Matching Items (699)
Description
Background: Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer deaths in females worldwide, accounting for 23% of all new cancer cases and 14% of all total cancer deaths in 2008. Five tumor-normal pairs of primary breast epithelial cells were treated for infinite proliferation by using a ROCK inhibitor and mouse feeder cells. Methods: Raw paired-end, 100x coverage RNA-Seq data was aligned to the Human Reference Genome Version 19 using BWA and Tophat. Gene differential expression analysis was completed using Cufflinks and Cuffdiff. Interactive Genome Viewer was used for data visualization. Results: 15 genes were found to be down-regulated by at least one log-fold change in 4/5 of tumor samples. 75 genes were found to be down-regulated in 3/5 of our tumor samples by at least one log-fold change. 11 genes were found to be up-regulated in 4/5 of our tumor samples, and 68 genes were identified to be up-regulated in 3/5 of the tumor samples by at least one-fold change. Conclusion: Expression changes in genes such as AZGP1, AGER, ALG11, and S1007 suggest a disruption in the glycosylation pathway. No correlation was found between Cufflink's Her2 gene-expression and DAKO score classification.
ContributorsHernandez, Fernando (Author) / Anderson, Karen (Thesis director) / Mangone, Marco (Committee member) / Park, Jin (Committee member) / Barrett, The Honors College (Contributor) / Department of Information Systems (Contributor)
Created2013-05
Description
Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution.
ContributorsLi, Dianfan (Author) / Stansfeld, Phillip J. (Author) / Sansom, Mark S. P. (Author) / Keogh, Aaron (Author) / Vogeley, Lutz (Author) / Howe, Nicole (Author) / Lyons, Joseph A. (Author) / Aragao, David (Author) / Fromme, Petra (Author) / Fromme, Raimund (Author) / Basu, Shibom (Author) / Grotjohann, Ingo (Author) / Kupitz, Christopher (Author) / Rendek, Kimberley (Author) / Weierstall, Uwe (Author) / Zatsepin, Nadia (Author) / Cherezov, Vadim (Author) / Liu, Wei (Author) / Bandaru, Sateesh (Author) / English, Niall J. (Author) / Gati, Cornelius (Author) / Barty, Anton (Author) / Yefanov, Oleksandr (Author) / Chapman, Henry N. (Author) / Diederichs, Kay (Author) / Messerschmidt, Marc (Author) / Boutet, Sebastien (Author) / Williams, Garth J. (Author) / Seibert, M. Marvin (Author) / Caffrey, Martin (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2015-12-17
Description
Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.
ContributorsEdlund, Petra (Author) / Takala, Heikki (Author) / Claesson, Elin (Author) / Henry, Leocadie (Author) / Dods, Robert (Author) / Lehtivuori, Heli (Author) / Panman, Matthijs (Author) / Pande, Kanupriya (Author) / White, Thomas (Author) / Nakane, Takanori (Author) / Berntsson, Oskar (Author) / Gustavsson, Emil (Author) / Bath, Petra (Author) / Modi, Vaibhav (Author) / Roy Chowdhury, Shatabdi (Author) / Zook, James (Author) / Berntsen, Peter (Author) / Pandey, Suraj (Author) / Poudyal, Ishwor (Author) / Tenboer, Jason (Author) / Kupitz, Christopher (Author) / Barty, Anton (Author) / Fromme, Petra (Author) / Koralek, Jake D. (Author) / Tanaka, Tomoyuki (Author) / Spence, John (Author) / Liang, Mengning (Author) / Hunter, Mark S. (Author) / Boutet, Sebastien (Author) / Nango, Eriko (Author) / Moffat, Keith (Author) / Groenhof, Gerrit (Author) / Ihalainen, Janne (Author) / Stojkovic, Emina A. (Author) / Schmidt, Marius (Author) / Westenhoff, Sebastian (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2016-10-19
Description
Antibodies are essential for structural determinations and functional studies of membrane proteins, but antibody generation is limited by the availability of properly-folded and purified antigen. We describe the first application of genetic immunization to a structurally diverse set of membrane proteins to show that immunization of mice with DNA alone produced antibodies against 71% (n = 17) of the bacterial and viral targets. Antibody production correlated with prior reports of target immunogenicity in host organisms, underscoring the efficiency of this DNA-gold micronanoplex approach. To generate each antigen for antibody characterization, we also developed a simple in vitro membrane protein expression and capture method. Antibody specificity was demonstrated upon identifying, for the first time, membrane-directed heterologous expression of the native sequences of the FopA and FTT1525 virulence determinants from the select agent Francisella tularensis SCHU S4. These approaches will accelerate future structural and functional investigations of therapeutically-relevant membrane proteins.
ContributorsHansen, Debra (Author) / Robida, Mark (Author) / Craciunescu, Felicia (Author) / Loskutov, Andrey (Author) / Dorner, Katerina (Author) / Rodenberry, John-Charles (Author) / Wang, Xiao (Author) / Olson, Tien (Author) / Patel, Hetal (Author) / Fromme, Petra (Author) / Sykes, Kathryn (Author) / Biodesign Institute (Contributor) / Innovations in Medicine (Contributor) / Applied Structural Discovery (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor)
Created2016-02-24
Description
Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.
ContributorsNogly, Przemyslaw (Author) / Panneels, Valerie (Author) / Nelson, Garrett (Author) / Gati, Cornelius (Author) / Kimura, Tetsunari (Author) / Milne, Christopher (Author) / Milathianaki, Despina (Author) / Kubo, Minoru (Author) / Wu, Wenting (Author) / Conrad, Chelsie (Author) / Coe, Jesse (Author) / Bean, Richard (Author) / Zhao, Yun (Author) / Bath, Petra (Author) / Dods, Robert (Author) / Harimoorthy, Rajiv (Author) / Beyerlein, Kenneth R. (Author) / Rheinberger, Jan (Author) / James, Daniel (Author) / Deponte, Daniel (Author) / Li, Chufeng (Author) / Sala, Leonardo (Author) / Williams, Garth J. (Author) / Hunter, Mark S. (Author) / Koglin, Jason E. (Author) / Berntsen, Peter (Author) / Nango, Eriko (Author) / Iwata, So (Author) / Chapman, Henry N. (Author) / Fromme, Petra (Author) / Frank, Matthias (Author) / Abela, Rafael (Author) / Boutet, Sebastien (Author) / Barty, Anton (Author) / White, Thomas A. (Author) / Weierstall, Uwe (Author) / Spence, John (Author) / Neutze, Richard (Author) / Schertler, Gebhard (Author) / Standfuss, Jorg (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / School of Molecular Sciences (Contributor)
Created2016-08-22
Description
This report analyzes the intersection that is present between law and technology. It covers the basics of patents and intellectual property law, and then touches briefly about the software side of patent law. The future of patent and technology law are explored as well. The main focus of this report is the patent that was created for a beacon that provides for a full enterprise resource planning solution at both supply chain and full business levels.
ContributorsShah, Dhara Vimesh (Author) / Michelle, Gross (Thesis director) / Stevens, Yvonne (Committee member) / Department of Information Systems (Contributor) / W. P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Over the course of 2015-2017, the ASU-SCMA/UASGC Outreach program was developed at Arizona State University (ASU) to support both high school students and college students interested in supply chain management careers. In particular, the program targets the high school students of the Urban Assembly School for Global Commerce (UASGC) and the college students of the ASU Supply Chain Management Association (ASU-SCMA). High school students are partnered with college students in a year-long mentoring program that allows both parties to develop professional supply chain skills. The work of the ASU-SCMA/UASGC Outreach Program is particularly important because it provides UASGC with much needed resources to address urban poverty issues in New York using career and technical education. The Urban Assembly describes its student group as "at-risk, under-resourced youth," and of those youth: - 85% are low-income - 83% enter high school below grade level in at least one subject - 20% require Individualized Education Plans (Special Needs) (urbanassembly.org). The Outreach Program addresses the above issues by providing the high school students with collegiate mentors that develop supply chain and college readiness resources in the form of a case study, site tour, supply chain simulation and presentations. In order to be considered successful, the program must first, equip the high school mentees with tools and skills for a professional career, specifically supply chain management, that they would not otherwise be exposed to; and second, motivate the collegiate participants who are about to enter the workforce to continue to participate in mentoring throughout their careers. This program documents the efforts and results of the pilot year for the Outreach Program that took place from September 2016 through March 2017. Through this pilot program, it was determined that the ASU-SCMA/UASGC Outreach Program is effective and valuable. In fact, the program found that: - 75% of the high school students agreed or strongly agreed that the program helped them learn new business skills. - 75% of the high school students agreed that the program taught them new, interesting things about supply chain. - 75% of the high school students became more interested in college. 100% of the college mentors agreed or strongly agreed that they gained new and important supply chain and professional skills. The success of the pilot year has led to plans for the Outreach Program to become an annual project for ASU-SCMA. This is a program that will continue for the foreseeable future.
ContributorsLam, Tiffany Ai (Author) / Davila, Eduardo (Thesis director) / Manfredo, Mark (Committee member) / Department of Economics (Contributor) / Department of Information Systems (Contributor) / Department of Supply Chain Management (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
This ethnography outlines the live storytelling culture in Phoenix, Arizona, and what each of its sub-cultures contributes to the city's community. Phoenix's live storytelling events incorporate elements of an ancient art form into contemporary entertainment and sophisticated platforms for community building. These events are described and delineated by stylistic, structural, and content-based differences into the following categories: open-mic, curated, scripted, non-scripted, micro-culture, and marginalized groups. Research presented in this report was collected by reviewing scholarly materials about the social power of storytelling, attending live storytelling events across all categories, and interviewing event organizers and storytellers. My research developed toward an auto-ethnographic direction when I joined the community of storytellers in Phoenix, shifting the thesis to assume a voice of solidarity with the community. This resulted in a research project framed primarily as an ethnography that also includes my initial, personal experiences as a storyteller. The thesis concludes with the art form's macro-influences on Phoenix's rapidly-expanding community.
ContributorsNorton, Maeve (Author) / Dombrowski, Rosemarie (Thesis director) / McAdams, Charity (Committee member) / School of International Letters and Cultures (Contributor) / Department of Information Systems (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
This thesis examines the value creation potential of renovating an existing commercial real estate asset to a medical office. It begins by examining commercial real estate and the medical sector at a high level. It then discusses the various criteria used to select a subject property for renovation. This renovation is then depicted through a modified pitch book that contains a financial model and pro forma.
ContributorsPeters, Matthew Scott (Co-author) / Larrea, Justin (Co-author) / Berger, Nicholas (Co-author) / Simonson, Mark (Thesis director) / Gray, William (Committee member) / Department of Finance (Contributor, Contributor) / Department of Information Systems (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
This thesis will bring together students to engage in entrepreneurship by finding, measuring and sharing strategic market opportunities. From a student’s perspective, it will take a deep dive into the world of startup ecosystems, markets and trends utilizing both qualitative and quantitative market research techniques. The information gathered has been curated into a productive, meaningful manner, through a report titled “The State of Startups: A Student Perspective.” <br/> The first key theme of this thesis is that market intelligence can be a powerful tool. The second key theme is the power of knowledge implementation towards competitive strategies. The first section of the thesis will focus on identifying and understanding the current “startup” landscape as a basis on which to build strategic and impactful business decisions. This will be accomplished as the team conducts a landscape analysis focused on the student perspective of the student-based North American “entrepreneurial” ecosystem. The second section of the thesis will focus specifically on the personal experiences of student startup founders. This will be accomplished through the analysis of interviews with founders of the startups researched from the first section of the thesis. This will provide us with a direct insight into the student perspective of the student-based North American “entrepreneurial” ecosystem.
ContributorsMinic, Jacob Michael (Co-author) / Callahan, Ryan (Co-author) / Rudick, Justin (Co-author) / Forshey, Cecilia (Co-author) / Hybert, Jacob (Co-author) / Byrne, Jared (Thesis director) / Olsen, Douglas (Committee member) / Curtiss, Ian (Committee member) / Department of Information Systems (Contributor) / Department of Economics (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05