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Biochemical Systematics of the Genus Sophora

Description: Three unusual amino acids, y-amino-n-butyric acid, pipecolic acid, and 4-hydroxypipecolic acid, and an uncommon dipeptide, y-glutamyltyrosine, have been isolated and characterized from the seeds of members of the genus Sophora. Structural proof of these compounds was carried out by paper chromatography, thin-layer chromatography, column chromatography on amino acid analyzer, infrared, nuclear magnetic resonance, mass spectrometry, and C, H, N analysis. The presence and absence of these compounds was used as a criterion for the classification of 23 species of the genus Sophora. A phylogenetic classification which seems to follow the morphological taxonomy of this genus was carried out on the basis of seeds that contained pipecolic acid, those which did not contain pipecolic acid, and plants which contained both pipecolic acid and 4-hydroxypipecolic acids. Another chemical classification was also introduced based on the presence and absence of y-amino-n-butyric acid and y-glutamyltyrosine.
Date: December 1973
Creator: Izaddoost, Mohamed
Partner: UNT Libraries

The Chlorination of Amino Acid in Municipal Waste Effluents

Description: In model reaction systems to test amino acids in chlorinated waste effluents, several amino acids were chlorinated at high chlorine doses. (2000-4000 mg/1). Amino acids present in municipal waste effluents before and after chlorination were concentrated and purified using cation exchange and Chelex resins. After concentration and cleanup of the samples, the amino acids were derivatized by esterification of the acid functional groups and acylation of the amine groups. Identification and quantification of the amino acids and chlorination products was carried out by gas chromatography/mass spectrometry, using a digital computer data system. Analysis of the waste products revealed the presence of new carbon-chlorine bonded derivatives of the amino acid tyrosine when the effluents were treated with heavy doses of chlorine.
Date: July 1977
Creator: Burleson, Jimmie L.
Partner: UNT Libraries

Part 1. Investigation of Aluminum Amino Acid Complexes; Part 2. Structural Studies of Aluminum Chalcogen Bonds

Description: Five different complexes of aluminum and amino acids have been synthesized and characterized. Reaction between aluminum halides and amino acids that do not contain either a carboxylate or a hydroxy group in the side chain produce complexes of the general formula, [Al(amino acid)_n(halide)_3-n]_m. The most prevalent form of this form of complex is where n = 2, and an example of this in which the halide is replaced by hydroxide ligand has been structurally characterized. The complex for which n = 3 may be obtained by employing a large excess of acid, and that for which n = 1 may be obtained by employing either equimolar conditions or an excess of aluminum halide. Reactions of aluminum halides with amino acids that contain either a carboxylate or hydroxy-containing side chain may result in complexes in which the side-chain is also bound. These proved impossible to characterize fully in the case of aspartic acid. For serine, however, a complex in which the amino acid binds in a chelating fashion through both the carboxylate and hydroxy groups was isolated. It was possible to form complexes when utilizing aluminum alkyls as the metal source. However, these complexes could only be isolated when the reactivity of the species was controlled by the presence of bulky groups. In these cases, the monomeric R_2Al(amino acid) complexes were obtained. Four complexes that contain aluminum-chalcogen bonds were structurally characterized. These included the bulky alkoxide complexes (BHT)_2AIH(OEt_2), (BHT)_3Al(cyclohexanone), and the cubane [(t-amyl)AlS]_4.
Date: May 1996
Creator: Gravelle, Philip W. (Philip Wyn)
Partner: UNT Libraries

Pseudo-stationary separation materials for highly parallel separations.

Description: Goal of this study was to develop and characterize novel polymeric materials as pseudostationary phases in electrokinetic chromatography. Fundamental studies have characterized the chromatographic selectivity of the materials as a function of chemical structure and molecular conformation. The selectivities of the polymers has been studied extensively, resulting in a large body of fundamental knowledge regarding the performance and selectivity of polymeric pseudostationary phases. Two polymers have also been used for amino acid and peptide separations, and with laser induced fluorescence detection. The polymers performed well for the separation of derivatized amino acids, and provided some significant differences in selectivity relative to a commonly used micellar pseudostationary phase. The polymers did not perform well for peptide separations. The polymers were compatible with laser induced fluorescence detection, indicating that they should also be compatible with chip-based separations.
Date: May 1, 2005
Creator: Singh, Anup K. & Palmer, Christopher (University of Montana, Missoula, MT)
Partner: UNT Libraries Government Documents Department

Site Directed Mutagenesis Of Dienelactone Hydrolase

Description: The role of individual amino acid residues of the enzyme dienelactone hydrolase was investigated. Using the polymerase chain reaction (PCR), a 1.9 kbp clcD fragment was amplified and subcloned yielding a 821 bp BamHI to EcoRI clcD subclone in the plasmid pUC19. Site-specific mutants of dienelactone hydrolase were created using mismatched oligonucleotides to prime DNA synthesis. Specifically modified proteins from mutated clcD genes (Arg 81 to alanine, Tyr 85 to phenylalanine and Arg 206 to alanine), were encoded by the mutant clones. Enzyme assays showed that dienelactone hydrolase activity of the mutants Arg 81 and Arg 206 was totally abolished. The DLHase enzyme activity of mutant Tyr 85 is greatly decreased by approximately two thirds.
Date: December 1992
Creator: Chen, Wei, 1965-
Partner: UNT Libraries

Posttranslational Modification of Proteins by ADP-ribosylation

Description: This work presents the development of a highly sensitive and selective chemical assay for mono(ADP-ribose) residues covalently bound to proteins in vivo. An extensive review of the literature is presented in the introduction of this work. The physiological.functions of mono(ADP-ribosyl)transferase activities associated with certain bacterial toxins (e.g., diphtheria, cholera and pertussis toxins) are well established. However, the roles of endogenous vertebrate transferases are unknown. The elucidation of the roles of these cellular transferases will likely require identification of the physiologically relevant target proteins. Toward this end, it will also be important to identify the types of (ADP-ribose)-protein linkages present in vivo. ADP-ribosylation reactions catalyzed by the different bacterial and vertebrate transferases are specific for different amino acid acceptors in vitro. However, the vertebrate transferases that have been characterized thus far are NAD:arginine mono(ADP-ribosyl)transferases. The work presented here describes the development of a chemical assay for the detection of in vivo modified, ADP-ribosylated proteins containing N-glycosylic linkages to arginine. The assay was applied to the analysis of ADP-ribose residues in adult rat liver. The strategy employed for detection of protein-bound ADP-ribose residues eliminated potential artifacts arising from trapped nucleotides (or their degradation products), since the acid-insoluble material was completely dissolved in a strongly denaturing solution and freed of non-covalently bound nucleotides prior to chemical release from proteins. Thus, the studies presented here demonstrate the unambiguous detection and quantification of protein-bound ADP-ribose residues in adult rat liver. "Arginine-linked" mono(ADP-ribose) residues (31.8 pmol/mg protein) were present in vivo at a level almost 400-fold higher than poly(ADP-ribose). A minor fraction (23%) of the ADP—ribose residues detected were bound via a second more labile linkage with chemical properties very similar to those described previously for carboxlylate esterlinked ADP-ribose. After fractionation of rat liver proteins by gel filtration HPLC, the major peak of "arginine-linked" ADP-ribose residues ...
Date: December 1984
Creator: Payne, David M. (David Michael)
Partner: UNT Libraries


Description: To investigate the extent of genetic stratification in structured microbial communities, we compared the metagenomes of 10 successive layers of a phylogenetically complex hypersaline mat from Guerrero Negro, Mexico. We found pronounced millimeter-scale genetic gradients that are consistent with the physicochemical profile of the mat. Despite these gradients, all layers displayed near identical and acid-shifted isoelectric point profiles due to a molecular convergence of amino acid usage indicating that hypersalinity enforces an overriding selective pressure on the mat community.
Date: April 30, 2008
Creator: Fenner, Marsha W; Kunin, Victor; Raes, Jeroen; Harris, J. Kirk; Spear, John R.; Walker, Jeffrey J. et al.
Partner: UNT Libraries Government Documents Department

Computer Analysis of Amino Acid Chromatography

Description: The problem with which this research was done was that of applying the IBM360 computer to the analysis of waveforms from a Beckman model 120C liquid chromatograph. Software to interpret these waveforms was written in the PLl language. For a control run, input to the computer consisted of a digital tape containing the raw results of the chromatograph run. Output consisted of several graphs and charts giving the results of the analysis. In addition, punched output was provided which gave the name of each amino acid, its elution time and color constant. These punched cards were then input to the computer as input to the experimental run, along with the raw data on the digital tape. From the known amounts of amino acids in the control run and the ratio of control to experimental peak area, the amino acids of the unknown were quantified. The resulting programs provided a complete and easy to use solution to the problem of chromatographic data analysis.
Date: May 1978
Creator: Hayes, Michael D.
Partner: UNT Libraries

Mathematical representation of solubility of amino acids in binary aqueous-organic solvent mixtures at various temperatures using the Jouyban-Acree model

Description: Article on mathematical representation of solubility of amino acids in binary aqueous-organic solvent mixtures at various temperatures using the Jouyban-Acree model.
Date: September 1, 2006
Creator: Jouyban, Abolghasem; Khoubnasabjafari, Maryam; Chan, Hak-Kim & Acree, William E. (William Eugene)
Partner: UNT College of Arts and Sciences

Metal (II) Complexes with N-Salicylideneamino Acids

Description: Transition metal complexes derived from Schiff bases have rendered an important contribution to the development of modern coordination chemistry. Various stable compounds have been prepared having synthetic, biological, and physicochemical interest. In particular, complexes of salicylaldimines, B-ketoamines, and closely related ligand systems have been investigated.
Date: August 1969
Creator: Carlisle, Gene Ozelle
Partner: UNT Libraries

Site Directed Mutagenesis of Dienelactone Hydrolase

Description: The clcD gene encoding dienelactone hydrolase (DLH) is part of the clc gene cluster for the utilization of the B-ketoadipate pathway intermediate chlorocatechol. The roles that individual amino acids residues play in catalysis and binding of the enzyme were investigated. Using PCR a 1.9 kbp clcD fragment was amplified and subcloned yielding a 821 bp BamHi to ZscoRI subclone in the plasmid pUC19.
Date: August 1995
Creator: Al-Khatib, Haifa Yousef
Partner: UNT Libraries

Studies on Human Plasma Lecithin:Cholesterol Acyltransferase: Physical and Chemical Characterization and Coupled Spectrophotometric Enzyme Assay

Description: The physico-chemical properties of lecithin:cholesterol acyltransferase were investigated. The amino acid composition analysis showed a relatively high content of glutamic acid, aspartic acid, glycine and leucine. The spectrophotometric titration of phenolic groups in the enzyme showed a large increase in absorbance at 295 nm with an apparent pK of about 12.0. The largest change in molar ellipticity at 222 nm was also observed above pH 11. Circular dichroism studies revealed that human lecithin:cholesterol acyltransferase has a relatively high content of β-pleated sheet structure (48%) with 20% α-helix, and 32% remaining structure. Human lecithin:cholesterol acyltransferase has a high extinction coefficient at neutral pH. Microsequencing of the amino terminal residues of the enzyme revealed a hydrophobic character. Inactivation of lecithin:cholesterol acyltransferase activity was observed using diisopropylfluorophosphate with a stoichiometry of 1 mole of diisopropylphosphate incorporated per mole of enzyme. This suggests the involvement of a serine residue in the active site of the enzyme, possibly for the formation of an acyl-intermediate. A new quicker assay method for lecithin:cholesterol acyltransferase was developed. This assay involved coupling reaction with acyl CoA synthetase, ΡΡᵢ-dependent phosphofructokinase, aldolase, triosephosphate isomerase and α-glycerol-3-phosphate dehydrogenase monitoring a change in the absorbance or fluorescence intensity due to the oxidation of NADH. The activity of each coupling enzyme was accurately determined to establish the optimum assay condition for lecithin:cholesterol acyltransferase. The coupled enzyme assay for lecithin:cholesterol acyltransferase by spectrofluorometry showed a significant change in relative fluorescence intensity whereas a UV absorption spectroscopy method showed no significant absorbance change for the initial rate of lecithin:cholesterol acyltransferase reaction.
Date: December 1984
Creator: Hara, Shinichi
Partner: UNT Libraries

Widespread Discordance of Gene Trees with Species Tree inDrosophila: Evidence for Incomplete Lineage Sorting

Description: The phylogenetic relationship of the now fully sequencedspecies Drosophila erecta and D. yakuba with respect to the D.melanogaster species complex has been a subject of controversy. All threepossible groupings of the species have been reported in the past, thoughrecent multi-gene studies suggest that D. erecta and D. yakuba are sisterspecies. Using the whole genomes of each of these species as well as thefour other fully sequenced species in the subgenus Sophophora, we set outto investigate the placement of D. erecta and D. yakuba in the D.melanogaster species group and to understand the cause of the pastincongruence. Though we find that the phylogeny grouping D. erecta and D.yakuba together is the best supported, we also find widespreadincongruence in nucleotide and amino acid substitutions, insertions anddeletions, and gene trees. The time inferred to span the two keyspeciation events is short enough that under the coalescent model, theincongruence could be the result of incomplete lineage sorting.Consistent with the lineage-sorting hypothesis, substitutions supportingthe same tree were spatially clustered. Support for the different treeswas found to be linked to recombination such that adjacent genes supportthe same tree most often in regions of low recombination andsubstitutions supporting the same tree are most enriched roughly on thesame scale as linkage disequilibrium, also consistent with lineagesorting. The incongruence was found to be statistically significant androbust to model and species choice. No systematic biases were found. Weconclude that phylogenetic incongruence in the D. melanogaster speciescomplex is the result, at least in part, of incomplete lineage sorting.Incomplete lineage sorting will likely cause phylogenetic incongruence inmany comparative genomics datasets. Methods to infer the correct speciestree, the history of every base in the genome, and comparative methodsthat control for and/or utilize this information will be valuableadvancements for the field of comparative genomics.
Date: August 28, 2006
Creator: Pollard, Daniel A.; Iyer, Venky N.; Moses, Alan M. & Eisen,Michael B.
Partner: UNT Libraries Government Documents Department

The Calyptogena magnifica chemoautotrophic symbiont genome

Description: Chemoautotrophic endosymbionts are the metabolic cornerstone of hydrothermal vent communities, providing invertebrate hosts with nearly all of their nutrition. The Calyptogena magnifica (Bivalvia: Vesicomyidae) symbiont, Candidatus Ruthia magnifica, is the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced, revealing a suite of metabolic capabilities. The genome encodes major chemoautotrophic pathways as well as pathways for biosynthesis of vitamins, cofactors, and all 20 amino acids required by the clam.
Date: March 1, 2007
Creator: Newton, I.L.; Woyke, T.; Auchtung, T.A.; Dilly, G.F.; Dutton,R.J.; Fisher, M.C. et al.
Partner: UNT Libraries Government Documents Department


Description: There is now experimental evidence for selectivity between the amino acid and the nucleic acid base which is the beginning of the chemical translation process from one linear system to the other. The linear system of the nucleic acid is, of course, an excellent place to store the information, whereas the linear system of the polypeptide, on the other hand, is the versatile system which can perform many different types of reactions but is unable to store information reliably. The experiments the author has described here may represent the beginning of the method of coupling of those two essential qualities which are required for the generation and evolution of a living organism.
Date: December 1, 1968
Creator: Calvin, Melvin
Partner: UNT Libraries Government Documents Department

Homology with vesicle fusion mediator syntaxin-1a predicts determinants ofepimorphin/syntaxin-2 function in mammary epithelial morphogenesis

Description: We have shown that branching morphogenesis of mammary ductal structures requires the action of the morphogen epimorphin/syntaxin-2. Epimorphin, originally identified as an extracellular molecule, is identical to syntaxin-2, an intracellular molecule that is a member of the extensively investigated syntaxin family of proteins that mediate vesicle trafficking. We show here that although epimorphin/syntaxin-2 is highly homologous to syntaxin-1a, only epimorphin/syntaxin-2 can stimulate mammary branching morphogenesis. We construct a homology model of epimorphin/syntaxin-2 based on the published structure of syntaxin-1a, and we use this model to identify the structural motif responsible for the morphogenic activity. We identify four residues located within the cleft between helices B and C that differ between syntaxin-1a and epimorphin/syntaxin-2; through site-directed mutagenesis of these four amino acids, we confer the properties of epimorphin for cell adhesion, gene activation, and branching morphogenesis onto the inactive syntaxin-1a template. These results provide a dramatic demonstration of the use of structural information about one molecule to define a functional motif of a second molecule that is related at the sequence level but highly divergent functionally.
Date: June 3, 2009
Creator: Chen, Connie S.; Nelson, Celeste M.; Khauv, Davitte; Bennett, Simone; Radisky, Evette S.; Hirai, Yohei et al.
Partner: UNT Libraries Government Documents Department


Description: OAK B202 INTEGRATION OF STRUCTURAL AND SEQUENCE INFORMATION FOR HOMOLOGY-BASED MODELING OF PROTEINS. In the six month supplement to this project the authors continued developing the approaches defined in the original proposal (evolutionary profile), and the family pairwise search (FPS) method for defining sequence patterns. This work resulted in several fundamental publications regarding methods for making statistical evaluations of sequence match scores, and a submitted manuscript validating the evolutionary profile approach. Homology modeling allows one to predict the three-dimensional structure of a novel query sequence based on the known three-dimensional structure of a homologous template sequence. This approach requires that one find a three-dimensional structure that is homologous to the query sequence. The query sequence must then be mapped onto the template sequence such that each amino acid residue appears in the correct position in the modeled structure. Both the identification of homologous sequences and the mapping of the query onto the template structure are achieved through sequence comparisons. Standard sequence comparison methods use a single amino acid residue comparison matrix, such as BLOSUM 62 or PAM250, to identify proteins that are more similar than average. When the similarity is high enough, one can infer that these proteins are homologous and thus likely to have similar structure and function.
Date: June 1, 2003
Partner: UNT Libraries Government Documents Department

Effect of Amino Acids on Growth and Cartenogenesis in Corynebacterium Species Strain 7E1C

Description: Studies were evaluated on the effects of known growth factors on the growth and carotenogenesis of Corynebacterium species strain 7ElC. The complex medium, Tryptic Soy Broth,was found to stimulate growth and production of more pigment in the light and in the dark than did a mineral salts-glucose medium. A complete amino acid mixture added to LSG enhanced carotenogenesis in the dark in Corynebacterium 7ElC, while B-vitamins retarded carotenogenesis. No absolute requirement for one or more amino acids was found,indicating a multiple amino acid requirement. The fewest amino acids found to stimulate carotenogenesis in the dark were a combination of those in the Serine and Histidine families which include serine, glycine, cysteine, and histidine.
Date: May 1977
Creator: Coughran, Carolyn S.
Partner: UNT Libraries