12th Advanced Accelerator Concept (AAC 2006) Workshop (open access)

12th Advanced Accelerator Concept (AAC 2006) Workshop

Summary of the 12th Advanced Accelerator Concept (AAC 2006) Workshop help by NIU and ANL on July 10th-15th 2006 in Lake Geneva WI. The proceedings of the workshop have been published as an AIP conference proceedings "12th Advanced Accelerator Concepts Workshop” volume 877.
Date: July 15, 2006
Creator: Piot, Philippe
Object Type: Text
System: The UNT Digital Library
2004 Toxic Chemical Release Inventory Report for the Emergency Planning and Community Right-to-Know Act of 1986, Title III, Section 313 (open access)

2004 Toxic Chemical Release Inventory Report for the Emergency Planning and Community Right-to-Know Act of 1986, Title III, Section 313

Section 313 of Emergency Planning and Community Right-to-Know Act (EPCRA) specifically requires facilities to submit a Toxic Chemical Release Inventory Report (Form R) to the U.S. Environmental Protection Agency (EPA) and state agencies if the owners and operators manufacture, process, or otherwise use any of the listed toxic chemicals above listed threshold quantities. EPA compiles this data in the Toxic Release Inventory database. Form R reports for each chemical over threshold quantities must be submitted on or before July 1 each year and must cover activities that occurred at the facility during the previous year. For reporting year 2004, Los Alamos National Laboratory (LANL or the Laboratory) submitted Form R reports for lead compounds, nitric acid, and nitrate compounds as required under the EPCRA Section 313. No other EPCRA Section 313 chemicals were used in 2004 above the reportable thresholds. This document provides a description of the evaluation of EPCRA Section 313 chemical use and threshold determinations for LANL for calendar year 2004, as well as background information about data included on the Form R reports.
Date: January 15, 2006
Creator: Stockton, M.
Object Type: Report
System: The UNT Digital Library
3D highly oriented nanoparticulate and microparticulate array ofmetal oxide materials (open access)

3D highly oriented nanoparticulate and microparticulate array ofmetal oxide materials

Advanced nano and micro particulate thin films of 3d transition and post-transition metal oxides consisting of nanorods and microrods with parallel and perpendicular orientation with respect to the substrate normal, have been successfully grown onto various substrates by heteronucleation, without template and/or surfactant, from the aqueous condensation of solution of metal salts or metal complexes (aqueous chemical growth). Three-dimensional arrays of iron oxide nanorods and zinc oxide nanorods with parallel and perpendicular orientation are presented as well as the oxygen K-edge polarization dependent x-ray absorption spectroscopy (XAS) study of anisotropic perpendicularly oriented microrod array of ZnO performed at synchrotron radiation source facility.
Date: September 15, 2006
Creator: Vayssieres, Lionel; Guo, Jinghua & Nordgren, Joseph
Object Type: Article
System: The UNT Digital Library
Accelerator-Driven Neutron Source for Cargo Screening (open access)

Accelerator-Driven Neutron Source for Cargo Screening

Advanced neutron interrogation systems for the screening ofsea-land cargo containers for shielded special nuclear materials (SNM)require a high-yield neutron source to achieve the desired detectionprobability, false alarm rate, and throughput. An accelerator-drivenneutron source is described that produces a forward directed beam ofhigh-energy (up to 8.5 MeV) neutrons utilizing the D(d,n)3He reaction atdeuteron beam energies of up to 6 MeV. The key components of the neutronsource are a high-current RFQ accelerator and an innovative neutronproduction target. A microwave-driven deuteron source is coupled to anelectrostatic LEBT that injects a 40 mA D+-beam into a 6 MeV, 5.1meter-long, 200 MHz RFQ. The RFQ is based on an unusual beam dynamicsdesign and is capable of operating at a duty factor that produces morethan 1.2 mA timeaverage beam current. The beam is transported to a2-atmosphere deuterium gas target with a specially-designed, thinentrance window. A high-frequency dipole magnet is used to spread thebeam over the long dimension of the 4 by 35 cm target window. The sourcewill be capable of delivering a neutron flux of ~;2 x 107 n/(cm2 x s) tothe center of a sea-land cargo container and is expected t o satisfy therequirements for full testing and demonstration of advanced neutroninterrogation techniques based on …
Date: November 15, 2006
Creator: Ludewigt, B. A.; Bleuel, D. L.; Hoff, M. D.; Kwan, J. W.; Li, D.; Ratti, A. et al.
Object Type: Article
System: The UNT Digital Library
Addressing an Uncertain Future Using Scenario Analysis (open access)

Addressing an Uncertain Future Using Scenario Analysis

The Office of Energy Efficiency and Renewable Energy (EERE) has had a longstanding goal of introducing uncertainty into the analysis it routinely conducts in compliance with the Government Performance and Results Act (GPRA) and for strategic management purposes. The need to introduce some treatment of uncertainty arises both because it would be good general management practice, and because intuitively many of the technologies under development by EERE have a considerable advantage in an uncertain world. For example, an expected kWh output from a wind generator in a future year, which is not exposed to volatile and unpredictable fuel prices, should be truly worth more than an equivalent kWh from an alternative fossil fuel fired technology. Indeed, analysts have attempted to measure this value by comparing the prices observed in fixed-price natural gas contracts compared to ones in which buyers are exposed to market prices (see Bolinger, Wiser, and Golove and (2004)). In addition to the routine reasons for exploring uncertainty given above, the history of energy markets appears to have exhibited infrequent, but troubling, regime shifts, i.e., historic turning points at which the center of gravity or fundamental nature of the system appears to have abruptly shifted. Figure 1 below …
Date: December 15, 2006
Creator: Siddiqui, Afzal S. & Marnay, Chris
Object Type: Report
System: The UNT Digital Library
Analysis of Energy Saving Impacts of New Commercial Energy Codes for the Gulf Coast (open access)

Analysis of Energy Saving Impacts of New Commercial Energy Codes for the Gulf Coast

Report on an analysis of the energy savings and cost impacts associated with the use of newer and more efficiently commercial building energy codes in the states of Louisiana and Mississippi.
Date: December 15, 2006
Creator: Halverson, Mark A.; Gowri, Krishnan & Richman, Eric E.
Object Type: Report
System: The UNT Digital Library
Appendix A; Appendix B (open access)

Appendix A; Appendix B

This is the summary page for the technical and other reports on the DOE Cooperative Agreement DE-FC36-94CH10604 for the period of January 1, 2000 to December 31, 2004. The progress, technical and other reports and publications are consolidated by the contracting year and also by the cooperative agreement tasks. The listing sorted by tasks is also sub-sorted by fiscal year for easier navigation. These listings are given in appendix A and Appendix B of this summary report. Individual report files are located in each fiscal year directory (i.e., FY00, FY01, etc. up to FY04). The complete listing and report files are also posted on the web site and is fully navigable by these two criteria. The web site is at: http://www.ceere.org/beep/beep{_}pubsanddownloads.html. More significant and less obvious part of deliverables are applications of this research, which are used in everyday operations of NFRC, software tools and manufacturers design practice, which has significantly changed as a result of this and related research efforts.
Date: September 15, 2006
Creator: Curcija, Dragan C.
Object Type: Report
System: The UNT Digital Library
A Barrel IFR Instrumented With Limited Streamer Tubes for BABAR Experiment (open access)

A Barrel IFR Instrumented With Limited Streamer Tubes for BABAR Experiment

The new barrel Instrumented Flux Return (IFR) of BABAR detector will be reported here. Limited Streamer Tubes (LSTs) have been chosen to replace the existing RPCs as active elements of the barrel IFR. The layout of the new detector will be discussed: in particular, a cell bigger than the standard one has been used to improve efficiency and reliability. The extruded profile is coated with a resistive layer of graphite having a typical surface resistivity between 0.2 and 0.4 MOhm/square. The tubes are assembled in modules and installed in 12 active layers of each sextant of the IFR detector. R&D studies to choose the final design and Quality Control procedure adopted during the tube production will be briefly discussed. Finally the performances of installed LSTs into 2/3 of IFR after 8 months of operations will be reported.
Date: November 15, 2006
Creator: Andreotti, M.
Object Type: Article
System: The UNT Digital Library
Biosynthesis of the Cyclotide MCoTI-II using an Engineered Intein (open access)

Biosynthesis of the Cyclotide MCoTI-II using an Engineered Intein

Cyclotides are an emerging family of naturally occurring circular mini-proteins ({approx}30-40 amino acids) characterized by six conserved Cys residues (forming 3 disulfide bridges) that create a topologically unique structure designated as a cyclic cysteine knot (CCK). The cysteine knot motif, which is embedded within the macrocylic backbone, is described as two disulfide bridges that form a ring that is penetrated by the third disulfide bridge. The cyclic backbone and CCK motif together confer cyclotides with a remarkable stability and resistance to proteolytic, chemical, and thermal degradation. Further, cyclotides are functionally diverse and display a wide range of functions including uterotonic activity, trypsin inhibition, cytotoxicity, neurotensin binding, anti-HIV, antimicrobial, and insecticidal activity. Together, these characteristics make cyclotides attractive candidates for both drug design and agricultural applications, both in their native forms and as molecular scaffolds for the incorporation of novel bioactivities. [1] The ability to manipulate production of cyclotides within biological systems is critical for mutagenesis studies, production of grafted products, and the mass production of cyclotides with novel activities. My adviser's hope is to achieve this capability by employing recombinant DNA expression techniques to generate large combinatorial libraries of cyclotides. The advantage in creating a biosynthetic library (containing {approx}10{sup 6}-10{sup …
Date: August 15, 2006
Creator: Cantor, J & Camarero, J A
Object Type: Report
System: The UNT Digital Library
Borehole Summary Report for Core Hole C4998 – Waste Treatment Plant Seismic Boreholes Project (open access)

Borehole Summary Report for Core Hole C4998 – Waste Treatment Plant Seismic Boreholes Project

Seismic borehole C4998 was cored through the upper portion of the Columbia River Basalt Group and Ellensburg Formation to provide detailed lithologic information and intact rock samples that represent the geology at the Waste Treatment Plant. This report describes the drilling of borehole C4998 and documents the geologic data collected during the drilling of the cored portion of the borehole.
Date: December 15, 2006
Creator: Barnett, D. BRENT & Garcia, Benjamin J.
Object Type: Report
System: The UNT Digital Library
CH-TRU Waste Content Codes (CH-TRUCON) (open access)

CH-TRU Waste Content Codes (CH-TRUCON)

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container. Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 …
Date: August 15, 2006
Creator: Westinghouse TRU Solutions LLC
Object Type: Report
System: The UNT Digital Library
CH-TRU Waste Content Codes (CH-TRUCON) (open access)

CH-TRU Waste Content Codes (CH-TRUCON)

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container. Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 …
Date: September 15, 2006
Creator: Westinghouse TRU Solutions LLC
Object Type: Report
System: The UNT Digital Library
The Characterization of Biotic and Abiotic Media Upgradient and Downgradient of the Los Alamos Canyon Weir (open access)

The Characterization of Biotic and Abiotic Media Upgradient and Downgradient of the Los Alamos Canyon Weir

As per the Mitigation Action Plan for the Special Environmental Analysis of the actions taken in response to the Cerro Grande Fire, sediments, vegetation, and small mammals were collected directly up- and downgradient of the Los Alamos Canyon weir, a low-head sediment control structure located on the northeastern boundary of Los Alamos National Laboratory, to determine contaminant impacts, if any. All radionuclides ({sup 3}H, {sup 137}Cs, {sup 238}Pu, {sup 239,240}Pu, {sup 90}Sr, {sup 241}Am, {sup 234}U, {sup 235}U and {sup 238}U) and trace elements (Ag, As, Ba, Be, Cd, Cr, Cu, Hg, Ni, Pb, Sb, Se, and Tl) in these media were low and most were below regional upper level background concentrations (mean plus three sigma). The very few constituents that were above regional background concentrations were far below screening levels (set from State and Federal standards) for the protection of the human food chain and the terrestrial environment.
Date: January 15, 2006
Creator: Fresquez, P.R.
Object Type: Report
System: The UNT Digital Library
Characterization of bubble core and cloudiness in Yb3+:Sr5(PO4)3F crystals using Micro-Raman spectroscopy (open access)

Characterization of bubble core and cloudiness in Yb3+:Sr5(PO4)3F crystals using Micro-Raman spectroscopy

Ytterbium doped strontium fluoroapatite Yb{sup 3+}:Sr{sub 5}(PO{sub 4}){sub 3}F (Yb: S-FAP) crystals have been used in High Average Power Laser systems as gain medium. Growth induced defects associated with the crystal often affect their performance. In order to improve the crystal quality and its optical applications, it is imperative to understand the nature of these defects. In this study, we utilize Micro-Raman spectroscopy to characterize two common growth-induced defects: bubble core and cloudiness. We find the bubble core consist of voids and microcrystals of Yb: S-FAP. These microcrystals have very different orientation from that of the pure crystal outside the bubble core. In contrast to a previous report, neither Sr{sub 3}(PO{sub 4}){sub 2} nor Yb{sub 2}O{sub 3} are observed in the bubble core regions. On the other hand, the cloudy regions are made up of the host materials blended with a structural deformation along with impurities which include CaCO{sub 3}, YbPO{sub 4}, SrHPO{sub 4} and Sr{sub 2}P{sub 2}O{sub 7}. The impurities are randomly distributed in the cloudy regions. This analysis is necessary for understanding and eliminating these growth defects in Yb:S-FAP crystals.
Date: November 15, 2006
Creator: Cui, Yunlong; Roy, Utpal N.; Bai, Lihua; Burger, Arnold; Qiu, S. Roger & Schaffers, Kathleen
Object Type: Article
System: The UNT Digital Library
Characterization of Suspect Fuel Rod Pieces from the 105 K West Basin (open access)

Characterization of Suspect Fuel Rod Pieces from the 105 K West Basin

This report provides physical and radiochemical characterization results from examinations and laboratory analyses performed on ~0.55-inch diameter rod pieces found in the 105 K West (KW) Basin that were suspected to be from nuclear reactor fuel. The characterization results will be used to establish the technical basis for adding this material to the contents of one of the final Multi-Canister Overpacks (MCOs) that will be loaded out of the KW Basin in late FY2006 or at a later time depending on project priorities. Fifteen fuel rod pieces were found during the clean out of the KW Basin. Based on lack of specific credentials, documentation, or obvious serial numbers, none of the items could be positively identified nor could their sources or compositions be described. Item weights and dimensions measured in the KW Basin indicated densities consistent with the suspect fuel rods containing uranium dioxide (UO2), uranium metal, or being empty. Extensive review of the Hanford Site technical literature led to the postulation that these pieces likely were irradiated test fuel prepared to support of the development of the Hanford “New Production Reactor,” later called N Reactor. To obtain definitive data on the composition of the suspect fuel, 4 representative fuel …
Date: September 15, 2006
Creator: Delegard, Calvin H.; Schmidt, Andrew J.; Pool, Karl N. & Thornton, Brenda M.
Object Type: Report
System: The UNT Digital Library
Characterization of Turbiditic Oil Reservoirs Based on Geophysical Models of their Formation (open access)

Characterization of Turbiditic Oil Reservoirs Based on Geophysical Models of their Formation

Models are developed and solved to describe the flow of and deposition from low and high concentration turbidity currents. The shallow water equations are amended to include particle transport to describe the low concentration turbidity currents. The suspension balance model is used to describe the high concentration turbidity currents. Numerical simulations are developed to solve the highly non-linear, free boundary problems associated with these models. Simpler, algebraic scaling relationships are also developed for these models. The models are successfully validated against field observations of turbidites. With these models, one can take seismic information on the shape of the turbiditic deposit and estimate the particle size, which can be used to determine the porosity and permeability.
Date: January 15, 2006
Creator: Bonnecaze, Roger
Object Type: Report
System: The UNT Digital Library
CHARACTERIZATION TESTING AND ANALYSIS OF SINGLE CELL SO2 DEPOLARIZED ELECTROLYZER (open access)

CHARACTERIZATION TESTING AND ANALYSIS OF SINGLE CELL SO2 DEPOLARIZED ELECTROLYZER

This document reports work performed at the Savannah River National Laboratory (SRNL) that further develops the use of a proton exchange membrane or PEM-type electrochemical cell to produce hydrogen via SO{sub 2}-depolarized water electrolysis. This work was begun at SRNL in 2005. This research is valuable in achieving the ultimate goal of an economical hydrogen production process based on the Hybrid Sulfur (HyS) Cycle. The HyS Process is a hybrid thermochemical cycle that may be used in conjunction with advanced nuclear reactors or centralized solar receivers to produce hydrogen by water-splitting. Like all other sulfur-based cycles, HyS utilizes the high temperature thermal decomposition of sulfuric acid to produce oxygen. The unique aspect of HyS is the generation of hydrogen in a water electrolyzer that is operated under conditions where dissolved sulfur dioxide depolarizes the anodic reaction, resulting in substantial voltage reduction. Sulfur dioxide is oxidized at the anode, producing sulfuric acid that is sent to the acid decomposition portion of the cycle. The focus of this work was to conduct single cell electrolyzer tests in order to prove the concept of SO{sub 2}-depolarization and to determine how the results can be used to evaluate the performance of key components of …
Date: September 15, 2006
Creator: Steimke, J & Timothy Steeper, T
Object Type: Report
System: The UNT Digital Library
Charge state dependence of cathodic vacuum arc ion energy andvelocity distributions (open access)

Charge state dependence of cathodic vacuum arc ion energy andvelocity distributions

In the literature, conflicting conclusions are reported concerning the charge state dependence of cathodic arc ion energy and velocity distributions. It appears that data from electrostatic energy analyzers indicate charge state dependence of ion energy, whereas time-of-flight methods support charge state independence of ion velocity. Here we present charge-state-resolved ion energy distributions and calculate the corresponding ion velocity distributions in aluminum vacuum arc plasma. We show that the conflicting conclusions reported in the literature for the two different characterization techniques may originate from the commonly employed data interpretation of energy and velocity, in which peak values and average values are not carefully distinguished.
Date: August 15, 2006
Creator: Rosen, Johanna; Schneider, Jochen M. & Anders, Andre
Object Type: Article
System: The UNT Digital Library
Climate Change Fuel Cell Program (open access)

Climate Change Fuel Cell Program

A 200 kW, natural gas fired fuel cell was installed at the Richard Stockton College of New Jersey. The purpose of this project was to demonstrate the financial and operational suitability of retrofit fuel cell technology at a medium sized college. Target audience was design professionals and the wider community, with emphasis on use in higher education. ''Waste'' heat from the fuel cell was utilized to supplement boiler operations and provide domestic hot water. Instrumentation was installed in order to measure the effectiveness of heat utilization. It was determined that 26% of the available heat was captured during the first year of operation. The economics of the fuel cell is highly dependent on the prices of electricity and natural gas. Considering only fuel consumed and energy produced (adjusted for boiler efficiency), the fuel cell saved $54,000 in its first year of operation. However, taking into account the price of maintenance and the cost of financing over the short five-year life span, the fuel cell operated at a loss, despite generous subsidies. As an educational tool and market stimulus, the fuel cell attracted considerable attention, both from design professionals and the general public.
Date: September 15, 2006
Creator: Gitchell, Alice M.
Object Type: Report
System: The UNT Digital Library
Compact Superconducting Final Focus Magnet Options for the ILC (open access)

Compact Superconducting Final Focus Magnet Options for the ILC

The QD0 quadrupole, the final focus magnet closest to the Interaction Point (IP) for the ILC 20 mr crossing angle layout, must provide strong focusing yet be adjustable to accommodate collision energy changes for energy scans and low energy calibration running. It must also be compact to allow disrupted beam and Beamstrahlung coming from the IP to pass outside into an independent instrumented beam line that leads to a high-power beam absorber. In designing QD0 we take advantage of recent BNL experience making direct wind superconducting magnets. Here we review important considerations for the present design, report on progress producing a prototype, describe our compact quadrupole concept in greater detail, and relate this work to other ILC design challenges.
Date: March 15, 2006
Creator: Parker, B.; Anerella, M.; Escallier, J.; Harrison, M.; He, P.; Jain, A. K. et al.
Object Type: Article
System: The UNT Digital Library
Comparison of Beam-Based Alignment Algorithms for the ILC (open access)

Comparison of Beam-Based Alignment Algorithms for the ILC

The main linac of the International Linear Collider (ILC) requires more sophisticated alignment techniques than those provided by survey alone. Various Beam-Based Alignment (BBA) algorithms have been proposed to achieve the desired low emittance preservation. Dispersion Free Steering, Ballistic Alignment and the Kubo method are compared. Alignment algorithms are also tested in the presence of an Earth-like stray field.
Date: March 15, 2006
Creator: Smith, J.C.; Gibbons, L.; Patterson, J.R.; Rubin, D.L.; /Cornell U., LEPP; Sagan, D. et al.
Object Type: Article
System: The UNT Digital Library
Comparisons Between Experimental Measurments and Numerical Simulations of Spheromak Formation in SSPX (open access)

Comparisons Between Experimental Measurments and Numerical Simulations of Spheromak Formation in SSPX

Data from a recently installed insertable magnetic probe array in the Sustained Spheromak Physics Experiment (SSPX) [E. B. Hooper et al., Nucl. Fusion 39, 863 (1999)] is compared against NIMROD [C. R. Sovinec et al., J. Comp. Phys. 195, 355 (2004)], a full 3D resistive magnetohydrodynamic code that is used to simulate SSPX plasmas. The experiment probe consists of a linear array of chip inductors arranged in clusters that are spaced every 2 cm, and spans the entire machine radius at the flux conserver midplane. Both the experiment and the numerical simulations show the appearance, shortly after breakdown, of a column with a hollow current profile that precedes magnetic reconnection, a process essential to the formation of closed magnetic flux surfaces. However, there are differences between the experiment and the simulation in how the column evolves after it is formed. These differences are studied to help identify the mechanisms that eventually lead to closed-flux surfaces (azimuthally averaged) and flux amplification, which occur in both the experiment and the simulation.
Date: March 15, 2006
Creator: Romero-Talam?s, C. A.; Hooper, E. B.; Hill, D. N.; Cohen, B. I.; McLean, H. S.; Wood, R. D. et al.
Object Type: Article
System: The UNT Digital Library
Complex Genetic Disorders and Intellectual Property Rights Final Report (open access)

Complex Genetic Disorders and Intellectual Property Rights Final Report

None
Date: November 15, 2006
Creator: Andrews, Lori, B.
Object Type: Report
System: The UNT Digital Library
Computational Analysis of an Evolutionarily Conserved VertebrateMuscle Alternative Splicing Program (open access)

Computational Analysis of an Evolutionarily Conserved VertebrateMuscle Alternative Splicing Program

A novel exon microarray format that probes gene expression with single exon resolution was employed to elucidate critical features of a vertebrate muscle alternative splicing program. A dataset of 56 microarray-defined, muscle-enriched exons and their flanking introns were examined computationally in order to investigate coordination of the muscle splicing program. Candidate intron regulatory motifs were required to meet several stringent criteria: significant over-representation near muscle-enriched exons, correlation with muscle expression, and phylogenetic conservation among genomes of several vertebrate orders. Three classes of regulatory motifs were identified in the proximal downstream intron, within 200nt of the target exons: UGCAUG, a specific binding site for Fox-1 related splicing factors; ACUAAC, a novel branchpoint-like element; and UG-/UGC-rich elements characteristic of binding sites for CELF splicing factors. UGCAUG was remarkably enriched, being present in nearly one-half of all cases. These studies suggest that Fox and CELF splicing factors play a major role in enforcing the muscle-specific alternative splicing program, facilitating expression of a set of unique isoforms of cytoskeletal proteins that are critical to muscle cell differentiation. Supplementary materials: There are four supplementary tables and one supplementary figure. The tables provide additional detailed information concerning the muscle-enriched datasets, and about over-represented oligonucleotide sequences in …
Date: June 15, 2006
Creator: Das, Debopriya; Clark, Tyson A.; Schweitzer, Anthony; Marr,Henry; Yamamoto, Miki L.; Parra, Marilyn K. et al.
Object Type: Article
System: The UNT Digital Library