The Epc-N domain: a predicted protein-protein interaction domain found in select chromatin associated proteins

BACKGROUND: An underlying tenet of the epigenetic code hypothesis is the existence of protein domains that can recognize various chromatin structures. To date, two major candidates have emerged: (i) the bromodomain, which can recognize certain acetylation marks and (ii) the chromodomain, which can recognize certain methylation marks. RESULTS: The Epc-N (Enhancer of Polycomb-N-terminus) domain is formally defined herein. This domain is conserved across eukaryotes and is predicted to form a right-handed orthogonal four-helix bundle with extended strands at both termini. The types of amino acid residues that define the Epc-N domain suggest a role in mediating protein-protein interactions, possibly specifically in the context of chromatin binding, and the types of proteins in which it is found (known components of histone acetyltransferase complexes) strongly suggest a role in epigenetic structure formation and/or recognition. There appear to be two major Epc-N protein families that can be divided into four unique protein subfamilies. Two of these subfamilies (I and II) may be related to one another in that subfamily I can be viewed as a plant-specific expansion of subfamily II. The other two subfamilies (III and IV) appear to be related to one another by duplication events in a primordial fungal-metazoan-mycetozoan ancestor. Subfamilies III and IV are further defined by the presence of an evolutionarily conserved five-center-zinc-binding motif in the loop connecting the second and third helices of the four-helix bundle. This motif appears to consist of a PHD followed by a mononuclear Zn knuckle, followed by a PHD-like derivative, and will thus be referred to as the PZPM. All non-Epc-N proteins studied thus far that contain the PZPM have been implicated in histone methylation and/or gene silencing. In addition, an unusual phyletic distribution of Epc-N-containing proteins is observed. CONCLUSION: The data suggest that the Epc-N domain is a protein-protein interaction module found in chromatin associated proteins. It is possible that the Epc-N domain serves as a direct link between histone acetylation and methylation statuses. The unusual phyletic distribution of Epc-N-containing proteins may provide a conduit for future insight into how different organisms form, perceive and respond to epigenetic information

An Investigation of Masked Priming Mechanisms in Binary Classification Tasks

The goal of the present research was to examine the nature of masked priming with an emphasis on the influence of stimulus-response (S-R) associations. In Chapter 2, both the magnitude of the category congruence (priming) effect and the nature of the priming distance effect were assessed in two number classification tasks. Participants made either magnitude (i.e., is the target larger or smaller than ‘5’?) or identification judgments (i.e., press one button if the target is a ‘1’, ‘2’, ‘3’ or ‘4’ or the other button if the target is a ‘6’, ‘7’, ‘8’ or ‘9’). Priming distance effects in both tasks indicated that, regardless of task instructions, semantic activation played a key role in producing masked priming even when the identification task showed evidence of priming from S-R associations. In Chapter 3, category learning tasks were used involving stimuli having neither the ability to activate semantic information nor any a priori response associations. Participants learned, through feedback, artificially-defined category sets. Each category contained a prototype item that served as a masked prime. In the single-session tasks, responses were faster when a stimulus was primed by its own prototype versus the prototype of the other category, however, this (priming) effect only increased in size when participants performed the task over multiple sessions, indicating that it takes considerable time for the S-R associations to develop and impact priming. The research in Chapters 2 and 3 was based on a prospective view of masked priming. There is, however, an alternative retrospective view supported by numerous demonstrations of prime validity effects (i.e., larger priming effects when the proportion of congruent trials is high). In Chapter 4, an arrow classification task with free choice stimuli was used to examine this debate. The prime-target relationship for the arrow targets was either: a) always congruent, b) always incongruent, or c) unpredictive. Prime validity effects for the free choice trials (i.e., trials involving “either way” stimuli, e.g., \u3c \u3e, for which either response was acceptable) occurred using both 77 ms and 165 ms prime-target intervals. The results in the unpredictive conditions support a prospective view of masked priming since they indicate that it was response bias suppression when the proportion of incongruent trials was high that produced the prime validity effects

Effects of Single Panel Replacement of a Full-Scale, Full-Depth, Precast Concrete Bridge Deck System

The use of precast concrete deck panels is becoming increasingly popular for bridge construction and rehabilitation in the state of Utah and across the country. It allows for the use of full depth concrete deck panels but removes the long construction times of traditional cast-in-place methods. One of the challenges to the use of precast deck panels is the transverse deck panel joints that exist between the panels. These joints are unreinforced using traditional methods and therefore are the weakest section of the bridge. In many situations the joint will fail and water seeps through and can damage the bridge superstructure. Post-tensioning of precast decks has become the standard. The post-tensioning provides reinforcing through the joints, reducing the cracking that occurs. Additionally, the post-tensioning provides pressure along the joint and closes cracks that have occurred, therefore preventing water from leaking through to the superstructure and damaging it. The Utah Department of Transportation uses post-tensioning cables that run along the length of the bridge deck, applying pressure on the joints. One of the problems with using this method is it does not allow for the replacement of a single deck panel should the need arise. Utah State University has been researching a new post-tensioned connection that would allow for the replacement of a single deck panel. The “curved bolt” connection connects each deck panel to adjacent panels, providing reinforcement and post-tensioning along the joint. Laboratory testing was undertaken to investigate the effects of single panel bridge rehabilitation on the existing deck system

A Study to Determine Criteria Essential to Technology Education at the Secondary Education Level

To accomplish the purpose of this study, the following goals were used: 1. Determine the list of curriculum criteria essential to technology education programs at the secondary level; 2. Validate the list of curriculum criteria essential to technology education programs at the secondary level

Do residents of food deserts express different food buying preferences compared to residents of food oases? A mixed-methods analysis

Background: Many people lack access to food stores that provide healthful food. Neighborhoods with poor supermarket access have been characterized as “food deserts” (as contrast with “food oases”). This study explored factors influencing food buying practices among residents of food deserts versus food oases in the city of Boston, USA. Methods: We used the mixed-methods approach of concept mapping, which allows participants to identify, list, and organize their perceptions according to importance. Resulting maps visually illustrate priority areas. Results: Sixty-seven low-income adults completed the concept mapping process that identified 163 unique statements (e.g. relating to affordability, taste, and convenience) that influence food buying practices. Multivariate statistical techniques grouped the 163 statements into 8 clusters or concepts. Results showed that average cluster ratings and rankings were similar between residents of food deserts and food oases. Conclusions: The implication of this study pertains to the importance of community resources and emergency food assistance programs that have served to minimize the burden associated with hunger and poor food access among low-income, urban populations

Theoretical studies of a hydrogen abstraction tool for nanotechnology

In the design of a nanoscale, site-specific hydrogen abstraction tool, the authors suggest the use of an alkynyl radical tip. Using ab initio quantum-chemistry techniques including electron correlation they model the abstraction of hydrogen from dihydrogen, methane, acetylene, benzene and isobutane by the acetylene radical. By conservative estimates, the abstraction barrier is small (less than 7.7 kcal mol^-1) in all cases except for acetylene and zero in the case of isobutane. Thermal vibrations at room temperature should be sufficient to supply the small activation energy. Several methods of creating the radical in a controlled vacuum setting should be feasible. The authors show how nanofabrication processes can be accurately and inexpensively designed in a computational framework

Photodiode-Based, Passive Ultraviolet Dosimeters

Simple, passive instruments have been developed for measuring the exposure of material specimens to vacuum ultraviolet (VUV) radiation from the Sun. Each instrument contains a silicon photodiode and a coulometer. The photocharge generated in the photodiode is stored in the coulometer. The accumulated electric charge measured by use of the coulometer is assumed to be proportional to the cumulative dose of VUV radiation expressed in such convenient units as equivalent Sun hours (ESH) [defined as the number of hours of exposure to sunlight at normal incidence]. Intended originally for use aboard spacecraft, these instruments could also be adapted to such terrestrial uses as monitoring the curing of ultraviolet-curable epoxies. Each instrument includes a photodiode and a coulometer assembly mounted on an interface plate (see figure). The photodiode assembly includes an aluminum housing that holds the photodiode, a poly(tetrafluoroehylene) cosine receptor, and a narrow-band optical filter. The cosine receptor ensures that the angular response of the instrument approximates the ideal angular response (proportional to the cosine of the angle of incidence). The filter is chosen to pass the ultraviolet wavelength of interest in a specific experiment. The photodiode is electrically connected to the coulometer. The factor of proportionality between the charge stored in the coulometer and ultraviolet dosage (in units of ESH) is established, prior to use, in calibration experiments that involve the use of lamps and current sources traceable to the National Institute of Standards and Technology