Matching Items (86)
Description
V(D)J Recombination is the mechanism responsible for generating diversity in the repertoire of antigen receptors of T and B cells. This recombination process proceeds in two steps: site-specific cleavage mediated lymphocyte-specific recombinase known as Recombination Activating Genes 1 and 2 complex (RAG) at the junction of coding gene segments and their flanking recombination signal sequence (RSS) and then followed by rejoining of the double strand broken DNA by the non-homologous end joining (NHEJ) complex. Mutations and truncations of the RAG-recombinase have been found associated with genomic instability and chromosomal translocation. It has been hypothesized that these RAG mutants may have abnormality in their interactions with recombination intermediates, ultimately causing premature release of the ends for aberrant joining. Additionally, these mutations have an increase in targeting non-B type DNA instead of legitimate recombination substrates that contain RSSs. To directly test these hypotheses, we have developed a fluorescence-based detection system to monitor in real time the recombination cleavage reaction from the pre-cleavage to the post-cleavage stages and to compare RAG-DNA interactions between wild type and mutant RAG1/2 during this process. Our study provides important insight into the ability of the C-terminus of RAG to regulate RAG recombinase activity.
ContributorsBushway, Kevin Thomas (Author) / Chang, Yung (Thesis director) / Levitus, Marcia (Committee member) / Wang, Guannan (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-12
Description
A literature review summarizing the current status of conservation efforts of the Mojave Desert tortoise (Gopherus agassizii) including a brief overview of the Endangered Species Act (ESA) and its applicability to this species' conservation. A genetic and physiological comparison of the morphologically similar Mojave species with the Sonoran (Gopherus morafkai) species proceeded by an analysis of if and how the ESA should apply to the Sonoran population. Analysis of current plans and interagency cooperations followed by a multi-step proposal on how best to conserve the Sonoran population of Desert tortoise.
ContributorsKulik, Elise Chikako (Author) / Kusumi, Kenro (Thesis director) / Tollis, Marc (Committee member) / Wilson Sayres, Melissa (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
The ringtail (Bassariscus astutus), a member of the Procyonidae, is capable of 180 degrees of hindlimb reversal during headfirst descent down a vertical substrate. The goal of this study was to determine the presence or absence of myological adaptations related to hindlimb reversal in the ringtail. Data for B. astutus are presented, including muscle weights and muscle maps ascertained from the dissection of four hindlimbs. Data from the current study were compared to published accounts of other species capable of hindlimb reversal, including procyonids (raccoon, coati, kinkajou, olingo), a mustelid (marten), palm civet, mongoose, tree squirrel, common tree shrew, and slow loris. Muscle mass data from this study demonstrate that the hip adductors of scansorial mammals are significantly more robust than those of terrestrial mammals, indicating a myological adaptation for climbing, but not necessarily hindlimb reversal. Among hindlimb reversers, the majority exhibit one belly of m. sartorius, the presence of m. extensor digiti I longus, and a fibular origin for m. fibularis longus. These characteristics indicate an emphasis on hip extension, ankle plantarflexion, and pes inversion. However, these characteristics are more likely due to phylogeny than hindlimb reversal because of their presence in closely-related non-reversers. Additional data on families outside of Carnivora may help determine if these myological traits are indeed due to phylogeny. Other myological data, such as moment arms and cross sectional areas, may provide evidence of adaptations for hindlimb reversal.
ContributorsLiu, Margaret Chuan (Author) / Fisher, Rebecca (Thesis director) / Hinrichs, Richard (Committee member) / Kusumi, Kenro (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
While a number of vertebrates, including fishes, salamanders, frogs, and lizards, display regenerative capacity, the process is not necessarily the same. It has been proposed that regeneration, while evolutionarily conserved, has diverged during evolution. However, the extent to which the mechanisms of regeneration have changed between taxa still remains elusive. In the salamander limb, cells dedifferentiate to a more plastic state and aggregate in the distal portion of the appendage to form a blastema, which is responsible for outgrowth and tissue development. In contrast, no such mechanism has been identified in lizards, and it is unclear to what extent evolutionary divergence between amniotes and anamniotes has altered this mechanism. Anolis carolinensis lizards are capable of regenerating their tails after stress-induced autotomy or self-amputation. In this investigation, the distribution of proliferating cells in early A. carolinensis tail regeneration was visualized by immunohistochemistry to examine the location and quantity of proliferating cells. An aggregate of proliferating cells at the distal region of the regenerate is considered indicative of blastema formation. Proliferating cell nuclear antigen (PCNA) and minichromosome maintenance complex component 2 (MCM2) were utilized as proliferation markers. Positive cells were counted for each tail (n=9, n=8 respectively). The percent of proliferating cells at the tip and base of the regenerating tail were compared with a one-way ANOVA statistical test. Both markers showed no significant difference (P=0.585, P=0.603 respectively) indicating absence of a blastema-like structure. These results suggest an alternative mechanism of regeneration in lizards and potentially other amniotes.
ContributorsTokuyama, Minami Adrianne (Author) / Kusumi, Kenro (Thesis director) / Wilson-Rawls, Jeanne (Committee member) / Menke, Douglas (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
Anole lizards that inhabit the islands and mainland of the Caribbean basin have evolved morphological traits adapted to the microhabitat that they occupy. The anoles on these islands have been characterized as "ecomorphs" or morphologically and behaviorally-adapted groups, including: crown-giant, trunk-crown, trunk, grass-bush, twig, and trunk-ground. Ecomorphs display morphological features that are specifically adapted to the habitat that the anole occupies. One key morphological difference is tail length. While the anoles Anolis carolinensis and A. sagrei have similar ratios of tail length versus snout-to-vent length (SVL), they occupy different microhabitats. Specifically, A. carolinensis inhabits trunk-crown habitats while A. sagrei is found in trunk-ground regions. In this study, I focused on analysis of the caudal vertebrae of these two species, to determine if the structure of the osteological elements reflected differences in microhabitat adaptation. Skeletal preparations reveal that A. carolinensis have 40 \u2014 46 caudal vertebrae, and A. sagrei have 38 \u2014 49 caudal vertebrae. Transverse processes are present in Ca1-8 in A. carolinensis whereas transverse processes in A. sagrei span from Ca1-42 vertebrae. Ca6\u201440 have autotomy planes in A. sagrei, whereas only Ca8\u201417 have autotomy planes in A. carolinensis. These findings indicate that A. carolinensis are limited in the ability to autotomize their tail compared to A. sagrei. A. carolinensis, living higher in the trees than A. sagrei, might incur a greater impairment of locomotor function if autotomized. There appears to be no differences between males and females of both species in respect to vertebrae lengths. Differences between A. carolinensis and A. sagrei in terms of vertebral length are found in Ca12-15, 29-30, 34, and 37. The finding indicates that almost all caudal vertebrae between A. carolinensis and A. sagrei have similar relative lengths, but seven vertebrae have statistically significant differences. The biological significance of the findings is not clear, but functional and myological studies may help elucidate the reason of the observed differences.
ContributorsLasku, Eris (Author) / Kusumi, Kenro (Thesis director) / Fisher, Rebecca (Committee member) / Hsieh, Tonia (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2013-05
Description
We propose the Bio-HCI framework, that focuses on three major components: biological materials, intermediate platforms, and interaction with the user. In this context, "biological materials" is meant to broadly cover biological matter (DNA, RNA, enzyme), biological information (gene, epigenetic), biological process (mutation, reproduction, self assembling), and biological form. These biological materials serve as the design elements for designers to use in the same way as digital materials. Intermediate Platform focuses on methods of connecting biological materials to a user, or a digital platform that connect to users. In most current use-cases, biological materials need an intermediate platform to transfer the information to the user and transfer the user's response back to biological materials. Examples include a DNA sequencer, microscope, or petri dish. User interaction emphasizes the interactivity between a user and the biological machine (biological materials + intermediate platform). The interaction ranges from a basic human-computer interaction such as using a biological machine as a file storage to a unique interaction such as having a biological machine that evolves to solve user's task. To examine this framework further, we present four experiments which focus on the different aspect of the Bio-HCI framework.
ContributorsPataranutaporn, Pat (Author) / Finn, Edward (Thesis director) / Kusumi, Kenro (Committee member) / Ingalls, Todd (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
As advanced as current cancer therapeutics are, there are still challenges that need to be addressed. One of them is the non-specific killing of normal cells in addition to cancerous cells. Ideal cancer therapeutics should be targeted specifically toward tumor cells. Due to the robust self-assembly and versatile addressability of DNA-nanostructures, a DNA tetrahedron nanostructure was explored as a drug carrier. The nanostructure can be decorated with various molecules to either increase immunogenicity, toxicity, or affinity to a specific cell type. The efficiency of the specific binding and internalization of the chosen molecules was measured via flow cytometry. Using a murine B cell lymphoma as the model system, several targeting molecules have been evaluated for their specific binding and induced internalization of DNA nanostructures, including an anti-Igκ antibody, an idiotype-binding peptide, and a g-quadruplex nucleolin specific aptamer. It was found that adding the anti-Igκ antibody appeared to provide increased binding and facilitated cellular internalization. Also, it was found that the presence of CpG appeared to aid in the binding of nanostructures decorated with other molecules, as compared to nanostructures without CpG. The g-quadruplex aptamer thought to specifically bind cancer cells that overexpress nucleolin was tested and found to have better binding to cells when linked to the nanostructure than when alone. The drug doxorubicin was used to load the DNA-nanostructure and attempt to inhibit cancer cell growth. The DNA-nanostructure has the benefit of being self-assembled and customizable, and it has been shown to bind to and internalize into a cancer cell line. The next steps are to test the toxicity of the nanostructure as well as its specificity for cancerous cells compared to noncancerous cells. Furthermore, once those tests are completed the structure’s drug delivery capacity will be tested in tumor bearing mice. The DNA-nanostructure exhibits potential as a cancer specific therapeutic.
ContributorsGomez, Amber Marie (Author) / Chang, Yung (Thesis director) / Anderson, Karen (Committee member) / Liu, Xiaowei (Committee member) / Sanford School of Social and Family Dynamics (Contributor) / School of Molecular Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Glioblastoma multiforme is the most common and aggressive primary malignant brain tumor in adults, exhibiting a median survival of only 15 months after diagnosis. A significant challenge in treating GBM is the ability of glioma cells to invade normal brain tissue, escape surgical resection, and resist radiotherapy and chemotherapy. We have previously demonstrated that the TWEAK-Fn14 signaling axis plays an important role in glioma cell invasion and discovered a small molecule, L524-0366, that specifically disrupts the TWEAK-Fn14 interaction. However, low affinity limits L524-0366’s clinical feasibility. By utilizing structure-activity relationship analyses of L524-0366, we identified additional small molecules that may inhibit TWEAK-Fn14 signaling. Here, we identify five additional novel Fn14 signaling inhibitors that specifically inhibited TWEAK-Fn14 NF-κB-dependent signaling and suppressed TWEAK-induced glioma cell migration. Furthermore, we demonstrate that two molecules exhibit improved affinity for Fn14, two molecules showed binding to the TWEAK ligand but not Fn14, and one showed no binding to either TWEAK or Fn14. These molecules will be further tested for in vitro and in vivo functionality, and serve as foundations for additional medicinal chemistry for drug modifications.
ContributorsMillard, Nghia Patrick (Author) / Misra, Rajeev (Thesis director) / Chang, Yung (Committee member) / Tran, Nhan (Committee member) / School of Life Sciences (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Invasive salmonellosis caused by Salmonella enterica serovar Typhimurium ST313 is a major health crisis in sub-Saharan Africa, with multidrug resistance and atypical clinical presentation challenging current treatment regimens and resulting in high mortality. Moreover, the increased risk of spreading ST313 pathovars worldwide is of major concern, given global public transportation networks and increased populations of immunocompromised individuals (as a result of HIV infection, drug use, cancer therapy, aging, etc). While it is unclear as to how Salmonella ST313 strains cause invasive disease in humans, it is intriguing that the genomic profile of some of these pathovars indicates key differences between classic Typhimurium (broad host range), but similarities to human-specific typhoidal Salmonella Typhi and Paratyphi. In an effort to advance fundamental understanding of the pathogenesis mechanisms of ST313 in humans, I report characterization of the molecular genetic, phenotypic and virulence profiles of D23580 (a representative ST313 strain). Preliminary studies to characterize D23580 virulence, baseline stress responses, and biochemical profiles, and in vitro infection profiles in human surrogate 3-D tissue culture models were done using conventional bacterial culture conditions; while subsequent studies integrated a range of incrementally increasing fluid shear levels relevant to those naturally encountered by D23580 in the infected host to understand the impact of biomechanical forces in altering these characteristics. In response to culture of D23580 under these conditions, distinct differences in transcriptional biosignatures, pathogenesis-related stress responses, in vitro infection profiles and in vivo virulence in mice were observed as compared to those of classic Salmonella pathovars tested.
Collectively, this work represents the first characterization of in vivo virulence and in vitro pathogenesis properties of D23580, the latter using advanced human surrogate models that mimic key aspects of the parental tissue. Results from these studies highlight the importance of studying infectious diseases using an integrated approach that combines actions of biological and physical networks that mimic the host-pathogen microenvironment and regulate pathogen responses.
Collectively, this work represents the first characterization of in vivo virulence and in vitro pathogenesis properties of D23580, the latter using advanced human surrogate models that mimic key aspects of the parental tissue. Results from these studies highlight the importance of studying infectious diseases using an integrated approach that combines actions of biological and physical networks that mimic the host-pathogen microenvironment and regulate pathogen responses.
ContributorsYang, Jiseon (Author) / Nickerson, Cheryl A. (Thesis advisor) / Chang, Yung (Committee member) / Stout, Valerie (Committee member) / Ott, C Mark (Committee member) / Roland, Kenneth (Committee member) / Barrila, Jennifer (Committee member) / Arizona State University (Publisher)
Created2015
Description
Damage to the central nervous system due to spinal cord or traumatic brain injury, as well as degenerative musculoskeletal disorders such as arthritis, drastically impact the quality of life. Regeneration of complex structures is quite limited in mammals, though other vertebrates possess this ability. Lizards are the most closely related organism to humans that can regenerate de novo skeletal muscle, hyaline cartilage, spinal cord, vasculature, and skin. Progress in studying the cellular and molecular mechanisms of lizard regeneration has previously been limited by a lack of genomic resources. Building on the release of the genome of the green anole, Anolis carolinensis, we developed a second generation, robust RNA-Seq-based genome annotation, and performed the first transcriptomic analysis of tail regeneration in this species. In order to investigate gene expression in regenerating tissue, we performed whole transcriptome and microRNA transcriptome analysis of regenerating tail tip and base and associated tissues, identifying key genetic targets in the regenerative process. These studies have identified components of a genetic program for regeneration in the lizard that includes both developmental and adult repair mechanisms shared with mammals, indicating value in the translation of these findings to future regenerative therapies.
ContributorsHutchins, Elizabeth (Author) / Kusumi, Kenro (Thesis advisor) / Rawls, Jeffrey A. (Committee member) / Denardo, Dale F. (Committee member) / Huentelman, Matthew J. (Committee member) / Arizona State University (Publisher)
Created2015