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Biosynthesis of the Cyclotide MCoTI-II using an Engineered Intein

Description: 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 confe… more
Date: August 15, 2006
Creator: Cantor, J & Camarero, J A
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
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In Vivo Enhancer Analysis Chromosome 16 Conserved NoncodingSequences

Description: The identification of enhancers with predicted specificitiesin vertebrate genomes remains a significant challenge that is hampered bya lack of experimentally validated training sets. In this study, weleveraged extreme evolutionary sequence conservation as a filter toidentify putative gene regulatory elements and characterized the in vivoenhancer activity of human-fish conserved and ultraconserved1 noncodingelements on human chromosome 16 as well as such elements from elsewherein the genome. We … more
Date: February 1, 2006
Creator: Pennacchio, Len A.; Ahituv, Nadav; Moses, Alan M.; Nobrega,Marcelo; Prabhakar, Shyam; Shoukry, Malak et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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In Vivo Characterization of Human APOA5 Haplotypes

Description: Increased plasma triglycerides concentrations are an independent risk factor for cardiovascular disease. Numerous studies support a reproducible genetic association between two minor haplotypes in the human apolipoprotein A5 gene (APOA5) and increased plasma triglyceride concentrations. We thus sought to investigate the effect of these minor haplotypes (APOA5*2 and APOA5*3) on ApoAV plasma levels through the precise insertion of single-copy intact APOA5 haplotypes at a targeted location in the … more
Date: October 1, 2006
Creator: Ahituv, Nadav; Akiyama, Jennifer; Chapman-Helleboid, Audrey; Fruchart, Jamila & Pennacchio, Len A.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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SATB1 tethers multiple gene loci to reprogram expression profiledriving breast cancer metastasis

Description: Global changes in gene expression occur during tumor progression, as indicated by expression profiling of metastatic tumors. How this occurs is poorly understood. SATB1 functions as a genome organizer by folding chromatin via tethering multiple genomic loci and recruiting chromatin remodeling enzymes to regulate chromatin structure and expression of a large number of genes. Here we show that SATB1 is expressed at high levels in aggressive breast cancer cells, and is undetectable in non-malignan… more
Date: July 13, 2006
Creator: Han, Hye-Jung; Kohwi, Yoshinori & Kohwi-Shigematsu, Terumi
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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Fox-2 Splicing Factor Binds to a Conserved Intron Motif to PromoteInclusion of Protein 4.1R Alternative Exon 16

Description: Activation of protein 4.1R exon 16 (E16) inclusion during erythropoiesis represents a physiologically important splicing switch that increases 4.1R affinity for spectrin and actin. Previous studies showed that negative regulation of E16 splicing is mediated by the binding of hnRNP A/B proteins to silencer elements in the exon and that downregulation of hnRNP A/B proteins in erythroblasts leads to activation of E16 inclusion. This paper demonstrates that positive regulation of E16 splicing can b… more
Date: March 1, 2006
Creator: Ponthier, Julie L.; Schluepen, Christina; Chen, Weiguo; Lersch,Robert A.; Gee, Sherry L.; Hou, Victor C. et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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SQUID-Detected Magnetic Resonance Imaging in MicroteslaFields

Description: Magnetic resonance imaging (MRI) has developed into a powerful clinical tool for imaging the human body (1). This technique is based on nuclear magnetic resonance (NMR) of protons (2, 3) in a static magnetic field B{sub 0}. An applied radiofrequency pulse causes the protons to precess about B{sub 0} at their Larmor frequency {nu}{sub 0} = ({gamma}/2{pi})B{sub 0}, where {gamma} is the gyromagnetic ratio; {gamma}/2{pi} = 42.58 MHz/tesla. The precessing protons generate an oscillating magnetic fie… more
Date: August 14, 2006
Creator: Moessle, Michael; Hatridge, Michael & Clarke, John
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Pseudomonas aeruginosa forms Biofilms in Acute InfectionIndependent of Cell-to-Cell Signaling

Description: Biofilms are bacterial communities residing within a polysaccharide matrix that are associated with persistence and antibiotic resistance in chronic infections. We show that the opportunistic pathogen Pseudomonas aeruginosa forms biofilms within 8 hours of infection in thermally-injured mice, demonstrating that biofilms contribute to bacterial colonization in acute infections. P. aeruginosa biofilms were visualized within burned tissue surrounding blood vessels and adipose cells. Although quoru… more
Date: September 20, 2006
Creator: Schaber, J. Andy; Triffo, W. J.; Suh, Sang J.; Oliver, Jeffrey W.; Hastert, Mary C.; Griswold, John A. et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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Proteomic Analysis of Calcium- and Phosphorylation-dependentCalmodulin Complexes in Mammalian Cells

Description: Protein conformational changes due to cofactor binding (e.g. metal ions, heme) and/or posttranslational modifications (e.g. phosphorylation) modulate dynamic protein complexes. Calmodulin (CaM) plays an essential role in regulating calcium (Ca{sup 2+}) signaling and homeostasis. No systematic approach on the identification of phosphorylation-dependent Ca{sup 2+}/CaM binding proteins has been published. Herein, we report a proteome-wide study of phosphorylation-dependent CaM binding proteins fro… more
Date: May 26, 2006
Creator: Jang, Deok-Jin & Wang, Daojing
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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Telomere dysfunction and cell survival: roles for distinctTIN2-containing complexes

Description: Telomeres are maintained by three DNA binding proteins, TRF1, TRF2 and POT1, and several associated factors. One factor, TIN2, binds TRF1 and TRF2 directly and POT1 indirectly. These and two other proteins form a soluble complex that may be the core telomere-maintenance complex. It is not clear whether subcomplexes exist or function in vivo. Here, we provide evidence for two TIN2 subcomplexes with distinct functions in human cells. TIN2 ablation by RNA interference caused telomere uncapping and… more
Date: November 7, 2006
Creator: Kim, Sahn-Ho; Davalos, Albert R.; Heo, Seok-Jin; Rodier, Francis; Beausejour, Christian; Kaminker, Patrick et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Enhancement of T1 and T2 relaxation by paramagnetic silica-coated nanocrystals

Description: We present the first comprehensive investigation on water-soluble nanoparticles embedded into a paramagnetic shell and their properties as an MRI contrast agent. The nanoprobes are constructed with an inorganic core embedded into an ultra-thin silica shell covalently linked to chelated Gd{sup 3+} paramagnetic ions that act as an MRI contrast agent. The chelator contains the molecule DOTA and the inorganic core contains a fluorescent CdSe/ZnS qdots in Au nanoparticles. Optical properties of the … more
Date: August 28, 2006
Creator: Gerion, D; Herberg, J; Gjersing, E; Ramon, E; Maxwell, R; Gray, J W et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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Human cathepsin L rescues the neurodegeneration and lethality incathepsin B/L double deficient mice

Description: Cathepsin B (CTSB) and cathepsin L (CTSL) are two widelyexpressed cysteine proteases thought to predominantly reside withinlysosomes. Functional analysis of CTSL in humans is complicated by theexistence of two CTSL-like homologues (CTSL and CTSL2), in contrast tomice which contain only one CTSL enzyme. Thus transgenic expression ofhuman CTSL in CTSL deficient mice provides an opportunity to study the invivo functions of this human protease without interference by its highlyrelated homologue. Wh… more
Date: January 9, 2006
Creator: Sevenich, Lisa; Pennacchio, Len A.; Peters, Christoph & Reinheckel, Thomas
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Metal inhibition of human alkylpurine-DNA-N-glycosylase activityin base excision repair

Description: Cadmium (Cd{sup 2+}), nickel (Ni{sup 2+}) and cobalt (Co{sup 2+}) are human and/or animal carcinogens. Zinc (Zn{sup 2+}) is not categorized as a carcinogen, and rather an essential element to humans. Metals were recently shown to inhibit DNA repair proteins that use metals for their function and/or structure. Here we report that the divalent ions Cd{sup 2+}, Ni{sup 2+}, and Zn{sup 2+} can inhibit the activity of a recombinant human N-methylpurine-DNA glycosylase (MPG) toward a deoxyoligonucleot… more
Date: February 28, 2006
Creator: Wang, Ping; Guliaev, Anton B. & Hang, Bo
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Accelerated Evolution of Conserved Noncoding Sequences in theHuman Genome

Description: Genomic comparisons between human and distant, non-primatemammals are commonly used to identify cis-regulatory elements based onconstrained sequence evolution. However, these methods fail to detect"cryptic" functional elements, which are too weakly conserved amongmammals to distinguish from nonfunctional DNA. To address this problem,we explored the potential of deep intra-primate sequence comparisons. Wesequenced the orthologs of 558 kb of human genomic sequence, coveringmultiple loci involved … more
Date: July 6, 2006
Creator: Prambhakar, Shyam; Noonan, James P.; Paabo, Svante & Rubin, EdwardM.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Role of Alcohol on the Fracture Resistance of Dentin

Description: Healthy dentin, the mineralized tissue that makes up the bulk of the tooth, is naturally hydrated in vivo; however, it is known that various chemical reagents including acetone and ethanol can induce dehydration and thereby affect its properties. Here, we seek to investigate this in light of the effect alcohol can have on the mechanical properties of dentin, specifically by measuring the stiffness, strength and toughness of dentin in simulated body fluid and scotch whisky. Results indicate that… more
Date: May 1, 2006
Creator: Nalla, Ravi K.; Kinney, John H.; Tomsia, Antoni P. & Ritchie,Robert O.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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Foundations for in vivo nano-scale measurement of memory processes.

Description: An ongoing program of research and development is utilizing nanomaterials as a basis for observing and measuring neurophysiological processes. Work commencing in fiscal year 2007 will focus on expanding current capabilities to create nanoelectrode arrays that will allow nanoscale measurement of the activity of 10's to 100's of neurons. This development is a vital step in gaining scientific insights concerning network properties associated with neural representations and processes. Specifically,… more
Date: September 1, 2006
Creator: Forsythe, James Chris
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
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Developing New Tools for the in vivo Generation/Screening of Cyclic Peptide Libraries. A New Combinatorial Approach for the Detection of Bacterial Toxin Inhibitors

Description: A new combinatorial approach for the biosynthesis and screening of small drug-like toxin inhibitors inside living cells is presented. This approach has been initially used as proof of principle for finding inhibitors against the LF factor from Bacillus anthracis. Key to our ''living combinatorial'' approach is the use of a living cell as a micro-chemical factory for both synthesis and screening of potential inhibitors for a given molecular recognition event (see Scheme 1). This powerful techniq… more
Date: November 28, 2006
Creator: Camarero, J A
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

Detection of Weakly Conserved Ancestral Mammalian RegulatorySequences by Primate Comparisons

Description: Genomic comparisons between human and distant, non-primatemammals are commonly used to identify cis-regulatory elements based onconstrained sequence evolution. However, these methods fail to detectcryptic functional elements, which are too weakly conserved among mammalsto distinguish from nonfunctional DNA. To address this problem, weexplored the potential of deep intra-primate sequence comparisons. Wesequenced the orthologs of 558 kb of human genomic sequence, coveringmultiple loci involved in… more
Date: June 1, 2006
Creator: Wang, Qian-fei; Prabhakar, Shyam; Chanan, Sumita; Cheng,Jan-Fang; Rubin, Edward M. & Boffelli, Dario
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Targeted Gene Deletion Demonstrates that Cell Adhesion MoleculeICAM-4 is Critical for Erythroblastic Island Formation

Description: Erythroid progenitors differentiate in erythroblastic islands, bone marrow niches composed of erythroblasts surrounding a central macrophage. Evidence suggests that within islands adhesive interactions regulate erythropoiesis and apoptosis. We are exploring whether erythroid intercellular adhesion molecule-4 (ICAM-4), animmunoglobulin superfamily member, participates in island formation. Earlier, we identified alpha V integrins as ICAM-4 counter receptors. Since macrophages express alpha V, ICA… more
Date: February 15, 2006
Creator: Lee, Gloria; Lo, Annie; Short, Sarah A.; Mankelow, Tosti J.; Spring, Frances; Parsons, Stephen F. et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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Large-scale turnover of functional transcription factor bindingsites in Drosophila

Description: The gain and loss of functional transcription-factor bindingsites has been proposed as a major source of evolutionary change incis-regulatory DNA and gene expression. We have developed an evolutionarymodel to study binding site turnover that uses multiple sequencealignments to assess the evolutionary constraint on individual bindingsites, and to map gain and loss events along a phylogenetic tree. Weapply this model to study the evolutionary dynamics of binding sites ofthe Drosophila melanogaste… more
Date: July 14, 2006
Creator: Moses, Alan M.; Pollard, Daniel A.; Nix, David A.; Iyer, VenkyN.; Li, Xiao-Yong; Biggin, Mark D. et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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VISTA Enhancer Browser--A Database of Tissue-Specific HumanEnhancers

Description: Despite the known existence of distant-acting cis-regulatoryelements in the human genome, only a small fraction of these elements hasbeen identified and experimentally characterized in vivo. This paucity ofenhancer collections with defined activities has thus hinderedcomputational approaches for the genome-wide prediction of enhancers andtheir functions. To fill this void, we utilize comparative genomeanalysis to identify candidate enhancer elements in the human genomecoupled with the experimen… more
Date: August 1, 2006
Creator: Visel, Axel; Minovitsky, Simon; Dubchak, Inna & Pennacchio, Len A.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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Predicting Tissue-Specific Enhancers in the Human Genome

Description: Determining how transcriptional regulatory signals areencoded in vertebrate genomes is essential for understanding the originsof multi-cellular complexity; yet the genetic code of vertebrate generegulation remains poorly understood. In an attempt to elucidate thiscode, we synergistically combined genome-wide gene expression profiling,vertebrate genome comparisons, and transcription factor binding siteanalysis to define sequence signatures characteristic of candidatetissue-specific enhancers in … more
Date: July 1, 2006
Creator: Pennacchio, Len A.; Loots, Gabriela G.; Nobrega, Marcelo A. & Ovcharenko, Ivan
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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Primate-Specific Evolution of an LDLR Enhancer

Description: Sequence changes in regulatory regions have often beeninvoked to explain phenotypic divergence among species, but molecularexamples of this have been difficult to obtain. In this study, weidentified an anthropoid primate specific sequence element thatcontributed to the regulatory evolution of the LDL receptor. Using acombination of close and distant species genomic sequence comparisonscoupled with in vivo and in vitro studies, we show that a functionalcholesterol-sensing sequence motif arose an… more
Date: June 28, 2006
Creator: Wang, Qian-fei; Prabhakar, Shyam; Wang, Qianben; Moses, Alan M.; Chanan, Sumita; Brown, Myles et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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Engineering intracellular active transport systems as in vivo biomolecular tools.

Description: Active transport systems provide essential functions in terms of cell physiology and metastasis. These systems, however, are also co-opted by invading viruses, enabling directed transport of the virus to and from the cell's nucleus (i.e., the site of virus replication). Based on this concept, fundamentally new approaches for interrogating and manipulating the inner workings of living cells may be achievable by co-opting Nature's active transport systems as an in vivo biomolecular tool. The over… more
Date: November 1, 2006
Creator: Bachand, George David & Carroll-Portillo, Amanda
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
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Identification of clustered YY1 binding sites in Imprinting Control Regions

Description: Mammalian genomic imprinting is regulated by Imprinting Control Regions (ICRs) that are usually associated with tandem arrays of transcription factor binding sites. In the current study, the sequence features derived from a tandem array of YY1 binding sites of Peg3-DMR (differentially methylated region) led us to identify three additional clustered YY1 binding sites, which are also localized within the DMRs of Xist, Tsix, and Nespas. These regions have been shown to play a critical role as ICRs… more
Date: April 19, 2006
Creator: Kim, J D; Hinz, A; Bergmann, A; Huang, J; Ovcharenko, I; Stubbs, L et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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