Comparative Studies of Processivity Clamp Loader ATP Site Function.

DNA replicases utilize ring-shaped sliding clamps to ensure polymerase processivity. An ATP-dependent clamp loader topologically links the clamp around DNA in a multi-step mechanism. Clamp loaders are ring-shaped pentamers of AAA+ subunits. The pentamer complex contains 3-4 ATP sites, each located at the interface of two subunits. In each ATP site, an arginine residue from one subunit is located near the γ-phosphate of ATP bound to the adjacent subunit. These arginines act as “arginine fingers†that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis. This thesis utilizes mutations in the arginine fingers of the E. coli and S. cerevisiae clamp loaders in order to examine steps in the clamp loading mechanism after the clamp loader binds ATP. The E. coli γ complex couples ATP hydrolysis to the loading of β sliding clamps onto DNA. We demonstrate that the δ\u27 subunit of γ complex contributes an arginine finger into ATP site D. Hydrolysis in site D is inhibited by mutation of the γ subunit arginine finger, which affects sites B and C. The δ\u27 arginine finger also mediates β binding and the γ arginine fingers are important for DNA binding. Utilizing a three-subunit fusion construct, we determined that a single arginine finger mutation in either site B or C causes inactivation of γ complex. Replication factor C (RFC) loads the processivity clamp, proliferating cell nuclear antigen (PCNA), onto DNA. ATP binding to RFC activates a γ-phosphate sensor in ATP site C that promotes DNA association by RFC-PCNA. DNA binding to the RFC-PCNA complex then triggers the ATP hydrolysis cycle which starts in site C and ends with ATP site D. ATP hydrolysis in site D is uniquely stimulated by PCNA and we propose that this site is coupled to closure of PCNA around DNA. PCNA closure severs contact to RFC subunits D and E, and the γ- phosphate sensor of ATP site C is switched off, leading to ejection of RFC from the site of PCNA loading. This work sheds light on conserved aspects of ATP site function that may extend to all clamp loaders

Understanding The In-School Literacies Of African American Males Through A Sociocultural Paradigm: Implications For Teacher Professional Development

ABSTRACT UNDERSTANDING THE IN-SCHOOL LITERACIES OF AFRICAN AMERICAN MALES THROUGH A SOCIOCULTURAL PARADIGM: IMPLICATIONS FOR TEACHER PROFESSIONAL DEVELOPMENT by AARON M. JOHNSON May 2016 Advisor: Dr. Gina DeBlase Major: Curriculum and Instruction Degree: Doctor of Philosophy There has been great debate about the reasons why African American male students reject the institution of school and school related content. Furthermore, data from multiple sources, including, national and local assessments and governmental studies, document a gap in achievement and school retention rates between African American students and their White counterparts. The data substantiates the notions that African American males have an aversion to the pedagogy of their teachers, schools’ environments, and the cultural mores and values of the institution of school that often run counter to their home or community values. This study explored how immersing teachers in a book club model of professional development could encourage them to use the practice in their classrooms and to use literacy as a means to connect students to the institution of school and school-related content. The book club model is heavily anchored in Vygotskian theory, and this study used Vygotsky’s social learning theory as a foundational theoretical framework while exposing teachers to a professional development series that encouraged them to address their perceptions of students by participating in inquiry about their instructional practice. Accordingly, teachers were asked to reflect on their pedagogy, text selections for their African America male students, and their thoughts about the nature of literacy and its components. The purpose of this study was twofold: 1) to engage teachers in professional development aimed at providing evidence-based literacy strategies to use with their students; and 2) to assist teachers to make connections between their perceptions of their African American students and their pedagogical decisions. The history of African Americans in this country, Supreme Court cases related to school desegregation, and the sociopolitical ideals of this nation were used as a backdrop to contextualize the current academic pandemic that faces African American children. This study used Tatum (2005) as the guiding text and his nesting ground framework was the main construct upon which the activities, conversations, and solutions were grounded. It was understood that human thought is varied and nuanced; therefore, it was necessary to employ a qualitative methodology using a sociocultural paradigm to understand how to improve teachers’ understandings of their students. Also, a robust data collection methodology was used to ensure that the findings could answer questions of validity and reliability

Toward a Theory of an Integrated Theoretical Approach of Literacy for Black Boys

In the education landscape the literacy of Black boys is viewed from deficit framing. Often, educators, politicians, and laypeople point to scores on standardized assessments such as the MSTEP, NAEP, ACT, SAT, and NWEA, these tests only tell a part of the story. The part of the story that those assessments do tell is the abject failure of schools’ ability to engage Black boys in school-based literacy and catapult them into proficient and advanced proficient reading levels. The part of the story that those assessments do not tell is the literate lives that Black boys lead. Furthermore, schools do a less than adequate job at employing their own theoretical framings that they themselves adopt to engage students in literacy instruction. Schools do not recognize how racism, antiblackness, deficit-oriented thinking held by society, and in schools specifically, impact the literate lives of Black boys. Asset-based framings allow us to conceive of literacy instruction and build school environments that value the textured identities of Black boys. This article compels educators to consider the complex identities of Black boys as they build instruction and to use multiple integrated socioculturally-based theoretical framings to underpin that instruction

EXERCISE AND DIET PROGRAMS DROSOPHILA SIMULANS OFFSPRING METABOLIC PHENOTYPE

Obesity in pediatric patients has increased significantly in recent decades, along with susceptibility to Type 2 Diabetes (T2D), cardiovascular disease, cancer, and mortality. The relative contribution of genetic and environmental conditions is unclear in these cases. Drosophila simulans contain an insulin-like growth pathway (IGF-1), which is a large contributing factor in anabolic stimulation and growth in children. The fat body of Drosophila is the equivalent of the vertebrate adipose tissue and liver regarding its storage and major metabolic functions. Thus, Drosophila is an ideal model to study the effects of environmental conditions, namely exercise and diet, on obesity phenotype. The purpose of this experiment was to characterize the model of obesity in Drosophila and determine how much diet and exercise act as epigenetic factors that affect metabolic function of parents and reprogram offspring phenotype trans-generationally. F0 male flies were broken into four groups, control (CF), exercise (EF), western diet (WF), and western diet with exercise (WEF), and exposed for a week. The F0 flies were then evaluated for behavioral and physical changes through monitoring locomotor activity, sleep-wake cycle, food preference, weights, and mortality. A subsection of each group was bred after exposure rather than tested, and their F1 offspring, in some instances, were tested. This process was repeated for F2 and F3. Western diet resulted in greater mortality and reduced activity in F0 and F1 flies. Locomotor data also showed increased nighttime activity in F0 western diet flies, and WFO flies from F1 and F3, suggesting a heritable disruption to the circadian rhythm. Food preference data shows that Western diet food is preferred by F0 flies that are pre-exposed to it, while control diet is preferred by those who were not. Naive F1 male and female flies with exposed parents prefer Western diet, while offspring whose parents were fed by control diet prefer control diet. Our results indicate that obesity characteristics in Drosophila are comparable in many instances with that of humans, making them a good study model for obesity

Robot Parkour: The Ground Reaction Complex & Dynamic Transitions

Many locomotion tasks on real, complex terrain are poorly modeled as deviations from limit cycles of steady state running. As obstacles become larger and larger relative to leg length, every step is novel and challenging: the leap onto a ledge in Fig. 1 is quite unlike any running step. We seek to organize and systematically reduce this space to a finite set of dynamic transition “words” in order to enable dramatic outdoor transitional behaviors. For moreinformation: Kod*La

Scholastic Liberation: Schools\u27 Impact on African American Academic Achievement

This article addresses some of the factors that contribute to low achievement observed in African American students. It is common that either schools or school districts are unable to fix the problem or they are unaware about how the beliefs and attitudes about African American students can contribute to their low performance in school. Furthermore, this article encourages school institutions to examine themselves and change school environments to align to the identities of African American students. African American students must be liberated from negative assumptions about them and to do that, individuals and the institution of school as a whole, has to stop assigning blame to students and families and get serious about reconceptualizing school to meet the needs of all learners

Antipredator Behavior in Desmognathus ochrophaeus: Threat-Specific Responses to Chemical Stimuli in a Foraging Context

Prey species may reduce the likelihood of injury or death by engaging in defensive behavior but often incur costs related to decreased foraging success or efficiency. To lessen these costs, prey may adjust the intensity or type of antipredator behavior according to the nature of the perceived threat. We evaluated the potential for threat-sensitive responses by Allegheny Mountain dusky salamanders (Desmognathus ochrophaeus) exposed to chemical stimuli associated with predation by asking three questions:(1) Do individual D. ochrophaeus respond to chemical cues in a threat-sensitive manner? (2) Do salamanders exhibit the same pattern of behavioral response while foraging? and (3) Is foraging efficiency reduced when focal individuals are exposed to stimuli from predators or predation events? In our first experiment, we evaluated salamander chemosensory movements (nose-taps), locomotor activity (steps), and edge behavior in response to chemical stimuli from disturbed and injured conspecifics as well as predatory Gyrinophilus porphyriticus and found that individual D. ochrophaeus show a significant graded increase in nose-taps when exposed to cues from conspecifics and a reduction in activity when exposed to the predator. In our second experiment, we again observed salamander responses to the same chemical stimuli but in this instance added five Drosophila prey to the test dishes. We found that salamanders exhibited a similar pat-tern of response to the chemical stimuli in the presence of prey, showing a graded increase in nose-taps to cues from conspecifics and a reduction in activity when exposed to the predator. However, foraging efficiency (i.e. the proportion of successful strikes) did not vary significantly among treatments. Our data show that individual D. ochrophaeus detect and differentially respond to chemical stimuli associated with predation, but do not significantly reduce foraging efficiency. Overall, the type and relative intensity of these responses is largely unaffected by the presence of potential prey

Cellular Decomposition and Classification of a Hybrid System

Robots are often modeled as hybrid systems providing a consistent, formal account of the varied dynamics associated with the loss and gain of kinematic freedom as a machine impacts and breaks away from its environment