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  • 1
    Article
    Article
    2010
    ISSN: 0009-2665 
    Language: English
    In: Chemical reviews, 12 May 2010, Vol.110(5), pp.3196-211
    Description: Combinatorial chemistry and phage display technologies provide robust means for the rapid discovery of tumor antigen-avid peptides. Combinatorial affinity maturation experiments have been performed on a small number of these peptides, including P30, in an attempt to improve affinity and in vivo binding. Phage display has also been performed using cultured human carcinoma cells or in situ with laser captured micro-dissected cancer cells resulting in many new peptides as potential imaging probes. Phage display-selected peptides been used in cancer imaging, but they have also been used in vivo to reduce tumor growth. The ability of unlabeled peptides to functionally modulate tumor growth and spread should positively impact future studies aimed at developing peptide-based cancer therapeutics. Thus, phage display technology has developed into a rapid, economical, and efficacious approach to the development of agents for the molecular imaging and diagnosis of cancer.
    Subject(s): Peptide Library ; Molecular Imaging -- Methods ; Neoplasms -- Diagnosis
    ISSN: 0009-2665
    E-ISSN: 1520-6890
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  • 2
    Language: English
    In: Journal of Applied Physics, 01 June 2012, Vol.111(11)
    Description: We review three different kinds of experiments that emphasize the non-BCS, inhomogeneous aspects of superconductivity in the high Tc cuprates. The first is the existence of two different energy scales in the superconducting state, initially identified by a comparison between tunneling and Andreev–Saint–James spectroscopies [Deutscher, Nature (London) 397 , 410 (1999)]. The second are EXAFS measurements of the Cu-O bond length distribution, which have shown that below a temperature T* 〉 Tc, it becomes broader than expected from the Debye-Waller broadening and presents a split [Bianconi et al. , Phys. Rev. Lett. 76 , 3412 (1996)]. The third one is the effect of frozen lattice disorder on critical current and vortex pinning, which profoundly affects the pairing landscape [Gutierrez et al. , Nature Mater. 6 , 367 (2007)]. We then discuss how these results fit with models in which the electron-lattice interaction plays a leading role.
    Subject(s): Special Topic: Invited Papers From The 6th Meeting Of The Study Of Matter At Extreme Conditions , Miami, Florida, USA, 2011
    ISSN: 0021-8979
    E-ISSN: 1089-7550
    Source: © 2012 American Institute of Physics (AIP)〈img src=http://exlibris-pub.s3.amazonaws.com/AIP_edited.gif style="vertical-align:middle;margin-left:7px"〉
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  • 3
    Language: English
    In: Applied Physics Letters, 22 March 2010, Vol.96(12)
    Description: Superconducting cuprates and pnictides composed of CuO 2 or AsFe planes, respectively, with intercalated insulating layers, are at the crossroads of three families of crystalline solids: Metals, doped Mott insulators, and ferroelectrics. The metallic and doped insulator approaches to high temperature superconductivity are essentially electronic ones, while in ferroelectrics atomic displacements play a key role. We show that pairing by contraction of in-plane Cu–O (or As–Fe) bonds, as proposed by the bond contraction pairing model, is prevented by the tensile strain generated by dislocations at grain boundaries. This explains why weak link behavior already sets in at low angle boundaries.
    Subject(s): Magnetism And Superconductivity
    ISSN: 0003-6951
    E-ISSN: 1077-3118
    E-ISSN: 23318422
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  • 4
    Language: English
    In: The Journal of biological chemistry, 03 May 2013, Vol.288(18), pp.12574-9
    Description: Processing of ribosomal RNA (rRNA) precursors is an important component of RNA metabolism in all cells. However, in no system have we yet identified all the RNases involved in this process. Here, we show that four 3'→5'-exoribonucleases, RNases II, R, and PH, and polynucleotide phosphorylase (PNPase), participate in maturation of the 3' end of 16S rRNA. In their absence, 16S precursor molecules with 33 extra 3'-nt accumulate; however, the presence of any one of the four RNases is sufficient to allow processing to occur, although with different efficiencies. Additionally, we find that in the absence of 3' maturation, 5' processing proceeds much less efficiently. Moreover, mutant 30S particles, containing immature 16S rRNA, form 70S ribosomes very poorly. These findings, together with the earlier discovery that RNases E and G are the 5'-processing enzymes, completes the catalogue of RNases involved in maturation of Escherichia coli 16S rRNA.
    Subject(s): RNA ; Ribonuclease ; Ribosome Assembly ; Ribosomes ; Rrna Processing ; 3' Untranslated Regions -- Physiology ; Escherichia Coli -- Metabolism ; Escherichia Coli Proteins -- Metabolism ; Exoribonucleases -- Metabolism ; RNA Processing, Post-Transcriptional -- Physiology ; RNA, Bacterial -- Metabolism ; RNA, Ribosomal, 16s -- Metabolism
    ISSN: 0021-9258
    E-ISSN: 1083-351X
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  • 5
    Article
    Article
    2012
    ISSN: 0263-2764 
    Language: English
    In: Theory, Culture & Society, January 2012, Vol.29(1), pp.119-137
    Description: This paper interrogates the status of the Malthusian couple and the policing and government of reproduction in the first volume of Foucault's History of Sexuality, Volume I (HS1), and the associated Collège de France lectures. Presented by Foucault as one of the four ‘strategic ensembles’ of the 18th century through which knowledge and power became centered on sex, what Foucault calls the socialization of procreative sexuality (HS1: 104) also constitutes a largely invisible hinge between the trajectories in HS1: biopolitics (vector of governmentality, management, administration and intensification of life) and sex (vector through which the repressive hypothesis is rejected). Particularly because it is one of the least discussed figures in Foucauldian commentary, my argument is that a reading of HS1 through the prism of its Malthusian couple produces unexpected results. A text that can be interpreted from the perspective of (a) its debate with psychoanalysis, or (b) its potential...
    Subject(s): Biopolitics ; Feminism ; Foucault ; Malthusian ; Population ; Sexuality ; Women ; Social Sciences (General)
    ISSN: 0263-2764
    E-ISSN: 1460-3616
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  • 6
    Language: English
    In: The Journal of biological chemistry, 28 September 2012, Vol.287(40), pp.33472-9
    Description: RNase R, an important exoribonuclease involved in degradation of structured RNA, is subject to a novel mechanism of regulation. The enzyme is extremely unstable in rapidly growing cells but becomes stabilized under conditions of stress, such as stationary phase or cold shock. RNase R instability results from acetylation which promotes binding of tmRNA-SmpB, two trans-translation factors, to its C-terminal region. Here, we examine how binding of tmRNA-SmpB leads to proteolysis of RNase R. We show that RNase R degradation is due to two proteases, HslUV and Lon. In their absence, RNase R is stable. We also show, using an in vitro system that accurately replicates the in vivo process, that tmRNA-SmpB is not essential, but it stimulates binding of the protease to the N-terminal region of RNase R and that it does so by a direct interaction between the protease and SmpB which stabilizes protease binding. Thus, a sequence of events, initiated by acetylation of a single Lys residue, results in proteolysis of RNase R in exponential phase cells. RNase R in stationary phase or in cold-shocked cells is not acetylated, and thereby remains stable. Such a regulatory mechanism, dependent on protein acetylation, has not been observed previously in bacterial cells.
    Subject(s): Gene Expression Regulation, Bacterial ; Endopeptidase Clp -- Metabolism ; Escherichia Coli Proteins -- Metabolism ; Exoribonucleases -- Metabolism ; Protease La -- Metabolism ; RNA, Bacterial -- Metabolism ; RNA-Binding Proteins -- Metabolism
    E-ISSN: 1083-351X
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  • 7
    Language: English
    In: The Journal of biological chemistry, 29 November 2013, Vol.288(48), pp.34791-8
    Description: Ribonucleases play an important role in RNA metabolism. Yet, they are also potentially destructive enzymes whose activity must be controlled. Here we describe a novel regulatory mechanism affecting RNase R, a 3' to 5' exoribonuclease able to act on essentially all RNAs including those with extensive secondary structure. Most RNase R is sequestered on ribosomes in growing cells where it is stable and participates in trans-translation. In contrast, the free form of the enzyme, which is deleterious to cells, is extremely unstable, turning over with a half-life of 2 min. RNase R binding to ribosomes is dependent on transfer-messenger RNA (tmRNA)-SmpB, nonstop mRNA, and the modified form of ribosomal protein S12. Degradation of the free form of RNase R also requires tmRNA-SmpB, but this process is independent of ribosomes, indicating two distinct roles for tmRNA-SmpB. Inhibition of RNase R binding to ribosomes leads to slower growth and a massive increase in RNA degradation. These studies indicate a previously unknown role for ribosomes in cellular homeostasis.
    Subject(s): Escherichia Coli ; Protein Stability ; RNA Metabolism ; Ribonuclease ; Ribosomes ; Escherichia Coli -- Enzymology ; Exoribonucleases -- Chemistry ; RNA -- Metabolism ; Ribosomes -- Enzymology
    E-ISSN: 1083-351X
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  • 8
    Language: English
    In: The Journal of biological chemistry, 29 April 2016, Vol.291(18), pp.9438-43
    Description: RNase R is a 3' to 5' hydrolytic exoribonuclease that has the unusual ability to digest highly structured RNA. The enzyme possesses an intrinsic, ATP-dependent RNA helicase activity that is essential in vitro for efficient nuclease activity against double-stranded RNA substrates, particularly at lower temperatures, with more stable RNA duplexes, and for duplexes with short 3' overhangs. Here, we inquired whether the helicase activity was also important for RNase R function in vivo and for RNA metabolism. We find that strains containing a helicase-deficient RNase R due to mutations in its ATP-binding Walker motifs exhibit growth defects at low temperatures. Most importantly, cells also lacking polynucleotide phosphorylase (PNPase), and dependent for growth on RNase R, grow extremely poorly at 34, 37, and 42 °C and do not grow at all at 31 °C. Northern analysis revealed that in these cells, fragments of 16S and 23S rRNA accumulate to high levels, leading to interference with ribosome maturation...
    Subject(s): Escherichia Coli (E. Coli) ; RNA Degradation ; RNA Helicase ; Bacteria ; Ribonuclease ; Ribosomal Ribonucleic Acid (Rrna) (Ribosomal RNA) ; Escherichia Coli ; Escherichia Coli Proteins ; Exoribonucleases ; RNA Helicases ; RNA, Bacterial ; RNA, Ribosomal, 23s
    ISSN: 0021-9258
    E-ISSN: 1083-351X
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  • 9
    Language: English
    In: The Journal of biological chemistry, 17 August 2012, Vol.287(34), pp.28816-9
    Description: A recent study (Wolfe-Simon, F., Switzer Blum, J., Kulp, T. R., Gordon, G. W., Hoeft, S. E., Pett-Ridge, J., Stolz, J. F., Webb, S. M., Weber, P. K., Davies, P. C., Anbar, A. D., and Oremland, R. S. (2011) Science 332, 1163-1166) described the isolation of a special bacterial strain, GFAJ-1, that could grow in medium containing arsenate, but lacking phosphate, and that supposedly could substitute arsenic for phosphorus in its biological macromolecules. Here, we provide an alternative explanation for these observations and show that they can be reproduced in a laboratory strain of Escherichia coli. We find that arsenate induces massive ribosome degradation, which provides a source of phosphate. A small number of arsenate-tolerant cells arise during the long lag period prior to initiation of growth in +As/-P medium, and it is this population that undergoes the very slow, limited growth observed for both E. coli and GFAJ-1. These results provide a simple explanation for the reported growth...
    Subject(s): Phosphorus ; Arsenic -- Metabolism ; Escherichia Coli -- Growth & Development ; Ribosomes -- Metabolism
    ISSN: 0021-9258
    E-ISSN: 1083-351X
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  • 10
    Language: English
    In: The Journal of biological chemistry, 18 October 2013, Vol.288(42), pp.30636-44
    Description: In many organisms, 3' maturation of tRNAs is catalyzed by the endoribonuclease, RNase BN/RNase Z, which cleaves after the discriminator nucleotide to generate a substrate for addition of the universal CCA sequence. However, tRNAs or tRNA precursors that already contain a CCA sequence are not cleaved, thereby avoiding a futile cycle of removal and readdition of these essential residues. We show here that the adjacent C residues of the CCA sequence and an Arg residue within a highly conserved sequence motif in the channel leading to the RNase catalytic site are both required for the protective effect of the CCA sequence. When both of these determinants are present, CCA-containing RNAs in the channel are unable to move into the catalytic site; however, substitution of either of the C residues by A or U or mutation of Arg(274) to Ala allows RNA movement and catalysis to proceed. These data define a novel mechanism for how tRNAs are protected against the promiscuous action of a processing enzyme....
    Subject(s): Enzyme Structure ; Nucleic Acid Chemistry ; Nucleic Acid Enzymology ; Phosphodiesterases ; Protein-Nucleic Acid Interaction ; RNA Catalysis ; RNA Processing ; RNA-Protein Interaction ; Structural Biology ; Transfer RNA (Trna) ; Endoribonucleases -- Metabolism ; Escherichia Coli -- Metabolism ; Escherichia Coli Proteins -- Metabolism ; Exoribonucleases -- Metabolism ; RNA Precursors -- Metabolism ; RNA Processing, Post-Transcriptional -- Physiology ; RNA, Bacterial -- Metabolism ; RNA, Transfer -- Metabolism
    ISSN: 0021-9258
    E-ISSN: 1083-351X
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