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  • 1
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    Riboswitches in eubacteria sense the second messenger cyclic di-GMP (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-19
    Description: Cyclic di-guanosine monophosphate (di-GMP) is a circular RNA dinucleotide that functions as a second messenger in diverse species of bacteria to trigger wide-ranging physiological changes, including cell differentiation, conversion between motile and biofilm lifestyles, and virulence gene expression. However, the mechanisms by which cyclic di-GMP regulates gene expression have remained a mystery. We found that cyclic di-GMP in many bacterial species is sensed by a riboswitch class in messenger RNA that controls the expression of genes involved in numerous fundamental cellular processes. A variety of cyclic di-GMP regulons are revealed, including some riboswitches associated with virulence gene expression, pilus formation, and flagellum biosynthesis. In addition, sequences matching the consensus for cyclic di-GMP riboswitches are present in the genome of a bacteriophage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sudarsan, N -- Lee, E R -- Weinberg, Z -- Moy, R H -- Kim, J N -- Link, K H -- Breaker, R R -- GM 068819/GM/NIGMS NIH HHS/ -- HV28186/HV/NHLBI NIH HHS/ -- R33 DK07027/DK/NIDDK NIH HHS/ -- RR19895-02/RR/NCRR NIH HHS/ -- T32GM007223/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Jul 18;321(5887):411-3. doi: 10.1126/science.1159519.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18635805" target="_blank"〉PubMed〈/a〉
    Keywords: Aptamers, Nucleotide/*metabolism ; Bacillus cereus/genetics/metabolism ; Bacteria/*genetics/metabolism ; Bacteriophages/genetics ; Base Sequence ; Clostridium difficile/genetics/metabolism ; Cyclic GMP/*analogs & derivatives/metabolism ; *Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Ligands ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Bacterial/chemistry/*metabolism ; RNA, Messenger/chemistry/*metabolism ; Regulon ; *Second Messenger Systems ; Vibrio cholerae/genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Widespread genetic switches and toxicity resistance proteins for fluoride (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-12-24
    Description: Most riboswitches are metabolite-binding RNA structures located in bacterial messenger RNAs where they control gene expression. We have discovered a riboswitch class in many bacterial and archaeal species whose members are selectively triggered by fluoride but reject other small anions, including chloride. These fluoride riboswitches activate expression of genes that encode putative fluoride transporters, enzymes that are known to be inhibited by fluoride, and additional proteins of unknown function. Our findings indicate that most organisms are naturally exposed to toxic levels of fluoride and that many species use fluoride-sensing RNAs to control the expression of proteins that alleviate the deleterious effects of this anion.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140402/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140402/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Jenny L -- Sudarsan, Narasimhan -- Weinberg, Zasha -- Roth, Adam -- Stockbridge, Randy B -- Breaker, Ronald R -- GM022778/GM/NIGMS NIH HHS/ -- P01 GM022778/GM/NIGMS NIH HHS/ -- R01 DE022340/DE/NIDCR NIH HHS/ -- RR19895-02/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jan 13;335(6065):233-5. doi: 10.1126/science.1215063. Epub 2011 Dec 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Yale University, Box 208103, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22194412" target="_blank"〉PubMed〈/a〉
    Keywords: Anion Transport Proteins/genetics/metabolism ; Aptamers, Nucleotide ; Bacterial Proteins/*genetics/metabolism ; Calcium/metabolism ; *Drug Resistance, Bacterial ; Escherichia coli/genetics/growth & development/metabolism ; Fluorides/metabolism/*pharmacology ; *Gene Expression Regulation, Bacterial ; Ion Channels/genetics/metabolism ; Nucleic Acid Conformation ; Pseudomonas syringae/drug effects/*genetics/metabolism ; RNA, Bacterial/chemistry/genetics/metabolism ; *Riboswitch ; Sodium Fluoride/metabolism/pharmacology ; Transformation, Bacterial
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    A glycine-dependent riboswitch that uses cooperative binding to control gene expression (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-09
    Description: We identified a previously unknown riboswitch class in bacteria that is selectively triggered by glycine. A representative of these glycine-sensing RNAs from Bacillus subtilis operates as a rare genetic on switch for the gcvT operon, which codes for proteins that form the glycine cleavage system. Most glycine riboswitches integrate two ligand-binding domains that function cooperatively to more closely approximate a two-state genetic switch. This advanced form of riboswitch may have evolved to ensure that excess glycine is efficiently used to provide carbon flux through the citric acid cycle and maintain adequate amounts of the amino acid for protein synthesis. Thus, riboswitches perform key regulatory roles and exhibit complex performance characteristics that previously had been observed only with protein factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mandal, Maumita -- Lee, Mark -- Barrick, Jeffrey E -- Weinberg, Zasha -- Emilsson, Gail Mitchell -- Ruzzo, Walter L -- Breaker, Ronald R -- New York, N.Y. -- Science. 2004 Oct 8;306(5694):275-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, Yale University, Post Office Box 208103, New Haven, CT 06520-8103, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15472076" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions/chemistry/*metabolism ; Allosteric Regulation ; Allosteric Site ; Bacillus subtilis/*genetics/metabolism ; Base Pairing ; Base Sequence ; Binding Sites ; *Gene Expression Regulation, Bacterial ; Glycine/*metabolism ; Ligands ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Operon ; RNA, Bacterial/chemistry/*metabolism ; RNA, Messenger/chemistry/*metabolism ; Transcription, Genetic ; Vibrio cholerae/*genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    An allosteric self-splicing ribozyme triggered by a bacterial second messenger (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-08-14
    Description: Group I self-splicing ribozymes commonly function as components of selfish mobile genetic elements. We identified an allosteric group I ribozyme, wherein self-splicing is regulated by a distinct riboswitch class that senses the bacterial second messenger c-di-GMP. The tandem RNA sensory system resides in the 5' untranslated region of the messenger RNA for a putative virulence gene in the pathogenic bacterium Clostridium difficile. c-di-GMP binding by the riboswitch induces folding changes at atypical splice site junctions to modulate alternative RNA processing. Our findings indicate that some self-splicing ribozymes are not selfish elements but are harnessed by cells as metabolite sensors and genetic regulators.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538695/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538695/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Elaine R -- Baker, Jenny L -- Weinberg, Zasha -- Sudarsan, Narasimhan -- Breaker, Ronald R -- P01 GM022778/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Aug 13;329(5993):845-8. doi: 10.1126/science.1190713.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20705859" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions ; Aptamers, Nucleotide/chemistry ; Base Pairing ; Base Sequence ; Clostridium difficile/*genetics/metabolism/pathogenicity ; Codon, Initiator ; Cyclic GMP/*analogs & derivatives/metabolism ; Exons ; Genes, Bacterial ; Guanosine Triphosphate/metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; *RNA Splicing ; RNA, Bacterial/chemistry/*genetics/metabolism ; RNA, Catalytic/chemistry/genetics/*metabolism ; RNA, Messenger/chemistry/genetics/metabolism ; *Regulatory Sequences, Ribonucleic Acid ; *Second Messenger Systems
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
    Electronic Resource
    Electronic Resource
    Positron annihilation studies in the field induced depletion regions of metal-oxide-semiconductor structures (1992)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 71 (1992), S. 5606-5609 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The centroid shifts of positron annihilation spectra are reported from the depletion regions of metal-oxide-semiconductor (MOS) capacitors at room temperature and at 35 K. The centroid shift measurement can be explained using the variation of the electric field strength and depletion layer thickness as a function of the applied gate bias. An estimate for the relevant MOS quantities is obtained by fitting the centroid shift versus beam energy data with a steady-state diffusion-annihilation equation and a derivative-gaussian positron implantation profile. Inadequacy of the present analysis scheme is evident from the derived quantities and alternate methods are required for better predictions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.350540
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  • 6
    Electronic Resource
    Electronic Resource
    Positron annihilation at the Si/SiO2 interface (1992)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 71 (1992), S. 530-532 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Variable-energy positron annihilation depth-profiling has been applied to the study of the Si/SiO2 interface in Al-gate metal-oxide-semiconductor (MOS) structures. For both n- and p-type silicon under conditions of negative gate bias, the positron annihilation S-factor characteristic of the interface (Sint) is substantially modified. Temperature and annealing behavior, combined with known MOS physics, suggest strongly that Sint depends directly on holes at interface states or traps at the Si/SiO2 interface.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.350694
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  • 7
    Electronic Resource
    Electronic Resource
    The effect of gate metal and SiO2 thickness on the generation of donor states at the Si-SiO2 interface (1985)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 57 (1985), S. 418-425 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Two experimental observations are reported concerning the degradation of the Si–SiO2 interface during electron injection in metal-oxide-semiconductor structures. First, the generation of the interfacial positive charge during avalanche injection can be strongly inhibited by employing magnesium, instead of aluminum, as gate metal, or enhanced by employing gold. This correlates with the different work functions of the metals. Second, during negative bias high-field injection in Al-gate capacitors with thin oxides ((approximately-less-than)100 A(ring)), a threshold in gate voltage, of 7–8 V, is found for the generation of the positive charge. Both observations are consistent with a model which assumes that holes generated in the anode by hot electrons, via emission of surface plasmons, are injected into the SiO2 and are subsequently trapped at the Si–SiO2 interface. Other possible mechanisms are also discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.334767
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  • 8
    Electronic Resource
    Electronic Resource
    Centroid shift of γ rays from positron annihilation in the depletion region of metal-oxide-semiconductor structures (1991)
    Woodbury, NY : American Institute of Physics (AIP)
    Applied Physics Letters 58 (1991), S. 86-88 
    Details
    ISSN: 1077-3118
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Using metal-oxide-semiconductor (MOS) structures, the shift of centroid (peak) of γ-ray energy distributions emitted from positron annihilation has been measured as a function of incident positron energy. The Doppler centroid shift was found to be consistent with the positron motion in the MOS depletion region. The results are described by a one-dimensional positron diffusion model, and provide information on "effective'' positron diffusion length under applied field.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.104399
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  • 9
    Electronic Resource
    Electronic Resource
    Ultrathin oxide-nitride-oxide films (1990)
    Woodbury, NY : American Institute of Physics (AIP)
    Applied Physics Letters 57 (1990), S. 1248-1250 
    Details
    ISSN: 1077-3118
    Source: AIP Digital Archive
    Topics: Physics
    Notes: It is demonstrated that the thickness limit of a thin nitride film which can withstand reoxidation is reduced to about 3.5 nm when it is deposited in situ on a thin-deposited oxide film. The deposited oxide apparently provides a better surface for nitride nucleation and initial growth. Using this finding an oxide-nitride-oxide (ONO) film as thin as 4.6 nm was fabricated and shown to have good electrical properties and low defect density. The current leakage through the film was close to the acceptable limit in dynamic-random-access-memory technology. It was also found that electron trapping is substantially higher in ONO films produced by reoxidation than in films having a top deposited oxide.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.103499
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  • 10
    Electronic Resource
    Electronic Resource
    The relation between positive charge and breakdown in metal-oxide-silicon structures (1987)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 61 (1987), S. 1947-1956 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The relation between positive-charge accumulation at the Si-SiO2 interface and the occurrence of high-field breakdown in metal-oxide-silicon structures has been investigated. Oxides having different hole-trapping properties were prepared with the addition of short rapid thermal anneals in O2. Experiments testing hole trapping, high-field stressing, the initial current transients at constant gate voltage, and breakdown statistics were performed on these oxides to examine the correlation between positive charge and breakdown. The conclusion is that positive-charge generation is only one of the processes occurring during high-field stress but is not the main cause for breakdown. Large current increases were observed for oxides that have large hole-trapping efficiencies, but the current increase is followed by fast current decay. The mechanism causing the current decay was investigated and was found to be an intrinsic mechanism which is related to the neutralization of the positive charge. These processes always accompany the formation of positive charge and explain why the effectiveness of the positive charge in causing current runaway is inhibited.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.338043
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