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Rife Resonance

Niyati Jain, Christopher E Morgan, Brittany D Rife, Marco Salemi, Blanton S Tolbert
Splicing patterns in human immunodeficiency virus type 1 (HIV-1) are maintained through cis regulatory elements that recruit antagonistic host RNA-binding proteins. The activity of the 3' acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b), and an exonic splicing enhancer (ESE3). Because HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites...
January 29, 2016: Journal of Biological Chemistry
Carrie Rollins, Jeffrey D Levengood, Brittany D Rife, Marco Salemi, Blanton S Tolbert
Complete expression of the HIV-1 genome requires balanced usage of suboptimal splice sites. The 3' acceptor site A7 (ssA7) is negatively regulated in part by an interaction between the host hnRNP A1 protein and a viral splicing silencer (ESS3). Binding of hnRNP A1 to ESS3 and other upstream silencers is sufficient to occlude spliceosome assembly. Efforts to understand the splicing repressive properties of hnRNP A1 on ssA7 have revealed hnRNP A1 binds specific sites within the context of a highly folded RNA structure; however, biochemical models assert hnRNP A1 disrupts RNA structure through cooperative spreading...
April 8, 2014: Biochemistry
Johan Lorenzen, Dirk Meyer-Olson, Marion Haubitz, Torsten Witte, Franz Bange, Reinhold Schmidt, Matthias Stoll
A 55-year-old woman with systemic lupus erythematosus was admitted with fever of unknown origin. She had been on an immunosuppressive regimen for the past 8 years including steroids and Azathioprine. Laboratory parameters revealed a markedly elevated C-reactive protein of 189 mg/l, antinuclear antibodies of 1:2,560, a hemoglobin level of 9.0 g/dl, and a severe lymphopenia (total lymphocytes 49.4/microl, CD4(+) cells 2/microl, CD8(+) cells 7/microl). Neither blood culture samples nor computed tomography and magnetic resonance imaging of the chest and abdomen nor a trans-esophageal echocardiography revealed positive results...
June 2009: Clinical Rheumatology
Adam W Anderson, Rubina A Heptulla, Naomi Driesen, Daniel Flanagan, Philip A Goldberg, Timothy W Jones, Fran Rife, Hedy Sarofin, William Tamborlane, Robert Sherwin, John C Gore
Functional magnetic resonance imaging (fMRI) was used to measure the effects of acute hypoglycemia caused by passive sensory stimulation on brain activation. Visual stimulation was used to generate blood-oxygen-level-dependent (BOLD) contrast, which was monitored during hyperinsulinemic hypoglycemic and euglycemic clamp studies. Hypoglycemia (50 +/- 1 mg glucose/dl) decreased the fMRI signal relative to euglycemia in 10 healthy human subjects: the fractional signal change was reduced by 28 +/- 12% (P < ...
July 2006: Magnetic Resonance Imaging
Ram Weiss, Sylvie Dufour, Sara E Taksali, William V Tamborlane, Kitt F Petersen, Riccardo C Bonadonna, Linda Boselli, Gina Barbetta, Karin Allen, Francis Rife, Mary Savoye, James Dziura, Robert Sherwin, Gerald I Shulman, Sonia Caprio
BACKGROUND: Impaired glucose tolerance is common among obese adolescents, but the changes in insulin sensitivity and secretion that lead to this prediabetic state are unknown. We investigated whether altered partitioning of myocellular and abdominal fat relates to abnormalities in glucose homoeostasis in obese adolescents with prediabetes. METHODS: We studied 14 obese children with impaired glucose tolerance and 14 with normal glucose tolerance, of similar ages, sex distribution, and degree of obesity...
September 20, 2003: Lancet
Stoyan K Smoukov, Joshua Telser, Bryan A Bernat, Chris L Rife, Richard N Armstrong, Brian M Hoffman
FosA is a manganese metalloglutathione transferase that confers resistance to the broad-spectrum antibiotic fosfomycin, (1R,2S)-epoxypropylphosphonic acid. The reaction catalyzed by FosA involves the attack by glutathione on fosfomycin to yield the product 1-(S-glutathionyl)-2-hydroxypropylphosphonic acid. The enzyme is a dimer of 16 kDa subunits, each of which harbors one mononuclear Mn(II) site. The coordination environment of the Mn(II) in the FosA x Mn(2+) complex is composed of a glutamate and two histidine ligands and three water molecules...
March 13, 2002: Journal of the American Chemical Society
P W Huber, J P Rife, P B Moore
The solution structure of an oligonucleotide containing the helix III sequence from Xenopus oocyte 5 S rRNA has been determined by NMR spectroscopy. Helix III includes two unpaired adenosine residues, flanked on either side by G:C base-pairs, that are required for binding of ribosomal protein L5. The consensus conformation of helix III in the context provided by this oligonucleotide has the two adenosine residues located in the minor groove and stacked upon the 3' flanking guanosine residue, consistent with biochemical studies of free 5 S rRNA in solution...
September 28, 2001: Journal of Molecular Biology
T F Fu, J P Rife, V Schirch
The role of cytosolic and mitochondrial serine hydroxymethyltransferase in supplying one-carbon groups for purine and thymidylate biosynthesis in MCF-7 cells was investigated by observing folate-mediated one-carbon metabolism of l-[3-(13)C]serine, [2-(13)C]glycine, and [(13)C]formate. (13)C NMR was used to follow the incorporation of label into carbons 2 and 8 of purines and the methyl group attached to carbon 5 of thymidylate. The percentage enrichment of the (13)C label in purines was determined from the splitting patterns of the (1)H NMR spectra of C2 and C8 of adenine and C8 of guanine...
September 1, 2001: Archives of Biochemistry and Biophysics
D J Cashman, J P Rife, G E Kellogg
The NMR structures of gentamicin and paromomycin in complex with the A-site of Escherichia coli 16S ribosomal RNA were modified with molecular modeling to 12 analogues. The intermolecular interactions between these molecules and RNA were examined using the HINT (Hydropathic INTeractions) computational model to obtain interaction scores that have been shown previously to be related to free energy. The calculations correlated well with experimental binding data, and the interaction scores were used to analyze the specific structural features of each aminoglycoside that contribute to the overall binding with the 16S rRNA...
January 22, 2001: Bioorganic & Medicinal Chemistry Letters
N P Ewing, C J Cassady
Collision-induced dissociation (CID) was performed on multiply deprotonated ions from three commercial peptides: hirudin (54-65), fibrinopeptide B, and oxidized insulin chain A. Ions were produced by electrospray ionization in a Fourier transform ion cyclotron resonance mass spectrometer. Each of these peptides contains multiple acidic residues, which makes them very difficult to ionize in the positive mode. However, the peptides deprotonate readily making negative ion studies a viable alternative. The CID spectra indicated that the likely deprotonation sites are acidic residues (aspartic, glutamic, and cysteic acids) and the C-terminus...
January 2001: Journal of the American Society for Mass Spectrometry
J P Rife, S C Stallings, C C Correll, A Dallas, T A Steitz, P B Moore
Until recently, there were no examples of RNAs whose structures had been determined by both NMR and x-ray crystallography, and thus there was no experimental basis for assessing the accuracy of RNA solution structures. A comparison of the solution and the crystal structures of two RNAs is presented, which demonstrates that NMR can produce solution structures that resemble crystal structures and thus validates the application to RNA of a methodology developed initially for the determination of protein conformations...
January 1999: Biophysical Journal
J P Rife, C S Cheng, P B Moore, S A Strobel
Modified nucleotides are resource-intensive alternatives to the four nucleotides that constitute the bulk of natural RNAs. Yet, even in cases where modifications are highly conserved, their functions are difficult to identify. One possible function might be to modulate the stability of RNA structures. To investigate this possibility for N 2-methylguanosine (m2G), which is present in a wide variety of RNAs, we have determined the thermodynamic consequences of substituting m2G for G in G-C Watson-Crick pairs and G@U wobble pairs within RNA duplexes...
August 15, 1998: Nucleic Acids Research
J P Rife, P B Moore
BACKGROUND: Ribosomal RNAs contain many modified nucleotides. The functions of these nucleotides are poorly understood and few of them are strongly conserved. The final stem loop in 16S-like rRNAs is an exception in both regards. In both prokaryotes and eukaryotes, the tetranucleotide loop that caps the 3'-terminal stem contains two N6, N6-dimethyladenosine residues. The sequence and pattern of methylation are conserved within the loop, and there is evidence that these methylated nucleotides play an important role in subunit association and the initiation of protein synthesis...
June 15, 1998: Structure
J Lapham, J P Rife, P B Moore, D M Crothers
Pulsed field-gradient NMR experiments can be used to measure the diffusion constants of nucleic acids. The diffusion constants measured in this way for double-helical DNAs of defined length agree well both with theory and with measurements done using other techniques. When applied to RNAs, this experiment easily distinguishes duplex RNAs from RNA hairpins and thus it can solve one of the perennial problems faced by RNA spectroscopists, i.e. assessing whether their samples are monomeric or not.
October 1997: Journal of Biomolecular NMR
E V Vyazovkina, J P Rife, A V Lebedev, E Wickstrom
Synthesis of stereoregular DNA methylphosphonates has been accomplished for homo-oligomers, but remains a formidable problem for oligomers of a defined antisense target sequence. In this work, four trimer and tetramer deoxynucleoside methylphosphonates of mixed sequence (dACA, dCCAA, dAGGG, and dGCAT) were prepared by block coupling of diastereomerically pure dimers with either monomers or other diastereomerically pure dimers. These oligomers were separated chromatographically into individual diastereomers, and the configurations of the chiral methylphosphonate linkages were assigned...
December 25, 1993: Nucleic Acids Research
D G Maggs, R Jacob, F Rife, R Lange, P Leone, M J During, W V Tamborlane, R S Sherwin
To determine the relationship between circulating metabolic fuels and their local concentrations in peripheral tissues we measured glycerol, glucose, and amino acids by microdialysis in muscle and adipose interstitium of 10 fasted, nonobese human subjects during (a) baseline, (b) euglycemic hyperinsulinemia (3 mU/kg per min for 3 h) and, (c) local norepinephrine reuptake blockade (NOR). At baseline, interstitial glycerol was strikingly higher (P < 0.0001) in muscle (3710 microM) and adipose tissue (2760 microM) compared with plasma (87 microM), whereas interstitial glucose (muscle 3...
July 1995: Journal of Clinical Investigation
R W Shaw, J E Rife, M H O'Leary, H Beinert
We have measured the increase in 18O content of water produced from single turnover oxidations of anerobically reduced cytochrome c oxidase with 18O2 in order to test the hypothesis that a reduced atom of oxygen, originating from dioxygen, remains bound to oxidized cytochrome c oxidase in the form of a mu-oxo-bridge between two metal components when a single turnover occurs. When water samples produced by oxidizing the reduced enzyme with 18O2 were compared to natural abundance control samples obtained by oxidizing with 16O2, all of the 18O2 reduced in a single turnover could be accounted for in the form of additional H218O produced...
February 10, 1981: Journal of Biological Chemistry
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