common cause of morbidity and mortality of heart diseases. Cardiac muscle contraction is regulated by calcium via the function of troponin, a protein complex associated with the myofilaments in muscle cells. The cardiac troponin subunits T (cTnT) and I (cTnI) have unique N-terminal extensions that can be selectively removed by restrictive proteolysis during cardiac adaptation to physiological and pathological stresses, indicating a role of these proteins in modulating cardiac contraction. This study aims to understand the effects of the N-terminal extensions of cTnT and cTnI on the actomyosin ATPase kinetics in response to Ca2+ signal, which is the foundation of cardiac muscle power generation. The ATP binding and ADP dissociation rates of the actomyosin ATPase of cardiac myofibrils containing cTnI lacking the N-terminal extension (cTnI-ND) have been measured using stopped flowmetry with mant-dATP and mant-dADP, respectively. The results showed that the second order mant-dATP binding rate for cTnI-ND myofibrils was three-fold as fast as that of wild type myofibrils. Moreover, the ADP dissociation rate of cTnI-ND myofibrils was positively dependent on calcium concentrations, while the wild type controls were not significantly affected. Further studies will be performed to determine the other steps of the ATPase cycle in cTnI-ND myofibrils, as well as the kinetic properties of cardiac myofibrils of which the N-terminus of cTnT has been genetically removed. The anticipated results will determine the rate-limiting steps of actomyosin ATPase cycle that are regulated by the N-terminal extensions of cTnI and cTnT. Completion of the proposed study will lead to new understanding of the function of the N-terminal segments of cTnI and cTnT as well as troponin-tropomyosin-mediated regulation of cardiac muscle contraction, which in turn, may provide useful information for the development of new treatment for heart failure. Advisors/Committee Members: Takeshi Sakamoto, Jian-Ping Jin.

Subjects/Keywords: Biophysics

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APA (6^th Edition):

Gunther, L. (2016). The Effects Of The N-Terminal Extensions Of Cardiac Troponins On The Ca2+ Regulation Of Myosin Atpase Kinetics In Cardiac Myofibrils. (Doctoral Dissertation). Wayne State University. Retrieved from https://digitalcommons.wayne.edu/oa_dissertations/1539

Chicago Manual of Style (16^th Edition):

Gunther, Laura. “The Effects Of The N-Terminal Extensions Of Cardiac Troponins On The Ca2+ Regulation Of Myosin Atpase Kinetics In Cardiac Myofibrils.” 2016. Doctoral Dissertation, Wayne State University. Accessed January 17, 2021. https://digitalcommons.wayne.edu/oa_dissertations/1539.

MLA Handbook (7^th Edition):

Gunther, Laura. “The Effects Of The N-Terminal Extensions Of Cardiac Troponins On The Ca2+ Regulation Of Myosin Atpase Kinetics In Cardiac Myofibrils.” 2016. Web. 17 Jan 2021.

Vancouver:

Gunther L. The Effects Of The N-Terminal Extensions Of Cardiac Troponins On The Ca2+ Regulation Of Myosin Atpase Kinetics In Cardiac Myofibrils. [Internet] [Doctoral dissertation]. Wayne State University; 2016. [cited 2021 Jan 17]. Available from: https://digitalcommons.wayne.edu/oa_dissertations/1539.

Council of Science Editors:

Gunther L. The Effects Of The N-Terminal Extensions Of Cardiac Troponins On The Ca2+ Regulation Of Myosin Atpase Kinetics In Cardiac Myofibrils. [Doctoral Dissertation]. Wayne State University; 2016. Available from: https://digitalcommons.wayne.edu/oa_dissertations/1539

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Open Access Theses and Dissertations