Regulatory elements are DNA sequences which have specialized activities that coordinate the functions of the genome. Promoters, enhancers, locus control regions, boundary elements (or insulator elements) are examples of DNA sequences that have regulatory properties. In transgenic assays insulator elements have been shown to block communication between regulatory regions, such as enhancers and promoters, when placed between these sequences and also protect genes from position effects when bracketing them, thereby affecting gene expression. Insulator sequences are bound by insulator proteins that direct the function of these sequences. One such insulator protein is the Boundary Element Associated Factor-32 (BEAF-32), a 32 kDa protein which was originally found to bind to the scs insulator sequence in the 87A heat shock locus of the Drosophila genome. BEAF-32 has two isoforms: 32A and 32B. BEAF was immunolocalized to numerous binding sites across the Drosophila genome. This was substantiated by various genome-wide mapping experiments, which have identified from 1800 to 6000 BEAF binding sites across the genome. Hence, BEAF-32 likely plays an important role in chromatin organization and gene regulation in combination with other proteins in the nucleus. However, it is not clear how BEAF-32 affects genome organization and gene regulation. We characterized essential domains in the BEAF-32 protein and identified protein partners, some of which include Transcription Factors (TFs). We further mapped the interaction regions inside BEAF and these TFs. We then attempted Fluorescent Recovery After Photobleaching (FRAP) to assess the dynamics of BEAF-32 on polytene chromosomes and also observed banding patterns, with the help of fluorescent protein labels, and evaluated its behavior during mitosis in early embryos. Finally, results obtained with BEAF prompted us to test for physical interactions between various insulator proteins and to check contradictory reported results from the literature to document interactions.

DNA double-strand breaks (DSBs) are the most lethal form of DNA damage; a single DSB, if left unrepaired, can cause cell death. Inaccurately repaired DSBs are sources of mutations, chromosomal rearrangements and genome instability. Telomeres, TG-rich nucleoprotein structures at the termini of eukaryotic chromosomes, protect chromosome ends from nucleolytic degradation and distinguish chromosome ends from those generated by DSBs. In most eukaryotes, proper telomere maintenance requires a specialized reverse transcriptase, telomerase, that utilizes an enzyme-associated RNA as template for new telomere synthesis. Increasingly, telomere-associated proteins are being recognized as playing roles in the repair of internal DSBs. At endonuclease-induced DSBs immediately preceded by ectopic, short telomere seeds, the telomeric single-stranded DNA binding protein Cdc13 recruits telomerase, promoting the addition of new (de novo) telomere sequences to the telomere seed. However, spontaneous DSBs occur very infrequently and as such, are rarely expected to occur immediately adjacent to telomere-like seed sequences. An experimental system in which a DSB is induced at a distance (~3 kb) from endogenous Sites of de novo Telomere Addition (SiRTAs) in budding yeast was utilized as a more representative model of de novo telomere addition following spontaneous DSBs. These telomere-like SiRTAs incurred high frequencies of de novo telomere addition relative to flanking sequences. Additionally, de novo telomere addition at these SiRTAs required a bipartite structure in which Cdc13 binding to a stimulatory (Stim) sequence strongly stimulates telomere addition at a nearby target (Core) sequence. The role of yet another budding yeast telomere-associated protein, Rif1, in DSB repair was also explored using an experimental system of an endonuclease-induced DSB that is primarily repaired by imprecise non-homologous end joining (NHEJ). Wild-type repair junctions contained only deletions. However, rif1â repair junctions contained relatively smaller deletions, as well as insertions, indicative of ends undergoing less resection in the absence of Rif1. A rif1 mutant lacking the protein phosphatase-1-interacting domain phenocopies the rif1â mutant, implicating this domain in Rif1âs role in regulating the fidelity of DSB repair.

No description available.

No description available.

Appropriate neuronal morphogenesis is essential for forming the distinct functional domains of each of the hundreds of types of neurons in the brain. Generating the correct size and shape of dendrites is essential for a neuron to satisfactorily sample and process the signals that converge on its dendritic field. Understanding the control of neuronal circuit development is key to understanding normal and abnormal brain function and behavior. The habenular nuclei of the limbic system regulate responses, such as anxiety, to aversive stimuli in the environment. The habenulae receive inputs from the telencephalon via elaborate dendrites that form in the center of the nuclei. The kinase Ulk2 positively regulates dendritogenesis on habenular neurons, and in turn is negatively regulated by the cytoplasmic protein Kctd12. Given that the habenulae are a nexus in the aversive response circuit, we suspected that incomplete habenular dendritogenesis would have profound implications for behavior. We find that Ulk2, which interacts with Kctd12 proteins via a small proline-serine rich domain, promotes branching and elaboration of dendrites. Loss of Kctd12 results in increased branching/elaboration and decreased anxiety. We conclude that fine-tuning of habenular dendritogenesis during development is essential for appropriate behavioral responses to negative stimuli. In addition to dendritic shaft development, dendritic spine development is a key event in synapse formation. Dendritic spines are protrusions emanating from the dendritic shaft that interact with axons to form excitatory synapses. Here we show that spinophilin/neurabin II, a scaffolding protein that is highly expressed in dendritic spines, has an important role in dendritic spine and synapse formation in hippocampal neurons. Knockdown of endogenous spinophilin with a short hairpin RNA (shRNA) causes a significant decrease in synapse and spine density, as shown by immunostaining for the presynaptic marker synaptic vesicle protein 2 and the postsynaptic marker postsynaptic density protein 95. On the other hand, expression of mCherry-spinophilin results in an increase in spine density. These results suggest that spinophilin is critical for dendritic spine and synapse formation. We hypothesized that spinophilin was promoting dendritic spine and synapse formation by regulating F-actin accumulation. Indeed, expression of GFP-spinophilin led to an increase in the amount of F-actin in spine heads. Collectively our data demonstrate an important function for spinophilin in modulating the formation of dendritic spines and synapses.

This paper examines the quality of education as it relates to the Iowa Communications Network (ICN). It reviews the literature to determine a working definition of quality that was used to create a list of characteristics desirable in teachers who use technology. A list of such teachers was solicited from three administrative committees of the ICN and from the directors of the state's 15 area education agencies. Four teachers were selected from the list and their approach to creating programs for delivery over the ICN was examined. Personal interviews were used to discover commonalities among the four teachers' approaches to distance education that had led to their success. These commonalities, along with the working definition of quality, were used to develop a set of guidelines that can be used by developers of future ICN offerings. The guidelines contain information on designing courses for distance education, overcoming obstacles, use of collaborative techniques, and distance learning methodology. The guidelines were developed into a small booklet that will be distributed to teachers and administrators across the state of lowa.

Software architecture appeared in the early 1990s as a distinct discipline within software engineering. Models based on software architecture attempt to reduce the complexity of software by providing relatively coarse-grained structures for representing different aspects of software development. A software architecture typically consists of various components and connections arranged in a specific topology. Elements of the topology can serve as abstractions on (for example) modules, objects, protocols or interfaces. The meaning of the topology depends on viewpoint. Software architectures' can be described using an architecture description language (ADL). The key goals of ADLs are to communicate alternate designs to the different individuals involved in software development (such individuals are referred to as "stakeholders"), to detect reusable structures, and to record design decisions. A major problem in software architecture has been the difficulty of creating different representations of an architecture to accommodate differing viewpoints of stakeholders. Ideally, different viewpoints would be conveyed in a way that is both comprehensive enough for specialists but consistent enough for generalists. The representation problem has been one of reconciling and integrating different viewpoints. This dissertation provided a solution to the representation problem by creating a tool for three-dimensional visualization of software architectures using the Virtual Reality Modeling Language (VRML). Different architectural viewpoints were first defined in an ADL called the Visually Translatable Architecture Description Language (VT ADL). When VT ADL was translated into VRML, software architectures were embodied within three-dimensional "worlds" through which stakeholders may navigate. Each viewpoint was a separate VRML world. A viewpoint could be related to other viewpoints, representing different facets of software architectures, to reflect different stakeholder requirements. Traceability from design to requirements was possible through VRML hyperlinks from the visualized architecture. The goal of the dissertation was to develop a prototype for demonstrating the visualization technique. Based on the successful results of two visualization case studies, we concluded that the goal was achieved. Refinement of the prototype into a polished visualization tool was recommended. In future research, the refined version should be used for realistic evaluation of the technique in an actual software development environment.

This thesis examines the performance of a custom built deep UV laser (257.5nm) for Raman spectroscopy and the advantages of Raman spectroscopy with a laser in the deep UV over a laser in the visible range (532 nm). It describes the theory of resonance Raman scattering, the experimental setup for Raman spectroscopy and a few Raman spectroscopy measurements. The measurements were performed on biological samples oak tree leaf and lactobacillus acidophilus and bifidobacteria from probotioc medicinal capsules. Fluorescence free Raman spectra were acquired for the two samples with 257.5 nm laser. The Raman spectra for the two samples with a 532nm laser was masked with fluorescence. Raman measurements for an inorganic salt sodium nitrate showed a resonance Raman effect with 257.5 nm laser which led to enhancement in the Raman intensity as compared to that with 532 nm laser. Therefore we were able to demonstrate two advantages of deep UV Raman spectroscopy. First one is the possibility of acquiring fluorescence free spectra for biological samples. Second is the possibility of gaining enhancement in Raman intensity due to resonance Raman effect. It was observed that 257.5 nm laser requires optimization to reduce the bandwidth of the laser to get better resolution. The 257.5 nm laser also needs to be optimized to obtain higher power to get better signal to noise ratio. The experimental setup can also be further improved to obtain better resolution. If the improvements required in the setup are implemented, the deep UV Raman setup will become an important tool for spectroscopy.

Fiber optic networks are no longer just pipelines for transporting data in the long haul backbone. Exponential growth in traffic in metro-regional areas has pushed higher capacity fiber toward the edge of the network, and highly dynamic patterns of heterogeneous traffic have emerged that are often bursty, severely stressing the historical "fat and dumb pipe" static optical network, which would need to be massively over-provisioned to deal with these loads. What is required is a more intelligent network with a span of control over the optical as well as electrical transport mechanisms which enables handling of service requests in a fast and efficient way that guarantees quality of service (QoS) while optimizing capacity efficiency. An "agile" optical network is a reconfigurable optical network comprised of high speed intelligent control system fed by real-time in situ network sensing. It provides fast response in the control and switching of optical signals in response to changing traffic demands and network conditions. This agile control of optical signals is enabled by pushing switching decisions downward in the network stack to the physical layer. Implementing such agility is challenging due to the response dynamics and interactions of signals in the physical layer. Control schemes must deal with issues such as dynamic power equalization, EDFA transients and cascaded noise effects, impairments due to self-phase modulation and dispersion, and channel-to-channel cross talk. If these issues are not properly predicted and mitigated, attempts at dynamic control can drive the optical network into an unstable state. In order to enable high speed actuation of signal modulators and switches, the network controller must be able to make decisions based on predictive models. In this thesis, we consider how to take advantage of Software Defined Networking (SDN) capabilities for network reconfiguration, combined with embedded models that access updates from deployed network monitoring sensors. In order to maintain signal quality while optimizing network resources, we find that it is essential to model and update estimates of the physical link impairments in real-time. In this thesis, we consider the key elements required to enable an agile optical network, with contributions as follows: *Control Framework: extended the SDN concept to include the optical transport network through extensions to the OpenFlow (OF) protocol. A unified SDN control plane is built to facilitate control and management capability across the electrical/packet-switched and optical/circuit-switched portions of the network seamlessly. The SDN control plane serves as a platform to abstract the resources of multilayer/multivendor networks. Through this platform, applications can dynamically request the network resources to meet their service requirements. *Use of In-situ Monitors: enabled real-time physical impairment sensing in the control plane using in-situ Optical Performance Monitoring (OPM) and bit error rate (BER) analyzers. OPM and BER values are used as quantitative indicators of the link status and are fed to the control plane through a high-speed data collection interface to form a closed-loop feedback system to enable adaptive resource allocation. *Predictive Network Model: used a network model embedded in the control layer to study the link status. The estimated results of network status is fed into the control decisions to precompute the network resources. The performance of the network model can be enhanced by the sensing results. *Real-Time Control Algorithms: investigated various dynamic resource allocation mechanisms supporting an agile optical network. Intelligent routing and wavelength switching for recovering from traffic impairments is achieved experimentally in the agile optical network within one second. A distance-adaptive spectrum allocation scheme to address transmission impairments caused by cascaded Wavelength Selective Switches (WSS) is proposed and evaluated for improving network spectral efficiency.

A preliminary causal-comparative study was conducted in an elementary suburban school in Massachusetts to investigate the impact of electronic portfolio assessments in student's intrinsic motivation and computer interest. The target population were two groups of fourth grade and two groups of fifth grade students for a total of 77 subjects. They were trained and introduced to electronic portfolio assessments, a program which lasted for the entire school year. The students used Hyper Studio, a multimedia software program developed and marketed by Roger Wagner Publishing, Inc. It was the intention of the elementary school program directors and teachers that students would take a proactive and self-administered approach to the management of portfolios. Participants were tested before initiation of the program and post-tested six months later using the "Children's Academic Intrinsic Motivation Inventory" "(CAIMI)," a Likert scale test developed by Adele Eskeles Gottfried, Ph.D. at California State University, Northridge. They were also given a pre-test and post-test computer interest Likert scale inventory adapted from a test named Moe Computer Educational Survey "(MCES)." This test was developed at South Dakota State University by Daniel J. Moe as part of his research and graduate work. The MCES test was used to determine if there had been a change of computer interest by girls after participation in the computer-based electronic portfolio assessment program. The motivation and interest pre-and post-test results were analyzed with t-tests (p < .05 for motivation, p < .01 for interest). There were no significant treatment effects. There were score increases at the lowest level of the motivation pre-test scoring level but no increases at the highest pre-test scoring levels. Thirty-four students (48 percent) showed an increase in intrinsic motivation scores, while thirty-seven students (52 percent) showed no change or experimented a decrease in scores. As a result, it was concluded that other factors, including subject maturation and teachers' skills in identifying and working intensely with the students who displayed symptoms of initial low motivation may have contributed to the increases. The study was inconclusive because it did not provide evidence to support the hypothesis that there was a change in intrinsic motivation or interest of all the students as a result of their participation in the electronic portfolio assessment program in the Massachusetts suburban elementary school. For confidentiality reasons, fictitious names were used to describe the suburban locality and the experimental school. The locality was named Best borough and the school site Pioneer.