Matching Items (141)
Description
The membrane proximal region (MPR, residues 649–683) and transmembrane domain (TMD, residues 684–705) of the gp41 subunit of HIV-1’s envelope protein are highly conserved and are important in viral mucosal transmission, virus attachment and membrane fusion with target cells. Several structures of the trimeric membrane proximal external region (residues 662–683) of MPR have been reported at the atomic level; however, the atomic structure of the TMD still remains unknown. To elucidate the structure of both MPR and TMD, we expressed the region spanning both domains, MPR-TM (residues 649–705), in Escherichia coli as a fusion protein with maltose binding protein (MBP). MPR-TM was initially fused to the C-terminus of MBP via a 42 aa-long linker containing a TEV protease recognition site (MBP-linker-MPR-TM).
Biophysical characterization indicated that the purified MBP-linker-MPR-TM protein was a monodisperse and stable candidate for crystallization. However, crystals of the MBP-linker-MPR-TM protein could not be obtained in extensive crystallization screens. It is possible that the 42 residue-long linker between MBP and MPR-TM was interfering with crystal formation. To test this hypothesis, the 42 residue-long linker was replaced with three alanine residues. The fusion protein, MBP-AAA-MPR-TM, was similarly purified and characterized. Significantly, both the MBP-linker-MPR-TM and MBP-AAA-MPR-TM proteins strongly interacted with broadly neutralizing monoclonal antibodies 2F5 and 4E10. With epitopes accessible to the broadly neutralizing antibodies, these MBP/MPR-TM recombinant proteins may be in immunologically relevant conformations that mimic a pre-hairpin intermediate of gp41.
ContributorsGong, Zhen (Author) / Martin Garcia, Jose Manuel (Author) / Daskalova, Sasha (Author) / Craciunescu, Felicia (Author) / Song, Lusheng (Author) / Dorner, Katerina (Author) / Hansen, Debra (Author) / Yang, Jay-How (Author) / LaBaer, Joshua (Author) / Hogue, Brenda (Author) / Mor, Tsafrir (Author) / Fromme, Petra (Author) / Department of Chemistry and Biochemistry (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Infectious Diseases and Vaccinology (Contributor) / Innovations in Medicine (Contributor) / Personalized Diagnostics (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2015-08-21
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
Honey bee workers display remarkable flexibility in the aging process. This plasticity is closely tied to behavioral maturation. Workers who initiate foraging behavior at earlier ages have shorter lifespans, and much of the variation in total lifespan can be explained by differences in pre-foraging lifespan. Vitellogenin (Vg), a yolk precursor protein, influences worker lifespan both as a regulator of behavioral maturation and through anti-oxidant and immune functions. Experimental reduction of Vg mRNA, and thus Vg protein levels, in wild-type bees results in precocious foraging behavior, decreased lifespan, and increased susceptibility to oxidative damage. We sought to separate the effects of Vg on lifespan due to behavioral maturation from those due to immune and antioxidant function using two selected strains of honey bees that differ in their phenotypic responsiveness to Vg gene knockdown. Surprisingly, we found that lifespans lengthen in the strain described as behaviorally and hormonally insensitive to Vg reduction. We then performed targeted gene expression analyses on genes hypothesized to mediate aging and lifespan: the insulin-like peptides (Ilp1 and 2) and manganese superoxide dismutase (mnSOD). The two honey bee Ilps are the most upstream components in the insulin-signaling pathway, which influences lifespan in Drosophila melanogaster and other organisms, while manganese superoxide dismutase encodes an enzyme with antioxidant functions in animals. We found expression differences in the llps in fat body related to behavior (llp1 and 2) and genetic background (Ilp2), but did not find strain by treatment effects. Expression of mnSOD was also affected by behavior and genetic background. Additionally, we observed a differential response to Vg knockdown in fat body expression of mnSOD, suggesting that antioxidant pathways may partially explain the strain-specific lifespan responses to Vg knockdown.
ContributorsIhle, Kate (Author) / Fondrk, M. Kim (Author) / Page, Robert (Author) / Amdam, Gro (Author) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2015-01-01
Description
The brain is considered the crux of identity, yet human behavior may be influenced by bacteria in gut microbiomes. Honeybees can exchange bacteria through their many social behaviors, making their microbiomes, and the effect they have on honeybee behavior, of interest. There is recent evidence suggesting the presence of bacteria existing in human brains, which can be investigated in honeybee brains due to their well-documented structure. The purpose of this study is to establish if lipopolysaccharide—a molecule on bacteria membranes—is present in the honeybee brain and if it colocalizes with vitellogenin—an immune mediator. Additionally, this study also seeks to establish the efficacy of embedding tissue samples in resin and performing immunohistochemistry for vitellogenin and lipopolysaccharide on sections.
ContributorsStrange, Amalie Sofie (Co-author) / Strange, Amalie (Co-author) / Amdam, Gro (Thesis director) / Baluch, Page (Committee member) / School of International Letters and Cultures (Contributor) / School of Life Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
The purpose of this thesis creative project was to create an educational video to present research findings on the increasingly important issue of human biospecimen preanalytic variables. When a human biospecimen, such as blood, urine, or tissue, is removed from the body, it is subjected to a plethora of variables that are not recorded or regulated in a vast majority of cases. Frequently, these samples arrive at the research or pathology lab with an unknown history, then undergo analysis for translational research purposes, or to guide clinical management decisions. Thus, compromised specimen quality caused by preanalytic variables has substantial, and potentially devastating, downstream effects. To identify the preanalytic variables with the greatest impact on blood and tissue specimen quality, 45 articles were gathered using PubMed and Google Scholar databases and cited. Based on the articles, the top five variables with the most detrimental effects were identified for both blood and tissue samples. Multiple sets of parameters ensuring specimen fitness were compared for each of the five variables for each specimen type. Then, specific parameters guaranteeing the fitness of the greatest number of analytes were verified. To present the research findings in greater detail, a paper was written that focused on identifying the top variables and key parameters to ensure analyte fitness. To present the overall issue in an easy-to-digest format, a storyboard and script were created as a guideline for a final video project. Ultimately, two alternate versions of the video were created to pertain to the audience of choice (one version for patients, one version for professionals). It is the hope that these videos will be used as educational tools to continue efforts to standardize and enforce human biospecimen preanalytic variable parameters. This is a necessary step to improve the accuracy of our biomedical research data and the healthcare of patients worldwide.
ContributorsAzcarate, Heather (Author) / Compton, Carolyn (Thesis director) / LaBaer, Joshua (Committee member) / Borges, Chad (Committee member) / Barrett, The Honors College (Contributor) / Department of Psychology (Contributor)
Created2018-12
Description
Cleavage and polyadenylation is a step in mRNA processing in which the 3’UTR is cleaved and a polyA tail is added to create a final mature transcript. This process relies on RNA sequence elements that guide a large multimeric protein complex named the Cleavage and Polyadenylation Complex to dock on the 3’UTR and execute the cleavage reaction. Interactions of the complex with the RNA and specific dynamics of complex recruitment and formation still remain largely uncharacterized. In our lab we have identified an Adenosine residue as the nucleotide most often present at the cleavage site, although it is unclear whether this specific element is a required instructor of cleavage and polyadenylation. To address whether the Adenosine residue is necessary and sufficient for the cleavage and polyadenylation reaction, we mutated this nucleotide at the cleavage site in three C. elegans protein coding genes, forcing the expression of these wt and mutant 3’UTRs, and studied how the cleavage and polyadenylation machinery process these genes in vivo. We found that interrupting the wt sequence elements found at the cleavage site interferes with the cleavage and polyadenylation reaction, suggesting that the sequence close to the end of the transcript plays a role in modulating the site of the RNA cleavage. This activity is also gene-specific. Genes such as ges-1 showed little disruption in the cleavage of the transcript, with similar location occurring in both the wt and mutant 3’UTRs. On the other hand, mutation of the cleavage site in genes such as Y106G6H.9 caused the activation of new cryptic cleavage sites within the transcript. Taken together, my experiments suggest that the sequence elements at the cleavage site somehow participate in the reaction to guide the cleavage reaction to occur at an exact site. This work will help to better understand the mechanisms of transcription termination in vivo and will push forward research aimed to study post-transcriptional gene regulation in eukaryotes.
ContributorsSteber, Hannah Suzanne (Author) / Mangone, Marco (Thesis director) / Harris, Robin (Committee member) / LaBaer, Joshua (Committee member) / School of Life Sciences (Contributor, Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
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
Background
The reproductive ground plan hypothesis of social evolution suggests that reproductive controls of a solitary ancestor have been co-opted during social evolution, facilitating the division of labor among social insect workers. Despite substantial empirical support, the generality of this hypothesis is not universally accepted. Thus, we investigated the prediction of particular genes with pleiotropic effects on ovarian traits and social behavior in worker honey bees as a stringent test of the reproductive ground plan hypothesis. We complemented these tests with a comprehensive genome scan for additional quantitative trait loci (QTL) to gain a better understanding of the genetic architecture of the ovary size of honey bee workers, a morphological trait that is significant for understanding social insect caste evolution and general insect biology.
Results
Back-crossing hybrid European x Africanized honey bee queens to the Africanized parent colony generated two study populations with extraordinarily large worker ovaries. Despite the transgressive ovary phenotypes, several previously mapped QTL for social foraging behavior demonstrated ovary size effects, confirming the prediction of pleiotropic genetic effects on reproductive traits and social behavior. One major QTL for ovary size was detected in each backcross, along with several smaller effects and two QTL for ovary asymmetry. One of the main ovary size QTL coincided with a major QTL for ovary activation, explaining 3/4 of the phenotypic variance, although no simple positive correlation between ovary size and activation was observed.
Conclusions
Our results provide strong support for the reproductive ground plan hypothesis of evolution in study populations that are independent of the genetic stocks that originally led to the formulation of this hypothesis. As predicted, worker ovary size is genetically linked to multiple correlated traits of the complex division of labor in worker honey bees, known as the pollen hoarding syndrome. The genetic architecture of worker ovary size presumably consists of a combination of trait-specific loci and general regulators that affect the whole behavioral syndrome and may even play a role in caste determination. Several promising candidate genes in the QTL intervals await further study to clarify their potential role in social insect evolution and the regulation of insect fertility in general.
The reproductive ground plan hypothesis of social evolution suggests that reproductive controls of a solitary ancestor have been co-opted during social evolution, facilitating the division of labor among social insect workers. Despite substantial empirical support, the generality of this hypothesis is not universally accepted. Thus, we investigated the prediction of particular genes with pleiotropic effects on ovarian traits and social behavior in worker honey bees as a stringent test of the reproductive ground plan hypothesis. We complemented these tests with a comprehensive genome scan for additional quantitative trait loci (QTL) to gain a better understanding of the genetic architecture of the ovary size of honey bee workers, a morphological trait that is significant for understanding social insect caste evolution and general insect biology.
Results
Back-crossing hybrid European x Africanized honey bee queens to the Africanized parent colony generated two study populations with extraordinarily large worker ovaries. Despite the transgressive ovary phenotypes, several previously mapped QTL for social foraging behavior demonstrated ovary size effects, confirming the prediction of pleiotropic genetic effects on reproductive traits and social behavior. One major QTL for ovary size was detected in each backcross, along with several smaller effects and two QTL for ovary asymmetry. One of the main ovary size QTL coincided with a major QTL for ovary activation, explaining 3/4 of the phenotypic variance, although no simple positive correlation between ovary size and activation was observed.
Conclusions
Our results provide strong support for the reproductive ground plan hypothesis of evolution in study populations that are independent of the genetic stocks that originally led to the formulation of this hypothesis. As predicted, worker ovary size is genetically linked to multiple correlated traits of the complex division of labor in worker honey bees, known as the pollen hoarding syndrome. The genetic architecture of worker ovary size presumably consists of a combination of trait-specific loci and general regulators that affect the whole behavioral syndrome and may even play a role in caste determination. Several promising candidate genes in the QTL intervals await further study to clarify their potential role in social insect evolution and the regulation of insect fertility in general.
ContributorsGraham, Allie M. (Author) / Munday, Michael D. (Author) / Kaftanoglu, Osman (Author) / Page, Robert (Author) / Amdam, Gro (Author) / Rueppell, Olav (Author) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2011-04-13