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Two Harpsichord Sonatas by Antonio Soler: Analysis and Transcription for Solo Guitar

Description: There is a puacity of original works from the Baroque Era for the guitar. Transcriptions, especially music originally for harpsichord, complement the guitarist's repertoire. Dominating the priviledged space in the guitar canon, represented by Baroque transcriptions, are the composers Johann Sebastian Bach, George Frideric Handel and Domenico Scarlatti. Underrepresented in the Baroque guitar canon is the music of Spanish composers, most noteworthy, the harpsichordist Padre Antonio Soler, who composed more than 120 sonatas for his instrument. Music is culturally defined and it is clear, through an analysis of the keyboard works of Soler, that his music was imbued with the salient features of his place and time. There is an implicit connection between the guitar and the non-guitar music produced in Spain as guitar gestures are part of the national emblem; this study makes an explicit connection between the harpsichord music of Soler and the modern guitar. The Spanish Baroque style, epitomized by the works of Soler, provide a clear objective for transcription. The current study produces a transcription of Padre Antonio Soler's Sonata No. R.27 and Sonata No. R.100, as well as an analysis of the sonatas to facilitate interpretation for performance and an explanation of the transcription process. The lacunae of Spanish Baroque guitar transcriptions that exists in the repertoire will be partially filled by adding Soler to the distinguished list of composers that currently inhabit the guitarists's library.
Date: August 2016
Creator: Daniel, Andrew Ray
Partner: UNT Libraries

Problem of the Arrangement for Two Pianos of Iberia by I. Albeniz

Description: The literal meaning of "transcription" is "written across"; in freer terminology it is "the musical counter-part of literary translation." The terms "arrangement" and "transcription: are used synonymously by nearly all musical dictionaries. However, even then , there is often a distinction made, an arrangement being considered to adhere strictly to the original text while a transcription admits of creative participation on part of the arranger, ranging from the simple transference of musical medium to the complete reworking of a composition with additions and modifications.
Date: August 1947
Creator: Bivens, Virginia L.
Partner: UNT Libraries

Transcriptome 2002 Conference

Description: The Transcriptome 2002 meeting was held March 11-13, 2002 in Seattle, Washington with attendance by more than 300 scientists representing the international community. The scientific program was developed by an international organizing committee. In association with the main meeting, an Image Consortium invitational meeting was organized by Charles Auffray of CNRS and held with approximately 40 participants immediately following the conclusion of the Transcriptome meeting.
Date: January 1, 2002
Creator: Quackenbush, John
Partner: UNT Libraries Government Documents Department

Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

Description: Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by patterns in mutation, suggesting thatselection which causes their conservation is not always verystrong.
Date: February 21, 2007
Creator: Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S. & Dubchak, Inna
Partner: UNT Libraries Government Documents Department

Conservation patterns in different functional sequence categories of divergent Drosophila species

Description: We have explored the distributions of fully conservedungapped blocks in genome-wide pairwise alignments of recently completedspecies of Drosophila: D.yakuba, D.ananassae, D.pseudoobscura, D.virilisand D.mojavensis. Based on these distributions we have found that nearlyevery functional sequence category possesses its own distinctiveconservation pattern, sometimes independent of the overall sequenceconservation level. In the coding and regulatory regions, the ungappedblocks were longer than in introns, UTRs and non-functional sequences. Atthe same time, the blocks in the coding regions carried 3N+2 signaturecharacteristic to synonymic substitutions in the 3rd codon positions.Larger block sizes in transcription regulatory regions can be explainedby the presence of conserved arrays of binding sites for transcriptionfactors. We also have shown that the longest ungapped blocks, or'ultraconserved' sequences, are associated with specific gene groups,including those encoding ion channels and components of the cytoskeleton.We discussed how restrained conservation patterns may help in mappingfunctional sequence categories and improving genomeannotation.
Date: October 1, 2005
Creator: Papatsenko, Dmitri; Kislyuk, Andrey; Levine, Michael & Dubchak, Inna
Partner: UNT Libraries Government Documents Department

Problems of Transcribing the Third Movement of Dvorak's Symphony Number Five in E Minor For Class A Band

Description: The problem of this study was to make a transcription of the third movement of Dvorak's Symphony Number Five in E Minor from the "New World" for a class A symphonic band. A critical discussion of the musical and technical problems involved was included as a supplement or complement, as was a brief history of the composers life and works. In the arrangement of the data, the discussions were presented before the transcription might be readily understood.
Date: August 1942
Creator: Turner, William Marion, 1913-
Partner: UNT Libraries

The Trichoplax Genome and the Nature of Placozoans

Description: Placozoans are arguably the simplest free-living animals, possibly evoking an early stage in metazoan evolution, yet their biology is poorly understood. Here we report the sequencing and analysis of the {approx}98 million base pair nuclear genome of the placozoan Trichoplax adhaerens. Whole genome phylogenetic analysis suggests that placozoans belong to a 'eumetazoan' clade that includes cnidarians and bilaterians, with sponges as the earliest diverging animals. The compact genome exhibits conserved gene content, gene structure, and synteny relative to the human and other complex eumetazoan genomes. Despite the apparent cellular and organismal simplicity of Trichoplax, its genome encodes a rich array of transcription factor and signaling pathway genes that are typically associated with diverse cell types and developmental processes in eumetazoans, motivating further searches for cryptic cellular complexity and/or as yet unobserved life history stages.
Date: August 1, 2008
Creator: Srivastava, Mansi; Begovic, Emina; Chapman, Jarrod; Putnam, Nicholas H.; Hellsten, Uffe; Kawashima, Takeshi et al.
Partner: UNT Libraries Government Documents Department

The Motif Tool Assessment Platform (MTAP) for Sequence-Based Transcription Factor Binding Site Prediction Tools.

Description: Predicting transcription factor binding sites (TFBS) from sequence is one of the most challenging problems in computational biology. The development of (semi-)automated computer-assisted prediction methods are needed to find TFBS over an entire genome, which is a first step in reconstructing mechanisms that controls gene activity. Bioinformatics journals continue to publish diverse methods for predicting TFBS on a monthly basis. To help practitioners in deciding which method to use to predict for a particular TFBS, we provide a platform to assess the quality and applicability of the available methods. Assessment tools allow researchers to determine how methods can be expected to perform on specific organisms or on specific transcription factor families. This chapter introduces the TFBS detection problem and reviews current strategies for evaluating algorithm effectiveness. In this chapter, a novel and robust assessment tool, the Motif Tool Assessment Platform (MTAP) is introduced and discussed.
Date: January 2010
Creator: Quest, Daniel J. & Ali, Hesham
Partner: UNT Libraries Government Documents Department

PointCloudXplore: a visualization tool for 3D gene expressiondata

Description: The Berkeley Drosophila Transcription Network Project (BDTNP) has developed a suite of methods that support quantitative, computational analysis of three-dimensional (3D) gene expression patterns with cellular resolution in early Drosophila embryos, aiming at a more in-depth understanding of gene regulatory networks. We describe a new tool, called PointCloudXplore (PCX), that supports effective 3D gene expression data exploration. PCX is a visualization tool that uses the established visualization techniques of multiple views, brushing, and linking to support the analysis of high-dimensional datasets that describe many genes' expression. Each of the views in PointCloudXplore shows a different gene expression data property. Brushing is used to select and emphasize data associated with defined subsets of embryo cells within a view. Linking is used to show in additional views the expression data for a group of cells that have first been highlighted as a brush in a single view, allowing further data subset properties to be determined. In PCX, physical views of the data are linked to abstract data displays such as parallel coordinates. Physical views show the spatial relationships between different genes' expression patterns within an embryo. Abstract gene expression data displays on the other hand allow for an analysis of relationships between different genes directly in the gene expression space. We discuss on parallel coordinates as one example abstract data view currently available in PCX. We have developed several extensions to standard parallel coordinates to facilitate brushing and the visualization of 3D gene expression data.
Date: October 1, 2006
Creator: Rubel, Oliver; Weber, Gunther H.; Keranen, Soile V.E.; Fowlkes,Charles C.; Luengo Hendriks, Cristian L.; Simirenko, Lisa et al.
Partner: UNT Libraries Government Documents Department

Transcription of Baroque Works for Classical Guitar: J S Bach's Sonata in D Minor (Bwv 964) As Model

Description: Continuing the common practice of composers of the Baroque period to transcribe their own or other composers' works for a different instrument, this dissertation contributes to studies of J. S. Bach's repertory as the source of program material for the classical guitar. It is from differences revealed through a comparative analysis of Bach's Violin Sonata No. 2 (BWV 1003) and his harpsichord arrangement thereof – Sonata in D minor (BWV 964) – that principles of transcription are derived and organized according to descriptive categories. Emulating the composer-transcriber with knowledge of the capabilities and limitations of the instruments involved, the arrangement procedures are applied to the classical guitar. In so doing, this study addresses the emerging challenges and complexities in creating an idiomatic arrangement.
Date: May 2013
Creator: Lang, Matthias
Partner: UNT Libraries

Extracellular Matrix-Regulated Gene Expression RequiresCooperation of SWI/SNF and Transcription Factors

Description: Extracellular cues play crucial roles in the transcriptional regulation of tissue-specific genes, but whether and how these signals lead to chromatin remodeling is not understood and subject to debate. Using chromatin immunoprecipitation (ChIP) assays and mammary-specific genes as models, we show here that extracellular matrix (ECM) molecules and prolactin cooperate to induce histone acetylation and binding of transcription factors and the SWI/SNF complex to the {beta}- and ?-casein promoters. Introduction of a dominant negative Brg1, an ATPase subunit of SWI/SNF complex, significantly reduced both {beta}- and ?-casein expression, suggesting that SWI/SNF-dependent chromatin remodeling is required for transcription of mammary-specific genes. ChIP analyses demonstrated that the ATPase activity of SWI/SNF is necessary for recruitment of RNA transcriptional machinery, but not for binding of transcription factors or for histone acetylation. Coimmunoprecipitation analyses showed that the SWI/SNF complex is associated with STAT5, C/EBP{beta}, and glucocorticoid receptor (GR). Thus, ECM- and prolactin-regulated transcription of the mammary-specific casein genes requires the concerted action of chromatin remodeling enzymes and transcription factors.
Date: May 25, 2006
Creator: Xu, Ren; Spencer, Virginia A. & Bissell, Mina J.
Partner: UNT Libraries Government Documents Department

Engineering phenolics metabolism in the grasses using transcription factors

Description: The economical competitiveness of agriculture-derived biofuels can be significantly enhanced by increasing biomass/acre yields and by furnishing the desired carbon balance for facilitating liquid fuel production (e.g., ethanol) or for high-energy solid waste availability to be used as biopower (e.g., for electricity production). Biomass production and carbon balance are tightly linked to the biosynthesis of phenolic compounds, which are found in crops and in agricultural residues either as lignins, as part of the cell wall, or as soluble phenolics which play a variety of functions in the biology of plants. The grasses, in particular maize, provide the single major source of agricultural biomass, offering significant opportunities for increasing renewable fuel production. Our laboratory has pioneered the use of transcription factors for manipulating plant metabolic pathways, an approach that will be applied here towards altering the composition of phenolic compounds in maize. Previously, we identified a small group of ten maize R2R3-MYB transcription factors with all the characteristics of regulators of different aspects of phenolic biosynthesis. Here, we propose to investigate the participation of these R2R3-MYB factors in the regulation of soluble and insoluble maize phenolics, using a combination of over-expression and down-regulation of these transcription factors in transgenic maize cultured cells and in maize plants. Maize cells and plants altered in the activity of these regulatory proteins will be analyzed for phenolic composition by targeted metabolic profiling. Specifically, we will I) Investigate the effect of gain- and loss-of-function of a select group of R2R3-MYB transcription factors on the phenolic composition of maize plants and II) Identify the biosynthetic genes regulated by each of the selected R2R3-MYB factors. While a likely outcome of these studies are transgenic maize plants with altered phenolic composition, this research will significantly contribute to understanding how different branches of the phenolic biosynthetic grid are regulated. Given ...
Date: July 26, 2013
Creator: Grotewold, Erich
Partner: UNT Libraries Government Documents Department

Final Report for Regulation of Embryonic Development in Higher Plants

Description: The overall goal of the project was to define the cellular processes that underlie embryo development in plants at a mechanistic level. Our studies focused on a critical transcriptional regulator, Arabidopsis LEAFY COTYLEDON (LEC1), that is necessary and sufficient to induce processes required for embryo development. Because LEC1 regulates lipid accumulation during the maturation phase of embryo development, information about LEC1 may be useful in designing approaches to enhance biofuel production in plants. During the tenure of this project, we determined the molecular mechanisms by which LEC1 acts as a transcription factor in embryos. We also identified genes directly regulated by LEC1 and showed that many of these genes are involved in maturation processes. This information has been useful in dissecting the gene regulatory networks controlling embryo development. Finally, LEC1 is a novel isoform of a transcription factor that is conserved among eukaryotes, and LEC1 is active primarily in seeds. Therefore, we determined that the LEC1-type transcription factors first appeared in lycophytes during land plant evolution. Together, this study provides basic information that has implications for biofuel production.
Date: October 22, 2013
Creator: Harada, John J.
Partner: UNT Libraries Government Documents Department

Crystal structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains

Description: The GntR superfamily of dimeric transcription factors, with more than 6200 members encoded in bacterial genomes, are characterized by N-terminal winged helix (WH) DNA-binding domains and diverse C-terminal, regulatory domains, which provide a basis for the classification of the constituent families. The largest of these families, FadR, contains nearly 3000 proteins with all a-helical regulatory domains classified into two related Pfam families: FadR{_}C and FCD. Only two crystal structures of the FadR family members, i.e. the E. coli FadR protein and the LldR from C. glutamicum, have been described to date in literature. Here we describe the crystal structure of TM0439, a GntR regulator with an FCD domain, found in the Thermotoga maritima genome. The FCD domain is similar to that of the LldR regulator, and contains a buried metal binding site. Using atomic absorption spectroscopy and Trp fluorescence, we show that the recombinant protein contains bound Ni{sup 2+} ions, but it is able to bind Zn{sup 2+} with K{sub D} < 70 nM . We conclude that Zn{sup 2+} is the likely physiological metal, where it may perform either or both structural and regulatory roles. Finally, we compare the TM0439 structure to two other FadR family structures recently deposited by Structural Genomics consortia. The results call for a revision in the classification of the FadR family of transcription factors.
Date: June 6, 2009
Creator: Zheng, Meiying; Cooper, David; Grossoehmerb, Nickolas; Yu, Minmin; Hung, Li-Wei; Cieslik, Murcin et al.
Partner: UNT Libraries Government Documents Department

A primer on regression methods for decoding cis-regulatory logic

Description: The rapidly emerging field of systems biology is helping us to understand the molecular determinants of phenotype on a genomic scale [1]. Cis-regulatory elements are major sequence-based determinants of biological processes in cells and tissues [2]. For instance, during transcriptional regulation, transcription factors (TFs) bind to very specific regions on the promoter DNA [2,3] and recruit the basal transcriptional machinery, which ultimately initiates mRNA transcription (Figure 1A). Learning cis-Regulatory Elements from Omics Data A vast amount of work over the past decade has shown that omics data can be used to learn cis-regulatory logic on a genome-wide scale [4-6]--in particular, by integrating sequence data with mRNA expression profiles. The most popular approach has been to identify over-represented motifs in promoters of genes that are coexpressed [4,7,8]. Though widely used, such an approach can be limiting for a variety of reasons. First, the combinatorial nature of gene regulation is difficult to explicitly model in this framework. Moreover, in many applications of this approach, expression data from multiple conditions are necessary to obtain reliable predictions. This can potentially limit the use of this method to only large data sets [9]. Although these methods can be adapted to analyze mRNA expression data from a pair of biological conditions, such comparisons are often confounded by the fact that primary and secondary response genes are clustered together--whereas only the primary response genes are expected to contain the functional motifs [10]. A set of approaches based on regression has been developed to overcome the above limitations [11-32]. These approaches have their foundations in certain biophysical aspects of gene regulation [26,33-35]. That is, the models are motivated by the expected transcriptional response of genes due to the binding of TFs to their promoters. While such methods have gathered popularity in the computational domain, they remain largely obscure ...
Date: March 3, 2009
Creator: Das, Debopriya; Pellegrini, Matteo & Gray, Joe W.
Partner: UNT Libraries Government Documents Department

Structural studies of bacterial transcriptional regulatory proteins by multidimensional heteronuclear NMR

Description: Nuclear magnetic resonance spectroscopy was used to elucidate detailed structural information for peptide and protein molecules. A small peptide was designed and synthesized, and its three-dimensional structure was calculated using distance information derived from two-dimensional NMR measurements. The peptide was used to induce antibodies in mice, and the cross-reactivity of the antibodies with a related protein was analyzed with enzyme-linked immunosorbent assays. Two proteins which are involved in regulation of transcription in bacteria were also studied. The ferric uptake regulation (Fur) protein is a metal-dependent repressor which controls iron uptake in bacteria. Two- and three-dimensional NMR techniques, coupled with uniform and selective isotope labeling allowed the nearly complete assignment of the resonances of the metal-binding domain of the Fur protein. NTRC is a transcriptional enhancer binding protein whose N-terminal domain is a {open_quote}receiver domain{close_quote} in the family of {open_quote}two-component{close_quote} regulatory systems. Phosphorylation of the N-terminal domain of NTRC activates the initiation of transcription of aeries encoding proteins involved in nitrogen regulation. Three- and four-dimensional NMR spectroscopy methods have been used to complete the resonance assignments and determine the solution structure of the N-terminal receiver domain of the NTRC protein. Comparison of the solution structure of the NTRC receiver domain with the crystal structures of the homologous protein CheY reveals a very similar fold, with the only significant difference being the position of helix 4 relative to the rest of the protein. The determination of the structure of the NTRC receiver domain is the first step toward understanding a mechanism of signal transduction which is common to many bacterial regulatory systems.
Date: February 1, 1995
Creator: Volkman, B.F.
Partner: UNT Libraries Government Documents Department

Transcription Factors in Xylem Development. Final report

Description: Answers to the following questions are answered in this report. do the two pine Byb proteins previously identified as candidate transcription factors bind to DNA and activate transcription? In what cell types are tehse Myb proteins expressed? Are these proteins localized to the nucleus? Do other proteins in pine xylem interact with these Myb proteins? Does altered expression of these genes have an impact on xylogenesis, specifically the expression of monolignol biosynthetic genes?
Date: July 1, 1999
Creator: Sederoff, Ronald; Whetten, Ross; O'Malley, David & Campbell, Malcolm
Partner: UNT Libraries Government Documents Department