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Recent Developments in the Site-Specific Immobilization of Proteins onto Solid Supports

Description: Immobilization of proteins onto surfaces is of great importance in numerous applications, including protein analysis, drug screening, and medical diagnostics, among others. The success of all these technologies relies on the immobilization technique employed to attach a protein to the corresponding surface. Non-specific physical adsorption or chemical cross-linking with appropriate surfaces results in the immobilization of the protein in random orientations. Site-specific covalent attachment, on the other hand, leads to molecules being arranged in a definite, orderly fashion and allows the use of spacers and linkers to help minimize steric hindrances between the protein and the surface. The present work reviews the latest chemical and biochemical developments for the site-specific covalent attachment of proteins onto solid supports.
Date: February 21, 2007
Creator: Camarero, J A
Partner: UNT Libraries Government Documents Department

Through the looking glass: Unraveling the network structure of coal

Description: Since the original idea by Sanada and Honda of treating coal as a three-dimensional cross-linked network, coal structure has been probed by monitoring ingress of solvents using traditional volumetric or gravimetric methods. However, using these techniques has allowed only an indirect observation of the swelling process. More recently, the authors have developed magnetic resonance microscopy (MRM) approaches for studying solvent ingress in polymeric systems, about which fundamental aspects of the swelling process can be deduced directly and quantitatively. The aim of their work is to utilize solvent transport and network response parameters obtained from these methods to assess fundamental properties of the system under investigation. Polymer and coal samples have been studied to date. Numerous swelling parameters measured by magnetic resonance microscopy are found to correlate with cross-link density of the polymer network under investigation. Use of these parameters to assess the three-dimensional network structure of coal is discussed.
Date: December 23, 1999
Creator: Gregory, D. M.; Stec, D. F. & Botto, R. E.
Partner: UNT Libraries Government Documents Department

Mechanistic Investigation into the Decarboxylation of Aromatic Carboxylic Acids

Description: It has been proposed that carboxylic acids and carboxylates are major contributors to cross-linking reactions in low-rank coals and inhibit its thermochemical processing. Therefore, the thermolysis of aromatic carboxylic acids was investigated to determine the mechanisms of decarboxylation at temperatures relevant to coal processing, and to determine if decarboxylation leads to cross-linking (i.e., formation of more refractory products). From the thcrmolysis of simple and polymeric coal model compounds containing aromatic carboxylic acids at 250-425 �C, decarboxylation was found to occur primarily by an acid promoted ionic pathway. Carboxylate salts were found to enhance the decarboxylation rate, which is consistent with the proposed cationic mechanism. Thermolysis of the acid in an aromatic solvent, such as naphthalene, produced a small amount of arylated products (~5 mol%)), which constitute a low-temperature cross-link. These arylated products were formed by the rapid decomposition of aromatic anhydrides, which are in equilibrium with the acid. These anhydrides decompose by a free radical induced decomposition pathway to form atyl radicals that can add to aromatic rings to form cross-links or abstract hydrogen. Large amounts of CO were formed in the thennolysis of the anhydrides which is consistent with the induced decomposition pathway. CO was also formed in the thermolysis of the carboxylic acids in aromatic solvents which is consistent with the formation and decomposition of the anhydride. The formation of anhydride linkages and cross-links was found to be very sensitive to the reactions conditions. Hydrogen donor solvents, such as tetralin, and water were found to decrease the formation of arylated products. Silar reaction pathways were also found in the thermolysis of a polymeric model that contained aromatic carboxylic acids. In this case, anhydride formation and decomposition produced an insoluble polymer, while the O-methylated polymer and the non-carboxylated polymer produced a soluble thermolysis product.
Date: August 22, 1999
Creator: Britt, P.F.; Buchanan, A.C., III; Eskay, T.P. & Mungall, W.S.
Partner: UNT Libraries Government Documents Department

Permeability Modification Using a Reactive Alkaline-Soluble Biopolymer

Description: Polymer injection has been used in reservoirs to alleviate contrasting permeability zones. Current technology relies on the use of cross-linking agents to initiate gelation. The use of biological polymers are advantageous in that they can block high permeability areas, are environmentally friendly, and have potential to form reversible gels without the use of hazardous cross-linkers. Recent efforts at the Idaho National Engineering and Environmental Laboratory (INEEL) have produced a reactive alkaline-soluble biopolymer from Agrobacterium sp. ATCC no. 31749 that gels upon decreasing the pH of the polymeric solution. The focus of this study was to determine the impact an alkaline-soluble biopolymer can have on sandstone permeability. Permeability modification was investigated by injecting solubilized biopolymer into Berea sandstone cores and defining the contribution of pH, salt, temperature, and Schuricht crude oil on biopolymer gelation. The biopolymer was soluble in KOH at a pH greater than 11.4 and gelled when the pH dropped below 10.8. The Berea sandstone core buffered the biopolymer solution, decreasing the pH sufficiently to form a gel, which subsequently decreased the permeability. The effluent pH of the control cores injected with 0.01 {und M} KOH (pH 12.0) and 0.10{und M} KOH (pH 13.0) decreased to 10.6 and 12.7, respectively. The permeability of the sandstone core injected with biopolymer was decreased to greater than 95% of the original permeability at 25 C in the presence of 2% NaCl, and Schuricht crude oil; however, the permeability increased when the temperature of the core was increased to 60 C. Residual resistance factors as high as 792 were seen in Berea cores treated with biopolymer. The buffering capacity of sandstone has been demonstrated to reduce the pH of a biopolymer solution sufficiently to cause the polymer to form a stable in-situ gel. This finding could potentially lead to alternate technology for permeability ...
Date: October 1, 2003
Creator: Fox, Snadra L.; Xie, X.; Schaller, K. D.; Robertson, E. P. & Bala, G. A.
Partner: UNT Libraries Government Documents Department

A NON-CLEAVABLE UmuD VARIANT THAT ACTS AS A UmuD' MIMIC

Description: UmuD{sub 2} cleaves and removes its N-terminal 24 amino acids to form UmuD'{sub 2}, which activates UmuC for its role in UV-induced mutagenesis in E. coli. Cells with a non-cleavable UmuD exhibit essentially no UV-induced mutagenesis and are hypersensitive to killing by UV light. UmuD has been shown to bind to the beta processivity clamp (''beta'') of the replicative DNA polymerase, pol III. A possible beta-binding motif has been predicted in the same region of UmuD shown to be important for its interaction with beta. We performed alanine-scanning mutagenesis of this motif (14-TFPLF-18) in UmuD and showed that it has a moderate influence on UV-induced mutagenesis but is required for the cold sensitive phenotype caused by elevated levels of wild-type UmuD and UmuC. Surprisingly, the wild-type and the beta-binding motif variant bind to beta with similar K{sub d} values as determined by changes in tryptophan fluorescence. However, this data also implies that the single tryptophan in beta is in strikingly different environments in the presence of the wild-type versus the variant UmuD proteins, suggesting a distinct change in some aspect of the interaction with little change in its strength. Despite the fact that this novel UmuD variant is noncleavable, we find that cells harboring it exhibit phenotypes more consistent with the cleaved form UmuD', such as resistance to killing by UV light and failure to exhibit the cold sensitive phenotype. Cross-linking and chemical modification experiments indicate that the N-terminal arms of the UmuD variant are less likely to be bound to the globular domain than those of the wild-type, which may be the mechanism by which this UmuD variant acts as a UmuD' mimic.
Date: October 26, 2005
Creator: Beuning, P J; Simon, S M; Zemla, A; Barsky, D & Walker, G C
Partner: UNT Libraries Government Documents Department

High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

Description: A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small ({approx}40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue. Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE. MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.
Date: February 24, 2009
Creator: Wang, Yuker; Carlton, Victoria E.H.; Karlin-Neumann, George; Sapolsky, Ronald; Zhang, Li; Moorhead, Martin et al.
Partner: UNT Libraries Government Documents Department

Thermolysis of a polymer model of aromatic carboxylic acids in low-rank coal

Description: To compliment our current investigation into the role that decarboxylation of aromatic carboxylic acids plays in the low-temperature cross-linking of low-rank coals, we are investigating the thermolysis of a polymeric coal model compound to determine if the polymeric network structure of coal can alter the decarboxylation pathways. In this investigation, a bibenzylic polymer, poly-(m-xylylene-co-5-carboxy-m-xylylene), 1, was synthesized containing 2.3 carboxylic acids per 100 carbons, which is similar to that found in Zapp lignite. The pyrolysis of 1 was compared to poly-m-xylylene, 2, and the methyl ester of 1, 3, to determine if the carboxy group enhances cross-linking reactions. The major product from the pyrolysis of 1 at 375{degrees} C or 400{degrees} C for 1 h was a THF insoluble residue (60-75 wt%), while pyrolysis of 2 or the methyl ester of 1 produced only a THF soluble product. The mechanistic pathways leading to cross-linking will be discussed.
Date: March 1997
Creator: Mungall, W. S.; Britt, P. F. & Buchanan, A. C., III
Partner: UNT Libraries Government Documents Department

Correlation of the crack initiation stress with epoxy network topology

Description: Much controversy surrounds the dependence of stress intensity factor of glassy thermosets, epoxies in particular, with crosslink density. One could scan the literature and find references that claim K{sub Ic} increases with crosslink density, decreases with crosslink density, or is independent of crosslink density. The authors feel that two factors contribute to this confusion. First, a typical method for assessing this dependence relies on modifying the crosslink density by changing the precursor epoxy molecular weight. On the other hand, one could change stoichiometry or quench the reaction at intermediate extents of reaction to obtain large changes in crosslink density. However, most studies have not measured the resulting stress intensity factor of these partially cured systems at constant T-T{sub g}, where T{sub g} is the glass transition temperature of the epoxy. Since T{sub g} can change significantly with cure and since fracture processes at the crack tip are dissipative, they must work at constant T-T{sub g} to ensure that the nonlinear viscoelastic mechanisms are fairly compared. In this study, they quenched the reaction of the diglycidyl ether of bisphenol A (DGEBA) and diethanolamine (DEA) at various stages past the gel point and measured the three-point-bend stress intensity factor at a constant T-T{sub g} = {minus}50 C. The trend is clear and significant; increasing crosslink density directly increases the load-to-fail.
Date: March 1, 1997
Creator: Adolf, D.; Weeks, T. & McCoy, J.
Partner: UNT Libraries Government Documents Department

Single-monolayer in situ modulus measurements using a SAW device: Photocrosslinking of a diacetylenic thiol-based monolayer

Description: We report direct measurement of the modulus change that accompanies the crosslinking of a single molecular monolayer. We measured a change in elastic modulus of 5 x 10{sup 10} dyn/cm{sup 2} as a result of ultraviolet-induced photocrosslinking of a single surface-confined monolayer of the conjugated diacetylenic thiol HS(CH{sub 2}){sub 10}C{triple_bond}CC{triple_bond}C(CH{sub 2}){sub 10}COOH, designated {open_quotes}DAT{close_quotes} hereafter. The modulus measurement was made on a monolayer of DAT chemisorbed upon a gold film on the surface of a 97-MHz ST-quartz surface acoustic wave delay line. The ratio of the changes recorded in SAW velocity and attenuation, approximately 4:1, suggests that the measured effect is mainly a change in the elastic (real) component of the complex shear modulus, viscous changes playing a lesser role. In relation to typical polymer modulus values, the change of 5 x 10{sup 10} dyn/cm{sup 2} is consistent with a change from a rubbery material (G{prime} {approximately} 10{sup 7} - 10{sup 8} dyn/cm{sup 2}) to a fairly rigid, glassy material (G{prime} {approximately} 10{sup 10} dyn/cm{sup 2}), reasonable for comparison of the monolayer in its as-adsorbed and crosslinked forms. This report of the direct SAW-based measurement of the modulus change associated with the crosslinking of a single molecular monolayer is complementary to and consistent with previous in-situ measurements of this process using thickness-shear mode resonators.
Date: October 1, 1997
Creator: Ricco, A.J.; Staton, A.W.; Crooks, R.M. & Kim, Taisun
Partner: UNT Libraries Government Documents Department

Depth-independent hardness improvements in ion irradiated polystyrene

Description: Polystyrene (PS) was irradiated with 2 MeV He{sup +} ions to a fluence of 3.3 {times} 10{sup 9} ions/m{sup 2}. A cross-section of the irradiated layer was subjected to hardness measurements across the section using a nanoindentation technique. Results showed that hardness increased as a function of irradiation depth and showed a maximum value of 12 GPa at a depth of approximately 6.5 {mu}m, for a total ion penetration range of 9 {mu}m, as compared to a hardness of 0.45 GPa for unirradiated PS. The hardness variation with depth followed the trend for Linear Energy Transfer (LET) for ionization from the energetic ions to substrate atoms. This investigation showed for the first time how hardness varies as a function of depth for ion-irradiated polymers; this variation approximately follows the ionization LET profile, suggesting that cross-linking in the polymers could be proportional to ionization.
Date: December 31, 1994
Creator: Rao, G.R.; Riester, L. & Lee, E.H.
Partner: UNT Libraries Government Documents Department

Top-surface imaging resists for lithography with strongly attenuated radiation

Description: Strong resist photoabsorption at wavelengths below 248 nm necessitates the use of a thin layer imaging (TLI) scheme for microlithography using 193 nm, 157 nm, or 13.4 nm radiation. Previous to this work, a TLI process commonly known as silylated top surface imaging (TSI) was developed by a Sandia/AT and T team for use in extreme ultraviolet lithography (EUVL) at 13.4 nm. Using this bilayer process, 0.13 {micro}m resolution with 87{degree} sidewalls in 0.7 {micro}m of resist was achieved for EUV exposures. New imaging layer polymers, silylation reagents and crosslinkers, and process conditions were screened for improvement in this TSI process with the ultimate goal of demonstrating a resist technology capable of 0.10 {micro}m critical dimension (CD). The results of these attempted improvements to the TSI process are described in this report.
Date: September 1, 1997
Creator: Ray-Chaudhuri, A.; Kubiak, G.; Henderson, C.; Wheeler, D. & Pollagi, T.
Partner: UNT Libraries Government Documents Department

Simulation of interfacial fracture in highly crosslinked adhesives

Description: The fracture of highly-crosslinked networks is investigated by molecular dynamics simulations. The network is modeled as a bead-spring polymer network between two solid surfaces. The network is dynamically formed by crosslinking an equilibrated liquid mixture. Tensile pull fracture is simulated as a function of the number of interracial bonds. The sequence of molecular structural deformations that lead to failure are determined, and the connectivity is found to strongly control the stress-strain response and failure modes. The failure strain is related to the minimal paths in the network that connect the two solid surfaces. The failure stress is a fraction of the ideal stress required to fracture all the interracial bonds, and is linearly proportional to the number of interracial bonds. By allowing only a single bond between a crosslinker and the surface, interracial failure always occurs. Allowing up to half of the crosslinker's bonds to occur with the surface, cohesive failure can occur.
Date: May 22, 2000
Creator: STEVENS,MARK J.
Partner: UNT Libraries Government Documents Department

Structure within thin epoxy films revealed by solvent swelling: A neutron reflectivity study

Description: The focus of this work is the structure within highly crosslinked, two component epoxy films. The authors examine variations in crosslink density within thin epoxy films on silicon substrates by solvent swelling. The method is based on the fact that the equilibrium volume fraction of a swelling solvent is strongly dependent upon the local crosslink density. The authors examine the volume fraction profile of the good solvent nitrobenzene through the epoxy films by neutron reflection. Isotopic substitution is used to provide contrast between the epoxy matrix and the swelling solvent.
Date: March 2, 2000
Creator: KENT,MICHAEL S.; YIM,HYUN; MCNAMARA,WILLIAM FRERE; IVKOV,R.; SATIJA,S. & MAJEWSKI,J.
Partner: UNT Libraries Government Documents Department

Investigation of coal structure. Quarterly report, July 1, 1993--September 30, 1993

Description: The objective of this project is to investigate the physical structure of coal: the extent to which coal molecules may be covalently cross-linked and/or physically associated. Coal structure should be well understood for its effective utilization, and better understanding of physical structure of coal is the first step for the development of coal utilization. Solvent swelling of coal and multistep sequences of extraction are the two main probes of investigation. No single solvent appears to disrupt all of the relatively strong secondary interactions in coal. Various relatively strong secondary interactions need to be solvated step by step by appropriate procedures. If physical association is considerable, it should be possible to extract coal by the multistep sequences. Secondly, physical association will be evaluated by coal swelling. For the investigation of the effects of low coal concentration and continuous mixing, a new method will be developed. The focus of the work will be on a specific bituminous coal low in sulfur and iron. As requested by DOE, Blind Canyon coal (DECS-16) obtained from the Penn State Coal Bank has been used in this project.
Date: October 1, 1993
Partner: UNT Libraries Government Documents Department

Functionalized nanoparticles for sensor applications.

Description: We will describe our work on functionalized arrays of nanoparticles crosslinked with short conducting molecules that contain sensing functionalities. These bridging ligands modulate their conductivity based on their interaction with analytes. This functionalized nanoparticles organic ligand composite material once it is assembled between nanogaps electrodes will provide nanosized sensors that can be easily interrogated. These nanogap sensors will be engineered so that they can be fabricated into arrays of different sensor elements. This project consists of a number of different requirements that must be met in order to enable the use of functionalized nanoparticles for sensor applications. The first requirement is the appropriately functionalized nanoparticle. The second is a method to assemble the particles. The third requirement is the generation of a nanogap to contain the nanoparticles. The successes in each of these areas will be discussed as will the sensing behavior of the final films.
Date: September 1, 2005
Creator: Simonson, Robert Joseph; Childs, Kenton David; Howell, Stephen Wayne; Dirk, Shawn M. & Wheeler, David Roger
Partner: UNT Libraries Government Documents Department

The interfacial bioscience grand challenge.

Description: This report is broken down into the following 3 sections: (1) Chemical Cross-linking and Mass Spectrometry Applied to Determination of Protein Structure and Dynamics; (2) Computational Modeling of Membrane Protein Structure and Dynamics; and (3) Studies of Toxin-Membrane Interactions using Single Molecule Biophysical Methods.
Date: March 1, 2004
Creator: Lane, Pamela; Stevens, Mark Jackson; Jacobsen, Richard B.; Hong, Joohee; Ayson, Marites J.; Crozier, Paul Stewart et al.
Partner: UNT Libraries Government Documents Department

The Multinational Arabidopsis Steering Subcommittee for Proteomics Assembles the Largest Proteome Database Resource for Plant Systems Biology

Description: In the past 10 years, we have witnessed remarkable advances in the field of plant molecular biology. The rapid development of proteomic technologies and the speed with which these techniques have been applied to the field have altered our perception of how we can analyze proteins in complex systems. At nearly the same time, the availability of the complete genome for the model plant Arabidopsis thaliana was released; this effort provides an unsurpassed resource for the identification of proteins when researchers use MS to analyze plant samples. Recognizing the growth in this area, the Multinational Arabidopsis Steering Committee (MASC) established a subcommittee for A. thaliana proteomics in 2006 with the objective of consolidating databases, technique standards, and experimentally validated candidate genes and functions. Since the establishment of the Multinational Arabidopsis Steering Subcommittee for Proteomics (MASCP), many new approaches and resources have become available. Recently, the subcommittee established a webpage to consolidate this information (www.masc-proteomics.org). It includes links to plant proteomic databases, general information about proteomic techniques, meeting information, a summary of proteomic standards, and other relevant resources. Altogether, this website provides a useful resource for the Arabidopsis proteomics community. In the future, the website will host discussions and investigate the cross-linking of databases. The subcommittee members have extensive experience in arabidopsis proteomics and collectively have produced some of the most extensive proteomics data sets for this model plant (Table S1 in the Supporting Information has a list of resources). The largest collection of proteomics data from a single study in A. thaliana was assembled into an accessible database (AtProteome; http://fgcz-atproteome.unizh.ch/index.php) and was recently published by the Baginsky lab.1 The database provides links to major Arabidopsis online resources, and raw data have been deposited in PRIDE and PRIDE BioMart. Included in this database is an Arabidopsis proteome map that provides evidence ...
Date: December 1, 2009
Creator: Weckwerth, Wolfram; Baginsky, Sacha; Van Wijk, Klass; Heazlewood, Joshua & Millar, Harvey
Partner: UNT Libraries Government Documents Department

Physical principles of ion-beam processing of polymeric materials and applications

Description: Irradiation of polymeric materials with energetic ions in the range of several hundreds of keV to several MeV causes drastic changes in physical, chemical, and mechanical properties. Studies indicate that irradiation produces many active radicals which then react with each other, transforming spaghetti-like tangled polymer chains into a highly cross-linked network structure. Analysis of experimental data shows that the most important parameter for cross-linking is the deposited energy density along the ion track, often expressed in terms of linear energy transfer (LET) in units of eV/nm. High LET produces a high number of free radicals over many neighboring molecular chains and thereby facilitates cross-linking. On the other hand, under low LET conditions, radicals are produced so sparsely that cross-linking efficiency decreases. Moreover, the deposited energy in the chain often leads to chain scission when there are no radicals in the neighboring chains for crosslinking. This paper reviews the current understanding of cross-linking mechanisms in terms of nuclear and electronic stopping and their impact on materials` properties.
Date: November 1, 1998
Creator: Lee, E.H.
Partner: UNT Libraries Government Documents Department

The preparation and characterization of linear and cross-linked poly(fluorenyl)

Description: Retrogressive reactions in coal processing are that class of reactions that lead to the formation of high molecular weight materials that are more intractable than those present in the coal prior to processing. This outcome almost always is regarded as deleterious. The present work focuses on the characterization of the acid-catalyzed polymerization of benzylic fluorides, and in particular the synthesis of poly(fluorenyl), as an example of the type of chemistry that may occur in the cross-linked organic matrix of coals when in contact with strong acids. Solution and solid state {sup 13}C NMR spectroscopy was used to characterize the soluble and insoluble polymers. The change in the value of the fraction of aromatic carbon that is protonated is the criterion used to monitor the extent of cross-linking in these polymer preparations. Benzylic fluorides are sensitive substances, prone to further reaction via acid catalyzed heterolytic scission of the C-F bond. The electron deficient reactive intermediate formed in this reaction undergoes electrophilic aromatic substitution. This reaction can be started with catalytic traces of acid and is self-sustaining as HF is generated in equivalent concentrations as the reaction proceeds. The relevance of this naturally non-occurring functional group in coal processing stems from the similar reaction pathway followed by both benzylic fluorides and benzylic alcohols. In the coal matrix, the operation of two exogenous processes--air oxidation and strong acid treatment of the coal (demineralization) creates a situation in which the polymerization discussed herein may occur in the coal. In addition to the polymerization reactions that produce poly(fluorenyl), the subsequent cross-linking of the linear polymer is also reported. In subsequent work, similar chemistry will be applied to soluble lignin as a model more similar to low rank coals.
Date: March 1, 1997
Creator: Hagaman, E.W. & Lee, S.K.
Partner: UNT Libraries Government Documents Department

Histone-DNA contacts in structure/function relationships of nucleosomes as revealed by crosslinking

Description: The magnitude of the problem of understanding the structure/function relationships of eukaryotic chromosomes can be appreciated from the fact that the human diploid genome contains more than 2 meters of DNA packaged into 46 chromosomes, each at metaphase being several microns in length. Each chromatid of a chromosome contains a single DNA molecule several centimeters in length. In addition to the DNA, chromosomes contain an equal weight of histones and an equal weight of non-histone chromosomal proteins. These histones are the major chromosomal structural proteins. The non-histone chromosomal proteins are involved in the DNA processes of transcription and replication, in chromosome organization and in nuclear architecture. Polytene chromosomes with their bands and interbands and puffs of active genetic loci provide visual evidence for long range order as do the bands and interbands of mammalian metaphase chromosomes. The gentle removal of histones and all but the most tightly bound 2--3% of non-histone proteins from metaphase chromosomes revealed by electron microscopy a residual protein scaffold constraining a halo of DNA loops extending out from the scaffold.
Date: December 31, 1998
Creator: Usachenko, S.I. & Bradbury, E.M.
Partner: UNT Libraries Government Documents Department

Investigation of the role of aromatic carboxylic acids in cross-linking processes in low-rank coals

Description: In the pyrolysis and liquefaction of low-rank coals, low-temperature cross-linking reactions have been correlated with the loss of carboxyl groups and the evolution of CO{sub 2} and H{sub 2}O. It is not clearly understood how decarboxylation leads to cross-linking beyond the suggestion that decarboxylation could be a radical process that involves radical recombination or radical addition reactions. We have recently conducted a study of the pyrolysis of 1,2-(3,3{prime}-dicarboxyphenyl)ethane (1) and 1,2-(4,4{prime}-dicarboxyphenyl)ethane (2) and found that decarboxylation occurs readily between 350-425 {degrees}C with no evidence of coupling products or products representative of cross-links. We proposed that decarboxylation occurred primarily by an acid-promoted cationic pathway, and the source of acid was a second carboxylic acid. The decarboxylation of 1 and 2 was investigated in diphenyl ether and naphthalene as inert diluents. In each solvent, the rate of decarboxylation dropped by roughly a factor of 2 upon dilution from the neat liquid to ca. 0.4 mole fraction of acid, but further dilution had no effect on the rate. This could be a consequence of hydrogen bonding or an intramolecular protonation. Molecular mechanics calculations indicated that 1 and 2 can adopt an appropriate conformation for internal proton transfer from a carboxy group on one ring to the second aryl ring without a significant energy penalty. In addition, the dicarboxylic acid could internally hydrogen bond, which may further complicate the reaction mechanism. Therefore, we have conducted a study of the pyrolysis of a monocarboxybibenzyl, 1-(3-carboxyphenyl)-2-(4-biphenyl)ethane (3), to determine if decarboxylation occurs by an ionic pathway in the absence of intramolecular pathways.
Date: March 1, 1997
Creator: Eskay, T.P.; Britt, P.F. & Buchanan, A.C. III
Partner: UNT Libraries Government Documents Department

Small angle neutron scattering studies of coal-extract solutions

Description: Interest in the physics and chemistry of coal extracts has extended for over 100 years. Early on it was recognized that pyridine was a particularly good solvent capable of extracting a significant weight percent of intermediate rank coals. Many of the current theories regarding the macromolecular structure of coals (type III kerogens) are based on the fact that there exists a physically definable limit in the extractability of soluble organics from coal in pyridine. The non-extractable residue is generally considered to be a cross-linked macromolecular network. The extract-solvent {open_quotes}solutions{close_quotes}, although acknowledged to be far from ideal (thermodynamically), are presumed to be {open_quotes}molecular solutions{close_quotes} in the sense that random mixing of the constituents occurs within a single solution phase. This research set out to characterize the solution structures of coal extracts to gain insight into the nature of coal-solvent interactions.
Date: August 1, 1997
Creator: Thiyagarajan, P. & Cody, G.D.
Partner: UNT Libraries Government Documents Department