Matching Items (151)
Description
Viral protein U (Vpu) is a type-III integral membrane protein encoded by Human Immunodeficiency Virus-1 (HIV- 1). It is expressed in infected host cells and plays several roles in viral progeny escape from infected cells, including down-regulation of CD4 receptors. But key structure/function questions remain regarding the mechanisms by which the Vpu protein contributes to HIV-1 pathogenesis. Here we describe expression of Vpu in bacteria, its purification and characterization. We report the successful expression of PelB-Vpu in Escherichia coli using the leader peptide pectate lyase B (PelB) from Erwinia carotovora. The protein was detergent extractable and could be isolated in a very pure form. We demonstrate that the PelB signal peptide successfully targets Vpu to the cell membranes and inserts it as a type I membrane protein. PelB-Vpu was biophysically characterized by circular dichroism and dynamic light scattering experiments and was shown to be an excellent candidate for elucidating structural models.
ContributorsDeb, Arpan (Author) / Johnson, William (Author) / Kline, Alexander (Author) / Scott, Boston (Author) / Meador, Lydia (Author) / Srinivas, Dustin (Author) / Martin Garcia, Jose Manuel (Author) / Dorner, Katerina (Author) / Borges, Chad (Author) / Misra, Rajeev (Author) / Hogue, Brenda (Author) / Fromme, Petra (Author) / Mor, Tsafrir (Author) / ASU Biodesign Center Immunotherapy, Vaccines and Virotherapy (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor) / Biodesign Institute (Contributor) / School of Molecular Sciences (Contributor) / Applied Structural Discovery (Contributor) / Personalized Diagnostics (Contributor)
Created2017-02-22
Description
Dielectrophoresis has been shown in the recent past to successfully separate bioparticles of very subtle differences at high resolutions using biophysical forces. In this study, we test the biophysical differences of methicillin resistant and susceptible Staph. aureus that are known to have very similar genomes by using a modified gradient insulator-based dielectrophoresis device (g-iDEP). MRSA is commonly seen in hospitals and is the leading killer of infectious bacteria, claiming the lives of around 10,000 people annually. G-iDEP improves many capabilities within the DEP field including sample size, cost, ease of use and analysis time. This is a promising foundation to creating a more clinically optimized diagnostic tool for both separation and detection of bacteria in the healthcare field. The capture on-set potential for fluorescently tagged MRSA (801 ± 34V) is higher than fluorescently tagged MSSA (610 ± 32V), resulting in a higher electrokinetic to dielectrophoretic mobility ratio for MRSA. Since the strains have proven to be genomically similar through sequencing, it is reasonable to attribute this significant biophysical difference to the added PBP2a enzyme in MRSA. These results are consistent with other bacterial studied within in this device and have proven to be reproducible.
ContributorsSmithers, Jared (Author) / Hayes, Mark (Thesis director) / Woodbury, Neal (Committee member) / School of Criminology and Criminal Justice (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
“Tell It to the Frogs: Fukushima’s nuclear disaster and its impact on the Japanese Tree Frog” is a representation of the work from Giraudeau et. al’s “Carotenoid distribution in wild Japanese tree frogs (Hyla japonica) exposed to ionizing radiation in Fukushima.” This paper looked to see if carotenoid levels in the tree frog’s vocal sac, liver, and blood were affected by radiation from Fukushima’s power plant explosion. Without carotenoids, the pigment that gives the frogs their orange color on their necks, their courtship practices would be impacted and would not be as able to show off their fitness to potential mates. The artwork inspired by this research displayed the tree frog’s degradation over time due to radiation, starting with normal life and ending with their death and open on the table. The sculptures also pinpoint where the carotenoids were being measured with a brilliant orange glaze. Through ceramic hand building, the artist created larger than life frogs in hopes to elicit curiosity about them and their plight. While the paper did not conclude any changes in the frog’s physiology after 18 months of exposure, there are still questions that are left unanswered. Why did these frogs not have any reaction? Could there be any effects after more time has passed? Is radiation leakage as big of a problem as previously thought? The only way to get the answers to these questions is to be aware of these amphibians, the circumstances that led them to be involved, and continued research on them and radiation.
ContributorsWesterfield, Savannah (Author) / Beiner, Susan (Thesis director) / McGraw, Kevin (Committee member) / School of Life Sciences (Contributor) / School of Art (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Diabesity is a global epidemic affecting millions worldwide. Diabesity is the term given to the link between obesity and Type II diabetes. It is estimated that ~90% of patients diagnosed with Type II diabetes are overweight or have struggled with excess body fat in the past. Type II diabetes is characterized by insulin resistance which is an impaired response of the body to insulin that leads to high blood glucose levels. Adipose tissue, previously thought of as an inert tissue, is now recognized as a major endocrine organ with an important role in the body's immune response and the development of chronic inflammation. It is speculated that adipose tissue inflammation is a major contributor to insulin resistance particular to Type II diabetes. This literature review explores the popular therapeutic targets and marketed drugs for the treatment of Type II diabetes and their role in decreasing adipose tissue inflammation. rAGE is currently in pre-clinical studies as a possible target to combat adipose tissue inflammation due to its relation to insulin resistance. Metformin and Pioglitazone are two drugs already being marketed that use unique chemical pathways to increase the production of insulin and/or decrease blood glucose levels. Sulfonylureas is one of the first FDA approved drugs used in the treatment of Type II diabetes, however, it has been discredited due to its life-threatening side effects. Bariatric surgery is a form of invasive surgery to rid the body of excess fat and has shown to normalize blood glucose levels. These treatments are all secondary to lifestyle changes, such as diet and exercise which can help halt the progression of Type II diabetes patients.
ContributorsRobles, Alondra Maria (Author) / Woodbury, Neal (Thesis director) / Redding, Kevin (Committee member) / Allen, James (Committee member) / Hendrickson, Kirstin (Committee member) / Sanford School of Social and Family Dynamics (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The Heliobacterial Reaction Center (HbRC) is the simplest Type I Reaction Center (RC) known today. However, upon illumination it has been found to produce menaquinol, and this has led to experiments investigating the function of this reduction scheme. The goal of the experiment was to investigate the mechanisms of menaquinol production through the use of Photosystem II (PSII) herbicides that are known to inhibit the QB quinone site in Type II RCs. Seven herbicides were chosen, and out of all of them terbuthylazine showed the greatest effect on the RC in isolated membranes when Transient Absorption Spectroscopy was used. In addition, terbuthylazine decreased menaquinone reduction to menaquinol by ~72%, slightly more than the reported effect of teburtryn (68%)1. In addition, terbuthylazine significantly impacted growth of whole cells under high light more than terbutryn.
ContributorsOdeh, Ahmad Osameh (Author) / Redding, Kevin (Thesis director) / Woodbury, Neal (Committee member) / Allen, James (Committee member) / School of Molecular Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Among the most ornate animal traits in nature are the angle-dependent (i.e. iridescent) structural colors of many birds, beetles, and butterflies. Though we now have a solid understanding of the mechanisms, function, and evolution of these features in several groups, less attention has been paid to the potential for angle-dependent reflectance in otherwise matte-appearing (i.e. not thought to be structurally colored) tissues. Here for the first time we describe non-iridescent angle-dependent coloration from the tail and wing feathers of several parrot species (Psittaciformes). We employed a novel approach \u2014 by calculating chromatic and achromatic contrasts (in just noticeable differences, JNDs) of straight and angled measurements of the same feather patch \u2014 to test for perceptually relevant angle-dependent changes in coloration on dorsal and ventral feather surfaces. We found, among the 15 parrot species studied, significant angle dependence for nearly all parameters (except chromatic JNDs on the ventral side of wing feathers). We then measured microstructural features on each side of feathers, including size and color of barbs and barbules, to attempt to predict interspecific variation in degree of angle-dependent reflectance. We found that hue, saturation, and brightness of feather barbs, barbule saturation, and barb:barbule coverage ratio were the strongest predictors of angle-dependent coloration. Interestingly, there was significant phylogenetic signal in only one of the seven angle-dependence models tested. These findings deepen our views on the importance of microscopic feather features in the production of directional animal coloration, especially in tissues that appear to be statically colored.
ContributorsReed, Steven Andrew (Co-author) / McGraw, Kevin (Thesis director) / Pratt, Stephen (Committee member) / Simpson, Richard (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Predicting the binding sites of proteins has historically relied on the determination of protein structural data. However, the ability to utilize binding data obtained from a simple assay and computationally make the same predictions using only sequence information would be more efficient, both in time and resources. The purpose of this study was to evaluate the effectiveness of an algorithm developed to predict regions of high-binding on proteins as it applies to determining the regions of interaction between binding partners. This approach was applied to tumor necrosis factor alpha (TNFα), its receptor TNFR2, programmed cell death protein-1 (PD-1), and one of its ligand PD-L1. The algorithms applied accurately predicted the binding region between TNFα and TNFR2 in which the interacting residues are sequential on TNFα, however failed to predict discontinuous regions of binding as accurately. The interface of PD-1 and PD-L1 contained continuous residues interacting with each other, however this region was predicted to bind weaker than the regions on the external portions of the molecules. Limitations of this approach include use of a linear search window (resulting in inability to predict discontinuous binding residues), and the use of proteins with unnaturally exposed regions, in the case of PD-1 and PD-L1 (resulting in observed interactions which would not occur normally). However, this method was overall very effective in utilizing the available information to make accurate predictions. The use of the microarray to obtain binding information and a computer algorithm to analyze is a versatile tool capable of being adapted to refine accuracy.
ContributorsBrooks, Meilia Catherine (Author) / Woodbury, Neal (Thesis director) / Diehnelt, Chris (Committee member) / Ghirlanda, Giovanna (Committee member) / Department of Psychology (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Historically, studies of condition-dependent signals in animals have been male-centric, but recent work suggests that female ornaments can also communicate individual quality (e.g., disease state, fecundity). There has been a surge of interest in how urbanization alters signaling traits, but we know little about if and how cities affect signal expression in female animals. We measured carotenoid-based plumage coloration and coccidian (Isospora spp) parasite burden in desert and city populations of house finches to examine urban impacts on male and female health and attractiveness. In earlier work, we showed that male house finches are less colorful and more parasitized in the city, and we again detected that pattern in this study for males. However, though city females are also less colorful than their rural counterparts, we found that rural females were more parasitized. Also, regardless of sex and unlike rural birds, more colorful birds in the city were more heavily infected with coccidia. These results show that urban environments can disrupt signal honesty in female animals and highlight the need for more studies on how cities affect disease and condition-dependent traits in both male and female animals.
ContributorsSykes, Brooke Emma (Author) / McGraw, Kevin (Thesis director) / Sweazea, Karen (Committee member) / Hutton, Pierce (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
The free-base tetra-tolyl-porphyrin and the corresponding cobalt and iron porphyrin complexes were synthesized and characterized to show that this class of compound can be promising, tunable catalysts for carbon dioxide reduction. During cyclic voltammetry experiments, the iron porphyrin showed an on-set of ‘catalytic current’ at an earlier potential than the cobalt porphyrin’s in organic solutions gassed with carbon dioxide. The cobalt porphyrin yielded larger catalytic currents, but at the same potential as the electrode. This difference, along with the significant changes in the porphyrin’s electronic, optical and redox properties, showed that its capabilities for carbon dioxide reduction can be controlled by metal ions, allotting it unique opportunities for applications in solar fuels catalysis and photochemical reactions.
ContributorsSkibo, Edward Kim (Author) / Moore, Gary (Thesis director) / Woodbury, Neal (Committee member) / School of Molecular Sciences (Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
There are two electrophysiological states of sleep in birds (rapid-eye-movement sleep [REM] and slow-wave sleep [SWS]), which have different functions and costs. REM improves memory consolidation, while SWS is neuro-restorative but also exposes the animal to more risk during this deep-sleep phase. Birds who sleep in more exposed microsites are known to invest proportionally less in SWS (presumably to ensure proper vigilance), but otherwise little else is known about the ecological or behavioral predictors of how much time birds devote to REM v. SWS sleep. In this comparative analysis, we examine how proportional time spent in SWS v. REM is related to brain mass and duration of the incubation period in adults. Brain mass and incubation period were chosen as predictors of sleep state investment because brain mass is positively correlated with body size (and may show a relationship between physical development and sleep) and incubation period can be a link used to show similarities and differences between birds and mammals (using mammalian gestation period). We hypothesized that (1) species with larger brains (relative to body size and also while controlling for phylogeny) would have higher demands for information processing, and possibly proportionally outweigh neuro-repair, and thus devote more time to REM and that (2) species with longer incubation periods would have proportionally more REM due to the extended time required for overnight predator vigilance (and not falling into deep sleep) while on the nest. We found, using neurophysiological data from literature on 27 bird species, that adults from species with longer incubation periods spent proportionally more time in REM sleep, but that relative brain size was not significantly associated with relative time spent in REM or SWS. We therefore provide evidence that mammalian and avian REM in response to incubation/gestation period have convergently evolved. Our results suggest that overnight environmental conditions (e.g. sleep site exposure) might have a greater effect on sleep parameters than gross morphological attributes.
ContributorsRaiffe, Joshua Sapell (Author) / McGraw, Kevin (Thesis director) / Deviche, Pierre (Committee member) / Hutton, Pierce (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05