Matching Items (97)
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
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
The purpose of this thesis is to compare ecolabeling to conservation easements for facilitating multi-use land between food production and conservation. Biodiversity has been on the decline as human agriculture uses more land. According to Encyclopedia Britannica “Half of the world’s habitable land (some 51 million square km [19.7 million square miles]) has been converted to agriculture, and some 77 percent of agricultural land (some 40 million square km [15.4 million square miles]) is used for grazing by cattle, sheep, goats, and other livestock. This massive conversion of forests, wetlands, grasslands, and other terrestrial ecosystems has produced a 60 percent decline (on average) in the number of vertebrates worldwide since 1970”(Rafferty 2010). The purpose of this paper is to explore ways individual landowners and private businesses can continue to operate profitably on their land while reversing the harmful loss to biodiversity observed in the past 50 years. Two of the most popular methods of achieving conservation on workable land are ecolabeling and conservation easements.
ContributorsWilcox, Christopher James (Author) / Leonard, Brian (Thesis director) / Schoon, Michael (Committee member) / Dean, W.P. Carey School of Business (Contributor) / Department of Supply Chain Management (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
Description
The issue of wild horse management in the American West has become prevalent in the media recently and management strategies are often criticized and opposed by the public. Horses have been a core feature of American history and culture nearly since the colonization of the western frontier, and popular media such as television and movies paint a romantic but often unrealistic picture of wild horses. Land management agencies must balance limited resources with an ever-growing wild horse population in order to properly manage public land so that it retains its ecological integrity and is still able to be used by multiple stakeholders, and they also must endure public criticism throughout the process. I used a photo elicitation survey to gather responses to photographic images of wild horses and determine how the public feels about wild horse management, given that horses are seen as a symbol of freedom and the American West. It was revealed that people who are unfamiliar with the issue still have opinions about how the horses should be managed, and these opinions often mirror what can be found in popular media.
ContributorsDuran, Kiana Alexis (Author) / Minteer, Ben (Thesis director) / Schoon, Michael (Thesis director) / Murphree, Julie (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
As human populations continue to expand, interactions with wildlife are expected to increase due to destruction of land and global climate change threatening native habitats. Established areas of protection are becoming essential to species survival and biodiversity protection. National Parks (NP) are a globally ubiquitous method employed to protect wildlife and habitats. Often NPs are mosaics of relatively small protected areas in a “sea” of human-dominated landscapes, and these remaining habitat “islands” are becoming essential to preventing species extinction. However, the establishment of a NP can lead to increased human-wildlife conflicts (HWC) and disenfranchisement of local communities, particularly along their borders. We conducted semi-structured interviews in six different countries to better understand the nature of HWCs at the borders of major NPs: (1) Khao Yai NP, Thailand; (2) Myall Lakes NP, Australia; (3) Chitwan NP, Nepal; (4) Kruger NP, South Africa; (5) Chingaza NP, Colombia, and (6) Yellowstone NP, United States. We evaluated affinity to wildlife, perception of conflicts, management success, and potential solutions at each park to better understand the global nature of HWCs.We also evaluated these data in relationship to the Human Development Index (HDI) to determine if there was a correlation between development and conflict issues. We found the intrinsic value of wildlife to not markedly differ between countries. Conflict was perceived as higher in the United States and Australia but was known to be of greater intensity in Nepal and South Africa. Management of NPs was well-regarded with a slight decrease from less-developed countries to more-developed countries, with solutions that were creative and unique to each region. Results appeared to be related to shifting baselines between countries and also to equivalency in a cross-cultural assessment. When these theories are taken into account, the complexity of HWCs globally is better understood. As our world continues to expand and NPs become some of the only contiguous native habitat and refuges for wildlife, it is important to understand the complex relationships occurring at the interface between natural and human communities and to explore effective solutions to these problems.
ContributorsRagan, Kinley Ann (Author) / Schoon, Michael (Thesis director) / Schipper, Jan (Committee member) / Senko, Jesse (Committee member) / School of Life Sciences (Contributor, Contributor) / School of Geographical Sciences and Urban Planning (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Human activities around the world are threatening scores of wildlife species, pushing them closer to extinction. In order to address what many conservationists view as a global biodiversity crisis, it is vital that more people are inspired to care about wild animals and motivated to act in ways that help protect them. The up-close experiences and personal connections that people form with wild animals in zoos accredited by the Association of Zoos and Aquariums (AZA) or the World Association of Zoos and Aquariums (WAZA) can help achieve this. However, it is not very well understood how different types of encounters within these zoos may inspire conservation mindedness and pro-environmental behaviors. During this thesis project, surveys were conducted at the AZA-accredited Arizona Center for Nature Conservation/Phoenix Zoo to understand how interactive, hands-on animal experiences within zoos differ from passively viewing zoo animals when it comes to inspiring people to care about conservation. The Phoenix Zoo is home to two different species of giraffes, and guests can view them from the front of the Savanna Exhibit. Guests can also participate in the Giraffe Encounter, which is a much more interactive, hands-on experience. After surveying guests at both locations, the results showed that fewer people at the Giraffe Encounter responded that they often engage in pro-environmental behaviors. This may indicate that the people who participated in the Giraffe Encounter came to the zoo more for recreation and entertainment than to learn about wildlife. Despite this, more people learned something new about nature or conservation at the Giraffe Encounter than they did at the Savanna Exhibit. On average, guests also felt that the Giraffe Encounter motivated them to learn more about how to help animals in the wild than the Savanna Exhibit did. Overall, there is a strong correlation between having an interactive, hands-on experience with a zoo animal and caring more about wildlife conservation. However, more research still needs to be done in order to conclusively provide evidence for causation.
ContributorsBurgess, Christa Noell (Author) / Schoon, Michael (Thesis director) / Minteer, Ben (Committee member) / Allard, Ruth (Committee member) / School of Life Sciences (Contributor) / School of Sustainability (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2019-12
Description
This paper covers the wild horse overpopulation case study at the Salt River in Arizona, exploring how Traditional Ecological Knowledge (TEK) might help foster solutions to a lengthy and heated controversy about how to manage wild horses and burros on the rangeland. Fikret Berke's Sacred Ecology defines traditional ecological knowledge as, "a cumulative body of knowledge, practice, and belief evolving by adaptive processes and handed down through generations by cultural transmission, about the relationship of living beings (including humans) with one another and with their environment," (Berkes, 3). In contrast to current management strategies, TEK utilizes knowledge that comes from direct experience and intuitive knowing, rather than science-based, techno-rational streams of knowledge. Drawing on three modern sustainability concepts that support and stem from TEK, including: everything is connected, complex solutions can further complicate problems and diversity as a key to resilience, this paper sets forth a number of specific solutions to be considered moving forward, guided by the wisdom of TEK.
ContributorsLyford, Rebecca (Author) / Schoon, Michael (Thesis director) / Murphey, Julia (Committee member) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Circles of Sustainability is a self-evaluation tool designed to build educator capacity in K-12 schools seeking sustainability solutions. Based on the Sustainable Schools Challenge Handbook from Memphis, Tennessee, Circles of Sustainability considers environmental impact and efficiency, a healthy and safe school environment, sustainability and environmental education, and engagement and empowerment as four key pillars of whole-school sustainability. Each pillar is composed of elements and rubric items, which are reviewed, totaled, and colored in on the front page of the tool to help educators visualize and evaluate the current state of sustainability at their school. Since its first iteration completed in May 2017, the tool has been used by 300 educators throughout the United States during ASU's Sustainability Teachers' Academy (STA) workshops. Circles of Sustainability is completed as part of an activity called "Evaluating Your Community," where educators complete the tool and then brainstorm sustainability projects and solutions for their school and community. This paper is a review and discussion of the research, informal feedback and formal feedback used to create the second iteration of the tool. A second iteration of the tool was created to make the tool more user-friendly and ensure each pillar, element, and rubric item are based in research. The informal feedback was conducted during STA workshops in Tempe, Arizona; Abingdon, Virginia; Princeton, New Jersey; Chicago, Illinois; Los Angeles, California; Tucson, Arizona; and Charlotte, North Carolina. The formal feedback was conducted using a survey distributed to teachers who participated in the Tucson and Charlotte workshops. Overall, educators have responded positively to the tool, and the second iteration will continue to be used in future STA workshops throughout the United States.
ContributorsColbert, Julia (Author) / Schoon, Michael (Thesis director) / Merritt, Eileen (Committee member) / School of Sustainability (Contributor) / Division of Teacher Preparation (Contributor) / School of Geographical Sciences and Urban Planning (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The fence between the US and Mexico had been and continues to be a controversial topic in both the U.S., Mexico and around the world. This study will look at the negative externalities related to the environment, society, and economy of the current fence on the border. The central question behind the thesis is whether or not the fence has a direct impact on the ecosystem and people around it.
ContributorsHoyt, Stephanie Alexis (Author) / Schoon, Michael (Thesis director) / Breetz, Hanna (Committee member) / School of Sustainability (Contributor) / School of Politics and Global Studies (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
ABSTRACT Over the past several decades, the dilemma of free-roaming horses in the U.S. has proven to be one of the most divisive issues in management of public lands. According to federal land management agencies, without population regulation, horses can increase at the rate of 15-20% a year on arid rangelands with inadequate numbers of natural, large predators. Horses compete for valuable forage and water resources alongside cattle and native wildlife in delicate riparian areas highly susceptible to the negative ecological effects of soil compaction and overgrazing. Most U.S. management policies, therefore, call for increased removal of free-roaming horses as they are categorized as “un-authorized livestock” or "non-native" species. Wild horse advocates, however, continue to petition for improvement in animal welfare and expansion of the horses’ territory. With heightened social conflict spurred by animal rights and ecological concerns, not to mention the often-stark differences over what really “belongs” on the landscape, the success of appropriate management strategies hinges on managing agencies’ preparedness and ability to respond in a timely and inclusive manner. A critical element of the management context is the public’s views toward the wild horse and the science used to manage them. Synthesizing the vast literature in the history and philosophy of wildlife management in the American West, and utilizing an ethnographic and case study approach, my research examines the range of stakeholder concerns and analyzes the factors that have led to the disconnect between public values of wild horses and public policy for the management of the federally protected free-roaming horses in Arizona’s Apache-Sitgreaves National Forests.
ContributorsMurphree, Julie Joan (Author) / Minteer, Ben A. (Thesis advisor) / Schoon, Michael (Thesis advisor) / Bradshaw, Karen (Committee member) / Chew, Matthew (Committee member) / Arizona State University (Publisher)
Created2022