Matching Items (271)
Filtering by
- All Subjects: Chemistry
- Creators: Arizona State University
Description
Serial crystallography (SX) is a relatively new structural biology technique that collects X-ray diffraction data from microcrystals via femtosecond pulses produced by an X-ray free electron laser (X-FEL) or by synchrotron radiation, allowing for challenging protein structures to be solved from microcrystals at room temperature. Because of the youth of this technique, method development is necessary for it to achieve its full potential.
Most serial crystallography experiments have relied on delivering sample in the mother liquor focused into a stream by compressed gas. This liquid stream moves at a fast rate, meaning that most of the valuable sample is wasted. For this reason, the liquid jet can require 10-100 milligrams of sample for a complete data set. Agarose has been developed as a slow moving microcrystal carrier to decrease sample consumption and waste. The agarose jet provides low background, no Debye-Sherrer rings, is compatible for sample delivery in vacuum environments, and is compatible with a wide variety of crystal systems. Additionally, poly(ethylene oxide) which is amenable for data collection in atmosphere has been developed for synchrotron experiments. Thus this work allows sample limited proteins of difficult to crystallize systems to be investigated by serial crystallography.
Time-resolved serial X-ray crystallography (TR-SX) studies have only been employed to study light-triggered reactions in photoactive systems. While these systems are very important, most proteins in Nature are not light-driven. However, fast mixing of two liquids, such as those containing enzyme protein crystals and substrates, immediately before being exposed to an X-ray beam would allow conformational changes and /or intermediates to be seen by diffraction. As a model, 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase (KDO8PS), has been developed for TR-SX. This enzyme initializes the first step of lipopolysaccharide synthesis by a net aldol condensation between arabinose-5-phosphate, phosphoenol pyruvate, and water. During this reaction, a short lived intermediate is formed and has been observed on a millisecond timescale using other methods. Thus KDO8PS is an ideal model protein for studying diffusion times into a crystal and short mixing times (<10 ms). For these experiments, microcrystals diffracting to high resolution have been developed and characterized.
Most serial crystallography experiments have relied on delivering sample in the mother liquor focused into a stream by compressed gas. This liquid stream moves at a fast rate, meaning that most of the valuable sample is wasted. For this reason, the liquid jet can require 10-100 milligrams of sample for a complete data set. Agarose has been developed as a slow moving microcrystal carrier to decrease sample consumption and waste. The agarose jet provides low background, no Debye-Sherrer rings, is compatible for sample delivery in vacuum environments, and is compatible with a wide variety of crystal systems. Additionally, poly(ethylene oxide) which is amenable for data collection in atmosphere has been developed for synchrotron experiments. Thus this work allows sample limited proteins of difficult to crystallize systems to be investigated by serial crystallography.
Time-resolved serial X-ray crystallography (TR-SX) studies have only been employed to study light-triggered reactions in photoactive systems. While these systems are very important, most proteins in Nature are not light-driven. However, fast mixing of two liquids, such as those containing enzyme protein crystals and substrates, immediately before being exposed to an X-ray beam would allow conformational changes and /or intermediates to be seen by diffraction. As a model, 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase (KDO8PS), has been developed for TR-SX. This enzyme initializes the first step of lipopolysaccharide synthesis by a net aldol condensation between arabinose-5-phosphate, phosphoenol pyruvate, and water. During this reaction, a short lived intermediate is formed and has been observed on a millisecond timescale using other methods. Thus KDO8PS is an ideal model protein for studying diffusion times into a crystal and short mixing times (<10 ms). For these experiments, microcrystals diffracting to high resolution have been developed and characterized.
ContributorsConrad, Chelsie E (Author) / Fromme, Petra (Thesis advisor) / Ros, Alexandra (Committee member) / Allen, James (Committee member) / Arizona State University (Publisher)
Created2016
Description
Multivalency is an important phenomenon that guides numerous biological interactions. It has been utilized in design of therapeutics and drug candidates. Hence, this study attempts to develop analytical tools to study multivalent interactions and design multivalent ligands for drug delivery and therapeutic applications.
Atomic Force Microscopy (AFM) has been envisioned as a means of nanodiagnostics due to its single molecule sensitivity. However, the AFM based recognition imaging lacks a multiplex capacity to detect multiple analytes in a single test. Also there is no user friendly wet chemistry to functionalize AFM tips. Hence, an uncatalyzed Click Chemistry protocol was developed to functionalize AFM tips. For multiplexed recognition imaging, recognition heads based on a C3 symmetrical three arm linker with azide functionalities at its ends were synthesized and the chemistry to attach them to AFM tips was developed, and these recognition heads were used in detecting multiple proteins simultaneously using AFM.
A bis-Angiopeptide-2 conjugate with this three-arm linker was synthesized and this was conjugated with anti-West Nile virus antibody E16 site specifically to target advanced West Nile virus infection in the Central Nervous System. The bis-Angiopeptide-2 conjugate of the antibody shows higher efficacy compared to a linear linker-Angiopeptide-2 conjugate of the antibody in in vitro studies and currently the efficacy of this antibody conjugate in studied in mice. Surface Plasmon Resonance imaging (SPRi) results indicate that the conjugation does not affect the antigen binding activity of the antibody very significantly.
A Y-shaped bisbiotin ligand was also prepared as a small sized antibody mimic. Compared to a monovalent biotin ligand, the y-Bisbiotin can cooperatively form a significantly more stable complex with streptavidin through intramolecular bivalent interactions, which were demonstrated by gel electrophoresis, SPR and AFM. Continuing on these lines, a four-arm linker was synthesized containing three single chain variable fragments (scFv) linked to the scaffold to form a tripod base, which would allow them to concomitantly interact with a trimeric Glycoprotein (GP) spike that has a “chalice” configuration. Meanwhile, a human IgG1 Fc is to be installed on the top of the tetrahedron, exerting effector functions of a monoclonal antibody.
Atomic Force Microscopy (AFM) has been envisioned as a means of nanodiagnostics due to its single molecule sensitivity. However, the AFM based recognition imaging lacks a multiplex capacity to detect multiple analytes in a single test. Also there is no user friendly wet chemistry to functionalize AFM tips. Hence, an uncatalyzed Click Chemistry protocol was developed to functionalize AFM tips. For multiplexed recognition imaging, recognition heads based on a C3 symmetrical three arm linker with azide functionalities at its ends were synthesized and the chemistry to attach them to AFM tips was developed, and these recognition heads were used in detecting multiple proteins simultaneously using AFM.
A bis-Angiopeptide-2 conjugate with this three-arm linker was synthesized and this was conjugated with anti-West Nile virus antibody E16 site specifically to target advanced West Nile virus infection in the Central Nervous System. The bis-Angiopeptide-2 conjugate of the antibody shows higher efficacy compared to a linear linker-Angiopeptide-2 conjugate of the antibody in in vitro studies and currently the efficacy of this antibody conjugate in studied in mice. Surface Plasmon Resonance imaging (SPRi) results indicate that the conjugation does not affect the antigen binding activity of the antibody very significantly.
A Y-shaped bisbiotin ligand was also prepared as a small sized antibody mimic. Compared to a monovalent biotin ligand, the y-Bisbiotin can cooperatively form a significantly more stable complex with streptavidin through intramolecular bivalent interactions, which were demonstrated by gel electrophoresis, SPR and AFM. Continuing on these lines, a four-arm linker was synthesized containing three single chain variable fragments (scFv) linked to the scaffold to form a tripod base, which would allow them to concomitantly interact with a trimeric Glycoprotein (GP) spike that has a “chalice” configuration. Meanwhile, a human IgG1 Fc is to be installed on the top of the tetrahedron, exerting effector functions of a monoclonal antibody.
ContributorsManna, Saikat (Author) / Lindsay, Stuart (Thesis advisor) / Zhang, Peiming (Thesis advisor) / Gould, Ian (Committee member) / Stephanopoulos, Nicholas (Committee member) / Arizona State University (Publisher)
Created2016
Description
This work demonstrates a capable reverse pulse deposition methodology to influence gap fill behavior inside microvia along with a uniform deposit in the fine line patterned regions for substrate packaging applications. Interconnect circuitry in IC substrate packages comprises of stacked microvia that varies in depth from 20µm to 100µm with an aspect ratio of 0.5 to 1.5 and fine line patterns defined by photolithography. Photolithography defined pattern regions incorporate a wide variety of feature sizes including large circular pad structures with diameter of 20µm - 200µm, fine traces with varying widths of 3µm - 30µm and additional planar regions to define a IC substrate package. Electrodeposition of copper is performed to establish the desired circuit. Electrodeposition of copper in IC substrate applications holds certain unique challenges in that they require a low cost manufacturing process that enables a void-free gap fill inside the microvia along with uniform deposition of copper on exposed patterned regions. Deposition time scales to establish the desired metal thickness for such packages could range from several minutes to few hours. This work showcases a reverse pulse electrodeposition methodology that achieves void-free gap fill inside the microvia and uniform plating in FLS (Fine Lines and Spaces) regions with significantly higher deposition rates than traditional approaches. In order to achieve this capability, systematic experimental and simulation studies were performed. A strong correlation of independent parameters that govern the electrodeposition process such as bath temperature, reverse pulse plating parameters and the ratio of electrolyte concentrations is shown to the deposition kinetics and deposition uniformity in fine patterned regions and gap fill rate inside the microvia. Additionally, insight into the physics of via fill process is presented with secondary and tertiary current simulation efforts. Such efforts lead to show “smart” control of deposition rate at the top and bottom of via to avoid void formation. Finally, a parametric effect on grain size and the ensuing copper metallurgical characteristics of bulk copper is also shown to enable high reliability substrate packages for the IC packaging industry.
ContributorsGanesan, Kousik (Author) / Tasooji, Amaneh (Thesis advisor) / Manepalli, Rahul (Committee member) / Alford, Terry (Committee member) / Chan, Candace (Committee member) / Arizona State University (Publisher)
Created2018
ContributorsMontilla, Jorge (Performer) / Tescarollo, Hamilton (Performer) / ASU Library. Music Library (Publisher)
Created2006-10-15
ContributorsMontilla, Jorge (Conductor) / Barefield, Robert (Performer) / Lehr, Natalie (Performer) / Lynch, Evan (Performer) / Clarinet Choir (Performer) / ASU Library. Music Library (Publisher)
Created2006-11-05
ContributorsMontilla, Jorge (Performer) / Undergraduate Clarinet Quartet (Performer) / Graduate Clarinet Quartet (Performer) / Clarinet Choir (Performer) / ASU Library. Music Library (Publisher)
Created2005-04-02
ContributorsVanOosthuyse, Eddy (Performer) / Montilla, Jorge (Performer) / Spring, Robert (Performer) / Campbell, Andrew (Pianist) (Performer) / Cosand, Walter, 1950- (Performer) / ASU Library. Music Library (Publisher)
Created2005-04-02
ContributorsNovak, Gail (Pianist) (Performer) / Paul, Evan C. (Performer) / Balzer, Shawna (Performer) / Rivas, Veronica (Performer) / McQuade, Jennifer (Performer) / Forney, Margaret (Performer) / MacWillie, Leslie (Performer) / Ratliff, Trevor (Performer) / Atchison, Jeff (Performer) / Ward, Ethan (Performer) / Karaffa, Patricia (Performer) / Clarinet Choir (Performer) / ASU Library. Music Library (Publisher)
Created2010-04-24
ContributorsMontilla, Jorge (Performer) / Novak, Gail (Pianist) (Performer) / Spring, Robert (Performer) / Montilla, Javier (Performer) / ASU Library. Music Library (Publisher)
Created2004-10-03
Description
Sexual minority youth experience significant health and mental health disparities compared to their heterosexual peers. Positive family relationships and effective parenting practices have been found to promote youth’s well-being broadly; however, there has been very little research conducted within the sexual and gender minority (SGM) populations. Furthermore, even though parental/familial acceptance of youth’s SGM identity has been consistently shown to be associated with better youth’s adjustment, very few studies have examined how the broader general parenting and familial processes intersect with SGM-acceptance. Hence, the aim of this study was to first examine the associations between (a) general parenting practices and family environment (i.e., positive parenting, negative parenting, mindful parenting, and family cohesion) and (b) SGM-specific practices (i.e., parental acceptance, parental microaggression and microaffirming behaviors) on SGM youth’s health (i.e., sleep disturbances & impairment, physical activity) and mental health (i.e., internalizing and externalizing symptoms) outcomes. The second aim of this study was to examine how SGM-specific practices may moderate the associations between general parenting and family environment variables and SGM youth health and mental health outcomes. The sample included 261 parents (Mage = 41.45, SD = 6.30, age range = 30 to 59) of sexual minority adolescents (Mage = 15.08, SD = 1.40, age range = 13 to 17) recruited nationwide in the U.S. via online recruitment. Results revealed that negative parenting was positively associated with child’s internalizing symptoms, externalizing symptoms, sleep disturbance, and sleep impairment. Meanwhile, mindful parenting was negatively associated with internalizing symptoms only. Parental acceptance, positive parenting, and family cohesion were not significantly associated with youth outcomes. No significant interaction emerged between parental acceptance and the four general parenting and family variables in predicting youth outcomes. Findings highlight the importance of examining how parenting practices and family processes were related to sexual minority adolescents physical and mental health outcomes.
ContributorsThamrin, Hardian (Author) / Gonzales, Nancy A (Thesis advisor) / Toomey, Russell B (Committee member) / Anderson, Samantha F (Committee member) / Perez, Marisol (Committee member) / Arizona State University (Publisher)
Created2024